Psyllid ID: psy7952

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440----
Protein Sequence
MAEGESKDASSAVGKSSSLTGNQQDRKGGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGYFLVILVFPC
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccHHHHHHHHHHHccccEEEEcccccccccccEEccccccccccccEEEEccccccccccccHHHHHccccccccccHHHHHHHcccEEEEEcccccHHHHHHHHHHHHcccccEEEEEEcccccccHHHHHHHHHHHHcccccEEEEEccccccccccccHHHHHHHHHHHHHccccccEEEEEccccHHHHHHHHHHHccccccccccccccccccEEEEEEccccccHHHHHHHHHHHHHccccccccccEEEEcccHHHHHHHHHHHccccHHHHHHHHHHHHcccccEEEEEccccccccccccEEEEEccccccccHHHHHcccccccccccEEEEccccccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccccHHHHHHHHHHHHccccEEEEEcccccHHHHHHHHHHHHHHcccccEEEEccccccEEEEEcHHHHHHHHHHHHHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHHccccEEEEEEccHHHccHHHHHHHHHHHHcccccEEEEEcHHHHHcccccccHHHHHHHHHHHHccccccEEEEEEcccHHHHHHHHHHHccccccEEEEEccccccEEEEEEEccccccHHHHHHHHHHHHHcHcccccccEEEEEccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccEEEEEEEEccccccccEEEEEEEcccccHHHHHHHHccccccccccEEEEEEcHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccccEEEEEccc
Coil and Loop (DISEMBL)
maegeskdassavgksssltgnqqdrkggkvSEQELTAKLKALFGFDSFKCELQKKAIRHILLRThdifvsmptgAVSLVGSVVsarsrvrippgadfilngnvrsrngwispilssfylrfrddktsivtgrsdlYQLELIVSGQTKTENKAILEELRLVKPrikllyvtperavTESFHYLLQHLVRYNKLAYIVVDEahcvsewghdfrptyrrlgelrqftgnsipiialtataepsvkQDIISVLkfnkpykvfktstfrsnLFYDVIFDDLLKDSYAHVKEFIEKClgkdnkanncgiiycrtrehtTDLADALRRKVNKHERSRVQESFMRGEINVITATIsfgmgidrqNVRFVVhwgmpssipayyqesgragrdgLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGYFLVILVFPC
Flexible Loop (DISEMBL)
maegeskdassavgksssltgnqqdrkggkvsEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSarsrvrippgadfilngnvrsrngWISPILSSFYLRFRDDKTSivtgrsdlyqlelivsgqtktenkaileelrlvkpriKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALtataepsvkQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIekclgkdnkannCGIIycrtrehttdladalrrkvnkhersrvqesfmrgeiNVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHsehskksleyvIKTDTSTKREQLELKFKNYLSMLEYCEQGYFLVILVFPC
Low Complexity Region (SEG)
MAEGESKDASSAVGKSSSLTGNQQDRKGGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTgavslvgsvvsarsrvrIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGYFLVILVFPC
Disordered region (IsUnstruct)
************************************TAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALR*************SFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGYFLVILVF**
Disordered Region (DISOPRED)
************************************TAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLE********************YLSMLEYCEQGYFLVILVFPC
Disordered Region (DISEMBL)
********************************EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALR***********QESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGYFLVILVFPC
Disordered Region (DISPRO)
**************************KGGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGYFLVILVFPC
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAEGESKDASSAVGKSSSLTGNQQDRKGGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGYFLVILVFPC
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	444	2.2.26 [Sep-21-2011]
O94762	991	ATP-dependent DNA helicas	no	N/A	0.851	0.381	0.400	7e-82
Q9FT72	713	ATP-dependent DNA helicas	yes	N/A	0.869	0.541	0.320	7e-56
Q9DEY9	1364	Bloom syndrome protein ho	N/A	N/A	0.795	0.258	0.355	1e-54
O18017	988	Bloom syndrome protein ho	no	N/A	0.835	0.375	0.353	2e-53
Q9FT74	606	ATP-dependent DNA helicas	no	N/A	0.790	0.579	0.349	7e-53
P54132	1417	Bloom syndrome protein OS	no	N/A	0.795	0.249	0.358	9e-53
Q9FT70	1150	ATP-dependent DNA helicas	no	N/A	0.797	0.307	0.349	2e-52
O88700	1416	Bloom syndrome protein ho	no	N/A	0.795	0.249	0.353	7e-51
Q8L840	1188	ATP-dependent DNA helicas	no	N/A	0.819	0.306	0.329	2e-50
Q9CL21	632	ATP-dependent DNA helicas	yes	N/A	0.581	0.408	0.368	2e-48

>sp|O94762|RECQ5_HUMAN ATP-dependent DNA helicase Q5 OS=Homo sapiens GN=RECQL5 PE=1 SV=2

 Score =  305 bits (780), Expect = 7e-82,   Method: Compositional matrix adjust.
 Identities = 168/419 (40%), Positives = 243/419 (57%), Gaps = 41/419 (9%)

Query: 33  EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRI 92
           E+ + + LK +FGFDSFK  LQ+ A   ++    D+FV MPTGA   +   + A      
Sbjct: 13  ERRVRSTLKKVFGFDSFKTPLQESATMAVVKGNKDVFVCMPTGAGKSLCYQLPA------ 66

Query: 93  PPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENK 152
                 +  G        I+ ++S      +D    ++T +  +  L   +S Q   E K
Sbjct: 67  -----LLAKG--------ITIVVSPLIALIQDQVDHLLTLKVRVSSLNSKLSAQ---ERK 110

Query: 153 AILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFR 212
            +L +L   KP+ K+LY+TPE A + SF   L  LV  + L+Y+VVDEAHCVS+WGHDFR
Sbjct: 111 ELLADLEREKPQTKILYITPEMAASSSFQPTLNSLVSRHLLSYLVVDEAHCVSQWGHDFR 170

Query: 213 PTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDV 272
           P Y RLG LR   G++ P +ALTATA P V++D+ + L   KP  +FKT  FR+NLFYDV
Sbjct: 171 PDYLRLGALRSRLGHA-PCVALTATATPQVQEDVFAALHLKKPVAIFKTPCFRANLFYDV 229

Query: 273 IFDDLLKDSYAHVKEFIEKCLGK--DNKANNCGIIYCRTREHTTDLADALR-RKVNKH-- 327
            F +L+ D Y ++K+F  K LG+  D   + CGI+YCRTRE    LA  L  R VN    
Sbjct: 230 QFKELISDPYGNLKDFCLKALGQEADKGLSGCGIVYCRTREACEQLAIELSCRGVNAKAY 289

Query: 328 -------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGR 380
                  ER+ VQ  +M  ++ VI ATISFGMG+D+ NVRFV HW +  S+  YYQESGR
Sbjct: 290 HAGLKASERTLVQNDWMEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGR 349

Query: 381 AGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKN------YLSMLEYCEQ 433
           AGRDG  S+CR+Y+S + +  + ++I+ + +  +E+   K  +      + +++ +CE+
Sbjct: 350 AGRDGKPSWCRLYYSRNDRDQVSFLIRKEVAKLQEKRGNKASDKATIMAFDALVTFCEE 408

May have an important role in DNA metabolism.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

>sp|Q9FT72|RQL3_ARATH ATP-dependent DNA helicase Q-like 3 OS=Arabidopsis thaliana GN=RECQL3 PE=1 SV=1

 Score =  218 bits (555), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 137/428 (32%), Positives = 215/428 (50%), Gaps = 42/428 (9%)

Query: 15  KSSSLTGNQQDRKGGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPT 74
           KS     N Q        ++ L   L+  FG   F+ + Q +AI+ ++    D F  MPT
Sbjct: 3   KSPLPVQNVQSSDKNVAGKEALVKLLRWHFGHADFRGK-QLEAIQAVV-SGRDCFCLMPT 60

Query: 75  GAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRS 134
           G    +   + A ++    PG   +           +SP+++         +  ++  + 
Sbjct: 61  GGGKSICYQIPALAK----PGIVLV-----------VSPLIALM-------ENQVMALKE 98

Query: 135 DLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLA 194
                E + S Q       I E+L   KP ++LLYVTPE   T+ F   L+ L     L 
Sbjct: 99  KGIAAEYLSSTQATHVKNKIHEDLDSGKPSVRLLYVTPELIATKGFMLKLRKLHSRGLLN 158

Query: 195 YIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNK 254
            I +DEAHC+S WGHDFRP+YR+L  LR    + +P++ALTATA P V++D+I  L    
Sbjct: 159 LIAIDEAHCISSWGHDFRPSYRQLSTLRDSLAD-VPVLALTATAAPKVQKDVIDSLNLRN 217

Query: 255 PYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTT 314
           P  V K+S  R N+FY+V + DLL ++Y  +   ++ C       N C IIYC  R    
Sbjct: 218 PL-VLKSSFNRPNIFYEVRYKDLLDNAYTDLGNLLKSC------GNICAIIYCLERTTCD 270

Query: 315 DLA----------DALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVH 364
           DL+           A    +N   RS V + ++  +  +I AT++FGMGID+++VR V H
Sbjct: 271 DLSVHLSSIGISSAAYHAGLNSKMRSTVLDDWLSSKKQIIVATVAFGMGIDKKDVRMVCH 330

Query: 365 WGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNY 424
           + +P S+ ++YQESGRAGRD L S   +Y+    +K +EY+++   + K    +    ++
Sbjct: 331 FNIPKSMESFYQESGRAGRDQLPSRSVLYYGVDDRKKMEYLLRNSENKKSSSSKKPTSDF 390

Query: 425 LSMLEYCE 432
             ++ YCE
Sbjct: 391 EQIVTYCE 398

3'-5' DNA helicase that may play a role in the repair of DNA. Exhibits an ATP or dATP-dependent DNA-helicase activity. Can not use GTP/dGTP, CTP/dCTP or UTP/dUTP as nucleotide cofactors. Catalyzes DNA strand annealing. On nicked Holliday junctions, unwinds the lagging strand. Can not act on intact Holliday junctions.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9DEY9|BLM_XENLA Bloom syndrome protein homolog OS=Xenopus laevis GN=blm PE=2 SV=1

 Score =  214 bits (544), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 144/405 (35%), Positives = 210/405 (51%), Gaps = 52/405 (12%)

Query: 44  FGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN 103
           FG   F+   Q +AI   L    D F+ MPTG     G  +  +    I PG   +    
Sbjct: 615 FGLHRFRTN-QLEAINACLC-GEDCFILMPTGG----GKSLCYQLPGCISPGVTIV---- 664

Query: 104 VRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLEL----IVSGQTKTENKAILEELR 159
                  ISP+           ++ IV     L  L++    +   +T  E  +I  +L 
Sbjct: 665 -------ISPL-----------RSLIVDQVQKLTSLDIPATYLTGDKTDAEAASIYLQLS 706

Query: 160 LVKPRIKLLYVTPERAVTES-FHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRL 218
              P IKLLYVTPE+    +     +++L     LA  V+DEAHCVS+WGHDFRP Y+RL
Sbjct: 707 KKDPIIKLLYVTPEKVCASTRLISTMENLYERQLLARFVIDEAHCVSQWGHDFRPDYKRL 766

Query: 219 GELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLL 278
             LRQ    S+P++ALTATA P VK+DI++ LK  KP ++F  S  R NL Y+V+     
Sbjct: 767 NVLRQ-KFQSVPMMALTATANPRVKKDILNQLKMTKP-QIFTMSFNRDNLKYEVLPKKPK 824

Query: 279 KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHE 328
           + +   V E+I+K     +  N+ GIIYC +R     +AD L+++          +    
Sbjct: 825 RVALDCV-EWIKK-----HHPNDSGIIYCLSRHECDTMADTLQKEGLAALAYHAGLADSN 878

Query: 329 RSRVQESFM-RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ 387
           R  VQ  ++ + +  VI ATI+FGMGID+ +VR+V+H  +P S+  YYQESGRAGRDG  
Sbjct: 879 RDYVQHKWINQDDCQVICATIAFGMGIDKPDVRYVIHASLPKSVEGYYQESGRAGRDGET 938

Query: 388 SYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCE 432
           S+C +++S H    +  +I+ +        +  F N  SM+ YCE
Sbjct: 939 SHCLLFYSYHDVTRIRRLIQMEKDGNSHTKQTHFNNLYSMVHYCE 983

Participates in DNA replication and repair. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|O18017|BLM_CAEEL Bloom syndrome protein homolog OS=Caenorhabditis elegans GN=him-6 PE=2 SV=2

 Score =  210 bits (534), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 147/416 (35%), Positives = 209/416 (50%), Gaps = 45/416 (10%)

Query: 29  GKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARS 88
           G    +EL   LK+ FGF+ F+   QK+ I   L+  HD FV MPTGA    G  +  + 
Sbjct: 228 GADMNKELYDTLKSKFGFNQFR-HRQKQCILSTLM-GHDTFVLMPTGA----GKSLCYQL 281

Query: 89  RVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTK 148
              I PG   +           +SP+ S       D K  +   +      E + +    
Sbjct: 282 PAVILPGVTVV-----------VSPLRS----LIEDQKMKM---KELGIGCEALTADLGA 323

Query: 149 TENKAILEELRLVKPRIKLLYVTPER-AVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEW 207
              + I  EL    P IKLLYVTPE+ + +   + +   L R   LA  V+DEAHCVS+W
Sbjct: 324 PAQEKIYAELGSGNPSIKLLYVTPEKISASGRLNSVFFDLHRRGLLARFVIDEAHCVSQW 383

Query: 208 GHDFRPTYRRLGELRQ-FTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRS 266
           GHDFRP Y +L  LR+ +    +PIIALTATA P +  D    LK     K+F +S  R 
Sbjct: 384 GHDFRPDYTKLSSLREKYANPPVPIIALTATATPKIVTDARDHLKMQN-SKLFISSFVRD 442

Query: 267 NLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDL---------- 316
           NL YD     L+  +   +   +EK   K       GI+YC +R+    +          
Sbjct: 443 NLKYD-----LIPKAARSLINVVEKM--KQLYPGKSGIVYCLSRKECETVQMMLTKAGLS 495

Query: 317 ADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ 376
           A+     +N + R  VQ S++  + +VI ATI+FGMGID+ +VRFV+H+ +P SI  YYQ
Sbjct: 496 AEVYHAGLNDNLRVSVQRSWIANKFDVICATIAFGMGIDKPDVRFVIHYSLPKSIEGYYQ 555

Query: 377 ESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCE 432
           E+GRAGRDG+ SYC + +S H    L  +I+   +T   +  +   N L ++ YCE
Sbjct: 556 ETGRAGRDGMPSYCLMLYSYHDSIRLRRMIEEGNTTTGVR-SMHLNNVLQVVAYCE 610

Participates in DNA replication and repair. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.

Caenorhabditis elegans (taxid: 6239)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9FT74|RQL1_ARATH ATP-dependent DNA helicase Q-like 1 OS=Arabidopsis thaliana GN=RECQL1 PE=2 SV=1

 Score =  208 bits (529), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 143/409 (34%), Positives = 206/409 (50%), Gaps = 58/409 (14%)

Query: 43  LFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG 102
           +FG   F+  LQ +A R  + R  D FV MPTG     G  +  +    +  G   +   
Sbjct: 201 IFGNKVFR-PLQHQACRASMER-KDCFVLMPTGG----GKSLCYQLPATLKAGVTIV--- 251

Query: 103 NVRSRNGWISPILS-------SFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAIL 155
                   ISP+LS       +  L+F    T              + S QT ++  A+L
Sbjct: 252 --------ISPLLSLIQDQIVALNLKFGIPAT-------------FLNSQQTSSQAAAVL 290

Query: 156 EELRLVKPRIKLLYVTPER-AVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPT 214
           +ELR   P  KLLYVTPE+ A + SF   L+ L R   LA  VVDEAHCVS+WGHDFRP 
Sbjct: 291 QELRRDNPSCKLLYVTPEKIAGSSSFLETLRCLDRKGLLAGFVVDEAHCVSQWGHDFRPD 350

Query: 215 YRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIF 274
           YR LG L+Q     +P++ALTATA  SV QD++  L+  +   V K S  R NL Y+VI 
Sbjct: 351 YRELGCLKQ-NFPRVPVMALTATATESVCQDVLKSLRIPRA-PVLKMSFDRINLKYEVIV 408

Query: 275 DDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------- 323
               K+    ++E +     +D   +  GI+YC ++    D+A  L  K           
Sbjct: 409 K--TKEPLKQLQELL-----RDRFKDQSGIVYCLSKSECVDVAKFLNEKCKVKTVYYHAG 461

Query: 324 VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGR 383
           V   +R  VQ  +  GE+ ++ ATI+FGMGID+ +VRFV+H  +  ++ +YYQESGRAGR
Sbjct: 462 VPAKQRVDVQRKWQTGEVRIVCATIAFGMGIDKADVRFVIHNTLSKAVESYYQESGRAGR 521

Query: 384 DGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCE 432
           DGLQ+ C   + +     +  +++       ++ +        M +YCE
Sbjct: 522 DGLQAQCICLYQKKDFSRVVCMLRNGQGRNMDRFKSAMAQAKKMQQYCE 570

3'-5' DNA helicase that may play a role in the repair of DNA.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P54132|BLM_HUMAN Bloom syndrome protein OS=Homo sapiens GN=BLM PE=1 SV=1

 Score =  207 bits (528), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 145/405 (35%), Positives = 209/405 (51%), Gaps = 52/405 (12%)

Query: 44   FGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN 103
            FG  +F+   Q +AI   LL   D F+ MPTG     G  +  +    + PG   +    
Sbjct: 663  FGLHNFRTN-QLEAINAALL-GEDCFILMPTGG----GKSLCYQLPACVSPGVTVV---- 712

Query: 104  VRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLEL----IVSGQTKTENKAILEELR 159
                   ISP+           ++ IV     L  L++    +   +T +E   I  +L 
Sbjct: 713  -------ISPL-----------RSLIVDQVQKLTSLDIPATYLTGDKTDSEATNIYLQLS 754

Query: 160  LVKPRIKLLYVTPER-AVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRL 218
               P IKLLYVTPE+   +      L++L     LA  V+DEAHCVS+WGHDFR  Y+R+
Sbjct: 755  KKDPIIKLLYVTPEKICASNRLISTLENLYERKLLARFVIDEAHCVSQWGHDFRQDYKRM 814

Query: 219  GELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLL 278
              LRQ    S+P++ALTATA P V++DI++ LK  +P +VF  S  R NL Y V+     
Sbjct: 815  NMLRQ-KFPSVPVMALTATANPRVQKDILTQLKILRP-QVFSMSFNRHNLKYYVLPKKPK 872

Query: 279  KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHE 328
            K ++  + E+I K    D+     GIIYC +R     +AD L+R           ++   
Sbjct: 873  KVAFDCL-EWIRKHHPYDS-----GIIYCLSRRECDTMADTLQRDGLAALAYHAGLSDSA 926

Query: 329  RSRVQESFMRGE-INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ 387
            R  VQ+ ++  +   VI ATI+FGMGID+ +VRFV+H  +P S+  YYQESGRAGRDG  
Sbjct: 927  RDEVQQKWINQDGCQVICATIAFGMGIDKPDVRFVIHASLPKSVEGYYQESGRAGRDGEI 986

Query: 388  SYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCE 432
            S+C ++++ H    L+ +I  +        E  F N  SM+ YCE
Sbjct: 987  SHCLLFYTYHDVTRLKRLIMMEKDGNHHTRETHFNNLYSMVHYCE 1031

Participates in DNA replication and repair. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9FT70|RQL4B_ARATH ATP-dependent DNA helicase Q-like 4B OS=Arabidopsis thaliana GN=RECQL4B PE=2 SV=1

 Score =  207 bits (526), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 147/421 (34%), Positives = 222/421 (52%), Gaps = 67/421 (15%)

Query: 41  KALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFIL 100
           K +FG  SF+    ++ I +  +   D+FV MPTG     G  ++ +    +  G   + 
Sbjct: 462 KLVFGNHSFR--PNQREIINATMSGCDVFVLMPTGG----GKSLTYQLPALLCAGITLV- 514

Query: 101 NGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRL 160
                     ISP++S    +  +   + ++  S       + +G    E   IL+EL  
Sbjct: 515 ----------ISPLVSLIQDQIMNLLQTNISAAS-------LSAGMEWAEQLEILQELSS 557

Query: 161 VKPRIKLLYVTPER-AVTESFHYLLQHLVRYNK---LAYIVVDEAHCVSEWGHDFRPTYR 216
            K + KLLYVTPE+ A +ES   LL+HL   N    LA  V+DEAHCVS+WGHDFRP Y+
Sbjct: 558 EKSKYKLLYVTPEKVAKSES---LLRHLEILNSRSLLARFVIDEAHCVSQWGHDFRPDYQ 614

Query: 217 RLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVI--F 274
            LG L+Q   N IP++ALTATA  SVK+D++  L       VF+ S  R NL+Y V+   
Sbjct: 615 GLGVLKQKFPN-IPMLALTATATTSVKEDVVQALGLVNCV-VFRQSFNRPNLWYSVVPKT 672

Query: 275 DDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALR----------RKV 324
           +  L+D    + +FI     ++N  + CGIIYC +R     + +ALR            +
Sbjct: 673 NKCLED----IDKFI-----RENHFDECGIIYCLSRMDCEKVTEALRVFGHKAAFYHGSM 723

Query: 325 NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD 384
           +  +R+ VQ+ + + EIN+I AT++FGMGI++ +VRFV+H  +P SI  Y+QE GRAGRD
Sbjct: 724 DPGKRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRD 783

Query: 385 GLQSYCRIYHSEHSKKSLEYVIKTD-------------TSTKREQLELKFKNYLSMLEYC 431
           G +S C +Y+S      ++++I                 ++    LE   +N L M+ YC
Sbjct: 784 GQRSSCVLYYSYTDYIRVKHMISQGGLGQGQMKMGYNCKASSGRMLETNTENLLRMVSYC 843

Query: 432 E 432
           E
Sbjct: 844 E 844

3'-5' DNA helicase that may play a role in the repair of DNA (By similarity). Required to promote but not to suppress crossovers.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|O88700|BLM_MOUSE Bloom syndrome protein homolog OS=Mus musculus GN=Blm PE=1 SV=1

 Score =  201 bits (512), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 143/405 (35%), Positives = 207/405 (51%), Gaps = 52/405 (12%)

Query: 44   FGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN 103
            FG  +F+   Q +AI   LL   D F+ MPTG     G  +  +    + PG   +    
Sbjct: 671  FGLHNFRTN-QLEAINAALL-GEDCFILMPTGG----GKSLCYQLPACVSPGVTIV---- 720

Query: 104  VRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLEL----IVSGQTKTENKAILEELR 159
                   ISP+           ++ IV     L   ++    +   +T +E   I  +L 
Sbjct: 721  -------ISPL-----------RSLIVDQVQKLTSFDIPATYLTGDKTDSEAANIYLQLS 762

Query: 160  LVKPRIKLLYVTPER-AVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRL 218
               P IKLLYVTPE+   +      L++L     LA  V+DEAHCVS+WGHDFR  Y+R+
Sbjct: 763  KKDPIIKLLYVTPEKVCASNRLISTLENLYERKLLARFVIDEAHCVSQWGHDFRQDYKRM 822

Query: 219  GELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLL 278
              LRQ    S+P++ALTATA P V++DI++ LK  +P +VF  S  R NL Y V+     
Sbjct: 823  NMLRQ-KFPSVPVMALTATANPRVQKDILTQLKILRP-QVFSMSFNRHNLKYYVLPKKPK 880

Query: 279  KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHE 328
            K ++  + E+I K    D+     GIIYC +R     +AD L+R+          ++   
Sbjct: 881  KVAFDCL-EWIRKHHPYDS-----GIIYCLSRRECDTMADTLQREGLAALAYHAGLSDSA 934

Query: 329  RSRVQESFM-RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ 387
            R  VQ  ++ +    VI ATI+FGMGID+ +VRFV+H  +P S+  YYQESGRAGRDG  
Sbjct: 935  RDEVQHKWINQDNCQVICATIAFGMGIDKPDVRFVIHASLPKSMEGYYQESGRAGRDGEI 994

Query: 388  SYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCE 432
            S+C ++++ H    L+ +I  +        E    N  SM+ YCE
Sbjct: 995  SHCVLFYTYHDVTRLKRLIMMEKDGNYHTKETHVNNLYSMVHYCE 1039

Participates in DNA replication and repair. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q8L840|RQL4A_ARATH ATP-dependent DNA helicase Q-like 4A OS=Arabidopsis thaliana GN=RECQL4A PE=2 SV=1

 Score =  200 bits (508), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 140/425 (32%), Positives = 212/425 (49%), Gaps = 61/425 (14%)

Query: 34  QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIP 93
           ++L    K +FG  SF+    ++ I +  +   D+FV MPTG     G  ++ +    I 
Sbjct: 439 RKLEVNNKKVFGNHSFR--PNQREIINATMSGSDVFVLMPTGG----GKSLTYQLPALIC 492

Query: 94  PGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKA 153
            G   +           ISP++S    +  +   + +   S       + +G    E   
Sbjct: 493 GGITLV-----------ISPLVSLIQDQIMNLLQANIPAAS-------LSAGMEWAEQLK 534

Query: 154 ILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK---LAYIVVDEAHCVSEWGHD 210
           I +EL     + KLLYVTPE+        LL+HL   N    LA  V+DEAHCVS+WGHD
Sbjct: 535 IFQELNSEHSKYKLLYVTPEKVAKSD--SLLRHLENLNSRGLLARFVIDEAHCVSQWGHD 592

Query: 211 FRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFY 270
           FRP Y+ LG L+Q   N IP++ALTATA  SVK+D++  L       VF+ S  R NL+Y
Sbjct: 593 FRPDYQSLGILKQKFPN-IPVLALTATATASVKEDVVQALGLVNCV-VFRQSFNRPNLWY 650

Query: 271 DVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR-------- 322
            V+     K     + +FI     K+N  + CGIIYC +R     +++ L+         
Sbjct: 651 SVV--PKTKKCLEDIDKFI-----KENHFDECGIIYCLSRMDCEKVSERLQEFGHKAAFY 703

Query: 323 --KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGR 380
              +   +R+ +Q  + + EIN+I AT++FGMGI++ +VRFV+H  +P SI  Y+QE GR
Sbjct: 704 HGSMEPEQRAFIQTQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGR 763

Query: 381 AGRDGLQSYCRIYHSEHSKKSLEYVIKTD-------------TSTKREQLELKFKNYLSM 427
           AGRDG +S C +Y+       ++++I                 ++    LE   +N L M
Sbjct: 764 AGRDGQRSSCVLYYGYGDYIRVKHMISQGGVDQSPMATGYNRVASSGRLLETNTENLLRM 823

Query: 428 LEYCE 432
           + YCE
Sbjct: 824 VRYCE 828

3'-5' DNA helicase that may play a role in the repair of DNA. Required for maintenance of genome stability by modulation of the DNA damage response and repression of crossovers. Confers resistance to genotoxic stress.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9CL21|RECQ_PASMU ATP-dependent DNA helicase RecQ OS=Pasteurella multocida (strain Pm70) GN=recQ PE=3 SV=1

 Score =  193 bits (490), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 105/285 (36%), Positives = 170/285 (59%), Gaps = 27/285 (9%)

Query: 144 SGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHC 203
           S QT TE + +  + +L+   +KLLYV+PE+ +T SF     HL+ + K++++ +DEAHC
Sbjct: 110 SSQTFTEQQQV--QNKLMSGTLKLLYVSPEKVMTTSFF----HLISHCKVSFVAIDEAHC 163

Query: 204 VSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST 263
           +S+WGHDFRP Y +LG L+    ++ PI+ALTATA+ + +QDI+  L    P+ V+  S 
Sbjct: 164 ISQWGHDFRPEYTQLGGLKSCFPHA-PIMALTATADHATRQDILRHLNLQSPH-VYIGSF 221

Query: 264 FRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK 323
            R N+ Y ++      + +  +++     LG+  K+   GIIYC +R     +A++LR K
Sbjct: 222 DRPNIRYTLV------EKFKPMEQLCRFVLGQKGKS---GIIYCNSRSKVERIAESLRNK 272

Query: 324 ----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPA 373
                     +   +R +VQ +F R  + V+ ATI+FGMGI++ NVRFVVH+ +P SI +
Sbjct: 273 GVSAQAYHAGLETSQREQVQRAFQRDNVQVVVATIAFGMGINKSNVRFVVHFDLPRSIES 332

Query: 374 YYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLE 418
           YYQE+GRAGRD L +   +++       L  ++     + + Q+E
Sbjct: 333 YYQETGRAGRDDLPAEAVLFYEPADYAWLHKILLEKPESPQRQIE 377

DNA helicase.

Pasteurella multocida (strain Pm70) (taxid: 272843)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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	444
328713283	1075	PREDICTED: ATP-dependent DNA helicase Q5	0.844	0.348	0.456	1e-91
157110525	846	DNA helicase recq5 [Aedes aegypti] gi|10	0.864	0.453	0.415	6e-86
312373020	1482	hypothetical protein AND_18377 [Anophele	0.894	0.267	0.428	7e-85
347965591	1523	AGAP001255-PA [Anopheles gambiae str. PE	0.849	0.247	0.424	1e-84
170039315	859	ATP-dependent DNA helicase recQ [Culex q	0.851	0.440	0.405	9e-84
270009277	1715	homolog of RecQ [Tribolium castaneum]	0.876	0.226	0.390	4e-82
334322907	996	PREDICTED: ATP-dependent DNA helicase Q5	0.851	0.379	0.411	1e-81
242008765	853	DNA helicase recq5, putative [Pediculus	0.846	0.440	0.419	1e-81
357627528	1133	DNA helicase recq5 [Danaus plexippus]	0.844	0.330	0.385	1e-81
193786741	435	unnamed protein product [Homo sapiens]	0.851	0.868	0.400	2e-80

>gi|328713283|ref|XP_001944776.2| PREDICTED: ATP-dependent DNA helicase Q5-like [Acyrthosiphon pisum]

 Score =  343 bits (879), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 193/423 (45%), Positives = 256/423 (60%), Gaps = 48/423 (11%)

Query: 36  LTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPG 95
           L  KLK  F   +FK +LQK AI  IL R  D+FVSMPTG+   +   + A   V   P 
Sbjct: 20  LLEKLKHFFHHPTFKSDLQKNAIIAILKRKFDVFVSMPTGSGKSLCYQLPA---VLHSPK 76

Query: 96  ADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAIL 155
              +            SP+++   ++ + D  + +  R+     E I S   ++E K ++
Sbjct: 77  VTIVF-----------SPLIA--LMKDQVDHLTRLKIRA-----ETINSKMPESERKRVI 118

Query: 156 EELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTY 215
            +L   +    LLYVTPE+A T+ F  LL +LVR NKLAYIVVDEAHCVS+WGHDFRP Y
Sbjct: 119 NDLYATQVSTSLLYVTPEQAATDFFKGLLSYLVRKNKLAYIVVDEAHCVSQWGHDFRPDY 178

Query: 216 RRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFD 275
            +LG LR+   + IP IALTATA   V +DI++ L    P   F T  FRSNLFYDVIFD
Sbjct: 179 LKLGMLRELYLH-IPWIALTATASADVVKDIMTALCLKTPVSKFTTPCFRSNLFYDVIFD 237

Query: 276 DLLKDSYAHVKEFIEKCLGKDNK-----------ANNCGIIYCRTREHTTDLADALRRK- 323
           D + +SY H+K+FI++CL  D                CGIIYCRTRE T ++A  L RK 
Sbjct: 238 DSITNSYQHLKDFIDQCLCDDLNCLEGTPNINPLTQPCGIIYCRTRELTEEIATVLSRKG 297

Query: 324 ---------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAY 374
                    +   ER  VQE+FM G I VITAT+SFGMGID+  VRFV+HWG+PSSIPAY
Sbjct: 298 ISIAPYHAGLKDKERLAVQEAFMSGHIQVITATVSFGMGIDKATVRFVIHWGIPSSIPAY 357

Query: 375 YQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKT-----DTSTKREQLELKFKNYLSMLE 429
           YQESGRAGRDG  + CRIYHS+ +K SL++++K+      T  K+++ +  +  +L M++
Sbjct: 358 YQESGRAGRDGKLARCRIYHSKQAKNSLDFILKSAITQAKTQDKQKKAKGSYSMFLKMIQ 417

Query: 430 YCE 432
           +CE
Sbjct: 418 FCE 420

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157110525|ref|XP_001651140.1| DNA helicase recq5 [Aedes aegypti] gi|108878672|gb|EAT42897.1| AAEL005597-PA [Aedes aegypti]

 Score =  324 bits (830), Expect = 6e-86,   Method: Compositional matrix adjust.
 Identities = 177/426 (41%), Positives = 253/426 (59%), Gaps = 42/426 (9%)

Query: 29  GKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARS 88
           G  SE  L  KLK  FG + FK  LQK+AI+ I+ RT D++VSMPTG         S +S
Sbjct: 231 GASSEGILQEKLKQYFGHNDFKSSLQKEAIQTIITRTRDVYVSMPTG---------SGKS 281

Query: 89  RVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTK 148
                PG   ++  N       ++ + S      +D   ++   +      + I S  + 
Sbjct: 282 LCFQLPG---VMQDNK------VTIVFSPLLALIKDQLDTLAKLK---IPADSINSKMSN 329

Query: 149 TENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWG 208
            +   +L +L+ ++  I+ LY+TPE+A T +F  L++ LV++ K+AY+VVDEAHCVSEWG
Sbjct: 330 KDRDRVLNDLKSIRTDIRFLYITPEQANTSTFKELMKMLVKHKKVAYVVVDEAHCVSEWG 389

Query: 209 HDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNL 268
           HDFRP Y +LG LR     SIP IALTATA   V  DI   L+  +P   FKT  FR NL
Sbjct: 390 HDFRPDYLKLGYLRS-EYPSIPWIALTATASKKVVDDIFKNLRLKEPIAKFKTPCFRKNL 448

Query: 269 FYDVIFDDLLKDSYAHVKEFIEKCLGKDNK-----ANNCGIIYCRTREHTTDLADALRR- 322
           +YDV+F + ++D Y H++++IE  L KD K        CGIIYCRTRE T  +A++L + 
Sbjct: 449 YYDVVFKNSIQDDYIHLRDYIESILDKDEKDIKPSKKACGIIYCRTRETTERVANSLTKL 508

Query: 323 ---------KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPA 373
                     + + ER  VQE +M G+   I+ATISFGMG+D+ +VRFV+HW +P S+ +
Sbjct: 509 GLKTAAYHAGLKQSERVAVQEDWMDGKYAAISATISFGMGVDKGSVRFVIHWDIPQSVAS 568

Query: 374 YYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI-----KTDTSTKREQLELKFKNYLSML 428
           YYQESGRAGRDG +S+CR+YH     KS+++++     KT  S K E+ +L  KN+  ++
Sbjct: 569 YYQESGRAGRDGKKSFCRVYHCRDQCKSIDFLLQQDLQKTKGSAKEEKAKLAVKNFEKIV 628

Query: 429 EYCEQG 434
           +YCE  
Sbjct: 629 QYCESA 634

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312373020|gb|EFR20851.1| hypothetical protein AND_18377 [Anopheles darlingi]

 Score =  320 bits (821), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 188/439 (42%), Positives = 250/439 (56%), Gaps = 42/439 (9%)

Query: 13  VGKSSSLTGNQQDRKGGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSM 72
           +G S    G     K  K  E  L  KL   FG   FK  LQK+AI  I+ RT D++VSM
Sbjct: 131 IGDSPDHLGRHALEKDTKADEL-LLEKLWKYFGHRDFKSHLQKEAIETIIARTRDVYVSM 189

Query: 73  PTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTG 132
           PTGA    G  +             F L G ++  +  ++ + S      +D   ++   
Sbjct: 190 PTGA----GKSLC------------FQLPGVMQ--DNKVTIVFSPLLALIKDQLDTLARI 231

Query: 133 RSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK 192
           +      + I S     + + +L +L+ VK  I+ LY+TPE+A T  F  ++QHLV++ K
Sbjct: 232 K---IPADSINSKMGSRDRERVLNDLKAVKTDIRFLYITPEQAQTAIFKEIIQHLVKHRK 288

Query: 193 LAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKF 252
           +AYIVVDEAHCVSEWGHDFRP Y +LG LR     SIP IALTATA   V  DI   L+ 
Sbjct: 289 VAYIVVDEAHCVSEWGHDFRPDYLKLGALRS-EYPSIPWIALTATASKQVVADIFKNLRL 347

Query: 253 NKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANN----CGIIYCR 308
            +P   FKT  FR NL+YDV+F + ++D Y H+KE+IE  LGK ++       CGIIYCR
Sbjct: 348 KEPVAKFKTQCFRHNLYYDVVFKNSIQDDYLHLKEYIESILGKQDEVKPSKRACGIIYCR 407

Query: 309 TREHTTDLADALR----RKVNKH------ERSRVQESFMRGEINVITATISFGMGIDRQN 358
           TRE T  +A +L     R V  H      ER  VQE +M G+   I ATISFGMG+D+ +
Sbjct: 408 TRETTERVAMSLTKLGLRTVPYHAGLKQSERETVQEDWMEGKYVAIAATISFGMGVDKGS 467

Query: 359 VRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTD-----TSTK 413
           VRFVVHW  P ++ AYYQESGRAGRDG +SYCRIYH     KS+++++K D      + K
Sbjct: 468 VRFVVHWDNPQNVAAYYQESGRAGRDGKKSYCRIYHCRDQCKSIDFLLKQDLQKSKDTGK 527

Query: 414 REQLELKFKNYLSMLEYCE 432
               +   KN+  M+E+CE
Sbjct: 528 EAAAKQAIKNFEKMIEFCE 546

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347965591|ref|XP_001238556.3| AGAP001255-PA [Anopheles gambiae str. PEST] gi|333470440|gb|EAU75726.3| AGAP001255-PA [Anopheles gambiae str. PEST]

 Score =  320 bits (819), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 179/422 (42%), Positives = 254/422 (60%), Gaps = 45/422 (10%)

Query: 32  SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVR 91
           S++ L  KL   FG   FK +LQK+AI  I+ RT D++VSMPTGA   +           
Sbjct: 174 SDELLQEKLWQYFGHRDFKSQLQKEAIETIIARTRDVYVSMPTGAGKSLC---------- 223

Query: 92  IPPGADFILNGNVRSRNGWI--SPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKT 149
                 F L G ++     I  SP+L+   ++ + D  + +   +D    ++ V  + + 
Sbjct: 224 ------FQLPGVMQDNKVTIVFSPLLA--LIKDQLDTLARIKIPADSINSKMGVRDRER- 274

Query: 150 ENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGH 209
               ++ +L+ VK  I+ LY+TPE+A T +F  ++QHLV++ K+AY+VVDEAHCVSEWGH
Sbjct: 275 ----VINDLKSVKTDIRFLYITPEQANTATFKDIMQHLVKFRKVAYVVVDEAHCVSEWGH 330

Query: 210 DFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLF 269
           DFRP Y +LG LR     S+P IALTATA   V +DI   L+  +P   FKT  FR NL+
Sbjct: 331 DFRPDYLKLGNLRA-EYPSVPWIALTATASKQVVEDIFRNLRLKEPVAKFKTPCFRHNLY 389

Query: 270 YDVIFDDLLKDSYAHVKEFIEKCLGKDNKANN----CGIIYCRTREHTTDLADALR---- 321
           YDV+F + ++D + H+K++IE  LGK ++       CGIIYCRTRE+T  +A  L     
Sbjct: 390 YDVVFKNSIQDDFLHLKDYIEGILGKQDEVKPSKRACGIIYCRTRENTERVATNLTKLGL 449

Query: 322 RKVNKH------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYY 375
           R V  H      ER +VQE +M G+   I ATISFGMG+D+ +VRFV+HW  P ++ AYY
Sbjct: 450 RTVPYHAGLKQSERDQVQEDWMEGKYVAIAATISFGMGVDKGSVRFVIHWDNPQNVAAYY 509

Query: 376 QESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTD-----TSTKREQLELKFKNYLSMLEY 430
           QESGRAGRDG +S+CRIYH     KS+E++++ D      + K E  +   KN+  M+E+
Sbjct: 510 QESGRAGRDGKKSFCRIYHCRDGCKSIEFLLRQDLQKSKDTPKEESAKQAVKNFEKMVEF 569

Query: 431 CE 432
           CE
Sbjct: 570 CE 571

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170039315|ref|XP_001847485.1| ATP-dependent DNA helicase recQ [Culex quinquefasciatus] gi|167862886|gb|EDS26269.1| ATP-dependent DNA helicase recQ [Culex quinquefasciatus]

 Score =  317 bits (811), Expect = 9e-84,   Method: Compositional matrix adjust.
 Identities = 172/424 (40%), Positives = 251/424 (59%), Gaps = 46/424 (10%)

Query: 36  LTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPG 95
           L  KLK  FG + FK  LQK+AI+ I+ RT D++VSMPTG         S +S     PG
Sbjct: 242 LQEKLKQYFGHNDFKSPLQKEAIQTIISRTRDVYVSMPTG---------SGKSLCFQLPG 292

Query: 96  ADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAIL 155
              ++  N       ++ + S      +D   ++   +      + I S  +  +   +L
Sbjct: 293 ---VMQDN------RVTIVFSPLLALIKDQLDTLAKLK---IPADSINSKMSNKDRDRVL 340

Query: 156 EELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTY 215
            +L+ ++  I+ LY+TPE+A T +F  L++ LV++ K+AY+VVDEAHCVSEWGHDFRP Y
Sbjct: 341 NDLKSIRTDIRFLYITPEQANTATFKELMKLLVKHKKVAYVVVDEAHCVSEWGHDFRPDY 400

Query: 216 RRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFD 275
            +LG LR     SIP IALTATA   V  DI   L+  +P   FKT  FR NLFYDV+F 
Sbjct: 401 LKLGYLRT-EYPSIPWIALTATASKQVVSDIFKNLRLKEPVAKFKTPCFRKNLFYDVVFK 459

Query: 276 DLLKDSYAHVKEFIEKCLGKDN-----KANNCGIIYCRTREHTTDLADALRR-------- 322
           + ++D Y H++++IE  L K++         CGIIYCRTRE T  +A++L +        
Sbjct: 460 NSIQDDYIHLRDYIESILEKEDVDVKPSKKACGIIYCRTRETTERVANSLSKLGLKAAAY 519

Query: 323 --KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGR 380
              + + ER  VQE +M G+  VI+ATISFGMG+D+ +VRFV+HW +P ++ +YYQESGR
Sbjct: 520 HAGLKQSERVAVQEDWMDGKYPVISATISFGMGVDKGSVRFVIHWDIPQNVASYYQESGR 579

Query: 381 AGRDGLQSYCRIYHSEHSKKSLEYVIKTD---------TSTKREQLELKFKNYLSMLEYC 431
           AGRDG +SYCRIYH     KS++++++ D            K ++ +L  KN+  ++++C
Sbjct: 580 AGRDGKKSYCRIYHCREQCKSIDFLLRQDLGKSKDKDGKEDKHDKAKLAVKNFEKIVDFC 639

Query: 432 EQGY 435
           E  Y
Sbjct: 640 ESAY 643

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270009277|gb|EFA05725.1| homolog of RecQ [Tribolium castaneum]

 Score =  311 bits (797), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 169/433 (39%), Positives = 259/433 (59%), Gaps = 44/433 (10%)

Query: 26   RKGGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVS 85
            +K  ++ E  + A LK+ F FDSFK ELQ+ A+  I  R HD+ VSMPTG+    G  + 
Sbjct: 903  KKPSEMDESTIKAALKSAFKFDSFKSELQQAAVTEICQRQHDVLVSMPTGS----GKSLC 958

Query: 86   ARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSG 145
             +    + P    I+           SP+L+   ++ + D  + +  R+     + + S 
Sbjct: 959  YQLPAVLRPNQTTIV----------FSPLLA--LIKDQIDHLNALKIRA-----KSLNSK 1001

Query: 146  QTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVS 205
             +K++  A++ +L+  +P  +LLY+TPE+A T++F  L  +LV+++K+A++VVDEAHCVS
Sbjct: 1002 TSKSDRDALIADLKSTQPLTRLLYITPEQAATKTFKSLYDNLVKFDKVAFVVVDEAHCVS 1061

Query: 206  EWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFR 265
            +WGHDFRP Y +LGELR      IP +ALTATA   V +DII+ LK     K+FKTS FR
Sbjct: 1062 QWGHDFRPDYLKLGELR---AKKIPFVALTATAGAEVTKDIITSLKL-ADLKLFKTSCFR 1117

Query: 266  SNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDL--------- 316
            +NL+YDV+F +L+++ + H+K+FI  CL     + +CGI+YCRTRE T  +         
Sbjct: 1118 ANLYYDVLFQNLIENEFLHLKKFIVGCL---EDSQDCGIVYCRTREQTEAVTFKLNSLGL 1174

Query: 317  -ADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYY 375
             A A    +   ER + QE + RG+  VI ATISFGMG+D+  VRFVVHWG+P    ++Y
Sbjct: 1175 KARAYHAGLKNTERLQCQEEWQRGDSQVICATISFGMGVDKATVRFVVHWGVPKDPASFY 1234

Query: 376  QESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK------TDTSTKREQLELKFKNYLSMLE 429
            QESGRAGRDG  + CRIY++    +++ + +        D  +++ + E   K++  M+E
Sbjct: 1235 QESGRAGRDGKPAKCRIYYNRGDSRAILFHLNHDLGKAKDKQSRKIKAENALKSFKKMVE 1294

Query: 430  YCEQGYFLVILVF 442
            +CE   +    +F
Sbjct: 1295 FCENSDYCRHKLF 1307

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|334322907|ref|XP_001377617.2| PREDICTED: ATP-dependent DNA helicase Q5 [Monodelphis domestica]

 Score =  310 bits (794), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 173/420 (41%), Positives = 244/420 (58%), Gaps = 42/420 (10%)

Query: 33  EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRI 92
           EQ +   LK +FGFDSFK  LQ+ A   ++    D+FV MPTGA    G  +  +    +
Sbjct: 14  EQRVRRTLKKIFGFDSFKTNLQENATMAVVKGEKDVFVCMPTGA----GKSLCYQLPALL 69

Query: 93  PPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENK 152
             G   +           ISP+++      +D    ++  +  +  L   +S Q   E K
Sbjct: 70  AAGITIV-----------ISPLIA----LIQDQVDHLLALKVHVCSLNSKLSAQ---ERK 111

Query: 153 AILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFR 212
            IL +L   KP+ K+LY+TPE A + SF  +L  LV  + L+Y+VVDEAHCVS+WGHDFR
Sbjct: 112 KILMDLEKEKPQTKILYITPEMAASASFQPILNSLVSRHLLSYLVVDEAHCVSQWGHDFR 171

Query: 213 PTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDV 272
           P Y RLG LR    ++ P +ALTATA   V++D+++ LK  +P  +FKTS FR+NLFYDV
Sbjct: 172 PDYLRLGALRNRIPDA-PCVALTATATQKVQEDVVTALKLRQPVAIFKTSCFRANLFYDV 230

Query: 273 IFDDLLKDSYAHVKEFIEKCLGKDNKA---NNCGIIYCRTREHTTDLADALRRK------ 323
            F DLL D Y ++K+F  K LG+ N     ++CGIIYCRTRE    LA  L  +      
Sbjct: 231 QFKDLLGDPYGNLKDFCLKALGQKNDKGAFSSCGIIYCRTREACEQLATELSSRGVKAKA 290

Query: 324 ----VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESG 379
               +   +R  VQ  +M  ++ VI ATISFGMG+D+ NVRFV HW +  S+  YYQESG
Sbjct: 291 YHAGLKAEDRMLVQNEWMEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESG 350

Query: 380 RAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSM------LEYCEQ 433
           RAGRDGL S+CR+Y+S   +  + ++IK + S  +E+   K  +  SM      +++CE+
Sbjct: 351 RAGRDGLPSWCRLYYSRKDRDQVSFLIKKEISKLQEKRGNKDSDKASMAAFEAVVDFCEK 410

Source: Monodelphis domestica

Species: Monodelphis domestica

Genus: Monodelphis

Family: Didelphidae

Order: Didelphimorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|242008765|ref|XP_002425170.1| DNA helicase recq5, putative [Pediculus humanus corporis] gi|212508872|gb|EEB12432.1| DNA helicase recq5, putative [Pediculus humanus corporis]

 Score =  310 bits (793), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 176/420 (41%), Positives = 246/420 (58%), Gaps = 44/420 (10%)

Query: 35  ELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPP 94
           +L  KLK  FG D F+ E+Q+ AI+ +L    D+++SMPTG         S +S     P
Sbjct: 3   KLLEKLKTYFGHDRFRSEIQENAIKTVLKGNQDVYISMPTG---------SGKSLCFQLP 53

Query: 95  GADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAI 154
               +L  N  +     SP++S         K  I   +    +   + S   + +  A 
Sbjct: 54  A---VLQENKVAI--VFSPLISLM-------KDQIDHLKKLNIKAVTLNSKMNEKDRTAT 101

Query: 155 LEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPT 214
           +  L+ VK  I L YV PE+  + +F  LL +L     ++Y VVDEAHC+S+WGHDFR  
Sbjct: 102 INGLKAVKCDISLFYVAPEQIKSATFLSLLTYLYSKKMISYFVVDEAHCISQWGHDFRSE 161

Query: 215 YRRLGELR-QFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVI 273
           Y +LG LR +F G  IP IALTATA   V++DII+ LK N+P+  FK   FR NL+YDV+
Sbjct: 162 YLKLGSLRIKFPG--IPYIALTATASCEVEKDIINNLKLNRPFGKFKVPCFRKNLYYDVV 219

Query: 274 FDDLLKDSYAHVKEFIEKCLGKDNKANN-----CGIIYCRTREHTTDLADALRRK----- 323
           F D+L D   H+K FI+KCL + +K         GIIYCRTRE T D+   L +K     
Sbjct: 220 FRDILDDDVEHLKTFIDKCLAQTSKTEKKSMLPSGIIYCRTRESTEDIVKLLLKKGLTIQ 279

Query: 324 -----VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQES 378
                ++  +R +VQ  +M G+  VI+AT+SFGMGID+  VRFVVHWGMP S+ AYYQES
Sbjct: 280 AYHAGLSDKQRIQVQNDWMSGKCPVISATVSFGMGIDKAAVRFVVHWGMPQSVAAYYQES 339

Query: 379 GRAGRDGLQSYCRIYHSEHSKKSLEYVIKTD-----TSTKREQLELKFKNYLSMLEYCEQ 433
           GRAGRDGL S CRIY+S+  +  +++++KT+     T  K E+ +L +K+Y  M+ YCE+
Sbjct: 340 GRAGRDGLPSLCRIYYSKIERDRVDFILKTEARKAKTEDKVEKAKLAYKSYERMVRYCEE 399

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357627528|gb|EHJ77194.1| DNA helicase recq5 [Danaus plexippus]

 Score =  310 bits (793), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 161/418 (38%), Positives = 246/418 (58%), Gaps = 43/418 (10%)

Query: 36  LTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPG 95
           +T KL   FG   FK ELQ++A+R I    HD+FVSMPTG+                  G
Sbjct: 4   VTEKLLQCFGHRRFKSELQERAVRAIARGVHDVFVSMPTGS------------------G 45

Query: 96  ADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAIL 155
                      +   ++ + S      +D    +   +      E I S  T+ + + +L
Sbjct: 46  KSLCFQLPAMLQENKVAVVFSPLLALIKDQVDHLTKLK---IAAESINSKMTQKDRERVL 102

Query: 156 EELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTY 215
            +LR +KP  + LYVTPE+A T +F  L++HLV+Y K++Y+VVDEAHCVSEWGHDFRP Y
Sbjct: 103 NDLRSMKPNTRFLYVTPEQAATGTFKALMEHLVKYKKVSYVVVDEAHCVSEWGHDFRPDY 162

Query: 216 RRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFD 275
            +LG LR+    SIP +ALTATA   V +DI+  LK   P   +KT +FR NL+YDV++ 
Sbjct: 163 LKLGNLRE-KFKSIPWVALTATASAEVTKDILENLKLLNPVAQYKTPSFRRNLYYDVVYQ 221

Query: 276 DLLKDSYAHVKEFIEKCLGKDN-----KANNCGIIYCRTREHTTDLADALRRK------- 323
           + ++D    + EF++K L KD      K  +  I+YCRTRE T D+A  L ++       
Sbjct: 222 NCIQDEIGDLVEFLKKNL-KDEISVKPKDKSAAIVYCRTREQTEDIASMLTKRGLNCLAY 280

Query: 324 ---VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGR 380
              +   ER  VQ+ +  GE+  ++AT+SFGMG+D+ +VR VVHWG+P ++ AYYQESGR
Sbjct: 281 HGGLKSSERVSVQDRWSNGEVPCVSATVSFGMGVDKASVRAVVHWGLPQNVAAYYQESGR 340

Query: 381 AGRDGLQSYCRIYHSEHSKKSLEYVIKTD-----TSTKREQLELKFKNYLSMLEYCEQ 433
           AGRDG  ++CRIY+    + ++++++K++     T  ++++ +  +K++  M++YCE+
Sbjct: 341 AGRDGKPAFCRIYYCRSERNAVDFLLKSEIARSKTPEQKQRCKNAYKSFEVMVKYCEE 398

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193786741|dbj|BAG52064.1| unnamed protein product [Homo sapiens]

 Score =  305 bits (782), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 168/419 (40%), Positives = 245/419 (58%), Gaps = 41/419 (9%)

Query: 33  EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRI 92
           E+ + + LK +FGFDSFK  LQ+ A   ++    D+FV MPTGA    G  +  +    +
Sbjct: 13  ERRVRSTLKKVFGFDSFKTPLQESATMAVVKGNKDVFVCMPTGA----GKSLCYQLPALL 68

Query: 93  PPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENK 152
             G   +           +SP+++      +D    ++T +  +  L   +S Q   E K
Sbjct: 69  AKGNTIV-----------VSPLIA----LIQDQVDHLLTLKVRVSSLNSKLSAQ---ERK 110

Query: 153 AILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFR 212
            +L +L   KP+ K+LY+TPE A + SF   L  LV  + L+Y+VVDEAHCVS+WGHDFR
Sbjct: 111 ELLADLEREKPQTKILYITPEMAASSSFQPTLNSLVSRHLLSYLVVDEAHCVSQWGHDFR 170

Query: 213 PTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDV 272
           P Y RLG LR   G++ P +ALTATA P V++D+ + L   KP  +FKT  FR+NLFYDV
Sbjct: 171 PDYLRLGALRSRLGHA-PCVALTATATPQVQEDVFAALHLKKPVAIFKTPCFRANLFYDV 229

Query: 273 IFDDLLKDSYAHVKEFIEKCLGK--DNKANNCGIIYCRTREHTTDLADALR-RKVNKH-- 327
            F +L+ D Y ++K+F  K LG+  D   + CGI+YCRTRE    LA  L  R VN    
Sbjct: 230 QFKELISDPYGNLKDFCLKALGQEADKGLSGCGIVYCRTREACEQLAIELSCRGVNAKAY 289

Query: 328 -------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGR 380
                  ER+ VQ  +M  ++ VI ATISFGMG+D+ NVRFV HW +  S+  YYQESGR
Sbjct: 290 HAGLKASERTLVQNDWMEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGR 349

Query: 381 AGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKN------YLSMLEYCEQ 433
           AGRDG  S+CR+Y+S + +  + ++I+ + +  +E+   K  +      + +++ +CE+
Sbjct: 350 AGRDGKPSWCRLYYSRNDRDQVSFLIRKEVAKLQEKRGNKASDKATIMAFDALVTFCEE 408

Source: Homo sapiens

Species: Homo sapiens

Genus: Homo

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

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	444
UNIPROTKB|Q6P4G0	964	RECQL5 "ATP-dependent DNA heli	0.680	0.313	0.449	2e-72
UNIPROTKB|J3KTQ2	480	RECQL5 "ATP-dependent DNA heli	0.813	0.752	0.411	4.1e-72
UNIPROTKB|O94762	991	RECQL5 "ATP-dependent DNA heli	0.813	0.364	0.411	4.1e-72
UNIPROTKB|E1BKM5	987	RECQL5 "Uncharacterized protei	0.844	0.379	0.404	2.9e-71
UNIPROTKB|I3LFW3	432	RECQL5 "Uncharacterized protei	0.813	0.835	0.411	6.1e-71
RGD|1310823	973	Recql5 "RecQ protein-like 5" [	0.844	0.385	0.401	6.1e-71
UNIPROTKB|F1PAG8	989	RECQL5 "Uncharacterized protei	0.844	0.379	0.399	3.3e-69
UNIPROTKB|F1NT69	451	F1NT69 "Uncharacterized protei	0.797	0.784	0.415	1.9e-67
UNIPROTKB|F1NWK5	1023	F1NWK5 "Uncharacterized protei	0.797	0.346	0.415	5.4e-67
FB|FBgn0027375	1058	RecQ5 "homolog of RecQ" [Droso	0.842	0.353	0.368	1.6e-55

UNIPROTKB|Q6P4G0 RECQL5 "ATP-dependent DNA helicase Q5" [Homo sapiens (taxid:9606)]

 Score = 685 (246.2 bits), Expect = 2.0e-72, Sum P(2) = 2.0e-72
 Identities = 143/318 (44%), Positives = 200/318 (62%)

Query:   111 ISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYV 170
             I+ ++S      +D    ++T +  +  L   +S Q   E K +L +L   KP+ K+LY+
Sbjct:    45 ITIVVSPLIALIQDQVDHLLTLKVRVSSLNSKLSAQ---ERKELLADLEREKPQTKILYI 101

Query:   171 TPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIP 230
             TPE A + SF   L  LV  + L+Y+VVDEAHCVS+WGHDFRP Y RLG LR   G++ P
Sbjct:   102 TPEMAASSSFQPTLNSLVSRHLLSYLVVDEAHCVSQWGHDFRPDYLRLGALRSRLGHA-P 160

Query:   231 IIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIE 290
              +ALTATA P V++D+ + L   KP  +FKT  FR+NLFYDV F +L+ D Y ++K+F  
Sbjct:   161 CVALTATATPQVQEDVFAALHLKKPVAIFKTPCFRANLFYDVQFKELISDPYGNLKDFCL 220

Query:   291 KCLGK--DNKANNCGIIYCRTREHTTDLADALR-RKVNK---H------ERSRVQESFMR 338
             K LG+  D   + CGI+YCRTRE    LA  L  R VN    H      ER+ VQ  +M 
Sbjct:   221 KALGQEADKGLSGCGIVYCRTREACEQLAIELSCRGVNAKAYHAGLKASERTLVQNDWME 280

Query:   339 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS 398
              ++ VI ATISFGMG+D+ NVRFV HW +  S+  YYQESGRAGRDG  S+CR+Y+S + 
Sbjct:   281 EKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGRAGRDGKPSWCRLYYSRND 340

Query:   399 KKSLEYVIKTDTSTKREQ 416
             +  + ++I+ + +  +E+
Sbjct:   341 RDQVSFLIRKEVAKLQEK 358

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|J3KTQ2 RECQL5 "ATP-dependent DNA helicase Q5" [Homo sapiens (taxid:9606)]

 Score = 729 (261.7 bits), Expect = 4.1e-72, P = 4.1e-72
 Identities = 163/396 (41%), Positives = 231/396 (58%)

Query:    33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTXXXXXXXXXXXXXXXXXI 92
             E+ + + LK +FGFDSFK  LQ+ A   ++    D+FV MPT                 +
Sbjct:    13 ERRVRSTLKKVFGFDSFKTPLQESATMAVVKGNKDVFVCMPTGAGKSLCYQLPAL----L 68

Query:    93 PPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENK 152
               G   +           +SP+++      +D    ++T +  +  L   +S Q   E K
Sbjct:    69 AKGITIV-----------VSPLIALI----QDQVDHLLTLKVRVSSLNSKLSAQ---ERK 110

Query:   153 AILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFR 212
              +L +L   KP+ K+LY+TPE A + SF   L  LV  + L+Y+VVDEAHCVS+WGHDFR
Sbjct:   111 ELLADLEREKPQTKILYITPEMAASSSFQPTLNSLVSRHLLSYLVVDEAHCVSQWGHDFR 170

Query:   213 PTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDV 272
             P Y RLG LR   G++ P +ALTATA P V++D+ + L   KP  +FKT  FR+NLFYDV
Sbjct:   171 PDYLRLGALRSRLGHA-PCVALTATATPQVQEDVFAALHLKKPVAIFKTPCFRANLFYDV 229

Query:   273 IFDDLLKDSYAHVKEFIEKCLGK--DNKANNCGIIYCRTREHTTDLADALR-RKVNK--- 326
              F +L+ D Y ++K+F  K LG+  D   + CGI+YCRTRE    LA  L  R VN    
Sbjct:   230 QFKELISDPYGNLKDFCLKALGQEADKGLSGCGIVYCRTREACEQLAIELSCRGVNAKAY 289

Query:   327 H------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGR 380
             H      ER+ VQ  +M  ++ VI ATISFGMG+D+ NVRFV HW +  S+  YYQESGR
Sbjct:   290 HAGLKASERTLVQNDWMEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGR 349

Query:   381 AGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQ 416
             AGRDG  S+CR+Y+S + +  + ++I+ + +  +E+
Sbjct:   350 AGRDGKPSWCRLYYSRNDRDQVSFLIRKEVAKLQEK 385

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|O94762 RECQL5 "ATP-dependent DNA helicase Q5" [Homo sapiens (taxid:9606)]

 Score = 729 (261.7 bits), Expect = 4.1e-72, P = 4.1e-72
 Identities = 163/396 (41%), Positives = 231/396 (58%)

Query:    33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTXXXXXXXXXXXXXXXXXI 92
             E+ + + LK +FGFDSFK  LQ+ A   ++    D+FV MPT                 +
Sbjct:    13 ERRVRSTLKKVFGFDSFKTPLQESATMAVVKGNKDVFVCMPTGAGKSLCYQLPAL----L 68

Query:    93 PPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENK 152
               G   +           +SP+++      +D    ++T +  +  L   +S Q   E K
Sbjct:    69 AKGITIV-----------VSPLIALI----QDQVDHLLTLKVRVSSLNSKLSAQ---ERK 110

Query:   153 AILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFR 212
              +L +L   KP+ K+LY+TPE A + SF   L  LV  + L+Y+VVDEAHCVS+WGHDFR
Sbjct:   111 ELLADLEREKPQTKILYITPEMAASSSFQPTLNSLVSRHLLSYLVVDEAHCVSQWGHDFR 170

Query:   213 PTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDV 272
             P Y RLG LR   G++ P +ALTATA P V++D+ + L   KP  +FKT  FR+NLFYDV
Sbjct:   171 PDYLRLGALRSRLGHA-PCVALTATATPQVQEDVFAALHLKKPVAIFKTPCFRANLFYDV 229

Query:   273 IFDDLLKDSYAHVKEFIEKCLGK--DNKANNCGIIYCRTREHTTDLADALR-RKVNK--- 326
              F +L+ D Y ++K+F  K LG+  D   + CGI+YCRTRE    LA  L  R VN    
Sbjct:   230 QFKELISDPYGNLKDFCLKALGQEADKGLSGCGIVYCRTREACEQLAIELSCRGVNAKAY 289

Query:   327 H------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGR 380
             H      ER+ VQ  +M  ++ VI ATISFGMG+D+ NVRFV HW +  S+  YYQESGR
Sbjct:   290 HAGLKASERTLVQNDWMEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGR 349

Query:   381 AGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQ 416
             AGRDG  S+CR+Y+S + +  + ++I+ + +  +E+
Sbjct:   350 AGRDGKPSWCRLYYSRNDRDQVSFLIRKEVAKLQEK 385

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003678 "DNA helicase activity" evidence=NAS

GO:0005654 "nucleoplasm" evidence=NAS

GO:0005737 "cytoplasm" evidence=IDA;NAS

GO:0006259 "DNA metabolic process" evidence=NAS

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IDA

GO:0006281 "DNA repair" evidence=TAS

GO:0032508 "DNA duplex unwinding" evidence=NAS;TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0031965 "nuclear membrane" evidence=IDA

UNIPROTKB|E1BKM5 RECQL5 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 721 (258.9 bits), Expect = 2.9e-71, P = 2.9e-71
 Identities = 166/410 (40%), Positives = 235/410 (57%)

Query:    33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTXXXXXXXXXXXXXXXXXI 92
             E+ + + LK +FGFDSFK  LQ+KAI  ++    D+FV MPT                 +
Sbjct:    12 ERRVRSTLKKVFGFDSFKTPLQEKAIMAVVKGDKDVFVCMPTGAGKSLCYQLPAL----L 67

Query:    93 PPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENK 152
               G   +           +SP+++      +D    ++  +  +  L   +S Q   E K
Sbjct:    68 AKGITIV-----------VSPLIALI----QDQVDHLLALKVRVSSLNSKLSVQ---ERK 109

Query:   153 AILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFR 212
              +L +L   KP+ KLLY+TPE A + SF   L  LV  + L+Y+VVDEAHCVS+WGHDFR
Sbjct:   110 ELLSDLEQEKPQTKLLYITPEMAASTSFQPTLNSLVSRHLLSYLVVDEAHCVSQWGHDFR 169

Query:   213 PTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDV 272
             P Y RLG LR    ++ P +ALTATA P V++D+ + L   +P   FKT  FR+NLFYDV
Sbjct:   170 PDYLRLGALRSRLADA-PCVALTATATPQVREDVFAALHLKQPVATFKTPCFRANLFYDV 228

Query:   273 IFDDLLKDSYAHVKEFIEKCLGK--DNKANNCGIIYCRTREHTTDLADALR-RKVNK--- 326
              F +LL D Y ++++F  K LG+  D   + CGIIYCRTRE    LA  L  R VN    
Sbjct:   229 QFKELLPDPYGNLRDFCLKALGQKADKGLSGCGIIYCRTREACEQLATELSYRGVNAKAY 288

Query:   327 H------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGR 380
             H      ER+ VQ  +M  ++ VI ATISFGMG+D+ NVRFV HW +  S+  YYQESGR
Sbjct:   289 HAGLKAPERTLVQNEWMEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGR 348

Query:   381 AGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEY 430
             AGRDG  S+CR+Y+S   +  + ++I+ + +  +E+   K  +  ++L +
Sbjct:   349 AGRDGKPSWCRLYYSRSDRDQVSFLIRKEVAKLQEKRGNKASDKAAVLAF 398

GO:0031965 "nuclear membrane" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0006310 "DNA recombination" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|I3LFW3 RECQL5 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 163/396 (41%), Positives = 230/396 (58%)

Query:    33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTXXXXXXXXXXXXXXXXXI 92
             E+ + + LK +FGFDSFK  LQ+ AI  ++    D+FV MPT                 +
Sbjct:     9 ERRVRSTLKKVFGFDSFKTPLQESAIMAVVKGDKDVFVCMPTGAGKSLCYQLPAL----L 64

Query:    93 PPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENK 152
               G   +           ISP+++      +D    ++  +  +  L   +S Q   E K
Sbjct:    65 AKGITIV-----------ISPLIALI----QDQVDHLLALKIHVCSLNSKLSAQ---ERK 106

Query:   153 AILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFR 212
              +L +L   KPR KLLY+TPE A + SF   L+ L+  + L+Y+VVDEAHCVS+WGHDFR
Sbjct:   107 ELLSDLEQEKPRTKLLYITPEMAASASFQPTLKSLLARHLLSYLVVDEAHCVSQWGHDFR 166

Query:   213 PTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDV 272
             P Y RLG LR    ++ P +ALTATA   V++D+ + L   +P   FKT  FR+NLFYDV
Sbjct:   167 PDYLRLGALRSRLAHA-PCVALTATATLQVQEDVFAALHLKQPVATFKTPCFRANLFYDV 225

Query:   273 IFDDLLKDSYAHVKEFIEKCLGK--DNKANNCGIIYCRTREHTTDLADALR-RKVNK--- 326
              F +LL D Y ++++F  K LG+  D   + CGI+YCRTRE    LA  L  R VN    
Sbjct:   226 QFKELLSDPYGNLRDFCLKALGQKADKGLSGCGIVYCRTREACEQLAIELSARGVNAKAY 285

Query:   327 H------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGR 380
             H      ER+ VQ  +M G++ VI ATISFGMG+D+ NVRFV HW +  S+  YYQESGR
Sbjct:   286 HAGLKAAERTLVQNEWMEGKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGR 345

Query:   381 AGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQ 416
             AGRDG  S+CR+Y+S + +  + ++I+ + +  +E+
Sbjct:   346 AGRDGRPSWCRLYYSRNDRDQVSFLIRKEVAKLQEK 381

GO:0031965 "nuclear membrane" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0006310 "DNA recombination" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

RGD|1310823 Recql5 "RecQ protein-like 5" [Rattus norvegicus (taxid:10116)]

 Score = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 165/411 (40%), Positives = 238/411 (57%)

Query:    33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTXXXXXXXXXXXXXXXXXI 92
             E+ + + LK +FGFDSFK  LQ+ AI  ++    D+FV MPT                 +
Sbjct:    13 ERRVRSTLKKVFGFDSFKTPLQESAIMAVVKGDKDVFVCMPTGAGKSLCYQLPAV----L 68

Query:    93 PPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENK 152
               G   +           +SP+++      +D    ++  +  +  L   +S Q   E K
Sbjct:    69 AKGITIV-----------VSPLIALI----QDQVDHLLALKVQVSSLNSKLSVQ---ERK 110

Query:   153 AILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFR 212
              +L +L   KPR KLLY+TPE A + SF   L  L+  N L+Y+VVDEAHCVS+WGHDFR
Sbjct:   111 ELLSDLERDKPRTKLLYITPEMAASASFQPTLNSLLSRNLLSYLVVDEAHCVSQWGHDFR 170

Query:   213 PTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDV 272
             P Y RLG LR    ++ P +ALTATA P V++D+ + L   +P   FKT  FR+NLFYDV
Sbjct:   171 PDYLRLGALRSRLAHA-PCVALTATATPQVQEDVFAALHLKQPVASFKTPCFRANLFYDV 229

Query:   273 IFDDLLKDSYAHVKEFIEKCLGK--DN-KANNCGIIYCRTREHTTDLADALR-RKVNK-- 326
              F +L+ D Y ++++F  K LG+  DN  ++ CGI+YCRTRE    LA  L  R VN   
Sbjct:   230 QFKELIPDVYGNLRDFCLKALGQKADNGSSSGCGIVYCRTREACEQLAIELSSRGVNAKA 289

Query:   327 -H------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESG 379
              H      ER++VQ  +M  ++ VI ATISFGMG+D+ NVRFV HW +  S+  YYQESG
Sbjct:   290 YHAGLKASERTQVQNEWMEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESG 349

Query:   380 RAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEY 430
             RAGRDG  S+CR+Y+S + +  + ++I+ + +  +E+   K  +  ++L +
Sbjct:   350 RAGRDGKPSWCRLYYSRNDRDQVSFLIRKELAKLQEKRGNKPSDKATLLAF 400

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005730 "nucleolus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA;ISO

GO:0031965 "nuclear membrane" evidence=IEA;ISO

UNIPROTKB|F1PAG8 RECQL5 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 702 (252.2 bits), Expect = 3.3e-69, P = 3.3e-69
 Identities = 164/411 (39%), Positives = 234/411 (56%)

Query:    33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTXXXXXXXXXXXXXXXXXI 92
             E+ + + LK +FGFDSFK  LQ+ A   ++    D+FV MPT                 +
Sbjct:     9 ERRVRSTLKKVFGFDSFKTPLQESATMAVVRGDKDVFVCMPTGAGKSLCYQLPAL----L 64

Query:    93 PPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENK 152
               G   +           +SP+++      +D    ++  +  +  L   +S Q   E K
Sbjct:    65 AKGITIV-----------VSPLIALI----QDQVDHLLALKVRVSSLNSKLSAQ---EKK 106

Query:   153 AILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFR 212
              +L +L   KP+ KLLY+TPE A + SF   L  LV  + L+Y+VVDEAHCVS+WGHDFR
Sbjct:   107 ELLSDLEREKPQTKLLYITPEMAASPSFQPTLNSLVSRHLLSYLVVDEAHCVSQWGHDFR 166

Query:   213 PTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDV 272
             P Y RLG LR    ++ P IALTATA   V++D+ + L   +P   FKT  FR+NLFYDV
Sbjct:   167 PDYLRLGTLRSRLAHA-PCIALTATATLQVQEDVFAALHLKQPVATFKTPCFRANLFYDV 225

Query:   273 IFDDLLKDSYAHVKEFIEKCLG-KDNKA--NNCGIIYCRTREHTTDLADALR-RKVNK-- 326
              F +LL D Y ++++F  K LG K +K   + CGI+YCRTRE    LA  L  R VN   
Sbjct:   226 QFKELLSDPYGNLRDFCLKALGQKADKGLLSGCGIVYCRTREACEQLATELSYRGVNAKA 285

Query:   327 -H------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESG 379
              H      ER+ VQ  +M  ++ VI ATISFGMG+D+ NVRFV HW +  S+  YYQESG
Sbjct:   286 YHAGLKASERTLVQNEWMEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESG 345

Query:   380 RAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEY 430
             RAGRDG  S+CR+Y+S + +  + ++I+ + +  +E+   K  +  ++L +
Sbjct:   346 RAGRDGKPSWCRLYYSRNDRDQVSFLIRKEVAKLQEKRGNKASDKAAILAF 396

GO:0005524 "ATP binding" evidence=IEA

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

GO:0006310 "DNA recombination" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1NT69 F1NT69 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 685 (246.2 bits), Expect = 1.9e-67, P = 1.9e-67
 Identities = 162/390 (41%), Positives = 218/390 (55%)

Query:    40 LKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTXXXXXXXXXXXXXXXXXIPPGADFI 99
             L  +FGF+SFK  LQ+ A   ++    D+FV MPT                 +  G   +
Sbjct:    25 LGKVFGFESFKTSLQESATMAVVRGEKDVFVCMPTGAGKSLCYQLPAV----LAVGITIV 80

Query:   100 LNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELR 159
                        ISP+++      +D    ++  +     L   +S Q   E K IL +L 
Sbjct:    81 -----------ISPLIALI----QDQVDHLLALKIKACSLNSKLSAQ---EKKTILADLA 122

Query:   160 LVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLG 219
               KP+IKLLY+TPE A   SF   L  LV  N L+Y+++DEAHCVS+WGHDFRP Y RLG
Sbjct:   123 SEKPQIKLLYITPEMAAASSFQPTLNSLVSRNLLSYLIIDEAHCVSQWGHDFRPDYLRLG 182

Query:   220 ELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLK 279
              LR    N+ P +ALTATA   V+ DI++ LK  +P   FKT  FRSNLFYDV F +LL 
Sbjct:   183 TLRTRIPNT-PCVALTATATKQVQDDIVTALKLKQPLATFKTPCFRSNLFYDVQFKELLT 241

Query:   280 DSYAHVKEFIEKCLGKDNKA---NNCGIIYCRTREHTTDLADALRRKVNK----H----- 327
             D YA++K+F  K L   N     + CGI+YCR R+    LA  L  +  K    H     
Sbjct:   242 DPYANLKDFCLKALEVKNTTGVYSGCGIVYCRMRDVCDQLAIELSYRGVKAKAYHAGLKA 301

Query:   328 -ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGL 386
              +R+ VQ  +M  +I VI ATISFGMG+D+ NVRFV HW +  S+  YYQESGRAGRDG 
Sbjct:   302 ADRTSVQNEWMEEKIPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGRAGRDGK 361

Query:   387 QSYCRIYHSEHSKKSLEYVIKTDTSTKREQ 416
              S CR+Y+S + +  + ++IK + S  +E+
Sbjct:   362 PSCCRLYYSRNDRDQVSFLIKKELSKIQEK 391

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0031965 "nuclear membrane" evidence=IEA

UNIPROTKB|F1NWK5 F1NWK5 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 685 (246.2 bits), Expect = 5.4e-67, P = 5.4e-67
 Identities = 162/390 (41%), Positives = 218/390 (55%)

Query:    40 LKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTXXXXXXXXXXXXXXXXXIPPGADFI 99
             L  +FGF+SFK  LQ+ A   ++    D+FV MPT                 +  G   +
Sbjct:    25 LGKVFGFESFKTSLQESATMAVVRGEKDVFVCMPTGAGKSLCYQLPAV----LAVGITIV 80

Query:   100 LNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELR 159
                        ISP+++      +D    ++  +     L   +S Q   E K IL +L 
Sbjct:    81 -----------ISPLIALI----QDQVDHLLALKIKACSLNSKLSAQ---EKKTILADLA 122

Query:   160 LVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLG 219
               KP+IKLLY+TPE A   SF   L  LV  N L+Y+++DEAHCVS+WGHDFRP Y RLG
Sbjct:   123 SEKPQIKLLYITPEMAAASSFQPTLNSLVSRNLLSYLIIDEAHCVSQWGHDFRPDYLRLG 182

Query:   220 ELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLK 279
              LR    N+ P +ALTATA   V+ DI++ LK  +P   FKT  FRSNLFYDV F +LL 
Sbjct:   183 TLRTRIPNT-PCVALTATATKQVQDDIVTALKLKQPLATFKTPCFRSNLFYDVQFKELLT 241

Query:   280 DSYAHVKEFIEKCLGKDNKA---NNCGIIYCRTREHTTDLADALRRKVNK----H----- 327
             D YA++K+F  K L   N     + CGI+YCR R+    LA  L  +  K    H     
Sbjct:   242 DPYANLKDFCLKALEVKNTTGVYSGCGIVYCRMRDVCDQLAIELSYRGVKAKAYHAGLKA 301

Query:   328 -ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGL 386
              +R+ VQ  +M  +I VI ATISFGMG+D+ NVRFV HW +  S+  YYQESGRAGRDG 
Sbjct:   302 ADRTSVQNEWMEEKIPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGRAGRDGK 361

Query:   387 QSYCRIYHSEHSKKSLEYVIKTDTSTKREQ 416
              S CR+Y+S + +  + ++IK + S  +E+
Sbjct:   362 PSCCRLYYSRNDRDQVSFLIKKELSKIQEK 391

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0031965 "nuclear membrane" evidence=IEA

FB|FBgn0027375 RecQ5 "homolog of RecQ" [Drosophila melanogaster (taxid:7227)]

 Score = 581 (209.6 bits), Expect = 1.6e-55, P = 1.6e-55
 Identities = 158/429 (36%), Positives = 231/429 (53%)

Query:    33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTXXXXXXXXXXXXXXXXXI 92
             E  +   LK  FG   FK +LQ+KA++  + +  D++VSMPT                  
Sbjct:     4 ESAVHEALKKHFGHSKFKSDLQEKAVKCAVKKKQDVYVSMPTGSGKSLC----------- 52

Query:    93 PPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENK 152
                  F L G + S N  I+ + S      +D    +   +     L   +S  TK  ++
Sbjct:    53 -----FQLPG-LMSENQ-ITIVFSPLLALIKDQIDHLTKLKVPADSLNSKMS--TKERDR 103

Query:   153 AILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFR 212
              I++ L+ V+  +K LY+TPE+A T+ F  LLQ L ++NKLAY  VDEAHCVS+WGHDFR
Sbjct:   104 VIMD-LKAVRTNLKFLYITPEQAATKFFQDLLQTLHKHNKLAYFAVDEAHCVSQWGHDFR 162

Query:   213 PTYRRLGELRQFTGNSIPI-IALTATAEPS---VKQDIIS--VLKFNKPYKVFKTSTFRS 266
             P Y +LGELR    + I + +  TA+ E      KQ  +   V +F+ P   F+ + F  
Sbjct:   163 PDYLKLGELRSKYSDVIWLALTATASREVKEDIYKQLRLHQPVAQFSTPS--FRKNLFYD 220

Query:   267 NLFYDVIFDDL--LKDSYAHV----KEFIEKCLGKDNKANNCGIIYCRTREHTTDLADAL 320
              ++ + I DD   L D   H     KEF  K   K  +   CGI+YCRTR+    +A  +
Sbjct:   221 IVYKNSIEDDFQHLADFARHCLGNPKEF--KDTPKPQRG--CGIVYCRTRDQVERMAIGV 276

Query:   321 RRK----VNKH------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSS 370
              ++    V  H      ER+ VQE++MRG+  +I AT SFGMG+D+ +VRFV+HW +P +
Sbjct:   277 TKQGIGAVAYHAGLKTGERTEVQEAWMRGDQPIICATNSFGMGVDKPSVRFVIHWDVPQN 336

Query:   371 IPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKR-----EQL-ELKFKNY 424
             + AYYQESGRAGRDGLQSYCR+Y+     +S+ ++++ D    R     E L E   K +
Sbjct:   337 VAAYYQESGRAGRDGLQSYCRLYYGREDVRSIRFLLQNDAHRARGRGDKELLTERAIKQF 396

Query:   425 LSMLEYCEQ 433
               + E+CE+
Sbjct:   397 EKITEFCER 405

GO:0004003 "ATP-dependent DNA helicase activity" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

GO:0003678 "DNA helicase activity" evidence=ISS

GO:0004386 "helicase activity" evidence=ISS

GO:0017116 "single-stranded DNA-dependent ATP-dependent DNA helicase activity" evidence=IDA

GO:0003924 "GTPase activity" evidence=IDA

GO:0005525 "GTP binding" evidence=IDA

GO:0006310 "DNA recombination" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0045930 "negative regulation of mitotic cell cycle" evidence=IMP

GO:0010165 "response to X-ray" evidence=IDA

GO:0045002 "double-strand break repair via single-strand annealing" evidence=IMP

GO:0090007 "regulation of mitotic anaphase" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.12	LOW CONFIDENCE 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	444
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	8e-87
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	2e-83
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	2e-78
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	2e-66
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	4e-61
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	4e-20
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	1e-14
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	2e-14
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	7e-13
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	5e-10
COG1205	851	COG1205, COG1205, Distinct helicase family with a	9e-10
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	2e-09
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	3e-09
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-07
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	2e-07
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	5e-06
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	1e-05
PRK02362	737	PRK02362, PRK02362, ski2-like helicase; Provisiona	1e-05
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	1e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-04
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	1e-04
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	3e-04
PRK09751	1490	PRK09751, PRK09751, putative ATP-dependent helicas	4e-04
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	0.001
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	0.002

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

 Score =  276 bits (707), Expect = 8e-87
 Identities = 139/414 (33%), Positives = 213/414 (51%), Gaps = 60/414 (14%)

Query: 34  QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRV-RI 92
           +E    LK +FG+ SF+   Q++ I  +L    D  V MPTG           +S   +I
Sbjct: 3   EEAQQVLKQVFGYASFR-PGQQEIIDALLSG-KDTLVVMPTG---------GGKSLCYQI 51

Query: 93  PPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENK 152
           P     +L G        +SP++S   L  +D    +    +   +   + S  ++ E +
Sbjct: 52  P---ALLLEGLTLV----VSPLIS---LM-KDQ---VDQLEAAGIRAAYLNSTLSREERQ 97

Query: 153 AILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFR 212
            +L   +L   ++KLLY++PER ++  F  LL+ L     ++ + +DEAHC+S+WGHDFR
Sbjct: 98  QVLN--QLKSGQLKLLYISPERLMSPRFLELLKRL----PISLVAIDEAHCISQWGHDFR 151

Query: 213 PTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDV 272
           P YRRLG LR    N  P++ALTATA P V+ DI   L       +F+ S  R NL   V
Sbjct: 152 PDYRRLGRLRAGLPN-PPVLALTATATPRVRDDIREQLGLQDA-NIFRGSFDRPNLALKV 209

Query: 273 IFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK--------- 323
           +      D  A +   + +           GIIYC TR+   +LA+ LR+          
Sbjct: 210 VEKGEPSDQLAFLATVLPQLSK-------SGIIYCLTRKKVEELAEWLRKNGISAGAYHA 262

Query: 324 -VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAG 382
            ++  ER RVQ++F+  EI V+ AT +FGMGID+ +VRFV+H+ +P SI +YYQE+GRAG
Sbjct: 263 GLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAG 322

Query: 383 RDGLQSYCRIYHSEHSKKSLEYVIKT----DTSTKREQLELKFKNYLSMLEYCE 432
           RDGL +   + +S    +   Y+I+     +   + E  +L+      M+ YCE
Sbjct: 323 RDGLPAEAILLYSPEDIRWQRYLIEQSKPDEEQKQIELAKLR-----QMIAYCE 371

Length = 590

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

 Score =  263 bits (674), Expect = 2e-83
 Identities = 145/413 (35%), Positives = 215/413 (52%), Gaps = 70/413 (16%)

Query: 40  LKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTG-AVSLVGSVVSARSRVRIPPGADF 98
           LK +FG  SF+  +Q + I + +L   D FV MPTG   SL           ++P     
Sbjct: 3   LKTVFGLSSFR-PVQLEVI-NAVLLGRDCFVVMPTGGGKSLC---------YQLPA---L 48

Query: 99  ILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLE-------LIVSGQTKTEN 151
             +G        ISP++S       +D+         + QL+        + S Q+K + 
Sbjct: 49  CSDGITLV----ISPLIS-----LMEDQ---------VLQLKASGIPATFLNSSQSKEQQ 90

Query: 152 KAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDF 211
           K +L +L+    +IKLLYVTPE+    +   LLQ L     +  I VDEAHC+S+WGHDF
Sbjct: 91  KNVLTDLKD--GKIKLLYVTPEKCSASN--RLLQTLEERKGITLIAVDEAHCISQWGHDF 146

Query: 212 RPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYD 271
           RP Y+ LG L+Q   N +PI+ALTATA PSV++DI+  L    P  +F TS  R NL+Y+
Sbjct: 147 RPDYKALGSLKQKFPN-VPIMALTATASPSVREDILRQLNLKNPQ-IFCTSFDRPNLYYE 204

Query: 272 VI--FDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------ 323
           V      +L+D    +  FI K     +     GIIYC +R+ +  +  +L+        
Sbjct: 205 VRRKTPKILED----LLRFIRKEFKGKS-----GIIYCPSRKKSEQVTASLQNLGIAAGA 255

Query: 324 ----VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESG 379
               +    R  V   F R EI V+ AT++FGMGI++ +VRFV+H+ +P S+ +YYQESG
Sbjct: 256 YHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESG 315

Query: 380 RAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCE 432
           RAGRDGL S C ++++      L  ++  +   ++   +LK      M+EYC 
Sbjct: 316 RAGRDGLPSECHLFYAPADINRLRRLLMEEPDGQQRTYKLKL---YEMMEYCL 365

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

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

 Score =  254 bits (650), Expect = 2e-78
 Identities = 139/410 (33%), Positives = 206/410 (50%), Gaps = 66/410 (16%)

Query: 40  LKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGA-VSLVGSVVSARSRVRIPPGADF 98
           LK  FG+D F+   Q++ I H+L    D+ V MPTG   SL   V          P    
Sbjct: 5   LKRTFGYDDFR-PGQEEIISHVL-DGRDVLVVMPTGGGKSLCYQV----------PA--L 50

Query: 99  ILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEEL 158
           +L G        ISP++S         K  +   R+       + S  +  E + I  E 
Sbjct: 51  LLKGLTVV----ISPLISLM-------KDQVDQLRAAGVAAAYLNSTLSAKEQQDI--EK 97

Query: 159 RLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRL 218
            LV   +KLLYV PER   + F  +LQ +     +A + VDEAHCVS+WGHDFRP Y+RL
Sbjct: 98  ALVNGELKLLYVAPERLEQDYFLNMLQRI----PIALVAVDEAHCVSQWGHDFRPEYQRL 153

Query: 219 GELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVI----- 273
           G L +     +P IALTATA+   +QDI  +L+     + F TS  R NL + V+     
Sbjct: 154 GSLAE-RFPQVPRIALTATADAETRQDIRELLRLADANE-FITSFDRPNLRFSVVKKNNK 211

Query: 274 FDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK---------- 323
              LL        ++++K  G+       GIIY  +R+   +LA+ L  +          
Sbjct: 212 QKFLL--------DYLKKHRGQS------GIIYASSRKKVEELAERLESQGISALAYHAG 257

Query: 324 VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGR 383
           ++   R+  QE F+  ++ V+ AT +FGMGID+ NVRFV+H+ MP ++ +YYQE+GRAGR
Sbjct: 258 LSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGR 317

Query: 384 DGLQSYCRIYHSEHSKKSLEYVIKTDTST-KREQLELKFKNYLSMLEYCE 432
           DGL +   + +S      L+  I+   +    +Q+E +     +M+ YCE
Sbjct: 318 DGLPAEAILLYSPADIALLKRRIEQSEADDDYKQIEREKLR--AMIAYCE 365

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

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

 Score =  222 bits (568), Expect = 2e-66
 Identities = 129/374 (34%), Positives = 196/374 (52%), Gaps = 65/374 (17%)

Query: 31  VSEQELTAK--LKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGA-VSLVGSVVSAR 87
           V   E  AK  L+  FG+  F+   Q   I   +L   D  V MPTG   SL        
Sbjct: 6   VLNLESLAKQVLQETFGYQQFRPGQQ--EIIDAVLSGRDCLVVMPTGGGKSLC------- 56

Query: 88  SRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQT 147
              +IP     +L+G        +SP++S         K  +    ++      + S QT
Sbjct: 57  --YQIPA---LVLDGLTLV----VSPLISLM-------KDQVDQLLANGVAAACLNSTQT 100

Query: 148 KTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEW 207
           + +   ++   R    +IKLLY+ PER + ++F   L+HL  +N  A + VDEAHC+S+W
Sbjct: 101 REQQLEVMAGCR--TGQIKLLYIAPERLMMDNF---LEHLAHWN-PALLAVDEAHCISQW 154

Query: 208 GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSN 267
           GHDFRP Y  LG+LRQ     +P +ALTATA+ + +QDI+ +L  N P  +  +S  R N
Sbjct: 155 GHDFRPEYAALGQLRQRFPT-LPFMALTATADDTTRQDIVRLLGLNDPL-IQISSFDRPN 212

Query: 268 LFYDVI-----FDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR 322
           + Y ++      D L++        ++++  GK       GIIYC +R    D A  L+ 
Sbjct: 213 IRYTLVEKFKPLDQLMR--------YVQEQRGK------SGIIYCNSRAKVEDTAARLQS 258

Query: 323 K----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIP 372
           +          ++   R+ VQE+F R ++ ++ AT++FGMGI++ NVRFVVH+ +P +I 
Sbjct: 259 RGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIE 318

Query: 373 AYYQESGRAGRDGL 386
           +YYQE+GRAGRDGL
Sbjct: 319 SYYQETGRAGRDGL 332

Length = 607

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

 Score =  214 bits (547), Expect = 4e-61
 Identities = 152/429 (35%), Positives = 226/429 (52%), Gaps = 69/429 (16%)

Query: 34  QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIP 93
           ++L    K +FG  SF+   Q++ I +  +  +D+FV MPTG     G  ++ +    I 
Sbjct: 446 KKLEVNNKKVFGNHSFRPN-QREII-NATMSGYDVFVLMPTGG----GKSLTYQLPALIC 499

Query: 94  PGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKA 153
           PG   +           ISP++S      +D   +++        L    +G    E   
Sbjct: 500 PGITLV-----------ISPLVS----LIQDQIMNLLQANIPAASLS---AGMEWAEQLE 541

Query: 154 ILEELRLVKPRIKLLYVTPER-AVTESFHYLLQHLVRYNK---LAYIVVDEAHCVSEWGH 209
           IL+EL     + KLLYVTPE+ A ++S   LL+HL   N    LA  V+DEAHCVS+WGH
Sbjct: 542 ILQELSSEYSKYKLLYVTPEKVAKSDS---LLRHLENLNSRGLLARFVIDEAHCVSQWGH 598

Query: 210 DFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLF 269
           DFRP Y+ LG L+Q   N IP++ALTATA  SVK+D++  L       VF+ S  R NL+
Sbjct: 599 DFRPDYQGLGILKQKFPN-IPVLALTATATASVKEDVVQALGLVNCV-VFRQSFNRPNLW 656

Query: 270 YDVI--FDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR----- 322
           Y V+      L+D    + +FI     K+N  + CGIIYC +R     +A+ L+      
Sbjct: 657 YSVVPKTKKCLED----IDKFI-----KENHFDECGIIYCLSRMDCEKVAERLQEFGHKA 707

Query: 323 -----KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQE 377
                 ++  +R+ VQ+ + + EIN+I AT++FGMGI++ +VRFV+H  +P SI  Y+QE
Sbjct: 708 AFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQE 767

Query: 378 SGRAGRDGLQSYCRIYHSEHSKKSLEYVI--------------KTDTSTKREQLELKFKN 423
            GRAGRDG +S C +Y+S      ++++I                  S+ R  LE   +N
Sbjct: 768 CGRAGRDGQRSSCVLYYSYSDYIRVKHMISQGGVEQSPMAMGYNRMASSGR-ILETNTEN 826

Query: 424 YLSMLEYCE 432
            L M+ YCE
Sbjct: 827 LLRMVSYCE 835

Length = 1195

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

 Score = 85.8 bits (213), Expect = 4e-20
 Identities = 38/137 (27%), Positives = 64/137 (46%), Gaps = 16/137 (11%)

Query: 267 NLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR---- 322
            +   V+  +  K     + E +++ L K  K     +I+C +++   +LA+ LR+    
Sbjct: 1   PIKQYVLPVEDEKLEA--LLELLKEHLKKGGKV----LIFCPSKKMLDELAELLRKPGIK 54

Query: 323 ------KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ 376
                   ++ ER  V + F  GEI V+ AT     GID  NV  V+++ +P S  +Y Q
Sbjct: 55  VAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQ 114

Query: 377 ESGRAGRDGLQSYCRIY 393
             GRAGR G +    + 
Sbjct: 115 RIGRAGRAGQKGTAILL 131

Length = 131

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

 Score = 68.3 bits (168), Expect = 1e-14
 Identities = 23/61 (37%), Positives = 35/61 (57%)

Query: 325 NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD 384
           ++ ER  + E F  G+  V+ AT   G GID  +V  V+++ +P +  +Y Q  GRAGR 
Sbjct: 18  SQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNPASYIQRIGRAGRA 77

Query: 385 G 385
           G
Sbjct: 78  G 78

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

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

 Score = 67.6 bits (166), Expect = 2e-14
 Identities = 22/61 (36%), Positives = 33/61 (54%)

Query: 325 NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD 384
           ++ ER  + + F  G+I V+ AT     G+D   V  V+ + +P S  +Y Q  GRAGR 
Sbjct: 22  SQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA 81

Query: 385 G 385
           G
Sbjct: 82  G 82

Length = 82

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

 Score = 66.1 bits (162), Expect = 7e-13
 Identities = 40/203 (19%), Positives = 70/203 (34%), Gaps = 50/203 (24%)

Query: 54  QKKAIRHILLRTHDIFVSMPTGAVSLVG-SVVSARSRVRIPPGADFILNGNVRSRNGWIS 112
           Q +AI  IL    D+ V  PTG+    G ++          P    +L      +   ++
Sbjct: 4   QAQAIPAIL-SGKDVLVQAPTGS----GKTLAFLL------PILQALLPKKGGPQALVLA 52

Query: 113 P-------ILSSF--YLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKP 163
           P       I        +    + +++TG            G +  E     +  +L K 
Sbjct: 53  PTRELAEQIYEELKKLFKILGLRVALLTG------------GTSLKE-----QARKLKKG 95

Query: 164 RIKLLYVTPERAVTESFHYLLQH--LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGEL 221
           +  +L  TP R        LL+   L     L  +V+DEAH + + G  F      +   
Sbjct: 96  KADILVGTPGR-----LLDLLRRGKLKLLKNLKLLVLDEAHRLLDMG--FGDDLEEILSR 148

Query: 222 RQFTGNSIPIIALTATAEPSVKQ 244
                    I+ L+AT   +++ 
Sbjct: 149 LP---PDRQILLLSATLPRNLED 168

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

 Score = 61.0 bits (148), Expect = 5e-10
 Identities = 35/148 (23%), Positives = 60/148 (40%), Gaps = 22/148 (14%)

Query: 283 AHVKEFIEKCLGKDNKA-----------NNCGIIYCRTREHTTDLADALRR--------- 322
             +K+F  +   ++ K                I++ RT+    +LA++LR+         
Sbjct: 245 KKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALH 304

Query: 323 -KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRA 381
             + + ER R  E F  GE+ V+ AT     G+D  +V  V+++ +P     Y    GR 
Sbjct: 305 GDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRT 364

Query: 382 GRDGLQSYC-RIYHSEHSKKSLEYVIKT 408
           GR G +         E   K L+ + K 
Sbjct: 365 GRAGRKGVAISFVTEEEEVKKLKRIEKR 392

Length = 513

>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 = 60.5 bits (147), Expect = 9e-10
 Identities = 66/311 (21%), Positives = 108/311 (34%), Gaps = 98/311 (31%)

Query: 145 GQTK-TENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL-----QHLVRYNKLAYIVV 198
           G T   E +AI+       P I  L   P+       HYLL       L     L Y+VV
Sbjct: 153 GDTPPEERRAIIRN----PPDI--LLTNPDM-----LHYLLLRNHDAWLWLLRNLKYLVV 201

Query: 199 DEAHCVSEWGHDFRPTY------------RRLGELRQFTGNSIPIIALTATA-------- 238
           DE H           TY            RRL    +  G+ + II  +AT         
Sbjct: 202 DELH-----------TYRGVQGSEVALLLRRLLRRLRRYGSPLQIICTSATLANPGEFAE 250

Query: 239 ------------EPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVK 286
                       E    + +   ++   P +    S  RS                A + 
Sbjct: 251 ELFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSA--------------LAELA 296

Query: 287 EFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKH------------------E 328
                 +    +     +++ R+R+    L  + RR++ +                   E
Sbjct: 297 TLAALLVRNGIQ----TLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREE 352

Query: 329 RSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQ 387
           R R++  F  GE+  + AT +  +GID  ++  V+ +G P  S+ ++ Q +GRAGR G +
Sbjct: 353 RRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQE 412

Query: 388 SY-CRIYHSEH 397
           S    +  S+ 
Sbjct: 413 SLVLVVLRSDP 423

Length = 851

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

 Score = 55.8 bits (135), Expect = 2e-09
 Identities = 16/98 (16%), Positives = 37/98 (37%), Gaps = 15/98 (15%)

Query: 140 ELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVD 199
             ++ G +  +      + +L+  +  ++  TP R        L +  +   KL  +++D
Sbjct: 61  GYLIGGTSIKQ------QEKLLSGKTDIVVGTPGRL----LDELERLKLSLKKLDLLILD 110

Query: 200 EAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTAT 237
           EAH +   G           ++         ++ L+AT
Sbjct: 111 EAHRLLNQGFGLLGL-----KILLKLPKDRQVLLLSAT 143

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

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

 Score = 56.3 bits (136), Expect = 3e-09
 Identities = 37/200 (18%), Positives = 70/200 (35%), Gaps = 41/200 (20%)

Query: 54  QKKAIRHILLRTHDIFVSMPTGA-VSLVGSVVSARSRVRIPPGADFI------LNGNVRS 106
           QK+AI  +L    D+ ++ PTG+  +L   + +  +  R   G   +      L      
Sbjct: 13  QKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAE 72

Query: 107 RNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIK 166
                   L             +  G S   QL  + SG+T                   
Sbjct: 73  E-------LKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTD------------------ 107

Query: 167 LLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTG 226
           +L  TP R        L    +  + +  +++DEAH + + G  F     +L +L     
Sbjct: 108 ILVTTPGRL----LDLLENDKLSLSNVDLVILDEAHRLLDGG--FGDQLEKLLKL---LP 158

Query: 227 NSIPIIALTATAEPSVKQDI 246
            ++ ++ L+AT    ++  +
Sbjct: 159 KNVQLLLLSATPPEEIENLL 178

Length = 201

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

 Score = 53.3 bits (128), Expect = 1e-07
 Identities = 68/249 (27%), Positives = 109/249 (43%), Gaps = 60/249 (24%)

Query: 165 IKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQF 224
           ++L+  TP R +      L +H +  + ++ +V+DE  C+ E G  FR    ++     F
Sbjct: 247 VELIVGTPGRLID----LLSKHDIELDNVSVLVLDEVDCMLERG--FRDQVMQI-----F 295

Query: 225 TGNSIPIIAL-TATAEPSVKQ---------DIISVLKFNKPYKVFK-------TSTFRSN 267
              S P + L +AT  P V++          +IS+   N+P K  K       T   +  
Sbjct: 296 QALSQPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQK 355

Query: 268 LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALR-----R 322
           LF      D+LK S  H K                 +++  +R     LA+A+      +
Sbjct: 356 LF------DILK-SKQHFKP--------------PAVVFVSSRLGADLLANAITVVTGLK 394

Query: 323 KVNKH------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ 376
            ++ H      ER  V +SF+ GE+ VI AT   G G+D   VR V+ + MP++I  Y  
Sbjct: 395 ALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIH 454

Query: 377 ESGRAGRDG 385
           + GRA R G
Sbjct: 455 QIGRASRMG 463

Length = 518

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

 Score = 53.4 bits (129), Expect = 2e-07
 Identities = 59/270 (21%), Positives = 104/270 (38%), Gaps = 85/270 (31%)

Query: 159 RLVK--PRIKLLYVTPERAVTESFHYLL------QHL--VRYNKLAYIVVDEAHCV--SE 206
           +++K  P I  L  TPE     S   LL      + L  VRY     ++VDE H +  S+
Sbjct: 118 KMLKNPPHI--LITTPE-----SLAILLNSPKFRELLRDVRY-----VIVDEIHALAESK 165

Query: 207 WGH----------DFRPTYRRLG---------ELRQF-TGNSIP--IIALTATAEPSVKQ 244
            G           +    ++R+G         E+ +F  G   P  I+ ++A  +  +K 
Sbjct: 166 RGVQLALSLERLRELAGDFQRIGLSATVGPPEEVAKFLVGFGDPCEIVDVSAAKKLEIK- 224

Query: 245 DIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGI 304
             +     +  Y              + ++  L +     + E ++K        +   +
Sbjct: 225 --VISPVEDLIY-------------DEELWAALYER----IAELVKK--------HRTTL 257

Query: 305 IYCRTREHTTDLADALRRK-----------VNKHERSRVQESFMRGEINVITATISFGMG 353
           I+  TR     LA  L++            +++  R  V+E    GE+  + AT S  +G
Sbjct: 258 IFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELG 317

Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGR 383
           ID  ++  V+  G P S+  + Q  GRAG 
Sbjct: 318 IDIGDIDLVIQLGSPKSVNRFLQRIGRAGH 347

Length = 814

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

 Score = 48.3 bits (115), Expect = 5e-06
 Identities = 26/92 (28%), Positives = 40/92 (43%), Gaps = 10/92 (10%)

Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
           IIYC TR     L   +  +          +++ +R  +   F  G   V+  T     G
Sbjct: 271 IIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARG 330

Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
           ID Q V  V+++ +P+S   Y    GR+GR G
Sbjct: 331 IDVQQVSLVINYDLPASPENYIHRIGRSGRFG 362

Length = 401

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

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 47/240 (19%), Positives = 73/240 (30%), Gaps = 59/240 (24%)

Query: 191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVL 250
           N+   I+ DE H      H   P+YRR+ EL      + P + LTAT E      I  + 
Sbjct: 145 NEFGLIIFDEVH------HLPAPSYRRILELLS---AAYPRLGLTATPEREDGGRIGDLF 195

Query: 251 ------------------KFNKPYK---VFKTST-------------FRSNLFYD----V 272
                              +  PYK   +  T T             FR  L        
Sbjct: 196 DLIGPIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGTLRA 255

Query: 273 IFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKV-------- 324
             +       +  K    + L   +   +  +I+    EH  ++A               
Sbjct: 256 ENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGIVEAITGE 315

Query: 325 -NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGR 383
             K ER  + E F  G I V+        G+D  +   ++    P+     +    R GR
Sbjct: 316 TPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLII-LRPTGSRRLFI--QRLGR 372

Length = 442

>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional

 Score = 46.9 bits (112), Expect = 1e-05
 Identities = 30/98 (30%), Positives = 43/98 (43%), Gaps = 16/98 (16%)

Query: 308 RTREHTTDLADALRRKVNKH-------ERSRVQESFMRGEINVITATISFGMG------- 353
              E + DLAD + +    H        R  V+++F    I VI++T +   G       
Sbjct: 290 SDTETSKDLADCVAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARR 349

Query: 354 -IDRQNVRFVVHWGM-PSSIPAYYQESGRAGRDGLQSY 389
            I R   R+    GM P  +  Y+Q +GRAGR GL  Y
Sbjct: 350 VIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPY 387

Length = 737

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

 Score = 44.1 bits (104), Expect = 1e-04
 Identities = 21/64 (32%), Positives = 31/64 (48%)

Query: 324 VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGR 383
           V +H+R +  E F  G+I V+ AT   G GI    +  V+++ +P     Y    GR GR
Sbjct: 369 VPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGR 428

Query: 384 DGLQ 387
            G  
Sbjct: 429 AGAS 432

Length = 475

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

 Score = 44.2 bits (105), Expect = 1e-04
 Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 10/93 (10%)

Query: 303 GIIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISFGM 352
            I++ RTRE   +LA  LR+          ++ + +R+   +    G +NV+ AT     
Sbjct: 248 SIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAAR 307

Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
           GID  +V  V+++ MP S   Y    GR GR G
Sbjct: 308 GIDIDDVSHVINFDMPRSADTYLHRIGRTGRAG 340

Length = 434

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

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 74/321 (23%), Positives = 118/321 (36%), Gaps = 81/321 (25%)

Query: 139 LELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVV 198
           + L+         K +LE +     +I L+  T         H L+Q  V + +LA +++
Sbjct: 315 VALLTGSLKGKRRKELLETIA--SGQIHLVVGT---------HALIQEKVEFKRLALVII 363

Query: 199 DEAHCVSEWGHDFRPTYRRLGE------LRQFTGNSIP-IIALTATAEPSVKQDIISVLK 251
           DE H    +G + R   R  G+      +   +   IP  +ALT   +  +   II  L 
Sbjct: 364 DEQH---RFGVEQRKKLREKGQGGFTPHVLVMSATPIPRTLALTVYGD--LDTSIIDELP 418

Query: 252 FNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTRE 311
                K   T          +I  D     Y    EFIE+ + K  +A    ++Y    E
Sbjct: 419 --PGRKPITTV---------LIKHDEKDIVY----EFIEEEIAKGRQAY---VVYPLIEE 460

Query: 312 -HTTDLADA------------------LRRKVNKHERSRVQESFMRGEINVITATISFGM 352
               DL  A                  L  ++   E+  V E F  GE++++ AT    +
Sbjct: 461 SEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEV 520

Query: 353 GIDRQNV---------RFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYH----SEHSK 399
           G+D  N          RF         +   +Q  GR GR   QSYC + +    SE +K
Sbjct: 521 GVDVPNATVMVIEDAERF--------GLSQLHQLRGRVGRGDHQSYCLLVYKNPKSESAK 572

Query: 400 KSLEYVIKTDTSTKREQLELK 420
           K L  +  T       + +L+
Sbjct: 573 KRLRVMADTLDGFVIAEEDLE 593

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

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

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 26/92 (28%), Positives = 45/92 (48%), Gaps = 10/92 (10%)

Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
           II+ RT+  T ++A+AL R           +N+  R +  E    G ++++ AT     G
Sbjct: 249 IIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARG 308

Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
           +D + +  VV++ +P    +Y    GR GR G
Sbjct: 309 LDVERISLVVNYDIPMDSESYVHRIGRTGRAG 340

Length = 629

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

 Score = 42.6 bits (100), Expect = 4e-04
 Identities = 22/75 (29%), Positives = 37/75 (49%)

Query: 308 RTREHTTDLADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGM 367
           R +     +A +    V+K +R+  +++   GE+  + AT S  +GID   V  V+    
Sbjct: 295 RVQSSDVFIARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVAT 354

Query: 368 PSSIPAYYQESGRAG 382
           P S+ +  Q  GRAG
Sbjct: 355 PLSVASGLQRIGRAG 369

Length = 1490

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

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 17/58 (29%), Positives = 32/58 (55%)

Query: 328 ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
           +R  ++ +   GE+  +  T +  +G+D   +  VV  G P +  + +Q++GRAGR G
Sbjct: 317 DRRELERALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRG 374

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|240273 PTZ00110, PTZ00110, helicase; Provisional

 Score = 40.5 bits (95), Expect = 0.002
 Identities = 27/115 (23%), Positives = 52/115 (45%), Gaps = 18/115 (15%)

Query: 283 AHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALR------------RKVNKHERS 330
             +K  +++ +   +K     +I+  T++    L   LR            +K  + ER+
Sbjct: 364 GKLKMLLQRIMRDGDKI----LIFVETKKGADFLTKELRLDGWPALCIHGDKK--QEERT 417

Query: 331 RVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
            V   F  G+  ++ AT     G+D ++V++V+++  P+ I  Y    GR GR G
Sbjct: 418 WVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAG 472

Length = 545

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	444
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
KOG0352|consensus	641		100.0
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	100.0
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	100.0
KOG0331|consensus	519		100.0
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	100.0
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	100.0
KOG0330|consensus	476		100.0
KOG0328|consensus	400		100.0
PTZ00110	545	helicase; Provisional	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
PTZ00424	401	helicase 45; Provisional	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0338|consensus	691		100.0
KOG0333|consensus	673		100.0
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	100.0
KOG0351|consensus	941		100.0
KOG0336|consensus	629		100.0
KOG0340|consensus	442		100.0
KOG0342|consensus	543		100.0
KOG0353|consensus	695		100.0
KOG0345|consensus	567		100.0
KOG0335|consensus	482		100.0
KOG0326|consensus	459		100.0
KOG0348|consensus	708		100.0
KOG0347|consensus	731		100.0
KOG0343|consensus	758		100.0
KOG0346|consensus	569		100.0
KOG4284|consensus	980		100.0
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	100.0
KOG0332|consensus	477		100.0
KOG0341|consensus	610		100.0
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	100.0
PRK13767	876	ATP-dependent helicase; Provisional	100.0
KOG0339|consensus	731		100.0
PRK02362	737	ski2-like helicase; Provisional	100.0
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	100.0
KOG0350|consensus	620		100.0
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	100.0
KOG0327|consensus	397		100.0
PRK10689	1147	transcription-repair coupling factor; Provisional	100.0
COG1201	814	Lhr Lhr-like helicases [General function predictio	100.0
PRK00254	720	ski2-like helicase; Provisional	100.0
KOG0334|consensus	997		100.0
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	100.0
KOG0329|consensus	387		100.0
PRK01172	674	ski2-like helicase; Provisional	100.0
KOG0952|consensus	1230		100.0
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	100.0
KOG0344|consensus	593		100.0
COG1204	766	Superfamily II helicase [General function predicti	100.0
PRK14701	1638	reverse gyrase; Provisional	100.0
KOG0337|consensus	529		100.0
COG1205	851	Distinct helicase family with a unique C-terminal	100.0
KOG0354|consensus	746		100.0
PHA02653	675	RNA helicase NPH-II; Provisional	100.0
PHA02558	501	uvsW UvsW helicase; Provisional	100.0
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	100.0
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	100.0
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	100.0
PRK09401	1176	reverse gyrase; Reviewed	100.0
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	100.0
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	100.0
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	100.0
COG1202	830	Superfamily II helicase, archaea-specific [General	100.0
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	100.0
PRK13766	773	Hef nuclease; Provisional	100.0
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.98
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.97
KOG0951|consensus	1674		99.97
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.97
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.97
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.97
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.97
PRK05580	679	primosome assembly protein PriA; Validated	99.97
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.96
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.95
PRK09694	878	helicase Cas3; Provisional	99.95
PRK04914	956	ATP-dependent helicase HepA; Validated	99.95
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.95
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.95
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.95
KOG0947|consensus	1248		99.95
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.94
KOG0950|consensus	1008		99.93
KOG0349|consensus	725		99.93
KOG0948|consensus	1041		99.93
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.92
COG4096	875	HsdR Type I site-specific restriction-modification	99.92
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.92
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.91
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.9
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.9
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.89
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.88
KOG0949|consensus	1330		99.88
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.88
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.88
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.88
KOG0922|consensus	674		99.88
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.87
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.87
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.86
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.84
KOG4150|consensus	1034		99.84
KOG1123|consensus	776		99.82
KOG0926|consensus	1172		99.82
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.81
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.81
KOG0924|consensus	1042		99.81
KOG0923|consensus	902		99.81
KOG0920|consensus	924		99.79
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.79
KOG0385|consensus	971		99.77
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.76
COG4889	1518	Predicted helicase [General function prediction on	99.75
KOG0387|consensus	923		99.72
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.72
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	99.72
KOG0384|consensus	1373		99.71
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.71
KOG0925|consensus	699		99.69
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.69
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.67
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.67
KOG0951|consensus	1674		99.67
KOG0389|consensus	941		99.64
KOG0390|consensus	776		99.64
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.64
PRK05298	652	excinuclease ABC subunit B; Provisional	99.64
KOG0953|consensus	700		99.62
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.61
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	99.6
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	99.58
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.58
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	99.56
PRK14873	665	primosome assembly protein PriA; Provisional	99.55
KOG1000|consensus	689		99.55
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.54
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.49
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.49
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	99.48
KOG0392|consensus	1549		99.46
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	99.42
KOG0386|consensus	1157		99.38
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.35
COG0610	962	Type I site-specific restriction-modification syst	99.32
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	99.24
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.2
KOG0388|consensus	1185		99.18
KOG1002|consensus	791		99.13
KOG0391|consensus	1958		99.11
KOG4439|consensus	901		99.1
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.0
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	98.99
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.78
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.78
KOG1015|consensus	1567		98.77
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	98.76
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	98.61
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.55
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	98.52
KOG0952|consensus	1230		98.49
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.41
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.35
PRK15483	986	type III restriction-modification system StyLTI en	98.2
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.14
KOG0921|consensus	1282		98.13
KOG1016|consensus	1387		98.1
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	98.0
KOG1803|consensus	649		97.99
KOG1513|consensus	1300		97.96
KOG1802|consensus	935		97.91
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.88
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.78
TIGR00376	637	DNA helicase, putative. The gene product may repre	97.74
KOG2340|consensus	698		97.71
PRK10536	262	hypothetical protein; Provisional	97.7
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.69
COG3587	985	Restriction endonuclease [Defense mechanisms]	97.64
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.62
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.56
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	97.42
PF13245	76	AAA_19: Part of AAA domain	97.42
KOG1805|consensus	1100		97.34
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	97.31
PRK08181	269	transposase; Validated	97.31
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.25
PRK06526	254	transposase; Provisional	97.15
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.12
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	96.95
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	96.95
KOG1132|consensus	945		96.84
KOG1133|consensus	821		96.83
PF13871	278	Helicase_C_4: Helicase_C-like	96.76
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	96.71
PRK12377	248	putative replication protein; Provisional	96.71
KOG0989|consensus	346		96.7
PRK08727	233	hypothetical protein; Validated	96.68
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	96.67
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.6
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.59
PRK13889	988	conjugal transfer relaxase TraA; Provisional	96.48
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	96.45
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.4
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	96.26
PRK06921	266	hypothetical protein; Provisional	96.22
KOG2028|consensus	554		96.2
PRK07952	244	DNA replication protein DnaC; Validated	96.2
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.2
PRK05642	234	DNA replication initiation factor; Validated	96.19
PRK14974	336	cell division protein FtsY; Provisional	96.11
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.11
PRK06835	329	DNA replication protein DnaC; Validated	96.08
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	96.06
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.05
KOG1131|consensus	755		96.05
PRK08084	235	DNA replication initiation factor; Provisional	96.04
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	96.03
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	96.03
PRK05707	328	DNA polymerase III subunit delta'; Validated	96.02
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	95.99
PRK04296	190	thymidine kinase; Provisional	95.98
PRK00149	450	dnaA chromosomal replication initiation protein; R	95.98
PRK12422	445	chromosomal replication initiation protein; Provis	95.91
PRK14087	450	dnaA chromosomal replication initiation protein; P	95.89
KOG0739|consensus	439		95.86
PRK14088	440	dnaA chromosomal replication initiation protein; P	95.84
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	95.83
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	95.82
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.82
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	95.75
PRK08116	268	hypothetical protein; Validated	95.72
PRK06893	229	DNA replication initiation factor; Validated	95.72
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	95.72
PRK09183	259	transposase/IS protein; Provisional	95.71
KOG1001|consensus	674		95.66
KOG0742|consensus	630		95.65
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	95.61
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	95.57
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	95.55
PRK00411	394	cdc6 cell division control protein 6; Reviewed	95.5
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	95.45
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	95.43
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	95.35
COG2256	436	MGS1 ATPase related to the helicase subunit of the	95.33
PRK13826	1102	Dtr system oriT relaxase; Provisional	95.27
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	95.24
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	95.23
PRK14086	617	dnaA chromosomal replication initiation protein; P	95.21
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.2
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	95.19
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	95.19
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	95.18
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	95.11
PF00004	132	AAA: ATPase family associated with various cellula	95.1
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	95.02
PTZ00112	1164	origin recognition complex 1 protein; Provisional	95.0
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	94.97
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	94.96
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	94.94
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	94.87
KOG0383|consensus	696		94.86
PLN03025	319	replication factor C subunit; Provisional	94.8
PRK08769	319	DNA polymerase III subunit delta'; Validated	94.79
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	94.79
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	94.77
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	94.73
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	94.73
PRK00771	437	signal recognition particle protein Srp54; Provisi	94.73
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	94.67
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	94.67
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	94.65
PRK05595	444	replicative DNA helicase; Provisional	94.62
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	94.55
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	94.54
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	94.49
PRK08939	306	primosomal protein DnaI; Reviewed	94.47
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	94.43
PRK06904	472	replicative DNA helicase; Validated	94.37
PRK06964	342	DNA polymerase III subunit delta'; Validated	94.31
PRK07940	394	DNA polymerase III subunit delta'; Validated	94.27
PRK12402	337	replication factor C small subunit 2; Reviewed	94.25
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	94.22
PRK08903	227	DnaA regulatory inactivator Hda; Validated	94.1
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	94.03
KOG0741|consensus	744		94.02
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	93.94
TIGR00064	272	ftsY signal recognition particle-docking protein F	93.92
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	93.86
PRK09112	351	DNA polymerase III subunit delta'; Validated	93.86
KOG0701|consensus	1606		93.84
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	93.84
COG3972	660	Superfamily I DNA and RNA helicases [General funct	93.78
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	93.77
PRK08760	476	replicative DNA helicase; Provisional	93.77
KOG1133|consensus	821		93.74
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	93.74
PRK05748	448	replicative DNA helicase; Provisional	93.69
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	93.57
KOG0734|consensus	752		93.57
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	93.56
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	93.51
PRK11054	684	helD DNA helicase IV; Provisional	93.51
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	93.49
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	93.48
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	93.41
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	93.4
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	93.32
PRK07993	334	DNA polymerase III subunit delta'; Validated	93.32
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	93.32
PRK06871	325	DNA polymerase III subunit delta'; Validated	93.27
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	93.25
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	93.24
KOG0744|consensus	423		93.24
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	93.24
PRK09376	416	rho transcription termination factor Rho; Provisio	93.2
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	93.15
PRK08506	472	replicative DNA helicase; Provisional	93.04
PRK06090	319	DNA polymerase III subunit delta'; Validated	92.97
TIGR00767	415	rho transcription termination factor Rho. Members	92.97
PRK05973	237	replicative DNA helicase; Provisional	92.92
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	92.89
PRK13341	725	recombination factor protein RarA/unknown domain f	92.89
PRK08699	325	DNA polymerase III subunit delta'; Validated	92.88
KOG0738|consensus	491		92.87
PRK07471	365	DNA polymerase III subunit delta'; Validated	92.86
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	92.84
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	92.76
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	92.74
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	92.7
PRK06067	234	flagellar accessory protein FlaH; Validated	92.69
PRK13833	323	conjugal transfer protein TrbB; Provisional	92.67
PRK13342	413	recombination factor protein RarA; Reviewed	92.55
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	92.55
PRK09165	497	replicative DNA helicase; Provisional	92.53
PRK05636	505	replicative DNA helicase; Provisional	92.53
PRK08840	464	replicative DNA helicase; Provisional	92.48
KOG0991|consensus	333		92.46
PRK08006	471	replicative DNA helicase; Provisional	92.45
PHA03368	738	DNA packaging terminase subunit 1; Provisional	92.43
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	92.36
PRK07004	460	replicative DNA helicase; Provisional	92.33
PRK04195	482	replication factor C large subunit; Provisional	92.3
PRK10416	318	signal recognition particle-docking protein FtsY;	92.3
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	92.26
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	92.24
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	92.21
PRK06321	472	replicative DNA helicase; Provisional	92.19
TIGR00665	434	DnaB replicative DNA helicase. This model describe	92.15
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	92.1
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	91.98
KOG0298|consensus	1394		91.97
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	91.91
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	91.59
PRK03992	389	proteasome-activating nucleotidase; Provisional	91.57
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	91.56
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	91.52
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	91.48
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	91.43
PRK13897	606	type IV secretion system component VirD4; Provisio	91.28
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	91.18
PRK05298	652	excinuclease ABC subunit B; Provisional	91.12
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	91.04
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	91.02
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	90.92
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	90.88
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	90.87
PRK10867	433	signal recognition particle protein; Provisional	90.83
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	90.83
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	90.76
PHA03333	752	putative ATPase subunit of terminase; Provisional	90.76
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	90.76
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	90.73
CHL00176	638	ftsH cell division protein; Validated	90.71
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	90.7
KOG1132|consensus	945		90.68
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	90.67
PRK10865	857	protein disaggregation chaperone; Provisional	90.62
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	90.6
PHA02542	473	41 41 helicase; Provisional	90.54
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	90.54
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	90.4
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	90.35
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	90.19
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	90.08
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	90.04
KOG2170|consensus	344		90.03
KOG0733|consensus	802		90.02
PRK07773	886	replicative DNA helicase; Validated	89.99
PRK00440	319	rfc replication factor C small subunit; Reviewed	89.95
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	89.91
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	89.86
PRK07399	314	DNA polymerase III subunit delta'; Validated	89.84
PRK13822	641	conjugal transfer coupling protein TraG; Provision	89.82
PRK11823	446	DNA repair protein RadA; Provisional	89.79
PHA02533	534	17 large terminase protein; Provisional	89.72
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	89.72
cd03115	173	SRP The signal recognition particle (SRP) mediates	89.64
PHA02544	316	44 clamp loader, small subunit; Provisional	89.54
COG0606	490	Predicted ATPase with chaperone activity [Posttran	89.53
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	89.5
TIGR00959	428	ffh signal recognition particle protein. This mode	89.38
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	89.36
PRK08058	329	DNA polymerase III subunit delta'; Validated	88.93
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	88.92
PRK13850	670	type IV secretion system protein VirD4; Provisiona	88.89
PRK10689	1147	transcription-repair coupling factor; Provisional	88.88
PRK13851	344	type IV secretion system protein VirB11; Provision	88.84
KOG0733|consensus	802		88.68
KOG0732|consensus	1080		88.48
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	88.35
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	88.35
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	88.25
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	88.2
PRK13880	636	conjugal transfer coupling protein TraG; Provision	88.17
KOG0331|consensus	519		87.99
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	87.96
COG0305	435	DnaB Replicative DNA helicase [DNA replication, re	87.83
COG1221	403	PspF Transcriptional regulators containing an AAA-	87.77
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	87.67
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	87.53
KOG0741|consensus	744		87.51
KOG0729|consensus	435		87.25
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	87.23
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	86.97
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	86.92
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	86.87
smart00382	148	AAA ATPases associated with a variety of cellular	86.83
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	86.47
PRK08533	230	flagellar accessory protein FlaH; Reviewed	86.47
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	86.47
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	86.37
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	86.35
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	86.34
KOG0344|consensus	593		86.21
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	86.12
KOG0333|consensus	673		86.09
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	86.0
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	85.79
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	85.73
PRK13876	663	conjugal transfer coupling protein TraG; Provision	85.55
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	85.54
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	85.39
PRK12608	380	transcription termination factor Rho; Provisional	85.2
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	85.16
PRK06749	428	replicative DNA helicase; Provisional	85.15
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	84.98
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	84.9
cd00983	325	recA RecA is a bacterial enzyme which has roles in	84.89
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	84.83
CHL00095	821	clpC Clp protease ATP binding subunit	84.78
PRK05917	290	DNA polymerase III subunit delta'; Validated	84.75
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	84.74
PHA03372	668	DNA packaging terminase subunit 1; Provisional	84.71
KOG0730|consensus	693		84.56
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	84.49
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	84.46
cd01128	249	rho_factor Transcription termination factor rho is	84.41
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	84.33
PRK10436	462	hypothetical protein; Provisional	84.33
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	84.31
PTZ00110	545	helicase; Provisional	84.12
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	84.08
TIGR02533	486	type_II_gspE general secretory pathway protein E.	83.96
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	83.86
KOG0298|consensus	1394		83.71
KOG2228|consensus	408		83.71
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	83.46
PHA00350	399	putative assembly protein	83.38
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	83.28
KOG0736|consensus	953		83.12
PRK09354	349	recA recombinase A; Provisional	82.91
PTZ00293	211	thymidine kinase; Provisional	82.9
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	82.86
COG0593	408	DnaA ATPase involved in DNA replication initiation	82.72
COG4128	398	Zot Zonula occludens toxin [General function predi	82.59
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	82.4
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	82.19
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	82.0
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	82.0
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	81.88
COG1134	249	TagH ABC-type polysaccharide/polyol phosphate tran	81.84
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	81.82
KOG1807|consensus	1025		81.77
PHA02244	383	ATPase-like protein	81.73
PRK13531	498	regulatory ATPase RavA; Provisional	81.73
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	81.69
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	81.64
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	81.53
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	81.2
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	81.2
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	81.15

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

Probab=100.00  E-value=5.1e-54  Score=440.12  Aligned_cols=382  Identities=36%  Similarity=0.594  Sum_probs=314.5

Q ss_pred             CCCCCCCC-HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC
Q psy7952          25 DRKGGKVS-EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN  103 (444)
Q Consensus        25 ~~~~~~~~-~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~  103 (444)
                      +|....++ ...+...++..||+..|+ ++|.++++.++.| +|+++.+|||+|||++        |++|+    +...+
T Consensus       436 ~W~~~~fpw~~~L~~~lk~~FG~~sFR-p~Q~eaI~aiL~G-rDVLVimPTGSGKSLc--------YQLPA----L~~~G  501 (1195)
T PLN03137        436 KWSSRNFPWTKKLEVNNKKVFGNHSFR-PNQREIINATMSG-YDVFVLMPTGGGKSLT--------YQLPA----LICPG  501 (1195)
T ss_pred             cccccCCCchHHHHHHHHHHcCCCCCC-HHHHHHHHHHHcC-CCEEEEcCCCccHHHH--------HHHHH----HHcCC
Confidence            35544444 567888999999999977 8999999999999 9999999999999999        99999    77777


Q ss_pred             ccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCcccccc-HH
Q psy7952         104 VRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTES-FH  181 (444)
Q Consensus       104 ~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~-~~  181 (444)
                      .+   |||+|+++|+     .+|+..+ ..+   +.+..+.++....+....+..+....+.++|+|+|||++.... +.
T Consensus       502 iT---LVISPLiSLm-----qDQV~~L~~~G---I~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll  570 (1195)
T PLN03137        502 IT---LVISPLVSLI-----QDQIMNLLQAN---IPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLL  570 (1195)
T ss_pred             cE---EEEeCHHHHH-----HHHHHHHHhCC---CeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHH
Confidence            77   9999999999     8899988 778   9999999999988888888777655578999999999986421 22


Q ss_pred             HHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEec
Q psy7952         182 YLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT  261 (444)
Q Consensus       182 ~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~  261 (444)
                      ..+........+.+|||||||++++||++|++.|..+..+.+.++. .+++++|||+++...+++...+++..+ .++..
T Consensus       571 ~~L~~L~~~~~LslIVIDEAHcVSqWGhDFRpdYr~L~~Lr~~fp~-vPilALTATAT~~V~eDI~~~L~l~~~-~vfr~  648 (1195)
T PLN03137        571 RHLENLNSRGLLARFVIDEAHCVSQWGHDFRPDYQGLGILKQKFPN-IPVLALTATATASVKEDVVQALGLVNC-VVFRQ  648 (1195)
T ss_pred             HHHHhhhhccccceeccCcchhhhhcccchHHHHHHHHHHHHhCCC-CCeEEEEecCCHHHHHHHHHHcCCCCc-EEeec
Confidence            2233333345689999999999999999999999998877777776 889999999999999999999987766 45666


Q ss_pred             CCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHH
Q psy7952         262 STFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSR  331 (444)
Q Consensus       262 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~  331 (444)
                      +..++++.|.+.....  .....+..++.    .. ..+.++||||+++++|+.++..|...          |++++|..
T Consensus       649 Sf~RpNL~y~Vv~k~k--k~le~L~~~I~----~~-~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~  721 (1195)
T PLN03137        649 SFNRPNLWYSVVPKTK--KCLEDIDKFIK----EN-HFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAF  721 (1195)
T ss_pred             ccCccceEEEEeccch--hHHHHHHHHHH----hc-ccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHH
Confidence            7889999887765421  11222333322    21 13567899999999999999999876          89999999


Q ss_pred             HHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhhccc
Q psy7952         332 VQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTS  411 (444)
Q Consensus       332 ~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~  411 (444)
                      +++.|..|+++|||||+++++|||+|+|++|||+++|.|++.|+||+||+||+|..|.|++|++..|...++.++.....
T Consensus       722 vqe~F~~Gei~VLVATdAFGMGIDkPDVR~VIHydlPkSiEsYyQriGRAGRDG~~g~cILlys~~D~~~~~~lI~~~~~  801 (1195)
T PLN03137        722 VQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMISQGGV  801 (1195)
T ss_pred             HHHHHhcCCCcEEEEechhhcCCCccCCcEEEEcCCCCCHHHHHhhhcccCCCCCCceEEEEecHHHHHHHHHHHhcccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999864432


Q ss_pred             hhH-------------HHHHHHHhhHHHHHHHhhh----------ceeeeec
Q psy7952         412 TKR-------------EQLELKFKNYLSMLEYCEQ----------GYFLVIL  440 (444)
Q Consensus       412 ~~~-------------~~~~~~~~~~~~~~~~~~~----------~~~~~~~  440 (444)
                      ...             ...+....++..|++||+.          .||.+..
T Consensus       802 ~~s~~~~~~~r~~~s~~~~e~~~~~L~~m~~yce~~~~CRR~~lL~yFGE~~  853 (1195)
T PLN03137        802 EQSPMAMGYNRMASSGRILETNTENLLRMVSYCENEVDCRRFLQLVHFGEKF  853 (1195)
T ss_pred             ccchhhhhhcccchhHHHHHHHHHHHHHHHHHHhChHhhHHHHHHHHccccc
Confidence            210             0123457889999999986          4677753

>KOG0352|consensus

Probab=100.00  E-value=7.4e-55  Score=394.29  Aligned_cols=379  Identities=43%  Similarity=0.766  Sum_probs=355.7

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      .+..+.++|++.||+..|.++.|..|+..+..+++||.+++|||+||+++        |++|+    +..+|.+   |++
T Consensus         3 ~Er~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLC--------yQLPa----L~~~gIT---IV~   67 (641)
T KOG0352|consen    3 MERKVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLC--------YQLPA----LVHGGIT---IVI   67 (641)
T ss_pred             hHHHHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhh--------hhchH----HHhCCeE---EEe
Confidence            46778899999999999999999999999999889999999999999999        99999    9999999   999


Q ss_pred             cchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhh
Q psy7952         112 SPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRY  190 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~  190 (444)
                      .|..+|+     .+|+..+ ...   +.+..+++.++..++..+.-++........+++.|||+..+..|..+++.+.+.
T Consensus        68 SPLiALI-----kDQiDHL~~LK---Vp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r  139 (641)
T KOG0352|consen   68 SPLIALI-----KDQIDHLKRLK---VPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANR  139 (641)
T ss_pred             hHHHHHH-----HHHHHHHHhcC---CchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhh
Confidence            9999999     9999999 888   999999999999999999999999899999999999999999999999999999


Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceE
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFY  270 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  270 (444)
                      ..+.|+|+||+|+.+.||++|++.|..+..+...++. +++|++|||.++.+.+++...+.+.+|+-++..+..|.|++|
T Consensus       140 ~~L~Y~vVDEAHCVSQWGHDFRPDYL~LG~LRS~~~~-vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~FR~NLFY  218 (641)
T KOG0352|consen  140 DVLRYIVVDEAHCVSQWGHDFRPDYLTLGSLRSVCPG-VPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTFRDNLFY  218 (641)
T ss_pred             ceeeeEEechhhhHhhhccccCcchhhhhhHHhhCCC-CceEEeecccChhHHHHHHHHHhhcCcHHhccCcchhhhhhH
Confidence            9999999999999999999999999999999998887 999999999999999999999999999999999999999999


Q ss_pred             EEEEcccchhhHHHHHHHHHHHhccCC-------CCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHH
Q psy7952         271 DVIFDDLLKDSYAHVKEFIEKCLGKDN-------KANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQ  333 (444)
Q Consensus       271 ~~~~~~~~~~~~~~~~~~l~~~l~~~~-------~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~  333 (444)
                      ++...+...+.+..+.++....+....       ...++.||||.|++.|++++-.|...          +...+|.++.
T Consensus       219 D~~~K~~I~D~~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQ  298 (641)
T KOG0352|consen  219 DNHMKSFITDCLTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQ  298 (641)
T ss_pred             HHHHHHHhhhHhHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHH
Confidence            999999999999999999888877332       13568999999999999999998777          7889999999


Q ss_pred             HHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhhccchh
Q psy7952         334 ESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTK  413 (444)
Q Consensus       334 ~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~  413 (444)
                      +.|.+++..||+||..++.|+|-|++++|||++.|.|+.-|.|-.||+||+|..+||-++++.+|...++.++.+++...
T Consensus       299 e~WM~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~qn~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~i~FLi~~e~akl  378 (641)
T KOG0352|consen  299 EKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPSQNLAGYYQESGRAGRDGKRSYCRLYYSRQDKNALNFLVSGELAKL  378 (641)
T ss_pred             HHHhcCCCCEEEEEeccccccCCcceeEEEecCchhhhHHHHHhccccccCCCccceeeeecccchHHHHHHHhhHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999998887765


Q ss_pred             HH------HHHHHHhhHHHHHHHhhhc
Q psy7952         414 RE------QLELKFKNYLSMLEYCEQG  434 (444)
Q Consensus       414 ~~------~~~~~~~~~~~~~~~~~~~  434 (444)
                      .+      ....-+..+.+|+.||++.
T Consensus       379 rek~~ke~~~k~~I~~F~k~~eFCE~~  405 (641)
T KOG0352|consen  379 REKAKKEMQIKSIITGFAKMLEFCESA  405 (641)
T ss_pred             HHhcchhhhHHHHHHHHHHHHHHHHHc
Confidence            54      4555688999999999964

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

Probab=100.00  E-value=5.5e-53  Score=410.13  Aligned_cols=369  Identities=38%  Similarity=0.660  Sum_probs=327.1

Q ss_pred             HHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcch
Q psy7952          35 ELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPI  114 (444)
Q Consensus        35 ~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~  114 (444)
                      .+...|++.||+..|| +-|.+++..++++ +++++..|||.|||++        |++|+    +...|.+   |||+|.
T Consensus         4 ~~~~~L~~~fGy~~FR-~gQ~evI~~~l~g-~d~lvvmPTGgGKSlC--------yQiPA----ll~~G~T---LVVSPL   66 (590)
T COG0514           4 EAQQVLKQVFGYASFR-PGQQEIIDALLSG-KDTLVVMPTGGGKSLC--------YQIPA----LLLEGLT---LVVSPL   66 (590)
T ss_pred             HHHHHHHHHhCccccC-CCHHHHHHHHHcC-CcEEEEccCCCCcchH--------hhhHH----HhcCCCE---EEECch
Confidence            3447799999999999 7999999999999 9999999999999999        99999    8889999   999999


Q ss_pred             hhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCc
Q psy7952         115 LSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKL  193 (444)
Q Consensus       115 ~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~  193 (444)
                      .+|.     .+|++++ ..|   +.+..+++..+..++..+...+.  .+..++++.+||++.++.|...+.    ...+
T Consensus        67 iSLM-----~DQV~~l~~~G---i~A~~lnS~l~~~e~~~v~~~l~--~g~~klLyisPErl~~~~f~~~L~----~~~i  132 (590)
T COG0514          67 ISLM-----KDQVDQLEAAG---IRAAYLNSTLSREERQQVLNQLK--SGQLKLLYISPERLMSPRFLELLK----RLPI  132 (590)
T ss_pred             HHHH-----HHHHHHHHHcC---ceeehhhcccCHHHHHHHHHHHh--cCceeEEEECchhhcChHHHHHHH----hCCC
Confidence            9999     9999999 889   99999999999999998888775  467999999999999876555444    5689


Q ss_pred             cEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEE
Q psy7952         194 AYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVI  273 (444)
Q Consensus       194 ~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  273 (444)
                      .+++|||||++++||++||+.|..+..+...+++ ++++++|||.++.+..++.+.+++..+ .++..+..|||+.|.+.
T Consensus       133 ~l~vIDEAHCiSqWGhdFRP~Y~~lg~l~~~~~~-~p~~AlTATA~~~v~~DI~~~L~l~~~-~~~~~sfdRpNi~~~v~  210 (590)
T COG0514         133 SLVAIDEAHCISQWGHDFRPDYRRLGRLRAGLPN-PPVLALTATATPRVRDDIREQLGLQDA-NIFRGSFDRPNLALKVV  210 (590)
T ss_pred             ceEEechHHHHhhcCCccCHhHHHHHHHHhhCCC-CCEEEEeCCCChHHHHHHHHHhcCCCc-ceEEecCCCchhhhhhh
Confidence            9999999999999999999999999999999995 999999999999999999999988776 56778899999999988


Q ss_pred             EcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccE
Q psy7952         274 FDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINV  343 (444)
Q Consensus       274 ~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~v  343 (444)
                      .......+..    ++.+.   ......++||||.|++.++.+++.|...          +..++|..+.++|..++++|
T Consensus       211 ~~~~~~~q~~----fi~~~---~~~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~i  283 (590)
T COG0514         211 EKGEPSDQLA----FLATV---LPQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKV  283 (590)
T ss_pred             hcccHHHHHH----HHHhh---ccccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcE
Confidence            7652222222    33331   1225677999999999999999999988          99999999999999999999


Q ss_pred             EEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhhccchhHHHHHHHHhh
Q psy7952         344 ITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKN  423 (444)
Q Consensus       344 LvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  423 (444)
                      +|||.+++.|||-|++++|||+++|.|++.|.|-+|||||+|.+..|++++++.|....+++++...+ ..+.......+
T Consensus       284 iVAT~AFGMGIdKpdVRfViH~~lP~s~EsYyQE~GRAGRDG~~a~aill~~~~D~~~~~~~i~~~~~-~~~~~~~~~~k  362 (590)
T COG0514         284 MVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLIEQSKP-DEEQKQIELAK  362 (590)
T ss_pred             EEEeccccCccCCCCceEEEEecCCCCHHHHHHHHhhccCCCCcceEEEeeccccHHHHHHHHHhhcc-hHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999998776 33455556788


Q ss_pred             HHHHHHHhhhc---------eeeeecccCC
Q psy7952         424 YLSMLEYCEQG---------YFLVILVFPC  444 (444)
Q Consensus       424 ~~~~~~~~~~~---------~~~~~~~~~~  444 (444)
                      +..|..+|+..         ||.+....||
T Consensus       363 l~~~~~~~e~~~crr~~ll~yfge~~~~~c  392 (590)
T COG0514         363 LRQMIAYCETQTCRRLVLLKYFGEDEPEPC  392 (590)
T ss_pred             HHHHHHhcccccchHHHHHHhcCccccccc
Confidence            89999999988         8888765555

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=100.00  E-value=5.1e-51  Score=404.88  Aligned_cols=336  Identities=40%  Similarity=0.709  Sum_probs=282.9

Q ss_pred             HHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          39 KLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        39 ~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      .|++.||++.|+ ++|.++++.++.| +++++.+|||+|||++        |++|+    +...+..   ||++|+++|+
T Consensus         2 ~l~~~~g~~~~r-~~Q~~ai~~~l~g-~dvlv~apTGsGKTl~--------y~lp~----l~~~~~~---lVi~P~~~L~   64 (470)
T TIGR00614         2 ILKTVFGLSSFR-PVQLEVINAVLLG-RDCFVVMPTGGGKSLC--------YQLPA----LCSDGIT---LVISPLISLM   64 (470)
T ss_pred             hhHhhcCCCCCC-HHHHHHHHHHHcC-CCEEEEcCCCCcHhHH--------HHHHH----HHcCCcE---EEEecHHHHH
Confidence            478889999955 8999999999999 8999999999999999        89998    6666666   9999999999


Q ss_pred             cccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEE
Q psy7952         119 YLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIV  197 (444)
Q Consensus       119 ~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iV  197 (444)
                           .+++..+ ..+   +.+..+.++....+......++.  .+.++|+++||+.+....  .+........++++||
T Consensus        65 -----~dq~~~l~~~g---i~~~~l~~~~~~~~~~~i~~~~~--~~~~~il~~TPe~l~~~~--~~~~~l~~~~~i~~iV  132 (470)
T TIGR00614        65 -----EDQVLQLKASG---IPATFLNSSQSKEQQKNVLTDLK--DGKIKLLYVTPEKCSASN--RLLQTLEERKGITLIA  132 (470)
T ss_pred             -----HHHHHHHHHcC---CcEEEEeCCCCHHHHHHHHHHHh--cCCCCEEEECHHHHcCch--hHHHHHHhcCCcCEEE
Confidence                 8889888 777   88889999888777766666653  467899999999986432  1222222567899999


Q ss_pred             EeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEccc
Q psy7952         198 VDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDL  277 (444)
Q Consensus       198 iDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  277 (444)
                      |||||++.+||++|++.+..+..+...+++ .+++++|||+++....++.+.+++..+. +...+..++++.+.+.....
T Consensus       133 iDEaH~i~~~g~~fr~~~~~l~~l~~~~~~-~~~l~lTAT~~~~~~~di~~~l~l~~~~-~~~~s~~r~nl~~~v~~~~~  210 (470)
T TIGR00614       133 VDEAHCISQWGHDFRPDYKALGSLKQKFPN-VPIMALTATASPSVREDILRQLNLKNPQ-IFCTSFDRPNLYYEVRRKTP  210 (470)
T ss_pred             EeCCcccCccccccHHHHHHHHHHHHHcCC-CceEEEecCCCHHHHHHHHHHcCCCCCc-EEeCCCCCCCcEEEEEeCCc
Confidence            999999999999999999999888887776 8999999999999988999988887774 44556778888777765432


Q ss_pred             chhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEc
Q psy7952         278 LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITAT  347 (444)
Q Consensus       278 ~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT  347 (444)
                        .....+...+..   .  ..+.++||||+++++++.++..|.+.          +++.+|..+++.|++|+++|||||
T Consensus       211 --~~~~~l~~~l~~---~--~~~~~~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT  283 (470)
T TIGR00614       211 --KILEDLLRFIRK---E--FKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVAT  283 (470)
T ss_pred             --cHHHHHHHHHHH---h--cCCCceEEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEe
Confidence              222333333332   1  14667799999999999999999876          899999999999999999999999


Q ss_pred             CccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhhccch
Q psy7952         348 ISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTST  412 (444)
Q Consensus       348 ~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~  412 (444)
                      +++++|||+|++++||++++|.|...|+||+||+||.|.+|.|++++.+.+...++.++......
T Consensus       284 ~~~~~GID~p~V~~VI~~~~P~s~~~y~Qr~GRaGR~G~~~~~~~~~~~~d~~~~~~~~~~~~~~  348 (470)
T TIGR00614       284 VAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLRRLLMEEPDG  348 (470)
T ss_pred             chhhccCCcccceEEEEeCCCCCHHHHHhhhcCcCCCCCCceEEEEechhHHHHHHHHHhcCCch
Confidence            99999999999999999999999999999999999999999999999999999999998765443

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

>KOG0331|consensus

Probab=100.00  E-value=7.9e-52  Score=394.77  Aligned_cols=337  Identities=22%  Similarity=0.303  Sum_probs=276.6

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc------CCccc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN------GNVRS  106 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~------~~~~~  106 (444)
                      ..+...+++.. ||+. ||++|...|+.++.| +|++..|.||||||++        |++|+ +.++..      .+..|
T Consensus        99 s~~~~~~lk~~-g~~~-PtpIQaq~wp~~l~G-rD~v~iA~TGSGKTLa--------y~lP~-i~~l~~~~~~~~~~~~P  166 (519)
T KOG0331|consen   99 SEELMKALKEQ-GFEK-PTPIQAQGWPIALSG-RDLVGIARTGSGKTLA--------YLLPA-IVHLNNEQGKLSRGDGP  166 (519)
T ss_pred             cHHHHHHHHhc-CCCC-CchhhhcccceeccC-CceEEEeccCCcchhh--------hhhHH-HHHHHhccccccCCCCC
Confidence            55667777775 9997 999999999999999 9999999999999999        99999 444443      34568


Q ss_pred             eeEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         107 RNGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       107 ~vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      ++||++|||+|+  +||.+.+..+  ...   ++...++|+.....+...+      ..+.+|+|+||+++.    +.+.
T Consensus       167 ~vLVL~PTRELA--~QV~~~~~~~~~~~~---~~~~cvyGG~~~~~Q~~~l------~~gvdiviaTPGRl~----d~le  231 (519)
T KOG0331|consen  167 IVLVLAPTRELA--VQVQAEAREFGKSLR---LRSTCVYGGAPKGPQLRDL------ERGVDVVIATPGRLI----DLLE  231 (519)
T ss_pred             eEEEEcCcHHHH--HHHHHHHHHHcCCCC---ccEEEEeCCCCccHHHHHH------hcCCcEEEeCChHHH----HHHH
Confidence            999999999999  6667777777  444   7799999999888665544      568999999999985    6666


Q ss_pred             HHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhh-CCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCC
Q psy7952         185 QHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFT-GNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST  263 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~  263 (444)
                      ....+++++.|+|+||||+|++.|  |.+.+..   ++... +...|.++.|||++..+......++.  ++..+.....
T Consensus       232 ~g~~~l~~v~ylVLDEADrMldmG--Fe~qI~~---Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~--~~~~i~ig~~  304 (519)
T KOG0331|consen  232 EGSLNLSRVTYLVLDEADRMLDMG--FEPQIRK---ILSQIPRPDRQTLMFSATWPKEVRQLAEDFLN--NPIQINVGNK  304 (519)
T ss_pred             cCCccccceeEEEeccHHhhhccc--cHHHHHH---HHHhcCCCcccEEEEeeeccHHHHHHHHHHhc--CceEEEecch
Confidence            777888999999999999999999  7765554   45566 44457999999999999888888876  5554444432


Q ss_pred             ----CCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHH
Q psy7952         264 ----FRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHER  329 (444)
Q Consensus       264 ----~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r  329 (444)
                          .+.++...+...+ ...+...+..++....   ...++++||||++++.|++++..|+..          .++.+|
T Consensus       305 ~~~~a~~~i~qive~~~-~~~K~~~l~~lL~~~~---~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR  380 (519)
T KOG0331|consen  305 KELKANHNIRQIVEVCD-ETAKLRKLGKLLEDIS---SDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSER  380 (519)
T ss_pred             hhhhhhcchhhhhhhcC-HHHHHHHHHHHHHHHh---ccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHH
Confidence                2333333333333 4445555555555554   236789999999999999999999885          889999


Q ss_pred             HHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         330 SRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       330 ~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      ..+++.|++|+..|||||+++++|+|+|+|++||+||+|.+.++|+||+||+||.|+.|.+++|+...+....+++.+
T Consensus       381 ~~~L~~FreG~~~vLVATdVAaRGLDi~dV~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~~~a~~l~~  458 (519)
T KOG0331|consen  381 DWVLKGFREGKSPVLVATDVAARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNAKLARELIK  458 (519)
T ss_pred             HHHHHhcccCCcceEEEcccccccCCCccccEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999988887777754

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=100.00  E-value=1.5e-50  Score=411.63  Aligned_cols=368  Identities=33%  Similarity=0.589  Sum_probs=300.0

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      +....+.+++.||++.|+ ++|+++++.++.| +++++.+|||+|||++        |++|+    +...+.+   ||++
T Consensus        10 ~~~~~~~l~~~fG~~~~r-~~Q~~ai~~il~g-~dvlv~apTGsGKTl~--------y~lpa----l~~~g~t---lVis   72 (607)
T PRK11057         10 ESLAKQVLQETFGYQQFR-PGQQEIIDAVLSG-RDCLVVMPTGGGKSLC--------YQIPA----LVLDGLT---LVVS   72 (607)
T ss_pred             hhHHHHHHHHHcCCCCCC-HHHHHHHHHHHcC-CCEEEEcCCCchHHHH--------HHHHH----HHcCCCE---EEEe
Confidence            444567899999999855 8999999999999 9999999999999999        89998    6667766   9999


Q ss_pred             chhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         113 PILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      |+++|+     .+++..+ ..+   +.+..+++.............+.  .+..+++++||+++....|..    .....
T Consensus        73 Pl~sL~-----~dqv~~l~~~g---i~~~~~~s~~~~~~~~~~~~~~~--~g~~~il~~tPe~l~~~~~~~----~l~~~  138 (607)
T PRK11057         73 PLISLM-----KDQVDQLLANG---VAAACLNSTQTREQQLEVMAGCR--TGQIKLLYIAPERLMMDNFLE----HLAHW  138 (607)
T ss_pred             cHHHHH-----HHHHHHHHHcC---CcEEEEcCCCCHHHHHHHHHHHh--CCCCcEEEEChHHhcChHHHH----HHhhC
Confidence            999999     8888888 777   88888888887776666655554  467899999999987533222    23345


Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEE
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYD  271 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~  271 (444)
                      ++++|||||||++.+||++|++.|..+..+...+++ .+++++|||+++....++...+++.++. +...+..++++.+.
T Consensus       139 ~l~~iVIDEaH~i~~~G~~fr~~y~~L~~l~~~~p~-~~~v~lTAT~~~~~~~di~~~l~l~~~~-~~~~~~~r~nl~~~  216 (607)
T PRK11057        139 NPALLAVDEAHCISQWGHDFRPEYAALGQLRQRFPT-LPFMALTATADDTTRQDIVRLLGLNDPL-IQISSFDRPNIRYT  216 (607)
T ss_pred             CCCEEEEeCccccccccCcccHHHHHHHHHHHhCCC-CcEEEEecCCChhHHHHHHHHhCCCCeE-EEECCCCCCcceee
Confidence            899999999999999999999999999888887765 8999999999999888888888887774 44456678888776


Q ss_pred             EEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCc
Q psy7952         272 VIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEI  341 (444)
Q Consensus       272 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~  341 (444)
                      +.....   ....+...+.    ..  .+.++||||+|+++|+.++..|.+.          +++.+|..+++.|++|+.
T Consensus       217 v~~~~~---~~~~l~~~l~----~~--~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~  287 (607)
T PRK11057        217 LVEKFK---PLDQLMRYVQ----EQ--RGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDL  287 (607)
T ss_pred             eeeccc---hHHHHHHHHH----hc--CCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCC
Confidence            654321   2222333322    22  5678999999999999999999876          889999999999999999


Q ss_pred             cEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhhccchhHHHHHHHH
Q psy7952         342 NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKF  421 (444)
Q Consensus       342 ~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  421 (444)
                      +|||||+++++|||+|++++||++++|.|...|+||+||+||.|.+|.+++++++.+...++.++.......  ......
T Consensus       288 ~VLVaT~a~~~GIDip~V~~VI~~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d~~~~~~~~~~~~~~~--~~~~~~  365 (607)
T PRK11057        288 QIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPAGQ--QQDIER  365 (607)
T ss_pred             CEEEEechhhccCCCCCcCEEEEeCCCCCHHHHHHHhhhccCCCCCceEEEEeCHHHHHHHHHHHhcCCcHH--HHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999998887654433  222334


Q ss_pred             hhHHHHHHHhh---------hceeeeecccCC
Q psy7952         422 KNYLSMLEYCE---------QGYFLVILVFPC  444 (444)
Q Consensus       422 ~~~~~~~~~~~---------~~~~~~~~~~~~  444 (444)
                      ..+..|..||+         -.||.+....||
T Consensus       366 ~~l~~~~~~~~~~~Crr~~~l~yf~e~~~~~c  397 (607)
T PRK11057        366 HKLNAMGAFAEAQTCRRLVLLNYFGEGRQEPC  397 (607)
T ss_pred             HHHHHHHHHHhcccCHHHHHHHHhCCCCCCCC
Confidence            56777888877         346666543343

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=100.00  E-value=2.1e-50  Score=411.88  Aligned_cols=354  Identities=35%  Similarity=0.616  Sum_probs=298.3

Q ss_pred             HHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhh
Q psy7952          37 TAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILS  116 (444)
Q Consensus        37 ~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~  116 (444)
                      .+.|++.|||+.|+ ++|.++++.+++| +|+++.+|||+|||++        |++|+    +...+.+   +|++|+++
T Consensus         2 ~~~l~~~fg~~~fr-~~Q~~~i~~il~g-~dvlv~~PTG~GKTl~--------y~lpa----l~~~g~~---lVisPl~s   64 (591)
T TIGR01389         2 QQVLKRTFGYDDFR-PGQEEIISHVLDG-RDVLVVMPTGGGKSLC--------YQVPA----LLLKGLT---VVISPLIS   64 (591)
T ss_pred             hHHHHHhcCCCCCC-HHHHHHHHHHHcC-CCEEEEcCCCccHhHH--------HHHHH----HHcCCcE---EEEcCCHH
Confidence            45789999999977 8999999999999 8999999999999999        88998    6667766   99999999


Q ss_pred             hhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccE
Q psy7952         117 SFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAY  195 (444)
Q Consensus       117 L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~  195 (444)
                      |+     .+|+..+ ..+   +.+..++++....+.......+.  .+..+|+++||+++.+..|    .......++++
T Consensus        65 L~-----~dq~~~l~~~g---i~~~~~~s~~~~~~~~~~~~~l~--~~~~~il~~tpe~l~~~~~----~~~l~~~~l~~  130 (591)
T TIGR01389        65 LM-----KDQVDQLRAAG---VAAAYLNSTLSAKEQQDIEKALV--NGELKLLYVAPERLEQDYF----LNMLQRIPIAL  130 (591)
T ss_pred             HH-----HHHHHHHHHcC---CcEEEEeCCCCHHHHHHHHHHHh--CCCCCEEEEChhHhcChHH----HHHHhcCCCCE
Confidence            99     8899988 777   88999999998887776666554  4678999999999975433    33345678999


Q ss_pred             EEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEc
Q psy7952         196 IVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFD  275 (444)
Q Consensus       196 iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  275 (444)
                      |||||||++++||++|++.|..+..+...+++ .+++++|||+++....++...+++.++.. +..+..++++.+.+...
T Consensus       131 iViDEaH~i~~~g~~frp~y~~l~~l~~~~~~-~~vi~lTAT~~~~~~~~i~~~l~~~~~~~-~~~~~~r~nl~~~v~~~  208 (591)
T TIGR01389       131 VAVDEAHCVSQWGHDFRPEYQRLGSLAERFPQ-VPRIALTATADAETRQDIRELLRLADANE-FITSFDRPNLRFSVVKK  208 (591)
T ss_pred             EEEeCCcccccccCccHHHHHHHHHHHHhCCC-CCEEEEEeCCCHHHHHHHHHHcCCCCCCe-EecCCCCCCcEEEEEeC
Confidence            99999999999999999999999988888877 66999999999999999999988877644 44567788888877654


Q ss_pred             ccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEE
Q psy7952         276 DLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVIT  345 (444)
Q Consensus       276 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLv  345 (444)
                      .   .....+.+.+..    .  .+.++||||+|++.++.++..|...          ++.++|..+++.|.+|+++|||
T Consensus       209 ~---~~~~~l~~~l~~----~--~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlV  279 (591)
T TIGR01389       209 N---NKQKFLLDYLKK----H--RGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMV  279 (591)
T ss_pred             C---CHHHHHHHHHHh----c--CCCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEE
Confidence            3   222333333332    2  3678999999999999999999865          8899999999999999999999


Q ss_pred             EcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhhccchhHHHHHHHHhhHH
Q psy7952         346 ATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYL  425 (444)
Q Consensus       346 aT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  425 (444)
                      ||+++++|||+|++++||++++|.|...|+|++||+||.|.++.|++++++.+...++.++....+... ........+.
T Consensus       280 aT~a~~~GID~p~v~~VI~~~~p~s~~~y~Q~~GRaGR~G~~~~~il~~~~~d~~~~~~~i~~~~~~~~-~~~~~~~~l~  358 (591)
T TIGR01389       280 ATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLKRRIEQSEADDD-YKQIEREKLR  358 (591)
T ss_pred             EechhhccCcCCCCCEEEEcCCCCCHHHHhhhhccccCCCCCceEEEecCHHHHHHHHHHHhccCCcHH-HHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999877554432 2223456677


Q ss_pred             HHHHHhhh
Q psy7952         426 SMLEYCEQ  433 (444)
Q Consensus       426 ~~~~~~~~  433 (444)
                      +|..||+.
T Consensus       359 ~~~~~~~~  366 (591)
T TIGR01389       359 AMIAYCET  366 (591)
T ss_pred             HHHHHHcc
Confidence            78888774

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.

>KOG0330|consensus

Probab=100.00  E-value=2.9e-51  Score=367.36  Aligned_cols=333  Identities=19%  Similarity=0.233  Sum_probs=274.0

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ...+.++.++. |+.. ||++|.++++.++.| +|++..|.||||||.+        |++|+ ++.++.....++++|++
T Consensus        69 ~~~L~~ac~~l-~~~~-PT~IQ~~aiP~~L~g-~dvIglAeTGSGKT~a--------faLPI-l~~LL~~p~~~~~lVLt  136 (476)
T KOG0330|consen   69 HPELLEACQEL-GWKK-PTKIQSEAIPVALGG-RDVIGLAETGSGKTGA--------FALPI-LQRLLQEPKLFFALVLT  136 (476)
T ss_pred             CHHHHHHHHHh-CcCC-CchhhhhhcchhhCC-CcEEEEeccCCCchhh--------hHHHH-HHHHHcCCCCceEEEec
Confidence            56677888875 8887 999999999999999 9999999999999999        99999 88888887778999999


Q ss_pred             chhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH-HHHHh
Q psy7952         113 PILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL-QHLVR  189 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~-~~~~~  189 (444)
                      |||+|+  +||.++++.+  ..|   +.+..+.|+.+.......+      ...++|+|+||++|.    +.+. ....+
T Consensus       137 PtRELA--~QI~e~fe~Lg~~ig---lr~~~lvGG~~m~~q~~~L------~kkPhilVaTPGrL~----dhl~~Tkgf~  201 (476)
T KOG0330|consen  137 PTRELA--QQIAEQFEALGSGIG---LRVAVLVGGMDMMLQANQL------SKKPHILVATPGRLW----DHLENTKGFS  201 (476)
T ss_pred             CcHHHH--HHHHHHHHHhccccC---eEEEEEecCchHHHHHHHh------hcCCCEEEeCcHHHH----HHHHhccCcc
Confidence            999999  7778899888  667   9999999999876554443      578999999999984    3333 23344


Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCC--CC
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFR--SN  267 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~--~~  267 (444)
                      +..++++|+||||++++..  |...++   .++..+|...|.+++|||++..+.+...  ..+.++..+...+...  +.
T Consensus       202 le~lk~LVlDEADrlLd~d--F~~~ld---~ILk~ip~erqt~LfsATMt~kv~kL~r--asl~~p~~v~~s~ky~tv~~  274 (476)
T KOG0330|consen  202 LEQLKFLVLDEADRLLDMD--FEEELD---YILKVIPRERQTFLFSATMTKKVRKLQR--ASLDNPVKVAVSSKYQTVDH  274 (476)
T ss_pred             HHHhHHHhhchHHhhhhhh--hHHHHH---HHHHhcCccceEEEEEeecchhhHHHHh--hccCCCeEEeccchhcchHH
Confidence            5688999999999999876  665555   4555677889999999999998877543  3456676666554332  22


Q ss_pred             ceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHh
Q psy7952         268 LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFM  337 (444)
Q Consensus       268 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~  337 (444)
                      +...+.+.. ...+..++..++.+.      .+..+||||++..++..++-.|+..          |+++.|...+++|+
T Consensus       275 lkQ~ylfv~-~k~K~~yLV~ll~e~------~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk  347 (476)
T KOG0330|consen  275 LKQTYLFVP-GKDKDTYLVYLLNEL------AGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFK  347 (476)
T ss_pred             hhhheEecc-ccccchhHHHHHHhh------cCCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHh
Confidence            222222222 123444566666654      5689999999999999999999887          99999999999999


Q ss_pred             cCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHH
Q psy7952         338 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI  406 (444)
Q Consensus       338 ~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  406 (444)
                      +|...||+|||++++|+|+|.+++||+||.|.+..+|+||+||++|.|.+|.++.+++..|.+-++++.
T Consensus       348 ~~~r~iLv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqyDve~~qrIE  416 (476)
T KOG0330|consen  348 AGARSILVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDVELVQRIE  416 (476)
T ss_pred             ccCCcEEEecchhcccCCCCCceEEEecCCCCcHHHHHHHcccccccCCCcceEEEEehhhhHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999988877774

>KOG0328|consensus

Probab=100.00  E-value=1.6e-49  Score=341.65  Aligned_cols=335  Identities=17%  Similarity=0.268  Sum_probs=279.9

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      .+++.+++-. +||+. |+.+|++|+++++.| +|++..+..|+|||.+        |.+.. ++.+--+.+...+++++
T Consensus        35 ~edlLrgiY~-yGfek-PS~IQqrAi~~IlkG-rdViaQaqSGTGKTa~--------~si~v-lq~~d~~~r~tQ~lils  102 (400)
T KOG0328|consen   35 KEDLLRGIYA-YGFEK-PSAIQQRAIPQILKG-RDVIAQAQSGTGKTAT--------FSISV-LQSLDISVRETQALILS  102 (400)
T ss_pred             hHHHHHHHHH-hccCC-chHHHhhhhhhhhcc-cceEEEecCCCCceEE--------EEeee-eeecccccceeeEEEec
Confidence            5677777766 59998 999999999999999 9999999999999999        77777 44444444545789999


Q ss_pred             chhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhh
Q psy7952         113 PILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRY  190 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~  190 (444)
                      ||++|+  .|+.+.+..+  .++   +.+....|+.+..+....+      .-+.+++.+||+++.    +.+.......
T Consensus       103 PTRELa--~Qi~~vi~alg~~mn---vq~hacigg~n~gedikkl------d~G~hvVsGtPGrv~----dmikr~~L~t  167 (400)
T KOG0328|consen  103 PTRELA--VQIQKVILALGDYMN---VQCHACIGGKNLGEDIKKL------DYGQHVVSGTPGRVL----DMIKRRSLRT  167 (400)
T ss_pred             ChHHHH--HHHHHHHHHhccccc---ceEEEEecCCccchhhhhh------cccceEeeCCCchHH----HHHHhccccc
Confidence            999999  5567777777  667   9999999998876544443      357899999999985    7777888888


Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEec--CCCCCCc
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT--STFRSNL  268 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~--~~~~~~~  268 (444)
                      ..+.++|+||++.+++.|  |.   ..+..+++.+|+++|++++|||++....+....+  +++|+.+...  ......+
T Consensus       168 r~vkmlVLDEaDemL~kg--fk---~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kf--mtdpvrilvkrdeltlEgI  240 (400)
T KOG0328|consen  168 RAVKMLVLDEADEMLNKG--FK---EQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKF--MTDPVRILVKRDELTLEGI  240 (400)
T ss_pred             cceeEEEeccHHHHHHhh--HH---HHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHh--cCCceeEEEecCCCchhhh
Confidence            899999999999998877  66   4455666788988999999999999998877665  4666655543  3333445


Q ss_pred             eEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhc
Q psy7952         269 FYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMR  338 (444)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~  338 (444)
                      ...+...+..+.+...++++...+      .-.+.+|||||+..+..+.+.+++.          |..++|+.+.+.|++
T Consensus       241 Kqf~v~ve~EewKfdtLcdLYd~L------tItQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRs  314 (400)
T KOG0328|consen  241 KQFFVAVEKEEWKFDTLCDLYDTL------TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRS  314 (400)
T ss_pred             hhheeeechhhhhHhHHHHHhhhh------ehheEEEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhc
Confidence            555565666666777777766665      4567899999999999999999887          899999999999999


Q ss_pred             CCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         339 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       339 g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      |..+||++|++.++|+|+|.+++||+||.|.+.+.|+||+||.||.|+.|.++-|+..++.+.++.+.+
T Consensus       315 g~SrvLitTDVwaRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainFVk~~d~~~lrdieq  383 (400)
T KOG0328|consen  315 GKSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDLRILRDIEQ  383 (400)
T ss_pred             CCceEEEEechhhccCCcceeEEEEecCCCccHHHHhhhhccccccCCcceEEEEecHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999988877754

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=7.9e-49  Score=393.66  Aligned_cols=338  Identities=18%  Similarity=0.272  Sum_probs=255.9

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccc----cCCcccee
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFIL----NGNVRSRN  108 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~----~~~~~~~v  108 (444)
                      ++.+.+++++ +||+. ||++|.++++.++.| +|+++++|||+|||++        |++|++.+...    ..+..+.+
T Consensus       138 ~~~l~~~l~~-~g~~~-pt~iQ~~aip~~l~G-~dvI~~ApTGSGKTla--------ylLP~l~~i~~~~~~~~~~gp~~  206 (545)
T PTZ00110        138 PDYILKSLKN-AGFTE-PTPIQVQGWPIALSG-RDMIGIAETGSGKTLA--------FLLPAIVHINAQPLLRYGDGPIV  206 (545)
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhcC-CCEEEEeCCCChHHHH--------HHHHHHHHHHhcccccCCCCcEE
Confidence            4578888887 59998 899999999999999 9999999999999999        77777222211    12334678


Q ss_pred             EEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         109 GWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       109 lil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      ||++||++|+  .|+.+.+..+  ..+   +++..+.++.........+      ..+++|+|+||++|.    +.+...
T Consensus       207 LIL~PTreLa--~Qi~~~~~~~~~~~~---i~~~~~~gg~~~~~q~~~l------~~~~~IlVaTPgrL~----d~l~~~  271 (545)
T PTZ00110        207 LVLAPTRELA--EQIREQCNKFGASSK---IRNTVAYGGVPKRGQIYAL------RRGVEILIACPGRLI----DFLESN  271 (545)
T ss_pred             EEECChHHHH--HHHHHHHHHHhcccC---ccEEEEeCCCCHHHHHHHH------HcCCCEEEECHHHHH----HHHHcC
Confidence            9999999999  4445666665  334   7788888887765443322      357899999999985    444444


Q ss_pred             HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCC---
Q psy7952         187 LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST---  263 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~---  263 (444)
                      ...+.++++||+||||++.+++  |...+..   ++...+.+.|++++|||++.........++. ..++.+.....   
T Consensus       272 ~~~l~~v~~lViDEAd~mld~g--f~~~i~~---il~~~~~~~q~l~~SAT~p~~v~~l~~~l~~-~~~v~i~vg~~~l~  345 (545)
T PTZ00110        272 VTNLRRVTYLVLDEADRMLDMG--FEPQIRK---IVSQIRPDRQTLMWSATWPKEVQSLARDLCK-EEPVHVNVGSLDLT  345 (545)
T ss_pred             CCChhhCcEEEeehHHhhhhcc--hHHHHHH---HHHhCCCCCeEEEEEeCCCHHHHHHHHHHhc-cCCEEEEECCCccc
Confidence            5567789999999999999887  6655544   4445666789999999998876655444432 33444333221   


Q ss_pred             CCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHH
Q psy7952         264 FRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQ  333 (444)
Q Consensus       264 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~  333 (444)
                      ...++...+.... ...+...+..++...    ...+.++||||++++.|+.++..|...          +++++|..++
T Consensus       346 ~~~~i~q~~~~~~-~~~k~~~L~~ll~~~----~~~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il  420 (545)
T PTZ00110        346 ACHNIKQEVFVVE-EHEKRGKLKMLLQRI----MRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVL  420 (545)
T ss_pred             cCCCeeEEEEEEe-chhHHHHHHHHHHHh----cccCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHH
Confidence            1223333332221 123333344444332    225789999999999999999999865          7899999999


Q ss_pred             HHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         334 ESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       334 ~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      +.|++|+.+|||||+++++|||+|++++||++|+|.+...|+||+||+||.|..|.+++|+++++......+.+
T Consensus       421 ~~F~~G~~~ILVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~~~~~~~~l~~  494 (545)
T PTZ00110        421 NEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVK  494 (545)
T ss_pred             HHHhcCCCcEEEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECcchHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999998877666644

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=1.6e-48  Score=387.71  Aligned_cols=337  Identities=15%  Similarity=0.195  Sum_probs=259.0

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ...+.+++.. +||+. ||++|.++++.+++| +|++++||||+|||++        |.+|+ ++.+.......+++|++
T Consensus        12 ~~~l~~~l~~-~g~~~-~t~iQ~~ai~~~l~g-~dvi~~a~TGsGKT~a--------~~lpi-l~~l~~~~~~~~~lil~   79 (460)
T PRK11776         12 PPALLANLNE-LGYTE-MTPIQAQSLPAILAG-KDVIAQAKTGSGKTAA--------FGLGL-LQKLDVKRFRVQALVLC   79 (460)
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhcC-CCEEEECCCCCcHHHH--------HHHHH-HHHhhhccCCceEEEEe
Confidence            4577888887 59998 889999999999999 9999999999999999        77777 44444333345789999


Q ss_pred             chhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCC
Q psy7952         113 PILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK  192 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~  192 (444)
                      ||++|+  .|+.+.++.+......+++..++|+.+.......+      ..+++|+|+||+++.    ..+......+.+
T Consensus        80 PtreLa--~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l------~~~~~IvV~Tp~rl~----~~l~~~~~~l~~  147 (460)
T PRK11776         80 PTRELA--DQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSL------EHGAHIIVGTPGRIL----DHLRKGTLDLDA  147 (460)
T ss_pred             CCHHHH--HHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHh------cCCCCEEEEChHHHH----HHHHcCCccHHH
Confidence            999999  44455555553222238899999998876554333      468899999999985    334444456778


Q ss_pred             ccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCC-CCCCceEE
Q psy7952         193 LAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST-FRSNLFYD  271 (444)
Q Consensus       193 ~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~-~~~~~~~~  271 (444)
                      +++||+||||++.+++  |...   +..++...+...|++++|||+++........++  ..+..+..... ..+.+...
T Consensus       148 l~~lViDEad~~l~~g--~~~~---l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~--~~~~~i~~~~~~~~~~i~~~  220 (460)
T PRK11776        148 LNTLVLDEADRMLDMG--FQDA---IDAIIRQAPARRQTLLFSATYPEGIAAISQRFQ--RDPVEVKVESTHDLPAIEQR  220 (460)
T ss_pred             CCEEEEECHHHHhCcC--cHHH---HHHHHHhCCcccEEEEEEecCcHHHHHHHHHhc--CCCEEEEECcCCCCCCeeEE
Confidence            9999999999998877  5544   445556677778999999999987766555544  34444433332 22333333


Q ss_pred             EEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCc
Q psy7952         272 VIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEI  341 (444)
Q Consensus       272 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~  341 (444)
                      +..... ..+.    +.+..++...  ...++||||++++.++.+++.|...          +++.+|..+++.|++|+.
T Consensus       221 ~~~~~~-~~k~----~~l~~ll~~~--~~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~  293 (460)
T PRK11776        221 FYEVSP-DERL----PALQRLLLHH--QPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSC  293 (460)
T ss_pred             EEEeCc-HHHH----HHHHHHHHhc--CCCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCC
Confidence            332221 1222    3333333332  4678999999999999999999876          899999999999999999


Q ss_pred             cEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         342 NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       342 ~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      ++||||+++++|+|+|++++||++|.|.+...|+||+||+||.|..|.+++++.+++...+..+.+
T Consensus       294 ~vLVaTdv~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~~e~~~~~~i~~  359 (460)
T PRK11776        294 SVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIED  359 (460)
T ss_pred             cEEEEecccccccchhcCCeEEEecCCCCHhHhhhhcccccCCCCcceEEEEEchhHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999988877666643

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=6.2e-49  Score=386.45  Aligned_cols=332  Identities=18%  Similarity=0.247  Sum_probs=251.1

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC-------Ccc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG-------NVR  105 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~-------~~~  105 (444)
                      +..+.+++.. +||.. ||++|.++++.++.| +|++++||||+|||++        |++|+ ++.+...       ...
T Consensus        16 ~~~l~~~l~~-~g~~~-pt~iQ~~aip~il~g-~dvi~~ApTGsGKTla--------~llp~-l~~l~~~~~~~~~~~~~   83 (423)
T PRK04837         16 HPQVVEALEK-KGFHN-CTPIQALALPLTLAG-RDVAGQAQTGTGKTMA--------FLTAT-FHYLLSHPAPEDRKVNQ   83 (423)
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CcEEEECCCCchHHHH--------HHHHH-HHHHHhcccccccccCC
Confidence            4678888887 69998 889999999999999 9999999999999999        76666 3333211       123


Q ss_pred             ceeEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYL  183 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~  183 (444)
                      +++||++||++|+  .|+.+++..+  ..+   +++..++|+.........+      ..+++|+|+||+++.    ..+
T Consensus        84 ~~~lil~PtreLa--~Qi~~~~~~l~~~~~---~~v~~~~gg~~~~~~~~~l------~~~~~IlV~TP~~l~----~~l  148 (423)
T PRK04837         84 PRALIMAPTRELA--VQIHADAEPLAQATG---LKLGLAYGGDGYDKQLKVL------ESGVDILIGTTGRLI----DYA  148 (423)
T ss_pred             ceEEEECCcHHHH--HHHHHHHHHHhccCC---ceEEEEECCCCHHHHHHHh------cCCCCEEEECHHHHH----HHH
Confidence            6789999999999  3345555555  345   8888889887765443333      457899999999985    444


Q ss_pred             HHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCC--CCcEEEEeccCCcchHHHHHHHhcCCCCeEEEec
Q psy7952         184 LQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGN--SIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT  261 (444)
Q Consensus       184 ~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~--~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~  261 (444)
                      ......+.+++++|+||||++.+++  |...+.   .+++..+.  ..+.+++|||++..........+  ..+..+...
T Consensus       149 ~~~~~~l~~v~~lViDEad~l~~~~--f~~~i~---~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~--~~p~~i~v~  221 (423)
T PRK04837        149 KQNHINLGAIQVVVLDEADRMFDLG--FIKDIR---WLFRRMPPANQRLNMLFSATLSYRVRELAFEHM--NNPEYVEVE  221 (423)
T ss_pred             HcCCcccccccEEEEecHHHHhhcc--cHHHHH---HHHHhCCCccceeEEEEeccCCHHHHHHHHHHC--CCCEEEEEc
Confidence            4455667899999999999998877  554443   34444543  24578999999987776655554  344433332


Q ss_pred             CCC--CCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHH
Q psy7952         262 STF--RSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHER  329 (444)
Q Consensus       262 ~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r  329 (444)
                      ...  ...+....... ..    ......+..++...  ...++||||+++..|+.++..|...          +++.+|
T Consensus       222 ~~~~~~~~i~~~~~~~-~~----~~k~~~l~~ll~~~--~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R  294 (423)
T PRK04837        222 PEQKTGHRIKEELFYP-SN----EEKMRLLQTLIEEE--WPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKR  294 (423)
T ss_pred             CCCcCCCceeEEEEeC-CH----HHHHHHHHHHHHhc--CCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHH
Confidence            221  22222222221 11    22233444444333  4678999999999999999999875          788999


Q ss_pred             HHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHH
Q psy7952         330 SRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV  405 (444)
Q Consensus       330 ~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~  405 (444)
                      ..+++.|++|+++|||||+++++|+|+|++++||+||+|.+...|+||+||+||.|+.|.+++|+.+++...+..+
T Consensus       295 ~~~l~~F~~g~~~vLVaTdv~~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~~~~~~~~i  370 (423)
T PRK04837        295 LRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYALNLPAI  370 (423)
T ss_pred             HHHHHHHHcCCCcEEEEechhhcCCCccccCEEEEeCCCCchhheEeccccccCCCCCeeEEEEeCHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999998877666665

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=3e-48  Score=383.99  Aligned_cols=335  Identities=19%  Similarity=0.266  Sum_probs=253.8

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC------Cccc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG------NVRS  106 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~------~~~~  106 (444)
                      ..++.+++.+ +||.. ||++|.++++.++++ +|+++++|||+|||++        |++|+ ++.+...      ....
T Consensus         9 ~~~l~~~l~~-~g~~~-pt~iQ~~ai~~il~g-~dvlv~apTGsGKTla--------~~lpi-l~~l~~~~~~~~~~~~~   76 (456)
T PRK10590          9 SPDILRAVAE-QGYRE-PTPIQQQAIPAVLEG-RDLMASAQTGTGKTAG--------FTLPL-LQHLITRQPHAKGRRPV   76 (456)
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CCEEEECCCCCcHHHH--------HHHHH-HHHhhhcccccccCCCc
Confidence            4568888988 59998 889999999999999 9999999999999999        77776 3333221      1224


Q ss_pred             eeEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         107 RNGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       107 ~vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      ++||++||++|+  .|+.+.+..+  ..+   +.+..++|+.........+      .+.++|+|+||+++.    ....
T Consensus        77 ~aLil~PtreLa--~Qi~~~~~~~~~~~~---~~~~~~~gg~~~~~~~~~l------~~~~~IiV~TP~rL~----~~~~  141 (456)
T PRK10590         77 RALILTPTRELA--AQIGENVRDYSKYLN---IRSLVVFGGVSINPQMMKL------RGGVDVLVATPGRLL----DLEH  141 (456)
T ss_pred             eEEEEeCcHHHH--HHHHHHHHHHhccCC---CEEEEEECCcCHHHHHHHH------cCCCcEEEEChHHHH----HHHH
Confidence            789999999999  3335555555  334   7788888888765543322      468899999999985    3334


Q ss_pred             HHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCC
Q psy7952         185 QHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTF  264 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~  264 (444)
                      .....+.++++||+||||++.+++  +.   ..+..++..++...|++++|||++..........+..+..+.+......
T Consensus       142 ~~~~~l~~v~~lViDEah~ll~~~--~~---~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~  216 (456)
T PRK10590        142 QNAVKLDQVEILVLDEADRMLDMG--FI---HDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTA  216 (456)
T ss_pred             cCCcccccceEEEeecHHHHhccc--cH---HHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEeccccc
Confidence            444567889999999999998877  44   3344455667777899999999998766655555432222222222222


Q ss_pred             CCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHH
Q psy7952         265 RSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQE  334 (444)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~  334 (444)
                      ...+...+.....     ....+++..++...  ...++||||+++..++.+++.|...          +++.+|..+++
T Consensus       217 ~~~i~~~~~~~~~-----~~k~~~l~~l~~~~--~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~  289 (456)
T PRK10590        217 SEQVTQHVHFVDK-----KRKRELLSQMIGKG--NWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALA  289 (456)
T ss_pred             ccceeEEEEEcCH-----HHHHHHHHHHHHcC--CCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHH
Confidence            3333333333221     12223344444332  4678999999999999999999876          88999999999


Q ss_pred             HHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHH
Q psy7952         335 SFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI  406 (444)
Q Consensus       335 ~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  406 (444)
                      .|++|+++|||||+++++|||+|++++||+|++|.+..+|+||+||+||.|..|.+++++...+...++.+.
T Consensus       290 ~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~d~~~~~~ie  361 (456)
T PRK10590        290 DFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIE  361 (456)
T ss_pred             HHHcCCCcEEEEccHHhcCCCcccCCEEEEeCCCCCHHHhhhhccccccCCCCeeEEEEecHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999988877666654

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

Probab=100.00  E-value=2.6e-48  Score=386.26  Aligned_cols=339  Identities=20%  Similarity=0.277  Sum_probs=270.9

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc-CCccce-eE
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN-GNVRSR-NG  109 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~-~~~~~~-vl  109 (444)
                      ...++.+++++ .||.. ||++|..+++.++.| +|++..|+||+|||++        |.+|. ++.+.. ...... +|
T Consensus        36 l~~~ll~~l~~-~gf~~-pt~IQ~~~IP~~l~g-~Dvi~~A~TGsGKT~A--------f~lP~-l~~l~~~~~~~~~~aL  103 (513)
T COG0513          36 LSPELLQALKD-LGFEE-PTPIQLAAIPLILAG-RDVLGQAQTGTGKTAA--------FLLPL-LQKILKSVERKYVSAL  103 (513)
T ss_pred             CCHHHHHHHHH-cCCCC-CCHHHHHHHHHHhCC-CCEEEECCCCChHHHH--------HHHHH-HHHHhcccccCCCceE
Confidence            46788899998 59998 999999999999999 9999999999999999        99999 555553 121112 79


Q ss_pred             EEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh
Q psy7952         110 WISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR  189 (444)
Q Consensus       110 il~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~  189 (444)
                      |++||++|+  .|+.+.+..+......+.+..++|+.+...+...+.      .+++|+|+||+++.    +.+......
T Consensus       104 il~PTRELA--~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~------~~~~ivVaTPGRll----D~i~~~~l~  171 (513)
T COG0513         104 ILAPTRELA--VQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALK------RGVDIVVATPGRLL----DLIKRGKLD  171 (513)
T ss_pred             EECCCHHHH--HHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHh------cCCCEEEECccHHH----HHHHcCCcc
Confidence            999999999  566777777722211388999999988876664442      36999999999986    555555677


Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEec--CC--CC
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT--ST--FR  265 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~--~~--~~  265 (444)
                      +..+.++|+||||+|++.|  |...+..   +....+.+.|.+++|||++.........++.  +|..+...  ..  ..
T Consensus       172 l~~v~~lVlDEADrmLd~G--f~~~i~~---I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~--~p~~i~v~~~~~~~~~  244 (513)
T COG0513         172 LSGVETLVLDEADRMLDMG--FIDDIEK---ILKALPPDRQTLLFSATMPDDIRELARRYLN--DPVEIEVSVEKLERTL  244 (513)
T ss_pred             hhhcCEEEeccHhhhhcCC--CHHHHHH---HHHhCCcccEEEEEecCCCHHHHHHHHHHcc--CCcEEEEccccccccc
Confidence            8899999999999999997  7755555   4456666799999999999987776666654  55444443  22  34


Q ss_pred             CCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHH
Q psy7952         266 SNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQES  335 (444)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~  335 (444)
                      ..+...+.......    .....+..++...  ...++||||+++..++.++..|...          +++++|...++.
T Consensus       245 ~~i~q~~~~v~~~~----~k~~~L~~ll~~~--~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~  318 (513)
T COG0513         245 KKIKQFYLEVESEE----EKLELLLKLLKDE--DEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEK  318 (513)
T ss_pred             cCceEEEEEeCCHH----HHHHHHHHHHhcC--CCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHH
Confidence            55665555554333    2334444444444  3447999999999999999999887          899999999999


Q ss_pred             HhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEeccc-chhhHHHHHh
Q psy7952         336 FMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEH-SKKSLEYVIK  407 (444)
Q Consensus       336 f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~~~~  407 (444)
                      |++|+.+||||||++++|||+|++++||+||.|.+.+.|+||+||+||.|..|.++.|+.+. +...+..+.+
T Consensus       319 F~~g~~~vLVaTDvaaRGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~~e~~~l~~ie~  391 (513)
T COG0513         319 FKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEK  391 (513)
T ss_pred             HHcCCCCEEEEechhhccCCccccceeEEccCCCCHHHheeccCccccCCCCCeEEEEeCcHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999875 6666655543

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

Probab=100.00  E-value=3.9e-48  Score=387.69  Aligned_cols=337  Identities=21%  Similarity=0.317  Sum_probs=250.1

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc-------CCcc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN-------GNVR  105 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~-------~~~~  105 (444)
                      +..+.+.++. .||.. ||++|.++++.++.| +|+++.+|||+|||++        |++|+ +..+..       .+..
T Consensus       129 ~~~l~~~L~~-~g~~~-ptpiQ~~aip~il~g-~dviv~ApTGSGKTla--------yllPi-l~~l~~~~~~~~~~~~~  196 (518)
T PLN00206        129 PPKLLLNLET-AGYEF-PTPIQMQAIPAALSG-RSLLVSADTGSGKTAS--------FLVPI-ISRCCTIRSGHPSEQRN  196 (518)
T ss_pred             CHHHHHHHHH-cCCCC-CCHHHHHHHHHHhcC-CCEEEEecCCCCccHH--------HHHHH-HHHHHhhccccccccCC
Confidence            5667888887 59997 889999999999999 9999999999999999        77776 322211       2244


Q ss_pred             ceeEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ  185 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~  185 (444)
                      +++||++||++|+  .|+.++++.+..+. .+++..+.|+........      .+..+++|+|+||+++.    ..+..
T Consensus       197 ~~aLIL~PTreLa--~Qi~~~~~~l~~~~-~~~~~~~~gG~~~~~q~~------~l~~~~~IiV~TPgrL~----~~l~~  263 (518)
T PLN00206        197 PLAMVLTPTRELC--VQVEDQAKVLGKGL-PFKTALVVGGDAMPQQLY------RIQQGVELIVGTPGRLI----DLLSK  263 (518)
T ss_pred             ceEEEEeCCHHHH--HHHHHHHHHHhCCC-CceEEEEECCcchHHHHH------HhcCCCCEEEECHHHHH----HHHHc
Confidence            6789999999999  44466666662221 267777777766543322      23467899999999985    34444


Q ss_pred             HHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCC
Q psy7952         186 HLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFR  265 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~  265 (444)
                      ....+.++++||+||||++.+++  |+..+..+   +..+++ .|++++|||+++.........  ..++..+.......
T Consensus       264 ~~~~l~~v~~lViDEad~ml~~g--f~~~i~~i---~~~l~~-~q~l~~SATl~~~v~~l~~~~--~~~~~~i~~~~~~~  335 (518)
T PLN00206        264 HDIELDNVSVLVLDEVDCMLERG--FRDQVMQI---FQALSQ-PQVLLFSATVSPEVEKFASSL--AKDIILISIGNPNR  335 (518)
T ss_pred             CCccchheeEEEeecHHHHhhcc--hHHHHHHH---HHhCCC-CcEEEEEeeCCHHHHHHHHHh--CCCCEEEEeCCCCC
Confidence            45567889999999999999887  77655544   334444 899999999998766544433  23444444333333


Q ss_pred             CC--ceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----------cCHHHHHHH
Q psy7952         266 SN--LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----------VNKHERSRV  332 (444)
Q Consensus       266 ~~--~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----------~~~~~r~~~  332 (444)
                      ++  +........ ...+...+.+.+.    .......++||||+++..++.++..|...           ++..+|..+
T Consensus       336 ~~~~v~q~~~~~~-~~~k~~~l~~~l~----~~~~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~i  410 (518)
T PLN00206        336 PNKAVKQLAIWVE-TKQKKQKLFDILK----SKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREV  410 (518)
T ss_pred             CCcceeEEEEecc-chhHHHHHHHHHH----hhcccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHH
Confidence            22  222222222 1222223333332    22223468999999999999999998753           789999999


Q ss_pred             HHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         333 QESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       333 ~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      ++.|++|+.+|||||+++++|||+|++++||++|+|.+..+|+||+||+||.|..|.+++|+.+++...+..+.+
T Consensus       411 l~~Fr~G~~~ILVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~~~~~~~~l~~  485 (518)
T PLN00206        411 MKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFPELVA  485 (518)
T ss_pred             HHHHHCCCCCEEEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEchhHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999888776666643

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=5.4e-48  Score=390.82  Aligned_cols=340  Identities=17%  Similarity=0.236  Sum_probs=260.7

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      ...++.+++.+ +||+. ||++|.++++.++.+ +++++.||||+|||.+        |.+|+ ++.+......+++||+
T Consensus        13 L~~~ll~al~~-~G~~~-ptpiQ~~ai~~ll~g-~dvl~~ApTGsGKT~a--------f~lpl-l~~l~~~~~~~~~LIL   80 (629)
T PRK11634         13 LKAPILEALND-LGYEK-PSPIQAECIPHLLNG-RDVLGMAQTGSGKTAA--------FSLPL-LHNLDPELKAPQILVL   80 (629)
T ss_pred             CCHHHHHHHHH-CCCCC-CCHHHHHHHHHHHcC-CCEEEEcCCCCcHHHH--------HHHHH-HHHhhhccCCCeEEEE
Confidence            35678889987 59998 889999999999999 9999999999999999        77777 4444333344678999


Q ss_pred             cchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         112 SPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      +||++|+  .|+.+.+..+......+.+..++|+.....+...+      ...++|+|+||+++.    +.+......+.
T Consensus        81 ~PTreLa--~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l------~~~~~IVVgTPgrl~----d~l~r~~l~l~  148 (629)
T PRK11634         81 APTRELA--VQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRAL------RQGPQIVVGTPGRLL----DHLKRGTLDLS  148 (629)
T ss_pred             eCcHHHH--HHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHh------cCCCCEEEECHHHHH----HHHHcCCcchh
Confidence            9999999  44455566662222238888899987765443322      467899999999985    44555556678


Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEE
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYD  271 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~  271 (444)
                      ++++||+||||++++++  |..   .+..++...+...|++++|||++.........++.-+..+.+.......+.+...
T Consensus       149 ~l~~lVlDEAd~ml~~g--f~~---di~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~  223 (629)
T PRK11634        149 KLSGLVLDEADEMLRMG--FIE---DVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQS  223 (629)
T ss_pred             hceEEEeccHHHHhhcc--cHH---HHHHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCccccCCceEEE
Confidence            99999999999998877  543   3445556677778999999999988776665554322222222222334444433


Q ss_pred             EEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCc
Q psy7952         272 VIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEI  341 (444)
Q Consensus       272 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~  341 (444)
                      +..... ..+..    .+..++...  ...++||||+++..++.++..|...          +++.+|..+++.|++|++
T Consensus       224 ~~~v~~-~~k~~----~L~~~L~~~--~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~  296 (629)
T PRK11634        224 YWTVWG-MRKNE----ALVRFLEAE--DFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRL  296 (629)
T ss_pred             EEEech-hhHHH----HHHHHHHhc--CCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCC
Confidence            333221 12222    333333332  4578999999999999999999876          889999999999999999


Q ss_pred             cEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         342 NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       342 ~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      +|||||+++++|||+|++++||+||.|.+...|+||+||+||.|+.|.+++++.+.+...++.+.+
T Consensus       297 ~ILVATdv~arGIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~~~e~~~l~~ie~  362 (629)
T PRK11634        297 DILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIER  362 (629)
T ss_pred             CEEEEcchHhcCCCcccCCEEEEeCCCCCHHHHHHHhccccCCCCcceEEEEechHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999888777776644

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=1.2e-47  Score=379.18  Aligned_cols=335  Identities=22%  Similarity=0.305  Sum_probs=257.7

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc----CCcccee
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN----GNVRSRN  108 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~----~~~~~~v  108 (444)
                      ...+.+++++ +||.. ||++|.++++.+++| +++++++|||+|||++        |++|+ ++.+..    .+...++
T Consensus         9 ~~~l~~~l~~-~g~~~-p~~iQ~~ai~~~~~g-~d~l~~apTGsGKT~~--------~~lp~-l~~l~~~~~~~~~~~~~   76 (434)
T PRK11192          9 DESLLEALQD-KGYTR-PTAIQAEAIPPALDG-RDVLGSAPTGTGKTAA--------FLLPA-LQHLLDFPRRKSGPPRI   76 (434)
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CCEEEECCCCChHHHH--------HHHHH-HHHHhhccccCCCCceE
Confidence            4577888888 59998 889999999999999 9999999999999999        66666 333321    1223578


Q ss_pred             EEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         109 GWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       109 lil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      ||++||++|+  .|+.+++..+  ..+   +++..++|+.........+      .++++|+|+||++|.    +.+...
T Consensus        77 lil~Pt~eLa--~Q~~~~~~~l~~~~~---~~v~~~~gg~~~~~~~~~l------~~~~~IlV~Tp~rl~----~~~~~~  141 (434)
T PRK11192         77 LILTPTRELA--MQVADQARELAKHTH---LDIATITGGVAYMNHAEVF------SENQDIVVATPGRLL----QYIKEE  141 (434)
T ss_pred             EEECCcHHHH--HHHHHHHHHHHccCC---cEEEEEECCCCHHHHHHHh------cCCCCEEEEChHHHH----HHHHcC
Confidence            9999999999  4445566666  345   8899999998877665444      457899999999985    444444


Q ss_pred             HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCC--C
Q psy7952         187 LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST--F  264 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~--~  264 (444)
                      .....++++||+||||++.+++  |...+..+   ....+...|++++|||++......+...+ +..+..+.....  .
T Consensus       142 ~~~~~~v~~lViDEah~~l~~~--~~~~~~~i---~~~~~~~~q~~~~SAT~~~~~~~~~~~~~-~~~~~~i~~~~~~~~  215 (434)
T PRK11192        142 NFDCRAVETLILDEADRMLDMG--FAQDIETI---AAETRWRKQTLLFSATLEGDAVQDFAERL-LNDPVEVEAEPSRRE  215 (434)
T ss_pred             CcCcccCCEEEEECHHHHhCCC--cHHHHHHH---HHhCccccEEEEEEeecCHHHHHHHHHHH-ccCCEEEEecCCccc
Confidence            4456789999999999999877  66555444   44455567899999999876555665554 344544433322  2


Q ss_pred             CCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHH
Q psy7952         265 RSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQE  334 (444)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~  334 (444)
                      +..+...+.....    .......+..++...  ...++||||+++++++.++..|...          ++..+|..+++
T Consensus       216 ~~~i~~~~~~~~~----~~~k~~~l~~l~~~~--~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~  289 (434)
T PRK11192        216 RKKIHQWYYRADD----LEHKTALLCHLLKQP--EVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIK  289 (434)
T ss_pred             ccCceEEEEEeCC----HHHHHHHHHHHHhcC--CCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHH
Confidence            2333333332222    223344555555432  4679999999999999999999876          88999999999


Q ss_pred             HHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHH
Q psy7952         335 SFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI  406 (444)
Q Consensus       335 ~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  406 (444)
                      .|++|+++|||||+++++|+|+|++++||++|+|.|...|+||+||+||.|..|.+++++...+...+..+.
T Consensus       290 ~f~~G~~~vLVaTd~~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~~d~~~~~~i~  361 (434)
T PRK11192        290 RLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIE  361 (434)
T ss_pred             HHhCCCCcEEEEccccccCccCCCCCEEEEECCCCCHHHHhhcccccccCCCCceEEEEecHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999988887766654

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.6e-47  Score=383.85  Aligned_cols=333  Identities=18%  Similarity=0.263  Sum_probs=251.3

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC-------Ccc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG-------NVR  105 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~-------~~~  105 (444)
                      ...+.++|.+ +||+. ||++|.++++.+++| +|+++.+|||+|||++        |++|+ ++.+...       ...
T Consensus        17 ~~~l~~~L~~-~g~~~-ptpiQ~~~ip~~l~G-~Dvi~~ApTGSGKTla--------fllpi-l~~l~~~~~~~~~~~~~   84 (572)
T PRK04537         17 HPALLAGLES-AGFTR-CTPIQALTLPVALPG-GDVAGQAQTGTGKTLA--------FLVAV-MNRLLSRPALADRKPED   84 (572)
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CCEEEEcCCCCcHHHH--------HHHHH-HHHHHhcccccccccCC
Confidence            4568888887 59998 889999999999999 9999999999999999        66666 3333221       123


Q ss_pred             ceeEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYL  183 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~  183 (444)
                      +++||++||++|+  .|+.+.+..+  ..+   +++..++|+.........+      ..+++|+|+||++|.    ..+
T Consensus        85 ~raLIl~PTreLa--~Qi~~~~~~l~~~~~---i~v~~l~Gg~~~~~q~~~l------~~~~dIiV~TP~rL~----~~l  149 (572)
T PRK04537         85 PRALILAPTRELA--IQIHKDAVKFGADLG---LRFALVYGGVDYDKQRELL------QQGVDVIIATPGRLI----DYV  149 (572)
T ss_pred             ceEEEEeCcHHHH--HHHHHHHHHHhccCC---ceEEEEECCCCHHHHHHHH------hCCCCEEEECHHHHH----HHH
Confidence            6889999999999  3334555555  344   8899999998876655444      357899999999985    322


Q ss_pred             HHH-HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCC--CCcEEEEeccCCcchHHHHHHHhcCCCCeEEEe
Q psy7952         184 LQH-LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGN--SIPIIALTATAEPSVKQDIISVLKFNKPYKVFK  260 (444)
Q Consensus       184 ~~~-~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~--~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~  260 (444)
                      ... ...+..+++||+||+|++.+++  |...+.   .++..++.  ..|++++|||++..........+.  .+..+..
T Consensus       150 ~~~~~~~l~~v~~lViDEAh~lld~g--f~~~i~---~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~--~p~~i~v  222 (572)
T PRK04537        150 KQHKVVSLHACEICVLDEADRMFDLG--FIKDIR---FLLRRMPERGTRQTLLFSATLSHRVLELAYEHMN--EPEKLVV  222 (572)
T ss_pred             HhccccchhheeeeEecCHHHHhhcc--hHHHHH---HHHHhcccccCceEEEEeCCccHHHHHHHHHHhc--CCcEEEe
Confidence            222 3456788999999999998877  554443   44444543  478999999999887776666554  3333322


Q ss_pred             c--CCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHH
Q psy7952         261 T--STFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHE  328 (444)
Q Consensus       261 ~--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~  328 (444)
                      .  ......+...+.... ...+    ...+..++...  .+.++||||++++.++.+++.|...          ++..+
T Consensus       223 ~~~~~~~~~i~q~~~~~~-~~~k----~~~L~~ll~~~--~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~e  295 (572)
T PRK04537        223 ETETITAARVRQRIYFPA-DEEK----QTLLLGLLSRS--EGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKK  295 (572)
T ss_pred             ccccccccceeEEEEecC-HHHH----HHHHHHHHhcc--cCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHH
Confidence            2  222222322222221 1222    23333333332  4779999999999999999999876          88999


Q ss_pred             HHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHH
Q psy7952         329 RSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI  406 (444)
Q Consensus       329 r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  406 (444)
                      |..+++.|++|+.+|||||+++++|||+|++++||+||.|.+...|+||+||+||.|..|.+++|+.+.+...+..+.
T Consensus       296 R~~il~~Fr~G~~~VLVaTdv~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~~~~~l~~i~  373 (572)
T PRK04537        296 RESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPDIE  373 (572)
T ss_pred             HHHHHHHHHcCCCeEEEEehhhhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999987776666553

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=3.7e-47  Score=372.94  Aligned_cols=367  Identities=17%  Similarity=0.254  Sum_probs=257.5

Q ss_pred             CCCCCCcccccccCCCCCCCCCcCC----CCCCCCCHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCC
Q psy7952           1 MAEGESKDASSAVGKSSSLTGNQQD----RKGGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGA   76 (444)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGs   76 (444)
                      ||.+|..+.+.-.......+.....    +..-.+ ...+.+++.. +|+.. |+++|.++++.++++ +++++.+|||+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l-~~~~~~~l~~-~~~~~-~~~~Q~~ai~~i~~~-~d~ii~apTGs   76 (401)
T PTZ00424          1 MATSEQKNQSEQVASTGTIESNYDEIVDSFDALKL-NEDLLRGIYS-YGFEK-PSAIQQRGIKPILDG-YDTIGQAQSGT   76 (401)
T ss_pred             CCchhhccchhhcccccccccccccccCCHhhCCC-CHHHHHHHHH-cCCCC-CCHHHHHHHHHHhCC-CCEEEECCCCC
Confidence            6666666665544444333222211    111122 4556677776 69997 789999999999999 99999999999


Q ss_pred             cccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHH
Q psy7952          77 VSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILE  156 (444)
Q Consensus        77 GKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~  156 (444)
                      |||++        |.+|+ +..+.......++||++|+++|+  .|+.+.+..+.. ...+.+....|+.........  
T Consensus        77 GKT~~--------~~l~~-l~~~~~~~~~~~~lil~Pt~~L~--~Q~~~~~~~~~~-~~~~~~~~~~g~~~~~~~~~~--  142 (401)
T PTZ00424         77 GKTAT--------FVIAA-LQLIDYDLNACQALILAPTRELA--QQIQKVVLALGD-YLKVRCHACVGGTVVRDDINK--  142 (401)
T ss_pred             hHHHH--------HHHHH-HHHhcCCCCCceEEEECCCHHHH--HHHHHHHHHHhh-hcCceEEEEECCcCHHHHHHH--
Confidence            99999        66665 33333223345789999999999  222333333311 112666667777654432222  


Q ss_pred             HHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEec
Q psy7952         157 ELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTA  236 (444)
Q Consensus       157 ~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSA  236 (444)
                          ...+++|+|+||+++.    ..+......+.++++||+||+|++.+++  +...   +..++...+.+.|++++||
T Consensus       143 ----~~~~~~Ivv~Tp~~l~----~~l~~~~~~l~~i~lvViDEah~~~~~~--~~~~---~~~i~~~~~~~~~~i~~SA  209 (401)
T PTZ00424        143 ----LKAGVHMVVGTPGRVY----DMIDKRHLRVDDLKLFILDEADEMLSRG--FKGQ---IYDVFKKLPPDVQVALFSA  209 (401)
T ss_pred             ----HcCCCCEEEECcHHHH----HHHHhCCcccccccEEEEecHHHHHhcc--hHHH---HHHHHhhCCCCcEEEEEEe
Confidence                2456799999999984    4444445567899999999999998766  4433   3344556667799999999


Q ss_pred             cCCcchHHHHHHHhcCCCCeEEEecC--CCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHH
Q psy7952         237 TAEPSVKQDIISVLKFNKPYKVFKTS--TFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTT  314 (444)
Q Consensus       237 T~~~~~~~~~~~~l~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~  314 (444)
                      |+++........++.  .+..+....  .....+...+..........    ..+..+....  ...++||||+++++++
T Consensus       210 T~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~l~~~~~~~--~~~~~ivF~~t~~~~~  281 (401)
T PTZ00424        210 TMPNEILELTTKFMR--DPKRILVKKDELTLEGIRQFYVAVEKEEWKF----DTLCDLYETL--TITQAIIYCNTRRKVD  281 (401)
T ss_pred             cCCHHHHHHHHHHcC--CCEEEEeCCCCcccCCceEEEEecChHHHHH----HHHHHHHHhc--CCCeEEEEecCcHHHH
Confidence            999876665555443  333322221  11222222222222212222    2233333222  4578999999999999


Q ss_pred             HHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCC
Q psy7952         315 DLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD  384 (444)
Q Consensus       315 ~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~  384 (444)
                      .++..|...          ++..+|..+++.|++|+++|||||+++++|+|+|++++||++|+|.|...|+||+||+||.
T Consensus       282 ~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~  361 (401)
T PTZ00424        282 YLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRF  361 (401)
T ss_pred             HHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCEEEEECCCCCHHHEeecccccccC
Confidence            999999876          8899999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCceeEEEEecccchhhHHHHH
Q psy7952         385 GLQSYCRIYHSEHSKKSLEYVI  406 (444)
Q Consensus       385 g~~g~~~~~~~~~~~~~~~~~~  406 (444)
                      |+.|.|++++.+++...+..+.
T Consensus       362 g~~G~~i~l~~~~~~~~~~~~e  383 (401)
T PTZ00424        362 GRKGVAINFVTPDDIEQLKEIE  383 (401)
T ss_pred             CCCceEEEEEcHHHHHHHHHHH
Confidence            9999999999988877776663

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=5.6e-47  Score=377.46  Aligned_cols=335  Identities=19%  Similarity=0.244  Sum_probs=248.0

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC-------cc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN-------VR  105 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~-------~~  105 (444)
                      ...+.+++.+ +|+.. +|++|.++++.+++| +|+++.+|||+|||++        |++|. ++.+....       ..
T Consensus        95 ~~~l~~~l~~-~g~~~-~~~iQ~~ai~~~~~G-~dvi~~apTGSGKTla--------y~lpi-l~~l~~~~~~~~~~~~~  162 (475)
T PRK01297         95 APELMHAIHD-LGFPY-CTPIQAQVLGYTLAG-HDAIGRAQTGTGKTAA--------FLISI-INQLLQTPPPKERYMGE  162 (475)
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CCEEEECCCCChHHHH--------HHHHH-HHHHHhcCcccccccCC
Confidence            5678889988 69998 779999999999999 9999999999999999        88887 44333221       13


Q ss_pred             ceeEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYL  183 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~  183 (444)
                      +++||++||++|+  +|+.+.+..+  ..+   +++..++|+.........+.     .+.++|+|+||++|.    ...
T Consensus       163 ~~aLil~PtreLa--~Q~~~~~~~l~~~~~---~~v~~~~gg~~~~~~~~~~~-----~~~~~Iiv~TP~~Ll----~~~  228 (475)
T PRK01297        163 PRALIIAPTRELV--VQIAKDAAALTKYTG---LNVMTFVGGMDFDKQLKQLE-----ARFCDILVATPGRLL----DFN  228 (475)
T ss_pred             ceEEEEeCcHHHH--HHHHHHHHHhhccCC---CEEEEEEccCChHHHHHHHh-----CCCCCEEEECHHHHH----HHH
Confidence            5789999999999  3334444455  334   78888888876654433321     357899999999984    323


Q ss_pred             HHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecC-
Q psy7952         184 LQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTS-  262 (444)
Q Consensus       184 ~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~-  262 (444)
                      ......+.++++|||||+|++.+++  +.+.+..+...... ..+.+++++|||++....+....++.  .+..+.... 
T Consensus       229 ~~~~~~l~~l~~lViDEah~l~~~~--~~~~l~~i~~~~~~-~~~~q~i~~SAT~~~~~~~~~~~~~~--~~~~v~~~~~  303 (475)
T PRK01297        229 QRGEVHLDMVEVMVLDEADRMLDMG--FIPQVRQIIRQTPR-KEERQTLLFSATFTDDVMNLAKQWTT--DPAIVEIEPE  303 (475)
T ss_pred             HcCCcccccCceEEechHHHHHhcc--cHHHHHHHHHhCCC-CCCceEEEEEeecCHHHHHHHHHhcc--CCEEEEeccC
Confidence            3334557789999999999998776  65555554433221 12468999999998877766555543  333332221 


Q ss_pred             -CCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHH
Q psy7952         263 -TFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSR  331 (444)
Q Consensus       263 -~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~  331 (444)
                       .....+...+.... ...+.    ..+..++...  ...++||||+++++++.++..|...          ++.++|..
T Consensus       304 ~~~~~~~~~~~~~~~-~~~k~----~~l~~ll~~~--~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~  376 (475)
T PRK01297        304 NVASDTVEQHVYAVA-GSDKY----KLLYNLVTQN--PWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIK  376 (475)
T ss_pred             cCCCCcccEEEEEec-chhHH----HHHHHHHHhc--CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHH
Confidence             11222222222221 12222    3333333332  4578999999999999999999765          78999999


Q ss_pred             HHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHH
Q psy7952         332 VQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV  405 (444)
Q Consensus       332 ~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~  405 (444)
                      +++.|++|++++||||+++++|||+|++++||++++|.|..+|+||+||+||.|..|.+++|+.++|...+..+
T Consensus       377 ~~~~Fr~G~~~vLvaT~~l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d~~~~~~~  450 (475)
T PRK01297        377 TLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEI  450 (475)
T ss_pred             HHHHHhCCCCcEEEEccccccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999998776554444

>KOG0338|consensus

Probab=100.00  E-value=2e-47  Score=353.02  Aligned_cols=337  Identities=22%  Similarity=0.305  Sum_probs=269.5

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC-C--ccceeE
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG-N--VRSRNG  109 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~-~--~~~~vl  109 (444)
                      ...+.+++.. +||.. |||+|..+++-.+-| +|+..+|.||||||.+        |++|+ +..+.-. .  ...|||
T Consensus       189 SRPlLka~~~-lGy~~-PTpIQ~a~IPvallg-kDIca~A~TGsGKTAA--------F~lPi-LERLlYrPk~~~~TRVL  256 (691)
T KOG0338|consen  189 SRPLLKACST-LGYKK-PTPIQVATIPVALLG-KDICACAATGSGKTAA--------FALPI-LERLLYRPKKVAATRVL  256 (691)
T ss_pred             chHHHHHHHh-cCCCC-CCchhhhcccHHhhc-chhhheecccCCchhh--------hHHHH-HHHHhcCcccCcceeEE
Confidence            3456677776 49997 999999999999999 9999999999999999        99999 4444433 2  335899


Q ss_pred             EEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH-
Q psy7952         110 WISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH-  186 (444)
Q Consensus       110 il~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~-  186 (444)
                      |+|||++|+  +||.+..+++  ...   +.++...|+.+...+...+      ...+||+|+||++|.    +.+.+. 
T Consensus       257 VL~PTRELa--iQv~sV~~qlaqFt~---I~~~L~vGGL~lk~QE~~L------Rs~PDIVIATPGRlI----DHlrNs~  321 (691)
T KOG0338|consen  257 VLVPTRELA--IQVHSVTKQLAQFTD---ITVGLAVGGLDLKAQEAVL------RSRPDIVIATPGRLI----DHLRNSP  321 (691)
T ss_pred             EEeccHHHH--HHHHHHHHHHHhhcc---ceeeeeecCccHHHHHHHH------hhCCCEEEecchhHH----HHhccCC
Confidence            999999999  7778888888  334   9999999999999888777      468999999999974    222222 


Q ss_pred             HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCC
Q psy7952         187 LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRS  266 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  266 (444)
                      ...+.++..+|+|||++|++.|  |...+..|   .+.++++.|.+++|||+...+.+.+  .+.+.+|+.++..+....
T Consensus       322 sf~ldsiEVLvlDEADRMLeeg--FademnEi---i~lcpk~RQTmLFSATMteeVkdL~--slSL~kPvrifvd~~~~~  394 (691)
T KOG0338|consen  322 SFNLDSIEVLVLDEADRMLEEG--FADEMNEI---IRLCPKNRQTMLFSATMTEEVKDLA--SLSLNKPVRIFVDPNKDT  394 (691)
T ss_pred             CccccceeEEEechHHHHHHHH--HHHHHHHH---HHhccccccceeehhhhHHHHHHHH--HhhcCCCeEEEeCCcccc
Confidence            2335688999999999999988  77655554   4567888999999999999887643  456789998887765433


Q ss_pred             Cc--e--EEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHH----------HhhcCHHHHHHH
Q psy7952         267 NL--F--YDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADAL----------RRKVNKHERSRV  332 (444)
Q Consensus       267 ~~--~--~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L----------~~~~~~~~r~~~  332 (444)
                      ..  .  +..+...........+..++...      -...+|||+.+++.|.++.-.|          ...+++++|...
T Consensus       395 a~~LtQEFiRIR~~re~dRea~l~~l~~rt------f~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRles  468 (691)
T KOG0338|consen  395 APKLTQEFIRIRPKREGDREAMLASLITRT------FQDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLES  468 (691)
T ss_pred             chhhhHHHheeccccccccHHHHHHHHHHh------cccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHH
Confidence            22  1  11122222333334444444443      2567899999999999875444          333899999999


Q ss_pred             HHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhhc
Q psy7952         333 QESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTD  409 (444)
Q Consensus       333 ~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~  409 (444)
                      +++|+.+++.||||||++++|+||+.+.+||+|.+|.+...|+||+||+.|.|+.|+.++++-..+...++.+++++
T Consensus       469 L~kFk~~eidvLiaTDvAsRGLDI~gV~tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~dRkllK~iik~~  545 (691)
T KOG0338|consen  469 LEKFKKEEIDVLIATDVASRGLDIEGVQTVINYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGESDRKLLKEIIKSS  545 (691)
T ss_pred             HHHHHhccCCEEEEechhhccCCccceeEEEeccCchhHHHHHHHhhhhhhcccCcceEEEeccccHHHHHHHHhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999998874

>KOG0333|consensus

Probab=100.00  E-value=1.3e-45  Score=342.17  Aligned_cols=360  Identities=20%  Similarity=0.251  Sum_probs=274.1

Q ss_pred             CCCCCCcCCCCCCCCCHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccce-EEeCCC
Q psy7952          17 SSLTGNQQDRKGGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSR-VRIPPG   95 (444)
Q Consensus        17 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~-~~~~~~   95 (444)
                      +-++...-.|+...++.+-+. .++.. |+.. ||++|..+++-.+++ +|+|..+.||||||.+-+++++.+ -.+|. 
T Consensus       238 ~~lpnplrnwEE~~~P~e~l~-~I~~~-~y~e-ptpIqR~aipl~lQ~-rD~igvaETgsGktaaf~ipLl~~IsslP~-  312 (673)
T KOG0333|consen  238 GRLPNPLRNWEESGFPLELLS-VIKKP-GYKE-PTPIQRQAIPLGLQN-RDPIGVAETGSGKTAAFLIPLLIWISSLPP-  312 (673)
T ss_pred             CCCCccccChhhcCCCHHHHH-HHHhc-CCCC-CchHHHhhccchhcc-CCeeeEEeccCCccccchhhHHHHHHcCCC-
Confidence            345555566776666655544 77764 9987 999999999999998 999999999999999933333221 11222 


Q ss_pred             ccccccCCccceeEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCC
Q psy7952          96 ADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPE  173 (444)
Q Consensus        96 ~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe  173 (444)
                      +..+....-.|+++++.||++|+  +||++....+  ..+   +++..+.|+....++.-.+      ..+|+|+|+||+
T Consensus       313 ~~~~en~~~gpyaiilaptReLa--qqIeeEt~kf~~~lg---~r~vsvigg~s~EEq~fql------s~gceiviatPg  381 (673)
T KOG0333|consen  313 MARLENNIEGPYAIILAPTRELA--QQIEEETNKFGKPLG---IRTVSVIGGLSFEEQGFQL------SMGCEIVIATPG  381 (673)
T ss_pred             cchhhhcccCceeeeechHHHHH--HHHHHHHHHhccccc---ceEEEEecccchhhhhhhh------hccceeeecCch
Confidence            11122233447889999999999  5555555556  445   8999999999887653333      468999999999


Q ss_pred             ccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhh----------------------CCCCcE
Q psy7952         174 RAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFT----------------------GNSIPI  231 (444)
Q Consensus       174 ~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~----------------------~~~~~~  231 (444)
                      +|.    ..+-+....+++..++|+||+++|.+.|  |.+.+..+.......                      ....|.
T Consensus       382 rLi----d~Lenr~lvl~qctyvvldeadrmiDmg--fE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT  455 (673)
T KOG0333|consen  382 RLI----DSLENRYLVLNQCTYVVLDEADRMIDMG--FEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQT  455 (673)
T ss_pred             HHH----HHHHHHHHHhccCceEeccchhhhhccc--ccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEE
Confidence            996    6667777788999999999999999988  666666554322111                      122578


Q ss_pred             EEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCC--ceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecc
Q psy7952         232 IALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSN--LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRT  309 (444)
Q Consensus       232 v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s  309 (444)
                      +++|||+++...+....++  .+|+.+......++.  +...+.... .+.+...+.+.+..    +  ...++|||+|+
T Consensus       456 ~mftatm~p~verlar~yl--r~pv~vtig~~gk~~~rveQ~v~m~~-ed~k~kkL~eil~~----~--~~ppiIIFvN~  526 (673)
T KOG0333|consen  456 VMFTATMPPAVERLARSYL--RRPVVVTIGSAGKPTPRVEQKVEMVS-EDEKRKKLIEILES----N--FDPPIIIFVNT  526 (673)
T ss_pred             EEEecCCChHHHHHHHHHh--hCCeEEEeccCCCCccchheEEEEec-chHHHHHHHHHHHh----C--CCCCEEEEEec
Confidence            9999999999988777775  577777666555443  333333332 23334444444444    3  47899999999


Q ss_pred             cchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhc
Q psy7952         310 REHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESG  379 (444)
Q Consensus       310 ~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~G  379 (444)
                      ++.|+.+++.|.+.          .++++|...+..|+.|...|||||+++++|||||+|.+||+||+++|+.+|+||+|
T Consensus       527 kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIG  606 (673)
T KOG0333|consen  527 KKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIG  606 (673)
T ss_pred             hhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEecccccCCCCCccceeeecchhhhHHHHHHHhc
Confidence            99999999999988          77899999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         380 RAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       380 R~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      |+||.|+.|.++.|+.+.+...+..|..
T Consensus       607 RTgRAGk~GtaiSflt~~dt~v~ydLkq  634 (673)
T KOG0333|consen  607 RTGRAGKSGTAISFLTPADTAVFYDLKQ  634 (673)
T ss_pred             cccccccCceeEEEeccchhHHHHHHHH
Confidence            9999999999999999999766555543

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

Probab=100.00  E-value=2.9e-45  Score=378.01  Aligned_cols=332  Identities=17%  Similarity=0.230  Sum_probs=244.3

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      +..+.+++++ .|++. |+++|.++++.+++| +|+++.+|||||||++        |.+|+ ++.+.. +...++||++
T Consensus        22 ~~~l~~~L~~-~g~~~-p~~~Q~~ai~~il~G-~nvvv~apTGSGKTla--------~~LPi-L~~l~~-~~~~~aL~l~   88 (742)
T TIGR03817        22 HPDVVAALEA-AGIHR-PWQHQARAAELAHAG-RHVVVATGTASGKSLA--------YQLPV-LSALAD-DPRATALYLA   88 (742)
T ss_pred             CHHHHHHHHH-cCCCc-CCHHHHHHHHHHHCC-CCEEEECCCCCcHHHH--------HHHHH-HHHHhh-CCCcEEEEEc
Confidence            5678899987 59997 789999999999999 9999999999999999        88888 554543 2345789999


Q ss_pred             chhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         113 PILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      ||++|+     .|+...+ .++...+++..++|+.....+..+       ..+++|+|+||+++..............+.
T Consensus        89 PtraLa-----~q~~~~l~~l~~~~i~v~~~~Gdt~~~~r~~i-------~~~~~IivtTPd~L~~~~L~~~~~~~~~l~  156 (742)
T TIGR03817        89 PTKALA-----ADQLRAVRELTLRGVRPATYDGDTPTEERRWA-------REHARYVLTNPDMLHRGILPSHARWARFLR  156 (742)
T ss_pred             ChHHHH-----HHHHHHHHHhccCCeEEEEEeCCCCHHHHHHH-------hcCCCEEEEChHHHHHhhccchhHHHHHHh
Confidence            999999     6666666 333334888889998875543222       246899999999985211111111123467


Q ss_pred             CccEEEEeccccccc-cCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCC-CCCCce
Q psy7952         192 KLAYIVVDEAHCVSE-WGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST-FRSNLF  269 (444)
Q Consensus       192 ~~~~iViDE~H~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~-~~~~~~  269 (444)
                      ++++||+||+|.|.+ .|.++...+..+.++....+.++|++++|||+++... ....+++  .+..+...+. ......
T Consensus       157 ~l~~vViDEah~~~g~fg~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~~-~~~~l~g--~~~~~i~~~~~~~~~~~  233 (742)
T TIGR03817       157 RLRYVVIDECHSYRGVFGSHVALVLRRLRRLCARYGASPVFVLASATTADPAA-AASRLIG--APVVAVTEDGSPRGART  233 (742)
T ss_pred             cCCEEEEeChhhccCccHHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCCHHH-HHHHHcC--CCeEEECCCCCCcCceE
Confidence            899999999999865 3334555566666666666777899999999988643 4444443  3433332221 122222


Q ss_pred             EEEEEccc-----------chhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh---------------
Q psy7952         270 YDVIFDDL-----------LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK---------------  323 (444)
Q Consensus       270 ~~~~~~~~-----------~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~---------------  323 (444)
                      +.......           ...........+..++.    .+.++||||+|++.++.++..|+..               
T Consensus       234 ~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~l~~l~~----~~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~  309 (742)
T TIGR03817       234 VALWEPPLTELTGENGAPVRRSASAEAADLLADLVA----EGARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAY  309 (742)
T ss_pred             EEEecCCccccccccccccccchHHHHHHHHHHHHH----CCCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhhe
Confidence            22211110           01112233444444443    3679999999999999999887642               


Q ss_pred             ---cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecc
Q psy7952         324 ---VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE  396 (444)
Q Consensus       324 ---~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~  396 (444)
                         +.+++|..++++|++|++++||||+++++|||+|++++||++|.|.+..+|+||+||+||.|+.|.++++...
T Consensus       310 hgg~~~~eR~~ie~~f~~G~i~vLVaTd~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~  385 (742)
T TIGR03817       310 RAGYLPEDRRELERALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARD  385 (742)
T ss_pred             ecCCCHHHHHHHHHHHHcCCceEEEECchHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCC
Confidence               7789999999999999999999999999999999999999999999999999999999999999999988863

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.

>KOG0351|consensus

Probab=100.00  E-value=5e-45  Score=374.28  Aligned_cols=369  Identities=38%  Similarity=0.611  Sum_probs=322.3

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      ++.+....++..||+..|| +-|.+++..++.| +++++.+|||.||+++        |++|+    +...+.+   |||
T Consensus       248 ~t~~~~~~l~~~Fg~~~FR-~~Q~eaI~~~l~G-kd~fvlmpTG~GKSLC--------YQlPA----~l~~git---vVI  310 (941)
T KOG0351|consen  248 ETKELELLLKEVFGHKGFR-PNQLEAINATLSG-KDCFVLMPTGGGKSLC--------YQLPA----LLLGGVT---VVI  310 (941)
T ss_pred             cchHHHHHHHHHhccccCC-hhHHHHHHHHHcC-CceEEEeecCCceeeE--------eeccc----cccCCce---EEe
Confidence            3456889999999999999 7999999999999 9999999999999999        99999    9999999   999


Q ss_pred             cchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCcccccc-HHHHHHHHHh
Q psy7952         112 SPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTES-FHYLLQHLVR  189 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~-~~~~~~~~~~  189 (444)
                      .|..+|+     .+|+..+ ..+   |....++++....++...++.+......++|++.|||++.... +...+.....
T Consensus       311 SPL~SLm-----~DQv~~L~~~~---I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~  382 (941)
T KOG0351|consen  311 SPLISLM-----QDQVTHLSKKG---IPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYA  382 (941)
T ss_pred             ccHHHHH-----HHHHHhhhhcC---cceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccC
Confidence            9999999     9999999 888   9999999999999999999998865568999999999997533 2223333333


Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCce
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLF  269 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  269 (444)
                      .+.+.++||||||+.+.|||+||+.|..+..++..++. .+++++|||.+..+..++.+.+++.++. ++..+..|+|+.
T Consensus       383 ~~~lal~vIDEAHCVSqWgHdFRp~Yk~l~~l~~~~~~-vP~iALTATAT~~v~~DIi~~L~l~~~~-~~~~sfnR~NL~  460 (941)
T KOG0351|consen  383 RGLLALFVIDEAHCVSQWGHDFRPSYKRLGLLRIRFPG-VPFIALTATATERVREDVIRSLGLRNPE-LFKSSFNRPNLK  460 (941)
T ss_pred             CCeeEEEEecHHHHhhhhcccccHHHHHHHHHHhhCCC-CCeEEeehhccHHHHHHHHHHhCCCCcc-eecccCCCCCce
Confidence            34489999999999999999999999999999999888 9999999999999999999999999884 778889999999


Q ss_pred             EEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcC
Q psy7952         270 YDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRG  339 (444)
Q Consensus       270 ~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g  339 (444)
                      |.+........ ...+...+..     .....++||||.++.+|+.++..|++.          |.+.+|..+.+.|..+
T Consensus       461 yeV~~k~~~~~-~~~~~~~~~~-----~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~  534 (941)
T KOG0351|consen  461 YEVSPKTDKDA-LLDILEESKL-----RHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSD  534 (941)
T ss_pred             EEEEeccCccc-hHHHHHHhhh-----cCCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcC
Confidence            99998764222 1122222222     226889999999999999999999887          9999999999999999


Q ss_pred             CccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhhccchhHHHHH-
Q psy7952         340 EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLE-  418 (444)
Q Consensus       340 ~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  418 (444)
                      +++|+|||=+++.|||-|+|+.||||+.|+|++.|.|-+|||||+|...+|++|+...|..+++.++.++ ..+..-.. 
T Consensus       535 ~~~VivATVAFGMGIdK~DVR~ViH~~lPks~E~YYQE~GRAGRDG~~s~C~l~y~~~D~~~l~~ll~s~-~~~~~~~~~  613 (941)
T KOG0351|consen  535 KIRVIVATVAFGMGIDKPDVRFVIHYSLPKSFEGYYQEAGRAGRDGLPSSCVLLYGYADISELRRLLTSG-NRLSGVKKF  613 (941)
T ss_pred             CCeEEEEEeeccCCCCCCceeEEEECCCchhHHHHHHhccccCcCCCcceeEEecchhHHHHHHHHHHcc-ccccchhhc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999888 33333222 


Q ss_pred             HHHhhHHHHHHHhhhc
Q psy7952         419 LKFKNYLSMLEYCEQG  434 (444)
Q Consensus       419 ~~~~~~~~~~~~~~~~  434 (444)
                      ....++..++.||++.
T Consensus       614 ~~~~~l~~~~~yCen~  629 (941)
T KOG0351|consen  614 TRLLELVQVVTYCENE  629 (941)
T ss_pred             cchhhHHHHHHhhcCc
Confidence            5678889999999853

>KOG0336|consensus

Probab=100.00  E-value=1.2e-45  Score=332.74  Aligned_cols=337  Identities=19%  Similarity=0.248  Sum_probs=263.8

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc-----CCccce
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN-----GNVRSR  107 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~-----~~~~~~  107 (444)
                      -.++++.+++. ||.. |||+|.+||+-+++| .|++.+|.||+|||++        |++|..++....     ....+.
T Consensus       228 ~pevmenIkK~-GFqK-PtPIqSQaWPI~LQG-~DliGVAQTgtgKtL~--------~L~pg~ihi~aqp~~~~qr~~p~  296 (629)
T KOG0336|consen  228 YPEVMENIKKT-GFQK-PTPIQSQAWPILLQG-IDLIGVAQTGTGKTLA--------FLLPGFIHIDAQPKRREQRNGPG  296 (629)
T ss_pred             hHHHHHHHHhc-cCCC-CCcchhcccceeecC-cceEEEEecCCCcCHH--------HhccceeeeeccchhhhccCCCc
Confidence            45677777774 9998 999999999999999 9999999999999999        888884443332     235578


Q ss_pred             eEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         108 NGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       108 vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      +|++.||++|++|  +.-.+... ..+   .+...+.|+....++.+.+      ..+.+|+++||++|.    +....+
T Consensus       297 ~lvl~ptreLalq--ie~e~~kysyng---~ksvc~ygggnR~eqie~l------krgveiiiatPgrln----dL~~~n  361 (629)
T KOG0336|consen  297 VLVLTPTRELALQ--IEGEVKKYSYNG---LKSVCVYGGGNRNEQIEDL------KRGVEIIIATPGRLN----DLQMDN  361 (629)
T ss_pred             eEEEeccHHHHHH--HHhHHhHhhhcC---cceEEEecCCCchhHHHHH------hcCceEEeeCCchHh----hhhhcC
Confidence            9999999999933  34444444 455   7777888887776655444      579999999999985    555667


Q ss_pred             HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCC
Q psy7952         187 LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRS  266 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  266 (444)
                      ..++..+.|+|+|||++|++.|  |.+....|   +-...++.+.++.|||+++.+.+....++  .+++.+...+....
T Consensus       362 ~i~l~siTYlVlDEADrMLDMg--FEpqIrki---lldiRPDRqtvmTSATWP~~VrrLa~sY~--Kep~~v~vGsLdL~  434 (629)
T KOG0336|consen  362 VINLASITYLVLDEADRMLDMG--FEPQIRKI---LLDIRPDRQTVMTSATWPEGVRRLAQSYL--KEPMIVYVGSLDLV  434 (629)
T ss_pred             eeeeeeeEEEEecchhhhhccc--ccHHHHHH---hhhcCCcceeeeecccCchHHHHHHHHhh--hCceEEEeccccee
Confidence            7788999999999999999999  77766554   33445569999999999999988666664  57777766654432


Q ss_pred             Cce--EEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHH
Q psy7952         267 NLF--YDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQE  334 (444)
Q Consensus       267 ~~~--~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~  334 (444)
                      ...  -+.........+.    +.+..++.. ...+.++||||.++..|+.+...|.-.          -.+.+|+..++
T Consensus       435 a~~sVkQ~i~v~~d~~k~----~~~~~f~~~-ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~  509 (629)
T KOG0336|consen  435 AVKSVKQNIIVTTDSEKL----EIVQFFVAN-MSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNREQSDREMALE  509 (629)
T ss_pred             eeeeeeeeEEecccHHHH----HHHHHHHHh-cCCCceEEEEEechhhhhhccchhhhcccchhhccCChhhhhHHHHHH
Confidence            211  1112222233333    333333332 337889999999999998887666444          66789999999


Q ss_pred             HHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         335 SFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       335 ~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      .|++|+++|||||+.+++|+|+|++.||++||+|.++++|+||+||.||.|+.|..+.++...|......|++
T Consensus       510 ~~ksG~vrILvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~lt~~D~~~a~eLI~  582 (629)
T KOG0336|consen  510 DFKSGEVRILVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISFLTRNDWSMAEELIQ  582 (629)
T ss_pred             hhhcCceEEEEEechhhcCCCchhcceeeccCCCccHHHHHHHhcccccCCCCcceEEEEehhhHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999988888765

>KOG0340|consensus

Probab=100.00  E-value=2.3e-45  Score=325.64  Aligned_cols=339  Identities=18%  Similarity=0.212  Sum_probs=260.7

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ..++.+.++. +|+.. |||+|..++++++.| +|++=+|.||||||.+        |.+|+ ++.+.....+-.++|++
T Consensus        15 ~~Wlve~l~~-l~i~~-pTpiQ~~cIpkILeG-rdcig~AkTGsGKT~A--------FaLPi-l~rLsedP~giFalvlT   82 (442)
T KOG0340|consen   15 SPWLVEQLKA-LGIKK-PTPIQQACIPKILEG-RDCIGCAKTGSGKTAA--------FALPI-LNRLSEDPYGIFALVLT   82 (442)
T ss_pred             cHHHHHHHHH-hcCCC-CCchHhhhhHHHhcc-cccccccccCCCcchh--------hhHHH-HHhhccCCCcceEEEec
Confidence            5678889998 59998 999999999999999 9999999999999999        99999 77777777777889999


Q ss_pred             chhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhh
Q psy7952         113 PILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRY  190 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~  190 (444)
                      ||++|++  |+.+|+..+  ..+   +++.++.|+++.-.....      +..++|++|+||+++....-...-.....+
T Consensus        83 PTrELA~--QiaEQF~alGk~l~---lK~~vivGG~d~i~qa~~------L~~rPHvVvatPGRlad~l~sn~~~~~~~~  151 (442)
T KOG0340|consen   83 PTRELAL--QIAEQFIALGKLLN---LKVSVIVGGTDMIMQAAI------LSDRPHVVVATPGRLADHLSSNLGVCSWIF  151 (442)
T ss_pred             chHHHHH--HHHHHHHHhccccc---ceEEEEEccHHHhhhhhh------cccCCCeEecCccccccccccCCccchhhh
Confidence            9999994  447777777  667   999999999876544333      367999999999999732111100112235


Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCC----CeEEEecCC--C
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNK----PYKVFKTST--F  264 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~----~~~~~~~~~--~  264 (444)
                      .++.++|+|||+++.+..  |...   +.......|...|.+++|||+.....+    ..+.+.    .+.+...+.  .
T Consensus       152 ~rlkflVlDEADrvL~~~--f~d~---L~~i~e~lP~~RQtLlfSATitd~i~q----l~~~~i~k~~a~~~e~~~~vst  222 (442)
T KOG0340|consen  152 QRLKFLVLDEADRVLAGC--FPDI---LEGIEECLPKPRQTLLFSATITDTIKQ----LFGCPITKSIAFELEVIDGVST  222 (442)
T ss_pred             hceeeEEecchhhhhccc--hhhH---HhhhhccCCCccceEEEEeehhhHHHH----hhcCCcccccceEEeccCCCCc
Confidence            689999999999998765  5544   444555677767999999999776644    333332    222222111  1


Q ss_pred             CCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHH
Q psy7952         265 RSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQE  334 (444)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~  334 (444)
                      .......+.... ...+..++...+...-.+   .++.++||+++..+|+.++..|+..          |++.+|...+.
T Consensus       223 vetL~q~yI~~~-~~vkdaYLv~~Lr~~~~~---~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLs  298 (442)
T KOG0340|consen  223 VETLYQGYILVS-IDVKDAYLVHLLRDFENK---ENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALS  298 (442)
T ss_pred             hhhhhhheeecc-hhhhHHHHHHHHhhhhhc---cCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHH
Confidence            111111222211 122333334444333221   5789999999999999999999877          99999999999


Q ss_pred             HHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         335 SFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       335 ~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      +|+++..++|||||++++|+|||.++.||++|.|.++.+|+||+||..|.|+.|.++.++...|.+.+..+.+
T Consensus       299 rFrs~~~~iliaTDVAsRGLDIP~V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv~l~~aiE~  371 (442)
T KOG0340|consen  299 RFRSNAARILIATDVASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRDVELLQAIEE  371 (442)
T ss_pred             HHhhcCccEEEEechhhcCCCCCceeEEEecCCCCCHHHHHHhhcchhcccCCcceEEEechhhHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999988777754

>KOG0342|consensus

Probab=100.00  E-value=3.8e-45  Score=337.56  Aligned_cols=343  Identities=18%  Similarity=0.227  Sum_probs=262.8

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCcc----cee
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVR----SRN  108 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~----~~v  108 (444)
                      .....+++++ +||+. .|++|+.+++.++.| +|++..|-||+|||++        |++|+ .+.+.+....    -.+
T Consensus        90 S~~t~kAi~~-~GF~~-MT~VQ~~ti~pll~g-kDvl~~AKTGtGKTlA--------FLiPa-ie~l~k~~~~~r~~~~v  157 (543)
T KOG0342|consen   90 SPLTLKAIKE-MGFET-MTPVQQKTIPPLLEG-KDVLAAAKTGTGKTLA--------FLLPA-IELLRKLKFKPRNGTGV  157 (543)
T ss_pred             CHHHHHHHHh-cCccc-hhHHHHhhcCccCCC-ccceeeeccCCCceee--------ehhHH-HHHHHhcccCCCCCeeE
Confidence            4456678887 59998 889999999999999 8999999999999999        99999 5555544322    268


Q ss_pred             EEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH
Q psy7952         109 GWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV  188 (444)
Q Consensus       109 lil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~  188 (444)
                      +|+||||+|++|  +...++.+-...+.+.+..+.|+.......+.+      ..++.|+|+||++|.    +.+.+...
T Consensus       158 lIi~PTRELA~Q--~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl------~k~~niliATPGRLl----DHlqNt~~  225 (543)
T KOG0342|consen  158 LIICPTRELAMQ--IFAEAKELLKYHESITVGIVIGGNNFSVEADKL------VKGCNILIATPGRLL----DHLQNTSG  225 (543)
T ss_pred             EEecccHHHHHH--HHHHHHHHHhhCCCcceEEEeCCccchHHHHHh------hccccEEEeCCchHH----hHhhcCCc
Confidence            999999999944  366667762222238888889888765433333      358999999999984    22222221


Q ss_pred             -hhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCC
Q psy7952         189 -RYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSN  267 (444)
Q Consensus       189 -~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  267 (444)
                       .+.+.+++|+||||++++.|  |+..+..|..   .++...|.+++|||.++.+.+...-.+. .++..+...+...+.
T Consensus       226 f~~r~~k~lvlDEADrlLd~G--F~~di~~Ii~---~lpk~rqt~LFSAT~~~kV~~l~~~~L~-~d~~~v~~~d~~~~~  299 (543)
T KOG0342|consen  226 FLFRNLKCLVLDEADRLLDIG--FEEDVEQIIK---ILPKQRQTLLFSATQPSKVKDLARGALK-RDPVFVNVDDGGERE  299 (543)
T ss_pred             chhhccceeEeecchhhhhcc--cHHHHHHHHH---hccccceeeEeeCCCcHHHHHHHHHhhc-CCceEeecCCCCCcc
Confidence             23456899999999999999  8866665554   5667789999999999988776555543 355555443322222


Q ss_pred             ----ceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHH
Q psy7952         268 ----LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQ  333 (444)
Q Consensus       268 ----~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~  333 (444)
                          +...+..... ......+..++++..     .+.++||||+|...+..+++.|+..          .++..|..+.
T Consensus       300 The~l~Qgyvv~~~-~~~f~ll~~~LKk~~-----~~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~  373 (543)
T KOG0342|consen  300 THERLEQGYVVAPS-DSRFSLLYTFLKKNI-----KRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTF  373 (543)
T ss_pred             hhhcccceEEeccc-cchHHHHHHHHHHhc-----CCceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHH
Confidence                1222222222 223444555555532     2389999999999999999999866          7888999999


Q ss_pred             HHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhhccc
Q psy7952         334 ESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTS  411 (444)
Q Consensus       334 ~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~  411 (444)
                      ..|+..+..||+|||++++|+|+|+|++||++|+|.+.++|+||+||+||.|+.|.+++++.+++...++++.+-++.
T Consensus       374 ~~F~kaesgIL~cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El~Flr~LK~lpl~  451 (543)
T KOG0342|consen  374 FEFCKAESGILVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGFLRYLKKLPLE  451 (543)
T ss_pred             HHHhhcccceEEecchhhccCCCCCceEEEEeCCCCCHHHHHHHhccccccCCCceEEEEeChhHHHHHHHHhhCCCc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999864443

>KOG0353|consensus

Probab=100.00  E-value=2.2e-44  Score=322.10  Aligned_cols=386  Identities=31%  Similarity=0.512  Sum_probs=328.4

Q ss_pred             ccccccCCCCCCCCCcCCCCCCCCC-HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccc
Q psy7952           8 DASSAVGKSSSLTGNQQDRKGGKVS-EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSA   86 (444)
Q Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~   86 (444)
                      ..+++.|....++.++-.|..++++ ..+..+.|++.|.++.|| |.|..+++....| .++++..|||.||+++     
T Consensus        53 ~edsdag~~~eyd~spaawdkd~fpws~e~~~ilk~~f~lekfr-plq~~ain~~ma~-ed~~lil~tgggkslc-----  125 (695)
T KOG0353|consen   53 LEDSDAGASNEYDRSPAAWDKDDFPWSDEAKDILKEQFHLEKFR-PLQLAAINATMAG-EDAFLILPTGGGKSLC-----  125 (695)
T ss_pred             cccccccccccccCCccccccCCCCCchHHHHHHHHHhhHHhcC-hhHHHHhhhhhcc-CceEEEEeCCCccchh-----
Confidence            3566777777888888888887776 667788999999999988 8999999999999 9999999999999999     


Q ss_pred             cceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCe
Q psy7952          87 RSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRI  165 (444)
Q Consensus        87 ~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (444)
                         |++|+    +...|-.   |++||..+|+     .+|+-.+ ..|   +....++.+.+..+....-..+-......
T Consensus       126 ---yqlpa----l~adg~a---lvi~plislm-----edqil~lkqlg---i~as~lnansske~~k~v~~~i~nkdse~  187 (695)
T KOG0353|consen  126 ---YQLPA----LCADGFA---LVICPLISLM-----EDQILQLKQLG---IDASMLNANSSKEEAKRVEAAITNKDSEF  187 (695)
T ss_pred             ---hhhhH----HhcCCce---EeechhHHHH-----HHHHHHHHHhC---cchhhccCcccHHHHHHHHHHHcCCCcee
Confidence               99999    9999999   9999999999     9999999 889   88888988888776666666666666778


Q ss_pred             eEEEECCCccccc-cHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHH
Q psy7952         166 KLLYVTPERAVTE-SFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQ  244 (444)
Q Consensus       166 ~Iiv~Tpe~l~~~-~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~  244 (444)
                      .+++.|||++... .|-..+........+.+|-+||+|+.+.||++|++.|..+.-+.+.|+. ++++++|||..+.+.+
T Consensus       188 kliyvtpekiaksk~~mnkleka~~~~~~~~iaidevhccsqwghdfr~dy~~l~ilkrqf~~-~~iigltatatn~vl~  266 (695)
T KOG0353|consen  188 KLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHCCSQWGHDFRPDYKALGILKRQFKG-APIIGLTATATNHVLD  266 (695)
T ss_pred             EEEEecHHHHHHHHHHHHHHHHHhhcceeEEEeecceeehhhhCcccCcchHHHHHHHHhCCC-Cceeeeehhhhcchhh
Confidence            9999999998642 2444445555667889999999999999999999999999888888887 9999999999999999


Q ss_pred             HHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-
Q psy7952         245 DIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-  323 (444)
Q Consensus       245 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-  323 (444)
                      +....+++... ..++.+..||++.|.+...+...+.   ..+.+.+++.... .+...||||-|.++|++++..|... 
T Consensus       267 d~k~il~ie~~-~tf~a~fnr~nl~yev~qkp~n~dd---~~edi~k~i~~~f-~gqsgiiyc~sq~d~ekva~alkn~g  341 (695)
T KOG0353|consen  267 DAKDILCIEAA-FTFRAGFNRPNLKYEVRQKPGNEDD---CIEDIAKLIKGDF-AGQSGIIYCFSQKDCEKVAKALKNHG  341 (695)
T ss_pred             HHHHHHhHHhh-heeecccCCCCceeEeeeCCCChHH---HHHHHHHHhcccc-CCCcceEEEeccccHHHHHHHHHhcC
Confidence            99999887666 4566788999999999988764332   2233333332222 5778999999999999999999887 


Q ss_pred             ---------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHH------------------
Q psy7952         324 ---------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ------------------  376 (444)
Q Consensus       324 ---------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Q------------------  376 (444)
                               +.+++|..+-+.|..|++.|+|||-.++.|||-|++++|||..+|+|+++|.|                  
T Consensus       342 i~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgidkpdvrfvihhsl~ksienyyqasarillrmtkqknksdt  421 (695)
T KOG0353|consen  342 IHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDKPDVRFVIHHSLPKSIENYYQASARILLRMTKQKNKSDT  421 (695)
T ss_pred             ccccccccccCccccccccccccccceEEEEEEeeecccCCCCCeeEEEecccchhHHHHHHHHHHHHHHHhhhcccccC
Confidence                     88999999999999999999999999999999999999999999999999999                  


Q ss_pred             -------------------------HhccCCCCCCceeEEEEecccchhhHHHHHhhccchhHHHHHHHHhhHHHHHHHh
Q psy7952         377 -------------------------ESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYC  431 (444)
Q Consensus       377 -------------------------r~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  431 (444)
                                               -.||+||++.+..|++++.-.+.-.+..+..        .-...+.++.+|++||
T Consensus       422 ggstqinilevctnfkiffavfsekesgragrd~~~a~cilyy~~~difk~ssmv~--------~e~~g~q~ly~mv~y~  493 (695)
T KOG0353|consen  422 GGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKADCILYYGFADIFKISSMVQ--------MENTGIQKLYEMVRYA  493 (695)
T ss_pred             CCcceeehhhhhccceeeeeeecchhccccccCCCcccEEEEechHHHHhHHHHHH--------HHhhhHHHHHHHHHHH
Confidence                                     6799999999999999999888777776654        2233577788888887


Q ss_pred             h
Q psy7952         432 E  432 (444)
Q Consensus       432 ~  432 (444)
                      .
T Consensus       494 ~  494 (695)
T KOG0353|consen  494 A  494 (695)
T ss_pred             h
Confidence            6

>KOG0345|consensus

Probab=100.00  E-value=1.4e-44  Score=331.66  Aligned_cols=336  Identities=18%  Similarity=0.273  Sum_probs=261.4

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC-cc----ce
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN-VR----SR  107 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~-~~----~~  107 (444)
                      ..++.+++.. +||.. .||.|..+++.++.+ +|+.+.+|||||||++        |++|. ++.+.++. ..    --
T Consensus        14 ~~~l~~~l~~-~GF~~-mTpVQa~tIPlll~~-KDVvveavTGSGKTlA--------FllP~-le~i~rr~~~~~~~~vg   81 (567)
T KOG0345|consen   14 SPWLLEALDE-SGFEK-MTPVQAATIPLLLKN-KDVVVEAVTGSGKTLA--------FLLPM-LEIIYRREAKTPPGQVG   81 (567)
T ss_pred             cHHHHHHHHh-cCCcc-cCHHHHhhhHHHhcC-CceEEEcCCCCCchhh--------HHHHH-HHHHHhhccCCCcccee
Confidence            4678888988 59997 789999999999999 9999999999999999        99998 66664432 11    14


Q ss_pred             eEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH
Q psy7952         108 NGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL  187 (444)
Q Consensus       108 vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~  187 (444)
                      +||++|||+|+  .|+.+.+..+......+++..+.|+.+..+....+.+     .++.|+||||++|.    +.+....
T Consensus        82 alIIsPTRELa--~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fke-----e~~nIlVgTPGRL~----di~~~~~  150 (567)
T KOG0345|consen   82 ALIISPTRELA--RQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKE-----EGPNILVGTPGRLL----DILQREA  150 (567)
T ss_pred             EEEecCcHHHH--HHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHH-----hCCcEEEeCchhHH----HHHhchh
Confidence            69999999999  5568888777222344999999999888776666643     57889999999984    3333323


Q ss_pred             Hh--hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCC
Q psy7952         188 VR--YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFR  265 (444)
Q Consensus       188 ~~--~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~  265 (444)
                      ..  +.++.++|+||||++++.|  |...+   ..++..+|+..+.=++|||......+...  .|+.+++.+.......
T Consensus       151 ~~l~~rsLe~LVLDEADrLldmg--Fe~~~---n~ILs~LPKQRRTGLFSATq~~~v~dL~r--aGLRNpv~V~V~~k~~  223 (567)
T KOG0345|consen  151 EKLSFRSLEILVLDEADRLLDMG--FEASV---NTILSFLPKQRRTGLFSATQTQEVEDLAR--AGLRNPVRVSVKEKSK  223 (567)
T ss_pred             hhccccccceEEecchHhHhccc--HHHHH---HHHHHhcccccccccccchhhHHHHHHHH--hhccCceeeeeccccc
Confidence            33  4489999999999999999  66444   45566788878899999999988877444  4566777666554332


Q ss_pred             ---C-CceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------------cCHHHH
Q psy7952         266 ---S-NLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------VNKHER  329 (444)
Q Consensus       266 ---~-~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------------~~~~~r  329 (444)
                         | .....+...+ ...+...+.+++..    .  ..+++|||++|...++..+..+...            +....|
T Consensus       224 ~~tPS~L~~~Y~v~~-a~eK~~~lv~~L~~----~--~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R  296 (567)
T KOG0345|consen  224 SATPSSLALEYLVCE-ADEKLSQLVHLLNN----N--KDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKAR  296 (567)
T ss_pred             ccCchhhcceeeEec-HHHHHHHHHHHHhc----c--ccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhH
Confidence               2 1222222222 23333344444433    2  5789999999999999888877665            888899


Q ss_pred             HHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHH
Q psy7952         330 SRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV  405 (444)
Q Consensus       330 ~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~  405 (444)
                      ..+++.|+...-.+|+|||++++|+|||++++||++|+|.+...|+||+||++|.|+.|.+++|+.+.+......+
T Consensus       297 ~k~~~~F~~~~~~vl~~TDVaARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E~aYveFl  372 (567)
T KOG0345|consen  297 AKVLEAFRKLSNGVLFCTDVAARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPREEAYVEFL  372 (567)
T ss_pred             HHHHHHHHhccCceEEeehhhhccCCCCCceEEEecCCCCChhHHHhhcchhhhccCccceEEEecccHHHHHHHH
Confidence            9999999998889999999999999999999999999999999999999999999999999999998665554444

>KOG0335|consensus

Probab=100.00  E-value=8.1e-45  Score=340.88  Aligned_cols=345  Identities=19%  Similarity=0.292  Sum_probs=266.9

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC---------
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN---------  103 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~---------  103 (444)
                      .+.+...++. .|++. ||++|+.+++.+..| ++.+++|+||+|||.+        |++|+ +.++...+         
T Consensus        82 ~~~l~~ni~~-~~~~~-ptpvQk~sip~i~~G-rdl~acAqTGsGKT~a--------FLiPi-i~~~~~~~~~~~~~~~~  149 (482)
T KOG0335|consen   82 GEALAGNIKR-SGYTK-PTPVQKYSIPIISGG-RDLMACAQTGSGKTAA--------FLIPI-ISYLLDEGPEDRGESGG  149 (482)
T ss_pred             hHHHhhcccc-ccccC-CCcceeeccceeecC-CceEEEccCCCcchHH--------HHHHH-HHHHHhcCcccCcccCC
Confidence            4445555555 38887 899999999999999 9999999999999999        99998 55555443         


Q ss_pred             -ccceeEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccH
Q psy7952         104 -VRSRNGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESF  180 (444)
Q Consensus       104 -~~~~vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~  180 (444)
                       ..|+++|++||++|+  .|+.+..+.+  ...   ++...++|+.......      +....+++|+|+||++|.    
T Consensus       150 ~~~P~~lIlapTReL~--~Qi~nea~k~~~~s~---~~~~~~ygg~~~~~q~------~~~~~gcdIlvaTpGrL~----  214 (482)
T KOG0335|consen  150 GVYPRALILAPTRELV--DQIYNEARKFSYLSG---MKSVVVYGGTDLGAQL------RFIKRGCDILVATPGRLK----  214 (482)
T ss_pred             CCCCceEEEeCcHHHh--hHHHHHHHhhccccc---ceeeeeeCCcchhhhh------hhhccCccEEEecCchhh----
Confidence             248999999999999  5556666666  334   7888888886655433      333679999999999986    


Q ss_pred             HHHHHHHHhhCCccEEEEeccccccc-cCCCcHHHHHHHHHHHHhhC-CCCcEEEEeccCCcchHHHHHHHhcC-CCCeE
Q psy7952         181 HYLLQHLVRYNKLAYIVVDEAHCVSE-WGHDFRPTYRRLGELRQFTG-NSIPIIALTATAEPSVKQDIISVLKF-NKPYK  257 (444)
Q Consensus       181 ~~~~~~~~~~~~~~~iViDE~H~~~~-~~~~~~~~~~~l~~~~~~~~-~~~~~v~lSAT~~~~~~~~~~~~l~~-~~~~~  257 (444)
                      +.+-.....+.+++++|+||+++|++ .+  |.+.+..|.......+ .+.|.+++|||.+.........++.- ...+.
T Consensus       215 d~~e~g~i~l~~~k~~vLDEADrMlD~mg--F~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~la  292 (482)
T KOG0335|consen  215 DLIERGKISLDNCKFLVLDEADRMLDEMG--FEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLA  292 (482)
T ss_pred             hhhhcceeehhhCcEEEecchHHhhhhcc--ccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEE
Confidence            55566667788899999999999998 77  7777777765443332 34789999999999877755555432 22344


Q ss_pred             EEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHh---ccCCCCCceEEEEecccchHHHHHHHHHhh----------c
Q psy7952         258 VFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCL---GKDNKANNCGIIYCRTREHTTDLADALRRK----------V  324 (444)
Q Consensus       258 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l---~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~  324 (444)
                      +.+-.....++...+.+... ..+...+.+++....   .......++++|||.+++.|..++..|...          .
T Consensus       293 V~rvg~~~~ni~q~i~~V~~-~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~  371 (482)
T KOG0335|consen  293 VGRVGSTSENITQKILFVNE-MEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDR  371 (482)
T ss_pred             EeeeccccccceeEeeeecc-hhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchh
Confidence            44556667777777766553 233334444444332   111123348999999999999999999888          6


Q ss_pred             CHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHH
Q psy7952         325 NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEY  404 (444)
Q Consensus       325 ~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~  404 (444)
                      .+.+|...++.|++|...+||||+++++|+|+|+|+|||+||+|.+..+|+||+||+||.|+.|.++.|++..+....+.
T Consensus       372 tq~er~~al~~Fr~g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~n~~~~~i~~~  451 (482)
T KOG0335|consen  372 TQIEREQALNDFRNGKAPVLVATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFFNEKNQNIAKA  451 (482)
T ss_pred             hhhHHHHHHHHhhcCCcceEEEehhhhcCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEeccccchhHHH
Confidence            77899999999999999999999999999999999999999999999999999999999999999999999666655555


Q ss_pred             HHh
Q psy7952         405 VIK  407 (444)
Q Consensus       405 ~~~  407 (444)
                      |.+
T Consensus       452 L~~  454 (482)
T KOG0335|consen  452 LVE  454 (482)
T ss_pred             HHH
Confidence            543

>KOG0326|consensus

Probab=100.00  E-value=8.3e-45  Score=317.69  Aligned_cols=331  Identities=19%  Similarity=0.276  Sum_probs=260.9

Q ss_pred             CCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCcc
Q psy7952          45 GFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRD  124 (444)
Q Consensus        45 g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~  124 (444)
                      ||+. |+|+|.++++.++.| +|++..|..|+|||.+        |.+|. ++.+-.....=..++++||++|+||.  .
T Consensus       104 G~ek-PSPiQeesIPiaLtG-rdiLaRaKNGTGKT~a--------~~IP~-Lekid~~~~~IQ~~ilVPtrelALQt--S  170 (459)
T KOG0326|consen  104 GFEK-PSPIQEESIPIALTG-RDILARAKNGTGKTAA--------YCIPV-LEKIDPKKNVIQAIILVPTRELALQT--S  170 (459)
T ss_pred             ccCC-CCCccccccceeecc-hhhhhhccCCCCCccc--------eechh-hhhcCccccceeEEEEeecchhhHHH--H
Confidence            9997 899999999999999 9999999999999999        99999 55555555445779999999999665  8


Q ss_pred             chHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccc
Q psy7952         125 DKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAH  202 (444)
Q Consensus       125 ~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H  202 (444)
                      +.+.++  ..+   +++...+|+++..+      ++-++.+..+++|+||+++.    +.....-..+++..++|+|||+
T Consensus       171 qvc~~lskh~~---i~vmvttGGT~lrD------DI~Rl~~~VH~~vgTPGRIl----DL~~KgVa~ls~c~~lV~DEAD  237 (459)
T KOG0326|consen  171 QVCKELSKHLG---IKVMVTTGGTSLRD------DIMRLNQTVHLVVGTPGRIL----DLAKKGVADLSDCVILVMDEAD  237 (459)
T ss_pred             HHHHHHhcccC---eEEEEecCCccccc------ceeeecCceEEEEcCChhHH----HHHhcccccchhceEEEechhh
Confidence            888888  556   99999999988653      34445788999999999985    4444555567888999999999


Q ss_pred             cccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCC-CCCc--eEEEEEcccch
Q psy7952         203 CVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTF-RSNL--FYDVIFDDLLK  279 (444)
Q Consensus       203 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~-~~~~--~~~~~~~~~~~  279 (444)
                      .+++..  |.+.+   .+++..+|++.|+++.|||.+-.+...+.+.+  .+|+.+..-... ...+  +|.+...   .
T Consensus       238 KlLs~~--F~~~~---e~li~~lP~~rQillySATFP~tVk~Fm~~~l--~kPy~INLM~eLtl~GvtQyYafV~e---~  307 (459)
T KOG0326|consen  238 KLLSVD--FQPIV---EKLISFLPKERQILLYSATFPLTVKGFMDRHL--KKPYEINLMEELTLKGVTQYYAFVEE---R  307 (459)
T ss_pred             hhhchh--hhhHH---HHHHHhCCccceeeEEecccchhHHHHHHHhc--cCcceeehhhhhhhcchhhheeeech---h
Confidence            998755  66544   45666789999999999999998888777765  566665543322 1222  2222221   1


Q ss_pred             hhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCc
Q psy7952         280 DSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATIS  349 (444)
Q Consensus       280 ~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~  349 (444)
                      .+    ..-+..++.+-  .-.+.||||||.+.++-+|..+.+.          |.++.|..++..|++|.++.|||||.
T Consensus       308 qK----vhCLntLfskL--qINQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL  381 (459)
T KOG0326|consen  308 QK----VHCLNTLFSKL--QINQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDL  381 (459)
T ss_pred             hh----hhhHHHHHHHh--cccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhh
Confidence            22    22233333322  4567899999999999999987666          89999999999999999999999999


Q ss_pred             cccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhhccchhHHHHH
Q psy7952         350 FGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLE  418 (444)
Q Consensus       350 ~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  418 (444)
                      +.+|||++.+++||+||+|++.++|+||+||.||.|..|.++.++.-+|...+..+.. .+..+..+++
T Consensus       382 ~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFGhlGlAInLityedrf~L~~IE~-eLGtEI~pip  449 (459)
T KOG0326|consen  382 FTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYEDRFNLYRIEQ-ELGTEIKPIP  449 (459)
T ss_pred             hhcccccceeeEEEecCCCCCHHHHHHHccCCccCCCcceEEEEEehhhhhhHHHHHH-HhccccccCC
Confidence            9999999999999999999999999999999999999999999999888777666643 3344443443

>KOG0348|consensus

Probab=100.00  E-value=2.4e-43  Score=327.81  Aligned_cols=345  Identities=19%  Similarity=0.241  Sum_probs=262.6

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC------Cccc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG------NVRS  106 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~------~~~~  106 (444)
                      ...+...++..+++.. ||.+|.++++.++.| +|++|.++||+|||++        |++|. .+.+...      ...+
T Consensus       144 ~~~lv~~L~~~m~i~~-pTsVQkq~IP~lL~g-rD~lV~aQTGSGKTLA--------YllPi-Vq~Lq~m~~ki~Rs~G~  212 (708)
T KOG0348|consen  144 HPHLVSHLNTKMKISA-PTSVQKQAIPVLLEG-RDALVRAQTGSGKTLA--------YLLPI-VQSLQAMEPKIQRSDGP  212 (708)
T ss_pred             CHHHHHHHHHHhccCc-cchHhhcchhhhhcC-cceEEEcCCCCcccHH--------HHHHH-HHHHHhcCccccccCCc
Confidence            5667888999999998 999999999999999 9999999999999999        99998 4444432      2335


Q ss_pred             eeEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH-
Q psy7952         107 RNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ-  185 (444)
Q Consensus       107 ~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~-  185 (444)
                      -+||++|||+|+  .|+.+.++.+-..+-+|-...+.|+......+..+      ..++.|+|+||++|.    +.+.+ 
T Consensus       213 ~ALVivPTREL~--~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARL------RKGiNILIgTPGRLv----DHLknT  280 (708)
T KOG0348|consen  213 YALVIVPTRELA--LQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARL------RKGINILIGTPGRLV----DHLKNT  280 (708)
T ss_pred             eEEEEechHHHH--HHHHHHHHHHhcCceEEeeceeecccccccHHHHH------hcCceEEEcCchHHH----HHHhcc
Confidence            789999999999  44588888885555567677777776554333333      478999999999985    22222 


Q ss_pred             HHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhh----------CCCCcEEEEeccCCcchHHHHHHHhcCCCC
Q psy7952         186 HLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFT----------GNSIPIIALTATAEPSVKQDIISVLKFNKP  255 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~----------~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~  255 (444)
                      ....+.+++++|+||+|++.+.|  |...+..|.......          +...+-+++|||+...+.+  ...+.+.++
T Consensus       281 ~~i~~s~LRwlVlDEaDrlleLG--fekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~r--La~~sLkDp  356 (708)
T KOG0348|consen  281 KSIKFSRLRWLVLDEADRLLELG--FEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNR--LADLSLKDP  356 (708)
T ss_pred             chheeeeeeEEEecchhHHHhcc--chhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHH--HhhccccCc
Confidence            23346789999999999999988  666666666555221          1124678999999987766  344556777


Q ss_pred             eEEEecC---CCCCC--------------------------ceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEE
Q psy7952         256 YKVFKTS---TFRSN--------------------------LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIY  306 (444)
Q Consensus       256 ~~~~~~~---~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf  306 (444)
                      +.+....   ...|.                          ..|.+..   .......+..++.......  ...++|||
T Consensus       357 v~I~ld~s~~~~~p~~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVP---pKLRLV~Laa~L~~~~k~~--~~qk~iVF  431 (708)
T KOG0348|consen  357 VYISLDKSHSQLNPKDKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVP---PKLRLVALAALLLNKVKFE--EKQKMIVF  431 (708)
T ss_pred             eeeeccchhhhcCcchhhhhhcCCcccccccccccCcHHhhhceEecC---CchhHHHHHHHHHHHhhhh--hhceeEEE
Confidence            6665111   00100                          0011111   1223344455555555544  45599999


Q ss_pred             ecccchHHHHHHHHHhh--------------------------------cCHHHHHHHHHHHhcCCccEEEEcCcccccc
Q psy7952         307 CRTREHTTDLADALRRK--------------------------------VNKHERSRVQESFMRGEINVITATISFGMGI  354 (444)
Q Consensus       307 ~~s~~~~~~l~~~L~~~--------------------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gi  354 (444)
                      +++.+.++.-++.|...                                |.+++|..+++.|....-.||+|||++++|+
T Consensus       432 ~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGL  511 (708)
T KOG0348|consen  432 FSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGL  511 (708)
T ss_pred             EechhHHHHHHHHHHhhhhcccccccCCcccCCChhhhhcceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccC
Confidence            99999999999988766                                8999999999999998888999999999999


Q ss_pred             ccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhhc
Q psy7952         355 DRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTD  409 (444)
Q Consensus       355 di~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~  409 (444)
                      |+|+|++||.||+|.+..+|+||+||+.|.|..|.+++|+.+.+.+.++.+....
T Consensus       512 DlP~V~~vVQYd~P~s~adylHRvGRTARaG~kG~alLfL~P~Eaey~~~l~~~~  566 (708)
T KOG0348|consen  512 DLPHVGLVVQYDPPFSTADYLHRVGRTARAGEKGEALLFLLPSEAEYVNYLKKHH  566 (708)
T ss_pred             CCCCcCeEEEeCCCCCHHHHHHHhhhhhhccCCCceEEEecccHHHHHHHHHhhc
Confidence            9999999999999999999999999999999999999999999988776665533

>KOG0347|consensus

Probab=100.00  E-value=7e-43  Score=325.72  Aligned_cols=348  Identities=20%  Similarity=0.275  Sum_probs=255.6

Q ss_pred             cCCCCCCCCCHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC
Q psy7952          23 QQDRKGGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG  102 (444)
Q Consensus        23 ~~~~~~~~~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~  102 (444)
                      ...|..- +.+..+.++|.. .||.. ||++|..+++.+..|..|++-.|.||||||++        |.+|++...+..+
T Consensus       180 vsAW~~l-~lp~~iL~aL~~-~gFs~-Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLA--------FGIPiv~~l~~~s  248 (731)
T KOG0347|consen  180 VSAWKNL-FLPMEILRALSN-LGFSR-PTEIQSLVLPAAIRGKVDILGAAETGSGKTLA--------FGIPIVERLLESS  248 (731)
T ss_pred             hHHHhcC-CCCHHHHHHHHh-cCCCC-CccchhhcccHhhccchhcccccccCCCceee--------ecchhhhhhhhcc
Confidence            3445555 346678888888 49998 99999999999999988999999999999999        9999944222222


Q ss_pred             C------------ccceeEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEE
Q psy7952         103 N------------VRSRNGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLL  168 (444)
Q Consensus       103 ~------------~~~~vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ii  168 (444)
                      +            ..+-.||++|||+|+  .||.+++..+  ..+   +.+..++|+.....+..++.      ..++|+
T Consensus       249 ~~s~e~~~~~~k~~k~~~LV~tPTRELa--~QV~~Hl~ai~~~t~---i~v~si~GGLavqKQqRlL~------~~p~IV  317 (731)
T KOG0347|consen  249 DDSQELSNTSAKYVKPIALVVTPTRELA--HQVKQHLKAIAEKTQ---IRVASITGGLAVQKQQRLLN------QRPDIV  317 (731)
T ss_pred             chHhhhhhHHhccCcceeEEecChHHHH--HHHHHHHHHhccccC---eEEEEeechhHHHHHHHHHh------cCCCEE
Confidence            2            112389999999999  7777777777  445   99999999999887777664      478999


Q ss_pred             EECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHH-hhCCCCcEEEEeccCCcchHH---
Q psy7952         169 YVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQ-FTGNSIPIIALTATAEPSVKQ---  244 (444)
Q Consensus       169 v~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~-~~~~~~~~v~lSAT~~~~~~~---  244 (444)
                      |+||++|-. .+..-..+..++.++.++|+||+|+|.+.|+ |...-..|..+.. ......|.+.+|||+.-...+   
T Consensus       318 VATPGRlwe-li~e~n~~l~~~k~vkcLVlDEaDRmvekgh-F~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~  395 (731)
T KOG0347|consen  318 VATPGRLWE-LIEEDNTHLGNFKKVKCLVLDEADRMVEKGH-FEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLS  395 (731)
T ss_pred             EecchHHHH-HHHhhhhhhhhhhhceEEEEccHHHHhhhcc-HHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhH
Confidence            999999821 1111112345678899999999999999886 6554444444331 122236899999997532221   


Q ss_pred             -----------------HHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHH--hccCC-------C
Q psy7952         245 -----------------DIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKC--LGKDN-------K  298 (444)
Q Consensus       245 -----------------~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~--l~~~~-------~  298 (444)
                                       .+...+++...-.+..              ..........+.+-...+  +++..       .
T Consensus       396 ~~~k~~~k~~~~~~kiq~Lmk~ig~~~kpkiiD--------------~t~q~~ta~~l~Es~I~C~~~eKD~ylyYfl~r  461 (731)
T KOG0347|consen  396 SSRKKKDKEDELNAKIQHLMKKIGFRGKPKIID--------------LTPQSATASTLTESLIECPPLEKDLYLYYFLTR  461 (731)
T ss_pred             HhhhccchhhhhhHHHHHHHHHhCccCCCeeEe--------------cCcchhHHHHHHHHhhcCCccccceeEEEEEee
Confidence                             1222222221111110              000111111111111111  00000       0


Q ss_pred             CCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCC
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMP  368 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p  368 (444)
                      -.+++|||||+.+.+.+++-.|...          |.+..|...+++|++....||||||++++|+|||+|.|||||..|
T Consensus       462 yPGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVP  541 (731)
T KOG0347|consen  462 YPGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVP  541 (731)
T ss_pred             cCCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHHHHHhHHHHhcCCCeEEEeehhhhccCCCCCcceEEEeecC
Confidence            3789999999999999999999877          889999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhh
Q psy7952         369 SSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKT  408 (444)
Q Consensus       369 ~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~  408 (444)
                      .+.+.|+||.||+.|.+..|..+.++.+.+...+.++.+.
T Consensus       542 rtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~~~KL~kt  581 (731)
T KOG0347|consen  542 RTSEIYVHRSGRTARANSEGVSVMLCGPQEVGPLKKLCKT  581 (731)
T ss_pred             CccceeEecccccccccCCCeEEEEeChHHhHHHHHHHHH
Confidence            9999999999999999999999999999999998888764

>KOG0343|consensus

Probab=100.00  E-value=1.2e-42  Score=324.20  Aligned_cols=340  Identities=20%  Similarity=0.225  Sum_probs=259.2

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC----cccee
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN----VRSRN  108 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~----~~~~v  108 (444)
                      .....++|++. +|.. +|++|+.+++..+.| +|++-.|.||||||++        |++|. ++.+++.+    ..-=+
T Consensus        77 s~~t~kgLke~-~fv~-~teiQ~~~Ip~aL~G-~DvlGAAkTGSGKTLA--------FlvPv-lE~L~r~kWs~~DGlGa  144 (758)
T KOG0343|consen   77 SQKTLKGLKEA-KFVK-MTEIQRDTIPMALQG-HDVLGAAKTGSGKTLA--------FLVPV-LEALYRLKWSPTDGLGA  144 (758)
T ss_pred             chHHHHhHhhc-CCcc-HHHHHHhhcchhccC-cccccccccCCCceee--------ehHHH-HHHHHHcCCCCCCCcee
Confidence            34455677765 7776 789999999999999 9999999999999999        99999 66666543    22347


Q ss_pred             EEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         109 GWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       109 lil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      ||++|||+|++|.  .+.+...  ...   +.+..+.|+..........       +...|+||||++|..   |.--.-
T Consensus       145 lIISPTRELA~Qt--FevL~kvgk~h~---fSaGLiiGG~~~k~E~eRi-------~~mNILVCTPGRLLQ---Hmde~~  209 (758)
T KOG0343|consen  145 LIISPTRELALQT--FEVLNKVGKHHD---FSAGLIIGGKDVKFELERI-------SQMNILVCTPGRLLQ---HMDENP  209 (758)
T ss_pred             EEecchHHHHHHH--HHHHHHHhhccc---cccceeecCchhHHHHHhh-------hcCCeEEechHHHHH---HhhhcC
Confidence            9999999999322  4444444  334   7889999998765444333       477899999999852   111111


Q ss_pred             HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCC---
Q psy7952         187 LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST---  263 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~---  263 (444)
                      .....++.++|+|||+++++.|  |...+..|.   ..+|...|.+++|||....+.+..+  +.+.+|..+.....   
T Consensus       210 ~f~t~~lQmLvLDEADR~LDMG--Fk~tL~~Ii---~~lP~~RQTLLFSATqt~svkdLaR--LsL~dP~~vsvhe~a~~  282 (758)
T KOG0343|consen  210 NFSTSNLQMLVLDEADRMLDMG--FKKTLNAII---ENLPKKRQTLLFSATQTKSVKDLAR--LSLKDPVYVSVHENAVA  282 (758)
T ss_pred             CCCCCcceEEEeccHHHHHHHh--HHHHHHHHH---HhCChhheeeeeecccchhHHHHHH--hhcCCCcEEEEeccccc
Confidence            2234578999999999999999  886666654   4788889999999999988766333  44667765554421   


Q ss_pred             -CCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------------cCHHHHH
Q psy7952         264 -FRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------VNKHERS  330 (444)
Q Consensus       264 -~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------------~~~~~r~  330 (444)
                       ...++...+...+ .    +..++++..++..+  ...+.|||++|.+++..++..+++.            |++..|.
T Consensus       283 atP~~L~Q~y~~v~-l----~~Ki~~L~sFI~sh--lk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~  355 (758)
T KOG0343|consen  283 ATPSNLQQSYVIVP-L----EDKIDMLWSFIKSH--LKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRI  355 (758)
T ss_pred             cChhhhhheEEEEe-h----hhHHHHHHHHHHhc--cccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHH
Confidence             1122222222221 1    23345555555544  4778999999999999999999888            8999999


Q ss_pred             HHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccc-hhhHHHHHhhc
Q psy7952         331 RVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS-KKSLEYVIKTD  409 (444)
Q Consensus       331 ~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~-~~~~~~~~~~~  409 (444)
                      .+.++|.....-||+||+++++|+|+|.|++||.+|-|.++.+|+||+||+.|.+..|.+.+++.+.+ ...+..+.+..
T Consensus       356 ev~~~F~~~~~~vLF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psEeE~~l~~Lq~k~  435 (758)
T KOG0343|consen  356 EVYKKFVRKRAVVLFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEEEAMLKKLQKKK  435 (758)
T ss_pred             HHHHHHHHhcceEEEeehhhhccCCCcccceEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchhHHHHHHHHHHcC
Confidence            99999999999999999999999999999999999999999999999999999999999999998887 56667776665


Q ss_pred             cchh
Q psy7952         410 TSTK  413 (444)
Q Consensus       410 ~~~~  413 (444)
                      ++.+
T Consensus       436 I~i~  439 (758)
T KOG0343|consen  436 IPIK  439 (758)
T ss_pred             CCHH
Confidence            6654

>KOG0346|consensus

Probab=100.00  E-value=1.2e-41  Score=309.68  Aligned_cols=339  Identities=19%  Similarity=0.233  Sum_probs=261.3

Q ss_pred             CCHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC------c
Q psy7952          31 VSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN------V  104 (444)
Q Consensus        31 ~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~------~  104 (444)
                      -.++++.+++.+. ||+. ||-+|..+++-+++| +|++..|.||||||.+        |++|. ++.+....      .
T Consensus        25 gLD~RllkAi~~l-G~ek-pTlIQs~aIplaLEg-KDvvarArTGSGKT~A--------YliPl-lqkll~~k~t~~~e~   92 (569)
T KOG0346|consen   25 GLDSRLLKAITKL-GWEK-PTLIQSSAIPLALEG-KDVVARARTGSGKTAA--------YLIPL-LQKLLAEKKTNDGEQ   92 (569)
T ss_pred             CCCHHHHHHHHHh-CcCC-cchhhhcccchhhcC-cceeeeeccCCCchHH--------HHHHH-HHHHHHhhhcccccc
Confidence            3478899999985 9998 999999999999999 8999999999999999        99999 65555432      3


Q ss_pred             cceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHH
Q psy7952         105 RSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYL  183 (444)
Q Consensus       105 ~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~  183 (444)
                      .+.++|++||++|+  +|+...++.+ ..-...+++.-+.++.+.......+      .+.++|+|+||.++.    ..+
T Consensus        93 ~~sa~iLvPTkEL~--qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L------~d~pdIvV~TP~~ll----~~~  160 (569)
T KOG0346|consen   93 GPSAVILVPTKELA--QQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVAL------MDLPDIVVATPAKLL----RHL  160 (569)
T ss_pred             cceeEEEechHHHH--HHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHH------ccCCCeEEeChHHHH----HHH
Confidence            36889999999999  7777777777 2222226666666666655544444      468999999999985    333


Q ss_pred             HHHH-HhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecC
Q psy7952         184 LQHL-VRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTS  262 (444)
Q Consensus       184 ~~~~-~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~  262 (444)
                      .... .....+.++|+||||.++.+|  |...   +.++...+|...|-++||||+...+..  ...+.+.+|+.+...+
T Consensus       161 ~~~~~~~~~~l~~LVvDEADLllsfG--Yeed---lk~l~~~LPr~~Q~~LmSATl~dDv~~--LKkL~l~nPviLkl~e  233 (569)
T KOG0346|consen  161 AAGVLEYLDSLSFLVVDEADLLLSFG--YEED---LKKLRSHLPRIYQCFLMSATLSDDVQA--LKKLFLHNPVILKLTE  233 (569)
T ss_pred             hhccchhhhheeeEEechhhhhhhcc--cHHH---HHHHHHhCCchhhheeehhhhhhHHHH--HHHHhccCCeEEEecc
Confidence            3333 446678999999999999988  6644   455556778888999999999887654  3445578887776655


Q ss_pred             CCCCC---ceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHH
Q psy7952         263 TFRSN---LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHER  329 (444)
Q Consensus       263 ~~~~~---~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r  329 (444)
                      ...++   ......... ..++.-.+..+++--+     ..++.|||+|+.+.|.++.-.|...          ++...|
T Consensus       234 ~el~~~dqL~Qy~v~cs-e~DKflllyallKL~L-----I~gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR  307 (569)
T KOG0346|consen  234 GELPNPDQLTQYQVKCS-EEDKFLLLYALLKLRL-----IRGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSR  307 (569)
T ss_pred             ccCCCcccceEEEEEec-cchhHHHHHHHHHHHH-----hcCceEEEEechhhhHHHHHHHHHhCcHhhhhcccccccch
Confidence            44442   222222222 4455444444444322     4788999999999999997777665          888999


Q ss_pred             HHHHHHHhcCCccEEEEcC-----------------------------------ccccccccCCccEEEEeCCCCCHHHH
Q psy7952         330 SRVQESFMRGEINVITATI-----------------------------------SFGMGIDRQNVRFVVHWGMPSSIPAY  374 (444)
Q Consensus       330 ~~~~~~f~~g~~~vLvaT~-----------------------------------~~~~Gidi~~~~~Vi~~~~p~s~~~~  374 (444)
                      -.+++.|..|-.+++||||                                   -.++|||+.+|..|++||+|.++..|
T Consensus       308 ~Hii~QFNkG~YdivIAtD~s~~~~~~eee~kgk~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sY  387 (569)
T KOG0346|consen  308 CHIIEQFNKGLYDIVIATDDSADGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSY  387 (569)
T ss_pred             hhHHHHhhCcceeEEEEccCccchhhhhccccccccccCCCCccccccccCchhchhccccchheeeeeecCCCCchHHH
Confidence            9999999999999999999                                   24689999999999999999999999


Q ss_pred             HHHhccCCCCCCceeEEEEecccchh---hHHHHH
Q psy7952         375 YQESGRAGRDGLQSYCRIYHSEHSKK---SLEYVI  406 (444)
Q Consensus       375 ~Qr~GR~~R~g~~g~~~~~~~~~~~~---~~~~~~  406 (444)
                      +||+||++|.+++|.++.|+.+.+..   .+..+.
T Consensus       388 IHRvGRTaRg~n~GtalSfv~P~e~~g~~~le~~~  422 (569)
T KOG0346|consen  388 IHRVGRTARGNNKGTALSFVSPKEEFGKESLESIL  422 (569)
T ss_pred             HHhccccccCCCCCceEEEecchHHhhhhHHHHHH
Confidence            99999999999999999999988766   444443

>KOG4284|consensus

Probab=100.00  E-value=1.8e-41  Score=321.41  Aligned_cols=334  Identities=15%  Similarity=0.176  Sum_probs=266.9

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      -..+..+|++. +|.. ||++|..|++.++.+ -|.||.+..|+|||++        |.+.+ ++.+........++|++
T Consensus        33 ~r~vl~glrrn-~f~~-ptkiQaaAIP~~~~k-mDliVQaKSGTGKTlV--------fsv~a-v~sl~~~~~~~q~~Iv~  100 (980)
T KOG4284|consen   33 WREVLLGLRRN-AFAL-PTKIQAAAIPAIFSK-MDLIVQAKSGTGKTLV--------FSVLA-VESLDSRSSHIQKVIVT  100 (980)
T ss_pred             HHHHHHHHHhh-cccC-CCchhhhhhhhhhcc-cceEEEecCCCCceEE--------EEeee-ehhcCcccCcceeEEEe
Confidence            34555677764 8886 999999999999999 9999999999999999        88777 66666677777889999


Q ss_pred             chhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCC
Q psy7952         113 PILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK  192 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~  192 (444)
                      |||+++  +||.+.+..++..+.+.++..+.|+.........+       +.++|+||||+++.    +.+-....+.+.
T Consensus       101 PTREia--VQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rl-------k~~rIvIGtPGRi~----qL~el~~~n~s~  167 (980)
T KOG4284|consen  101 PTREIA--VQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRL-------KQTRIVIGTPGRIA----QLVELGAMNMSH  167 (980)
T ss_pred             cchhhh--hHHHHHHHHhcccccCcceEEEecCchhhhhhhhh-------hhceEEecCchHHH----HHHHhcCCCccc
Confidence            999999  88899999885555559999999998765443333       46789999999986    556667778889


Q ss_pred             ccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCC--CCceE
Q psy7952         193 LAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFR--SNLFY  270 (444)
Q Consensus       193 ~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~--~~~~~  270 (444)
                      ++++|+||||.+.+.+. |.   ..|..+...+|...|++++|||.+....+.+..++  .+|..+.......  -.+..
T Consensus       168 vrlfVLDEADkL~~t~s-fq---~~In~ii~slP~~rQv~a~SATYp~nLdn~Lsk~m--rdp~lVr~n~~d~~L~GikQ  241 (980)
T KOG4284|consen  168 VRLFVLDEADKLMDTES-FQ---DDINIIINSLPQIRQVAAFSATYPRNLDNLLSKFM--RDPALVRFNADDVQLFGIKQ  241 (980)
T ss_pred             eeEEEeccHHhhhchhh-HH---HHHHHHHHhcchhheeeEEeccCchhHHHHHHHHh--cccceeecccCCceeechhh
Confidence            99999999999987443 55   44555666888889999999999999999888875  4665554433222  12222


Q ss_pred             EEEEcccchhhHHH---HHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHh
Q psy7952         271 DVIFDDLLKDSYAH---VKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFM  337 (444)
Q Consensus       271 ~~~~~~~~~~~~~~---~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~  337 (444)
                      .+..........+.   ....+.+++...  +..+.||||+....|+.++..|...          |++.+|..+++.++
T Consensus       242 yv~~~~s~nnsveemrlklq~L~~vf~~i--py~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr  319 (980)
T KOG4284|consen  242 YVVAKCSPNNSVEEMRLKLQKLTHVFKSI--PYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLR  319 (980)
T ss_pred             eeeeccCCcchHHHHHHHHHHHHHHHhhC--chHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhh
Confidence            22222222222222   233333443333  6789999999999999999999888          99999999999999


Q ss_pred             cCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         338 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       338 ~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                      .-..+|||+||..++|||-|+++.||+.|.|.+..+|.||+|||||+|..|.+++|+..+..
T Consensus       320 ~f~~rILVsTDLtaRGIDa~~vNLVVNiD~p~d~eTY~HRIGRAgRFG~~G~aVT~~~~~~e  381 (980)
T KOG4284|consen  320 AFRVRILVSTDLTARGIDADNVNLVVNIDAPADEETYFHRIGRAGRFGAHGAAVTLLEDERE  381 (980)
T ss_pred             hceEEEEEecchhhccCCccccceEEecCCCcchHHHHHHhhhcccccccceeEEEeccchh
Confidence            99999999999999999999999999999999999999999999999999999999976543

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=100.00  E-value=3.3e-40  Score=343.51  Aligned_cols=351  Identities=21%  Similarity=0.222  Sum_probs=252.2

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHcc-----CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccce
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLR-----THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSR  107 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~-----~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~  107 (444)
                      +..+.+.+.+.|||+  ||+.|.++++.++++     .+++++++|||+|||.+        ++.++ +..+..+   .+
T Consensus       437 ~~~~~~~~~~~~~f~--~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~v--------al~a~-l~al~~g---~q  502 (926)
T TIGR00580       437 DLEWQQEFEDSFPFE--ETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEV--------AMRAA-FKAVLDG---KQ  502 (926)
T ss_pred             CHHHHHHHHHhCCCC--CCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHH--------HHHHH-HHHHHhC---Ce
Confidence            455677788889997  589999999999974     26899999999999999        44444 2223333   46


Q ss_pred             eEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH
Q psy7952         108 NGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ  185 (444)
Q Consensus       108 vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~  185 (444)
                      ++|++||++|+     .|+.+.+  .+...++++..+++.....+.......+.  .+.++|+|+||..         +.
T Consensus       503 vlvLvPT~~LA-----~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~--~g~~dIVIGTp~l---------l~  566 (926)
T TIGR00580       503 VAVLVPTTLLA-----QQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELA--SGKIDILIGTHKL---------LQ  566 (926)
T ss_pred             EEEEeCcHHHH-----HHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHH--cCCceEEEchHHH---------hh
Confidence            79999999999     5555554  12222388889998888777777666654  3578999999843         33


Q ss_pred             HHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCC
Q psy7952         186 HLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFR  265 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~  265 (444)
                      ....+.+++++||||+|++   |...+       ..++..+.++++++|||||.+.....  ...+..+...+......+
T Consensus       567 ~~v~f~~L~llVIDEahrf---gv~~~-------~~L~~~~~~~~vL~~SATpiprtl~~--~l~g~~d~s~I~~~p~~R  634 (926)
T TIGR00580       567 KDVKFKDLGLLIIDEEQRF---GVKQK-------EKLKELRTSVDVLTLSATPIPRTLHM--SMSGIRDLSIIATPPEDR  634 (926)
T ss_pred             CCCCcccCCEEEeeccccc---chhHH-------HHHHhcCCCCCEEEEecCCCHHHHHH--HHhcCCCcEEEecCCCCc
Confidence            4456788999999999994   31111       12233455689999999998765543  233444544444333334


Q ss_pred             CCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------------cCHHHHHHHH
Q psy7952         266 SNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------VNKHERSRVQ  333 (444)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------------~~~~~r~~~~  333 (444)
                      .++...+....     ...+...+...+.    .+++++|||+++++++.+++.|.+.            |++.+|..++
T Consensus       635 ~~V~t~v~~~~-----~~~i~~~i~~el~----~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im  705 (926)
T TIGR00580       635 LPVRTFVMEYD-----PELVREAIRRELL----RGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVM  705 (926)
T ss_pred             cceEEEEEecC-----HHHHHHHHHHHHH----cCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHH
Confidence            44433322211     1122222222222    4689999999999999999999873            8999999999


Q ss_pred             HHHhcCCccEEEEcCccccccccCCccEEEEeCCCC-CHHHHHHHhccCCCCCCceeEEEEecc------cchhhHHHHH
Q psy7952         334 ESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQSYCRIYHSE------HSKKSLEYVI  406 (444)
Q Consensus       334 ~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~-s~~~~~Qr~GR~~R~g~~g~~~~~~~~------~~~~~~~~~~  406 (444)
                      ++|++|+.+|||||+++++|+|+|++++||+++.|. +..+|+||+||+||.|+.|+|++++++      ...++++.+.
T Consensus       706 ~~F~~Gk~~ILVaT~iie~GIDIp~v~~VIi~~a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~~~l~~~~~~RL~~~~  785 (926)
T TIGR00580       706 LEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQ  785 (926)
T ss_pred             HHHHcCCCCEEEECChhhcccccccCCEEEEecCCCCCHHHHHHHhcCCCCCCCCeEEEEEECCcccCCHHHHHHHHHHH
Confidence            999999999999999999999999999999998864 688999999999999999999999864      3445666666


Q ss_pred             hhcc---chhHHHHHHHHhhHHHHHHHhhhc
Q psy7952         407 KTDT---STKREQLELKFKNYLSMLEYCEQG  434 (444)
Q Consensus       407 ~~~~---~~~~~~~~~~~~~~~~~~~~~~~~  434 (444)
                      +...   ..+....+.++++..++.-..++|
T Consensus       786 ~~~~~g~gf~ia~~Dl~~Rg~G~~lG~~QsG  816 (926)
T TIGR00580       786 EFSELGAGFKIALHDLEIRGAGNLLGEEQSG  816 (926)
T ss_pred             HhhcchhhHHHHHHHHHhcCCcCCCCCcccC
Confidence            5544   556667777777766666544444

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.

>KOG0332|consensus

Probab=100.00  E-value=4.8e-41  Score=299.98  Aligned_cols=346  Identities=15%  Similarity=0.188  Sum_probs=263.1

Q ss_pred             CCCCCCcCCCCCCCCCHHHHHHHHHHHhCCcccCchHHHHHHHHHHccC-CcEEEEccCCCcccccccccccceEEeCCC
Q psy7952          17 SSLTGNQQDRKGGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRT-HDIFVSMPTGAVSLVGSVVSARSRVRIPPG   95 (444)
Q Consensus        17 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~-~~~ii~apTGsGKT~~a~~~~~~~~~~~~~   95 (444)
                      +.++........+--...++.+++-. ++|.. |+.+|..+++-++... ++.|..+..|+|||.+        |.+.. 
T Consensus        82 pnsPlyS~ksFeeL~LkPellkgly~-M~F~k-PskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaa--------FvL~M-  150 (477)
T KOG0332|consen   82 PNSPLYSAKSFEELRLKPELLKGLYA-MKFQK-PSKIQETALPLLLAEPPQNLIAQSQSGTGKTAA--------FVLTM-  150 (477)
T ss_pred             CCCCccccccHHhhCCCHHHHhHHHH-hccCC-cchHHHhhcchhhcCCchhhhhhhcCCCchhHH--------HHHHH-
Confidence            33333333333333335567777776 69997 9999999999999875 7899999999999999        66666 


Q ss_pred             ccccccCCccceeEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCcc
Q psy7952          96 ADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERA  175 (444)
Q Consensus        96 ~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l  175 (444)
                      +.++-..-..|.++.++||++|+  .|.-+.+..+... ..+.......+.......         .-..+|+|+||+.+
T Consensus       151 Lsrvd~~~~~PQ~iCLaPtrELA--~Q~~eVv~eMGKf-~~ita~yair~sk~~rG~---------~i~eqIviGTPGtv  218 (477)
T KOG0332|consen  151 LSRVDPDVVVPQCICLAPTRELA--PQTGEVVEEMGKF-TELTASYAIRGSKAKRGN---------KLTEQIVIGTPGTV  218 (477)
T ss_pred             HHhcCccccCCCceeeCchHHHH--HHHHHHHHHhcCc-eeeeEEEEecCcccccCC---------cchhheeeCCCccH
Confidence            33344445668899999999999  2224444444111 125665555544221111         12358999999998


Q ss_pred             ccccHHHHHH-HHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCC
Q psy7952         176 VTESFHYLLQ-HLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNK  254 (444)
Q Consensus       176 ~~~~~~~~~~-~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~  254 (444)
                      .    +++.. .......+..+|+|||+.+.+-.. |.....   ++....|.+.|++++|||.....+......+.-.+
T Consensus       219 ~----Dlm~klk~id~~kikvfVlDEAD~Mi~tqG-~~D~S~---rI~~~lP~~~QllLFSATf~e~V~~Fa~kivpn~n  290 (477)
T KOG0332|consen  219 L----DLMLKLKCIDLEKIKVFVLDEADVMIDTQG-FQDQSI---RIMRSLPRNQQLLLFSATFVEKVAAFALKIVPNAN  290 (477)
T ss_pred             H----HHHHHHHhhChhhceEEEecchhhhhhccc-ccccch---hhhhhcCCcceEEeeechhHHHHHHHHHHhcCCCc
Confidence            6    44444 556678899999999999976321 332223   34456777899999999999999888888877777


Q ss_pred             CeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------c
Q psy7952         255 PYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------V  324 (444)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~  324 (444)
                      ++.+.+......++...+........++..+.++....      .-++.||||.++..|.+++..+...          +
T Consensus       291 ~i~Lk~eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~------tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l  364 (477)
T KOG0332|consen  291 VIILKREELALDNIKQLYVLCACRDDKYQALVNLYGLL------TIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDL  364 (477)
T ss_pred             eeeeehhhccccchhhheeeccchhhHHHHHHHHHhhh------hhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccc
Confidence            77777777778888777777777777776666633322      4678899999999999999999887          8


Q ss_pred             CHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCC------CHHHHHHHhccCCCCCCceeEEEEecccc
Q psy7952         325 NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPS------SIPAYYQESGRAGRDGLQSYCRIYHSEHS  398 (444)
Q Consensus       325 ~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~------s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~  398 (444)
                      ..++|..++++|+.|..+|||+|+++++|||++.++.||+||+|.      +.+.|+||+||+||+|+.|.++-+++.++
T Consensus       365 ~~~~R~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~  444 (477)
T KOG0332|consen  365 TVEQRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKD  444 (477)
T ss_pred             hhHHHHHHHHHHhcCcceEEEEechhhcccccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccC
Confidence            889999999999999999999999999999999999999999985      78999999999999999999999887654


Q ss_pred             h
Q psy7952         399 K  399 (444)
Q Consensus       399 ~  399 (444)
                      -
T Consensus       445 s  445 (477)
T KOG0332|consen  445 S  445 (477)
T ss_pred             c
Confidence            3

>KOG0341|consensus

Probab=100.00  E-value=4.7e-42  Score=307.70  Aligned_cols=330  Identities=19%  Similarity=0.257  Sum_probs=254.1

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccc-------cCCcc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFIL-------NGNVR  105 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~-------~~~~~  105 (444)
                      +..+.+.+++ -|+.. ||++|.+-++.++.| +|++-.|-||||||++        |.+|.+.-.+.       ..+-.
T Consensus       178 P~~~L~~lk~-KGI~~-PTpIQvQGlPvvLsG-RDmIGIAfTGSGKTlv--------FvLP~imf~LeqE~~lPf~~~EG  246 (610)
T KOG0341|consen  178 PKPLLRGLKK-KGIVH-PTPIQVQGLPVVLSG-RDMIGIAFTGSGKTLV--------FVLPVIMFALEQEMMLPFARGEG  246 (610)
T ss_pred             CHHHHHHHHh-cCCCC-CCceeecCcceEeec-CceeeEEeecCCceEE--------EeHHHHHHHHHHHhcCccccCCC
Confidence            5677888888 49998 999999999999999 9999999999999999        77777433332       23344


Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESF  180 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~  180 (444)
                      |-.||+||+++|+  .|..+.++.+     .-+.+.++.....|+.+..++.+..      ..+.+|+|+||++|.    
T Consensus       247 P~gLiicPSRELA--rQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v------~~GvHivVATPGRL~----  314 (610)
T KOG0341|consen  247 PYGLIICPSRELA--RQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVV------RRGVHIVVATPGRLM----  314 (610)
T ss_pred             CeeEEEcCcHHHH--HHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHH------hcCeeEEEcCcchHH----
Confidence            5669999999999  5556555554     4566778888999999887665554      468999999999986    


Q ss_pred             HHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEe
Q psy7952         181 HYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFK  260 (444)
Q Consensus       181 ~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~  260 (444)
                      +.+......+.-.+|+.+||++++.+.|  |..   .+..++..|....|.+++|||++..........  +-+|+.+..
T Consensus       315 DmL~KK~~sLd~CRyL~lDEADRmiDmG--FEd---dir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSA--LVKPvtvNV  387 (610)
T KOG0341|consen  315 DMLAKKIMSLDACRYLTLDEADRMIDMG--FED---DIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSA--LVKPVTVNV  387 (610)
T ss_pred             HHHHHhhccHHHHHHhhhhhHHHHhhcc--chh---hHHHHHHHHhhhhheeeeeccccHHHHHHHHhh--cccceEEec
Confidence            5556666667778999999999999998  664   444555566666889999999998876655444  346655544


Q ss_pred             cCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHH
Q psy7952         261 TSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERS  330 (444)
Q Consensus       261 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~  330 (444)
                      ....-.+  ..+.. +..-.+.+...-.+.+.+.+   ...+++|||..+.+++.+.+.|--+          .++++|.
T Consensus       388 GRAGAAs--ldViQ-evEyVkqEaKiVylLeCLQK---T~PpVLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKDQedR~  461 (610)
T KOG0341|consen  388 GRAGAAS--LDVIQ-EVEYVKQEAKIVYLLECLQK---TSPPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRH  461 (610)
T ss_pred             ccccccc--hhHHH-HHHHHHhhhhhhhHHHHhcc---CCCceEEEeccccChHHHHHHHHHccceeEEeecCcchhHHH
Confidence            3221111  11110 00011112222233333333   6889999999999999999887555          7899999


Q ss_pred             HHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccc
Q psy7952         331 RVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS  398 (444)
Q Consensus       331 ~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~  398 (444)
                      ..++.|+.|+..|||||++++.|+|+|++.|||+||+|..+++|+||+||+||.|+.|.+.+|+.+..
T Consensus       462 ~ai~afr~gkKDVLVATDVASKGLDFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~~  529 (610)
T KOG0341|consen  462 YAIEAFRAGKKDVLVATDVASKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGIATTFINKNQ  529 (610)
T ss_pred             HHHHHHhcCCCceEEEecchhccCCCccchhhccCCChHHHHHHHHHhcccCCCCCcceeeeeecccc
Confidence            99999999999999999999999999999999999999999999999999999999999999998653

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=100.00  E-value=1.5e-39  Score=334.37  Aligned_cols=352  Identities=20%  Similarity=0.242  Sum_probs=253.9

Q ss_pred             HHHHHHHHHHhCCcccCchHHHHHHHHHHccC-----CcEEEEccCCCcccccccccccceEEeCCCccccccCCcccee
Q psy7952          34 QELTAKLKALFGFDSFKCELQKKAIRHILLRT-----HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRN  108 (444)
Q Consensus        34 ~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~-----~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~v  108 (444)
                      ..+.+.+...++|+  +|++|.++++.+..+-     .++++++|||||||.+        +.+++ +..+..+   .++
T Consensus       248 ~~~~~~~~~~l~f~--lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~v--------a~~~i-l~~~~~g---~q~  313 (681)
T PRK10917        248 GELLKKFLASLPFE--LTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVV--------AALAA-LAAIEAG---YQA  313 (681)
T ss_pred             hHHHHHHHHhCCCC--CCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHH--------HHHHH-HHHHHcC---CeE
Confidence            45667777778997  5789999999999862     4799999999999999        55555 3323332   356


Q ss_pred             EEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         109 GWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       109 lil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      +|++||++|+  .|+.+.++.+  ..+   +++..++|+....++...+..+.  .+.++|+|+||+.+.         .
T Consensus       314 lilaPT~~LA--~Q~~~~l~~l~~~~~---i~v~ll~G~~~~~~r~~~~~~l~--~g~~~IvVgT~~ll~---------~  377 (681)
T PRK10917        314 ALMAPTEILA--EQHYENLKKLLEPLG---IRVALLTGSLKGKERREILEAIA--SGEADIVIGTHALIQ---------D  377 (681)
T ss_pred             EEEeccHHHH--HHHHHHHHHHHhhcC---cEEEEEcCCCCHHHHHHHHHHHh--CCCCCEEEchHHHhc---------c
Confidence            9999999999  2223333333  335   89999999999887777776654  457999999987753         2


Q ss_pred             HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCC
Q psy7952         187 LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRS  266 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  266 (444)
                      ...+.+++++|+||+|++..   ..+.   .   +. ..+..+++++|||||.+.....  ...+..+...+......+.
T Consensus       378 ~v~~~~l~lvVIDE~Hrfg~---~qr~---~---l~-~~~~~~~iL~~SATp~prtl~~--~~~g~~~~s~i~~~p~~r~  445 (681)
T PRK10917        378 DVEFHNLGLVIIDEQHRFGV---EQRL---A---LR-EKGENPHVLVMTATPIPRTLAM--TAYGDLDVSVIDELPPGRK  445 (681)
T ss_pred             cchhcccceEEEechhhhhH---HHHH---H---HH-hcCCCCCEEEEeCCCCHHHHHH--HHcCCCceEEEecCCCCCC
Confidence            34567899999999999532   1221   1   11 2233488999999997755432  2222222222222222233


Q ss_pred             CceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccc--------hHHHHHHHHHhh------------cCH
Q psy7952         267 NLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTRE--------HTTDLADALRRK------------VNK  326 (444)
Q Consensus       267 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~--------~~~~l~~~L~~~------------~~~  326 (444)
                      ++...+...    .....+.+.+...+    ..+++++|||+.++        .++.+++.|.+.            |++
T Consensus       446 ~i~~~~~~~----~~~~~~~~~i~~~~----~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~  517 (681)
T PRK10917        446 PITTVVIPD----SRRDEVYERIREEI----AKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKP  517 (681)
T ss_pred             CcEEEEeCc----ccHHHHHHHHHHHH----HcCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCH
Confidence            343333322    22233334444443    25789999999654        345566666554            889


Q ss_pred             HHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCC-CHHHHHHHhccCCCCCCceeEEEEec-c---cchhh
Q psy7952         327 HERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQSYCRIYHS-E---HSKKS  401 (444)
Q Consensus       327 ~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~-s~~~~~Qr~GR~~R~g~~g~~~~~~~-~---~~~~~  401 (444)
                      .+|..++++|++|+.+|||||+++++|+|+|++++||+++.|. +...+.||+||+||.|..|+|++++. +   ...++
T Consensus       518 ~eR~~i~~~F~~g~~~ILVaT~vie~GiDip~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~~~~~~~~~~r  597 (681)
T PRK10917        518 AEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARER  597 (681)
T ss_pred             HHHHHHHHHHHcCCCCEEEECcceeeCcccCCCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEECCCCChhHHHH
Confidence            9999999999999999999999999999999999999999986 57889999999999999999999995 3   35567


Q ss_pred             HHHHHhhccchhHHHHHHHHhhHHHHHHHhhhce
Q psy7952         402 LEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGY  435 (444)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  435 (444)
                      +..+.++....+..+.+.++++..++.....+|.
T Consensus       598 l~~~~~~~dgf~iae~dl~~rg~g~~~g~~q~g~  631 (681)
T PRK10917        598 LKIMRETNDGFVIAEKDLELRGPGELLGTRQSGL  631 (681)
T ss_pred             HHHHHHhcchHHHHHHhHhhCCCccccCceecCC
Confidence            7888888888888888888999999888777774

>PRK13767 ATP-dependent helicase; Provisional

Probab=100.00  E-value=1.4e-39  Score=342.50  Aligned_cols=322  Identities=22%  Similarity=0.308  Sum_probs=220.6

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC------Cccc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG------NVRS  106 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~------~~~~  106 (444)
                      +..+.+.+++  ++.. ||++|.++++.+++| ++++++||||+|||++        +.+|+ ++.+...      ....
T Consensus        19 ~~~v~~~~~~--~~~~-~tpiQ~~Ai~~il~g-~nvli~APTGSGKTla--------a~Lpi-l~~l~~~~~~~~~~~~~   85 (876)
T PRK13767         19 RPYVREWFKE--KFGT-FTPPQRYAIPLIHEG-KNVLISSPTGSGKTLA--------AFLAI-IDELFRLGREGELEDKV   85 (876)
T ss_pred             CHHHHHHHHH--ccCC-CCHHHHHHHHHHHcC-CCEEEECCCCCcHHHH--------HHHHH-HHHHHhhccccCCCCCe
Confidence            4555566665  5565 779999999999999 9999999999999999        55555 3223221      1234


Q ss_pred             eeEEEcchhhhhcccCccchHhhh------------c--CCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECC
Q psy7952         107 RNGWISPILSSFYLRFRDDKTSIV------------T--GRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTP  172 (444)
Q Consensus       107 ~vlil~P~~~L~~~~q~~~~~~~l------------~--~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tp  172 (444)
                      ++||++|+++|+     .++.+.+            .  ...+.+.+...+|+....++...+      ...++|+|+||
T Consensus        86 ~~LyIsPtraLa-----~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l------~~~p~IlVtTP  154 (876)
T PRK13767         86 YCLYVSPLRALN-----NDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKML------KKPPHILITTP  154 (876)
T ss_pred             EEEEEcCHHHHH-----HHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHH------hCCCCEEEecH
Confidence            689999999999     4444322            1  122248899999998877665544      35789999999


Q ss_pred             CccccccHHHHHHHH---HhhCCccEEEEeccccccccC--CCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHH
Q psy7952         173 ERAVTESFHYLLQHL---VRYNKLAYIVVDEAHCVSEWG--HDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDII  247 (444)
Q Consensus       173 e~l~~~~~~~~~~~~---~~~~~~~~iViDE~H~~~~~~--~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~  247 (444)
                      |++.     .++...   ..+.++++||+||+|.+.+..  ..+...+.   ++....+...|++++|||+++.  +.+.
T Consensus       155 E~L~-----~ll~~~~~~~~l~~l~~VVIDE~H~l~~~~RG~~l~~~L~---rL~~l~~~~~q~IglSATl~~~--~~va  224 (876)
T PRK13767        155 ESLA-----ILLNSPKFREKLRTVKWVIVDEIHSLAENKRGVHLSLSLE---RLEELAGGEFVRIGLSATIEPL--EEVA  224 (876)
T ss_pred             HHHH-----HHhcChhHHHHHhcCCEEEEechhhhccCccHHHHHHHHH---HHHHhcCCCCeEEEEecccCCH--HHHH
Confidence            9974     222211   246789999999999997533  22222223   3333334558899999999763  3445


Q ss_pred             HHhcC------CCCeEEEecCCCCCCceEEEEEc------ccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHH
Q psy7952         248 SVLKF------NKPYKVFKTSTFRSNLFYDVIFD------DLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTD  315 (444)
Q Consensus       248 ~~l~~------~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~  315 (444)
                      .++..      +.+..+..... .......+...      .........+...+.+.+.    .++++||||||+..|+.
T Consensus       225 ~~L~~~~~~~~~r~~~iv~~~~-~k~~~i~v~~p~~~l~~~~~~~~~~~l~~~L~~~i~----~~~~~LVF~nTr~~ae~  299 (876)
T PRK13767        225 KFLVGYEDDGEPRDCEIVDARF-VKPFDIKVISPVDDLIHTPAEEISEALYETLHELIK----EHRTTLIFTNTRSGAER  299 (876)
T ss_pred             HHhcCccccCCCCceEEEccCC-CccceEEEeccCccccccccchhHHHHHHHHHHHHh----cCCCEEEEeCCHHHHHH
Confidence            55543      22223322211 11111111110      0011112233344444332    36789999999999999


Q ss_pred             HHHHHHhh----------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhc
Q psy7952         316 LADALRRK----------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESG  379 (444)
Q Consensus       316 l~~~L~~~----------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~G  379 (444)
                      ++..|.+.                +++++|..+++.|++|++++||||+++++|||+|++++||+++.|.|...|+||+|
T Consensus       300 la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~Le~GIDip~Vd~VI~~~~P~sv~~ylQRiG  379 (876)
T PRK13767        300 VLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIG  379 (876)
T ss_pred             HHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChHHhcCCCCCCcEEEEeCCCCCHHHHHHhcc
Confidence            99998761                88999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC-CCceeEEEE
Q psy7952         380 RAGRD-GLQSYCRIY  393 (444)
Q Consensus       380 R~~R~-g~~g~~~~~  393 (444)
                      |+||. |..+.+.++
T Consensus       380 RaGR~~g~~~~g~ii  394 (876)
T PRK13767        380 RAGHRLGEVSKGRII  394 (876)
T ss_pred             cCCCCCCCCCcEEEE
Confidence            99987 433333333

>KOG0339|consensus

Probab=100.00  E-value=1.1e-39  Score=301.62  Aligned_cols=336  Identities=16%  Similarity=0.235  Sum_probs=276.6

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc-----CCccce
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN-----GNVRSR  107 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~-----~~~~~~  107 (444)
                      ++.|..+.+.. .|.. ||++|-++++..+.| ++++-.|-||+|||.+        |+.|.+.+ ++.     .+..|-
T Consensus       231 DkqLm~airk~-Ey~k-ptpiq~qalptalsg-rdvigIAktgSgktaA--------fi~pm~~h-imdq~eL~~g~gPi  298 (731)
T KOG0339|consen  231 DKQLMTAIRKS-EYEK-PTPIQCQALPTALSG-RDVIGIAKTGSGKTAA--------FIWPMIVH-IMDQPELKPGEGPI  298 (731)
T ss_pred             hHHHHHHHhhh-hccc-CCccccccccccccc-ccchheeeccCcchhH--------HHHHHHHH-hcchhhhcCCCCCe
Confidence            45566777765 7776 899999999999999 9999999999999999        88888333 332     245577


Q ss_pred             eEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH
Q psy7952         108 NGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ  185 (444)
Q Consensus       108 vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~  185 (444)
                      .+|+|||++|+  .||...++.|  ..+   +++..++|+.+.+++..-++      .++.|+|+||++|.    +.+..
T Consensus       299 ~vilvPTrela--~Qi~~eaKkf~K~yg---l~~v~~ygGgsk~eQ~k~Lk------~g~EivVaTPgRli----d~Vkm  363 (731)
T KOG0339|consen  299 GVILVPTRELA--SQIFSEAKKFGKAYG---LRVVAVYGGGSKWEQSKELK------EGAEIVVATPGRLI----DMVKM  363 (731)
T ss_pred             EEEEeccHHHH--HHHHHHHHHhhhhcc---ceEEEeecCCcHHHHHHhhh------cCCeEEEechHHHH----HHHHh
Confidence            89999999999  6667777888  667   99999999999987766664      58999999999986    66777


Q ss_pred             HHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecC--C
Q psy7952         186 HLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTS--T  263 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~--~  263 (444)
                      ...++.+..|+|+||+++|.+.|  |.+++..|..   ...++.|.+++|||....+....+..|.  +++.++..+  .
T Consensus       364 Katn~~rvS~LV~DEadrmfdmG--fe~qVrSI~~---hirpdrQtllFsaTf~~kIe~lard~L~--dpVrvVqg~vge  436 (731)
T KOG0339|consen  364 KATNLSRVSYLVLDEADRMFDMG--FEPQVRSIKQ---HIRPDRQTLLFSATFKKKIEKLARDILS--DPVRVVQGEVGE  436 (731)
T ss_pred             hcccceeeeEEEEechhhhhccc--cHHHHHHHHh---hcCCcceEEEeeccchHHHHHHHHHHhc--CCeeEEEeehhc
Confidence            77888999999999999999988  8877776654   4556689999999999988888888765  555555443  3


Q ss_pred             CCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHH
Q psy7952         264 FRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQ  333 (444)
Q Consensus       264 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~  333 (444)
                      ....+...+........++   ..++..+.+..  ..+++|||+..+..+++++..|.-+          +.+.+|.+++
T Consensus       437 an~dITQ~V~V~~s~~~Kl---~wl~~~L~~f~--S~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~l  511 (731)
T KOG0339|consen  437 ANEDITQTVSVCPSEEKKL---NWLLRHLVEFS--SEGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVL  511 (731)
T ss_pred             cccchhheeeeccCcHHHH---HHHHHHhhhhc--cCCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHH
Confidence            3445555555555444443   33444444333  5789999999999999999998776          8899999999


Q ss_pred             HHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         334 ESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       334 ~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      .+|+.+...||++|++..+|+|||++..||+||+-.+++.+.||+||.||.|..|.+++++.+.+.+....|..
T Consensus       512 s~fKkk~~~VlvatDvaargldI~~ikTVvnyD~ardIdththrigrtgRag~kGvayTlvTeKDa~fAG~LVn  585 (731)
T KOG0339|consen  512 SKFKKKRKPVLVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEKDAEFAGHLVN  585 (731)
T ss_pred             HHHhhcCCceEEEeeHhhcCCCccccceeecccccchhHHHHHHhhhcccccccceeeEEechhhHHHhhHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999887776654

>PRK02362 ski2-like helicase; Provisional

Probab=100.00  E-value=1.1e-39  Score=340.35  Aligned_cols=318  Identities=18%  Similarity=0.254  Sum_probs=223.4

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHH-HHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRH-ILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~-~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      +..+.+++++ .|+.. ++++|.++++. +..| +++++++|||+|||++        +.+++ +..+..+   .+++|+
T Consensus         9 p~~~~~~l~~-~g~~~-l~p~Q~~ai~~~~~~g-~nvlv~APTGSGKTli--------a~lai-l~~l~~~---~kal~i   73 (737)
T PRK02362          9 PEGVIEFYEA-EGIEE-LYPPQAEAVEAGLLDG-KNLLAAIPTASGKTLI--------AELAM-LKAIARG---GKALYI   73 (737)
T ss_pred             CHHHHHHHHh-CCCCc-CCHHHHHHHHHHHhCC-CcEEEECCCcchHHHH--------HHHHH-HHHHhcC---CcEEEE
Confidence            4577788887 59998 56999999998 5566 9999999999999999        44444 3333333   356999


Q ss_pred             cchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH-HHh
Q psy7952         112 SPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH-LVR  189 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~-~~~  189 (444)
                      +|+++|+     .|+++.+ .+...++++..++|+......  .       ...++|+|+|||++.     .+.++ ...
T Consensus        74 ~P~raLa-----~q~~~~~~~~~~~g~~v~~~tGd~~~~~~--~-------l~~~~IiV~Tpek~~-----~llr~~~~~  134 (737)
T PRK02362         74 VPLRALA-----SEKFEEFERFEELGVRVGISTGDYDSRDE--W-------LGDNDIIVATSEKVD-----SLLRNGAPW  134 (737)
T ss_pred             eChHHHH-----HHHHHHHHHhhcCCCEEEEEeCCcCcccc--c-------cCCCCEEEECHHHHH-----HHHhcChhh
Confidence            9999999     6777666 332123889999998754321  1       246799999999973     33332 233


Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCC-c
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSN-L  268 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~-~  268 (444)
                      +.+++++|+||+|.+.+.+  +...+..+...+.......|+|++|||+++  .+.+.++++....     ....+|. +
T Consensus       135 l~~v~lvViDE~H~l~d~~--rg~~le~il~rl~~~~~~~qii~lSATl~n--~~~la~wl~~~~~-----~~~~rpv~l  205 (737)
T PRK02362        135 LDDITCVVVDEVHLIDSAN--RGPTLEVTLAKLRRLNPDLQVVALSATIGN--ADELADWLDAELV-----DSEWRPIDL  205 (737)
T ss_pred             hhhcCEEEEECccccCCCc--chHHHHHHHHHHHhcCCCCcEEEEcccCCC--HHHHHHHhCCCcc-----cCCCCCCCC
Confidence            5689999999999997644  455555554444444556899999999976  3466777753210     0111111 0


Q ss_pred             eEEEE------Ecc----cchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh---------------
Q psy7952         269 FYDVI------FDD----LLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK---------------  323 (444)
Q Consensus       269 ~~~~~------~~~----~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~---------------  323 (444)
                      ...+.      ...    ............+...+.    .++++||||+|++.|+.++..|...               
T Consensus       206 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~  281 (737)
T PRK02362        206 REGVFYGGAIHFDDSQREVEVPSKDDTLNLVLDTLE----EGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAE  281 (737)
T ss_pred             eeeEecCCeeccccccccCCCccchHHHHHHHHHHH----cCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHH
Confidence            00000      000    000000122233333322    4789999999999998887766421               


Q ss_pred             -------------------------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEE----eC--
Q psy7952         324 -------------------------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVH----WG--  366 (444)
Q Consensus       324 -------------------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~----~~--  366 (444)
                                                     +++.+|..+++.|++|.++|||||+++++|+|+|..++||+    |+  
T Consensus       282 ~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR~~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~  361 (737)
T PRK02362        282 LAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGG  361 (737)
T ss_pred             HHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHHHHHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCC
Confidence                                           77899999999999999999999999999999999999996    55  


Q ss_pred             ---CCCCHHHHHHHhccCCCCCCc--eeEEEEeccc
Q psy7952         367 ---MPSSIPAYYQESGRAGRDGLQ--SYCRIYHSEH  397 (444)
Q Consensus       367 ---~p~s~~~~~Qr~GR~~R~g~~--g~~~~~~~~~  397 (444)
                         .|.+..+|.||+|||||.|.+  |.++++....
T Consensus       362 ~g~~~~s~~~y~Qm~GRAGR~g~d~~G~~ii~~~~~  397 (737)
T PRK02362        362 AGMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSY  397 (737)
T ss_pred             CCceeCCHHHHHHHhhcCCCCCCCCCceEEEEecCc
Confidence               588999999999999999875  8888888764

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=100.00  E-value=1.4e-38  Score=325.26  Aligned_cols=352  Identities=21%  Similarity=0.252  Sum_probs=245.0

Q ss_pred             HHHHHHHHHhCCcccCchHHHHHHHHHHccC-----CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeE
Q psy7952          35 ELTAKLKALFGFDSFKCELQKKAIRHILLRT-----HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNG  109 (444)
Q Consensus        35 ~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~-----~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vl  109 (444)
                      .....+...++|+  +|+.|+++++.++.+-     .+.++++|||+|||.+        +.+++ +..+..+   .+++
T Consensus       223 ~~~~~~~~~lpf~--lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~v--------a~l~i-l~~~~~g---~qvl  288 (630)
T TIGR00643       223 ELLTKFLASLPFK--LTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLV--------AALAM-LAAIEAG---YQVA  288 (630)
T ss_pred             HHHHHHHHhCCCC--CCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHH--------HHHHH-HHHHHcC---CcEE
Confidence            3444444457996  5789999999998751     3589999999999999        55554 2223333   3569


Q ss_pred             EEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH
Q psy7952         110 WISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL  187 (444)
Q Consensus       110 il~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~  187 (444)
                      |++||++|+  .|+.+.+..+  ..+   +++..++|+....++......+.  .+.++|+|+||..+.         ..
T Consensus       289 ilaPT~~LA--~Q~~~~~~~l~~~~g---i~v~lltg~~~~~~r~~~~~~i~--~g~~~IiVgT~~ll~---------~~  352 (630)
T TIGR00643       289 LMAPTEILA--EQHYNSLRNLLAPLG---IEVALLTGSLKGKRRKELLETIA--SGQIHLVVGTHALIQ---------EK  352 (630)
T ss_pred             EECCHHHHH--HHHHHHHHHHhcccC---cEEEEEecCCCHHHHHHHHHHHh--CCCCCEEEecHHHHh---------cc
Confidence            999999999  2223334443  335   89999999998877766666554  467899999987653         33


Q ss_pred             HhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhC--CCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCC
Q psy7952         188 VRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTG--NSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFR  265 (444)
Q Consensus       188 ~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~--~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~  265 (444)
                      ..+.+++++|+||+|++..   ..+..      +.....  ..+++++|||||.+.....  ...+..+...+......+
T Consensus       353 ~~~~~l~lvVIDEaH~fg~---~qr~~------l~~~~~~~~~~~~l~~SATp~prtl~l--~~~~~l~~~~i~~~p~~r  421 (630)
T TIGR00643       353 VEFKRLALVIIDEQHRFGV---EQRKK------LREKGQGGFTPHVLVMSATPIPRTLAL--TVYGDLDTSIIDELPPGR  421 (630)
T ss_pred             ccccccceEEEechhhccH---HHHHH------HHHhcccCCCCCEEEEeCCCCcHHHHH--HhcCCcceeeeccCCCCC
Confidence            4567899999999999532   12211      222222  2478999999987754332  111111111111111122


Q ss_pred             CCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccc--------hHHHHHHHHHhh------------cC
Q psy7952         266 SNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTRE--------HTTDLADALRRK------------VN  325 (444)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~--------~~~~l~~~L~~~------------~~  325 (444)
                      ..+...+....    ....+...+.+.+.    .+++++|||+..+        .++.+++.|...            |+
T Consensus       422 ~~i~~~~~~~~----~~~~~~~~i~~~l~----~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~  493 (630)
T TIGR00643       422 KPITTVLIKHD----EKDIVYEFIEEEIA----KGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMK  493 (630)
T ss_pred             CceEEEEeCcc----hHHHHHHHHHHHHH----hCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCC
Confidence            33333222221    11333333333322    4788999998764        455666666643            88


Q ss_pred             HHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCC-CHHHHHHHhccCCCCCCceeEEEEec----ccchh
Q psy7952         326 KHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQSYCRIYHS----EHSKK  400 (444)
Q Consensus       326 ~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~-s~~~~~Qr~GR~~R~g~~g~~~~~~~----~~~~~  400 (444)
                      +.+|..+++.|++|+.+|||||+++++|+|+|++++||+++.|. +...|.||+||+||.|..|+|++++.    +....
T Consensus       494 ~~eR~~i~~~F~~g~~~ILVaT~vie~GvDiP~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~~~~~~~~~~  573 (630)
T TIGR00643       494 SDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKNPKSESAKK  573 (630)
T ss_pred             HHHHHHHHHHHHcCCCCEEEECceeecCcccCCCcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEECCCCCHHHHH
Confidence            99999999999999999999999999999999999999999886 68899999999999999999999992    33344


Q ss_pred             hHHHHHhhccchhHHHHHHHHhhHHHHHHHhhhce
Q psy7952         401 SLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGY  435 (444)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  435 (444)
                      .+..+..+.......+.+.++++..++....++|.
T Consensus       574 rl~~~~~~~dgf~iae~dl~~Rg~g~~~g~~QsG~  608 (630)
T TIGR00643       574 RLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGY  608 (630)
T ss_pred             HHHHHHhhcccHHHHHHHHhcCCCcccCCCcccCC
Confidence            56777777777778888888999999988877774

>KOG0350|consensus

Probab=100.00  E-value=4.9e-39  Score=297.09  Aligned_cols=340  Identities=21%  Similarity=0.275  Sum_probs=231.3

Q ss_pred             HHHHHHhCCcccCchHHHHHHHHHHcc--------CCcEEEEccCCCcccccccccccceEEeCCCccccccCC-cccee
Q psy7952          38 AKLKALFGFDSFKCELQKKAIRHILLR--------THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN-VRSRN  108 (444)
Q Consensus        38 ~~l~~~~g~~~~~t~~Q~~~~~~~~~~--------~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~-~~~~v  108 (444)
                      +.+.+ ++++.+. |+|..+++.++..        .+|+.+.||||||||++        |.+|+ .+.+..+. ..-|+
T Consensus       150 q~l~k-~~is~~F-PVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLa--------Y~iPI-VQ~L~~R~v~~LRa  218 (620)
T KOG0350|consen  150 QLLVK-MAISRLF-PVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLA--------YVIPI-VQLLSSRPVKRLRA  218 (620)
T ss_pred             HHHHH-hhccccc-chHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceee--------ehhHH-HHHHccCCccceEE
Confidence            34555 3777644 5999999998641        37899999999999999        99999 66666553 33689


Q ss_pred             EEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH-H
Q psy7952         109 GWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL-Q  185 (444)
Q Consensus       109 lil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~-~  185 (444)
                      +|++|+++|+  .||.+.+..+  ..+   +.|..+.|..+.......+...- .....||+|+||++|.    +.+. .
T Consensus       219 vVivPtr~L~--~QV~~~f~~~~~~tg---L~V~~~sgq~sl~~E~~qL~~~~-~~~~~DIlVaTPGRLV----DHl~~~  288 (620)
T KOG0350|consen  219 VVIVPTRELA--LQVYDTFKRLNSGTG---LAVCSLSGQNSLEDEARQLASDP-PECRIDILVATPGRLV----DHLNNT  288 (620)
T ss_pred             EEEeeHHHHH--HHHHHHHHHhccCCc---eEEEecccccchHHHHHHHhcCC-CccccceEEcCchHHH----HhccCC
Confidence            9999999999  4447777777  445   78888888776543333222100 0123599999999985    2222 2


Q ss_pred             HHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhh----------------------------C---CCCcEEEE
Q psy7952         186 HLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFT----------------------------G---NSIPIIAL  234 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~----------------------------~---~~~~~v~l  234 (444)
                      ....+.+++++||||+|++.+..  |..++..+..+.+..                            .   .....+.+
T Consensus       289 k~f~Lk~LrfLVIDEADRll~qs--fQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~~  366 (620)
T KOG0350|consen  289 KSFDLKHLRFLVIDEADRLLDQS--FQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLVF  366 (620)
T ss_pred             CCcchhhceEEEechHHHHHHHH--HHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHhhhc
Confidence            23346789999999999997643  444333333222211                            0   11125666


Q ss_pred             eccCCcchHHHHHHHhcCCCC--eEEEecC---CCCC-CceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEec
Q psy7952         235 TATAEPSVKQDIISVLKFNKP--YKVFKTS---TFRS-NLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCR  308 (444)
Q Consensus       235 SAT~~~~~~~~~~~~l~~~~~--~~~~~~~---~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~  308 (444)
                      |||+...-.. + ..+.+..|  ..+..+.   ...| .+.......+ ...+.-.+...+..    .  ...++|+|++
T Consensus       367 satLsqdP~K-l-~~l~l~~Prl~~v~~~~~~ryslp~~l~~~~vv~~-~~~kpl~~~~lI~~----~--k~~r~lcf~~  437 (620)
T KOG0350|consen  367 SATLSQDPSK-L-KDLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVTE-PKFKPLAVYALITS----N--KLNRTLCFVN  437 (620)
T ss_pred             chhhhcChHH-H-hhhhcCCCceEEeecccceeeecChhhhhceeecc-cccchHhHHHHHHH----h--hcceEEEEec
Confidence            7776553222 1 12223333  1111100   0000 0111111100 01111122222222    2  5778999999


Q ss_pred             ccchHHHHHHHHHhh--------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHH
Q psy7952         309 TREHTTDLADALRRK--------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAY  374 (444)
Q Consensus       309 s~~~~~~l~~~L~~~--------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~  374 (444)
                      +.+.+.+++..|.-.              ++...|...+++|..|.+++|||+|++++|+|+-+++.||+||+|.+...|
T Consensus       438 S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~~v~~VINYd~P~~~kty  517 (620)
T KOG0350|consen  438 SVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVDNVINYDPPASDKTY  517 (620)
T ss_pred             chHHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEEehhhhhcCCcccccceEeecCCCchhhHH
Confidence            999999999988722              778899999999999999999999999999999999999999999999999


Q ss_pred             HHHhccCCCCCCceeEEEEecccchhhHHHHHhhc
Q psy7952         375 YQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTD  409 (444)
Q Consensus       375 ~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~  409 (444)
                      +||+||++|.|+.|+++.+....+...+.++++..
T Consensus       518 VHR~GRTARAgq~G~a~tll~~~~~r~F~klL~~~  552 (620)
T KOG0350|consen  518 VHRAGRTARAGQDGYAITLLDKHEKRLFSKLLKKT  552 (620)
T ss_pred             HHhhcccccccCCceEEEeeccccchHHHHHHHHh
Confidence            99999999999999999999999999999887643

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

Probab=100.00  E-value=3.3e-38  Score=293.95  Aligned_cols=310  Identities=17%  Similarity=0.248  Sum_probs=229.2

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-  130 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-  130 (444)
                      .||.......+.+  +.+++.|||.|||++|++.+.+++..          ... ++|+++||+.|+     .|+++.+ 
T Consensus        18 ~YQ~~i~a~al~~--NtLvvlPTGLGKT~IA~~V~~~~l~~----------~~~-kvlfLAPTKPLV-----~Qh~~~~~   79 (542)
T COG1111          18 LYQLNIAAKALFK--NTLVVLPTGLGKTFIAAMVIANRLRW----------FGG-KVLFLAPTKPLV-----LQHAEFCR   79 (542)
T ss_pred             HHHHHHHHHHhhc--CeEEEecCCccHHHHHHHHHHHHHHh----------cCC-eEEEecCCchHH-----HHHHHHHH
Confidence            7999999999986  99999999999999987765543221          112 679999999999     7888887 


Q ss_pred             -cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCC
Q psy7952         131 -TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGH  209 (444)
Q Consensus       131 -~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~  209 (444)
                       ..+.+.-.+..++|.....++...+       ...+|+|+||+.+.    ..++.+..+..++.++|+||||+-.+.  
T Consensus        80 ~v~~ip~~~i~~ltGev~p~~R~~~w-------~~~kVfvaTPQvve----NDl~~Grid~~dv~~lifDEAHRAvGn--  146 (542)
T COG1111          80 KVTGIPEDEIAALTGEVRPEEREELW-------AKKKVFVATPQVVE----NDLKAGRIDLDDVSLLIFDEAHRAVGN--  146 (542)
T ss_pred             HHhCCChhheeeecCCCChHHHHHHH-------hhCCEEEeccHHHH----hHHhcCccChHHceEEEechhhhccCc--
Confidence             5675667888999999888777666       46789999999997    567788888899999999999996432  


Q ss_pred             CcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHH--HHHHHhcCCCCeEEEecCCC---CCC---ceEEE---------
Q psy7952         210 DFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQ--DIISVLKFNKPYKVFKTSTF---RSN---LFYDV---------  272 (444)
Q Consensus       210 ~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~--~~~~~l~~~~~~~~~~~~~~---~~~---~~~~~---------  272 (444)
                       +.  |-.+.+..-...+++.+++|||||.+....  .+.+.|++.+-  .......   ++.   +...+         
T Consensus       147 -yA--Yv~Va~~y~~~~k~~~ilgLTASPGs~~ekI~eV~~nLgIe~v--evrTE~d~DV~~Yv~~~kve~ikV~lp~e~  221 (542)
T COG1111         147 -YA--YVFVAKEYLRSAKNPLILGLTASPGSDLEKIQEVVENLGIEKV--EVRTEEDPDVRPYVKKIKVEWIKVDLPEEI  221 (542)
T ss_pred             -ch--HHHHHHHHHHhccCceEEEEecCCCCCHHHHHHHHHhCCcceE--EEecCCCccHHHhhccceeEEEeccCcHHH
Confidence             22  344444444455668899999998764432  22333333211  0111000   000   00000         


Q ss_pred             --------------------------------------------------------------------------------
Q psy7952         273 --------------------------------------------------------------------------------  272 (444)
Q Consensus       273 --------------------------------------------------------------------------------  272 (444)
                                                                                                      
T Consensus       222 ~~ir~~l~~~l~~~Lk~L~~~g~~~~~~~~~~kdl~~~~~~~~~~a~~~~~~~~~~l~~~a~~~kl~~a~elletqGi~~  301 (542)
T COG1111         222 KEIRDLLRDALKPRLKPLKELGVIESSSPVSKKDLLELRQIRLIMAKNEDSDKFRLLSVLAEAIKLAHALELLETQGIRP  301 (542)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCceeccCcccHhHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHHHHHHhhChHH
Confidence                                                                                            


Q ss_pred             ---------------------------------------EEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchH
Q psy7952         273 ---------------------------------------IFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHT  313 (444)
Q Consensus       273 ---------------------------------------~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~  313 (444)
                                                             ......+.+.+.+.+++.+.+.+.  .+.++|||++.+++|
T Consensus       302 ~~~Yl~~l~e~~~~~~sk~a~~l~~d~~~~~al~~~~~~~~~~v~HPKl~~l~eilke~~~k~--~~~RvIVFT~yRdTa  379 (542)
T COG1111         302 FYQYLEKLEEEATKGGSKAAKSLLADPYFKRALRLLIRADESGVEHPKLEKLREILKEQLEKN--GDSRVIVFTEYRDTA  379 (542)
T ss_pred             HHHHHHHHHHHhcccchHHHHHHhcChhhHHHHHHHHHhccccCCCccHHHHHHHHHHHHhcC--CCceEEEEehhHhHH
Confidence                                                   000001111123334444445444  468999999999999


Q ss_pred             HHHHHHHHhh-------------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHH
Q psy7952         314 TDLADALRRK-------------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAY  374 (444)
Q Consensus       314 ~~l~~~L~~~-------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~  374 (444)
                      +.++..|.+.                   |++.++.++++.|+.|+.+|||||+++++|+|||++++||+|++..|..-+
T Consensus       380 e~i~~~L~~~~~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~  459 (542)
T COG1111         380 EEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRS  459 (542)
T ss_pred             HHHHHHHHhcCCcceeEEeeccccccccccCHHHHHHHHHHHhcCCceEEEEcccccccCCCCcccEEEEecCCcHHHHH
Confidence            9999999876                   999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccCCCCCCceeEEEEecccchh
Q psy7952         375 YQESGRAGRDGLQSYCRIYHSEHSKK  400 (444)
Q Consensus       375 ~Qr~GR~~R~g~~g~~~~~~~~~~~~  400 (444)
                      +||.||+||. ++|.+++++..+...
T Consensus       460 IQR~GRTGR~-r~Grv~vLvt~gtrd  484 (542)
T COG1111         460 IQRKGRTGRK-RKGRVVVLVTEGTRD  484 (542)
T ss_pred             HHhhCccccC-CCCeEEEEEecCchH
Confidence            9999999999 889999998877443

>KOG0327|consensus

Probab=100.00  E-value=3.6e-39  Score=290.33  Aligned_cols=332  Identities=19%  Similarity=0.287  Sum_probs=258.1

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      .+++.+.+-. +||+. |+.+|++|+..+..| .|+.+.+++|+|||.+        |.+++ ++.+-.......++++.
T Consensus        34 ~e~LLrgiy~-yGFek-PSaIQqraI~p~i~G-~dv~~qaqsgTgKt~a--------f~i~i-Lq~iD~~~ke~qalila  101 (397)
T KOG0327|consen   34 KESLLRGIYA-YGFEK-PSAIQQRAILPCIKG-HDVIAQAQSGTGKTAA--------FLISI-LQQIDMSVKETQALILA  101 (397)
T ss_pred             CHHHHhHHHh-hccCC-chHHHhccccccccC-CceeEeeeccccchhh--------hHHHH-HhhcCcchHHHHHHHhc
Confidence            4566666665 69998 999999999999999 9999999999999999        88777 44444344556789999


Q ss_pred             chhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhh
Q psy7952         113 PILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRY  190 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~  190 (444)
                      |+++|+  .|+...+..+  ..+   .++....|+.........+.     ...++|+++||+++.    +.+.......
T Consensus       102 PtreLa--~qi~~v~~~lg~~~~---~~v~~~igg~~~~~~~~~i~-----~~~~hivvGTpgrV~----dml~~~~l~~  167 (397)
T KOG0327|consen  102 PTRELA--QQIQKVVRALGDHMD---VSVHACIGGTNVRREDQALL-----KDKPHIVVGTPGRVF----DMLNRGSLST  167 (397)
T ss_pred             chHHHH--HHHHHHHHhhhcccc---eeeeeecCcccchhhhhhhh-----ccCceeecCCchhHH----Hhhccccccc
Confidence            999999  4445555555  445   77887888777654433332     356899999999985    5444554556


Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEe--cCCCCCCc
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFK--TSTFRSNL  268 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~--~~~~~~~~  268 (444)
                      ..+.++|+||++.+...|  |+   ..|..+++..+++.|++++|||.++.....-.++..  +|..+..  .......+
T Consensus       168 ~~iKmfvlDEaDEmLs~g--fk---dqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~--~pv~i~vkk~~ltl~gi  240 (397)
T KOG0327|consen  168 DGIKMFVLDEADEMLSRG--FK---DQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMR--EPVRILVKKDELTLEGI  240 (397)
T ss_pred             cceeEEeecchHhhhccc--hH---HHHHHHHHHcCcchhheeecccCcHHHHHHHHHhcc--CceEEEecchhhhhhhe
Confidence            679999999999998877  66   445556667888899999999999988876666654  4444433  33333333


Q ss_pred             eEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhc
Q psy7952         269 FYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMR  338 (444)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~  338 (444)
                      ...+....... +..-+.++..        .-.+.+||||+++.+..+...|...          +.+.+|....+.|+.
T Consensus       241 kq~~i~v~k~~-k~~~l~dl~~--------~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~  311 (397)
T KOG0327|consen  241 KQFYINVEKEE-KLDTLCDLYR--------RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRS  311 (397)
T ss_pred             eeeeeeccccc-cccHHHHHHH--------hhhcceEEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhc
Confidence            33333222212 3333334333        2566799999999999999999666          889999999999999


Q ss_pred             CCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHH
Q psy7952         339 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI  406 (444)
Q Consensus       339 g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  406 (444)
                      |..++||+|+.+++|+|+..+..||+|+.|....+|+||+||+||.|.+|.++.++...+...++++.
T Consensus       312 gssrvlIttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~d~~~lk~ie  379 (397)
T KOG0327|consen  312 GSSRVLITTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVRDLKDIE  379 (397)
T ss_pred             CCceEEeeccccccccchhhcceeeeeccccchhhhhhhcccccccCCCceeeeeehHhhHHHHHhHH
Confidence            99999999999999999999999999999999999999999999999999999999998888877775

>PRK10689 transcription-repair coupling factor; Provisional

Probab=100.00  E-value=1.2e-37  Score=331.00  Aligned_cols=351  Identities=19%  Similarity=0.182  Sum_probs=247.8

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHcc-----CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccce
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLR-----THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSR  107 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~-----~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~  107 (444)
                      +....+.+...|+|+  +|+.|.++++.++.+     .+++++++|||+|||.+|+.        ++ ...+..   ..+
T Consensus       586 ~~~~~~~~~~~~~~~--~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~--------aa-~~~~~~---g~q  651 (1147)
T PRK10689        586 DREQYQLFCDSFPFE--TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMR--------AA-FLAVEN---HKQ  651 (1147)
T ss_pred             CHHHHHHHHHhCCCC--CCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHH--------HH-HHHHHc---CCe
Confidence            455667777778996  689999999999985     26899999999999998433        22 111222   346


Q ss_pred             eEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH
Q psy7952         108 NGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ  185 (444)
Q Consensus       108 vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~  185 (444)
                      ++|++||++|+     .|+.+.+  .+....+++..+++..+..++...+..+.  .+.++|+|+||+.+         .
T Consensus       652 vlvLvPT~eLA-----~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~--~g~~dIVVgTp~lL---------~  715 (1147)
T PRK10689        652 VAVLVPTTLLA-----QQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAA--EGKIDILIGTHKLL---------Q  715 (1147)
T ss_pred             EEEEeCcHHHH-----HHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHH--hCCCCEEEECHHHH---------h
Confidence            79999999999     4555544  12222378888999888877777666554  35789999998653         2


Q ss_pred             HHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCC
Q psy7952         186 HLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFR  265 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~  265 (444)
                      ....+.+++++||||+|++   |  +..     ...++..+.+++++++||||.+........  ++.++..+......+
T Consensus       716 ~~v~~~~L~lLVIDEahrf---G--~~~-----~e~lk~l~~~~qvLl~SATpiprtl~l~~~--gl~d~~~I~~~p~~r  783 (1147)
T PRK10689        716 SDVKWKDLGLLIVDEEHRF---G--VRH-----KERIKAMRADVDILTLTATPIPRTLNMAMS--GMRDLSIIATPPARR  783 (1147)
T ss_pred             CCCCHhhCCEEEEechhhc---c--hhH-----HHHHHhcCCCCcEEEEcCCCCHHHHHHHHh--hCCCcEEEecCCCCC
Confidence            2334678999999999995   3  221     112234556799999999998876654333  345555554443333


Q ss_pred             CCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------------cCHHHHHHHH
Q psy7952         266 SNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------VNKHERSRVQ  333 (444)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------------~~~~~r~~~~  333 (444)
                      ..+...+....    ........+.++.     .+++++||||+++.++.+++.|.+.            |+..+|..++
T Consensus       784 ~~v~~~~~~~~----~~~~k~~il~el~-----r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im  854 (1147)
T PRK10689        784 LAVKTFVREYD----SLVVREAILREIL-----RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVM  854 (1147)
T ss_pred             CCceEEEEecC----cHHHHHHHHHHHh-----cCCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHH
Confidence            33332222211    1111112222222     3678999999999999999999775            8999999999


Q ss_pred             HHHhcCCccEEEEcCccccccccCCccEEEEeCCC-CCHHHHHHHhccCCCCCCceeEEEEeccc------chhhHHHHH
Q psy7952         334 ESFMRGEINVITATISFGMGIDRQNVRFVVHWGMP-SSIPAYYQESGRAGRDGLQSYCRIYHSEH------SKKSLEYVI  406 (444)
Q Consensus       334 ~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p-~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~------~~~~~~~~~  406 (444)
                      .+|++|+.+|||||+++++|+|+|++++||..+.. .+...|+||+||+||.|+.|+|++++.+.      ..+++..+.
T Consensus       855 ~~Fr~Gk~~VLVaTdIierGIDIP~v~~VIi~~ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~~~~~~~~~~~rl~~~~  934 (1147)
T PRK10689        855 NDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIA  934 (1147)
T ss_pred             HHHHhcCCCEEEECchhhcccccccCCEEEEecCCCCCHHHHHHHhhccCCCCCceEEEEEeCCCcccCHHHHHHHHHHH
Confidence            99999999999999999999999999999955442 46778999999999999999999998543      345555555


Q ss_pred             hhcc---chhHHHHHHHHhhHHHHHHHhhhc
Q psy7952         407 KTDT---STKREQLELKFKNYLSMLEYCEQG  434 (444)
Q Consensus       407 ~~~~---~~~~~~~~~~~~~~~~~~~~~~~~  434 (444)
                      +...   ..+....+.++++..++..--++|
T Consensus       935 ~~~~lg~gf~~a~~dl~~rg~g~~~g~~q~g  965 (1147)
T PRK10689        935 SLEDLGAGFALATHDLEIRGAGELLGEEQSG  965 (1147)
T ss_pred             HhcCCcchHHHHHHHHHhcCCccCCCCccCC
Confidence            5444   666777777777776665444444

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

Probab=100.00  E-value=6.5e-38  Score=315.80  Aligned_cols=323  Identities=24%  Similarity=0.339  Sum_probs=240.5

Q ss_pred             CCHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC-----cc
Q psy7952          31 VSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN-----VR  105 (444)
Q Consensus        31 ~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~-----~~  105 (444)
                      ..+..+.+.++..  |.. ||+.|.+|++.+.+| +|+++.||||+|||++|.++++.         .+...+     ..
T Consensus         7 ~l~~~v~~~~~~~--~~~-~t~~Q~~a~~~i~~G-~nvLiiAPTGsGKTeAAfLpil~---------~l~~~~~~~~~~~   73 (814)
T COG1201           7 ILDPRVREWFKRK--FTS-LTPPQRYAIPEIHSG-ENVLIIAPTGSGKTEAAFLPVIN---------ELLSLGKGKLEDG   73 (814)
T ss_pred             hcCHHHHHHHHHh--cCC-CCHHHHHHHHHHhCC-CceEEEcCCCCChHHHHHHHHHH---------HHHhccCCCCCCc
Confidence            3466778888875  666 789999999999999 99999999999999997665443         233331     12


Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESF  180 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~  180 (444)
                      -.+|+++|.++|.     .+...++     ..|   +.+...+|+++..++....      .+.+||+++|||+|.    
T Consensus        74 i~~lYIsPLkALn-----~Di~~rL~~~~~~~G---~~v~vRhGDT~~~er~r~~------~~PPdILiTTPEsL~----  135 (814)
T COG1201          74 IYALYISPLKALN-----NDIRRRLEEPLRELG---IEVAVRHGDTPQSEKQKML------KNPPHILITTPESLA----  135 (814)
T ss_pred             eEEEEeCcHHHHH-----HHHHHHHHHHHHHcC---CccceecCCCChHHhhhcc------CCCCcEEEeChhHHH----
Confidence            3689999999999     7888777     556   8889999999988776655      578999999999985    


Q ss_pred             HHHHH---HHHhhCCccEEEEeccccccc--cCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCC-
Q psy7952         181 HYLLQ---HLVRYNKLAYIVVDEAHCVSE--WGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNK-  254 (444)
Q Consensus       181 ~~~~~---~~~~~~~~~~iViDE~H~~~~--~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~-  254 (444)
                       .++.   ....+.++.+|||||+|.+.+  .|.+..-.   +.++....+ +.|.+++|||..+.  ..+.+++.-.. 
T Consensus       136 -lll~~~~~r~~l~~vr~VIVDEiHel~~sKRG~~Lsl~---LeRL~~l~~-~~qRIGLSATV~~~--~~varfL~g~~~  208 (814)
T COG1201         136 -ILLNSPKFRELLRDVRYVIVDEIHALAESKRGVQLALS---LERLRELAG-DFQRIGLSATVGPP--EEVAKFLVGFGD  208 (814)
T ss_pred             -HHhcCHHHHHHhcCCcEEEeehhhhhhccccchhhhhh---HHHHHhhCc-ccEEEeehhccCCH--HHHHHHhcCCCC
Confidence             2222   233467999999999999954  45443333   334443344 69999999999864  45677776554 


Q ss_pred             CeEEEecCCCCCCceEEEEEcccc----hhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-------
Q psy7952         255 PYKVFKTSTFRSNLFYDVIFDDLL----KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-------  323 (444)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-------  323 (444)
                      +..+...... .+..+.+......    ..........+.++...    ...++||+||+..++.++..|++.       
T Consensus       209 ~~~Iv~~~~~-k~~~i~v~~p~~~~~~~~~~~~~~~~~i~~~v~~----~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~  283 (814)
T COG1201         209 PCEIVDVSAA-KKLEIKVISPVEDLIYDEELWAALYERIAELVKK----HRTTLIFTNTRSGAERLAFRLKKLGPDIIEV  283 (814)
T ss_pred             ceEEEEcccC-CcceEEEEecCCccccccchhHHHHHHHHHHHhh----cCcEEEEEeChHHHHHHHHHHHHhcCCceee
Confidence            4444433322 2222333222221    12223333444444332    458999999999999999999887       


Q ss_pred             ----cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCC-CCceeEEEEecc
Q psy7952         324 ----VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD-GLQSYCRIYHSE  396 (444)
Q Consensus       324 ----~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~-g~~g~~~~~~~~  396 (444)
                          ++.+.|..++++|++|+.+++|||+.++-|||+.+++.||+++.|.++..++||+||+|+. |....++++...
T Consensus       284 HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDiG~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~  361 (814)
T COG1201         284 HHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAED  361 (814)
T ss_pred             ecccccHHHHHHHHHHHhcCCceEEEEccchhhccccCCceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEecC
Confidence                8899999999999999999999999999999999999999999999999999999999964 665666665554

>PRK00254 ski2-like helicase; Provisional

Probab=100.00  E-value=2.9e-38  Score=328.72  Aligned_cols=324  Identities=18%  Similarity=0.255  Sum_probs=221.8

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHH-HHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRH-ILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~-~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      ++.+.+.+++ .|++. ++++|.++++. +..| +++++++|||+|||++        +.+++ +..+...  ..++|++
T Consensus         9 ~~~~~~~l~~-~g~~~-l~~~Q~~ai~~~~~~g-~nvlv~apTGsGKT~~--------~~l~i-l~~l~~~--~~~~l~l   74 (720)
T PRK00254          9 DERIKRVLKE-RGIEE-LYPPQAEALKSGVLEG-KNLVLAIPTASGKTLV--------AEIVM-VNKLLRE--GGKAVYL   74 (720)
T ss_pred             CHHHHHHHHh-CCCCC-CCHHHHHHHHHHHhCC-CcEEEECCCCcHHHHH--------HHHHH-HHHHHhc--CCeEEEE
Confidence            5677888888 59998 56999999987 5666 9999999999999999        54554 2223222  2467999


Q ss_pred             cchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH-HHHh
Q psy7952         112 SPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ-HLVR  189 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~-~~~~  189 (444)
                      +|+++|+     .++++.+ .+...++++..++|+......  .       .+.++|+|+||+++.     .+++ ....
T Consensus        75 ~P~~aLa-----~q~~~~~~~~~~~g~~v~~~~Gd~~~~~~--~-------~~~~~IiV~Tpe~~~-----~ll~~~~~~  135 (720)
T PRK00254         75 VPLKALA-----EEKYREFKDWEKLGLRVAMTTGDYDSTDE--W-------LGKYDIIIATAEKFD-----SLLRHGSSW  135 (720)
T ss_pred             eChHHHH-----HHHHHHHHHHhhcCCEEEEEeCCCCCchh--h-------hccCCEEEEcHHHHH-----HHHhCCchh
Confidence            9999999     6666666 221123889999998764321  1       246899999999963     2332 2234


Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCC-c
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSN-L  268 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~-~  268 (444)
                      +.++++||+||+|.+.+.+  +...+..   ++.....+.|+|++|||+++  ...+.++++....     ....+|. .
T Consensus       136 l~~l~lvViDE~H~l~~~~--rg~~le~---il~~l~~~~qiI~lSATl~n--~~~la~wl~~~~~-----~~~~rpv~l  203 (720)
T PRK00254        136 IKDVKLVVADEIHLIGSYD--RGATLEM---ILTHMLGRAQILGLSATVGN--AEELAEWLNAELV-----VSDWRPVKL  203 (720)
T ss_pred             hhcCCEEEEcCcCccCCcc--chHHHHH---HHHhcCcCCcEEEEEccCCC--HHHHHHHhCCccc-----cCCCCCCcc
Confidence            5789999999999997655  3333333   34445566899999999976  3566777764321     1111221 1


Q ss_pred             eEEEE------Ecccchhh-HHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHh-------------------
Q psy7952         269 FYDVI------FDDLLKDS-YAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR-------------------  322 (444)
Q Consensus       269 ~~~~~------~~~~~~~~-~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~-------------------  322 (444)
                      ...+.      ........ .......+.+.+.    .++++||||+|++.|+.++..|.+                   
T Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~----~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~  279 (720)
T PRK00254        204 RKGVFYQGFLFWEDGKIERFPNSWESLVYDAVK----KGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELAD  279 (720)
T ss_pred             eeeEecCCeeeccCcchhcchHHHHHHHHHHHH----hCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHH
Confidence            00000      00100000 1122233333332    367899999999999887655521                   


Q ss_pred             -----------------h-------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEE-------eCCCC-C
Q psy7952         323 -----------------K-------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVH-------WGMPS-S  370 (444)
Q Consensus       323 -----------------~-------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~-------~~~p~-s  370 (444)
                                       .       +++++|..+++.|++|.++|||||+++++|+|+|..++||.       ++.|. +
T Consensus       280 ~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~  359 (720)
T PRK00254        280 SLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIP  359 (720)
T ss_pred             HHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHHHHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCC
Confidence                             0       88999999999999999999999999999999999999984       34432 5


Q ss_pred             HHHHHHHhccCCCCC--CceeEEEEecccc-hhhHHHH
Q psy7952         371 IPAYYQESGRAGRDG--LQSYCRIYHSEHS-KKSLEYV  405 (444)
Q Consensus       371 ~~~~~Qr~GR~~R~g--~~g~~~~~~~~~~-~~~~~~~  405 (444)
                      ..+|.||+|||||.|  ..|.++++....+ .+.+..+
T Consensus       360 ~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~~~~~~~~~~  397 (720)
T PRK00254        360 VLEIQQMMGRAGRPKYDEVGEAIIVATTEEPSKLMERY  397 (720)
T ss_pred             HHHHHHhhhccCCCCcCCCceEEEEecCcchHHHHHHH
Confidence            789999999999975  5688898887654 2334444

>KOG0334|consensus

Probab=100.00  E-value=1.9e-37  Score=310.95  Aligned_cols=336  Identities=21%  Similarity=0.292  Sum_probs=268.9

Q ss_pred             HHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc----CCccceeE
Q psy7952          34 QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN----GNVRSRNG  109 (444)
Q Consensus        34 ~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~----~~~~~~vl  109 (444)
                      ..+...+++ +|+.. ||++|.+||+++..| +++|.+|-||+|||++        |.+|.+.+....    .+..|-++
T Consensus       374 ~~il~tlkk-l~y~k-~~~IQ~qAiP~ImsG-rdvIgvakTgSGKT~a--------f~LPmirhi~dQr~~~~gdGPi~l  442 (997)
T KOG0334|consen  374 SKILETLKK-LGYEK-PTPIQAQAIPAIMSG-RDVIGVAKTGSGKTLA--------FLLPMIRHIKDQRPLEEGDGPIAL  442 (997)
T ss_pred             HHHHHHHHH-hcCCC-CcchhhhhcchhccC-cceEEeeccCCccchh--------hhcchhhhhhcCCChhhCCCceEE
Confidence            445555565 69998 889999999999999 9999999999999999        999994332222    23457889


Q ss_pred             EEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH
Q psy7952         110 WISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL  187 (444)
Q Consensus       110 il~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~  187 (444)
                      |++||++|+  .|+...+..|  ..+   +.++...|+.........+      ..++.|+||||+++.    +.+..+.
T Consensus       443 i~aPtrela--~QI~r~~~kf~k~l~---ir~v~vygg~~~~~qiael------kRg~eIvV~tpGRmi----D~l~~n~  507 (997)
T KOG0334|consen  443 ILAPTRELA--MQIHREVRKFLKLLG---IRVVCVYGGSGISQQIAEL------KRGAEIVVCTPGRMI----DILCANS  507 (997)
T ss_pred             EEcCCHHHH--HHHHHHHHHHHhhcC---ceEEEecCCccHHHHHHHH------hcCCceEEeccchhh----hhHhhcC
Confidence            999999999  5557777777  445   9999999998877655444      356999999999975    4444444


Q ss_pred             HhhCCc---cEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEec--C
Q psy7952         188 VRYNKL---AYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT--S  262 (444)
Q Consensus       188 ~~~~~~---~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~--~  262 (444)
                      ....++   .++|+||+|++.+.+  |.+....   +++..+...|.+++|||.+..++......+.  .|+.+...  +
T Consensus       508 grvtnlrR~t~lv~deaDrmfdmg--fePq~~~---Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~--~Pveiiv~~~s  580 (997)
T KOG0334|consen  508 GRVTNLRRVTYLVLDEADRMFDMG--FEPQITR---ILQNLRPDRQTVLFSATFPRSMEALARKVLK--KPVEIIVGGRS  580 (997)
T ss_pred             Cccccccccceeeechhhhhheec--cCcccch---HHhhcchhhhhhhhhhhhhHHHHHHHHHhhc--CCeeEEEccce
Confidence            444444   599999999999877  6665554   4455577799999999999987776666665  45444433  3


Q ss_pred             CCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHH
Q psy7952         263 TFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRV  332 (444)
Q Consensus       263 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~  332 (444)
                      .....+...+........+...+.+++.+..     ...++||||.+.+.|..+.+.|.+.          .+..+|..+
T Consensus       581 vV~k~V~q~v~V~~~e~eKf~kL~eLl~e~~-----e~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~st  655 (997)
T KOG0334|consen  581 VVCKEVTQVVRVCAIENEKFLKLLELLGERY-----EDGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSST  655 (997)
T ss_pred             eEeccceEEEEEecCchHHHHHHHHHHHHHh-----hcCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCchHHHHhH
Confidence            3445566666666666777777777777653     3789999999999999999998866          678999999


Q ss_pred             HHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         333 QESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       333 ~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      ++.|++|.+.+||+|+.+++|+|++++..||+|+.|.-.+.|+||.||+||.|..|.+++|+.+++......|.+
T Consensus       656 i~dfK~~~~~LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtFi~p~q~~~a~dl~~  730 (997)
T KOG0334|consen  656 IEDFKNGVVNLLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITPDQLKYAGDLCK  730 (997)
T ss_pred             HHHHhccCceEEEehhhhhcccccccceEEEEcccchhHHHHHHHhcccccCCccceeEEEeChHHhhhHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999977766665554

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

Probab=100.00  E-value=2.2e-36  Score=306.43  Aligned_cols=329  Identities=14%  Similarity=0.118  Sum_probs=216.1

Q ss_pred             HHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcc
Q psy7952          34 QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISP  113 (444)
Q Consensus        34 ~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P  113 (444)
                      +++.+.++...||+  ||+||.++++.++.|..++++.+|||||||.++.+     |.++.    ........++++++|
T Consensus         2 ~~f~~ff~~~~G~~--PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aa-----fll~~----~~~~~~~~rLv~~vP   70 (844)
T TIGR02621         2 LKFDEWYQGLHGYS--PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAA-----WLLAV----EIGAKVPRRLVYVVN   70 (844)
T ss_pred             chHHHHHHHHhCCC--CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHH-----hhccc----cccccccceEEEeCc
Confidence            35678888888999  68899999999999944788899999999986221     23322    222222235566789


Q ss_pred             hhhhhcccCccchHhhh--cCC--------------------CCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEEC
Q psy7952         114 ILSSFYLRFRDDKTSIV--TGR--------------------SDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVT  171 (444)
Q Consensus       114 ~~~L~~~~q~~~~~~~l--~~~--------------------~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~T  171 (444)
                      +++|+  .|+.+.++.+  ...                    ...+++..+.|+.......      ..+..+++|+|+|
T Consensus        71 tReLa--~Qi~~~~~~~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~------~~l~~~p~IIVgT  142 (844)
T TIGR02621        71 RRTVV--DQVTEEAEKIGERLPDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEW------MLDPHRPAVIVGT  142 (844)
T ss_pred             hHHHH--HHHHHHHHHHHHHhcccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHH------HhcCCCCcEEEEC
Confidence            99999  4446666666  221                    1248899999998876443      3345688999999


Q ss_pred             CCccccccHH--------HHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCC--CCcEEEEeccCCcc
Q psy7952         172 PERAVTESFH--------YLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGN--SIPIIALTATAEPS  241 (444)
Q Consensus       172 pe~l~~~~~~--------~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~--~~~~v~lSAT~~~~  241 (444)
                      ++.+.+..+.        ..--+...++++.++|+||||  ++.+  |...+..|.+.....+.  ..|+++||||++..
T Consensus       143 ~D~i~sr~L~~gYg~~~~~~pi~ag~L~~v~~LVLDEAD--Ld~g--F~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~e  218 (844)
T TIGR02621       143 VDMIGSRLLFSGYGCGFKSRPLHAGFLGQDALIVHDEAH--LEPA--FQELLKQIMNEQQRPPDFLPLRVVELTATSRTD  218 (844)
T ss_pred             HHHHcCCccccccccccccccchhhhhccceEEEEehhh--hccc--cHHHHHHHHHhcccCcccccceEEEEecCCCcc
Confidence            8877543210        000011236789999999999  3445  77666666554211111  25899999999876


Q ss_pred             hHHHHHHHhcCCCCeEEEec--CCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHH
Q psy7952         242 VKQDIISVLKFNKPYKVFKT--STFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADA  319 (444)
Q Consensus       242 ~~~~~~~~l~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~  319 (444)
                      ..+......  .++..+...  ......+.. +.... ...+...+...+...+.   ..++++||||||++.|+.+++.
T Consensus       219 i~~l~~~~~--~~p~~i~V~~~~l~a~ki~q-~v~v~-~e~Kl~~lv~~L~~ll~---e~g~~vLVF~NTv~~Aq~L~~~  291 (844)
T TIGR02621       219 GPDRTTLLS--AEDYKHPVLKKRLAAKKIVK-LVPPS-DEKFLSTMVKELNLLMK---DSGGAILVFCRTVKHVRKVFAK  291 (844)
T ss_pred             HHHHHHHHc--cCCceeecccccccccceEE-EEecC-hHHHHHHHHHHHHHHHh---hCCCcEEEEECCHHHHHHHHHH
Confidence            655433332  233222211  111112221 11111 11222222222222222   2467899999999999999999


Q ss_pred             HHhh--------cCHHHHH-----HHHHHHhc----CC-------ccEEEEcCccccccccCCccEEEEeCCCCCHHHHH
Q psy7952         320 LRRK--------VNKHERS-----RVQESFMR----GE-------INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYY  375 (444)
Q Consensus       320 L~~~--------~~~~~r~-----~~~~~f~~----g~-------~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~  375 (444)
                      |.+.        |.+.+|.     .+++.|++    |.       .+|||||+++++|+||+. ++||+...|  .+.|+
T Consensus       292 L~~~g~~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVATdVaerGLDId~-d~VI~d~aP--~esyI  368 (844)
T TIGR02621       292 LPKEKFELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCTSAGEVGVNISA-DHLVCDLAP--FESMQ  368 (844)
T ss_pred             HHhcCCeEeeCCCCHHHHhhHHHHHHHHHHhccccccccccccccceEEeccchhhhcccCCc-ceEEECCCC--HHHHH
Confidence            9876        7889999     77889987    44       689999999999999986 888887666  79999


Q ss_pred             HHhccCCCCCCc-eeEEEEec
Q psy7952         376 QESGRAGRDGLQ-SYCRIYHS  395 (444)
Q Consensus       376 Qr~GR~~R~g~~-g~~~~~~~  395 (444)
                      ||+||+||.|+. +..+.++.
T Consensus       369 QRiGRtgR~G~~~~~~i~vv~  389 (844)
T TIGR02621       369 QRFGRVNRFGELQACQIAVVH  389 (844)
T ss_pred             HHhcccCCCCCCCCceEEEEe
Confidence            999999999885 33355553

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.

>KOG0329|consensus

Probab=100.00  E-value=4.9e-38  Score=267.19  Aligned_cols=322  Identities=16%  Similarity=0.216  Sum_probs=245.7

Q ss_pred             CCCCCcCCCCCCCCCHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcc
Q psy7952          18 SLTGNQQDRKGGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGAD   97 (444)
Q Consensus        18 ~~~~~~~~~~~~~~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~   97 (444)
                      ++..-.....+..+...++.+++-+ .||+. |++.|+++++...-| .++++.|..|.|||.+        |.+.. ++
T Consensus        35 syv~ihssgfrdfllkpellraivd-cgfeh-psevqhecipqailg-mdvlcqaksgmgktav--------fvl~t-lq  102 (387)
T KOG0329|consen   35 SYVSIHSSGFRDFLLKPELLRAIVD-CGFEH-PSEVQHECIPQAILG-MDVLCQAKSGMGKTAV--------FVLAT-LQ  102 (387)
T ss_pred             cEEEEeccchhhhhcCHHHHHHHHh-ccCCC-chHhhhhhhhHHhhc-chhheecccCCCceee--------eehhh-hh
Confidence            3444444455566678888899988 69998 999999999999999 9999999999999999        88888 66


Q ss_pred             ccccCCccceeEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCcccc
Q psy7952          98 FILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVT  177 (444)
Q Consensus        98 ~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~  177 (444)
                      .+..-...-.++++|.|++|+  -|+.+...++....+.+++..+.|+.......+.+.      +.++|+|+||+++. 
T Consensus       103 qiepv~g~vsvlvmchtrela--fqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk------~~PhivVgTPGril-  173 (387)
T KOG0329|consen  103 QIEPVDGQVSVLVMCHTRELA--FQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLK------NCPHIVVGTPGRIL-  173 (387)
T ss_pred             hcCCCCCeEEEEEEeccHHHH--HHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHh------CCCeEEEcCcHHHH-
Confidence            666655555789999999999  444777778866777799999999999887777663      57899999999985 


Q ss_pred             ccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeE
Q psy7952         178 ESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYK  257 (444)
Q Consensus       178 ~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~  257 (444)
                         ........+++++..+|+|||+.++++- +++   ..+..+.+..|...|+..+|||++........++  +.+|+.
T Consensus       174 ---ALvr~k~l~lk~vkhFvlDEcdkmle~l-DMr---RDvQEifr~tp~~KQvmmfsatlskeiRpvC~kF--mQdPmE  244 (387)
T KOG0329|consen  174 ---ALVRNRSLNLKNVKHFVLDECDKMLEQL-DMR---RDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKF--MQDPME  244 (387)
T ss_pred             ---HHHHhccCchhhcceeehhhHHHHHHHH-HHH---HHHHHHhhcCcccceeeeeeeecchhhHHHHHhh--hcCchh
Confidence               4445556678899999999999987643 244   4455666678888999999999999877765555  457777


Q ss_pred             EEecCCCCCCceE--EEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhhcCHHHHHHHHHH
Q psy7952         258 VFKTSTFRSNLFY--DVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERSRVQES  335 (444)
Q Consensus       258 ~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~~~~~~r~~~~~~  335 (444)
                      ++..+.......-  +.........+...+.+++..+      ...+++||+.|+....                     
T Consensus       245 i~vDdE~KLtLHGLqQ~YvkLke~eKNrkl~dLLd~L------eFNQVvIFvKsv~Rl~---------------------  297 (387)
T KOG0329|consen  245 IFVDDEAKLTLHGLQQYYVKLKENEKNRKLNDLLDVL------EFNQVVIFVKSVQRLS---------------------  297 (387)
T ss_pred             hhccchhhhhhhhHHHHHHhhhhhhhhhhhhhhhhhh------hhcceeEeeehhhhhh---------------------
Confidence            7766543322110  0011111223333444444443      5788999999866411                     


Q ss_pred             HhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchh
Q psy7952         336 FMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK  400 (444)
Q Consensus       336 f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~  400 (444)
                      |   ..+ +|||+.+++|+|+..++.+++||+|.+.++|+||+|||||.|..|.++.+++.++..
T Consensus       298 f---~kr-~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~da  358 (387)
T KOG0329|consen  298 F---QKR-LVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDA  358 (387)
T ss_pred             h---hhh-hHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhhH
Confidence            2   233 899999999999999999999999999999999999999999999999999866543

>PRK01172 ski2-like helicase; Provisional

Probab=100.00  E-value=9e-37  Score=316.30  Aligned_cols=356  Identities=20%  Similarity=0.273  Sum_probs=234.1

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      +..+.+.++. .|++  ++++|.++++.+.++ +++++++|||+|||+++.+        ++ +..+..+   .++++++
T Consensus         9 ~~~~~~~~~~-~~~~--l~~~Q~~ai~~l~~~-~nvlv~apTGSGKTl~a~l--------ai-l~~l~~~---~k~v~i~   72 (674)
T PRK01172          9 DDEFLNLFTG-NDFE--LYDHQRMAIEQLRKG-ENVIVSVPTAAGKTLIAYS--------AI-YETFLAG---LKSIYIV   72 (674)
T ss_pred             CHHHHHHHhh-CCCC--CCHHHHHHHHHHhcC-CcEEEECCCCchHHHHHHH--------HH-HHHHHhC---CcEEEEe
Confidence            4556777776 4777  358999999999888 9999999999999999443        33 2223333   3569999


Q ss_pred             chhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH-HHhh
Q psy7952         113 PILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH-LVRY  190 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~-~~~~  190 (444)
                      |+++|+     .++.+.+ .+...++++...+|+......  .       ...++|+|+||+++.     .+... ...+
T Consensus        73 P~raLa-----~q~~~~~~~l~~~g~~v~~~~G~~~~~~~--~-------~~~~dIiv~Tpek~~-----~l~~~~~~~l  133 (674)
T PRK01172         73 PLRSLA-----MEKYEELSRLRSLGMRVKISIGDYDDPPD--F-------IKRYDVVILTSEKAD-----SLIHHDPYII  133 (674)
T ss_pred             chHHHH-----HHHHHHHHHHhhcCCeEEEEeCCCCCChh--h-------hccCCEEEECHHHHH-----HHHhCChhHH
Confidence            999999     5666655 221122788888887654321  1       136799999999863     33332 2346


Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCC-ce
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSN-LF  269 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~-~~  269 (444)
                      .++++||+||+|.+.+.+  +...+..+.......+.+.|+|++|||+++.  ..+.++++...    +. ...++. +.
T Consensus       134 ~~v~lvViDEaH~l~d~~--rg~~le~ll~~~~~~~~~~riI~lSATl~n~--~~la~wl~~~~----~~-~~~r~vpl~  204 (674)
T PRK01172        134 NDVGLIVADEIHIIGDED--RGPTLETVLSSARYVNPDARILALSATVSNA--NELAQWLNASL----IK-SNFRPVPLK  204 (674)
T ss_pred             hhcCEEEEecchhccCCC--ccHHHHHHHHHHHhcCcCCcEEEEeCccCCH--HHHHHHhCCCc----cC-CCCCCCCeE
Confidence            789999999999987654  3444555554444555668999999999753  45677765321    11 111211 11


Q ss_pred             EEEEE-----cccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh---------------------
Q psy7952         270 YDVIF-----DDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK---------------------  323 (444)
Q Consensus       270 ~~~~~-----~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~---------------------  323 (444)
                      ..+..     ..........+...+.+..    ..++++||||++++.++.++..|...                     
T Consensus       205 ~~i~~~~~~~~~~~~~~~~~~~~~i~~~~----~~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L  280 (674)
T PRK01172        205 LGILYRKRLILDGYERSQVDINSLIKETV----NDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSL  280 (674)
T ss_pred             EEEEecCeeeecccccccccHHHHHHHHH----hCCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHH
Confidence            11111     0000001111223333322    24789999999999999998877531                     


Q ss_pred             --------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCC---------CCCHHHHHHHhcc
Q psy7952         324 --------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGM---------PSSIPAYYQESGR  380 (444)
Q Consensus       324 --------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~---------p~s~~~~~Qr~GR  380 (444)
                                    ++.++|..+++.|++|.++|||||+++++|+|+|+..+|| .+.         |.|..+|.||+||
T Consensus       281 ~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~i~VLvaT~~la~Gvnipa~~VII-~~~~~~~~~~~~~~s~~~~~Qm~GR  359 (674)
T PRK01172        281 NEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIV-RDITRYGNGGIRYLSNMEIKQMIGR  359 (674)
T ss_pred             HHHHhcCEEEecCCCCHHHHHHHHHHHHcCCCeEEEecchhhccCCCcceEEEE-cCceEeCCCCceeCCHHHHHHHhhc
Confidence                          7789999999999999999999999999999999865554 332         5688999999999


Q ss_pred             CCCCCC--ceeEEEEeccc-chhhHHHHHh-hccchhH-------------HHHHH-HHhhHHHHHHHhhhceee
Q psy7952         381 AGRDGL--QSYCRIYHSEH-SKKSLEYVIK-TDTSTKR-------------EQLEL-KFKNYLSMLEYCEQGYFL  437 (444)
Q Consensus       381 ~~R~g~--~g~~~~~~~~~-~~~~~~~~~~-~~~~~~~-------------~~~~~-~~~~~~~~~~~~~~~~~~  437 (444)
                      |||.|.  .|.++++.... +...+++++. .+.+.+.             ..+-. ...+..+.++|....|+.
T Consensus       360 AGR~g~d~~g~~~i~~~~~~~~~~~~~~l~~~~~pi~S~l~~~~~~~~~~l~~i~~g~~~~~~d~~~~l~~tf~~  434 (674)
T PRK01172        360 AGRPGYDQYGIGYIYAASPASYDAAKKYLSGEPEPVISYMGSQRKVRFNTLAAISMGLASSMEDLILFYNETLMA  434 (674)
T ss_pred             CCCCCCCCcceEEEEecCcccHHHHHHHHcCCCCceeecCCCcccHHHHHHHHHHhcccCCHHHHHHHHHhhhhH
Confidence            999985  56677776544 3555666653 3222110             11111 234567788887776664

>KOG0952|consensus

Probab=100.00  E-value=5e-36  Score=298.52  Aligned_cols=374  Identities=18%  Similarity=0.241  Sum_probs=268.0

Q ss_pred             HHHHHHHHH-HHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          33 EQELTAKLK-ALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        33 ~~~~~~~l~-~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      -.++....+ ..|+|..|. .+|.++++.++..+.|++|+||||+|||.+|++.|+..+-- . ..........-|++++
T Consensus        94 isdld~~~rk~~f~f~~fN-~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~-~-~~~~~i~k~~fKiVYI  170 (1230)
T KOG0952|consen   94 ISDLDDVGRKGFFSFEEFN-RIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKE-H-EEQGDIAKDDFKIVYI  170 (1230)
T ss_pred             EEecchhhhhhcccHHHHH-HHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHh-h-ccccccccCCceEEEE
Confidence            445555554 667889866 79999999999988999999999999999977665431100 0 0000001122478999


Q ss_pred             cchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH---
Q psy7952         112 SPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH---  186 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~---  186 (444)
                      +|+++|+     .+.++.+  ++..-++.|..++|++.....+ +        .+++|+|+|||+.-     -..+.   
T Consensus       171 aPmKALa-----~Em~~~~~kkl~~~gi~v~ELTGD~ql~~te-i--------~~tqiiVTTPEKwD-----vvTRk~~~  231 (1230)
T KOG0952|consen  171 APMKALA-----AEMVDKFSKKLAPLGISVRELTGDTQLTKTE-I--------ADTQIIVTTPEKWD-----VVTRKSVG  231 (1230)
T ss_pred             echHHHH-----HHHHHHHhhhcccccceEEEecCcchhhHHH-H--------HhcCEEEeccccee-----eeeeeecc
Confidence            9999999     8999988  4444459999999999876554 2        26899999999952     22222   


Q ss_pred             -HHhhCCccEEEEeccccccc-cCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEE-ecCC
Q psy7952         187 -LVRYNKLAYIVVDEAHCVSE-WGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVF-KTST  263 (444)
Q Consensus       187 -~~~~~~~~~iViDE~H~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~-~~~~  263 (444)
                       ...+..+++|||||+|.+.+ .|......+.+..++........++|++|||+|+  ..++..+++.+....++ ....
T Consensus       232 d~~l~~~V~LviIDEVHlLhd~RGpvlEtiVaRtlr~vessqs~IRivgLSATlPN--~eDvA~fL~vn~~~glfsFd~~  309 (1230)
T KOG0952|consen  232 DSALFSLVRLVIIDEVHLLHDDRGPVLETIVARTLRLVESSQSMIRIVGLSATLPN--YEDVARFLRVNPYAGLFSFDQR  309 (1230)
T ss_pred             chhhhhheeeEEeeeehhhcCcccchHHHHHHHHHHHHHhhhhheEEEEeeccCCC--HHHHHHHhcCCCccceeeeccc
Confidence             23456789999999999966 4655666666666665556667899999999987  45789999876333222 2223


Q ss_pred             CCCC-ceEEEEEccc----------chhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh---------
Q psy7952         264 FRSN-LFYDVIFDDL----------LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK---------  323 (444)
Q Consensus       264 ~~~~-~~~~~~~~~~----------~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~---------  323 (444)
                      .||- +...+.-...          ....++.+.+++.        .+++++|||++++.+.+.|+.|.+.         
T Consensus       310 yRPvpL~~~~iG~k~~~~~~~~~~~d~~~~~kv~e~~~--------~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~  381 (1230)
T KOG0952|consen  310 YRPVPLTQGFIGIKGKKNRQQKKNIDEVCYDKVVEFLQ--------EGHQVLVFVHSRNETIRTAKKLRERAETNGEKDL  381 (1230)
T ss_pred             ccccceeeeEEeeecccchhhhhhHHHHHHHHHHHHHH--------cCCeEEEEEecChHHHHHHHHHHHHHHhcCcccc
Confidence            3332 2222221111          1122233333333        4999999999999999999988776         


Q ss_pred             ------------------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCC-----------
Q psy7952         324 ------------------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMP-----------  368 (444)
Q Consensus       324 ------------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p-----------  368 (444)
                                              +..++|..+++.|..|.++||+||..+..|+|+|+-.++| -|.+           
T Consensus       382 f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~F~~G~i~vL~cTaTLAwGVNLPA~aViI-KGT~~ydsskg~f~d  460 (1230)
T KOG0952|consen  382 FLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFKEGHIKVLCCTATLAWGVNLPAYAVII-KGTQVYDSSKGSFVD  460 (1230)
T ss_pred             cCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHHHhcCCceEEEecceeeeccCCcceEEEe-cCCcccccccCceee
Confidence                                    7788999999999999999999999999999999544444 3332           


Q ss_pred             CCHHHHHHHhccCCCC--CCceeEEEEecccchhhHHHHHhhccchhHHHHHHHH------------hhHHHHHHHhhhc
Q psy7952         369 SSIPAYYQESGRAGRD--GLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKF------------KNYLSMLEYCEQG  434 (444)
Q Consensus       369 ~s~~~~~Qr~GR~~R~--g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~  434 (444)
                      .++.+.+|..|||||.  +..|.++++.+.+...++..++...-+.+..-...-+            .+.++-++|....
T Consensus       461 lgilDVlQifGRAGRPqFd~~G~giIiTt~dkl~~Y~sLl~~~~piES~~~~~L~dnLnAEi~LgTVt~VdeAVeWL~yT  540 (1230)
T KOG0952|consen  461 LGILDVLQIFGRAGRPQFDSSGEGIIITTRDKLDHYESLLTGQNPIESQLLPCLIDNLNAEISLGTVTNVDEAVEWLKYT  540 (1230)
T ss_pred             ehHHHHHHHHhccCCCCCCCCceEEEEecccHHHHHHHHHcCCChhHHHHHHHHHHhhhhheeeceeecHHHHHHHhhce
Confidence            1577889999999996  5679999999999999999998877766655444333            4556778888888


Q ss_pred             eeeee
Q psy7952         435 YFLVI  439 (444)
Q Consensus       435 ~~~~~  439 (444)
                      |++.-
T Consensus       541 ylYVR  545 (1230)
T KOG0952|consen  541 YLYVR  545 (1230)
T ss_pred             eEEEE
Confidence            87653

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=100.00  E-value=1.7e-36  Score=323.81  Aligned_cols=291  Identities=22%  Similarity=0.295  Sum_probs=202.2

Q ss_pred             EEccCCCcccccccccccceEEeCCCccccccC----------CccceeEEEcchhhhhcccCccchHhhhc--------
Q psy7952          70 VSMPTGAVSLVGSVVSARSRVRIPPGADFILNG----------NVRSRNGWISPILSSFYLRFRDDKTSIVT--------  131 (444)
Q Consensus        70 i~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~----------~~~~~vlil~P~~~L~~~~q~~~~~~~l~--------  131 (444)
                      |++|||||||++        +.+|+ ++.+...          ....++|||+|+++|+     .++.+.+.        
T Consensus         1 V~APTGSGKTLA--------A~Lpa-L~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa-----~Dv~~~L~~pl~~i~~   66 (1490)
T PRK09751          1 VIAPTGSGKTLA--------AFLYA-LDRLFREGGEDTREAHKRKTSRILYISPIKALG-----TDVQRNLQIPLKGIAD   66 (1490)
T ss_pred             CcCCCCcHHHHH--------HHHHH-HHHHHhcccccccccccCCCCEEEEEeChHHHH-----HHHHHHHHHHHHhhhh
Confidence            579999999999        55555 3333321          1235789999999999     45444431        


Q ss_pred             ----CC--CCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH-HHhhCCccEEEEeccccc
Q psy7952         132 ----GR--SDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH-LVRYNKLAYIVVDEAHCV  204 (444)
Q Consensus       132 ----~~--~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~-~~~~~~~~~iViDE~H~~  204 (444)
                          ++  ...+++...+|+.+..++....      .+.++|+|+|||++.    ..+.+. ...+.++++|||||+|.+
T Consensus        67 ~~~~~g~~~~~i~V~vrtGDt~~~eR~rll------~~ppdILVTTPEsL~----~LLtsk~r~~L~~Vr~VIVDE~H~L  136 (1490)
T PRK09751         67 ERRRRGETEVNLRVGIRTGDTPAQERSKLT------RNPPDILITTPESLY----LMLTSRARETLRGVETVIIDEVHAV  136 (1490)
T ss_pred             hhhhcccccCceEEEEEECCCCHHHHHHHh------cCCCCEEEecHHHHH----HHHhhhhhhhhccCCEEEEecHHHh
Confidence                11  1248999999999888765554      357899999999984    222222 235789999999999999


Q ss_pred             cc--cCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCC-CceEEEEEcccch--
Q psy7952         205 SE--WGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRS-NLFYDVIFDDLLK--  279 (444)
Q Consensus       205 ~~--~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~--  279 (444)
                      .+  .|.++...+..|..   ..+.+.|+|++|||+.+.  +.+.++++...+..++.....++ .+.+.+.......  
T Consensus       137 ~g~kRG~~Lel~LeRL~~---l~~~~~QrIgLSATI~n~--eevA~~L~g~~pv~Iv~~~~~r~~~l~v~vp~~d~~~~~  211 (1490)
T PRK09751        137 AGSKRGAHLALSLERLDA---LLHTSAQRIGLSATVRSA--SDVAAFLGGDRPVTVVNPPAMRHPQIRIVVPVANMDDVS  211 (1490)
T ss_pred             cccccccHHHHHHHHHHH---hCCCCCeEEEEEeeCCCH--HHHHHHhcCCCCEEEECCCCCcccceEEEEecCchhhcc
Confidence            75  35555555555544   345568999999999873  46778886555555544333222 2222111111000  


Q ss_pred             ----------------hhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHh---------------------
Q psy7952         280 ----------------DSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR---------------------  322 (444)
Q Consensus       280 ----------------~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~---------------------  322 (444)
                                      .....+...+...+    ..+.++||||||+..|+.++..|++                     
T Consensus       212 ~~~~~~~~~~~~~r~~~i~~~v~~~il~~i----~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~  287 (1490)
T PRK09751        212 SVASGTGEDSHAGREGSIWPYIETGILDEV----LRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFES  287 (1490)
T ss_pred             ccccccccccchhhhhhhhHHHHHHHHHHH----hcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhh
Confidence                            00001111111111    1367899999999999999887753                     


Q ss_pred             -----------------h-----cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhcc
Q psy7952         323 -----------------K-----VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGR  380 (444)
Q Consensus       323 -----------------~-----~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR  380 (444)
                                       .     +++++|..+++.|++|++++||||++++.|||++++++||+++.|.|+.+|+||+||
T Consensus       288 ~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~~IE~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGR  367 (1490)
T PRK09751        288 TSGATSNRVQSSDVFIARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR  367 (1490)
T ss_pred             ccccchhccccccceeeeeccccCCHHHHHHHHHHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCC
Confidence                             0     789999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC-CCceeEEEE
Q psy7952         381 AGRD-GLQSYCRIY  393 (444)
Q Consensus       381 ~~R~-g~~g~~~~~  393 (444)
                      +||. |..+.++++
T Consensus       368 AGR~~gg~s~gli~  381 (1490)
T PRK09751        368 AGHQVGGVSKGLFF  381 (1490)
T ss_pred             CCCCCCCccEEEEE
Confidence            9997 334455533

>KOG0344|consensus

Probab=100.00  E-value=5.7e-37  Score=289.95  Aligned_cols=343  Identities=20%  Similarity=0.244  Sum_probs=245.6

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC-----Cccce
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG-----NVRSR  107 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~-----~~~~~  107 (444)
                      +..+.+.+... ||.. ||+.|.++++.++.+ ++++.++|||+|||++        |.+|+ +..+...     ...-+
T Consensus       144 ~~~ll~nl~~~-~F~~-Pt~iq~~aipvfl~~-r~~lAcapTGsgKtla--------f~~Pi-l~~L~~~~~~~~~~gl~  211 (593)
T KOG0344|consen  144 NKRLLENLQEL-GFDE-PTPIQKQAIPVFLEK-RDVLACAPTGSGKTLA--------FNLPI-LQHLKDLSQEKHKVGLR  211 (593)
T ss_pred             cHHHHHhHhhC-CCCC-CCcccchhhhhhhcc-cceEEeccCCCcchhh--------hhhHH-HHHHHHhhcccCccceE
Confidence            44455555553 8998 899999999999999 9999999999999999        99998 4444332     23358


Q ss_pred             eEEEcchhhhhcccCccchHhhhc-CCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         108 NGWISPILSSFYLRFRDDKTSIVT-GRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       108 vlil~P~~~L~~~~q~~~~~~~l~-~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      ++|+.|+++|+  .|+...+..+. ..+..+.+..+..............     ...++|+++||-++.    ..+-..
T Consensus       212 a~Il~ptreLa--~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~-----~~k~dili~TP~ri~----~~~~~~  280 (593)
T KOG0344|consen  212 ALILSPTRELA--AQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLS-----DEKYDILISTPMRIV----GLLGLG  280 (593)
T ss_pred             EEEecchHHHH--HHHHHHHHhcCCCCCCchhhhhcccccchhhccchhH-----HHHHHHHhcCHHHHH----HHhcCC
Confidence            89999999999  33344444442 1222244444443322222211111     236799999999964    111111


Q ss_pred             H--HhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCC
Q psy7952         187 L--VRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTF  264 (444)
Q Consensus       187 ~--~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~  264 (444)
                      .  ..+..+..+|+||++.+.+. ..|..++..|...++.  ++..+=++|||.+..+.+...........+.+...+..
T Consensus       281 ~~~idl~~V~~lV~dEaD~lfe~-~~f~~Qla~I~sac~s--~~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~~sa  357 (593)
T KOG0344|consen  281 KLNIDLSKVEWLVVDEADLLFEP-EFFVEQLADIYSACQS--PDIRVALFSATISVYVEEWAELIKSDLKRVIVGLRNSA  357 (593)
T ss_pred             CccchhheeeeEeechHHhhhCh-hhHHHHHHHHHHHhcC--cchhhhhhhccccHHHHHHHHHhhccceeEEEecchhH
Confidence            1  35678899999999999876 2277666666554443  44777799999998887765554433333333333222


Q ss_pred             CCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----------cCHHHHHHHH
Q psy7952         265 RSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----------VNKHERSRVQ  333 (444)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----------~~~~~r~~~~  333 (444)
                      ...+.....+.-....+.-.    +.+++...  -..+++||+.+.+.|.+|+..|...           .++.+|..++
T Consensus       358 ~~~V~QelvF~gse~~K~lA----~rq~v~~g--~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~  431 (593)
T KOG0344|consen  358 NETVDQELVFCGSEKGKLLA----LRQLVASG--FKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETM  431 (593)
T ss_pred             hhhhhhhheeeecchhHHHH----HHHHHhcc--CCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHH
Confidence            22333333343333333333    34444333  4789999999999999999999411           6889999999


Q ss_pred             HHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         334 ESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       334 ~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      ++|+.|++.+|+||+++++|+|+.++++||+||+|.+...|+||+||+||.|+.|.+++||...+...++.+..
T Consensus       432 ~~FR~g~IwvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~ir~iae  505 (593)
T KOG0344|consen  432 ERFRIGKIWVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPRIRSIAE  505 (593)
T ss_pred             HHHhccCeeEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEEeccccchhhhhHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999988777753

>COG1204 Superfamily II helicase [General function prediction only]

Probab=100.00  E-value=8.9e-36  Score=304.38  Aligned_cols=319  Identities=19%  Similarity=0.275  Sum_probs=219.0

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      .+.+.+.++. .|+..+. +.|++++.+.+-+++|+++++|||+|||++|+++|++         .+.++  ..+++++|
T Consensus        17 ~~~v~~i~~~-~~~~el~-~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~---------~l~~~--~~k~vYiv   83 (766)
T COG1204          17 DDRVLEILKG-DGIDELF-NPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILS---------TLLEG--GGKVVYIV   83 (766)
T ss_pred             cHHHHHHhcc-CChHHhh-HHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHH---------HHHhc--CCcEEEEe
Confidence            4445555554 5776544 4577776666655599999999999999997765443         13322  23459999


Q ss_pred             chhhhhcccCccchHhhh----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH
Q psy7952         113 PILSSFYLRFRDDKTSIV----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV  188 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~  188 (444)
                      |+++|+     .+.++.+    .+|   +++...+|+......  .       ..+++|+|+|||++-     ...++..
T Consensus        84 PlkALa-----~Ek~~~~~~~~~~G---irV~~~TgD~~~~~~--~-------l~~~~ViVtT~EK~D-----sl~R~~~  141 (766)
T COG1204          84 PLKALA-----EEKYEEFSRLEELG---IRVGISTGDYDLDDE--R-------LARYDVIVTTPEKLD-----SLTRKRP  141 (766)
T ss_pred             ChHHHH-----HHHHHHhhhHHhcC---CEEEEecCCcccchh--h-------hccCCEEEEchHHhh-----HhhhcCc
Confidence            999999     7777777    456   999999999875431  1       258899999999973     3343332


Q ss_pred             -hhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCC
Q psy7952         189 -RYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSN  267 (444)
Q Consensus       189 -~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  267 (444)
                       -...+++||+||+|.+.+...  .+.+..+...........+++++|||+++.  ..+..+++-.......+.......
T Consensus       142 ~~~~~V~lvViDEiH~l~d~~R--G~~lE~iv~r~~~~~~~~rivgLSATlpN~--~evA~wL~a~~~~~~~rp~~l~~~  217 (766)
T COG1204         142 SWIEEVDLVVIDEIHLLGDRTR--GPVLESIVARMRRLNELIRIVGLSATLPNA--EEVADWLNAKLVESDWRPVPLRRG  217 (766)
T ss_pred             chhhcccEEEEeeeeecCCccc--CceehhHHHHHHhhCcceEEEEEeeecCCH--HHHHHHhCCcccccCCCCcccccC
Confidence             345799999999999976421  122333332222333338999999999874  577888876543223333222222


Q ss_pred             ceEEEE--Ecccch-----hhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----------------
Q psy7952         268 LFYDVI--FDDLLK-----DSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----------------  323 (444)
Q Consensus       268 ~~~~~~--~~~~~~-----~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----------------  323 (444)
                      +.+...  ......     .........+...    ...+++++|||+|+..+...+..+...                 
T Consensus       218 v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~~----~~~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a  293 (766)
T COG1204         218 VPYVGAFLGADGKKKTWPLLIDNLALELVLES----LAEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGA  293 (766)
T ss_pred             CccceEEEEecCccccccccchHHHHHHHHHH----HhcCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccc
Confidence            222211  111111     1122223333333    236899999999999999999999842                 


Q ss_pred             ------------------------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEE----EeC---
Q psy7952         324 ------------------------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVV----HWG---  366 (444)
Q Consensus       324 ------------------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi----~~~---  366 (444)
                                                    ++.++|..+++.|+.|.++||+||++++.|+|+|.-.+||    .++   
T Consensus       294 ~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~~R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~  373 (766)
T COG1204         294 SPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKG  373 (766)
T ss_pred             cccccccccccchHHHHHHHHhCccccccCCCHHHHHHHHHHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCC
Confidence                                          8899999999999999999999999999999999766666    455   


Q ss_pred             --CCCCHHHHHHHhccCCCCCCc--eeEEEEe
Q psy7952         367 --MPSSIPAYYQESGRAGRDGLQ--SYCRIYH  394 (444)
Q Consensus       367 --~p~s~~~~~Qr~GR~~R~g~~--g~~~~~~  394 (444)
                        .+.+.-+++||.|||||.|-.  |.++++.
T Consensus       374 g~~~i~~~dv~QM~GRAGRPg~d~~G~~~i~~  405 (766)
T COG1204         374 GIVDIPVLDVLQMAGRAGRPGYDDYGEAIILA  405 (766)
T ss_pred             CeEECchhhHhhccCcCCCCCcCCCCcEEEEe
Confidence              455789999999999998754  5666666

>PRK14701 reverse gyrase; Provisional

Probab=100.00  E-value=1.5e-34  Score=314.36  Aligned_cols=337  Identities=17%  Similarity=0.196  Sum_probs=230.5

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ..++.+.+++.+|++  |+++|.++++.+++| +++++.||||+|||+.        +++++    +.......+++|++
T Consensus        65 ~~~~~~~f~~~~G~~--pt~iQ~~~i~~il~G-~d~li~APTGsGKTl~--------~~~~a----l~~~~~g~~aLVl~  129 (1638)
T PRK14701         65 VEEFEEFFEKITGFE--FWSIQKTWAKRILRG-KSFSIVAPTGMGKSTF--------GAFIA----LFLALKGKKCYIIL  129 (1638)
T ss_pred             HHHHHHHHHHhhCCC--CCHHHHHHHHHHHcC-CCEEEEEcCCCCHHHH--------HHHHH----HHHHhcCCeEEEEE
Confidence            566778888888995  678999999999999 9999999999999986        34433    21111224679999


Q ss_pred             chhhhhcccCccchHhhhcCC-CCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         113 PILSSFYLRFRDDKTSIVTGR-SDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l~~~-~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      ||++|+  .|+.+++..+... ...+.+..++|+.+..++......+.  .+.++|+|+||+.+..    .+ .... ..
T Consensus       130 PTreLa--~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~--~g~~dILV~TPgrL~~----~~-~~l~-~~  199 (1638)
T PRK14701        130 PTTLLV--KQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIE--NGDFDILVTTAQFLAR----NF-PEMK-HL  199 (1638)
T ss_pred             CHHHHH--HHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHh--cCCCCEEEECCchhHH----hH-HHHh-hC
Confidence            999999  3334444444111 12378888999998877666555543  3568999999998742    11 1222 26


Q ss_pred             CccEEEEeccccccccCC---------CcHHHHHH----H-------------------HHHHHhhCCCCc-EEEEeccC
Q psy7952         192 KLAYIVVDEAHCVSEWGH---------DFRPTYRR----L-------------------GELRQFTGNSIP-IIALTATA  238 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~---------~~~~~~~~----l-------------------~~~~~~~~~~~~-~v~lSAT~  238 (444)
                      +++++|+||||++++|++         +|++.+..    +                   ......+++..+ ++.+|||+
T Consensus       200 ~i~~iVVDEAD~ml~~~knid~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~  279 (1638)
T PRK14701        200 KFDFIFVDDVDAFLKASKNIDRSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATG  279 (1638)
T ss_pred             CCCEEEEECceeccccccccchhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCC
Confidence            799999999999988654         46666543    1                   111112344455 57799999


Q ss_pred             CcchHHHHHHHhcCCCCeEEEecCCCCC---CceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccch---
Q psy7952         239 EPSVKQDIISVLKFNKPYKVFKTSTFRS---NLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREH---  312 (444)
Q Consensus       239 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~---  312 (444)
                      ++..  .....+  ..+..+... ..++   ++...+.....  .....+.+++..    .   +.++||||++++.   
T Consensus       280 ~~r~--~~~~l~--~~~l~f~v~-~~~~~lr~i~~~yi~~~~--~~k~~L~~ll~~----~---g~~gIVF~~t~~~~e~  345 (1638)
T PRK14701        280 KAKG--DRVKLY--RELLGFEVG-SGRSALRNIVDVYLNPEK--IIKEHVRELLKK----L---GKGGLIFVPIDEGAEK  345 (1638)
T ss_pred             Cchh--HHHHHh--hcCeEEEec-CCCCCCCCcEEEEEECCH--HHHHHHHHHHHh----C---CCCeEEEEeccccchH
Confidence            8632  222333  233333222 2232   33333222221  111233333332    2   4678999999875   


Q ss_pred             HHHHHHHHHhh-----cCHHHHHHHHHHHhcCCccEEEEc----CccccccccCC-ccEEEEeCCCC---CHHHHHHHh-
Q psy7952         313 TTDLADALRRK-----VNKHERSRVQESFMRGEINVITAT----ISFGMGIDRQN-VRFVVHWGMPS---SIPAYYQES-  378 (444)
Q Consensus       313 ~~~l~~~L~~~-----~~~~~r~~~~~~f~~g~~~vLvaT----~~~~~Gidi~~-~~~Vi~~~~p~---s~~~~~Qr~-  378 (444)
                      |++++..|...     .--..|...+++|++|+.+|||||    +++++|||+|+ +++|||+|+|+   |++.|.|-. 
T Consensus       346 ae~la~~L~~~Gi~a~~~h~~R~~~l~~F~~G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~  425 (1638)
T PRK14701        346 AEEIEKYLLEDGFKIELVSAKNKKGFDLFEEGEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIY  425 (1638)
T ss_pred             HHHHHHHHHHCCCeEEEecchHHHHHHHHHcCCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchh
Confidence            58999999886     222359999999999999999999    58999999998 99999999999   888776655 


Q ss_pred             ------------ccCCCCCCceeEEEEecccchhhHHHHHhh
Q psy7952         379 ------------GRAGRDGLQSYCRIYHSEHSKKSLEYVIKT  408 (444)
Q Consensus       379 ------------GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~  408 (444)
                                  ||+||.|..+.++..+...+...++.++..
T Consensus       426 ~~~~~~~~~~~~~~a~~~g~~~~~~~~~~~~~~~~~~~~l~~  467 (1638)
T PRK14701        426 RILGLLSEILKIEEELKEGIPIEGVLDVFPEDVEFLRSILKD  467 (1638)
T ss_pred             hhhcchHHHHHhhhhcccCCcchhHHHhHHHHHHHHHHHhcc
Confidence                        999999998888766667777777777654

>KOG0337|consensus

Probab=100.00  E-value=6e-36  Score=271.32  Aligned_cols=336  Identities=18%  Similarity=0.194  Sum_probs=250.1

Q ss_pred             CCHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC-ccceeE
Q psy7952          31 VSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN-VRSRNG  109 (444)
Q Consensus        31 ~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~-~~~~vl  109 (444)
                      ++..- .+++.+- ||.. |||+|++.++-++++ +++.-.+-||+|||.+        |.+|+ +..+.... ..-|.+
T Consensus        28 L~~~v-~raI~kk-g~~~-ptpiqRKTipliLe~-~dvv~martgsgktaa--------f~ipm-~e~Lk~~s~~g~Ral   94 (529)
T KOG0337|consen   28 LDYKV-LRAIHKK-GFNT-PTPIQRKTIPLILEG-RDVVGMARTGSGKTAA--------FLIPM-IEKLKSHSQTGLRAL   94 (529)
T ss_pred             CCHHH-HHHHHHh-hcCC-CCchhcccccceeec-cccceeeecCCcchhh--------HHHHH-HHHHhhcccccccee
Confidence            44443 4444442 8887 999999999999999 9999999999999999        99999 55555444 334779


Q ss_pred             EEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh
Q psy7952         110 WISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR  189 (444)
Q Consensus       110 il~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~  189 (444)
                      +++||++|++  |..+.++.+..+ ..+.+..+.|+....++-..+      ..++||+++||+++.    +....-...
T Consensus        95 ilsptreLa~--qtlkvvkdlgrg-t~lr~s~~~ggD~~eeqf~~l------~~npDii~ATpgr~~----h~~vem~l~  161 (529)
T KOG0337|consen   95 ILSPTRELAL--QTLKVVKDLGRG-TKLRQSLLVGGDSIEEQFILL------NENPDIIIATPGRLL----HLGVEMTLT  161 (529)
T ss_pred             eccCcHHHHH--HHHHHHHHhccc-cchhhhhhcccchHHHHHHHh------ccCCCEEEecCceee----eeehheecc
Confidence            9999999992  224444555222 226777777776665443333      468999999999986    333333456


Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecC--CCCCC
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTS--TFRSN  267 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~--~~~~~  267 (444)
                      +..+.|||+||++.+.+.|  |.+.+   .+++...+.+.|.++||||++....+....  |+.+|+.+....  ...+.
T Consensus       162 l~sveyVVfdEadrlfemg--fqeql---~e~l~rl~~~~QTllfSatlp~~lv~faka--Gl~~p~lVRldvetkise~  234 (529)
T KOG0337|consen  162 LSSVEYVVFDEADRLFEMG--FQEQL---HEILSRLPESRQTLLFSATLPRDLVDFAKA--GLVPPVLVRLDVETKISEL  234 (529)
T ss_pred             ccceeeeeehhhhHHHhhh--hHHHH---HHHHHhCCCcceEEEEeccCchhhHHHHHc--cCCCCceEEeehhhhcchh
Confidence            7789999999999999887  66444   455567777889999999999988775554  455665555332  22222


Q ss_pred             ceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHh
Q psy7952         268 LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFM  337 (444)
Q Consensus       268 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~  337 (444)
                      ......... ...+...+..    ++.... ...+++|||.+..+++.+...|+..          +++..|...+.+|+
T Consensus       235 lk~~f~~~~-~a~K~aaLl~----il~~~~-~~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~  308 (529)
T KOG0337|consen  235 LKVRFFRVR-KAEKEAALLS----ILGGRI-KDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFR  308 (529)
T ss_pred             hhhheeeec-cHHHHHHHHH----HHhccc-cccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhcccccc
Confidence            222222111 1222222222    222221 3568999999999999999999877          88999999999999


Q ss_pred             cCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHH
Q psy7952         338 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV  405 (444)
Q Consensus       338 ~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~  405 (444)
                      .++..+||.|+.+.+|+|+|-.+.||+||+|.+...|+||+||+.|.|..|+++.++.+.+...+..+
T Consensus       309 ~~k~~~lvvTdvaaRG~diplldnvinyd~p~~~klFvhRVgr~aragrtg~aYs~V~~~~~~yl~DL  376 (529)
T KOG0337|consen  309 GRKTSILVVTDVAARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRTGRAYSLVASTDDPYLLDL  376 (529)
T ss_pred             CCccceEEEehhhhccCCCccccccccccCCCCCceEEEEecchhhccccceEEEEEecccchhhhhh
Confidence            99999999999999999999999999999999999999999999999999999999988777665554

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

Probab=100.00  E-value=2e-34  Score=298.52  Aligned_cols=338  Identities=21%  Similarity=0.267  Sum_probs=250.7

Q ss_pred             CCHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEE
Q psy7952          31 VSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGW  110 (444)
Q Consensus        31 ~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vli  110 (444)
                      .....+..++... |...+. .+|.+|+..+..| ++++|++|||||||.+        |++|+ ++.+...... ++|+
T Consensus        54 ~~~~~l~~~l~~~-g~~~lY-~HQ~~A~~~~~~G-~~vvVtTgTgSGKTe~--------FllPI-ld~~l~~~~a-~AL~  120 (851)
T COG1205          54 LRDESLKSALVKA-GIERLY-SHQVDALRLIREG-RNVVVTTGTGSGKTES--------FLLPI-LDHLLRDPSA-RALL  120 (851)
T ss_pred             hhhhHHHHHHHHh-cccccc-HHHHHHHHHHHCC-CCEEEECCCCCchhHH--------HHHHH-HHHHhhCcCc-cEEE
Confidence            4455556666664 777745 7999999999999 9999999999999999        99999 5555554444 8899


Q ss_pred             EcchhhhhcccCccchHhhh----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         111 ISPILSSFYLRFRDDKTSIV----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       111 l~P~~~L~~~~q~~~~~~~l----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      +.||++|+     ++|.+++    ...+..+....++|+....++..++      .+.++|+++||+|+.......-...
T Consensus       121 lYPtnALa-----~DQ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~------~~pp~IllTNpdMLh~~llr~~~~~  189 (851)
T COG1205         121 LYPTNALA-----NDQAERLRELISDLPGKVTFGRYTGDTPPEERRAII------RNPPDILLTNPDMLHYLLLRNHDAW  189 (851)
T ss_pred             EechhhhH-----hhHHHHHHHHHHhCCCcceeeeecCCCChHHHHHHH------hCCCCEEEeCHHHHHHHhccCcchH
Confidence            99999999     8999988    1112258999999999988877666      4789999999999842111111111


Q ss_pred             HHhhCCccEEEEeccccccc-cCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCC
Q psy7952         187 LVRYNKLAYIVVDEAHCVSE-WGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFR  265 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~  265 (444)
                      ...+.++++||+||+|.|-. .|+++...+.++.++++..+.+.++|++|||+.... +...++++..-... +..+...
T Consensus       190 ~~~~~~Lk~lVvDElHtYrGv~GS~vA~llRRL~~~~~~~~~~~q~i~~SAT~~np~-e~~~~l~~~~f~~~-v~~~g~~  267 (851)
T COG1205         190 LWLLRNLKYLVVDELHTYRGVQGSEVALLLRRLLRRLRRYGSPLQIICTSATLANPG-EFAEELFGRDFEVP-VDEDGSP  267 (851)
T ss_pred             HHHHhcCcEEEEecceeccccchhHHHHHHHHHHHHHhccCCCceEEEEeccccChH-HHHHHhcCCcceee-ccCCCCC
Confidence            23355799999999999954 677888889999999888888899999999997754 34455544322211 2233222


Q ss_pred             CCceEEEEEccc--------chhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh--------------
Q psy7952         266 SNLFYDVIFDDL--------LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK--------------  323 (444)
Q Consensus       266 ~~~~~~~~~~~~--------~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~--------------  323 (444)
                      ....+.+.....        ..+.......++..++.    .+-++|+|+.++..++.++...++.              
T Consensus       268 ~~~~~~~~~~p~~~~~~~~~r~s~~~~~~~~~~~~~~----~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~  343 (851)
T COG1205         268 RGLRYFVRREPPIRELAESIRRSALAELATLAALLVR----NGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVST  343 (851)
T ss_pred             CCceEEEEeCCcchhhhhhcccchHHHHHHHHHHHHH----cCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheee
Confidence            233333332220        01122222222222222    5789999999999999986333222              


Q ss_pred             ----cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCC-CHHHHHHHhccCCCCCCceeEEEEecccc
Q psy7952         324 ----VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQSYCRIYHSEHS  398 (444)
Q Consensus       324 ----~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~-s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~  398 (444)
                          +..++|..++..|+.|++.++++|++++.|+|+.+++.||..+.|. +..++.||.||+||.++.+..+.+...+.
T Consensus       344 ~~~~~~~~er~~ie~~~~~g~~~~~~st~AlelgidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~~~  423 (851)
T COG1205         344 YRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRSDP  423 (851)
T ss_pred             ccccCCHHHHHHHHHHHhcCCccEEecchhhhhceeehhhhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCCCc
Confidence                8899999999999999999999999999999999999999999999 99999999999999998888777776443

>KOG0354|consensus

Probab=100.00  E-value=2.9e-34  Score=282.69  Aligned_cols=311  Identities=19%  Similarity=0.272  Sum_probs=207.8

Q ss_pred             ccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchH
Q psy7952          48 SFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKT  127 (444)
Q Consensus        48 ~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~  127 (444)
                      .+| .||.+.+..++ | ++++|++|||+|||++|+..|.+          .++.....+|+|++|++.|+     .||.
T Consensus        62 ~lR-~YQ~eivq~AL-g-kNtii~lPTG~GKTfIAa~Vm~n----------h~rw~p~~KiVF~aP~~pLv-----~QQ~  123 (746)
T KOG0354|consen   62 ELR-NYQEELVQPAL-G-KNTIIALPTGSGKTFIAAVIMKN----------HFEWRPKGKVVFLAPTRPLV-----NQQI  123 (746)
T ss_pred             ccc-HHHHHHhHHhh-c-CCeEEEeecCCCccchHHHHHHH----------HHhcCCcceEEEeeCCchHH-----HHHH
Confidence            456 69999999999 8 99999999999999997665444          23333346889999999999     7777


Q ss_pred             hhh-cCCCCceeEEEEeCCCC-hhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh-hCCccEEEEeccccc
Q psy7952         128 SIV-TGRSDLYQLELIVSGQT-KTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR-YNKLAYIVVDEAHCV  204 (444)
Q Consensus       128 ~~l-~~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~-~~~~~~iViDE~H~~  204 (444)
                      ..+ ..+.+ ..+....++.. ...+..       +....+|+|+||+.+.+..    ...... ++.|.++||||||+-
T Consensus       124 a~~~~~~~~-~~~T~~l~~~~~~~~r~~-------i~~s~~vff~TpQil~ndL----~~~~~~~ls~fs~iv~DE~Hra  191 (746)
T KOG0354|consen  124 ACFSIYLIP-YSVTGQLGDTVPRSNRGE-------IVASKRVFFRTPQILENDL----KSGLHDELSDFSLIVFDECHRT  191 (746)
T ss_pred             HHHhhccCc-ccceeeccCccCCCchhh-------hhcccceEEeChHhhhhhc----ccccccccceEEEEEEcccccc
Confidence            666 33322 44555555533 333222       2357899999999987433    333222 578999999999997


Q ss_pred             cccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHh-cCCCCeEEEecC---------------------
Q psy7952         205 SEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVL-KFNKPYKVFKTS---------------------  262 (444)
Q Consensus       205 ~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l-~~~~~~~~~~~~---------------------  262 (444)
                      ... +.+...+..+..+.   ....|+++|||||.....+ +.+.+ ++...+.+...+                     
T Consensus       192 ~kn-~~Y~~Vmr~~l~~k---~~~~qILgLTASpG~~~~~-v~~~I~~L~asldvr~~ssi~~~y~~lr~~~~i~v~~~~  266 (746)
T KOG0354|consen  192 SKN-HPYNNIMREYLDLK---NQGNQILGLTASPGSKLEQ-VQNVIDNLCASLDVRTESSIKSNYEELREHVQIPVDLSL  266 (746)
T ss_pred             ccc-ccHHHHHHHHHHhh---hccccEEEEecCCCccHHH-HHHHHHhhheecccchhhhhhhhHHHHhccCcccCcHHH
Confidence            542 23444443333322   2224899999999864433 22221 111000000000                     


Q ss_pred             ----------------------------------C----------CCCCc----e------------------EEEE---
Q psy7952         263 ----------------------------------T----------FRSNL----F------------------YDVI---  273 (444)
Q Consensus       263 ----------------------------------~----------~~~~~----~------------------~~~~---  273 (444)
                                                        .          ..++.    .                  ....   
T Consensus       267 ~~~~~~~~f~~~i~p~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~f~~~~~~~~~~~ll~~~gir~~~  346 (746)
T KOG0354|consen  267 CERDIEDPFGMIIEPLLQQLQEEGLIEISDKSTSYEQWVVQAEKAAAPNGPENQRNCFYALHLRKYNLALLISDGIRFVD  346 (746)
T ss_pred             hhhhhhhhHHHHHHHHHHHHHhcCccccccccccccchhhhhhhhhccCCCccchhhHHHHHHHHHHHHHHhhcchhhHH
Confidence                                              0          00000    0                  0000   


Q ss_pred             ------------------------------------------EcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccc
Q psy7952         274 ------------------------------------------FDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTRE  311 (444)
Q Consensus       274 ------------------------------------------~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~  311 (444)
                                                                .......+.+.+.+.+.+...  ..+..++||||.+++
T Consensus       347 ~l~~~~~f~~e~~~~k~~~~~~e~~~~~~~~~~m~~~~~l~~~~~~~npkle~l~~~l~e~f~--~~~dsR~IIFve~R~  424 (746)
T KOG0354|consen  347 ALDYLEDFYEEVALKKYLKLELEARLIRNFTENMNELEHLSLDPPKENPKLEKLVEILVEQFE--QNPDSRTIIFVETRE  424 (746)
T ss_pred             HHhhhhhhccccchhHHHHHHhcchhhHHHHHHHHhhhhhhcCCCccChhHHHHHHHHHHHhh--cCCCccEEEEEehHH
Confidence                                                      000001111223333333333  236779999999999


Q ss_pred             hHHHHHHHHHhh---------------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCC
Q psy7952         312 HTTDLADALRRK---------------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSS  370 (444)
Q Consensus       312 ~~~~l~~~L~~~---------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s  370 (444)
                      .|..+...|.+.                     |++.+..++++.|++|++++||||+++++|+||+.|++||.||...|
T Consensus       425 sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI~ec~lVIcYd~~sn  504 (746)
T KOG0354|consen  425 SALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDIGECNLVICYDYSSN  504 (746)
T ss_pred             HHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCCCccEEEEecchhccCCcccccEEEEecCCcc
Confidence            999999999844                     89999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhccCCCCCCceeEEEEeccc
Q psy7952         371 IPAYYQESGRAGRDGLQSYCRIYHSEH  397 (444)
Q Consensus       371 ~~~~~Qr~GR~~R~g~~g~~~~~~~~~  397 (444)
                      +..++||.|| ||. +.|.+++++...
T Consensus       505 pIrmIQrrGR-gRa-~ns~~vll~t~~  529 (746)
T KOG0354|consen  505 PIRMVQRRGR-GRA-RNSKCVLLTTGS  529 (746)
T ss_pred             HHHHHHHhcc-ccc-cCCeEEEEEcch
Confidence            9999999999 898 677788877733

>PHA02653 RNA helicase NPH-II; Provisional

Probab=100.00  E-value=3.8e-33  Score=281.49  Aligned_cols=320  Identities=13%  Similarity=0.079  Sum_probs=203.7

Q ss_pred             CCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccc-eEEeCCCccccc---cCCccceeEEEcchhhhhcc
Q psy7952          45 GFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARS-RVRIPPGADFIL---NGNVRSRNGWISPILSSFYL  120 (444)
Q Consensus        45 g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~-~~~~~~~~~~l~---~~~~~~~vlil~P~~~L~~~  120 (444)
                      .+.++...+|+++++.++.+ ++++++|+||+|||.+.-.+++- .|++|. +..+.   ..+...++++++|+++|+  
T Consensus       160 ~l~~~~~~iQ~qil~~i~~g-kdvIv~A~TGSGKTtqvPq~l~~~~flf~~-l~~l~~~~~~~~~~~ilvt~PrreLa--  235 (675)
T PHA02653        160 PLASLQPDVQLKIFEAWISR-KPVVLTGGTGVGKTSQVPKLLLWFNYLFGG-FDNLDKIDPNFIERPIVLSLPRVALV--  235 (675)
T ss_pred             cCCchhHHHHHHHHHHHHhC-CCEEEECCCCCCchhHHHHHHHHhhhccch-hhhhhhcccccCCcEEEEECcHHHHH--
Confidence            34444557999999999999 99999999999999752111111 033333 22121   122345789999999999  


Q ss_pred             cCccchHhhh-c-CCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEE
Q psy7952         121 RFRDDKTSIV-T-GRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVV  198 (444)
Q Consensus       121 ~q~~~~~~~l-~-~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iVi  198 (444)
                      .|+.+.+... . .......+....|+......       .......+++++|+....           ..+.++++||+
T Consensus       236 ~qi~~~i~~~vg~~~~~g~~v~v~~Gg~~~~~~-------~t~~k~~~Ilv~T~~L~l-----------~~L~~v~~VVI  297 (675)
T PHA02653        236 RLHSITLLKSLGFDEIDGSPISLKYGSIPDELI-------NTNPKPYGLVFSTHKLTL-----------NKLFDYGTVII  297 (675)
T ss_pred             HHHHHHHHHHhCccccCCceEEEEECCcchHHh-------hcccCCCCEEEEeCcccc-----------cccccCCEEEc
Confidence            2233333332 1 12223667777887762100       001235689999976421           13568999999


Q ss_pred             eccccccccCCCcHHHHHHHHHHHHhh-CCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEccc
Q psy7952         199 DEAHCVSEWGHDFRPTYRRLGELRQFT-GNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDL  277 (444)
Q Consensus       199 DE~H~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  277 (444)
                      ||||.....+.       .+..+++.. +...|+++||||++.... .+.++++  ++..+........++...+.....
T Consensus       298 DEaHEr~~~~D-------llL~llk~~~~~~rq~ILmSATl~~dv~-~l~~~~~--~p~~I~I~grt~~pV~~~yi~~~~  367 (675)
T PHA02653        298 DEVHEHDQIGD-------IIIAVARKHIDKIRSLFLMTATLEDDRD-RIKEFFP--NPAFVHIPGGTLFPISEVYVKNKY  367 (675)
T ss_pred             cccccCccchh-------HHHHHHHHhhhhcCEEEEEccCCcHhHH-HHHHHhc--CCcEEEeCCCcCCCeEEEEeecCc
Confidence            99999876542       122222222 222589999999987654 4555553  454444443322333322221110


Q ss_pred             c----hhh-HHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------------cCHHHHHHHHHHH-hcC
Q psy7952         278 L----KDS-YAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------VNKHERSRVQESF-MRG  339 (444)
Q Consensus       278 ~----~~~-~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------------~~~~~r~~~~~~f-~~g  339 (444)
                      .    ... .......+..+.......++++||||+++++++.+++.|.+.            +++  +++.+++| ++|
T Consensus       368 ~~~~~~~y~~~~k~~~l~~L~~~~~~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq--~eq~l~~ff~~g  445 (675)
T PHA02653        368 NPKNKRAYIEEEKKNIVTALKKYTPPKGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPN--IDEILEKVYSSK  445 (675)
T ss_pred             ccccchhhhHHHHHHHHHHHHHhhcccCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCH--HHHHHHHHhccC
Confidence            0    000 011111122221111123568999999999999999999753            333  35666777 689


Q ss_pred             CccEEEEcCccccccccCCccEEEEeC---CCC---------CHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         340 EINVITATISFGMGIDRQNVRFVVHWG---MPS---------SIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       340 ~~~vLvaT~~~~~Gidi~~~~~Vi~~~---~p~---------s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                      +.+|||||+++++|+|+|++++||++|   .|.         |..+|.||+||+||. ++|.|+.++++++.
T Consensus       446 k~kILVATdIAERGIDIp~V~~VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~~  516 (675)
T PHA02653        446 NPSIIISTPYLESSVTIRNATHVYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDLL  516 (675)
T ss_pred             ceeEEeccChhhccccccCeeEEEECCCccCCCcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHHh
Confidence            999999999999999999999999998   554         889999999999999 88999999998764

>PHA02558 uvsW UvsW helicase; Provisional

Probab=100.00  E-value=2.8e-33  Score=279.39  Aligned_cols=298  Identities=18%  Similarity=0.154  Sum_probs=189.2

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhh
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      |+++|.+++..++.+ ++.++++|||+|||.++..        .  .......+ ..++||++||++|+     .|..+.
T Consensus       115 ~r~~Q~~av~~~l~~-~~~il~apTGsGKT~i~~~--------l--~~~~~~~~-~~~vLilvpt~eL~-----~Q~~~~  177 (501)
T PHA02558        115 PHWYQYDAVYEGLKN-NRRLLNLPTSAGKSLIQYL--------L--SRYYLENY-EGKVLIIVPTTSLV-----TQMIDD  177 (501)
T ss_pred             CCHHHHHHHHHHHhc-CceEEEeCCCCCHHHHHHH--------H--HHHHHhcC-CCeEEEEECcHHHH-----HHHHHH
Confidence            558999999999988 8899999999999987321        0  11111222 22679999999999     444444


Q ss_pred             h-cCC-CCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccccc
Q psy7952         130 V-TGR-SDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEW  207 (444)
Q Consensus       130 l-~~~-~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~  207 (444)
                      + .+. .+...+..+.++....             ...+|+|+||+++...       ....+.++++||+||||++.+.
T Consensus       178 l~~~~~~~~~~~~~i~~g~~~~-------------~~~~I~VaT~qsl~~~-------~~~~~~~~~~iIvDEaH~~~~~  237 (501)
T PHA02558        178 FVDYRLFPREAMHKIYSGTAKD-------------TDAPIVVSTWQSAVKQ-------PKEWFDQFGMVIVDECHLFTGK  237 (501)
T ss_pred             HHHhccccccceeEEecCcccC-------------CCCCEEEeeHHHHhhc-------hhhhccccCEEEEEchhcccch
Confidence            4 221 1112333444443221             3578999999997521       1123568999999999998642


Q ss_pred             CCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHH--HHHHhcCCCCeEEEec-C----CCCCCceEEEEEcccc--
Q psy7952         208 GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQD--IISVLKFNKPYKVFKT-S----TFRSNLFYDVIFDDLL--  278 (444)
Q Consensus       208 ~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~--~~~~l~~~~~~~~~~~-~----~~~~~~~~~~~~~~~~--  278 (444)
                      .  +       ..++..+++..++++|||||.......  +...++  +....... .    .......+........  
T Consensus       238 ~--~-------~~il~~~~~~~~~lGLTATp~~~~~~~~~~~~~fG--~i~~~v~~~~li~~g~l~~~~~~~v~~~~~~~  306 (501)
T PHA02558        238 S--L-------TSIITKLDNCKFKFGLTGSLRDGKANILQYVGLFG--DIFKPVTTSQLMEEGQVTDLKINSIFLRYPDE  306 (501)
T ss_pred             h--H-------HHHHHhhhccceEEEEeccCCCccccHHHHHHhhC--CceEEecHHHHHhCCCcCCceEEEEeccCCHH
Confidence            2  2       233334444477999999997643221  111222  11110000 0    0000011110000000  


Q ss_pred             ----------hh------hHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHH
Q psy7952         279 ----------KD------SYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRV  332 (444)
Q Consensus       279 ----------~~------~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~  332 (444)
                                ..      ..+.....+..........+.+++|||++.++++.+++.|.+.          ++.++|..+
T Consensus       307 ~~~~~~~~~~~~~~~~l~~~~~Rn~~I~~~~~~~~~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i  386 (501)
T PHA02558        307 DRVKLKGEDYQEEIKYITSHTKRNKWIANLALKLAKKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEM  386 (501)
T ss_pred             HhhhhcccchHHHHHHHhccHHHHHHHHHHHHHHHhcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHH
Confidence                      00      0001112222222211224678899999999999999999876          888999999


Q ss_pred             HHHHhcCCccEEEEc-CccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEec
Q psy7952         333 QESFMRGEINVITAT-ISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHS  395 (444)
Q Consensus       333 ~~~f~~g~~~vLvaT-~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~  395 (444)
                      ++.|+.|...+|||| +++++|+|+|++++||++.++.|...|+||+||++|.+.++....+++
T Consensus       387 ~~~~~~~~~~vLvaT~~~l~eG~Dip~ld~vIl~~p~~s~~~~~QriGR~~R~~~~K~~~~i~D  450 (501)
T PHA02558        387 KKIAEGGKGIIIVASYGVFSTGISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGSKSIATVWD  450 (501)
T ss_pred             HHHHhCCCCeEEEEEcceeccccccccccEEEEecCCcchhhhhhhhhccccCCCCCceEEEEE
Confidence            999999999999998 899999999999999999999999999999999999876654444443

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

Probab=100.00  E-value=7.2e-33  Score=269.07  Aligned_cols=356  Identities=22%  Similarity=0.280  Sum_probs=268.5

Q ss_pred             HHHHHHHHHHhCCcccCchHHHHHHHHHHcc-----CCcEEEEccCCCcccccccccccceEEeCCCccccccCCcccee
Q psy7952          34 QELTAKLKALFGFDSFKCELQKKAIRHILLR-----THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRN  108 (444)
Q Consensus        34 ~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~-----~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~v  108 (444)
                      .++.+.+.+..+|+  .|..|++++..|...     ..+-++.+.-|||||.+|+++++.     +    +..+...   
T Consensus       249 ~~l~~~~~~~LPF~--LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~-----a----i~~G~Q~---  314 (677)
T COG1200         249 GELLAKFLAALPFK--LTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLA-----A----IEAGYQA---  314 (677)
T ss_pred             HHHHHHHHHhCCCC--ccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHH-----H----HHcCCee---
Confidence            34555565557988  488999999999863     245799999999999997765443     1    3334444   


Q ss_pred             EEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         109 GWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       109 lil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      .+++||.-||     .|++..+  .+..-++.+..++|......+.+.+..+.  .+..+|+|||         |.+++.
T Consensus       315 ALMAPTEILA-----~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~--~G~~~ivVGT---------HALiQd  378 (677)
T COG1200         315 ALMAPTEILA-----EQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLA--SGEIDIVVGT---------HALIQD  378 (677)
T ss_pred             EEeccHHHHH-----HHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHh--CCCCCEEEEc---------chhhhc
Confidence            9999999999     7777776  22222399999999999999999988886  5789999999         777888


Q ss_pred             HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhc-CCCCeEEEecCCCC
Q psy7952         187 LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLK-FNKPYKVFKTSTFR  265 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~-~~~~~~~~~~~~~~  265 (444)
                      ...+.+++++|+||=|++   |..-|      ..+...-..++.++.|||||.|...-  ...++ +.-. .+-.-+..|
T Consensus       379 ~V~F~~LgLVIiDEQHRF---GV~QR------~~L~~KG~~~Ph~LvMTATPIPRTLA--lt~fgDldvS-~IdElP~GR  446 (677)
T COG1200         379 KVEFHNLGLVIIDEQHRF---GVHQR------LALREKGEQNPHVLVMTATPIPRTLA--LTAFGDLDVS-IIDELPPGR  446 (677)
T ss_pred             ceeecceeEEEEeccccc---cHHHH------HHHHHhCCCCCcEEEEeCCCchHHHH--HHHhccccch-hhccCCCCC
Confidence            899999999999999994   42111      12222222157899999999987654  33333 2222 222223445


Q ss_pred             CCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchH--------HHHHHHHHhh------------cC
Q psy7952         266 SNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHT--------TDLADALRRK------------VN  325 (444)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~--------~~l~~~L~~~------------~~  325 (444)
                      .++.-.+...+.    ...+.+.+.+.+.    .++++.|.|+-.++.        ..++..|...            |+
T Consensus       447 kpI~T~~i~~~~----~~~v~e~i~~ei~----~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~  518 (677)
T COG1200         447 KPITTVVIPHER----RPEVYERIREEIA----KGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMK  518 (677)
T ss_pred             CceEEEEecccc----HHHHHHHHHHHHH----cCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCC
Confidence            555555555433    3334444444333    489999999877655        4556666633            99


Q ss_pred             HHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCC-CCCHHHHHHHhccCCCCCCceeEEEEecccc----hh
Q psy7952         326 KHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGM-PSSIPAYYQESGRAGRDGLQSYCRIYHSEHS----KK  400 (444)
Q Consensus       326 ~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~-p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~----~~  400 (444)
                      ..++++++++|++|+++|||||.+.++|||+|+.+++|..+. -.....+.|-.||+||.+..++|++++.+..    ..
T Consensus       519 ~~eKd~vM~~Fk~~e~~ILVaTTVIEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~~~~a~~  598 (677)
T COG1200         519 PAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPLSEVAKQ  598 (677)
T ss_pred             hHHHHHHHHHHHcCCCcEEEEeeEEEecccCCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCCChhHHH
Confidence            999999999999999999999999999999999999776664 3468889999999999999999999998665    57


Q ss_pred             hHHHHHhhccchhHHHHHHHHhhHHHHHHHhhhceeeee
Q psy7952         401 SLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGYFLVI  439 (444)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  439 (444)
                      +++.+.++.......+.+.++++..++..-.++|+..+.
T Consensus       599 RL~im~~t~DGF~IAE~DLklRGpGe~lG~rQSG~~~f~  637 (677)
T COG1200         599 RLKIMRETTDGFVIAEEDLKLRGPGELLGTRQSGLPEFR  637 (677)
T ss_pred             HHHHHHhcCCcceehhhhHhccCCccccCCcccCCcceE
Confidence            899999999999999999999999999988888765443

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=100.00  E-value=1.1e-32  Score=284.49  Aligned_cols=303  Identities=16%  Similarity=0.140  Sum_probs=201.9

Q ss_pred             HHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh--
Q psy7952          53 LQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV--  130 (444)
Q Consensus        53 ~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l--  130 (444)
                      +-.+.+..+..+ ++++++|+||||||..        +..+. ++..   ....+++++.|+++++     .+..+++  
T Consensus         6 ~~~~i~~~l~~~-~~vIi~a~TGSGKTT~--------vpl~l-L~~~---~~~~~ilvlqPrR~aA-----~qiA~rva~   67 (819)
T TIGR01970         6 VLPALRDALAAH-PQVVLEAPPGAGKSTA--------VPLAL-LDAP---GIGGKIIMLEPRRLAA-----RSAAQRLAS   67 (819)
T ss_pred             HHHHHHHHHHcC-CcEEEECCCCCCHHHH--------HHHHH-HHhh---ccCCeEEEEeCcHHHH-----HHHHHHHHH
Confidence            334556666566 8999999999999998        55555 2222   2234789999999999     4444444  


Q ss_pred             cCC-CCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccc-ccccC
Q psy7952         131 TGR-SDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHC-VSEWG  208 (444)
Q Consensus       131 ~~~-~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~-~~~~~  208 (444)
                      .++ ..+..+.........            ...+.+|+|+||+.|.    . .+.....+.++++|||||+|. ..+..
T Consensus        68 ~~~~~~g~~VGy~vr~~~~------------~s~~t~I~v~T~G~Ll----r-~l~~d~~L~~v~~VIiDEaHER~L~~D  130 (819)
T TIGR01970        68 QLGEAVGQTVGYRVRGENK------------VSRRTRLEVVTEGILT----R-MIQDDPELDGVGALIFDEFHERSLDAD  130 (819)
T ss_pred             HhCCCcCcEEEEEEccccc------------cCCCCcEEEECCcHHH----H-HHhhCcccccCCEEEEeccchhhhccc
Confidence            122 001334333332211            1346789999999985    2 233345678999999999995 44322


Q ss_pred             CCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHH
Q psy7952         209 HDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEF  288 (444)
Q Consensus       209 ~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  288 (444)
                        +.  +..+..+.+.++++.++|+||||++...   +.++++  ++..+....... ++...+............+...
T Consensus       131 --l~--L~ll~~i~~~lr~dlqlIlmSATl~~~~---l~~~l~--~~~vI~~~gr~~-pVe~~y~~~~~~~~~~~~v~~~  200 (819)
T TIGR01970       131 --LG--LALALDVQSSLREDLKILAMSATLDGER---LSSLLP--DAPVVESEGRSF-PVEIRYLPLRGDQRLEDAVSRA  200 (819)
T ss_pred             --hH--HHHHHHHHHhcCCCceEEEEeCCCCHHH---HHHHcC--CCcEEEecCcce-eeeeEEeecchhhhHHHHHHHH
Confidence              21  1222334444566789999999998653   344443  222233222111 1222222111111111122233


Q ss_pred             HHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-------------cCHHHHHHHHHHHhcCCccEEEEcCccccccc
Q psy7952         289 IEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-------------VNKHERSRVQESFMRGEINVITATISFGMGID  355 (444)
Q Consensus       289 l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gid  355 (444)
                      +..++..   ..+++|||+++.++++.++..|.+.             +++++|..+++.|++|..+|||||+++++|||
T Consensus       201 l~~~l~~---~~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgIt  277 (819)
T TIGR01970       201 VEHALAS---ETGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLT  277 (819)
T ss_pred             HHHHHHh---cCCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhccc
Confidence            4444332   3678999999999999999999862             88899999999999999999999999999999


Q ss_pred             cCCccEEEEeCCCC------------------CHHHHHHHhccCCCCCCceeEEEEecccchhhHHH
Q psy7952         356 RQNVRFVVHWGMPS------------------SIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEY  404 (444)
Q Consensus       356 i~~~~~Vi~~~~p~------------------s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~  404 (444)
                      ||+|++||++|.|.                  |..++.||.||+||. .+|.|+.+++..+...+..
T Consensus       278 Ip~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~-~~G~cyrL~t~~~~~~l~~  343 (819)
T TIGR01970       278 IEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRL-EPGVCYRLWSEEQHQRLPA  343 (819)
T ss_pred             ccCceEEEEcCcccccccccccCCceeeEEEECHHHHHhhhhhcCCC-CCCEEEEeCCHHHHHhhhc
Confidence            99999999999875                  345699999999999 8999999999877655433

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.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=100.00  E-value=6.6e-33  Score=286.91  Aligned_cols=300  Identities=14%  Similarity=0.135  Sum_probs=201.8

Q ss_pred             HHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhhcCC-
Q psy7952          55 KKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGR-  133 (444)
Q Consensus        55 ~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l~~~-  133 (444)
                      .+.+..+.++ +++++.||||||||.+        |.++.    +.......+++++.|+++++  .|+.+.+... ++ 
T Consensus        11 ~~i~~~l~~~-~~vvv~A~TGSGKTt~--------~pl~l----L~~~~~~~~ilvlqPrR~aA--~qia~rva~~-l~~   74 (812)
T PRK11664         11 PELLTALKTA-PQVLLKAPTGAGKSTW--------LPLQL----LQHGGINGKIIMLEPRRLAA--RNVAQRLAEQ-LGE   74 (812)
T ss_pred             HHHHHHHHhC-CCEEEEcCCCCCHHHH--------HHHHH----HHcCCcCCeEEEECChHHHH--HHHHHHHHHH-hCc
Confidence            3455666566 8999999999999999        65555    32222234789999999999  3333333222 11 


Q ss_pred             CCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccc-cccCCCcH
Q psy7952         134 SDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCV-SEWGHDFR  212 (444)
Q Consensus       134 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~-~~~~~~~~  212 (444)
                      ..+..+....++....            ....+|+|+||+.+.    + .+.....+.++++||+||+|.. .+..  + 
T Consensus        75 ~~g~~VGy~vr~~~~~------------~~~t~I~v~T~G~Ll----r-~l~~d~~L~~v~~IIlDEaHER~l~~D--l-  134 (812)
T PRK11664         75 KPGETVGYRMRAESKV------------GPNTRLEVVTEGILT----R-MIQRDPELSGVGLVILDEFHERSLQAD--L-  134 (812)
T ss_pred             ccCceEEEEecCcccc------------CCCCcEEEEChhHHH----H-HHhhCCCcCcCcEEEEcCCCccccccc--h-
Confidence            1114555544443321            235689999999984    2 2333456789999999999973 2211  1 


Q ss_pred             HHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHH
Q psy7952         213 PTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKC  292 (444)
Q Consensus       213 ~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  292 (444)
                       .+..+..+++.++++.++++||||++..   .+.+++  +++..+....... .+...+............+...+..+
T Consensus       135 -~L~ll~~i~~~lr~~lqlilmSATl~~~---~l~~~~--~~~~~I~~~gr~~-pV~~~y~~~~~~~~~~~~v~~~l~~~  207 (812)
T PRK11664        135 -ALALLLDVQQGLRDDLKLLIMSATLDND---RLQQLL--PDAPVIVSEGRSF-PVERRYQPLPAHQRFDEAVARATAEL  207 (812)
T ss_pred             -HHHHHHHHHHhCCccceEEEEecCCCHH---HHHHhc--CCCCEEEecCccc-cceEEeccCchhhhHHHHHHHHHHHH
Confidence             1222334445556678999999999764   234444  2332333322211 22222222111111112222334444


Q ss_pred             hccCCCCCceEEEEecccchHHHHHHHHHhh-------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCc
Q psy7952         293 LGKDNKANNCGIIYCRTREHTTDLADALRRK-------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNV  359 (444)
Q Consensus       293 l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~  359 (444)
                      +..   ..+.+|||+++.++++.+++.|...             ++..+|..+++.|++|..+|||||+++++|||||++
T Consensus       208 l~~---~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V  284 (812)
T PRK11664        208 LRQ---ESGSLLLFLPGVGEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGI  284 (812)
T ss_pred             HHh---CCCCEEEEcCCHHHHHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCc
Confidence            432   3688999999999999999999862             888999999999999999999999999999999999


Q ss_pred             cEEEEeCCCC------------------CHHHHHHHhccCCCCCCceeEEEEecccchhh
Q psy7952         360 RFVVHWGMPS------------------SIPAYYQESGRAGRDGLQSYCRIYHSEHSKKS  401 (444)
Q Consensus       360 ~~Vi~~~~p~------------------s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~  401 (444)
                      ++||++|.+.                  |..+|.||.||+||. .+|.|+.++++.+...
T Consensus       285 ~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~~~~~  343 (812)
T PRK11664        285 RLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL-EPGICLHLYSKEQAER  343 (812)
T ss_pred             eEEEECCCcccccccccCCcceeEEEeechhhhhhhccccCCC-CCcEEEEecCHHHHhh
Confidence            9999988764                  446899999999999 6999999999876644

>PRK09401 reverse gyrase; Reviewed

Probab=100.00  E-value=2.2e-32  Score=291.60  Aligned_cols=306  Identities=19%  Similarity=0.247  Sum_probs=198.6

Q ss_pred             HHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcc
Q psy7952          34 QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISP  113 (444)
Q Consensus        34 ~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P  113 (444)
                      .++.+.+++.+|+.  |+++|..+++.++.| ++++++||||+|||..         .+++ +..+.  ....+++|++|
T Consensus        67 ~~~~~~f~~~~G~~--pt~iQ~~~i~~il~g-~dv~i~ApTGsGKT~f---------~l~~-~~~l~--~~g~~alIL~P  131 (1176)
T PRK09401         67 KEFEKFFKKKTGSK--PWSLQRTWAKRLLLG-ESFAIIAPTGVGKTTF---------GLVM-SLYLA--KKGKKSYIIFP  131 (1176)
T ss_pred             HHHHHHHHHhcCCC--CcHHHHHHHHHHHCC-CcEEEEcCCCCCHHHH---------HHHH-HHHHH--hcCCeEEEEec
Confidence            45566777777985  578999999999999 9999999999999954         2222 11111  12356799999


Q ss_pred             hhhhhcccCccchHhhh--cCCCCceeEEEEeCCCC--hhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh
Q psy7952         114 ILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQT--KTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR  189 (444)
Q Consensus       114 ~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~  189 (444)
                      |++|+  .|+.+.++.+  ..+   +.+..+.++..  .....+....+.  .+.++|+|+||+.+..     ... ...
T Consensus       132 TreLa--~Qi~~~l~~l~~~~~---~~~~~~~g~~~~~~~ek~~~~~~l~--~~~~~IlV~Tp~rL~~-----~~~-~l~  198 (1176)
T PRK09401        132 TRLLV--EQVVEKLEKFGEKVG---CGVKILYYHSSLKKKEKEEFLERLK--EGDFDILVTTSQFLSK-----NFD-ELP  198 (1176)
T ss_pred             cHHHH--HHHHHHHHHHhhhcC---ceEEEEEccCCcchhHHHHHHHHHh--cCCCCEEEECHHHHHH-----HHH-hcc
Confidence            99999  3334555555  223   55655655543  233333333332  3568999999999742     122 233


Q ss_pred             hCCccEEEEeccccccccCCC---------cH-HHHHHH-----------------HHHHHhh----CCCCcEEEEeccC
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHD---------FR-PTYRRL-----------------GELRQFT----GNSIPIIALTATA  238 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~---------~~-~~~~~l-----------------~~~~~~~----~~~~~~v~lSAT~  238 (444)
                      ..+++++|+||||++++++..         |. ..+..+                 ..+...+    ++..|++++|||+
T Consensus       199 ~~~~~~lVvDEaD~~L~~~k~id~~l~~lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~  278 (1176)
T PRK09401        199 KKKFDFVFVDDVDAVLKSSKNIDKLLYLLGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATG  278 (1176)
T ss_pred             ccccCEEEEEChHHhhhcccchhhHHHhCCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCC
Confidence            456999999999999874422         32 112211                 1111111    1257899999999


Q ss_pred             CcchHHH--HHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccch---H
Q psy7952         239 EPSVKQD--IISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREH---T  313 (444)
Q Consensus       239 ~~~~~~~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~---~  313 (444)
                      ++.....  +.+.++    +.+........++...+....   .+...+..++..    .   +.++||||++...   +
T Consensus       279 ~~~~~~~~l~~~ll~----~~v~~~~~~~rnI~~~yi~~~---~k~~~L~~ll~~----l---~~~~LIFv~t~~~~~~a  344 (1176)
T PRK09401        279 RPRGNRVKLFRELLG----FEVGSPVFYLRNIVDSYIVDE---DSVEKLVELVKR----L---GDGGLIFVPSDKGKEYA  344 (1176)
T ss_pred             CccchHHHHhhccce----EEecCcccccCCceEEEEEcc---cHHHHHHHHHHh----c---CCCEEEEEecccChHHH
Confidence            8743221  222221    122222222334444333322   233333343332    2   4579999999888   9


Q ss_pred             HHHHHHHHhh-------cCHHHHHHHHHHHhcCCccEEEE----cCccccccccCC-ccEEEEeCCCC------CHHHHH
Q psy7952         314 TDLADALRRK-------VNKHERSRVQESFMRGEINVITA----TISFGMGIDRQN-VRFVVHWGMPS------SIPAYY  375 (444)
Q Consensus       314 ~~l~~~L~~~-------~~~~~r~~~~~~f~~g~~~vLva----T~~~~~Gidi~~-~~~Vi~~~~p~------s~~~~~  375 (444)
                      +.+++.|...       ....  ...+++|++|+.+||||    |+++++|||+|+ +++|||+|.|.      ....+.
T Consensus       345 e~l~~~L~~~gi~v~~~hg~l--~~~l~~F~~G~~~VLVatas~tdv~aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~~  422 (1176)
T PRK09401        345 EELAEYLEDLGINAELAISGF--ERKFEKFEEGEVDVLVGVASYYGVLVRGIDLPERIRYAIFYGVPKFKFSLEEELAPP  422 (1176)
T ss_pred             HHHHHHHHHCCCcEEEEeCcH--HHHHHHHHCCCCCEEEEecCCCCceeecCCCCcceeEEEEeCCCCEEEeccccccCH
Confidence            9999999887       1112  33459999999999999    699999999999 89999999998      678899


Q ss_pred             HHhccCCC
Q psy7952         376 QESGRAGR  383 (444)
Q Consensus       376 Qr~GR~~R  383 (444)
                      +|+||+..
T Consensus       423 ~~~~r~~~  430 (1176)
T PRK09401        423 FLLLRLLS  430 (1176)
T ss_pred             HHHHHHHh
Confidence            99999963

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=100.00  E-value=5.8e-33  Score=268.10  Aligned_cols=299  Identities=15%  Similarity=0.106  Sum_probs=177.5

Q ss_pred             cEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-c-CCCCceeEEEEeC
Q psy7952          67 DIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-T-GRSDLYQLELIVS  144 (444)
Q Consensus        67 ~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~-~~~~~i~~~~~~~  144 (444)
                      ++++.+|||+|||.+        +..++ +..+. .+...++++++|+++|+     .++.+.+ . ++   .++..+++
T Consensus         1 ~vvi~apTGsGKT~~--------~~~~~-l~~~~-~~~~~~ii~v~P~~~L~-----~q~~~~l~~~f~---~~~~~~~~   62 (358)
T TIGR01587         1 LLVIEAPTGYGKTEA--------ALLWA-LHSIK-SQKADRVIIALPTRATI-----NAMYRRAKELFG---SNLGLLHS   62 (358)
T ss_pred             CEEEEeCCCCCHHHH--------HHHHH-HHHHh-hCCCCeEEEEeehHHHH-----HHHHHHHHHHhC---cccEEeec
Confidence            579999999999999        55554 22222 23345789999999999     6777776 2 24   34445555


Q ss_pred             CCChhh---------HHHHHHHHHh---cCCCeeEEEECCCccccccHHHHHHHHHhh--CCccEEEEeccccccccCCC
Q psy7952         145 GQTKTE---------NKAILEELRL---VKPRIKLLYVTPERAVTESFHYLLQHLVRY--NKLAYIVVDEAHCVSEWGHD  210 (444)
Q Consensus       145 ~~~~~~---------~~~~~~~~~~---~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~--~~~~~iViDE~H~~~~~~~~  210 (444)
                      ......         ..........   .....+|+|+||+++....+..+......+  -..++||+||+|.+.+.+  
T Consensus        63 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~--  140 (358)
T TIGR01587        63 SSSFKRIKEMGDSEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYT--  140 (358)
T ss_pred             cHHHHHHhccCCchhHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHH--
Confidence            432110         0011110000   012467999999998532222111111111  133899999999987653  


Q ss_pred             cHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCC-CCCceEEEE-EcccchhhHHHHHHH
Q psy7952         211 FRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTF-RSNLFYDVI-FDDLLKDSYAHVKEF  288 (444)
Q Consensus       211 ~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~  288 (444)
                      ... +..+...+.  ..+.|+++||||++....+.+... ... .......... .....+.+. .......+...+..+
T Consensus       141 ~~~-l~~~l~~l~--~~~~~~i~~SATlp~~l~~~~~~~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l  215 (358)
T TIGR01587       141 LAL-ILAVLEVLK--DNDVPILLMSATLPKFLKEYAEKI-GYV-EFNEPLDLKEERRFERHRFIKIESDKVGEISSLERL  215 (358)
T ss_pred             HHH-HHHHHHHHH--HcCCCEEEEecCchHHHHHHHhcC-CCc-ccccCCCCccccccccccceeeccccccCHHHHHHH
Confidence            222 233222222  235899999999985543332221 111 0000000000 000011111 111111222223333


Q ss_pred             HHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------------cCHHHHHH----HHHHHhcCCccEEEEcCcccc
Q psy7952         289 IEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------VNKHERSR----VQESFMRGEINVITATISFGM  352 (444)
Q Consensus       289 l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------------~~~~~r~~----~~~~f~~g~~~vLvaT~~~~~  352 (444)
                      +...     ..++++||||+++++++.++..|.+.            +++.+|..    +++.|++|..++||||+++++
T Consensus       216 ~~~~-----~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~  290 (358)
T TIGR01587       216 LEFI-----KKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEA  290 (358)
T ss_pred             HHHh-----hCCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhc
Confidence            3221     14689999999999999999999765            56777765    488999999999999999999


Q ss_pred             ccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCc----eeEEEEecccc
Q psy7952         353 GIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ----SYCRIYHSEHS  398 (444)
Q Consensus       353 Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~----g~~~~~~~~~~  398 (444)
                      |+|++ +++||++..|  ..+|+||+||+||.|+.    |.++++....+
T Consensus       291 GiDi~-~~~vi~~~~~--~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~~  337 (358)
T TIGR01587       291 SLDIS-ADVMITELAP--IDSLIQRLGRLHRYGRKNGENFEVYIITIAPE  337 (358)
T ss_pred             eeccC-CCEEEEcCCC--HHHHHHHhccccCCCCCCCCCCeEEEEeecCC
Confidence            99996 7888887665  88999999999998754    35666655443

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.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=100.00  E-value=9.4e-32  Score=257.04  Aligned_cols=292  Identities=17%  Similarity=0.200  Sum_probs=183.6

Q ss_pred             HHHHHHHHHHccCC-cEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-
Q psy7952          53 LQKKAIRHILLRTH-DIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-  130 (444)
Q Consensus        53 ~Q~~~~~~~~~~~~-~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-  130 (444)
                      +|.++++.+.+++. .+++.+|||+|||.+        +.+++    +...+.   +++++|+++|+     .++.+++ 
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~--------~~~~~----l~~~~~---~~~~~P~~aL~-----~~~~~~~~   60 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLA--------WLTPL----LHGEND---TIALYPTNALI-----EDQTEAIK   60 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHH--------HHHHH----HHcCCC---EEEEeChHHHH-----HHHHHHHH
Confidence            59999999999843 478999999999999        66666    433334   49999999999     6666665 


Q ss_pred             --c--C-CCCceeEEEEeCCCChh--hHH-------------HH-HHHHHhcCCCeeEEEECCCccccccHHHHHHHH--
Q psy7952         131 --T--G-RSDLYQLELIVSGQTKT--ENK-------------AI-LEELRLVKPRIKLLYVTPERAVTESFHYLLQHL--  187 (444)
Q Consensus       131 --~--~-~~~~i~~~~~~~~~~~~--~~~-------------~~-~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~--  187 (444)
                        .  + +.....+..++|....+  ...             .. ...+  ....++|+++||+++.     .+++..  
T Consensus        61 ~~~~~~~~~~~~~v~~~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~--~~~~p~illT~p~~l~-----~llr~~~~  133 (357)
T TIGR03158        61 EFVDVFKPERDVNLLHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPI--GTSTPIILLTNPDIFV-----YLTRFAYI  133 (357)
T ss_pred             HHHHhcCCCCCceEEEecCCchHHHHHhhhhhcccCccchhhhhHHHHH--hcCCCCEEEecHHHHH-----HHHhhhcc
Confidence              1  1 11236667777753221  000             00 0011  1346789999999974     222211  


Q ss_pred             -------HhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEe
Q psy7952         188 -------VRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFK  260 (444)
Q Consensus       188 -------~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~  260 (444)
                             ..+.++++||+||+|.+..++......+.....+........+++++|||+++...+.+.....+..++....
T Consensus       134 ~~~~~~~~~~~~~~~iV~DE~H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~~~v~  213 (357)
T TIGR03158       134 DRGDIAAGFYTKFSTVIFDEFHLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPALILRLQNAKQAGVKIAPID  213 (357)
T ss_pred             CcccchhhhhcCCCEEEEecccccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHHHHHHHHhccccCceeeeec
Confidence                   1246899999999999876543222222222233333333478999999999887777665432333332222


Q ss_pred             cC-----------CC------C---CCceEEEEEccc-chhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHH
Q psy7952         261 TS-----------TF------R---SNLFYDVIFDDL-LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADA  319 (444)
Q Consensus       261 ~~-----------~~------~---~~~~~~~~~~~~-~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~  319 (444)
                      ..           ..      +   +.+...+..... .......+.+.+.+.+...  .++++||||+|++.++.++..
T Consensus       214 g~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~i~~~~~~~--~~~k~LIf~nt~~~~~~l~~~  291 (357)
T TIGR03158       214 GEKYQFPDNPELEADNKTQSFRPVLPPVELELIPAPDFKEEELSELAEEVIERFRQL--PGERGAIILDSLDEVNRLSDL  291 (357)
T ss_pred             CcccccCCChhhhccccccccceeccceEEEEEeCCchhHHHHHHHHHHHHHHHhcc--CCCeEEEEECCHHHHHHHHHH
Confidence            21           00      1   233333333111 1111222223333333222  467999999999999999999


Q ss_pred             HHhh------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCC
Q psy7952         320 LRRK------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAG  382 (444)
Q Consensus       320 L~~~------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~  382 (444)
                      |+..            +++.+|..      .++..+||||+++++|+|+|.+ +|| ++ |.+...|+||+||+|
T Consensus       292 L~~~~~~~~~~~l~g~~~~~~R~~------~~~~~iLVaTdv~~rGiDi~~~-~vi-~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       292 LQQQGLGDDIGRITGFAPKKDRER------AMQFDILLGTSTVDVGVDFKRD-WLI-FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             HhhhCCCceEEeeecCCCHHHHHH------hccCCEEEEecHHhcccCCCCc-eEE-EC-CCCHHHHhhhcccCC
Confidence            9863            44555543      3478999999999999999986 555 45 889999999999997

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.

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=100.00  E-value=1.1e-31  Score=266.87  Aligned_cols=320  Identities=18%  Similarity=0.145  Sum_probs=216.6

Q ss_pred             HHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhh
Q psy7952          37 TAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILS  116 (444)
Q Consensus        37 ~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~  116 (444)
                      .++.++.+|..+  +++|..++..++.| +  +..+.||+|||++        +.+|+    +......+.++|++||++
T Consensus        93 rEa~~R~lg~~p--~~VQ~~~~~~ll~G-~--Iae~~TGeGKTla--------~~lp~----~~~al~G~~v~VvTptre  155 (656)
T PRK12898         93 REASGRVLGQRH--FDVQLMGGLALLSG-R--LAEMQTGEGKTLT--------ATLPA----GTAALAGLPVHVITVNDY  155 (656)
T ss_pred             HHHHHHHhCCCC--ChHHHHHHHHHhCC-C--eeeeeCCCCcHHH--------HHHHH----HHHhhcCCeEEEEcCcHH
Confidence            456677778885  56999999999999 5  9999999999999        77777    322223346799999999


Q ss_pred             hhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh-----
Q psy7952         117 SFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR-----  189 (444)
Q Consensus       117 L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~-----  189 (444)
                      |+  .|..+.+..+  .++   +++..+.|+.+...+...        ..++|+|+|...+.   |+++..++..     
T Consensus       156 LA--~qdae~~~~l~~~lG---lsv~~i~gg~~~~~r~~~--------y~~dIvygT~~e~~---FDyLrd~~~~~~~~~  219 (656)
T PRK12898        156 LA--ERDAELMRPLYEALG---LTVGCVVEDQSPDERRAA--------YGADITYCTNKELV---FDYLRDRLALGQRAS  219 (656)
T ss_pred             HH--HHHHHHHHHHHhhcC---CEEEEEeCCCCHHHHHHH--------cCCCEEEECCCchh---hhhcccccccccccc
Confidence            99  4446666665  556   999999998765433322        37899999998886   3444433221     


Q ss_pred             --------------------hCCccEEEEecccccc-ccC-----------CC-cHHHHHHHHHHHHh------------
Q psy7952         190 --------------------YNKLAYIVVDEAHCVS-EWG-----------HD-FRPTYRRLGELRQF------------  224 (444)
Q Consensus       190 --------------------~~~~~~iViDE~H~~~-~~~-----------~~-~~~~~~~l~~~~~~------------  224 (444)
                                          ...+.+.||||+|.++ |..           .. ....|..+..+.+.            
T Consensus       220 ~~~~~~~~l~~~~~~~~~~v~r~~~~aIvDEvDSiLiDeartpliis~~~~~~~~~~~y~~~~~~~~~l~~~~~y~~d~~  299 (656)
T PRK12898        220 DARLALESLHGRSSRSTQLLLRGLHFAIVDEADSVLIDEARTPLIISAPAKEADEAEVYRQALELAAQLKEGEDYTIDAA  299 (656)
T ss_pred             chhhhhhhhccccCchhhhcccccceeEeecccceeeccCCCceEEECCCCCCchhHHHHHHHHHHHhcCCCCceEEECC
Confidence                                2457999999999773 311           00 00011110000000            


Q ss_pred             --------------------------------------------------------------------------------
Q psy7952         225 --------------------------------------------------------------------------------  224 (444)
Q Consensus       225 --------------------------------------------------------------------------------  224 (444)
                                                                                                      
T Consensus       300 ~~~v~lt~~g~~~~e~~~~~l~~~~~~~~~~~~~i~~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~w~~GLhQ  379 (656)
T PRK12898        300 EKRIELTEAGRARIAELAESLPPAWRGAVRREELVRQALSALHLFRRDEHYIVRDGKVVIVDEFTGRVMPDRSWEDGLHQ  379 (656)
T ss_pred             CCeEEEcHHHHHHHHHHhCcchhhcccchHHHHHHHHHHHHHHHHhcCCceEEECCeEEEEECCCCeECCCCCcChHHHH
Confidence                                                                                            


Q ss_pred             -------------------------hCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceE--E-EEEcc
Q psy7952         225 -------------------------TGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFY--D-VIFDD  276 (444)
Q Consensus       225 -------------------------~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~--~-~~~~~  276 (444)
                                               |....++.+||||.... .+.+.+..++. ++.+   +..+|....  . .....
T Consensus       380 aieaKE~v~i~~e~~t~a~It~q~~Fr~Y~kl~GmTGTa~~~-~~El~~~y~l~-vv~I---Pt~kp~~r~~~~~~v~~t  454 (656)
T PRK12898        380 MIEAKEGCELTDPRETLARITYQRFFRRYLRLAGMTGTAREV-AGELWSVYGLP-VVRI---PTNRPSQRRHLPDEVFLT  454 (656)
T ss_pred             HHHHhcCCCCCcCceeeeeehHHHHHHhhHHHhcccCcChHH-HHHHHHHHCCC-eEEe---CCCCCccceecCCEEEeC
Confidence                                     00011247788887753 45556655543 2222   222333211  1 12221


Q ss_pred             cchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh--------cCHHHHHHHHHHHhcCCccEEEEcC
Q psy7952         277 LLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK--------VNKHERSRVQESFMRGEINVITATI  348 (444)
Q Consensus       277 ~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~--------~~~~~r~~~~~~f~~g~~~vLvaT~  348 (444)
                       ...+...+.+.+...    ...+.++||||+|++.++.++..|.+.        -....|+..+..++.+...|+|||+
T Consensus       455 -~~~K~~aL~~~i~~~----~~~~~pvLIft~t~~~se~L~~~L~~~gi~~~~Lhg~~~~rE~~ii~~ag~~g~VlVATd  529 (656)
T PRK12898        455 -AAAKWAAVAARVREL----HAQGRPVLVGTRSVAASERLSALLREAGLPHQVLNAKQDAEEAAIVARAGQRGRITVATN  529 (656)
T ss_pred             -HHHHHHHHHHHHHHH----HhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEeeCCcHHHHHHHHHHcCCCCcEEEEcc
Confidence             234444555554442    224578999999999999999999877        2345666667777777778999999


Q ss_pred             ccccccccC---Ccc-----EEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         349 SFGMGIDRQ---NVR-----FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       349 ~~~~Gidi~---~~~-----~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                      ++++|+||+   ++.     +||+++.|.|.+.|.||+||+||.|.+|.++.+++.+|.
T Consensus       530 mAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRTGRqG~~G~s~~~is~eD~  588 (656)
T PRK12898        530 MAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRCGRQGDPGSYEAILSLEDD  588 (656)
T ss_pred             chhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccccCCCCCeEEEEEechhHH
Confidence            999999999   666     999999999999999999999999999999999997653

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

Probab=100.00  E-value=1.2e-31  Score=252.16  Aligned_cols=328  Identities=18%  Similarity=0.229  Sum_probs=229.1

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHH-ccCCcEEEEccCCCcccccccccccceEEeCCCcccccc-CCccceeEE
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHIL-LRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN-GNVRSRNGW  110 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~-~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~-~~~~~~vli  110 (444)
                      ++.+.+.++. .|++.+. |.|.-++..-+ .| +|.+++++|+||||+++.+        .. +..+.. ++.-   ||
T Consensus       202 pe~fk~~lk~-~G~~eLl-PVQ~laVe~GLLeG-~nllVVSaTasGKTLIgEl--------AG-i~~~l~~g~Km---lf  266 (830)
T COG1202         202 PEKFKRMLKR-EGIEELL-PVQVLAVEAGLLEG-ENLLVVSATASGKTLIGEL--------AG-IPRLLSGGKKM---LF  266 (830)
T ss_pred             cHHHHHHHHh-cCcceec-chhhhhhhhccccC-CceEEEeccCCCcchHHHh--------hC-cHHHHhCCCeE---EE
Confidence            4445555555 3899866 79999998655 56 9999999999999999544        33 222444 4455   99


Q ss_pred             EcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH
Q psy7952         111 ISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV  188 (444)
Q Consensus       111 l~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~  188 (444)
                      ++|..+|+     +|..+.|  +...-.+++..-.|-........-  ..-....++||+|+|+|-+     +++++.-.
T Consensus       267 LvPLVALA-----NQKy~dF~~rYs~LglkvairVG~srIk~~~~p--v~~~t~~dADIIVGTYEGi-----D~lLRtg~  334 (830)
T COG1202         267 LVPLVALA-----NQKYEDFKERYSKLGLKVAIRVGMSRIKTREEP--VVVDTSPDADIIVGTYEGI-----DYLLRTGK  334 (830)
T ss_pred             EehhHHhh-----cchHHHHHHHhhcccceEEEEechhhhcccCCc--cccCCCCCCcEEEeechhH-----HHHHHcCC
Confidence            99999999     4555555  222222555544443322211100  0011246789999999986     77777778


Q ss_pred             hhCCccEEEEeccccccc--cCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCC
Q psy7952         189 RYNKLAYIVVDEAHCVSE--WGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRS  266 (444)
Q Consensus       189 ~~~~~~~iViDE~H~~~~--~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  266 (444)
                      .+.+++.|||||+|.+.+  .|+-..   ..|.++...++ .+|+|++|||..++.  .+...++..    .+.-.....
T Consensus       335 ~lgdiGtVVIDEiHtL~deERG~RLd---GLI~RLr~l~~-~AQ~i~LSATVgNp~--elA~~l~a~----lV~y~~RPV  404 (830)
T COG1202         335 DLGDIGTVVIDEIHTLEDEERGPRLD---GLIGRLRYLFP-GAQFIYLSATVGNPE--ELAKKLGAK----LVLYDERPV  404 (830)
T ss_pred             cccccceEEeeeeeeccchhcccchh---hHHHHHHHhCC-CCeEEEEEeecCChH--HHHHHhCCe----eEeecCCCC
Confidence            889999999999999966  343322   22334444455 499999999997754  446666543    122222234


Q ss_pred             CceEEEEEcccchhhHHHHHHHHHHHhccCCC--CCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHH
Q psy7952         267 NLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNK--ANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQE  334 (444)
Q Consensus       267 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~--~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~  334 (444)
                      ++.....+......++..+..+++.-.....+  -.+++|||++|+..|..+++.|..+          ++..+|..+..
T Consensus       405 plErHlvf~~~e~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~  484 (830)
T COG1202         405 PLERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVER  484 (830)
T ss_pred             ChhHeeeeecCchHHHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHH
Confidence            55666666666666766666666654433332  3579999999999999999999966          88999999999


Q ss_pred             HHhcCCccEEEEcCccccccccCCccEEE---EeC-CCCCHHHHHHHhccCCCCCC--ceeEEEEeccc
Q psy7952         335 SFMRGEINVITATISFGMGIDRQNVRFVV---HWG-MPSSIPAYYQESGRAGRDGL--QSYCRIYHSEH  397 (444)
Q Consensus       335 ~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi---~~~-~p~s~~~~~Qr~GR~~R~g~--~g~~~~~~~~~  397 (444)
                      .|.++++.++|+|-+++.|+|+|.-.+|+   -++ ---|+.+|.||.|||||.+.  .|.+++++.+.
T Consensus       485 ~F~~q~l~~VVTTAAL~AGVDFPASQVIFEsLaMG~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg  553 (830)
T COG1202         485 AFAAQELAAVVTTAALAAGVDFPASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPG  553 (830)
T ss_pred             HHhcCCcceEeehhhhhcCCCCchHHHHHHHHHcccccCCHHHHHHHhcccCCCCcccCceEEEEecCC
Confidence            99999999999999999999999655544   122 23489999999999999864  58888877643

>TIGR00603 rad25 DNA repair helicase rad25

Probab=100.00  E-value=1.3e-31  Score=269.32  Aligned_cols=309  Identities=15%  Similarity=0.107  Sum_probs=193.8

Q ss_pred             hHHHHHHHHHHccC--CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhh
Q psy7952          52 ELQKKAIRHILLRT--HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~--~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      +||.+++..+..+.  ++.++++|||+|||++++.++.          .+  .   .++||+||+..|+  .||.+++..
T Consensus       258 pYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~----------~l--~---k~tLILvps~~Lv--~QW~~ef~~  320 (732)
T TIGR00603       258 PYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAAC----------TV--K---KSCLVLCTSAVSV--EQWKQQFKM  320 (732)
T ss_pred             HHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHH----------Hh--C---CCEEEEeCcHHHH--HHHHHHHHH
Confidence            79999999988542  4789999999999999543211          11  2   3459999999999  444555554


Q ss_pred             hcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHH--HHHH--HHHhhCCccEEEEecccccc
Q psy7952         130 VTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFH--YLLQ--HLVRYNKLAYIVVDEAHCVS  205 (444)
Q Consensus       130 l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~--~~~~--~~~~~~~~~~iViDE~H~~~  205 (444)
                      +. ..+...+..++|+....           ..+..+|+|+|++++.+..-.  ....  .......+++||+||||++.
T Consensus       321 ~~-~l~~~~I~~~tg~~k~~-----------~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lp  388 (732)
T TIGR00603       321 WS-TIDDSQICRFTSDAKER-----------FHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVP  388 (732)
T ss_pred             hc-CCCCceEEEEecCcccc-----------cccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEcccccc
Confidence            41 21224555666643221           023478999999987532100  0011  11222478999999999974


Q ss_pred             ccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHH--HHHHHhcCCCCeEEEec----CCCCCCceEEEEEcccch
Q psy7952         206 EWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQ--DIISVLKFNKPYKVFKT----STFRSNLFYDVIFDDLLK  279 (444)
Q Consensus       206 ~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~--~~~~~l~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~  279 (444)
                      ..      .+..+   ...+.. ...++|||||.+....  .+...+| +.-+.....    .....+..+.....+...
T Consensus       389 A~------~fr~i---l~~l~a-~~RLGLTATP~ReD~~~~~L~~LiG-P~vye~~~~eLi~~G~LA~~~~~ev~v~~t~  457 (732)
T TIGR00603       389 AA------MFRRV---LTIVQA-HCKLGLTATLVREDDKITDLNFLIG-PKLYEANWMELQKKGFIANVQCAEVWCPMTP  457 (732)
T ss_pred             HH------HHHHH---HHhcCc-CcEEEEeecCcccCCchhhhhhhcC-CeeeecCHHHHHhCCccccceEEEEEecCCH
Confidence            32      22222   222222 5689999999764322  2222222 111111000    111112222111111111


Q ss_pred             h------------------hHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----cCHHHHHHHHHHH
Q psy7952         280 D------------------SYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----VNKHERSRVQESF  336 (444)
Q Consensus       280 ~------------------~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----~~~~~r~~~~~~f  336 (444)
                      .                  ....+...+..++......+.++||||.+...++.++..|...     ++..+|..+++.|
T Consensus       458 ~~~~~yl~~~~~~k~~l~~~np~K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L~~~~I~G~ts~~ER~~il~~F  537 (732)
T TIGR00603       458 EFYREYLRENSRKRMLLYVMNPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQQERMQILQNF  537 (732)
T ss_pred             HHHHHHHHhcchhhhHHhhhChHHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHcCCceEECCCCHHHHHHHHHHH
Confidence            0                  0011122333333332236789999999999999999988544     8899999999999


Q ss_pred             hcC-CccEEEEcCccccccccCCccEEEEeCCC-CCHHHHHHHhccCCCCCCcee-------EEEEecccchh
Q psy7952         337 MRG-EINVITATISFGMGIDRQNVRFVVHWGMP-SSIPAYYQESGRAGRDGLQSY-------CRIYHSEHSKK  400 (444)
Q Consensus       337 ~~g-~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p-~s~~~~~Qr~GR~~R~g~~g~-------~~~~~~~~~~~  400 (444)
                      +.| .+++||+|+++.+|+|+|++++||+++.| .|...|+||+||++|.+.+|.       ++.+++++..+
T Consensus       538 r~~~~i~vLv~SkVgdeGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~E  610 (732)
T TIGR00603       538 QHNPKVNTIFLSKVGDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQE  610 (732)
T ss_pred             HhCCCccEEEEecccccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCchH
Confidence            875 78999999999999999999999999987 599999999999999876544       37777766554

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).

>PRK13766 Hef nuclease; Provisional

Probab=100.00  E-value=6e-31  Score=277.88  Aligned_cols=313  Identities=16%  Similarity=0.239  Sum_probs=205.5

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      .+||.++...++.+  ++++++|||+|||++|++.        + ...+  .....++||++|+++|+     .|+.+.+
T Consensus        17 r~yQ~~~~~~~l~~--n~lv~~ptG~GKT~~a~~~--------i-~~~l--~~~~~~vLvl~Pt~~L~-----~Q~~~~~   78 (773)
T PRK13766         17 RLYQQLLAATALKK--NTLVVLPTGLGKTAIALLV--------I-AERL--HKKGGKVLILAPTKPLV-----EQHAEFF   78 (773)
T ss_pred             cHHHHHHHHHHhcC--CeEEEcCCCccHHHHHHHH--------H-HHHH--HhCCCeEEEEeCcHHHH-----HHHHHHH
Confidence            47999999998886  8999999999999984332        2 1112  12335779999999999     5555555


Q ss_pred             --cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccC
Q psy7952         131 --TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWG  208 (444)
Q Consensus       131 --~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~  208 (444)
                        ..+....++..++|+.....+...+       .+++|+|+||+.+.    ..++.......++++||+||||++.+..
T Consensus        79 ~~~~~~~~~~v~~~~g~~~~~~r~~~~-------~~~~iiv~T~~~l~----~~l~~~~~~~~~~~liVvDEaH~~~~~~  147 (773)
T PRK13766         79 RKFLNIPEEKIVVFTGEVSPEKRAELW-------EKAKVIVATPQVIE----NDLIAGRISLEDVSLLIFDEAHRAVGNY  147 (773)
T ss_pred             HHHhCCCCceEEEEeCCCCHHHHHHHH-------hCCCEEEECHHHHH----HHHHcCCCChhhCcEEEEECCccccccc
Confidence              2332224778888887766544433       46799999999875    3334445556789999999999986422


Q ss_pred             CCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHH--HHHHHhcCCCCeEEEecC-------CCCCCceEEE-------
Q psy7952         209 HDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQ--DIISVLKFNKPYKVFKTS-------TFRSNLFYDV-------  272 (444)
Q Consensus       209 ~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~--~~~~~l~~~~~~~~~~~~-------~~~~~~~~~~-------  272 (444)
                      . +    ..+...+......+++++|||||......  .+.+.++... +.+....       ...+.+.+..       
T Consensus       148 ~-~----~~i~~~~~~~~~~~~il~lTaTP~~~~~~i~~~~~~L~i~~-v~~~~~~~~~v~~~~~~~~v~~~~v~l~~~~  221 (773)
T PRK13766        148 A-Y----VYIAERYHEDAKNPLVLGLTASPGSDEEKIKEVCENLGIEH-VEVRTEDDPDVKPYVHKVKIEWVRVELPEEL  221 (773)
T ss_pred             c-H----HHHHHHHHhcCCCCEEEEEEcCCCCCHHHHHHHHHhCCceE-EEEcCCCChhHHhhhccceeEEEEeCCcHHH
Confidence            1 1    22333332333447799999998654211  1122221110 0000000       0000000000       


Q ss_pred             -----------------------EE--c----------------------------------------------------
Q psy7952         273 -----------------------IF--D----------------------------------------------------  275 (444)
Q Consensus       273 -----------------------~~--~----------------------------------------------------  275 (444)
                                             ..  .                                                    
T Consensus       222 ~~i~~~l~~~~~~~l~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~  301 (773)
T PRK13766        222 KEIRDLLNEALKDRLKKLKELGVIVSISPDVSKKELLGLQKKLQQEIANDDSEGYEAISILAEAMKLRHAVELLETQGVE  301 (773)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCcccCCCCcCHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHHHHHHHHhCHH
Confidence                                   00  0                                                    


Q ss_pred             -----------------------------------------ccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHH
Q psy7952         276 -----------------------------------------DLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTT  314 (444)
Q Consensus       276 -----------------------------------------~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~  314 (444)
                                                               .....+...+.+.+.+....  ..+.++||||+++++|+
T Consensus       302 ~~~~y~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~pK~~~L~~il~~~~~~--~~~~kvlIF~~~~~t~~  379 (773)
T PRK13766        302 ALRRYLERLREEARSSGGSKASKRLVEDPRFRKAVRKAKELDIEHPKLEKLREIVKEQLGK--NPDSRIIVFTQYRDTAE  379 (773)
T ss_pred             HHHHHHHHHHhhccccCCcHHHHHHHhCHHHHHHHHHHHhcccCChHHHHHHHHHHHHHhc--CCCCeEEEEeCcHHHHH
Confidence                                                     00001111222222222221  25789999999999999


Q ss_pred             HHHHHHHhh------------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHH
Q psy7952         315 DLADALRRK------------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ  376 (444)
Q Consensus       315 ~l~~~L~~~------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Q  376 (444)
                      .+++.|...                  +++.+|..++++|++|+.++||||+++++|+|+|++++||+||+|++...|+|
T Consensus       380 ~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~~vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQ  459 (773)
T PRK13766        380 KIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQ  459 (773)
T ss_pred             HHHHHHHhCCCceEEEEccccccccCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHH
Confidence            999999553                  56688999999999999999999999999999999999999999999999999


Q ss_pred             HhccCCCCCCceeEEEEecccchhh
Q psy7952         377 ESGRAGRDGLQSYCRIYHSEHSKKS  401 (444)
Q Consensus       377 r~GR~~R~g~~g~~~~~~~~~~~~~  401 (444)
                      |+||+||.|. |.++.++..+..+.
T Consensus       460 R~GR~gR~~~-~~v~~l~~~~t~ee  483 (773)
T PRK13766        460 RKGRTGRQEE-GRVVVLIAKGTRDE  483 (773)
T ss_pred             HhcccCcCCC-CEEEEEEeCCChHH
Confidence            9999999865 67777776655443

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

Probab=99.98  E-value=8.5e-31  Score=268.17  Aligned_cols=314  Identities=19%  Similarity=0.221  Sum_probs=248.8

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHcc-----CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccce
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLR-----THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSR  107 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~-----~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~  107 (444)
                      +.+..+.+...|+|+.  |+-|..|++.+.+.     ..|-+||+.-|.|||.+|+=|     ++.+    +..+   +.
T Consensus       580 d~~~q~~F~~~FPyeE--T~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRA-----AFkA----V~~G---KQ  645 (1139)
T COG1197         580 DTEWQEEFEASFPYEE--TPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRA-----AFKA----VMDG---KQ  645 (1139)
T ss_pred             ChHHHHHHHhcCCCcC--CHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHH-----HHHH----hcCC---Ce
Confidence            5566788999999997  78999999999862     267899999999999995432     2223    4444   45


Q ss_pred             eEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH
Q psy7952         108 NGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ  185 (444)
Q Consensus       108 vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~  185 (444)
                      |.++|||.-|+     +|+++.+  ++.+-++++..+..-.+..+....++.+.  .+..||+|||         |.+++
T Consensus       646 VAvLVPTTlLA-----~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la--~G~vDIvIGT---------HrLL~  709 (1139)
T COG1197         646 VAVLVPTTLLA-----QQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLA--EGKVDIVIGT---------HRLLS  709 (1139)
T ss_pred             EEEEcccHHhH-----HHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHh--cCCccEEEec---------hHhhC
Confidence            69999999999     8999988  55555599999999999999999999887  5899999999         88888


Q ss_pred             HHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCC
Q psy7952         186 HLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFR  265 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~  265 (444)
                      ....+++++++||||=|++   |..-.   ..|+    .+..++-++-|||||.|...++  ...|+.+--.+..++..|
T Consensus       710 kdv~FkdLGLlIIDEEqRF---GVk~K---EkLK----~Lr~~VDvLTLSATPIPRTL~M--sm~GiRdlSvI~TPP~~R  777 (1139)
T COG1197         710 KDVKFKDLGLLIIDEEQRF---GVKHK---EKLK----ELRANVDVLTLSATPIPRTLNM--SLSGIRDLSVIATPPEDR  777 (1139)
T ss_pred             CCcEEecCCeEEEechhhc---CccHH---HHHH----HHhccCcEEEeeCCCCcchHHH--HHhcchhhhhccCCCCCC
Confidence            8899999999999999994   42122   2222    2334588999999999988874  445555554444444555


Q ss_pred             CCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------------cCHHHHHHHH
Q psy7952         266 SNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------VNKHERSRVQ  333 (444)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------------~~~~~r~~~~  333 (444)
                      -++.-.+...+.         ..+++.+.+....++++...+|.++..++++..|+..            |+..+-+.++
T Consensus       778 ~pV~T~V~~~d~---------~~ireAI~REl~RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM  848 (1139)
T COG1197         778 LPVKTFVSEYDD---------LLIREAILRELLRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVM  848 (1139)
T ss_pred             cceEEEEecCCh---------HHHHHHHHHHHhcCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHH
Confidence            554433333221         2333444444447999999999999999999999988            9999999999


Q ss_pred             HHHhcCCccEEEEcCccccccccCCccEEEEeCCC-CCHHHHHHHhccCCCCCCceeEEEEeccc
Q psy7952         334 ESFMRGEINVITATISFGMGIDRQNVRFVVHWGMP-SSIPAYYQESGRAGRDGLQSYCRIYHSEH  397 (444)
Q Consensus       334 ~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p-~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~  397 (444)
                      ..|-+|+.+|||||.+.+.|||||+++++|..+.. ....++.|..||+||....+||+.++.+.
T Consensus       849 ~~F~~g~~dVLv~TTIIEtGIDIPnANTiIIe~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~~  913 (1139)
T COG1197         849 LDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSNKQAYAYFLYPPQ  913 (1139)
T ss_pred             HHHHcCCCCEEEEeeeeecCcCCCCCceEEEeccccccHHHHHHhccccCCccceEEEEEeecCc
Confidence            99999999999999999999999999998855543 36899999999999999999999999854

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.97  E-value=9e-31  Score=265.68  Aligned_cols=319  Identities=20%  Similarity=0.206  Sum_probs=210.0

Q ss_pred             HHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchh
Q psy7952          36 LTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPIL  115 (444)
Q Consensus        36 ~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~  115 (444)
                      +.++.++.+|..  |+++|..+...+++| +  +..+.||+|||++        +.+|+++. ...+   +.++|++||+
T Consensus        67 vrea~~R~~g~~--p~~vQl~~~~~l~~G-~--Iaem~TGeGKTL~--------a~lp~~l~-al~G---~~v~VvTpt~  129 (790)
T PRK09200         67 VREAAKRVLGMR--PYDVQLIGALVLHEG-N--IAEMQTGEGKTLT--------ATMPLYLN-ALEG---KGVHLITVND  129 (790)
T ss_pred             HHHHHHHHhCCC--CchHHHHhHHHHcCC-c--eeeecCCCcchHH--------HHHHHHHH-HHcC---CCeEEEeCCH
Confidence            346677777886  467999999988877 4  9999999999999        66666212 2233   3459999999


Q ss_pred             hhhcccCccchHhhh--cCCCCceeEEEEeCCCC-hhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH-----
Q psy7952         116 SSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQT-KTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL-----  187 (444)
Q Consensus       116 ~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~-----  187 (444)
                      .||  .|..+.+..+  ..+   +.+..+.|+.+ ...+...        ..++|+++||..+.   |+++..+.     
T Consensus       130 ~LA--~qd~e~~~~l~~~lG---l~v~~i~g~~~~~~~r~~~--------y~~dIvygT~~~l~---fDyLrd~~~~~~~  193 (790)
T PRK09200        130 YLA--KRDAEEMGQVYEFLG---LTVGLNFSDIDDASEKKAI--------YEADIIYTTNSELG---FDYLRDNLADSKE  193 (790)
T ss_pred             HHH--HHHHHHHHHHHhhcC---CeEEEEeCCCCcHHHHHHh--------cCCCEEEECCcccc---chhHHhccccchh
Confidence            999  3334444555  556   99999999988 4444332        25899999999985   34333332     


Q ss_pred             -HhhCCccEEEEecccccc-ccC--------C--CcHHHHHHHHHHHHhh------------------------------
Q psy7952         188 -VRYNKLAYIVVDEAHCVS-EWG--------H--DFRPTYRRLGELRQFT------------------------------  225 (444)
Q Consensus       188 -~~~~~~~~iViDE~H~~~-~~~--------~--~~~~~~~~l~~~~~~~------------------------------  225 (444)
                       .....+.++|+||+|.++ +..        .  .-...|..+..+.+.+                              
T Consensus       194 ~~~~r~~~~~IvDEaDsiLiDea~tpliisg~~~~~~~~y~~~~~~~~~l~~~~dy~~d~~~~~~~lt~~g~~~~e~~~~  273 (790)
T PRK09200        194 DKVQRPLNYAIIDEIDSILLDEAQTPLIISGKPRVQSNLYHIAAKFVKTLEEDVDYEFDEEKKEVWLTDQGIEKAESYFG  273 (790)
T ss_pred             hhcccccceEEEeccccceeccCCCceeeeCCCccccHHHHHHHHHHHhcccCCCeEEecCCCeEEecHhHHHHHHHhcC
Confidence             234678999999999883 311        0  0000000000000000                              


Q ss_pred             --------------------------------------------------------------------------------
Q psy7952         226 --------------------------------------------------------------------------------  225 (444)
Q Consensus       226 --------------------------------------------------------------------------------  225 (444)
                                                                                                      
T Consensus       274 i~~l~~~~~~~~~~~i~~Al~A~~~~~~d~dYiV~~~~v~ivD~~TGr~~~gr~~s~GlhQaieaKe~v~i~~e~~t~a~  353 (790)
T PRK09200        274 IDNLYSLEHQVLYRHIILALRAHVLFKRDVDYIVYDGEIVLVDRFTGRVLPGRKLQDGLHQAIEAKEGVEITEENRTMAS  353 (790)
T ss_pred             CccccChhhhHHHHHHHHHHHHHHHhhcCCcEEEECCEEEEEECCCCcCCCCCccChHHHHHHHHhcCCCcCCCceehhh
Confidence                                                                                            


Q ss_pred             -------CCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEE---EEcccchhhHHHHHHHHHHHhcc
Q psy7952         226 -------GNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDV---IFDDLLKDSYAHVKEFIEKCLGK  295 (444)
Q Consensus       226 -------~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~l~~~l~~  295 (444)
                             ....++.+||+|... ....+.+..++    .+..-+..+|......   ... ....+...+...+...   
T Consensus       354 It~q~~fr~Y~kl~GmTGTa~t-~~~e~~~~Y~l----~v~~IPt~kp~~r~d~~~~i~~-~~~~K~~al~~~i~~~---  424 (790)
T PRK09200        354 ITIQNLFRMFPKLSGMTGTAKT-EEKEFFEVYNM----EVVQIPTNRPIIRIDYPDKVFV-TLDEKYKAVIEEVKER---  424 (790)
T ss_pred             hhHHHHHHHhHHHhccCCCChH-HHHHHHHHhCC----cEEECCCCCCcccccCCCeEEc-CHHHHHHHHHHHHHHH---
Confidence                   000124666777533 22333333332    2222334455443222   111 1233444444444432   


Q ss_pred             CCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCcccccccc---CCcc--
Q psy7952         296 DNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDR---QNVR--  360 (444)
Q Consensus       296 ~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi---~~~~--  360 (444)
                       ...+.++||||+|++.++.++..|.+.          +...++..+...++.|  +|+|||++++||+|+   |++.  
T Consensus       425 -~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~  501 (790)
T PRK09200        425 -HETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNMAGRGTDIKLGEGVHEL  501 (790)
T ss_pred             -HhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCccHHHHHHHHHcCCCC--eEEEEccchhcCcCCCcccccccc
Confidence             225889999999999999999999887          4455555555555444  899999999999999   6898  


Q ss_pred             ---EEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         361 ---FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       361 ---~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                         +||+++.|.|.+.|.||+||+||.|.+|.++.|++.+|.
T Consensus       502 GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~is~eD~  543 (790)
T PRK09200        502 GGLAVIGTERMESRRVDLQLRGRSGRQGDPGSSQFFISLEDD  543 (790)
T ss_pred             cCcEEEeccCCCCHHHHHHhhccccCCCCCeeEEEEEcchHH
Confidence               999999999999999999999999999999999986554

>KOG0951|consensus

Probab=99.97  E-value=4.2e-30  Score=259.55  Aligned_cols=368  Identities=17%  Similarity=0.221  Sum_probs=250.4

Q ss_pred             hCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCcc---ceeEEEcchhhhhcc
Q psy7952          44 FGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVR---SRNGWISPILSSFYL  120 (444)
Q Consensus        44 ~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~---~~vlil~P~~~L~~~  120 (444)
                      +|...|. .+|.......+.+..+++++||||+|||.+|++.|+.-.--..    -..++..   -++++++|.++|+  
T Consensus       305 ~g~~sLN-rIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~----r~dgs~nl~~fKIVYIAPmKaLv--  377 (1674)
T KOG0951|consen  305 FGKQSLN-RIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHL----REDGSVNLAPFKIVYIAPMKALV--  377 (1674)
T ss_pred             ccchhhh-HHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhccc----ccccceecccceEEEEeeHHHHH--
Confidence            3666655 7999999999999899999999999999997776543111111    0011111   3789999999999  


Q ss_pred             cCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhh---CCccE
Q psy7952         121 RFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRY---NKLAY  195 (444)
Q Consensus       121 ~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~---~~~~~  195 (444)
                         ++++..+  ++.+-++.|...+|+.......         .....|+|+|||+-     +-+.+...+.   .-+++
T Consensus       378 ---qE~VgsfSkRla~~GI~V~ElTgD~~l~~~q---------ieeTqVIV~TPEK~-----DiITRk~gdraY~qlvrL  440 (1674)
T KOG0951|consen  378 ---QEMVGSFSKRLAPLGITVLELTGDSQLGKEQ---------IEETQVIVTTPEKW-----DIITRKSGDRAYEQLVRL  440 (1674)
T ss_pred             ---HHHHHHHHhhccccCcEEEEecccccchhhh---------hhcceeEEeccchh-----hhhhcccCchhHHHHHHH
Confidence               8888877  3334449999999987643221         24689999999993     3333332222   23689


Q ss_pred             EEEeccccccc-cCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCC-CceEEEE
Q psy7952         196 IVVDEAHCVSE-WGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRS-NLFYDVI  273 (444)
Q Consensus       196 iViDE~H~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~-~~~~~~~  273 (444)
                      +||||+|.+.+ .|.-......+..+....-...++++++|||+|+  +.++..+++...+-.....+..|| ++.++++
T Consensus       441 lIIDEIHLLhDdRGpvLESIVaRt~r~ses~~e~~RlVGLSATLPN--y~DV~~Fl~v~~~glf~fd~syRpvPL~qq~I  518 (1674)
T KOG0951|consen  441 LIIDEIHLLHDDRGPVLESIVARTFRRSESTEEGSRLVGLSATLPN--YEDVASFLRVDPEGLFYFDSSYRPVPLKQQYI  518 (1674)
T ss_pred             HhhhhhhhcccccchHHHHHHHHHHHHhhhcccCceeeeecccCCc--hhhhHHHhccCcccccccCcccCcCCccceEe
Confidence            99999999855 4543333333333332233446899999999987  567788776655433333333343 3444443


Q ss_pred             Ec--ccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------------------------
Q psy7952         274 FD--DLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------------------------  323 (444)
Q Consensus       274 ~~--~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------------------------  323 (444)
                      -.  ...........+.+-+.+..+. ..+++|||++|++++.+.|..++..                            
T Consensus       519 gi~ek~~~~~~qamNe~~yeKVm~~a-gk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~  597 (1674)
T KOG0951|consen  519 GITEKKPLKRFQAMNEACYEKVLEHA-GKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQA  597 (1674)
T ss_pred             ccccCCchHHHHHHHHHHHHHHHHhC-CCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcc
Confidence            22  2222333444444444444433 3489999999999999999999854                            


Q ss_pred             -------------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEE----EeCC------CCCHHHH
Q psy7952         324 -------------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVV----HWGM------PSSIPAY  374 (444)
Q Consensus       324 -------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi----~~~~------p~s~~~~  374 (444)
                                         |+..+|..+++.|+.|.++++++|-.+++|+|+|.-.++|    .|++      +.|+.+.
T Consensus       598 kn~dLkdLLpygfaIHhAGl~R~dR~~~EdLf~~g~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv  677 (1674)
T KOG0951|consen  598 KNPDLKDLLPYGFAIHHAGLNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDV  677 (1674)
T ss_pred             cChhHHHHhhccceeeccCCCcchHHHHHHHHhcCceeEEEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHH
Confidence                               8899999999999999999999999999999999655555    3332      3489999


Q ss_pred             HHHhccCCCCCCc--eeEEEEecccchhhHHHHHhhccchhHH-----------HHHHHHhhHHHHHHHhhhceeee
Q psy7952         375 YQESGRAGRDGLQ--SYCRIYHSEHSKKSLEYVIKTDTSTKRE-----------QLELKFKNYLSMLEYCEQGYFLV  438 (444)
Q Consensus       375 ~Qr~GR~~R~g~~--g~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~  438 (444)
                      +||.||+||.+..  |..+++....+......+....++.+..           ++-..+++.+++++|...+|-+.
T Consensus       678 ~qmlgragrp~~D~~gegiiit~~se~qyyls~mn~qLpiesq~~~rl~d~lnaeiv~Gv~~~~d~~~wl~yTylyv  754 (1674)
T KOG0951|consen  678 MQMLGRAGRPQYDTCGEGIIITDHSELQYYLSLMNQQLPIESQFVSRLADCLNAEIVLGVRSARDAVDWLGYTYLYV  754 (1674)
T ss_pred             HHHHhhcCCCccCcCCceeeccCchHhhhhHHhhhhcCCChHHHHHHhhhhhhhhhhcchhhHHHHHhhhcceeeEE
Confidence            9999999998654  5556666666666666666666555433           33333566888888888777654

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.97  E-value=2.4e-30  Score=258.50  Aligned_cols=321  Identities=17%  Similarity=0.156  Sum_probs=218.9

Q ss_pred             HHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchh
Q psy7952          36 LTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPIL  115 (444)
Q Consensus        36 ~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~  115 (444)
                      +.++.++.+|..+  ++.|..+...+..| +  +..++||+|||++        +.+|+++..+. +.   .|.|++||.
T Consensus        45 vrEa~~R~lg~~p--~~vQlig~~~l~~G-~--Iaem~TGeGKTLv--------a~lpa~l~aL~-G~---~V~VvTpt~  107 (745)
T TIGR00963        45 VREASKRVLGMRP--FDVQLIGGIALHKG-K--IAEMKTGEGKTLT--------ATLPAYLNALT-GK---GVHVVTVND  107 (745)
T ss_pred             HHHHHHHHhCCCc--cchHHhhhhhhcCC-c--eeeecCCCccHHH--------HHHHHHHHHHh-CC---CEEEEcCCH
Confidence            4467777789886  45899888888777 3  8999999999999        55565223232 22   469999999


Q ss_pred             hhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH------H
Q psy7952         116 SSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH------L  187 (444)
Q Consensus       116 ~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~------~  187 (444)
                      .||  .|..+.+..+  ..+   +++..+.|+.+...+...+        .++|+|+||..|.   |+.+..+      .
T Consensus       108 ~LA--~qdae~~~~l~~~LG---Lsv~~i~g~~~~~~r~~~y--------~~dIvyGT~~rlg---fDyLrd~~~~~~~~  171 (745)
T TIGR00963       108 YLA--QRDAEWMGQVYRFLG---LSVGLILSGMSPEERREAY--------ACDITYGTNNELG---FDYLRDNMAHSKEE  171 (745)
T ss_pred             HHH--HHHHHHHHHHhccCC---CeEEEEeCCCCHHHHHHhc--------CCCEEEECCCchh---hHHHhcccccchhh
Confidence            999  3334555555  456   9999999998866544433        5799999999984   2444433      2


Q ss_pred             HhhCCccEEEEeccccccc-cC--------C--CcHHHHH----------------------------------------
Q psy7952         188 VRYNKLAYIVVDEAHCVSE-WG--------H--DFRPTYR----------------------------------------  216 (444)
Q Consensus       188 ~~~~~~~~iViDE~H~~~~-~~--------~--~~~~~~~----------------------------------------  216 (444)
                      ..+..++++|+||+|.++- ..        .  .....|.                                        
T Consensus       172 ~~~r~l~~aIIDEaDs~LIDeaRtpLiisg~~~~~~~ly~~a~~i~r~L~~~~dy~~de~~k~v~Lt~~G~~~~e~~~~~  251 (745)
T TIGR00963       172 KVQRPFHFAIIDEVDSILIDEARTPLIISGPAEKSTELYLQANRFAKALEKEVHYEVDEKNRAVLLTEKGIKKAEDLLGV  251 (745)
T ss_pred             hhccccceeEeecHHHHhHHhhhhHHhhcCCCCCchHHHHHHHHHHHhhccCCCeEEecCCCceeECHHHHHHHHHHcCC
Confidence            4567899999999999843 11        0  0000000                                        


Q ss_pred             -------------HHHHHHHh-----------------------------------------------------------
Q psy7952         217 -------------RLGELRQF-----------------------------------------------------------  224 (444)
Q Consensus       217 -------------~l~~~~~~-----------------------------------------------------------  224 (444)
                                   .+...+++                                                           
T Consensus       252 ~~ly~~~~~~~~~~i~~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~ws~GLhQaiEaKE~v~i~~e~~t~a~I  331 (745)
T TIGR00963       252 DNLYDLENSPLIHYINNALKAKELFEKDVDYIVRDGEVVIVDEFTGRIMEGRRWSDGLHQAIEAKEGVEIQNENQTLATI  331 (745)
T ss_pred             ccccChhhhHHHHHHHHHHHHHHHHhcCCcEEEECCEEEEEECCCCcCCCCCccchHHHHHHHHhcCCCcCCCceeeeee
Confidence                         00000000                                                           


Q ss_pred             -----hCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEE---EEcccchhhHHHHHHHHHHHhccC
Q psy7952         225 -----TGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDV---IFDDLLKDSYAHVKEFIEKCLGKD  296 (444)
Q Consensus       225 -----~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~l~~~l~~~  296 (444)
                           |....++.+||+|... ....+.+..++.    +..-+..+|......   .+.. ...++..+.+.+.+.    
T Consensus       332 t~qn~Fr~Y~kl~GmTGTa~t-e~~E~~~iY~l~----vv~IPtnkp~~R~d~~d~i~~t-~~~k~~ai~~~i~~~----  401 (745)
T TIGR00963       332 TYQNFFRLYEKLSGMTGTAKT-EEEEFEKIYNLE----VVVVPTNRPVIRKDLSDLVYKT-EEEKWKAVVDEIKER----  401 (745)
T ss_pred             eHHHHHhhCchhhccCCCcHH-HHHHHHHHhCCC----EEEeCCCCCeeeeeCCCeEEcC-HHHHHHHHHHHHHHH----
Confidence                 0011134677777643 233344433322    222233444433221   1111 233444444444443    


Q ss_pred             CCCCceEEEEecccchHHHHHHHHHhh--------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCC-------ccE
Q psy7952         297 NKANNCGIIYCRTREHTTDLADALRRK--------VNKHERSRVQESFMRGEINVITATISFGMGIDRQN-------VRF  361 (444)
Q Consensus       297 ~~~~~~~iVf~~s~~~~~~l~~~L~~~--------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~-------~~~  361 (444)
                      ...+.++||||+|++.++.++..|.+.        -...+|+..+..|+.+...|+|||++++||+||+.       ..+
T Consensus       402 ~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl~  481 (745)
T TIGR00963       402 HAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAKNHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELGGLY  481 (745)
T ss_pred             HhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCChHHHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcCCcE
Confidence            236889999999999999999999886        34778999999999999999999999999999997       559


Q ss_pred             EEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         362 VVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       362 Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                      ||+++.|.|.+.|.|++||+||.|.+|.+..+++.+|.
T Consensus       482 VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~ls~eD~  519 (745)
T TIGR00963       482 VIGTERHESRRIDNQLRGRSGRQGDPGSSRFFLSLEDN  519 (745)
T ss_pred             EEecCCCCcHHHHHHHhccccCCCCCcceEEEEeccHH
Confidence            99999999999999999999999999999999987654

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.

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

Probab=99.97  E-value=9.1e-30  Score=249.26  Aligned_cols=286  Identities=19%  Similarity=0.169  Sum_probs=184.1

Q ss_pred             CchHHHHHHHHHHcc---CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccch
Q psy7952          50 KCELQKKAIRHILLR---THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDK  126 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~---~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~  126 (444)
                      +.+||++++..+...   .++.++++|||+|||.+|+-        .+    .....   ++|||||+.+|+     .|.
T Consensus        37 lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~--------~~----~~~~~---~~Lvlv~~~~L~-----~Qw   96 (442)
T COG1061          37 LRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAE--------AI----AELKR---STLVLVPTKELL-----DQW   96 (442)
T ss_pred             CcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHH--------HH----HHhcC---CEEEEECcHHHH-----HHH
Confidence            348999999999983   38999999999999988321        11    11111   259999999999     333


Q ss_pred             Hhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccc
Q psy7952         127 TSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVS  205 (444)
Q Consensus       127 ~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~  205 (444)
                      .+.+ ...........+.++....            .+ ..|.|+|.+.+....    .........+++||+||||++.
T Consensus        97 ~~~~~~~~~~~~~~g~~~~~~~~~------------~~-~~i~vat~qtl~~~~----~l~~~~~~~~~liI~DE~Hh~~  159 (442)
T COG1061          97 AEALKKFLLLNDEIGIYGGGEKEL------------EP-AKVTVATVQTLARRQ----LLDEFLGNEFGLIIFDEVHHLP  159 (442)
T ss_pred             HHHHHHhcCCccccceecCceecc------------CC-CcEEEEEhHHHhhhh----hhhhhcccccCEEEEEccccCC
Confidence            3444 2221112334444433221            11 469999999975311    1111222369999999999976


Q ss_pred             ccCCCcHHHHHHHHHHHHhhCCCCc-EEEEeccCCcchHHHHHHHhcCCCCeEEEec------CCCCCCceEEEEEc-cc
Q psy7952         206 EWGHDFRPTYRRLGELRQFTGNSIP-IIALTATAEPSVKQDIISVLKFNKPYKVFKT------STFRSNLFYDVIFD-DL  277 (444)
Q Consensus       206 ~~~~~~~~~~~~l~~~~~~~~~~~~-~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~------~~~~~~~~~~~~~~-~~  277 (444)
                      +..  +    ..+.....   . .. +++|||||................+......      .....+..+..... ..
T Consensus       160 a~~--~----~~~~~~~~---~-~~~~LGLTATp~R~D~~~~~~l~~~~g~~vy~~~~~~li~~g~Lap~~~~~i~~~~t  229 (442)
T COG1061         160 APS--Y----RRILELLS---A-AYPRLGLTATPEREDGGRIGDLFDLIGPIVYEVSLKELIDEGYLAPYKYVEIKVTLT  229 (442)
T ss_pred             cHH--H----HHHHHhhh---c-ccceeeeccCceeecCCchhHHHHhcCCeEeecCHHHHHhCCCccceEEEEEEeccc
Confidence            533  2    22322222   2 33 8999999886543333333322222211111      01112222222221 11


Q ss_pred             chhh--------------------------------HHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh--
Q psy7952         278 LKDS--------------------------------YAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK--  323 (444)
Q Consensus       278 ~~~~--------------------------------~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~--  323 (444)
                      ....                                .+.....+..++.... .+.+++|||.++.++..++..+...  
T Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~lif~~~~~~a~~i~~~~~~~~~  308 (442)
T COG1061         230 EDEEREYAKESARFRELLRARGTLRAENEARRIAIASERKIAAVRGLLLKHA-RGDKTLIFASDVEHAYEIAKLFLAPGI  308 (442)
T ss_pred             hHHHHHhhhhhhhhhhhhhhhhhhhHHHHHHHHhhccHHHHHHHHHHHHHhc-CCCcEEEEeccHHHHHHHHHHhcCCCc
Confidence            0000                                0111223333333333 4779999999999999999998754  


Q ss_pred             -------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCC
Q psy7952         324 -------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGR  383 (444)
Q Consensus       324 -------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R  383 (444)
                             .+..+|..+++.|+.|.+++|+++.++.+|+|+|+++++|...++.|...|+||+||+.|
T Consensus       309 ~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~vl~EGvDiP~~~~~i~~~~t~S~~~~~Q~lGR~LR  375 (442)
T COG1061         309 VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLR  375 (442)
T ss_pred             eEEEECCCCHHHHHHHHHHHHcCCCCEEEEeeeccceecCCCCcEEEEeCCCCcHHHHHHHhhhhcc
Confidence                   789999999999999999999999999999999999999999999999999999999999

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.97  E-value=9.5e-30  Score=255.84  Aligned_cols=323  Identities=18%  Similarity=0.177  Sum_probs=199.9

Q ss_pred             HHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchh
Q psy7952          36 LTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPIL  115 (444)
Q Consensus        36 ~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~  115 (444)
                      +.++-++.+|..  |.+.|  ++..+... +..++.++||+|||++        +.+|+.+. ...+   +.++|++|++
T Consensus        59 vrEa~~R~lglr--pydVQ--lig~l~l~-~G~Iaem~TGeGKTLt--------a~Lpa~l~-aL~g---~~V~VVTpn~  121 (762)
T TIGR03714        59 VREADKRVLGMF--PYDVQ--VLGAIVLH-QGNIAEMKTGEGKTLT--------ATMPLYLN-ALTG---KGAMLVTTND  121 (762)
T ss_pred             HHHHHHhhcCCC--ccHHH--HHHHHHhc-CCceeEecCCcchHHH--------HHHHHHHH-hhcC---CceEEeCCCH
Confidence            345666666764  33355  55444444 4469999999999999        66666222 2222   2469999999


Q ss_pred             hhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH------
Q psy7952         116 SSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL------  187 (444)
Q Consensus       116 ~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~------  187 (444)
                      +|+  .|+.+.+..+  .+|   +++....++.......   .+.+....+++|+++||+.|..   +.+..+.      
T Consensus       122 yLA--~Rdae~m~~l~~~LG---Lsv~~~~~~s~~~~~~---~~~rr~~y~~dIvygTp~~Lgf---DyLrD~l~~~~~~  190 (762)
T TIGR03714       122 YLA--KRDAEEMGPVYEWLG---LTVSLGVVDDPDEEYD---ANEKRKIYNSDIVYTTNSALGF---DYLIDNLASNKEG  190 (762)
T ss_pred             HHH--HHHHHHHHHHHhhcC---CcEEEEECCCCccccC---HHHHHHhCCCCEEEECchhhhh---hHHHHHhhcchhh
Confidence            999  4445555555  556   7777766542111110   0001112478999999999952   3333322      


Q ss_pred             HhhCCccEEEEeccccccccC---------C--CcHHHHHHHHHHHHh--------------------------------
Q psy7952         188 VRYNKLAYIVVDEAHCVSEWG---------H--DFRPTYRRLGELRQF--------------------------------  224 (444)
Q Consensus       188 ~~~~~~~~iViDE~H~~~~~~---------~--~~~~~~~~l~~~~~~--------------------------------  224 (444)
                      .....+.++|+||||.++-..         .  .-...|.....+.+.                                
T Consensus       191 ~~~r~l~~~IVDEaDsILiDeartpliisg~~~~~~~~y~~~~~~v~~l~~~~dy~~d~~~~~v~lt~~G~~~~e~~~~~  270 (762)
T TIGR03714       191 KFLRPFNYVIVDEVDSVLLDSAQTPLVISGAPRVQSNLYHIADTFVRTLKEDVDYIFKKDKKEVWLTDKGIEKAEQYFKI  270 (762)
T ss_pred             cccccCcEEEEecHhhHhhccCcCCeeeeCCCccchHHHHHHHHHHHhcCCCCCeEEEcCCCeeeecHhHHHHHHHHcCC
Confidence            225678999999999984311         0  000000000000000                                


Q ss_pred             --------------------------------------------------------------------------------
Q psy7952         225 --------------------------------------------------------------------------------  224 (444)
Q Consensus       225 --------------------------------------------------------------------------------  224 (444)
                                                                                                      
T Consensus       271 ~~l~~~~~~~~~~~i~~al~A~~~~~~d~dYiV~~~~v~ivD~~TGr~~~gr~~~~GLhQaieaKE~v~i~~e~~t~a~I  350 (762)
T TIGR03714       271 DNLYSEEYFELVRHINLALRAHYLFKRNKDYVVTNGEVVLLDRITGRLLEGTKLQSGIHQAIEAKEHVELSKETRAMASI  350 (762)
T ss_pred             CccCChhhHHHHHHHHHHHHHHHHHhcCCceEEECCEEEEEECCCCcCCCCCCcchHHHHHHHhhcCCCCCCCceeeeee
Confidence                                                                                            


Q ss_pred             -----hCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEE---EEcccchhhHHHHHHHHHHHhccC
Q psy7952         225 -----TGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDV---IFDDLLKDSYAHVKEFIEKCLGKD  296 (444)
Q Consensus       225 -----~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~l~~~l~~~  296 (444)
                           |....++.+||+|... ....+.+..++    .+..-+..+|.+....   .+.. ...++..+.+.+.+.    
T Consensus       351 t~qn~Fr~Y~kl~GmTGTa~~-~~~Ef~~iY~l----~v~~IPt~kp~~r~d~~d~i~~~-~~~K~~ai~~~i~~~----  420 (762)
T TIGR03714       351 TYQNLFKMFNKLSGMTGTGKV-AEKEFIETYSL----SVVKIPTNKPIIRIDYPDKIYAT-LPEKLMATLEDVKEY----  420 (762)
T ss_pred             eHHHHHhhCchhcccCCCChh-HHHHHHHHhCC----CEEEcCCCCCeeeeeCCCeEEEC-HHHHHHHHHHHHHHH----
Confidence                 0111234677777543 23334443332    2233334455444332   1211 233444455544443    


Q ss_pred             CCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccC---------
Q psy7952         297 NKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQ---------  357 (444)
Q Consensus       297 ~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~---------  357 (444)
                      ...+.++||||+|++.++.++..|.+.          +...++..+.+.++.|  .|+|||++++||+|||         
T Consensus       421 ~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~v~~~G  498 (762)
T TIGR03714       421 HETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKEAQIIAEAGQKG--AVTVATSMAGRGTDIKLGKGVAELG  498 (762)
T ss_pred             hhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHHHHHHHHcCCCC--eEEEEccccccccCCCCCccccccC
Confidence            225789999999999999999999887          5555555555544444  8999999999999999         


Q ss_pred             CccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         358 NVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       358 ~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                      ++++|+++++|....+ .||+||+||.|.+|.++.|++.++.
T Consensus       499 GL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~eD~  539 (762)
T TIGR03714       499 GLAVIGTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSLEDD  539 (762)
T ss_pred             CeEEEEecCCCCcHHH-HHhhhcccCCCCceeEEEEEccchh
Confidence            8999999999987666 9999999999999999999987654

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.

>TIGR01054 rgy reverse gyrase

Probab=99.97  E-value=1.3e-29  Score=270.84  Aligned_cols=296  Identities=19%  Similarity=0.234  Sum_probs=187.7

Q ss_pred             HHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcc
Q psy7952          34 QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISP  113 (444)
Q Consensus        34 ~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P  113 (444)
                      .++.+.+++..|+.  |+++|+.+++.++.| +++++.||||+|||..         .+++ ...+..  ..++++|++|
T Consensus        65 ~~f~~~f~~~~g~~--p~~iQ~~~i~~il~G-~d~vi~ApTGsGKT~f---------~l~~-~~~l~~--~g~~vLIL~P  129 (1171)
T TIGR01054        65 KEFEEFFKKAVGSE--PWSIQKMWAKRVLRG-DSFAIIAPTGVGKTTF---------GLAM-SLFLAK--KGKRCYIILP  129 (1171)
T ss_pred             HHHHHHHHHhcCCC--CcHHHHHHHHHHhCC-CeEEEECCCCCCHHHH---------HHHH-HHHHHh--cCCeEEEEeC
Confidence            44556666666765  578999999999999 9999999999999964         2233 111211  2356799999


Q ss_pred             hhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         114 ILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       114 ~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      |++|+  .|+.+.+..+  ..+.....+..++|+.+..++......+.  .++++|+|+||+.+.    . ...   .+.
T Consensus       130 TreLa--~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~--~~~~dIlV~Tp~rL~----~-~~~---~l~  197 (1171)
T TIGR01054       130 TTLLV--IQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIE--NGDFDILITTTMFLS----K-NYD---ELG  197 (1171)
T ss_pred             HHHHH--HHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHh--cCCCCEEEECHHHHH----H-HHH---Hhc
Confidence            99999  4445555555  23311122345788888776655555443  356899999999874    1 111   222


Q ss_pred             -CccEEEEeccccccccCCC---------cHHH-HHHH-------------------HHHHHhhCCCCc--EEEEeccC-
Q psy7952         192 -KLAYIVVDEAHCVSEWGHD---------FRPT-YRRL-------------------GELRQFTGNSIP--IIALTATA-  238 (444)
Q Consensus       192 -~~~~iViDE~H~~~~~~~~---------~~~~-~~~l-------------------~~~~~~~~~~~~--~v~lSAT~-  238 (444)
                       +++++|+||||++++.+..         |... +..+                   ...++..++..|  ++++|||+ 
T Consensus       198 ~~~~~iVvDEaD~~L~~~k~vd~il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~  277 (1171)
T TIGR01054       198 PKFDFIFVDDVDALLKASKNVDKLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGR  277 (1171)
T ss_pred             CCCCEEEEeChHhhhhccccHHHHHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCC
Confidence             8999999999999874321         3321 1111                   112233344444  56789994 


Q ss_pred             CcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEeccc---chHHH
Q psy7952         239 EPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTR---EHTTD  315 (444)
Q Consensus       239 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~---~~~~~  315 (444)
                      +......+   +...-.+.+........++...+....   .....+.+++..       .+.++||||+++   +.|++
T Consensus       278 p~~~~~~l---~r~ll~~~v~~~~~~~r~I~~~~~~~~---~~~~~L~~ll~~-------l~~~~IVFv~t~~~~~~a~~  344 (1171)
T TIGR01054       278 PRGKRAKL---FRELLGFEVGGGSDTLRNVVDVYVEDE---DLKETLLEIVKK-------LGTGGIVYVSIDYGKEKAEE  344 (1171)
T ss_pred             ccccHHHH---cccccceEecCccccccceEEEEEecc---cHHHHHHHHHHH-------cCCCEEEEEeccccHHHHHH
Confidence            44333221   111111122222222233333332221   112233333333       245789999999   99999


Q ss_pred             HHHHHHhh------cCHHHHHHHHHHHhcCCccEEEE----cCccccccccCC-ccEEEEeCCCC
Q psy7952         316 LADALRRK------VNKHERSRVQESFMRGEINVITA----TISFGMGIDRQN-VRFVVHWGMPS  369 (444)
Q Consensus       316 l~~~L~~~------~~~~~r~~~~~~f~~g~~~vLva----T~~~~~Gidi~~-~~~Vi~~~~p~  369 (444)
                      ++..|.+.      +....+...++.|++|+++||||    |+++++|||+|+ +++||++|+|.
T Consensus       345 l~~~L~~~g~~a~~lhg~~~~~~l~~Fr~G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P~  409 (1171)
T TIGR01054       345 IAEFLENHGVKAVAYHATKPKEDYEKFAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVPK  409 (1171)
T ss_pred             HHHHHHhCCceEEEEeCCCCHHHHHHHHcCCCCEEEEeccccCcccccCCCCccccEEEEECCCC
Confidence            99999875      11111247899999999999999    599999999999 89999999996

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.

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.97  E-value=2.1e-29  Score=258.39  Aligned_cols=315  Identities=18%  Similarity=0.161  Sum_probs=208.2

Q ss_pred             CchHHHHHHHHHHcc--CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchH
Q psy7952          50 KCELQKKAIRHILLR--THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKT  127 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~--~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~  127 (444)
                      +|+.|+++++.+..+  .+++++.+|||+|||.+        |+.++ ...+..+   .++||++|+++|+     .|+.
T Consensus       145 Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v--------~l~~i-~~~l~~g---~~vLvLvPt~~L~-----~Q~~  207 (679)
T PRK05580        145 LNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEV--------YLQAI-AEVLAQG---KQALVLVPEIALT-----PQML  207 (679)
T ss_pred             CCHHHHHHHHHHHhccCCCcEEEECCCCChHHHH--------HHHHH-HHHHHcC---CeEEEEeCcHHHH-----HHHH
Confidence            468999999999973  47899999999999999        54433 3333333   3569999999999     7777


Q ss_pred             hhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccc
Q psy7952         128 SIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVS  205 (444)
Q Consensus       128 ~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~  205 (444)
                      +.+  .++   ..+..++|+.+..++...+..+.  .+..+|+|+|+..+.           ..+.++++||+||+|...
T Consensus       208 ~~l~~~fg---~~v~~~~s~~s~~~r~~~~~~~~--~g~~~IVVgTrsal~-----------~p~~~l~liVvDEeh~~s  271 (679)
T PRK05580        208 ARFRARFG---APVAVLHSGLSDGERLDEWRKAK--RGEAKVVIGARSALF-----------LPFKNLGLIIVDEEHDSS  271 (679)
T ss_pred             HHHHHHhC---CCEEEEECCCCHHHHHHHHHHHH--cCCCCEEEeccHHhc-----------ccccCCCEEEEECCCccc
Confidence            777  456   78999999988877766655543  467899999987652           246789999999999875


Q ss_pred             ccCCCcHHHH--HHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEe-cC----CCCCCceEEEEEcccc
Q psy7952         206 EWGHDFRPTY--RRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFK-TS----TFRSNLFYDVIFDDLL  278 (444)
Q Consensus       206 ~~~~~~~~~~--~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~-~~----~~~~~~~~~~~~~~~~  278 (444)
                      -++.. .+.+  ..+.... ....+.+++++||||+......+..     ..+.... ..    ...|.+...-......
T Consensus       272 ~~~~~-~p~y~~r~va~~r-a~~~~~~~il~SATps~~s~~~~~~-----g~~~~~~l~~r~~~~~~p~v~~id~~~~~~  344 (679)
T PRK05580        272 YKQQE-GPRYHARDLAVVR-AKLENIPVVLGSATPSLESLANAQQ-----GRYRLLRLTKRAGGARLPEVEIIDMRELLR  344 (679)
T ss_pred             cccCc-CCCCcHHHHHHHH-hhccCCCEEEEcCCCCHHHHHHHhc-----cceeEEEeccccccCCCCeEEEEechhhhh
Confidence            43221 1111  2232222 2334589999999988665543321     1111111 11    1122221111100000


Q ss_pred             h----hhHHHHHHHHHHHhccCCCCCceEEEEecccc-------------------------------------------
Q psy7952         279 K----DSYAHVKEFIEKCLGKDNKANNCGIIYCRTRE-------------------------------------------  311 (444)
Q Consensus       279 ~----~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~-------------------------------------------  311 (444)
                      .    .-...+.+.+.+.+.    .++++|||+|.+.                                           
T Consensus       345 ~~~~~~ls~~l~~~i~~~l~----~g~qvll~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~  420 (679)
T PRK05580        345 GENGSFLSPPLLEAIKQRLE----RGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPI  420 (679)
T ss_pred             hcccCCCCHHHHHHHHHHHH----cCCeEEEEEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCC
Confidence            0    011233344444332    4678888877532                                           


Q ss_pred             -----------------hHHHHHHHHHhh--------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCcc
Q psy7952         312 -----------------HTTDLADALRRK--------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVR  360 (444)
Q Consensus       312 -----------------~~~~l~~~L~~~--------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~  360 (444)
                                       .++++++.|.+.              ..+.+++.+++.|++|+.+|||+|+++++|+|+|+++
T Consensus       421 ~~~Cp~Cg~~~l~~~g~G~e~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~  500 (679)
T PRK05580        421 PKACPECGSTDLVPVGPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVT  500 (679)
T ss_pred             CCCCCCCcCCeeEEeeccHHHHHHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcC
Confidence                             345666666664              1246788999999999999999999999999999999


Q ss_pred             EEEEeCC--CCC----------HHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhh
Q psy7952         361 FVVHWGM--PSS----------IPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKT  408 (444)
Q Consensus       361 ~Vi~~~~--p~s----------~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~  408 (444)
                      +|+.++.  +.+          ...|.|++||+||.+.+|.+++.....+...++.+...
T Consensus       501 lV~il~aD~~l~~pdfra~Er~~~~l~q~~GRagR~~~~g~viiqT~~p~~~~~~~~~~~  560 (679)
T PRK05580        501 LVGVLDADLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQALLAQ  560 (679)
T ss_pred             EEEEEcCchhccCCccchHHHHHHHHHHHHhhccCCCCCCEEEEEeCCCCCHHHHHHHhC
Confidence            9865543  322          36789999999999999999987766555555555443

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.96  E-value=4.6e-28  Score=255.26  Aligned_cols=294  Identities=18%  Similarity=0.151  Sum_probs=183.0

Q ss_pred             HHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchh----hhhcccCccchHhhh
Q psy7952          55 KKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPIL----SSFYLRFRDDKTSIV  130 (444)
Q Consensus        55 ~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~----~L~~~~q~~~~~~~l  130 (444)
                      .+.+..+..+ +.++++|+||||||..          +|.++... ..+...+|++.-|.+    +|+     .+..+.+
T Consensus        80 ~~Il~ai~~~-~VviI~GeTGSGKTTq----------lPq~lle~-g~g~~g~I~~TQPRRlAArsLA-----~RVA~El  142 (1294)
T PRK11131         80 QDILEAIRDH-QVVIVAGETGSGKTTQ----------LPKICLEL-GRGVKGLIGHTQPRRLAARTVA-----NRIAEEL  142 (1294)
T ss_pred             HHHHHHHHhC-CeEEEECCCCCCHHHH----------HHHHHHHc-CCCCCCceeeCCCcHHHHHHHH-----HHHHHHH
Confidence            3445555555 7789999999999965          56411111 112212334445754    566     2333333


Q ss_pred             --cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccc-cccc
Q psy7952         131 --TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHC-VSEW  207 (444)
Q Consensus       131 --~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~-~~~~  207 (444)
                        ..|   -.+..-......            ...+++|+|+||++|.    ..+ .....+.++++|||||+|. ..+.
T Consensus       143 ~~~lG---~~VGY~vrf~~~------------~s~~t~I~v~TpG~LL----~~l-~~d~~Ls~~~~IIIDEAHERsLn~  202 (1294)
T PRK11131        143 ETELG---GCVGYKVRFNDQ------------VSDNTMVKLMTDGILL----AEI-QQDRLLMQYDTIIIDEAHERSLNI  202 (1294)
T ss_pred             hhhhc---ceeceeecCccc------------cCCCCCEEEEChHHHH----HHH-hcCCccccCcEEEecCcccccccc
Confidence              122   111111110000            1346899999999985    222 2334478899999999994 5553


Q ss_pred             CCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccc-----hhhH
Q psy7952         208 GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLL-----KDSY  282 (444)
Q Consensus       208 ~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~  282 (444)
                      +  |.  +..+..++...+ +.++|+||||++..   .+.++++ ..++ +.......+ +...+......     .+..
T Consensus       203 D--fL--Lg~Lk~lL~~rp-dlKvILmSATid~e---~fs~~F~-~apv-I~V~Gr~~p-Vei~y~p~~~~~~~~~~d~l  271 (1294)
T PRK11131        203 D--FI--LGYLKELLPRRP-DLKVIITSATIDPE---RFSRHFN-NAPI-IEVSGRTYP-VEVRYRPIVEEADDTERDQL  271 (1294)
T ss_pred             c--hH--HHHHHHhhhcCC-CceEEEeeCCCCHH---HHHHHcC-CCCE-EEEcCcccc-ceEEEeecccccchhhHHHH
Confidence            3  33  223444443333 48999999999643   4455543 3343 333222211 22222221111     1122


Q ss_pred             HHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-------------cCHHHHHHHHHHHhcCCccEEEEcCc
Q psy7952         283 AHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-------------VNKHERSRVQESFMRGEINVITATIS  349 (444)
Q Consensus       283 ~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-------------~~~~~r~~~~~~f~~g~~~vLvaT~~  349 (444)
                      ..+...+..+.   ....+.+|||+++..+++.+++.|.+.             ++..+|..+++.  .|..+|||||++
T Consensus       272 ~~ll~~V~~l~---~~~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNI  346 (1294)
T PRK11131        272 QAIFDAVDELG---REGPGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNV  346 (1294)
T ss_pred             HHHHHHHHHHh---cCCCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccH
Confidence            22223333222   224678999999999999999999864             677888888875  578899999999


Q ss_pred             cccccccCCccEEEEeCC------------------CCCHHHHHHHhccCCCCCCceeEEEEecccchhhH
Q psy7952         350 FGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL  402 (444)
Q Consensus       350 ~~~Gidi~~~~~Vi~~~~------------------p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~  402 (444)
                      +++|||||++++||++|.                  |.|..+|.||+||+||. .+|.|+.+++.++...+
T Consensus       347 AEtSITIpgI~yVID~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~d~~~~  416 (1294)
T PRK11131        347 AETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSEDDFLSR  416 (1294)
T ss_pred             HhhccccCcceEEEECCCccccccccccCcccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHHHHHhh
Confidence            999999999999999873                  34678999999999999 78999999998776544

>TIGR00595 priA primosomal protein N'

Probab=99.95  E-value=2.4e-27  Score=234.94  Aligned_cols=294  Identities=17%  Similarity=0.166  Sum_probs=187.6

Q ss_pred             EEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCC
Q psy7952          69 FVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQ  146 (444)
Q Consensus        69 ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~  146 (444)
                      ++++|||+|||.+        |...+ .+.+..++   ++||++|+.+|+     .|+.+.+  .++   .++..++++.
T Consensus         1 LL~g~TGsGKT~v--------~l~~i-~~~l~~g~---~vLvlvP~i~L~-----~Q~~~~l~~~f~---~~v~vlhs~~   60 (505)
T TIGR00595         1 LLFGVTGSGKTEV--------YLQAI-EKVLALGK---SVLVLVPEIALT-----PQMIQRFKYRFG---SQVAVLHSGL   60 (505)
T ss_pred             CccCCCCCCHHHH--------HHHHH-HHHHHcCC---eEEEEeCcHHHH-----HHHHHHHHHHhC---CcEEEEECCC
Confidence            4789999999999        43221 22233333   459999999999     7788888  456   7788999998


Q ss_pred             ChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHH--HHHHHHHHh
Q psy7952         147 TKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTY--RRLGELRQF  224 (444)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~--~~l~~~~~~  224 (444)
                      +..++...+..+.  .+..+|+|||+..+.           ..+.++++|||||.|...-++... +.|  ..+..++..
T Consensus        61 ~~~er~~~~~~~~--~g~~~IVVGTrsalf-----------~p~~~l~lIIVDEeh~~sykq~~~-p~y~ar~~a~~ra~  126 (505)
T TIGR00595        61 SDSEKLQAWRKVK--NGEILVVIGTRSALF-----------LPFKNLGLIIVDEEHDSSYKQEEG-PRYHARDVAVYRAK  126 (505)
T ss_pred             CHHHHHHHHHHHH--cCCCCEEECChHHHc-----------CcccCCCEEEEECCCccccccccC-CCCcHHHHHHHHHH
Confidence            8777766665553  467899999976542           246789999999999976433211 112  223333333


Q ss_pred             hCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEec-----CCCCCCceEEEEEcccc-hhhHHHHHHHHHHHhccCCC
Q psy7952         225 TGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT-----STFRSNLFYDVIFDDLL-KDSYAHVKEFIEKCLGKDNK  298 (444)
Q Consensus       225 ~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~l~~~~~  298 (444)
                      .. +.++|++||||+......+..     ..+.....     ....+.+...-...... ..-...+.+.+.+.+.    
T Consensus       127 ~~-~~~vil~SATPsles~~~~~~-----g~~~~~~l~~r~~~~~~p~v~vid~~~~~~~~~ls~~l~~~i~~~l~----  196 (505)
T TIGR00595       127 KF-NCPVVLGSATPSLESYHNAKQ-----KAYRLLVLTRRVSGRKPPEVKLIDMRKEPRQSFLSPELITAIEQTLA----  196 (505)
T ss_pred             hc-CCCEEEEeCCCCHHHHHHHhc-----CCeEEeechhhhcCCCCCeEEEEecccccccCCccHHHHHHHHHHHH----
Confidence            33 489999999987655443321     11111111     11112222111111100 0111234444444433    


Q ss_pred             CCceEEEEecccch------------------------------------------------------------HHHHHH
Q psy7952         299 ANNCGIIYCRTREH------------------------------------------------------------TTDLAD  318 (444)
Q Consensus       299 ~~~~~iVf~~s~~~------------------------------------------------------------~~~l~~  318 (444)
                      .++++|||+|++..                                                            ++++.+
T Consensus       197 ~g~qvLvflnrrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~l~~~g~Gte~~~e  276 (505)
T TIGR00595       197 AGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEE  276 (505)
T ss_pred             cCCcEEEEEeCCcCCCeeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCeeEeecccHHHHHH
Confidence            47789999776543                                                            466777


Q ss_pred             HHHhh------------cC--HHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCC------------CHH
Q psy7952         319 ALRRK------------VN--KHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPS------------SIP  372 (444)
Q Consensus       319 ~L~~~------------~~--~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~------------s~~  372 (444)
                      .|.+.            +.  ......+++.|++|+.+|||+|++++.|+|+|++++|+..+...            ...
T Consensus       277 ~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra~E~~~~  356 (505)
T TIGR00595       277 ELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQ  356 (505)
T ss_pred             HHHhhCCCCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccchHHHHHH
Confidence            77665            12  23347899999999999999999999999999999886444321            246


Q ss_pred             HHHHHhccCCCCCCceeEEEEecccchhhHHHHH
Q psy7952         373 AYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI  406 (444)
Q Consensus       373 ~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  406 (444)
                      .|+|++||+||.+..|.+++.....+...++.+.
T Consensus       357 ll~q~~GRagR~~~~g~viiqt~~p~~~~~~~~~  390 (505)
T TIGR00595       357 LLTQVAGRAGRAEDPGQVIIQTYNPNHPAIQAAL  390 (505)
T ss_pred             HHHHHHhccCCCCCCCEEEEEeCCCCCHHHHHHH
Confidence            7899999999999999988766444444444443

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).

>PRK09694 helicase Cas3; Provisional

Probab=99.95  E-value=5.5e-27  Score=242.39  Aligned_cols=306  Identities=15%  Similarity=0.122  Sum_probs=183.0

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhh
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      |+++|..+... ..++..+++.+|||+|||.+|+.++.          .+...+...+++|..||++++     .+.+++
T Consensus       287 p~p~Q~~~~~~-~~~pgl~ileApTGsGKTEAAL~~A~----------~l~~~~~~~gi~~aLPT~Ata-----n~m~~R  350 (878)
T PRK09694        287 PRQLQTLVDAL-PLQPGLTIIEAPTGSGKTEAALAYAW----------RLIDQGLADSIIFALPTQATA-----NAMLSR  350 (878)
T ss_pred             ChHHHHHHHhh-ccCCCeEEEEeCCCCCHHHHHHHHHH----------HHHHhCCCCeEEEECcHHHHH-----HHHHHH
Confidence            56899977543 23336799999999999999654322          233344445789999999999     666666


Q ss_pred             h----cCCCCceeEEEEeCCCChhhH---------------------HHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         130 V----TGRSDLYQLELIVSGQTKTEN---------------------KAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       130 l----~~~~~~i~~~~~~~~~~~~~~---------------------~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      +    ...++..++...+|.......                     ..++.+.+.-.--.+|+|||++++....+.   
T Consensus       351 l~~~~~~~f~~~~v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~---  427 (878)
T PRK09694        351 LEALASKLFPSPNLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLP---  427 (878)
T ss_pred             HHHHHHHhcCCCceEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHc---
Confidence            5    112223467777776542211                     011111000011268999999988632111   


Q ss_pred             HHHHhhCC----ccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCC-----
Q psy7952         185 QHLVRYNK----LAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKP-----  255 (444)
Q Consensus       185 ~~~~~~~~----~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~-----  255 (444)
                      ........    -++|||||+|.+..+   +...+..+.+.+..  ...++|+||||++....+.+.+.++...+     
T Consensus       428 ~kh~~lR~~~La~svvIiDEVHAyD~y---m~~lL~~~L~~l~~--~g~~vIllSATLP~~~r~~L~~a~~~~~~~~~~~  502 (878)
T PRK09694        428 VKHRFIRGFGLGRSVLIVDEVHAYDAY---MYGLLEAVLKAQAQ--AGGSVILLSATLPATLKQKLLDTYGGHDPVELSS  502 (878)
T ss_pred             cchHHHHHHhhccCeEEEechhhCCHH---HHHHHHHHHHHHHh--cCCcEEEEeCCCCHHHHHHHHHHhcccccccccc
Confidence            10111111    258999999997432   23333333333333  23679999999999887776654432100     


Q ss_pred             -eEEE--ec---------CCC----CCCceEEEEEcccc-hhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHH
Q psy7952         256 -YKVF--KT---------STF----RSNLFYDVIFDDLL-KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLAD  318 (444)
Q Consensus       256 -~~~~--~~---------~~~----~~~~~~~~~~~~~~-~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~  318 (444)
                       +-..  ..         ...    .......+...... ......+.+.+.+.+    ..+++++|||||++.|+++++
T Consensus       503 ~YPlvt~~~~~~~~~~~~~~~~~~~~~~~~v~v~~~~~~~~~~~~~~l~~i~~~~----~~g~~vLVf~NTV~~Aq~ly~  578 (878)
T PRK09694        503 AYPLITWRGVNGAQRFDLSAHPEQLPARFTIQLEPICLADMLPDLTLLQRMIAAA----NAGAQVCLICNLVDDAQKLYQ  578 (878)
T ss_pred             ccccccccccccceeeeccccccccCcceEEEEEeeccccccCHHHHHHHHHHHH----hcCCEEEEEECCHHHHHHHHH
Confidence             0000  00         000    00011111111000 011122233333322    157899999999999999999


Q ss_pred             HHHhh-------------cCHHHH----HHHHHHH-hcCC---ccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHH
Q psy7952         319 ALRRK-------------VNKHER----SRVQESF-MRGE---INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQE  377 (444)
Q Consensus       319 ~L~~~-------------~~~~~r----~~~~~~f-~~g~---~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr  377 (444)
                      .|++.             +...+|    ..+++.| ++|+   .+|||||+++++|+|+ +++++|....|  ++.++||
T Consensus       579 ~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLDI-d~DvlItdlaP--idsLiQR  655 (878)
T PRK09694        579 RLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQSLDL-DFDWLITQLCP--VDLLFQR  655 (878)
T ss_pred             HHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhheeec-CCCeEEECCCC--HHHHHHH
Confidence            99864             556677    4567778 5665   4799999999999999 47999987777  7899999


Q ss_pred             hccCCCCCC
Q psy7952         378 SGRAGRDGL  386 (444)
Q Consensus       378 ~GR~~R~g~  386 (444)
                      +||++|.+.
T Consensus       656 aGR~~R~~~  664 (878)
T PRK09694        656 LGRLHRHHR  664 (878)
T ss_pred             HhccCCCCC
Confidence            999999875

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.95  E-value=7.8e-27  Score=242.74  Aligned_cols=329  Identities=15%  Similarity=0.089  Sum_probs=200.3

Q ss_pred             chHHHHHHHHHHcc-CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhh
Q psy7952          51 CELQKKAIRHILLR-THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        51 t~~Q~~~~~~~~~~-~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      -|||..++..++.. ..++++.-..|.|||..|.+.          +..+...+...++||+||. .|.     .+-...
T Consensus       154 ~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAgli----------l~~l~~~g~~~rvLIVvP~-sL~-----~QW~~E  217 (956)
T PRK04914        154 IPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMI----------IHQQLLTGRAERVLILVPE-TLQ-----HQWLVE  217 (956)
T ss_pred             CHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHH----------HHHHHHcCCCCcEEEEcCH-HHH-----HHHHHH
Confidence            47999999887654 257999999999999885432          2224445555688999998 566     233333


Q ss_pred             h--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccccc
Q psy7952         130 V--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEW  207 (444)
Q Consensus       130 l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~  207 (444)
                      +  .++   +....+.++.......    .-.......+++|+|.+.+....   -.........+++||+||||++...
T Consensus       218 l~~kF~---l~~~i~~~~~~~~~~~----~~~~pf~~~~~vI~S~~~l~~~~---~~~~~l~~~~wdlvIvDEAH~lk~~  287 (956)
T PRK04914        218 MLRRFN---LRFSLFDEERYAEAQH----DADNPFETEQLVICSLDFLRRNK---QRLEQALAAEWDLLVVDEAHHLVWS  287 (956)
T ss_pred             HHHHhC---CCeEEEcCcchhhhcc----cccCccccCcEEEEEHHHhhhCH---HHHHHHhhcCCCEEEEechhhhccC
Confidence            3  344   4555554433211000    00011235689999988875311   0111222347999999999998531


Q ss_pred             CCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCe-------------------------------
Q psy7952         208 GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPY-------------------------------  256 (444)
Q Consensus       208 ~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~-------------------------------  256 (444)
                      ...-...|..+..+...   ...++++||||.......+...+.+-+|.                               
T Consensus       288 ~~~~s~~y~~v~~La~~---~~~~LLLTATP~q~~~~e~falL~lLdP~~f~~~~~F~~e~~~~~~~a~~v~~l~~~~~~  364 (956)
T PRK04914        288 EEAPSREYQVVEQLAEV---IPGVLLLTATPEQLGQESHFARLRLLDPDRFHDYEAFVEEQQQYRPVADAVQALLAGEKL  364 (956)
T ss_pred             CCCcCHHHHHHHHHhhc---cCCEEEEEcCcccCCcHHHHHhhhhhCCCcCCCHHHHHHHHHhhHHHHHHHHHHhcCCcC
Confidence            11112235555554332   24689999998753322222222111100                               


Q ss_pred             --------------------------------------------------EEEecC----CCCCCceEEEEEcccchh--
Q psy7952         257 --------------------------------------------------KVFKTS----TFRSNLFYDVIFDDLLKD--  280 (444)
Q Consensus       257 --------------------------------------------------~~~~~~----~~~~~~~~~~~~~~~~~~--  280 (444)
                                                                        ..++..    ..-|.-.+.....+....  
T Consensus       365 ~~~~~~~l~~ll~~~~~~~l~~~~~~~~~~~~~~~~~~i~~L~d~hg~~rvm~RntR~~v~~fp~R~~~~~~l~~~~~y~  444 (956)
T PRK04914        365 SDDALNALGELLGEQDIEPLLQAANSDSEEAQAARQELISELLDRHGTGRVLFRNTRAAVKGFPKRELHPIPLPLPEQYQ  444 (956)
T ss_pred             CHHHHHHHHHHhcccchhHHHhhhcccccccHHHHHHHHHHHHhhcCcceEEEeccHHhhcCCCcCceeEeecCCCHHHH
Confidence                                                              000000    000000011110100000  


Q ss_pred             -------------------------------hHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------
Q psy7952         281 -------------------------------SYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------  323 (444)
Q Consensus       281 -------------------------------~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------  323 (444)
                                                     ......+.+.+++...  .+.|+||||+++.++..+++.|...      
T Consensus       445 ~~~~~~~~~~~~~~l~pe~~~~~~~~~~~~~~~d~Ki~~L~~~L~~~--~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~  522 (956)
T PRK04914        445 TAIKVSLEARARDMLYPEQIYQEFEDNATWWNFDPRVEWLIDFLKSH--RSEKVLVICAKAATALQLEQALREREGIRAA  522 (956)
T ss_pred             HHHHHhHHHHHHhhcCHHHHHHHHhhhhhccccCHHHHHHHHHHHhc--CCCeEEEEeCcHHHHHHHHHHHhhccCeeEE
Confidence                                           0001122333333333  4789999999999999999999543      


Q ss_pred             -----cCHHHHHHHHHHHhcC--CccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecc
Q psy7952         324 -----VNKHERSRVQESFMRG--EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE  396 (444)
Q Consensus       324 -----~~~~~r~~~~~~f~~g--~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~  396 (444)
                           ++..+|...++.|+++  ..+|||||+++++|+|++.+++||+||+|+++..|.||+||++|.|+.+.+.+++..
T Consensus       523 ~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTdvgseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~  602 (956)
T PRK04914        523 VFHEGMSIIERDRAAAYFADEEDGAQVLLCSEIGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPY  602 (956)
T ss_pred             EEECCCCHHHHHHHHHHHhcCCCCccEEEechhhccCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEcc
Confidence                 8999999999999974  599999999999999999999999999999999999999999999999887666542


Q ss_pred             c---chhhHHHHHhhcc
Q psy7952         397 H---SKKSLEYVIKTDT  410 (444)
Q Consensus       397 ~---~~~~~~~~~~~~~  410 (444)
                      .   ..+.+..+...++
T Consensus       603 ~~~t~~e~i~~~~~~~l  619 (956)
T PRK04914        603 LEGTAQERLFRWYHEGL  619 (956)
T ss_pred             CCCCHHHHHHHHHhhhc
Confidence            2   2344444444433

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.95  E-value=6.9e-27  Score=247.30  Aligned_cols=297  Identities=17%  Similarity=0.176  Sum_probs=188.0

Q ss_pred             HHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh--cCC
Q psy7952          56 KAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV--TGR  133 (444)
Q Consensus        56 ~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l--~~~  133 (444)
                      +.+..+..+ +.++|+|+||||||..          +|.++... ..+...+|++.-|.+-.+     .....++  ..+
T Consensus        74 ~Il~~l~~~-~vvii~g~TGSGKTTq----------lPq~lle~-~~~~~~~I~~tQPRRlAA-----~svA~RvA~elg  136 (1283)
T TIGR01967        74 DIAEAIAEN-QVVIIAGETGSGKTTQ----------LPKICLEL-GRGSHGLIGHTQPRRLAA-----RTVAQRIAEELG  136 (1283)
T ss_pred             HHHHHHHhC-ceEEEeCCCCCCcHHH----------HHHHHHHc-CCCCCceEecCCccHHHH-----HHHHHHHHHHhC
Confidence            445555444 7889999999999965          45411111 112223456666888766     4555555  333


Q ss_pred             CCceeEEEEeCCC-ChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccc-ccccCCCc
Q psy7952         134 SDLYQLELIVSGQ-TKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHC-VSEWGHDF  211 (444)
Q Consensus       134 ~~~i~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~-~~~~~~~~  211 (444)
                         ..+....|.. .....         ...+..|.++|++.|..    . +.....+.++++|||||+|. ..+.+  +
T Consensus       137 ---~~lG~~VGY~vR~~~~---------~s~~T~I~~~TdGiLLr----~-l~~d~~L~~~~~IIIDEaHERsL~~D--~  197 (1283)
T TIGR01967       137 ---TPLGEKVGYKVRFHDQ---------VSSNTLVKLMTDGILLA----E-TQQDRFLSRYDTIIIDEAHERSLNID--F  197 (1283)
T ss_pred             ---CCcceEEeeEEcCCcc---------cCCCceeeeccccHHHH----H-hhhCcccccCcEEEEcCcchhhccch--h
Confidence               2222222211 00000         13467899999999852    2 22333577899999999994 54432  2


Q ss_pred             HHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCC-CCCceEEEEEccc---chhhHHHHHH
Q psy7952         212 RPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTF-RSNLFYDVIFDDL---LKDSYAHVKE  287 (444)
Q Consensus       212 ~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~---~~~~~~~~~~  287 (444)
                      .  +..+..++...+ +.++|+||||+..   ..+.++++ ..++ +...... ...+.|.......   .....+.+..
T Consensus       198 L--L~lLk~il~~rp-dLKlIlmSATld~---~~fa~~F~-~apv-I~V~Gr~~PVev~Y~~~~~~~~~~~~~~~~~i~~  269 (1283)
T TIGR01967       198 L--LGYLKQLLPRRP-DLKIIITSATIDP---ERFSRHFN-NAPI-IEVSGRTYPVEVRYRPLVEEQEDDDLDQLEAILD  269 (1283)
T ss_pred             H--HHHHHHHHhhCC-CCeEEEEeCCcCH---HHHHHHhc-CCCE-EEECCCcccceeEEecccccccchhhhHHHHHHH
Confidence            2  223444444444 4889999999964   34555553 2343 3222221 2222222111110   0122233444


Q ss_pred             HHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-------------cCHHHHHHHHHHHhcCCccEEEEcCcccccc
Q psy7952         288 FIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-------------VNKHERSRVQESFMRGEINVITATISFGMGI  354 (444)
Q Consensus       288 ~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gi  354 (444)
                      .+..+...   ..+.+|||+++..+++.+++.|.+.             ++.++|..+++.+  +..+||+||+++++|+
T Consensus       270 ~I~~l~~~---~~GdILVFLpg~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSL  344 (1283)
T TIGR01967       270 AVDELFAE---GPGDILIFLPGEREIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSL  344 (1283)
T ss_pred             HHHHHHhh---CCCCEEEeCCCHHHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhcc
Confidence            45444332   4678999999999999999999864             6788888876543  3479999999999999


Q ss_pred             ccCCccEEEEeCCC------------------CCHHHHHHHhccCCCCCCceeEEEEecccchhhH
Q psy7952         355 DRQNVRFVVHWGMP------------------SSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL  402 (444)
Q Consensus       355 di~~~~~Vi~~~~p------------------~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~  402 (444)
                      |||++++||++|.+                  .|..+|.||.||+||.| +|.|+.+++.++...+
T Consensus       345 TIpgV~yVIDsGl~r~~~yd~~~~~~~L~~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~~~~~~  409 (1283)
T TIGR01967       345 TVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVA-PGICIRLYSEEDFNSR  409 (1283)
T ss_pred             ccCCeeEEEeCCCccccccccccCccccCCccCCHHHHHHHhhhhCCCC-CceEEEecCHHHHHhh
Confidence            99999999999853                  36789999999999996 9999999998776554

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.

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

Probab=99.95  E-value=2e-26  Score=204.75  Aligned_cols=308  Identities=18%  Similarity=0.119  Sum_probs=202.5

Q ss_pred             CCcccCchHHHHHHHHHHc---cCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhccc
Q psy7952          45 GFDSFKCELQKKAIRHILL---RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLR  121 (444)
Q Consensus        45 g~~~~~t~~Q~~~~~~~~~---~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~  121 (444)
                      ++..-.|+.|+.+-+.+.+   ..++.+++|.||+|||..         ++..+...+..++..   .+.+|....+   
T Consensus        93 ~W~G~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEM---------if~~i~~al~~G~~v---ciASPRvDVc---  157 (441)
T COG4098          93 QWKGTLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEM---------IFQGIEQALNQGGRV---CIASPRVDVC---  157 (441)
T ss_pred             eeccccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhh---------hHHHHHHHHhcCCeE---EEecCcccch---
Confidence            4444357899998877765   238999999999999988         344423334444455   8889999888   


Q ss_pred             CccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecc
Q psy7952         122 FRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEA  201 (444)
Q Consensus       122 q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~  201 (444)
                        -+...++...+.......++|+....             -..+++|+|--++.        +   ....|+++||||+
T Consensus       158 --lEl~~Rlk~aF~~~~I~~Lyg~S~~~-------------fr~plvVaTtHQLl--------r---Fk~aFD~liIDEV  211 (441)
T COG4098         158 --LELYPRLKQAFSNCDIDLLYGDSDSY-------------FRAPLVVATTHQLL--------R---FKQAFDLLIIDEV  211 (441)
T ss_pred             --HHHHHHHHHhhccCCeeeEecCCchh-------------ccccEEEEehHHHH--------H---HHhhccEEEEecc
Confidence              78888884444447788888887653             24678888844432        1   1235899999999


Q ss_pred             ccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCC--CCCceEEEEEcccch
Q psy7952         202 HCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTF--RSNLFYDVIFDDLLK  279 (444)
Q Consensus       202 H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~  279 (444)
                      |.+.-..  -...+.++   .+....+...|.+|||++....+.+...-  .....+...-..  .|-..+.....-...
T Consensus       212 DAFP~~~--d~~L~~Av---~~ark~~g~~IylTATp~k~l~r~~~~g~--~~~~klp~RfH~~pLpvPkf~w~~~~~k~  284 (441)
T COG4098         212 DAFPFSD--DQSLQYAV---KKARKKEGATIYLTATPTKKLERKILKGN--LRILKLPARFHGKPLPVPKFVWIGNWNKK  284 (441)
T ss_pred             ccccccC--CHHHHHHH---HHhhcccCceEEEecCChHHHHHHhhhCC--eeEeecchhhcCCCCCCCceEEeccHHHH
Confidence            9974211  11112222   23344456689999999988777654321  111111111111  111122222211111


Q ss_pred             hhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCc
Q psy7952         280 DSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATIS  349 (444)
Q Consensus       280 ~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~  349 (444)
                      -....+.-.+...+++....+.+++||+++.+..++++..|...          .....|.+..+.|++|+..+|++|.+
T Consensus       285 l~r~kl~~kl~~~lekq~~~~~P~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~d~~R~EkV~~fR~G~~~lLiTTTI  364 (441)
T COG4098         285 LQRNKLPLKLKRWLEKQRKTGRPVLIFFPEIETMEQVAAALKKKLPKETIASVHSEDQHRKEKVEAFRDGKITLLITTTI  364 (441)
T ss_pred             hhhccCCHHHHHHHHHHHhcCCcEEEEecchHHHHHHHHHHHhhCCccceeeeeccCccHHHHHHHHHcCceEEEEEeeh
Confidence            11122333455566666667899999999999999999999766          44567899999999999999999999


Q ss_pred             cccccccCCccEEEEeCC--CCCHHHHHHHhccCCCCCC--ceeEEEEecccchh
Q psy7952         350 FGMGIDRQNVRFVVHWGM--PSSIPAYYQESGRAGRDGL--QSYCRIYHSEHSKK  400 (444)
Q Consensus       350 ~~~Gidi~~~~~Vi~~~~--p~s~~~~~Qr~GR~~R~g~--~g~~~~~~~~~~~~  400 (444)
                      +++|+.+|++++.|.-.-  -.+...++|..||+||.-.  .|.+..|.......
T Consensus       365 LERGVTfp~vdV~Vlgaeh~vfTesaLVQIaGRvGRs~~~PtGdv~FFH~G~ska  419 (441)
T COG4098         365 LERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVGRSLERPTGDVLFFHYGKSKA  419 (441)
T ss_pred             hhcccccccceEEEecCCcccccHHHHHHHhhhccCCCcCCCCcEEEEeccchHH
Confidence            999999999998664332  2578899999999999743  46655554444433

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

Probab=99.95  E-value=3.8e-27  Score=250.30  Aligned_cols=302  Identities=17%  Similarity=0.137  Sum_probs=179.0

Q ss_pred             chHHHHHHHHHH----ccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccch
Q psy7952          51 CELQKKAIRHIL----LRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDK  126 (444)
Q Consensus        51 t~~Q~~~~~~~~----~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~  126 (444)
                      .+||.+|+..+.    +|.+++++++|||||||++|+.         . +..+...+..+||||++|+.+|+     .|.
T Consensus       415 R~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~---------l-i~~L~~~~~~~rVLfLvDR~~L~-----~Qa  479 (1123)
T PRK11448        415 RYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIA---------L-MYRLLKAKRFRRILFLVDRSALG-----EQA  479 (1123)
T ss_pred             CHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHH---------H-HHHHHhcCccCeEEEEecHHHHH-----HHH
Confidence            379999998776    3547899999999999988321         1 22244444556889999999999     566


Q ss_pred             Hhhh-cCCCCce-eEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH-HHHhhCCccEEEEecccc
Q psy7952         127 TSIV-TGRSDLY-QLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ-HLVRYNKLAYIVVDEAHC  203 (444)
Q Consensus       127 ~~~l-~~~~~~i-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~-~~~~~~~~~~iViDE~H~  203 (444)
                      ...+ ..+.... ....+.+.   ..    +.+.. .....+|+|+|++++.+..+..... .......+++||+||||+
T Consensus       480 ~~~F~~~~~~~~~~~~~i~~i---~~----L~~~~-~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHR  551 (1123)
T PRK11448        480 EDAFKDTKIEGDQTFASIYDI---KG----LEDKF-PEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHR  551 (1123)
T ss_pred             HHHHHhcccccccchhhhhch---hh----hhhhc-ccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCC
Confidence            6666 3331101 11001110   00    00000 1245789999999875321110000 012346789999999999


Q ss_pred             cccc------C-CCcH---HHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEec------CCC---
Q psy7952         204 VSEW------G-HDFR---PTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT------STF---  264 (444)
Q Consensus       204 ~~~~------~-~~~~---~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~------~~~---  264 (444)
                      -...      + ..++   ..+....+++..+.  ...|+|||||.....    ..++.  ++....-      ...   
T Consensus       552 s~~~d~~~~~~~~~~~~~~~~~~~yr~iL~yFd--A~~IGLTATP~r~t~----~~FG~--pv~~Ysl~eAI~DG~Lv~~  623 (1123)
T PRK11448        552 GYTLDKEMSEGELQFRDQLDYVSKYRRVLDYFD--AVKIGLTATPALHTT----EIFGE--PVYTYSYREAVIDGYLIDH  623 (1123)
T ss_pred             CCccccccccchhccchhhhHHHHHHHHHhhcC--ccEEEEecCCccchh----HHhCC--eeEEeeHHHHHhcCCcccC
Confidence            5310      0 0011   11233334444442  568999999976443    23331  1110000      000   


Q ss_pred             CCCceEEEEE-------------------------cccch----------------hhHHHHHHHHHHHhccCCCCCceE
Q psy7952         265 RSNLFYDVIF-------------------------DDLLK----------------DSYAHVKEFIEKCLGKDNKANNCG  303 (444)
Q Consensus       265 ~~~~~~~~~~-------------------------~~~~~----------------~~~~~~~~~l~~~l~~~~~~~~~~  303 (444)
                      .+++.+....                         .....                .....+.+.+.+.+...  ..+++
T Consensus       624 ~~p~~i~t~~~~~gi~~~~~e~~~~~~~~~~~i~~~~l~d~~~~~~~~~~~~vi~~~~~~~i~~~l~~~l~~~--~~~Kt  701 (1123)
T PRK11448        624 EPPIRIETRLSQEGIHFEKGEEVEVINTQTGEIDLATLEDEVDFEVEDFNRRVITESFNRVVCEELAKYLDPT--GEGKT  701 (1123)
T ss_pred             cCCEEEEEEeccccccccccchhhhcchhhhhhhhccCcHHHhhhHHHHHHHHhhHHHHHHHHHHHHHHHhcc--CCCcE
Confidence            0111111000                         00000                00001112222223222  24799


Q ss_pred             EEEecccchHHHHHHHHHhh-----------------cCHHHHHHHHHHHhcCCc-cEEEEcCccccccccCCccEEEEe
Q psy7952         304 IIYCRTREHTTDLADALRRK-----------------VNKHERSRVQESFMRGEI-NVITATISFGMGIDRQNVRFVVHW  365 (444)
Q Consensus       304 iVf~~s~~~~~~l~~~L~~~-----------------~~~~~r~~~~~~f~~g~~-~vLvaT~~~~~Gidi~~~~~Vi~~  365 (444)
                      ||||.++++|+.+++.|.+.                 .+..++..++++|+++.. +|+|+++++.+|+|+|.+++||++
T Consensus       702 iIF~~s~~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg~~~~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~v~~vVf~  781 (1123)
T PRK11448        702 LIFAATDAHADMVVRLLKEAFKKKYGQVEDDAVIKITGSIDKPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSICNLVFL  781 (1123)
T ss_pred             EEEEcCHHHHHHHHHHHHHHHHhhcCCcCccceEEEeCCccchHHHHHHHhCCCCCeEEEEecccccCCCcccccEEEEe
Confidence            99999999999999887653                 122367889999999876 689999999999999999999999


Q ss_pred             CCCCCHHHHHHHhccCCCCC
Q psy7952         366 GMPSSIPAYYQESGRAGRDG  385 (444)
Q Consensus       366 ~~p~s~~~~~Qr~GR~~R~g  385 (444)
                      .++.|...|.||+||+.|.-
T Consensus       782 rpvkS~~lf~QmIGRgtR~~  801 (1123)
T PRK11448        782 RRVRSRILYEQMLGRATRLC  801 (1123)
T ss_pred             cCCCCHHHHHHHHhhhccCC
Confidence            99999999999999999963

>KOG0947|consensus

Probab=99.95  E-value=2.2e-26  Score=227.66  Aligned_cols=315  Identities=22%  Similarity=0.242  Sum_probs=211.7

Q ss_pred             HhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccC
Q psy7952          43 LFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRF  122 (444)
Q Consensus        43 ~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q  122 (444)
                      .|+|+.  ..+|++|+-++.+| .++++.|+|.+|||.+|..+      +..    ...+  ..|.++.+|.++|.    
T Consensus       293 ~~pFel--D~FQk~Ai~~lerg-~SVFVAAHTSAGKTvVAEYA------ial----aq~h--~TR~iYTSPIKALS----  353 (1248)
T KOG0947|consen  293 IYPFEL--DTFQKEAIYHLERG-DSVFVAAHTSAGKTVVAEYA------IAL----AQKH--MTRTIYTSPIKALS----  353 (1248)
T ss_pred             hCCCCc--cHHHHHHHHHHHcC-CeEEEEecCCCCcchHHHHH------HHH----HHhh--ccceEecchhhhhc----
Confidence            367774  46999999999999 99999999999999997643      222    1111  12459999999999    


Q ss_pred             ccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccc
Q psy7952         123 RDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAH  202 (444)
Q Consensus       123 ~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H  202 (444)
                       .|.++.|+..+++  +..++|+....             +.+.++|+|-|.|.    .+++++.--..++..||+||+|
T Consensus       354 -NQKfRDFk~tF~D--vgLlTGDvqin-------------PeAsCLIMTTEILR----sMLYrgadliRDvE~VIFDEVH  413 (1248)
T KOG0947|consen  354 -NQKFRDFKETFGD--VGLLTGDVQIN-------------PEASCLIMTTEILR----SMLYRGADLIRDVEFVIFDEVH  413 (1248)
T ss_pred             -cchHHHHHHhccc--cceeecceeeC-------------CCcceEeehHHHHH----HHHhcccchhhccceEEEeeee
Confidence             7888888333222  33888887653             67889999988875    4445555556789999999999


Q ss_pred             cccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCC-CCCC-ceEEEEEcccch-
Q psy7952         203 CVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST-FRSN-LFYDVIFDDLLK-  279 (444)
Q Consensus       203 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~-  279 (444)
                      .+.+..++  ..|..+.   =++|..+++|++|||.++..  .+..|+|-.+.-.+...++ .||. ..+......... 
T Consensus       414 YiND~eRG--vVWEEVi---IMlP~HV~~IlLSATVPN~~--EFA~WIGRtK~K~IyViST~kRPVPLEh~l~t~~~l~k  486 (1248)
T KOG0947|consen  414 YINDVERG--VVWEEVI---IMLPRHVNFILLSATVPNTL--EFADWIGRTKQKTIYVISTSKRPVPLEHYLYTKKSLFK  486 (1248)
T ss_pred             eccccccc--ccceeee---eeccccceEEEEeccCCChH--HHHHHhhhccCceEEEEecCCCccceEEEEEeccceeh
Confidence            99774321  1233322   25677899999999998764  4577777544333333333 2322 111111100000 


Q ss_pred             --------------hhH---------------------------------------------H----HHHHHHHHHhccC
Q psy7952         280 --------------DSY---------------------------------------------A----HVKEFIEKCLGKD  296 (444)
Q Consensus       280 --------------~~~---------------------------------------------~----~~~~~l~~~l~~~  296 (444)
                                    +..                                             .    ...+++..+ ...
T Consensus       487 iidq~g~fl~~~~~~a~~~~~~~ak~~~~~~~~~~~~rgs~~~ggk~~~~~g~~r~~~~~~nrr~~~~~l~lin~L-~k~  565 (1248)
T KOG0947|consen  487 IIDQNGIFLLKGIKDAKDSLKKEAKFVDVEKSDARGGRGSQKRGGKTNYHNGGSRGSGIGKNRRKQPTWLDLINHL-RKK  565 (1248)
T ss_pred             hhcccchhhhhcchhhhhhhcccccccccccccccccccccccCCcCCCCCCCcccccccccccccchHHHHHHHH-hhc
Confidence                          000                                             0    011111111 111


Q ss_pred             CCCCceEEEEecccchHHHHHHHHHhh-------------------------------------------------cCHH
Q psy7952         297 NKANNCGIIYCRTREHTTDLADALRRK-------------------------------------------------VNKH  327 (444)
Q Consensus       297 ~~~~~~~iVf~~s~~~~~~l~~~L~~~-------------------------------------------------~~~~  327 (444)
                        .--++||||.|++.|++-++.|...                                                 .-+-
T Consensus       566 --~lLP~VvFvFSkkrCde~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPi  643 (1248)
T KOG0947|consen  566 --NLLPVVVFVFSKKRCDEYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPI  643 (1248)
T ss_pred             --ccCceEEEEEccccHHHHHHHHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchHH
Confidence              2347999999999999999999766                                                 4455


Q ss_pred             HHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCC---------CCHHHHHHHhccCCCCCC--ceeEEEEecc
Q psy7952         328 ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMP---------SSIPAYYQESGRAGRDGL--QSYCRIYHSE  396 (444)
Q Consensus       328 ~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p---------~s~~~~~Qr~GR~~R~g~--~g~~~~~~~~  396 (444)
                      -+.-++-.|..|-++||+||.+++.|+|+|. ++||+...-         -++-+|.||+|||||.|-  .|+++++...
T Consensus       644 vKE~VE~LFqrGlVKVLFATETFAMGVNMPA-RtvVF~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~  722 (1248)
T KOG0947|consen  644 VKEVVELLFQRGLVKVLFATETFAMGVNMPA-RTVVFSSLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKD  722 (1248)
T ss_pred             HHHHHHHHHhcCceEEEeehhhhhhhcCCCc-eeEEeeehhhccCcceeecCChhHHhhhccccccccCcCceEEEEecC
Confidence            6677778899999999999999999999995 444433332         267899999999999985  4776666654


Q ss_pred             c--chhhHHHHHh
Q psy7952         397 H--SKKSLEYVIK  407 (444)
Q Consensus       397 ~--~~~~~~~~~~  407 (444)
                      .  +...++.++-
T Consensus       723 ~vp~~a~l~~li~  735 (1248)
T KOG0947|consen  723 SVPSAATLKRLIM  735 (1248)
T ss_pred             CCCCHHHHhhHhc
Confidence            3  4555666654

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

Probab=99.94  E-value=8.8e-26  Score=231.48  Aligned_cols=321  Identities=20%  Similarity=0.222  Sum_probs=211.8

Q ss_pred             HhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccC
Q psy7952          43 LFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRF  122 (444)
Q Consensus        43 ~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q  122 (444)
                      .+||+. . ++|++++..+.+| ++|+++||||+|||.+|..+      +..   .+.++.+   +++..|.++|.    
T Consensus       115 ~~~F~L-D-~fQ~~a~~~Ler~-esVlV~ApTssGKTvVaeyA------i~~---al~~~qr---viYTsPIKALs----  175 (1041)
T COG4581         115 EYPFEL-D-PFQQEAIAILERG-ESVLVCAPTSSGKTVVAEYA------IAL---ALRDGQR---VIYTSPIKALS----  175 (1041)
T ss_pred             hCCCCc-C-HHHHHHHHHHhCC-CcEEEEccCCCCcchHHHHH------HHH---HHHcCCc---eEeccchhhhh----
Confidence            378885 4 7999999999999 99999999999999996532      222   1222233   59999999999    


Q ss_pred             ccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEec
Q psy7952         123 RDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDE  200 (444)
Q Consensus       123 ~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE  200 (444)
                       .|....+  .++.-.--+..++|+...+             +++.++|+|-|.|.    .+++........+..||+||
T Consensus       176 -NQKyrdl~~~fgdv~~~vGL~TGDv~IN-------------~~A~clvMTTEILR----nMlyrg~~~~~~i~~ViFDE  237 (1041)
T COG4581         176 -NQKYRDLLAKFGDVADMVGLMTGDVSIN-------------PDAPCLVMTTEILR----NMLYRGSESLRDIEWVVFDE  237 (1041)
T ss_pred             -hhHHHHHHHHhhhhhhhccceecceeeC-------------CCCceEEeeHHHHH----HHhccCcccccccceEEEEe
Confidence             7788887  3330011247778887764             68889999988764    33344445567899999999


Q ss_pred             cccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcC--CCCeEEEecCCCCCC-ceEEEEEccc
Q psy7952         201 AHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKF--NKPYKVFKTSTFRSN-LFYDVIFDDL  277 (444)
Q Consensus       201 ~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~-~~~~~~~~~~  277 (444)
                      +|.+.+...+  ..+..+..   .+|+..++|+||||.++..  .+..|+..  ..+..+.... .||. ..+.+.....
T Consensus       238 vHyi~D~eRG--~VWEE~Ii---~lP~~v~~v~LSATv~N~~--EF~~Wi~~~~~~~~~vv~t~-~RpvPL~~~~~~~~~  309 (1041)
T COG4581         238 VHYIGDRERG--VVWEEVII---LLPDHVRFVFLSATVPNAE--EFAEWIQRVHSQPIHVVSTE-HRPVPLEHFVYVGKG  309 (1041)
T ss_pred             eeeccccccc--hhHHHHHH---hcCCCCcEEEEeCCCCCHH--HHHHHHHhccCCCeEEEeec-CCCCCeEEEEecCCc
Confidence            9999875432  22333322   4677789999999998754  45666652  3343333333 3332 2222111100


Q ss_pred             ----chhhH-------HHHHHH--------------------------------------HHHHhccCCCCCceEEEEec
Q psy7952         278 ----LKDSY-------AHVKEF--------------------------------------IEKCLGKDNKANNCGIIYCR  308 (444)
Q Consensus       278 ----~~~~~-------~~~~~~--------------------------------------l~~~l~~~~~~~~~~iVf~~  308 (444)
                          .+...       ......                                      +...+..  ...-++|+|+.
T Consensus       310 l~~lvde~~~~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~iv~~l~~--~~~lP~I~F~F  387 (1041)
T COG4581         310 LFDLVDEKKKFNAENFPSANRSLSCFSEKVRETDDGDVGRYARRTKALRGSAKGPAGRPEIVNKLDK--DNLLPAIVFSF  387 (1041)
T ss_pred             eeeeecccccchhhcchhhhhhhhccchhccccCccccccccccccccCCcccccccchHHHhhhhh--hcCCceEEEEE
Confidence                00000       000000                                      0011111  13568999999


Q ss_pred             ccchHHHHHHHHHhh---------------------------------------------------cCHHHHHHHHHHHh
Q psy7952         309 TREHTTDLADALRRK---------------------------------------------------VNKHERSRVQESFM  337 (444)
Q Consensus       309 s~~~~~~l~~~L~~~---------------------------------------------------~~~~~r~~~~~~f~  337 (444)
                      |+..|+..+..+...                                                   +-+..|..+...|.
T Consensus       388 Sr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~~K~~vE~Lfq  467 (1041)
T COG4581         388 SRRGCEEAAQILSTLDLVLTEEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAIKELVEELFQ  467 (1041)
T ss_pred             chhhHHHHHHHhcccccccCCcHHHHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchHHHHHHHHHHh
Confidence            999999988877633                                                   66778889999999


Q ss_pred             cCCccEEEEcCccccccccCCccEEEEeCC---------CCCHHHHHHHhccCCCCCCc--eeEEEEec--ccchhhHHH
Q psy7952         338 RGEINVITATISFGMGIDRQNVRFVVHWGM---------PSSIPAYYQESGRAGRDGLQ--SYCRIYHS--EHSKKSLEY  404 (444)
Q Consensus       338 ~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~---------p~s~~~~~Qr~GR~~R~g~~--g~~~~~~~--~~~~~~~~~  404 (444)
                      .|-++|++||.+++.|+|+|. +.|++...         +.+..+|.|+.|||||.|-+  |.+++.-.  +.+......
T Consensus       468 ~GLvkvvFaTeT~s~GiNmPa-rtvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~~~~~~~e~~~  546 (1041)
T COG4581         468 EGLVKVVFATETFAIGINMPA-RTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPPFESEPSEAAG  546 (1041)
T ss_pred             ccceeEEeehhhhhhhcCCcc-cceeeeeeEEecCCceeecChhHHHHhhhhhccccccccceEEEecCCCCCChHHHHH
Confidence            999999999999999999994 44443332         34799999999999999865  77666633  223555566


Q ss_pred             HHhhccc
Q psy7952         405 VIKTDTS  411 (444)
Q Consensus       405 ~~~~~~~  411 (444)
                      +......
T Consensus       547 l~~~~~~  553 (1041)
T COG4581         547 LASGKLD  553 (1041)
T ss_pred             hhcCCCc
Confidence            5544433

>KOG0950|consensus

Probab=99.93  E-value=3.2e-25  Score=220.78  Aligned_cols=328  Identities=21%  Similarity=0.262  Sum_probs=219.0

Q ss_pred             hCCcccCchHHHHHH--HHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhccc
Q psy7952          44 FGFDSFKCELQKKAI--RHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLR  121 (444)
Q Consensus        44 ~g~~~~~t~~Q~~~~--~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~  121 (444)
                      +|...+- +||.+++  +.++.+ ++.+..+||+.|||++|.+.++.+.        +..++..   +++.|..+.+   
T Consensus       219 kgi~~~f-ewq~ecls~~~~~e~-~nliys~Pts~gktlvaeilml~~~--------l~~rr~~---llilp~vsiv---  282 (1008)
T KOG0950|consen  219 KGILKLF-EWQAECLSLPRLLER-KNLIYSLPTSAGKTLVAEILMLREV--------LCRRRNV---LLILPYVSIV---  282 (1008)
T ss_pred             hhHHHHH-HHHHHHhcchhhhcc-cceEEeCCCccchHHHHHHHHHHHH--------HHHhhce---eEecceeehh---
Confidence            5777744 7999997  467766 9999999999999999877655422        3333444   9999999999   


Q ss_pred             CccchHhhh-----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh---hCCc
Q psy7952         122 FRDDKTSIV-----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR---YNKL  193 (444)
Q Consensus       122 q~~~~~~~l-----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~---~~~~  193 (444)
                        .+.+..+     ..|   +.+..+.|.......          ...-++.|+|.|+-.     .+.+....   ...+
T Consensus       283 --~Ek~~~l~~~~~~~G---~~ve~y~g~~~p~~~----------~k~~sv~i~tiEkan-----slin~lie~g~~~~~  342 (1008)
T KOG0950|consen  283 --QEKISALSPFSIDLG---FPVEEYAGRFPPEKR----------RKRESVAIATIEKAN-----SLINSLIEQGRLDFL  342 (1008)
T ss_pred             --HHHHhhhhhhccccC---CcchhhcccCCCCCc----------ccceeeeeeehHhhH-----hHHHHHHhcCCcccc
Confidence              7888777     344   777777766554432          346689999999963     23444433   4567


Q ss_pred             cEEEEeccccccccCCCcHHHHHHHH-H-HHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEE
Q psy7952         194 AYIVVDEAHCVSEWGHDFRPTYRRLG-E-LRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYD  271 (444)
Q Consensus       194 ~~iViDE~H~~~~~~~~~~~~~~~l~-~-~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~  271 (444)
                      ++||+||.|.+.+.+.+..  +..+. + ++.......|+|+||||+++..  .+..++.  ..+...   ..||.....
T Consensus       343 g~vvVdElhmi~d~~rg~~--lE~~l~k~~y~~~~~~~~iIGMSATi~N~~--lL~~~L~--A~~y~t---~fRPv~L~E  413 (1008)
T KOG0950|consen  343 GMVVVDELHMIGDKGRGAI--LELLLAKILYENLETSVQIIGMSATIPNNS--LLQDWLD--AFVYTT---RFRPVPLKE  413 (1008)
T ss_pred             CcEEEeeeeeeeccccchH--HHHHHHHHHHhccccceeEeeeecccCChH--HHHHHhh--hhheec---ccCcccchh
Confidence            9999999999988664322  22221 1 1112222367999999998743  4455543  111111   111111111


Q ss_pred             EEEccc--chhhHHHHHHHHH----HHhccC------------CCCCceEEEEecccchHHHHHHHHHhh----------
Q psy7952         272 VIFDDL--LKDSYAHVKEFIE----KCLGKD------------NKANNCGIIYCRTREHTTDLADALRRK----------  323 (444)
Q Consensus       272 ~~~~~~--~~~~~~~~~~~l~----~~l~~~------------~~~~~~~iVf~~s~~~~~~l~~~L~~~----------  323 (444)
                      ......  .+.....+...+.    ......            ..++.++||||+++..|+.++..+...          
T Consensus       414 ~ik~G~~i~~~~r~~~lr~ia~l~~~~~g~~dpD~~v~L~tet~~e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~  493 (1008)
T KOG0950|consen  414 YIKPGSLIYESSRNKVLREIANLYSSNLGDEDPDHLVGLCTETAPEGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKR  493 (1008)
T ss_pred             ccCCCcccccchhhHHHHHhhhhhhhhcccCCCcceeeehhhhhhcCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhh
Confidence            111000  0000111111111    111101            114556999999999999998766544          


Q ss_pred             --------------------------------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEe
Q psy7952         324 --------------------------------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHW  365 (444)
Q Consensus       324 --------------------------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~  365 (444)
                                                            +..++|+.+...|+.|.+.|++||+++..|+|+|.-++++-.
T Consensus       494 ~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~GvAyHhaGLT~eER~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIira  573 (1008)
T KOG0950|consen  494 LGLWELLSISNLLRRIPGILDPVLAKTIPYGVAYHHAGLTSEEREIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRA  573 (1008)
T ss_pred             hhHHHHHHHHhHhhcCCcccchHHheeccccceecccccccchHHHHHHHHHhcCeEEEEecchhhccCcCCcceeEEeC
Confidence                                                  678999999999999999999999999999999988887743


Q ss_pred             C----CCCCHHHHHHHhccCCCCCC--ceeEEEEecccchhhHHHHHhhccchhHHH
Q psy7952         366 G----MPSSIPAYYQESGRAGRDGL--QSYCRIYHSEHSKKSLEYVIKTDTSTKREQ  416 (444)
Q Consensus       366 ~----~p~s~~~~~Qr~GR~~R~g~--~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  416 (444)
                      -    ...+..+|.||+|||||.|-  .|.+++++...+.+...+++..+.+....-
T Consensus       574 P~~g~~~l~~~~YkQM~GRAGR~gidT~GdsiLI~k~~e~~~~~~lv~~~~~~~~S~  630 (1008)
T KOG0950|consen  574 PYVGREFLTRLEYKQMVGRAGRTGIDTLGDSILIIKSSEKKRVRELVNSPLKPLNSC  630 (1008)
T ss_pred             CccccchhhhhhHHhhhhhhhhcccccCcceEEEeeccchhHHHHHHhccccccccc
Confidence            2    23478899999999999975  488999999999999999988877765443

>KOG0349|consensus

Probab=99.93  E-value=1.8e-25  Score=204.01  Aligned_cols=277  Identities=16%  Similarity=0.193  Sum_probs=183.0

Q ss_pred             ceeEEEcchhhhhcccCccchHhhhcCC--CCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIVTGR--SDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYL  183 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l~~~--~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~  183 (444)
                      +..+|+-|+++|+  .|..++++.+.+.  .+.++...+.++....++...      +.++.+|+|+||.++.    ..+
T Consensus       287 p~avivepsrela--Eqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~q------l~~g~~ivvGtpgRl~----~~i  354 (725)
T KOG0349|consen  287 PEAVIVEPSRELA--EQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQ------LKDGTHIVVGTPGRLL----QPI  354 (725)
T ss_pred             cceeEecCcHHHH--HHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHH------hhcCceeeecCchhhh----hhh
Confidence            3589999999999  5557777777333  334555566666555444333      3578999999999985    445


Q ss_pred             HHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhC------CCCcEEEEeccCCcchHHHHHH-HhcCCCCe
Q psy7952         184 LQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTG------NSIPIIALTATAEPSVKQDIIS-VLKFNKPY  256 (444)
Q Consensus       184 ~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~------~~~~~v~lSAT~~~~~~~~~~~-~l~~~~~~  256 (444)
                      ......+...+++|.||++.++..+  +...   |.++....+      ...+.+.+|||+..-....+.+ .+.++.-+
T Consensus       355 s~g~~~lt~crFlvlDead~lL~qg--y~d~---I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwV  429 (725)
T KOG0349|consen  355 SKGLVTLTHCRFLVLDEADLLLGQG--YDDK---IYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWV  429 (725)
T ss_pred             hccceeeeeeEEEEecchhhhhhcc--cHHH---HHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeE
Confidence            5556677788999999999998765  3333   333332222      2367899999976533222221 11111111


Q ss_pred             EEEecCCCCCCceEEEE-Eccc----------------------------chhhHHHHHHHH-----HHHhccCCCCCce
Q psy7952         257 KVFKTSTFRSNLFYDVI-FDDL----------------------------LKDSYAHVKEFI-----EKCLGKDNKANNC  302 (444)
Q Consensus       257 ~~~~~~~~~~~~~~~~~-~~~~----------------------------~~~~~~~~~~~l-----~~~l~~~~~~~~~  302 (444)
                      .+.-.+.........+. ....                            ..........++     ...+.+.  .-.+
T Consensus       430 dLkgeD~vpetvHhvv~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~ai~~h--~mdk  507 (725)
T KOG0349|consen  430 DLKGEDLVPETVHHVVKLVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRRH--AMDK  507 (725)
T ss_pred             ecccccccchhhccceeecCCccCccHHHHhhhhccCCcccccccccccCCCCChhhhhHHhcCchhhhhhhhh--ccCc
Confidence            11100000000000000 0000                            000011111111     1111111  4668


Q ss_pred             EEEEecccchHHHHHHHHHhh-------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCC
Q psy7952         303 GIIYCRTREHTTDLADALRRK-------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPS  369 (444)
Q Consensus       303 ~iVf~~s~~~~~~l~~~L~~~-------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~  369 (444)
                      .||||.++.+|+.+.+++.++             ..+.+|.+.++.|+.+..+.||||+++.+|+||..+-++|+...|.
T Consensus       508 aiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~invtlpd  587 (725)
T KOG0349|consen  508 AIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINVTLPD  587 (725)
T ss_pred             eEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEEEecCc
Confidence            999999999999999999988             5689999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHhccCCCCCCceeEEEEecccchhh
Q psy7952         370 SIPAYYQESGRAGRDGLQSYCRIYHSEHSKKS  401 (444)
Q Consensus       370 s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~  401 (444)
                      ...+|+||+||+||..+-|.++.++.....+.
T Consensus       588 ~k~nyvhrigrvgraermglaislvat~~ekv  619 (725)
T KOG0349|consen  588 DKTNYVHRIGRVGRAERMGLAISLVATVPEKV  619 (725)
T ss_pred             ccchhhhhhhccchhhhcceeEEEeeccchhe
Confidence            99999999999999988899999887554443

>KOG0948|consensus

Probab=99.93  E-value=2.5e-25  Score=215.16  Aligned_cols=315  Identities=17%  Similarity=0.218  Sum_probs=210.6

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      .++|..++.-+-++ +++++.|.|.+|||.+|..++.      .   .+...   -|||+.+|.++|.     .|..+.+
T Consensus       131 DpFQ~~aI~Cidr~-eSVLVSAHTSAGKTVVAeYAIA------~---sLr~k---QRVIYTSPIKALS-----NQKYREl  192 (1041)
T KOG0948|consen  131 DPFQSTAIKCIDRG-ESVLVSAHTSAGKTVVAEYAIA------M---SLREK---QRVIYTSPIKALS-----NQKYREL  192 (1041)
T ss_pred             CchHhhhhhhhcCC-ceEEEEeecCCCcchHHHHHHH------H---HHHhc---CeEEeeChhhhhc-----chhHHHH
Confidence            46999999998888 9999999999999999764322      2   12222   2569999999999     7788887


Q ss_pred             -cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCC
Q psy7952         131 -TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGH  209 (444)
Q Consensus       131 -~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~  209 (444)
                       ..-   -.|...+|+.+..             +++..+|+|-|.|.    .++.++..-...+.-||+||+|.|-+..+
T Consensus       193 ~~EF---~DVGLMTGDVTIn-------------P~ASCLVMTTEILR----sMLYRGSEvmrEVaWVIFDEIHYMRDkER  252 (1041)
T KOG0948|consen  193 LEEF---KDVGLMTGDVTIN-------------PDASCLVMTTEILR----SMLYRGSEVMREVAWVIFDEIHYMRDKER  252 (1041)
T ss_pred             HHHh---cccceeecceeeC-------------CCCceeeeHHHHHH----HHHhccchHhheeeeEEeeeehhcccccc
Confidence             333   4578889988764             67889999988875    44555666677899999999999966332


Q ss_pred             CcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcC--CCCeEEEecCCCCCCceEEE------------EEc
Q psy7952         210 DFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKF--NKPYKVFKTSTFRSNLFYDV------------IFD  275 (444)
Q Consensus       210 ~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~~~~~~------------~~~  275 (444)
                      +.-  |..   -.=.+|++.+.+++|||+++..  .+.+|+.-  ..|..++-.+ .||.....+            ...
T Consensus       253 GVV--WEE---TIIllP~~vr~VFLSATiPNA~--qFAeWI~~ihkQPcHVVYTd-yRPTPLQHyifP~ggdGlylvVDe  324 (1041)
T KOG0948|consen  253 GVV--WEE---TIILLPDNVRFVFLSATIPNAR--QFAEWICHIHKQPCHVVYTD-YRPTPLQHYIFPAGGDGLYLVVDE  324 (1041)
T ss_pred             cee--eee---eEEeccccceEEEEeccCCCHH--HHHHHHHHHhcCCceEEeec-CCCCcceeeeecCCCCeeEEEEec
Confidence            111  111   1113677899999999998743  34555431  2233333222 222211111            110


Q ss_pred             c--cchhhHH-----------------------------------HHHHHHHHHhccCCCCCceEEEEecccchHHHHHH
Q psy7952         276 D--LLKDSYA-----------------------------------HVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLAD  318 (444)
Q Consensus       276 ~--~~~~~~~-----------------------------------~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~  318 (444)
                      .  ..++...                                   .+...++-.+.+   ...++|||+.|+++|+..|-
T Consensus       325 k~~FrednF~~am~~l~~~~~~~~~~~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~---~~~PVIvFSFSkkeCE~~Al  401 (1041)
T KOG0948|consen  325 KGKFREDNFQKAMSVLRKAGESDGKKKANKKGRKGGTGGKGPGDSDIYKIVKMIMER---NYLPVIVFSFSKKECEAYAL  401 (1041)
T ss_pred             ccccchHHHHHHHHHhhccCCCccccccccccccCCcCCCCCCcccHHHHHHHHHhh---cCCceEEEEecHhHHHHHHH
Confidence            0  0111111                                   111222222222   46789999999999999998


Q ss_pred             HHHhh-------------------------------------------------cCHHHHHHHHHHHhcCCccEEEEcCc
Q psy7952         319 ALRRK-------------------------------------------------VNKHERSRVQESFMRGEINVITATIS  349 (444)
Q Consensus       319 ~L~~~-------------------------------------------------~~~~~r~~~~~~f~~g~~~vLvaT~~  349 (444)
                      .+.+.                                                 +-+--++-++-.|..|-+++|.||.+
T Consensus       402 qm~kldfN~deEk~~V~~iF~nAi~~LseeDr~LPqie~iLPLL~RGIGIHHsGLLPIlKE~IEILFqEGLvKvLFATET  481 (1041)
T KOG0948|consen  402 QMSKLDFNTDEEKELVETIFNNAIDQLSEEDRELPQIENILPLLRRGIGIHHSGLLPILKEVIEILFQEGLVKVLFATET  481 (1041)
T ss_pred             hhccCcCCChhHHHHHHHHHHHHHHhcChhhccchHHHHHHHHHHhccccccccchHHHHHHHHHHHhccHHHHHHhhhh
Confidence            88766                                                 44556667777889999999999999


Q ss_pred             cccccccCCccEEEEeCCC---------CCHHHHHHHhccCCCCCCc--eeEEEEeccc-chhhHHHHHhhccchhHH
Q psy7952         350 FGMGIDRQNVRFVVHWGMP---------SSIPAYYQESGRAGRDGLQ--SYCRIYHSEH-SKKSLEYVIKTDTSTKRE  415 (444)
Q Consensus       350 ~~~Gidi~~~~~Vi~~~~p---------~s~~~~~Qr~GR~~R~g~~--g~~~~~~~~~-~~~~~~~~~~~~~~~~~~  415 (444)
                      ++.|+|+|.-.+|+ ...-         -|.-+|+||.|||||.|..  |.|++.++.. +....+.+.+-.....++
T Consensus       482 FsiGLNMPAkTVvF-T~~rKfDG~~fRwissGEYIQMSGRAGRRG~DdrGivIlmiDekm~~~~ak~m~kG~aD~LnS  558 (1041)
T KOG0948|consen  482 FSIGLNMPAKTVVF-TAVRKFDGKKFRWISSGEYIQMSGRAGRRGIDDRGIVILMIDEKMEPQVAKDMLKGSADPLNS  558 (1041)
T ss_pred             hhhccCCcceeEEE-eeccccCCcceeeecccceEEecccccccCCCCCceEEEEecCcCCHHHHHHHhcCCCcchhh
Confidence            99999999554444 3322         2667899999999999865  7777777644 556666666655444433

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.92  E-value=3.6e-24  Score=217.12  Aligned_cols=322  Identities=19%  Similarity=0.162  Sum_probs=216.0

Q ss_pred             HHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchh
Q psy7952          36 LTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPIL  115 (444)
Q Consensus        36 ~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~  115 (444)
                      +.++.++.+|..+|.  .|.-..-.+.+|   -+..++||+|||++        +.+|+++..+. +..   |-|++|+.
T Consensus        70 vrEa~~R~lg~~~~d--vQlig~l~L~~G---~Iaem~TGeGKTLv--------a~lpa~l~aL~-G~~---V~IvTpn~  132 (830)
T PRK12904         70 VREASKRVLGMRHFD--VQLIGGMVLHEG---KIAEMKTGEGKTLV--------ATLPAYLNALT-GKG---VHVVTVND  132 (830)
T ss_pred             HHHHHHHHhCCCCCc--cHHHhhHHhcCC---chhhhhcCCCcHHH--------HHHHHHHHHHc-CCC---EEEEecCH
Confidence            346677777988744  797777777666   48999999999999        55555333332 223   47999999


Q ss_pred             hhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH------
Q psy7952         116 SSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL------  187 (444)
Q Consensus       116 ~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~------  187 (444)
                      .||  .|..+.+..+  ..|   +++..+.++.+..++...+        .++|+++||..+.   |+.+..+.      
T Consensus       133 yLA--~rd~e~~~~l~~~LG---lsv~~i~~~~~~~er~~~y--------~~dI~ygT~~elg---fDyLrd~~~~~~~~  196 (830)
T PRK12904        133 YLA--KRDAEWMGPLYEFLG---LSVGVILSGMSPEERREAY--------AADITYGTNNEFG---FDYLRDNMVFSLEE  196 (830)
T ss_pred             HHH--HHHHHHHHHHHhhcC---CeEEEEcCCCCHHHHHHhc--------CCCeEEECCcchh---hhhhhcccccchhh
Confidence            999  3334444444  556   9999999998887776655        4899999999985   24444333      


Q ss_pred             HhhCCccEEEEecccccc-ccC----------CCcHHHHHHHHHHHHhh-------------------------------
Q psy7952         188 VRYNKLAYIVVDEAHCVS-EWG----------HDFRPTYRRLGELRQFT-------------------------------  225 (444)
Q Consensus       188 ~~~~~~~~iViDE~H~~~-~~~----------~~~~~~~~~l~~~~~~~-------------------------------  225 (444)
                      .....+.++|+||+|.++ +..          ......|..+..+.+.+                               
T Consensus       197 ~~~r~~~~aIvDEaDsiLIDeArtpLiiSg~~~~~~~~y~~~~~~v~~l~~~~dy~vde~~~~v~lte~G~~~~e~~~~~  276 (830)
T PRK12904        197 RVQRGLNYAIVDEVDSILIDEARTPLIISGPAEDSSELYKRANKIVPTLEKEGDYTVDEKSRTVGLTEEGIEKAEKLLGI  276 (830)
T ss_pred             hcccccceEEEechhhheeccCCCceeeECCCCcccHHHHHHHHHHHhcCCCCCeEEEcCCCeeeECHHHHHHHHHHhCC
Confidence            225678999999999883 311          00001111111111111                               


Q ss_pred             --------------------------------------------------------------------------------
Q psy7952         226 --------------------------------------------------------------------------------  225 (444)
Q Consensus       226 --------------------------------------------------------------------------------  225 (444)
                                                                                                      
T Consensus       277 ~~ly~~~~~~~~~~i~~AL~A~~l~~~d~dYiV~dg~V~ivDe~TGR~~~gr~ws~GLHQaiEaKE~v~i~~e~~t~a~I  356 (830)
T PRK12904        277 ENLYDPENIALVHHLNQALRAHELFKRDVDYIVKDGEVVIVDEFTGRLMPGRRYSDGLHQAIEAKEGVKIQNENQTLASI  356 (830)
T ss_pred             ccccChhhhHHHHHHHHHHHHHHHHhcCCcEEEECCEEEEEECCCCccCCCCccchHHHHHHHHhcCCCCCCCceeeeee
Confidence                                                                                            


Q ss_pred             ------CCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEE--EcccchhhHHHHHHHHHHHhccCC
Q psy7952         226 ------GNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVI--FDDLLKDSYAHVKEFIEKCLGKDN  297 (444)
Q Consensus       226 ------~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~l~~~~  297 (444)
                            .-..++.+||+|.... ...+.+..++    .+..-+..+|.+.....  .......++..+.+.+.+..    
T Consensus       357 t~qn~Fr~Y~kl~GmTGTa~te-~~E~~~iY~l----~vv~IPtnkp~~r~d~~d~i~~t~~~K~~aI~~~I~~~~----  427 (830)
T PRK12904        357 TFQNYFRMYEKLAGMTGTADTE-AEEFREIYNL----DVVVIPTNRPMIRIDHPDLIYKTEKEKFDAVVEDIKERH----  427 (830)
T ss_pred             eHHHHHHhcchhcccCCCcHHH-HHHHHHHhCC----CEEEcCCCCCeeeeeCCCeEEECHHHHHHHHHHHHHHHH----
Confidence                  0111246666666432 3333333332    22222334454443311  11122344555555554432    


Q ss_pred             CCCceEEEEecccchHHHHHHHHHhh--------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCc----------
Q psy7952         298 KANNCGIIYCRTREHTTDLADALRRK--------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNV----------  359 (444)
Q Consensus       298 ~~~~~~iVf~~s~~~~~~l~~~L~~~--------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~----------  359 (444)
                      ..+.++||||+|++.++.++..|.+.        -...+|...+..|+.++..|+|||++++||+||+=-          
T Consensus       428 ~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnakq~eREa~Iia~Ag~~g~VtIATNmAGRGtDI~LgGn~~~~~~~~  507 (830)
T PRK12904        428 KKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAKNHEREAEIIAQAGRPGAVTIATNMAGRGTDIKLGGNPEMLAAAL  507 (830)
T ss_pred             hcCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCchHHHHHHHHHhcCCCceEEEecccccCCcCccCCCchhhhhhhh
Confidence            25789999999999999999999877        346789999999999999999999999999999732          


Q ss_pred             ----------------------------cEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         360 ----------------------------RFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       360 ----------------------------~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                                                  -+||-...|.|.+---|-.||+||.|.+|.+..|++-+|.
T Consensus       508 ~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVigTerhesrRid~QlrGRagRQGdpGss~f~lSleD~  575 (830)
T PRK12904        508 LEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLEDD  575 (830)
T ss_pred             hhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEecccCchHHHHHHhhcccccCCCCCceeEEEEcCcH
Confidence                                        2688888999999999999999999999999999986654

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

Probab=99.92  E-value=1.8e-24  Score=213.45  Aligned_cols=305  Identities=13%  Similarity=0.065  Sum_probs=195.9

Q ss_pred             chHHHHHHHHHH----ccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccch
Q psy7952          51 CELQKKAIRHIL----LRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDK  126 (444)
Q Consensus        51 t~~Q~~~~~~~~----~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~  126 (444)
                      ..||..|+.++.    +|++.++++++||+|||.+|+         . ++..+++.+..+||||++-+++|+     .|.
T Consensus       167 RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAi---------a-ii~rL~r~~~~KRVLFLaDR~~Lv-----~QA  231 (875)
T COG4096         167 RYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAI---------A-IIDRLIKSGWVKRVLFLADRNALV-----DQA  231 (875)
T ss_pred             hHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHH---------H-HHHHHHhcchhheeeEEechHHHH-----HHH
Confidence            369999987655    466779999999999998843         2 256688888889999999999999     666


Q ss_pred             Hhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHH-HHHHHHhhCCccEEEEeccccc
Q psy7952         127 TSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHY-LLQHLVRYNKLAYIVVDEAHCV  204 (444)
Q Consensus       127 ~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~-~~~~~~~~~~~~~iViDE~H~~  204 (444)
                      ...+ .+.+..-....+.+...              ...++|.++|++.+....-.. ..........+++|||||||+-
T Consensus       232 ~~af~~~~P~~~~~n~i~~~~~--------------~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRg  297 (875)
T COG4096         232 YGAFEDFLPFGTKMNKIEDKKG--------------DTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRG  297 (875)
T ss_pred             HHHHHHhCCCccceeeeecccC--------------CcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhh
Confidence            6555 33222122222222221              236799999999875311010 0011112345899999999983


Q ss_pred             cccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHh-cCCCC------------------eEEEecCCCC
Q psy7952         205 SEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVL-KFNKP------------------YKVFKTSTFR  265 (444)
Q Consensus       205 ~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l-~~~~~------------------~~~~~~~~~~  265 (444)
                            .-..+..+...+.     ...+++||||......+-..++ |.+..                  +.+. .....
T Consensus       298 ------i~~~~~~I~dYFd-----A~~~gLTATP~~~~d~~T~~~F~g~Pt~~YsleeAV~DGfLvpy~vi~i~-~~~~~  365 (875)
T COG4096         298 ------IYSEWSSILDYFD-----AATQGLTATPKETIDRSTYGFFNGEPTYAYSLEEAVEDGFLVPYKVIRID-TDFDL  365 (875)
T ss_pred             ------HHhhhHHHHHHHH-----HHHHhhccCcccccccccccccCCCcceeecHHHHhhccccCCCCceEEe-eeccc
Confidence                  2233344433333     2245669999886655555555 32210                  0000 00000


Q ss_pred             CCc---------------------eEEEEE---cccchhhHHHHHHHHHHHhcc--CCCCCceEEEEecccchHHHHHHH
Q psy7952         266 SNL---------------------FYDVIF---DDLLKDSYAHVKEFIEKCLGK--DNKANNCGIIYCRTREHTTDLADA  319 (444)
Q Consensus       266 ~~~---------------------~~~~~~---~~~~~~~~~~~~~~l~~~l~~--~~~~~~~~iVf~~s~~~~~~l~~~  319 (444)
                      ..+                     .+....   ........+.+...+.+.+..  .+..-+|+||||.+..+|+.+...
T Consensus       366 ~G~~~~~~serek~~g~~i~~dd~~~~~~d~dr~~v~~~~~~~V~r~~~~~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~  445 (875)
T COG4096         366 DGWKPDAGSEREKLQGEAIDEDDQNFEARDFDRTLVIPFRTETVARELTEYLKRGATGDEIGKTIVFAKNHDHAERIREA  445 (875)
T ss_pred             cCcCcCccchhhhhhccccCcccccccccccchhccccchHHHHHHHHHHHhccccCCCccCceEEEeeCcHHHHHHHHH
Confidence            000                     000000   001112334566777777777  443467999999999999999999


Q ss_pred             HHhh-------------cCHHHHHHHHHHHhc--CCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCC
Q psy7952         320 LRRK-------------VNKHERSRVQESFMR--GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD  384 (444)
Q Consensus       320 L~~~-------------~~~~~r~~~~~~f~~--g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~  384 (444)
                      |...             ...+.-...+..|..  .-.+|.|+.+++..|||+|.|..+|++..-.|...|-||+||+.|.
T Consensus       446 ~~~~ype~~~~~a~~IT~d~~~~q~~Id~f~~ke~~P~IaitvdlL~TGiDvpev~nlVF~r~VrSktkF~QMvGRGTRl  525 (875)
T COG4096         446 LVNEYPEYNGRYAMKITGDAEQAQALIDNFIDKEKYPRIAITVDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRGTRL  525 (875)
T ss_pred             HHHhCccccCceEEEEeccchhhHHHHHHHHhcCCCCceEEehhhhhcCCCchheeeeeehhhhhhHHHHHHHhcCcccc
Confidence            9887             344555566777754  3468999999999999999999999999999999999999999994


Q ss_pred             -C------CceeEEEEecc
Q psy7952         385 -G------LQSYCRIYHSE  396 (444)
Q Consensus       385 -g------~~g~~~~~~~~  396 (444)
                       +      +....+.+++-
T Consensus       526 ~~~~~~~~~dK~~F~ifDf  544 (875)
T COG4096         526 CPDLGGPEQDKEFFTIFDF  544 (875)
T ss_pred             CccccCccccceeEEEEEh
Confidence             2      22455666653

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.92  E-value=2.6e-23  Score=210.12  Aligned_cols=325  Identities=18%  Similarity=0.149  Sum_probs=199.9

Q ss_pred             HHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcch
Q psy7952          35 ELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPI  114 (444)
Q Consensus        35 ~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~  114 (444)
                      -+.++.++.+|..++  +.|.-..-.+.+| +  +..+.||.|||++|++        |+ .-....+..   |-+++|+
T Consensus        68 ~vrEa~~R~~g~~~~--dvQlig~l~l~~G-~--iaEm~TGEGKTLvA~l--------~a-~l~al~G~~---v~vvT~n  130 (796)
T PRK12906         68 VAREGAKRVLGLRPF--DVQIIGGIVLHEG-N--IAEMKTGEGKTLTATL--------PV-YLNALTGKG---VHVVTVN  130 (796)
T ss_pred             HHHHHHHHHhCCCCc--hhHHHHHHHHhcC-C--cccccCCCCCcHHHHH--------HH-HHHHHcCCC---eEEEecc
Confidence            345677788898864  4798877777776 3  8999999999999554        33 111223333   4899999


Q ss_pred             hhhhcccCccchHhhh-----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH-
Q psy7952         115 LSSFYLRFRDDKTSIV-----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV-  188 (444)
Q Consensus       115 ~~L~~~~q~~~~~~~l-----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~-  188 (444)
                      .-||     .+..+.+     .+|   +.+..+.++.+..++...+        .+||+++|...+.   |+++..++. 
T Consensus       131 eyLA-----~Rd~e~~~~~~~~LG---l~vg~i~~~~~~~~r~~~y--------~~dI~Y~t~~e~g---fDyLRD~m~~  191 (796)
T PRK12906        131 EYLS-----SRDATEMGELYRWLG---LTVGLNLNSMSPDEKRAAY--------NCDITYSTNSELG---FDYLRDNMVV  191 (796)
T ss_pred             HHHH-----HhhHHHHHHHHHhcC---CeEEEeCCCCCHHHHHHHh--------cCCCeecCCcccc---ccchhhcccc
Confidence            9999     6666655     566   9999999988887776666        6899999988886   344444321 


Q ss_pred             -----hhCCccEEEEecccccc-ccC----------CCcHHHHHHHHHHHHhhCC-------------------CCcEEE
Q psy7952         189 -----RYNKLAYIVVDEAHCVS-EWG----------HDFRPTYRRLGELRQFTGN-------------------SIPIIA  233 (444)
Q Consensus       189 -----~~~~~~~iViDE~H~~~-~~~----------~~~~~~~~~l~~~~~~~~~-------------------~~~~v~  233 (444)
                           ....+.+.||||+|.++ +..          ......|..+..+...+..                   ..+.+.
T Consensus       192 ~~~~~v~r~~~~aIvDEvDSiLiDeartPLiisg~~~~~~~~y~~~~~~v~~l~~~~~~~~~~~~~~~dy~id~~~k~v~  271 (796)
T PRK12906        192 YKEQMVQRPLNYAIVDEVDSILIDEARTPLIISGQAEKATDLYIRADRFVKTLIKDEAEDGDDDEDTGDYKIDEKTKTIS  271 (796)
T ss_pred             chhhhhccCcceeeeccchheeeccCCCceecCCCCCcchHHHHHHHHHHHHHHhhhhccccccCCCCceEEEcccCcee
Confidence                 13468999999999873 211          1122233333333322211                   012222


Q ss_pred             Eecc-------------C-Ccc---hHHHHHHH------hcCCCC-------eE--------------------------
Q psy7952         234 LTAT-------------A-EPS---VKQDIISV------LKFNKP-------YK--------------------------  257 (444)
Q Consensus       234 lSAT-------------~-~~~---~~~~~~~~------l~~~~~-------~~--------------------------  257 (444)
                      +|..             + ...   ....+...      +.-...       +.                          
T Consensus       272 lte~G~~~~e~~~~i~~l~~~~~~~~~~~i~~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~ws~GLHQaieaK  351 (796)
T PRK12906        272 LTEQGIRKAEKLFGLDNLYDSENTALAHHIDQALRANYIMLKDIDYVVQDGEVLIVDEFTGRVMEGRRYSDGLHQAIEAK  351 (796)
T ss_pred             ecHHHHHHHHHHcCCccccCchhhhHHHHHHHHHHHHHHHhcCCcEEEECCEEEEEeCCCCCcCCCCccChHHHHHHHHh
Confidence            3321             0 000   00000000      000000       00                          


Q ss_pred             ------------------------------------------------EEecCCCCCCceEEEE--EcccchhhHHHHHH
Q psy7952         258 ------------------------------------------------VFKTSTFRSNLFYDVI--FDDLLKDSYAHVKE  287 (444)
Q Consensus       258 ------------------------------------------------~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~  287 (444)
                                                                      +..-+..+|.+.....  .......++..+.+
T Consensus       352 e~v~i~~e~~t~a~It~qnfFr~Y~kl~GmTGTa~~e~~Ef~~iY~l~vv~IPtnkp~~r~d~~d~i~~t~~~K~~al~~  431 (796)
T PRK12906        352 EGVKIQEENQTLATITYQNFFRMYKKLSGMTGTAKTEEEEFREIYNMEVITIPTNRPVIRKDSPDLLYPTLDSKFNAVVK  431 (796)
T ss_pred             cCCCcCCCceeeeeehHHHHHHhcchhhccCCCCHHHHHHHHHHhCCCEEEcCCCCCeeeeeCCCeEEcCHHHHHHHHHH
Confidence                                                            1111111222111110  00011223333333


Q ss_pred             HHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh--------cCHHHHHHHHHHHhcCCccEEEEcCccccccccC--
Q psy7952         288 FIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK--------VNKHERSRVQESFMRGEINVITATISFGMGIDRQ--  357 (444)
Q Consensus       288 ~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~--------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~--  357 (444)
                      .+..    ....+.++||||+|++.++.++..|.+.        -...+++..+-.+.-.+..|+|||++++||.||+  
T Consensus       432 ~i~~----~~~~g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~VtIATnmAGRGtDI~l~  507 (796)
T PRK12906        432 EIKE----RHAKGQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGAVTIATNMAGRGTDIKLG  507 (796)
T ss_pred             HHHH----HHhCCCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCceEEEEeccccCCCCCCCC
Confidence            3333    2336899999999999999999999887        1122444444343434455999999999999995  


Q ss_pred             -Ccc-----EEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         358 -NVR-----FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       358 -~~~-----~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                       ++.     +||+++.|.|.+.|.|++||+||.|.+|.+..+++.+|.
T Consensus       508 ~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG~~G~s~~~~sleD~  555 (796)
T PRK12906        508 PGVKELGGLAVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLEDD  555 (796)
T ss_pred             cchhhhCCcEEEeeecCCcHHHHHHHhhhhccCCCCcceEEEEeccch
Confidence             788     999999999999999999999999999999999987653

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.91  E-value=7.5e-23  Score=207.80  Aligned_cols=324  Identities=17%  Similarity=0.152  Sum_probs=206.3

Q ss_pred             HHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhh
Q psy7952          37 TAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILS  116 (444)
Q Consensus        37 ~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~  116 (444)
                      .++-++.+|..+|.  .|.-.--.+.+|   -+..++||+|||++        +.+|+++.. ..+.   .|+|++||+.
T Consensus        72 rEa~~R~lg~~~yd--vQliGg~~Lh~G---~Iaem~TGeGKTL~--------a~Lpa~~~a-l~G~---~V~VvTpn~y  134 (896)
T PRK13104         72 REVSLRTLGLRHFD--VQLIGGMVLHEG---NIAEMRTGEGKTLV--------ATLPAYLNA-ISGR---GVHIVTVNDY  134 (896)
T ss_pred             HHHHHHHcCCCcch--HHHhhhhhhccC---ccccccCCCCchHH--------HHHHHHHHH-hcCC---CEEEEcCCHH
Confidence            45566667877644  787666666655   47999999999999        677772222 2332   4599999999


Q ss_pred             hhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH-h----
Q psy7952         117 SFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV-R----  189 (444)
Q Consensus       117 L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~-~----  189 (444)
                      ||  .|..+.+..+  ..|   +.+..+.|+.+...+...+        .++|+|+||..|.   |+++..+.. .    
T Consensus       135 LA--~qd~e~m~~l~~~lG---Ltv~~i~gg~~~~~r~~~y--------~~dIvygT~grlg---fDyLrd~~~~~~~~~  198 (896)
T PRK13104        135 LA--KRDSQWMKPIYEFLG---LTVGVIYPDMSHKEKQEAY--------KADIVYGTNNEYG---FDYLRDNMAFSLTDK  198 (896)
T ss_pred             HH--HHHHHHHHHHhcccC---ceEEEEeCCCCHHHHHHHh--------CCCEEEECChhhh---HHHHhcCCccchHhh
Confidence            99  4445566665  456   9999999998877654444        5899999999984   244444321 1    


Q ss_pred             -hCCccEEEEecccccc-ccC----------CCcHHHHHHHHHHHHhhCC--------------CCcEEEEecc------
Q psy7952         190 -YNKLAYIVVDEAHCVS-EWG----------HDFRPTYRRLGELRQFTGN--------------SIPIIALTAT------  237 (444)
Q Consensus       190 -~~~~~~iViDE~H~~~-~~~----------~~~~~~~~~l~~~~~~~~~--------------~~~~v~lSAT------  237 (444)
                       ...+.++|+||+|.++ |..          ......|..+..+...+..              ..+-+.+|-.      
T Consensus       199 v~r~l~~~IvDEaDsiLIDeArtPLIISg~~~~~~~~y~~~~~~v~~l~~~~~~~~~~dy~idek~~~v~Lte~G~~~~e  278 (896)
T PRK13104        199 VQRELNFAIVDEVDSILIDEARTPLIISGAAEDSSELYIKINSLIPQLKKQEEEGDEGDYTIDEKQKQAHLTDAGHLHIE  278 (896)
T ss_pred             hccccceEEeccHhhhhhhccCCceeeeCCCccchHHHHHHHHHHHHHHhccccCCCCCEEEEcCCCceEEchHHHHHHH
Confidence             2579999999999883 311          1122334333333332211              1233444433      


Q ss_pred             --------CC--cchHH--------HHHHHh------cCCCC-------eEEE---------------------------
Q psy7952         238 --------AE--PSVKQ--------DIISVL------KFNKP-------YKVF---------------------------  259 (444)
Q Consensus       238 --------~~--~~~~~--------~~~~~l------~~~~~-------~~~~---------------------------  259 (444)
                              ++  .+.++        .+...+      .-...       +.++                           
T Consensus       279 ~~~~~~~il~~~~~l~~~~~~~~~~~i~~aL~A~~lf~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQaiEaKE~v  358 (896)
T PRK13104        279 ELLTKAKLLDPGESLYHASNIMLMHHVNAALKAHAMFHRDIDYIVKDNQVVIVDEHTGRTMPGRRWSEGLHQAVEAKEGV  358 (896)
T ss_pred             HHHHhCCccCCcccccCchhhhHHHHHHHHHHHHHHhcCCCceEEECCEEEEEECCCCCcCCCCCcChHHHHHHHHHcCC
Confidence                    00  00000        000000      00000       0111                           


Q ss_pred             -----------------------------------------------ecCCCCCCceEEE--EEcccchhhHHHHHHHHH
Q psy7952         260 -----------------------------------------------KTSTFRSNLFYDV--IFDDLLKDSYAHVKEFIE  290 (444)
Q Consensus       260 -----------------------------------------------~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~  290 (444)
                                                                     .-+..+|.+....  ........++..+.+.+.
T Consensus       359 ~i~~e~~t~AsIT~Qn~Fr~Y~kLsGMTGTa~te~~Ef~~iY~l~Vv~IPtnkp~~R~d~~d~v~~t~~~k~~av~~~i~  438 (896)
T PRK13104        359 PIQNENQTLASITFQNFFRMYNKLSGMTGTADTEAYEFQQIYNLEVVVIPTNRSMIRKDEADLVYLTQADKFQAIIEDVR  438 (896)
T ss_pred             CCCCCceeeeeehHHHHHHhcchhccCCCCChhHHHHHHHHhCCCEEECCCCCCcceecCCCeEEcCHHHHHHHHHHHHH
Confidence                                                           1111111111110  001112233444444444


Q ss_pred             HHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCC--
Q psy7952         291 KCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQN--  358 (444)
Q Consensus       291 ~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~--  358 (444)
                      +.    ...+.|+||||+|++.++.++..|.+.          +...++..+.+.|+.|  .|+|||++++||+||.=  
T Consensus       439 ~~----~~~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G--~VtIATNmAGRGtDI~Lgg  512 (896)
T PRK13104        439 EC----GVRKQPVLVGTVSIEASEFLSQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPG--AVTIATNMAGRGTDIVLGG  512 (896)
T ss_pred             HH----HhCCCCEEEEeCcHHHHHHHHHHHHHcCCCeEeecCCCChHHHHHHHhCCCCC--cEEEeccCccCCcceecCC
Confidence            33    336899999999999999999999888          6788999999999998  49999999999999861  


Q ss_pred             ------------------------------------ccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         359 ------------------------------------VRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       359 ------------------------------------~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                                                          --+||-...+.|.+---|-.||+||.|.+|.+..|++-+|.
T Consensus       513 n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~f~lSleD~  589 (896)
T PRK13104        513 SLAADLANLPADASEQEKEAVKKEWQKRHDEVIAAGGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDN  589 (896)
T ss_pred             chhhhhhccccchhhHHHHHHHHHhhhhhhHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcH
Confidence                                                12688888899999999999999999999999999986654

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

Probab=99.90  E-value=1.2e-22  Score=203.68  Aligned_cols=293  Identities=19%  Similarity=0.230  Sum_probs=199.1

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      -+++.+.+++..|+.+ . ..|+-+...+..| +++.+.||||.|||.-        .++.+    ++-....+|+++++
T Consensus        68 ~e~~~~fF~k~~G~~~-w-s~QR~WakR~~rg-~SFaiiAPTGvGKTTf--------g~~~s----l~~a~kgkr~yii~  132 (1187)
T COG1110          68 YEEFEEFFKKATGFRP-W-SAQRVWAKRLVRG-KSFAIIAPTGVGKTTF--------GLLMS----LYLAKKGKRVYIIV  132 (1187)
T ss_pred             HHHHHHHHHHhhCCCc-h-HHHHHHHHHHHcC-CceEEEcCCCCchhHH--------HHHHH----HHHHhcCCeEEEEe
Confidence            4567778888889975 3 5999999999999 9999999999999965        23333    33333446779999


Q ss_pred             chhhhhcccCccchHhhhc--CCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhh
Q psy7952         113 PILSSFYLRFRDDKTSIVT--GRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRY  190 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l~--~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~  190 (444)
                      ||..|+  .|+.+.++.+.  .+...+... +|+.....+..+..+.+.  .++.||+|+|..-+.        .+...+
T Consensus       133 PT~~Lv--~Q~~~kl~~~~e~~~~~~~~~~-yh~~l~~~ekee~le~i~--~gdfdIlitTs~FL~--------k~~e~L  199 (1187)
T COG1110         133 PTTTLV--RQVYERLKKFAEDAGSLDVLVV-YHSALPTKEKEEALERIE--SGDFDILITTSQFLS--------KRFEEL  199 (1187)
T ss_pred             cCHHHH--HHHHHHHHHHHhhcCCcceeee-eccccchHHHHHHHHHHh--cCCccEEEEeHHHHH--------hhHHHh
Confidence            999999  44445555551  222234444 888888888888888876  588999999955542        222223


Q ss_pred             --CCccEEEEeccccccccCCCcHHHH-----------------------------HHHHHHHHh--------hCCCCcE
Q psy7952         191 --NKLAYIVVDEAHCVSEWGHDFRPTY-----------------------------RRLGELRQF--------TGNSIPI  231 (444)
Q Consensus       191 --~~~~~iViDE~H~~~~~~~~~~~~~-----------------------------~~l~~~~~~--------~~~~~~~  231 (444)
                        .+|++|++|++|.++..+......+                             ..+.+....        -.+...+
T Consensus       200 ~~~kFdfifVDDVDA~LkaskNvDriL~LlGf~eE~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~L  279 (1187)
T COG1110         200 SKLKFDFIFVDDVDAILKASKNVDRLLRLLGFSEEVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGIL  279 (1187)
T ss_pred             cccCCCEEEEccHHHHHhccccHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCceE
Confidence              4799999999999865331111100                             001111000        1223568


Q ss_pred             EEEeccCCcch--HHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecc
Q psy7952         232 IALTATAEPSV--KQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRT  309 (444)
Q Consensus       232 v~lSAT~~~~~--~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s  309 (444)
                      +..|||..+.-  ...+++.+++...    .......|+.-.+..    ....+...++++.+       +..+|||++.
T Consensus       280 vvsSATg~~rg~R~~LfReLlgFevG----~~~~~LRNIvD~y~~----~~~~e~~~elvk~l-------G~GgLIfV~~  344 (1187)
T COG1110         280 VVSSATGKPRGSRLKLFRELLGFEVG----SGGEGLRNIVDIYVE----SESLEKVVELVKKL-------GDGGLIFVPI  344 (1187)
T ss_pred             EEeeccCCCCCchHHHHHHHhCCccC----ccchhhhheeeeecc----CccHHHHHHHHHHh-------CCCeEEEEEc
Confidence            99999976644  2345666665422    111222232222221    15556666777775       6678999999


Q ss_pred             ---cchHHHHHHHHHhh-----cCHHHHHHHHHHHhcCCccEEEEc----CccccccccCC-ccEEEEeCCC
Q psy7952         310 ---REHTTDLADALRRK-----VNKHERSRVQESFMRGEINVITAT----ISFGMGIDRQN-VRFVVHWGMP  368 (444)
Q Consensus       310 ---~~~~~~l~~~L~~~-----~~~~~r~~~~~~f~~g~~~vLvaT----~~~~~Gidi~~-~~~Vi~~~~p  368 (444)
                         ++.++++++.|++.     .-...+...++.|..|++++||+.    .++-+|+|+|. ++.+|++|.|
T Consensus       345 d~G~e~aeel~e~Lr~~Gi~a~~~~a~~~~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvP  416 (1187)
T COG1110         345 DYGREKAEELAEYLRSHGINAELIHAEKEEALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVP  416 (1187)
T ss_pred             HHhHHHHHHHHHHHHhcCceEEEeeccchhhhhhhccCceeEEEEecccccceeecCCchhheeEEEEecCC
Confidence               89999999999988     222334888999999999999986    57899999996 8899999988

>cd00268 DEADc DEAD-box helicases

Probab=99.90  E-value=1.9e-23  Score=185.33  Aligned_cols=188  Identities=19%  Similarity=0.240  Sum_probs=136.1

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC--CccceeEE
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG--NVRSRNGW  110 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~--~~~~~vli  110 (444)
                      +.++.+.+++ +|++. ++++|.++++.+.++ +++++.+|||+|||++        |.+++ +..+...  ...++++|
T Consensus         7 ~~~i~~~l~~-~~~~~-~~~~Q~~~~~~~~~~-~~~li~~~TG~GKT~~--------~~~~~-l~~~~~~~~~~~~~vii   74 (203)
T cd00268           7 SPELLRGIYA-LGFEK-PTPIQARAIPPLLSG-RDVIGQAQTGSGKTAA--------FLIPI-LEKLDPSPKKDGPQALI   74 (203)
T ss_pred             CHHHHHHHHH-cCCCC-CCHHHHHHHHHHhcC-CcEEEECCCCCcHHHH--------HHHHH-HHHHHhhcccCCceEEE
Confidence            4557888888 69997 568999999999998 9999999999999999        66666 4444444  34568899


Q ss_pred             EcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhh
Q psy7952         111 ISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRY  190 (444)
Q Consensus       111 l~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~  190 (444)
                      ++|+++|+  .|+.+.++.+... ..+++..++|+.........+      ..+++|+|+||+.+.    ..+......+
T Consensus        75 i~p~~~L~--~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~------~~~~~iiv~T~~~l~----~~l~~~~~~~  141 (203)
T cd00268          75 LAPTRELA--LQIAEVARKLGKH-TNLKVVVIYGGTSIDKQIRKL------KRGPHIVVATPGRLL----DLLERGKLDL  141 (203)
T ss_pred             EcCCHHHH--HHHHHHHHHHhcc-CCceEEEEECCCCHHHHHHHh------cCCCCEEEEChHHHH----HHHHcCCCCh
Confidence            99999999  2223334444211 238888889888765544333      357899999999974    3333444456


Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHh
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVL  250 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l  250 (444)
                      .+++++|+||+|.+.+.+  +...+..+   ...++.+.+++++|||+++...+.+...+
T Consensus       142 ~~l~~lIvDE~h~~~~~~--~~~~~~~~---~~~l~~~~~~~~~SAT~~~~~~~~~~~~~  196 (203)
T cd00268         142 SKVKYLVLDEADRMLDMG--FEDQIREI---LKLLPKDRQTLLFSATMPKEVRDLARKFL  196 (203)
T ss_pred             hhCCEEEEeChHHhhccC--hHHHHHHH---HHhCCcccEEEEEeccCCHHHHHHHHHHC
Confidence            789999999999987544  44444443   34455578999999999987766655554

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.

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.89  E-value=1.1e-21  Score=205.19  Aligned_cols=310  Identities=14%  Similarity=0.133  Sum_probs=196.1

Q ss_pred             cCchHHHHHHHHHHc---cCCcEEEEccCCCcccccccccccceEEeCCCccccc-cCCccceeEEEcchhhhhcccCcc
Q psy7952          49 FKCELQKKAIRHILL---RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFIL-NGNVRSRNGWISPILSSFYLRFRD  124 (444)
Q Consensus        49 ~~t~~Q~~~~~~~~~---~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~-~~~~~~~vlil~P~~~L~~~~q~~  124 (444)
                      ++ +||.+.+..+..   ...+.|+.-..|.|||+.++.++          ..+. ..+...++|||||...+..   |.
T Consensus       170 Lr-~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIalL----------~~L~~~~~~~gp~LIVvP~SlL~n---W~  235 (1033)
T PLN03142        170 MR-DYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLL----------GYLHEYRGITGPHMVVAPKSTLGN---WM  235 (1033)
T ss_pred             hH-HHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHHH----------HHHHHhcCCCCCEEEEeChHHHHH---HH
Confidence            44 799999998863   22788999999999998733211          1121 2233345599999877762   34


Q ss_pred             chHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccc
Q psy7952         125 DKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCV  204 (444)
Q Consensus       125 ~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~  204 (444)
                      +.+..+...   +.+..++|.....  ........ ..+.++|+|+|++.+..      .........+++||+||+|++
T Consensus       236 ~Ei~kw~p~---l~v~~~~G~~~eR--~~~~~~~~-~~~~~dVvITSYe~l~~------e~~~L~k~~W~~VIvDEAHrI  303 (1033)
T PLN03142        236 NEIRRFCPV---LRAVKFHGNPEER--AHQREELL-VAGKFDVCVTSFEMAIK------EKTALKRFSWRYIIIDEAHRI  303 (1033)
T ss_pred             HHHHHHCCC---CceEEEeCCHHHH--HHHHHHHh-cccCCCcceecHHHHHH------HHHHhccCCCCEEEEcCcccc
Confidence            555555444   7777787754322  12111111 24578999999888642      112223346899999999997


Q ss_pred             cccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEec---------C-------------
Q psy7952         205 SEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT---------S-------------  262 (444)
Q Consensus       205 ~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~---------~-------------  262 (444)
                      -...       ..+.+.+..+.. ...+++||||..+...++...+.+-.|-.....         .             
T Consensus       304 KN~~-------Sklskalr~L~a-~~RLLLTGTPlqNnl~ELwsLL~FL~P~~f~s~~~F~~~f~~~~~~~~~e~i~~L~  375 (1033)
T PLN03142        304 KNEN-------SLLSKTMRLFST-NYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQQEVVQQLH  375 (1033)
T ss_pred             CCHH-------HHHHHHHHHhhc-CcEEEEecCCCCCCHHHHHHHHhcCCCCcCCCHHHHHHHHccccccchHHHHHHHH
Confidence            5432       222222333333 556899999988777766666554322110000         0             


Q ss_pred             ----------------CCCCCceEEEEEcccch---hhH-----------------------------------------
Q psy7952         263 ----------------TFRSNLFYDVIFDDLLK---DSY-----------------------------------------  282 (444)
Q Consensus       263 ----------------~~~~~~~~~~~~~~~~~---~~~-----------------------------------------  282 (444)
                                      ...|+............   ..+                                         
T Consensus       376 ~~L~pf~LRR~KsdV~~~LPpK~e~iv~v~LS~~Qk~lY~~ll~k~~~~l~~g~~~~~LlnilmqLRk~cnHP~L~~~~e  455 (1033)
T PLN03142        376 KVLRPFLLRRLKSDVEKGLPPKKETILKVGMSQMQKQYYKALLQKDLDVVNAGGERKRLLNIAMQLRKCCNHPYLFQGAE  455 (1033)
T ss_pred             HHhhHHHhhhhHHHHhhhCCCceeEEEeeCCCHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCHHhhhccc
Confidence                            00111111111111000   000                                         


Q ss_pred             --------------HHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhc
Q psy7952         283 --------------AHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMR  338 (444)
Q Consensus       283 --------------~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~  338 (444)
                                    .....++..++......+.++|||+........+.+.|...          ++..+|...++.|..
T Consensus       456 p~~~~~~~e~lie~SgKl~lLdkLL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~  535 (1033)
T PLN03142        456 PGPPYTTGEHLVENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNK  535 (1033)
T ss_pred             ccCcccchhHHhhhhhHHHHHHHHHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhcc
Confidence                          00111222233333335789999999999898888888655          888999999999975


Q ss_pred             C---CccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEE
Q psy7952         339 G---EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRI  392 (444)
Q Consensus       339 g---~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~  392 (444)
                      .   ...+|++|.+++.|||+..+++||+||+++++....|++||+.|-|+...+.+
T Consensus       536 ~~s~~~VfLLSTrAGGlGINLt~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~V  592 (1033)
T PLN03142        536 PGSEKFVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQV  592 (1033)
T ss_pred             ccCCceEEEEeccccccCCchhhCCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEE
Confidence            3   23568999999999999999999999999999999999999999998866544

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

Probab=99.88  E-value=2.8e-22  Score=201.72  Aligned_cols=322  Identities=18%  Similarity=0.157  Sum_probs=213.8

Q ss_pred             chHHHHHHHHHHcc---CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchH
Q psy7952          51 CELQKKAIRHILLR---THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKT  127 (444)
Q Consensus        51 t~~Q~~~~~~~~~~---~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~  127 (444)
                      ++-|+.++..+...   ....++.+.||||||.+        |+ .++.+.+..+...   |+++|..+|.     .+.+
T Consensus       200 n~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEv--------Yl-~~i~~~L~~Gkqv---LvLVPEI~Lt-----pq~~  262 (730)
T COG1198         200 NQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEV--------YL-EAIAKVLAQGKQV---LVLVPEIALT-----PQLL  262 (730)
T ss_pred             CHHHHHHHHHHHHhcccccceeEeCCCCCcHHHH--------HH-HHHHHHHHcCCEE---EEEeccccch-----HHHH
Confidence            46899999988765   47799999999999999        54 3324444445444   9999999999     8888


Q ss_pred             hhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccc
Q psy7952         128 SIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVS  205 (444)
Q Consensus       128 ~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~  205 (444)
                      .++  +++   .++..++++.+..++...+....  .+...|+|||=           ..-+..+.++++||+||=|.-.
T Consensus       263 ~rf~~rFg---~~v~vlHS~Ls~~er~~~W~~~~--~G~~~vVIGtR-----------SAlF~Pf~~LGLIIvDEEHD~s  326 (730)
T COG1198         263 ARFKARFG---AKVAVLHSGLSPGERYRVWRRAR--RGEARVVIGTR-----------SALFLPFKNLGLIIVDEEHDSS  326 (730)
T ss_pred             HHHHHHhC---CChhhhcccCChHHHHHHHHHHh--cCCceEEEEec-----------hhhcCchhhccEEEEecccccc
Confidence            999  778   99999999999888877776664  58899999992           2334457799999999999753


Q ss_pred             ccCC-CcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCC--CCCCceEEEEEcccchh--
Q psy7952         206 EWGH-DFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST--FRSNLFYDVIFDDLLKD--  280 (444)
Q Consensus       206 ~~~~-~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~--  280 (444)
                      -... ..+..-..+.-++.... ++++|+-||||.=.....+..  +-.....+.....  ..|.+...-...+....  
T Consensus       327 YKq~~~prYhARdvA~~Ra~~~-~~pvvLgSATPSLES~~~~~~--g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~  403 (730)
T COG1198         327 YKQEDGPRYHARDVAVLRAKKE-NAPVVLGSATPSLESYANAES--GKYKLLRLTNRAGRARLPRVEIIDMRKEPLETGR  403 (730)
T ss_pred             ccCCcCCCcCHHHHHHHHHHHh-CCCEEEecCCCCHHHHHhhhc--CceEEEEccccccccCCCcceEEeccccccccCc
Confidence            2211 12222233333333333 489999999996554443311  1001111111111  12222222222221111  


Q ss_pred             -hHHHHHHHHHHHhccCCCCCceEEEEecccchHHHH-------------------------------------------
Q psy7952         281 -SYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDL-------------------------------------------  316 (444)
Q Consensus       281 -~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l-------------------------------------------  316 (444)
                       -...+.+.+.+.++    .++++|+|.|.+..+-.+                                           
T Consensus       404 ~lS~~Ll~~i~~~l~----~geQ~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp  479 (730)
T COG1198         404 SLSPALLEAIRKTLE----RGEQVLLFLNRRGYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCP  479 (730)
T ss_pred             cCCHHHHHHHHHHHh----cCCeEEEEEccCCccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCC
Confidence             12344555555444    477888888776654332                                           


Q ss_pred             -----------------HHHHHhh--------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEe
Q psy7952         317 -----------------ADALRRK--------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHW  365 (444)
Q Consensus       317 -----------------~~~L~~~--------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~  365 (444)
                                       .+.|.+.              ..+..-...++.|.+|+.+|||+|+++.-|.|+|++..|...
T Consensus       480 ~Cgs~~L~~~G~GterieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl  559 (730)
T COG1198         480 ECGSEHLRAVGPGTERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVL  559 (730)
T ss_pred             CCCCCeeEEecccHHHHHHHHHHHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEE
Confidence                             1111111              345556788999999999999999999999999999987655


Q ss_pred             CCCC------------CHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhhccch
Q psy7952         366 GMPS------------SIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTST  412 (444)
Q Consensus       366 ~~p~------------s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~  412 (444)
                      +...            ....+.|..||+||.+.+|.+++-.-..+...++.+...+...
T Consensus       560 ~aD~~L~~~DfRA~Er~fqll~QvaGRAgR~~~~G~VvIQT~~P~hp~i~~~~~~dy~~  618 (730)
T COG1198         560 DADTGLGSPDFRASERTFQLLMQVAGRAGRAGKPGEVVIQTYNPDHPAIQALKRGDYEA  618 (730)
T ss_pred             echhhhcCCCcchHHHHHHHHHHHHhhhccCCCCCeEEEEeCCCCcHHHHHHHhcCHHH
Confidence            5322            3555789999999999999999888877877777777655443

>KOG0949|consensus

Probab=99.88  E-value=3.9e-22  Score=198.13  Aligned_cols=88  Identities=26%  Similarity=0.388  Sum_probs=70.9

Q ss_pred             cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCC--CCCHHHHHHHhccCCCCCCceeEEEEecccchhh
Q psy7952         324 VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGM--PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKS  401 (444)
Q Consensus       324 ~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~--p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~  401 (444)
                      ++..+|..++-.|+.|...||+||.+++-|||+| |++|++.+-  --++-+|.|+.|||||.|-.-.+-+++-.-...+
T Consensus       972 lNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMP-CrTVvF~gDsLQL~plny~QmaGRAGRRGFD~lGnV~FmgiP~~k 1050 (1330)
T KOG0949|consen  972 LNRKYRSLVEVLFRQGHLQVLFATETLSLGINMP-CRTVVFAGDSLQLDPLNYKQMAGRAGRRGFDTLGNVVFMGIPRQK 1050 (1330)
T ss_pred             cchHHHHHHHHHhhcCceEEEEEeeehhcccCCC-ceeEEEeccccccCchhHHhhhccccccccccccceEEEeCcHHH
Confidence            8899999999999999999999999999999999 555554442  3478899999999999998755555555566667


Q ss_pred             HHHHHhhccch
Q psy7952         402 LEYVIKTDTST  412 (444)
Q Consensus       402 ~~~~~~~~~~~  412 (444)
                      ++.+....++.
T Consensus      1051 v~rLlts~L~d 1061 (1330)
T KOG0949|consen 1051 VQRLLTSLLPD 1061 (1330)
T ss_pred             HHHHHHHhhhc
Confidence            77777665554

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.88  E-value=1e-21  Score=203.71  Aligned_cols=327  Identities=17%  Similarity=0.159  Sum_probs=186.6

Q ss_pred             chHHHHHHHHHHccC--C-cEEEEccCCCcccccccccccceEEeCCCcccccc-CCccceeEEEcchhhhhcccCccch
Q psy7952          51 CELQKKAIRHILLRT--H-DIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN-GNVRSRNGWISPILSSFYLRFRDDK  126 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~--~-~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~-~~~~~~vlil~P~~~L~~~~q~~~~  126 (444)
                      .++|..++..+....  . .+++.||||+|||.+++.++..         .+.. ....+|++++.|+++++     +++
T Consensus       197 ~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~---------~~~~~~~~~~r~i~vlP~~t~i-----e~~  262 (733)
T COG1203         197 YELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALA---------LLDEKIKLKSRVIYVLPFRTII-----EDM  262 (733)
T ss_pred             hHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHH---------HhhccccccceEEEEccHHHHH-----HHH
Confidence            468999999888742  4 7899999999999996554332         1222 22456789999999999     666


Q ss_pred             Hhhh--cCCCCceeEEEEeCCCChhhHHHHHH---HH-----HhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEE
Q psy7952         127 TSIV--TGRSDLYQLELIVSGQTKTENKAILE---EL-----RLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYI  196 (444)
Q Consensus       127 ~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~---~~-----~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~i  196 (444)
                      .+++  ..+...+.....++..........-.   ..     .....-..+.++||.......+..........-..+++
T Consensus       263 ~~r~~~~~~~~~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~v  342 (733)
T COG1203         263 YRRAKEIFGLFSVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLV  342 (733)
T ss_pred             HHHHHhhhcccccccccccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhch
Confidence            6666  12211122221344332221110000   00     00001123333333332210000000000000123789


Q ss_pred             EEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcc
Q psy7952         197 VVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDD  276 (444)
Q Consensus       197 ViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  276 (444)
                      |+||+|.+.+..  ....+..+...+...  +.++|+||||+|+...+.+....+-......  .....+..........
T Consensus       343 IlDE~h~~~~~~--~~~~l~~~i~~l~~~--g~~ill~SATlP~~~~~~l~~~~~~~~~~~~--~~~~~~~~~e~~~~~~  416 (733)
T COG1203         343 ILDEVHLYADET--MLAALLALLEALAEA--GVPVLLMSATLPPFLKEKLKKALGKGREVVE--NAKFCPKEDEPGLKRK  416 (733)
T ss_pred             hhccHHhhcccc--hHHHHHHHHHHHHhC--CCCEEEEecCCCHHHHHHHHHHHhcccceec--cccccccccccccccc
Confidence            999999987653  233333333443333  3789999999999998888777653322211  1110000000000000


Q ss_pred             cchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHH----hcCCcc
Q psy7952         277 LLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESF----MRGEIN  342 (444)
Q Consensus       277 ~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f----~~g~~~  342 (444)
                      .......................+.+++|.|||+..|.+++..|+..          +...+|.+.++.+    +.+...
T Consensus       417 ~~~~~~~~~~~~~~~~~~~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~  496 (733)
T COG1203         417 ERVDVEDGPQEELIELISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGF  496 (733)
T ss_pred             cchhhhhhhhHhhhhcchhhhccCCcEEEEEecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCe
Confidence            00000000001122222223346889999999999999999999887          5566777666654    467899


Q ss_pred             EEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCC--CceeEEEEecccchh
Q psy7952         343 VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG--LQSYCRIYHSEHSKK  400 (444)
Q Consensus       343 vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g--~~g~~~~~~~~~~~~  400 (444)
                      |+|||++.+.|+|+. .+.+|-  -+..+++.+||+||++|.|  .+|..+++.......
T Consensus       497 IvVaTQVIEagvDid-fd~mIT--e~aPidSLIQR~GRv~R~g~~~~~~~~v~~~~~~~~  553 (733)
T COG1203         497 IVVATQVIEAGVDID-FDVLIT--ELAPIDSLIQRAGRVNRHGKKENGKIYVYNDEERGP  553 (733)
T ss_pred             EEEEeeEEEEEeccc-cCeeee--cCCCHHHHHHHHHHHhhcccccCCceeEeecccCCC
Confidence            999999999999996 676664  3445999999999999999  677777776544433

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.88  E-value=4.5e-21  Score=194.64  Aligned_cols=133  Identities=16%  Similarity=0.175  Sum_probs=100.1

Q ss_pred             CCccc--CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccC
Q psy7952          45 GFDSF--KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRF  122 (444)
Q Consensus        45 g~~~~--~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q  122 (444)
                      |++..  .+|+|.++++.+..+ ++++..++||+|||++        |.+|+ +..+..+.   .++|++||++|+  .|
T Consensus        86 G~~~p~~~tp~qvQ~I~~i~l~-~gvIAeaqTGeGKTLA--------f~LP~-l~~aL~g~---~v~IVTpTrELA--~Q  150 (970)
T PRK12899         86 GYHQQWDMVPYDVQILGAIAMH-KGFITEMQTGEGKTLT--------AVMPL-YLNALTGK---PVHLVTVNDYLA--QR  150 (970)
T ss_pred             cccCCCCCChHHHHHhhhhhcC-CCeEEEeCCCCChHHH--------HHHHH-HHHHhhcC---CeEEEeCCHHHH--HH
Confidence            67762  278999999999999 9999999999999999        88887 32233333   358999999999  55


Q ss_pred             ccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhh-------CCc
Q psy7952         123 RDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRY-------NKL  193 (444)
Q Consensus       123 ~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~-------~~~  193 (444)
                      +.+.+..+  ..+   +++..+.|+.+...+...+        .++|+|+||.+|.   |+.+.......       ..+
T Consensus       151 dae~m~~L~k~lG---LsV~~i~GG~~~~eq~~~y--------~~DIVygTPgRLg---fDyLrd~~~~~~~~~~vqr~~  216 (970)
T PRK12899        151 DCEWVGSVLRWLG---LTTGVLVSGSPLEKRKEIY--------QCDVVYGTASEFG---FDYLRDNSIATRKEEQVGRGF  216 (970)
T ss_pred             HHHHHHHHHhhcC---CeEEEEeCCCCHHHHHHHc--------CCCEEEECCChhH---HHHhhCCCCCcCHHHhhcccc
Confidence            56777766  456   8999999998877665433        5899999999983   13333332222       356


Q ss_pred             cEEEEeccccccc
Q psy7952         194 AYIVVDEAHCVSE  206 (444)
Q Consensus       194 ~~iViDE~H~~~~  206 (444)
                      .++|+||||.++-
T Consensus       217 ~~~IIDEADsmLi  229 (970)
T PRK12899        217 YFAIIDEVDSILI  229 (970)
T ss_pred             cEEEEechhhhhh
Confidence            8999999999853

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

Probab=99.88  E-value=7.3e-23  Score=176.11  Aligned_cols=162  Identities=23%  Similarity=0.341  Sum_probs=117.2

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      |++|.++++.+.++ +++++.+|||+|||++        +.+++ +..+... ...++++++|+++|+     .++.+.+
T Consensus         1 t~~Q~~~~~~i~~~-~~~li~aptGsGKT~~--------~~~~~-l~~~~~~-~~~~~lii~P~~~l~-----~q~~~~~   64 (169)
T PF00270_consen    1 TPLQQEAIEAIISG-KNVLISAPTGSGKTLA--------YILPA-LNRLQEG-KDARVLIIVPTRALA-----EQQFERL   64 (169)
T ss_dssp             -HHHHHHHHHHHTT-SEEEEECSTTSSHHHH--------HHHHH-HHHHHTT-SSSEEEEEESSHHHH-----HHHHHHH
T ss_pred             CHHHHHHHHHHHcC-CCEEEECCCCCccHHH--------HHHHH-HhhhccC-CCceEEEEeeccccc-----ccccccc
Confidence            68999999999987 8999999999999999        55555 4434444 334779999999999     6666666


Q ss_pred             --cCCCCceeEEEEeCCCChh-hHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccccc
Q psy7952         131 --TGRSDLYQLELIVSGQTKT-ENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEW  207 (444)
Q Consensus       131 --~~~~~~i~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~  207 (444)
                        ......+++..++++.... ......      .++++|+|+||+++.    ..+......+.++++||+||+|.+..+
T Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~ilv~T~~~l~----~~~~~~~~~~~~~~~iViDE~h~l~~~  134 (169)
T PF00270_consen   65 RKFFSNTNVRVVLLHGGQSISEDQREVL------SNQADILVTTPEQLL----DLISNGKINISRLSLIVIDEAHHLSDE  134 (169)
T ss_dssp             HHHTTTTTSSEEEESTTSCHHHHHHHHH------HTTSSEEEEEHHHHH----HHHHTTSSTGTTESEEEEETHHHHHHT
T ss_pred             cccccccccccccccccccccccccccc------cccccccccCcchhh----ccccccccccccceeeccCcccccccc
Confidence              2222347888888887744 222222      357999999999974    222222224566999999999999876


Q ss_pred             CCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcc
Q psy7952         208 GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPS  241 (444)
Q Consensus       208 ~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~  241 (444)
                      +  +...+..+...+.... +.+++++|||+++.
T Consensus       135 ~--~~~~~~~i~~~~~~~~-~~~~i~~SAT~~~~  165 (169)
T PF00270_consen  135 T--FRAMLKSILRRLKRFK-NIQIILLSATLPSN  165 (169)
T ss_dssp             T--HHHHHHHHHHHSHTTT-TSEEEEEESSSTHH
T ss_pred             c--HHHHHHHHHHHhcCCC-CCcEEEEeeCCChh
Confidence            4  6666666665554444 38899999999843

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 ....

>KOG0922|consensus

Probab=99.88  E-value=1e-20  Score=182.90  Aligned_cols=295  Identities=17%  Similarity=0.187  Sum_probs=194.2

Q ss_pred             HHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCcc--ceeEEEcchhhhhcccCccchHhhh
Q psy7952          53 LQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVR--SRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        53 ~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~--~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      +-.+.+..+.++ +-++|.++||+|||.-          +|.   ++...|-.  .++.+.-|.|..+     -...++.
T Consensus        55 ~r~~il~~ve~n-qvlIviGeTGsGKSTQ----------ipQ---yL~eaG~~~~g~I~~TQPRRVAa-----vslA~RV  115 (674)
T KOG0922|consen   55 YRDQILYAVEDN-QVLIVIGETGSGKSTQ----------IPQ---YLAEAGFASSGKIACTQPRRVAA-----VSLAKRV  115 (674)
T ss_pred             HHHHHHHHHHHC-CEEEEEcCCCCCcccc----------HhH---HHHhcccccCCcEEeecCchHHH-----HHHHHHH
Confidence            444567777777 8899999999999944          555   34444422  2367777998665     3444443


Q ss_pred             ------cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccc
Q psy7952         131 ------TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCV  204 (444)
Q Consensus       131 ------~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~  204 (444)
                            ..|   -.|..-..-.+..            .....|.+.|-++|..    . ......+.+.++||+||||. 
T Consensus       116 AeE~~~~lG---~~VGY~IRFed~t------------s~~TrikymTDG~LLR----E-~l~Dp~LskYsvIIlDEAHE-  174 (674)
T KOG0922|consen  116 AEEMGCQLG---EEVGYTIRFEDST------------SKDTRIKYMTDGMLLR----E-ILKDPLLSKYSVIILDEAHE-  174 (674)
T ss_pred             HHHhCCCcC---ceeeeEEEecccC------------CCceeEEEecchHHHH----H-HhcCCccccccEEEEechhh-
Confidence                  333   2332222211111            2467899999998742    1 11222467899999999998 


Q ss_pred             cccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHH
Q psy7952         205 SEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAH  284 (444)
Q Consensus       205 ~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  284 (444)
                        ..-.-.-.+..++++.+..+. .++|.||||+..   +.+.++++. -++...........+.|..  .. ..+..+.
T Consensus       175 --Rsl~TDiLlGlLKki~~~R~~-LklIimSATlda---~kfS~yF~~-a~i~~i~GR~fPVei~y~~--~p-~~dYv~a  244 (674)
T KOG0922|consen  175 --RSLHTDILLGLLKKILKKRPD-LKLIIMSATLDA---EKFSEYFNN-APILTIPGRTFPVEILYLK--EP-TADYVDA  244 (674)
T ss_pred             --hhhHHHHHHHHHHHHHhcCCC-ceEEEEeeeecH---HHHHHHhcC-CceEeecCCCCceeEEecc--CC-chhhHHH
Confidence              332122333445555554444 889999999964   445666542 2333332222222222222  21 2222233


Q ss_pred             HHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------------------cCHHHHHHHHHHHhcCCccEEEE
Q psy7952         285 VKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------------VNKHERSRVQESFMRGEINVITA  346 (444)
Q Consensus       285 ~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------------------~~~~~r~~~~~~f~~g~~~vLva  346 (444)
                      ....+.+.-..  .+.+-++||....++.+.+++.|.+.                  ++.+++..+++.--.|..+|+++
T Consensus       245 ~~~tv~~Ih~~--E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIls  322 (674)
T KOG0922|consen  245 ALITVIQIHLT--EPPGDILVFLTGQEEIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILS  322 (674)
T ss_pred             HHHHHHHHHcc--CCCCCEEEEeCCHHHHHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEE
Confidence            33333333222  35779999999999999999998877                  67778888887777899999999


Q ss_pred             cCccccccccCCccEEEEeCC------------------CCCHHHHHHHhccCCCCCCceeEEEEecccchh
Q psy7952         347 TISFGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK  400 (444)
Q Consensus       347 T~~~~~Gidi~~~~~Vi~~~~------------------p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~  400 (444)
                      |++++..+.||++..||+.|+                  |-|-..-.||.|||||. .+|.|+-+++..+..
T Consensus       323 TNIAETSlTI~GI~YVVDsG~vK~~~y~p~~g~~~L~v~~ISkasA~QRaGRAGRt-~pGkcyRLYte~~~~  393 (674)
T KOG0922|consen  323 TNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGRAGRT-GPGKCYRLYTESAYD  393 (674)
T ss_pred             cceeeeeEEecceEEEEcCCceEEEeeccccCccceeEEechHHHHhhhcccCCCC-CCceEEEeeeHHHHh
Confidence            999999999999999997775                  44888899999999999 589999999877763

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.87  E-value=5.7e-21  Score=193.61  Aligned_cols=324  Identities=18%  Similarity=0.148  Sum_probs=203.3

Q ss_pred             HHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhh
Q psy7952          37 TAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILS  116 (444)
Q Consensus        37 ~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~  116 (444)
                      .++-++.+|..+|.  .|.-.--.+.+|   -+..++||.|||++        +.+|+++..+ .+..   |.|++|+..
T Consensus        72 rEaa~R~lgm~~yd--VQliGgl~L~~G---~IaEm~TGEGKTL~--------a~lp~~l~al-~g~~---VhIvT~ndy  134 (908)
T PRK13107         72 REASKRVFEMRHFD--VQLLGGMVLDSN---RIAEMRTGEGKTLT--------ATLPAYLNAL-TGKG---VHVITVNDY  134 (908)
T ss_pred             HHHHHHHhCCCcCc--hHHhcchHhcCC---ccccccCCCCchHH--------HHHHHHHHHh-cCCC---EEEEeCCHH
Confidence            45666677887644  787666666555   57999999999999        6667622222 2223   599999999


Q ss_pred             hhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH-h----
Q psy7952         117 SFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV-R----  189 (444)
Q Consensus       117 L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~-~----  189 (444)
                      |+  .|..+.+..+  ..|   +.+..+.++.+...+...+        .++|+++||..|.   |+++..++. .    
T Consensus       135 LA--~RD~e~m~~l~~~lG---lsv~~i~~~~~~~~r~~~Y--------~~dI~YgT~~e~g---fDyLrdnm~~~~~~~  198 (908)
T PRK13107        135 LA--RRDAENNRPLFEFLG---LTVGINVAGLGQQEKKAAY--------NADITYGTNNEFG---FDYLRDNMAFSPQER  198 (908)
T ss_pred             HH--HHHHHHHHHHHHhcC---CeEEEecCCCCHHHHHhcC--------CCCeEEeCCCccc---chhhhccCccchhhh
Confidence            99  3335555555  667   9999999888765443333        6899999999985   344444421 1    


Q ss_pred             -hCCccEEEEeccccccccC-----------CCcHHHHHHHHHHHHhhC-------------------CCCcEEEEecc-
Q psy7952         190 -YNKLAYIVVDEAHCVSEWG-----------HDFRPTYRRLGELRQFTG-------------------NSIPIIALTAT-  237 (444)
Q Consensus       190 -~~~~~~iViDE~H~~~~~~-----------~~~~~~~~~l~~~~~~~~-------------------~~~~~v~lSAT-  237 (444)
                       ...+.++|+||+|.++-..           ..-...|..+..+...+.                   ...+.+.+|-. 
T Consensus       199 vqr~~~~aIvDEvDsiLiDEArtPLIISg~~~~~~~~y~~~~~~v~~L~~~~~~~~~~~~~~~dy~idek~~~v~LTe~G  278 (908)
T PRK13107        199 VQRPLHYALIDEVDSILIDEARTPLIISGAAEDSSELYIKINTLIPNLIRQDKEDTEEYVGEGDYSIDEKAKQVHFTERG  278 (908)
T ss_pred             hccccceeeecchhhhccccCCCceeecCCCccchHHHHHHHHHHHHHHhhhhccccccCCCCCEEEecCCCeeeechHH
Confidence             2678999999999884311           111223333332222111                   01122333311 


Q ss_pred             -------C---C-----cch--------HHHHHHH------hcCCCC-------eEE-----------------------
Q psy7952         238 -------A---E-----PSV--------KQDIISV------LKFNKP-------YKV-----------------------  258 (444)
Q Consensus       238 -------~---~-----~~~--------~~~~~~~------l~~~~~-------~~~-----------------------  258 (444)
                             +   .     ...        ...+...      +.-...       +.+                       
T Consensus       279 ~~~~e~~l~~~~~~~~~~~l~~~~~~~~~~~i~~aL~A~~lf~~d~dYiV~dg~V~IVDe~TGRim~grrwsdGLHQaIE  358 (908)
T PRK13107        279 QEKVENLLIERGMLAEGDSLYSAANISLLHHVNAALRAHTLFEKDVDYIVQDNEVIIVDEHTGRTMPGRRWSEGLHQAVE  358 (908)
T ss_pred             HHHHHHHHHhCCcccCcccccCchhhHHHHHHHHHHHHHHHHhcCCceEEECCEEEEEECCCCCCCCCCccchHHHHHHH
Confidence                   0   0     000        0000000      000000       011                       


Q ss_pred             ---------------------------------------------------EecCCCCCCceEEEE--EcccchhhHHHH
Q psy7952         259 ---------------------------------------------------FKTSTFRSNLFYDVI--FDDLLKDSYAHV  285 (444)
Q Consensus       259 ---------------------------------------------------~~~~~~~~~~~~~~~--~~~~~~~~~~~~  285 (444)
                                                                         ..-+..+|.+.....  .......++..+
T Consensus       359 aKE~v~I~~e~~t~AsIT~QnfFr~Y~kL~GMTGTa~te~~Ef~~iY~l~Vv~IPTnkp~~R~d~~d~iy~t~~~K~~Ai  438 (908)
T PRK13107        359 AKEGVHIQNENQTLASITFQNYFRQYEKLAGMTGTADTEAFEFQHIYGLDTVVVPTNRPMVRKDMADLVYLTADEKYQAI  438 (908)
T ss_pred             HhcCCCCCCCceeeeeehHHHHHHhhhHhhcccCCChHHHHHHHHHhCCCEEECCCCCCccceeCCCcEEeCHHHHHHHH
Confidence                                                               111111221111110  011123344455


Q ss_pred             HHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccc
Q psy7952         286 KEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGID  355 (444)
Q Consensus       286 ~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gid  355 (444)
                      .+.+.+..    ..+.++||||+|++.++.++..|...          .+..++..+.+.|+.|.  |+|||+++++|.|
T Consensus       439 i~ei~~~~----~~GrpVLV~t~sv~~se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRGTD  512 (908)
T PRK13107        439 IKDIKDCR----ERGQPVLVGTVSIEQSELLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRGTD  512 (908)
T ss_pred             HHHHHHHH----HcCCCEEEEeCcHHHHHHHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCCcc
Confidence            55555442    36889999999999999999999887          67788999999999888  9999999999999


Q ss_pred             cCC-------------------------------------ccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccc
Q psy7952         356 RQN-------------------------------------VRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS  398 (444)
Q Consensus       356 i~~-------------------------------------~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~  398 (444)
                      |.=                                     --+||-...+.|.+---|-.||+||.|.+|.+..|++-+|
T Consensus       513 IkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~lSlED  592 (908)
T PRK13107        513 IVLGGNWNMEIEALENPTAEQKAKIKADWQIRHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYLSMED  592 (908)
T ss_pred             eecCCchHHhhhhhcchhhHHHHHHHHHHHhhHHHHHHcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEEEeCc
Confidence            861                                     2268888899999999999999999999999999998666


Q ss_pred             h
Q psy7952         399 K  399 (444)
Q Consensus       399 ~  399 (444)
                      .
T Consensus       593 ~  593 (908)
T PRK13107        593 S  593 (908)
T ss_pred             H
Confidence            4

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

Probab=99.87  E-value=3.4e-21  Score=196.74  Aligned_cols=300  Identities=17%  Similarity=0.201  Sum_probs=199.8

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC--ccceeEEEcchhhhhcccCccchHhh
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN--VRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~--~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      ....+.+..+.++ +-++|.+|||+|||..          +|.   .+...+  ...++.+.-|.|--+     ....++
T Consensus        53 ~~~~~i~~ai~~~-~vvii~getGsGKTTq----------lP~---~lle~g~~~~g~I~~tQPRRlAA-----rsvA~R  113 (845)
T COG1643          53 AVRDEILKAIEQN-QVVIIVGETGSGKTTQ----------LPQ---FLLEEGLGIAGKIGCTQPRRLAA-----RSVAER  113 (845)
T ss_pred             HHHHHHHHHHHhC-CEEEEeCCCCCChHHH----------HHH---HHHhhhcccCCeEEecCchHHHH-----HHHHHH
Confidence            3455566666666 8899999999999955          444   122222  223556677998655     455555


Q ss_pred             h--cCCC-CceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccc
Q psy7952         130 V--TGRS-DLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSE  206 (444)
Q Consensus       130 l--~~~~-~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~  206 (444)
                      +  .++. .+-.|..-....+.            ...+..|-++|.+.|.     ..+.....++.+++||+||+|+   
T Consensus       114 vAeel~~~~G~~VGY~iRfe~~------------~s~~Trik~mTdGiLl-----rei~~D~~Ls~ys~vIiDEaHE---  173 (845)
T COG1643         114 VAEELGEKLGETVGYSIRFESK------------VSPRTRIKVMTDGILL-----REIQNDPLLSGYSVVIIDEAHE---  173 (845)
T ss_pred             HHHHhCCCcCceeeEEEEeecc------------CCCCceeEEeccHHHH-----HHHhhCcccccCCEEEEcchhh---
Confidence            5  2221 01222222211111            1357789999999975     2344444578899999999998   


Q ss_pred             cCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchh-hHHHH
Q psy7952         207 WGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKD-SYAHV  285 (444)
Q Consensus       207 ~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~  285 (444)
                      ..-+..-.+..+..++...+.+.++|.||||+...   .+.++++. -|+...........+.|.....  .+. -...+
T Consensus       174 RSl~tDilLgllk~~~~~rr~DLKiIimSATld~~---rfs~~f~~-apvi~i~GR~fPVei~Y~~~~~--~d~~l~~ai  247 (845)
T COG1643         174 RSLNTDILLGLLKDLLARRRDDLKLIIMSATLDAE---RFSAYFGN-APVIEIEGRTYPVEIRYLPEAE--ADYILLDAI  247 (845)
T ss_pred             hhHHHHHHHHHHHHHHhhcCCCceEEEEecccCHH---HHHHHcCC-CCEEEecCCccceEEEecCCCC--cchhHHHHH
Confidence            22212233444556566667679999999999654   55666642 3433333333333344322221  222 23334


Q ss_pred             HHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh--------------cCHHHHHHHHHHHhcCCccEEEEcCccc
Q psy7952         286 KEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK--------------VNKHERSRVQESFMRGEINVITATISFG  351 (444)
Q Consensus       286 ~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~--------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~  351 (444)
                      ...+..++..   ..+.++||.+...+.+.+++.|.+.              ++.++...+++.-..|..+|++||++++
T Consensus       248 ~~~v~~~~~~---~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAE  324 (845)
T COG1643         248 VAAVDIHLRE---GSGSILVFLPGQREIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAE  324 (845)
T ss_pred             HHHHHHhccC---CCCCEEEECCcHHHHHHHHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccc
Confidence            4444444433   4889999999999999999999982              7888888887777677777999999999


Q ss_pred             cccccCCccEEEEeCC------------------CCCHHHHHHHhccCCCCCCceeEEEEecccchh
Q psy7952         352 MGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK  400 (444)
Q Consensus       352 ~Gidi~~~~~Vi~~~~------------------p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~  400 (444)
                      .++.||+++.||+.|.                  |-|-.+..||.|||||. .+|.|+-+++.++..
T Consensus       325 TSLTI~gIr~VIDsG~ak~~~y~~~~g~~~L~~~~ISqAsA~QRaGRAGR~-~pGicyRLyse~~~~  390 (845)
T COG1643         325 TSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRT-GPGICYRLYSEEDFL  390 (845)
T ss_pred             cceeeCCeEEEecCCcccccccccccCceeeeEEEechhhhhhhccccccC-CCceEEEecCHHHHH
Confidence            9999999999997775                  34788899999999999 689999999986655

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

Probab=99.86  E-value=6.4e-21  Score=195.88  Aligned_cols=314  Identities=11%  Similarity=0.092  Sum_probs=175.5

Q ss_pred             CCHHHHHHHHHHHh------C--CcccCchHHHHHHHHHHc---------cCCcEEEEccCCCcccccccccccceEEeC
Q psy7952          31 VSEQELTAKLKALF------G--FDSFKCELQKKAIRHILL---------RTHDIFVSMPTGAVSLVGSVVSARSRVRIP   93 (444)
Q Consensus        31 ~~~~~~~~~l~~~~------g--~~~~~t~~Q~~~~~~~~~---------~~~~~ii~apTGsGKT~~a~~~~~~~~~~~   93 (444)
                      +.+..+.+.++...      |  ...++..+|.+|+..+..         +.+..+++.|||||||++|+..+       
T Consensus       212 ~~~~~ll~~i~~~~~~~~~~~~~~k~~~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la-------  284 (667)
T TIGR00348       212 LKKERLLDFIRNFIIFDKDTGLVTKPYQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAA-------  284 (667)
T ss_pred             cCHHHHHHHHHheEEEECCCCceeeeehHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHH-------
Confidence            45666666665411      1  123455789999887653         23579999999999999843221       


Q ss_pred             CCccccccCCccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECC
Q psy7952          94 PGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTP  172 (444)
Q Consensus        94 ~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tp  172 (444)
                         ..+......+++||++|+.+|.     .|..+.+ ..+   ....  .+..+..   .....+.  ....+|+|+|.
T Consensus       285 ---~~l~~~~~~~~vl~lvdR~~L~-----~Q~~~~f~~~~---~~~~--~~~~s~~---~L~~~l~--~~~~~iivtTi  346 (667)
T TIGR00348       285 ---RKALELLKNPKVFFVVDRRELD-----YQLMKEFQSLQ---KDCA--ERIESIA---ELKRLLE--KDDGGIIITTI  346 (667)
T ss_pred             ---HHHHhhcCCCeEEEEECcHHHH-----HHHHHHHHhhC---CCCC--cccCCHH---HHHHHHh--CCCCCEEEEEh
Confidence               1123334456889999999999     5666666 333   1100  1111111   1111121  23578999999


Q ss_pred             CccccccHHHHHHHHHhh--CCc-cEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHH
Q psy7952         173 ERAVTESFHYLLQHLVRY--NKL-AYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISV  249 (444)
Q Consensus       173 e~l~~~~~~~~~~~~~~~--~~~-~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~  249 (444)
                      +++...    .......+  ... .+||+||||+...     .. +..  .+...+++ ..+++|||||...........
T Consensus       347 Qk~~~~----~~~~~~~~~~~~~~~lvIvDEaHrs~~-----~~-~~~--~l~~~~p~-a~~lGfTaTP~~~~d~~t~~~  413 (667)
T TIGR00348       347 QKFDKK----LKEEEEKFPVDRKEVVVIFDEAHRSQY-----GE-LAK--NLKKALKN-ASFFGFTGTPIFKKDRDTSLT  413 (667)
T ss_pred             HHhhhh----HhhhhhccCCCCCCEEEEEEcCccccc-----hH-HHH--HHHhhCCC-CcEEEEeCCCccccccccccc
Confidence            997531    11111111  111 2899999999532     11 111  12234555 789999999965321111122


Q ss_pred             hcC--CCCeEEEec-----CCCCCCceEEEEEccc--chh----------------------------------------
Q psy7952         250 LKF--NKPYKVFKT-----STFRSNLFYDVIFDDL--LKD----------------------------------------  280 (444)
Q Consensus       250 l~~--~~~~~~~~~-----~~~~~~~~~~~~~~~~--~~~----------------------------------------  280 (444)
                      ++.  ...+....-     .....++.|.......  ...                                        
T Consensus       414 f~~~fg~~i~~Y~~~~AI~dG~~~~i~Y~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  493 (667)
T TIGR00348       414 FAYVFGRYLHRYFITDAIRDGLTVKIDYEDRLPEDHLDRKKLDAFFDEIFELLPERIREITKESLKEKLQKTKKILFNED  493 (667)
T ss_pred             ccCCCCCeEEEeeHHHHhhcCCeeeEEEEecchhhccChHHHHHHHHHHHHhhhccccHHHHHHHHHHHHHHHhhhcChH
Confidence            221  111111100     0111112222111100  000                                        


Q ss_pred             hHHHHHHHHHHHhcc-CCCCCceEEEEecccchHHHHHHHHHhhcCH---------------------------------
Q psy7952         281 SYAHVKEFIEKCLGK-DNKANNCGIIYCRTREHTTDLADALRRKVNK---------------------------------  326 (444)
Q Consensus       281 ~~~~~~~~l~~~l~~-~~~~~~~~iVf~~s~~~~~~l~~~L~~~~~~---------------------------------  326 (444)
                      ....+...+.+.... ....+.+++|||.++.+|..+++.|.+..+.                                 
T Consensus       494 ~~~~ia~~i~~h~~~~~~~~~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~  573 (667)
T TIGR00348       494 RLESIAKDIAEHYAKFKELFKFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKS  573 (667)
T ss_pred             HHHHHHHHHHHHHHHhhhcccCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccc
Confidence            001111222222221 1113589999999999999998887553100                                 


Q ss_pred             ---HHHHHHHHHHhc-CCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCC
Q psy7952         327 ---HERSRVQESFMR-GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGR  383 (444)
Q Consensus       327 ---~~r~~~~~~f~~-g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R  383 (444)
                         .....++++|+. +.+++||.++++..|+|.|.+++++...+..+ ..++|.+||+.|
T Consensus       574 ~~~~~~~~~~~~Fk~~~~~~ilIVvdmllTGFDaP~l~tLyldKplk~-h~LlQai~R~nR  633 (667)
T TIGR00348       574 DGFEIYYKDLERFKKEENPKLLIVVDMLLTGFDAPILNTLYLDKPLKY-HGLLQAIARTNR  633 (667)
T ss_pred             hhhhHHHHHHHHhcCCCCceEEEEEcccccccCCCccceEEEeccccc-cHHHHHHHHhcc
Confidence               022467888875 68899999999999999999999997776554 568999999999

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

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

Probab=99.84  E-value=3.6e-19  Score=188.63  Aligned_cols=180  Identities=17%  Similarity=0.112  Sum_probs=119.3

Q ss_pred             CcEEEEeccCCcc-hHHHHHHHhcCCCCeEEEe-cCCCC--CCceEEEEEccc-------chhhHHHHHHHHHHHhccCC
Q psy7952         229 IPIIALTATAEPS-VKQDIISVLKFNKPYKVFK-TSTFR--SNLFYDVIFDDL-------LKDSYAHVKEFIEKCLGKDN  297 (444)
Q Consensus       229 ~~~v~lSAT~~~~-~~~~~~~~l~~~~~~~~~~-~~~~~--~~~~~~~~~~~~-------~~~~~~~~~~~l~~~l~~~~  297 (444)
                      ..+|++|||+... ..+.+.+.+|+.+...... ++...  .+... +.....       .....+.+.+.+.+++..  
T Consensus       596 ~~~il~SATL~~~~~~~~~~~~lGl~~~~~~~~~~spf~~~~~~~l-~v~~d~~~~~~~~~~~~~~~ia~~i~~l~~~--  672 (850)
T TIGR01407       596 KSLIFTSATLKFSHSFESFPQLLGLTDVHFNTIEPTPLNYAENQRV-LIPTDAPAIQNKSLEEYAQEIASYIIEITAI--  672 (850)
T ss_pred             CeEEEEecccccCCChHHHHHhcCCCccccceecCCCCCHHHcCEE-EecCCCCCCCCCChHHHHHHHHHHHHHHHHh--
Confidence            3578999999743 3567778888865432221 11111  11111 111111       122233555566565544  


Q ss_pred             CCCceEEEEecccchHHHHHHHHHhh-----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCcc--EEEE
Q psy7952         298 KANNCGIIYCRTREHTTDLADALRRK-----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVR--FVVH  364 (444)
Q Consensus       298 ~~~~~~iVf~~s~~~~~~l~~~L~~~-----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~--~Vi~  364 (444)
                       .+++++||++|.+..+.++..|...           .....|..+++.|++++..||+||+.+++|||+|+..  .||.
T Consensus       673 -~~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~~l~q~~~~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~viI  751 (850)
T TIGR01407       673 -TSPKILVLFTSYEMLHMVYDMLNELPEFEGYEVLAQGINGSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCLVI  751 (850)
T ss_pred             -cCCCEEEEeCCHHHHHHHHHHHhhhccccCceEEecCCCccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEEEE
Confidence             3679999999999999999999752           1124788999999999999999999999999999755  5777


Q ss_pred             eCCCCC------------------------------HHHHHHHhccCCCCCCceeEEEEeccc-chhhHHHHHhhccch
Q psy7952         365 WGMPSS------------------------------IPAYYQESGRAGRDGLQSYCRIYHSEH-SKKSLEYVIKTDTST  412 (444)
Q Consensus       365 ~~~p~s------------------------------~~~~~Qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~  412 (444)
                      .+.|..                              ...+.|.+||+-|..++.-+++++++. ....+.+.+-..++.
T Consensus       752 ~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~lP~A~~~l~Qa~GRlIRs~~D~G~v~ilD~R~~~~~Yg~~~~~sLp~  830 (850)
T TIGR01407       752 PRLPFANPKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVILDRRLVGKRYGKRFEKSLPE  830 (850)
T ss_pred             eCCCCCCCCCHHHHHHHHHHHHhcCCchHHhhHHHHHHHHHHhhccccccCCceEEEEEEccccccchHHHHHHHhCCC
Confidence            887641                              234579999999986654456666655 455666666666664

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.

>KOG4150|consensus

Probab=99.84  E-value=1.7e-19  Score=170.33  Aligned_cols=323  Identities=14%  Similarity=0.069  Sum_probs=213.8

Q ss_pred             cccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccch
Q psy7952          47 DSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDK  126 (444)
Q Consensus        47 ~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~  126 (444)
                      +.+- .+|.++++.+.+| +++++...|.+||+.+        +.+.+ .+.+.... ....++..|+.+++     +++
T Consensus       285 E~~~-~~~~~~~~~~~~G-~~~~~~~~~~~GK~~~--------~~~~s-~~~~~~~~-~s~~~~~~~~~~~~-----~~~  347 (1034)
T KOG4150|consen  285 ESGI-AISLELLKFASEG-RADGGNEARQAGKGTC--------PTSGS-RKFQTLCH-ATNSLLPSEMVEHL-----RNG  347 (1034)
T ss_pred             cchh-hhhHHHHhhhhhc-ccccccchhhcCCccC--------cccch-hhhhhcCc-ccceecchhHHHHh-----hcc
Confidence            3444 5999999999999 9999999999999999        77666 33222221 12348899999999     566


Q ss_pred             Hhhhc---CCCCce---eEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEec
Q psy7952         127 TSIVT---GRSDLY---QLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDE  200 (444)
Q Consensus       127 ~~~l~---~~~~~i---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE  200 (444)
                      -+.+.   ...+..   -+.+..+.. ..+ +..+.     ..+..++++.|+++.+.....-.......-...+++.||
T Consensus       348 ~~~~~V~~~~I~~~K~A~V~~~D~~s-E~~-~~A~~-----R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~  420 (1034)
T KOG4150|consen  348 SKGQVVHVEVIKARKSAYVEMSDKLS-ETT-KSALK-----RIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNS  420 (1034)
T ss_pred             CCceEEEEEehhhhhcceeecccCCC-chh-HHHHH-----hcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccc
Confidence            55440   000001   122222222 222 22221     247789999998875322111111112222357889999


Q ss_pred             cccccc-cCCCcHHHHHHHHHHHHhhC--CCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEccc
Q psy7952         201 AHCVSE-WGHDFRPTYRRLGELRQFTG--NSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDL  277 (444)
Q Consensus       201 ~H~~~~-~~~~~~~~~~~l~~~~~~~~--~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  277 (444)
                      +|.+.. .++.....+.++.++...|.  .+.+++-.+||+.... +...+.+++..-..+.........-.+.++....
T Consensus       421 ~~~Y~~~~~~~~~~~~R~L~~L~~~F~~~~~~~~~~~~~~~K~~~-~~~~~~~~~~E~~Li~~DGSPs~~K~~V~WNP~~  499 (1034)
T KOG4150|consen  421 CALYLFPTKALAQDQLRALSDLIKGFEASINMGVYDGDTPYKDRT-RLRSELANLSELELVTIDGSPSSEKLFVLWNPSA  499 (1034)
T ss_pred             eeeeecchhhHHHHHHHHHHHHHHHHHhhcCcceEeCCCCcCCHH-HHHHHhcCCcceEEEEecCCCCccceEEEeCCCC
Confidence            999854 34444555666666666553  3478999999988765 4456666766554444444333333333332222


Q ss_pred             ch-------hhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------------------cCHHHHHHH
Q psy7952         278 LK-------DSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------------VNKHERSRV  332 (444)
Q Consensus       278 ~~-------~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------------------~~~~~r~~~  332 (444)
                      ..       ....+...++.+++.    .+-++|-||.+++-|+-+....+.-                  ...++|.++
T Consensus       500 ~P~~~~~~~~~i~E~s~~~~~~i~----~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKI  575 (1034)
T KOG4150|consen  500 PPTSKSEKSSKVVEVSHLFAEMVQ----HGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKI  575 (1034)
T ss_pred             CCcchhhhhhHHHHHHHHHHHHHH----cCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHH
Confidence            11       122233333334333    4778999999999988776555443                  778999999


Q ss_pred             HHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccc
Q psy7952         333 QESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS  398 (444)
Q Consensus       333 ~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~  398 (444)
                      +..+..|+..-+|+|+.++.||||..++.|++.|+|.|..++.|..|||||..+++.++.+.....
T Consensus       576 E~~~F~G~L~giIaTNALELGIDIG~LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~P  641 (1034)
T KOG4150|consen  576 ESDLFGGKLCGIIATNALELGIDIGHLDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGP  641 (1034)
T ss_pred             HHHhhCCeeeEEEecchhhhccccccceeEEEccCchhHHHHHHHhccccccCCCceEEEEEeccc
Confidence            999999999999999999999999999999999999999999999999999999988887776443

>KOG1123|consensus

Probab=99.82  E-value=1.4e-18  Score=161.88  Aligned_cols=300  Identities=13%  Similarity=0.112  Sum_probs=193.6

Q ss_pred             chHHHHHHHHHHccC--CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHh
Q psy7952          51 CELQKKAIRHILLRT--HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTS  128 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~--~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~  128 (444)
                      .|||.+.+..+.-+.  ++-+|+.|+|+|||++        -.-.+       -...+++|++|.+..-+  .||.+|+.
T Consensus       304 RpYQEksL~KMFGNgRARSGiIVLPCGAGKtLV--------GvTAa-------~tikK~clvLcts~VSV--eQWkqQfk  366 (776)
T KOG1123|consen  304 RPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLV--------GVTAA-------CTIKKSCLVLCTSAVSV--EQWKQQFK  366 (776)
T ss_pred             CchHHHHHHHHhCCCcccCceEEEecCCCCcee--------eeeee-------eeecccEEEEecCccCH--HHHHHHHH
Confidence            479999999998643  6789999999999998        22222       11335679999998888  67788888


Q ss_pred             hh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccH----HHHHHHHHhhCCccEEEEecccc
Q psy7952         129 IV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESF----HYLLQHLVRYNKLAYIVVDEAHC  203 (444)
Q Consensus       129 ~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~----~~~~~~~~~~~~~~~iViDE~H~  203 (444)
                      .| ....  -.++.++++....           ...++.|+|+|+.++....-    ..-.-.+.....++++++||+|.
T Consensus       367 ~wsti~d--~~i~rFTsd~Ke~-----------~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHv  433 (776)
T KOG1123|consen  367 QWSTIQD--DQICRFTSDAKER-----------FPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHV  433 (776)
T ss_pred             hhcccCc--cceEEeecccccc-----------CCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhcc
Confidence            88 3321  4566677665432           24688999999999874221    11122334456799999999999


Q ss_pred             ccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHH--H----------HHHhcCCCCeEEEecCCCCCCceEE
Q psy7952         204 VSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQD--I----------ISVLKFNKPYKVFKTSTFRSNLFYD  271 (444)
Q Consensus       204 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~--~----------~~~l~~~~~~~~~~~~~~~~~~~~~  271 (444)
                      +...-  |+..+..+....+        +++|||+.+...+.  +          .+|+.+.....+.       ++...
T Consensus       434 vPA~M--FRRVlsiv~aHcK--------LGLTATLvREDdKI~DLNFLIGPKlYEAnWmdL~~kGhIA-------~VqCa  496 (776)
T KOG1123|consen  434 VPAKM--FRRVLSIVQAHCK--------LGLTATLVREDDKITDLNFLIGPKLYEANWMDLQKKGHIA-------KVQCA  496 (776)
T ss_pred             chHHH--HHHHHHHHHHHhh--------ccceeEEeeccccccccceeecchhhhccHHHHHhCCcee-------EEeee
Confidence            86544  6665555554332        79999986543221  0          0111111110000       00000


Q ss_pred             EEEccc---------------------chhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----cC
Q psy7952         272 VIFDDL---------------------LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----VN  325 (444)
Q Consensus       272 ~~~~~~---------------------~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----~~  325 (444)
                      -....-                     .....-...+++.+.-+.   .+.++|||..++=...+-+-.|.+-     .+
T Consensus       497 EVWCpMt~eFy~eYL~~~t~kr~lLyvMNP~KFraCqfLI~~HE~---RgDKiIVFsDnvfALk~YAikl~KpfIYG~Ts  573 (776)
T KOG1123|consen  497 EVWCPMTPEFYREYLRENTRKRMLLYVMNPNKFRACQFLIKFHER---RGDKIIVFSDNVFALKEYAIKLGKPFIYGPTS  573 (776)
T ss_pred             eeecCCCHHHHHHHHhhhhhhhheeeecCcchhHHHHHHHHHHHh---cCCeEEEEeccHHHHHHHHHHcCCceEECCCc
Confidence            000000                     000111233444444333   5889999999877666666666555     88


Q ss_pred             HHHHHHHHHHHh-cCCccEEEEcCccccccccCCccEEEEeCCCC-CHHHHHHHhccCCCCCC------ceeEEEEeccc
Q psy7952         326 KHERSRVQESFM-RGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGL------QSYCRIYHSEH  397 (444)
Q Consensus       326 ~~~r~~~~~~f~-~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~-s~~~~~Qr~GR~~R~g~------~g~~~~~~~~~  397 (444)
                      +.+|..+++.|+ +..++.|.-+.+....+|+|..+++|...... |...=.||.||..|..+      ..+++.+++.+
T Consensus       574 q~ERm~ILqnFq~n~~vNTIFlSKVgDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAKk~~de~fnafFYSLVS~D  653 (776)
T KOG1123|consen  574 QNERMKILQNFQTNPKVNTIFLSKVGDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKRNDEEFNAFFYSLVSKD  653 (776)
T ss_pred             hhHHHHHHHhcccCCccceEEEeeccCccccCCcccEEEEEcccccchHHHHHHHHHHHHHhhcCccccceeeeeeeecc
Confidence            999999999998 55688999999999999999999999766543 78888999999988532      34556666655


Q ss_pred             chh
Q psy7952         398 SKK  400 (444)
Q Consensus       398 ~~~  400 (444)
                      ..+
T Consensus       654 TqE  656 (776)
T KOG1123|consen  654 TQE  656 (776)
T ss_pred             hHH
Confidence            544

>KOG0926|consensus

Probab=99.82  E-value=3.4e-19  Score=174.15  Aligned_cols=300  Identities=18%  Similarity=0.206  Sum_probs=189.4

Q ss_pred             HHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCcc------c-eeEEEcchhhhhcccCccchHh
Q psy7952          56 KAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVR------S-RNGWISPILSSFYLRFRDDKTS  128 (444)
Q Consensus        56 ~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~------~-~vlil~P~~~L~~~~q~~~~~~  128 (444)
                      +.++.|..+ .-+||++.||+|||.-          +|.   .++..|-.      + -+-|.-|.|..+     -...+
T Consensus       263 ~IMEaIn~n-~vvIIcGeTGsGKTTQ----------vPQ---FLYEAGf~s~~~~~~gmIGITqPRRVAa-----iamAk  323 (1172)
T KOG0926|consen  263 RIMEAINEN-PVVIICGETGSGKTTQ----------VPQ---FLYEAGFASEQSSSPGMIGITQPRRVAA-----IAMAK  323 (1172)
T ss_pred             HHHHHhhcC-CeEEEecCCCCCcccc----------chH---HHHHcccCCccCCCCCeeeecCchHHHH-----HHHHH
Confidence            455566666 6789999999999954          555   22222211      1 234566888776     45555


Q ss_pred             hh--cCC--CCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccc
Q psy7952         129 IV--TGR--SDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCV  204 (444)
Q Consensus       129 ~l--~~~--~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~  204 (444)
                      +.  .++  +..+....-..+..              .....|-++|.+.|..+.     .+...+...+.||+||||.=
T Consensus       324 RVa~EL~~~~~eVsYqIRfd~ti--------------~e~T~IkFMTDGVLLrEi-----~~DflL~kYSvIIlDEAHER  384 (1172)
T KOG0926|consen  324 RVAFELGVLGSEVSYQIRFDGTI--------------GEDTSIKFMTDGVLLREI-----ENDFLLTKYSVIILDEAHER  384 (1172)
T ss_pred             HHHHHhccCccceeEEEEecccc--------------CCCceeEEecchHHHHHH-----HHhHhhhhceeEEechhhhc
Confidence            55  222  11122222222211              246789999999986432     33334567899999999974


Q ss_pred             cccCCCcHHHHHHHHHHHHhhCC------CCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccc
Q psy7952         205 SEWGHDFRPTYRRLGELRQFTGN------SIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLL  278 (444)
Q Consensus       205 ~~~~~~~~~~~~~l~~~~~~~~~------~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  278 (444)
                      +-...-.-..+.++..+++...+      ..++|.||||+.-.....=...+-++.|+.-+...+..    ..+++....
T Consensus       385 SvnTDILiGmLSRiV~LR~k~~ke~~~~kpLKLIIMSATLRVsDFtenk~LFpi~pPlikVdARQfP----VsIHF~krT  460 (1172)
T KOG0926|consen  385 SVNTDILIGMLSRIVPLRQKYYKEQCQIKPLKLIIMSATLRVSDFTENKRLFPIPPPLIKVDARQFP----VSIHFNKRT  460 (1172)
T ss_pred             cchHHHHHHHHHHHHHHHHHHhhhhcccCceeEEEEeeeEEecccccCceecCCCCceeeeecccCc----eEEEeccCC
Confidence            32222234455666667666554      46799999998654332223334444553222221111    122222221


Q ss_pred             hhhHHHHHHHHHHHhcc-CCCCCceEEEEecccchHHHHHHHHHhh----------------------------------
Q psy7952         279 KDSYAHVKEFIEKCLGK-DNKANNCGIIYCRTREHTTDLADALRRK----------------------------------  323 (444)
Q Consensus       279 ~~~~~~~~~~l~~~l~~-~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------------------------------  323 (444)
                      ..  .++.+..++.... ..-+.+.++||+....++++++..|++.                                  
T Consensus       461 ~~--DYi~eAfrKtc~IH~kLP~G~ILVFvTGQqEV~qL~~kLRK~~p~~f~~~k~~k~~k~~~e~k~~~s~~~~~~k~~  538 (1172)
T KOG0926|consen  461 PD--DYIAEAFRKTCKIHKKLPPGGILVFVTGQQEVDQLCEKLRKRFPESFGGVKMKKNVKAFKELKENPSDIGDSNKTD  538 (1172)
T ss_pred             Cc--hHHHHHHHHHHHHhhcCCCCcEEEEEeChHHHHHHHHHHHhhCccccccchhhhhhhhccccccchhhhccCcccc
Confidence            11  3333333332222 2337889999999999999999999887                                  


Q ss_pred             ---------------------------------------------------------------------------cCHHH
Q psy7952         324 ---------------------------------------------------------------------------VNKHE  328 (444)
Q Consensus       324 ---------------------------------------------------------------------------~~~~~  328 (444)
                                                                                                 ++.+.
T Consensus       539 dfe~Ed~~~~~ed~d~~~~~~~~~~~raa~~~~~De~~~~nge~e~d~~e~~~E~~~~~~~~~~~pLyvLPLYSLLs~~~  618 (1172)
T KOG0926|consen  539 DFEEEDMYESDEDIDQELVDSGFASLRAAFNALADENGSVNGEPEKDESEEGQEAEQGKGKFSPGPLYVLPLYSLLSTEK  618 (1172)
T ss_pred             cchhcccccchhhhhhhhhcccchhhhhhhhccccccccccCCcccchhhhchhhhhccCCCCCCceEEeehhhhcCHHH
Confidence                                                                                       56677


Q ss_pred             HHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCC------------------CHHHHHHHhccCCCCCCceeE
Q psy7952         329 RSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPS------------------SIPAYYQESGRAGRDGLQSYC  390 (444)
Q Consensus       329 r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~------------------s~~~~~Qr~GR~~R~g~~g~~  390 (444)
                      +..++..--.|..-++|||++++..+.||++.+||+.|.-+                  |-.+--||+|||||.| +|+|
T Consensus       619 Q~RVF~~~p~g~RLcVVaTNVAETSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRAGRAGRtg-pGHc  697 (1172)
T KOG0926|consen  619 QMRVFDEVPKGERLCVVATNVAETSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQRAGRAGRTG-PGHC  697 (1172)
T ss_pred             hhhhccCCCCCceEEEEeccchhcccccCCeeEEEeccchhhhccccccCceeEEEEeeeccccchhccccCCCC-CCce
Confidence            77777777788888999999999999999999999877543                  4455579999999994 8999


Q ss_pred             EEEecccchh
Q psy7952         391 RIYHSEHSKK  400 (444)
Q Consensus       391 ~~~~~~~~~~  400 (444)
                      +-+|+..-+.
T Consensus       698 YRLYSSAVf~  707 (1172)
T KOG0926|consen  698 YRLYSSAVFS  707 (1172)
T ss_pred             eehhhhHHhh
Confidence            9999865443

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.81  E-value=1.9e-18  Score=176.21  Aligned_cols=102  Identities=26%  Similarity=0.231  Sum_probs=92.7

Q ss_pred             CCCceEEEEecccchHHHHHHHHHhh--------cCHHHHHHHHHHHhcCCccEEEEcCccccccccC---Ccc-----E
Q psy7952         298 KANNCGIIYCRTREHTTDLADALRRK--------VNKHERSRVQESFMRGEINVITATISFGMGIDRQ---NVR-----F  361 (444)
Q Consensus       298 ~~~~~~iVf~~s~~~~~~l~~~L~~~--------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~---~~~-----~  361 (444)
                      ..+.++||||+|++.++.++..|...        ....+|...+..|+.+...|+|||++++||+||+   .|.     +
T Consensus       596 ~~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLnakq~~REa~Iia~AG~~g~VtIATNMAGRGtDIkl~~~V~~vGGL~  675 (1025)
T PRK12900        596 KKGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNAKQHDREAEIVAEAGQKGAVTIATNMAGRGTDIKLGEGVRELGGLF  675 (1025)
T ss_pred             hCCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecCCHHHhHHHHHHhcCCCCeEEEeccCcCCCCCcCCccchhhhCCce
Confidence            36889999999999999999999887        5678899999999999999999999999999999   443     4


Q ss_pred             EEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         362 VVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       362 Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                      ||.+..|.|.+.|.|++||+||.|.+|.++.|++.+|.
T Consensus       676 VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD~  713 (1025)
T PRK12900        676 ILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLEDE  713 (1025)
T ss_pred             eeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhHH
Confidence            58999999999999999999999999999999987664

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.81  E-value=2.1e-18  Score=171.18  Aligned_cols=317  Identities=18%  Similarity=0.169  Sum_probs=204.8

Q ss_pred             HHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchh
Q psy7952          36 LTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPIL  115 (444)
Q Consensus        36 ~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~  115 (444)
                      +.++.++.+|..++  +.|.-..-.+++|   -+..+.||.|||++|++        |+++. ...+..+   .+++|+.
T Consensus        67 vREa~~R~lg~r~y--dvQlig~l~Ll~G---~VaEM~TGEGKTLvA~l--------~a~l~-AL~G~~V---hvvT~Nd  129 (764)
T PRK12326         67 AREAAERTLGLRPF--DVQLLGALRLLAG---DVIEMATGEGKTLAGAI--------AAAGY-ALQGRRV---HVITVND  129 (764)
T ss_pred             HHHHHHHHcCCCcc--hHHHHHHHHHhCC---CcccccCCCCHHHHHHH--------HHHHH-HHcCCCe---EEEcCCH
Confidence            34566777788864  4899999999987   35799999999999544        44111 2333344   8999999


Q ss_pred             hhhcccCccchHhhh-----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh-
Q psy7952         116 SSFYLRFRDDKTSIV-----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR-  189 (444)
Q Consensus       116 ~L~~~~q~~~~~~~l-----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~-  189 (444)
                      .|+     .+..+.+     .+|   +.+..+.++.+..++...+        .+||+++|...+.   |+++..++.. 
T Consensus       130 yLA-----~RDae~m~~ly~~LG---Lsvg~i~~~~~~~err~aY--------~~DItYgTn~e~g---FDyLRDnm~~~  190 (764)
T PRK12326        130 YLA-----RRDAEWMGPLYEALG---LTVGWITEESTPEERRAAY--------ACDVTYASVNEIG---FDVLRDQLVTD  190 (764)
T ss_pred             HHH-----HHHHHHHHHHHHhcC---CEEEEECCCCCHHHHHHHH--------cCCCEEcCCcccc---cccchhhhccC
Confidence            999     6666655     456   9999999998887777666        6899999988876   4444444321 


Q ss_pred             -----hCCccEEEEecccccc-ccC--------C-CcHHHHHHHHHHHHh------------------------------
Q psy7952         190 -----YNKLAYIVVDEAHCVS-EWG--------H-DFRPTYRRLGELRQF------------------------------  224 (444)
Q Consensus       190 -----~~~~~~iViDE~H~~~-~~~--------~-~~~~~~~~l~~~~~~------------------------------  224 (444)
                           ...+.+.||||+|.++ |..        . .-...|..+..+.+.                              
T Consensus       191 ~~~~v~R~~~faIVDEvDSiLIDeArtPLiISg~~~~~~~y~~~~~~v~~L~~~~dy~ide~~k~v~LTe~G~~~~e~~l  270 (764)
T PRK12326        191 VADLVSPNPDVAIIDEADSVLVDEALVPLVLAGSTPGEAPRGEIAELVRRLREGKDYEIDDDGRNVHLTDKGARKVEKAL  270 (764)
T ss_pred             hHhhcCCccceeeecchhhheeccccCceeeeCCCcchhHHHHHHHHHHhcCcCCcEEEEcCCCeeEecHHHHHHHHHHc
Confidence                 2468999999999873 211        0 000001110000000                              


Q ss_pred             --------------------------------------------------------------------------------
Q psy7952         225 --------------------------------------------------------------------------------  224 (444)
Q Consensus       225 --------------------------------------------------------------------------------  224 (444)
                                                                                                      
T Consensus       271 ~~~~ly~~~~~~~~~~~i~~AL~A~~l~~~d~dYiV~dgeV~iVDe~TGRvm~grrwsdGLHQaIEaKE~v~i~~e~~t~  350 (764)
T PRK12326        271 GGIDLYSEEHVGTTLTQVNVALHAHALLQRDVHYIVRDGKVHLINASRGRIAQLQRWPDGLQAAVEAKEGLETTETGEVL  350 (764)
T ss_pred             CCccccCcchhHHHHHHHHHHHHHHHHHhcCCcEEEECCEEEEEECCCCCcCCCCccChHHHHHHHHHcCCCCCCCceee
Confidence                                                                                            


Q ss_pred             --------hCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEE--EcccchhhHHHHHHHHHHHhc
Q psy7952         225 --------TGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVI--FDDLLKDSYAHVKEFIEKCLG  294 (444)
Q Consensus       225 --------~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~l~  294 (444)
                              |....++.+||+|.... ...+.+..++.    +..-+..+|.+.....  .......++..+.+.+.+.  
T Consensus       351 AsIT~QnfFr~Y~kLsGMTGTa~t~-~~Ef~~iY~l~----Vv~IPtnkp~~R~d~~d~iy~t~~~k~~Aii~ei~~~--  423 (764)
T PRK12326        351 DTITVQALIGRYPTVCGMTGTAVAA-GEQLRQFYDLG----VSVIPPNKPNIREDEADRVYATAAEKNDAIVEHIAEV--  423 (764)
T ss_pred             ehhhHHHHHHhcchheeecCCChhH-HHHHHHHhCCc----EEECCCCCCceeecCCCceEeCHHHHHHHHHHHHHHH--
Confidence                    00111246777776443 33344443332    2233334444433211  1111234455555555543  


Q ss_pred             cCCCCCceEEEEecccchHHHHHHHHHhh------cCH--HHHH-HHHHHHhcC-CccEEEEcCccccccccC-------
Q psy7952         295 KDNKANNCGIIYCRTREHTTDLADALRRK------VNK--HERS-RVQESFMRG-EINVITATISFGMGIDRQ-------  357 (444)
Q Consensus       295 ~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------~~~--~~r~-~~~~~f~~g-~~~vLvaT~~~~~Gidi~-------  357 (444)
                        ...+.|+||.|.|++.++.++..|.+.      ++.  .+++ .++.  ..| ...|.|||++++||.||.       
T Consensus       424 --~~~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vLNAk~~~~EA~IIa--~AG~~gaVTIATNMAGRGTDIkLg~~~~~  499 (764)
T PRK12326        424 --HETGQPVLVGTHDVAESEELAERLRAAGVPAVVLNAKNDAEEARIIA--EAGKYGAVTVSTQMAGRGTDIRLGGSDEA  499 (764)
T ss_pred             --HHcCCCEEEEeCCHHHHHHHHHHHHhCCCcceeeccCchHhHHHHHH--hcCCCCcEEEEecCCCCccCeecCCCccc
Confidence              236899999999999999999999987      211  1222 2221  245 467899999999999986       


Q ss_pred             --------CccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         358 --------NVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       358 --------~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                              +--+||-...+.|.+--.|-.||+||.|.+|.+..|++-+|.
T Consensus       500 ~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQGDpGss~f~lSleDd  549 (764)
T PRK12326        500 DRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQGDPGSSVFFVSLEDD  549 (764)
T ss_pred             chHHHHHcCCcEEEeccCCchHHHHHHHhcccccCCCCCceeEEEEcchh
Confidence                    122789899999999999999999999999999999986553

>KOG0924|consensus

Probab=99.81  E-value=2.2e-18  Score=165.86  Aligned_cols=295  Identities=17%  Similarity=0.156  Sum_probs=188.2

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEE--EcchhhhhcccCccchHhh
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGW--ISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vli--l~P~~~L~~~~q~~~~~~~  129 (444)
                      ..+.+.+..+..+ +-++|++.||||||.-          +   .+++...|-...-+|  .-|.+..+     --.+++
T Consensus       359 ~~R~~ll~~ir~n-~vvvivgETGSGKTTQ----------l---~QyL~edGY~~~GmIGcTQPRRvAA-----iSVAkr  419 (1042)
T KOG0924|consen  359 ACRDQLLSVIREN-QVVVIVGETGSGKTTQ----------L---AQYLYEDGYADNGMIGCTQPRRVAA-----ISVAKR  419 (1042)
T ss_pred             HHHHHHHHHHhhC-cEEEEEecCCCCchhh----------h---HHHHHhcccccCCeeeecCchHHHH-----HHHHHH
Confidence            3677788888887 8899999999999966          2   334555553322233  34888877     455555


Q ss_pred             h--cCCCC-ceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccc
Q psy7952         130 V--TGRSD-LYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSE  206 (444)
Q Consensus       130 l--~~~~~-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~  206 (444)
                      +  .++.+ +-.+..-..-.+..            .....|-+.|-+.|..+.   +  ....+.+.+.||+||||.=  
T Consensus       420 Va~EM~~~lG~~VGYsIRFEdvT------------~~~T~IkymTDGiLLrEs---L--~d~~L~kYSviImDEAHER--  480 (1042)
T KOG0924|consen  420 VAEEMGVTLGDTVGYSIRFEDVT------------SEDTKIKYMTDGILLRES---L--KDRDLDKYSVIIMDEAHER--  480 (1042)
T ss_pred             HHHHhCCccccccceEEEeeecC------------CCceeEEEeccchHHHHH---h--hhhhhhheeEEEechhhhc--
Confidence            5  22200 01222111111111            135677899988875321   1  1223557899999999983  


Q ss_pred             cCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHH
Q psy7952         207 WGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVK  286 (444)
Q Consensus       207 ~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  286 (444)
                       .....-.+..++..+.. ..+.++|.+|||+.   .+.+..+++ .-|........      |.+..........+++.
T Consensus       481 -slNtDilfGllk~~lar-RrdlKliVtSATm~---a~kf~nfFg-n~p~f~IpGRT------yPV~~~~~k~p~eDYVe  548 (1042)
T KOG0924|consen  481 -SLNTDILFGLLKKVLAR-RRDLKLIVTSATMD---AQKFSNFFG-NCPQFTIPGRT------YPVEIMYTKTPVEDYVE  548 (1042)
T ss_pred             -ccchHHHHHHHHHHHHh-hccceEEEeecccc---HHHHHHHhC-CCceeeecCCc------cceEEEeccCchHHHHH
Confidence             21122223333333333 33588999999985   456777776 23322222222      22222222223334555


Q ss_pred             HHHHHHhccCCC-CCceEEEEecccchHHHHHHHHHhh--------------------cCHHHHHHHHHHHhcCCccEEE
Q psy7952         287 EFIEKCLGKDNK-ANNCGIIYCRTREHTTDLADALRRK--------------------VNKHERSRVQESFMRGEINVIT  345 (444)
Q Consensus       287 ~~l~~~l~~~~~-~~~~~iVf~~s~~~~~~l~~~L~~~--------------------~~~~~r~~~~~~f~~g~~~vLv  345 (444)
                      ..+.+.+..+.. ..+-++||....++.+..+..+...                    ++..-+.+++.....|..++||
T Consensus       549 aavkq~v~Ihl~~~~GdilIfmtGqediE~t~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~Iv  628 (1042)
T KOG0924|consen  549 AAVKQAVQIHLSGPPGDILIFMTGQEDIECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIV  628 (1042)
T ss_pred             HHHhhheEeeccCCCCCEEEecCCCcchhHHHHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEE
Confidence            666666555443 4478999999998888877777665                    5666666777666678889999


Q ss_pred             EcCccccccccCCccEEEEeCC------------------CCCHHHHHHHhccCCCCCCceeEEEEeccc
Q psy7952         346 ATISFGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQSYCRIYHSEH  397 (444)
Q Consensus       346 aT~~~~~Gidi~~~~~Vi~~~~------------------p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~  397 (444)
                      ||++++..+.+|++.+||..|.                  |-|-.+--||.|||||. .+|.|+-++...
T Consensus       629 ATNIAETSLTi~gI~yVID~Gy~K~kvyn~~~G~D~L~~~pIS~AnA~QRaGRAGRt-~pG~cYRlYTe~  697 (1042)
T KOG0924|consen  629 ATNIAETSLTIPGIRYVIDTGYCKLKVYNPRIGMDALQIVPISQANADQRAGRAGRT-GPGTCYRLYTED  697 (1042)
T ss_pred             eccchhhceeecceEEEEecCceeeeecccccccceeEEEechhccchhhccccCCC-CCcceeeehhhh
Confidence            9999999999999999998775                  44777888999999999 588899888753

>KOG0923|consensus

Probab=99.81  E-value=1.5e-18  Score=166.60  Aligned_cols=296  Identities=15%  Similarity=0.188  Sum_probs=187.6

Q ss_pred             HHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCcc---ceeEEEcchhhhhcccCccchHhh
Q psy7952          53 LQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVR---SRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        53 ~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~---~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      +-.+.+.++... +-++|.+.||||||.-          +|.   ++...|-+   +++-+.-|.|..+     .-...+
T Consensus       269 ykdell~av~e~-QVLiI~GeTGSGKTTQ----------iPQ---yL~EaGytk~gk~IgcTQPRRVAA-----mSVAaR  329 (902)
T KOG0923|consen  269 YKDELLKAVKEH-QVLIIVGETGSGKTTQ----------IPQ---YLYEAGYTKGGKKIGCTQPRRVAA-----MSVAAR  329 (902)
T ss_pred             hHHHHHHHHHhC-cEEEEEcCCCCCcccc----------ccH---HHHhcccccCCceEeecCcchHHH-----HHHHHH
Confidence            556677777777 8899999999999944          666   45555422   3456666988766     444444


Q ss_pred             h--cCCCC-ceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccc
Q psy7952         130 V--TGRSD-LYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSE  206 (444)
Q Consensus       130 l--~~~~~-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~  206 (444)
                      .  .++-. +..|..-+.-.++.            ....-+=++|.++|.    .. +.....+...++|||||||.   
T Consensus       330 VA~EMgvkLG~eVGYsIRFEdcT------------SekTvlKYMTDGmLl----RE-fL~epdLasYSViiiDEAHE---  389 (902)
T KOG0923|consen  330 VAEEMGVKLGHEVGYSIRFEDCT------------SEKTVLKYMTDGMLL----RE-FLSEPDLASYSVIIVDEAHE---  389 (902)
T ss_pred             HHHHhCcccccccceEEEecccc------------CcceeeeeecchhHH----HH-HhccccccceeEEEeehhhh---
Confidence            4  22200 02222221111111            234566799999874    22 22334567789999999998   


Q ss_pred             cCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHH
Q psy7952         207 WGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVK  286 (444)
Q Consensus       207 ~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  286 (444)
                      ...+..-.+..+..+.+. .++.+++.+|||+.-   +.+..+++ ..|+  +..+..|-++...+...+..    .++-
T Consensus       390 RTL~TDILfgLvKDIar~-RpdLKllIsSAT~DA---ekFS~fFD-dapI--F~iPGRRyPVdi~Yt~~PEA----dYld  458 (902)
T KOG0923|consen  390 RTLHTDILFGLVKDIARF-RPDLKLLISSATMDA---EKFSAFFD-DAPI--FRIPGRRYPVDIFYTKAPEA----DYLD  458 (902)
T ss_pred             hhhhhhHHHHHHHHHHhh-CCcceEEeeccccCH---HHHHHhcc-CCcE--EeccCcccceeeecccCCch----hHHH
Confidence            332222333444444443 445899999999854   45566653 2333  33333333333223222211    1222


Q ss_pred             HHHHHHhccC-CCCCceEEEEecccchHHHHHHHHHhh-------------------cCHHHHHHHHHHHhcCCccEEEE
Q psy7952         287 EFIEKCLGKD-NKANNCGIIYCRTREHTTDLADALRRK-------------------VNKHERSRVQESFMRGEINVITA  346 (444)
Q Consensus       287 ~~l~~~l~~~-~~~~~~~iVf~~s~~~~~~l~~~L~~~-------------------~~~~~r~~~~~~f~~g~~~vLva  346 (444)
                      ..+...+..+ ..+.+-+|||....++.+.+...|...                   ++.+.+..+++.--.|..+|++|
T Consensus       459 Aai~tVlqIH~tqp~GDILVFltGQeEIEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVVLA  538 (902)
T KOG0923|consen  459 AAIVTVLQIHLTQPLGDILVFLTGQEEIETVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLA  538 (902)
T ss_pred             HHHhhheeeEeccCCccEEEEeccHHHHHHHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEEEe
Confidence            2222222222 125678999999988877776666555                   77788888888777899999999


Q ss_pred             cCccccccccCCccEEEEeCC------------------CCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         347 TISFGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       347 T~~~~~Gidi~~~~~Vi~~~~------------------p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                      |++++..+.|+++.+||+-|+                  |-|..+-.||.|||||.| +|.|+-++.....
T Consensus       539 TNIAETSlTIdgI~yViDpGf~K~nsynprtGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfRLYt~~aY  608 (902)
T KOG0923|consen  539 TNIAETSLTIDGIKYVIDPGFVKQNSYNPRTGMESLLVTPISKASANQRAGRAGRTG-PGKCFRLYTAWAY  608 (902)
T ss_pred             ecchhhceeecCeEEEecCccccccCcCCCcCceeEEEeeechhhhhhhccccCCCC-CCceEEeechhhh
Confidence            999999999999999997665                  447888899999999995 8889999985443

>KOG0920|consensus

Probab=99.79  E-value=2.4e-18  Score=175.34  Aligned_cols=308  Identities=18%  Similarity=0.135  Sum_probs=192.8

Q ss_pred             cC-chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCC-CccccccCCccceeEEEcchhhhhcccCccch
Q psy7952          49 FK-CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPP-GADFILNGNVRSRNGWISPILSSFYLRFRDDK  126 (444)
Q Consensus        49 ~~-t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~-~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~  126 (444)
                      +| .+.+.+.++.+.++ +-+++.+.||+|||.-          +|. +++.....+..-++++.-|.|--|     -..
T Consensus       172 LPa~~~r~~Il~~i~~~-qVvvIsGeTGcGKTTQ----------vpQfiLd~~~~~~~~~~IicTQPRRIsA-----Isv  235 (924)
T KOG0920|consen  172 LPAYKMRDTILDAIEEN-QVVVISGETGCGKTTQ----------VPQFILDEAIESGAACNIICTQPRRISA-----ISV  235 (924)
T ss_pred             CccHHHHHHHHHHHHhC-ceEEEeCCCCCCchhh----------hhHHHHHHHHhcCCCCeEEecCCchHHH-----HHH
Confidence            44 34566666777666 8999999999999955          333 122233344444677777998665     344


Q ss_pred             Hhhh--cCCC-CceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccc
Q psy7952         127 TSIV--TGRS-DLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHC  203 (444)
Q Consensus       127 ~~~l--~~~~-~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~  203 (444)
                      .++.  ..+. .+-.|..-.+-...            ......+.+||.+.+.    . .+.....+..+..||+||+|.
T Consensus       236 AeRVa~ER~~~~g~~VGYqvrl~~~------------~s~~t~L~fcTtGvLL----r-~L~~~~~l~~vthiivDEVHE  298 (924)
T KOG0920|consen  236 AERVAKERGESLGEEVGYQVRLESK------------RSRETRLLFCTTGVLL----R-RLQSDPTLSGVTHIIVDEVHE  298 (924)
T ss_pred             HHHHHHHhccccCCeeeEEEeeecc------------cCCceeEEEecHHHHH----H-HhccCcccccCceeeeeeEEE
Confidence            4544  1110 01112111111111            1235789999988874    2 233345567889999999998


Q ss_pred             ccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCce-----------EEE
Q psy7952         204 VSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLF-----------YDV  272 (444)
Q Consensus       204 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~-----------~~~  272 (444)
                      =.-. .+|-  +-.++.++... ++.++|+||||+..   +.+..+++.. + .+......-|-..           |..
T Consensus       299 R~i~-~Dfl--Li~lk~lL~~~-p~LkvILMSAT~da---e~fs~YF~~~-p-vi~i~grtfpV~~~fLEDil~~~~~~~  369 (924)
T KOG0920|consen  299 RSIN-TDFL--LILLKDLLPRN-PDLKVILMSATLDA---ELFSDYFGGC-P-VITIPGRTFPVKEYFLEDILSKTGYVS  369 (924)
T ss_pred             ccCC-cccH--HHHHHHHhhhC-CCceEEEeeeecch---HHHHHHhCCC-c-eEeecCCCcchHHHHHHHHHHHhcccc
Confidence            3322 1222  22333444433 45999999999873   4455666522 2 1222221111100           000


Q ss_pred             --------EEcc----------cchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----------
Q psy7952         273 --------IFDD----------LLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----------  323 (444)
Q Consensus       273 --------~~~~----------~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----------  323 (444)
                              ....          ..+..+..+..++......  ...+.+|||.+...+...+.+.|...           
T Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~~~~id~~Li~~li~~I~~~--~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~i  447 (924)
T KOG0920|consen  370 EDDSARSGPERSQLRLARLKLWEPEIDYDLIEDLIEYIDER--EFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAI  447 (924)
T ss_pred             cccccccccccCccccccchhccccccHHHHHHHHHhcccC--CCCceEEEEcCCHHHHHHHHHHhhhccccccccceEE
Confidence                    0000          0011222333333333322  35789999999999999999999754           


Q ss_pred             ------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCC------------------CHHHHHHHhc
Q psy7952         324 ------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPS------------------SIPAYYQESG  379 (444)
Q Consensus       324 ------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~------------------s~~~~~Qr~G  379 (444)
                            ++.+++..+++..-.|..+||++|++++.+|.|+++.+||+.+.-+                  |..+-.||.|
T Consensus       448 lplHs~~~s~eQ~~VF~~pp~g~RKIIlaTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~G  527 (924)
T KOG0920|consen  448 LPLHSSIPSEEQQAVFKRPPKGTRKIILATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRG  527 (924)
T ss_pred             EeccccCChHHHHHhcCCCCCCcchhhhhhhhHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcc
Confidence                  7888999999998899999999999999999999999999766422                  6777899999


Q ss_pred             cCCCCCCceeEEEEecccchhh
Q psy7952         380 RAGRDGLQSYCRIYHSEHSKKS  401 (444)
Q Consensus       380 R~~R~g~~g~~~~~~~~~~~~~  401 (444)
                      ||||. ..|.|+.+++....+.
T Consensus       528 RAGRv-~~G~cy~L~~~~~~~~  548 (924)
T KOG0920|consen  528 RAGRV-RPGICYHLYTRSRYEK  548 (924)
T ss_pred             cccCc-cCCeeEEeechhhhhh
Confidence            99999 8999999998765543

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

Probab=99.79  E-value=1.4e-17  Score=174.16  Aligned_cols=178  Identities=16%  Similarity=0.096  Sum_probs=112.2

Q ss_pred             CcEEEEeccCCc-chHHHHHHHhcCCCCeEEEecCCCCCCceEEEEE--cc-----cchhhHHHHHHHHHHHhccCCCCC
Q psy7952         229 IPIIALTATAEP-SVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIF--DD-----LLKDSYAHVKEFIEKCLGKDNKAN  300 (444)
Q Consensus       229 ~~~v~lSAT~~~-~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~--~~-----~~~~~~~~~~~~l~~~l~~~~~~~  300 (444)
                      ..+|++|||+.- .... +.+.+|+..............+.. .+..  ..     ......+.+.+.+..+. .   .+
T Consensus       574 ~~~i~tSATL~v~~~f~-~~~~lGl~~~~~~~~~~~~~~~~~-~~i~~~~p~~~~~~~~~~~~~~~~~i~~~~-~---~~  647 (820)
T PRK07246        574 CKTYFVSATLQISPRVS-LADLLGFEEYLFHKIEKDKKQDQL-VVVDQDMPLVTETSDEVYAEEIAKRLEELK-Q---LQ  647 (820)
T ss_pred             CeEEEEecccccCCCCc-HHHHcCCCccceecCCCChHHccE-EEeCCCCCCCCCCChHHHHHHHHHHHHHHH-h---cC
Confidence            357999999962 2223 677788754322211111111111 1111  11     11222335555555543 2   47


Q ss_pred             ceEEEEecccchHHHHHHHHHhh-------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCC--ccEEEEeCCCCC-
Q psy7952         301 NCGIIYCRTREHTTDLADALRRK-------VNKHERSRVQESFMRGEINVITATISFGMGIDRQN--VRFVVHWGMPSS-  370 (444)
Q Consensus       301 ~~~iVf~~s~~~~~~l~~~L~~~-------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~--~~~Vi~~~~p~s-  370 (444)
                      ++++|+++|.+..+.+++.|...       -....+..++++|++++..||++|+.+.+|||+|.  ...||....|.. 
T Consensus       648 g~~LVLFtS~~~l~~v~~~l~~~~~~~l~Qg~~~~~~~l~~~F~~~~~~vLlG~~sFwEGVD~p~~~~~~viI~kLPF~~  727 (820)
T PRK07246        648 QPILVLFNSKKHLLAVSDLLDQWQVSHLAQEKNGTAYNIKKRFDRGEQQILLGLGSFWEGVDFVQADRMIEVITRLPFDN  727 (820)
T ss_pred             CCEEEEECcHHHHHHHHHHHhhcCCcEEEeCCCccHHHHHHHHHcCCCeEEEecchhhCCCCCCCCCeEEEEEecCCCCC
Confidence            89999999999999999988643       11123567899999998999999999999999973  455677776631 


Q ss_pred             -----------------------------HHHHHHHhccCCCCCCceeEEEEeccc-chhhHHHHHhhccch
Q psy7952         371 -----------------------------IPAYYQESGRAGRDGLQSYCRIYHSEH-SKKSLEYVIKTDTST  412 (444)
Q Consensus       371 -----------------------------~~~~~Qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~  412 (444)
                                                   ...+.|.+||.-|...+.-+++++++. ..+.+.+.+-+.+|.
T Consensus       728 P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gvv~ilD~R~~~k~Yg~~~l~sLP~  799 (820)
T PRK07246        728 PEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLILDRRILTKSYGKQILASLAE  799 (820)
T ss_pred             CCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEEEEEECCcccccHHHHHHHHhCCC
Confidence                                         344689999999986543356666655 555666666666664

>KOG0385|consensus

Probab=99.77  E-value=9.9e-18  Score=163.64  Aligned_cols=312  Identities=15%  Similarity=0.119  Sum_probs=198.3

Q ss_pred             cCchHHHHHHHHHHc---cCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccc
Q psy7952          49 FKCELQKKAIRHILL---RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDD  125 (444)
Q Consensus        49 ~~t~~Q~~~~~~~~~---~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~  125 (444)
                      ++ +||.+-++++..   +.-+.|+.-..|-|||+- .|++++ |+..    ..-..|+.   ||+||...|.+|   ..
T Consensus       168 lr-~YQveGlnWLi~l~engingILaDEMGLGKTlQ-tIs~l~-yl~~----~~~~~GPf---LVi~P~StL~NW---~~  234 (971)
T KOG0385|consen  168 LR-DYQLEGLNWLISLYENGINGILADEMGLGKTLQ-TISLLG-YLKG----RKGIPGPF---LVIAPKSTLDNW---MN  234 (971)
T ss_pred             cc-hhhhccHHHHHHHHhcCcccEeehhcccchHHH-HHHHHH-HHHH----hcCCCCCe---EEEeeHhhHHHH---HH
Confidence            44 799999888774   336799999999999976 222222 1110    02224566   999999999844   34


Q ss_pred             hHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccc
Q psy7952         126 KTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVS  205 (444)
Q Consensus       126 ~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~  205 (444)
                      .+.+|...   +++..++|+.  .++....+++- ..+..+|+|+|+|+...      -......-+++|+||||+|++-
T Consensus       235 Ef~rf~P~---l~~~~~~Gdk--~eR~~~~r~~~-~~~~fdV~iTsYEi~i~------dk~~lk~~~W~ylvIDEaHRiK  302 (971)
T KOG0385|consen  235 EFKRFTPS---LNVVVYHGDK--EERAALRRDIM-LPGRFDVCITSYEIAIK------DKSFLKKFNWRYLVIDEAHRIK  302 (971)
T ss_pred             HHHHhCCC---cceEEEeCCH--HHHHHHHHHhh-ccCCCceEeehHHHHHh------hHHHHhcCCceEEEechhhhhc
Confidence            44555555   9999999976  44444444443 24589999999998642      2333444578999999999975


Q ss_pred             ccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecC-----------------------
Q psy7952         206 EWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTS-----------------------  262 (444)
Q Consensus       206 ~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~-----------------------  262 (444)
                      ...       ..+.+.++.+.. ..-+++|+||-.+....+...+.+--|-......                       
T Consensus       303 N~~-------s~L~~~lr~f~~-~nrLLlTGTPLQNNL~ELWaLLnFllPdiF~~~e~F~swF~~~~~~~~~e~v~~Lh~  374 (971)
T KOG0385|consen  303 NEK-------SKLSKILREFKT-DNRLLLTGTPLQNNLHELWALLNFLLPDIFNSAEDFDSWFDFTNCEGDQELVSRLHK  374 (971)
T ss_pred             chh-------hHHHHHHHHhcc-cceeEeeCCcccccHHHHHHHHHhhchhhccCHHHHHHHHcccccccCHHHHHHHHh
Confidence            432       344455555554 4568999999887777666666543221111000                       


Q ss_pred             ----------------CCCCCceEEEEEcc--cchhhHHHHH--------------------------------------
Q psy7952         263 ----------------TFRSNLFYDVIFDD--LLKDSYAHVK--------------------------------------  286 (444)
Q Consensus       263 ----------------~~~~~~~~~~~~~~--~~~~~~~~~~--------------------------------------  286 (444)
                                      ...|...+.+...-  .....+..+.                                      
T Consensus       375 vL~pFlLRR~K~dVe~sLppKkE~~iyvgms~mQkk~Y~~iL~kdl~~~n~~~~~~k~kL~NI~mQLRKccnHPYLF~g~  454 (971)
T KOG0385|consen  375 VLRPFLLRRIKSDVEKSLPPKKELIIYVGMSSMQKKWYKAILMKDLDALNGEGKGEKTKLQNIMMQLRKCCNHPYLFDGA  454 (971)
T ss_pred             hhhHHHHHHHHHhHhhcCCCcceeeEeccchHHHHHHHHHHHHhcchhhcccccchhhHHHHHHHHHHHhcCCccccCCC
Confidence                            00011111111100  0111111110                                      


Q ss_pred             -------------------HHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHh
Q psy7952         287 -------------------EFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFM  337 (444)
Q Consensus       287 -------------------~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~  337 (444)
                                         .++.+++.+-...+++|+||........-+-+...-+          ++-++|...++.|.
T Consensus       455 ePg~pyttdehLv~nSGKm~vLDkLL~~Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn  534 (971)
T KOG0385|consen  455 EPGPPYTTDEHLVTNSGKMLVLDKLLPKLKEQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFN  534 (971)
T ss_pred             CCCCCCCcchHHHhcCcceehHHHHHHHHHhCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcC
Confidence                               0111111111125777888877666666555544333          78899999999997


Q ss_pred             cCC--c-cEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEE
Q psy7952         338 RGE--I-NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIY  393 (444)
Q Consensus       338 ~g~--~-~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~  393 (444)
                      ...  . -.|++|.+.+.|||+-..++||.||..+++..-+|..-||.|-|+..-+.+|
T Consensus       535 ~~~s~~FiFlLSTRAGGLGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~  593 (971)
T KOG0385|consen  535 APPSEKFIFLLSTRAGGLGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVY  593 (971)
T ss_pred             CCCcceEEEEEeccccccccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEE
Confidence            543  3 3499999999999999999999999999999999999999999988765543

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.76  E-value=1.5e-16  Score=161.92  Aligned_cols=133  Identities=16%  Similarity=0.124  Sum_probs=94.6

Q ss_pred             HHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhh
Q psy7952          37 TAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILS  116 (444)
Q Consensus        37 ~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~  116 (444)
                      .++-++..|..+|.  .|.-.--.+.+|   -+..+.||.|||++|++        |+ .-....+..   |.+++|+..
T Consensus        72 rEa~~R~lGm~~yd--VQliGg~~Lh~G---~iaEM~TGEGKTLvA~l--------~a-~l~al~G~~---VhvvT~ndy  134 (913)
T PRK13103         72 REAGKRVMGMRHFD--VQLIGGMTLHEG---KIAEMRTGEGKTLVGTL--------AV-YLNALSGKG---VHVVTVNDY  134 (913)
T ss_pred             HHHHHHHhCCCcch--hHHHhhhHhccC---ccccccCCCCChHHHHH--------HH-HHHHHcCCC---EEEEeCCHH
Confidence            45566667877644  787666666555   67999999999999544        44 111223333   489999999


Q ss_pred             hhcccCccchHhhh-----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH---
Q psy7952         117 SFYLRFRDDKTSIV-----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV---  188 (444)
Q Consensus       117 L~~~~q~~~~~~~l-----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~---  188 (444)
                      ||     .+..+.+     .+|   +.+..+.++....++...+        .++|++||...+.   |+++..+..   
T Consensus       135 LA-----~RD~e~m~~l~~~lG---l~v~~i~~~~~~~err~~Y--------~~dI~YGT~~e~g---FDYLrD~~~~~~  195 (913)
T PRK13103        135 LA-----RRDANWMRPLYEFLG---LSVGIVTPFQPPEEKRAAY--------AADITYGTNNEFG---FDYLRDNMAFSL  195 (913)
T ss_pred             HH-----HHHHHHHHHHhcccC---CEEEEECCCCCHHHHHHHh--------cCCEEEEcccccc---cchhhccceech
Confidence            99     6666665     445   9999999998888777766        4899999988875   344333322   


Q ss_pred             ---hhCCccEEEEecccccc
Q psy7952         189 ---RYNKLAYIVVDEAHCVS  205 (444)
Q Consensus       189 ---~~~~~~~iViDE~H~~~  205 (444)
                         ....++++||||+|.++
T Consensus       196 ~~~vqr~l~~aIVDEvDsiL  215 (913)
T PRK13103        196 DDKFQRELNFAVIDEVDSIL  215 (913)
T ss_pred             hhhcccccceeEechhhhee
Confidence               13678999999999873

>COG4889 Predicted helicase [General function prediction only]

Probab=99.75  E-value=4.2e-18  Score=167.97  Aligned_cols=337  Identities=15%  Similarity=0.173  Sum_probs=192.6

Q ss_pred             CCCCCcCCCCCCCCCHHHHHHHHHHHhCCcccCchHHHHHHHHHHcc---CCcEEEEccCCCcccccccccccceEEeCC
Q psy7952          18 SLTGNQQDRKGGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLR---THDIFVSMPTGAVSLVGSVVSARSRVRIPP   94 (444)
Q Consensus        18 ~~~~~~~~~~~~~~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~---~~~~ii~apTGsGKT~~a~~~~~~~~~~~~   94 (444)
                      .+..++++|.....  .++...+.-. .... |.++|+.|+....++   +.+-=+.++||+|||++++         .+
T Consensus       134 ei~es~IDW~~f~p--~e~~~nl~l~-~~kk-~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsL---------ki  200 (1518)
T COG4889         134 EIAESPIDWDIFDP--TELQDNLPLK-KPKK-PRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSL---------KI  200 (1518)
T ss_pred             HHhcCCCChhhcCc--cccccccccC-CCCC-CChhHHHHHHHHHhhcccccCCcEEEecCCCccchHH---------HH
Confidence            44556788876553  4444444322 2333 348999999998875   2344567789999999832         11


Q ss_pred             CccccccCCccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCCh-----------------hhHHHHHH
Q psy7952          95 GADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTK-----------------TENKAILE  156 (444)
Q Consensus        95 ~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~-----------------~~~~~~~~  156 (444)
                       .+.+.    ..++|+++|+.+|.     .|.++.+ .....++....++++...                 .....++.
T Consensus       201 -sEala----~~~iL~LvPSIsLL-----sQTlrew~~~~~l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~  270 (1518)
T COG4889         201 -SEALA----AARILFLVPSISLL-----SQTLREWTAQKELDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILS  270 (1518)
T ss_pred             -HHHHh----hhheEeecchHHHH-----HHHHHHHhhccCccceeEEEecCccccccccccccccCCCCCcccHHHHHH
Confidence             11111    15679999999999     8899988 444344766667665322                 11233444


Q ss_pred             HHHh--cCCCeeEEEECCCccccccHHHHHHHH--HhhCCccEEEEecccccccc---C---CCcHHHH--HHHHHHHHh
Q psy7952         157 ELRL--VKPRIKLLYVTPERAVTESFHYLLQHL--VRYNKLAYIVVDEAHCVSEW---G---HDFRPTY--RRLGELRQF  224 (444)
Q Consensus       157 ~~~~--~~~~~~Iiv~Tpe~l~~~~~~~~~~~~--~~~~~~~~iViDE~H~~~~~---~---~~~~~~~--~~l~~~~~~  224 (444)
                      .+..  ...+--|+++|++.+.      .....  ..+..|++||+||+|+-...   +   +.|....  ..++.    
T Consensus       271 ~~~~~~k~~~~~vvFsTYQSl~------~i~eAQe~G~~~fDliicDEAHRTtGa~~a~dd~saFt~vHs~~niKa----  340 (1518)
T COG4889         271 EMEHRQKANGLTVVFSTYQSLP------RIKEAQEAGLDEFDLIICDEAHRTTGATLAGDDKSAFTRVHSDQNIKA----  340 (1518)
T ss_pred             HHHHhhccCCcEEEEEcccchH------HHHHHHHcCCCCccEEEecchhccccceecccCcccceeecCcchhHH----
Confidence            3332  2456679999999974      22222  34678999999999997431   1   1111000  11111    


Q ss_pred             hCCCCcEEEEeccCCcchHHHHHHHhc--------CC-----------------------CCeEEEecCCCCCCc---eE
Q psy7952         225 TGNSIPIIALTATAEPSVKQDIISVLK--------FN-----------------------KPYKVFKTSTFRSNL---FY  270 (444)
Q Consensus       225 ~~~~~~~v~lSAT~~~~~~~~~~~~l~--------~~-----------------------~~~~~~~~~~~~~~~---~~  270 (444)
                          .+.+.|||||.--... ....-.        +.                       ..+.+..-......+   ..
T Consensus       341 ----~kRlYmTATPkiy~eS-~K~kAkd~s~~l~SMDDe~~fGeef~rl~FgeAv~rdlLTDYKVmvlaVd~~~i~~~~~  415 (1518)
T COG4889         341 ----AKRLYMTATPKIYSES-SKAKAKDHSAELSSMDDELTFGEEFHRLGFGEAVERDLLTDYKVMVLAVDKEVIAGVLQ  415 (1518)
T ss_pred             ----HHhhhcccCchhhchh-hhhhhhhccceeeccchhhhhchhhhcccHHHHHHhhhhccceEEEEEechhhhhhhhh
Confidence                3457899997421110 000000        00                       001111000000000   00


Q ss_pred             EEEEcccchhhH---HHHHHHHHHHhccCC------------CCCceEEEEecccchHHHHHHHHHhh------------
Q psy7952         271 DVIFDDLLKDSY---AHVKEFIEKCLGKDN------------KANNCGIIYCRTREHTTDLADALRRK------------  323 (444)
Q Consensus       271 ~~~~~~~~~~~~---~~~~~~l~~~l~~~~------------~~~~~~iVf~~s~~~~~~l~~~L~~~------------  323 (444)
                      ............   ..++-...-+..+..            .+-.+.|-||.+.++.+++++.+..-            
T Consensus       416 ~~~~~~~~~L~~dd~~kIvG~wnGlakr~g~~n~~~~~~~d~ap~~RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~  495 (1518)
T COG4889         416 SVLSGPSKGLALDDVSKIVGCWNGLAKRNGEDNDLKNIKADTAPMQRAIAFAKDIKTSKQIAESFETVVEAYDEELKKDF  495 (1518)
T ss_pred             hhccCcccccchhhhhhhhhhhhhhhhhccccccccCCcCCchHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            000000000011   111111111111111            12346788999999999988877554            


Q ss_pred             -------------cCHHHHHHHHH---HHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCC-
Q psy7952         324 -------------VNKHERSRVQE---SFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGL-  386 (444)
Q Consensus       324 -------------~~~~~r~~~~~---~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~-  386 (444)
                                   |+..+|...+.   .|...+++||-....+++|||+|.++.||++++-.|..+.+|.+||+.|... 
T Consensus       496 ~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~neckIlSNaRcLSEGVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~g  575 (1518)
T COG4889         496 KNLKISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCLSEGVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKG  575 (1518)
T ss_pred             CCceEEeecccccccHHHHHHHHhccCCCCcchheeeccchhhhcCCCccccceEEEecCchhHHHHHHHHHHHHHhCcC
Confidence                         66667644333   3456789999999999999999999999999999999999999999999632 


Q ss_pred             c--eeEEE
Q psy7952         387 Q--SYCRI  392 (444)
Q Consensus       387 ~--g~~~~  392 (444)
                      +  ||.++
T Consensus       576 K~yGYIIL  583 (1518)
T COG4889         576 KKYGYIIL  583 (1518)
T ss_pred             CccceEEE
Confidence            2  55544

>KOG0387|consensus

Probab=99.72  E-value=8.6e-17  Score=157.86  Aligned_cols=316  Identities=14%  Similarity=0.104  Sum_probs=203.9

Q ss_pred             hHHHHHHHHHHc---cCCcEEEEccCCCcccccccccccceEEeCCCccccccC-CccceeEEEcchhhhhcccCccchH
Q psy7952          52 ELQKKAIRHILL---RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG-NVRSRNGWISPILSSFYLRFRDDKT  127 (444)
Q Consensus        52 ~~Q~~~~~~~~~---~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~-~~~~~vlil~P~~~L~~~~q~~~~~  127 (444)
                      +||++.++++.+   .+..-|+.-..|-|||.-.+.     |     +..+... ....++|||||..-+.      +-+
T Consensus       208 ~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiis-----F-----LaaL~~S~k~~~paLIVCP~Tii~------qW~  271 (923)
T KOG0387|consen  208 PYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIIS-----F-----LAALHHSGKLTKPALIVCPATIIH------QWM  271 (923)
T ss_pred             HHHHHHHHHHHHHHhccCCCeecccccCccchhHHH-----H-----HHHHhhcccccCceEEEccHHHHH------HHH
Confidence            599999888774   225678999999999966211     1     1223333 3446679999998887      555


Q ss_pred             hhh-cCCCCceeEEEEeCCCChh---------hHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEE
Q psy7952         128 SIV-TGRSDLYQLELIVSGQTKT---------ENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIV  197 (444)
Q Consensus       128 ~~l-~~~~~~i~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iV  197 (444)
                      ..+ ... +.+.+..+++.....         .+...+.  +....+..|+++|++.+.      ..........++|+|
T Consensus       272 ~E~~~w~-p~~rv~ilh~t~s~~r~~~~~~~~~~~~~L~--r~~~~~~~ilitty~~~r------~~~d~l~~~~W~y~I  342 (923)
T KOG0387|consen  272 KEFQTWW-PPFRVFILHGTGSGARYDASHSSHKKDKLLI--RKVATDGGILITTYDGFR------IQGDDLLGILWDYVI  342 (923)
T ss_pred             HHHHHhC-cceEEEEEecCCcccccccchhhhhhhhhhe--eeecccCcEEEEehhhhc------ccCcccccccccEEE
Confidence            555 222 228888888876521         1111111  112345679999988863      222333445789999


Q ss_pred             EeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecC--------------C
Q psy7952         198 VDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTS--------------T  263 (444)
Q Consensus       198 iDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~--------------~  263 (444)
                      +||.|.+-....       .+...+..++. .+.+.+|+||..+....+...+.+-.|..+....              .
T Consensus       343 LDEGH~IrNpns-------~islackki~T-~~RiILSGTPiQNnL~ELwsLfDFv~PG~Lgt~~~F~~~f~~pI~~Ggy  414 (923)
T KOG0387|consen  343 LDEGHRIRNPNS-------KISLACKKIRT-VHRIILSGTPIQNNLTELWSLFDFVFPGKLGTLPVFQQNFEHPINRGGY  414 (923)
T ss_pred             ecCcccccCCcc-------HHHHHHHhccc-cceEEeeCccccchHHHHHHHhhhccCCcccchHHHHhhhhhheecccc
Confidence            999999866553       22222233333 6678999999887777666555432111100000              0


Q ss_pred             -------------------------------------CCCCceEEEEE--------------------------------
Q psy7952         264 -------------------------------------FRSNLFYDVIF--------------------------------  274 (444)
Q Consensus       264 -------------------------------------~~~~~~~~~~~--------------------------------  274 (444)
                                                           ..|.-.-.+.+                                
T Consensus       415 aNAs~~qv~~aykca~~Lr~lI~PylLRR~K~dv~~~~Lp~K~E~VlfC~LT~~QR~~Y~~fl~s~~v~~i~ng~~~~l~  494 (923)
T KOG0387|consen  415 ANASPRQVQTAYKCAVALRDLISPYLLRRMKSDVKGLKLPKKEEIVLFCRLTKLQRRLYQRFLNSSEVNKILNGKRNCLS  494 (923)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhhhccCCCccceEEEEeccHHHHHHHHHHhhhHHHHHHHcCCcccee
Confidence                                                 00000000000                                


Q ss_pred             -------------------------ccc-chhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----
Q psy7952         275 -------------------------DDL-LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----  323 (444)
Q Consensus       275 -------------------------~~~-~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----  323 (444)
                                               .+. ...+..-....+..++......+.++++|..++....-+...|...     
T Consensus       495 Gi~iLrkICnHPdll~~~~~~~~~~~D~~g~~k~sGKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysy  574 (923)
T KOG0387|consen  495 GIDILRKICNHPDLLDRRDEDEKQGPDYEGDPKRSGKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSY  574 (923)
T ss_pred             chHHHHhhcCCcccccCcccccccCCCcCCChhhcchHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceE
Confidence                                     000 0111123345555555555567889999999999999988888842     


Q ss_pred             ------cCHHHHHHHHHHHhcCCc-cE-EEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEE--E
Q psy7952         324 ------VNKHERSRVQESFMRGEI-NV-ITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRI--Y  393 (444)
Q Consensus       324 ------~~~~~r~~~~~~f~~g~~-~v-LvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~--~  393 (444)
                            .+...|..++++|.+++. .| |++|.+.+-|+|+..++.||.||+.+++.+-.|..-||=|.|+...+++  +
T Consensus       575 lRmDGtT~~~~R~~lVd~Fne~~s~~VFLLTTrvGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VYRL  654 (923)
T KOG0387|consen  575 LRMDGTTPAALRQKLVDRFNEDESIFVFLLTTRVGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVYRL  654 (923)
T ss_pred             EEecCCCccchhhHHHHhhcCCCceEEEEEEecccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEEEE
Confidence                  677899999999997753 44 9999999999999999999999999999999999999999999877655  4


Q ss_pred             ecccchh
Q psy7952         394 HSEHSKK  400 (444)
Q Consensus       394 ~~~~~~~  400 (444)
                      +.....+
T Consensus       655 ~t~gTIE  661 (923)
T KOG0387|consen  655 MTAGTIE  661 (923)
T ss_pred             ecCCcHH
Confidence            4544433

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

Probab=99.72  E-value=1.6e-15  Score=161.62  Aligned_cols=180  Identities=18%  Similarity=0.172  Sum_probs=118.4

Q ss_pred             cEEEEeccCCcc-hHHHHHHHhcCCCC--eEEEecCCCC-CCceEEEEEccc-------chhhHHHHHHHHHHHhccCCC
Q psy7952         230 PIIALTATAEPS-VKQDIISVLKFNKP--YKVFKTSTFR-SNLFYDVIFDDL-------LKDSYAHVKEFIEKCLGKDNK  298 (444)
Q Consensus       230 ~~v~lSAT~~~~-~~~~~~~~l~~~~~--~~~~~~~~~~-~~~~~~~~~~~~-------~~~~~~~~~~~l~~~l~~~~~  298 (444)
                      .+|++|||+... ..+.+.+.+|+.+.  .....++... .+....+.....       .......+.+.+.+++..   
T Consensus       674 ~~iltSATL~~~~~f~~~~~~lGl~~~~~~~~~~~SpF~~~~q~~l~vp~d~p~~~~~~~~~~~~~la~~i~~l~~~---  750 (928)
T PRK08074        674 SVILTSATLTVNGSFDYIIERLGLEDFYPRTLQIPSPFSYEEQAKLMIPTDMPPIKDVPIEEYIEEVAAYIAKIAKA---  750 (928)
T ss_pred             cEEEEeeecccCCCcHHHHHhcCCCCCCccEEEeCCCCCHHHhcEEEeecCCCCCCCCChHHHHHHHHHHHHHHHHh---
Confidence            368999998743 23455677787542  1222222111 111111111111       122234555556555443   


Q ss_pred             CCceEEEEecccchHHHHHHHHHhh------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCC--ccEEEE
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQN--VRFVVH  364 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~--~~~Vi~  364 (444)
                      .+++++|+++|.+..+.+++.|...            +....|..+++.|++++-.||++|+.+++|||+|+  +.+||.
T Consensus       751 ~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg~~l~~viI  830 (928)
T PRK08074        751 TKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDELSCLVI  830 (928)
T ss_pred             CCCCEEEEECCHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCCCceEEEEE
Confidence            4679999999999999999998643            12356889999999998899999999999999996  578888


Q ss_pred             eCCCCC------------------------------HHHHHHHhccCCCCCCceeEEEEeccc-chhhHHHHHhhccch
Q psy7952         365 WGMPSS------------------------------IPAYYQESGRAGRDGLQSYCRIYHSEH-SKKSLEYVIKTDTST  412 (444)
Q Consensus       365 ~~~p~s------------------------------~~~~~Qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~  412 (444)
                      ...|..                              ...+.|.+||+-|..++.-+++++++. ..+.+.+.+-+.+|.
T Consensus       831 ~kLPF~~p~dp~~~a~~~~~~~~g~~~F~~~~lP~A~~~lkQg~GRlIRs~~D~G~v~ilD~R~~~k~Yg~~~l~sLP~  909 (928)
T PRK08074        831 VRLPFAPPDQPVMEAKSEWAKEQGENPFQELSLPQAVLRFKQGFGRLIRTETDRGTVFVLDRRLTTTSYGKYFLESLPT  909 (928)
T ss_pred             ecCCCCCCCCHHHHHHHHHHHHhCCCchhhhhhHHHHHHHHhhhhhhcccCCceEEEEEecCccccchHHHHHHHhCCC
Confidence            887641                              334579999999987554456666655 566677777777764

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=99.72  E-value=2.1e-15  Score=152.09  Aligned_cols=318  Identities=17%  Similarity=0.144  Sum_probs=196.6

Q ss_pred             HHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchh
Q psy7952          36 LTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPIL  115 (444)
Q Consensus        36 ~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~  115 (444)
                      +.++.++.+|..+|+  .|.-..-.+..|   -+..+.||-|||++|+        +|+.+..+...+.    -|++...
T Consensus        67 vREA~~R~lG~r~yd--VQliGglvLh~G---~IAEMkTGEGKTLvAt--------LpayLnAL~GkgV----hVVTvNd  129 (925)
T PRK12903         67 AREATKRVLGKRPYD--VQIIGGIILDLG---SVAEMKTGEGKTITSI--------APVYLNALTGKGV----IVSTVNE  129 (925)
T ss_pred             HHHHHHHHhCCCcCc--hHHHHHHHHhcC---CeeeecCCCCccHHHH--------HHHHHHHhcCCce----EEEecch
Confidence            446777778988644  788777777666   4699999999999954        4442332433333    5667777


Q ss_pred             hhhcccCccchHhhh-----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH--
Q psy7952         116 SSFYLRFRDDKTSIV-----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV--  188 (444)
Q Consensus       116 ~L~~~~q~~~~~~~l-----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~--  188 (444)
                      -|+     ....+.+     .+|   +.+..+..+.....+...+        .+||+++|...|.   |+++..++.  
T Consensus       130 YLA-----~RDae~mg~vy~fLG---LsvG~i~~~~~~~~rr~aY--------~~DItYgTn~E~g---FDYLRDnm~~~  190 (925)
T PRK12903        130 YLA-----ERDAEEMGKVFNFLG---LSVGINKANMDPNLKREAY--------ACDITYSVHSELG---FDYLRDNMVSS  190 (925)
T ss_pred             hhh-----hhhHHHHHHHHHHhC---CceeeeCCCCChHHHHHhc--------cCCCeeecCcccc---hhhhhhccccc
Confidence            787     5666555     567   9999998888777766666        6899999988876   555554432  


Q ss_pred             ----hhCCccEEEEecccccc-ccC----------CCcHHHHHHHHHHHHhhCC-------CCcEEEEec----------
Q psy7952         189 ----RYNKLAYIVVDEAHCVS-EWG----------HDFRPTYRRLGELRQFTGN-------SIPIIALTA----------  236 (444)
Q Consensus       189 ----~~~~~~~iViDE~H~~~-~~~----------~~~~~~~~~l~~~~~~~~~-------~~~~v~lSA----------  236 (444)
                          -...+.+.||||+|.++ +..          ......|..+..+...+..       ..+.+.+|.          
T Consensus       191 ~~~~vqR~~~faIVDEVDSILIDEArTPLIISg~~~~~~~~Y~~~~~~v~~L~~~dy~iDek~k~v~LTe~G~~~~E~~l  270 (925)
T PRK12903        191 KEEKVQRGLNFCLIDEVDSILIDEAKTPLIISGGQSNDSNLYLAADQFVRTLKEDDYKIDEETKAISLTEKGIKKANKFF  270 (925)
T ss_pred             HHHhcCcccceeeeccchheeecccCCcccccCCCccchHHHHHHHHHHHhccccceEEecccceEEECHhHHHHHHHHc
Confidence                13568999999999873 311          1111233333333332211       112233332          


Q ss_pred             --------------------------------------------------------------------------------
Q psy7952         237 --------------------------------------------------------------------------------  236 (444)
Q Consensus       237 --------------------------------------------------------------------------------  236 (444)
                                                                                                      
T Consensus       271 ~i~nLy~~~n~~l~h~i~~AL~A~~lf~rd~dYiV~dg~V~IVDefTGR~m~gRrwsdGLHQaIEAKEgv~I~~e~~TlA  350 (925)
T PRK12903        271 KLKNLYDIENSELVHRIQNALRAHKVMKEDVEYIVRDGKIELVDQFTGRIMEGRSYSEGLQQAIQAKEMVEIEPETKTLA  350 (925)
T ss_pred             CCCcccChhhHHHHHHHHHHHHHHHHHhcCCceEEECCEEEEEECCCCCCCCCCccchHHHHHHHHHcCCCCCCCceeee
Confidence                                                                                            


Q ss_pred             -------------------cCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEE--EcccchhhHHHHHHHHHHHhcc
Q psy7952         237 -------------------TAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVI--FDDLLKDSYAHVKEFIEKCLGK  295 (444)
Q Consensus       237 -------------------T~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~l~~  295 (444)
                                         |.... ...+.+..+    ..+..-+..+|.+.....  .......++..+.+.+.+..  
T Consensus       351 sIT~QnfFr~Y~kLsGMTGTA~te-~~Ef~~iY~----l~Vv~IPTnkP~~R~D~~d~iy~t~~~K~~Aii~ei~~~~--  423 (925)
T PRK12903        351 TITYQNFFRLFKKLSGMTGTAKTE-EQEFIDIYN----MRVNVVPTNKPVIRKDEPDSIFGTKHAKWKAVVKEVKRVH--  423 (925)
T ss_pred             eehHHHHHHhcchhhccCCCCHHH-HHHHHHHhC----CCEEECCCCCCeeeeeCCCcEEEcHHHHHHHHHHHHHHHH--
Confidence                               21110 011111111    011111222232222111  00112234444444444432  


Q ss_pred             CCCCCceEEEEecccchHHHHHHHHHhh------cC--HHHHHHHHHHHhcC-CccEEEEcCccccccccCCcc------
Q psy7952         296 DNKANNCGIIYCRTREHTTDLADALRRK------VN--KHERSRVQESFMRG-EINVITATISFGMGIDRQNVR------  360 (444)
Q Consensus       296 ~~~~~~~~iVf~~s~~~~~~l~~~L~~~------~~--~~~r~~~~~~f~~g-~~~vLvaT~~~~~Gidi~~~~------  360 (444)
                        ..+.|+||.|.|++.++.++..|.+.      ++  ..+++..+-. ..| ...|.|||++++||.||.--.      
T Consensus       424 --~~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~e~EA~IIa-~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~G  500 (925)
T PRK12903        424 --KKGQPILIGTAQVEDSETLHELLLEANIPHTVLNAKQNAREAEIIA-KAGQKGAITIATNMAGRGTDIKLSKEVLELG  500 (925)
T ss_pred             --hcCCCEEEEeCcHHHHHHHHHHHHHCCCCceeecccchhhHHHHHH-hCCCCCeEEEecccccCCcCccCchhHHHcC
Confidence              36889999999999999999999887      22  1222222222 345 567899999999999996222      


Q ss_pred             --EEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         361 --FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       361 --~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                        +||....|.|.+---|-.||+||.|.+|.+..|++-+|.
T Consensus       501 GLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f~lSLeD~  541 (925)
T PRK12903        501 GLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFISLDDQ  541 (925)
T ss_pred             CcEEEecccCchHHHHHHHhcccccCCCCCcceEEEecchH
Confidence              899999999999999999999999999999888886543

>KOG0384|consensus

Probab=99.71  E-value=3.7e-17  Score=166.94  Aligned_cols=320  Identities=16%  Similarity=0.150  Sum_probs=207.6

Q ss_pred             cccCchHHHHHHHHHHc---cCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCc
Q psy7952          47 DSFKCELQKKAIRHILL---RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFR  123 (444)
Q Consensus        47 ~~~~t~~Q~~~~~~~~~---~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~  123 (444)
                      ..+| +||.+-+++++.   +++++|+.-..|.|||.-.+.. +. |++..    ....|+.   |+++|...+..|   
T Consensus       369 ~~LR-dyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqti~f-l~-~l~~~----~~~~gpf---lvvvplst~~~W---  435 (1373)
T KOG0384|consen  369 NELR-DYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITF-LS-YLFHS----LQIHGPF---LVVVPLSTITAW---  435 (1373)
T ss_pred             chhh-hhhcccchhHHHHHHhcccceehhhcCCCcchHHHHH-HH-HHHHh----hhccCCe---EEEeehhhhHHH---
Confidence            3456 799998887774   2289999999999999762221 11 11111    3345566   999999988844   


Q ss_pred             cchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhc---CCCeeEEEECCCccccccHHHHHHHHHhh--CCccEEEE
Q psy7952         124 DDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLV---KPRIKLLYVTPERAVTESFHYLLQHLVRY--NKLAYIVV  198 (444)
Q Consensus       124 ~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~--~~~~~iVi  198 (444)
                      ...+..+. .   .++.+++|+.........+.-...-   .-..+++++|++.+.        .....+  -.+.+++|
T Consensus       436 ~~ef~~w~-~---mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~L--------kDk~~L~~i~w~~~~v  503 (1373)
T KOG0384|consen  436 EREFETWT-D---MNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVL--------KDKAELSKIPWRYLLV  503 (1373)
T ss_pred             HHHHHHHh-h---hceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHh--------ccHhhhccCCcceeee
Confidence            34445555 6   8899999988776555555433221   114789999988864        333333  35799999


Q ss_pred             eccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecC----------------
Q psy7952         199 DEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTS----------------  262 (444)
Q Consensus       199 DE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~----------------  262 (444)
                      ||||++-...       ..+...+..+.- ..-+++|+||-.+....+..++.+..|.......                
T Consensus       504 DeahrLkN~~-------~~l~~~l~~f~~-~~rllitgTPlQNsikEL~sLl~Fl~P~kf~~~~~f~~~~~~~~e~~~~~  575 (1373)
T KOG0384|consen  504 DEAHRLKNDE-------SKLYESLNQFKM-NHRLLITGTPLQNSLKELWSLLHFLMPGKFDSWDEFLEEFDEETEEQVRK  575 (1373)
T ss_pred             cHHhhcCchH-------HHHHHHHHHhcc-cceeeecCCCccccHHHHHHHhcccCCCCCCcHHHHHHhhcchhHHHHHH
Confidence            9999985322       222222333433 4468899998877766666665443221110000                


Q ss_pred             ---------------------CCCCCceEEEEEcccchhhH---------------------------------------
Q psy7952         263 ---------------------TFRSNLFYDVIFDDLLKDSY---------------------------------------  282 (444)
Q Consensus       263 ---------------------~~~~~~~~~~~~~~~~~~~~---------------------------------------  282 (444)
                                           .........+.........+                                       
T Consensus       576 L~~~L~P~~lRr~kkdvekslp~k~E~IlrVels~lQk~yYk~ILtkN~~~LtKG~~g~~~~lLNimmELkKccNHpyLi  655 (1373)
T KOG0384|consen  576 LQQILKPFLLRRLKKDVEKSLPPKEETILRVELSDLQKQYYKAILTKNFSALTKGAKGSTPSLLNIMMELKKCCNHPYLI  655 (1373)
T ss_pred             HHHHhhHHHHHHHHhhhccCCCCCcceEEEeehhHHHHHHHHHHHHhhHHHHhccCCCCCchHHHHHHHHHHhcCCcccc
Confidence                                 00000111111000000000                                       


Q ss_pred             -----------------HHHH---------HHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCH
Q psy7952         283 -----------------AHVK---------EFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNK  326 (444)
Q Consensus       283 -----------------~~~~---------~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~  326 (444)
                                       ..+.         -++.++|.+-...+++||||...+....-|++.|..+          +..
T Consensus       656 ~gaee~~~~~~~~~~~d~~L~~lI~sSGKlVLLDKLL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrg  735 (1373)
T KOG0384|consen  656 KGAEEKILGDFRDKMRDEALQALIQSSGKLVLLDKLLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRG  735 (1373)
T ss_pred             CcHHHHHHHhhhhcchHHHHHHHHHhcCcEEeHHHHHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcch
Confidence                             0010         1122334443447899999999999999999999877          778


Q ss_pred             HHHHHHHHHHhc---CCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEE--Eecccch
Q psy7952         327 HERSRVQESFMR---GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRI--YHSEHSK  399 (444)
Q Consensus       327 ~~r~~~~~~f~~---g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~--~~~~~~~  399 (444)
                      +.|+..++.|..   .....|+||.+.+.|||+-..++||.||..+++.+-+|.-.||.|-|+...+-+  +++....
T Consensus       736 elRq~AIDhFnap~SddFvFLLSTRAGGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~Tv  813 (1373)
T KOG0384|consen  736 ELRQQAIDHFNAPDSDDFVFLLSTRAGGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNTV  813 (1373)
T ss_pred             HHHHHHHHhccCCCCCceEEEEecccCcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCCch
Confidence            999999999973   345569999999999999999999999999999999999999999999876543  5555543

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.71  E-value=4.2e-16  Score=158.72  Aligned_cols=122  Identities=19%  Similarity=0.256  Sum_probs=101.9

Q ss_pred             hHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCcc
Q psy7952         281 SYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISF  350 (444)
Q Consensus       281 ~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~  350 (444)
                      +.+.+.+.+....    ..+.+++|||++++.++.+++.|...          ++..+|..+++.|+.|++.|+|||+.+
T Consensus       427 qi~~Ll~eI~~~~----~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L  502 (655)
T TIGR00631       427 QVDDLLSEIRQRV----ARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLL  502 (655)
T ss_pred             hHHHHHHHHHHHH----cCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChh
Confidence            3344444444432    25789999999999999999999876          678999999999999999999999999


Q ss_pred             ccccccCCccEEEEeC-----CCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         351 GMGIDRQNVRFVVHWG-----MPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       351 ~~Gidi~~~~~Vi~~~-----~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      ++|+|+|++++||+++     .|.+...|+||+||+||. ..|.++++++..+......+.+
T Consensus       503 ~rGfDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~~~~~~~ai~~  563 (655)
T TIGR00631       503 REGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVIMYADKITDSMQKAIEE  563 (655)
T ss_pred             cCCeeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCCCHHHHHHHHH
Confidence            9999999999999888     799999999999999998 6899999998766544444433

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

>KOG0925|consensus

Probab=99.69  E-value=3.3e-15  Score=139.29  Aligned_cols=311  Identities=18%  Similarity=0.156  Sum_probs=183.2

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCC-ccccccCCccceeEEE
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPG-ADFILNGNVRSRNGWI  111 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~-~~~l~~~~~~~~vlil  111 (444)
                      ...+.+.+++.-.   +|---|++-+-.++.+++-+++++.||+|||.-          +|.. +.......  .-|...
T Consensus        33 s~rY~~ilk~R~~---LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQ----------iPq~~~~~~~~~~--~~v~CT   97 (699)
T KOG0925|consen   33 SQRYYDILKKRRE---LPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQ----------IPQFVLEYELSHL--TGVACT   97 (699)
T ss_pred             cHHHHHHHHHHhc---CchHHhHHHHHHHHhcCceEEEEecCCCCcccc----------CcHHHHHHHHhhc--cceeec
Confidence            4566777777633   342234444555555449999999999999955          3330 01111111  122555


Q ss_pred             cchhhhhcccCccchHhhh------cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH
Q psy7952         112 SPILSSFYLRFRDDKTSIV------TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ  185 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l------~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~  185 (444)
                      -|.+..+     -....+.      ..|   ..|.....-.++....-+            .-++|.++|..+     ..
T Consensus        98 Qprrvaa-----msva~RVadEMDv~lG---~EVGysIrfEdC~~~~T~------------Lky~tDgmLlrE-----am  152 (699)
T KOG0925|consen   98 QPRRVAA-----MSVAQRVADEMDVTLG---EEVGYSIRFEDCTSPNTL------------LKYCTDGMLLRE-----AM  152 (699)
T ss_pred             CchHHHH-----HHHHHHHHHHhccccc---hhccccccccccCChhHH------------HHHhcchHHHHH-----Hh
Confidence            5887665     3333333      233   222222222221111111            124455554211     01


Q ss_pred             HHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCC
Q psy7952         186 HLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFR  265 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~  265 (444)
                      ....+...++||+||+|.   ..-.-.-.+..++......+ +.++|.||||+...   .+..+++ ..| .+..+....
T Consensus       153 s~p~l~~y~viiLDeahE---RtlATDiLmGllk~v~~~rp-dLk~vvmSatl~a~---Kfq~yf~-n~P-ll~vpg~~P  223 (699)
T KOG0925|consen  153 SDPLLGRYGVIILDEAHE---RTLATDILMGLLKEVVRNRP-DLKLVVMSATLDAE---KFQRYFG-NAP-LLAVPGTHP  223 (699)
T ss_pred             hCcccccccEEEechhhh---hhHHHHHHHHHHHHHHhhCC-CceEEEeecccchH---HHHHHhC-CCC-eeecCCCCc
Confidence            112356789999999998   22111222334444444445 58999999998654   4445553 334 333333222


Q ss_pred             CCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh---------------cCHHHHH
Q psy7952         266 SNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK---------------VNKHERS  330 (444)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~---------------~~~~~r~  330 (444)
                      ..+   +...+...+..+.....+.++-...  ..+-++||....++.+..++.+...               +.+..+.
T Consensus       224 vEi---~Yt~e~erDylEaairtV~qih~~e--e~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLyP~~qq  298 (699)
T KOG0925|consen  224 VEI---FYTPEPERDYLEAAIRTVLQIHMCE--EPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLYPAQQQ  298 (699)
T ss_pred             eEE---EecCCCChhHHHHHHHHHHHHHhcc--CCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecCchhhc
Confidence            222   2223334455555556555554443  4788999999999999998888755               4454444


Q ss_pred             HHHHHHh---cC--CccEEEEcCccccccccCCccEEEEeCC------------------CCCHHHHHHHhccCCCCCCc
Q psy7952         331 RVQESFM---RG--EINVITATISFGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQ  387 (444)
Q Consensus       331 ~~~~~f~---~g--~~~vLvaT~~~~~Gidi~~~~~Vi~~~~------------------p~s~~~~~Qr~GR~~R~g~~  387 (444)
                      .+++...   .|  ..+|+|+|++++..+-++++.+||+-|+                  |-|..+-.||.||+||. .+
T Consensus       299 ~iFep~p~~~~~~~~RkvVvstniaetsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt-~p  377 (699)
T KOG0925|consen  299 RIFEPAPEKRNGAYGRKVVVSTNIAETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RP  377 (699)
T ss_pred             cccCCCCcccCCCccceEEEEecchheeeeeccEEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCC-CC
Confidence            4443322   12  3589999999999999999999997774                  55888899999999998 78


Q ss_pred             eeEEEEecccc
Q psy7952         388 SYCRIYHSEHS  398 (444)
Q Consensus       388 g~~~~~~~~~~  398 (444)
                      |.|+.++..+-
T Consensus       378 GkcfrLYte~~  388 (699)
T KOG0925|consen  378 GKCFRLYTEEA  388 (699)
T ss_pred             CceEEeecHHh
Confidence            99999998543

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

Probab=99.69  E-value=2.2e-15  Score=151.11  Aligned_cols=178  Identities=14%  Similarity=0.010  Sum_probs=116.8

Q ss_pred             cEEEEeccCCcch------HHHHHHHhcCCCCeEEEecCCC----CCC--ceEEEEE----cccch--------------
Q psy7952         230 PIIALTATAEPSV------KQDIISVLKFNKPYKVFKTSTF----RSN--LFYDVIF----DDLLK--------------  279 (444)
Q Consensus       230 ~~v~lSAT~~~~~------~~~~~~~l~~~~~~~~~~~~~~----~~~--~~~~~~~----~~~~~--------------  279 (444)
                      .+|++|||+.-..      .+.+.+.+|++........+..    +..  ..|....    .+...              
T Consensus       373 ~~I~TSATL~v~~~~~~~~F~~f~~~lGL~~~~l~~~SPFd~~y~~qa~~~LyvP~~~~~~lP~p~~~~~~~~~~~~~~~  452 (636)
T TIGR03117       373 GAIIVSATLYLPDRFGQMSCDYLKRVLSLPLSRLDTPSPIVAPWVRNAIPHLHVPNAKARFLRPVGKDEQGDANLQEAER  452 (636)
T ss_pred             eEEEEccccccCCcCCCcCcHHHHHhcCCCccceeCCCCCCchhHhcCceEEEEcCccccCCCCCCCCcccchhhhcchh
Confidence            4699999998744      6888999998654222222222    222  1221100    00111              


Q ss_pred             hhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-------cC-HHHHHHHHHHHhc----CCccEEEEc
Q psy7952         280 DSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-------VN-KHERSRVQESFMR----GEINVITAT  347 (444)
Q Consensus       280 ~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-------~~-~~~r~~~~~~f~~----g~~~vLvaT  347 (444)
                      ...+.+.+.+..++..   .++.++|.+.|....+.++..|...       -. ...+...+++|+.    |...||++|
T Consensus       453 ~~~~~~~~~~~~~~~~---~~G~~lvLfTS~~~~~~~~~~l~~~l~~~~l~qg~~~~~~~l~~~f~~~~~~~~~~vL~gt  529 (636)
T TIGR03117       453 TWLENVSLSTAAILRK---AQGGTLVLTTAFSHISAIGQLVELGIPAEIVIQSEKNRLASAEQQFLALYANGIQPVLIAA  529 (636)
T ss_pred             hHHHHHHHHHHHHHHH---cCCCEEEEechHHHHHHHHHHHHhhcCCCEEEeCCCccHHHHHHHHHHhhcCCCCcEEEeC
Confidence            1222355555555554   4779999999999999999999766       11 1245778999987    478999999


Q ss_pred             Ccccccccc--------C--CccEEEEeCCCC-------------------------CHHHHHHHhccCCCCCCc--eeE
Q psy7952         348 ISFGMGIDR--------Q--NVRFVVHWGMPS-------------------------SIPAYYQESGRAGRDGLQ--SYC  390 (444)
Q Consensus       348 ~~~~~Gidi--------~--~~~~Vi~~~~p~-------------------------s~~~~~Qr~GR~~R~g~~--g~~  390 (444)
                      +.+.+|||+        |  .+++||....|.                         ....+.|.+||.-|....  --.
T Consensus       530 ~sfweGvDv~~~~~~p~~G~~Ls~ViI~kLPF~~~dp~a~~~~~~~~g~~~f~~~p~a~i~lkQg~GRLIR~~~D~~~G~  609 (636)
T TIGR03117       530 GGAWTGIDLTHKPVSPDKDNLLTDLIITCAPFGLNRSLSMLKRIRKTSVRPWEIINESLMMLRQGLGRLVRHPDMPQNRR  609 (636)
T ss_pred             CccccccccCCccCCCCCCCcccEEEEEeCCCCcCChHHHHHHHHhcCCChHhhhHHHHHHHHHhcCceeecCCCcCceE
Confidence            999999999        3  478898887773                         134468999999998665  445


Q ss_pred             EEEecccchhhHHHHHhhcc
Q psy7952         391 RIYHSEHSKKSLEYVIKTDT  410 (444)
Q Consensus       391 ~~~~~~~~~~~~~~~~~~~~  410 (444)
                      ++++++.-.+.+...+.+.+
T Consensus       610 i~ilD~R~~~~yg~~~~~~~  629 (636)
T TIGR03117       610 IHMLDGRIHWPYMESWQESV  629 (636)
T ss_pred             EEEEeCCCCchhHHHHHHHH
Confidence            67777665455555555443

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.

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.67  E-value=1.6e-15  Score=153.87  Aligned_cols=133  Identities=17%  Similarity=0.161  Sum_probs=94.5

Q ss_pred             HHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchh
Q psy7952          36 LTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPIL  115 (444)
Q Consensus        36 ~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~  115 (444)
                      +.++.++.+|..+++  .|.-..-.+..   .-+..+.||.|||++|        .+|+.+..+ .+..   |-|++++.
T Consensus        65 vrEa~~R~lG~r~yd--vQlig~l~L~~---G~IaEm~TGEGKTL~a--------~l~ayl~aL-~G~~---VhVvT~Nd  127 (870)
T CHL00122         65 TREASFRTLGLRHFD--VQLIGGLVLND---GKIAEMKTGEGKTLVA--------TLPAYLNAL-TGKG---VHIVTVND  127 (870)
T ss_pred             HHHHHHHHhCCCCCc--hHhhhhHhhcC---CccccccCCCCchHHH--------HHHHHHHHh-cCCc---eEEEeCCH
Confidence            446777778988644  78766555544   5789999999999994        445522223 2333   37889999


Q ss_pred             hhhcccCccchHhhh-----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH--
Q psy7952         116 SSFYLRFRDDKTSIV-----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV--  188 (444)
Q Consensus       116 ~L~~~~q~~~~~~~l-----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~--  188 (444)
                      .|+     ....+.+     .+|   +.+..+.++.+..++...+        .+||+++|...+.   |+++..++.  
T Consensus       128 yLA-----~RD~e~m~pvy~~LG---Lsvg~i~~~~~~~err~aY--------~~DItYgTn~e~g---FDyLRDnm~~~  188 (870)
T CHL00122        128 YLA-----KRDQEWMGQIYRFLG---LTVGLIQEGMSSEERKKNY--------LKDITYVTNSELG---FDYLRDNMALS  188 (870)
T ss_pred             HHH-----HHHHHHHHHHHHHcC---CceeeeCCCCChHHHHHhc--------CCCCEecCCcccc---ccchhhccCcC
Confidence            999     4544444     667   9999998888887776666        6799999988776   444444432  


Q ss_pred             ----hhCCccEEEEeccccc
Q psy7952         189 ----RYNKLAYIVVDEAHCV  204 (444)
Q Consensus       189 ----~~~~~~~iViDE~H~~  204 (444)
                          ....+.+.||||+|.+
T Consensus       189 ~~~~v~r~~~faIVDEvDSi  208 (870)
T CHL00122        189 LSDVVQRPFNYCIIDEVDSI  208 (870)
T ss_pred             hHHhhccccceeeeecchhh
Confidence                2356899999999987

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

Probab=99.67  E-value=8.4e-15  Score=138.42  Aligned_cols=156  Identities=19%  Similarity=0.166  Sum_probs=112.7

Q ss_pred             CcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEec
Q psy7952         229 IPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCR  308 (444)
Q Consensus       229 ~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~  308 (444)
                      .|+|++||||.+...+.-.     ..-+.....+.........+...   ....+.+...+.+...    .+.+++|-+=
T Consensus       387 ~q~i~VSATPg~~E~e~s~-----~~vveQiIRPTGLlDP~ievRp~---~~QvdDL~~EI~~r~~----~~eRvLVTtL  454 (663)
T COG0556         387 PQTIYVSATPGDYELEQSG-----GNVVEQIIRPTGLLDPEIEVRPT---KGQVDDLLSEIRKRVA----KNERVLVTTL  454 (663)
T ss_pred             CCEEEEECCCChHHHHhcc-----CceeEEeecCCCCCCCceeeecC---CCcHHHHHHHHHHHHh----cCCeEEEEee
Confidence            5799999999775433111     11111122222222222222222   2333444444444332    4789999999


Q ss_pred             ccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCC-----CCCHHH
Q psy7952         309 TREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGM-----PSSIPA  373 (444)
Q Consensus       309 s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~-----p~s~~~  373 (444)
                      |++.|+.+.+.|...          .+.-+|.++++.++.|...|||+.+.+-+|+|+|.|..|..+|.     ..|..+
T Consensus       455 TKkmAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRse~S  534 (663)
T COG0556         455 TKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERS  534 (663)
T ss_pred             hHHHHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEeecCccccccccch
Confidence            999999999999888          67789999999999999999999999999999999999988875     458999


Q ss_pred             HHHHhccCCCCCCceeEEEEeccc
Q psy7952         374 YYQESGRAGRDGLQSYCRIYHSEH  397 (444)
Q Consensus       374 ~~Qr~GR~~R~g~~g~~~~~~~~~  397 (444)
                      ++|-+|||.|. -.|.++.+.+.-
T Consensus       535 LIQtIGRAARN-~~GkvIlYAD~i  557 (663)
T COG0556         535 LIQTIGRAARN-VNGKVILYADKI  557 (663)
T ss_pred             HHHHHHHHhhc-cCCeEEEEchhh
Confidence            99999999998 578888887643

>KOG0951|consensus

Probab=99.67  E-value=6.8e-16  Score=157.74  Aligned_cols=341  Identities=14%  Similarity=0.163  Sum_probs=225.0

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      +++|.++++.+.+.++++++.+|+|||||.+|..+++.             .....+++++.|..+.+     ..++..+
T Consensus      1145 n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~-------------~~~~~~~vyi~p~~~i~-----~~~~~~w 1206 (1674)
T KOG0951|consen 1145 NPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR-------------PDTIGRAVYIAPLEEIA-----DEQYRDW 1206 (1674)
T ss_pred             CCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC-------------CccceEEEEecchHHHH-----HHHHHHH
Confidence            36899999999988789999999999999996544332             33345789999999999     8888877


Q ss_pred             --cCC-CCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccccc
Q psy7952         131 --TGR-SDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEW  207 (444)
Q Consensus       131 --~~~-~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~  207 (444)
                        +++ ..+..+..++|..+.+...         ....+|+|+||++.     +.+ +   ....+++.|.||.|.+.+.
T Consensus      1207 ~~~f~~~~G~~~~~l~ge~s~~lkl---------~~~~~vii~tpe~~-----d~l-q---~iQ~v~l~i~d~lh~igg~ 1268 (1674)
T KOG0951|consen 1207 EKKFSKLLGLRIVKLTGETSLDLKL---------LQKGQVIISTPEQW-----DLL-Q---SIQQVDLFIVDELHLIGGV 1268 (1674)
T ss_pred             HHhhccccCceEEecCCccccchHH---------hhhcceEEechhHH-----HHH-h---hhhhcceEeeehhhhhccc
Confidence              221 1347788888877655321         23578999999994     333 2   4557899999999998652


Q ss_pred             -CCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCc-eEEEEEcccch--hhHH
Q psy7952         208 -GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNL-FYDVIFDDLLK--DSYA  283 (444)
Q Consensus       208 -~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~--~~~~  283 (444)
                       |.-+.-... +..+...+.++.+++++|..+.+.     ...++....-........|+.. ...+.......  ....
T Consensus      1269 ~g~v~evi~S-~r~ia~q~~k~ir~v~ls~~lana-----~d~ig~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~ 1342 (1674)
T KOG0951|consen 1269 YGAVYEVICS-MRYIASQLEKKIRVVALSSSLANA-----RDLIGASSSGVFNFSPSVRPVPLEIHIQSVDISHFESRML 1342 (1674)
T ss_pred             CCceEEEEee-HHHHHHHHHhheeEEEeehhhccc-----hhhccccccceeecCcccCCCceeEEEEEeccchhHHHHH
Confidence             222222222 344444556668999999988653     2236665554455555555543 22222222111  1111


Q ss_pred             HHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh--------------------------------cCHHHHHH
Q psy7952         284 HVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK--------------------------------VNKHERSR  331 (444)
Q Consensus       284 ~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~--------------------------------~~~~~r~~  331 (444)
                      ...+..-..+......+++.+||++++++|..++..+-..                                ++..+..-
T Consensus      1343 am~~~~~~ai~~~a~~~k~~~vf~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~i 1422 (1674)
T KOG0951|consen 1343 AMTKPTYTAIVRHAGNRKPAIVFLPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEI 1422 (1674)
T ss_pred             HhhhhHHHHHHHHhcCCCCeEEEeccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHH
Confidence            1112222223333346889999999999999887765333                                55666667


Q ss_pred             HHHHHhcCCccEEEEcCccccccccCCccEEEEeC-----------CCCCHHHHHHHhccCCCCCCceeEEEEecccchh
Q psy7952         332 VQESFMRGEINVITATISFGMGIDRQNVRFVVHWG-----------MPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK  400 (444)
Q Consensus       332 ~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~-----------~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~  400 (444)
                      +-..|..|.+.|+|...- -.|+-.. .+.||..|           .+.++.++.|+.|+|.|   .|.|+++.......
T Consensus      1423 v~~l~e~g~i~v~v~s~~-~~~~~~~-~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~---~~k~vi~~~~~~k~ 1497 (1674)
T KOG0951|consen 1423 VQQLFEAGAIQVCVMSRD-CYGTKLK-AHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG---AGKCVIMCHTPKKE 1497 (1674)
T ss_pred             HHHHHhcCcEEEEEEEcc-ccccccc-ceEEEEecceeecccccccccCchhHHHHHhhhhcC---CccEEEEecCchHH
Confidence            777888999999887766 6677664 33344333           35579999999999988   47899999999999


Q ss_pred             hHHHHHhhccchhHH-----------HHHH-HHhhHHHHHHHhhhceeee
Q psy7952         401 SLEYVIKTDTSTKRE-----------QLEL-KFKNYLSMLEYCEQGYFLV  438 (444)
Q Consensus       401 ~~~~~~~~~~~~~~~-----------~~~~-~~~~~~~~~~~~~~~~~~~  438 (444)
                      .++++...++|.+.-           ++.. -+.+-.+-++|..-.|++.
T Consensus      1498 yykkfl~e~lPves~lq~~lhd~~n~ei~~~tienkqd~vd~lt~s~~yr 1547 (1674)
T KOG0951|consen 1498 YYKKFLYEPLPVESHLQHCLHDNFNAEIVTKTIENKQDAVDYLTWSFMYR 1547 (1674)
T ss_pred             HHHHhccCcCchHHHHHHHHHhhhhHHHHHHHHHhHHHHHHHHHHHHhhh
Confidence            999999999988633           2222 2444455555655555443

>KOG0389|consensus

Probab=99.64  E-value=2.8e-15  Score=147.19  Aligned_cols=171  Identities=16%  Similarity=0.150  Sum_probs=116.3

Q ss_pred             hHHHHHHHHHH---ccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHh
Q psy7952          52 ELQKKAIRHIL---LRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTS  128 (444)
Q Consensus        52 ~~Q~~~~~~~~---~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~  128 (444)
                      +||.--++++.   ...-+.|+.-..|-|||.-++ +      +-+.+...-..|++   |||||+..|-+|   ...+.
T Consensus       402 dYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQvI-a------FlayLkq~g~~gpH---LVVvPsSTleNW---lrEf~  468 (941)
T KOG0389|consen  402 DYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQVI-A------FLAYLKQIGNPGPH---LVVVPSSTLENW---LREFA  468 (941)
T ss_pred             chhhhhHHHHHHHHHccccceehhhccCcchhHHH-H------HHHHHHHcCCCCCc---EEEecchhHHHH---HHHHH
Confidence            58888777765   232567999999999996622 1      11112223345677   999999999844   34455


Q ss_pred             hhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccC
Q psy7952         129 IVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWG  208 (444)
Q Consensus       129 ~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~  208 (444)
                      .|+..   +++..++|..  .++.++...+.....+++|+++|+..+.+..   --+.+....+++++|+||.|.+-..+
T Consensus       469 kwCPs---l~Ve~YyGSq--~ER~~lR~~i~~~~~~ydVllTTY~la~~~k---dDRsflk~~~~n~viyDEgHmLKN~~  540 (941)
T KOG0389|consen  469 KWCPS---LKVEPYYGSQ--DERRELRERIKKNKDDYDVLLTTYNLAASSK---DDRSFLKNQKFNYVIYDEGHMLKNRT  540 (941)
T ss_pred             HhCCc---eEEEeccCcH--HHHHHHHHHHhccCCCccEEEEEeecccCCh---HHHHHHHhccccEEEecchhhhhccc
Confidence            55666   9999999876  6677777777766779999999999987533   22334455689999999999986654


Q ss_pred             CCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhc
Q psy7952         209 HDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLK  251 (444)
Q Consensus       209 ~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~  251 (444)
                      +   ..|..+..+    +. ...+++|+||-.+....+...+.
T Consensus       541 S---eRy~~LM~I----~A-n~RlLLTGTPLQNNL~ELiSLL~  575 (941)
T KOG0389|consen  541 S---ERYKHLMSI----NA-NFRLLLTGTPLQNNLKELISLLA  575 (941)
T ss_pred             h---HHHHHhccc----cc-cceEEeeCCcccccHHHHHHHHH
Confidence            2   334444433    22 44689999987766655544443

>KOG0390|consensus

Probab=99.64  E-value=2.3e-14  Score=144.21  Aligned_cols=313  Identities=14%  Similarity=0.112  Sum_probs=184.5

Q ss_pred             hHHHHHHHHHHcc---------CCcEEEEccCCCcccccccccccceEEeCCCccccccCCcc-----ceeEEEcchhhh
Q psy7952          52 ELQKKAIRHILLR---------THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVR-----SRNGWISPILSS  117 (444)
Q Consensus        52 ~~Q~~~~~~~~~~---------~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~-----~~vlil~P~~~L  117 (444)
                      |+|++.+.-+.++         ...+|+.-.+|+|||+..+..          +..+.+..+.     .+.|||+|..-+
T Consensus       241 PHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~Isf----------lwtlLrq~P~~~~~~~k~lVV~P~sLv  310 (776)
T KOG0390|consen  241 PHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISF----------IWTLLRQFPQAKPLINKPLVVAPSSLV  310 (776)
T ss_pred             chHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHHH----------HHHHHHhCcCccccccccEEEccHHHH
Confidence            7999999877742         245788888999999873222          2223334333     688999998777


Q ss_pred             hcccCccchHhhhcCCCCceeEEEEeCCCCh--hhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccE
Q psy7952         118 FYLRFRDDKTSIVTGRSDLYQLELIVSGQTK--TENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAY  195 (444)
Q Consensus       118 ~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~  195 (444)
                      -+|   .+.+..| .+...+....+.+....  .....++ .+....-...|.+.+.|.+.      ..-.......+++
T Consensus       311 ~nW---kkEF~KW-l~~~~i~~l~~~~~~~~~w~~~~sil-~~~~~~~~~~vli~sye~~~------~~~~~il~~~~gl  379 (776)
T KOG0390|consen  311 NNW---KKEFGKW-LGNHRINPLDFYSTKKSSWIKLKSIL-FLGYKQFTTPVLIISYETAS------DYCRKILLIRPGL  379 (776)
T ss_pred             HHH---HHHHHHh-ccccccceeeeecccchhhhhhHHHH-HhhhhheeEEEEeccHHHHH------HHHHHHhcCCCCe
Confidence            633   3444444 11123777777776653  1111111 11111123455666655542      2233445668999


Q ss_pred             EEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEc
Q psy7952         196 IVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFD  275 (444)
Q Consensus       196 iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  275 (444)
                      +|+||.|.+-..   -...+..+.    ...- .+-|++|+||-.+....+...+++-.|..+......+..........
T Consensus       380 LVcDEGHrlkN~---~s~~~kaL~----~l~t-~rRVLLSGTp~QNdl~EyFnlL~fvrP~~Lgs~~sf~k~~~~~i~~~  451 (776)
T KOG0390|consen  380 LVCDEGHRLKNS---DSLTLKALS----SLKT-PRRVLLTGTPIQNDLKEYFNLLDFVRPGFLGSISSFKKKFEIPILRG  451 (776)
T ss_pred             EEECCCCCccch---hhHHHHHHH----hcCC-CceEEeeCCcccccHHHHHHHHhhcChhhccchHHHHHHhhcccccc
Confidence            999999996332   122233333    2332 67899999998888877777777655543332221111111000000


Q ss_pred             c------c---chhhHHHHHHHHHHHhccCCC--------CCceEEEEecccchHHHHHHHHHh---h------------
Q psy7952         276 D------L---LKDSYAHVKEFIEKCLGKDNK--------ANNCGIIYCRTREHTTDLADALRR---K------------  323 (444)
Q Consensus       276 ~------~---~~~~~~~~~~~l~~~l~~~~~--------~~~~~iVf~~s~~~~~~l~~~L~~---~------------  323 (444)
                      .      .   ...+..++.+++..++-....        ...-.+|||+-...-..++..|..   .            
T Consensus       452 ~~~~~s~e~~~~~~rl~eL~~~t~~fi~rrt~~il~k~LP~k~e~vv~~n~t~~Q~~~~~~l~~~~~~~~~~~~~l~~~~  531 (776)
T KOG0390|consen  452 RDADASEEDREREERLQELRELTNKFILRRTGDILLKYLPGKYEYVVFCNPTPIQKELYKKLLDSMKMRTLKGYALELIT  531 (776)
T ss_pred             cCCCcchhhhhhHHHHHHHHHHHHhheeecccchhhhhCCCceeEEEEeCCcHHHHHHHHHHHHHHHhhhhhcchhhHHH
Confidence            0      0   011233333333333222211        112345666544333333222221   0            


Q ss_pred             --------------------------------------------------------------------------------
Q psy7952         324 --------------------------------------------------------------------------------  323 (444)
Q Consensus       324 --------------------------------------------------------------------------------  323 (444)
                                                                                                      
T Consensus       532 ~L~k~cnhP~L~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~ks~kl~~L~~ll~~~~ek~~~~~v~Isny~~tldl~  611 (776)
T KOG0390|consen  532 KLKKLCNHPSLLLLCEKTEKEKAFKNPALLLDPGKLKLDAGDGSKSGKLLVLVFLLEVIREKLLVKSVLISNYTQTLDLF  611 (776)
T ss_pred             HHHHHhcCHHhhcccccccccccccChHhhhcccccccccccchhhhHHHHHHHHHHHHhhhcceEEEEeccHHHHHHHH
Confidence                                                                                            


Q ss_pred             -----------------cCHHHHHHHHHHHhcC--CccE-EEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCC
Q psy7952         324 -----------------VNKHERSRVQESFMRG--EINV-ITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGR  383 (444)
Q Consensus       324 -----------------~~~~~r~~~~~~f~~g--~~~v-LvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R  383 (444)
                                       ++..+|+.+++.|.+.  ...| |.+|.++++||++-+.+.+|.+|+++++..-.|.++|+=|
T Consensus       612 e~~~~~~g~~~~rLdG~~~~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~R  691 (776)
T KOG0390|consen  612 EQLCRWRGYEVLRLDGKTSIKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWR  691 (776)
T ss_pred             HHHHhhcCceEEEEcCCCchHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEEEeCCCCCchhHHHHHHHhcc
Confidence                             8899999999999854  3345 7778899999999999999999999999999999999999


Q ss_pred             CCCceeEEEE
Q psy7952         384 DGLQSYCRIY  393 (444)
Q Consensus       384 ~g~~g~~~~~  393 (444)
                      .|+..-|+++
T Consensus       692 dGQKk~v~iY  701 (776)
T KOG0390|consen  692 DGQKKPVYIY  701 (776)
T ss_pred             CCCcceEEEE
Confidence            9998766553

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

Probab=99.64  E-value=1.8e-15  Score=123.95  Aligned_cols=110  Identities=31%  Similarity=0.510  Sum_probs=95.4

Q ss_pred             hhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCc
Q psy7952         280 DSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATIS  349 (444)
Q Consensus       280 ~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~  349 (444)
                      .+...+.+.+...    ...++++||||++.+.++.+++.|.+.          ++..+|..+.+.|.++...+|++|++
T Consensus        12 ~k~~~i~~~i~~~----~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~   87 (131)
T cd00079          12 EKLEALLELLKEH----LKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDV   87 (131)
T ss_pred             HHHHHHHHHHHhc----ccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcCh
Confidence            3444454544443    225789999999999999999999864          77899999999999999999999999


Q ss_pred             cccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEE
Q psy7952         350 FGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIY  393 (444)
Q Consensus       350 ~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~  393 (444)
                      +++|+|+|.+++||++++|++...++|++||++|.|+.|.++++
T Consensus        88 ~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~  131 (131)
T cd00079          88 IARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             hhcCcChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEeC
Confidence            99999999999999999999999999999999999998887653

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.64  E-value=1.4e-14  Score=148.78  Aligned_cols=111  Identities=21%  Similarity=0.268  Sum_probs=96.2

Q ss_pred             HHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccc
Q psy7952         282 YAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFG  351 (444)
Q Consensus       282 ~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~  351 (444)
                      ...+.+.+....    ..+.+++|||++.+.++.+++.|...          ++..+|..+++.|+.|.+.++|||+.++
T Consensus       432 ~~~L~~~L~~~~----~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~  507 (652)
T PRK05298        432 VDDLLSEIRKRV----AKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLR  507 (652)
T ss_pred             HHHHHHHHHHHH----hCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHh
Confidence            344444444432    25789999999999999999999876          6789999999999999999999999999


Q ss_pred             cccccCCccEEEEeCC-----CCCHHHHHHHhccCCCCCCceeEEEEeccc
Q psy7952         352 MGIDRQNVRFVVHWGM-----PSSIPAYYQESGRAGRDGLQSYCRIYHSEH  397 (444)
Q Consensus       352 ~Gidi~~~~~Vi~~~~-----p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~  397 (444)
                      +|+|+|++++||+++.     |.+...|+||+||+||. ..|.++.+++..
T Consensus       508 rGfdlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~  557 (652)
T PRK05298        508 EGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKI  557 (652)
T ss_pred             CCccccCCcEEEEeCCcccccCCCHHHHHHHhccccCC-CCCEEEEEecCC
Confidence            9999999999998874     78999999999999996 789999999843

>KOG0953|consensus

Probab=99.62  E-value=8.5e-15  Score=138.74  Aligned_cols=273  Identities=16%  Similarity=0.172  Sum_probs=175.7

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeC
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVS  144 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~  144 (444)
                      +-++-++||.||||.-             +++.+......   ++.-|.+-|+     .+.+.++ +.|   +.+..++|
T Consensus       192 kIi~H~GPTNSGKTy~-------------ALqrl~~aksG---vycGPLrLLA-----~EV~~r~na~g---ipCdL~TG  247 (700)
T KOG0953|consen  192 KIIMHVGPTNSGKTYR-------------ALQRLKSAKSG---VYCGPLRLLA-----HEVYDRLNALG---IPCDLLTG  247 (700)
T ss_pred             eEEEEeCCCCCchhHH-------------HHHHHhhhccc---eecchHHHHH-----HHHHHHhhhcC---CCcccccc
Confidence            4567788999999977             35556666777   9999999999     8999999 888   99999998


Q ss_pred             CCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHh
Q psy7952         145 GQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQF  224 (444)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~  224 (444)
                      ........        ....+..+-||.|++.-            ...+++.||||+++|.+..+++...    ..++..
T Consensus       248 eE~~~~~~--------~~~~a~hvScTVEM~sv------------~~~yeVAViDEIQmm~Dp~RGwAWT----rALLGl  303 (700)
T KOG0953|consen  248 EERRFVLD--------NGNPAQHVSCTVEMVSV------------NTPYEVAVIDEIQMMRDPSRGWAWT----RALLGL  303 (700)
T ss_pred             ceeeecCC--------CCCcccceEEEEEEeec------------CCceEEEEehhHHhhcCcccchHHH----HHHHhh
Confidence            76432110        01346788899998741            1257899999999998765543322    122222


Q ss_pred             hCCCCcEEEEeccCCcchHHHHHHHhcCCC-CeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceE
Q psy7952         225 TGNSIPIIALTATAEPSVKQDIISVLKFNK-PYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCG  303 (444)
Q Consensus       225 ~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~  303 (444)
                      ..+...+.+=-     ...+.+...+.+.. .+.+..  ..|..       ...       +.+.+...+.. ..++.++
T Consensus       304 ~AdEiHLCGep-----svldlV~~i~k~TGd~vev~~--YeRl~-------pL~-------v~~~~~~sl~n-lk~GDCv  361 (700)
T KOG0953|consen  304 AADEIHLCGEP-----SVLDLVRKILKMTGDDVEVRE--YERLS-------PLV-------VEETALGSLSN-LKPGDCV  361 (700)
T ss_pred             hhhhhhccCCc-----hHHHHHHHHHhhcCCeeEEEe--ecccC-------cce-------ehhhhhhhhcc-CCCCCeE
Confidence            22223333322     23333344333222 221111  11110       000       00111111111 1134444


Q ss_pred             EEEecccchHHHHHHHHHhh-----------cCHHHHHHHHHHHhc--CCccEEEEcCccccccccCCccEEEEeCCC--
Q psy7952         304 IIYCRTREHTTDLADALRRK-----------VNKHERSRVQESFMR--GEINVITATISFGMGIDRQNVRFVVHWGMP--  368 (444)
Q Consensus       304 iVf~~s~~~~~~l~~~L~~~-----------~~~~~r~~~~~~f~~--g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p--  368 (444)
                      +  |.|+++.-.+...+.+.           ++++.|..--..|.+  ++.+||||||+++.|+|+ +++.||+++.-  
T Consensus       362 V--~FSkk~I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL-~IrRiiF~sl~Ky  438 (700)
T KOG0953|consen  362 V--AFSKKDIFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNL-NIRRIIFYSLIKY  438 (700)
T ss_pred             E--EeehhhHHHHHHHHHHhcCcceEEEecCCCCchhHHHHHHhCCCCCccceEEeeccccccccc-ceeEEEEeecccC
Confidence            4  44566776676677666           899999999999986  899999999999999999 69999988753  


Q ss_pred             -------CCHHHHHHHhccCCCCCC---ceeEEEEecccchhhHHHHHhhccch
Q psy7952         369 -------SSIPAYYQESGRAGRDGL---QSYCRIYHSEHSKKSLEYVIKTDTST  412 (444)
Q Consensus       369 -------~s~~~~~Qr~GR~~R~g~---~g~~~~~~~~~~~~~~~~~~~~~~~~  412 (444)
                             .+..+..|..|||||.|.   .|. ++-+..+|...++..++.+...
T Consensus       439 sg~e~~~it~sqikQIAGRAGRf~s~~~~G~-vTtl~~eDL~~L~~~l~~p~ep  491 (700)
T KOG0953|consen  439 SGRETEDITVSQIKQIAGRAGRFGSKYPQGE-VTTLHSEDLKLLKRILKRPVEP  491 (700)
T ss_pred             CcccceeccHHHHHHHhhcccccccCCcCce-EEEeeHhhHHHHHHHHhCCchH
Confidence                   468889999999999864   355 4445567888888887755443

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.61  E-value=5e-15  Score=130.43  Aligned_cols=176  Identities=22%  Similarity=0.350  Sum_probs=108.0

Q ss_pred             hCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCc
Q psy7952          44 FGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFR  123 (444)
Q Consensus        44 ~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~  123 (444)
                      +++.. ++++|.+++..+..+.+++++.+|||+|||.++.        ..+ ...+... ...++++++|+..++     
T Consensus         4 ~~~~~-~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~--------~~~-~~~~~~~-~~~~~l~~~p~~~~~-----   67 (201)
T smart00487        4 FGFEP-LRPYQKEAIEALLSGLRDVILAAPTGSGKTLAAL--------LPA-LEALKRG-KGKRVLVLVPTRELA-----   67 (201)
T ss_pred             cCCCC-CCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHH--------HHH-HHHhccc-CCCcEEEEeCCHHHH-----
Confidence            34555 4689999999999754689999999999999732        222 2212222 134679999999999     


Q ss_pred             cchHhhh-c-CCCC-ceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEec
Q psy7952         124 DDKTSIV-T-GRSD-LYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDE  200 (444)
Q Consensus       124 ~~~~~~l-~-~~~~-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE  200 (444)
                      .+....+ . .... ......+.+........    .+.  .+..+++++|++.+.    ............++++|+||
T Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~--~~~~~v~~~t~~~l~----~~~~~~~~~~~~~~~iIiDE  137 (201)
T smart00487       68 EQWAEELKKLGPSLGLKVVGLYGGDSKREQLR----KLE--SGKTDILVTTPGRLL----DLLENDLLELSNVDLVILDE  137 (201)
T ss_pred             HHHHHHHHHHhccCCeEEEEEeCCcchHHHHH----HHh--cCCCCEEEeChHHHH----HHHHcCCcCHhHCCEEEEEC
Confidence            5555555 1 2111 13333344333222211    111  233499999999874    22222223455789999999


Q ss_pred             cccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHh
Q psy7952         201 AHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVL  250 (444)
Q Consensus       201 ~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l  250 (444)
                      +|.+....  +...+   ..+....++..+++++||||++..........
T Consensus       138 ~h~~~~~~--~~~~~---~~~~~~~~~~~~~v~~saT~~~~~~~~~~~~~  182 (201)
T smart00487      138 AHRLLDGG--FGDQL---EKLLKLLPKNVQLLLLSATPPEEIENLLELFL  182 (201)
T ss_pred             HHHHhcCC--cHHHH---HHHHHhCCccceEEEEecCCchhHHHHHHHhc
Confidence            99986432  33333   33444445568899999999877666555543

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=99.60  E-value=1.6e-13  Score=143.04  Aligned_cols=162  Identities=17%  Similarity=0.140  Sum_probs=102.2

Q ss_pred             EEEEeccCCcchHHHHHHHhcCCCCeEEEecCC-CCCCceEEEEE-c-----------cc-chhhHHHHHHHHHHHhccC
Q psy7952         231 IIALTATAEPSVKQDIISVLKFNKPYKVFKTST-FRSNLFYDVIF-D-----------DL-LKDSYAHVKEFIEKCLGKD  296 (444)
Q Consensus       231 ~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~-~~~~~~~~~~~-~-----------~~-~~~~~~~~~~~l~~~l~~~  296 (444)
                      +|++|||+.+..  .+...+++..+........ ...+....+.. .           .. .......+.+.+.++... 
T Consensus       444 vil~SgTL~p~~--~~~~~Lg~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~l~~~~~~r~~~~~~~~l~~~i~~~~~~-  520 (705)
T TIGR00604       444 VILASGTLSPLD--AFPRNLGFNPVSQDSPTHILKRENLLTLIVTRGSDQVPLSSTFEIRNDPSLVRNLGELLVEFSKI-  520 (705)
T ss_pred             EEEecccCCcHH--HHHHHhCCCCccceecCcccchHHeEEEEEeeCCCCCeeeeehhccCCHHHHHHHHHHHHHHhhc-
Confidence            589999998843  4566677654332211111 11111111111 1           01 122334555555555444 


Q ss_pred             CCCCceEEEEecccchHHHHHHHHHhh----------------cCHHHHHHHHHHHhc----CCccEEEEc--Ccccccc
Q psy7952         297 NKANNCGIIYCRTREHTTDLADALRRK----------------VNKHERSRVQESFMR----GEINVITAT--ISFGMGI  354 (444)
Q Consensus       297 ~~~~~~~iVf~~s~~~~~~l~~~L~~~----------------~~~~~r~~~~~~f~~----g~~~vLvaT--~~~~~Gi  354 (444)
                        .++.++||++|....+++++.+...                -...++..+++.|+.    |...||+|+  ..+++||
T Consensus       521 --~pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~~~~~~~~~~l~~f~~~~~~~~gavL~av~gGk~sEGI  598 (705)
T TIGR00604       521 --IPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVETKDAQETSDALERYKQAVSEGRGAVLLSVAGGKVSEGI  598 (705)
T ss_pred             --CCCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeCCCcchHHHHHHHHHHHHhcCCceEEEEecCCcccCcc
Confidence              3688999999999999988877642                112467889999964    456799998  8999999


Q ss_pred             ccCC--ccEEEEeCCCC-C------------------------------HHHHHHHhccCCCCCCceeEEEEeccc
Q psy7952         355 DRQN--VRFVVHWGMPS-S------------------------------IPAYYQESGRAGRDGLQSYCRIYHSEH  397 (444)
Q Consensus       355 di~~--~~~Vi~~~~p~-s------------------------------~~~~~Qr~GR~~R~g~~g~~~~~~~~~  397 (444)
                      |+++  ++.||.++.|. +                              .....|.+||+-|..++--++++++..
T Consensus       599 Df~~~~~r~ViivGlPf~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~a~~~v~QaiGR~IR~~~D~G~iillD~R  674 (705)
T TIGR00604       599 DFCDDLGRAVIMVGIPYEYTESRILLARLEFLRDQYPIRENQDFYEFDAMRAVNQAIGRVIRHKDDYGSIVLLDKR  674 (705)
T ss_pred             ccCCCCCcEEEEEccCCCCCCCHHHHHHHHHHHhhcCCCccHHHHHHHHHHHHHHHhCccccCcCceEEEEEEehh
Confidence            9986  68899999886 1                              123469999999986554355566543

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).

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=99.58  E-value=3.7e-13  Score=136.65  Aligned_cols=133  Identities=17%  Similarity=0.176  Sum_probs=95.8

Q ss_pred             HHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchh
Q psy7952          36 LTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPIL  115 (444)
Q Consensus        36 ~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~  115 (444)
                      +.++-++..|..+|+  .|.-.--.+.+|   -+..+.||-|||++|        .+|+.+..+. +..   |-|++++.
T Consensus        74 vREa~~R~lG~r~yd--VQliGgl~Lh~G---~IAEM~TGEGKTL~a--------tlpaylnAL~-Gkg---VhVVTvNd  136 (939)
T PRK12902         74 VREASKRVLGMRHFD--VQLIGGMVLHEG---QIAEMKTGEGKTLVA--------TLPSYLNALT-GKG---VHVVTVND  136 (939)
T ss_pred             HHHHHHHHhCCCcch--hHHHhhhhhcCC---ceeeecCCCChhHHH--------HHHHHHHhhc-CCC---eEEEeCCH
Confidence            345667777888644  887766666655   679999999999994        4555222232 223   37888999


Q ss_pred             hhhcccCccchHhhh-----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh-
Q psy7952         116 SSFYLRFRDDKTSIV-----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR-  189 (444)
Q Consensus       116 ~L~~~~q~~~~~~~l-----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~-  189 (444)
                      .||     ....+.+     .+|   +.+..+.++....++...+        .+||+++|+..+.   |+++..++.. 
T Consensus       137 YLA-----~RDae~m~~vy~~LG---Ltvg~i~~~~~~~err~aY--------~~DItYgTn~e~g---FDYLRDnm~~~  197 (939)
T PRK12902        137 YLA-----RRDAEWMGQVHRFLG---LSVGLIQQDMSPEERKKNY--------ACDITYATNSELG---FDYLRDNMATD  197 (939)
T ss_pred             HHH-----HhHHHHHHHHHHHhC---CeEEEECCCCChHHHHHhc--------CCCeEEecCCccc---ccchhhhhccc
Confidence            999     5555554     567   9999998888777766655        7899999999886   4555555432 


Q ss_pred             -----hCCccEEEEeccccc
Q psy7952         190 -----YNKLAYIVVDEAHCV  204 (444)
Q Consensus       190 -----~~~~~~iViDE~H~~  204 (444)
                           ...+.+.||||+|.+
T Consensus       198 ~~~~vqR~~~faIVDEvDSI  217 (939)
T PRK12902        198 ISEVVQRPFNYCVIDEVDSI  217 (939)
T ss_pred             ccccccCccceEEEecccce
Confidence                 256899999999987

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.58  E-value=4.6e-13  Score=138.63  Aligned_cols=177  Identities=19%  Similarity=0.140  Sum_probs=111.4

Q ss_pred             EEEEeccCCcc-hHHHHHHHhcCCC---CeEEEecCCCC-CCceEEEEE----cc-cchhhHHHHHHHHHHHhccCCCCC
Q psy7952         231 IIALTATAEPS-VKQDIISVLKFNK---PYKVFKTSTFR-SNLFYDVIF----DD-LLKDSYAHVKEFIEKCLGKDNKAN  300 (444)
Q Consensus       231 ~v~lSAT~~~~-~~~~~~~~l~~~~---~~~~~~~~~~~-~~~~~~~~~----~~-~~~~~~~~~~~~l~~~l~~~~~~~  300 (444)
                      +|++|||+.+. ..+.+.+.+|++.   ......++... .+....+..    .. ........+.+.+.+++. .   +
T Consensus       459 vIltSATL~~~~~f~~~~~~lGL~~~~~~~~~~~~SpF~~~~q~~l~vp~~~~~p~~~~~~~~~~~~~i~~l~~-~---~  534 (697)
T PRK11747        459 AVLTSATLRSLNSFDRFQEQSGLPEKDGDRFLALPSPFDYPNQGKLVIPKMRAEPDNEEAHTAEMAEFLPELLE-K---H  534 (697)
T ss_pred             EEEEeeeCCCCCchHHHHHHcCCCCCCCceEEEcCCCCCHHHccEEEeCCCCCCCCCcHHHHHHHHHHHHHHHh-c---C
Confidence            48889998762 3456667777763   22222222211 111111111    10 122334566666666655 2   4


Q ss_pred             ceEEEEecccchHHHHHHHHHhh-------cCHHHHHHHHHHHh----cCCccEEEEcCccccccccCC--ccEEEEeCC
Q psy7952         301 NCGIIYCRTREHTTDLADALRRK-------VNKHERSRVQESFM----RGEINVITATISFGMGIDRQN--VRFVVHWGM  367 (444)
Q Consensus       301 ~~~iVf~~s~~~~~~l~~~L~~~-------~~~~~r~~~~~~f~----~g~~~vLvaT~~~~~Gidi~~--~~~Vi~~~~  367 (444)
                      +.++|+++|.+..++++..|...       -....+..+++.|+    .|+..||++|..+.+|||+|+  +++||..+.
T Consensus       535 gg~LVlFtSy~~l~~v~~~l~~~~~~~ll~Q~~~~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~vII~kL  614 (697)
T PRK11747        535 KGSLVLFASRRQMQKVADLLPRDLRLMLLVQGDQPRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQVIITKI  614 (697)
T ss_pred             CCEEEEeCcHHHHHHHHHHHHHhcCCcEEEeCCchHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEEEEEEcC
Confidence            44899999999999999988643       12245677887776    467889999999999999986  788998887


Q ss_pred             CCC------------------------------HHHHHHHhccCCCCCCceeEEEEeccc-chhhHHHHHhhccc
Q psy7952         368 PSS------------------------------IPAYYQESGRAGRDGLQSYCRIYHSEH-SKKSLEYVIKTDTS  411 (444)
Q Consensus       368 p~s------------------------------~~~~~Qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~~~~~~~~  411 (444)
                      |..                              ...+.|.+||+-|...+--+++++++. ..+.+.+.+-+.+|
T Consensus       615 PF~~p~dp~~~ar~~~~~~~g~~~F~~~~lP~A~~kl~Qg~GRlIRs~~D~G~i~ilD~R~~~~~Yg~~~l~sLP  689 (697)
T PRK11747        615 PFAVPDSPVEATLAEWLKSRGGNPFMEISVPDASFKLIQAVGRLIRSEQDRGRVTILDRRLLTKRYGKRLLDALP  689 (697)
T ss_pred             CCCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhccccccCCceEEEEEEcccccchhHHHHHHHhCC
Confidence            741                              223479999999986554356666655 44555555555554

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

Probab=99.56  E-value=3.3e-13  Score=140.55  Aligned_cols=180  Identities=17%  Similarity=0.215  Sum_probs=114.3

Q ss_pred             cEEEEeccCCcchH-HHHHHHhcCCCCe-EEEecCCCC-CCceEEEEEccc--ch--hhHHHHHHHHHHHhccCCCCCce
Q psy7952         230 PIIALTATAEPSVK-QDIISVLKFNKPY-KVFKTSTFR-SNLFYDVIFDDL--LK--DSYAHVKEFIEKCLGKDNKANNC  302 (444)
Q Consensus       230 ~~v~lSAT~~~~~~-~~~~~~l~~~~~~-~~~~~~~~~-~~~~~~~~~~~~--~~--~~~~~~~~~l~~~l~~~~~~~~~  302 (444)
                      .+|++|||+.+... ..+....+..... .....+... ............  ..  .....+...+...+...   +++
T Consensus       405 ~~vl~SaTL~~~~~f~~~~~~~~~~~~~~~~~~~spf~~~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~~~~~~---~~~  481 (654)
T COG1199         405 SVVLTSATLSPLDSFSSLLGLLGLEEKLRFLSLPSPFNYEEQGQLYVPTDLPEPREPELLAKLAAYLREILKAS---PGG  481 (654)
T ss_pred             cEEEeeeeccCCCcHHHHHHHcCCccccceeccCCCCChhhcceEeccccCCCCCChHHHHHHHHHHHHHHhhc---CCC
Confidence            46999999877432 2244444444333 122222111 111111111111  11  34556666666666554   569


Q ss_pred             EEEEecccchHHHHHHHHHhh--------cCHHHHHHHHHHHhcCCc-cEEEEcCccccccccCC--ccEEEEeCCCC--
Q psy7952         303 GIIYCRTREHTTDLADALRRK--------VNKHERSRVQESFMRGEI-NVITATISFGMGIDRQN--VRFVVHWGMPS--  369 (444)
Q Consensus       303 ~iVf~~s~~~~~~l~~~L~~~--------~~~~~r~~~~~~f~~g~~-~vLvaT~~~~~Gidi~~--~~~Vi~~~~p~--  369 (444)
                      ++||++|.+..+.+++.+...        .+...+...++.|+.+.- .++|+|..+++|||+|+  +..||..+.|.  
T Consensus       482 ~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~~~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~vvI~~lPfp~  561 (654)
T COG1199         482 VLVLFPSYEYLKRVAERLKDERSTLPVLTQGEDEREELLEKFKASGEGLILVGGGSFWEGVDFPGDALRLVVIVGLPFPN  561 (654)
T ss_pred             EEEEeccHHHHHHHHHHHhhcCccceeeecCCCcHHHHHHHHHHhcCCeEEEeeccccCcccCCCCCeeEEEEEecCCCC
Confidence            999999999999999998853        445666688999986655 89999999999999985  57788888775  


Q ss_pred             ----------------------------CHHHHHHHhccCCCCCCceeEEEEeccc-chhhHHHHHhhccch
Q psy7952         370 ----------------------------SIPAYYQESGRAGRDGLQSYCRIYHSEH-SKKSLEYVIKTDTST  412 (444)
Q Consensus       370 ----------------------------s~~~~~Qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~  412 (444)
                                                  -...+.|.+||+-|.....-++++++.. ....++..+...++.
T Consensus       562 p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivllD~R~~~~~y~~~l~~~l~~  633 (654)
T COG1199         562 PDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLDKRYATKRYGKLLLDSLPP  633 (654)
T ss_pred             CCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEEEEecccchhhhHHHHHHHhCCC
Confidence                                        2556789999999975443344555543 444466666655554

>PRK14873 primosome assembly protein PriA; Provisional

Probab=99.55  E-value=6.4e-14  Score=142.48  Aligned_cols=296  Identities=8%  Similarity=-0.012  Sum_probs=169.3

Q ss_pred             EEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCCh
Q psy7952          69 FVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTK  148 (444)
Q Consensus        69 ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~  148 (444)
                      +..+.+|+|||.+        |+-.+ .+.+..++.   +|+++|...|.     .+..+++...++...+..+|++.+.
T Consensus       164 i~~~~~GSGKTev--------yl~~i-~~~l~~Gk~---vLvLvPEi~lt-----~q~~~rl~~~f~~~~v~~lhS~l~~  226 (665)
T PRK14873        164 VWQALPGEDWARR--------LAAAA-AATLRAGRG---ALVVVPDQRDV-----DRLEAALRALLGAGDVAVLSAGLGP  226 (665)
T ss_pred             HhhcCCCCcHHHH--------HHHHH-HHHHHcCCe---EEEEecchhhH-----HHHHHHHHHHcCCCcEEEECCCCCH
Confidence            3444469999999        54322 333334444   49999999999     7777888332222458889999998


Q ss_pred             hhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCC-CcHHHHHHHHHHHHhhCC
Q psy7952         149 TENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGH-DFRPTYRRLGELRQFTGN  227 (444)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~-~~~~~~~~l~~~~~~~~~  227 (444)
                      .++...+..+.  .+..+|+|||-.-+           +..+.++++||+||=|.-+-... ..+..-..+..++... .
T Consensus       227 ~~R~~~w~~~~--~G~~~IViGtRSAv-----------FaP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~-~  292 (665)
T PRK14873        227 ADRYRRWLAVL--RGQARVVVGTRSAV-----------FAPVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQ-H  292 (665)
T ss_pred             HHHHHHHHHHh--CCCCcEEEEcceeE-----------EeccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHHH-c
Confidence            88877776664  57789999995544           23567899999999997532111 1111122233333333 3


Q ss_pred             CCcEEEEeccCCcchHHHHHHHhcCCCCeEEEe--cCCCCCCceEEEEEc-cc-----chh--hHHHHHHHHHHHhccCC
Q psy7952         228 SIPIIALTATAEPSVKQDIISVLKFNKPYKVFK--TSTFRSNLFYDVIFD-DL-----LKD--SYAHVKEFIEKCLGKDN  297 (444)
Q Consensus       228 ~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~-~~-----~~~--~~~~~~~~l~~~l~~~~  297 (444)
                      +.++|+.||||+-.....+...  .........  .....|.+...-... +.     ...  -...+.+.+.+.++   
T Consensus       293 ~~~lvLgSaTPSles~~~~~~g--~~~~~~~~~~~~~~~~P~v~~vd~~~~~~~~~~~~~g~~ls~~l~~~i~~~L~---  367 (665)
T PRK14873        293 GCALLIGGHARTAEAQALVESG--WAHDLVAPRPVVRARAPRVRALGDSGLALERDPAARAARLPSLAFRAARDALE---  367 (665)
T ss_pred             CCcEEEECCCCCHHHHHHHhcC--cceeeccccccccCCCCeEEEEeCchhhhccccccccCccCHHHHHHHHHHHh---
Confidence            4889999999976554432211  101000000  011122222111110 00     000  11233444444443   


Q ss_pred             CCCceEEEEecccchHHHHHH-----------------------------------------------------------
Q psy7952         298 KANNCGIIYCRTREHTTDLAD-----------------------------------------------------------  318 (444)
Q Consensus       298 ~~~~~~iVf~~s~~~~~~l~~-----------------------------------------------------------  318 (444)
                       .+ ++|||.|.+..+-.+..                                                           
T Consensus       368 -~g-qvll~lnRrGyap~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~~l~~~g~Gter~ee  445 (665)
T PRK14873        368 -HG-PVLVQVPRRGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSDRLRAVVVGARRTAE  445 (665)
T ss_pred             -cC-cEEEEecCCCCCCeeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCCcceeeeccHHHHHH
Confidence             35 88888776655433221                                                           


Q ss_pred             HHHhhc-----CHHHHHHHHHHHhcCCccEEEEcC----ccccccccCCccEEEEeCCCC------------CHHHHHHH
Q psy7952         319 ALRRKV-----NKHERSRVQESFMRGEINVITATI----SFGMGIDRQNVRFVVHWGMPS------------SIPAYYQE  377 (444)
Q Consensus       319 ~L~~~~-----~~~~r~~~~~~f~~g~~~vLvaT~----~~~~Gidi~~~~~Vi~~~~p~------------s~~~~~Qr  377 (444)
                      .|.+.+     -..+++.+++.|. ++..|||+|+    ++.     +++..|+..|...            ....+.|.
T Consensus       446 eL~~~FP~~~V~r~d~d~~l~~~~-~~~~IlVGTqgaepm~~-----g~~~lV~ildaD~~L~~pDfRA~Er~~qll~qv  519 (665)
T PRK14873        446 ELGRAFPGVPVVTSGGDQVVDTVD-AGPALVVATPGAEPRVE-----GGYGAALLLDAWALLGRQDLRAAEDTLRRWMAA  519 (665)
T ss_pred             HHHHHCCCCCEEEEChHHHHHhhc-cCCCEEEECCCCccccc-----CCceEEEEEcchhhhcCCCcChHHHHHHHHHHH
Confidence            111111     1113445778886 5899999999    665     3456665544321            24556899


Q ss_pred             hccCCCCCCceeEEEEecccchhhHHHHHhhc
Q psy7952         378 SGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTD  409 (444)
Q Consensus       378 ~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~  409 (444)
                      .||+||.+.+|.+++...++ ...++.+...+
T Consensus       520 agragr~~~~G~V~iq~~p~-~~~~~~l~~~d  550 (665)
T PRK14873        520 AALVRPRADGGQVVVVAESS-LPTVQALIRWD  550 (665)
T ss_pred             HHhhcCCCCCCEEEEEeCCC-CHHHHHHHhCC
Confidence            99999998999988876444 35566665544

>KOG1000|consensus

Probab=99.55  E-value=2.4e-14  Score=133.91  Aligned_cols=302  Identities=14%  Similarity=0.120  Sum_probs=180.8

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-  130 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-  130 (444)
                      |+|++-+...++...++++.-..|-|||+-|+..          +.+....+.-   ||+||.....-|   .+++.+| 
T Consensus       201 PFQreGv~faL~RgGR~llADeMGLGKTiQAlaI----------A~yyraEwpl---liVcPAsvrftW---a~al~r~l  264 (689)
T KOG1000|consen  201 PFQREGVIFALERGGRILLADEMGLGKTIQALAI----------ARYYRAEWPL---LIVCPASVRFTW---AKALNRFL  264 (689)
T ss_pred             chhhhhHHHHHhcCCeEEEecccccchHHHHHHH----------HHHHhhcCcE---EEEecHHHhHHH---HHHHHHhc
Confidence            5999999888875488999999999999874432          2223344555   999998776522   5666766 


Q ss_pred             cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCC
Q psy7952         131 TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHD  210 (444)
Q Consensus       131 ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~  210 (444)
                      ..-.+ +.+..-..+...+           ..-...|.|.+++++.      .+........+++||+||+|++-+... 
T Consensus       265 ps~~p-i~vv~~~~D~~~~-----------~~t~~~v~ivSye~ls------~l~~~l~~~~~~vvI~DEsH~Lk~skt-  325 (689)
T KOG1000|consen  265 PSIHP-IFVVDKSSDPLPD-----------VCTSNTVAIVSYEQLS------LLHDILKKEKYRVVIFDESHMLKDSKT-  325 (689)
T ss_pred             ccccc-eEEEecccCCccc-----------cccCCeEEEEEHHHHH------HHHHHHhcccceEEEEechhhhhccch-
Confidence            22211 3333333322211           1123467888877754      233334445699999999999854221 


Q ss_pred             cHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHH-------------------HHHHHhcCCCCeEEEec--C-------
Q psy7952         211 FRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQ-------------------DIISVLKFNKPYKVFKT--S-------  262 (444)
Q Consensus       211 ~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~-------------------~~~~~l~~~~~~~~~~~--~-------  262 (444)
                           .+.+........-.++|++|+||.-.-..                   .-.++... ..+.....  .       
T Consensus       326 -----kr~Ka~~dllk~akhvILLSGTPavSRP~elytqi~avd~tlfp~f~efa~rYCd~-k~vr~~~Dykg~tnl~EL  399 (689)
T KOG1000|consen  326 -----KRTKAATDLLKVAKHVILLSGTPAVSRPSELYTQIRAVDHTLFPNFHEFAIRYCDG-KQVRFCFDYKGCTNLEEL  399 (689)
T ss_pred             -----hhhhhhhhHHHHhhheEEecCCcccCCchhhhhhhhhhcccccccHHHHHHHhcCc-cccceeeecCCCCCHHHH
Confidence                 11222222222235699999996321000                   00000000 00000000  0       


Q ss_pred             -------------------CCCCCceEEEE-Ecccchhh---------------------------HH----HHHHHHHH
Q psy7952         263 -------------------TFRSNLFYDVI-FDDLLKDS---------------------------YA----HVKEFIEK  291 (444)
Q Consensus       263 -------------------~~~~~~~~~~~-~~~~~~~~---------------------------~~----~~~~~l~~  291 (444)
                                         ...+.....+. ........                           +.    .....+.+
T Consensus       400 ~~lL~k~lMIRRlK~dvL~qLPpKrr~Vv~~~~gr~da~~~~lv~~a~~~t~~~~~e~~~~~l~l~y~~tgiaK~~av~e  479 (689)
T KOG1000|consen  400 AALLFKRLMIRRLKADVLKQLPPKRREVVYVSGGRIDARMDDLVKAAADYTKVNSMERKHESLLLFYSLTGIAKAAAVCE  479 (689)
T ss_pred             HHHHHHHHHHHHHHHHHHhhCCccceEEEEEcCCccchHHHHHHHHhhhcchhhhhhhhhHHHHHHHHHhcccccHHHHH
Confidence                               00000000000 00000000                           00    01122222


Q ss_pred             Hhcc----CCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHh-cCCccE-EEEcCccccccc
Q psy7952         292 CLGK----DNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFM-RGEINV-ITATISFGMGID  355 (444)
Q Consensus       292 ~l~~----~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~-~g~~~v-LvaT~~~~~Gid  355 (444)
                      .+..    ....+.+.+|||+-....+.+...+.++          .++..|...-+.|. +.+.+| +++...++.|++
T Consensus       480 yi~~~~~l~d~~~~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt  559 (689)
T KOG1000|consen  480 YILENYFLPDAPPRKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLT  559 (689)
T ss_pred             HHHhCcccccCCCceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeeccccee
Confidence            2222    3346789999999999999999998887          78899999999998 446777 778888999999


Q ss_pred             cCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEe
Q psy7952         356 RQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYH  394 (444)
Q Consensus       356 i~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~  394 (444)
                      +...+.|++...++++--++|.--|+.|.|+..-+.+.+
T Consensus       560 ~tAa~~VVFaEL~wnPgvLlQAEDRaHRiGQkssV~v~y  598 (689)
T KOG1000|consen  560 LTAASVVVFAELHWNPGVLLQAEDRAHRIGQKSSVFVQY  598 (689)
T ss_pred             eeccceEEEEEecCCCceEEechhhhhhccccceeeEEE
Confidence            999999999999999999999999999999876554433

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

Probab=99.54  E-value=1.4e-14  Score=107.03  Aligned_cols=62  Identities=39%  Similarity=0.590  Sum_probs=60.2

Q ss_pred             cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCC
Q psy7952         324 VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG  385 (444)
Q Consensus       324 ~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g  385 (444)
                      +++.+|..+++.|++++..+||||+++++|+|+|.+++||++++|+|...|.|++||++|.|
T Consensus        17 ~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~g   78 (78)
T PF00271_consen   17 MSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGRIG   78 (78)
T ss_dssp             SHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSSTTT
T ss_pred             CCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCCCC
Confidence            67889999999999999999999999999999999999999999999999999999999986

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

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.49  E-value=7.6e-14  Score=115.62  Aligned_cols=143  Identities=15%  Similarity=0.232  Sum_probs=88.0

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeC
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVS  144 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~  144 (444)
                      +++++.+|||+|||.+++.++.         . +...+..+++++++|++.++     .+..+.+ ......+.+..+.+
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~---------~-~~~~~~~~~~lv~~p~~~l~-----~~~~~~~~~~~~~~~~~~~~~~   65 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPIL---------E-LLDSLKGGQVLVLAPTRELA-----NQVAERLKELFGEGIKVGYLIG   65 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHH---------H-HHhcccCCCEEEEcCcHHHH-----HHHHHHHHHHhhCCcEEEEEec
Confidence            4689999999999988332211         1 22223345779999999999     5555555 11110366777777


Q ss_pred             CCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHh
Q psy7952         145 GQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQF  224 (444)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~  224 (444)
                      ..........      .....+|+++|++.+.    ............++++|+||+|.+....  .....   ......
T Consensus        66 ~~~~~~~~~~------~~~~~~i~i~t~~~~~----~~~~~~~~~~~~~~~iiiDE~h~~~~~~--~~~~~---~~~~~~  130 (144)
T cd00046          66 GTSIKQQEKL------LSGKTDIVVGTPGRLL----DELERLKLSLKKLDLLILDEAHRLLNQG--FGLLG---LKILLK  130 (144)
T ss_pred             CcchhHHHHH------hcCCCCEEEECcHHHH----HHHHcCCcchhcCCEEEEeCHHHHhhcc--hHHHH---HHHHhh
Confidence            6554433211      2467899999999874    2222222234578999999999986533  11111   112223


Q ss_pred             hCCCCcEEEEeccC
Q psy7952         225 TGNSIPIIALTATA  238 (444)
Q Consensus       225 ~~~~~~~v~lSAT~  238 (444)
                      .....+++++||||
T Consensus       131 ~~~~~~~i~~saTp  144 (144)
T cd00046         131 LPKDRQVLLLSATP  144 (144)
T ss_pred             CCccceEEEEeccC
Confidence            34558899999997

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

>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=99.49  E-value=6.7e-14  Score=121.84  Aligned_cols=154  Identities=19%  Similarity=0.165  Sum_probs=87.5

Q ss_pred             hHHHHHHHHHHc------cCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccc
Q psy7952          52 ELQKKAIRHILL------RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDD  125 (444)
Q Consensus        52 ~~Q~~~~~~~~~------~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~  125 (444)
                      ++|.+++..+.+      ..+++++.+|||+|||.+|+..+          ..+..     +++|++|+..|+     .|
T Consensus         6 ~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~----------~~l~~-----~~l~~~p~~~l~-----~Q   65 (184)
T PF04851_consen    6 PYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALI----------LELAR-----KVLIVAPNISLL-----EQ   65 (184)
T ss_dssp             HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHH----------HHHHC-----EEEEEESSHHHH-----HH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhh----------hcccc-----ceeEecCHHHHH-----HH
Confidence            799999999995      13789999999999999843211          11222     669999999999     55


Q ss_pred             hHhhh-cCCCCceeEEEE-----------eCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHH-------HHH
Q psy7952         126 KTSIV-TGRSDLYQLELI-----------VSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYL-------LQH  186 (444)
Q Consensus       126 ~~~~l-~~~~~~i~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~-------~~~  186 (444)
                      ....+ ............           ...........     .......+++++|.+.+........       ...
T Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~  140 (184)
T PF04851_consen   66 WYDEFDDFGSEKYNFFEKSIKPAYDSKEFISIQDDISDKS-----ESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSY  140 (184)
T ss_dssp             HHHHHHHHSTTSEEEEE--GGGCCE-SEEETTTTEEEHHH-----HHCBSS-SEEEEEHHHHHHHHHH---------GCH
T ss_pred             HHHHHHHhhhhhhhhccccccccccccccccccccccccc-----ccccccccchhhHHHHHHhhcccccccccchhhhh
Confidence            55555 222111111110           11111111111     1124678899999888753210000       001


Q ss_pred             HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCc
Q psy7952         187 LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEP  240 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~  240 (444)
                      .......++||+||||++...     ..+..+.+     .+...+|+|||||.+
T Consensus       141 ~~~~~~~~~vI~DEaH~~~~~-----~~~~~i~~-----~~~~~~l~lTATp~r  184 (184)
T PF04851_consen  141 KLLKNKFDLVIIDEAHHYPSD-----SSYREIIE-----FKAAFILGLTATPFR  184 (184)
T ss_dssp             HGGGGSESEEEEETGGCTHHH-----HHHHHHHH-----SSCCEEEEEESS-S-
T ss_pred             hhccccCCEEEEehhhhcCCH-----HHHHHHHc-----CCCCeEEEEEeCccC
Confidence            122346799999999996431     11344433     333779999999963

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 ....

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=99.48  E-value=1.5e-12  Score=134.25  Aligned_cols=82  Identities=23%  Similarity=0.265  Sum_probs=57.9

Q ss_pred             EEEEecccchHHHHHHHHHhh----------------cCHHHHHHHHHH----------------------Hhc----CC
Q psy7952         303 GIIYCRTREHTTDLADALRRK----------------VNKHERSRVQES----------------------FMR----GE  340 (444)
Q Consensus       303 ~iVf~~s~~~~~~l~~~L~~~----------------~~~~~r~~~~~~----------------------f~~----g~  340 (444)
                      ++|-+++++.+..++..|...                .....|..+++.                      .++    +.
T Consensus       759 GliR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~  838 (1110)
T TIGR02562       759 GLIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNH  838 (1110)
T ss_pred             EEEEEcCchHHHHHHHHHHhhccccCCceeEEEecccChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCC
Confidence            577788888888888887655                222233332222                      122    46


Q ss_pred             ccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCc
Q psy7952         341 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ  387 (444)
Q Consensus       341 ~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~  387 (444)
                      ..|+|+|++.+.|+|+. .+.+|.  -|.+++..+|+.||+.|.|..
T Consensus       839 ~~i~v~Tqv~E~g~D~d-fd~~~~--~~~~~~sliQ~aGR~~R~~~~  882 (1110)
T TIGR02562       839 LFIVLATPVEEVGRDHD-YDWAIA--DPSSMRSIIQLAGRVNRHRLE  882 (1110)
T ss_pred             CeEEEEeeeEEEEeccc-CCeeee--ccCcHHHHHHHhhcccccccC
Confidence            78999999999999984 555553  466799999999999998653

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.

>KOG0392|consensus

Probab=99.46  E-value=1.3e-12  Score=133.97  Aligned_cols=92  Identities=22%  Similarity=0.263  Sum_probs=82.5

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh-------------cCHHHHHHHHHHHhcC-CccE-EEEcCccccccccCCccEEE
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK-------------VNKHERSRVQESFMRG-EINV-ITATISFGMGIDRQNVRFVV  363 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~-------------~~~~~r~~~~~~f~~g-~~~v-LvaT~~~~~Gidi~~~~~Vi  363 (444)
                      .+++++|||.-+...+-+.+.|-+.             .++.+|.++.++|.++ .+.+ |++|.+.+.|+|+.+.++||
T Consensus      1339 sqHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDGSVpp~~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTVV 1418 (1549)
T KOG0392|consen 1339 SQHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDGSVPPGDRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTVV 1418 (1549)
T ss_pred             ccceeEEeeeHHHHHHHHHHHHhhhhcCceeEEEecCCCCcHHHHHHHHHhcCCCceeEEEEeeeccccccccCCCceEE
Confidence            4679999999999998888877666             7899999999999988 6787 67889999999999999999


Q ss_pred             EeCCCCCHHHHHHHhccCCCCCCceeE
Q psy7952         364 HWGMPSSIPAYYQESGRAGRDGLQSYC  390 (444)
Q Consensus       364 ~~~~p~s~~~~~Qr~GR~~R~g~~g~~  390 (444)
                      +++-.|++-.-+|..-||.|-|++..+
T Consensus      1419 FvEHDWNPMrDLQAMDRAHRIGQKrvV 1445 (1549)
T KOG0392|consen 1419 FVEHDWNPMRDLQAMDRAHRIGQKRVV 1445 (1549)
T ss_pred             EEecCCCchhhHHHHHHHHhhcCceee
Confidence            999999999999999999999987643

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=99.42  E-value=1.5e-11  Score=126.47  Aligned_cols=114  Identities=24%  Similarity=0.200  Sum_probs=85.6

Q ss_pred             hHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------cCH--HHHHHHHHHHhcC-CccEEEEcCccc
Q psy7952         281 SYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------VNK--HERSRVQESFMRG-EINVITATISFG  351 (444)
Q Consensus       281 ~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------~~~--~~r~~~~~~f~~g-~~~vLvaT~~~~  351 (444)
                      ++..+.+.+.+.    ...+.|+||-+.|++.++.++..|...      ++.  .+++.-+-. ..| ...|-|||+|++
T Consensus       613 K~~Aii~ei~~~----~~~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~EAeIVA-~AG~~GaVTIATNMAG  687 (1112)
T PRK12901        613 KYNAVIEEITEL----SEAGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKEAEIVA-EAGQPGTVTIATNMAG  687 (1112)
T ss_pred             HHHHHHHHHHHH----HHCCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhHHHHHH-hcCCCCcEEEeccCcC
Confidence            344444444443    236899999999999999999999887      211  122221111 234 467899999999


Q ss_pred             cccccC--------CccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         352 MGIDRQ--------NVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       352 ~Gidi~--------~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                      ||-||.        +--+||-...+.|.+---|-.||+||.|.+|.+..|++-+|.
T Consensus       688 RGTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLEDd  743 (1112)
T PRK12901        688 RGTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLEDN  743 (1112)
T ss_pred             CCcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEcccH
Confidence            999996        334788899999999999999999999999999999886654

>KOG0386|consensus

Probab=99.38  E-value=1.7e-12  Score=131.00  Aligned_cols=315  Identities=16%  Similarity=0.162  Sum_probs=194.6

Q ss_pred             ccCchHHHHHHHHHH---ccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCcc
Q psy7952          48 SFKCELQKKAIRHIL---LRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRD  124 (444)
Q Consensus        48 ~~~t~~Q~~~~~~~~---~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~  124 (444)
                      .++ +||...+.++.   +|+=+-|+.-.+|-|||... |++.. |+.-.    ....|+.   +|+||+-.|.+|   .
T Consensus       394 ~Lk-~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQt-IsLit-YLmE~----K~~~GP~---LvivPlstL~NW---~  460 (1157)
T KOG0386|consen  394 ELK-EYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQT-ISLIT-YLMEH----KQMQGPF---LIIVPLSTLVNW---S  460 (1157)
T ss_pred             CCc-hhhhhhhHHHhhccCCCcccccchhcccchHHHH-HHHHH-HHHHH----cccCCCe---EEeccccccCCc---h
Confidence            356 79999887765   45456799999999999762 11111 11111    3345666   999999999955   2


Q ss_pred             chHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccc
Q psy7952         125 DKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCV  204 (444)
Q Consensus       125 ~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~  204 (444)
                      ..+..|+..   +....+.|  +...+.....+++.  ++.+|+++|++.+..      -...+..-++.|+||||-|+|
T Consensus       461 ~Ef~kWaPS---v~~i~YkG--tp~~R~~l~~qir~--gKFnVLlTtyEyiik------dk~lLsKI~W~yMIIDEGHRm  527 (1157)
T KOG0386|consen  461 SEFPKWAPS---VQKIQYKG--TPQQRSGLTKQQRH--GKFNVLLTTYEYIIK------DKALLSKISWKYMIIDEGHRM  527 (1157)
T ss_pred             hhccccccc---eeeeeeeC--CHHHHhhHHHHHhc--ccceeeeeeHHHhcC------CHHHHhccCCcceeecccccc
Confidence            444444333   55544444  44555666666653  789999999888753      223333447899999999997


Q ss_pred             cccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCC----------------e------------
Q psy7952         205 SEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKP----------------Y------------  256 (444)
Q Consensus       205 ~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~----------------~------------  256 (444)
                      ...       ...+...+.......+.+++|+||-.+....+...+.+--|                +            
T Consensus       528 KNa-------~~KLt~~L~t~y~~q~RLLLTGTPLQN~LpELWaLLNFlLP~IFnS~~~FeqWFN~PFantGek~eLteE  600 (1157)
T KOG0386|consen  528 KNA-------ICKLTDTLNTHYRAQRRLLLTGTPLQNNLPELWALLNFLLPNIFNSCKAFEQWFNQPFANTGEKVELTEE  600 (1157)
T ss_pred             cch-------hhHHHHHhhccccchhhhhhcCChhhhccHHHHHHHHHhccchhhhHhHHHHHhhhhhhhcCCcccccch
Confidence            542       13333333322223456788888654433333333221100                0            


Q ss_pred             --------------------------------------------------------EEEecC-----CCC----------
Q psy7952         257 --------------------------------------------------------KVFKTS-----TFR----------  265 (444)
Q Consensus       257 --------------------------------------------------------~~~~~~-----~~~----------  265 (444)
                                                                              .+....     ..+          
T Consensus       601 EtlLIIrRLHkVLRPFlLRRlKkeVE~~LPdKve~viKC~mSalQq~lY~~m~~~g~l~~d~~~g~~g~k~L~N~imqLR  680 (1157)
T KOG0386|consen  601 ETLLIIRRLHKVLRPFLLRRLKKEVEQELPDKVEDVIKCDMSALQQSLYKQMQNKGQLLKDTAKGKKGYKPLFNTIMQLR  680 (1157)
T ss_pred             HHHHHHHHHHHhhhHHHHHhhhHHHhhhCchhhhHhhheehhhhhHhhhHHHHhCCCCCcCchhccccchhhhhHhHHHH
Confidence                                                                    000000     000          


Q ss_pred             -----CCce----EEE--EEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------c
Q psy7952         266 -----SNLF----YDV--IFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------V  324 (444)
Q Consensus       266 -----~~~~----~~~--~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~  324 (444)
                           |..+    ..+  ......-.......+++...+-+-...+++++.||....-..-+.+.|.-.          .
T Consensus       681 KiCNHP~lf~~ve~~~~~~~~~~dL~R~sGKfELLDRiLPKLkatgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~T  760 (1157)
T KOG0386|consen  681 KLCNHPYLFANVENSYTLHYDIKDLVRVSGKFELLDRILPKLKATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQT  760 (1157)
T ss_pred             HhcCCchhhhhhccccccccChhHHHHhccHHHHHHhhhHHHHhcCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCc
Confidence                 0000    000  000001111122234555555555557999999998877666666666544          7


Q ss_pred             CHHHHHHHHHHHhcC--C-ccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEec
Q psy7952         325 NKHERSRVQESFMRG--E-INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHS  395 (444)
Q Consensus       325 ~~~~r~~~~~~f~~g--~-~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~  395 (444)
                      ...+|-..++.|..-  . ..+|.+|...+.|+|+...+.||.||..+++..+.|+--||-|.|+...+-++.-
T Consensus       761 K~~eRg~ll~~FN~Pds~yf~FllstragglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~rl  834 (1157)
T KOG0386|consen  761 KVEERGDLLEIFNAPDSPYFIFLLSTRAGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLRL  834 (1157)
T ss_pred             chhhHHHHHHHhcCCCCceeeeeeeecccccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeeeee
Confidence            788999999999733  2 3459999999999999999999999999999999999999999998877665543

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.35  E-value=3.5e-12  Score=95.02  Aligned_cols=62  Identities=37%  Similarity=0.599  Sum_probs=59.4

Q ss_pred             cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCC
Q psy7952         324 VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG  385 (444)
Q Consensus       324 ~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g  385 (444)
                      +++.+|...++.|..+...+|++|+++++|+|+|++++||.+++|.+...|.|++||++|.|
T Consensus        21 ~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~g   82 (82)
T smart00490       21 LSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG   82 (82)
T ss_pred             CCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcccccCC
Confidence            67888999999999999999999999999999999999999999999999999999999975

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=99.32  E-value=1e-10  Score=124.55  Aligned_cols=289  Identities=13%  Similarity=0.136  Sum_probs=155.9

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeC
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVS  144 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~  144 (444)
                      +..+|+--||||||+++.-+          ...+......++|+||+-++.|-     .|....+ ..+.......   .
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~----------A~~l~~~~~~~~v~fvvDR~dLd-----~Q~~~~f~~~~~~~~~~~---~  335 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKL----------ARLLLELPKNPKVLFVVDRKDLD-----DQTSDEFQSFGKVAFNDP---K  335 (962)
T ss_pred             CceEEEeecCCchHHHHHHH----------HHHHHhccCCCeEEEEechHHHH-----HHHHHHHHHHHHhhhhcc---c
Confidence            45899999999999993321          22244445667889999999999     4455544 2220001111   2


Q ss_pred             CCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH---HhhCCccEEEEeccccccccCCCcHHHHHHHHHH
Q psy7952         145 GQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL---VRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGEL  221 (444)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~---~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~  221 (444)
                      ..+..   +..+.+..  ....|+|+|.++|..     .....   ....+=-+||+||||+-- .|    ..-..   +
T Consensus       336 ~~s~~---~Lk~~l~~--~~~~ii~TTIQKf~~-----~~~~~~~~~~~~~~ivvI~DEaHRSQ-~G----~~~~~---~  397 (962)
T COG0610         336 AESTS---ELKELLED--GKGKIIVTTIQKFNK-----AVKEDELELLKRKNVVVIIDEAHRSQ-YG----ELAKL---L  397 (962)
T ss_pred             ccCHH---HHHHHHhc--CCCcEEEEEecccch-----hhhcccccccCCCcEEEEEechhhcc-cc----HHHHH---H
Confidence            22222   22233322  355899999999853     22111   111222478999999932 23    11122   2


Q ss_pred             HHhhCCCCcEEEEeccCCcchHHH-HHHHhcCCCCeEEEec-CCCC----CCceEEEE-EcccchhhH------------
Q psy7952         222 RQFTGNSIPIIALTATAEPSVKQD-IISVLKFNKPYKVFKT-STFR----SNLFYDVI-FDDLLKDSY------------  282 (444)
Q Consensus       222 ~~~~~~~~~~v~lSAT~~~~~~~~-~~~~l~~~~~~~~~~~-~~~~----~~~~~~~~-~~~~~~~~~------------  282 (444)
                      ...+++ +.++++|+||.-..... ....+|  ..+....- ...+    ..+.|... .........            
T Consensus       398 ~~~~~~-a~~~gFTGTPi~~~d~~tt~~~fg--~ylh~Y~i~daI~Dg~vl~i~y~~~~~~~~~~~~~~~~~~~~~~~~~  474 (962)
T COG0610         398 KKALKK-AIFIGFTGTPIFKEDKDTTKDVFG--DYLHTYTITDAIRDGAVLPVYYENRVELELIEESIKEEAEELDERIE  474 (962)
T ss_pred             HHHhcc-ceEEEeeCCccccccccchhhhhc--ceeEEEecchhhccCceeeEEEeecccccccccchhhhhhhhHHHHh
Confidence            334555 88999999997544433 122222  22111111 0001    01222221 000000000            


Q ss_pred             ---------------------------H-HHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----------
Q psy7952         283 ---------------------------A-HVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----------  323 (444)
Q Consensus       283 ---------------------------~-~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----------  323 (444)
                                                 . ...+....... ....+.++++.+.++..+..+++.....           
T Consensus       475 ~~~~~~~~~~~k~~~~~~~~~~~~~r~~~~a~~i~~~f~~-~~~~~~kam~V~~sr~~~~~~~~~~~~~~~~~~~~~~~~  553 (962)
T COG0610         475 EITEDILEKIKKKTKNLEFLAMLAVRLIRAAKDIYDHFKK-EEVFDLKAMVVASSRKVAVELYEAEIAARLDWHSKESLE  553 (962)
T ss_pred             hhHHHHHHHHHHHHhhhhHHhcchHHHHHHHHHHHHHHHh-hcccCceEEEEEechHHHHHhHHHHhhhhhhhhhhhhhh
Confidence                                       0 01112222222 2335678888888887555444443222           


Q ss_pred             ---------------------cCHHHHHHHHHHH--hcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhcc
Q psy7952         324 ---------------------VNKHERSRVQESF--MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGR  380 (444)
Q Consensus       324 ---------------------~~~~~r~~~~~~f--~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR  380 (444)
                                           .....+.....+|  .....++||.++++-.|+|.|.++++. +|.|.--..++|.+.|
T Consensus       554 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~d~~kilIV~dmlLTGFDaP~L~TmY-vDK~Lk~H~L~QAisR  632 (962)
T COG0610         554 GAIKDYNTEFETDFDKKQSHAKLKDEKKDLIKRFKLKDDPLDLLIVVDMLLTGFDAPCLNTLY-VDKPLKYHNLIQAISR  632 (962)
T ss_pred             hHHHHHHhhcccchhhhhhhHHHHHHHhhhhhhhcCcCCCCCEEEEEccccccCCccccceEE-eccccccchHHHHHHH
Confidence                                 1122333444443  356789999999999999999888877 5677888889999999


Q ss_pred             CCCC--C--CceeEEEEec
Q psy7952         381 AGRD--G--LQSYCRIYHS  395 (444)
Q Consensus       381 ~~R~--g--~~g~~~~~~~  395 (444)
                      ++|.  +  ..|..+.|..
T Consensus       633 tNR~~~~~K~~G~IVDf~g  651 (962)
T COG0610         633 TNRVFPGKKKFGLIVDFRG  651 (962)
T ss_pred             hccCCCCCCCCcEEEECcc
Confidence            9995  3  2355444443

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=99.24  E-value=1.3e-10  Score=117.24  Aligned_cols=288  Identities=15%  Similarity=0.111  Sum_probs=160.0

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCccccccC--CccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEE
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG--NVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELI  142 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~--~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~  142 (444)
                      .-.+|.+|.|||||.+        . +..    +...  ....+++++...++|+     .+...++ ..+-+++....-
T Consensus        50 ~V~vVRSpMGTGKTta--------L-i~w----Lk~~l~~~~~~VLvVShRrSL~-----~sL~~rf~~~~l~gFv~Y~d  111 (824)
T PF02399_consen   50 GVLVVRSPMGTGKTTA--------L-IRW----LKDALKNPDKSVLVVSHRRSLT-----KSLAERFKKAGLSGFVNYLD  111 (824)
T ss_pred             CeEEEECCCCCCcHHH--------H-HHH----HHHhccCCCCeEEEEEhHHHHH-----HHHHHHHhhcCCCcceeeec
Confidence            3468999999999977        1 222    3222  3445779999999999     7888887 443111221111


Q ss_pred             eCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHH----H
Q psy7952         143 VSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRR----L  218 (444)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~----l  218 (444)
                      ..+....            ...++-+++..+.+.     .+.  ...+.+.++||+||+-.....-  +.+.+..    +
T Consensus       112 ~~~~~i~------------~~~~~rLivqIdSL~-----R~~--~~~l~~yDvVIIDEv~svL~qL--~S~Tm~~~~~v~  170 (824)
T PF02399_consen  112 SDDYIID------------GRPYDRLIVQIDSLH-----RLD--GSLLDRYDVVIIDEVMSVLNQL--FSPTMRQREEVD  170 (824)
T ss_pred             ccccccc------------ccccCeEEEEehhhh-----hcc--cccccccCEEEEehHHHHHHHH--hHHHHhhHHHHH
Confidence            1111110            123567888877763     111  2235568999999997664311  2121111    2


Q ss_pred             HHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEE---EEEcc-----------cc---hh-
Q psy7952         219 GELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYD---VIFDD-----------LL---KD-  280 (444)
Q Consensus       219 ~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~---~~~~~-----------~~---~~-  280 (444)
                      ..+.....+...+|++-|++.....+.+... .-.+++.++......+.....   ....-           ..   +. 
T Consensus       171 ~~L~~lI~~ak~VI~~DA~ln~~tvdFl~~~-Rp~~~i~vI~n~y~~~~fs~R~~~~~~~l~~~~l~~~~~~~~~~~~~~  249 (824)
T PF02399_consen  171 NLLKELIRNAKTVIVMDADLNDQTVDFLASC-RPDENIHVIVNTYASPGFSNRRCTFLRSLGTDTLAAALNPEDENADTS  249 (824)
T ss_pred             HHHHHHHHhCCeEEEecCCCCHHHHHHHHHh-CCCCcEEEEEeeeecCCcccceEEEecccCcHHHHHHhCCcccccccC
Confidence            2233334455779999999999888776654 334555555444222211000   00000           00   00 


Q ss_pred             -------------hH-HHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------cCHHHHHHHHHHHhcCC
Q psy7952         281 -------------SY-AHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------VNKHERSRVQESFMRGE  340 (444)
Q Consensus       281 -------------~~-~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------~~~~~r~~~~~~f~~g~  340 (444)
                                   .. .....+...+.. ....++++-||++|...++.+++.....      ++......-.+.+  ++
T Consensus       250 ~~~~~~~~~~~~~~~~~~~~tF~~~L~~-~L~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~dv~~W--~~  326 (824)
T PF02399_consen  250 PTPKHSPDPTATAAISNDETTFFSELLA-RLNAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLEDVESW--KK  326 (824)
T ss_pred             CCcCCCCccccccccccchhhHHHHHHH-HHhCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCccccccc--cc
Confidence                         00 000111111111 1125788899999999888888777665      1111111112222  56


Q ss_pred             ccEEEEcCccccccccCCcc--EEEEeCCC----CCHHHHHHHhccCCCCCCceeEEEEeccc
Q psy7952         341 INVITATISFGMGIDRQNVR--FVVHWGMP----SSIPAYYQESGRAGRDGLQSYCRIYHSEH  397 (444)
Q Consensus       341 ~~vLvaT~~~~~Gidi~~~~--~Vi~~~~p----~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~  397 (444)
                      .+|++=|++++.|+++...+  .++.|=.|    .+..+..|++||+ |.-.....+++++..
T Consensus       327 ~~VviYT~~itvG~Sf~~~HF~~~f~yvk~~~~gpd~~s~~Q~lgRv-R~l~~~ei~v~~d~~  388 (824)
T PF02399_consen  327 YDVVIYTPVITVGLSFEEKHFDSMFAYVKPMSYGPDMVSVYQMLGRV-RSLLDNEIYVYIDAS  388 (824)
T ss_pred             eeEEEEeceEEEEeccchhhceEEEEEecCCCCCCcHHHHHHHHHHH-HhhccCeEEEEEecc
Confidence            89999999999999987544  35544223    3566789999999 544556667777644

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

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

Probab=99.20  E-value=1e-11  Score=99.46  Aligned_cols=134  Identities=14%  Similarity=0.044  Sum_probs=71.9

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCC-CccccccCCccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEe
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPP-GADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIV  143 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~-~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~  143 (444)
                      +--++...||+|||.-         .+|. +.+.+.++.   |+|++.||+.++     .+..+.+ ...   +...   
T Consensus         5 ~~~~~d~hpGaGKTr~---------vlp~~~~~~i~~~~---rvLvL~PTRvva-----~em~~aL~~~~---~~~~---   61 (148)
T PF07652_consen    5 ELTVLDLHPGAGKTRR---------VLPEIVREAIKRRL---RVLVLAPTRVVA-----EEMYEALKGLP---VRFH---   61 (148)
T ss_dssp             EEEEEE--TTSSTTTT---------HHHHHHHHHHHTT-----EEEEESSHHHH-----HHHHHHTTTSS---EEEE---
T ss_pred             ceeEEecCCCCCCccc---------ccHHHHHHHHHccC---eEEEecccHHHH-----HHHHHHHhcCC---cccC---
Confidence            4568999999999986         2443 112233334   459999999999     7777777 333   3322   


Q ss_pred             CCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHH
Q psy7952         144 SGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQ  223 (444)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~  223 (444)
                      .......          ..++.-|-++|...+     ..++.......++++||+||||......-.++..   + +.+.
T Consensus        62 t~~~~~~----------~~g~~~i~vMc~at~-----~~~~~~p~~~~~yd~II~DEcH~~Dp~sIA~rg~---l-~~~~  122 (148)
T PF07652_consen   62 TNARMRT----------HFGSSIIDVMCHATY-----GHFLLNPCRLKNYDVIIMDECHFTDPTSIAARGY---L-RELA  122 (148)
T ss_dssp             STTSS--------------SSSSEEEEEHHHH-----HHHHHTSSCTTS-SEEEECTTT--SHHHHHHHHH---H-HHHH
T ss_pred             ceeeecc----------ccCCCcccccccHHH-----HHHhcCcccccCccEEEEeccccCCHHHHhhhee---H-HHhh
Confidence            1111110          124566778886664     3344444556789999999999854322112221   1 1122


Q ss_pred             hhCCCCcEEEEeccCCcch
Q psy7952         224 FTGNSIPIIALTATAEPSV  242 (444)
Q Consensus       224 ~~~~~~~~v~lSAT~~~~~  242 (444)
                      . .....+|+|||||+...
T Consensus       123 ~-~g~~~~i~mTATPPG~~  140 (148)
T PF07652_consen  123 E-SGEAKVIFMTATPPGSE  140 (148)
T ss_dssp             H-TTS-EEEEEESS-TT--
T ss_pred             h-ccCeeEEEEeCCCCCCC
Confidence            2 22367999999998864

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 ....

>KOG0388|consensus

Probab=99.18  E-value=3e-10  Score=110.98  Aligned_cols=93  Identities=19%  Similarity=0.211  Sum_probs=82.4

Q ss_pred             CCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccE-EEEcCccccccccCCccEEEEe
Q psy7952         297 NKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINV-ITATISFGMGIDRQNVRFVVHW  365 (444)
Q Consensus       297 ~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~v-LvaT~~~~~Gidi~~~~~Vi~~  365 (444)
                      ...++++++|+...+...-+.+.|..+          ...++|..++..|....+-| |++|.+.+.|||+...++||+|
T Consensus      1041 kaegHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAGGLGINLTAADTViFY 1120 (1185)
T KOG0388|consen 1041 KAEGHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAGGLGINLTAADTVIFY 1120 (1185)
T ss_pred             hcCCceEEehhHHHHHHHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecccCcccccccccceEEEe
Confidence            346889999999888888888888766          66789999999999877765 9999999999999999999999


Q ss_pred             CCCCCHHHHHHHhccCCCCCCcee
Q psy7952         366 GMPSSIPAYYQESGRAGRDGLQSY  389 (444)
Q Consensus       366 ~~p~s~~~~~Qr~GR~~R~g~~g~  389 (444)
                      |..+++..-.|..-||.|.|+...
T Consensus      1121 dSDWNPT~D~QAMDRAHRLGQTrd 1144 (1185)
T KOG0388|consen 1121 DSDWNPTADQQAMDRAHRLGQTRD 1144 (1185)
T ss_pred             cCCCCcchhhHHHHHHHhccCccc
Confidence            999999999999999999987654

>KOG1002|consensus

Probab=99.13  E-value=5.4e-10  Score=105.12  Aligned_cols=108  Identities=12%  Similarity=0.079  Sum_probs=80.6

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcC-CccE-EEEcCccccccccCCccEEEEeC
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRG-EINV-ITATISFGMGIDRQNVRFVVHWG  366 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g-~~~v-LvaT~~~~~Gidi~~~~~Vi~~~  366 (444)
                      ...+.|||..-.....-+...|.+.          |++..|...++.|++. .++| |++-.+.+..+|+....+|+++|
T Consensus       637 ~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLkAGGVALNLteASqVFmmD  716 (791)
T KOG1002|consen  637 RTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLKAGGVALNLTEASQVFMMD  716 (791)
T ss_pred             cchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEeccCceEeeechhceeEeec
Confidence            3457788877666666666666655          9999999999999976 4665 78888899999999999999999


Q ss_pred             CCCCHHHHHHHhccCCCCCC--ceeEEEEecccch-hhHHHHH
Q psy7952         367 MPSSIPAYYQESGRAGRDGL--QSYCRIYHSEHSK-KSLEYVI  406 (444)
Q Consensus       367 ~p~s~~~~~Qr~GR~~R~g~--~g~~~~~~~~~~~-~~~~~~~  406 (444)
                      +-+++.---|.--|..|-|+  +=.++.|+..... +++-.+-
T Consensus       717 PWWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iEnsiE~kIieLQ  759 (791)
T KOG1002|consen  717 PWWNPAVEWQAQDRIHRIGQYRPVKVVRFCIENSIEEKIIELQ  759 (791)
T ss_pred             ccccHHHHhhhhhhHHhhcCccceeEEEeehhccHHHHHHHHH
Confidence            99999888887777777775  3445555554433 3344443

>KOG0391|consensus

Probab=99.11  E-value=9.4e-10  Score=112.64  Aligned_cols=169  Identities=12%  Similarity=0.107  Sum_probs=107.3

Q ss_pred             hHHHHHHHHHH---ccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHh
Q psy7952          52 ELQKKAIRHIL---LRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTS  128 (444)
Q Consensus        52 ~~Q~~~~~~~~---~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~  128 (444)
                      +||..-++++.   +.+-|.|+.-..|.|||.- .|.++. ++...    -...|.+   ||||||-.+.+|   .-.++
T Consensus       618 eYQkiGLdWLatLYeknlNGILADEmGLGKTIQ-tISllA-hLACe----egnWGPH---LIVVpTsviLnW---EMElK  685 (1958)
T KOG0391|consen  618 EYQKIGLDWLATLYEKNLNGILADEMGLGKTIQ-TISLLA-HLACE----EGNWGPH---LIVVPTSVILNW---EMELK  685 (1958)
T ss_pred             HHHHhhHHHHHHHHHhcccceehhhhcccchhH-HHHHHH-HHHhc----ccCCCCc---eEEeechhhhhh---hHHHh
Confidence            58887777655   4445789999999999965 222111 11111    1234688   999999999965   45667


Q ss_pred             hhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccC
Q psy7952         129 IVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWG  208 (444)
Q Consensus       129 ~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~  208 (444)
                      +|+-+   +++..++|...  +++.-.+.|. ..+..+|.|+++..+...      .......++.|+|+||+|.+-.+.
T Consensus       686 RwcPg---lKILTYyGs~k--ErkeKRqgW~-kPnaFHVCItSYklv~qd------~~AFkrkrWqyLvLDEaqnIKnfk  753 (1958)
T KOG0391|consen  686 RWCPG---LKILTYYGSHK--ERKEKRQGWA-KPNAFHVCITSYKLVFQD------LTAFKRKRWQYLVLDEAQNIKNFK  753 (1958)
T ss_pred             hhCCc---ceEeeecCCHH--HHHHHhhccc-CCCeeEEeehhhHHHHhH------HHHHHhhccceeehhhhhhhcchh
Confidence            77888   99999988653  3333344443 356778888887765321      122234579999999999987654


Q ss_pred             CCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcC
Q psy7952         209 HDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKF  252 (444)
Q Consensus       209 ~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~  252 (444)
                      +   ..|..   +++. .. .+.+++|+||-.+..-.++..+.+
T Consensus       754 s---qrWQA---llnf-ns-qrRLLLtgTPLqNslmELWSLmhF  789 (1958)
T KOG0391|consen  754 S---QRWQA---LLNF-NS-QRRLLLTGTPLQNSLMELWSLMHF  789 (1958)
T ss_pred             H---HHHHH---Hhcc-ch-hheeeecCCchhhHHHHHHHHHHH
Confidence            2   12333   3322 22 567899999866555545444443

>KOG4439|consensus

Probab=99.10  E-value=6.1e-10  Score=108.92  Aligned_cols=69  Identities=17%  Similarity=0.205  Sum_probs=60.5

Q ss_pred             cCHHHHHHHHHHHh--cCCccE-EEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEE
Q psy7952         324 VNKHERSRVQESFM--RGEINV-ITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRI  392 (444)
Q Consensus       324 ~~~~~r~~~~~~f~--~g~~~v-LvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~  392 (444)
                      ....+|..+++.|.  .|..+| |++-...+.|+|+-..+|+|..|+.+++.-=.|..-|..|.|+...+++
T Consensus       780 v~vK~Rq~iv~~FN~~k~~~rVmLlSLtAGGVGLNL~GaNHlilvDlHWNPaLEqQAcDRIYR~GQkK~V~I  851 (901)
T KOG4439|consen  780 VLVKDRQEIVDEFNQEKGGARVMLLSLTAGGVGLNLIGANHLILVDLHWNPALEQQACDRIYRMGQKKDVFI  851 (901)
T ss_pred             cchhHHHHHHHHHHhccCCceEEEEEEccCcceeeecccceEEEEecccCHHHHHHHHHHHHHhcccCceEE
Confidence            67889999999997  454666 6667788999999999999999999999999999999999999877655

>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=99.00  E-value=2e-10  Score=108.21  Aligned_cols=170  Identities=15%  Similarity=0.118  Sum_probs=89.1

Q ss_pred             HHHHHHHHHHcc------------CCcEEEEccCCCcccccccccccceEEeCCCccccccCC---ccceeEEEcchhhh
Q psy7952          53 LQKKAIRHILLR------------THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN---VRSRNGWISPILSS  117 (444)
Q Consensus        53 ~Q~~~~~~~~~~------------~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~---~~~~vlil~P~~~L  117 (444)
                      +|.+++..++..            .+.+++...+|+|||..++.++.          .+...+   ...++||+||. .+
T Consensus         1 ~Q~~~v~~m~~~~~~~~~~~~~~~~~g~lL~de~GlGKT~~~i~~~~----------~l~~~~~~~~~~~~LIv~P~-~l   69 (299)
T PF00176_consen    1 HQLEAVRWMLDRELVEEYPNSESPPRGGLLADEMGLGKTITAIALIS----------YLKNEFPQRGEKKTLIVVPS-SL   69 (299)
T ss_dssp             HHHHHHHHHHHHH----TTSSSTTT-EEEE---TTSSHHHHHHHHHH----------HHHHCCTTSS-S-EEEEE-T-TT
T ss_pred             CHHHHHHHHHHHhhhhcccccccCCCCEEEEECCCCCchhhhhhhhh----------hhhhccccccccceeEeecc-ch
Confidence            577777766432            26789999999999988443221          122222   21246999999 55


Q ss_pred             hcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEE
Q psy7952         118 FYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIV  197 (444)
Q Consensus       118 ~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iV  197 (444)
                      .  .||.+.+..+.. ....++..+.+.....      ..........+++++|++.+....-.... ......++++||
T Consensus        70 ~--~~W~~E~~~~~~-~~~~~v~~~~~~~~~~------~~~~~~~~~~~vvi~ty~~~~~~~~~~~~-~~l~~~~~~~vI  139 (299)
T PF00176_consen   70 L--SQWKEEIEKWFD-PDSLRVIIYDGDSERR------RLSKNQLPKYDVVITTYETLRKARKKKDK-EDLKQIKWDRVI  139 (299)
T ss_dssp             H--HHHHHHHHHHSG-T-TS-EEEESSSCHHH------HTTSSSCCCSSEEEEEHHHHH--TSTHTT-HHHHTSEEEEEE
T ss_pred             h--hhhhhhhccccc-cccccccccccccccc------cccccccccceeeeccccccccccccccc-cccccccceeEE
Confidence            5  233344444421 1126777777665110      11111246789999998886400000011 112224589999


Q ss_pred             EeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhc
Q psy7952         198 VDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLK  251 (444)
Q Consensus       198 iDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~  251 (444)
                      +||+|.+-+...   ..+..+.    .+. ....+++||||..+...++...+.
T Consensus       140 vDEaH~~k~~~s---~~~~~l~----~l~-~~~~~lLSgTP~~n~~~dl~~~l~  185 (299)
T PF00176_consen  140 VDEAHRLKNKDS---KRYKALR----KLR-ARYRWLLSGTPIQNSLEDLYSLLR  185 (299)
T ss_dssp             ETTGGGGTTTTS---HHHHHHH----CCC-ECEEEEE-SS-SSSGSHHHHHHHH
T ss_pred             Eecccccccccc---ccccccc----ccc-cceEEeeccccccccccccccchh
Confidence            999999854332   2222222    233 367889999998887776666554

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.

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=98.99  E-value=1.2e-08  Score=103.96  Aligned_cols=138  Identities=18%  Similarity=0.210  Sum_probs=91.3

Q ss_pred             HHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcc
Q psy7952          34 QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISP  113 (444)
Q Consensus        34 ~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P  113 (444)
                      .-+.++-++.+|..+|.  .|.-..-.+..   .-+..+.||-|||++|.+        |+.+..+...+.+    +++.
T Consensus        67 av~REa~~Rvlg~~~~d--VQliG~i~lh~---g~iaEM~TGEGKTL~atl--------p~ylnaL~gkgVh----vVTv  129 (822)
T COG0653          67 AVVREASKRVLGMRHFD--VQLLGGIVLHL---GDIAEMRTGEGKTLVATL--------PAYLNALAGKGVH----VVTV  129 (822)
T ss_pred             HhhhHHHHHhcCCChhh--HHHhhhhhhcC---CceeeeecCCchHHHHHH--------HHHHHhcCCCCcE----Eeee
Confidence            34456777777888644  67554444444   467999999999999554        4433334444444    5555


Q ss_pred             hhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh--
Q psy7952         114 ILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR--  189 (444)
Q Consensus       114 ~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~--  189 (444)
                      ..-|+  ..=.+++..+  ..|   +.+.....+....++...+        .+||.++|...+-   |+++..++..  
T Consensus       130 NdYLA--~RDae~m~~l~~~LG---lsvG~~~~~m~~~ek~~aY--------~~DItY~TnnElG---FDYLRDNm~~~~  193 (822)
T COG0653         130 NDYLA--RRDAEWMGPLYEFLG---LSVGVILAGMSPEEKRAAY--------ACDITYGTNNELG---FDYLRDNMVTSQ  193 (822)
T ss_pred             hHHhh--hhCHHHHHHHHHHcC---CceeeccCCCChHHHHHHH--------hcCceeccccccC---cchhhhhhhccH
Confidence            55566  1112333334  567   9999999999888888777        6899999988776   4444444221  


Q ss_pred             ----hCCccEEEEeccccc
Q psy7952         190 ----YNKLAYIVVDEAHCV  204 (444)
Q Consensus       190 ----~~~~~~iViDE~H~~  204 (444)
                          ...+.+.|+||++-+
T Consensus       194 ee~vqr~~~faIvDEvDSI  212 (822)
T COG0653         194 EEKVQRGLNFAIVDEVDSI  212 (822)
T ss_pred             HHhhhccCCeEEEcchhhe
Confidence                246899999999977

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.78  E-value=1.2e-08  Score=94.72  Aligned_cols=63  Identities=11%  Similarity=0.138  Sum_probs=44.7

Q ss_pred             hCCcccCchHHHHHHHHHH----ccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCc---cceeEEEcchhh
Q psy7952          44 FGFDSFKCELQKKAIRHIL----LRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNV---RSRNGWISPILS  116 (444)
Q Consensus        44 ~g~~~~~t~~Q~~~~~~~~----~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~---~~~vlil~P~~~  116 (444)
                      |+|++  ++.|.+.+..+.    +| .++++.+|||+|||++        ++.|+ +.++...+.   ..+++|+++|..
T Consensus         5 FPy~~--r~~Q~~~m~~v~~~~~~~-~~~~~eapTGtGKTl~--------~L~~a-l~~~~~~~~~~~~~kvi~~t~T~~   72 (289)
T smart00489        5 FPYEP--YPIQYEFMEELKRVLDRG-KIGILESPTGTGKTLS--------LLCLT-LTWLRSFPERIQKIKLIYLSRTVS   72 (289)
T ss_pred             CCCCC--CHHHHHHHHHHHHHHHcC-CcEEEECCCCcchhHH--------HHHHH-HHHHHhCcccccccceeEEeccHH
Confidence            67775  479999655544    45 8899999999999999        66665 322232222   236799999988


Q ss_pred             hh
Q psy7952         117 SF  118 (444)
Q Consensus       117 L~  118 (444)
                      +.
T Consensus        73 ~~   74 (289)
T smart00489       73 EI   74 (289)
T ss_pred             HH
Confidence            86

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.78  E-value=1.2e-08  Score=94.72  Aligned_cols=63  Identities=11%  Similarity=0.138  Sum_probs=44.7

Q ss_pred             hCCcccCchHHHHHHHHHH----ccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCc---cceeEEEcchhh
Q psy7952          44 FGFDSFKCELQKKAIRHIL----LRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNV---RSRNGWISPILS  116 (444)
Q Consensus        44 ~g~~~~~t~~Q~~~~~~~~----~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~---~~~vlil~P~~~  116 (444)
                      |+|++  ++.|.+.+..+.    +| .++++.+|||+|||++        ++.|+ +.++...+.   ..+++|+++|..
T Consensus         5 FPy~~--r~~Q~~~m~~v~~~~~~~-~~~~~eapTGtGKTl~--------~L~~a-l~~~~~~~~~~~~~kvi~~t~T~~   72 (289)
T smart00488        5 FPYEP--YPIQYEFMEELKRVLDRG-KIGILESPTGTGKTLS--------LLCLT-LTWLRSFPERIQKIKLIYLSRTVS   72 (289)
T ss_pred             CCCCC--CHHHHHHHHHHHHHHHcC-CcEEEECCCCcchhHH--------HHHHH-HHHHHhCcccccccceeEEeccHH
Confidence            67775  479999655544    45 8899999999999999        66665 322232222   236799999988


Q ss_pred             hh
Q psy7952         117 SF  118 (444)
Q Consensus       117 L~  118 (444)
                      +.
T Consensus        73 ~~   74 (289)
T smart00488       73 EI   74 (289)
T ss_pred             HH
Confidence            86

>KOG1015|consensus

Probab=98.77  E-value=1.3e-07  Score=95.74  Aligned_cols=69  Identities=17%  Similarity=0.081  Sum_probs=59.6

Q ss_pred             cCHHHHHHHHHHHhcC-C--c-cEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEE
Q psy7952         324 VNKHERSRVQESFMRG-E--I-NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRI  392 (444)
Q Consensus       324 ~~~~~r~~~~~~f~~g-~--~-~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~  392 (444)
                      .....|..+...|.+- .  . -.||+|.+.+.|||+=..+.||.||..|++.--+|-+=|+-|.|+..-|++
T Consensus      1198 t~s~~R~k~~~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyi 1270 (1567)
T KOG1015|consen 1198 TTSQSRKKWAEEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYI 1270 (1567)
T ss_pred             ccHHHHHHHHHHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceee
Confidence            6678899999999743 2  2 359999999999999999999999999999999999999999998765554

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

Probab=98.76  E-value=2.7e-06  Score=82.02  Aligned_cols=235  Identities=12%  Similarity=0.133  Sum_probs=148.6

Q ss_pred             CCeeEEEECCCccccccHHHHHH-------HHHhhCCccEEEEeccccccc--cCCCcHHHHHHHHHHHHhhC-------
Q psy7952         163 PRIKLLYVTPERAVTESFHYLLQ-------HLVRYNKLAYIVVDEAHCVSE--WGHDFRPTYRRLGELRQFTG-------  226 (444)
Q Consensus       163 ~~~~Iiv~Tpe~l~~~~~~~~~~-------~~~~~~~~~~iViDE~H~~~~--~~~~~~~~~~~l~~~~~~~~-------  226 (444)
                      ..+||||++|=-|.     ..+.       ..-.++.|.++|+|.+|.+.-  |.+ +.    .+...++..|       
T Consensus       130 y~SDIIiASPLGLr-----~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQNW~H-v~----~v~~~lN~~P~~~~~~D  199 (442)
T PF06862_consen  130 YSSDIIIASPLGLR-----MIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQNWEH-VL----HVFEHLNLQPKKSHDTD  199 (442)
T ss_pred             ccCCEEEEChHHHH-----HHhccccccccccchhheeeeEeechhhHHHHhhHHH-HH----HHHHHhccCCCCCCCCC
Confidence            35799999998763     2222       233467899999999998742  221 11    1111222112       


Q ss_pred             --------------CCCcEEEEeccCCcchHHHHHHHhcC-CCCeEEEecC-------CCCCCceEEEEE--cccc----
Q psy7952         227 --------------NSIPIIALTATAEPSVKQDIISVLKF-NKPYKVFKTS-------TFRSNLFYDVIF--DDLL----  278 (444)
Q Consensus       227 --------------~~~~~v~lSAT~~~~~~~~~~~~l~~-~~~~~~~~~~-------~~~~~~~~~~~~--~~~~----  278 (444)
                                    ...|.|++|+...+.....+.....- ...+.+....       ...+.+......  ....    
T Consensus       200 fsRVR~w~Ldg~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r~~~~s~~~~~  279 (442)
T PF06862_consen  200 FSRVRPWYLDGQAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQRFDCSSPADDP  279 (442)
T ss_pred             HHHHHHHHHcCcchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEEecCCCcchhh
Confidence                          12478999999988766555543211 1111111111       111222222221  2221    


Q ss_pred             hhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcC
Q psy7952         279 KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATI  348 (444)
Q Consensus       279 ~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~  348 (444)
                      +.........+...+.+ ......+|||++|-=+=..+...|++.          .+..+-...-..|..|+.++|+-|.
T Consensus       280 d~Rf~yF~~~iLP~l~~-~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TE  358 (442)
T PF06862_consen  280 DARFKYFTKKILPQLKR-DSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPILLYTE  358 (442)
T ss_pred             hHHHHHHHHHHHHHhhh-ccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEh
Confidence            22223333333333332 235789999999998888888888866          7778888888999999999999997


Q ss_pred             cc--ccccccCCccEEEEeCCCCCHHHHHHHhccCCCCC------CceeEEEEecccchhhHHHHHhh
Q psy7952         349 SF--GMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG------LQSYCRIYHSEHSKKSLEYVIKT  408 (444)
Q Consensus       349 ~~--~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g------~~g~~~~~~~~~~~~~~~~~~~~  408 (444)
                      =+  =+-..+.++++||+|++|..+.-|-..++-.+...      ....|.++++.-|.-.+..++.+
T Consensus       359 R~HFfrRy~irGi~~viFY~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~D~~~LErIVGt  426 (442)
T PF06862_consen  359 RFHFFRRYRIRGIRHVIFYGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKYDALRLERIVGT  426 (442)
T ss_pred             HHhhhhhceecCCcEEEEECCCCChhHHHHHHhhhcccccccccccCceEEEEecHhHHHHHHHHhCH
Confidence            54  34567889999999999999888877776554443      25789999999998888888753

; GO: 0005634 nucleus

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=98.61  E-value=2.1e-06  Score=89.66  Aligned_cols=69  Identities=17%  Similarity=0.059  Sum_probs=53.7

Q ss_pred             CCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCc
Q psy7952         163 PRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEP  240 (444)
Q Consensus       163 ~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~  240 (444)
                      ....|+++||..+.    ..++.+......+..|||||||++.+..     .+.-|.++++...+...+.++||+|..
T Consensus         6 ~~ggi~~~T~rIl~----~DlL~~ri~~~~itgiiv~~Ahr~~~~~-----~eaFI~rlyr~~n~~gfIkafSdsP~~   74 (814)
T TIGR00596         6 LEGGIFSITSRILV----VDLLTGIIPPELITGILVLRADRIIESS-----QEAFILRLYRQKNKTGFIKAFSDNPEA   74 (814)
T ss_pred             hcCCEEEEechhhH----hHHhcCCCCHHHccEEEEeecccccccc-----cHHHHHHHHHHhCCCcceEEecCCCcc
Confidence            46789999999997    5668888888999999999999986422     134455666666666779999999775

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

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

Probab=98.55  E-value=5.2e-07  Score=97.88  Aligned_cols=95  Identities=17%  Similarity=0.178  Sum_probs=81.8

Q ss_pred             CCc--eEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcC--CccEEEEcCccccccccCCccEEEE
Q psy7952         299 ANN--CGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRG--EINVITATISFGMGIDRQNVRFVVH  364 (444)
Q Consensus       299 ~~~--~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g--~~~vLvaT~~~~~Gidi~~~~~Vi~  364 (444)
                      .+.  +++||+.......-+...+...          ++...|...++.|.++  ..-+++++..++.|+|+...++||+
T Consensus       708 ~~~~~kvlifsq~t~~l~il~~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~kagg~glnLt~a~~vi~  787 (866)
T COG0553         708 EGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVIL  787 (866)
T ss_pred             hcccccEEEEeCcHHHHHHHHHHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEecccccceeecccceEEE
Confidence            455  8999999999888888888776          4478999999999986  3455888899999999999999999


Q ss_pred             eCCCCCHHHHHHHhccCCCCCCceeEEEE
Q psy7952         365 WGMPSSIPAYYQESGRAGRDGLQSYCRIY  393 (444)
Q Consensus       365 ~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~  393 (444)
                      +|+.+++....|...|+.|.|+...+.++
T Consensus       788 ~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~  816 (866)
T COG0553         788 FDPWWNPAVELQAIDRAHRIGQKRPVKVY  816 (866)
T ss_pred             eccccChHHHHHHHHHHHHhcCcceeEEE
Confidence            99999999999999999999887765443

>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=98.52  E-value=1.2e-07  Score=85.87  Aligned_cols=133  Identities=14%  Similarity=0.189  Sum_probs=90.0

Q ss_pred             HHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhh
Q psy7952          37 TAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILS  116 (444)
Q Consensus        37 ~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~  116 (444)
                      .++.++.+|+.+  .+.|.-+.-.+..| +  ++...||-|||++++        +++++..+ .+..   |-|++.+..
T Consensus        67 rea~~r~~g~~p--~~vQll~~l~L~~G-~--laEm~TGEGKTli~~--------l~a~~~AL-~G~~---V~vvT~Ndy  129 (266)
T PF07517_consen   67 REAARRTLGLRP--YDVQLLGALALHKG-R--LAEMKTGEGKTLIAA--------LPAALNAL-QGKG---VHVVTSNDY  129 (266)
T ss_dssp             HHHHHHHTS------HHHHHHHHHHHTT-S--EEEESTTSHHHHHHH--------HHHHHHHT-TSS----EEEEESSHH
T ss_pred             HHHHHHHcCCcc--cHHHHhhhhhcccc-e--eEEecCCCCcHHHHH--------HHHHHHHH-hcCC---cEEEeccHH
Confidence            345566668775  46899888888766 3  899999999999944        44422223 2333   368888889


Q ss_pred             hhcccCccchHhhh-----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh--
Q psy7952         117 SFYLRFRDDKTSIV-----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR--  189 (444)
Q Consensus       117 L~~~~q~~~~~~~l-----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~--  189 (444)
                      |+     ....+.+     .+|   +.+..+.++.....+.+.+        .++|+++|...+.   |+.+..+...  
T Consensus       130 LA-----~RD~~~~~~~y~~LG---lsv~~~~~~~~~~~r~~~Y--------~~dI~Y~t~~~~~---fD~Lrd~~~~~~  190 (266)
T PF07517_consen  130 LA-----KRDAEEMRPFYEFLG---LSVGIITSDMSSEERREAY--------AADIVYGTNSEFG---FDYLRDNLALSK  190 (266)
T ss_dssp             HH-----HHHHHHHHHHHHHTT-----EEEEETTTEHHHHHHHH--------HSSEEEEEHHHHH---HHHHHHTT-SSG
T ss_pred             Hh-----hccHHHHHHHHHHhh---hccccCccccCHHHHHHHH--------hCcccccccchhh---HHHHHHHHhhcc
Confidence            98     6666655     677   9999999998877666666        4689999988876   3444433221  


Q ss_pred             ----hCCccEEEEecccccc
Q psy7952         190 ----YNKLAYIVVDEAHCVS  205 (444)
Q Consensus       190 ----~~~~~~iViDE~H~~~  205 (444)
                          ...++++||||+|.++
T Consensus       191 ~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  191 NEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             GG--SSSSSEEEECTHHHHT
T ss_pred             chhccCCCCEEEEeccceEE
Confidence                3578999999999873

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 ....

>KOG0952|consensus

Probab=98.49  E-value=2e-08  Score=102.69  Aligned_cols=227  Identities=15%  Similarity=0.107  Sum_probs=132.8

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-  130 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-  130 (444)
                      +.|...+..+..-+.++++.+|||+|||.+|..+++.          .....+..+++++.|-++|+     .+-+..+ 
T Consensus       930 ~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~----------~~~~~p~~kvvyIap~kalv-----ker~~Dw~  994 (1230)
T KOG0952|consen  930 PIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFR----------ALSYYPGSKVVYIAPDKALV-----KERSDDWS  994 (1230)
T ss_pred             CccceEEEEEeecchhhhhcCCccCcchhHHHHHHHH----------HhccCCCccEEEEcCCchhh-----cccccchh
Confidence            4666666665555578999999999999996554332          22233346789999999999     8888887 


Q ss_pred             -cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH---HHhhCCccEEEEeccccccc
Q psy7952         131 -TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH---LVRYNKLAYIVVDEAHCVSE  206 (444)
Q Consensus       131 -~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~---~~~~~~~~~iViDE~H~~~~  206 (444)
                       +...+++++...+|+...+..     .    -...+++|+||++..     ...+.   ...+.+++.+|+||.|++.+
T Consensus       995 ~r~~~~g~k~ie~tgd~~pd~~-----~----v~~~~~~ittpek~d-----gi~Rsw~~r~~v~~v~~iv~de~hllg~ 1060 (1230)
T KOG0952|consen  995 KRDELPGIKVIELTGDVTPDVK-----A----VREADIVITTPEKWD-----GISRSWQTRKYVQSVSLIVLDEIHLLGE 1060 (1230)
T ss_pred             hhcccCCceeEeccCccCCChh-----h----eecCceEEccccccc-----CccccccchhhhccccceeecccccccC
Confidence             344345889999888765521     1    136799999999963     22332   23356789999999999865


Q ss_pred             c-CCCcHHHHHHHHHHH----HhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEE-ccc---
Q psy7952         207 W-GHDFRPTYRRLGELR----QFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIF-DDL---  277 (444)
Q Consensus       207 ~-~~~~~~~~~~l~~~~----~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~---  277 (444)
                      . |.    .+..+..-.    ...++..+.+++|--+.  ..+++..+++..+. .-++ +..+|........ .+.   
T Consensus      1061 ~rgP----Vle~ivsr~n~~s~~t~~~vr~~glsta~~--na~dla~wl~~~~~-~nf~-~svrpvp~~~~i~gfp~~~~ 1132 (1230)
T KOG0952|consen 1061 DRGP----VLEVIVSRMNYISSQTEEPVRYLGLSTALA--NANDLADWLNIKDM-YNFR-PSVRPVPLEVHIDGFPGQHY 1132 (1230)
T ss_pred             CCcc----eEEEEeeccccCccccCcchhhhhHhhhhh--ccHHHHHHhCCCCc-CCCC-cccccCCceEeecCCCchhc
Confidence            3 32    111111111    11222355666665543  34678888887665 2222 2223322211111 111   


Q ss_pred             ---chhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHH
Q psy7952         278 ---LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADAL  320 (444)
Q Consensus       278 ---~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L  320 (444)
                         .....+.....++.     ..+..+++||+.+++...--+..|
T Consensus      1133 cprm~smnkpa~qaik~-----~sp~~p~lifv~srrqtrlta~~l 1173 (1230)
T KOG0952|consen 1133 CPRMMSMNKPAFQAIKT-----HSPIKPVLIFVSSRRQTRLTALDL 1173 (1230)
T ss_pred             chhhhhcccHHHHHHhc-----CCCCCceEEEeecccccccchHhH
Confidence               11111122222222     347889999999887654443333

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

Probab=98.41  E-value=2.5e-07  Score=83.60  Aligned_cols=64  Identities=16%  Similarity=0.133  Sum_probs=44.5

Q ss_pred             chHHHHHHHHHHccCCc-EEEEccCCCcccccccccccceEEeCCCcccc------ccCCccceeEEEcchhhhhcccCc
Q psy7952          51 CELQKKAIRHILLRTHD-IFVSMPTGAVSLVGSVVSARSRVRIPPGADFI------LNGNVRSRNGWISPILSSFYLRFR  123 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~-~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l------~~~~~~~~vlil~P~~~L~~~~q~  123 (444)
                      ++.|.+|+..++.. .. .+|.||+|||||.+..-         + +..+      .......++|+++|+...+     
T Consensus         3 n~~Q~~Ai~~~~~~-~~~~~i~GpPGTGKT~~l~~---------~-i~~~~~~~~~~~~~~~~~il~~~~sN~av-----   66 (236)
T PF13086_consen    3 NESQREAIQSALSS-NGITLIQGPPGTGKTTTLAS---------I-IAQLLQRFKSRSADRGKKILVVSPSNAAV-----   66 (236)
T ss_dssp             -HHHHHHHHHHCTS-SE-EEEE-STTSSHHHHHHH---------H-HHHH-------HCCCSS-EEEEESSHHHH-----
T ss_pred             CHHHHHHHHHHHcC-CCCEEEECCCCCChHHHHHH---------H-HHHhccchhhhhhhccccceeecCCchhH-----
Confidence            36899999999998 66 99999999999965111         1 1112      1133445779999999998     


Q ss_pred             cchHhhh
Q psy7952         124 DDKTSIV  130 (444)
Q Consensus       124 ~~~~~~l  130 (444)
                      .+.++++
T Consensus        67 d~~~~~l   73 (236)
T PF13086_consen   67 DNILERL   73 (236)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7777776

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

Probab=98.35  E-value=2.4e-06  Score=72.70  Aligned_cols=99  Identities=23%  Similarity=0.305  Sum_probs=71.6

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcC--ccccccccCC--ccEEEE
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATI--SFGMGIDRQN--VRFVVH  364 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~--~~~~Gidi~~--~~~Vi~  364 (444)
                      .++.++||++|....+.+.+.+...          -....+...++.|+.++..+|+++.  .+++|||+|+  ++.||.
T Consensus         8 ~~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~r~vii   87 (167)
T PF13307_consen    8 VPGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQGSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLLRAVII   87 (167)
T ss_dssp             CSSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEESTCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESEEEEEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHhhcccccceeeecCcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchhheeee
Confidence            4689999999999999999988765          1356788999999999999999998  9999999996  778999


Q ss_pred             eCCCCC------------------------------HHHHHHHhccCCCCCCceeEEEEeccc
Q psy7952         365 WGMPSS------------------------------IPAYYQESGRAGRDGLQSYCRIYHSEH  397 (444)
Q Consensus       365 ~~~p~s------------------------------~~~~~Qr~GR~~R~g~~g~~~~~~~~~  397 (444)
                      .+.|..                              .....|.+||+-|..++--+++++++.
T Consensus        88 ~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD~R  150 (167)
T PF13307_consen   88 VGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLDSR  150 (167)
T ss_dssp             ES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEESGG
T ss_pred             cCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEcCc
Confidence            998851                              223369999999986654445555543

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=98.20  E-value=7.7e-06  Score=85.76  Aligned_cols=45  Identities=22%  Similarity=0.172  Sum_probs=42.1

Q ss_pred             CccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCC
Q psy7952         340 EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD  384 (444)
Q Consensus       340 ~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~  384 (444)
                      ..+.|++-+++-+|-|.|++-.++......|...-.|.+||+.|.
T Consensus       501 ~~~fifs~~al~egwd~~~~~~~~~l~~~~s~~~~~q~~gr~lr~  545 (986)
T PRK15483        501 TRRFLFSKWTLREGWDNPNVFQIAKLRSSGSETSKLQEVGRGLRL  545 (986)
T ss_pred             CeEEEEEhHHhhhcCCCCCeEEEEEeccCCchHHHHHHhccceec
Confidence            678999999999999999999999999888999999999999985

>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=98.14  E-value=2.5e-06  Score=74.15  Aligned_cols=57  Identities=19%  Similarity=0.183  Sum_probs=37.1

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhh
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSS  117 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L  117 (444)
                      +|+.|..++..+... +-+++.+|.|||||+.|+..+         ++.+.. +...+++++-|..+.
T Consensus         5 ~~~~Q~~~~~al~~~-~~v~~~G~AGTGKT~LA~a~A---------l~~v~~-g~~~kiii~Rp~v~~   61 (205)
T PF02562_consen    5 KNEEQKFALDALLNN-DLVIVNGPAGTGKTFLALAAA---------LELVKE-GEYDKIIITRPPVEA   61 (205)
T ss_dssp             -SHHHHHHHHHHHH--SEEEEE--TTSSTTHHHHHHH---------HHHHHT-TS-SEEEEEE-S--T
T ss_pred             CCHHHHHHHHHHHhC-CeEEEECCCCCcHHHHHHHHH---------HHHHHh-CCCcEEEEEecCCCC
Confidence            578999999999966 889999999999998844322         333433 666678888787754

; GO: 0005524 ATP binding; PDB: 3B85_A.

>KOG0921|consensus

Probab=98.13  E-value=5.9e-06  Score=83.71  Aligned_cols=98  Identities=20%  Similarity=0.269  Sum_probs=72.9

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh-----------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccE
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK-----------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRF  361 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~-----------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~  361 (444)
                      -.+-++||.+-....-.+...+-..                 ....+..++.+....|..++|++|.+.+..+.+.++..
T Consensus       642 i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkvf~~~p~gv~kii~stniaetsiTidd~v~  721 (1282)
T KOG0921|consen  642 IDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQRKVFEPVPEGVTKIILSTNIAETSITIDDVVY  721 (1282)
T ss_pred             CccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhhhccCcccccccccccccceeeEeeeecceeE
Confidence            4567888988888777777766544                 23344455566666788899999999999999888777


Q ss_pred             EEEeCCC------------------CCHHHHHHHhccCCCCCCceeEEEEeccc
Q psy7952         362 VVHWGMP------------------SSIPAYYQESGRAGRDGLQSYCRIYHSEH  397 (444)
Q Consensus       362 Vi~~~~p------------------~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~  397 (444)
                      |++.+.-                  .|..+..||.||+||. ++|+|..+.+.-
T Consensus       722 vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grv-R~G~~f~lcs~a  774 (1282)
T KOG0921|consen  722 VIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRV-RPGFCFHLCSRA  774 (1282)
T ss_pred             EEeeeeeeeeeeccccceeeeeeecccccchHhhcccCcee-cccccccccHHH
Confidence            7754432                  2677789999999998 788888877643

>KOG1016|consensus

Probab=98.10  E-value=0.00042  Score=69.69  Aligned_cols=96  Identities=15%  Similarity=0.173  Sum_probs=77.5

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh----------------------------cCHHHHHHHHHHHhcC---CccEEEEc
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK----------------------------VNKHERSRVQESFMRG---EINVITAT  347 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~----------------------------~~~~~r~~~~~~f~~g---~~~vLvaT  347 (444)
                      .+.++|||..+.....-+...|.+.                            .+..+|.+.++.|.+-   .+-++++|
T Consensus       718 ~g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~~lsWlfllst  797 (1387)
T KOG1016|consen  718 IGEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEPGLSWLFLLST  797 (1387)
T ss_pred             cCceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCCCceeeeeehh
Confidence            4667888888777776666666555                            5678899999999743   24678999


Q ss_pred             CccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEe
Q psy7952         348 ISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYH  394 (444)
Q Consensus       348 ~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~  394 (444)
                      .....|||+-..+.++.++..++..--.|.+-|+-|-|+..-|+++=
T Consensus       798 rag~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvYR  844 (1387)
T KOG1016|consen  798 RAGSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVYR  844 (1387)
T ss_pred             ccccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEEe
Confidence            99999999987888888898999999999999999999887777654

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=98.00  E-value=2.2e-05  Score=71.53  Aligned_cols=165  Identities=19%  Similarity=0.124  Sum_probs=96.2

Q ss_pred             chHHHHHHHHHHc--------c-CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhccc
Q psy7952          51 CELQKKAIRHILL--------R-THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLR  121 (444)
Q Consensus        51 t~~Q~~~~~~~~~--------~-~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~  121 (444)
                      +..|.+++-.+.+        + ...+++--.||.||-..        .+ .++.+....++  +|.||++.+..|.   
T Consensus        39 S~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~--------iA-giI~~n~l~Gr--~r~vwvS~s~dL~---  104 (303)
T PF13872_consen   39 SALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQ--------IA-GIILENWLRGR--KRAVWVSVSNDLK---  104 (303)
T ss_pred             cHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccch--------hH-HHHHHHHHcCC--CceEEEECChhhh---
Confidence            4678887765542        1 15688999999999977        22 12123233332  2569999999999   


Q ss_pred             CccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCcccccc-----HHHHHHHHHhh---CC
Q psy7952         122 FRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTES-----FHYLLQHLVRY---NK  192 (444)
Q Consensus       122 q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~-----~~~~~~~~~~~---~~  192 (444)
                        .+..+.+ ..+...+.+..+..-.....          ..-...|+++|+..|....     ....+......   ..
T Consensus       105 --~Da~RDl~DIG~~~i~v~~l~~~~~~~~----------~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~df  172 (303)
T PF13872_consen  105 --YDAERDLRDIGADNIPVHPLNKFKYGDI----------IRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDF  172 (303)
T ss_pred             --hHHHHHHHHhCCCcccceechhhccCcC----------CCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCC
Confidence              7877777 45544455554443111100          0124579999988875431     11122222221   22


Q ss_pred             ccEEEEeccccccccCC---CcHHHHHHHHHHHHhhCCCCcEEEEeccCCcch
Q psy7952         193 LAYIVVDEAHCVSEWGH---DFRPTYRRLGELRQFTGNSIPIIALTATAEPSV  242 (444)
Q Consensus       193 ~~~iViDE~H~~~~~~~---~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~  242 (444)
                      -++||+||||.......   .-...-..+..+.+.+|+ .++|.+|||--..-
T Consensus       173 dgvivfDEcH~akn~~~~~~~~sk~g~avl~LQ~~LP~-ARvvY~SATgasep  224 (303)
T PF13872_consen  173 DGVIVFDECHKAKNLSSGSKKPSKTGIAVLELQNRLPN-ARVVYASATGASEP  224 (303)
T ss_pred             CceEEeccchhcCCCCccCccccHHHHHHHHHHHhCCC-CcEEEecccccCCC
Confidence            37899999999854321   011222344556666776 88999999965543

>KOG1803|consensus

Probab=97.99  E-value=1.2e-05  Score=78.67  Aligned_cols=63  Identities=13%  Similarity=0.080  Sum_probs=46.4

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      ..-|..|+..+...+.-.++++|+|+|||.+          +..++..+...+  ++||++.||..-+     .+.++++
T Consensus       187 n~SQk~Av~~~~~~k~l~~I~GPPGTGKT~T----------lvEiI~qlvk~~--k~VLVcaPSn~AV-----dNiverl  249 (649)
T KOG1803|consen  187 NSSQKAAVSFAINNKDLLIIHGPPGTGKTRT----------LVEIISQLVKQK--KRVLVCAPSNVAV-----DNIVERL  249 (649)
T ss_pred             cHHHHHHHHHHhccCCceEeeCCCCCCceee----------HHHHHHHHHHcC--CeEEEEcCchHHH-----HHHHHHh
Confidence            4578888888888755689999999999977          222233343333  4679999999988     7888764

>KOG1513|consensus

Probab=97.96  E-value=0.00031  Score=70.79  Aligned_cols=74  Identities=23%  Similarity=0.301  Sum_probs=54.8

Q ss_pred             HHHHhcCCccEEEEcCccccccccCCccEE--------EEeCCCCCHHHHHHHhccCCCCCC---ceeEEEEecccchhh
Q psy7952         333 QESFMRGEINVITATISFGMGIDRQNVRFV--------VHWGMPSSIPAYYQESGRAGRDGL---QSYCRIYHSEHSKKS  401 (444)
Q Consensus       333 ~~~f~~g~~~vLvaT~~~~~Gidi~~~~~V--------i~~~~p~s~~~~~Qr~GR~~R~g~---~g~~~~~~~~~~~~~  401 (444)
                      -++|.+|+..|-|-+..++.||-+..-+.|        |-...|+|.+.-+|.+||+.|..+   +.|++++.+-...++
T Consensus       850 KqrFM~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQVsaPEYvFlIseLAGErR  929 (1300)
T KOG1513|consen  850 KQRFMDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQVSAPEYVFLISELAGERR  929 (1300)
T ss_pred             HhhhccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCcchhHHHHHhcccccccccCCCeEEEEehhhccchH
Confidence            346888998888888899999988754443        467799999999999999999865   466666655444444


Q ss_pred             HHHHH
Q psy7952         402 LEYVI  406 (444)
Q Consensus       402 ~~~~~  406 (444)
                      +..+.
T Consensus       930 FAS~V  934 (1300)
T KOG1513|consen  930 FASIV  934 (1300)
T ss_pred             HHHHH
Confidence            44443

>KOG1802|consensus

Probab=97.91  E-value=2.7e-05  Score=76.71  Aligned_cols=80  Identities=14%  Similarity=0.114  Sum_probs=55.9

Q ss_pred             CCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCcc
Q psy7952          45 GFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRD  124 (444)
Q Consensus        45 g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~  124 (444)
                      ++..+ +.-|..|+.++++. .--+|.+|+|+|||.+.          ..+...+... ...+||+++|+...+     +
T Consensus       407 ~lpkL-N~SQ~~AV~~VL~r-plsLIQGPPGTGKTvts----------a~IVyhl~~~-~~~~VLvcApSNiAV-----D  468 (935)
T KOG1802|consen  407 NLPKL-NASQSNAVKHVLQR-PLSLIQGPPGTGKTVTS----------ATIVYHLARQ-HAGPVLVCAPSNIAV-----D  468 (935)
T ss_pred             Cchhh-chHHHHHHHHHHcC-CceeeecCCCCCceehh----------HHHHHHHHHh-cCCceEEEcccchhH-----H
Confidence            44443 46899999999998 77899999999999772          1112222222 223559999999999     6


Q ss_pred             chHhhh-cCCCCceeEEEEeCC
Q psy7952         125 DKTSIV-TGRSDLYQLELIVSG  145 (444)
Q Consensus       125 ~~~~~l-~~~~~~i~~~~~~~~  145 (444)
                      +..+.+ ..|   +++..+...
T Consensus       469 qLaeKIh~tg---LKVvRl~ak  487 (935)
T KOG1802|consen  469 QLAEKIHKTG---LKVVRLCAK  487 (935)
T ss_pred             HHHHHHHhcC---ceEeeeehh
Confidence            666666 667   777766553

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.88  E-value=4.4e-05  Score=77.85  Aligned_cols=84  Identities=23%  Similarity=0.142  Sum_probs=57.0

Q ss_pred             CCHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc--CCcccee
Q psy7952          31 VSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN--GNVRSRN  108 (444)
Q Consensus        31 ~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~--~~~~~~v  108 (444)
                      +++..+.+.+...|+...-..++|+.|+...+.+ +-.+|.+++|+|||.+.          ..++..+..  .+...++
T Consensus       134 ~~~~~~~~~l~~lf~~~~~~~d~Qk~Av~~a~~~-~~~vItGgpGTGKTt~v----------~~ll~~l~~~~~~~~~~i  202 (615)
T PRK10875        134 VDEALLRQTLDALFGPVTDEVDWQKVAAAVALTR-RISVISGGPGTGKTTTV----------AKLLAALIQLADGERCRI  202 (615)
T ss_pred             CChHHHHHHHHHhcCcCCCCCHHHHHHHHHHhcC-CeEEEEeCCCCCHHHHH----------HHHHHHHHHhcCCCCcEE
Confidence            3456777788887766531247999999999987 88999999999999771          111111222  1223467


Q ss_pred             EEEcchhhhhcccCccchHhhh
Q psy7952         109 GWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus       109 lil~P~~~L~~~~q~~~~~~~l  130 (444)
                      +++.||...+     ....+.+
T Consensus       203 ~l~APTgkAA-----~rL~e~~  219 (615)
T PRK10875        203 RLAAPTGKAA-----ARLTESL  219 (615)
T ss_pred             EEECCcHHHH-----HHHHHHH
Confidence            8889999888     4554444

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.78  E-value=4.4e-05  Score=77.66  Aligned_cols=56  Identities=13%  Similarity=-0.005  Sum_probs=40.4

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC---ccceeEEEcchhhhh
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN---VRSRNGWISPILSSF  118 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~---~~~~vlil~P~~~L~  118 (444)
                      ++|+.|+..++.+ +-++|.+++|||||.+..          .++..+....   ...++++++||-..+
T Consensus       148 ~~Qk~A~~~al~~-~~~vitGgpGTGKTt~v~----------~ll~~l~~~~~~~~~~~I~l~APTGkAA  206 (586)
T TIGR01447       148 NWQKVAVALALKS-NFSLITGGPGTGKTTTVA----------RLLLALVKQSPKQGKLRIALAAPTGKAA  206 (586)
T ss_pred             HHHHHHHHHHhhC-CeEEEEcCCCCCHHHHHH----------HHHHHHHHhccccCCCcEEEECCcHHHH
Confidence            6999999999998 889999999999997611          1111122111   124679999998887

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.

>TIGR00376 DNA helicase, putative

Probab=97.74  E-value=5e-05  Score=78.31  Aligned_cols=63  Identities=17%  Similarity=0.097  Sum_probs=46.4

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      ++.|.+|+..++.....++|++|+|||||.++.         .. +..+...+  .+|++++||...+     .+.++++
T Consensus       159 n~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~---------~i-i~~~~~~g--~~VLv~a~sn~Av-----d~l~e~l  221 (637)
T TIGR00376       159 NESQKEAVSFALSSKDLFLIHGPPGTGKTRTLV---------EL-IRQLVKRG--LRVLVTAPSNIAV-----DNLLERL  221 (637)
T ss_pred             CHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHH---------HH-HHHHHHcC--CCEEEEcCcHHHH-----HHHHHHH
Confidence            679999999998764678999999999997621         11 11122222  2679999999988     7777777

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.

>KOG2340|consensus

Probab=97.71  E-value=0.0011  Score=64.02  Aligned_cols=108  Identities=19%  Similarity=0.189  Sum_probs=79.8

Q ss_pred             CceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCcc--ccccccCCccEEEEeCC
Q psy7952         300 NNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISF--GMGIDRQNVRFVVHWGM  367 (444)
Q Consensus       300 ~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~--~~Gidi~~~~~Vi~~~~  367 (444)
                      ...+|||.+|-=+-..+...+++.          .+++.-...-.-|-.|...+|+-|.=+  -+-.++.+++.||+|.+
T Consensus       552 ~s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLyTER~hffrR~~ikGVk~vVfYqp  631 (698)
T KOG2340|consen  552 ESGILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLYTERAHFFRRYHIKGVKNVVFYQP  631 (698)
T ss_pred             cCceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEEehhhhhhhhheecceeeEEEecC
Confidence            345799999987777777777665          444555566667889999999998754  35688999999999999


Q ss_pred             CCCHHHH---HHHhccCCCC----CCceeEEEEecccchhhHHHHHh
Q psy7952         368 PSSIPAY---YQESGRAGRD----GLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       368 p~s~~~~---~Qr~GR~~R~----g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      |..+.-|   +-+.+|+.-.    +....|.+++++-|.-.+..+..
T Consensus       632 P~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD~i~Le~ivG  678 (698)
T KOG2340|consen  632 PNNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYDRIRLENIVG  678 (698)
T ss_pred             CCCcHHHHHHHhhhhhhhccCCccccceEEEEEeechhhHHHHHhhh
Confidence            9886655   5666665432    33467888999888877777754

>PRK10536 hypothetical protein; Provisional

Probab=97.70  E-value=0.00017  Score=64.73  Aligned_cols=61  Identities=18%  Similarity=0.153  Sum_probs=41.2

Q ss_pred             CCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhh
Q psy7952          45 GFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSS  117 (444)
Q Consensus        45 g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L  117 (444)
                      ++.+ ++..|...+..+.++ ..+++.+|+|+|||+.|...        + ++.+.. +...++++.-|+...
T Consensus        56 ~i~p-~n~~Q~~~l~al~~~-~lV~i~G~aGTGKT~La~a~--------a-~~~l~~-~~~~kIiI~RP~v~~  116 (262)
T PRK10536         56 PILA-RNEAQAHYLKAIESK-QLIFATGEAGCGKTWISAAK--------A-AEALIH-KDVDRIIVTRPVLQA  116 (262)
T ss_pred             cccC-CCHHHHHHHHHHhcC-CeEEEECCCCCCHHHHHHHH--------H-HHHHhc-CCeeEEEEeCCCCCc
Confidence            4455 578999999988887 78999999999999884321        1 112323 334466666666543

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.69  E-value=5.9e-05  Score=65.99  Aligned_cols=56  Identities=20%  Similarity=0.143  Sum_probs=38.3

Q ss_pred             chHHHHHHHHHHccCC-cEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          51 CELQKKAIRHILLRTH-DIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~-~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      ++-|.+++..++.+.+ -.++.+|.|+|||.+          +..+...+...+  .++++++||...+
T Consensus         3 ~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~----------l~~~~~~~~~~g--~~v~~~apT~~Aa   59 (196)
T PF13604_consen    3 NEEQREAVRAILTSGDRVSVLQGPAGTGKTTL----------LKALAEALEAAG--KRVIGLAPTNKAA   59 (196)
T ss_dssp             -HHHHHHHHHHHHCTCSEEEEEESTTSTHHHH----------HHHHHHHHHHTT----EEEEESSHHHH
T ss_pred             CHHHHHHHHHHHhcCCeEEEEEECCCCCHHHH----------HHHHHHHHHhCC--CeEEEECCcHHHH
Confidence            4689999999986533 467889999999976          222122233332  4679999999888

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=97.64  E-value=0.00087  Score=68.42  Aligned_cols=47  Identities=23%  Similarity=0.179  Sum_probs=43.4

Q ss_pred             cCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCC
Q psy7952         338 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD  384 (444)
Q Consensus       338 ~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~  384 (444)
                      +...+.|.+-.++-+|-|-|+|=.++-.....|..+=+|.+||+.|-
T Consensus       481 d~plRFIFS~waLrEGWDNPNVFtIckL~~S~SeiSK~QeVGRGLRL  527 (985)
T COG3587         481 DEPLRFIFSKWALREGWDNPNVFTICKLRSSGSEISKLQEVGRGLRL  527 (985)
T ss_pred             CCcceeeeehhHHhhcCCCCCeeEEEEecCCCcchHHHHHhccceee
Confidence            34689999999999999999999999999999999999999999994

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=97.62  E-value=8.6e-05  Score=68.64  Aligned_cols=70  Identities=11%  Similarity=0.112  Sum_probs=52.9

Q ss_pred             HHHHHhCCcccCchHHHHHHHHHHccC-CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhh
Q psy7952          39 KLKALFGFDSFKCELQKKAIRHILLRT-HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSS  117 (444)
Q Consensus        39 ~l~~~~g~~~~~t~~Q~~~~~~~~~~~-~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L  117 (444)
                      .-++.||+.+ ++..|.-|+..+++.+ .-|.+.++.|||||+.|+.+         .+......+...++++.-|+..+
T Consensus       219 ~~~~vwGi~p-rn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaA---------gleqv~e~~~y~KiiVtRp~vpv  288 (436)
T COG1875         219 EDQEVWGIRP-RNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAA---------GLEQVLERKRYRKIIVTRPTVPV  288 (436)
T ss_pred             CchhhhccCc-ccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHH---------HHHHHHHHhhhceEEEecCCcCc
Confidence            4457789998 6678999999999864 44789999999999884432         24446666666778888888877


Q ss_pred             h
Q psy7952         118 F  118 (444)
Q Consensus       118 ~  118 (444)
                      -
T Consensus       289 G  289 (436)
T COG1875         289 G  289 (436)
T ss_pred             c
Confidence            5

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.56  E-value=0.00019  Score=75.27  Aligned_cols=67  Identities=10%  Similarity=-0.008  Sum_probs=46.0

Q ss_pred             HHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          39 KLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        39 ~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      .+...+++.  .++.|.+|+..+..+ +-+++.+++|+|||.+          +..++..+...+...++++++||-..+
T Consensus       315 ~~~~~~~~~--l~~~Q~~Ai~~~~~~-~~~iitGgpGTGKTt~----------l~~i~~~~~~~~~~~~v~l~ApTg~AA  381 (720)
T TIGR01448       315 EVEKKLRKG--LSEEQKQALDTAIQH-KVVILTGGPGTGKTTI----------TRAIIELAEELGGLLPVGLAAPTGRAA  381 (720)
T ss_pred             HHHHhcCCC--CCHHHHHHHHHHHhC-CeEEEECCCCCCHHHH----------HHHHHHHHHHcCCCceEEEEeCchHHH
Confidence            344445655  358999999999877 7899999999999976          122122233333223568888998887

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.

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.42  E-value=0.00086  Score=65.84  Aligned_cols=58  Identities=22%  Similarity=0.141  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHh--cCCccEEEEcCccccccccCCc---cEEE---EeCCCCC----HHHHHHHhccCCCC
Q psy7952         327 HERSRVQESFM--RGEINVITATISFGMGIDRQNV---RFVV---HWGMPSS----IPAYYQESGRAGRD  384 (444)
Q Consensus       327 ~~r~~~~~~f~--~g~~~vLvaT~~~~~Gidi~~~---~~Vi---~~~~p~s----~~~~~Qr~GR~~R~  384 (444)
                      ++-...++.+.  +.++++|.+.+.+.+|-|+-++   +.+.   ...-...    ...=.|-+||+.|-
T Consensus       315 ~e~~lllnsled~dnpir~if~vd~lnegwdvlnlfdmr~i~rrk~~an~kk~~~~TikekQLIGRGaRY  384 (812)
T COG3421         315 EESMLLLNSLEDRDNPIRVIFSVDKLNEGWDVLNLFDMRGIKRRKKMANDKKLAAATIKEKQLIGRGARY  384 (812)
T ss_pred             HHHHHHHhhhhhcCCCeEEEEEeecccccchhhhhhhHHHHHHHHhhhcccchhhhhhhHHHHHhcccee
Confidence            34445555553  5689999999999999886431   1111   0001112    33346889998884

>PF13245 AAA_19: Part of AAA domain

Probab=97.42  E-value=5.5e-05  Score=54.79  Aligned_cols=60  Identities=17%  Similarity=0.160  Sum_probs=35.8

Q ss_pred             HHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccc-cCCccceeEEEcchhhhhcccCccchHhhh
Q psy7952          57 AIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFIL-NGNVRSRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        57 ~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~-~~~~~~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      ++...+.+++-++|.+|+|||||.++         +..+...+. ......++++++|++..+     .+..+++
T Consensus         2 av~~al~~~~~~vv~g~pGtGKT~~~---------~~~i~~l~~~~~~~~~~vlv~a~t~~aa-----~~l~~rl   62 (76)
T PF13245_consen    2 AVRRALAGSPLFVVQGPPGTGKTTTL---------AARIAELLAARADPGKRVLVLAPTRAAA-----DELRERL   62 (76)
T ss_pred             HHHHHHhhCCeEEEECCCCCCHHHHH---------HHHHHHHHHHhcCCCCeEEEECCCHHHH-----HHHHHHH
Confidence            45544444244566999999999661         111112121 111255789999999999     6555554

>KOG1805|consensus

Probab=97.34  E-value=0.00034  Score=72.22  Aligned_cols=127  Identities=13%  Similarity=0.028  Sum_probs=81.9

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-  130 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-  130 (444)
                      .-|++|+.+++......+|.+=+|||||.+          +..++..+...|.  +||+.+-|...+     ++....+ 
T Consensus       672 ~dQr~A~~k~L~aedy~LI~GMPGTGKTTt----------I~~LIkiL~~~gk--kVLLtsyThsAV-----DNILiKL~  734 (1100)
T KOG1805|consen  672 NDQRQALLKALAAEDYALILGMPGTGKTTT----------ISLLIKILVALGK--KVLLTSYTHSAV-----DNILIKLK  734 (1100)
T ss_pred             HHHHHHHHHHHhccchheeecCCCCCchhh----------HHHHHHHHHHcCC--eEEEEehhhHHH-----HHHHHHHh
Confidence            589999999998856689999999999977          1111222333333  457777777777     7888777 


Q ss_pred             cCCCCceeEEEEeCCCChhhH-----------HHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEe
Q psy7952         131 TGRSDLYQLELIVSGQTKTEN-----------KAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVD  199 (444)
Q Consensus       131 ~~~~~~i~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViD  199 (444)
                      ..+   +....+..+......           ...+.+++...+...|+.+|-=-+..+        ....+.|||.|||
T Consensus       735 ~~~---i~~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~p--------lf~~R~FD~cIiD  803 (1100)
T KOG1805|consen  735 GFG---IYILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINHP--------LFVNRQFDYCIID  803 (1100)
T ss_pred             ccC---cceeecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCch--------hhhccccCEEEEc
Confidence            556   444433333222111           233445556678889999995444321        1223469999999


Q ss_pred             ccccccc
Q psy7952         200 EAHCVSE  206 (444)
Q Consensus       200 E~H~~~~  206 (444)
                      ||-.+..
T Consensus       804 EASQI~l  810 (1100)
T KOG1805|consen  804 EASQILL  810 (1100)
T ss_pred             ccccccc
Confidence            9998754

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=97.31  E-value=0.0021  Score=52.80  Aligned_cols=68  Identities=21%  Similarity=0.268  Sum_probs=47.9

Q ss_pred             HHHHHHHHhcCC-ccEEEEcCccccccccCC--ccEEEEeCCCCC-------------------------------HHHH
Q psy7952         329 RSRVQESFMRGE-INVITATISFGMGIDRQN--VRFVVHWGMPSS-------------------------------IPAY  374 (444)
Q Consensus       329 r~~~~~~f~~g~-~~vLvaT~~~~~Gidi~~--~~~Vi~~~~p~s-------------------------------~~~~  374 (444)
                      ...+++.|+... ..||+++..+++|+|+|+  ++.||..+.|..                               ...+
T Consensus        36 ~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l  115 (141)
T smart00492       36 TGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPFPYPDSPILKARLELLRDKGQIRPFDFVSLPDAMRTL  115 (141)
T ss_pred             HHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhCCCCchhHHHHHHHHHHH
Confidence            455667776543 379999988999999996  567998887741                               2334


Q ss_pred             HHHhccCCCCCCceeEEEEecc
Q psy7952         375 YQESGRAGRDGLQSYCRIYHSE  396 (444)
Q Consensus       375 ~Qr~GR~~R~g~~g~~~~~~~~  396 (444)
                      .|.+||+-|..++--+++++++
T Consensus       116 ~Qa~GR~iR~~~D~g~i~l~D~  137 (141)
T smart00492      116 AQCVGRLIRGANDYGVVVIADK  137 (141)
T ss_pred             HHHhCccccCcCceEEEEEEec
Confidence            7999999998654334555543

>PRK08181 transposase; Validated

Probab=97.31  E-value=0.00087  Score=61.37  Aligned_cols=30  Identities=20%  Similarity=0.142  Sum_probs=21.0

Q ss_pred             hHHHHHHH---HHHccCCcEEEEccCCCccccc
Q psy7952          52 ELQKKAIR---HILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~---~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      +.|..++.   .+....+++++.||+|+|||..
T Consensus        90 ~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHL  122 (269)
T PRK08181         90 KAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHL  122 (269)
T ss_pred             HHHHHHHHHHHHHHhcCceEEEEecCCCcHHHH
Confidence            45555553   2333338899999999999966

>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=97.25  E-value=0.00092  Score=58.35  Aligned_cols=57  Identities=12%  Similarity=0.080  Sum_probs=37.7

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHh
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVL  250 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l  250 (444)
                      ..+.++|+||-+.+...    -...+..+..+.....+...++.+|||......+.+..+.
T Consensus        81 ~~~~D~vlIDT~Gr~~~----d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~~~~~  137 (196)
T PF00448_consen   81 KKGYDLVLIDTAGRSPR----DEELLEELKKLLEALNPDEVHLVLSATMGQEDLEQALAFY  137 (196)
T ss_dssp             HTTSSEEEEEE-SSSST----HHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHHHHHHHH
T ss_pred             hcCCCEEEEecCCcchh----hHHHHHHHHHHhhhcCCccceEEEecccChHHHHHHHHHh
Confidence            34689999999877432    2344566666666665556688999999877666555443

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 ....

>PRK06526 transposase; Provisional

Probab=97.15  E-value=0.00052  Score=62.47  Aligned_cols=17  Identities=12%  Similarity=0.088  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCCccccc
Q psy7952          65 THDIFVSMPTGAVSLVG   81 (444)
Q Consensus        65 ~~~~ii~apTGsGKT~~   81 (444)
                      .+++++.||+|+|||..
T Consensus        98 ~~nlll~Gp~GtGKThL  114 (254)
T PRK06526         98 KENVVFLGPPGTGKTHL  114 (254)
T ss_pred             CceEEEEeCCCCchHHH
Confidence            38999999999999976

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.12  E-value=0.0034  Score=60.51  Aligned_cols=57  Identities=16%  Similarity=0.141  Sum_probs=36.4

Q ss_pred             hhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCC-CcEEEEeccCCcchHHHHHHH
Q psy7952         189 RYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNS-IPIIALTATAEPSVKQDIISV  249 (444)
Q Consensus       189 ~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~-~~~v~lSAT~~~~~~~~~~~~  249 (444)
                      ...+.++|+||++.+...    -...+..+..++...... -.++.+|||........+...
T Consensus       251 ~~~~~DlVLIDTaGr~~~----~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~~~~~~~~  308 (388)
T PRK12723        251 QSKDFDLVLVDTIGKSPK----DFMKLAEMKELLNACGRDAEFHLAVSSTTKTSDVKEIFHQ  308 (388)
T ss_pred             HhCCCCEEEEcCCCCCcc----CHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHHHHHHHHH
Confidence            346789999999998642    112245666666554432 467899999876555544333

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=96.95  E-value=0.00039  Score=66.94  Aligned_cols=43  Identities=12%  Similarity=-0.006  Sum_probs=28.5

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      +-++|.+.+|||||++|+-         . +..+.......+++++++...|.
T Consensus         2 ~v~~I~G~aGTGKTvla~~---------l-~~~l~~~~~~~~~~~l~~n~~l~   44 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALN---------L-AKELQNSEEGKKVLYLCGNHPLR   44 (352)
T ss_pred             eEEEEEecCCcCHHHHHHH---------H-HHHhhccccCCceEEEEecchHH
Confidence            3579999999999988331         1 11121122334559999999998

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=96.95  E-value=0.0028  Score=52.10  Aligned_cols=67  Identities=22%  Similarity=0.208  Sum_probs=45.3

Q ss_pred             HHHHHHHhcCC---ccEEEEcCc--cccccccCC--ccEEEEeCCCCC-------------------------------H
Q psy7952         330 SRVQESFMRGE---INVITATIS--FGMGIDRQN--VRFVVHWGMPSS-------------------------------I  371 (444)
Q Consensus       330 ~~~~~~f~~g~---~~vLvaT~~--~~~Gidi~~--~~~Vi~~~~p~s-------------------------------~  371 (444)
                      ..+++.|++..   ..||+++.-  +++|||+|+  ++.||..+.|..                               .
T Consensus        34 ~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~a~  113 (142)
T smart00491       34 EELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPFPNPDSPILRARLEYLDEKGGIRPFDEVYLFDAM  113 (142)
T ss_pred             HHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHH
Confidence            34555565432   257877766  999999996  678998887741                               2


Q ss_pred             HHHHHHhccCCCCCCceeEEEEecc
Q psy7952         372 PAYYQESGRAGRDGLQSYCRIYHSE  396 (444)
Q Consensus       372 ~~~~Qr~GR~~R~g~~g~~~~~~~~  396 (444)
                      ....|.+||+-|..++--+++++++
T Consensus       114 ~~~~Qa~GR~iR~~~D~g~i~l~D~  138 (142)
T smart00491      114 RALAQAIGRAIRHKNDYGVVVLLDK  138 (142)
T ss_pred             HHHHHHhCccccCccceEEEEEEec
Confidence            3347999999998654334555553

>KOG1132|consensus

Probab=96.84  E-value=0.0014  Score=67.29  Aligned_cols=45  Identities=18%  Similarity=0.248  Sum_probs=33.3

Q ss_pred             HHHhCCcccCchHHHHHHHHHHcc---CCcEEEEccCCCccccccccccc
Q psy7952          41 KALFGFDSFKCELQKKAIRHILLR---THDIFVSMPTGAVSLVGSVVSAR   87 (444)
Q Consensus        41 ~~~~g~~~~~t~~Q~~~~~~~~~~---~~~~ii~apTGsGKT~~a~~~~~   87 (444)
                      .-.|.|.++|  .|...+..+++.   .++.++..|||+|||+.-++..+
T Consensus        15 ~V~fP~qpY~--~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~L   62 (945)
T KOG1132|consen   15 PVEFPFQPYP--TQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTL   62 (945)
T ss_pred             eeeccCCcch--HHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHH
Confidence            3347777644  799888877752   37899999999999988555444

>KOG1133|consensus

Probab=96.83  E-value=0.025  Score=56.83  Aligned_cols=114  Identities=18%  Similarity=0.151  Sum_probs=74.3

Q ss_pred             hhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh--------------cCHHHHHHHHHHHh----cCCc
Q psy7952         280 DSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK--------------VNKHERSRVQESFM----RGEI  341 (444)
Q Consensus       280 ~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~--------------~~~~~r~~~~~~f~----~g~~  341 (444)
                      .....+...+..+....   .+.+++|++|.+-..++...+...              -+...-..+++.|.    .|..
T Consensus       612 ~~l~~l~~~~~nL~~~V---PgGvV~FfPSy~yL~~v~k~w~~~gil~ri~~kK~vF~E~k~~~~dvl~~Ya~a~~~g~G  688 (821)
T KOG1133|consen  612 EMIKDLGSSISNLSNAV---PGGVVCFFPSYAYLGQVRKRWEQNGILARIVGKKKVFYEPKDTVEDVLEGYAEAAERGRG  688 (821)
T ss_pred             HHHHHHHHHHHHHHhhC---CCcEEEEeccHHHHHHHHHHHHhcchHHHhhccchhhccCcccHHHHHHHHHHHhhcCCC
Confidence            33445555555554443   588999999999888888777644              01111245555554    4554


Q ss_pred             cEEEEc--CccccccccCC--ccEEEEeCCCCC--------------------------------HHHHHHHhccCCCCC
Q psy7952         342 NVITAT--ISFGMGIDRQN--VRFVVHWGMPSS--------------------------------IPAYYQESGRAGRDG  385 (444)
Q Consensus       342 ~vLvaT--~~~~~Gidi~~--~~~Vi~~~~p~s--------------------------------~~~~~Qr~GR~~R~g  385 (444)
                      .+|+|.  .-+++|||+.+  ++.|+..|+|..                                ....-|-+|||-|..
T Consensus       689 aiLlaVVGGKlSEGINF~D~LgRaVvvVGlPyPN~~s~EL~er~k~l~~k~~~~gagke~yEnlCMkAVNQsIGRAIRH~  768 (821)
T KOG1133|consen  689 AILLAVVGGKLSEGINFSDDLGRAVVVVGLPYPNIQSVELQERMKHLDGKLPTPGAGKELYENLCMKAVNQSIGRAIRHR  768 (821)
T ss_pred             eEEEEEeccccccccccccccccEEEEeecCCCCCCCHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHhhh
Confidence            566554  67899999975  778999998862                                112248899999995


Q ss_pred             CceeEEEEecc
Q psy7952         386 LQSYCRIYHSE  396 (444)
Q Consensus       386 ~~g~~~~~~~~  396 (444)
                      ++=.++++++.
T Consensus       769 ~DYA~i~LlD~  779 (821)
T KOG1133|consen  769 KDYASIYLLDK  779 (821)
T ss_pred             ccceeEEEehh
Confidence            55555555553

>PF13871 Helicase_C_4: Helicase_C-like

Probab=96.76  E-value=0.0053  Score=55.95  Aligned_cols=57  Identities=25%  Similarity=0.281  Sum_probs=49.1

Q ss_pred             HHHHHHhcCCccEEEEcCccccccccCCc--------cEEEEeCCCCCHHHHHHHhccCCCCCCc
Q psy7952         331 RVQESFMRGEINVITATISFGMGIDRQNV--------RFVVHWGMPSSIPAYYQESGRAGRDGLQ  387 (444)
Q Consensus       331 ~~~~~f~~g~~~vLvaT~~~~~Gidi~~~--------~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~  387 (444)
                      ...+.|.+|+..|+|-++..+.|+-++.-        ++-|...+|+|+...+|..||+.|.++.
T Consensus        52 ~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~  116 (278)
T PF13871_consen   52 AEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQV  116 (278)
T ss_pred             HHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccc
Confidence            34678999999999999999999987632        3567788999999999999999999874

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=96.71  E-value=0.0027  Score=66.98  Aligned_cols=72  Identities=15%  Similarity=0.002  Sum_probs=46.7

Q ss_pred             CCHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEE
Q psy7952          31 VSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGW  110 (444)
Q Consensus        31 ~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vli  110 (444)
                      +++..+...+..  ++.  .++.|.+|+..++.+++-++|.+++|+|||.+          +..+...+...+  .++++
T Consensus       338 ~~~~~~~~~l~~--~~~--Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtl----------l~~i~~~~~~~g--~~V~~  401 (744)
T TIGR02768       338 VSPPIVDAAIDQ--HYR--LSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTM----------LKAAREAWEAAG--YRVIG  401 (744)
T ss_pred             CCHHHHHHHHhc--cCC--CCHHHHHHHHHHhcCCCEEEEEecCCCCHHHH----------HHHHHHHHHhCC--CeEEE
Confidence            344455555542  222  24799999999998646689999999999966          222122222222  35688


Q ss_pred             Ecchhhhh
Q psy7952         111 ISPILSSF  118 (444)
Q Consensus       111 l~P~~~L~  118 (444)
                      ++||-..+
T Consensus       402 ~ApTg~Aa  409 (744)
T TIGR02768       402 AALSGKAA  409 (744)
T ss_pred             EeCcHHHH
Confidence            88998776

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.

>PRK12377 putative replication protein; Provisional

Probab=96.71  E-value=0.0038  Score=56.48  Aligned_cols=40  Identities=8%  Similarity=-0.037  Sum_probs=25.8

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      .++++.+|+|+|||..|          .++...+...+..   +++++..+|.
T Consensus       102 ~~l~l~G~~GtGKThLa----------~AIa~~l~~~g~~---v~~i~~~~l~  141 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLA----------AAIGNRLLAKGRS---VIVVTVPDVM  141 (248)
T ss_pred             CeEEEECCCCCCHHHHH----------HHHHHHHHHcCCC---eEEEEHHHHH
Confidence            57999999999999662          2223334444555   5555666666

>KOG0989|consensus

Probab=96.70  E-value=0.002  Score=58.51  Aligned_cols=41  Identities=12%  Similarity=0.145  Sum_probs=30.0

Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccC
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATA  238 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~  238 (444)
                      .+..||+||||.|..      ..+..+.+....++...++++.+.-+
T Consensus       129 ~fKiiIlDEcdsmts------daq~aLrr~mE~~s~~trFiLIcnyl  169 (346)
T KOG0989|consen  129 PFKIIILDECDSMTS------DAQAALRRTMEDFSRTTRFILICNYL  169 (346)
T ss_pred             cceEEEEechhhhhH------HHHHHHHHHHhccccceEEEEEcCCh
Confidence            568999999999853      23456666666677778888877664

>PRK08727 hypothetical protein; Validated

Probab=96.68  E-value=0.0035  Score=56.51  Aligned_cols=16  Identities=19%  Similarity=0.171  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus        42 ~~l~l~G~~G~GKThL   57 (233)
T PRK08727         42 DWLYLSGPAGTGKTHL   57 (233)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4699999999999965

>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=96.67  E-value=0.0063  Score=53.63  Aligned_cols=111  Identities=14%  Similarity=0.118  Sum_probs=62.4

Q ss_pred             cCchHHHHHHHHHHcc--CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccch
Q psy7952          49 FKCELQKKAIRHILLR--THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDK  126 (444)
Q Consensus        49 ~~t~~Q~~~~~~~~~~--~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~  126 (444)
                      +| +.|.+...++.+.  ..+.+..+-+|.|||.+         .+|+ +..+...+.. -+.+++|. +|.     .+.
T Consensus        24 iR-~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsV---------I~Pm-la~~LAdg~~-LvrviVpk-~Ll-----~q~   85 (229)
T PF12340_consen   24 IR-PVQVEIAREMISPPSGKNSVMQLNMGEGKTSV---------IVPM-LALALADGSR-LVRVIVPK-ALL-----EQM   85 (229)
T ss_pred             ee-HHHHHHHHHHhCCCCCCCeEeeecccCCccch---------HHHH-HHHHHcCCCc-EEEEEcCH-HHH-----HHH
Confidence            45 7999999999873  26889999999999988         5566 3333333322 23445554 455     333


Q ss_pred             Hhhh--cCC---CCceeEEEEeCCCChhhH--HHHHHHHHhcCCCeeEEEECCCcccc
Q psy7952         127 TSIV--TGR---SDLYQLELIVSGQTKTEN--KAILEELRLVKPRIKLLYVTPERAVT  177 (444)
Q Consensus       127 ~~~l--~~~---~~~i~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~Iiv~Tpe~l~~  177 (444)
                      ...+  +++   ...+-...+.........  ..+..-+........|+++|||.+.+
T Consensus        86 ~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilS  143 (229)
T PF12340_consen   86 RQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILS  143 (229)
T ss_pred             HHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHH
Confidence            3333  111   112444445544443221  11222222223466799999998864

There are two conserved sequence motifs: LLE and NMG.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.60  E-value=0.05  Score=52.18  Aligned_cols=55  Identities=18%  Similarity=0.175  Sum_probs=33.4

Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHh
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVL  250 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l  250 (444)
                      +.++|+||-+-+...    -...+..+.++++...+...++.+|||........+.+.+
T Consensus       320 ~~DvVLIDTaGRs~k----d~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i~~~F  374 (436)
T PRK11889        320 RVDYILIDTAGKNYR----ASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIITNF  374 (436)
T ss_pred             CCCEEEEeCccccCc----CHHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHHHHHh
Confidence            589999999877432    2333455555555443334467799987765544444444

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=96.59  E-value=0.015  Score=55.41  Aligned_cols=64  Identities=19%  Similarity=0.148  Sum_probs=39.2

Q ss_pred             HHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhc
Q psy7952         184 LQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLK  251 (444)
Q Consensus       184 ~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~  251 (444)
                      ......+.+.++|.||=+-+-..    -......+..+.+...+.-..+.+|||........+...+.
T Consensus       273 ~~ai~~l~~~d~ILVDTaGrs~~----D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlkei~~~f~  336 (407)
T COG1419         273 AEAIEALRDCDVILVDTAGRSQY----DKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKEIIKQFS  336 (407)
T ss_pred             HHHHHHhhcCCEEEEeCCCCCcc----CHHHHHHHHHHHhccccceEEEEEecCcchHHHHHHHHHhc
Confidence            44445556778888888876321    12334555555555444345688999987777766666554

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=96.48  E-value=0.0058  Score=65.68  Aligned_cols=74  Identities=14%  Similarity=-0.079  Sum_probs=47.3

Q ss_pred             CCHHHHHHHHHHH--hCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCcccee
Q psy7952          31 VSEQELTAKLKAL--FGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRN  108 (444)
Q Consensus        31 ~~~~~~~~~l~~~--~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~v  108 (444)
                      +++......+...  .|+.  .++-|.+++..++.+.+-+++.++.|+|||.+          +..+...+...+  .+|
T Consensus       328 v~~~~~~~~l~~~~~~g~~--Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~----------l~~~~~~~e~~G--~~V  393 (988)
T PRK13889        328 VSDADREAALARAEARGLV--LSGEQADALAHVTDGRDLGVVVGYAGTGKSAM----------LGVAREAWEAAG--YEV  393 (988)
T ss_pred             CCHHHHHHHHHHHHhcCCC--CCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH----------HHHHHHHHHHcC--CeE
Confidence            4455555544431  2443  35799999999998745579999999999976          222122222222  346


Q ss_pred             EEEcchhhhh
Q psy7952         109 GWISPILSSF  118 (444)
Q Consensus       109 lil~P~~~L~  118 (444)
                      +.++||-..+
T Consensus       394 ~~~ApTGkAA  403 (988)
T PRK13889        394 RGAALSGIAA  403 (988)
T ss_pred             EEecCcHHHH
Confidence            8888988776

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=96.45  E-value=0.0057  Score=49.48  Aligned_cols=16  Identities=19%  Similarity=0.169  Sum_probs=12.4

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.++|.||+|+|||..
T Consensus         5 ~~~~i~G~~G~GKT~~   20 (131)
T PF13401_consen    5 RILVISGPPGSGKTTL   20 (131)
T ss_dssp             --EEEEE-TTSSHHHH
T ss_pred             cccEEEcCCCCCHHHH
Confidence            6789999999999987

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=96.40  E-value=0.0023  Score=61.86  Aligned_cols=55  Identities=16%  Similarity=0.123  Sum_probs=37.7

Q ss_pred             chHHHHHHHHH------HccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          51 CELQKKAIRHI------LLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        51 t~~Q~~~~~~~------~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      ++-|++++..+      .++ ..+++.+|-|+|||++          +.++.+.+..  ....+++++||-..|
T Consensus         3 n~eQ~~~~~~v~~~~~~~~~-~~~fv~G~~GtGKs~l----------~~~i~~~~~~--~~~~~~~~a~tg~AA   63 (364)
T PF05970_consen    3 NEEQRRVFDTVIEAIENEEG-LNFFVTGPAGTGKSFL----------IKAIIDYLRS--RGKKVLVTAPTGIAA   63 (364)
T ss_pred             CHHHHHHHHHHHHHHHccCC-cEEEEEcCCCCChhHH----------HHHHHHHhcc--ccceEEEecchHHHH
Confidence            36799998887      445 7899999999999976          3331222222  233568888888776

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=96.26  E-value=0.0014  Score=61.84  Aligned_cols=63  Identities=13%  Similarity=0.075  Sum_probs=42.3

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC-CccceeEEEcchhhhhcccCccchHhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG-NVRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~-~~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      |+-|.+++.. ..  ++++|.|+.|||||.+        ....+ +..+... ....+++++++|+..+     .+.-.+
T Consensus         2 ~~eQ~~~i~~-~~--~~~lV~a~AGSGKT~~--------l~~ri-~~ll~~~~~~~~~Il~lTft~~aa-----~e~~~r   64 (315)
T PF00580_consen    2 TDEQRRIIRS-TE--GPLLVNAGAGSGKTTT--------LLERI-AYLLYEGGVPPERILVLTFTNAAA-----QEMRER   64 (315)
T ss_dssp             -HHHHHHHHS--S--SEEEEEE-TTSSHHHH--------HHHHH-HHHHHTSSSTGGGEEEEESSHHHH-----HHHHHH
T ss_pred             CHHHHHHHhC-CC--CCEEEEeCCCCCchHH--------HHHHH-HHhhccccCChHHheecccCHHHH-----HHHHHH
Confidence            4679999988 33  6999999999999988        11111 2223333 2345889999999998     566565


Q ss_pred             h
Q psy7952         130 V  130 (444)
Q Consensus       130 l  130 (444)
                      +
T Consensus        65 i   65 (315)
T PF00580_consen   65 I   65 (315)
T ss_dssp             H
T ss_pred             H
Confidence            5

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 ....

>PRK06921 hypothetical protein; Provisional

Probab=96.22  E-value=0.013  Score=53.89  Aligned_cols=16  Identities=13%  Similarity=-0.074  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +++++.+|+|+|||..
T Consensus       118 ~~l~l~G~~G~GKThL  133 (266)
T PRK06921        118 NSIALLGQPGSGKTHL  133 (266)
T ss_pred             CeEEEECCCCCcHHHH
Confidence            6799999999999966

>KOG2028|consensus

Probab=96.20  E-value=0.0058  Score=56.81  Aligned_cols=42  Identities=14%  Similarity=0.169  Sum_probs=30.1

Q ss_pred             HHHHHHhCCcccCchHHHHHHHHHHccC--CcEEEEccCCCccccc
Q psy7952          38 AKLKALFGFDSFKCELQKKAIRHILLRT--HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        38 ~~l~~~~g~~~~~t~~Q~~~~~~~~~~~--~~~ii~apTGsGKT~~   81 (444)
                      +.|.+.+|-+.+-  -|.-.+..++..+  .++++++|+|+|||..
T Consensus       135 ktL~dyvGQ~hlv--~q~gllrs~ieq~~ipSmIlWGppG~GKTtl  178 (554)
T KOG2028|consen  135 KTLDDYVGQSHLV--GQDGLLRSLIEQNRIPSMILWGPPGTGKTTL  178 (554)
T ss_pred             chHHHhcchhhhc--CcchHHHHHHHcCCCCceEEecCCCCchHHH
Confidence            4566666666544  4666677766543  5799999999999966

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.20  E-value=0.011  Score=53.33  Aligned_cols=30  Identities=17%  Similarity=-0.035  Sum_probs=20.5

Q ss_pred             hHHHHHHHHHHc-------cCCcEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHILL-------RTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~~-------~~~~~ii~apTGsGKT~~   81 (444)
                      +.|..++..+.+       +...+++.+++|+|||..
T Consensus        79 ~~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThL  115 (244)
T PRK07952         79 EGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHL  115 (244)
T ss_pred             chHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHH
Confidence            355555554442       114799999999999966

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=96.20  E-value=0.004  Score=56.75  Aligned_cols=54  Identities=13%  Similarity=0.130  Sum_probs=36.6

Q ss_pred             hHHHHHHHHHHc------cCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          52 ELQKKAIRHILL------RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        52 ~~Q~~~~~~~~~------~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      ..+..++..+..      ...++++.||+|+|||..|          .++...+...|..   +.++++.+++
T Consensus        86 ~~~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa----------~Ai~~~l~~~g~s---v~f~~~~el~  145 (254)
T COG1484          86 GIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLA----------IAIGNELLKAGIS---VLFITAPDLL  145 (254)
T ss_pred             chhHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHH----------HHHHHHHHHcCCe---EEEEEHHHHH
Confidence            455555554432      2279999999999999762          2223334466777   8888888888

>PRK05642 DNA replication initiation factor; Validated

Probab=96.19  E-value=0.0083  Score=54.09  Aligned_cols=16  Identities=13%  Similarity=-0.122  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      ..++++||+|+|||..
T Consensus        46 ~~l~l~G~~G~GKTHL   61 (234)
T PRK05642         46 SLIYLWGKDGVGRSHL   61 (234)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4689999999999965

>PRK14974 cell division protein FtsY; Provisional

Probab=96.11  E-value=0.055  Score=51.25  Aligned_cols=54  Identities=13%  Similarity=0.097  Sum_probs=35.0

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHH
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIIS  248 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~  248 (444)
                      ...++|+||.++++..    -...+..+.++......+..++.++||......+.+..
T Consensus       221 ~~~DvVLIDTaGr~~~----~~~lm~eL~~i~~~~~pd~~iLVl~a~~g~d~~~~a~~  274 (336)
T PRK14974        221 RGIDVVLIDTAGRMHT----DANLMDELKKIVRVTKPDLVIFVGDALAGNDAVEQARE  274 (336)
T ss_pred             CCCCEEEEECCCccCC----cHHHHHHHHHHHHhhCCceEEEeeccccchhHHHHHHH
Confidence            4578999999998642    23344555555555555566888999876655544433

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=96.11  E-value=0.0017  Score=55.76  Aligned_cols=41  Identities=10%  Similarity=0.001  Sum_probs=25.6

Q ss_pred             CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          65 THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        65 ~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      .+++++.+|+|+|||..|.          ++...+...+..   +..++...|+
T Consensus        47 ~~~l~l~G~~G~GKThLa~----------ai~~~~~~~g~~---v~f~~~~~L~   87 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAV----------AIANEAIRKGYS---VLFITASDLL   87 (178)
T ss_dssp             --EEEEEESTTSSHHHHHH----------HHHHHHHHTT-----EEEEEHHHHH
T ss_pred             CeEEEEEhhHhHHHHHHHH----------HHHHHhccCCcc---eeEeecCcee
Confidence            3889999999999997732          112234445555   6666777777

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.08  E-value=0.018  Score=54.47  Aligned_cols=40  Identities=13%  Similarity=-0.083  Sum_probs=26.1

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      +++++.||||+|||..|          .++...+...+..   ++..+...|.
T Consensus       184 ~~Lll~G~~GtGKThLa----------~aIa~~l~~~g~~---V~y~t~~~l~  223 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLS----------NCIAKELLDRGKS---VIYRTADELI  223 (329)
T ss_pred             CcEEEECCCCCcHHHHH----------HHHHHHHHHCCCe---EEEEEHHHHH
Confidence            78999999999999662          2223334444544   5555656665

>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=96.06  E-value=0.016  Score=51.61  Aligned_cols=49  Identities=10%  Similarity=0.105  Sum_probs=28.4

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhh-CCCCcEEEEeccCCcch
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFT-GNSIPIIALTATAEPSV  242 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~v~lSAT~~~~~  242 (444)
                      +...+++++|++|.+.+..    .....+.++++.+ ..+.++|+.|..+|...
T Consensus        95 ~~~~DlL~iDDi~~l~~~~----~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l  144 (219)
T PF00308_consen   95 LRSADLLIIDDIQFLAGKQ----RTQEELFHLFNRLIESGKQLILTSDRPPSEL  144 (219)
T ss_dssp             HCTSSEEEEETGGGGTTHH----HHHHHHHHHHHHHHHTTSEEEEEESS-TTTT
T ss_pred             hhcCCEEEEecchhhcCch----HHHHHHHHHHHHHHhhCCeEEEEeCCCCccc
Confidence            4578999999999975421    1123333444333 23366777776666543

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.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.05  E-value=0.18  Score=49.67  Aligned_cols=58  Identities=17%  Similarity=0.090  Sum_probs=34.3

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHH-hhCCCCcEEEEeccCCcchHHHHHHHhc
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQ-FTGNSIPIIALTATAEPSVKQDIISVLK  251 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~-~~~~~~~~v~lSAT~~~~~~~~~~~~l~  251 (444)
                      ..+.++|+||.+-+...    -......+..+.. ........+.+|||........+...+.
T Consensus       297 ~~~~DlVlIDt~G~~~~----d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~~~~~~f~  355 (424)
T PRK05703        297 LRDCDVILIDTAGRSQR----DKRLIEELKALIEFSGEPIDVYLVLSATTKYEDLKDIYKHFS  355 (424)
T ss_pred             hCCCCEEEEeCCCCCCC----CHHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHHHHHHHhC
Confidence            44689999999876322    1222344444444 1122244788999988766666555543

>KOG1131|consensus

Probab=96.05  E-value=0.025  Score=54.95  Aligned_cols=96  Identities=17%  Similarity=0.126  Sum_probs=56.9

Q ss_pred             CceEEEEecccchHHHHHHHHHhh----------------cCHHHHHHHHHHHh----cCCccE--EEEcCccccccccC
Q psy7952         300 NNCGIIYCRTREHTTDLADALRRK----------------VNKHERSRVQESFM----RGEINV--ITATISFGMGIDRQ  357 (444)
Q Consensus       300 ~~~~iVf~~s~~~~~~l~~~L~~~----------------~~~~~r~~~~~~f~----~g~~~v--LvaT~~~~~Gidi~  357 (444)
                      .+.++.|+.+.-..+.++......                -+..+-...++.++    .|...|  =|+-.-.++|+|+.
T Consensus       530 pdG~v~ff~sylYmesiv~~w~~~gil~ei~k~KL~fIetpD~~ETs~al~ny~~aC~~gRGavl~sVargkVsEgidF~  609 (755)
T KOG1131|consen  530 PDGIVCFFPSYLYMESIVSRWYEQGILDEIMKYKLLFIETPDFRETSLALANYRYACDNGRGAVLLSVARGKVSEGIDFD  609 (755)
T ss_pred             CCceEEEEehHHHHHHHHHHHHHHhHHHHHhhCceEEEeCCchhhhHHHHHHHHHHhcCCCCceEEEEecCccccCcccc
Confidence            344566777665555554443332                12222234444443    344444  46678889999997


Q ss_pred             Ccc--EEEEeCCCCC---------------------------HH---HHHHHhccCCCCCCceeEEEEecc
Q psy7952         358 NVR--FVVHWGMPSS---------------------------IP---AYYQESGRAGRDGLQSYCRIYHSE  396 (444)
Q Consensus       358 ~~~--~Vi~~~~p~s---------------------------~~---~~~Qr~GR~~R~g~~g~~~~~~~~  396 (444)
                      +-.  .||+++.|.-                           .+   .-.|-.||+.|. +..|...++.+
T Consensus       610 hhyGR~ViM~gIP~qytesriLkarle~Lrd~~~irE~dflTFDAmRhaAQC~GrvLr~-K~dYg~mI~aD  679 (755)
T KOG1131|consen  610 HHYGREVIMEGIPYQYTESRILKARLEYLRDQFQIRENDFLTFDAMRHAAQCLGRVLRG-KTDYGLMIFAD  679 (755)
T ss_pred             cccCceEEEEeccchhhHHHHHHHHHHHHHHHhcccccceechHhHHHHHHHHHHHHhc-cccceeeEeee
Confidence            644  8999999861                           11   124778999886 66666666643

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.04  E-value=0.036  Score=49.98  Aligned_cols=16  Identities=19%  Similarity=-0.039  Sum_probs=14.5

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      ..++++||+|+|||..
T Consensus        46 ~~l~l~Gp~G~GKThL   61 (235)
T PRK08084         46 GYIYLWSREGAGRSHL   61 (235)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            5799999999999966

>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=96.03  E-value=0.015  Score=47.59  Aligned_cols=16  Identities=13%  Similarity=0.210  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus        20 ~~v~i~G~~G~GKT~l   35 (151)
T cd00009          20 KNLLLYGPPGTGKTTL   35 (151)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            7899999999999976

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.

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.03  E-value=0.014  Score=59.37  Aligned_cols=41  Identities=12%  Similarity=0.254  Sum_probs=27.0

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEecc
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTAT  237 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT  237 (444)
                      .+.+++||||+|.|....      .+.+.+.+..-+.++.+|+.|.-
T Consensus       123 gr~KViIIDEah~Ls~~A------aNALLKTLEEPP~~v~FILaTte  163 (700)
T PRK12323        123 GRFKVYMIDEVHMLTNHA------FNAMLKTLEEPPEHVKFILATTD  163 (700)
T ss_pred             CCceEEEEEChHhcCHHH------HHHHHHhhccCCCCceEEEEeCC
Confidence            467899999999986422      34455555555555666666643

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=96.02  E-value=0.015  Score=55.05  Aligned_cols=31  Identities=16%  Similarity=0.154  Sum_probs=25.9

Q ss_pred             hHHHHHHHHHHccC---CcEEEEccCCCcccccc
Q psy7952          52 ELQKKAIRHILLRT---HDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~---~~~ii~apTGsGKT~~a   82 (444)
                      |||...++.+.+.+   +-.++++|.|.|||..|
T Consensus         6 PWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A   39 (328)
T PRK05707          6 PWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALA   39 (328)
T ss_pred             CCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHH
Confidence            59999999998753   34889999999999774

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.99  E-value=0.099  Score=50.19  Aligned_cols=55  Identities=11%  Similarity=0.153  Sum_probs=30.3

Q ss_pred             hhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHH
Q psy7952         189 RYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDII  247 (444)
Q Consensus       189 ~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~  247 (444)
                      .+.+.++|+||.+-.....    ......+..+.........++.+|||........+.
T Consensus       212 ~l~~~DlVLIDTaG~~~~d----~~l~e~La~L~~~~~~~~~lLVLsAts~~~~l~evi  266 (374)
T PRK14722        212 ELRNKHMVLIDTIGMSQRD----RTVSDQIAMLHGADTPVQRLLLLNATSHGDTLNEVV  266 (374)
T ss_pred             HhcCCCEEEEcCCCCCccc----HHHHHHHHHHhccCCCCeEEEEecCccChHHHHHHH
Confidence            4556799999999763210    112222322222222224588999998776655443

>PRK04296 thymidine kinase; Provisional

Probab=95.98  E-value=0.0064  Score=52.91  Aligned_cols=15  Identities=7%  Similarity=-0.150  Sum_probs=12.9

Q ss_pred             cEEEEccCCCccccc
Q psy7952          67 DIFVSMPTGAVSLVG   81 (444)
Q Consensus        67 ~~ii~apTGsGKT~~   81 (444)
                      -.++.+|+|+|||..
T Consensus         4 i~litG~~GsGKTT~   18 (190)
T PRK04296          4 LEFIYGAMNSGKSTE   18 (190)
T ss_pred             EEEEECCCCCHHHHH
Confidence            468899999999976

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=95.98  E-value=0.016  Score=57.78  Aligned_cols=16  Identities=13%  Similarity=0.021  Sum_probs=14.2

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.||+|+|||..
T Consensus       149 ~~l~l~G~~G~GKThL  164 (450)
T PRK00149        149 NPLFIYGGVGLGKTHL  164 (450)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4689999999999966

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=95.91  E-value=0.014  Score=57.72  Aligned_cols=16  Identities=19%  Similarity=0.198  Sum_probs=14.2

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +++++.||+|+|||..
T Consensus       142 npl~L~G~~G~GKTHL  157 (445)
T PRK12422        142 NPIYLFGPEGSGKTHL  157 (445)
T ss_pred             ceEEEEcCCCCCHHHH
Confidence            4689999999999966

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=95.89  E-value=0.015  Score=57.72  Aligned_cols=16  Identities=13%  Similarity=0.085  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.|++|+|||..
T Consensus       142 npl~i~G~~G~GKTHL  157 (450)
T PRK14087        142 NPLFIYGESGMGKTHL  157 (450)
T ss_pred             CceEEECCCCCcHHHH
Confidence            4689999999999966

>KOG0739|consensus

Probab=95.86  E-value=0.029  Score=50.91  Aligned_cols=57  Identities=26%  Similarity=0.254  Sum_probs=31.8

Q ss_pred             hhCCccEEEEeccccccccCC-CcHHHHHHHH-HHH-H--hh-CCCCcEEEEeccCCcchHHH
Q psy7952         189 RYNKLAYIVVDEAHCVSEWGH-DFRPTYRRLG-ELR-Q--FT-GNSIPIIALTATAEPSVKQD  245 (444)
Q Consensus       189 ~~~~~~~iViDE~H~~~~~~~-~~~~~~~~l~-~~~-~--~~-~~~~~~v~lSAT~~~~~~~~  245 (444)
                      .-...+.|+|||++.+..... .-.....+|+ .++ +  .. .++--++.+.||-.+...+.
T Consensus       222 Re~kPSIIFiDEiDslcg~r~enEseasRRIKTEfLVQMqGVG~d~~gvLVLgATNiPw~LDs  284 (439)
T KOG0739|consen  222 RENKPSIIFIDEIDSLCGSRSENESEASRRIKTEFLVQMQGVGNDNDGVLVLGATNIPWVLDS  284 (439)
T ss_pred             HhcCCcEEEeehhhhhccCCCCCchHHHHHHHHHHHHhhhccccCCCceEEEecCCCchhHHH
Confidence            345789999999998854221 1122223332 111 1  12 23355889999976655443

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=95.84  E-value=0.02  Score=56.76  Aligned_cols=16  Identities=13%  Similarity=0.021  Sum_probs=14.3

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +++++.||+|+|||..
T Consensus       131 n~l~lyG~~G~GKTHL  146 (440)
T PRK14088        131 NPLFIYGGVGLGKTHL  146 (440)
T ss_pred             CeEEEEcCCCCcHHHH
Confidence            4699999999999966

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=95.83  E-value=0.034  Score=57.58  Aligned_cols=39  Identities=13%  Similarity=0.241  Sum_probs=25.4

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      .+.+++||||+|.|....      .+.+.+.+...+.+..+|+.|
T Consensus       118 gr~KVIIIDEah~LT~~A------~NALLKtLEEPP~~v~FILaT  156 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHA------FNAMLKTLEEPPPHVKFILAT  156 (830)
T ss_pred             CCceEEEEeChhhCCHHH------HHHHHHHHHhcCCCeEEEEEE
Confidence            357899999999986422      344555555555556666555

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=95.82  E-value=0.031  Score=51.44  Aligned_cols=49  Identities=24%  Similarity=0.278  Sum_probs=27.5

Q ss_pred             HHHhhCCccEEEEeccccccccCC-CcHHHHHHHHHHHHhhCCCCcEEEEecc
Q psy7952         186 HLVRYNKLAYIVVDEAHCVSEWGH-DFRPTYRRLGELRQFTGNSIPIIALTAT  237 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~v~lSAT  237 (444)
                      +....-..+++||||+|.++.... ..+..+..|+.+-+.+  ..++|++ +|
T Consensus       139 ~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL--~ipiV~v-Gt  188 (302)
T PF05621_consen  139 RLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNEL--QIPIVGV-GT  188 (302)
T ss_pred             HHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhcc--CCCeEEe-cc
Confidence            344455789999999999865331 2233333333332222  2567765 55

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>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=95.82  E-value=0.012  Score=51.03  Aligned_cols=18  Identities=17%  Similarity=0.071  Sum_probs=14.3

Q ss_pred             hhCCccEEEEeccccccc
Q psy7952         189 RYNKLAYIVVDEAHCVSE  206 (444)
Q Consensus       189 ~~~~~~~iViDE~H~~~~  206 (444)
                      ...+.+++|+||...+.+
T Consensus        92 ~~~~~~~lviD~~~~~~~  109 (187)
T cd01124          92 EEFKAKRVVIDSVSGLLL  109 (187)
T ss_pred             HHhCCCEEEEeCcHHHhh
Confidence            345789999999998754

A related protein is found in archaea.

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=95.75  E-value=0.083  Score=48.67  Aligned_cols=33  Identities=18%  Similarity=0.147  Sum_probs=23.1

Q ss_pred             cCchHHHHHHHHHH----ccCCcEEEEccCCCccccc
Q psy7952          49 FKCELQKKAIRHIL----LRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        49 ~~t~~Q~~~~~~~~----~~~~~~ii~apTGsGKT~~   81 (444)
                      |+++.+.+++..+.    .+...+++.||+|+|||..
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl   59 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTL   59 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHH
Confidence            34556666666553    2324689999999999977

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>PRK08116 hypothetical protein; Validated

Probab=95.72  E-value=0.023  Score=52.35  Aligned_cols=16  Identities=6%  Similarity=-0.091  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      ..+++.|++|+|||..
T Consensus       115 ~gl~l~G~~GtGKThL  130 (268)
T PRK08116        115 VGLLLWGSVGTGKTYL  130 (268)
T ss_pred             ceEEEECCCCCCHHHH
Confidence            3499999999999976

>PRK06893 DNA replication initiation factor; Validated

Probab=95.72  E-value=0.015  Score=52.30  Aligned_cols=49  Identities=10%  Similarity=0.171  Sum_probs=27.5

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhh-CCCCcEEEEeccCCcchH
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFT-GNSIPIIALTATAEPSVK  243 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~v~lSAT~~~~~~  243 (444)
                      .+.+++++||+|.+..... ..   ..+..+++.. ..+.+++++|++..+...
T Consensus        90 ~~~dlLilDDi~~~~~~~~-~~---~~l~~l~n~~~~~~~~illits~~~p~~l  139 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNEE-WE---LAIFDLFNRIKEQGKTLLLISADCSPHAL  139 (229)
T ss_pred             ccCCEEEEeChhhhcCChH-HH---HHHHHHHHHHHHcCCcEEEEeCCCChHHc
Confidence            3678999999998753211 11   1233333322 223557778887655443

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=95.72  E-value=0.037  Score=50.84  Aligned_cols=17  Identities=6%  Similarity=-0.029  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCcccccc
Q psy7952          66 HDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a   82 (444)
                      .++++.+|+|+|||.+|
T Consensus        43 ~~vll~GppGtGKTtlA   59 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVA   59 (261)
T ss_pred             ceEEEEcCCCCCHHHHH
Confidence            57899999999999873

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.

>PRK09183 transposase/IS protein; Provisional

Probab=95.71  E-value=0.041  Score=50.41  Aligned_cols=19  Identities=16%  Similarity=0.057  Sum_probs=16.2

Q ss_pred             HccCCcEEEEccCCCccccc
Q psy7952          62 LLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        62 ~~~~~~~ii~apTGsGKT~~   81 (444)
                      ..+ .++++.+|+|+|||..
T Consensus       100 ~~~-~~v~l~Gp~GtGKThL  118 (259)
T PRK09183        100 ERN-ENIVLLGPSGVGKTHL  118 (259)
T ss_pred             hcC-CeEEEEeCCCCCHHHH
Confidence            345 7899999999999966

>KOG1001|consensus

Probab=95.66  E-value=0.021  Score=58.94  Aligned_cols=69  Identities=13%  Similarity=0.061  Sum_probs=56.0

Q ss_pred             cCHHHHHHHHHHHhcCC-ccE-EEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEE
Q psy7952         324 VNKHERSRVQESFMRGE-INV-ITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRI  392 (444)
Q Consensus       324 ~~~~~r~~~~~~f~~g~-~~v-LvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~  392 (444)
                      |....|...+..|..+. .++ +++..+...|+|+-...+|+..|+-+++...-|.+-|+-|-|+...+.+
T Consensus       573 ~~~~~r~~s~~~~~~~~~~~vll~Slkag~~glnlt~a~~v~~~d~~wnp~~eeQaidR~hrigq~k~v~v  643 (674)
T KOG1001|consen  573 MLMKIRTKSFTDFPCDPLVTALLMSLKAGKVGLNLTAASHVLLMDPWWNPAVEEQAIDRAHRIGQTKPVKV  643 (674)
T ss_pred             hHHHHHHhhhcccccCccHHHHHHHHHHhhhhhchhhhhHHHhhchhcChHHHHHHHHHHHHhcccceeee
Confidence            66677888888887443 333 6778889999999999999999999999999999999999988765443

>KOG0742|consensus

Probab=95.65  E-value=0.036  Score=52.47  Aligned_cols=16  Identities=19%  Similarity=0.216  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +++++.+|+|+|||..
T Consensus       385 RNilfyGPPGTGKTm~  400 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMF  400 (630)
T ss_pred             hheeeeCCCCCCchHH
Confidence            6899999999999977

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=95.61  E-value=0.018  Score=56.60  Aligned_cols=16  Identities=13%  Similarity=0.021  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.||+|+|||..
T Consensus       137 n~l~l~G~~G~GKThL  152 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHL  152 (405)
T ss_pred             CeEEEECCCCCcHHHH
Confidence            4589999999999976

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).

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.57  E-value=0.089  Score=53.07  Aligned_cols=39  Identities=18%  Similarity=0.274  Sum_probs=26.6

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      .+.+++||||+|.+...      ....+.+.+...++++.+|+.|
T Consensus       118 ~~~kV~iIDE~~~ls~~------a~naLLk~LEepp~~~~fIlat  156 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGH------SFNALLKTLEEPPSHVKFILAT  156 (509)
T ss_pred             CCcEEEEEEChHhcCHH------HHHHHHHHHhccCCCeEEEEEE
Confidence            36789999999998642      2345556666666666676655

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.55  E-value=0.058  Score=56.96  Aligned_cols=38  Identities=13%  Similarity=0.270  Sum_probs=25.1

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEE
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIAL  234 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~l  234 (444)
                      .+..++||||+|.|..      .....+.+.+...+.+.++|+.
T Consensus       118 gk~KViIIDEAh~LT~------eAqNALLKtLEEPP~~vrFILa  155 (944)
T PRK14949        118 GRFKVYLIDEVHMLSR------SSFNALLKTLEEPPEHVKFLLA  155 (944)
T ss_pred             CCcEEEEEechHhcCH------HHHHHHHHHHhccCCCeEEEEE
Confidence            4678999999999753      2235555555555555666664

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=95.50  E-value=0.088  Score=51.59  Aligned_cols=16  Identities=13%  Similarity=0.260  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .++++.||+|+|||.+
T Consensus        56 ~~~lI~G~~GtGKT~l   71 (394)
T PRK00411         56 LNVLIYGPPGTGKTTT   71 (394)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            5799999999999977

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=95.45  E-value=0.067  Score=51.81  Aligned_cols=16  Identities=19%  Similarity=0.235  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .+++|.||+|+|||.+
T Consensus        41 ~~i~I~G~~GtGKT~l   56 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAV   56 (365)
T ss_pred             CcEEEECCCCCCHHHH
Confidence            5799999999999977

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.

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=95.43  E-value=0.061  Score=55.20  Aligned_cols=40  Identities=18%  Similarity=0.191  Sum_probs=26.8

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      +...+++||||+|.+...      ....+.+.+...+....+|+.+
T Consensus       130 ~a~~KVvIIDEad~Ls~~------a~naLLKtLEePp~~~~fIl~t  169 (598)
T PRK09111        130 SARYKVYIIDEVHMLSTA------AFNALLKTLEEPPPHVKFIFAT  169 (598)
T ss_pred             cCCcEEEEEEChHhCCHH------HHHHHHHHHHhCCCCeEEEEEe
Confidence            456789999999998542      2355555565666656666655

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=95.35  E-value=0.14  Score=59.88  Aligned_cols=56  Identities=14%  Similarity=-0.065  Sum_probs=39.8

Q ss_pred             chHHHHHHHHHHccC-CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          51 CELQKKAIRHILLRT-HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~-~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      ++-|.+++..++.+. +-.+|.++.|+|||.+          +..+...+...|  .+|+.++||-.-+
T Consensus       431 s~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~----------l~~l~~~~~~~G--~~V~~lAPTgrAA  487 (1960)
T TIGR02760       431 SPSNKDAVSTLFTSTKRFIIINGFGGTGSTEI----------AQLLLHLASEQG--YEIQIITAGSLSA  487 (1960)
T ss_pred             CHHHHHHHHHHHhCCCCeEEEEECCCCCHHHH----------HHHHHHHHHhcC--CeEEEEeCCHHHH
Confidence            578999999998753 5579999999999977          222122222222  3568899998876

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.

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=95.33  E-value=0.067  Score=50.78  Aligned_cols=26  Identities=19%  Similarity=0.246  Sum_probs=19.6

Q ss_pred             HHHHHHHccC--CcEEEEccCCCccccc
Q psy7952          56 KAIRHILLRT--HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        56 ~~~~~~~~~~--~~~ii~apTGsGKT~~   81 (444)
                      ..+..+++..  .++|+++|+|+|||..
T Consensus        37 ~~lrr~v~~~~l~SmIl~GPPG~GKTTl   64 (436)
T COG2256          37 KPLRRAVEAGHLHSMILWGPPGTGKTTL   64 (436)
T ss_pred             chHHHHHhcCCCceeEEECCCCCCHHHH
Confidence            3455555532  5799999999999977

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=95.27  E-value=0.026  Score=61.29  Aligned_cols=56  Identities=16%  Similarity=-0.062  Sum_probs=39.6

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      ++-|.+++..+..+++-+++.++.|+|||.+          +..+...+...|  .+|+.+.||-.-+
T Consensus       383 s~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~----------l~~~~~~~e~~G--~~V~g~ApTgkAA  438 (1102)
T PRK13826        383 SDEQKTAIEHVAGPARIAAVVGRAGAGKTTM----------MKAAREAWEAAG--YRVVGGALAGKAA  438 (1102)
T ss_pred             CHHHHHHHHHHhccCCeEEEEeCCCCCHHHH----------HHHHHHHHHHcC--CeEEEEcCcHHHH
Confidence            5789999999876546789999999999977          222122222223  3458888988777

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.24  E-value=0.083  Score=54.07  Aligned_cols=39  Identities=15%  Similarity=0.251  Sum_probs=25.2

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      .+.+++||||+|++....      ...+.+.+...++...+|+.|
T Consensus       117 gk~KV~IIDEVh~LS~~A------~NALLKtLEEPP~~v~FILaT  155 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTHS------FNALLKTLEEPPEHVKFLFAT  155 (702)
T ss_pred             CCcEEEEEechHhcCHHH------HHHHHHHHhcCCCCcEEEEEE
Confidence            457899999999976422      344555555555556566544

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.23  E-value=0.099  Score=52.12  Aligned_cols=39  Identities=21%  Similarity=0.282  Sum_probs=24.7

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      .+.+++||||+|.+...      ....+.+.+..-++...+|+.|
T Consensus       115 ~~~KVvIIDEah~Ls~~------A~NaLLK~LEePp~~v~fIlat  153 (491)
T PRK14964        115 SKFKVYIIDEVHMLSNS------AFNALLKTLEEPAPHVKFILAT  153 (491)
T ss_pred             CCceEEEEeChHhCCHH------HHHHHHHHHhCCCCCeEEEEEe
Confidence            46789999999997542      2344555555555545555544

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=95.21  E-value=0.032  Score=56.67  Aligned_cols=16  Identities=13%  Similarity=0.075  Sum_probs=13.9

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.++|.+++|+|||..
T Consensus       315 NpL~LyG~sGsGKTHL  330 (617)
T PRK14086        315 NPLFIYGESGLGKTHL  330 (617)
T ss_pred             CcEEEECCCCCCHHHH
Confidence            4589999999999966

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.20  E-value=0.049  Score=49.33  Aligned_cols=18  Identities=6%  Similarity=-0.165  Sum_probs=15.3

Q ss_pred             ccCCcEEEEccCCCccccc
Q psy7952          63 LRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        63 ~~~~~~ii~apTGsGKT~~   81 (444)
                      .| +-++|.|+||+|||..
T Consensus        12 ~G-~l~lI~G~~G~GKT~~   29 (242)
T cd00984          12 PG-DLIIIAARPSMGKTAF   29 (242)
T ss_pred             CC-eEEEEEeCCCCCHHHH
Confidence            44 6789999999999976

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.

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=95.19  E-value=0.12  Score=55.05  Aligned_cols=39  Identities=23%  Similarity=0.372  Sum_probs=27.5

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      .+.+++||||+|.|...+      .+.|.+++...+.+..+|+.|
T Consensus       119 ~~~KV~IIDEad~lt~~a------~NaLLK~LEEpP~~~~fIl~t  157 (824)
T PRK07764        119 SRYKIFIIDEAHMVTPQG------FNALLKIVEEPPEHLKFIFAT  157 (824)
T ss_pred             CCceEEEEechhhcCHHH------HHHHHHHHhCCCCCeEEEEEe
Confidence            467899999999986532      355666666666666666665

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=95.19  E-value=0.042  Score=49.18  Aligned_cols=16  Identities=6%  Similarity=-0.081  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .++++.||+|+|||..
T Consensus        39 ~~lll~G~~G~GKT~l   54 (226)
T TIGR03420        39 RFLYLWGESGSGKSHL   54 (226)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            6899999999999977

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.

>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=95.18  E-value=0.031  Score=47.18  Aligned_cols=43  Identities=21%  Similarity=0.183  Sum_probs=29.7

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCC
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAE  239 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~  239 (444)
                      ...+++||||+|.|...      ....+.+.+..-+.+..++++|..+.
T Consensus       101 ~~~KviiI~~ad~l~~~------a~NaLLK~LEepp~~~~fiL~t~~~~  143 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTEE------AQNALLKTLEEPPENTYFILITNNPS  143 (162)
T ss_dssp             SSSEEEEEETGGGS-HH------HHHHHHHHHHSTTTTEEEEEEES-GG
T ss_pred             CCceEEEeehHhhhhHH------HHHHHHHHhcCCCCCEEEEEEECChH
Confidence            35789999999997542      24666677777777677777776543

...

>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=95.11  E-value=0.021  Score=50.13  Aligned_cols=16  Identities=13%  Similarity=0.090  Sum_probs=14.0

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .++++++|+|+|||..
T Consensus        51 ~h~lf~GPPG~GKTTL   66 (233)
T PF05496_consen   51 DHMLFYGPPGLGKTTL   66 (233)
T ss_dssp             -EEEEESSTTSSHHHH
T ss_pred             ceEEEECCCccchhHH
Confidence            4799999999999977

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.

>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=95.10  E-value=0.2  Score=40.20  Aligned_cols=14  Identities=21%  Similarity=0.242  Sum_probs=12.8

Q ss_pred             EEEEccCCCccccc
Q psy7952          68 IFVSMPTGAVSLVG   81 (444)
Q Consensus        68 ~ii~apTGsGKT~~   81 (444)
                      +++++|+|+|||..
T Consensus         1 ill~G~~G~GKT~l   14 (132)
T PF00004_consen    1 ILLHGPPGTGKTTL   14 (132)
T ss_dssp             EEEESSTTSSHHHH
T ss_pred             CEEECcCCCCeeHH
Confidence            58999999999977

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 ....

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=95.02  E-value=0.13  Score=49.56  Aligned_cols=28  Identities=18%  Similarity=0.330  Sum_probs=18.9

Q ss_pred             HHHHHHHHhhCCccEEEEeccccccccC
Q psy7952         181 HYLLQHLVRYNKLAYIVVDEAHCVSEWG  208 (444)
Q Consensus       181 ~~~~~~~~~~~~~~~iViDE~H~~~~~~  208 (444)
                      ..+..........-+||+||++.+.+..
T Consensus       112 ~~l~~~~~~~~~~~IvvLDEid~L~~~~  139 (366)
T COG1474         112 KRLYDNLSKKGKTVIVILDEVDALVDKD  139 (366)
T ss_pred             HHHHHHHHhcCCeEEEEEcchhhhcccc
Confidence            3344444444566789999999997654

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=95.00  E-value=0.15  Score=53.69  Aligned_cols=15  Identities=20%  Similarity=0.251  Sum_probs=13.1

Q ss_pred             cE-EEEccCCCccccc
Q psy7952          67 DI-FVSMPTGAVSLVG   81 (444)
Q Consensus        67 ~~-ii~apTGsGKT~~   81 (444)
                      ++ +|.|+||+|||.+
T Consensus       782 nvLYIyG~PGTGKTAT  797 (1164)
T PTZ00112        782 QILYISGMPGTGKTAT  797 (1164)
T ss_pred             ceEEEECCCCCCHHHH
Confidence            44 5999999999988

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.97  E-value=0.07  Score=52.72  Aligned_cols=18  Identities=11%  Similarity=0.023  Sum_probs=15.1

Q ss_pred             cEEEEccCCCcccccccc
Q psy7952          67 DIFVSMPTGAVSLVGSVV   84 (444)
Q Consensus        67 ~~ii~apTGsGKT~~a~~   84 (444)
                      .++++||.|+|||.+|-+
T Consensus        42 a~Lf~GP~GtGKTTlAri   59 (484)
T PRK14956         42 AYIFFGPRGVGKTTIARI   59 (484)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            379999999999988543

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=94.96  E-value=0.094  Score=43.84  Aligned_cols=20  Identities=20%  Similarity=0.177  Sum_probs=15.4

Q ss_pred             HHHhhCCccEEEEecccccc
Q psy7952         186 HLVRYNKLAYIVVDEAHCVS  205 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~~~  205 (444)
                      ........+++|+||++.+.
T Consensus        79 ~~~~~~~~~~lviDe~~~~~   98 (165)
T cd01120          79 RLRERGGDDLIILDELTRLV   98 (165)
T ss_pred             HHHhCCCCEEEEEEcHHHHH
Confidence            34445678999999999874

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.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.94  E-value=0.22  Score=50.93  Aligned_cols=40  Identities=23%  Similarity=0.265  Sum_probs=27.2

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      ..+.+++||||+|.+...      ....|.+.+...+.+..+|+.|
T Consensus       116 ~~~~KVvIIDEah~Lt~~------A~NALLK~LEEpp~~~~fIL~t  155 (584)
T PRK14952        116 QSRYRIFIVDEAHMVTTA------GFNALLKIVEEPPEHLIFIFAT  155 (584)
T ss_pred             cCCceEEEEECCCcCCHH------HHHHHHHHHhcCCCCeEEEEEe
Confidence            356789999999998642      2355556666666656666666

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.87  E-value=0.037  Score=51.64  Aligned_cols=17  Identities=12%  Similarity=0.200  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCCccccc
Q psy7952          65 THDIFVSMPTGAVSLVG   81 (444)
Q Consensus        65 ~~~~ii~apTGsGKT~~   81 (444)
                      .+.+++.+|+|||||+.
T Consensus       185 PKGVLLYGPPGTGKTLL  201 (406)
T COG1222         185 PKGVLLYGPPGTGKTLL  201 (406)
T ss_pred             CCceEeeCCCCCcHHHH
Confidence            37899999999999977

>KOG0383|consensus

Probab=94.86  E-value=0.024  Score=58.05  Aligned_cols=61  Identities=21%  Similarity=0.276  Sum_probs=42.3

Q ss_pred             hccCCCCCceEEEEecccchHHHHHHHHHhh---------cCHHHHHHHHHHHh-cC--CccEEEEcCccccc
Q psy7952         293 LGKDNKANNCGIIYCRTREHTTDLADALRRK---------VNKHERSRVQESFM-RG--EINVITATISFGMG  353 (444)
Q Consensus       293 l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~---------~~~~~r~~~~~~f~-~g--~~~vLvaT~~~~~G  353 (444)
                      +.+....+++++||..-....+-+-+.+...         .....|+..+.+|. .|  ....|.+|...+.|
T Consensus       624 ~~~l~~~ghrvl~~~q~~~~ldlled~~~~~~~~~r~dG~~~~~~rq~ai~~~n~~~~~~~cfllstra~g~g  696 (696)
T KOG0383|consen  624 LKKLKSSGHRVLIFSQMIHMLDLLEDYLTYEGKYERIDGPITGPERQAAIDRFNAPGSNQFCFLLSTRAGGLG  696 (696)
T ss_pred             HHHHHhcchhhHHHHHHHHHHHHhHHHHhccCcceeccCCccchhhhhhccccCCCCccceEEEeecccccCC
Confidence            3333446888888888777776666666554         55677888899987 33  34568888877665

>PLN03025 replication factor C subunit; Provisional

Probab=94.80  E-value=0.061  Score=51.03  Aligned_cols=38  Identities=13%  Similarity=0.183  Sum_probs=23.3

Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      ..+++|+||+|.+....      ...+.+.+...++..++++.+
T Consensus        99 ~~kviiiDE~d~lt~~a------q~aL~~~lE~~~~~t~~il~~  136 (319)
T PLN03025         99 RHKIVILDEADSMTSGA------QQALRRTMEIYSNTTRFALAC  136 (319)
T ss_pred             CeEEEEEechhhcCHHH------HHHHHHHHhcccCCceEEEEe
Confidence            46899999999975421      244445555555545555433

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=94.79  E-value=0.033  Score=52.36  Aligned_cols=42  Identities=12%  Similarity=0.080  Sum_probs=29.1

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccC
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATA  238 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~  238 (444)
                      ...+++|||++|.|....      -+.+.+.+..-+.+..+|++|..+
T Consensus       112 g~~kV~iI~~ae~m~~~A------aNaLLKtLEEPp~~~~fiL~~~~~  153 (319)
T PRK08769        112 GIAQVVIVDPADAINRAA------CNALLKTLEEPSPGRYLWLISAQP  153 (319)
T ss_pred             CCcEEEEeccHhhhCHHH------HHHHHHHhhCCCCCCeEEEEECCh
Confidence            356899999999986432      355666666666667777776553

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.79  E-value=0.13  Score=52.18  Aligned_cols=39  Identities=15%  Similarity=0.262  Sum_probs=25.5

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      .+.+++||||+|.+....      ...+.+.+...+.+..+|+.|
T Consensus       118 ~~~kVvIIDEad~ls~~a------~naLLK~LEepp~~~~fIL~t  156 (527)
T PRK14969        118 GRFKVYIIDEVHMLSKSA------FNAMLKTLEEPPEHVKFILAT  156 (527)
T ss_pred             CCceEEEEcCcccCCHHH------HHHHHHHHhCCCCCEEEEEEe
Confidence            457899999999976422      344555555555556666665

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=94.77  E-value=0.22  Score=51.35  Aligned_cols=39  Identities=15%  Similarity=0.274  Sum_probs=25.8

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      ...+++||||+|+|...      ....+.+.+..-+.+..+|+.|
T Consensus       118 g~~KV~IIDEah~Ls~~------a~NALLKtLEEPp~~v~FIL~T  156 (647)
T PRK07994        118 GRFKVYLIDEVHMLSRH------SFNALLKTLEEPPEHVKFLLAT  156 (647)
T ss_pred             CCCEEEEEechHhCCHH------HHHHHHHHHHcCCCCeEEEEec
Confidence            46789999999998642      2355555555555555566653

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=94.73  E-value=0.081  Score=52.31  Aligned_cols=160  Identities=11%  Similarity=0.086  Sum_probs=71.7

Q ss_pred             HHHHHHcc---CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh---
Q psy7952          57 AIRHILLR---THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV---  130 (444)
Q Consensus        57 ~~~~~~~~---~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l---  130 (444)
                      .++.+..|   ..-+++.|+||+|||..|+-.+.         ......+  .+|+|++.-. -.     .+.+.++   
T Consensus       183 ~LD~~~~G~~~g~liviag~pg~GKT~~al~ia~---------~~a~~~g--~~v~~fSlEm-~~-----~~l~~Rl~~~  245 (421)
T TIGR03600       183 KLDRLTNGLVKGDLIVIGARPSMGKTTLALNIAE---------NVALREG--KPVLFFSLEM-SA-----EQLGERLLAS  245 (421)
T ss_pred             hHHHHhcCCCCCceEEEEeCCCCCHHHHHHHHHH---------HHHHhCC--CcEEEEECCC-CH-----HHHHHHHHHH
Confidence            45555543   15689999999999976332111         1111222  2346765221 11     2333333   


Q ss_pred             cCCCCceeEEEE-eCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh-hCCccEEEEeccccccc-c
Q psy7952         131 TGRSDLYQLELI-VSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR-YNKLAYIVVDEAHCVSE-W  207 (444)
Q Consensus       131 ~~~~~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~-~~~~~~iViDE~H~~~~-~  207 (444)
                      ..+   +....+ .+.....++.........+. +..+.|.....+.-............ ...+++||||=.|.+.. .
T Consensus       246 ~~~---v~~~~~~~~~l~~~~~~~~~~~~~~l~-~~~l~i~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDyLql~~~~~  321 (421)
T TIGR03600       246 KSG---INTGNIRTGRFNDSDFNRLLNAVDRLS-EKDLYIDDTGGLTVAQIRSIARRIKRKKGGLDLIVVDYIQLMAPTR  321 (421)
T ss_pred             HcC---CCHHHHhcCCCCHHHHHHHHHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEecccccCCCC
Confidence            122   221111 23334444433333333322 33456554433321111222222222 23699999999998853 2


Q ss_pred             CCCcHHHHHHHHHHHHhhC--CCCcEEEEecc
Q psy7952         208 GHDFRPTYRRLGELRQFTG--NSIPIIALTAT  237 (444)
Q Consensus       208 ~~~~~~~~~~l~~~~~~~~--~~~~~v~lSAT  237 (444)
                      +..-...+..+.+-++.+.  -+++++++|-.
T Consensus       322 ~~~~~~~~~~i~~~Lk~lAke~~i~Vi~lsQl  353 (421)
T TIGR03600       322 GRDRNEELGGISRGLKALAKELDVPVVLLAQL  353 (421)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHhCCcEEEeccc
Confidence            2222222333333333221  23778887754

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.

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=94.73  E-value=0.13  Score=47.57  Aligned_cols=21  Identities=14%  Similarity=-0.029  Sum_probs=16.7

Q ss_pred             HHHccCCcEEEEccCCCccccc
Q psy7952          60 HILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        60 ~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      -+..| .-+++.||||+|||..
T Consensus        26 G~~~g-~~~~i~g~~G~GKT~l   46 (271)
T cd01122          26 GLRKG-ELIILTAGTGVGKTTF   46 (271)
T ss_pred             EEcCC-cEEEEEcCCCCCHHHH
Confidence            34445 6789999999999976

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=94.73  E-value=0.16  Score=49.92  Aligned_cols=16  Identities=13%  Similarity=0.084  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      ..+++++++|+|||.+
T Consensus        96 ~vI~lvG~~GsGKTTt  111 (437)
T PRK00771         96 QTIMLVGLQGSGKTTT  111 (437)
T ss_pred             eEEEEECCCCCcHHHH
Confidence            4578999999999987

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=94.67  E-value=0.16  Score=52.40  Aligned_cols=40  Identities=18%  Similarity=0.226  Sum_probs=26.0

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      ..+.+++||||+|.+...      ....+.+.+...+..+.+|+.|
T Consensus       117 ~gk~KVIIIDEad~Ls~~------A~NALLKtLEEPp~~v~fILaT  156 (709)
T PRK08691        117 AGKYKVYIIDEVHMLSKS------AFNAMLKTLEEPPEHVKFILAT  156 (709)
T ss_pred             hCCcEEEEEECccccCHH------HHHHHHHHHHhCCCCcEEEEEe
Confidence            346789999999997532      2344555555555556666655

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.67  E-value=0.6  Score=44.78  Aligned_cols=16  Identities=19%  Similarity=-0.041  Sum_probs=14.3

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus       207 ~ii~lvGptGvGKTTt  222 (407)
T PRK12726        207 RIISLIGQTGVGKTTT  222 (407)
T ss_pred             eEEEEECCCCCCHHHH
Confidence            5678999999999977

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.65  E-value=0.1  Score=53.37  Aligned_cols=19  Identities=11%  Similarity=-0.024  Sum_probs=15.9

Q ss_pred             CcEEEEccCCCcccccccc
Q psy7952          66 HDIFVSMPTGAVSLVGSVV   84 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~   84 (444)
                      +.+++++|.|+|||.+|.+
T Consensus        39 ha~Lf~GPpG~GKTtiAri   57 (624)
T PRK14959         39 PAYLFSGTRGVGKTTIARI   57 (624)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            4588999999999988544

>PRK05595 replicative DNA helicase; Provisional

Probab=94.62  E-value=0.15  Score=50.67  Aligned_cols=167  Identities=9%  Similarity=0.024  Sum_probs=76.9

Q ss_pred             ccCchHHHHHHHHHHccC---CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCcc
Q psy7952          48 SFKCELQKKAIRHILLRT---HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRD  124 (444)
Q Consensus        48 ~~~t~~Q~~~~~~~~~~~---~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~  124 (444)
                      .+||.++  .++.+..|-   .-++|.|.||+|||..|+-         .+.+.....+  .+|++++.-..-      .
T Consensus       183 gi~tg~~--~ld~~~~G~~~g~liviaarpg~GKT~~al~---------ia~~~a~~~g--~~vl~fSlEms~------~  243 (444)
T PRK05595        183 GVASGFR--ELDAKTSGFQKGDMILIAARPSMGKTTFALN---------IAEYAALREG--KSVAIFSLEMSK------E  243 (444)
T ss_pred             cccCChH--HHHHhcCCCCCCcEEEEEecCCCChHHHHHH---------HHHHHHHHcC--CcEEEEecCCCH------H
Confidence            3455443  566665431   4578899999999976321         1011111222  234676543222      1


Q ss_pred             chHhhh---cCCCCceeEEEE-eCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEec
Q psy7952         125 DKTSIV---TGRSDLYQLELI-VSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDE  200 (444)
Q Consensus       125 ~~~~~l---~~~~~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE  200 (444)
                      +.+.++   ..+   +....+ .+.....++.........+. ...+.|-.+..+.-...............+++||||=
T Consensus       244 ~l~~R~~a~~~~---v~~~~~~~~~l~~~e~~~~~~~~~~l~-~~~l~i~d~~~~t~~~i~~~~r~~~~~~~~~~vvIDy  319 (444)
T PRK05595        244 QLAYKLLCSEAN---VDMLRLRTGNLEDKDWENIARASGPLA-AAKIFIDDTAGVSVMEMRSKCRRLKIEHGIDMILIDY  319 (444)
T ss_pred             HHHHHHHHHhcC---CCHHHHhcCCCCHHHHHHHHHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHHHHhcCCCEEEEeH
Confidence            333333   222   222222 23344444444444433322 2345554333232111222233333345699999999


Q ss_pred             cccccccCC-CcH-HHHHHHHHHHHhhC--CCCcEEEEecc
Q psy7952         201 AHCVSEWGH-DFR-PTYRRLGELRQFTG--NSIPIIALTAT  237 (444)
Q Consensus       201 ~H~~~~~~~-~~~-~~~~~l~~~~~~~~--~~~~~v~lSAT  237 (444)
                      .|.+...+. .-+ ..+..+.+-++.+.  -+++++++|-.
T Consensus       320 lql~~~~~~~~~r~~~v~~is~~LK~lAke~~i~vi~lsQL  360 (444)
T PRK05595        320 LQLMSGGKGSESRQQEVSEISRSIKALAKEMECPVIALSQL  360 (444)
T ss_pred             HHhccCCCCCccHHHHHHHHHHHHHHHHHHhCCeEEEeecc
Confidence            999853221 111 22333333333332  24778877643

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.55  E-value=1.2  Score=40.81  Aligned_cols=57  Identities=18%  Similarity=0.151  Sum_probs=35.1

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHh
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVL  250 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l  250 (444)
                      ..+.++|+||-+-+...    -...+..+..+.....+...++.+|||........+.+.+
T Consensus       152 ~~~~D~ViIDt~Gr~~~----~~~~l~el~~~~~~~~~~~~~LVl~a~~~~~d~~~~~~~f  208 (270)
T PRK06731        152 EARVDYILIDTAGKNYR----ASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIITNF  208 (270)
T ss_pred             cCCCCEEEEECCCCCcC----CHHHHHHHHHHHhhhCCCeEEEEEcCccCHHHHHHHHHHh
Confidence            34689999999977432    1334455555555444434577899998765554444443

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.54  E-value=0.23  Score=50.34  Aligned_cols=40  Identities=18%  Similarity=0.223  Sum_probs=26.4

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      ..+.+++||||+|.+...      ....+.+.+...+....+|+.|
T Consensus       117 ~g~~kViIIDEa~~ls~~------a~naLLK~LEepp~~v~fIL~T  156 (546)
T PRK14957        117 QGRYKVYLIDEVHMLSKQ------SFNALLKTLEEPPEYVKFILAT  156 (546)
T ss_pred             cCCcEEEEEechhhccHH------HHHHHHHHHhcCCCCceEEEEE
Confidence            356789999999997542      2345555555555556666655

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.49  E-value=0.31  Score=48.78  Aligned_cols=55  Identities=20%  Similarity=0.218  Sum_probs=29.3

Q ss_pred             hhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHH
Q psy7952         189 RYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIIS  248 (444)
Q Consensus       189 ~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~  248 (444)
                      .+.+.++|+||.+-.....    ......+..+... .....++.++++........+.+
T Consensus       425 ~l~~~DLVLIDTaG~s~~D----~~l~eeL~~L~aa-~~~a~lLVLpAtss~~Dl~eii~  479 (559)
T PRK12727        425 RLRDYKLVLIDTAGMGQRD----RALAAQLNWLRAA-RQVTSLLVLPANAHFSDLDEVVR  479 (559)
T ss_pred             HhccCCEEEecCCCcchhh----HHHHHHHHHHHHh-hcCCcEEEEECCCChhHHHHHHH
Confidence            3456899999999764211    1112222222222 22356888888876544444433

>PRK08939 primosomal protein DnaI; Reviewed

Probab=94.47  E-value=0.1  Score=48.97  Aligned_cols=16  Identities=6%  Similarity=-0.039  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +++++.||+|+|||..
T Consensus       157 ~gl~L~G~~G~GKThL  172 (306)
T PRK08939        157 KGLYLYGDFGVGKSYL  172 (306)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            5799999999999966

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=94.43  E-value=0.13  Score=51.74  Aligned_cols=19  Identities=5%  Similarity=0.034  Sum_probs=16.0

Q ss_pred             CcEEEEccCCCcccccccc
Q psy7952          66 HDIFVSMPTGAVSLVGSVV   84 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~   84 (444)
                      +.++++||.|+|||.+|-+
T Consensus        44 ~a~Lf~Gp~G~GKTT~Ari   62 (507)
T PRK06645         44 GGYLLTGIRGVGKTTSARI   62 (507)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            4689999999999988544

>PRK06904 replicative DNA helicase; Validated

Probab=94.37  E-value=0.16  Score=50.81  Aligned_cols=152  Identities=11%  Similarity=0.079  Sum_probs=69.0

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEE-e
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELI-V  143 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~-~  143 (444)
                      .-+++.|.||+|||..|+-.+         .......+  .+|+|++.-..-      .+.+.++ +.... +....+ .
T Consensus       222 ~LiiIaarPg~GKTafalnia---------~~~a~~~g--~~Vl~fSlEMs~------~ql~~Rlla~~s~-v~~~~i~~  283 (472)
T PRK06904        222 DLIIVAARPSMGKTTFAMNLC---------ENAAMASE--KPVLVFSLEMPA------EQIMMRMLASLSR-VDQTKIRT  283 (472)
T ss_pred             cEEEEEeCCCCChHHHHHHHH---------HHHHHhcC--CeEEEEeccCCH------HHHHHHHHHhhCC-CCHHHhcc
Confidence            557889999999997632111         11111222  234676543322      2344443 11100 222222 3


Q ss_pred             C-CCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh-hCCccEEEEeccccccccCC--CcHHHHHHHH
Q psy7952         144 S-GQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR-YNKLAYIVVDEAHCVSEWGH--DFRPTYRRLG  219 (444)
Q Consensus       144 ~-~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~-~~~~~~iViDE~H~~~~~~~--~~~~~~~~l~  219 (444)
                      | ..+..++..+......+.....+.|-....+.-.......+.... ...+++||||=.+.+...+.  .-...+..+.
T Consensus       284 g~~l~~~e~~~~~~a~~~l~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~~~~~~~~r~~ei~~is  363 (472)
T PRK06904        284 GQNLDQQDWAKISSTVGMFKQKPNLYIDDSSGLTPTELRSRARRVYRENGGLSLIMVDYLQLMRAPGFEDNRTLEIAEIS  363 (472)
T ss_pred             CCCCCHHHHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEecHHhcCCCCCCCcHHHHHHHHH
Confidence            3 345555544443333333334455542111211111222222222 23689999999998854321  1122334444


Q ss_pred             HHHHhhCC--CCcEEEEe
Q psy7952         220 ELRQFTGN--SIPIIALT  235 (444)
Q Consensus       220 ~~~~~~~~--~~~~v~lS  235 (444)
                      +-++.+.+  +++++++|
T Consensus       364 r~LK~lAkel~ipVi~ls  381 (472)
T PRK06904        364 RSLKALAKELKVPVVALS  381 (472)
T ss_pred             HHHHHHHHHhCCeEEEEE
Confidence            33333322  47888888

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=94.31  E-value=0.051  Score=51.62  Aligned_cols=33  Identities=12%  Similarity=0.039  Sum_probs=25.2

Q ss_pred             hHHHHHHHHHHcc--C--CcEEEEccCCCcccccccc
Q psy7952          52 ELQKKAIRHILLR--T--HDIFVSMPTGAVSLVGSVV   84 (444)
Q Consensus        52 ~~Q~~~~~~~~~~--~--~~~ii~apTGsGKT~~a~~   84 (444)
                      |||...++.+...  .  +-+++++|.|.||+..|..
T Consensus         4 PW~~~~~~~l~~~~~rl~ha~Lf~Gp~G~GK~~lA~~   40 (342)
T PRK06964          4 PWQTDDWNRLQALRARLPHALLLHGQAGIGKLDFAQH   40 (342)
T ss_pred             cccHHHHHHHHHhcCCcceEEEEECCCCCCHHHHHHH
Confidence            4888888877752  1  4578999999999987543

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=94.27  E-value=0.12  Score=50.33  Aligned_cols=41  Identities=10%  Similarity=0.093  Sum_probs=24.8

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEecc
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTAT  237 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT  237 (444)
                      .+..++||||+|.+....      ...+.+.+..-+++..+|+.|.+
T Consensus       116 ~~~kViiIDead~m~~~a------anaLLk~LEep~~~~~fIL~a~~  156 (394)
T PRK07940        116 GRWRIVVIEDADRLTERA------ANALLKAVEEPPPRTVWLLCAPS  156 (394)
T ss_pred             CCcEEEEEechhhcCHHH------HHHHHHHhhcCCCCCeEEEEECC
Confidence            456799999999985422      23444555554554545555544

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=94.25  E-value=0.22  Score=47.60  Aligned_cols=29  Identities=10%  Similarity=0.169  Sum_probs=20.0

Q ss_pred             HHHHHHHHHccCC--cEEEEccCCCcccccc
Q psy7952          54 QKKAIRHILLRTH--DIFVSMPTGAVSLVGS   82 (444)
Q Consensus        54 Q~~~~~~~~~~~~--~~ii~apTGsGKT~~a   82 (444)
                      ..+.+..+...++  +++++||+|+|||..|
T Consensus        23 ~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la   53 (337)
T PRK12402         23 VVERLSRAVDSPNLPHLLVQGPPGSGKTAAV   53 (337)
T ss_pred             HHHHHHHHHhCCCCceEEEECCCCCCHHHHH
Confidence            3334444444434  7999999999999773

>TIGR01075 uvrD DNA helicase II

Probab=94.22  E-value=0.027  Score=59.71  Aligned_cols=62  Identities=10%  Similarity=0.040  Sum_probs=44.2

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc-CC-ccceeEEEcchhhhhcccCccchHh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN-GN-VRSRNGWISPILSSFYLRFRDDKTS  128 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~-~~-~~~~vlil~P~~~L~~~~q~~~~~~  128 (444)
                      ++-|++++.+  .. .+++|.|.+|||||.+        . ..- +.++.. .+ ...++|+++.|+..+     .+.-+
T Consensus         6 n~~Q~~av~~--~~-g~~lV~AgaGSGKT~~--------L-~~R-ia~Li~~~~v~p~~IL~lTFTnkAA-----~em~~   67 (715)
T TIGR01075         6 NDKQREAVAA--PP-GNLLVLAGAGSGKTRV--------L-THR-IAWLLSVENASPHSIMAVTFTNKAA-----AEMRH   67 (715)
T ss_pred             CHHHHHHHcC--CC-CCEEEEecCCCCHHHH--------H-HHH-HHHHHHcCCCCHHHeEeeeccHHHH-----HHHHH
Confidence            4789998875  23 5899999999999988        1 111 222333 33 234889999999999     77777


Q ss_pred             hh
Q psy7952         129 IV  130 (444)
Q Consensus       129 ~l  130 (444)
                      ++
T Consensus        68 Rl   69 (715)
T TIGR01075        68 RI   69 (715)
T ss_pred             HH
Confidence            76

Designed to identify uvrD members of the uvrD/rep subfamily.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=94.10  E-value=0.19  Score=45.01  Aligned_cols=29  Identities=7%  Similarity=-0.071  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHc---cCCcEEEEccCCCccccc
Q psy7952          53 LQKKAIRHILL---RTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        53 ~Q~~~~~~~~~---~~~~~ii~apTGsGKT~~   81 (444)
                      .....+..+..   ..+.+++++|+|+|||..
T Consensus        27 ~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~L   58 (227)
T PRK08903         27 ELVARLRELAAGPVADRFFYLWGEAGSGRSHL   58 (227)
T ss_pred             HHHHHHHHHHhccCCCCeEEEECCCCCCHHHH
Confidence            34444544433   126799999999999966

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=94.03  E-value=0.028  Score=59.59  Aligned_cols=62  Identities=8%  Similarity=0.039  Sum_probs=44.1

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc-CCc-cceeEEEcchhhhhcccCccchHh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN-GNV-RSRNGWISPILSSFYLRFRDDKTS  128 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~-~~~-~~~vlil~P~~~L~~~~q~~~~~~  128 (444)
                      ++-|++++.+.  . .+++|.|.+|||||.+        . ..- +.++.. .+. ..++|+++-|+..+     .+.-+
T Consensus        11 n~~Q~~av~~~--~-g~~lV~AgaGSGKT~v--------l-~~R-ia~Li~~~~v~p~~IL~lTFT~kAA-----~Em~~   72 (721)
T PRK11773         11 NDKQREAVAAP--L-GNMLVLAGAGSGKTRV--------L-VHR-IAWLMQVENASPYSIMAVTFTNKAA-----AEMRH   72 (721)
T ss_pred             CHHHHHHHhCC--C-CCEEEEecCCCCHHHH--------H-HHH-HHHHHHcCCCChhHeEeeeccHHHH-----HHHHH
Confidence            47899998753  3 5899999999999988        1 111 222332 342 34789999999999     77777


Q ss_pred             hh
Q psy7952         129 IV  130 (444)
Q Consensus       129 ~l  130 (444)
                      ++
T Consensus        73 Rl   74 (721)
T PRK11773         73 RI   74 (721)
T ss_pred             HH
Confidence            76

>KOG0741|consensus

Probab=94.02  E-value=0.076  Score=52.07  Aligned_cols=50  Identities=18%  Similarity=0.256  Sum_probs=34.8

Q ss_pred             CCCCCHHHHHHHHHHHhCCcccCchHHHHHHHHHHcc-CCcEEEEccCCCccccc
Q psy7952          28 GGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLR-THDIFVSMPTGAVSLVG   81 (444)
Q Consensus        28 ~~~~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~-~~~~ii~apTGsGKT~~   81 (444)
                      +..-.+.++.+.+++.|-..-||.+    .++.+-=. -+.+++.+|+|+|||+.
T Consensus       222 GIGGLd~EFs~IFRRAFAsRvFpp~----vie~lGi~HVKGiLLyGPPGTGKTLi  272 (744)
T KOG0741|consen  222 GIGGLDKEFSDIFRRAFASRVFPPE----VIEQLGIKHVKGILLYGPPGTGKTLI  272 (744)
T ss_pred             ccccchHHHHHHHHHHHHhhcCCHH----HHHHcCccceeeEEEECCCCCChhHH
Confidence            3344588888999988877777733    23322211 15689999999999988

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=93.94  E-value=0.14  Score=53.21  Aligned_cols=39  Identities=21%  Similarity=0.250  Sum_probs=24.0

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      ....++||||+|.+...      ....+.+.+...+....+|+.|
T Consensus       117 g~~KV~IIDEa~~LT~~------A~NALLKtLEEPP~~tifILaT  155 (725)
T PRK07133        117 SKYKIYIIDEVHMLSKS------AFNALLKTLEEPPKHVIFILAT  155 (725)
T ss_pred             CCCEEEEEEChhhCCHH------HHHHHHHHhhcCCCceEEEEEc
Confidence            56789999999997532      2345555555544444445444

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=93.92  E-value=0.47  Score=43.73  Aligned_cols=16  Identities=13%  Similarity=-0.004  Sum_probs=13.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +-+++.+|+|+|||.+
T Consensus        73 ~vi~l~G~~G~GKTTt   88 (272)
T TIGR00064        73 NVILFVGVNGVGKTTT   88 (272)
T ss_pred             eEEEEECCCCCcHHHH
Confidence            4578889999999977

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.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.86  E-value=0.17  Score=52.02  Aligned_cols=39  Identities=10%  Similarity=0.229  Sum_probs=24.6

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      .+++++||||+|.+....      ++.+.+.+..-+....+|+.|
T Consensus       123 g~~KV~IIDEvh~Ls~~a------~NaLLKtLEEPP~~~~fIL~T  161 (618)
T PRK14951        123 GRFKVFMIDEVHMLTNTA------FNAMLKTLEEPPEYLKFVLAT  161 (618)
T ss_pred             CCceEEEEEChhhCCHHH------HHHHHHhcccCCCCeEEEEEE
Confidence            357899999999986422      344445554445545565554

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=93.86  E-value=0.16  Score=48.61  Aligned_cols=42  Identities=7%  Similarity=0.068  Sum_probs=27.3

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccC
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATA  238 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~  238 (444)
                      ....++||||+|.+....      ...+.+.+...+.+..++++|..+
T Consensus       140 g~~rVviIDeAd~l~~~a------anaLLk~LEEpp~~~~fiLit~~~  181 (351)
T PRK09112        140 GNWRIVIIDPADDMNRNA------ANAILKTLEEPPARALFILISHSS  181 (351)
T ss_pred             CCceEEEEEchhhcCHHH------HHHHHHHHhcCCCCceEEEEECCh
Confidence            467899999999985422      344555555555556666766443

>KOG0701|consensus

Probab=93.84  E-value=0.037  Score=61.65  Aligned_cols=84  Identities=27%  Similarity=0.375  Sum_probs=72.3

Q ss_pred             ceEEEEecccchHHHHHHHHHhh----------------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCC
Q psy7952         301 NCGIIYCRTREHTTDLADALRRK----------------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQN  358 (444)
Q Consensus       301 ~~~iVf~~s~~~~~~l~~~L~~~----------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~  358 (444)
                      -..++|++.+..+....+.++..                      -....+.++++.|....+++|++|.++.+|+|++.
T Consensus       293 l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~  372 (1606)
T KOG0701|consen  293 LSGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPK  372 (1606)
T ss_pred             hhheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhh
Confidence            45689999888888888877766                      11223678899999999999999999999999999


Q ss_pred             ccEEEEeCCCCCHHHHHHHhccCCCC
Q psy7952         359 VRFVVHWGMPSSIPAYYQESGRAGRD  384 (444)
Q Consensus       359 ~~~Vi~~~~p~s~~~~~Qr~GR~~R~  384 (444)
                      ++.|+.++.|.....|+|..||+.+.
T Consensus       373 ~~~~~~~~~~~~~~~~vq~~~r~~~~  398 (1606)
T KOG0701|consen  373 CNLVVLFDAPTYYRSYVQKKGRARAA  398 (1606)
T ss_pred             hhhheeccCcchHHHHHHhhcccccc
Confidence            99999999999999999999999655

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.84  E-value=0.18  Score=51.77  Aligned_cols=40  Identities=18%  Similarity=0.219  Sum_probs=26.0

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      ..+.+++||||+|.+...      ....+.+.+...+.+..+|+.|
T Consensus       117 ~~~~KVvIIdev~~Lt~~------a~naLLk~LEepp~~~~fIl~t  156 (576)
T PRK14965        117 RSRYKIFIIDEVHMLSTN------AFNALLKTLEEPPPHVKFIFAT  156 (576)
T ss_pred             cCCceEEEEEChhhCCHH------HHHHHHHHHHcCCCCeEEEEEe
Confidence            346789999999997642      2345555555555556666555

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=93.78  E-value=0.049  Score=52.82  Aligned_cols=159  Identities=11%  Similarity=0.013  Sum_probs=82.6

Q ss_pred             CCCCCHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccce
Q psy7952          28 GGKVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSR  107 (444)
Q Consensus        28 ~~~~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~  107 (444)
                      ....+...+.+.++.  .+..|-+ .|.++.-..-.|.+  -|.+-.|||||.+        .+..+  ..+...++..+
T Consensus       144 ~~~~~a~a~l~~ies--kIanfD~-~Q~kaa~~~~~G~q--rIrGLAGSGKT~~--------La~Ka--a~lh~knPd~~  208 (660)
T COG3972         144 RINLEANALLDTIES--KIANFDT-DQTKAAFQSGFGKQ--RIRGLAGSGKTEL--------LAHKA--AELHSKNPDSR  208 (660)
T ss_pred             cccchhHHHHHHHHH--HHhcccc-hhheeeeecCCchh--hhhcccCCCchhH--------HHHHH--HHHhcCCCCce
Confidence            333445555555553  2334443 78887766666633  5788899999988        44333  33556667779


Q ss_pred             eEEEcchhhhhcccCccchHhhh-----cCCCCceeE--EEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccH
Q psy7952         108 NGWISPILSSFYLRFRDDKTSIV-----TGRSDLYQL--ELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESF  180 (444)
Q Consensus       108 vlil~P~~~L~~~~q~~~~~~~l-----~~~~~~i~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~  180 (444)
                      ++|.+-|+.|+  +|....+..+     ...+++-+.  .--.|+.+.......+....   ....+-++--+.-.....
T Consensus       209 I~~Tfftk~L~--s~~r~lv~~F~f~~~e~~pdW~~~l~~h~wgG~t~~g~y~~~~~~~---~~~~~~fsg~g~~F~~aC  283 (660)
T COG3972         209 IAFTFFTKILA--STMRTLVPEFFFMRVEKQPDWGTKLFCHNWGGLTKEGFYGMYRYIC---HYYEIPFSGFGNGFDAAC  283 (660)
T ss_pred             EEEEeehHHHH--HHHHHHHHHHHHHHhhcCCCccceEEEeccCCCCCCcchHHHHHHh---cccccccCCCCcchHHHH
Confidence            99999999998  2223333333     112222222  22223333322222222221   222333331111111112


Q ss_pred             HHHHHHHHhhCCccEEEEeccccccc
Q psy7952         181 HYLLQHLVRYNKLAYIVVDEAHCVSE  206 (444)
Q Consensus       181 ~~~~~~~~~~~~~~~iViDE~H~~~~  206 (444)
                      ..++.......-.++|.|||.+-+.+
T Consensus       284 ~eli~~~~~~~~yD~ilIDE~QDFP~  309 (660)
T COG3972         284 KELIADINNKKAYDYILIDESQDFPQ  309 (660)
T ss_pred             HHHHHhhhccccccEEEecccccCCH
Confidence            33444455566789999999988643

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.77  E-value=0.15  Score=50.88  Aligned_cols=17  Identities=12%  Similarity=0.073  Sum_probs=14.5

Q ss_pred             cEEEEccCCCccccccc
Q psy7952          67 DIFVSMPTGAVSLVGSV   83 (444)
Q Consensus        67 ~~ii~apTGsGKT~~a~   83 (444)
                      .++++||+|+|||..|-
T Consensus        38 ~~Lf~GPpGtGKTTlA~   54 (472)
T PRK14962         38 AYIFAGPRGTGKTTVAR   54 (472)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            37999999999998844

>PRK08760 replicative DNA helicase; Provisional

Probab=93.77  E-value=0.17  Score=50.75  Aligned_cols=166  Identities=12%  Similarity=0.111  Sum_probs=75.2

Q ss_pred             cCchHHHHHHHHHHcc---CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccc
Q psy7952          49 FKCELQKKAIRHILLR---THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDD  125 (444)
Q Consensus        49 ~~t~~Q~~~~~~~~~~---~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~  125 (444)
                      +||.+.  .+..+..|   ..-++|.|.||+|||..|+-.+         .......+  .+|+|++.-..-.      +
T Consensus       212 i~TG~~--~LD~~t~G~~~G~LivIaarPg~GKTafal~iA---------~~~a~~~g--~~V~~fSlEMs~~------q  272 (476)
T PRK08760        212 LPTGYN--DFDAMTAGLQPTDLIILAARPAMGKTTFALNIA---------EYAAIKSK--KGVAVFSMEMSAS------Q  272 (476)
T ss_pred             ccCCcH--HHHHHhcCCCCCceEEEEeCCCCChhHHHHHHH---------HHHHHhcC--CceEEEeccCCHH------H
Confidence            454332  45555433   1557899999999997633211         11111222  2346765433222      3


Q ss_pred             hHhhh-cCCCCceeEEEE-eCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccc
Q psy7952         126 KTSIV-TGRSDLYQLELI-VSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHC  203 (444)
Q Consensus       126 ~~~~l-~~~~~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~  203 (444)
                      .+.++ +.... +....+ .|..+..++......+..+. +..+.|.....+.-...............+++||||=.+.
T Consensus       273 l~~Rl~a~~s~-i~~~~i~~g~l~~~e~~~~~~a~~~l~-~~~l~I~d~~~~t~~~I~~~~r~l~~~~~~~lVvIDyLql  350 (476)
T PRK08760        273 LAMRLISSNGR-INAQRLRTGALEDEDWARVTGAIKMLK-ETKIFIDDTPGVSPEVLRSKCRRLKREHDLGLIVIDYLQL  350 (476)
T ss_pred             HHHHHHHhhCC-CcHHHHhcCCCCHHHHHHHHHHHHHHh-cCCEEEeCCCCCCHHHHHHHHHHHHHhcCCCEEEEecHHh
Confidence            33343 11100 211111 23444444444433333333 3456555433332222222333333445789999999998


Q ss_pred             ccccCC--CcHHHHHHHHHHHHhhCC--CCcEEEEe
Q psy7952         204 VSEWGH--DFRPTYRRLGELRQFTGN--SIPIIALT  235 (444)
Q Consensus       204 ~~~~~~--~~~~~~~~l~~~~~~~~~--~~~~v~lS  235 (444)
                      +...+.  .-...+..+.+-++.+.+  +++++++|
T Consensus       351 ~~~~~~~~~r~~ei~~Isr~LK~lAkel~ipVi~ls  386 (476)
T PRK08760        351 MSVPGNSENRATEISEISRSLKGLAKELNVPVIALS  386 (476)
T ss_pred             cCCCCCCcccHHHHHHHHHHHHHHHHHhCCEEEEee
Confidence            853221  111223333333332221  37777777

>KOG1133|consensus

Probab=93.74  E-value=0.034  Score=55.96  Aligned_cols=44  Identities=18%  Similarity=0.249  Sum_probs=33.9

Q ss_pred             hCCcccCchHHHHHHHHHHc----cCCcEEEEccCCCcccccccccccc
Q psy7952          44 FGFDSFKCELQKKAIRHILL----RTHDIFVSMPTGAVSLVGSVVSARS   88 (444)
Q Consensus        44 ~g~~~~~t~~Q~~~~~~~~~----~~~~~ii~apTGsGKT~~a~~~~~~   88 (444)
                      |+|..-|..+|.+.+..+++    | +-.|+.+|||||||+.-+++++.
T Consensus        10 F~fPy~PYdIQ~~lM~elyrvLe~G-kIgIfESPTGTGKSLSLiCaalt   57 (821)
T KOG1133|consen   10 FPFPYTPYDIQEDLMRELYRVLEEG-KIGIFESPTGTGKSLSLICAALT   57 (821)
T ss_pred             cCCCCCchhHHHHHHHHHHHHHhcC-CeeeeeCCCCCCchHHHHHHHHH
Confidence            55554467799998887774    6 77899999999999986666643

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=93.74  E-value=0.091  Score=54.66  Aligned_cols=59  Identities=12%  Similarity=-0.054  Sum_probs=42.7

Q ss_pred             CchHHHHHHHHHHcc----CCcEEEEccCCCcccccccccccceEEeCCCcccccc--CCccceeEEEcchhhhhcccCc
Q psy7952          50 KCELQKKAIRHILLR----THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN--GNVRSRNGWISPILSSFYLRFR  123 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~----~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~--~~~~~~vlil~P~~~L~~~~q~  123 (444)
                      |+..|..++..+.++    .+..++.+.||+|||+++          ..    +..  +.+.   ||++|...++     
T Consensus        10 ~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~----------a~----~~~~~~~p~---Lvi~~n~~~A-----   67 (655)
T TIGR00631        10 PAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTM----------AN----VIAQVNRPT---LVIAHNKTLA-----   67 (655)
T ss_pred             CChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHH----------HH----HHHHhCCCE---EEEECCHHHH-----
Confidence            577899998887654    236679999999999881          11    222  2344   9999999999     


Q ss_pred             cchHhhh
Q psy7952         124 DDKTSIV  130 (444)
Q Consensus       124 ~~~~~~l  130 (444)
                      .+....+
T Consensus        68 ~ql~~el   74 (655)
T TIGR00631        68 AQLYNEF   74 (655)
T ss_pred             HHHHHHH
Confidence            5666666

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

>PRK05748 replicative DNA helicase; Provisional

Probab=93.69  E-value=0.2  Score=49.92  Aligned_cols=168  Identities=10%  Similarity=0.080  Sum_probs=74.6

Q ss_pred             ccCchHHHHHHHHHHcc---CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCcc
Q psy7952          48 SFKCELQKKAIRHILLR---THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRD  124 (444)
Q Consensus        48 ~~~t~~Q~~~~~~~~~~---~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~  124 (444)
                      .+||.+  ..++.+..|   ..-++|.|+||+|||..|+-.+         .+.....+  .+|++++.-.. .     .
T Consensus       185 gi~TG~--~~LD~~~~G~~~G~livIaarpg~GKT~~al~ia---------~~~a~~~g--~~v~~fSlEms-~-----~  245 (448)
T PRK05748        185 GIPTGF--TDLDKMTSGLQPNDLIIVAARPSVGKTAFALNIA---------QNVATKTD--KNVAIFSLEMG-A-----E  245 (448)
T ss_pred             CccCCh--HHHHHhcCCCCCCceEEEEeCCCCCchHHHHHHH---------HHHHHhCC--CeEEEEeCCCC-H-----H
Confidence            345433  355555543   1558999999999997632211         11111222  23366643222 1     2


Q ss_pred             chHhhh-cCCCCceeEE-EEeCCCChhhHHHHHHHHHhcCCCeeEEEE-CCCccccccHHHHHHHHHhhC-CccEEEEec
Q psy7952         125 DKTSIV-TGRSDLYQLE-LIVSGQTKTENKAILEELRLVKPRIKLLYV-TPERAVTESFHYLLQHLVRYN-KLAYIVVDE  200 (444)
Q Consensus       125 ~~~~~l-~~~~~~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~-Tpe~l~~~~~~~~~~~~~~~~-~~~~iViDE  200 (444)
                      +.+.++ +... .+... ...+.....++.........+.. ..+.|. +|. +.-..+........... ++++||||=
T Consensus       246 ~l~~R~l~~~~-~v~~~~i~~~~l~~~e~~~~~~a~~~l~~-~~~~i~d~~~-~ti~~i~~~~r~~~~~~~~~~~vvIDy  322 (448)
T PRK05748        246 SLVMRMLCAEG-NIDAQRLRTGQLTDDDWPKLTIAMGSLSD-APIYIDDTPG-IKVTEIRARCRRLAQEHGGLGLILIDY  322 (448)
T ss_pred             HHHHHHHHHhc-CCCHHHhhcCCCCHHHHHHHHHHHHHHhc-CCEEEECCCC-CCHHHHHHHHHHHHHhcCCCCEEEEcc
Confidence            333333 1100 02221 11234444444444444433333 345554 333 22111122223333333 789999999


Q ss_pred             cccccccCC---CcHHHHHHHHHHHHhhC--CCCcEEEEecc
Q psy7952         201 AHCVSEWGH---DFRPTYRRLGELRQFTG--NSIPIIALTAT  237 (444)
Q Consensus       201 ~H~~~~~~~---~~~~~~~~l~~~~~~~~--~~~~~v~lSAT  237 (444)
                      .|.+...+.   .....+..+.+-++.+.  -+++++++|-.
T Consensus       323 L~li~~~~~~~~~r~~~i~~i~~~LK~lAke~~i~vi~lsQl  364 (448)
T PRK05748        323 LQLIQGSGRSGENRQQEVSEISRSLKALAKELKVPVIALSQL  364 (448)
T ss_pred             chhcCCCCCCCcCHHHHHHHHHHHHHHHHHHhCCeEEEeccc
Confidence            999853221   11122333333332221  23777777754

>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=93.57  E-value=0.08  Score=48.56  Aligned_cols=149  Identities=14%  Similarity=0.091  Sum_probs=70.4

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcc---hhhhhcccCccchHhhhcCCCCceeEEEE
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISP---ILSSFYLRFRDDKTSIVTGRSDLYQLELI  142 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P---~~~L~~~~q~~~~~~~l~~~~~~i~~~~~  142 (444)
                      .=+++.|+||.|||..|+-         .+.+.....+  ..|++++.   ...++     ...+... .+   +....+
T Consensus        20 ~L~vi~a~pg~GKT~~~l~---------ia~~~a~~~~--~~vly~SlEm~~~~l~-----~R~la~~-s~---v~~~~i   79 (259)
T PF03796_consen   20 ELTVIAARPGVGKTAFALQ---------IALNAALNGG--YPVLYFSLEMSEEELA-----ARLLARL-SG---VPYNKI   79 (259)
T ss_dssp             -EEEEEESTTSSHHHHHHH---------HHHHHHHTTS--SEEEEEESSS-HHHHH-----HHHHHHH-HT---STHHHH
T ss_pred             cEEEEEecccCCchHHHHH---------HHHHHHHhcC--CeEEEEcCCCCHHHHH-----HHHHHHh-hc---chhhhh
Confidence            5589999999999977322         2122233322  34477764   33444     3333333 11   111111


Q ss_pred             e-CCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhh-CCccEEEEecccccccc--CCCcHHHHHH-
Q psy7952         143 V-SGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRY-NKLAYIVVDEAHCVSEW--GHDFRPTYRR-  217 (444)
Q Consensus       143 ~-~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~-~~~~~iViDE~H~~~~~--~~~~~~~~~~-  217 (444)
                      . +.....+..........+....-.+..+|. +............... ..+++||||=+|.+...  .......+.. 
T Consensus        80 ~~g~l~~~e~~~~~~~~~~l~~~~l~i~~~~~-~~~~~i~~~i~~~~~~~~~~~~v~IDyl~ll~~~~~~~~~~~~~~~i  158 (259)
T PF03796_consen   80 RSGDLSDEEFERLQAAAEKLSDLPLYIEDTPS-LTIDDIESKIRRLKREGKKVDVVFIDYLQLLKSEDSSDNRRQEIGEI  158 (259)
T ss_dssp             HCCGCHHHHHHHHHHHHHHHHTSEEEEEESSS--BHHHHHHHHHHHHHHSTTEEEEEEEEGGGSBTSCSSSCCHHHHHHH
T ss_pred             hccccCHHHHHHHHHHHHHHhhCcEEEECCCC-CCHHHHHHHHHHHHhhccCCCEEEechHHHhcCCCCCCCHHHHHHHH
Confidence            1 223333333333333333333333344444 2222223333333333 78999999999998552  1122333333 


Q ss_pred             ---HHHHHHhhCCCCcEEEEecc
Q psy7952         218 ---LGELRQFTGNSIPIIALTAT  237 (444)
Q Consensus       218 ---l~~~~~~~~~~~~~v~lSAT  237 (444)
                         ++.+...+  +.+++++|-.
T Consensus       159 ~~~Lk~lA~~~--~i~vi~~sQl  179 (259)
T PF03796_consen  159 SRELKALAKEL--NIPVIALSQL  179 (259)
T ss_dssp             HHHHHHHHHHH--TSEEEEEEEB
T ss_pred             HHHHHHHHHHc--CCeEEEcccc
Confidence               34433333  3777777765

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 ....

>KOG0734|consensus

Probab=93.57  E-value=0.18  Score=49.60  Aligned_cols=53  Identities=23%  Similarity=0.118  Sum_probs=32.9

Q ss_pred             CCccEEEEecccccccc-----CCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchH
Q psy7952         191 NKLAYIVVDEAHCVSEW-----GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVK  243 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~-----~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~  243 (444)
                      .-...|+|||+|.+...     .+..+..+..+..-+..|.++-.+|.+.||--+...
T Consensus       395 ~APcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe~L  452 (752)
T KOG0734|consen  395 RAPCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFPEAL  452 (752)
T ss_pred             cCCeEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCChhhh
Confidence            34678999999998542     111223333344444456667789999999555443

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.56  E-value=0.2  Score=50.52  Aligned_cols=16  Identities=19%  Similarity=0.162  Sum_probs=13.9

Q ss_pred             EEEEccCCCccccccc
Q psy7952          68 IFVSMPTGAVSLVGSV   83 (444)
Q Consensus        68 ~ii~apTGsGKT~~a~   83 (444)
                      +++++|+|+|||.+|.
T Consensus        39 ~Lf~GppGtGKTTlA~   54 (504)
T PRK14963         39 YLFSGPRGVGKTTTAR   54 (504)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5999999999998843

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=93.51  E-value=0.4  Score=46.91  Aligned_cols=15  Identities=13%  Similarity=-0.039  Sum_probs=13.3

Q ss_pred             cEEEEccCCCccccc
Q psy7952          67 DIFVSMPTGAVSLVG   81 (444)
Q Consensus        67 ~~ii~apTGsGKT~~   81 (444)
                      -+++++++|+|||.+
T Consensus       102 vi~lvG~~GvGKTTt  116 (429)
T TIGR01425       102 VIMFVGLQGSGKTTT  116 (429)
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999977

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.

>PRK11054 helD DNA helicase IV; Provisional

Probab=93.51  E-value=0.034  Score=58.09  Aligned_cols=77  Identities=9%  Similarity=0.024  Sum_probs=49.9

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccc-cCC-ccceeEEEcchhhhhcccCccchH
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFIL-NGN-VRSRNGWISPILSSFYLRFRDDKT  127 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~-~~~-~~~~vlil~P~~~L~~~~q~~~~~  127 (444)
                      .|+-|++++..  .. .+++|.|..|||||.++         +.. +.++. .++ ...++++++.++..+     .+.-
T Consensus       197 L~~~Q~~av~~--~~-~~~lV~agaGSGKT~vl---------~~r-~ayLl~~~~~~~~~IL~ltft~~AA-----~em~  258 (684)
T PRK11054        197 LNPSQARAVVN--GE-DSLLVLAGAGSGKTSVL---------VAR-AGWLLARGQAQPEQILLLAFGRQAA-----EEMD  258 (684)
T ss_pred             CCHHHHHHHhC--CC-CCeEEEEeCCCCHHHHH---------HHH-HHHHHHhCCCCHHHeEEEeccHHHH-----HHHH
Confidence            46889998864  22 57899999999999881         111 11222 222 234789999999999     6777


Q ss_pred             hhh--cCCCCceeEEEEeC
Q psy7952         128 SIV--TGRSDLYQLELIVS  144 (444)
Q Consensus       128 ~~l--~~~~~~i~~~~~~~  144 (444)
                      +++  ..+...+.+.++|+
T Consensus       259 eRL~~~lg~~~v~v~TFHS  277 (684)
T PRK11054        259 ERIRERLGTEDITARTFHA  277 (684)
T ss_pred             HHHHHhcCCCCcEEEeHHH
Confidence            666  33323356666554

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.49  E-value=0.31  Score=47.12  Aligned_cols=39  Identities=21%  Similarity=0.285  Sum_probs=23.6

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      ....++||||+|.+....      ...+.+.+...+.+..+++.|
T Consensus       118 ~~~kviIIDEa~~l~~~a------~naLLk~lEe~~~~~~fIl~t  156 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRHS------FNALLKTLEEPPQHIKFILAT  156 (363)
T ss_pred             CCceEEEEEChhhcCHHH------HHHHHHHHhcCCCCeEEEEEc
Confidence            356799999999975421      234444444445545565554

>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=93.48  E-value=0.074  Score=45.22  Aligned_cols=39  Identities=10%  Similarity=0.025  Sum_probs=19.2

Q ss_pred             EEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          69 FVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        69 ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      ++.|+-|-|||.+..+++          ..+...+. .+|+|.+|+.+-+
T Consensus         1 VltA~RGRGKSa~lGl~~----------a~l~~~~~-~~I~vtAP~~~~~   39 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAA----------AALIQKGK-IRILVTAPSPENV   39 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCC----------CCSSS------EEEE-SS--S-
T ss_pred             CccCCCCCCHHHHHHHHH----------HHHHHhcC-ceEEEecCCHHHH
Confidence            478999999997733322          12333333 3678889999877

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.

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=93.41  E-value=0.23  Score=44.47  Aligned_cols=17  Identities=12%  Similarity=0.221  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCCccccc
Q psy7952          65 THDIFVSMPTGAVSLVG   81 (444)
Q Consensus        65 ~~~~ii~apTGsGKT~~   81 (444)
                      .+++++.+|||+|||..
T Consensus       151 PknVLFyGppGTGKTm~  167 (368)
T COG1223         151 PKNVLFYGPPGTGKTMM  167 (368)
T ss_pred             cceeEEECCCCccHHHH
Confidence            37899999999999976

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=93.40  E-value=1.3  Score=43.32  Aligned_cols=58  Identities=14%  Similarity=0.150  Sum_probs=32.2

Q ss_pred             hhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHh
Q psy7952         189 RYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVL  250 (444)
Q Consensus       189 ~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l  250 (444)
                      .+.+.++++||.+-+...    .......+..+.........++.+|||........+...+
T Consensus       266 ~l~~~d~VLIDTaGrsqr----d~~~~~~l~~l~~~~~~~~~~LVl~at~~~~~~~~~~~~f  323 (420)
T PRK14721        266 ELRGKHMVLIDTVGMSQR----DQMLAEQIAMLSQCGTQVKHLLLLNATSSGDTLDEVISAY  323 (420)
T ss_pred             HhcCCCEEEecCCCCCcc----hHHHHHHHHHHhccCCCceEEEEEcCCCCHHHHHHHHHHh
Confidence            455678888888633211    1222334444332222334578899998777666655544

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=93.32  E-value=0.54  Score=40.66  Aligned_cols=40  Identities=13%  Similarity=0.076  Sum_probs=24.0

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      .....+|||||+|.+...      ....+.+.+...+++..+|+++
T Consensus        94 ~~~~kviiide~~~l~~~------~~~~Ll~~le~~~~~~~~il~~  133 (188)
T TIGR00678        94 ESGRRVVIIEDAERMNEA------AANALLKTLEEPPPNTLFILIT  133 (188)
T ss_pred             cCCeEEEEEechhhhCHH------HHHHHHHHhcCCCCCeEEEEEE
Confidence            346789999999997542      1244555555444444455544

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.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=93.32  E-value=0.084  Score=50.21  Aligned_cols=42  Identities=5%  Similarity=-0.077  Sum_probs=27.8

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccC
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATA  238 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~  238 (444)
                      +..+++|||++|.|....      -+.+.+.+.+-+.+..++++|.-+
T Consensus       107 g~~kV~iI~~ae~m~~~A------aNaLLKtLEEPp~~t~fiL~t~~~  148 (334)
T PRK07993        107 GGAKVVWLPDAALLTDAA------ANALLKTLEEPPENTWFFLACREP  148 (334)
T ss_pred             CCceEEEEcchHhhCHHH------HHHHHHHhcCCCCCeEEEEEECCh
Confidence            467899999999986422      255556666655555566666543

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=93.32  E-value=0.44  Score=46.73  Aligned_cols=28  Identities=11%  Similarity=0.280  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHccCCcEEEEccCCCccccc
Q psy7952          53 LQKKAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        53 ~Q~~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      .....+..+..+ +++++.+|+|+|||..
T Consensus       183 ~le~l~~~L~~~-~~iil~GppGtGKT~l  210 (459)
T PRK11331        183 TIETILKRLTIK-KNIILQGPPGVGKTFV  210 (459)
T ss_pred             HHHHHHHHHhcC-CCEEEECCCCCCHHHH
Confidence            445556666666 8999999999999977

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=93.27  E-value=0.12  Score=48.84  Aligned_cols=42  Identities=7%  Similarity=-0.049  Sum_probs=27.9

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccC
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATA  238 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~  238 (444)
                      +..+++|||++|.|....      ...+.+.+..-+.+..+++.|..+
T Consensus       106 g~~KV~iI~~a~~m~~~A------aNaLLKtLEEPp~~~~fiL~t~~~  147 (325)
T PRK06871        106 GGNKVVYIQGAERLTEAA------ANALLKTLEEPRPNTYFLLQADLS  147 (325)
T ss_pred             CCceEEEEechhhhCHHH------HHHHHHHhcCCCCCeEEEEEECCh
Confidence            467899999999986432      355666666656656566655443

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=93.25  E-value=2.1  Score=45.15  Aligned_cols=16  Identities=19%  Similarity=0.100  Sum_probs=13.9

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +-+.+++|||+|||.+
T Consensus       186 ~Vi~lVGpnGvGKTTT  201 (767)
T PRK14723        186 GVLALVGPTGVGKTTT  201 (767)
T ss_pred             eEEEEECCCCCcHHHH
Confidence            3478999999999977

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.24  E-value=0.4  Score=49.47  Aligned_cols=41  Identities=15%  Similarity=0.137  Sum_probs=25.3

Q ss_pred             hhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         189 RYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       189 ~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      .+...+++||||+|.+...      ....+.+.+..-+....+|+++
T Consensus       124 ~~~~~KVvIIdEad~Lt~~------a~naLLK~LEePp~~tv~IL~t  164 (620)
T PRK14954        124 QKGRYRVYIIDEVHMLSTA------AFNAFLKTLEEPPPHAIFIFAT  164 (620)
T ss_pred             hcCCCEEEEEeChhhcCHH------HHHHHHHHHhCCCCCeEEEEEe
Confidence            3456789999999997542      2344555555544444455554

>KOG0744|consensus

Probab=93.24  E-value=0.16  Score=46.91  Aligned_cols=30  Identities=17%  Similarity=0.408  Sum_probs=19.3

Q ss_pred             cccccHHHHHHHHHhhCCccEEEEeccccc
Q psy7952         175 AVTESFHYLLQHLVRYNKLAYIVVDEAHCV  204 (444)
Q Consensus       175 l~~~~~~~~~~~~~~~~~~~~iViDE~H~~  204 (444)
                      +....|..+..-..+.+.+-+|.|||+..+
T Consensus       233 lV~kmF~kI~ELv~d~~~lVfvLIDEVESL  262 (423)
T KOG0744|consen  233 LVAKMFQKIQELVEDRGNLVFVLIDEVESL  262 (423)
T ss_pred             HHHHHHHHHHHHHhCCCcEEEEEeHHHHHH
Confidence            333334444444445667889999999876

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=93.24  E-value=0.43  Score=44.49  Aligned_cols=125  Identities=9%  Similarity=0.087  Sum_probs=67.9

Q ss_pred             cEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc---chhhhhcccCccchHhhh--cCCCCceeEEE
Q psy7952          67 DIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS---PILSSFYLRFRDDKTSIV--TGRSDLYQLEL  141 (444)
Q Consensus        67 ~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~---P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~  141 (444)
                      -+++++..|+|||.+          +.-+.+++...|..   ++++   ..|+-+     -+|++.|  +.+     +..
T Consensus       141 Vil~vGVNG~GKTTT----------IaKLA~~l~~~g~~---VllaA~DTFRAaA-----iEQL~~w~er~g-----v~v  197 (340)
T COG0552         141 VILFVGVNGVGKTTT----------IAKLAKYLKQQGKS---VLLAAGDTFRAAA-----IEQLEVWGERLG-----VPV  197 (340)
T ss_pred             EEEEEecCCCchHhH----------HHHHHHHHHHCCCe---EEEEecchHHHHH-----HHHHHHHHHHhC-----CeE
Confidence            368999999999987          23323445555554   4443   467777     7888888  445     333


Q ss_pred             EeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHH
Q psy7952         142 IVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGEL  221 (444)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~  221 (444)
                      +.+....+...-.+..                         +.  ...-.++++|++|=+-++...    .+.+..|.++
T Consensus       198 I~~~~G~DpAaVafDA-------------------------i~--~Akar~~DvvliDTAGRLhnk----~nLM~EL~KI  246 (340)
T COG0552         198 ISGKEGADPAAVAFDA-------------------------IQ--AAKARGIDVVLIDTAGRLHNK----KNLMDELKKI  246 (340)
T ss_pred             EccCCCCCcHHHHHHH-------------------------HH--HHHHcCCCEEEEeCcccccCc----hhHHHHHHHH
Confidence            3322222222112211                         11  112347888999988887543    2334444444


Q ss_pred             HHhhCCCC------cEEEEeccCCcchHHH
Q psy7952         222 RQFTGNSI------PIIALTATAEPSVKQD  245 (444)
Q Consensus       222 ~~~~~~~~------~~v~lSAT~~~~~~~~  245 (444)
                      .+-..+..      -++.+=||...+..+-
T Consensus       247 ~rV~~k~~~~ap~e~llvlDAttGqnal~Q  276 (340)
T COG0552         247 VRVIKKDDPDAPHEILLVLDATTGQNALSQ  276 (340)
T ss_pred             HHHhccccCCCCceEEEEEEcccChhHHHH
Confidence            44333222      2455578877655543

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=93.20  E-value=0.24  Score=47.59  Aligned_cols=19  Identities=16%  Similarity=-0.071  Sum_probs=16.3

Q ss_pred             HccCCcEEEEccCCCccccc
Q psy7952          62 LLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        62 ~~~~~~~ii~apTGsGKT~~   81 (444)
                      -.| ++.+|.+|.|+|||..
T Consensus       167 GkG-QR~lIvgppGvGKTTL  185 (416)
T PRK09376        167 GKG-QRGLIVAPPKAGKTVL  185 (416)
T ss_pred             ccC-ceEEEeCCCCCChhHH
Confidence            356 8999999999999955

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=93.15  E-value=0.034  Score=58.26  Aligned_cols=63  Identities=11%  Similarity=-0.013  Sum_probs=43.6

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCc-cceeEEEcchhhhhcccCccchHhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNV-RSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~-~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      ++-|++++.+.  . .+++|.|.+|||||.+        . ...+...+...+. -.++|+++.|+..+     .+..++
T Consensus         4 n~~Q~~av~~~--~-g~~lV~AgpGSGKT~v--------L-~~Ria~Li~~~~v~p~~IL~lTFT~kAA-----~em~~R   66 (672)
T PRK10919          4 NPGQQQAVEFV--T-GPCLVLAGAGSGKTRV--------I-TNKIAHLIRGCGYQARHIAAVTFTNKAA-----REMKER   66 (672)
T ss_pred             CHHHHHHHhCC--C-CCEEEEecCCCCHHHH--------H-HHHHHHHHHhcCCCHHHeeeEechHHHH-----HHHHHH
Confidence            46899998762  3 5899999999999988        2 1221222323343 34789999999999     676666


Q ss_pred             h
Q psy7952         130 V  130 (444)
Q Consensus       130 l  130 (444)
                      +
T Consensus        67 l   67 (672)
T PRK10919         67 V   67 (672)
T ss_pred             H
Confidence            6

>PRK08506 replicative DNA helicase; Provisional

Probab=93.04  E-value=0.27  Score=49.30  Aligned_cols=165  Identities=13%  Similarity=0.100  Sum_probs=74.5

Q ss_pred             ccCchHHHHHHHHHHccC---CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCcc
Q psy7952          48 SFKCELQKKAIRHILLRT---HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRD  124 (444)
Q Consensus        48 ~~~t~~Q~~~~~~~~~~~---~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~  124 (444)
                      .+||.  ...++.+..|-   .-+++.|.||+|||..|+-.+         .+ ....+  .+|+|++.-..-      .
T Consensus       174 Gi~TG--~~~LD~~~~G~~~G~LivIaarpg~GKT~fal~ia---------~~-~~~~g--~~V~~fSlEMs~------~  233 (472)
T PRK08506        174 GLDTG--FVELNKMTKGFNKGDLIIIAARPSMGKTTLCLNMA---------LK-ALNQD--KGVAFFSLEMPA------E  233 (472)
T ss_pred             cccCC--hHHHHhhcCCCCCCceEEEEcCCCCChHHHHHHHH---------HH-HHhcC--CcEEEEeCcCCH------H
Confidence            34543  33556655431   557899999999997633211         11 11222  234666533222      2


Q ss_pred             chHhhh-c--CCCCceeEEE-EeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh-hCCccEEEEe
Q psy7952         125 DKTSIV-T--GRSDLYQLEL-IVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR-YNKLAYIVVD  199 (444)
Q Consensus       125 ~~~~~l-~--~~~~~i~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~-~~~~~~iViD  199 (444)
                      +.+.++ +  .+   +.... ..+.....++.........+.. ..+.|-....+.-.......+.... ...+++||||
T Consensus       234 ql~~Rlla~~s~---v~~~~i~~~~l~~~e~~~~~~a~~~l~~-~~l~I~d~~~~ti~~I~~~~r~l~~~~~~~~lvvID  309 (472)
T PRK08506        234 QLMLRMLSAKTS---IPLQNLRTGDLDDDEWERLSDACDELSK-KKLFVYDSGYVNIHQVRAQLRKLKSQHPEIGLAVID  309 (472)
T ss_pred             HHHHHHHHHhcC---CCHHHHhcCCCCHHHHHHHHHHHHHHHc-CCeEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEc
Confidence            333333 1  22   21111 1244444444444333333333 3455543222211111222222222 2468999999


Q ss_pred             ccccccccCC--CcHHHHHHHHHHHHhhCC--CCcEEEEec
Q psy7952         200 EAHCVSEWGH--DFRPTYRRLGELRQFTGN--SIPIIALTA  236 (444)
Q Consensus       200 E~H~~~~~~~--~~~~~~~~l~~~~~~~~~--~~~~v~lSA  236 (444)
                      =.+.+...+.  .-...+..+.+-++.+.+  +++++++|-
T Consensus       310 yLql~~~~~~~~~r~~ev~~isr~LK~lAkel~ipVi~lsQ  350 (472)
T PRK08506        310 YLQLMSGSGNFKDRHLQISEISRGLKLLARELDIPIIALSQ  350 (472)
T ss_pred             ChhhccCCCCCCCHHHHHHHHHHHHHHHHHHhCCcEEEEee
Confidence            9998853321  112223333333332222  477888873

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=92.97  E-value=0.1  Score=49.13  Aligned_cols=42  Identities=14%  Similarity=0.120  Sum_probs=28.5

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccC
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATA  238 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~  238 (444)
                      +..+++|||++|.|....      -..+.+.+.+-+.+..++++|..+
T Consensus       107 ~~~kV~iI~~ae~m~~~A------aNaLLKtLEEPp~~t~fiL~t~~~  148 (319)
T PRK06090        107 NGYRLFVIEPADAMNESA------SNALLKTLEEPAPNCLFLLVTHNQ  148 (319)
T ss_pred             CCceEEEecchhhhCHHH------HHHHHHHhcCCCCCeEEEEEECCh
Confidence            457899999999986422      355666666666656666666554

>TIGR00767 rho transcription termination factor Rho

Probab=92.97  E-value=0.49  Score=45.71  Aligned_cols=18  Identities=17%  Similarity=0.006  Sum_probs=16.0

Q ss_pred             ccCCcEEEEccCCCccccc
Q psy7952          63 LRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        63 ~~~~~~ii~apTGsGKT~~   81 (444)
                      .| +.+.|.+|+|+|||..
T Consensus       167 ~G-q~~~IvG~~g~GKTtL  184 (415)
T TIGR00767       167 KG-QRGLIVAPPKAGKTVL  184 (415)
T ss_pred             CC-CEEEEECCCCCChhHH
Confidence            46 8899999999999966

Members of this family differ in the specificity of RNA binding.

>PRK05973 replicative DNA helicase; Provisional

Probab=92.92  E-value=0.2  Score=44.98  Aligned_cols=18  Identities=6%  Similarity=0.060  Sum_probs=15.4

Q ss_pred             CcEEEEccCCCccccccc
Q psy7952          66 HDIFVSMPTGAVSLVGSV   83 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~   83 (444)
                      .-++|.|+||+|||..|+
T Consensus        65 sl~LIaG~PG~GKT~lal   82 (237)
T PRK05973         65 DLVLLGARPGHGKTLLGL   82 (237)
T ss_pred             CEEEEEeCCCCCHHHHHH
Confidence            668999999999998743

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.89  E-value=0.14  Score=52.93  Aligned_cols=19  Identities=11%  Similarity=0.172  Sum_probs=15.7

Q ss_pred             CcEEEEccCCCcccccccc
Q psy7952          66 HDIFVSMPTGAVSLVGSVV   84 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~   84 (444)
                      +.++++||.|+|||.+|..
T Consensus        39 ~a~Lf~Gp~G~GKttlA~~   57 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSARI   57 (620)
T ss_pred             ceEEEECCCCCChHHHHHH
Confidence            4579999999999988543

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=92.89  E-value=0.83  Score=48.15  Aligned_cols=25  Identities=12%  Similarity=0.149  Sum_probs=18.2

Q ss_pred             HHHHHHccC--CcEEEEccCCCccccc
Q psy7952          57 AIRHILLRT--HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        57 ~~~~~~~~~--~~~ii~apTGsGKT~~   81 (444)
                      .+..+..+.  .++++.+|+|+|||..
T Consensus        42 ~L~~~i~~~~~~slLL~GPpGtGKTTL   68 (725)
T PRK13341         42 LLRRAIKADRVGSLILYGPPGVGKTTL   68 (725)
T ss_pred             HHHHHHhcCCCceEEEECCCCCCHHHH
Confidence            444444432  4799999999999977

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=92.88  E-value=0.36  Score=45.71  Aligned_cols=32  Identities=9%  Similarity=0.012  Sum_probs=24.8

Q ss_pred             hHHHHHHHHHHcc----CCcEEEEccCCCccccccc
Q psy7952          52 ELQKKAIRHILLR----THDIFVSMPTGAVSLVGSV   83 (444)
Q Consensus        52 ~~Q~~~~~~~~~~----~~~~ii~apTGsGKT~~a~   83 (444)
                      |||...+..+...    .+-+++++|.|.|||..|.
T Consensus         4 PW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la~   39 (325)
T PRK08699          4 PWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFAR   39 (325)
T ss_pred             CccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHHH
Confidence            4888888887742    1458999999999998743

>KOG0738|consensus

Probab=92.87  E-value=0.19  Score=47.58  Aligned_cols=24  Identities=25%  Similarity=0.430  Sum_probs=18.3

Q ss_pred             HHHHHHhhCCccEEEEeccccccc
Q psy7952         183 LLQHLVRYNKLAYIVVDEAHCVSE  206 (444)
Q Consensus       183 ~~~~~~~~~~~~~iViDE~H~~~~  206 (444)
                      ++..+..+.-.+.|+|||++.+..
T Consensus       295 lLFemARfyAPStIFiDEIDslcs  318 (491)
T KOG0738|consen  295 LLFEMARFYAPSTIFIDEIDSLCS  318 (491)
T ss_pred             HHHHHHHHhCCceeehhhHHHHHh
Confidence            455555666789999999999854

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=92.86  E-value=0.24  Score=47.73  Aligned_cols=42  Identities=10%  Similarity=0.050  Sum_probs=27.1

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccC
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATA  238 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~  238 (444)
                      ....++||||+|.+...      ....+.+.+..-+.+..+|++|..+
T Consensus       140 ~~~kVviIDead~m~~~------aanaLLK~LEepp~~~~~IL~t~~~  181 (365)
T PRK07471        140 GGWRVVIVDTADEMNAN------AANALLKVLEEPPARSLFLLVSHAP  181 (365)
T ss_pred             CCCEEEEEechHhcCHH------HHHHHHHHHhcCCCCeEEEEEECCc
Confidence            45689999999997532      2345556665555555566666554

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.84  E-value=0.21  Score=48.95  Aligned_cols=19  Identities=21%  Similarity=0.141  Sum_probs=15.5

Q ss_pred             CcEEEEccCCCcccccccc
Q psy7952          66 HDIFVSMPTGAVSLVGSVV   84 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~   84 (444)
                      +.+++++|+|+|||.+|.+
T Consensus        39 ha~lf~Gp~G~GKtt~A~~   57 (397)
T PRK14955         39 HGYIFSGLRGVGKTTAARV   57 (397)
T ss_pred             eeEEEECCCCCCHHHHHHH
Confidence            3488999999999988543

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=92.76  E-value=0.076  Score=50.09  Aligned_cols=30  Identities=23%  Similarity=0.148  Sum_probs=25.9

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      +.|.+.+..+..+..++++.++||+|||..
T Consensus       135 ~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl  164 (319)
T PRK13894        135 AAQREAIIAAVRAHRNILVIGGTGSGKTTL  164 (319)
T ss_pred             HHHHHHHHHHHHcCCeEEEECCCCCCHHHH
Confidence            678888888777668999999999999965

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=92.74  E-value=0.11  Score=59.36  Aligned_cols=58  Identities=19%  Similarity=0.054  Sum_probs=40.1

Q ss_pred             chHHHHHHHHHHccC-CcEEEEccCCCcccccccccccceEEeCCCccccc--cCCccceeEEEcchhhhh
Q psy7952          51 CELQKKAIRHILLRT-HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFIL--NGNVRSRNGWISPILSSF  118 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~-~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~--~~~~~~~vlil~P~~~L~  118 (444)
                      ++.|.+|+..++.+. +-++|.+..|+|||.+          +..+...+.  ......+|+.++||-.-+
T Consensus       969 t~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~----------l~~v~~~~~~l~~~~~~~V~glAPTgrAA 1029 (1747)
T PRK13709        969 TSGQRAATRMILESTDRFTVVQGYAGVGKTTQ----------FRAVMSAVNTLPESERPRVVGLGPTHRAV 1029 (1747)
T ss_pred             CHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHH----------HHHHHHHHHHhhcccCceEEEECCcHHHH
Confidence            689999999999852 5689999999999977          222111121  111223568889998887

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=92.70  E-value=0.54  Score=48.01  Aligned_cols=19  Identities=21%  Similarity=0.186  Sum_probs=15.7

Q ss_pred             CcEEEEccCCCcccccccc
Q psy7952          66 HDIFVSMPTGAVSLVGSVV   84 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~   84 (444)
                      +.++++||.|+|||..|..
T Consensus        39 hA~Lf~GP~GvGKTTlA~~   57 (605)
T PRK05896         39 HAYIFSGPRGIGKTSIAKI   57 (605)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            4589999999999988543

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=92.69  E-value=0.8  Score=41.19  Aligned_cols=25  Identities=16%  Similarity=0.003  Sum_probs=18.6

Q ss_pred             HHHHHHccC----CcEEEEccCCCccccc
Q psy7952          57 AIRHILLRT----HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        57 ~~~~~~~~~----~~~ii~apTGsGKT~~   81 (444)
                      .++.++.|.    .-+++.+++|+|||..
T Consensus        13 ~LD~~l~gG~~~g~~~~i~G~~GsGKt~l   41 (234)
T PRK06067         13 ELDRKLGGGIPFPSLILIEGDHGTGKSVL   41 (234)
T ss_pred             HHHHhhCCCCcCCcEEEEECCCCCChHHH
Confidence            455665531    5689999999999977

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=92.67  E-value=0.11  Score=49.06  Aligned_cols=30  Identities=27%  Similarity=0.190  Sum_probs=26.4

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      +.|.+.+..+.....+++++++||||||..
T Consensus       131 ~~~~~~L~~~v~~~~nilI~G~tGSGKTTl  160 (323)
T PRK13833        131 EAQASVIRSAIDSRLNIVISGGTGSGKTTL  160 (323)
T ss_pred             HHHHHHHHHHHHcCCeEEEECCCCCCHHHH
Confidence            678888888887768999999999999976

>PRK13342 recombination factor protein RarA; Reviewed

Probab=92.55  E-value=0.31  Score=48.04  Aligned_cols=24  Identities=13%  Similarity=0.192  Sum_probs=17.6

Q ss_pred             HHHHHccC--CcEEEEccCCCccccc
Q psy7952          58 IRHILLRT--HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        58 ~~~~~~~~--~~~ii~apTGsGKT~~   81 (444)
                      +..++.+.  .++++.||+|+|||..
T Consensus        27 L~~~i~~~~~~~ilL~GppGtGKTtL   52 (413)
T PRK13342         27 LRRMIEAGRLSSMILWGPPGTGKTTL   52 (413)
T ss_pred             HHHHHHcCCCceEEEECCCCCCHHHH
Confidence            44444432  4799999999999977

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=92.55  E-value=0.086  Score=59.44  Aligned_cols=59  Identities=17%  Similarity=0.027  Sum_probs=39.9

Q ss_pred             CchHHHHHHHHHHcc-CCcEEEEccCCCcccccccccccceEEeCCCccccc--cCCccceeEEEcchhhhh
Q psy7952          50 KCELQKKAIRHILLR-THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFIL--NGNVRSRNGWISPILSSF  118 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~-~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~--~~~~~~~vlil~P~~~L~  118 (444)
                      .|+.|.+|+..++.+ ++-++|.+..|+|||.+          +..++..+.  ......+++.++||-..+
T Consensus       836 Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~----------l~~i~~~~~~l~e~~g~~V~glAPTgkAa  897 (1623)
T PRK14712        836 LTSGQRAATRMILETSDRFTVVQGYAGVGKTTQ----------FRAVMSAVNMLPESERPRVVGLGPTHRAV  897 (1623)
T ss_pred             cCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHH----------HHHHHHHHHHHhhccCceEEEEechHHHH
Confidence            357999999999964 25689999999999976          111111111  112223568899998887

>PRK09165 replicative DNA helicase; Provisional

Probab=92.53  E-value=0.33  Score=48.96  Aligned_cols=168  Identities=13%  Similarity=0.065  Sum_probs=77.4

Q ss_pred             ccCchHHHHHHHHHHccC---CcEEEEccCCCcccccccccccceEEeCCCccccccC------------CccceeEEEc
Q psy7952          48 SFKCELQKKAIRHILLRT---HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG------------NVRSRNGWIS  112 (444)
Q Consensus        48 ~~~t~~Q~~~~~~~~~~~---~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~------------~~~~~vlil~  112 (444)
                      .++|.+.  -++.+..|-   .-++|.|+||+|||..|+-.+.+     .    ....            ....+|+|++
T Consensus       199 gi~TG~~--~LD~~~gG~~~g~livIaarpg~GKT~~al~ia~~-----~----a~~~~~~~~~~~~~~~~~g~~vl~fS  267 (497)
T PRK09165        199 GISTGLR--DLDSKLGGLHPSDLIILAGRPSMGKTALATNIAFN-----A----AKAYRREAQPDGSKKAVNGGVVGFFS  267 (497)
T ss_pred             cccCChH--HHhhhcCCCCCCceEEEEeCCCCChHHHHHHHHHH-----H----HHhhcccccccccccccCCCeEEEEe
Confidence            3444443  455554431   45799999999999764322111     0    1110            0123457775


Q ss_pred             chhhhhcccCccchHhhh---cCCCCceeEEE-EeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH
Q psy7952         113 PILSSFYLRFRDDKTSIV---TGRSDLYQLEL-IVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV  188 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l---~~~~~~i~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~  188 (444)
                      .-..-.      +.+.++   ..+   +.... ..+.....++..+......+. ...+.|-....+.-.......+...
T Consensus       268 lEMs~~------ql~~R~la~~s~---v~~~~i~~~~l~~~e~~~l~~a~~~l~-~~~l~I~d~~~~ti~~i~~~ir~l~  337 (497)
T PRK09165        268 LEMSAE------QLATRILSEQSE---ISSSKIRRGKISEEDFEKLVDASQELQ-KLPLYIDDTPALSISQLRARARRLK  337 (497)
T ss_pred             CcCCHH------HHHHHHHHHhcC---CCHHHHhcCCCCHHHHHHHHHHHHHHh-cCCeEEeCCCCCCHHHHHHHHHHHH
Confidence            333222      333443   122   22211 233445555554444443332 3445555433332111122233333


Q ss_pred             hhCCccEEEEeccccccccCC---CcH-HHHHHHHHHHHhhC--CCCcEEEEec
Q psy7952         189 RYNKLAYIVVDEAHCVSEWGH---DFR-PTYRRLGELRQFTG--NSIPIIALTA  236 (444)
Q Consensus       189 ~~~~~~~iViDE~H~~~~~~~---~~~-~~~~~l~~~~~~~~--~~~~~v~lSA  236 (444)
                      ....+++||||=.|.+...+.   .-+ ..+..+.+-++.+.  -+++++++|-
T Consensus       338 ~~~~~~lvvIDyLqli~~~~~~~~~~r~~ev~~is~~LK~lAkel~ipVi~lsQ  391 (497)
T PRK09165        338 RQHGLDLLVVDYLQLIRGSSKRSSDNRVQEISEITQGLKALAKELNIPVIALSQ  391 (497)
T ss_pred             HhcCCCEEEEcchHhccCCCCCCCCchHHHHHHHHHHHHHHHHHhCCeEEEeec
Confidence            345689999999998853221   111 22333333333332  2367777764

>PRK05636 replicative DNA helicase; Provisional

Probab=92.53  E-value=0.28  Score=49.38  Aligned_cols=163  Identities=11%  Similarity=0.065  Sum_probs=73.7

Q ss_pred             cCchHHHHHHHHHHcc---CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcc---hhhhhcccC
Q psy7952          49 FKCELQKKAIRHILLR---THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISP---ILSSFYLRF  122 (444)
Q Consensus        49 ~~t~~Q~~~~~~~~~~---~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P---~~~L~~~~q  122 (444)
                      +||.+.  -+..+..|   ..-+++.|.||+|||..|+-.+         .......+  ..++|++.   ...++    
T Consensus       248 i~TG~~--~LD~~t~Gl~~G~Liiiaarpg~GKT~~al~~a---------~~~a~~~g--~~v~~fSlEMs~~ql~----  310 (505)
T PRK05636        248 IPTGFK--DLDDLTNGLRGGQMIIVAARPGVGKSTLALDFM---------RSASIKHN--KASVIFSLEMSKSEIV----  310 (505)
T ss_pred             eecChH--HHhhhcCCCCCCceEEEEeCCCCCHHHHHHHHH---------HHHHHhCC--CeEEEEEeeCCHHHHH----
Confidence            455433  45555443   1456889999999996632211         11111222  23466643   33333    


Q ss_pred             ccchHhhhcCCCCceeEEE-EeCCCChhhHHHHHHHHHhcCCCeeEEEE-CCCccccccHHHHHHHHHhhCCccEEEEec
Q psy7952         123 RDDKTSIVTGRSDLYQLEL-IVSGQTKTENKAILEELRLVKPRIKLLYV-TPERAVTESFHYLLQHLVRYNKLAYIVVDE  200 (444)
Q Consensus       123 ~~~~~~~l~~~~~~i~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~-Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE  200 (444)
                       ...+... .+   ++... ..+..+..++..+...+..+. +..+.|- +|. +.-.......+.......+++||||=
T Consensus       311 -~R~ls~~-s~---v~~~~i~~g~l~~~e~~~~~~a~~~l~-~~~l~I~d~~~-~ti~~I~~~~r~~~~~~~~~lvvIDY  383 (505)
T PRK05636        311 -MRLLSAE-AE---VRLSDMRGGKMDEDAWEKLVQRLGKIA-QAPIFIDDSAN-LTMMEIRSKARRLKQKHDLKLIVVDY  383 (505)
T ss_pred             -HHHHHHh-cC---CCHHHHhcCCCCHHHHHHHHHHHHHHh-cCCEEEECCCC-CCHHHHHHHHHHHHHhcCCCEEEEcc
Confidence             2222211 11   11111 133445555555444444333 3445554 333 21111122223333345699999999


Q ss_pred             cccccccC--CCcHHHHHHHHHHHHhhCC--CCcEEEEe
Q psy7952         201 AHCVSEWG--HDFRPTYRRLGELRQFTGN--SIPIIALT  235 (444)
Q Consensus       201 ~H~~~~~~--~~~~~~~~~l~~~~~~~~~--~~~~v~lS  235 (444)
                      .|.+....  ..-...+..+.+-++.+.+  +++++++|
T Consensus       384 Lql~~~~~~~~~r~~ei~~isr~LK~lAkel~ipVi~ls  422 (505)
T PRK05636        384 LQLMSSGKRVESRQQEVSEFSRQLKLLAKELDVPLIAIS  422 (505)
T ss_pred             hHhcCCCCCCCcHHHHHHHHHHHHHHHHHHhCCeEEEEe
Confidence            99985321  1111223333333333322  47788887

>PRK08840 replicative DNA helicase; Provisional

Probab=92.48  E-value=0.34  Score=48.36  Aligned_cols=166  Identities=8%  Similarity=0.036  Sum_probs=74.5

Q ss_pred             ccCchHHHHHHHHHHcc---CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCcc
Q psy7952          48 SFKCELQKKAIRHILLR---THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRD  124 (444)
Q Consensus        48 ~~~t~~Q~~~~~~~~~~---~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~  124 (444)
                      .++|.+.  .++.+..|   .+-+++.|.||.|||..|+-.+.         ......+  ..|+|++.-..-.      
T Consensus       199 gi~TG~~--~LD~~~~G~~~g~LiviaarPg~GKTafalnia~---------~~a~~~~--~~v~~fSlEMs~~------  259 (464)
T PRK08840        199 GVDTGFT--DLNKKTAGLQGSDLIIVAARPSMGKTTFAMNLCE---------NAAMDQD--KPVLIFSLEMPAE------  259 (464)
T ss_pred             CcCCCcH--HHHHhhcCCCCCceEEEEeCCCCchHHHHHHHHH---------HHHHhCC--CeEEEEeccCCHH------
Confidence            4555543  44444433   15578899999999976322111         1111222  2346665332222      


Q ss_pred             chHhhh---cCCCCceeEEEE-eCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh-hCCccEEEEe
Q psy7952         125 DKTSIV---TGRSDLYQLELI-VSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR-YNKLAYIVVD  199 (444)
Q Consensus       125 ~~~~~l---~~~~~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~-~~~~~~iViD  199 (444)
                      +.+.++   ..+   +....+ .+..+..++.........+.....+.|-....+.-.......+.... ...+++||||
T Consensus       260 ql~~Rlla~~s~---v~~~~i~~~~l~~~e~~~~~~a~~~l~~~~~l~I~d~~~~ti~~i~~~~r~~~~~~~~~~lvvID  336 (464)
T PRK08840        260 QLMMRMLASLSR---VDQTKIRTGQLDDEDWARISSTMGILMEKKNMYIDDSSGLTPTEVRSRARRIAREHGGLSMIMVD  336 (464)
T ss_pred             HHHHHHHHhhCC---CCHHHHhcCCCCHHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEc
Confidence            333333   112   221111 33445555554443333332233455542211211111222222222 2358999999


Q ss_pred             ccccccccCC--CcHHHHHHHHHHHHhhC--CCCcEEEEe
Q psy7952         200 EAHCVSEWGH--DFRPTYRRLGELRQFTG--NSIPIIALT  235 (444)
Q Consensus       200 E~H~~~~~~~--~~~~~~~~l~~~~~~~~--~~~~~v~lS  235 (444)
                      =.|.+...+.  .-...+..+.+-++.+.  -+++++++|
T Consensus       337 YLql~~~~~~~~~r~~ei~~isr~LK~lAkel~ipVi~Ls  376 (464)
T PRK08840        337 YLQLMRVPALSDNRTLEIAEISRSLKALAKELNVPVVALS  376 (464)
T ss_pred             cHHhcCCCCCCCchHHHHHHHHHHHHHHHHHhCCeEEEEE
Confidence            9998853221  11122333433333332  247788887

>KOG0991|consensus

Probab=92.46  E-value=0.16  Score=44.55  Aligned_cols=19  Identities=16%  Similarity=0.251  Sum_probs=16.1

Q ss_pred             ccC-CcEEEEccCCCccccc
Q psy7952          63 LRT-HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        63 ~~~-~~~ii~apTGsGKT~~   81 (444)
                      +|+ .++++.+|+|+|||..
T Consensus        45 ~gnmP~liisGpPG~GKTTs   64 (333)
T KOG0991|consen   45 EGNMPNLIISGPPGTGKTTS   64 (333)
T ss_pred             cCCCCceEeeCCCCCchhhH
Confidence            343 6799999999999988

>PRK08006 replicative DNA helicase; Provisional

Probab=92.45  E-value=0.38  Score=48.06  Aligned_cols=165  Identities=8%  Similarity=0.020  Sum_probs=75.9

Q ss_pred             cCchHHHHHHHHHHcc---CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccc
Q psy7952          49 FKCELQKKAIRHILLR---THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDD  125 (444)
Q Consensus        49 ~~t~~Q~~~~~~~~~~---~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~  125 (444)
                      ++|.+.  .++.+..|   ..-++|.|.||+|||..|+-.+         .......+  .+|+|++.-..-.      +
T Consensus       207 i~TG~~--~LD~~~~Gl~~G~LiiIaarPgmGKTafalnia---------~~~a~~~g--~~V~~fSlEM~~~------q  267 (471)
T PRK08006        207 VNTGYD--DLNKKTAGLQPSDLIIVAARPSMGKTTFAMNLC---------ENAAMLQD--KPVLIFSLEMPGE------Q  267 (471)
T ss_pred             ccCCCH--HHHHhhcCCCCCcEEEEEeCCCCCHHHHHHHHH---------HHHHHhcC--CeEEEEeccCCHH------H
Confidence            455443  44444433   1557889999999996632211         11111222  2346665432222      3


Q ss_pred             hHhhh---cCCCCceeEEEE-eCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh-hCCccEEEEec
Q psy7952         126 KTSIV---TGRSDLYQLELI-VSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR-YNKLAYIVVDE  200 (444)
Q Consensus       126 ~~~~l---~~~~~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~-~~~~~~iViDE  200 (444)
                      .+.++   ..+   +....+ .+..+..++..+......+.....+.|-....+.-.......+.... ...+++||||=
T Consensus       268 l~~Rlla~~~~---v~~~~i~~~~l~~~e~~~~~~a~~~~~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDY  344 (471)
T PRK08006        268 IMMRMLASLSR---VDQTRIRTGQLDDEDWARISGTMGILLEKRNMYIDDSSGLTPTEVRSRARRIFREHGGLSLIMIDY  344 (471)
T ss_pred             HHHHHHHHhcC---CCHHHhhcCCCCHHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEcc
Confidence            33444   122   222222 34455555555444443332334455543222211111222222222 23699999999


Q ss_pred             cccccccC--CCcHHHHHHHHHHHHhhC--CCCcEEEEe
Q psy7952         201 AHCVSEWG--HDFRPTYRRLGELRQFTG--NSIPIIALT  235 (444)
Q Consensus       201 ~H~~~~~~--~~~~~~~~~l~~~~~~~~--~~~~~v~lS  235 (444)
                      .|.+...+  ..-...+..+.+-++.+.  -++++|++|
T Consensus       345 Lqli~~~~~~~~r~~ei~~isr~LK~lAkel~ipVi~Ls  383 (471)
T PRK08006        345 LQLMRVPSLSDNRTLEIAEISRSLKALAKELQVPVVALS  383 (471)
T ss_pred             HHHccCCCCCCCcHHHHHHHHHHHHHHHHHhCCeEEEEE
Confidence            99885321  111223344433333332  247888888

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=92.43  E-value=0.84  Score=46.75  Aligned_cols=169  Identities=13%  Similarity=0.142  Sum_probs=90.2

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      .+.+.+.|+..|+...+.    ..+++...+  +-.++..|=-.|||....         +. +..+...-..-+|++.+
T Consensus       228 a~r~~~~lk~~Fdi~~~s----~~~~~~fkq--k~tVflVPRR~GKTwivv---------~i-I~~ll~s~~Gi~IgytA  291 (738)
T PHA03368        228 AERVERFLRTVFNTPLFS----DAAVRHFRQ--RATVFLVPRRHGKTWFLV---------PL-IALALATFRGIKIGYTA  291 (738)
T ss_pred             HHHHHHHHHHHcCCcccc----HHHHHHhhc--cceEEEecccCCchhhHH---------HH-HHHHHHhCCCCEEEEEc
Confidence            566778888888877533    234555444  567888899999998622         22 11122222234569999


Q ss_pred             chhhhhcccCccchHhhh----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCC--eeEEEECCCccccccHHHHHHH
Q psy7952         113 PILSSFYLRFRDDKTSIV----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPR--IKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      |.+..+     +..++++    ...++.-.+....|. ...     +    .+.++  ..|.+++.-          ..+
T Consensus       292 H~~~ts-----~~vF~eI~~~le~~f~~~~v~~vkGe-~I~-----i----~f~nG~kstI~FaSar----------ntN  346 (738)
T PHA03368        292 HIRKAT-----EPVFEEIGARLRQWFGASRVDHVKGE-TIS-----F----SFPDGSRSTIVFASSH----------NTN  346 (738)
T ss_pred             CcHHHH-----HHHHHHHHHHHhhhcchhheeeecCc-EEE-----E----EecCCCccEEEEEecc----------CCC
Confidence            999888     5555555    111111112122221 110     0    00111  244454311          111


Q ss_pred             HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHh
Q psy7952         187 LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVL  250 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l  250 (444)
                      ...-..++++|+|||+.+.+.      .+..+.-.+.  ..++++|++|.|-.......+...+
T Consensus       347 siRGqtfDLLIVDEAqFIk~~------al~~ilp~l~--~~n~k~I~ISS~Ns~~~sTSFL~nL  402 (738)
T PHA03368        347 GIRGQDFNLLFVDEANFIRPD------AVQTIMGFLN--QTNCKIIFVSSTNTGKASTSFLYNL  402 (738)
T ss_pred             CccCCcccEEEEechhhCCHH------HHHHHHHHHh--ccCccEEEEecCCCCccchHHHHhh
Confidence            122237899999999997542      2333333322  2358899999997775555544433

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=92.36  E-value=0.11  Score=48.74  Aligned_cols=30  Identities=23%  Similarity=0.272  Sum_probs=25.1

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      +-|.+.+..+..+..++++++|||||||..
T Consensus       119 ~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl  148 (299)
T TIGR02782       119 AAQRDVLREAVLARKNILVVGGTGSGKTTL  148 (299)
T ss_pred             HHHHHHHHHHHHcCCeEEEECCCCCCHHHH
Confidence            567777777777658999999999999976

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.

>PRK07004 replicative DNA helicase; Provisional

Probab=92.33  E-value=0.43  Score=47.63  Aligned_cols=164  Identities=13%  Similarity=0.067  Sum_probs=75.2

Q ss_pred             cCchHHHHHHHHHHcc---CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc---chhhhhcccC
Q psy7952          49 FKCELQKKAIRHILLR---THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS---PILSSFYLRF  122 (444)
Q Consensus        49 ~~t~~Q~~~~~~~~~~---~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~---P~~~L~~~~q  122 (444)
                      +||.+.  -++.+..|   ..-+++.|.||+|||..|+-.+         .+.....+  ..++|++   +...|+    
T Consensus       196 i~TG~~--~LD~~t~G~~~g~liviaarpg~GKT~~al~ia---------~~~a~~~~--~~v~~fSlEM~~~ql~----  258 (460)
T PRK07004        196 TPTGFV--DLDRMTSGMHGGELIIVAGRPSMGKTAFSMNIG---------EYVAVEYG--LPVAVFSMEMPGTQLA----  258 (460)
T ss_pred             ccCCcH--HhcccccCCCCCceEEEEeCCCCCccHHHHHHH---------HHHHHHcC--CeEEEEeCCCCHHHHH----
Confidence            454433  44444432   1568899999999997632211         11111222  2336664   333343    


Q ss_pred             ccchHhhhcCCCCceeEEEE-eCCCChhhHHHHHHHHHhcCCCeeEEEE-CCCccccccHHHHHHHHHh-hCCccEEEEe
Q psy7952         123 RDDKTSIVTGRSDLYQLELI-VSGQTKTENKAILEELRLVKPRIKLLYV-TPERAVTESFHYLLQHLVR-YNKLAYIVVD  199 (444)
Q Consensus       123 ~~~~~~~l~~~~~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~Iiv~-Tpe~l~~~~~~~~~~~~~~-~~~~~~iViD  199 (444)
                       ...+... .+   +....+ .|.....++..+...+..+. +..+.|. +|. +.............. ...+++||||
T Consensus       259 -~R~la~~-~~---v~~~~i~~g~l~~~e~~~~~~a~~~l~-~~~l~I~d~~~-~~~~~i~~~~r~l~~~~~~~~lviID  331 (460)
T PRK07004        259 -MRMLGSV-GR---LDQHRMRTGRLTDEDWPKLTHAVQKMS-EAQLFIDETGG-LNPMELRSRARRLARQCGKLGLIIID  331 (460)
T ss_pred             -HHHHHhh-cC---CCHHHHhcCCCCHHHHHHHHHHHHHHh-cCCEEEECCCC-CCHHHHHHHHHHHHHhCCCCCEEEEC
Confidence             2222221 11   221111 34555555555554444443 3445554 333 221111222222222 2458999999


Q ss_pred             ccccccccC--CCcHHHHHHHHHHHHhhC--CCCcEEEEec
Q psy7952         200 EAHCVSEWG--HDFRPTYRRLGELRQFTG--NSIPIIALTA  236 (444)
Q Consensus       200 E~H~~~~~~--~~~~~~~~~l~~~~~~~~--~~~~~v~lSA  236 (444)
                      =.|.+...+  ..-...+..+.+-++.+.  -+++++++|-
T Consensus       332 YLql~~~~~~~~~r~~ei~~Isr~LK~lAkel~ipVi~lsQ  372 (460)
T PRK07004        332 YLQLMSGSSQGENRATEISEISRSLKSLAKELDVPVIALSQ  372 (460)
T ss_pred             hhhhccCCCCCCcHHHHHHHHHHHHHHHHHHhCCeEEEEec
Confidence            999985322  112222333333333332  2377888773

>PRK04195 replication factor C large subunit; Provisional

Probab=92.30  E-value=0.29  Score=49.35  Aligned_cols=16  Identities=13%  Similarity=0.127  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.||+|+|||..
T Consensus        40 ~~lLL~GppG~GKTtl   55 (482)
T PRK04195         40 KALLLYGPPGVGKTSL   55 (482)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            6799999999999977

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=92.30  E-value=1.4  Score=41.73  Aligned_cols=58  Identities=9%  Similarity=0.142  Sum_probs=30.4

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHh---hCCCCcEEEEeccCCcchHHHHHHH
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQF---TGNSIPIIALTATAEPSVKQDIISV  249 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~---~~~~~~~v~lSAT~~~~~~~~~~~~  249 (444)
                      .++++||||=+-++..... ....+..+.+..+.   ..+...++.++||...........+
T Consensus       195 ~~~D~ViIDTaGr~~~~~~-l~~eL~~~~~v~~~~~~~~p~~~~LVl~a~~g~~~~~~a~~f  255 (318)
T PRK10416        195 RGIDVLIIDTAGRLHNKTN-LMEELKKIKRVIKKADPDAPHEVLLVLDATTGQNALSQAKAF  255 (318)
T ss_pred             CCCCEEEEeCCCCCcCCHH-HHHHHHHHHHHHhhhcCCCCceEEEEEECCCChHHHHHHHHH
Confidence            5688999998877532111 22233333333221   1222357889999665544444433

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=92.26  E-value=0.46  Score=47.98  Aligned_cols=39  Identities=15%  Similarity=0.256  Sum_probs=26.2

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      ...+++||||+|.+...      ....+.+.+...++...+|+.+
T Consensus       116 ~~~KVvIIDEad~Lt~~------A~NALLK~LEEpp~~t~FIL~t  154 (535)
T PRK08451        116 ARFKIFIIDEVHMLTKE------AFNALLKTLEEPPSYVKFILAT  154 (535)
T ss_pred             CCeEEEEEECcccCCHH------HHHHHHHHHhhcCCceEEEEEE
Confidence            46789999999997542      2345555555556656666655

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=92.24  E-value=0.26  Score=53.02  Aligned_cols=28  Identities=14%  Similarity=0.251  Sum_probs=20.4

Q ss_pred             HHHHHHHHH----cc-CCcEEEEccCCCccccc
Q psy7952          54 QKKAIRHIL----LR-THDIFVSMPTGAVSLVG   81 (444)
Q Consensus        54 Q~~~~~~~~----~~-~~~~ii~apTGsGKT~~   81 (444)
                      |..-+..+.    ++ ..+.++++|+|+|||.+
T Consensus       192 r~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal  224 (852)
T TIGR03345       192 RDDEIRQMIDILLRRRQNNPILTGEAGVGKTAV  224 (852)
T ss_pred             CHHHHHHHHHHHhcCCcCceeEECCCCCCHHHH
Confidence            555555554    32 26899999999999977

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.21  E-value=4.5  Score=39.57  Aligned_cols=56  Identities=13%  Similarity=0.176  Sum_probs=33.8

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhC---CCCcEEEEeccCCcchHHHHHHHh
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTG---NSIPIIALTATAEPSVKQDIISVL  250 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~---~~~~~v~lSAT~~~~~~~~~~~~l  250 (444)
                      ...++|+||=+-+...    -...+..+..+.....   +.-.++.+|||........+...+
T Consensus       298 ~~~D~VLIDTaGr~~r----d~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~~~~f  356 (432)
T PRK12724        298 DGSELILIDTAGYSHR----NLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTVLKAY  356 (432)
T ss_pred             CCCCEEEEeCCCCCcc----CHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHHHHHh
Confidence            5678999997655321    2244455555555432   224578999998876655555544

>PRK06321 replicative DNA helicase; Provisional

Probab=92.19  E-value=0.41  Score=47.85  Aligned_cols=167  Identities=9%  Similarity=0.117  Sum_probs=78.1

Q ss_pred             ccCchHHHHHHHHHHccC---CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc---chhhhhccc
Q psy7952          48 SFKCELQKKAIRHILLRT---HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS---PILSSFYLR  121 (444)
Q Consensus        48 ~~~t~~Q~~~~~~~~~~~---~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~---P~~~L~~~~  121 (444)
                      .+||.+.  -++.+..|-   .=++|.|.||+|||..|+-         .+.......+  ..|+|++   |...|+   
T Consensus       208 Gi~tG~~--~LD~~t~Gl~~G~LiiiaarPgmGKTafal~---------ia~~~a~~~g--~~v~~fSLEMs~~ql~---  271 (472)
T PRK06321        208 GIPTHFI--DLDKMINGFSPSNLMILAARPAMGKTALALN---------IAENFCFQNR--LPVGIFSLEMTVDQLI---  271 (472)
T ss_pred             ccccCcH--HHHHHhcCCCCCcEEEEEeCCCCChHHHHHH---------HHHHHHHhcC--CeEEEEeccCCHHHHH---
Confidence            4565543  566665531   4468899999999976322         1011111212  2346665   333444   


Q ss_pred             CccchHhhhcCCCCceeEEEE-eCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEec
Q psy7952         122 FRDDKTSIVTGRSDLYQLELI-VSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDE  200 (444)
Q Consensus       122 q~~~~~~~l~~~~~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE  200 (444)
                        ...+.. ..+   +....+ .+.....++.........+.. ..+.|-....+.-..+....+.......+++||||=
T Consensus       272 --~Rlla~-~s~---v~~~~i~~~~l~~~e~~~~~~a~~~l~~-~~~~idd~~~~ti~~i~~~~r~~~~~~~~~lvvIDy  344 (472)
T PRK06321        272 --HRIICS-RSE---VESKKISVGDLSGRDFQRIVSVVNEMQE-HTLLIDDQPGLKITDLRARARRMKESYDIQFLIIDY  344 (472)
T ss_pred             --HHHHHh-hcC---CCHHHhhcCCCCHHHHHHHHHHHHHHHc-CCEEEeCCCCCCHHHHHHHHHHHHHhcCCCEEEEcc
Confidence              222211 112   222222 344445555544444444333 345554222221111222233333345689999999


Q ss_pred             cccccccC-----CCcHHHHHHHHHHHHhhCC--CCcEEEEecc
Q psy7952         201 AHCVSEWG-----HDFRPTYRRLGELRQFTGN--SIPIIALTAT  237 (444)
Q Consensus       201 ~H~~~~~~-----~~~~~~~~~l~~~~~~~~~--~~~~v~lSAT  237 (444)
                      .+.+...+     ..-...+..+.+-++.+.+  +++++++|-.
T Consensus       345 Lql~~~~~~~~~~~~r~~ei~~Isr~LK~lAkel~vpVi~lsQL  388 (472)
T PRK06321        345 LQLLSGSGNLRNSESRQTEISEISRMLKNLARELNIPILCLSQL  388 (472)
T ss_pred             hHHcCCCCccCCcchHHHHHHHHHHHHHHHHHHhCCcEEEEeec
Confidence            99885322     1112233334333333322  4788888754

>TIGR00665 DnaB replicative DNA helicase

Probab=92.15  E-value=0.39  Score=47.76  Aligned_cols=25  Identities=4%  Similarity=-0.093  Sum_probs=18.3

Q ss_pred             HHHHHHccC---CcEEEEccCCCccccc
Q psy7952          57 AIRHILLRT---HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        57 ~~~~~~~~~---~~~ii~apTGsGKT~~   81 (444)
                      .+..+..|-   .-++|.|+||+|||..
T Consensus       184 ~LD~~~~G~~~G~l~vi~g~pg~GKT~~  211 (434)
T TIGR00665       184 DLDKLTSGLQPSDLIILAARPSMGKTAF  211 (434)
T ss_pred             hhHhhcCCCCCCeEEEEEeCCCCChHHH
Confidence            556655431   5579999999999976

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.

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=92.10  E-value=0.2  Score=48.92  Aligned_cols=38  Identities=26%  Similarity=0.266  Sum_probs=28.5

Q ss_pred             cEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          67 DIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        67 ~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      ++++.||||+|||..        +.+|.    +...+.  .++|+=|.-++.
T Consensus         1 H~lv~g~tGsGKt~~--------~viP~----ll~~~~--s~vv~D~Kge~~   38 (384)
T cd01126           1 HVLVFAPTRSGKGVG--------FVIPN----LLTWPG--SVVVLDPKGENF   38 (384)
T ss_pred             CeeEecCCCCCCccE--------EEccc----hhcCCC--CEEEEccchhHH
Confidence            578999999999999        88888    443332  336666888887

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.

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=91.98  E-value=0.15  Score=51.20  Aligned_cols=59  Identities=14%  Similarity=0.117  Sum_probs=36.8

Q ss_pred             hHHHHHHHHHH-----ccC---CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          52 ELQKKAIRHIL-----LRT---HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        52 ~~Q~~~~~~~~-----~~~---~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      |||.-.+..++     .|.   +.+++..|=|.|||..+...++  |.+      +..+.....++++++++.-+
T Consensus         1 PwQ~fi~~~i~G~~~~~g~rrf~~~~l~v~RkNGKS~l~a~i~l--y~l------~~~g~~~~~i~~~A~~~~QA   67 (477)
T PF03354_consen    1 PWQKFILRSIFGWRKDDGRRRFREVYLEVPRKNGKSTLAAAIAL--YML------FLDGEPGAEIYCAANTRDQA   67 (477)
T ss_pred             CcHHHHHHHHhceEcCCCCEEEEEEEEEEcCccCccHHHHHHHH--HHH------hcCCccCceEEEEeCCHHHH
Confidence            47777766666     121   4578899999999977332211  111      12233445678899999888

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>KOG0298|consensus

Probab=91.97  E-value=0.073  Score=57.27  Aligned_cols=152  Identities=14%  Similarity=0.034  Sum_probs=82.9

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCc-----------cccccCCccceeEEEcchhhhhcccCccchHhhh-cCC
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGA-----------DFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGR  133 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~-----------~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~  133 (444)
                      .++++.--.|.|||...++..+  +..|...           ..+...|.+   ||+||.--|.      |-+... ..-
T Consensus       375 ~~~~~ade~~~qk~~~~l~~~l--~~~~k~~~~~cS~~~~e~~n~~~tgaT---LII~P~aIl~------QW~~EI~kH~  443 (1394)
T KOG0298|consen  375 KRVQCADEMGWQKTSEKLILEL--SDLPKLCPSCCSELVKEGENLVETGAT---LIICPNAILM------QWFEEIHKHI  443 (1394)
T ss_pred             cceeehhhhhccchHHHHHHHH--hcccccchhhhhHHHhcccceeecCce---EEECcHHHHH------HHHHHHHHhc
Confidence            5567777779999977433322  1122200           111123455   9999998887      555555 222


Q ss_pred             CCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH---Hh-------h-C-----CccEEE
Q psy7952         134 SDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL---VR-------Y-N-----KLAYIV  197 (444)
Q Consensus       134 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~---~~-------~-~-----~~~~iV  197 (444)
                      .+.+++..+.|-........  .+    -..+|||++|++.|.++..+..-.+.   ..       . +     .+=.|+
T Consensus       444 ~~~lKv~~Y~Girk~~~~~~--~e----l~~yDIVlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWRIc  517 (1394)
T KOG0298|consen  444 SSLLKVLLYFGIRKTFWLSP--FE----LLQYDIVLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWRIC  517 (1394)
T ss_pred             cccceEEEEechhhhcccCc--hh----hhccCEEEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHHHh
Confidence            22278887777543221111  11    24799999999999765433211000   00       0 0     134579


Q ss_pred             EeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcch
Q psy7952         198 VDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSV  242 (444)
Q Consensus       198 iDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~  242 (444)
                      +||++++-...       ....++...++. ...-+.|+||...+
T Consensus       518 lDEaQMvesss-------S~~a~M~~rL~~-in~W~VTGTPiq~I  554 (1394)
T KOG0298|consen  518 LDEAQMVESSS-------SAAAEMVRRLHA-INRWCVTGTPIQKI  554 (1394)
T ss_pred             hhHHHhhcchH-------HHHHHHHHHhhh-hceeeecCCchhhh
Confidence            99999975422       222222222332 44569999998773

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=91.91  E-value=0.068  Score=56.30  Aligned_cols=63  Identities=13%  Similarity=-0.018  Sum_probs=42.0

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC-ccceeEEEcchhhhhcccCccchHhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN-VRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~-~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      ++-|.+++..  .. .+++|.|.+|||||.+        . +..+.+.+...+ ...++++++.|+..+     .+.-++
T Consensus         3 n~~Q~~av~~--~~-~~~~V~Ag~GSGKT~~--------L-~~ri~~ll~~~~~~p~~IL~vTFt~~Aa-----~em~~R   65 (664)
T TIGR01074         3 NPQQQEAVEY--VT-GPCLVLAGAGSGKTRV--------I-TNKIAYLIQNCGYKARNIAAVTFTNKAA-----REMKER   65 (664)
T ss_pred             CHHHHHHHhC--CC-CCEEEEecCCCCHHHH--------H-HHHHHHHHHhcCCCHHHeEEEeccHHHH-----HHHHHH
Confidence            4679888875  23 6899999999999988        2 222122232333 234788888888888     566555


Q ss_pred             h
Q psy7952         130 V  130 (444)
Q Consensus       130 l  130 (444)
                      +
T Consensus        66 l   66 (664)
T TIGR01074        66 V   66 (664)
T ss_pred             H
Confidence            5

Designed to identify rep members of the uvrD/rep subfamily.

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=91.59  E-value=0.15  Score=46.14  Aligned_cols=40  Identities=15%  Similarity=0.164  Sum_probs=24.7

Q ss_pred             HHHHhCCcccCchHHHHHHHHHHcc--C--CcEEEEccCCCccccc
Q psy7952          40 LKALFGFDSFKCELQKKAIRHILLR--T--HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        40 l~~~~g~~~~~t~~Q~~~~~~~~~~--~--~~~ii~apTGsGKT~~   81 (444)
                      |.+..|-+...  -|.+.+-.+...  .  .++++.+|+|.|||..
T Consensus        25 l~efiGQ~~vk--~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTL   68 (332)
T COG2255          25 LDEFIGQEKVK--EQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTL   68 (332)
T ss_pred             HHHhcChHHHH--HHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHH
Confidence            34433555433  355554444432  1  5799999999999976

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=91.57  E-value=0.29  Score=47.73  Aligned_cols=16  Identities=13%  Similarity=0.210  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++++|+|+|||..
T Consensus       166 ~gvLL~GppGtGKT~l  181 (389)
T PRK03992        166 KGVLLYGPPGTGKTLL  181 (389)
T ss_pred             CceEEECCCCCChHHH
Confidence            6799999999999977

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin

Probab=91.56  E-value=0.11  Score=44.46  Aligned_cols=43  Identities=16%  Similarity=0.193  Sum_probs=27.4

Q ss_pred             cCCCeeEEEECCCccccccHHHHHHHHH-hhCCccEEEEeccccccc
Q psy7952         161 VKPRIKLLYVTPERAVTESFHYLLQHLV-RYNKLAYIVVDEAHCVSE  206 (444)
Q Consensus       161 ~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~-~~~~~~~iViDE~H~~~~  206 (444)
                      ....++|+|+++..+..+...   .... ...+-.+|||||||.+.+
T Consensus       116 ~~~~adivi~~y~yl~~~~~~---~~~~~~~~~~~ivI~DEAHNL~~  159 (174)
T PF06733_consen  116 LAKNADIVICNYNYLFDPSIR---KSLFGIDLKDNIVIFDEAHNLED  159 (174)
T ss_dssp             CGGG-SEEEEETHHHHSHHHH---HHHCT--CCCEEEEETTGGGCGG
T ss_pred             hcccCCEEEeCHHHHhhHHHH---hhhccccccCcEEEEecccchHH
Confidence            356789999998888653321   1111 123447899999999865

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=91.52  E-value=0.46  Score=48.64  Aligned_cols=19  Identities=21%  Similarity=0.315  Sum_probs=15.3

Q ss_pred             CcEEEEccCCCcccccccc
Q psy7952          66 HDIFVSMPTGAVSLVGSVV   84 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~   84 (444)
                      +-++++||.|+|||.+|-+
T Consensus        39 hayLf~Gp~GtGKTt~Ak~   57 (559)
T PRK05563         39 HAYLFSGPRGTGKTSAAKI   57 (559)
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4478999999999988443

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=91.48  E-value=0.56  Score=47.99  Aligned_cols=58  Identities=3%  Similarity=-0.019  Sum_probs=41.0

Q ss_pred             CchHHHHHHHHHHccC-CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          50 KCELQKKAIRHILLRT-HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~-~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      ++|||.+.++.+.... +.+.+..++-+|||.+++.++ + |        .....+ ..++++.||..++
T Consensus        17 ~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~~~~n~~-g-~--------~i~~~P-~~~l~v~Pt~~~a   75 (557)
T PF05876_consen   17 RTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLNWI-G-Y--------SIDQDP-GPMLYVQPTDDAA   75 (557)
T ss_pred             CChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHhhc-e-E--------EEEeCC-CCEEEEEEcHHHH
Confidence            3679999999988754 678999999999998733222 1 1        112222 1349999999998

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 [].

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=91.43  E-value=3.4  Score=41.27  Aligned_cols=16  Identities=19%  Similarity=0.054  Sum_probs=14.2

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +-+.+.+|||+|||.+
T Consensus       257 ~Vi~LvGpnGvGKTTT  272 (484)
T PRK06995        257 GVFALMGPTGVGKTTT  272 (484)
T ss_pred             cEEEEECCCCccHHHH
Confidence            4588999999999988

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=91.28  E-value=0.27  Score=50.54  Aligned_cols=42  Identities=21%  Similarity=0.130  Sum_probs=31.5

Q ss_pred             ccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          63 LRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        63 ~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      .+.+++++.||||+|||..        +.+|.    +..-+.+  ++|+=|--++.
T Consensus       156 ~g~~hvLviapTgSGKg~g--------~VIPn----LL~~~~S--~VV~DpKGEl~  197 (606)
T PRK13897        156 DGFQHALLFAPTGSGKGVG--------FVIPN----LLFWEDS--VVVHDIKLENY  197 (606)
T ss_pred             cCCceEEEEcCCCCCcceE--------Eehhh----HHhCCCC--EEEEeCcHHHH
Confidence            3447899999999999999        88999    4443333  35566877887

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=91.18  E-value=0.2  Score=50.44  Aligned_cols=39  Identities=23%  Similarity=0.198  Sum_probs=29.3

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      .++++.||||+|||..        +.+|.    +...+..  ++|.=|--+|.
T Consensus        45 ~h~lvig~tgSGKt~~--------~viP~----ll~~~~s--~iV~D~KgEl~   83 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTS--------FVIPN----LLNYPGS--MIVTDPKGELY   83 (469)
T ss_pred             eEEEEEeCCCCCccce--------eeHhH----HHhccCC--EEEEECCCcHH
Confidence            3799999999999999        88888    4443323  35666888887

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

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=91.12  E-value=0.27  Score=51.40  Aligned_cols=61  Identities=10%  Similarity=-0.024  Sum_probs=43.0

Q ss_pred             CchHHHHHHHHHHcc----CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccc
Q psy7952          50 KCELQKKAIRHILLR----THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDD  125 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~----~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~  125 (444)
                      |++.|..++..+.++    .++.++.+.+|+|||+.        +  ..    +... ....+|||+|+...+     .+
T Consensus        13 ~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~l--------i--a~----l~~~-~~r~vLIVt~~~~~A-----~~   72 (652)
T PRK05298         13 PAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFT--------M--AN----VIAR-LQRPTLVLAHNKTLA-----AQ   72 (652)
T ss_pred             CChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHH--------H--HH----HHHH-hCCCEEEEECCHHHH-----HH
Confidence            578999999888653    23577999999999977        1  11    2221 112459999999999     56


Q ss_pred             hHhhh
Q psy7952         126 KTSIV  130 (444)
Q Consensus       126 ~~~~l  130 (444)
                      ....+
T Consensus        73 l~~dL   77 (652)
T PRK05298         73 LYSEF   77 (652)
T ss_pred             HHHHH
Confidence            66666

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=91.04  E-value=1.5  Score=43.60  Aligned_cols=39  Identities=13%  Similarity=0.226  Sum_probs=24.1

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      ...+++||||+|.+...      ....+.+.+...+....+|+.+
T Consensus       120 ~~~kvvIIdead~lt~~------~~n~LLk~lEep~~~~~~Il~t  158 (451)
T PRK06305        120 SRYKIYIIDEVHMLTKE------AFNSLLKTLEEPPQHVKFFLAT  158 (451)
T ss_pred             CCCEEEEEecHHhhCHH------HHHHHHHHhhcCCCCceEEEEe
Confidence            46789999999997532      2344555555544445555544

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.02  E-value=1.1  Score=46.32  Aligned_cols=18  Identities=17%  Similarity=0.218  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccccc
Q psy7952          66 HDIFVSMPTGAVSLVGSV   83 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~   83 (444)
                      +.++++||.|+|||.+|-
T Consensus        39 ~a~Lf~Gp~G~GKTtlA~   56 (585)
T PRK14950         39 HAYLFTGPRGVGKTSTAR   56 (585)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            346999999999998843

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=90.92  E-value=0.46  Score=42.51  Aligned_cols=117  Identities=15%  Similarity=0.132  Sum_probs=68.1

Q ss_pred             HHHccC--CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-cCCCCc
Q psy7952          60 HILLRT--HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDL  136 (444)
Q Consensus        60 ~~~~~~--~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~  136 (444)
                      .+++|.  ++++++++.|+|||-.          +.+++......+-.   +|=++...|.   .+.+.+..+ ...   
T Consensus        45 ~Fl~G~pannvLL~G~rGtGKSSl----------Vkall~~y~~~GLR---lIev~k~~L~---~l~~l~~~l~~~~---  105 (249)
T PF05673_consen   45 QFLQGLPANNVLLWGARGTGKSSL----------VKALLNEYADQGLR---LIEVSKEDLG---DLPELLDLLRDRP---  105 (249)
T ss_pred             HHHcCCCCcceEEecCCCCCHHHH----------HHHHHHHHhhcCce---EEEECHHHhc---cHHHHHHHHhcCC---
Confidence            444542  7899999999999965          33323335556666   7777777765   123444444 334   


Q ss_pred             eeEEEEeCCCChhhHHHHHHHHHhc-------CCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccc
Q psy7952         137 YQLELIVSGQTKTENKAILEELRLV-------KPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHC  203 (444)
Q Consensus       137 i~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~  203 (444)
                      .+...+..+.+.......+..++..       .+..-++++|..+-     +.+...+.+...   +.=||+|.
T Consensus       106 ~kFIlf~DDLsFe~~d~~yk~LKs~LeGgle~~P~NvliyATSNRR-----HLv~E~~~d~~~---~~~~eih~  171 (249)
T PF05673_consen  106 YKFILFCDDLSFEEGDTEYKALKSVLEGGLEARPDNVLIYATSNRR-----HLVPESFSDRED---IQDDEIHP  171 (249)
T ss_pred             CCEEEEecCCCCCCCcHHHHHHHHHhcCccccCCCcEEEEEecchh-----hccchhhhhccC---CCccccCc
Confidence            5667777777665555555544432       33345677886652     333333333333   55667776

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=90.88  E-value=0.3  Score=42.49  Aligned_cols=55  Identities=20%  Similarity=0.088  Sum_probs=23.8

Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCC-CCcEEEEeccCCcchHHHHH
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGN-SIPIIALTATAEPSVKQDII  247 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~-~~~~v~lSAT~~~~~~~~~~  247 (444)
                      .-.++|+||||.+.................+..... +.-++++|=.+. .+...++
T Consensus        79 ~~~liviDEa~~~~~~r~~~~~~~~~~~~~l~~hRh~g~diiliTQ~~~-~id~~ir  134 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSWKGKKVPEIIEFLAQHRHYGWDIILITQSPS-QIDKFIR  134 (193)
T ss_dssp             TT-EEEETTGGGTSB---T-T----HHHHGGGGCCCTT-EEEEEES-GG-GB-HHHH
T ss_pred             CCcEEEEECChhhcCCCccccccchHHHHHHHHhCcCCcEEEEEeCCHH-HHhHHHH
Confidence            568999999999854221101111222233333333 244667665553 3444444

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=90.87  E-value=0.27  Score=49.79  Aligned_cols=16  Identities=13%  Similarity=0.229  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus        89 ~giLL~GppGtGKT~l  104 (495)
T TIGR01241        89 KGVLLVGPPGTGKTLL  104 (495)
T ss_pred             CcEEEECCCCCCHHHH
Confidence            5799999999999977

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>PRK10867 signal recognition particle protein; Provisional

Probab=90.83  E-value=1.3  Score=43.65  Aligned_cols=15  Identities=20%  Similarity=0.023  Sum_probs=13.4

Q ss_pred             cEEEEccCCCccccc
Q psy7952          67 DIFVSMPTGAVSLVG   81 (444)
Q Consensus        67 ~~ii~apTGsGKT~~   81 (444)
                      -+++++|+|+|||.+
T Consensus       102 vI~~vG~~GsGKTTt  116 (433)
T PRK10867        102 VIMMVGLQGAGKTTT  116 (433)
T ss_pred             EEEEECCCCCcHHHH
Confidence            478999999999987

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=90.83  E-value=0.084  Score=56.14  Aligned_cols=63  Identities=14%  Similarity=0.026  Sum_probs=42.8

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCcc-ceeEEEcchhhhhcccCccchHhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVR-SRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~-~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      ++-|++++.+.  . .+++|.|..|||||.+        .. .-+...+...+.. .++|+++-|+..+     .+..++
T Consensus         6 n~~Q~~av~~~--~-g~~lV~AgaGSGKT~~--------l~-~ria~Li~~~~i~P~~IL~lTFT~kAA-----~em~~R   68 (726)
T TIGR01073         6 NPEQREAVKTT--E-GPLLIMAGAGSGKTRV--------LT-HRIAHLIAEKNVAPWNILAITFTNKAA-----REMKER   68 (726)
T ss_pred             CHHHHHHHhCC--C-CCEEEEeCCCCCHHHH--------HH-HHHHHHHHcCCCCHHHeeeeeccHHHH-----HHHHHH
Confidence            47899998753  3 5899999999999988        21 1112222233333 4789999998887     666666


Q ss_pred             h
Q psy7952         130 V  130 (444)
Q Consensus       130 l  130 (444)
                      +
T Consensus        69 l   69 (726)
T TIGR01073        69 V   69 (726)
T ss_pred             H
Confidence            5

Designed to identify pcrA members of the uvrD/rep subfamily.

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=90.76  E-value=0.12  Score=48.93  Aligned_cols=16  Identities=6%  Similarity=-0.270  Sum_probs=14.0

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .-+++++|+|+|||+.
T Consensus       149 lgllL~GPPGcGKTll  164 (413)
T PLN00020        149 LILGIWGGKGQGKSFQ  164 (413)
T ss_pred             eEEEeeCCCCCCHHHH
Confidence            4578999999999977

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=90.76  E-value=2  Score=44.28  Aligned_cols=44  Identities=16%  Similarity=0.171  Sum_probs=27.4

Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchH
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVK  243 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~  243 (444)
                      .++++|+|||+.+..      ..+..+.-.+..  .+.+++.+|.+-....+
T Consensus       294 ~~DLLIVDEAAfI~~------~~l~aIlP~l~~--~~~k~IiISS~~~~~s~  337 (752)
T PHA03333        294 NPDLVIVDEAAFVNP------GALLSVLPLMAV--KGTKQIHISSPVDADSW  337 (752)
T ss_pred             CCCEEEEECcccCCH------HHHHHHHHHHcc--CCCceEEEeCCCCcchH
Confidence            579999999999753      223344333332  34677888877654443

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=90.76  E-value=0.11  Score=58.27  Aligned_cols=63  Identities=17%  Similarity=0.047  Sum_probs=44.7

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      |+-|++++..  .+ ++++|.|..|||||.+        .. ..++..+..+....++++++-|+..+     .+.-.++
T Consensus         3 t~~Q~~ai~~--~~-~~~lv~A~AGsGKT~~--------lv-~r~~~~~~~~~~~~~il~~tFt~~aa-----~e~~~ri   65 (1232)
T TIGR02785         3 TDEQWQAIYT--RG-QNILVSASAGSGKTAV--------LV-ERIIKKILRGVDIDRLLVVTFTNAAA-----REMKERI   65 (1232)
T ss_pred             CHHHHHHHhC--CC-CCEEEEecCCCcHHHH--------HH-HHHHHHHhcCCCHhhEEEEeccHHHH-----HHHHHHH
Confidence            5789999983  55 8999999999999988        21 11122233332335789999999998     6766665

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.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=90.73  E-value=0.21  Score=49.18  Aligned_cols=30  Identities=27%  Similarity=0.309  Sum_probs=24.7

Q ss_pred             hHHHHHHHHHHccCC-cEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHILLRTH-DIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~-~~ii~apTGsGKT~~   81 (444)
                      +.|...+..++...+ -+++.+|||||||.+
T Consensus       244 ~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT  274 (500)
T COG2804         244 PFQLARLLRLLNRPQGLILVTGPTGSGKTTT  274 (500)
T ss_pred             HHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH
Confidence            578888888887643 479999999999987

>CHL00176 ftsH cell division protein; Validated

Probab=90.71  E-value=0.52  Score=48.90  Aligned_cols=16  Identities=13%  Similarity=0.229  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus       217 ~gVLL~GPpGTGKT~L  232 (638)
T CHL00176        217 KGVLLVGPPGTGKTLL  232 (638)
T ss_pred             ceEEEECCCCCCHHHH
Confidence            5799999999999977

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=90.70  E-value=0.25  Score=42.78  Aligned_cols=30  Identities=20%  Similarity=0.116  Sum_probs=25.6

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      +-|.+.+.........+++.+|||+|||..
T Consensus        12 ~~~~~~l~~~v~~g~~i~I~G~tGSGKTTl   41 (186)
T cd01130          12 PLQAAYLWLAVEARKNILISGGTGSGKTTL   41 (186)
T ss_pred             HHHHHHHHHHHhCCCEEEEECCCCCCHHHH
Confidence            678888887777658999999999999966

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.

>KOG1132|consensus

Probab=90.68  E-value=5.4  Score=42.04  Aligned_cols=70  Identities=17%  Similarity=0.208  Sum_probs=45.2

Q ss_pred             CceEEEEecccchHHHHHHHHHhh----------------cCHHHHHHHHHHHh--------cCCccEEEEcCccccccc
Q psy7952         300 NNCGIIYCRTREHTTDLADALRRK----------------VNKHERSRVQESFM--------RGEINVITATISFGMGID  355 (444)
Q Consensus       300 ~~~~iVf~~s~~~~~~l~~~L~~~----------------~~~~~r~~~~~~f~--------~g~~~vLvaT~~~~~Gid  355 (444)
                      ...++||+++-...+++.......                -++.+-.+++..|.        .|..-..||-...++|+|
T Consensus       561 p~G~L~FfPSY~vmdk~~tfw~~~~~we~~~~vk~l~vEPr~k~~f~e~m~~y~~~i~~pes~ga~~~aVcRGKVSEGlD  640 (945)
T KOG1132|consen  561 PYGLLIFFPSYPVMDKLITFWQNRGLWERMEKVKKLVVEPRSKSEFTEVMSRYYNAIADPESSGAVFFAVCRGKVSEGLD  640 (945)
T ss_pred             ccceEEeccchHHHHHHHHHHHcchHHHHhhcccCceeccCCccchHHHHHHHHHHhhCccccceEEEEEecccccCCCC
Confidence            445999999988777774444332                12222233344443        233456788899999999


Q ss_pred             cCC--ccEEEEeCCCC
Q psy7952         356 RQN--VRFVVHWGMPS  369 (444)
Q Consensus       356 i~~--~~~Vi~~~~p~  369 (444)
                      ..+  .+.||..|.|.
T Consensus       641 FsD~~~RaVI~tGlPy  656 (945)
T KOG1132|consen  641 FSDDNGRAVIITGLPY  656 (945)
T ss_pred             ccccCCceeEEecCCC
Confidence            964  66799999875

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=90.67  E-value=0.1  Score=47.94  Aligned_cols=19  Identities=21%  Similarity=0.261  Sum_probs=16.1

Q ss_pred             CcEEEEccCCCcccccccc
Q psy7952          66 HDIFVSMPTGAVSLVGSVV   84 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~   84 (444)
                      .|+++.+|||||||+.|-.
T Consensus        98 SNILLiGPTGsGKTlLAqT  116 (408)
T COG1219          98 SNILLIGPTGSGKTLLAQT  116 (408)
T ss_pred             ccEEEECCCCCcHHHHHHH
Confidence            5799999999999988443

>PRK10865 protein disaggregation chaperone; Provisional

Probab=90.62  E-value=0.36  Score=52.17  Aligned_cols=16  Identities=6%  Similarity=-0.105  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .+.++++|+|+|||.+
T Consensus       200 ~n~lL~G~pGvGKT~l  215 (857)
T PRK10865        200 NNPVLIGEPGVGKTAI  215 (857)
T ss_pred             CceEEECCCCCCHHHH
Confidence            5899999999999977

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=90.60  E-value=0.21  Score=45.09  Aligned_cols=86  Identities=16%  Similarity=0.108  Sum_probs=55.4

Q ss_pred             ccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCC-CChhhHHHHHHHHHhcCCCeeEEEECCCccccccHH
Q psy7952         104 VRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSG-QTKTENKAILEELRLVKPRIKLLYVTPERAVTESFH  181 (444)
Q Consensus       104 ~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~  181 (444)
                      ..|.+||++.+--=+     .+..+.+ .+......+..+... ....++...+.     ....+|.||||+++.    .
T Consensus       125 gsP~~lvvs~SalRa-----~dl~R~l~~~~~k~~~v~KLFaKH~Kl~eqv~~L~-----~~~~~i~vGTP~Rl~----k  190 (252)
T PF14617_consen  125 GSPHVLVVSSSALRA-----ADLIRALRSFKGKDCKVAKLFAKHIKLEEQVKLLK-----KTRVHIAVGTPGRLS----K  190 (252)
T ss_pred             CCCEEEEEcchHHHH-----HHHHHHHHhhccCCchHHHHHHhhccHHHHHHHHH-----hCCceEEEeChHHHH----H
Confidence            446778888776656     5677766 332111334334333 35555555553     357899999999985    3


Q ss_pred             HHHHHHHhhCCccEEEEecccc
Q psy7952         182 YLLQHLVRYNKLAYIVVDEAHC  203 (444)
Q Consensus       182 ~~~~~~~~~~~~~~iViDE~H~  203 (444)
                      .+-.....+.++.+||+|--|.
T Consensus       191 Lle~~~L~l~~l~~ivlD~s~~  212 (252)
T PF14617_consen  191 LLENGALSLSNLKRIVLDWSYL  212 (252)
T ss_pred             HHHcCCCCcccCeEEEEcCCcc
Confidence            3445556678899999998765

>PHA02542 41 41 helicase; Provisional

Probab=90.54  E-value=0.8  Score=45.79  Aligned_cols=35  Identities=6%  Similarity=-0.046  Sum_probs=22.8

Q ss_pred             CcccCchHHHHHHHHHHc-cC---CcEEEEccCCCcccccc
Q psy7952          46 FDSFKCELQKKAIRHILL-RT---HDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        46 ~~~~~t~~Q~~~~~~~~~-~~---~~~ii~apTGsGKT~~a   82 (444)
                      ...+||.  ..-+..+.. |-   .-+++.|+||+|||..|
T Consensus       169 ~~gi~TG--~~~LD~~t~gGl~~G~LiiIaarPgmGKTtfa  207 (473)
T PHA02542        169 ANKIPFK--LEILNKITKGGAERKTLNVLLAGVNVGKSLGL  207 (473)
T ss_pred             CCccCCC--cHHHHHhccCCCCCCcEEEEEcCCCccHHHHH
Confidence            3344553  346666663 21   44788999999999773

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=90.54  E-value=0.28  Score=53.01  Aligned_cols=16  Identities=6%  Similarity=-0.105  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .+.++++|+|+|||.+
T Consensus       195 ~n~lL~G~pGvGKT~l  210 (852)
T TIGR03346       195 NNPVLIGEPGVGKTAI  210 (852)
T ss_pred             CceEEEcCCCCCHHHH
Confidence            6899999999999977

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=90.40  E-value=0.57  Score=45.25  Aligned_cols=25  Identities=12%  Similarity=0.030  Sum_probs=19.2

Q ss_pred             HHHHHHccC----CcEEEEccCCCccccc
Q psy7952          57 AIRHILLRT----HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        57 ~~~~~~~~~----~~~ii~apTGsGKT~~   81 (444)
                      -++.++.|.    .-+++.+++|+|||..
T Consensus        70 eLD~vLgGGi~~GslvLI~G~pG~GKStL   98 (372)
T cd01121          70 ELDRVLGGGLVPGSVILIGGDPGIGKSTL   98 (372)
T ss_pred             HHHHhhcCCccCCeEEEEEeCCCCCHHHH
Confidence            566666541    5589999999999977

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.

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=90.35  E-value=0.095  Score=47.12  Aligned_cols=14  Identities=21%  Similarity=0.005  Sum_probs=12.4

Q ss_pred             EEEEccCCCccccc
Q psy7952          68 IFVSMPTGAVSLVG   81 (444)
Q Consensus        68 ~ii~apTGsGKT~~   81 (444)
                      ++|+|++|+|||..
T Consensus         1 ~vv~G~pGsGKSt~   14 (234)
T PF01443_consen    1 IVVHGVPGSGKSTL   14 (234)
T ss_pred             CEEEcCCCCCHHHH
Confidence            47899999999977

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

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=90.19  E-value=0.23  Score=43.29  Aligned_cols=29  Identities=17%  Similarity=0.189  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHccCCcEEEEccCCCccccc
Q psy7952          53 LQKKAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        53 ~Q~~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      .-.+|+.-+..|.+++++.+|+|+|||..
T Consensus        10 ~aKrAL~iAAaG~h~lLl~GppGtGKTml   38 (206)
T PF01078_consen   10 EAKRALEIAAAGGHHLLLIGPPGTGKTML   38 (206)
T ss_dssp             HHHHHHHHHHHCC--EEEES-CCCTHHHH
T ss_pred             HHHHHHHHHHcCCCCeEEECCCCCCHHHH
Confidence            34456666666669999999999999977

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>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=90.08  E-value=0.19  Score=46.38  Aligned_cols=26  Identities=12%  Similarity=0.129  Sum_probs=20.7

Q ss_pred             HHHHHHHccCCcEEEEccCCCccccc
Q psy7952          56 KAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        56 ~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      ..+..++.++++++++||+|+|||..
T Consensus        24 ~ll~~l~~~~~pvLl~G~~GtGKT~l   49 (272)
T PF12775_consen   24 YLLDLLLSNGRPVLLVGPSGTGKTSL   49 (272)
T ss_dssp             HHHHHHHHCTEEEEEESSTTSSHHHH
T ss_pred             HHHHHHHHcCCcEEEECCCCCchhHH
Confidence            34555555558999999999999977

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=90.04  E-value=1.2  Score=47.34  Aligned_cols=26  Identities=15%  Similarity=0.148  Sum_probs=18.6

Q ss_pred             HHHHHHHc-cCCcEEEEccCCCccccc
Q psy7952          56 KAIRHILL-RTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        56 ~~~~~~~~-~~~~~ii~apTGsGKT~~   81 (444)
                      +++..+.+ ...++++.+|+|+|||..
T Consensus       197 ~~i~iL~r~~~~n~LLvGppGvGKT~l  223 (758)
T PRK11034        197 RAIQVLCRRRKNNPLLVGESGVGKTAI  223 (758)
T ss_pred             HHHHHHhccCCCCeEEECCCCCCHHHH
Confidence            34443333 236899999999999977

>KOG2170|consensus

Probab=90.03  E-value=1.6  Score=40.14  Aligned_cols=57  Identities=11%  Similarity=0.108  Sum_probs=36.9

Q ss_pred             HhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCC-------CCcEEEEeccCCcchHHHHHHHh
Q psy7952         188 VRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGN-------SIPIIALTATAEPSVKQDIISVL  250 (444)
Q Consensus       188 ~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~-------~~~~v~lSAT~~~~~~~~~~~~l  250 (444)
                      .....=+++|+||++.|..      ..++.|.-+++..+.       +.-+|++|.+-...+.+...+..
T Consensus       174 v~~C~rslFIFDE~DKmp~------gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg~eI~~~aL~~~  237 (344)
T KOG2170|consen  174 VQACQRSLFIFDEVDKLPP------GLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGGSEIARIALENA  237 (344)
T ss_pred             HHhcCCceEEechhhhcCH------hHHHHHhhhhccccccccccccceEEEEEcCCcchHHHHHHHHHH
Confidence            3345668999999999743      345666666664332       13478999887766665555544

>KOG0733|consensus

Probab=90.02  E-value=0.96  Score=45.54  Aligned_cols=16  Identities=13%  Similarity=0.185  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++++|+|+|||..
T Consensus       224 rGvLlHGPPGCGKT~l  239 (802)
T KOG0733|consen  224 RGVLLHGPPGCGKTSL  239 (802)
T ss_pred             CceeeeCCCCccHHHH
Confidence            6799999999999976

>PRK07773 replicative DNA helicase; Validated

Probab=89.99  E-value=0.77  Score=49.95  Aligned_cols=33  Identities=6%  Similarity=-0.112  Sum_probs=21.5

Q ss_pred             ccCchHHHHHHHHHHccC---CcEEEEccCCCcccccc
Q psy7952          48 SFKCELQKKAIRHILLRT---HDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        48 ~~~t~~Q~~~~~~~~~~~---~~~ii~apTGsGKT~~a   82 (444)
                      .+||.  ...++.+..|-   .-++|.|+||+|||..|
T Consensus       199 Gi~TG--~~~LD~l~~Gl~~G~livIagrPg~GKT~fa  234 (886)
T PRK07773        199 GVPTG--FTELDAMTNGLHPGQLIIVAARPSMGKTTFG  234 (886)
T ss_pred             CccCC--hhHhccccCCCCCCcEEEEEeCCCCCcHHHH
Confidence            34543  33555555431   44789999999999763

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=89.95  E-value=1.3  Score=41.80  Aligned_cols=16  Identities=13%  Similarity=0.266  Sum_probs=14.3

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .++++.||+|+|||.+
T Consensus        39 ~~~ll~G~~G~GKt~~   54 (319)
T PRK00440         39 PHLLFAGPPGTGKTTA   54 (319)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            3599999999999977

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=89.91  E-value=0.42  Score=46.67  Aligned_cols=16  Identities=13%  Similarity=0.206  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus       180 kgvLL~GppGTGKT~L  195 (398)
T PTZ00454        180 RGVLLYGPPGTGKTML  195 (398)
T ss_pred             ceEEEECCCCCCHHHH
Confidence            7799999999999977

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=89.86  E-value=0.47  Score=50.56  Aligned_cols=16  Identities=13%  Similarity=0.191  Sum_probs=14.5

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus       488 ~giLL~GppGtGKT~l  503 (733)
T TIGR01243       488 KGVLLFGPPGTGKTLL  503 (733)
T ss_pred             ceEEEECCCCCCHHHH
Confidence            5689999999999977

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=89.84  E-value=0.82  Score=43.13  Aligned_cols=41  Identities=15%  Similarity=0.186  Sum_probs=27.1

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccC
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATA  238 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~  238 (444)
                      ...+++|||++|.|....      ...+.+.+..-+ +..++++|..+
T Consensus       123 ~~~kVvII~~ae~m~~~a------aNaLLK~LEEPp-~~~fILi~~~~  163 (314)
T PRK07399        123 APRKVVVIEDAETMNEAA------ANALLKTLEEPG-NGTLILIAPSP  163 (314)
T ss_pred             CCceEEEEEchhhcCHHH------HHHHHHHHhCCC-CCeEEEEECCh
Confidence            467999999999985422      355556666555 46566666543

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=89.82  E-value=0.45  Score=49.34  Aligned_cols=41  Identities=15%  Similarity=0.071  Sum_probs=31.3

Q ss_pred             cCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          64 RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        64 ~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      |+.++++.||||+|||..        +.+|.    +...+..  ++++=|..++.
T Consensus       223 g~~H~Lv~ApTgsGKt~g--------~VIPn----LL~~~gS--~VV~DpKgEl~  263 (641)
T PRK13822        223 GSTHGLVFAGSGGFKTTS--------VVVPT----ALKWGGP--LVVLDPSTEVA  263 (641)
T ss_pred             CCceEEEEeCCCCCccce--------Eehhh----hhcCCCC--EEEEeCcHHHH
Confidence            347899999999999999        89998    5554434  25555888876

>PRK11823 DNA repair protein RadA; Provisional

Probab=89.79  E-value=0.83  Score=45.40  Aligned_cols=26  Identities=8%  Similarity=-0.009  Sum_probs=19.7

Q ss_pred             HHHHHHccC----CcEEEEccCCCcccccc
Q psy7952          57 AIRHILLRT----HDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        57 ~~~~~~~~~----~~~ii~apTGsGKT~~a   82 (444)
                      -++.++.|.    .-+++.+++|+|||..+
T Consensus        68 ~LD~~LgGGi~~Gs~~lI~G~pG~GKTtL~   97 (446)
T PRK11823         68 ELDRVLGGGLVPGSVVLIGGDPGIGKSTLL   97 (446)
T ss_pred             HHHHHhcCCccCCEEEEEECCCCCCHHHHH
Confidence            566666541    56799999999999773

>PHA02533 17 large terminase protein; Provisional

Probab=89.72  E-value=1  Score=45.79  Aligned_cols=57  Identities=9%  Similarity=-0.052  Sum_probs=38.1

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      .++|.+.+..+..+ +-.++..+=..|||.++...++.        ..+...  ...+++++|+..-+
T Consensus        61 ~p~Q~~i~~~~~~~-R~~ii~~aRq~GKStl~a~~al~--------~a~~~~--~~~v~i~A~~~~QA  117 (534)
T PHA02533         61 RDYQKDMLKIMHKN-RFNACNLSRQLGKTTVVAIFLLH--------YVCFNK--DKNVGILAHKASMA  117 (534)
T ss_pred             cHHHHHHHHHHhcC-eEEEEEEcCcCChHHHHHHHHHH--------HHHhCC--CCEEEEEeCCHHHH
Confidence            57999999887655 55678888999999884322111        011122  23678899988877

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=89.72  E-value=1.2  Score=47.40  Aligned_cols=16  Identities=6%  Similarity=-0.049  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .++++.+|+|+|||..
T Consensus       204 ~n~lL~G~pG~GKT~l  219 (731)
T TIGR02639       204 NNPLLVGEPGVGKTAI  219 (731)
T ss_pred             CceEEECCCCCCHHHH
Confidence            6899999999999977

>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=89.64  E-value=3.2  Score=35.23  Aligned_cols=14  Identities=14%  Similarity=0.052  Sum_probs=12.7

Q ss_pred             EEEEccCCCccccc
Q psy7952          68 IFVSMPTGAVSLVG   81 (444)
Q Consensus        68 ~ii~apTGsGKT~~   81 (444)
                      +++.+|+|+|||..
T Consensus         3 ~~~~G~~G~GKTt~   16 (173)
T cd03115           3 ILLVGLQGVGKTTT   16 (173)
T ss_pred             EEEECCCCCCHHHH
Confidence            57899999999977

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.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=89.54  E-value=1.4  Score=41.60  Aligned_cols=39  Identities=15%  Similarity=0.110  Sum_probs=23.9

Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      ..++||+||+|.+...     .....+..++...+.+.++|+.|
T Consensus       100 ~~~vliiDe~d~l~~~-----~~~~~L~~~le~~~~~~~~Ilt~  138 (316)
T PHA02544        100 GGKVIIIDEFDRLGLA-----DAQRHLRSFMEAYSKNCSFIITA  138 (316)
T ss_pred             CCeEEEEECcccccCH-----HHHHHHHHHHHhcCCCceEEEEc
Confidence            5689999999987321     12234455555556656666644

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=89.53  E-value=0.27  Score=48.02  Aligned_cols=28  Identities=18%  Similarity=0.260  Sum_probs=22.8

Q ss_pred             HHHHHHHHHccCCcEEEEccCCCccccc
Q psy7952          54 QKKAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        54 Q~~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      =++++.....|.++.++.+|+|||||..
T Consensus       187 AKrAleiAAAGgHnLl~~GpPGtGKTml  214 (490)
T COG0606         187 AKRALEIAAAGGHNLLLVGPPGTGKTML  214 (490)
T ss_pred             HHHHHHHHHhcCCcEEEecCCCCchHHh
Confidence            3456666667779999999999999976

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=89.50  E-value=0.24  Score=45.45  Aligned_cols=25  Identities=16%  Similarity=0.150  Sum_probs=19.2

Q ss_pred             HHHHHHccCCcEEEEccCCCcccccc
Q psy7952          57 AIRHILLRTHDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        57 ~~~~~~~~~~~~ii~apTGsGKT~~a   82 (444)
                      ++..+..+ +++++.+|+|+|||..|
T Consensus        14 ~l~~l~~g-~~vLL~G~~GtGKT~lA   38 (262)
T TIGR02640        14 ALRYLKSG-YPVHLRGPAGTGKTTLA   38 (262)
T ss_pred             HHHHHhcC-CeEEEEcCCCCCHHHHH
Confidence            33344456 89999999999999873

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).

>TIGR00959 ffh signal recognition particle protein

Probab=89.38  E-value=2.7  Score=41.38  Aligned_cols=15  Identities=13%  Similarity=0.003  Sum_probs=13.6

Q ss_pred             cEEEEccCCCccccc
Q psy7952          67 DIFVSMPTGAVSLVG   81 (444)
Q Consensus        67 ~~ii~apTGsGKT~~   81 (444)
                      -+++++++|+|||.+
T Consensus       101 vi~~vG~~GsGKTTt  115 (428)
T TIGR00959       101 VILMVGLQGSGKTTT  115 (428)
T ss_pred             EEEEECCCCCcHHHH
Confidence            478999999999987

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.

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.36  E-value=1.4  Score=44.40  Aligned_cols=16  Identities=13%  Similarity=0.059  Sum_probs=13.7

Q ss_pred             EEEEccCCCccccccc
Q psy7952          68 IFVSMPTGAVSLVGSV   83 (444)
Q Consensus        68 ~ii~apTGsGKT~~a~   83 (444)
                      +++.||.|+|||.+|-
T Consensus        41 yLf~Gp~G~GKTtlAr   56 (486)
T PRK14953         41 YIFAGPRGTGKTTIAR   56 (486)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6889999999998743

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=88.93  E-value=1.2  Score=42.35  Aligned_cols=42  Identities=12%  Similarity=0.085  Sum_probs=27.4

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEecc
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTAT  237 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT  237 (444)
                      ....+++||||+|.+....      ...+.+.+..-+++..+|+.|..
T Consensus       108 ~~~~kvviI~~a~~~~~~a------~NaLLK~LEEPp~~~~~Il~t~~  149 (329)
T PRK08058        108 ESNKKVYIIEHADKMTASA------ANSLLKFLEEPSGGTTAILLTEN  149 (329)
T ss_pred             ccCceEEEeehHhhhCHHH------HHHHHHHhcCCCCCceEEEEeCC
Confidence            3467899999999975422      34555666665665666665543

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.92  E-value=2.1  Score=44.48  Aligned_cols=40  Identities=18%  Similarity=0.173  Sum_probs=24.9

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEe
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALT  235 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lS  235 (444)
                      ....+++||||+|.+...      ....+.+.+...+.+..+|+.|
T Consensus       119 ~~~~KVvIIdea~~Ls~~------a~naLLK~LEepp~~tifIL~t  158 (614)
T PRK14971        119 IGKYKIYIIDEVHMLSQA------AFNAFLKTLEEPPSYAIFILAT  158 (614)
T ss_pred             cCCcEEEEEECcccCCHH------HHHHHHHHHhCCCCCeEEEEEe
Confidence            346789999999998542      2345555555555544454444

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=88.89  E-value=0.45  Score=49.55  Aligned_cols=41  Identities=27%  Similarity=0.147  Sum_probs=30.5

Q ss_pred             cCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          64 RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        64 ~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      +++++++.||||+|||..        +.+|.    +..-+.+  ++|+=|--++.
T Consensus       138 ~~~hvlviApTgSGKgvg--------~VIPn----LL~~~gS--~VV~DpKGE~~  178 (670)
T PRK13850        138 EQPHSLVVAPTRAGKGVG--------VVIPT----LLTFKGS--VIALDVKGELF  178 (670)
T ss_pred             CCceEEEEecCCCCceee--------ehHhH----HhcCCCC--EEEEeCCchHH
Confidence            346899999999999999        88888    4443322  35666777777

>PRK10689 transcription-repair coupling factor; Provisional

Probab=88.88  E-value=1.9  Score=48.11  Aligned_cols=81  Identities=7%  Similarity=0.143  Sum_probs=61.7

Q ss_pred             eeEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         107 RNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       107 ~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      +++|++|+..-+     ....+.+....+...+..+||+++..++.....+..  .+..+|+|+|.          +...
T Consensus       811 qv~vf~n~i~~i-----e~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr--~Gk~~VLVaTd----------Iier  873 (1147)
T PRK10689        811 QVYYLYNDVENI-----QKAAERLAELVPEARIAIGHGQMRERELERVMNDFH--HQRFNVLVCTT----------IIET  873 (1147)
T ss_pred             eEEEEECCHHHH-----HHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHH--hcCCCEEEECc----------hhhc
Confidence            569999999877     555555522222278899999999998888887776  47899999991          2445


Q ss_pred             HHhhCCccEEEEeccccc
Q psy7952         187 LVRYNKLAYIVVDEAHCV  204 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~  204 (444)
                      -.+..++++||++.++++
T Consensus       874 GIDIP~v~~VIi~~ad~f  891 (1147)
T PRK10689        874 GIDIPTANTIIIERADHF  891 (1147)
T ss_pred             ccccccCCEEEEecCCCC
Confidence            567788999999999874

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=88.84  E-value=0.39  Score=45.81  Aligned_cols=28  Identities=11%  Similarity=0.140  Sum_probs=21.4

Q ss_pred             HHHHHHHHHccCCcEEEEccCCCccccc
Q psy7952          54 QKKAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        54 Q~~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      ....+..+.....++++.+|||||||..
T Consensus       151 ~~~~l~~~v~~~~nilI~G~tGSGKTTl  178 (344)
T PRK13851        151 LEAFLHACVVGRLTMLLCGPTGSGKTTM  178 (344)
T ss_pred             HHHHHHHHHHcCCeEEEECCCCccHHHH
Confidence            3445555555558999999999999966

>KOG0733|consensus

Probab=88.68  E-value=0.71  Score=46.43  Aligned_cols=16  Identities=13%  Similarity=0.233  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      ..+++++|+|+|||+.
T Consensus       546 sGvLL~GPPGCGKTLl  561 (802)
T KOG0733|consen  546 SGVLLCGPPGCGKTLL  561 (802)
T ss_pred             CceEEeCCCCccHHHH
Confidence            5699999999999977

>KOG0732|consensus

Probab=88.48  E-value=0.62  Score=50.14  Aligned_cols=54  Identities=15%  Similarity=0.097  Sum_probs=35.3

Q ss_pred             hhCCccEEEEeccccccc----cCC-CcHHHHHHHHHHHHhhCCCCcEEEEeccCCcch
Q psy7952         189 RYNKLAYIVVDEAHCVSE----WGH-DFRPTYRRLGELRQFTGNSIPIIALTATAEPSV  242 (444)
Q Consensus       189 ~~~~~~~iViDE~H~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~  242 (444)
                      .......|.+||++-+.-    +.. .-...+..+..++..++...|++..+||..+..
T Consensus       360 ~k~qPSIIffdeIdGlapvrSskqEqih~SIvSTLLaLmdGldsRgqVvvigATnRpda  418 (1080)
T KOG0732|consen  360 QKTQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDSRGQVVVIGATNRPDA  418 (1080)
T ss_pred             hccCceEEeccccccccccccchHHHhhhhHHHHHHHhccCCCCCCceEEEcccCCccc
Confidence            345678999999995421    111 112344556677777777789999999965533

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=88.35  E-value=1.1  Score=47.74  Aligned_cols=16  Identities=13%  Similarity=0.210  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++++|+|+|||..
T Consensus       213 ~giLL~GppGtGKT~l  228 (733)
T TIGR01243       213 KGVLLYGPPGTGKTLL  228 (733)
T ss_pred             ceEEEECCCCCChHHH
Confidence            6799999999999976

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=88.35  E-value=1.2  Score=52.47  Aligned_cols=59  Identities=15%  Similarity=0.032  Sum_probs=39.1

Q ss_pred             CchHHHHHHHHHHccC-CcEEEEccCCCcccccccccccceEE--eCCCccccccCCccceeEEEcchhhhh
Q psy7952          50 KCELQKKAIRHILLRT-HDIFVSMPTGAVSLVGSVVSARSRVR--IPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~-~~~ii~apTGsGKT~~a~~~~~~~~~--~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      .|+.|.+|+..++.+. +-++|.++.|+|||.+        +.  ...+.+.+...+  .+|+.++||...+
T Consensus      1020 Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~--------l~~~~~~i~~~~~~~g--~~v~glApT~~Aa 1081 (1960)
T TIGR02760      1020 LTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTM--------LESRYKPVLQAFESEQ--LQVIGLAPTHEAV 1081 (1960)
T ss_pred             CCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHh--------HHHHHHHHHHHHHhcC--CeEEEEeChHHHH
Confidence            3689999999998763 4568899999999977        10  011111122222  3468889998877

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.

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=88.25  E-value=1.2  Score=42.11  Aligned_cols=40  Identities=18%  Similarity=0.150  Sum_probs=27.0

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEec
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTA  236 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSA  236 (444)
                      ....+||+||++.+...      ....+.+.....+.+.++++.+-
T Consensus       108 ~~~kviiidead~mt~~------A~nallk~lEep~~~~~~il~~n  147 (325)
T COG0470         108 GGYKVVIIDEADKLTED------AANALLKTLEEPPKNTRFILITN  147 (325)
T ss_pred             CCceEEEeCcHHHHhHH------HHHHHHHHhccCCCCeEEEEEcC
Confidence            46789999999998542      23555555556666666666664

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=88.20  E-value=0.44  Score=45.30  Aligned_cols=27  Identities=19%  Similarity=0.209  Sum_probs=20.8

Q ss_pred             HHHHHHHHccCCcEEEEccCCCccccc
Q psy7952          55 KKAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        55 ~~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      ...+..+..+..+++++++||||||..
T Consensus       150 ~~~L~~~v~~~~nili~G~tgSGKTTl  176 (332)
T PRK13900        150 KEFLEHAVISKKNIIISGGTSTGKTTF  176 (332)
T ss_pred             HHHHHHHHHcCCcEEEECCCCCCHHHH
Confidence            344555555558999999999999966

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=88.17  E-value=0.41  Score=49.79  Aligned_cols=41  Identities=15%  Similarity=0.133  Sum_probs=31.0

Q ss_pred             cCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          64 RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        64 ~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      +.+++++.||||+|||..        +.+|.    +...+.+  ++|+=|--++.
T Consensus       174 g~~HvlviapTgSGKgvg--------~ViPn----LL~~~~S--~VV~D~KGE~~  214 (636)
T PRK13880        174 GPEHVLTYAPTRSGKGVG--------LVVPT----LLSWGHS--SVITDLKGELW  214 (636)
T ss_pred             CCceEEEEecCCCCCceE--------EEccc----hhhCCCC--EEEEeCcHHHH
Confidence            347899999999999999        88899    5544333  35666777776

>KOG0331|consensus

Probab=87.99  E-value=0.83  Score=45.50  Aligned_cols=75  Identities=9%  Similarity=0.104  Sum_probs=57.7

Q ss_pred             ccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHH
Q psy7952         104 VRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHY  182 (444)
Q Consensus       104 ~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~  182 (444)
                      ...|+||+|-|+.-+     .+....+ ..+   +++..+||+.+..++...+.+.+  .+++.|+|+|--         
T Consensus       340 ~~~KvIIFc~tkr~~-----~~l~~~l~~~~---~~a~~iHGd~sQ~eR~~~L~~Fr--eG~~~vLVATdV---------  400 (519)
T KOG0331|consen  340 SEGKVIIFCETKRTC-----DELARNLRRKG---WPAVAIHGDKSQSERDWVLKGFR--EGKSPVLVATDV---------  400 (519)
T ss_pred             CCCcEEEEecchhhH-----HHHHHHHHhcC---cceeeecccccHHHHHHHHHhcc--cCCcceEEEccc---------
Confidence            335789999999999     6666666 557   88999999999999998888865  588999999922         


Q ss_pred             HHHHHHhhCCccEEEE
Q psy7952         183 LLQHLVRYNKLAYIVV  198 (444)
Q Consensus       183 ~~~~~~~~~~~~~iVi  198 (444)
                       -.+-++..++++||-
T Consensus       401 -AaRGLDi~dV~lVIn  415 (519)
T KOG0331|consen  401 -AARGLDVPDVDLVIN  415 (519)
T ss_pred             -ccccCCCccccEEEe
Confidence             234445667777773

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=87.96  E-value=0.64  Score=43.58  Aligned_cols=62  Identities=15%  Similarity=0.029  Sum_probs=40.8

Q ss_pred             CCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcc
Q psy7952          45 GFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYL  120 (444)
Q Consensus        45 g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~  120 (444)
                      .|.. .++-|...+..+.+...++++++.||||||..          +.+... ...  ...|++.+=-|.+|-++
T Consensus       154 ~~gt-~~~~~a~~L~~av~~r~NILisGGTGSGKTTl----------LNal~~-~i~--~~eRvItiEDtaELql~  215 (355)
T COG4962         154 IFGT-MIRRAAKFLRRAVGIRCNILISGGTGSGKTTL----------LNALSG-FID--SDERVITIEDTAELQLA  215 (355)
T ss_pred             HcCC-cCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH----------HHHHHh-cCC--CcccEEEEeehhhhccC
Confidence            3344 34689999998888856999999999999966          111000 111  12255777777777643

>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]

Probab=87.83  E-value=2.2  Score=41.78  Aligned_cols=91  Identities=13%  Similarity=0.175  Sum_probs=48.2

Q ss_pred             eCCCChhhHHHHHHHHHhcCCCeeEEEE-CCCccccccHHHHHHHHHhhCCccEEEEeccccccccCC--CcHHHHHHHH
Q psy7952         143 VSGQTKTENKAILEELRLVKPRIKLLYV-TPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGH--DFRPTYRRLG  219 (444)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~Iiv~-Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~--~~~~~~~~l~  219 (444)
                      +|.....++.........+.... |.|- ||+.=. .......+.......++++++|=.+.+...+.  .....+..+.
T Consensus       258 tg~l~~~d~~~l~~a~~~l~~~~-i~IdD~~~~si-~eir~~aRrlk~~~~l~~i~iDYLqLm~~~~~~~~r~qevs~iS  335 (435)
T COG0305         258 TGRLSDDEWERLIKAASELSEAP-IFIDDTPGLTI-TEIRSKARRLKLKHNLGLIVIDYLQLMTGGKKSENRKQEVSEIS  335 (435)
T ss_pred             cccccHHHHHHHHHHHHHHhhCC-eeecCCCcCCH-HHHHHHHHHHHHhcCccEEEEEEEEeecccccchhHHHHHHHHH
Confidence            33445566665555555544444 5443 444322 11233344445556699999999999865442  1233334444


Q ss_pred             HHHHhhCC--CCcEEEEe
Q psy7952         220 ELRQFTGN--SIPIIALT  235 (444)
Q Consensus       220 ~~~~~~~~--~~~~v~lS  235 (444)
                      +-++.+.+  +++++++|
T Consensus       336 r~LK~lAkEl~vpvialS  353 (435)
T COG0305         336 RSLKGLAKELGVPVIALS  353 (435)
T ss_pred             HHHHHHHHhcCCcEEehh
Confidence            33333322  36777776

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=87.77  E-value=0.87  Score=44.04  Aligned_cols=17  Identities=12%  Similarity=0.026  Sum_probs=15.8

Q ss_pred             CcEEEEccCCCcccccc
Q psy7952          66 HDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a   82 (444)
                      .++++.++||+||++.|
T Consensus       102 ~~vLi~GetGtGKel~A  118 (403)
T COG1221         102 LPVLIIGETGTGKELFA  118 (403)
T ss_pred             CcEEEecCCCccHHHHH
Confidence            89999999999999884

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=87.67  E-value=0.24  Score=44.28  Aligned_cols=17  Identities=18%  Similarity=0.225  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCcccccc
Q psy7952          66 HDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a   82 (444)
                      ..+++.+|+|+|||..+
T Consensus        20 s~~li~G~~GsGKT~l~   36 (226)
T PF06745_consen   20 SVVLISGPPGSGKTTLA   36 (226)
T ss_dssp             SEEEEEESTTSSHHHHH
T ss_pred             cEEEEEeCCCCCcHHHH
Confidence            66899999999999773

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 ....

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=87.53  E-value=0.99  Score=45.70  Aligned_cols=50  Identities=16%  Similarity=0.101  Sum_probs=28.3

Q ss_pred             CCccEEEEeccccccccCC-Cc----HHHHHHHHHHHHhhCCCCcEEEEeccCCc
Q psy7952         191 NKLAYIVVDEAHCVSEWGH-DF----RPTYRRLGELRQFTGNSIPIIALTATAEP  240 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~~v~lSAT~~~  240 (444)
                      .....|++||++.+..... ..    ......+...+........++.+-||=.+
T Consensus       334 ~~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p  388 (494)
T COG0464         334 LAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRP  388 (494)
T ss_pred             CCCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCc
Confidence            4568999999999855321 11    23444444444434444456666666444

>KOG0741|consensus

Probab=87.51  E-value=3.5  Score=41.05  Aligned_cols=61  Identities=15%  Similarity=0.211  Sum_probs=34.0

Q ss_pred             CCccEEEEeccccccccC---CCcHHH-HHHHHHHHHhhCC-CCcEEEEeccCCcchHHHHHHHhcCCCC
Q psy7952         191 NKLAYIVVDEAHCVSEWG---HDFRPT-YRRLGELRQFTGN-SIPIIALTATAEPSVKQDIISVLKFNKP  255 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~---~~~~~~-~~~l~~~~~~~~~-~~~~v~lSAT~~~~~~~~~~~~l~~~~~  255 (444)
                      +.+++||+|++.++.+|.   ..|.+. ++.+.-+++..|+ ..+++.+..|-    ...+.+.+++.+.
T Consensus       597 S~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS----~~~vL~~m~i~~~  662 (744)
T KOG0741|consen  597 SPLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTS----RREVLQEMGILDC  662 (744)
T ss_pred             CcceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEeccc----HHHHHHHcCHHHh
Confidence            468999999999998864   233332 3334444444443 34555555553    3344444444443

>KOG0729|consensus

Probab=87.25  E-value=2.4  Score=38.22  Aligned_cols=17  Identities=12%  Similarity=0.247  Sum_probs=15.6

Q ss_pred             CCcEEEEccCCCccccc
Q psy7952          65 THDIFVSMPTGAVSLVG   81 (444)
Q Consensus        65 ~~~~ii~apTGsGKT~~   81 (444)
                      .+.+++.+|+|+|||++
T Consensus       211 pkgvllygppgtgktl~  227 (435)
T KOG0729|consen  211 PKGVLLYGPPGTGKTLC  227 (435)
T ss_pred             CCceEEeCCCCCchhHH
Confidence            47899999999999988

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=87.23  E-value=0.81  Score=47.68  Aligned_cols=56  Identities=7%  Similarity=-0.021  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHccCC-cEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          53 LQKKAIRHILLRTH-DIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        53 ~Q~~~~~~~~~~~~-~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      -|.+.+..+++..+ -+++.|+-|=|||.++.+++.      +    +.......+++|..|+.+-+
T Consensus       218 ~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~------~----~~~~~~~~~iiVTAP~~~nv  274 (758)
T COG1444         218 EALEILERLLDAPKRALVLTADRGRGKSAALGIALA------A----AARLAGSVRIIVTAPTPANV  274 (758)
T ss_pred             HHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHH------H----HHHhcCCceEEEeCCCHHHH
Confidence            34445566666543 578999999999988554321      1    11222134678999999887

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=86.97  E-value=0.22  Score=44.95  Aligned_cols=26  Identities=19%  Similarity=0.161  Sum_probs=19.1

Q ss_pred             HHHHHHcc----CCcEEEEccCCCcccccc
Q psy7952          57 AIRHILLR----THDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        57 ~~~~~~~~----~~~~ii~apTGsGKT~~a   82 (444)
                      -++.++.|    ...+++.+|+|+|||..|
T Consensus         9 ~LD~~l~GG~~~gs~~lI~G~pGsGKT~la   38 (237)
T TIGR03877         9 GMDEILHGGIPERNVVLLSGGPGTGKSIFS   38 (237)
T ss_pred             hHHHHhcCCCcCCeEEEEEcCCCCCHHHHH
Confidence            45555543    166899999999999873

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.

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=86.92  E-value=1.6  Score=47.41  Aligned_cols=82  Identities=11%  Similarity=0.163  Sum_probs=61.9

Q ss_pred             ceeEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ  185 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~  185 (444)
                      .+++|+||+.+-+     ....+.+....+..++..+||.++..++.....+..  .+..+|+|+|-          ++.
T Consensus       661 ~qv~if~n~i~~~-----e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~--~Gk~~ILVaT~----------iie  723 (926)
T TIGR00580       661 GQVFYVHNRIESI-----EKLATQLRELVPEARIAIAHGQMTENELEEVMLEFY--KGEFQVLVCTT----------IIE  723 (926)
T ss_pred             CeEEEEECCcHHH-----HHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHH--cCCCCEEEECC----------hhh
Confidence            3579999998777     444455522122388999999999998888888776  47899999992          245


Q ss_pred             HHHhhCCccEEEEeccccc
Q psy7952         186 HLVRYNKLAYIVVDEAHCV  204 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~~  204 (444)
                      .-.+..++++||++.++++
T Consensus       724 ~GIDIp~v~~VIi~~a~~~  742 (926)
T TIGR00580       724 TGIDIPNANTIIIERADKF  742 (926)
T ss_pred             cccccccCCEEEEecCCCC
Confidence            5667788999999999873

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.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=86.87  E-value=1.6  Score=41.47  Aligned_cols=22  Identities=5%  Similarity=-0.023  Sum_probs=17.5

Q ss_pred             HHHccCCcEEEEccCCCccccc
Q psy7952          60 HILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        60 ~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      .+...+.+++|.+++|+||+.+
T Consensus        17 ~~a~~~~pVLI~GE~GtGK~~l   38 (329)
T TIGR02974        17 RLAPLDRPVLIIGERGTGKELI   38 (329)
T ss_pred             HHhCCCCCEEEECCCCChHHHH
Confidence            3334448899999999999977

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=86.83  E-value=0.31  Score=39.18  Aligned_cols=16  Identities=19%  Similarity=0.181  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus         3 ~~~~l~G~~G~GKTtl   18 (148)
T smart00382        3 EVILIVGPPGSGKTTL   18 (148)
T ss_pred             CEEEEECCCCCcHHHH
Confidence            6799999999999987

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=86.47  E-value=1.2  Score=48.13  Aligned_cols=14  Identities=14%  Similarity=0.207  Sum_probs=13.2

Q ss_pred             EEEEccCCCccccc
Q psy7952          68 IFVSMPTGAVSLVG   81 (444)
Q Consensus        68 ~ii~apTGsGKT~~   81 (444)
                      +++.+|||+|||..
T Consensus       599 ~lf~Gp~GvGKT~l  612 (852)
T TIGR03345       599 FLLVGPSGVGKTET  612 (852)
T ss_pred             EEEECCCCCCHHHH
Confidence            79999999999977

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=86.47  E-value=1.8  Score=38.84  Aligned_cols=16  Identities=6%  Similarity=-0.097  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .-+++.+|+|+|||..
T Consensus        25 ~~~~i~G~~G~GKTtl   40 (230)
T PRK08533         25 SLILIEGDESTGKSIL   40 (230)
T ss_pred             cEEEEECCCCCCHHHH
Confidence            6789999999999977

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=86.47  E-value=4.8  Score=42.43  Aligned_cols=55  Identities=20%  Similarity=0.354  Sum_probs=38.0

Q ss_pred             HHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCc
Q psy7952         181 HYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEP  240 (444)
Q Consensus       181 ~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~  240 (444)
                      ..++.......+.=++|+|+.|.+.+.-  ..   ..+..+++..|.+..+++.|=+-++
T Consensus       118 ~~L~~Ela~~~~pl~LVlDDyHli~~~~--l~---~~l~fLl~~~P~~l~lvv~SR~rP~  172 (894)
T COG2909         118 SSLLNELASYEGPLYLVLDDYHLISDPA--LH---EALRFLLKHAPENLTLVVTSRSRPQ  172 (894)
T ss_pred             HHHHHHHHhhcCceEEEeccccccCccc--HH---HHHHHHHHhCCCCeEEEEEeccCCC
Confidence            3444444445555699999999987643  22   4566777788888888888877544

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=86.37  E-value=1  Score=38.65  Aligned_cols=16  Identities=13%  Similarity=-0.145  Sum_probs=13.6

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +-.++.+|..||||..
T Consensus         5 ~l~~i~gpM~SGKT~e   20 (201)
T COG1435           5 WLEFIYGPMFSGKTEE   20 (201)
T ss_pred             EEEEEEccCcCcchHH
Confidence            3468999999999987

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=86.35  E-value=1.6  Score=43.76  Aligned_cols=74  Identities=9%  Similarity=0.095  Sum_probs=56.4

Q ss_pred             cceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHH
Q psy7952         105 RSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYL  183 (444)
Q Consensus       105 ~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~  183 (444)
                      ..++||+|+++.-+     ....+.+ ..+   +.+..++++.+..++...+..++  .+..+|+|+|.          .
T Consensus       245 ~~~~lVF~~t~~~~-----~~l~~~L~~~g---~~~~~lhg~~~~~~R~~~l~~F~--~g~~~iLVaTd----------v  304 (456)
T PRK10590        245 WQQVLVFTRTKHGA-----NHLAEQLNKDG---IRSAAIHGNKSQGARTRALADFK--SGDIRVLVATD----------I  304 (456)
T ss_pred             CCcEEEEcCcHHHH-----HHHHHHHHHCC---CCEEEEECCCCHHHHHHHHHHHH--cCCCcEEEEcc----------H
Confidence            35789999999988     6666666 667   88999999999999988888776  47889999992          2


Q ss_pred             HHHHHhhCCccEEEE
Q psy7952         184 LQHLVRYNKLAYIVV  198 (444)
Q Consensus       184 ~~~~~~~~~~~~iVi  198 (444)
                      ...-.++.++++||.
T Consensus       305 ~~rGiDip~v~~VI~  319 (456)
T PRK10590        305 AARGLDIEELPHVVN  319 (456)
T ss_pred             HhcCCCcccCCEEEE
Confidence            334445667777763

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=86.34  E-value=2.9  Score=42.92  Aligned_cols=18  Identities=17%  Similarity=0.152  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCccccccc
Q psy7952          66 HDIFVSMPTGAVSLVGSV   83 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~   83 (444)
                      +-+++.||.|+|||.+|-
T Consensus        39 hayLf~Gp~G~GKTt~Ar   56 (563)
T PRK06647         39 NAYIFSGPRGVGKTSSAR   56 (563)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            347999999999998843

>KOG0344|consensus

Probab=86.21  E-value=3.6  Score=41.22  Aligned_cols=87  Identities=10%  Similarity=0.128  Sum_probs=66.4

Q ss_pred             cccCCccceeEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccc
Q psy7952          99 ILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTE  178 (444)
Q Consensus        99 l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~  178 (444)
                      +...+..|.++|.+-+.+-+     .+.+..+. -.+.+++.+++|..+...+.+.....+  .+...++|||       
T Consensus       381 ~v~~g~~PP~lIfVQs~eRa-----k~L~~~L~-~~~~i~v~vIh~e~~~~qrde~~~~FR--~g~IwvLicT-------  445 (593)
T KOG0344|consen  381 LVASGFKPPVLIFVQSKERA-----KQLFEELE-IYDNINVDVIHGERSQKQRDETMERFR--IGKIWVLICT-------  445 (593)
T ss_pred             HHhccCCCCeEEEEecHHHH-----HHHHHHhh-hccCcceeeEecccchhHHHHHHHHHh--ccCeeEEEeh-------
Confidence            55666777889999998888     66666662 223399999999998888888777776  4788999999       


Q ss_pred             cHHHHHHHHHhhCCccEEEEecccc
Q psy7952         179 SFHYLLQHLVRYNKLAYIVVDEAHC  203 (444)
Q Consensus       179 ~~~~~~~~~~~~~~~~~iViDE~H~  203 (444)
                        . ++.+-.++..+++||.+++-.
T Consensus       446 --d-ll~RGiDf~gvn~VInyD~p~  467 (593)
T KOG0344|consen  446 --D-LLARGIDFKGVNLVINYDFPQ  467 (593)
T ss_pred             --h-hhhccccccCcceEEecCCCc
Confidence              3 344557889999999977754

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=86.12  E-value=2.3  Score=43.85  Aligned_cols=76  Identities=9%  Similarity=0.206  Sum_probs=59.1

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||+|+++..+     ....+.+ ..+   +.+..++++....++...++.++  .+..+|+|+|.          ..
T Consensus       258 ~k~LVF~nt~~~a-----e~l~~~L~~~g---~~v~~lhg~l~~~eR~~il~~Fr--~G~~~VLVaTd----------v~  317 (572)
T PRK04537        258 ARTMVFVNTKAFV-----ERVARTLERHG---YRVGVLSGDVPQKKRESLLNRFQ--KGQLEILVATD----------VA  317 (572)
T ss_pred             CcEEEEeCCHHHH-----HHHHHHHHHcC---CCEEEEeCCCCHHHHHHHHHHHH--cCCCeEEEEeh----------hh
Confidence            4679999999999     5666666 667   88999999999999988888876  47899999992          23


Q ss_pred             HHHHhhCCccEEEEecc
Q psy7952         185 QHLVRYNKLAYIVVDEA  201 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE~  201 (444)
                      ..-.++.++++||.-++
T Consensus       318 arGIDip~V~~VInyd~  334 (572)
T PRK04537        318 ARGLHIDGVKYVYNYDL  334 (572)
T ss_pred             hcCCCccCCCEEEEcCC
Confidence            34456778888886544

>KOG0333|consensus

Probab=86.09  E-value=1.3  Score=43.74  Aligned_cols=75  Identities=12%  Similarity=0.185  Sum_probs=58.5

Q ss_pred             CccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHH
Q psy7952         103 NVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFH  181 (444)
Q Consensus       103 ~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~  181 (444)
                      +..+.++|+++++.-+     ....+.| ..+   +++..+||+.+...+...+.+++  .+..+|+|+|.--       
T Consensus       515 ~~~ppiIIFvN~kk~~-----d~lAk~LeK~g---~~~~tlHg~k~qeQRe~aL~~fr--~~t~dIlVaTDvA-------  577 (673)
T KOG0333|consen  515 NFDPPIIIFVNTKKGA-----DALAKILEKAG---YKVTTLHGGKSQEQRENALADFR--EGTGDILVATDVA-------  577 (673)
T ss_pred             CCCCCEEEEEechhhH-----HHHHHHHhhcc---ceEEEeeCCccHHHHHHHHHHHH--hcCCCEEEEeccc-------
Confidence            3457889999999988     6666777 778   99999999999999999998887  3678999999322       


Q ss_pred             HHHHHHHhhCCccEEE
Q psy7952         182 YLLQHLVRYNKLAYIV  197 (444)
Q Consensus       182 ~~~~~~~~~~~~~~iV  197 (444)
                         -.-.+..++++||
T Consensus       578 ---gRGIDIpnVSlVi  590 (673)
T KOG0333|consen  578 ---GRGIDIPNVSLVI  590 (673)
T ss_pred             ---ccCCCCCccceee
Confidence               2334556676666

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=86.00  E-value=0.82  Score=41.99  Aligned_cols=30  Identities=23%  Similarity=0.259  Sum_probs=23.5

Q ss_pred             hHHHHHHHHHHccC-CcEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHILLRT-HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~-~~~ii~apTGsGKT~~   81 (444)
                      +.|.+.+..++... ..+++.+|||+|||..
T Consensus        66 ~~~~~~l~~~~~~~~GlilisG~tGSGKTT~   96 (264)
T cd01129          66 PENLEIFRKLLEKPHGIILVTGPTGSGKTTT   96 (264)
T ss_pred             HHHHHHHHHHHhcCCCEEEEECCCCCcHHHH
Confidence            46777887777532 4689999999999977

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.

>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=85.79  E-value=0.49  Score=43.64  Aligned_cols=30  Identities=23%  Similarity=0.222  Sum_probs=22.1

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      +...+.+....++..++++.||||||||..
T Consensus       114 ~~~~~~l~~~v~~~~~ili~G~tGSGKTT~  143 (270)
T PF00437_consen  114 EEIAEFLRSAVRGRGNILISGPTGSGKTTL  143 (270)
T ss_dssp             HHHHHHHHHCHHTTEEEEEEESTTSSHHHH
T ss_pred             HHHHHHHhhccccceEEEEECCCccccchH
Confidence            344555555544447999999999999977

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 ....

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=85.73  E-value=2.2  Score=42.24  Aligned_cols=75  Identities=11%  Similarity=0.132  Sum_probs=58.2

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||+|+++.-+     ......+ ..+   +++..++|+....++...+++++  .+..+|+|+|.          ..
T Consensus       256 ~~~lVF~~t~~~~-----~~l~~~L~~~g---~~v~~lhg~~~~~~R~~~l~~F~--~g~~~vLVaTd----------v~  315 (423)
T PRK04837        256 DRAIIFANTKHRC-----EEIWGHLAADG---HRVGLLTGDVAQKKRLRILEEFT--RGDLDILVATD----------VA  315 (423)
T ss_pred             CeEEEEECCHHHH-----HHHHHHHHhCC---CcEEEecCCCChhHHHHHHHHHH--cCCCcEEEEec----------hh
Confidence            4679999999998     6666666 667   89999999999988888888776  57899999992          23


Q ss_pred             HHHHhhCCccEEEEec
Q psy7952         185 QHLVRYNKLAYIVVDE  200 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE  200 (444)
                      ..-.++.++++||.-+
T Consensus       316 ~rGiDip~v~~VI~~d  331 (423)
T PRK04837        316 ARGLHIPAVTHVFNYD  331 (423)
T ss_pred             hcCCCccccCEEEEeC
Confidence            3445666788777544

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=85.55  E-value=0.6  Score=48.58  Aligned_cols=41  Identities=15%  Similarity=0.084  Sum_probs=30.6

Q ss_pred             cCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          64 RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        64 ~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      +++++++.||||+|||..        +.+|.    +..-..+  +||.=|.-++.
T Consensus       143 g~~hvLviApTrSGKgvg--------~VIPn----LL~~~~S--~VV~D~KGEl~  183 (663)
T PRK13876        143 GPEHVLCFAPTRSGKGVG--------LVVPT----LLTWPGS--AIVHDIKGENW  183 (663)
T ss_pred             CCceEEEEecCCCCccee--------Eehhh----HHhCCCC--EEEEeCcchHH
Confidence            457999999999999999        88898    5443333  25555777776

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=85.54  E-value=3.1  Score=33.82  Aligned_cols=23  Identities=4%  Similarity=0.089  Sum_probs=17.3

Q ss_pred             HHHHccCCcEEEEccCCCccccc
Q psy7952          59 RHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        59 ~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      ..+...+.++++.+++|+||+.+
T Consensus        15 ~~~a~~~~pvli~GE~GtGK~~~   37 (138)
T PF14532_consen   15 ERLAKSSSPVLITGEPGTGKSLL   37 (138)
T ss_dssp             HHHHCSSS-EEEECCTTSSHHHH
T ss_pred             HHHhCCCCcEEEEcCCCCCHHHH
Confidence            33444448999999999999987

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=85.39  E-value=4.1  Score=36.75  Aligned_cols=20  Identities=20%  Similarity=-0.006  Sum_probs=15.9

Q ss_pred             cEEEEccCCCcccccccccc
Q psy7952          67 DIFVSMPTGAVSLVGSVVSA   86 (444)
Q Consensus        67 ~~ii~apTGsGKT~~a~~~~   86 (444)
                      -.++.+|.|+|||..++..+
T Consensus         3 ~~ll~g~~G~GKS~lal~la   22 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLA   22 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHH
Confidence            35899999999998865544

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PRK12608 transcription termination factor Rho; Provisional

Probab=85.20  E-value=3.7  Score=39.42  Aligned_cols=28  Identities=14%  Similarity=0.106  Sum_probs=22.0

Q ss_pred             HHHHHHHHHH---ccCCcEEEEccCCCccccc
Q psy7952          53 LQKKAIRHIL---LRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        53 ~Q~~~~~~~~---~~~~~~ii~apTGsGKT~~   81 (444)
                      .-.++++.+.   .| ++.+|.+|.|+|||..
T Consensus       119 ~~~RvID~l~PiGkG-QR~LIvG~pGtGKTTL  149 (380)
T PRK12608        119 LSMRVVDLVAPIGKG-QRGLIVAPPRAGKTVL  149 (380)
T ss_pred             hhHhhhhheeecCCC-ceEEEECCCCCCHHHH
Confidence            4445666555   56 8999999999999977

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=85.16  E-value=4.5  Score=34.35  Aligned_cols=50  Identities=14%  Similarity=0.164  Sum_probs=31.3

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcch
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSV  242 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~  242 (444)
                      -..+++||+||+-...+.+  +-+. ..+..+++..|...-+|+..-.+++..
T Consensus        95 ~~~~DlvVLDEi~~A~~~g--li~~-~~v~~lL~~rp~~~evVlTGR~~p~~l  144 (173)
T TIGR00708        95 DPELDLVLLDELTYALKYG--YLDV-EEVVEALQERPGHQHVIITGRGCPQDL  144 (173)
T ss_pred             cCCCCEEEehhhHHHHHCC--CcCH-HHHHHHHHhCCCCCEEEEECCCCCHHH
Confidence            4679999999998777665  2222 345566666666555555444444433

Alternate name: corrinoid adenosyltransferase.

>PRK06749 replicative DNA helicase; Provisional

Probab=85.15  E-value=2.6  Score=41.63  Aligned_cols=33  Identities=0%  Similarity=-0.053  Sum_probs=21.5

Q ss_pred             ccCchHHHHHHHHHHccC---CcEEEEccCCCcccccc
Q psy7952          48 SFKCELQKKAIRHILLRT---HDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        48 ~~~t~~Q~~~~~~~~~~~---~~~ii~apTGsGKT~~a   82 (444)
                      .+||.+.  .++.+..|-   .-++|.|.||.|||..|
T Consensus       168 Gi~TG~~--~LD~~t~Gl~~G~LiiIaarPgmGKTafa  203 (428)
T PRK06749        168 GIETGYT--SLNKMTCGLQEGDFVVLGARPSMGKTAFA  203 (428)
T ss_pred             CccCCcH--HHHHHhCCCCCCcEEEEEeCCCCCchHHH
Confidence            3555543  455554431   55789999999999763

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=84.98  E-value=0.29  Score=45.50  Aligned_cols=17  Identities=6%  Similarity=-0.076  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCcccccc
Q psy7952          66 HDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a   82 (444)
                      .++++.+|+|+|||.+|
T Consensus        59 ~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        59 LHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             ceEEEEcCCCCCHHHHH
Confidence            47999999999999874

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.

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=84.90  E-value=2.6  Score=40.46  Aligned_cols=17  Identities=24%  Similarity=0.227  Sum_probs=14.4

Q ss_pred             CcEEEEccCCCcccccc
Q psy7952          66 HDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a   82 (444)
                      +.+++.||+|+|||..|
T Consensus        37 ~~~Ll~G~~G~GKt~~a   53 (355)
T TIGR02397        37 HAYLFSGPRGTGKTSIA   53 (355)
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            35799999999999773

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.

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=84.89  E-value=0.63  Score=43.86  Aligned_cols=27  Identities=11%  Similarity=-0.050  Sum_probs=20.2

Q ss_pred             HHHHHHc-cC----CcEEEEccCCCccccccc
Q psy7952          57 AIRHILL-RT----HDIFVSMPTGAVSLVGSV   83 (444)
Q Consensus        57 ~~~~~~~-~~----~~~ii~apTGsGKT~~a~   83 (444)
                      .++.++. |.    +-+.+.+|+|+|||..|+
T Consensus        42 ~LD~~Lg~GGlp~G~iteI~Gp~GsGKTtLal   73 (325)
T cd00983          42 SLDIALGIGGYPKGRIIEIYGPESSGKTTLAL   73 (325)
T ss_pred             HHHHHhcCCCccCCeEEEEECCCCCCHHHHHH
Confidence            5667776 31    457899999999997743

RecA couples ATP hydrolysis to DNA strand exchange.

>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases

Probab=84.83  E-value=3.2  Score=37.41  Aligned_cols=105  Identities=14%  Similarity=0.241  Sum_probs=76.3

Q ss_pred             hhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhhcCHHHHHHHHHHHhcC----CccEEEEcCccccccc
Q psy7952         280 DSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERSRVQESFMRG----EINVITATISFGMGID  355 (444)
Q Consensus       280 ~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~~~~~~r~~~~~~f~~g----~~~vLvaT~~~~~Gid  355 (444)
                      .+++.+...+...+..     +--|+.+||....+.    |              .+.++    ...|+|+=+.++||+.
T Consensus        94 ~s~~ei~~~l~~~~~~-----~~~v~~vNS~~~~~~----l--------------dy~~~~~~~~~~I~VGGn~LsRGlT  150 (239)
T PF10593_consen   94 PSWEEIKPELPKAISD-----GIEVVVVNSGSSDDS----L--------------DYDDGENLGLNVIAVGGNKLSRGLT  150 (239)
T ss_pred             cCHHHHHHHHHHHHhc-----CceEEEEeCCCcccc----c--------------cccccccCCceEEEECCccccCcee
Confidence            4455666666665542     233777776543332    1              12222    3788999999999999


Q ss_pred             cCCccEEEEeCCCCCHHHHHHHhccCC-CCCCceeEEEEecccchhhHHHHHh
Q psy7952         356 RQNVRFVVHWGMPSSIPAYYQESGRAG-RDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       356 i~~~~~Vi~~~~p~s~~~~~Qr~GR~~-R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      ++++.+-.+...+...++++||.-=.| |.|-.+.|-++.+++-...+..+..
T Consensus       151 leGL~vsYf~R~s~~~DTL~QmgRwFGYR~gY~dl~Ri~~~~~l~~~f~~i~~  203 (239)
T PF10593_consen  151 LEGLTVSYFLRNSKQYDTLMQMGRWFGYRPGYEDLCRIYMPEELYDWFRHIAE  203 (239)
T ss_pred             ECCcEEEEecCCCchHHHHHHHhhcccCCcccccceEEecCHHHHHHHHHHHH
Confidence            999999999999998999988864455 7888899999999888888777764

This domain is found associated with a helicase domain of superfamily type II [].

>CHL00095 clpC Clp protease ATP binding subunit

Probab=84.78  E-value=2.1  Score=46.23  Aligned_cols=104  Identities=16%  Similarity=0.060  Sum_probs=0.0

Q ss_pred             EEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCC
Q psy7952          68 IFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSG  145 (444)
Q Consensus        68 ~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~  145 (444)
                      +++++|||+|||..                                          ...+...  ...   .....+...
T Consensus       542 ~lf~Gp~GvGKt~l------------------------------------------A~~LA~~l~~~~---~~~~~~d~s  576 (821)
T CHL00095        542 FLFSGPTGVGKTEL------------------------------------------TKALASYFFGSE---DAMIRLDMS  576 (821)
T ss_pred             EEEECCCCCcHHHH------------------------------------------HHHHHHHhcCCc---cceEEEEch


Q ss_pred             CChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHh-
Q psy7952         146 QTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQF-  224 (444)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~-  224 (444)
                      .-..            .....-++++|..-....-...+......+..++|++||+|.+      -......+..++.. 
T Consensus       577 ~~~~------------~~~~~~l~g~~~gyvg~~~~~~l~~~~~~~p~~VvllDeieka------~~~v~~~Llq~le~g  638 (821)
T CHL00095        577 EYME------------KHTVSKLIGSPPGYVGYNEGGQLTEAVRKKPYTVVLFDEIEKA------HPDIFNLLLQILDDG  638 (821)
T ss_pred             hccc------------cccHHHhcCCCCcccCcCccchHHHHHHhCCCeEEEECChhhC------CHHHHHHHHHHhccC


Q ss_pred             -----------hCCCCcEEEEe
Q psy7952         225 -----------TGNSIPIIALT  235 (444)
Q Consensus       225 -----------~~~~~~~v~lS  235 (444)
                                 +.+ +-+|+.|
T Consensus       639 ~~~d~~g~~v~~~~-~i~I~Ts  659 (821)
T CHL00095        639 RLTDSKGRTIDFKN-TLIIMTS  659 (821)
T ss_pred             ceecCCCcEEecCc-eEEEEeC

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=84.75  E-value=2.8  Score=38.88  Aligned_cols=43  Identities=12%  Similarity=0.027  Sum_probs=30.2

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCC
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAE  239 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~  239 (444)
                      +..+++|||++|.|....      ...+.+.+..-+++..++++|..+.
T Consensus        94 ~~~kv~ii~~ad~mt~~A------aNaLLK~LEEPp~~~~fiL~~~~~~  136 (290)
T PRK05917         94 SPYKIYIIHEADRMTLDA------ISAFLKVLEDPPQHGVIILTSAKPQ  136 (290)
T ss_pred             CCceEEEEechhhcCHHH------HHHHHHHhhcCCCCeEEEEEeCChh
Confidence            467899999999986422      3566667777676677777776643

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=84.74  E-value=1  Score=41.75  Aligned_cols=16  Identities=25%  Similarity=0.125  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++++|||+|||.+
T Consensus       195 ~vi~~vGptGvGKTTt  210 (282)
T TIGR03499       195 GVIALVGPTGVGKTTT  210 (282)
T ss_pred             eEEEEECCCCCCHHHH
Confidence            4588999999999977

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=84.71  E-value=6.6  Score=39.98  Aligned_cols=166  Identities=13%  Similarity=0.090  Sum_probs=84.9

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ...+.+.++..||...+.    ..+++...+  +--+.-.|---|||..         .+|+ +..+...-..=++.+++
T Consensus       176 a~r~~~~lk~~Fdi~~~s----~~~l~~FKQ--kaTVFLVPRRHGKTWf---------~Vpi-IsllL~s~~gI~IGYvA  239 (668)
T PHA03372        176 ANRVLEYLLHVFDIEFLS----ESSLNIFKQ--KATVFLVPRRHGKTWF---------IIPI-ISFLLKNIIGISIGYVA  239 (668)
T ss_pred             HHHHHHHHHHHcCCcccC----HHHHHHhhc--cceEEEecccCCceeh---------HHHH-HHHHHHhhcCceEEEEe
Confidence            566778889998988633    345666555  3455667899999965         2333 33333322223567888


Q ss_pred             chhhhhcccCccchHhhh----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHH-HHHHH
Q psy7952         113 PILSSFYLRFRDDKTSIV----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHY-LLQHL  187 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~-~~~~~  187 (444)
                      .-+..+     +-.+++.    +.-++.-.+...                    .+..|.+.-|+.=....|.. ...+.
T Consensus       240 HqKhvs-----~~Vf~EI~~~lrrwF~~~~vi~~--------------------k~~tI~~s~pg~Kst~~fasc~n~Ns  294 (668)
T PHA03372        240 HQKHVS-----QFVLKEVEFRCRRMFPRKHTIEN--------------------KDNVISIDHRGAKSTALFASCYNTNS  294 (668)
T ss_pred             eHHHHH-----HHHHHHHHHHHhhhcCccceeee--------------------cCcEEEEecCCCcceeeehhhccCcc
Confidence            877665     3333332    111110111100                    11234444443211111111 11122


Q ss_pred             HhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHH
Q psy7952         188 VRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDII  247 (444)
Q Consensus       188 ~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~  247 (444)
                      ..-.+++++++||+|-+..      ..+..|.-++  ..+++++|..|.|-.......+.
T Consensus       295 iRGQ~fnll~VDEA~FI~~------~a~~tilgfm--~q~~~KiIfISS~Nsg~~sTSfL  346 (668)
T PHA03372        295 IRGQNFHLLLVDEAHFIKK------DAFNTILGFL--AQNTTKIIFISSTNTTNDATCFL  346 (668)
T ss_pred             ccCCCCCEEEEehhhccCH------HHHHHhhhhh--cccCceEEEEeCCCCCCccchHH
Confidence            2334789999999998643      1223333222  23458899999886555444333

>KOG0730|consensus

Probab=84.56  E-value=2.4  Score=43.19  Aligned_cols=27  Identities=7%  Similarity=0.062  Sum_probs=19.2

Q ss_pred             HHHHHHHH-ccCCcEEEEccCCCccccc
Q psy7952          55 KKAIRHIL-LRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        55 ~~~~~~~~-~~~~~~ii~apTGsGKT~~   81 (444)
                      -+.+..+- +-.+.|++.+|+|+|||..
T Consensus       457 pe~F~r~Gi~ppkGVLlyGPPGC~KT~l  484 (693)
T KOG0730|consen  457 PEKFARFGISPPKGVLLYGPPGCGKTLL  484 (693)
T ss_pred             hHHHHHhcCCCCceEEEECCCCcchHHH
Confidence            33444433 2237899999999999977

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

Probab=84.49  E-value=1.9  Score=43.74  Aligned_cols=72  Identities=8%  Similarity=0.152  Sum_probs=57.9

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||+|.|+..+     ......+ ..+   +++..+||+.+...+...+...+  .+..+|+|+|-          +.
T Consensus       274 ~~~IVF~~tk~~~-----~~l~~~l~~~g---~~~~~lhG~l~q~~R~~~l~~F~--~g~~~vLVaTD----------va  333 (513)
T COG0513         274 GRVIVFVRTKRLV-----EELAESLRKRG---FKVAALHGDLPQEERDRALEKFK--DGELRVLVATD----------VA  333 (513)
T ss_pred             CeEEEEeCcHHHH-----HHHHHHHHHCC---CeEEEecCCCCHHHHHHHHHHHH--cCCCCEEEEec----------hh
Confidence            3589999999999     6666666 788   99999999999999999998887  58899999992          22


Q ss_pred             HHHHhhCCccEEE
Q psy7952         185 QHLVRYNKLAYIV  197 (444)
Q Consensus       185 ~~~~~~~~~~~iV  197 (444)
                      .+-.+..++++||
T Consensus       334 aRGiDi~~v~~Vi  346 (513)
T COG0513         334 ARGLDIPDVSHVI  346 (513)
T ss_pred             hccCCccccceeE
Confidence            3445566677775

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=84.46  E-value=1.5  Score=43.04  Aligned_cols=41  Identities=2%  Similarity=-0.107  Sum_probs=24.4

Q ss_pred             cEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhh
Q psy7952          67 DIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILS  116 (444)
Q Consensus        67 ~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~  116 (444)
                      -.++.+..|||||.++.+.        . +..+.......+++++-|+..
T Consensus         3 ~~i~~GgrgSGKS~~~~~~--------~-~~~~~~~~~~~~~~~~r~~~~   43 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALK--------L-VEKLAINKKQQNILAARKVQN   43 (396)
T ss_pred             eEEEeCCCCcccHHHHHHH--------H-HHHHHhcCCCcEEEEEehhhh
Confidence            4678999999999883322        2 111222112245677878776

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.

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=84.41  E-value=2.4  Score=38.54  Aligned_cols=21  Identities=14%  Similarity=-0.072  Sum_probs=17.5

Q ss_pred             HHHccCCcEEEEccCCCccccc
Q psy7952          60 HILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        60 ~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      .+-.| +.+++.+|.|+|||..
T Consensus        12 ~i~~G-qr~~I~G~~G~GKTTL   32 (249)
T cd01128          12 PIGKG-QRGLIVAPPKAGKTTL   32 (249)
T ss_pred             ccCCC-CEEEEECCCCCCHHHH
Confidence            34467 8999999999999965

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=84.33  E-value=0.57  Score=47.18  Aligned_cols=28  Identities=11%  Similarity=-0.044  Sum_probs=20.9

Q ss_pred             HHHHHHHccC----CcEEEEccCCCccccccc
Q psy7952          56 KAIRHILLRT----HDIFVSMPTGAVSLVGSV   83 (444)
Q Consensus        56 ~~~~~~~~~~----~~~ii~apTGsGKT~~a~   83 (444)
                      .-++.++.|.    .-+++.+|+|+|||..++
T Consensus       250 ~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~  281 (484)
T TIGR02655       250 VRLDEMCGGGFFKDSIILATGATGTGKTLLVS  281 (484)
T ss_pred             HhHHHHhcCCccCCcEEEEECCCCCCHHHHHH
Confidence            4566767542    558999999999998743

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.

>PRK10436 hypothetical protein; Provisional

Probab=84.33  E-value=0.9  Score=45.20  Aligned_cols=30  Identities=30%  Similarity=0.290  Sum_probs=23.6

Q ss_pred             hHHHHHHHHHHccC-CcEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHILLRT-HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~-~~~ii~apTGsGKT~~   81 (444)
                      +.|.+.+..+.... .-+++++|||||||.+
T Consensus       204 ~~~~~~l~~~~~~~~GliLvtGpTGSGKTTt  234 (462)
T PRK10436        204 PAQLAQFRQALQQPQGLILVTGPTGSGKTVT  234 (462)
T ss_pred             HHHHHHHHHHHHhcCCeEEEECCCCCChHHH
Confidence            46777887776532 4689999999999987

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=84.31  E-value=0.79  Score=47.36  Aligned_cols=41  Identities=12%  Similarity=0.106  Sum_probs=31.5

Q ss_pred             cCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          64 RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        64 ~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      |+.++++.||||+|||..        +.+|.    +...+..  ++++=|.-++.
T Consensus       210 g~~H~lv~ApTgsGKgvg--------~VIPn----LL~~~gS--~VV~DpKgE~~  250 (623)
T TIGR02767       210 GSTHMIFFAGSGGFKTTS--------VVVPT----ALKYGGP--LVCLDPSTEVA  250 (623)
T ss_pred             CCceEEEEeCCCCCccce--------eehhh----hhcCCCC--EEEEEChHHHH
Confidence            347899999999999999        88998    5554433  26666888887

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>PTZ00110 helicase; Provisional

Probab=84.12  E-value=2.8  Score=43.03  Aligned_cols=74  Identities=11%  Similarity=0.094  Sum_probs=57.2

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||+|+++.-+     ....+.+ ..+   +.+..++|+....++...+..++  .+...|+|+|.          ..
T Consensus       378 ~k~LIF~~t~~~a-----~~l~~~L~~~g---~~~~~ihg~~~~~eR~~il~~F~--~G~~~ILVaTd----------v~  437 (545)
T PTZ00110        378 DKILIFVETKKGA-----DFLTKELRLDG---WPALCIHGDKKQEERTWVLNEFK--TGKSPIMIATD----------VA  437 (545)
T ss_pred             CeEEEEecChHHH-----HHHHHHHHHcC---CcEEEEECCCcHHHHHHHHHHHh--cCCCcEEEEcc----------hh
Confidence            4779999999998     5666666 566   78899999999999988888876  47788999992          13


Q ss_pred             HHHHhhCCccEEEEe
Q psy7952         185 QHLVRYNKLAYIVVD  199 (444)
Q Consensus       185 ~~~~~~~~~~~iViD  199 (444)
                      ..-.+..++++||.-
T Consensus       438 ~rGIDi~~v~~VI~~  452 (545)
T PTZ00110        438 SRGLDVKDVKYVINF  452 (545)
T ss_pred             hcCCCcccCCEEEEe
Confidence            344566778888753

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

Probab=84.08  E-value=3.6  Score=44.87  Aligned_cols=66  Identities=6%  Similarity=0.215  Sum_probs=59.2

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh--------------cCHHHHHHHHHHHhcCCccEEEEcCc-cccccccCCccEEE
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK--------------VNKHERSRVQESFMRGEINVITATIS-FGMGIDRQNVRFVV  363 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~--------------~~~~~r~~~~~~f~~g~~~vLvaT~~-~~~Gidi~~~~~Vi  363 (444)
                      .++++.|.++|---|++-++-++.+              .+..+...+++..++|+++|+|+|.- ++.+|-+.++..+|
T Consensus       642 ~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLlI  721 (1139)
T COG1197         642 DGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLI  721 (1139)
T ss_pred             CCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhCCCcEEecCCeEE
Confidence            5799999999999999999999888              67899999999999999999999965 67888888888887


Q ss_pred             E
Q psy7952         364 H  364 (444)
Q Consensus       364 ~  364 (444)
                      .
T Consensus       722 I  722 (1139)
T COG1197         722 I  722 (1139)
T ss_pred             E
Confidence            3

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=83.96  E-value=1.1  Score=45.17  Aligned_cols=30  Identities=23%  Similarity=0.274  Sum_probs=23.9

Q ss_pred             hHHHHHHHHHHccCC-cEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHILLRTH-DIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~-~~ii~apTGsGKT~~   81 (444)
                      +-|.+.+..+....+ -+++.+|||||||..
T Consensus       228 ~~~~~~l~~~~~~~~GlilitGptGSGKTTt  258 (486)
T TIGR02533       228 PELLSRFERLIRRPHGIILVTGPTGSGKTTT  258 (486)
T ss_pred             HHHHHHHHHHHhcCCCEEEEEcCCCCCHHHH
Confidence            468888888776534 478999999999977

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.

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=83.86  E-value=1  Score=42.96  Aligned_cols=30  Identities=17%  Similarity=0.086  Sum_probs=25.9

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      +.+.+.+..+.....++++.++||+|||..
T Consensus       165 ~~~~~~L~~~v~~~~~ili~G~tGsGKTTl  194 (340)
T TIGR03819       165 PGVARLLRAIVAARLAFLISGGTGSGKTTL  194 (340)
T ss_pred             HHHHHHHHHHHhCCCeEEEECCCCCCHHHH
Confidence            678888888887768999999999999965

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.

>KOG0298|consensus

Probab=83.71  E-value=2  Score=46.91  Aligned_cols=89  Identities=11%  Similarity=-0.021  Sum_probs=65.4

Q ss_pred             CCCceEEEEecccchHHHHHHHHHhh-------cCHHHHHHHHHHHhcCCccE-EEEcCccccccccCCccEEEEeCCCC
Q psy7952         298 KANNCGIIYCRTREHTTDLADALRRK-------VNKHERSRVQESFMRGEINV-ITATISFGMGIDRQNVRFVVHWGMPS  369 (444)
Q Consensus       298 ~~~~~~iVf~~s~~~~~~l~~~L~~~-------~~~~~r~~~~~~f~~g~~~v-LvaT~~~~~Gidi~~~~~Vi~~~~p~  369 (444)
                      +...++|||..-.....-+...+...       ...++....+..|++  +.+ ++-++..+.|+|+-+..||+..++-.
T Consensus      1219 ~~qekvIvfsqws~~ldV~e~~~~~N~I~~~~~~~t~d~~dc~~~fk~--I~clll~~~~~~~GLNL~eA~Hvfl~ePiL 1296 (1394)
T KOG0298|consen 1219 NEQEKVIVFSQWSVVLDVKELRYLMNLIKKQLDGETEDFDDCIICFKS--IDCLLLFVSKGSKGLNLIEATHVFLVEPIL 1296 (1394)
T ss_pred             CcCceEEEEEehHHHHHHHHHHHHhhhhHhhhccCCcchhhhhhhccc--ceEEEEEeccCcccccHHhhhhhheecccc
Confidence            35678999987554433333333222       223445566666665  554 67788899999999999999999999


Q ss_pred             CHHHHHHHhccCCCCCCce
Q psy7952         370 SIPAYYQESGRAGRDGLQS  388 (444)
Q Consensus       370 s~~~~~Qr~GR~~R~g~~g  388 (444)
                      +...-.|.+||+.|.|+.-
T Consensus      1297 N~~~E~QAigRvhRiGQ~~ 1315 (1394)
T KOG0298|consen 1297 NPGDEAQAIGRVHRIGQKR 1315 (1394)
T ss_pred             CchHHHhhhhhhhhccccc
Confidence            9999999999999999864

>KOG2228|consensus

Probab=83.71  E-value=6.7  Score=36.85  Aligned_cols=16  Identities=13%  Similarity=0.270  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +++++.+|-|+|||..
T Consensus        50 nsviiigprgsgkT~l   65 (408)
T KOG2228|consen   50 NSVIIIGPRGSGKTIL   65 (408)
T ss_pred             CceEEEccCCCCceEe
Confidence            7899999999999954

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=83.46  E-value=4.1  Score=38.86  Aligned_cols=56  Identities=9%  Similarity=-0.097  Sum_probs=31.6

Q ss_pred             HHHHHHccC----CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          57 AIRHILLRT----HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        57 ~~~~~~~~~----~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      .++.++.|.    .-..|.+|+|+|||..++..+.. .++|.     ..++...+++|+......-
T Consensus       114 ~LD~lLgGGi~~G~ItEI~G~~GsGKTql~lqlav~-~qlp~-----~~gg~~~~vvyIdTE~tF~  173 (344)
T PLN03187        114 ALDELLGGGIETRCITEAFGEFRSGKTQLAHTLCVT-TQLPT-----EMGGGNGKVAYIDTEGTFR  173 (344)
T ss_pred             hHHhhcCCCCCCCeEEEEecCCCCChhHHHHHHHHH-Hhcch-----hhCCCCceEEEEEcCCCCC
Confidence            456666642    34679999999999875433221 11221     1233334668887655433

>PHA00350 putative assembly protein

Probab=83.38  E-value=6  Score=38.44  Aligned_cols=16  Identities=13%  Similarity=0.044  Sum_probs=13.4

Q ss_pred             EEEEccCCCccccccc
Q psy7952          68 IFVSMPTGAVSLVGSV   83 (444)
Q Consensus        68 ~ii~apTGsGKT~~a~   83 (444)
                      .++.+.+|+|||+.|+
T Consensus         4 ~l~tG~pGSGKT~~aV   19 (399)
T PHA00350          4 YAIVGRPGSYKSYEAV   19 (399)
T ss_pred             EEEecCCCCchhHHHH
Confidence            5789999999998843

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=83.28  E-value=3  Score=42.52  Aligned_cols=52  Identities=29%  Similarity=0.318  Sum_probs=31.5

Q ss_pred             ccEEEEeccccccc-c------CCCcH-HHHHHHHHHHHhhCCCCcEEEEeccCCcchHH
Q psy7952         193 LAYIVVDEAHCVSE-W------GHDFR-PTYRRLGELRQFTGNSIPIIALTATAEPSVKQ  244 (444)
Q Consensus       193 ~~~iViDE~H~~~~-~------~~~~~-~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~  244 (444)
                      ...|+|||++.... .      |++.+ ..+..+.--...+..+..++.+.||..+.+.+
T Consensus       243 P~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmDGF~~~~gviviaaTNRpdVlD  302 (596)
T COG0465         243 PCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGNEGVIVIAATNRPDVLD  302 (596)
T ss_pred             CCeEEEehhhhcccccCCCCCCCchHHHHHHHHHHhhhccCCCCCceEEEecCCCcccch
Confidence            36899999999843 1      22212 12233333333445556899999998776654

>KOG0736|consensus

Probab=83.12  E-value=1.5  Score=45.38  Aligned_cols=52  Identities=17%  Similarity=0.125  Sum_probs=31.2

Q ss_pred             CccEEEEeccccccc-------cCCCcHHHHHHHHHHHHhhC--CCCcEEEEeccCCcchH
Q psy7952         192 KLAYIVVDEAHCVSE-------WGHDFRPTYRRLGELRQFTG--NSIPIIALTATAEPSVK  243 (444)
Q Consensus       192 ~~~~iViDE~H~~~~-------~~~~~~~~~~~l~~~~~~~~--~~~~~v~lSAT~~~~~~  243 (444)
                      ....|++||.|-+--       .|.-+...+..+..-+..+.  ....+..+.||-.|...
T Consensus       764 ~PCVIFFDELDSlAP~RG~sGDSGGVMDRVVSQLLAELDgls~~~s~~VFViGATNRPDLL  824 (953)
T KOG0736|consen  764 APCVIFFDELDSLAPNRGRSGDSGGVMDRVVSQLLAELDGLSDSSSQDVFVIGATNRPDLL  824 (953)
T ss_pred             CCeEEEeccccccCccCCCCCCccccHHHHHHHHHHHhhcccCCCCCceEEEecCCCcccc
Confidence            567899999998821       22233444444444444443  34568888899666543

>PRK09354 recA recombinase A; Provisional

Probab=82.91  E-value=1.1  Score=42.74  Aligned_cols=27  Identities=11%  Similarity=-0.045  Sum_probs=20.3

Q ss_pred             HHHHHHc-cC----CcEEEEccCCCccccccc
Q psy7952          57 AIRHILL-RT----HDIFVSMPTGAVSLVGSV   83 (444)
Q Consensus        57 ~~~~~~~-~~----~~~ii~apTGsGKT~~a~   83 (444)
                      .++.++. |.    +-+.|.+|+|+|||..|+
T Consensus        47 ~LD~~LG~GGip~G~IteI~G~~GsGKTtLal   78 (349)
T PRK09354         47 ALDIALGIGGLPRGRIVEIYGPESSGKTTLAL   78 (349)
T ss_pred             HHHHHhcCCCCcCCeEEEEECCCCCCHHHHHH
Confidence            5667776 42    457899999999998743

>PTZ00293 thymidine kinase; Provisional

Probab=82.90  E-value=3  Score=36.62  Aligned_cols=16  Identities=6%  Similarity=-0.213  Sum_probs=13.3

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .--++.+|.++|||.-
T Consensus         5 ~i~vi~GpMfSGKTte   20 (211)
T PTZ00293          5 TISVIIGPMFSGKTTE   20 (211)
T ss_pred             EEEEEECCCCChHHHH
Confidence            4468899999999975

>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=82.86  E-value=0.6  Score=38.01  Aligned_cols=15  Identities=13%  Similarity=0.173  Sum_probs=13.7

Q ss_pred             cEEEEccCCCccccc
Q psy7952          67 DIFVSMPTGAVSLVG   81 (444)
Q Consensus        67 ~~ii~apTGsGKT~~   81 (444)
                      ++++.+|+|+|||..
T Consensus         1 ~vlL~G~~G~GKt~l   15 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTL   15 (139)
T ss_dssp             EEEEEESSSSSHHHH
T ss_pred             CEEEECCCCCCHHHH
Confidence            589999999999977

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.

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=82.72  E-value=8.2  Score=37.61  Aligned_cols=125  Identities=12%  Similarity=0.094  Sum_probs=74.7

Q ss_pred             eEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHH---HHHHHhcCCCeeEEEECCCccccccHHHH
Q psy7952         108 NGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAI---LEELRLVKPRIKLLYVTPERAVTESFHYL  183 (444)
Q Consensus       108 vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~  183 (444)
                      -+|+.|+..++     ......+ ...+...+...+.|+.+....+-.   .........+..++..|.+.+.+.....+
T Consensus        88 nFv~g~~N~~A-----~aa~~~va~~~g~~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~f~~~~v~a~  162 (408)
T COG0593          88 NFVVGPSNRLA-----YAAAKAVAENPGGAYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVKAL  162 (408)
T ss_pred             heeeCCchHHH-----HHHHHHHHhccCCcCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccHHHHHHHHHHHH
Confidence            38889999888     6777777 322224678888888877665422   22333345667899999888764333332


Q ss_pred             HHH----HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCC-CcEEEEeccCCcc
Q psy7952         184 LQH----LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNS-IPIIALTATAEPS  241 (444)
Q Consensus       184 ~~~----~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~-~~~v~lSAT~~~~  241 (444)
                      ..+    +....++++++||.++.+......    ...+.+.++.+..+ .|+|+.|-.+|..
T Consensus       163 ~~~~~~~Fk~~y~~dlllIDDiq~l~gk~~~----qeefFh~FN~l~~~~kqIvltsdr~P~~  221 (408)
T COG0593         163 RDNEMEKFKEKYSLDLLLIDDIQFLAGKERT----QEEFFHTFNALLENGKQIVLTSDRPPKE  221 (408)
T ss_pred             HhhhHHHHHHhhccCeeeechHhHhcCChhH----HHHHHHHHHHHHhcCCEEEEEcCCCchh
Confidence            221    111127999999999998654321    23444444444332 4566666555543

>COG4128 Zot Zonula occludens toxin [General function prediction only]

Probab=82.59  E-value=1.6  Score=39.83  Aligned_cols=22  Identities=27%  Similarity=0.336  Sum_probs=16.1

Q ss_pred             EEEccCCCcccccccccccceEEeCC
Q psy7952          69 FVSMPTGAVSLVGSVVSARSRVRIPP   94 (444)
Q Consensus        69 ii~apTGsGKT~~a~~~~~~~~~~~~   94 (444)
                      +-++++||+||..|++-    -++|+
T Consensus         5 ihhG~pGSyKTsgAv~~----~~iPA   26 (398)
T COG4128           5 IHHGIPGSYKTSGAVCN----VIIPA   26 (398)
T ss_pred             EEecCCCCcccchhHHh----hhhhh
Confidence            56899999999886543    34565

>TIGR02012 tigrfam_recA protein RecA

Probab=82.40  E-value=2.6  Score=39.76  Aligned_cols=27  Identities=11%  Similarity=-0.047  Sum_probs=19.5

Q ss_pred             HHHHHHc-cC----CcEEEEccCCCccccccc
Q psy7952          57 AIRHILL-RT----HDIFVSMPTGAVSLVGSV   83 (444)
Q Consensus        57 ~~~~~~~-~~----~~~ii~apTGsGKT~~a~   83 (444)
                      .++.++. |.    .-+.|.+|+|+|||..|+
T Consensus        42 ~LD~~Lg~GGlp~G~iteI~G~~GsGKTtLaL   73 (321)
T TIGR02012        42 SLDLALGVGGLPRGRIIEIYGPESSGKTTLAL   73 (321)
T ss_pred             HHHHHhcCCCCcCCeEEEEECCCCCCHHHHHH
Confidence            4566665 31    457899999999997743

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.

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=82.19  E-value=5.1  Score=41.40  Aligned_cols=51  Identities=8%  Similarity=-0.007  Sum_probs=28.3

Q ss_pred             HHhcCCCeeEEEECCCccccccHHHHH-HHHHhhCCccEEEEeccccccccC
Q psy7952         158 LRLVKPRIKLLYVTPERAVTESFHYLL-QHLVRYNKLAYIVVDEAHCVSEWG  208 (444)
Q Consensus       158 ~~~~~~~~~Iiv~Tpe~l~~~~~~~~~-~~~~~~~~~~~iViDE~H~~~~~~  208 (444)
                      +..++++++-.|+--+.-.+..-...+ -.....++-.++|+||+..-.|..
T Consensus       448 I~~lp~g~dt~vge~G~~LSgGQrQrlaiARall~~~~ILILDEaTSalD~~  499 (567)
T COG1132         448 IANLPDGYDTIVGERGVNLSGGQRQRLAIARALLRNPPILILDEATSALDTE  499 (567)
T ss_pred             HHhCcccccceecCCCccCCHHHHHHHHHHHHHhcCCCEEEEeccccccCHH
Confidence            334456788888843332222211111 122234566999999999877643

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=82.00  E-value=1.6  Score=38.85  Aligned_cols=17  Identities=29%  Similarity=0.053  Sum_probs=14.5

Q ss_pred             CcEEEEccCCCcccccc
Q psy7952          66 HDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a   82 (444)
                      .-+++.+++|+|||..|
T Consensus        17 ~~~li~G~~G~GKt~~~   33 (224)
T TIGR03880        17 HVIVVIGEYGTGKTTFS   33 (224)
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            56899999999999763

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.

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=82.00  E-value=0.65  Score=42.64  Aligned_cols=15  Identities=33%  Similarity=0.330  Sum_probs=13.6

Q ss_pred             cEEEEccCCCccccc
Q psy7952          67 DIFVSMPTGAVSLVG   81 (444)
Q Consensus        67 ~~ii~apTGsGKT~~   81 (444)
                      -++|.+|||||||.+
T Consensus       127 LILVTGpTGSGKSTT  141 (353)
T COG2805         127 LILVTGPTGSGKSTT  141 (353)
T ss_pred             eEEEeCCCCCcHHHH
Confidence            489999999999977

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=81.88  E-value=17  Score=31.38  Aligned_cols=49  Identities=12%  Similarity=0.125  Sum_probs=30.2

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcc
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPS  241 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~  241 (444)
                      -..+++||+||+-...+.|  +-+. ..+..+++..|...-+|+..-.+++.
T Consensus       113 ~~~ydlvVLDEi~~Al~~g--li~~-eevi~~L~~rp~~~evVlTGR~~p~~  161 (191)
T PRK05986        113 DESYDLVVLDELTYALKYG--YLDV-EEVLEALNARPGMQHVVITGRGAPRE  161 (191)
T ss_pred             CCCCCEEEEehhhHHHHCC--CccH-HHHHHHHHcCCCCCEEEEECCCCCHH
Confidence            4678999999998887766  2222 44555666666644454444444443

>COG1134 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]

Probab=81.84  E-value=0.85  Score=40.60  Aligned_cols=45  Identities=16%  Similarity=0.272  Sum_probs=27.3

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccC
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATA  238 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~  238 (444)
                      .-+.+++++||+=...|..  |..  ..+.++.....++..+|+.|-.+
T Consensus       163 ~~~pdILllDEvlavGD~~--F~~--K~~~rl~e~~~~~~tiv~VSHd~  207 (249)
T COG1134         163 HVEPDILLLDEVLAVGDAA--FQE--KCLERLNELVEKNKTIVLVSHDL  207 (249)
T ss_pred             hcCCCEEEEehhhhcCCHH--HHH--HHHHHHHHHHHcCCEEEEEECCH
Confidence            3478999999998876644  432  22233333334556677777553

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=81.82  E-value=2.9  Score=40.77  Aligned_cols=52  Identities=12%  Similarity=0.163  Sum_probs=31.5

Q ss_pred             CCCHHHHHHHHHHHhCCcc--cCchHHHHHHHH---HHccCCcEEEEccCCCccccc
Q psy7952          30 KVSEQELTAKLKALFGFDS--FKCELQKKAIRH---ILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        30 ~~~~~~~~~~l~~~~g~~~--~~t~~Q~~~~~~---~~~~~~~~ii~apTGsGKT~~   81 (444)
                      .++.++-.+.|-+..|+++  +-+..+...+..   +.+.+.|++..+|+|+|||..
T Consensus       169 ~FT~dEWid~LlrSiG~~P~~~~~r~k~~~L~rl~~fve~~~Nli~lGp~GTGKThl  225 (449)
T TIGR02688       169 EFTLEEWIDVLIRSIGYEPEGFEARQKLLLLARLLPLVEPNYNLIELGPKGTGKSYI  225 (449)
T ss_pred             hcCHHHHHHHHHHhcCCCcccCChHHHHHHHHhhHHHHhcCCcEEEECCCCCCHHHH
Confidence            4455555566666678884  222222222222   233338999999999999966

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.

>KOG1807|consensus

Probab=81.77  E-value=1.8  Score=44.75  Aligned_cols=63  Identities=13%  Similarity=-0.006  Sum_probs=45.3

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC----ccceeEEEcchhhhhcccCccchH
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN----VRSRNGWISPILSSFYLRFRDDKT  127 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~----~~~~vlil~P~~~L~~~~q~~~~~  127 (444)
                      .-|+.|....+.. +--++.+|+|+|||++.+.         + .+.+....    ....++++|-|...+     .|..
T Consensus       381 sSq~~A~qs~lty-elsliqgppGTgkt~vtlk---------a-v~tLL~n~s~~~~~epIlvvC~Tnhav-----dq~l  444 (1025)
T KOG1807|consen  381 SSQQFAKQSKLTY-ELSLIQGPPGTGKTLVTLK---------A-VDTLLLNSSGYTEPEPILVVCLTNHAV-----DQYL  444 (1025)
T ss_pred             HHHHHHHHHHhhh-hhheeecCCCCCceeehHH---------H-HHHHHhcccccccccceeeeehhhHHH-----HHHH
Confidence            4699999998887 7789999999999988222         2 11122211    224679999999998     6777


Q ss_pred             hhh
Q psy7952         128 SIV  130 (444)
Q Consensus       128 ~~l  130 (444)
                      ..+
T Consensus       445 igi  447 (1025)
T KOG1807|consen  445 IGI  447 (1025)
T ss_pred             HHH
Confidence            766

>PHA02244 ATPase-like protein

Probab=81.73  E-value=1.5  Score=42.05  Aligned_cols=24  Identities=17%  Similarity=0.090  Sum_probs=18.6

Q ss_pred             HHHHHccCCcEEEEccCCCccccc
Q psy7952          58 IRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        58 ~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      +..+++.+.++++.+|||+|||..
T Consensus       112 i~r~l~~~~PVLL~GppGtGKTtL  135 (383)
T PHA02244        112 IAKIVNANIPVFLKGGAGSGKNHI  135 (383)
T ss_pred             HHHHHhcCCCEEEECCCCCCHHHH
Confidence            334444448999999999999966

>PRK13531 regulatory ATPase RavA; Provisional

Probab=81.73  E-value=1.6  Score=43.44  Aligned_cols=24  Identities=17%  Similarity=0.231  Sum_probs=19.3

Q ss_pred             HHHHHHccCCcEEEEccCCCccccc
Q psy7952          57 AIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        57 ~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      ++..++.+ .++++.+|+|+|||..
T Consensus        32 ll~aalag-~hVLL~GpPGTGKT~L   55 (498)
T PRK13531         32 CLLAALSG-ESVFLLGPPGIAKSLI   55 (498)
T ss_pred             HHHHHccC-CCEEEECCCChhHHHH
Confidence            34444556 8999999999999977

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=81.69  E-value=1.2  Score=45.65  Aligned_cols=30  Identities=23%  Similarity=0.236  Sum_probs=23.2

Q ss_pred             hHHHHHHHHHHccC-CcEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHILLRT-HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~-~~~ii~apTGsGKT~~   81 (444)
                      +.|.+.+..+.... .-+++++|||||||.+
T Consensus       302 ~~~~~~l~~~~~~~~Glilv~G~tGSGKTTt  332 (564)
T TIGR02538       302 PDQKALFLEAIHKPQGMVLVTGPTGSGKTVS  332 (564)
T ss_pred             HHHHHHHHHHHHhcCCeEEEECCCCCCHHHH
Confidence            46777777776532 4688999999999977

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.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=81.64  E-value=1.7  Score=45.56  Aligned_cols=16  Identities=13%  Similarity=0.225  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++++|+|+|||..
T Consensus       186 ~gill~G~~G~GKt~~  201 (644)
T PRK10733        186 KGVLMVGPPGTGKTLL  201 (644)
T ss_pred             CcEEEECCCCCCHHHH
Confidence            5699999999999977

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=81.53  E-value=7  Score=38.05  Aligned_cols=57  Identities=7%  Similarity=0.015  Sum_probs=33.9

Q ss_pred             EEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc--chhhhhcccCccchHhhhcCCCCceeEEEEeC
Q psy7952          68 IFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS--PILSSFYLRFRDDKTSIVTGRSDLYQLELIVS  144 (444)
Q Consensus        68 ~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~--P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~  144 (444)
                      +++++=-|+|||.++.         .. ..++.+  ...++++++  ..|.-+     .+|++.+...   +.+..+..
T Consensus       103 ImmvGLQGsGKTTt~~---------KL-A~~lkk--~~~kvllVaaD~~RpAA-----~eQL~~La~q---~~v~~f~~  161 (451)
T COG0541         103 ILMVGLQGSGKTTTAG---------KL-AKYLKK--KGKKVLLVAADTYRPAA-----IEQLKQLAEQ---VGVPFFGS  161 (451)
T ss_pred             EEEEeccCCChHhHHH---------HH-HHHHHH--cCCceEEEecccCChHH-----HHHHHHHHHH---cCCceecC
Confidence            7888889999998821         11 222333  333445554  466777     7899888444   44444443

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=81.20  E-value=1.3  Score=41.72  Aligned_cols=26  Identities=19%  Similarity=0.174  Sum_probs=19.5

Q ss_pred             HHHHHHHccCCcEEEEccCCCccccc
Q psy7952          56 KAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        56 ~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      +.+.....+..++++.+|||+|||..
T Consensus       135 ~~l~~~v~~~~~ili~G~tGsGKTTl  160 (308)
T TIGR02788       135 EFLRLAIASRKNIIISGGTGSGKTTF  160 (308)
T ss_pred             HHHHHHhhCCCEEEEECCCCCCHHHH
Confidence            33444444448999999999999976

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.

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=81.20  E-value=2.6  Score=41.83  Aligned_cols=74  Identities=7%  Similarity=0.089  Sum_probs=56.8

Q ss_pred             cceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHH
Q psy7952         105 RSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYL  183 (444)
Q Consensus       105 ~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~  183 (444)
                      ..++||+|++++-+     ......+ ..+   +.+..++|+....++...+..++  .+..+|+|+|. .         
T Consensus       245 ~~~~lVF~~s~~~~-----~~l~~~L~~~~---~~~~~l~g~~~~~~R~~~l~~f~--~G~~~vLVaTd-~---------  304 (434)
T PRK11192        245 VTRSIVFVRTRERV-----HELAGWLRKAG---INCCYLEGEMVQAKRNEAIKRLT--DGRVNVLVATD-V---------  304 (434)
T ss_pred             CCeEEEEeCChHHH-----HHHHHHHHhCC---CCEEEecCCCCHHHHHHHHHHHh--CCCCcEEEEcc-c---------
Confidence            35779999999998     5666666 566   88999999999999988888776  47899999992 2         


Q ss_pred             HHHHHhhCCccEEEE
Q psy7952         184 LQHLVRYNKLAYIVV  198 (444)
Q Consensus       184 ~~~~~~~~~~~~iVi  198 (444)
                      ...-.+..++++||.
T Consensus       305 ~~~GiDip~v~~VI~  319 (434)
T PRK11192        305 AARGIDIDDVSHVIN  319 (434)
T ss_pred             cccCccCCCCCEEEE
Confidence            223345667888774

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=81.15  E-value=4.5  Score=42.73  Aligned_cols=68  Identities=16%  Similarity=0.237  Sum_probs=56.6

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh--------------cCHHHHHHHHHHHhcCCccEEEEcCc-cccccccCCccEEE
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK--------------VNKHERSRVQESFMRGEINVITATIS-FGMGIDRQNVRFVV  363 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~--------------~~~~~r~~~~~~f~~g~~~vLvaT~~-~~~Gidi~~~~~Vi  363 (444)
                      .+.+++|.++|+.-|.+.++.+.+.              ++..+|...++...+|+..|+|+|.. +...+.++++.+||
T Consensus       309 ~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~v~~~~l~lvV  388 (681)
T PRK10917        309 AGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVI  388 (681)
T ss_pred             cCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcccchhcccceEE
Confidence            4678999999999999998887765              66788899999999999999999975 45567788888888


Q ss_pred             EeC
Q psy7952         364 HWG  366 (444)
Q Consensus       364 ~~~  366 (444)
                      ...
T Consensus       389 IDE  391 (681)
T PRK10917        389 IDE  391 (681)
T ss_pred             Eec
Confidence            544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	444
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		1e-46
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		3e-44
2v1x_A	591	Crystal Structure Of Human Recq-Like Dna Helicase L		2e-37
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		5e-08
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		6e-06
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		7e-06
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		3e-05
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		1e-04
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		1e-04
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		1e-04
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		4e-04
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		5e-04
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		6e-04
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		7e-04

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score =  184 bits (466), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 127/415 (30%), Positives = 210/415 (50%), Gaps = 55/415 (13%)
Query: 40  LKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTXXXXXXXXXXXXXXXXXIPPGADFI 99
           L+  FG+  F+    ++ I   +L   D  V MPT                 IP     +
Sbjct: 17  LQETFGYQQFRPG--QEEIIDTVLSGRDCLVVMPTGGGKSLCYQ--------IPA---LL 63
Query: 100 LNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELR 159
           LNG        +SP++S         K  +   +++      + S QT+ +   ++   R
Sbjct: 64  LNGLTVV----VSPLISLM-------KDQVDQLQANGVAAACLNSTQTREQQLEVMTGCR 112
Query: 160 LVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLG 219
               +I+LLY+ PER + ++F   L+HL  +N +  + VDEAHC+S+WGHDFRP Y  LG
Sbjct: 113 --TGQIRLLYIAPERLMLDNF---LEHLAHWNPV-LLAVDEAHCISQWGHDFRPEYAALG 166
Query: 220 ELRQ-FTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTF-RSNLFYDVIFDDL 277
           +LRQ F   ++P +ALTATA+ + +QDI+ +L  N P  + + S+F R N+ Y      +
Sbjct: 167 QLRQRFP--TLPFMALTATADDTTRQDIVRLLGLNDP--LIQISSFDRPNIRY------M 216
Query: 278 LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKH 327
           L + +  + + +     +  K+   GIIYC +R    D A  L+ K          +  +
Sbjct: 217 LMEKFKPLDQLMRYVQEQRGKS---GIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENN 273
Query: 328 ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ 387
            R+ VQE F R ++ ++ AT++FGMGI++ NVRFVVH+ +P +I +YYQE+GRAGRDGL 
Sbjct: 274 VRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLP 333
Query: 388 SYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGYFLVILVF 442
           +   +++       L   ++     + + +E    N +      +    LV+L +
Sbjct: 334 AEAMLFYDPADMAWLRRCLEEKPQGQLQDIERHKLNAMGAFAEAQTCRRLVLLNY 388

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score =  176 bits (445), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 104/293 (35%), Positives = 163/293 (55%), Gaps = 33/293 (11%)
Query: 164 RIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQ 223
           +I+LLY+ PER   ++F   L+HL  +N +  + VDEAHC+S+WGHDFRP Y  LG+LRQ
Sbjct: 115 QIRLLYIAPERLXLDNF---LEHLAHWNPV-LLAVDEAHCISQWGHDFRPEYAALGQLRQ 170
Query: 224 -FTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTF-RSNLFYDVI--FDDLLK 279
            F   ++P  ALTATA+ + +QDI+ +L  N P  + + S+F R N+ Y +   F  L  
Sbjct: 171 RFP--TLPFXALTATADDTTRQDIVRLLGLNDP--LIQISSFDRPNIRYXLXEKFKPL-- 224
Query: 280 DSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHER 329
                +  ++++  GK       GIIYC +R    D A  L+ K          +  + R
Sbjct: 225 ---DQLXRYVQEQRGKS------GIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVR 275
Query: 330 SRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSY 389
           + VQE F R ++ ++ AT++FG GI++ NVRFVVH+ +P +I +YYQE+GRAGRDGL + 
Sbjct: 276 ADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAE 335
Query: 390 CRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQGYFLVILVF 442
             +++       L   ++     + + +E    N        +    LV+L +
Sbjct: 336 AXLFYDPADXAWLRRCLEEKPQGQLQDIERHKLNAXGAFAEAQTCRRLVLLNY 388

>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase Length = 591

Iteration: 1
 Score =  153 bits (386), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 95/268 (35%), Positives = 143/268 (53%), Gaps = 23/268 (8%)
Query: 141 LIVSGQTKTENKAILEELRLVKPRIKLLYVTPER-AVTESFHYLLQHLVRYNKLAYIVVD 199
           ++ +  +K   K +  E+      +KL+YVTPE+ A ++ F   L+      +   I VD
Sbjct: 113 MLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVD 172
Query: 200 EAHCVSEWGHDFRPTYRRLGEL-RQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKV 258
           E HC S+WGHDFRP Y+ LG L RQF   S+  I LTATA   V  D   +L   K +  
Sbjct: 173 EVHCCSQWGHDFRPDYKALGILKRQFPNASL--IGLTATATNHVLTDAQKILCIEKCF-T 229
Query: 259 FKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNK--ANNCGIIYCRTREHTTDL 316
           F  S  R NL+Y+V      +   ++ ++FIE  +   N       GIIYC +++ +  +
Sbjct: 230 FTASFNRPNLYYEV------RQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQV 283
Query: 317 ----------ADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWG 366
                     A A    +   +++ V   +   EI V+ AT++FGMGID+ +VRFV+H  
Sbjct: 284 TVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHS 343
Query: 367 MPSSIPAYYQESGRAGRDGLQSYCRIYH 394
           M  S+  YYQESGRAGRD +++ C +Y+
Sbjct: 344 MSKSMENYYQESGRAGRDDMKADCILYY 371

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score = 55.5 bits (132), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 46/92 (50%), Gaps = 10/92 (10%)
Query: 304 IIYCRTREHTTDLADALRR------KVN----KHERSRVQESFMRGEINVITATISFGMG 353
           II+CRT+EH   L D L        K++    + +R  V   F RGE   + AT     G
Sbjct: 39  IIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARG 98
Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
           ID +N+  V+++ +P    +Y   +GR GR G
Sbjct: 99  IDIENISLVINYDLPLEKESYVHRTGRTGRAG 130

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 48.9 bits (115), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 28/113 (24%), Positives = 54/113 (47%), Gaps = 10/113 (8%)
Query: 303 GIIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISFGM 352
           G+++C+T+  T +LA  LR            +++ +R +V   F + +I ++ AT     
Sbjct: 241 GLVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSR 300
Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV 405
           GID  ++  V+++ +P +  +Y    GR GR G +       +    K L Y+
Sbjct: 301 GIDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISIINRREYKKLRYI 353

>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including The C-Terminal Reca Domain, The Dimerization Domain, And The Rna Binding Domain Length = 300

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 40/146 (27%), Positives = 68/146 (46%), Gaps = 18/146 (12%)
Query: 301 NCGIIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISF 350
           +  +++ RT+  T ++A  L R           +++ ER RV  +F +GE+ V+ AT   
Sbjct: 29  DRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVA 88
Query: 351 GMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV----- 405
             G+D   V  VVH+ MP    AY   SGR GR G      + +    ++ +E +     
Sbjct: 89  ARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVG 148
Query: 406 ---IKTDTSTKREQLELKFKNYLSML 428
               + +  T  E LE K+++ L+ L
Sbjct: 149 RRFKRVNPPTPEEVLEAKWRHLLARL 174

>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera Form 2, Complete Dimer, Symmetric Length = 212

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 39/146 (26%), Positives = 68/146 (46%), Gaps = 18/146 (12%)
Query: 301 NCGIIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISF 350
           +  +++ RT+  T ++A  L R           +++ ER RV  +F +GE+ V+ AT   
Sbjct: 32  DRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVA 91
Query: 351 GMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV----- 405
             G+D   V  VVH+ +P    AY   SGR GR G      + +    ++ +E +     
Sbjct: 92  ARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVG 151
Query: 406 ---IKTDTSTKREQLELKFKNYLSML 428
               + +  T  E LE K+++ L+ L
Sbjct: 152 RRFKRVNPPTPEEVLEAKWRHLLARL 177

>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 = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 58/263 (22%), Positives = 113/263 (42%), Gaps = 39/263 (14%)
Query: 149 TENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK-----LAYIVVDEAHC 203
           T+ +A + ++  ++P I  +  TP R        L+  L +Y+      + Y V+DEA  
Sbjct: 137 TDFRAAMNKMNKLRPNI--VIATPGR--------LIDVLEKYSNKFFRFVDYKVLDEADR 186
Query: 204 VSEWG--HDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT 261
           + E G   D       L E    + ++I  +  +AT +  V++   +++  NK   +F  
Sbjct: 187 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIM--NKKECLFLD 244
Query: 262 STFRSN------LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTD 315
           +  ++       +   V+  +   +S     E I+K + K+  +N   II+  T + T+ 
Sbjct: 245 TVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFTSF 303
Query: 316 LADALRR-------------KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFV 362
           L   L+              K+ +++R+ + + F + E  ++  T     G+D  NV  V
Sbjct: 304 LCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEV 363
Query: 363 VHWGMPSSIPAYYQESGRAGRDG 385
           +  G+PS +  Y    GR  R G
Sbjct: 364 LQIGVPSELANYIHRIGRTARSG 386

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 58/263 (22%), Positives = 113/263 (42%), Gaps = 39/263 (14%)
Query: 149 TENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK-----LAYIVVDEAHC 203
           T+ +A + ++  ++P I  +  TP R        L+  L +Y+      + Y V+DEA  
Sbjct: 188 TDFRAAMNKMNKLRPNI--VIATPGR--------LIDVLEKYSNKFFRFVDYKVLDEADR 237
Query: 204 VSEWG--HDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT 261
           + E G   D       L E    + ++I  +  +AT +  V++   +++  NK   +F  
Sbjct: 238 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIM--NKKECLFLD 295
Query: 262 STFRSN------LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTD 315
           +  ++       +   V+  +   +S     E I+K + K+  +N   II+  T + T+ 
Sbjct: 296 TVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFTSF 354
Query: 316 LADALRR-------------KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFV 362
           L   L+              K+ +++R+ + + F + E  ++  T     G+D  NV  V
Sbjct: 355 LCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEV 414
Query: 363 VHWGMPSSIPAYYQESGRAGRDG 385
           +  G+PS +  Y    GR  R G
Sbjct: 415 LQIGVPSELANYIHRIGRTARSG 437

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 56/258 (21%), Positives = 111/258 (43%), Gaps = 29/258 (11%)
Query: 149 TENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWG 208
           T+ +A + ++  ++P I  +  TP R + +          R+  + Y V+DEA  + E G
Sbjct: 137 TDFRAAMNKMNKLRPNI--VIATPGRLI-DVLEKYSNKFFRF--VDYKVLDEADRLLEIG 191
Query: 209 --HDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRS 266
              D       L E    + ++I  +  +AT +  V++   +++  NK   +F  +  ++
Sbjct: 192 FRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIM--NKKECLFLDTVDKN 249
Query: 267 N------LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADAL 320
                  +   V+  +   +S     E I+K + K+  +N   II+  T + T+ L   L
Sbjct: 250 EPEAHERIDQSVVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFTSFLCSIL 308
Query: 321 RR-------------KVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGM 367
           +              K+ +++R+ + + F + E  ++  T     G+D  NV  V+  G+
Sbjct: 309 KNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGV 368
Query: 368 PSSIPAYYQESGRAGRDG 385
           PS +  Y    GR  R G
Sbjct: 369 PSELANYIHRIGRTARSG 386

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 326 KHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
           + +R +    F  G + V+ AT     G+D +N++ V+++ MPS I  Y    GR GR G
Sbjct: 336 QSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVG 395

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/95 (25%), Positives = 42/95 (44%), Gaps = 10/95 (10%)
Query: 301 NCGIIYCRTREHTTDLADAL----------RRKVNKHERSRVQESFMRGEINVITATISF 350
           N  II+C +      LA  +            ++ + ER++V   F +G++  +  +   
Sbjct: 259 NQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLL 318
Query: 351 GMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
             GID Q V  V+++  P +   Y    GR+GR G
Sbjct: 319 TRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFG 353

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 36/69 (52%)
Query: 317 ADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ 376
           A A+    ++ ER++  E+F  G+ +V+ AT     G+D   ++ V+++ MP  I  Y  
Sbjct: 81  AVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVH 140
Query: 377 ESGRAGRDG 385
             GR G  G
Sbjct: 141 RIGRTGCSG 149

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 53/246 (21%), Positives = 101/246 (41%), Gaps = 29/246 (11%)
Query: 154 ILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRP 213
           I +++R ++    LL  TP R V      + +  +  +   Y+V+DEA  + + G  F P
Sbjct: 141 IGQQIRDLERGCHLLVATPGRLVD----MMERGKIGLDFCKYLVLDEADRMLDMG--FEP 194
Query: 214 TYRRLGELRQFTGNSIPIIALTATAEPS----VKQDIISVLKFNKPYKVFKTSTFRSNLF 269
             RR+ E        +    + +   P     + +D +    F    +V  TS    N+ 
Sbjct: 195 QIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTS---ENIT 251
Query: 270 YDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKV----- 324
             V++ +      +  + F+   L    K ++  +++  T++    L D L  +      
Sbjct: 252 QKVVWVE-----ESDKRSFLLDLLNATGK-DSLTLVFVETKKGADSLEDFLYHEGYACTS 305
Query: 325 -----NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESG 379
                ++ +R      F  G+  ++ AT     G+D  NV+ V+++ +PS I  Y    G
Sbjct: 306 IHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIG 365
Query: 380 RAGRDG 385
           R GR G
Sbjct: 366 RTGRVG 371

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	444
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	1e-104
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	8e-06
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	4e-99
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	2e-05
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	3e-10
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	2e-09
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	8e-09
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	1e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	2e-08
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	3e-08
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	5e-08
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	9e-08
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	1e-07
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-07
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	2e-07
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	2e-07
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	4e-07
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	6e-07
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-06
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	1e-06
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	2e-06
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	3e-06
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	4e-06
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	5e-06
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-05
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	3e-05
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	5e-05
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	6e-05
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	6e-05
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	7e-05
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	3e-04
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	4e-04
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	6e-04
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	7e-04

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A* Length = 591

 Score =  320 bits (821), Expect = e-104
 Identities = 92/301 (30%), Positives = 146/301 (48%), Gaps = 27/301 (8%)

Query: 144 SGQTKTENKAILEELRLVKPRIKLLYVTPERAVTE-SFHYLLQHLVRYNKLAYIVVDEAH 202
           +  +K   K +  E+      +KL+YVTPE+      F   L+      +   I VDE H
Sbjct: 116 ASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVH 175

Query: 203 CVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTS 262
           C S+WGHDFRP Y+ LG L++   N   +I LTATA   V  D   +L   K    F  S
Sbjct: 176 CCSQWGHDFRPDYKALGILKRQFPN-ASLIGLTATATNHVLTDAQKILCIEKC-FTFTAS 233

Query: 263 TFRSNLFYDVIF-DDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALR 321
             R NL+Y+V       +D    + + I             GIIYC +++ +  +  +L+
Sbjct: 234 FNRPNLYYEVRQKPSNTEDFIEDIVKLI-----NGRYKGQSGIIYCFSQKDSEQVTVSLQ 288

Query: 322 RK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSI 371
                       +   +++ V   +   EI V+ AT++FGMGID+ +VRFV+H  M  S+
Sbjct: 289 NLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSM 348

Query: 372 PAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYC 431
             YYQESGRAGRD +++ C +Y+       +  ++  + +  +++L         M+ YC
Sbjct: 349 ENYYQESGRAGRDDMKADCILYYGFGDIFRISSMVVME-NVGQQKLY-------EMVSYC 400

Query: 432 E 432
           +
Sbjct: 401 Q 401

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A* Length = 591

 Score = 47.3 bits (113), Expect = 8e-06
 Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 3/68 (4%)

Query: 10 SSAVGKSSSLTGNQQDRKGGKVS-EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDI 68
           S  G S+    +             ++   L+ +F  + F+  LQ + I   +    ++
Sbjct: 5  DSDAGASNEYDSSPAAWNKEDFPWSGKVKDILQNVFKLEKFR-PLQLETINVTMAG-KEV 62

Query: 69 FVSMPTGA 76
          F+ MPTG 
Sbjct: 63 FLVMPTGG 70

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A* Length = 523

 Score =  305 bits (783), Expect = 4e-99
 Identities = 98/299 (32%), Positives = 161/299 (53%), Gaps = 29/299 (9%)

Query: 144 SGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHC 203
           S QT+ +   ++   R    +I+LLY+ PER + ++F   L H         + VDEAHC
Sbjct: 97  STQTREQQLEVMTGCR--TGQIRLLYIAPERLMLDNFLEHLAHW----NPVLLAVDEAHC 150

Query: 204 VSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST 263
           +S+WGHDFRP Y  LG+LRQ     +P +ALTATA+ + +QDI+ +L  N P  +  +S 
Sbjct: 151 ISQWGHDFRPEYAALGQLRQRFPT-LPFMALTATADDTTRQDIVRLLGLNDP-LIQISSF 208

Query: 264 FRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK 323
            R N+ Y ++           +  ++++      +    GIIYC +R    D A  L+ K
Sbjct: 209 DRPNIRYMLMEKF---KPLDQLMRYVQE------QRGKSGIIYCNSRAKVEDTAARLQSK 259

Query: 324 ----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPA 373
                     +  + R+ VQE F R ++ ++ AT++FGMGI++ NVRFVVH+ +P +I +
Sbjct: 260 GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIES 319

Query: 374 YYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCE 432
           YYQE+GRAGRDGL +   +++       L   +  +   + +  +++     +M  + E
Sbjct: 320 YYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL--EEKPQGQLQDIERHKLNAMGAFAE 376

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A* Length = 523

 Score = 45.6 bits (109), Expect = 2e-05
 Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 2/44 (4%)

Query: 33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGA 76
          E      L+  FG+  F+   Q++ I  +L    D  V MPTG 
Sbjct: 10 ESGAKQVLQETFGYQQFR-PGQEEIIDTVLSG-RDCLVVMPTGG 51

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A Length = 212

 Score = 58.5 bits (142), Expect = 3e-10
 Identities = 35/120 (29%), Positives = 54/120 (45%), Gaps = 15/120 (12%)

Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
            +++ RT+  T ++A  L R           +++ ER RV  +F +GE+ V+ AT     
Sbjct: 34  AMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAAR 93

Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESG---RAGRDGLQSYCRIYHSEHSK-KSLEYVIKT 408
           G+D   V  VVH+ +P    AY   SG   RAGR G          E    ++LE  +  
Sbjct: 94  GLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGR-VVLLYGPRERRDVEALERAVGR 152

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 58.2 bits (141), Expect = 2e-09
 Identities = 51/328 (15%), Positives = 103/328 (31%), Gaps = 65/328 (19%)

Query: 142 IVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL--VRYNKLAYIVVD 199
             S   K E +   +        I  L  + +         + ++   +   +  ++ VD
Sbjct: 97  FYSSMKKEEKEKFEKSFEEDDYHI--LVFSTQF--------VSKNREKLSQKRFDFVFVD 146

Query: 200 EAHCVSEWGHD------FRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFN 253
           +         D             L  +       I   A +   +  + +         
Sbjct: 147 DV--------DAVLKASRNI--DTLLMMVGIPEEII-RKAFSTIKQGKIYERP---KNLK 192

Query: 254 KPYKVFKTSTFRSNLFYDVIFDDLL--------------KDSYAHVKEFIEKCLGKDNKA 299
               V  ++T +      ++F DLL                     +   EK +      
Sbjct: 193 PGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSRSK-EKLVELLEIF 251

Query: 300 NNCGIIYCRTREHTTDLADALRRK-----VNKHERSRVQESFMRGEINVITATISFGM-- 352
            +  +I+ +T E   +L + L+R          E  +  E F  G+IN++    ++    
Sbjct: 252 RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKNFEDFKVGKINILIGVQAYYGKL 311

Query: 353 --GID-RQNVRFVVHWGMPSSIPA--YYQESGRAGRDGLQSYCRIY-----HSEHSKKSL 402
             G+D  + +++V+ WG PS      Y Q SGR+ R       +         E   +SL
Sbjct: 312 TRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESL 371

Query: 403 EYVIKTDT-STKREQLELKFKNYLSMLE 429
           +  +         E+ E  +K  +  +E
Sbjct: 372 KTRLLLIAEEEIIEEAEANWKELVHEVE 399

>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 = 56.0 bits (136), Expect = 8e-09
 Identities = 32/131 (24%), Positives = 64/131 (48%), Gaps = 19/131 (14%)

Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
           G+++C+T+  T +LA  LR            +++ +R +V   F + +I ++ AT     
Sbjct: 241 GLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSR 300

Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESG---RAGRDGLQSYCRIYHSEHSK-KSLEYVIKT 408
           GID  ++  V+++ +P +  +Y    G   RAG+ G  +   I   E+ K + +E  +K 
Sbjct: 301 GIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGK-AISIINRREYKKLRYIERAMK- 358

Query: 409 DTSTKREQLEL 419
               K ++L+ 
Sbjct: 359 ---LKIKKLKF 366

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus} Length = 300

 Score = 55.1 bits (133), Expect = 1e-08
 Identities = 36/120 (30%), Positives = 54/120 (45%), Gaps = 15/120 (12%)

Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
            +++ RT+  T ++A  L R           +++ ER RV  +F +GE+ V+ AT     
Sbjct: 31  AMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAAR 90

Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESG---RAGRDGLQSYCRIYHSEHSK-KSLEYVIKT 408
           G+D   V  VVH+ MP    AY   SG   RAGR G          E    ++LE  +  
Sbjct: 91  GLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGR-VVLLYGPRERRDVEALERAVGR 149

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 56.0 bits (134), Expect = 2e-08
 Identities = 54/350 (15%), Positives = 108/350 (30%), Gaps = 96/350 (27%)

Query: 27  KG-GK---VSEQELTAKLKALFGFDSF-----KCELQKKAIRHILLRTHDI---FVSMPT 74
            G GK     +  L+ K++    F  F      C   +  +  +    + I   + S   
Sbjct: 159 LGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD 218

Query: 75  GAVSLVGSVVSARSRVRI----PPGAD--FILNGNVRSRNGWISPILSSFYL-------- 120
            + ++   + S ++ +R      P  +   +L  NV       +   ++F L        
Sbjct: 219 HSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL-NV-----QNAKAWNAFNLSCKILLTT 272

Query: 121 RFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVT--- 177
           RF+     +    +    L+      T  E K++L  L+ +  R + L   P   +T   
Sbjct: 273 RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL--LKYLDCRPQDL---PREVLTTNP 327

Query: 178 -------ESFHYLLQHLVRYNKLAYIVVDEAHCVSEWG------HDFRPTYRRLGELRQF 224
                  ES       L  ++   ++  D+   + E         ++R  + RL      
Sbjct: 328 RRLSIIAESIR---DGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFP-- 382

Query: 225 TGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAH 284
              S  I                       P  +         +++DVI  D++      
Sbjct: 383 --PSAHI-----------------------PTILLSL------IWFDVIKSDVMVV---- 407

Query: 285 VKEFIEKCL-GKDNKANNCGI--IYCRTREHTTDLADALRRKVNKHERSR 331
           V +  +  L  K  K +   I  IY   +    +     R  V+ +   +
Sbjct: 408 VNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPK 457

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 44.1 bits (103), Expect = 1e-04
 Identities = 31/209 (14%), Positives = 67/209 (32%), Gaps = 44/209 (21%)

Query: 90  VRIPPGADFILNGNVRSRNGWISPILSSFY---LRFRDDKTSIVTGRSDLYQLELIVSGQ 146
             IP     ++  +V   +  +  +++  +   L  +  K S ++    +  + L +  +
Sbjct: 385 AHIPTILLSLIWFDVIKSD--VMVVVNKLHKYSLVEKQPKESTIS----IPSIYLELKVK 438

Query: 147 TKTE---NKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHC 203
            + E   +++I++   + K       + P       + ++  HL           +    
Sbjct: 439 LENEYALHRSIVDHYNIPK-TFDSDDLIPPYLDQYFYSHIGHHLKNIEH-----PERMTL 492

Query: 204 VSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST 263
                 DFR           F    I     TA        + +  LKF KPY       
Sbjct: 493 FRMVFLDFR-----------FLEQKI-RHDSTAWNASGSILNTLQQLKFYKPY------- 533

Query: 264 FRSNLFYDVIFDDLLKDSYAHVKEFIEKC 292
              N   D  ++ L+      + +F+ K 
Sbjct: 534 ICDN---DPKYERLVNA----ILDFLPKI 555

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.3 bits (101), Expect = 1e-04
 Identities = 38/251 (15%), Positives = 72/251 (28%), Gaps = 73/251 (29%)

Query: 244 QDIISVL--KFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAH----------------- 284
           +DI+SV    F   +          ++      D ++    A                  
Sbjct: 19  KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM 78

Query: 285 VKEFIEKCLGKDNK--------------ANNCGIIYCRTREHTTDLADALRRKVNKHERS 330
           V++F+E+ L  + K                    I  R R +  +      +   K+  S
Sbjct: 79  VQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN------QVFAKYNVS 132

Query: 331 RVQESF--------MRGEINVITATISFGM-GIDRQ----NV--RFVVHWGMPSSIPAYY 375
           R+Q           +R   NV+      G+ G  +     +V   + V   M   I  ++
Sbjct: 133 RLQPYLKLRQALLELRPAKNVLI----DGVLGSGKTWVALDVCLSYKVQCKMDFKI--FW 186

Query: 376 QESGRAGRDG-----LQSYC-RIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLE 429
                          LQ    +I  +  S+      IK         ++ + +  L    
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI----HSIQAELRRLLKSKP 242

Query: 430 YCEQGYFLVIL 440
           Y      L++L
Sbjct: 243 YENC---LLVL 250

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19 Length = 172

 Score = 53.0 bits (128), Expect = 2e-08
 Identities = 22/92 (23%), Positives = 38/92 (41%), Gaps = 10/92 (10%)

Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
           +I+ ++ +    LA  L  +          + + ER    + F   +  ++ AT  FG G
Sbjct: 35  VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 94

Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
           +D + V    ++ MP     Y     RAGR G
Sbjct: 95  MDIERVNIAFNYDMPEDSDTYLHRVARAGRFG 126

>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 = 53.7 bits (130), Expect = 5e-08
 Identities = 22/92 (23%), Positives = 37/92 (40%), Gaps = 10/92 (10%)

Query: 304 IIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISFGMG 353
           +I+ ++ +    LA  L             + + ER    + F   +  ++ AT  FG G
Sbjct: 254 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG 313

Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
           +D + V    ++ MP     Y     RAGR G
Sbjct: 314 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFG 345

>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 = 52.9 bits (128), Expect = 9e-08
 Identities = 25/96 (26%), Positives = 42/96 (43%), Gaps = 13/96 (13%)

Query: 304 IIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISFGMG 353
           +I+C TR    +L   LR            + + ER  + + F  G   ++ +T     G
Sbjct: 263 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 322

Query: 354 IDRQNVRFVVHWGMPSSIPAYYQ---ESGRAGRDGL 386
           ID Q V  V+++ +P++   Y       GR GR G+
Sbjct: 323 IDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGV 358

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens} Length = 175

 Score = 50.7 bits (122), Expect = 1e-07
 Identities = 23/102 (22%), Positives = 41/102 (40%), Gaps = 19/102 (18%)

Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
           II+C+TR +   L   + +           +   +R+ + + F  G+  V+  T     G
Sbjct: 38  IIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARG 97

Query: 354 IDRQNVRFVVHWGMPSSIPAYYQE---------SGRAGRDGL 386
           ID + V  VV++ +P                  +GR G+ GL
Sbjct: 98  IDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGL 139

>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 = 52.6 bits (127), Expect = 1e-07
 Identities = 23/96 (23%), Positives = 39/96 (40%), Gaps = 13/96 (13%)

Query: 304 IIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISFGMG 353
           +I+  TR     L + +             +++ ER  +   F  G   V+  T     G
Sbjct: 284 VIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARG 343

Query: 354 IDRQNVRFVVHWGMPSSIPAYYQ---ESGRAGRDGL 386
           ID Q V  V+++ +P++   Y       GR GR G+
Sbjct: 344 IDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGV 379

>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 = 52.2 bits (126), Expect = 2e-07
 Identities = 22/97 (22%), Positives = 43/97 (44%), Gaps = 13/97 (13%)

Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
            +I+C T+     L + +R            + + ER  + + F  G   V+ +T  +  
Sbjct: 279 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR 338

Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQ---ESGRAGRDGL 386
           G+D   V  ++++ +P++   Y      SGR GR G+
Sbjct: 339 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGV 375

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score = 49.9 bits (120), Expect = 2e-07
 Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 10/92 (10%)

Query: 304 IIYCRTREHTTDLADALR----------RKVNKHERSRVQESFMRGEINVITATISFGMG 353
           +I+C TR    +L   LR            + + ER  + + F  G   ++ +T     G
Sbjct: 34  VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 93

Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
           ID Q V  V+++ +P++   Y    GR GR G
Sbjct: 94  IDVQQVSLVINYDLPANKENYIHRIGRGGRFG 125

>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 = 51.0 bits (123), Expect = 4e-07
 Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 15/97 (15%)

Query: 304 IIYCRTREHTTDLADALRR----------KVNKHERSRVQESFMRGEINVITATISFGMG 353
           II+C +      LA  +            ++ + ER++V   F +G++  +  +     G
Sbjct: 262 IIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRG 321

Query: 354 IDRQNVRFVVHWGMPSSIPAYY----QESGRAGRDGL 386
           ID Q V  V+++  P +    Y      SGR G  GL
Sbjct: 322 IDIQAVNVVINFDFPKT-AETYLHRIGRSGRFGHLGL 357

>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 = 50.2 bits (121), Expect = 6e-07
 Identities = 25/102 (24%), Positives = 43/102 (42%), Gaps = 19/102 (18%)

Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
           +I+C TR+  + LA  L ++          +   +R+ V E F  G+  V+  T     G
Sbjct: 270 MIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARG 329

Query: 354 IDRQNVRFVVHWGMPSSIPAYYQE---------SGRAGRDGL 386
           ID + V  V+++ +P                  +GR G+ GL
Sbjct: 330 IDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGL 371

>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 = 50.0 bits (120), Expect = 1e-06
 Identities = 25/102 (24%), Positives = 43/102 (42%), Gaps = 19/102 (18%)

Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
           +I+C TR+  + LA  L ++          +   +R+ V E F  G+  V+  T     G
Sbjct: 337 MIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARG 396

Query: 354 IDRQNVRFVVHWGMPSSIPAYYQE---------SGRAGRDGL 386
           ID + V  V+++ +P                  +GR G+ GL
Sbjct: 397 IDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGL 438

>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 = 49.8 bits (118), Expect = 1e-06
 Identities = 28/118 (23%), Positives = 46/118 (38%), Gaps = 20/118 (16%)

Query: 284 HVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------------VN 325
            +KE I + L +   +    I++   RE    + + L +                   ++
Sbjct: 347 KLKEIIREQLQRKQNSK--IIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLS 404

Query: 326 KHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGR 383
           + E+  + + F RGE NV+ AT     G+D   V  VV +    S     Q  GR GR
Sbjct: 405 QREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR 462

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score = 46.7 bits (112), Expect = 2e-06
 Identities = 30/97 (30%), Positives = 43/97 (44%), Gaps = 15/97 (15%)

Query: 303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGM 352
            II+CRT+EH   L D L             + + +R  V   F RGE   + AT     
Sbjct: 38  CIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAAR 97

Query: 353 GIDRQNVRFVVHWGMPSSIPAYY----QESGRAGRDG 385
           GID +N+  V+++ +P      Y      +GRAG  G
Sbjct: 98  GIDIENISLVINYDLPLE-KESYVHRTGRTGRAGNKG 133

>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 = 48.3 bits (116), Expect = 3e-06
 Identities = 24/102 (23%), Positives = 39/102 (38%), Gaps = 19/102 (18%)

Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
           II+  T++    L   L+ +          +   ER R+ + F  G   V+  T     G
Sbjct: 247 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 306

Query: 354 IDRQNVRFVVHWGMPSSIPAYYQE---------SGRAGRDGL 386
           ID   V  VV++ +P+                 +GR GR G+
Sbjct: 307 IDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGV 348

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score = 46.5 bits (111), Expect = 4e-06
 Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 10/92 (10%)

Query: 304 IIYCRTREHTTDLADALRRK----VNKH------ERSRVQESFMRGEINVITATISFGMG 353
           +I+   +     + + L  K    V  H      ER++  E+F  G+ +V+ AT     G
Sbjct: 58  LIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKG 117

Query: 354 IDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
           +D   ++ V+++ MP  I  Y    GR G  G
Sbjct: 118 LDFPAIQHVINYDMPEEIENYVHRIGRTGCSG 149

>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 = 47.5 bits (113), Expect = 5e-06
 Identities = 55/265 (20%), Positives = 101/265 (38%), Gaps = 55/265 (20%)

Query: 156 EELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR-----YNKLAYIVVDEAHCVSEWGHD 210
              ++ K R  ++  TP R        L+  L +     +  + Y V+DEA        D
Sbjct: 193 AMNKMNKLRPNIVIATPGR--------LIDVLEKYSNKFFRFVDYKVLDEA--------D 236

Query: 211 ------FRPTYRR----LGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVF- 259
                 FR         L E    + ++I  +  +AT +  V++  ++    NK   +F 
Sbjct: 237 RLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQK--LANNIMNKKECLFL 294

Query: 260 ------KTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHT 313
                 +       +   V+  +   +S     E I+K + K+  +N   II+  T + T
Sbjct: 295 DTVDKNEPEA-HERIDQSVVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFT 352

Query: 314 TDLADALRRKVNK-------------HERSRVQESFMRGEINVITATISFGMGIDRQNVR 360
           + L   L+ +  K             ++R+ + + F + E  ++  T     G+D  NV 
Sbjct: 353 SFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVH 412

Query: 361 FVVHWGMPSSIPAYYQESGRAGRDG 385
            V+  G+PS +  Y    GR  R G
Sbjct: 413 EVLQIGVPSELANYIHRIGRTARSG 437

>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 = 46.7 bits (111), Expect = 1e-05
 Identities = 56/262 (21%), Positives = 101/262 (38%), Gaps = 55/262 (20%)

Query: 159 RLVKPRIKLLYVTPERAVTESFHYLLQHLVR-----YNKLAYIVVDEAHCVSEWGHD--- 210
           ++ K R  ++  TP R        L+  L +     +  + Y V+DEA        D   
Sbjct: 145 KMNKLRPNIVIATPGR--------LIDVLEKYSNKFFRFVDYKVLDEA--------DRLL 188

Query: 211 ---FRPTYRR----LGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVF---- 259
              FR         L E    + ++I  +  +AT +  V++  ++    NK   +F    
Sbjct: 189 EIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQK--LANNIMNKKECLFLDTV 246

Query: 260 ---KTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDL 316
              +       +   V+  +   +S     E I+K + K+  +N   II+  T + T+ L
Sbjct: 247 DKNEPEA-HERIDQSVVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFTSFL 304

Query: 317 ADALRRKVNK-------H------ERSRVQESFMRGEINVITATISFGMGIDRQNVRFVV 363
              L+ +  K       H      +R+ + + F + E  ++  T     G+D  NV  V+
Sbjct: 305 CSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVL 364

Query: 364 HWGMPSSIPAYYQESGRAGRDG 385
             G+PS +  Y    GR  R G
Sbjct: 365 QIGVPSELANYIHRIGRTARSG 386

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens} Length = 185

 Score = 43.3 bits (103), Expect = 3e-05
 Identities = 27/110 (24%), Positives = 47/110 (42%), Gaps = 11/110 (10%)

Query: 286 KEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----VNKH------ERSRVQES 335
           + F+   L    K +   +++  T++    L D L  +     + H      +R      
Sbjct: 33  RSFLLDLLNATGKDSLT-LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQ 91

Query: 336 FMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
           F  G+  ++ AT     G+D  NV+ V+++ +PS I  Y    GR GR G
Sbjct: 92  FRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVG 141

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli} Length = 170

 Score = 42.6 bits (101), Expect = 5e-05
 Identities = 28/96 (29%), Positives = 43/96 (44%), Gaps = 13/96 (13%)

Query: 304 IIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMG 353
           I++ R RE   +LA+ LR            + + +R+   +    G +NV+ AT     G
Sbjct: 34  IVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARG 93

Query: 354 IDRQNVRFVVHWGMPSSIPAYYQE---SGRAGRDGL 386
           ID  +V  V ++ MP S   Y      + RAGR G 
Sbjct: 94  IDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGT 129

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12} Length = 968

 Score = 44.7 bits (105), Expect = 6e-05
 Identities = 22/128 (17%), Positives = 43/128 (33%), Gaps = 14/128 (10%)

Query: 304 IIYCRTREHTTDLADALRRK-----------VNKHERSRVQESFMRGE--INVITATISF 350
           ++ C        L   LR +           ++  ER R    F   +    V+  +   
Sbjct: 507 LVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIG 566

Query: 351 GMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDT 410
             G + Q    +V + +P +     Q  GR  R G     +I+   + +K+ + V+    
Sbjct: 567 SEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHV-PYLEKTAQSVLVRWY 625

Query: 411 STKREQLE 418
               +  E
Sbjct: 626 HEGLDAFE 633

>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 = 44.5 bits (105), Expect = 6e-05
 Identities = 31/133 (23%), Positives = 50/133 (37%), Gaps = 22/133 (16%)

Query: 315 DLADALRRKVNKH-------ERSRVQESFMRGEINVITATISFGMGID--------RQNV 359
            LA A+R  V  H       ER  V+E+F +G I  + AT +   GI+        R   
Sbjct: 288 KLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIW 347

Query: 360 RFVVHWGMPSSIPAYYQESGRAGRDGLQSYCR---IYHSEHSKKSLEYVIKTDTSTKREQ 416
           R+         I   +Q  GRAGR           +  S+  ++ + + I        E+
Sbjct: 348 RYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREVMNHYIFGKP----EK 403

Query: 417 LELKFKNYLSMLE 429
           L  +  N  ++  
Sbjct: 404 LFSQLSNESNLRS 416

>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 = 43.6 bits (104), Expect = 7e-05
 Identities = 22/93 (23%), Positives = 36/93 (38%), Gaps = 11/93 (11%)

Query: 303 GIIYCRTREHTTDLADALRRKVNKH------ERSRVQESFMRGEINVITATISFGMGIDR 356
            I++ RTR     L       +          R+R  ++F  GE +++  T     G+D 
Sbjct: 223 VIVFVRTRNRVAKLVRLFDNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDI 282

Query: 357 QNVRFVVHWGMPSSIPAYY----QESGRAGRDG 385
             V  V+++  P      Y      +GR GR G
Sbjct: 283 PLVEKVINFDAP-QDLRTYIHRIGRTGRMGRKG 314

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 42.0 bits (99), Expect = 3e-04
 Identities = 30/135 (22%), Positives = 49/135 (36%), Gaps = 20/135 (14%)

Query: 315 DLADALRRKVNKH-------ERSRVQESFMRGEINVITATISFGMGI------------D 355
            L   + + V  H        R  ++E F + +I VI AT +   G+             
Sbjct: 306 LLKSLISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIY 365

Query: 356 RQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKRE 415
           R N +   ++     I  Y Q SGRAGR G             K+ ++ V K    +  E
Sbjct: 366 RFNKKIAGYY-DEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKEDVDRVFKKYVLSDVE 424

Query: 416 QLELKFKNYLSMLEY 430
            +E K  +  +   +
Sbjct: 425 PIESKLGSERAFYTF 439

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score = 41.8 bits (99), Expect = 4e-04
 Identities = 27/110 (24%), Positives = 47/110 (42%), Gaps = 11/110 (10%)

Query: 286 KEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----VNKH------ERSRVQES 335
           + F+   L    K +   +++  T++    L D L  +     + H      +R      
Sbjct: 263 RSFLLDLLNATGKDSLT-LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQ 321

Query: 336 FMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
           F  G+  ++ AT     G+D  NV+ V+++ +PS I  Y    GR GR G
Sbjct: 322 FRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVG 371

>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 = 41.3 bits (97), Expect = 6e-04
 Identities = 29/132 (21%), Positives = 51/132 (38%), Gaps = 21/132 (15%)

Query: 315 DLADALRRKVNKH-------ERSRVQESFMRGEINVITATISFGMGIDRQNV--RFVV-- 363
            LA+ +R+    H       +R  V+++F RG I V+ AT +   G+   N+  R V+  
Sbjct: 290 KLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGV---NLPARRVIVR 346

Query: 364 ------HWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQL 417
                  +     +  Y Q +GRAGR G+            +   E  +K     + E++
Sbjct: 347 SLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRD-REIAVKRYIFGEPERI 405

Query: 418 ELKFKNYLSMLE 429
             K      +  
Sbjct: 406 TSKLGVETHLRF 417

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 39.2 bits (90), Expect = 7e-04
 Identities = 8/25 (32%), Positives = 15/25 (60%), Gaps = 1/25 (4%)

Query: 216 RRL-GELRQFTGNSIPIIALTATAE 239
           ++L   L+ +  +S P +A+ AT E
Sbjct: 23  KKLQASLKLYADDSAPALAIKATME 47

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	444
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	100.0
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	100.0
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	100.0
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	100.0
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	100.0
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	100.0
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	100.0
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	100.0
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	100.0
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	100.0
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	100.0
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	100.0
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	100.0
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	100.0
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	100.0
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	100.0
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	100.0
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	100.0
4gl2_A	699	Interferon-induced helicase C domain-containing P;	100.0
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	100.0
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	100.0
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	100.0
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	100.0
3h1t_A	590	Type I site-specific restriction-modification syst	100.0
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	100.0
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	100.0
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	100.0
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	100.0
1yks_A	440	Genome polyprotein [contains: flavivirin protease	100.0
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	100.0
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	100.0
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	100.0
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.98
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.98
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.97
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.97
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.97
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.97
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.95
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.95
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.95
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.95
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.94
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.93
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.93
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.93
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.93
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.93
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.93
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.92
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.92
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.92
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.92
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.92
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.91
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.91
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.91
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.9
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.9
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.88
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.87
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.87
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.86
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.86
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.86
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.86
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.84
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.83
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.71
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.81
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.79
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.78
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.73
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.69
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.69
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.67
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.56
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.51
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.03
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	97.86
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	97.71
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	97.68
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.6
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.55
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.18
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	96.53
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	96.5
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	96.49
3co5_A	143	Putative two-component system transcriptional RES	96.26
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.04
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	96.01
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	95.75
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	95.54
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	95.52
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	95.51
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	95.09
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	95.03
3bos_A	242	Putative DNA replication factor; P-loop containing	94.83
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	94.79
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	94.76
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	94.68
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	94.64
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	94.61
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	94.54
2chg_A	226	Replication factor C small subunit; DNA-binding pr	94.5
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	94.41
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	94.37
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	94.23
2r6a_A	454	DNAB helicase, replicative helicase; replication,	94.16
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	94.13
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	94.05
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	93.98
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	93.82
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	93.58
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	93.49
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	93.38
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	93.37
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	93.37
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	93.34
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	93.33
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	93.33
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	93.32
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	93.26
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	93.26
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	93.19
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	92.93
3pvs_A	447	Replication-associated recombination protein A; ma	92.92
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	92.9
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	92.89
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	92.87
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	92.52
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	92.5
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	92.48
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	92.28
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	92.27
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	92.24
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	92.2
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	92.17
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	91.99
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	91.91
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	91.87
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	90.85
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	90.83
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	89.83
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	89.63
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	88.78
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	88.67
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	88.66
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	88.37
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	88.02
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	87.09
1u94_A	356	RECA protein, recombinase A; homologous recombinat	87.01
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	86.94
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	86.77
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	86.62
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	86.37
1xp8_A	366	RECA protein, recombinase A; recombination, radior	85.83
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	85.76
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	85.71
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	85.41
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	85.17
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	85.13
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	84.4
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	83.7
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	83.36
2z43_A	324	DNA repair and recombination protein RADA; archaea	82.83
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	82.47
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	82.26
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	81.89
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	81.64
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	81.46
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	81.44
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	81.2
3io5_A	333	Recombination and repair protein; storage dimer, i	80.93
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	80.67
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	80.5
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	80.31

>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=100.00  E-value=4e-52  Score=422.22  Aligned_cols=376  Identities=29%  Similarity=0.513  Sum_probs=309.3

Q ss_pred             CCCCCcCCCCCCCCC-HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCc
Q psy7952          18 SLTGNQQDRKGGKVS-EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGA   96 (444)
Q Consensus        18 ~~~~~~~~~~~~~~~-~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~   96 (444)
                      ..+....+|....++ ...+.+.|++.||+..++ ++|.++++.++.| +++++.+|||+|||++        |++|+  
T Consensus        13 ~~~~~~~~w~~~~~~l~~~l~~~L~~~fg~~~~r-p~Q~~~i~~il~g-~d~lv~~pTGsGKTl~--------~~lpa--   80 (591)
T 2v1x_A           13 EYDSSPAAWNKEDFPWSGKVKDILQNVFKLEKFR-PLQLETINVTMAG-KEVFLVMPTGGGKSLC--------YQLPA--   80 (591)
T ss_dssp             ---CCGGGGCCSCSTTHHHHHHHHHHTSCCCSCC-TTHHHHHHHHHTT-CCEEEECCTTSCTTHH--------HHHHH--
T ss_pred             CCCcchhccccccCCCCHHHHHHHHHHhCCCCCC-HHHHHHHHHHHcC-CCEEEEECCCChHHHH--------HHHHH--
Confidence            344455666665554 778999999999999844 8999999999999 9999999999999999        88888  


Q ss_pred             cccccCCccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCcc
Q psy7952          97 DFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERA  175 (444)
Q Consensus        97 ~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l  175 (444)
                        +...+..   ||++|+++|+     .++++.+ ..+   +.+..++++....+.......+....+.++|+|+||+++
T Consensus        81 --l~~~g~~---lVisP~~~L~-----~q~~~~l~~~g---i~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L  147 (591)
T 2v1x_A           81 --LCSDGFT---LVICPLISLM-----EDQLMVLKQLG---ISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKI  147 (591)
T ss_dssp             --HTSSSEE---EEECSCHHHH-----HHHHHHHHHHT---CCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHH
T ss_pred             --HHcCCcE---EEEeCHHHHH-----HHHHHHHHhcC---CcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHh
Confidence              6655555   9999999999     7888888 667   889999999988877777666654467899999999998


Q ss_pred             ccc-cHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCC
Q psy7952         176 VTE-SFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNK  254 (444)
Q Consensus       176 ~~~-~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~  254 (444)
                      ... .|...+.......++++|||||||++.+||++|++.+..+..+...+++ .+++++|||+++....++...++++.
T Consensus       148 ~~~~~~~~~l~~~~~~~~i~~iViDEAH~is~~g~dfr~~~~~l~~l~~~~~~-~~ii~lSAT~~~~v~~~i~~~l~~~~  226 (591)
T 2v1x_A          148 AKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPN-ASLIGLTATATNHVLTDAQKILCIEK  226 (591)
T ss_dssp             HSCHHHHHHHHHHHHTTCEEEEEEETGGGGSTTCTTCCGGGGGGGHHHHHCTT-SEEEEEESSCCHHHHHHHHHHTTCCS
T ss_pred             hccHHHHHHHHhhhhccCCcEEEEECcccccccccccHHHHHHHHHHHHhCCC-CcEEEEecCCCHHHHHHHHHHhCCCC
Confidence            642 3444555566678999999999999999999999988877666666665 89999999999999899999988876


Q ss_pred             CeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------c
Q psy7952         255 PYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------V  324 (444)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~  324 (444)
                      +. .+..+..++++.+.+......   .......+.+++.... .+.++||||++++.++.++..|...          +
T Consensus       227 ~~-~~~~~~~r~nl~~~v~~~~~~---~~~~~~~l~~~l~~~~-~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l  301 (591)
T 2v1x_A          227 CF-TFTASFNRPNLYYEVRQKPSN---TEDFIEDIVKLINGRY-KGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANL  301 (591)
T ss_dssp             CE-EEECCCCCTTEEEEEEECCSS---HHHHHHHHHHHHTTTT-TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTS
T ss_pred             cE-EEecCCCCcccEEEEEeCCCc---HHHHHHHHHHHHHHhc-cCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCC
Confidence            64 455667788988887765422   1223333444443322 5789999999999999999999876          8


Q ss_pred             CHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHH
Q psy7952         325 NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEY  404 (444)
Q Consensus       325 ~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~  404 (444)
                      ++.+|..+++.|++|+.+|||||+++++|||+|++++||++++|.|...|+||+||+||.|++|.|++++.+.|...+..
T Consensus       302 ~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~l~~~~D~~~~~~  381 (591)
T 2v1x_A          302 EPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISS  381 (591)
T ss_dssp             CHHHHHHHHHHHHTTSSSEEEECTTSCTTCCCSCEEEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCeEEEEechhhcCCCcccccEEEEeCCCCCHHHHHHHhccCCcCCCCceEEEEEChHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             HHhhccchhHHHHHHHHhhHHHHHHHhh
Q psy7952         405 VIKTDTSTKREQLELKFKNYLSMLEYCE  432 (444)
Q Consensus       405 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~  432 (444)
                      ++..+.        .....+.+|+.||+
T Consensus       382 ~~~~~~--------~~~~~l~~~~~~~~  401 (591)
T 2v1x_A          382 MVVMEN--------VGQQKLYEMVSYCQ  401 (591)
T ss_dssp             HTTTST--------THHHHHHHHHHHHT
T ss_pred             HHhhhh--------hhHHHHHHHHHHHh
Confidence            876432        13455677888876

>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=100.00  E-value=2.2e-51  Score=412.75  Aligned_cols=357  Identities=33%  Similarity=0.589  Sum_probs=300.6

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ..++.+.+++.||+..++ ++|.++++.+++| +++++.+|||+|||++        |++|+    +...+..   ||++
T Consensus        10 ~~~~~~~l~~~~g~~~~r-~~Q~~~i~~il~g-~d~lv~apTGsGKTl~--------~~lp~----l~~~g~~---lvi~   72 (523)
T 1oyw_A           10 ESGAKQVLQETFGYQQFR-PGQEEIIDTVLSG-RDCLVVMPTGGGKSLC--------YQIPA----LLLNGLT---VVVS   72 (523)
T ss_dssp             HHHHHHHHHHTTCCSSCC-TTHHHHHHHHHTT-CCEEEECSCHHHHHHH--------HHHHH----HHSSSEE---EEEC
T ss_pred             CHHHHHHHHHHhCCCCCC-HHHHHHHHHHHcC-CCEEEECCCCcHHHHH--------HHHHH----HHhCCCE---EEEC
Confidence            677889999999999855 8999999999999 8999999999999999        88888    5555655   9999


Q ss_pred             chhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         113 PILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      |+++|+     .++++.+ ..+   +.+..++++............+.  .+.++|+|+||+++.+..+...    ....
T Consensus        73 P~~aL~-----~q~~~~l~~~g---i~~~~l~~~~~~~~~~~~~~~~~--~~~~~ilv~Tpe~l~~~~~~~~----l~~~  138 (523)
T 1oyw_A           73 PLISLM-----KDQVDQLQANG---VAAACLNSTQTREQQLEVMTGCR--TGQIRLLYIAPERLMLDNFLEH----LAHW  138 (523)
T ss_dssp             SCHHHH-----HHHHHHHHHTT---CCEEEECTTSCHHHHHHHHHHHH--HTCCSEEEECHHHHTSTTHHHH----HTTS
T ss_pred             ChHHHH-----HHHHHHHHHcC---CcEEEEeCCCCHHHHHHHHHHHh--cCCCCEEEECHHHHhChHHHHH----HhhC
Confidence            999999     8888888 777   88999999888776666555554  3678999999999975543332    3347


Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEE
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYD  271 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~  271 (444)
                      ++++|||||+|++.+||++|++.+..+..+.+.+++ .+++++|||+++....++.+.+++..+. +...+..++++.+.
T Consensus       139 ~~~~vViDEaH~i~~~g~~fr~~~~~l~~l~~~~~~-~~~i~lSAT~~~~~~~~i~~~l~~~~~~-~~~~~~~r~~l~~~  216 (523)
T 1oyw_A          139 NPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPT-LPFMALTATADDTTRQDIVRLLGLNDPL-IQISSFDRPNIRYM  216 (523)
T ss_dssp             CEEEEEESSGGGGCTTSSCCCHHHHGGGGHHHHCTT-SCEEEEESCCCHHHHHHHHHHHTCCSCE-EEECCCCCTTEEEE
T ss_pred             CCCEEEEeCccccCcCCCccHHHHHHHHHHHHhCCC-CCEEEEeCCCCHHHHHHHHHHhCCCCCe-EEeCCCCCCceEEE
Confidence            899999999999999999999999988888777765 8999999999999888899988887774 44566778888877


Q ss_pred             EEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCc
Q psy7952         272 VIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEI  341 (444)
Q Consensus       272 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~  341 (444)
                      +....   .....+.+.+..    .  .+.++||||+|+++++.+++.|...          ++.++|..+++.|++|+.
T Consensus       217 v~~~~---~~~~~l~~~l~~----~--~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~  287 (523)
T 1oyw_A          217 LMEKF---KPLDQLMRYVQE----Q--RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDL  287 (523)
T ss_dssp             EEECS---SHHHHHHHHHHH----T--TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             EEeCC---CHHHHHHHHHHh----c--CCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCC
Confidence            76542   233344444443    2  5679999999999999999999876          899999999999999999


Q ss_pred             cEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhhccchhHHHHHHHH
Q psy7952         342 NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKF  421 (444)
Q Consensus       342 ~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  421 (444)
                      +|||||+++++|||+|++++||++++|.|...|+||+||+||.|.+|.+++++++.+...++.++....+..  ......
T Consensus       288 ~vlVaT~a~~~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~d~~~~~~~~~~~~~~~--~~~~~~  365 (523)
T 1oyw_A          288 QIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQGQ--LQDIER  365 (523)
T ss_dssp             SEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHHHTSCCSH--HHHHHH
T ss_pred             eEEEEechhhCCCCccCccEEEEECCCCCHHHHHHHhccccCCCCCceEEEEeCHHHHHHHHHHHhccCcHH--HHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999988743332  334456


Q ss_pred             hhHHHHHHHhhh
Q psy7952         422 KNYLSMLEYCEQ  433 (444)
Q Consensus       422 ~~~~~~~~~~~~  433 (444)
                      ..+.+|..||+.
T Consensus       366 ~~l~~m~~~~~~  377 (523)
T 1oyw_A          366 HKLNAMGAFAEA  377 (523)
T ss_dssp             HHHHHHHHHHTC
T ss_pred             HHHHHHHHHHhc
Confidence            677888888763

>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=2.1e-48  Score=383.96  Aligned_cols=335  Identities=17%  Similarity=0.239  Sum_probs=251.2

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC-----Cccce
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG-----NVRSR  107 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~-----~~~~~  107 (444)
                      ...+.+++++ +||.. ||++|.++++.++.| +++++++|||+|||++        |++|+ +..+...     ...++
T Consensus        64 ~~~l~~~l~~-~g~~~-pt~iQ~~ai~~i~~g-~d~i~~a~TGsGKT~a--------~~lpi-l~~l~~~~~~~~~~~~~  131 (434)
T 2db3_A           64 RDIIIDNVNK-SGYKI-PTPIQKCSIPVISSG-RDLMACAQTGSGKTAA--------FLLPI-LSKLLEDPHELELGRPQ  131 (434)
T ss_dssp             CHHHHHHHHH-TTCCS-CCHHHHHHHHHHHTT-CCEEEECCTTSSHHHH--------HHHHH-HHHHHHSCCCCCTTCCS
T ss_pred             CHHHHHHHHH-cCCCC-CCHHHHHHHHHHhcC-CCEEEECCCCCCchHH--------HHHHH-HHHHHhcccccccCCcc
Confidence            5677888887 59998 889999999999999 9999999999999999        67776 4333332     23467


Q ss_pred             eEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH
Q psy7952         108 NGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL  187 (444)
Q Consensus       108 vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~  187 (444)
                      +||++||++|+  .|+.+.++.+.. ...+++..++|+.........+      ..+++|+|+||+++.    ..+....
T Consensus       132 ~lil~PtreLa--~Q~~~~~~~~~~-~~~~~~~~~~gg~~~~~~~~~l------~~~~~Ivv~Tp~~l~----~~l~~~~  198 (434)
T 2db3_A          132 VVIVSPTRELA--IQIFNEARKFAF-ESYLKIGIVYGGTSFRHQNECI------TRGCHVVIATPGRLL----DFVDRTF  198 (434)
T ss_dssp             EEEECSSHHHH--HHHHHHHHHHTT-TSSCCCCEECTTSCHHHHHHHH------TTCCSEEEECHHHHH----HHHHTTS
T ss_pred             EEEEecCHHHH--HHHHHHHHHHhc-cCCcEEEEEECCCCHHHHHHHh------hcCCCEEEEChHHHH----HHHHhCC
Confidence            89999999999  333444444421 1227888889988766543333      468999999999984    3333334


Q ss_pred             HhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCC--CC
Q psy7952         188 VRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST--FR  265 (444)
Q Consensus       188 ~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~--~~  265 (444)
                      ..+.+++++|+||||++.+++  |...+..+..... .+.+.+++++|||+++...+....++  .++..+.....  ..
T Consensus       199 ~~l~~~~~lVlDEah~~~~~g--f~~~~~~i~~~~~-~~~~~q~l~~SAT~~~~~~~~~~~~l--~~~~~i~~~~~~~~~  273 (434)
T 2db3_A          199 ITFEDTRFVVLDEADRMLDMG--FSEDMRRIMTHVT-MRPEHQTLMFSATFPEEIQRMAGEFL--KNYVFVAIGIVGGAC  273 (434)
T ss_dssp             CCCTTCCEEEEETHHHHTSTT--THHHHHHHHHCTT-SCSSCEEEEEESCCCHHHHHHHHTTC--SSCEEEEESSTTCCC
T ss_pred             cccccCCeEEEccHhhhhccC--cHHHHHHHHHhcC-CCCCceEEEEeccCCHHHHHHHHHhc--cCCEEEEeccccccc
Confidence            457789999999999999887  7766666544322 24458999999999988766555443  35544443322  22


Q ss_pred             CCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHH
Q psy7952         266 SNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQES  335 (444)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~  335 (444)
                      .++...+.... ...+...+.+.+..    .   ..++||||++++.++.+++.|.+.          +++.+|..+++.
T Consensus       274 ~~i~~~~~~~~-~~~k~~~l~~~l~~----~---~~~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~  345 (434)
T 2db3_A          274 SDVKQTIYEVN-KYAKRSKLIEILSE----Q---ADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRD  345 (434)
T ss_dssp             TTEEEEEEECC-GGGHHHHHHHHHHH----C---CTTEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHH
T ss_pred             cccceEEEEeC-cHHHHHHHHHHHHh----C---CCCEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHH
Confidence            33333333322 23333444444433    2   345999999999999999999876          889999999999


Q ss_pred             HhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEeccc-chhhHHHH
Q psy7952         336 FMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEH-SKKSLEYV  405 (444)
Q Consensus       336 f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~~  405 (444)
                      |++|+.+|||||+++++|+|+|++++||++|+|.+..+|+||+||+||.|+.|.+++|+.++ +......+
T Consensus       346 F~~g~~~vLvaT~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~~~~~~~~~l  416 (434)
T 2db3_A          346 FKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADL  416 (434)
T ss_dssp             HHTSSCSEEEECGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTTTCGGGHHHH
T ss_pred             HHcCCCcEEEEchhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCCCCEEEEEEeccccHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999854 44444444

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=100.00  E-value=1e-46  Score=370.27  Aligned_cols=336  Identities=15%  Similarity=0.251  Sum_probs=252.6

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ..++.+++++ +|+.. |+++|.++++.++++ +++++.+|||+|||++        |.+|+ ++.+.......++||++
T Consensus        45 ~~~l~~~l~~-~g~~~-~~~~Q~~ai~~i~~~-~~~lv~a~TGsGKT~~--------~~~~~-~~~l~~~~~~~~~lil~  112 (410)
T 2j0s_A           45 REDLLRGIYA-YGFEK-PSAIQQRAIKQIIKG-RDVIAQSQSGTGKTAT--------FSISV-LQCLDIQVRETQALILA  112 (410)
T ss_dssp             CHHHHHHHHH-HTCCS-CCHHHHHHHHHHHTT-CCEEEECCTTSSHHHH--------HHHHH-HHTCCTTSCSCCEEEEC
T ss_pred             CHHHHHHHHH-cCCCC-CCHHHHHHHHHHhCC-CCEEEECCCCCCchHH--------HHHHH-HHHHhhccCCceEEEEc
Confidence            4678888887 69998 679999999999999 9999999999999999        66555 33343333445789999


Q ss_pred             chhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCC
Q psy7952         113 PILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK  192 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~  192 (444)
                      |+++|+  .|+.+.+..+. ....+.+..+.|+.........+      ..+++|+|+||+++.    ..+........+
T Consensus       113 Pt~~L~--~q~~~~~~~~~-~~~~~~~~~~~g~~~~~~~~~~~------~~~~~ivv~Tp~~l~----~~l~~~~~~~~~  179 (410)
T 2j0s_A          113 PTRELA--VQIQKGLLALG-DYMNVQCHACIGGTNVGEDIRKL------DYGQHVVAGTPGRVF----DMIRRRSLRTRA  179 (410)
T ss_dssp             SSHHHH--HHHHHHHHHHT-TTTTCCEEEECTTSCHHHHHHHH------HHCCSEEEECHHHHH----HHHHTTSSCCTT
T ss_pred             CcHHHH--HHHHHHHHHHh-ccCCeEEEEEECCCCHHHHHHHh------hcCCCEEEcCHHHHH----HHHHhCCccHhh
Confidence            999999  22233333441 11237888888888766544333      236799999999974    333333345677


Q ss_pred             ccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecC--CCCCCceE
Q psy7952         193 LAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTS--TFRSNLFY  270 (444)
Q Consensus       193 ~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~--~~~~~~~~  270 (444)
                      +++||+||+|++.+++  +...   +..++...+.+.+++++|||+++...+....+  +..+..+....  .....+..
T Consensus       180 ~~~vViDEah~~~~~~--~~~~---~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~  252 (410)
T 2j0s_A          180 IKMLVLDEADEMLNKG--FKEQ---IYDVYRYLPPATQVVLISATLPHEILEMTNKF--MTDPIRILVKRDELTLEGIKQ  252 (410)
T ss_dssp             CCEEEEETHHHHTSTT--THHH---HHHHHTTSCTTCEEEEEESCCCHHHHTTGGGT--CSSCEEECCCGGGCSCTTEEE
T ss_pred             eeEEEEccHHHHHhhh--hHHH---HHHHHHhCccCceEEEEEcCCCHHHHHHHHHH--cCCCEEEEecCccccCCCceE
Confidence            9999999999998776  5543   44455566677899999999988655433333  33444433222  22334444


Q ss_pred             EEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCC
Q psy7952         271 DVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGE  340 (444)
Q Consensus       271 ~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~  340 (444)
                      .+........+...+.+.+...      ..+++||||+++++++.+++.|...          ++..+|..+++.|++|+
T Consensus       253 ~~~~~~~~~~k~~~l~~~~~~~------~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~  326 (410)
T 2j0s_A          253 FFVAVEREEWKFDTLCDLYDTL------TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGA  326 (410)
T ss_dssp             EEEEESSTTHHHHHHHHHHHHH------TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTS
T ss_pred             EEEEeCcHHhHHHHHHHHHHhc------CCCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCC
Confidence            4444433333444555544443      4569999999999999999999876          88999999999999999


Q ss_pred             ccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHH
Q psy7952         341 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI  406 (444)
Q Consensus       341 ~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  406 (444)
                      .+|||||+++++|+|+|++++||++++|.+...|+||+||+||.|+.|.+++++.+.+...++.+.
T Consensus       327 ~~vlv~T~~~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~  392 (410)
T 2j0s_A          327 SRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIE  392 (410)
T ss_dssp             SCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHH
T ss_pred             CCEEEECChhhCcCCcccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEEecHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999998877776654

>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=1.2e-46  Score=370.47  Aligned_cols=338  Identities=18%  Similarity=0.259  Sum_probs=249.9

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC---------
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN---------  103 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~---------  103 (444)
                      ...+.++++. +|+.. ||++|.++++.++.+ +++++.+|||+|||++        |++|+ +..+...+         
T Consensus        23 ~~~l~~~l~~-~~~~~-~~~~Q~~~i~~i~~~-~~~lv~a~TGsGKT~~--------~~~~~-l~~~~~~~~~~~~~~~~   90 (417)
T 2i4i_A           23 GEIIMGNIEL-TRYTR-PTPVQKHAIPIIKEK-RDLMACAQTGSGKTAA--------FLLPI-LSQIYSDGPGEALRAMK   90 (417)
T ss_dssp             CHHHHHHHHH-HTCCS-CCHHHHHHHHHHHTT-CCEEEECCTTSCHHHH--------HHHHH-HHHHHHHCCCHHHHHHH
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHccC-CCEEEEcCCCCHHHHH--------HHHHH-HHHHHhccccchhhccc
Confidence            5678888887 59997 789999999999999 9999999999999999        66666 33232211         


Q ss_pred             ---------ccceeEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECC
Q psy7952         104 ---------VRSRNGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTP  172 (444)
Q Consensus       104 ---------~~~~vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tp  172 (444)
                               ..+++||++|+++|+  .|+.+.+..+  ..+   +++..++|+.........+      ..+++|+|+||
T Consensus        91 ~~~~~~~~~~~~~~lil~Pt~~L~--~q~~~~~~~~~~~~~---~~~~~~~g~~~~~~~~~~~------~~~~~I~v~Tp  159 (417)
T 2i4i_A           91 ENGRYGRRKQYPISLVLAPTRELA--VQIYEEARKFSYRSR---VRPCVVYGGADIGQQIRDL------ERGCHLLVATP  159 (417)
T ss_dssp             HCBTTBSCSBCCSEEEECSSHHHH--HHHHHHHHHHHTTSS---CCEEEECSSSCHHHHHHHH------TTCCSEEEECH
T ss_pred             cccccccccCCccEEEECCcHHHH--HHHHHHHHHHhCcCC---ceEEEEECCCCHHHHHHHh------hCCCCEEEECh
Confidence                     225789999999999  2234444444  234   8888899887765443322      46789999999


Q ss_pred             CccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhC-CCCcEEEEeccCCcchHHHHHHHhc
Q psy7952         173 ERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTG-NSIPIIALTATAEPSVKQDIISVLK  251 (444)
Q Consensus       173 e~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~-~~~~~v~lSAT~~~~~~~~~~~~l~  251 (444)
                      +++.    ..+......+.++++||+||+|++.+++  +...+..+.......+ ...+++++|||+++........++.
T Consensus       160 ~~l~----~~l~~~~~~~~~~~~iViDEah~~~~~~--~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~  233 (417)
T 2i4i_A          160 GRLV----DMMERGKIGLDFCKYLVLDEADRMLDMG--FEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLD  233 (417)
T ss_dssp             HHHH----HHHHTTSBCCTTCCEEEESSHHHHHHTT--CHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCS
T ss_pred             HHHH----HHHHcCCcChhhCcEEEEEChhHhhccC--cHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcC
Confidence            9984    2233333346788999999999998876  6666655543211111 2468999999998877666555543


Q ss_pred             CCCCeEEEec--CCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------
Q psy7952         252 FNKPYKVFKT--STFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------  323 (444)
Q Consensus       252 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------  323 (444)
                        .+..+...  ....+++...+..... ..+...    +..++... ..++++||||+++++++.+++.|.+.      
T Consensus       234 --~~~~~~~~~~~~~~~~i~~~~~~~~~-~~~~~~----l~~~l~~~-~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~  305 (417)
T 2i4i_A          234 --EYIFLAVGRVGSTSENITQKVVWVEE-SDKRSF----LLDLLNAT-GKDSLTLVFVETKKGADSLEDFLYHEGYACTS  305 (417)
T ss_dssp             --SCEEEEEC----CCSSEEEEEEECCG-GGHHHH----HHHHHHTC-CTTCEEEEECSSHHHHHHHHHHHHHTTCCEEE
T ss_pred             --CCEEEEeCCCCCCccCceEEEEEecc-HhHHHH----HHHHHHhc-CCCCeEEEEECCHHHHHHHHHHHHHCCCCeeE
Confidence              44333322  2234444444443322 223333    33333332 25789999999999999999999875      


Q ss_pred             ----cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         324 ----VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       324 ----~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                          ++.++|..+++.|++|+.+|||||+++++|+|+|++++||++++|.|...|+||+||+||.|+.|.+++++++.+.
T Consensus       306 ~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~  385 (417)
T 2i4i_A          306 IHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNI  385 (417)
T ss_dssp             ECTTSCHHHHHHHHHHHHHTSSCEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGG
T ss_pred             ecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccccH
Confidence                8899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hhHHHHHh
Q psy7952         400 KSLEYVIK  407 (444)
Q Consensus       400 ~~~~~~~~  407 (444)
                      ..+..+.+
T Consensus       386 ~~~~~l~~  393 (417)
T 2i4i_A          386 NITKDLLD  393 (417)
T ss_dssp             GGHHHHHH
T ss_pred             HHHHHHHH
Confidence            88777754

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=100.00  E-value=8e-46  Score=378.85  Aligned_cols=350  Identities=19%  Similarity=0.264  Sum_probs=258.9

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHH--ccCCcEEEEccCCCcccccccccccceEEeCCCccccccC----Ccc
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHIL--LRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG----NVR  105 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~--~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~----~~~  105 (444)
                      ....+.++++. +|+.. |+++|.++++.++  .+ +++++.+|||+|||++        |++|+ +..+...    +..
T Consensus        28 l~~~l~~~l~~-~g~~~-~~~~Q~~~i~~il~~~~-~dvlv~apTGsGKTl~--------~~lpi-l~~l~~~~~~~~~~   95 (579)
T 3sqw_A           28 LDKEIHKAITR-MEFPG-LTPVQQKTIKPILSSED-HDVIARAKTGTGKTFA--------FLIPI-FQHLINTKFDSQYM   95 (579)
T ss_dssp             SCHHHHHHHHT-TTCSS-CCHHHHHHHHHHHCSSS-EEEEEECCTTSCHHHH--------HHHHH-HHHHHHTTTSSTTS
T ss_pred             CCHHHHHHHHH-CCCCC-CCHHHHHHHHHHHccCC-CeEEEEcCCCcHHHHH--------HHHHH-HHHHHhccccccCC
Confidence            46778888887 69998 6699999999999  55 8999999999999999        67776 3333332    223


Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-c--CCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-T--GRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHY  182 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~--~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~  182 (444)
                      +++||++||++|+  .|+.+.+..+ .  .+...+.+..+.++.........+.     ..+++|+|+||+++.    ..
T Consensus        96 ~~~lvl~Ptr~La--~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~-----~~~~~IlV~Tp~~l~----~~  164 (579)
T 3sqw_A           96 VKAVIVAPTRDLA--LQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMN-----KLRPNIVIATPGRLI----DV  164 (579)
T ss_dssp             CCEEEECSSHHHH--HHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHH-----HHCCSEEEECHHHHH----HH
T ss_pred             CeEEEEcchHHHH--HHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHh-----cCCCCEEEECHHHHH----HH
Confidence            5789999999999  3334455544 1  1333366777888776554433332     236899999999985    22


Q ss_pred             HHHH-HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhC----CCCcEEEEeccCCcchHHHHHHHhcCCCCeE
Q psy7952         183 LLQH-LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTG----NSIPIIALTATAEPSVKQDIISVLKFNKPYK  257 (444)
Q Consensus       183 ~~~~-~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~----~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~  257 (444)
                      +... ...+..+++||+||||++.+++  |+..+..+...+....    .+.+++++|||+++.....+...+..+....
T Consensus       165 l~~~~~~~~~~~~~lViDEah~l~~~g--f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~  242 (579)
T 3sqw_A          165 LEKYSNKFFRFVDYKVLDEADRLLEIG--FRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLF  242 (579)
T ss_dssp             HHHHHHHHCTTCCEEEEETHHHHTSTT--THHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEE
T ss_pred             HHhccccccccCCEEEEEChHHhhcCC--CHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEE
Confidence            2222 3457889999999999999988  8888888776665543    2578999999999877665554443222222


Q ss_pred             EEecCC----CCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------
Q psy7952         258 VFKTST----FRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------  323 (444)
Q Consensus       258 ~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------  323 (444)
                      +.....    ....+....................+...+... ..+.++||||+++..++.++..|...          
T Consensus       243 ~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~  321 (579)
T 3sqw_A          243 LDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKER-DSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEF  321 (579)
T ss_dssp             EESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHT-TTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEE
T ss_pred             EeecCccccccccccceEEEEecchhhhHHHHHHHHHHHHhhc-CCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEe
Confidence            221111    122333333333332333333333344333321 25789999999999999999999864          


Q ss_pred             ---cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchh
Q psy7952         324 ---VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK  400 (444)
Q Consensus       324 ---~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~  400 (444)
                         +++.+|..+++.|++|+.+|||||+++++|+|+|++++||++++|.+...|+||+||+||.|+.|.+++++.+.+..
T Consensus       322 hg~~~~~~R~~~~~~F~~g~~~vLVaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~  401 (579)
T 3sqw_A          322 HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELP  401 (579)
T ss_dssp             STTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHH
T ss_pred             cCCCCHHHHHHHHHHhhcCCCeEEEEcchhhcCCCcccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEEEcccHHH
Confidence               78999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             hHHHHHh
Q psy7952         401 SLEYVIK  407 (444)
Q Consensus       401 ~~~~~~~  407 (444)
                      .++.+.+
T Consensus       402 ~~~~l~~  408 (579)
T 3sqw_A          402 FVRELED  408 (579)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8888864

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=100.00  E-value=1.6e-45  Score=376.17  Aligned_cols=349  Identities=19%  Similarity=0.280  Sum_probs=256.1

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHcc-CCcEEEEccCCCcccccccccccceEEeCCCccccccCC----ccc
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLR-THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN----VRS  106 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~-~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~----~~~  106 (444)
                      .+..+.+++++ +|+.. ++++|.++++.++.+ .+++++.+|||+|||++        |++|+ ++.+....    ..+
T Consensus        79 l~~~l~~~l~~-~g~~~-~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~--------~~lpi-l~~l~~~~~~~~~~~  147 (563)
T 3i5x_A           79 LDKEIHKAITR-MEFPG-LTPVQQKTIKPILSSEDHDVIARAKTGTGKTFA--------FLIPI-FQHLINTKFDSQYMV  147 (563)
T ss_dssp             SCHHHHHHHHT-TCCSS-CCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHH--------HHHHH-HHHHHHTTTSSTTSC
T ss_pred             CCHHHHHHHHH-CCCCC-CCHHHHHHHHHHhcCCCCeEEEECCCCCCccHH--------HHHHH-HHHHHhccccccCCe
Confidence            34566777876 59998 669999999999942 28999999999999999        67776 44343332    234


Q ss_pred             eeEEEcchhhhhcccCccchHhhh---cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHH
Q psy7952         107 RNGWISPILSSFYLRFRDDKTSIV---TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYL  183 (444)
Q Consensus       107 ~vlil~P~~~L~~~~q~~~~~~~l---~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~  183 (444)
                      ++||++||++|+  .|+.+.+..+   ..+.....+..+.++.........+.     ..+++|+|+||+++.    ..+
T Consensus       148 ~~lil~Ptr~La--~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-----~~~~~Iiv~Tp~~l~----~~l  216 (563)
T 3i5x_A          148 KAVIVAPTRDLA--LQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMN-----KLRPNIVIATPGRLI----DVL  216 (563)
T ss_dssp             CEEEECSSHHHH--HHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHH-----HHCCSEEEECHHHHH----HHH
T ss_pred             eEEEEcCcHHHH--HHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHh-----cCCCCEEEECcHHHH----HHH
Confidence            789999999999  3334444443   12323366777888776554433322     236899999999985    222


Q ss_pred             HHH-HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhC----CCCcEEEEeccCCcchHHHHHHHhcCCCCeEE
Q psy7952         184 LQH-LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTG----NSIPIIALTATAEPSVKQDIISVLKFNKPYKV  258 (444)
Q Consensus       184 ~~~-~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~----~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~  258 (444)
                      ... ...+..+++||+||||++.+++  |++.+..+...+....    .+.|++++|||+++.....+...+.  .+..+
T Consensus       217 ~~~~~~~~~~~~~lViDEah~l~~~~--f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~--~~~~~  292 (563)
T 3i5x_A          217 EKYSNKFFRFVDYKVLDEADRLLEIG--FRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMN--KKECL  292 (563)
T ss_dssp             HHHHHHHCTTCCEEEEETHHHHTSTT--THHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCC--SSEEE
T ss_pred             HhccccccccceEEEEeCHHHHhccc--hHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcC--CCceE
Confidence            222 3456789999999999999888  8888888776665443    2578999999999877665544433  33222


Q ss_pred             Eec--CC----CCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh---------
Q psy7952         259 FKT--ST----FRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK---------  323 (444)
Q Consensus       259 ~~~--~~----~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~---------  323 (444)
                      ...  ..    ....+....................+...+... ..+.++||||++++.++.++..|...         
T Consensus       293 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~  371 (563)
T 3i5x_A          293 FLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKER-DSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILE  371 (563)
T ss_dssp             EEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHT-TTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEE
T ss_pred             EEeccCCCCccccccCceEEEECchhHhhHHHHHHHHHHHHhhc-CCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEE
Confidence            221  11    122233333333332333333333343333322 25789999999999999999999864         


Q ss_pred             ----cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         324 ----VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       324 ----~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                          +++.+|..+++.|++|+.+|||||+++++|+|+|++++||++++|.|...|+||+||+||.|+.|.+++++.+.+.
T Consensus       372 ~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~  451 (563)
T 3i5x_A          372 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDEL  451 (563)
T ss_dssp             ESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGH
T ss_pred             ecCCCCHHHHHHHHHHHhcCCCCEEEEcchhhcCCCcccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEEEchhHH
Confidence                7899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHh
Q psy7952         400 KSLEYVIK  407 (444)
Q Consensus       400 ~~~~~~~~  407 (444)
                      ..++.+.+
T Consensus       452 ~~~~~l~~  459 (563)
T 3i5x_A          452 PFVRELED  459 (563)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88888864

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=100.00  E-value=7.1e-46  Score=361.87  Aligned_cols=332  Identities=16%  Similarity=0.216  Sum_probs=247.6

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ...+.+++++ +|+.. |+++|.++++.++.+ +++++.+|||+|||++        +.+++ +..+.......++||++
T Consensus        16 ~~~l~~~l~~-~g~~~-~~~~Q~~~i~~~~~~-~~~lv~a~TGsGKT~~--------~~~~~-~~~l~~~~~~~~~lil~   83 (391)
T 1xti_A           16 KPELLRAIVD-CGFEH-PSEVQHECIPQAILG-MDVLCQAKSGMGKTAV--------FVLAT-LQQLEPVTGQVSVLVMC   83 (391)
T ss_dssp             CHHHHHHHHH-HSCCS-CCHHHHHHHHHHTTT-CCEEEECSSCSSHHHH--------HHHHH-HHHCCCCTTCCCEEEEC
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhcC-CcEEEECCCCCcHHHH--------HHHHH-HHhhcccCCCeeEEEEC
Confidence            4678888887 59997 669999999999999 9999999999999999        55555 33333333445779999


Q ss_pred             chhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCC
Q psy7952         113 PILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK  192 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~  192 (444)
                      |+++|+  .|+.+.+..+....+.+++..++|+.........+.     .+.++|+|+||+++.    ..+......+.+
T Consensus        84 P~~~L~--~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-----~~~~~iiv~T~~~l~----~~~~~~~~~~~~  152 (391)
T 1xti_A           84 HTRELA--FQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLK-----KNCPHIVVGTPGRIL----ALARNKSLNLKH  152 (391)
T ss_dssp             SCHHHH--HHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHH-----HSCCSEEEECHHHHH----HHHHTTSSCCTT
T ss_pred             CCHHHH--HHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHh-----cCCCCEEEECHHHHH----HHHHcCCccccc
Confidence            999999  333444444422222488999999887665544432     245799999999975    222233344678


Q ss_pred             ccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCC---CCCce
Q psy7952         193 LAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTF---RSNLF  269 (444)
Q Consensus       193 ~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~---~~~~~  269 (444)
                      +++||+||||++.++. .+.   ..+..++...+...+++++|||+++.....+..++.  .+..+......   ...+.
T Consensus       153 ~~~vViDEaH~~~~~~-~~~---~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~  226 (391)
T 1xti_A          153 IKHFILDECDKMLEQL-DMR---RDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQ--DPMEIFVDDETKLTLHGLQ  226 (391)
T ss_dssp             CSEEEECSHHHHTSSH-HHH---HHHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCS--SCEEEECCCCCCCCCTTCE
T ss_pred             cCEEEEeCHHHHhhcc-chH---HHHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcC--CCeEEEecCccccCcccce
Confidence            9999999999987631 133   334455556666789999999999987776666653  44444433222   12233


Q ss_pred             EEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcC
Q psy7952         270 YDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRG  339 (444)
Q Consensus       270 ~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g  339 (444)
                      ..+.... ...+...+.+++..    .  .++++||||+++++++.+++.|...          ++..+|..+++.|++|
T Consensus       227 ~~~~~~~-~~~~~~~l~~~l~~----~--~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~  299 (391)
T 1xti_A          227 QYYVKLK-DNEKNRKLFDLLDV----L--EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDF  299 (391)
T ss_dssp             EEEEECC-GGGHHHHHHHHHHH----S--CCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             EEEEEcC-chhHHHHHHHHHHh----c--CCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcC
Confidence            2222222 23333344444433    2  5789999999999999999999876          7899999999999999


Q ss_pred             CccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchh
Q psy7952         340 EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK  400 (444)
Q Consensus       340 ~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~  400 (444)
                      +.+|||||+++++|+|+|++++||++++|.|...|+||+||+||.|+.|.+++++++.+..
T Consensus       300 ~~~vlv~T~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~  360 (391)
T 1xti_A          300 QRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDA  360 (391)
T ss_dssp             CCSEEEESCCCSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSSSCCCCEEEEEECSHHHH
T ss_pred             CCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHhcccccCCCCceEEEEEEcccchH
Confidence            9999999999999999999999999999999999999999999999999999999876543

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=100.00  E-value=2e-46  Score=368.55  Aligned_cols=336  Identities=17%  Similarity=0.212  Sum_probs=240.0

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ...+.+.+++ +|+.. |+++|.++++.++.| +++++.+|||+|||++        |.+++ ++.+.......+++|++
T Consensus        48 ~~~~~~~l~~-~~~~~-~~~~Q~~~i~~~~~~-~~~lv~a~TGsGKT~~--------~~~~~-~~~~~~~~~~~~~lil~  115 (414)
T 3eiq_A           48 SESLLRGIYA-YGFEK-PSAIQQRAILPCIKG-YDVIAQAQSGTGKTAT--------FAISI-LQQIELDLKATQALVLA  115 (414)
T ss_dssp             CHHHHHHHHH-TTCCS-CCHHHHHHHHHHHTT-CCEEECCCSCSSSHHH--------HHHHH-HHHCCTTSCSCCEEEEC
T ss_pred             CHHHHHHHHH-cCCCC-CCHHHHHHhHHHhCC-CCEEEECCCCCcccHH--------HHHHH-HHHHhhcCCceeEEEEe
Confidence            5567788887 69998 679999999999999 8999999999999999        55555 33344333455779999


Q ss_pred             chhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhh
Q psy7952         113 PILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRY  190 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~  190 (444)
                      |+++|+  .|+.+.+..+  ..+   ..+....++..........     ....++|+|+||+++.    ..+.......
T Consensus       116 P~~~L~--~q~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~-----~~~~~~iiv~T~~~l~----~~l~~~~~~~  181 (414)
T 3eiq_A          116 PTRELA--QQIQKVVMALGDYMG---ASCHACIGGTNVRAEVQKL-----QMEAPHIIVGTPGRVF----DMLNRRYLSP  181 (414)
T ss_dssp             SSHHHH--HHHHHHHHHHGGGSC---CCEEECCCCTTHHHHHHHH-----TTTCCSEEEECHHHHH----HHHHHTSSCS
T ss_pred             ChHHHH--HHHHHHHHHHhcccC---ceEEEEECCcchHHHHHHH-----hcCCCCEEEECHHHHH----HHHHcCCccc
Confidence            999999  3334444444  234   7777777777654433222     1367899999999985    4444444456


Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecC--CCCCCc
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTS--TFRSNL  268 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~--~~~~~~  268 (444)
                      .++++||+||+|++.+++  +.   ..+..++...+.+.+++++|||+++........++  .++..+....  .....+
T Consensus       182 ~~~~~vViDEah~~~~~~--~~---~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~  254 (414)
T 3eiq_A          182 KYIKMFVLDEADEMLSRG--FK---DQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFM--RDPIRILVKKEELTLEGI  254 (414)
T ss_dssp             TTCCEEEECSHHHHHHTT--TH---HHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTC--SSCEEECCCCCCCCTTSC
T ss_pred             ccCcEEEEECHHHhhccC--cH---HHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHc--CCCEEEEecCCccCCCCc
Confidence            779999999999987766  44   33445555666779999999999887766554443  3443333222  222333


Q ss_pred             eEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhc
Q psy7952         269 FYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMR  338 (444)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~  338 (444)
                      ............+...+    ..++...  ..+++||||+++++++.+++.|...          ++..+|..+++.|++
T Consensus       255 ~~~~~~~~~~~~~~~~l----~~~~~~~--~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~  328 (414)
T 3eiq_A          255 RQFYINVEREEWKLDTL----CDLYETL--TITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRS  328 (414)
T ss_dssp             CEEEEECSSSTTHHHHH----HHHHHSS--CCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSC
T ss_pred             eEEEEEeChHHhHHHHH----HHHHHhC--CCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHc
Confidence            33344433333333333    3333333  4679999999999999999999876          778999999999999


Q ss_pred             CCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         339 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       339 g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      |+.+|||||+++++|+|+|++++||+++.|.|...|+||+||+||.|+.|.+++++++.+...++.+.+
T Consensus       329 g~~~vlv~T~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~  397 (414)
T 3eiq_A          329 GSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIET  397 (414)
T ss_dssp             C---CEEECSSCC--CCGGGCSCEEESSCCSSTHHHHHHSCCC-------CEEEEECSTHHHHHHHHHH
T ss_pred             CCCcEEEECCccccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEEEcHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999988877776643

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=100.00  E-value=5.3e-45  Score=356.83  Aligned_cols=336  Identities=17%  Similarity=0.249  Sum_probs=249.0

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ...+.+++.+ +|+.. |+++|.++++.++++ +++++.+|||+|||++        +.+|+ +..+.......+++|++
T Consensus        29 ~~~l~~~l~~-~g~~~-~~~~Q~~~i~~i~~~-~~~li~a~TGsGKT~~--------~~~~~-~~~~~~~~~~~~~lil~   96 (400)
T 1s2m_A           29 KRELLMGIFE-AGFEK-PSPIQEEAIPVAITG-RDILARAKNGTGKTAA--------FVIPT-LEKVKPKLNKIQALIMV   96 (400)
T ss_dssp             CHHHHHHHHH-TTCCS-CCHHHHHHHHHHHHT-CCEEEECCTTSCHHHH--------HHHHH-HHHCCTTSCSCCEEEEC
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhcC-CCEEEECCCCcHHHHH--------HHHHH-HHHHhhccCCccEEEEc
Confidence            5677788887 59997 669999999999999 8999999999999999        55555 33333333445779999


Q ss_pred             chhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCC
Q psy7952         113 PILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK  192 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~  192 (444)
                      |+++|+  .|+.+.+..+. ....+.+..+.|+........      .....++|+|+||+++.    ..+......+.+
T Consensus        97 P~~~L~--~q~~~~~~~~~-~~~~~~~~~~~g~~~~~~~~~------~~~~~~~Ivv~T~~~l~----~~~~~~~~~~~~  163 (400)
T 1s2m_A           97 PTRELA--LQTSQVVRTLG-KHCGISCMVTTGGTNLRDDIL------RLNETVHILVGTPGRVL----DLASRKVADLSD  163 (400)
T ss_dssp             SSHHHH--HHHHHHHHHHT-TTTTCCEEEECSSSCHHHHHH------HTTSCCSEEEECHHHHH----HHHHTTCSCCTT
T ss_pred             CCHHHH--HHHHHHHHHHh-cccCceEEEEeCCcchHHHHH------HhcCCCCEEEEchHHHH----HHHHhCCccccc
Confidence            999999  22233333331 111278888888876543322      23467899999999974    223333345678


Q ss_pred             ccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecC-CCCCCceEE
Q psy7952         193 LAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTS-TFRSNLFYD  271 (444)
Q Consensus       193 ~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~-~~~~~~~~~  271 (444)
                      +++||+||+|++.+.+  +..   .+..+...++...+++++|||++....+.+...+.  .+..+.... ....++...
T Consensus       164 ~~~vIiDEaH~~~~~~--~~~---~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~  236 (400)
T 1s2m_A          164 CSLFIMDEADKMLSRD--FKT---IIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLH--KPYEINLMEELTLKGITQY  236 (400)
T ss_dssp             CCEEEEESHHHHSSHH--HHH---HHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCS--SCEEESCCSSCBCTTEEEE
T ss_pred             CCEEEEeCchHhhhhc--hHH---HHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcC--CCeEEEeccccccCCceeE
Confidence            9999999999986543  443   34445556666789999999999887777666553  443332222 222333333


Q ss_pred             EEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCc
Q psy7952         272 VIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEI  341 (444)
Q Consensus       272 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~  341 (444)
                      ..... ...+...+..++    ...  ..+++||||+++++++.+++.|...          ++..+|..+++.|++|+.
T Consensus       237 ~~~~~-~~~k~~~l~~~~----~~~--~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~  309 (400)
T 1s2m_A          237 YAFVE-ERQKLHCLNTLF----SKL--QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKV  309 (400)
T ss_dssp             EEECC-GGGHHHHHHHHH----HHS--CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSS
T ss_pred             EEEec-hhhHHHHHHHHH----hhc--CCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCC
Confidence            33222 222333333333    322  4679999999999999999999875          789999999999999999


Q ss_pred             cEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         342 NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       342 ~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      +|||||+++++|+|+|++++||++++|.|...|+||+||+||.|+.|.+++++++.+...+..+.+
T Consensus       310 ~vLv~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~  375 (400)
T 1s2m_A          310 RTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQ  375 (400)
T ss_dssp             SEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHH
T ss_pred             cEEEEcCccccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEEeccchHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999888777754

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=100.00  E-value=3.2e-45  Score=359.73  Aligned_cols=336  Identities=17%  Similarity=0.220  Sum_probs=245.6

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHcc-CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEE
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLR-THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGW  110 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~-~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vli  110 (444)
                      ....+.+++++ +|+.. |+++|.++++.++.+ ++++++.+|||+|||++        |.+|+ +..+...+..++++|
T Consensus        32 l~~~l~~~l~~-~g~~~-~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~--------~~~~~-~~~~~~~~~~~~~li  100 (412)
T 3fht_A           32 LKPQLLQGVYA-MGFNR-PSKIQENALPLMLAEPPQNLIAQSQSGTGKTAA--------FVLAM-LSQVEPANKYPQCLC  100 (412)
T ss_dssp             CCHHHHHHHHH-TTCCS-CCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHH--------HHHHH-HHHCCTTSCSCCEEE
T ss_pred             CCHHHHHHHHH-cCCCC-CCHHHHHHHHHHhcCCCCeEEEECCCCchHHHH--------HHHHH-HHHhhhcCCCCCEEE
Confidence            35667788887 69998 779999999999986 48999999999999999        55555 444554555567899


Q ss_pred             EcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH-HHHh
Q psy7952         111 ISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ-HLVR  189 (444)
Q Consensus       111 l~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~-~~~~  189 (444)
                      ++|+++|+  .|+.+.++.+....+.+.+....++......         ....++|+|+||+++.    ..+.. ....
T Consensus       101 l~P~~~L~--~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~ivv~T~~~l~----~~~~~~~~~~  165 (412)
T 3fht_A          101 LSPTYELA--LQTGKVIEQMGKFYPELKLAYAVRGNKLERG---------QKISEQIVIGTPGTVL----DWCSKLKFID  165 (412)
T ss_dssp             ECSSHHHH--HHHHHHHHHHTTTSTTCCEEEECTTCCCCTT---------CCCCCSEEEECHHHHH----HHHTTSCSSC
T ss_pred             ECCCHHHH--HHHHHHHHHHHhhcccceEEEeecCcchhhh---------hcCCCCEEEECchHHH----HHHHhcCCcC
Confidence            99999999  2223334444222233777777776554321         1346799999999974    21111 2234


Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEe--cCCCCCC
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFK--TSTFRSN  267 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~--~~~~~~~  267 (444)
                      +.++++||+||+|++.+... +...+.   .+....+.+.+++++|||+++.........+.  .+..+..  .......
T Consensus       166 ~~~~~~iViDEah~~~~~~~-~~~~~~---~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~  239 (412)
T 3fht_A          166 PKKIKVFVLDEADVMIATQG-HQDQSI---RIQRMLPRNCQMLLFSATFEDSVWKFAQKVVP--DPNVIKLKREEETLDT  239 (412)
T ss_dssp             GGGCCEEEEETHHHHHSTTT-THHHHH---HHHHTSCTTCEEEEEESCCCHHHHHHHHHHSS--SCEEECCCGGGSSCTT
T ss_pred             hhhCcEEEEeCHHHHhhcCC-cHHHHH---HHHhhCCCCceEEEEEeecCHHHHHHHHHhcC--CCeEEeeccccccccC
Confidence            56899999999999876321 443333   44455667789999999999987776666543  3333322  2223344


Q ss_pred             ceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHh
Q psy7952         268 LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFM  337 (444)
Q Consensus       268 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~  337 (444)
                      +................+...+...      .++++||||+++++++.++..|...          ++..+|..+++.|+
T Consensus       240 ~~~~~~~~~~~~~~~~~l~~~~~~~------~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~  313 (412)
T 3fht_A          240 IKQYYVLCSSRDEKFQALCNLYGAI------TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFR  313 (412)
T ss_dssp             EEEEEEECSSHHHHHHHHHHHHHHH------SSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHH
T ss_pred             ceEEEEEcCChHHHHHHHHHHHhhc------CCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHH
Confidence            4444444443344444444444432      4679999999999999999999876          88999999999999


Q ss_pred             cCCccEEEEcCccccccccCCccEEEEeCCC------CCHHHHHHHhccCCCCCCceeEEEEecccc-hhhHHHH
Q psy7952         338 RGEINVITATISFGMGIDRQNVRFVVHWGMP------SSIPAYYQESGRAGRDGLQSYCRIYHSEHS-KKSLEYV  405 (444)
Q Consensus       338 ~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p------~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~-~~~~~~~  405 (444)
                      +|+.+|||||+++++|+|+|++++||+++.|      .+...|+||+||+||.|+.|.+++++++.+ ...++.+
T Consensus       314 ~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i  388 (412)
T 3fht_A          314 EGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRI  388 (412)
T ss_dssp             TTSCSEEEECGGGTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHH
T ss_pred             CCCCcEEEEcCccccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChhhHHHHHHH
Confidence            9999999999999999999999999999999      578999999999999999999999998765 4444443

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=100.00  E-value=1.1e-44  Score=353.70  Aligned_cols=335  Identities=16%  Similarity=0.248  Sum_probs=243.9

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccC-CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRT-HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~-~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      ...+.+++++ +|+.. |+++|.++++.++.+. +++++.+|||+|||++        +.+++ +..+...+..+++||+
T Consensus        13 ~~~l~~~l~~-~~~~~-~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~--------~~~~~-~~~~~~~~~~~~~lil   81 (395)
T 3pey_A           13 APELLKGIYA-MKFQK-PSKIQERALPLLLHNPPRNMIAQSQSGTGKTAA--------FSLTM-LTRVNPEDASPQAICL   81 (395)
T ss_dssp             CHHHHHHHHH-TTCCS-CCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHH--------HHHHH-HHHCCTTCCSCCEEEE
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHH--------HHHHH-HHHhccCCCCccEEEE
Confidence            5677888887 59998 7799999999999874 7899999999999999        55555 3334444455678999


Q ss_pred             cchhhhhcccCccchHhhh-c-CCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh
Q psy7952         112 SPILSSFYLRFRDDKTSIV-T-GRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR  189 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l-~-~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~  189 (444)
                      +|+++|+     .|+.+.+ . .....+.+....++......          ..+++|+|+||+++.    ..+......
T Consensus        82 ~P~~~L~-----~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~iiv~T~~~l~----~~~~~~~~~  142 (395)
T 3pey_A           82 APSRELA-----RQTLEVVQEMGKFTKITSQLIVPDSFEKNK----------QINAQVIVGTPGTVL----DLMRRKLMQ  142 (395)
T ss_dssp             CSSHHHH-----HHHHHHHHHHTTTSCCCEEEESTTSSCTTS----------CBCCSEEEECHHHHH----HHHHTTCBC
T ss_pred             CCCHHHH-----HHHHHHHHHHhcccCeeEEEEecCchhhhc----------cCCCCEEEEcHHHHH----HHHHcCCcc
Confidence            9999999     4444444 1 11222667777766543221          346899999999974    333333445


Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCce
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLF  269 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  269 (444)
                      +.++++||+||||++.+... +...+   ..+....+.+.+++++|||+++.........+.................+.
T Consensus       143 ~~~~~~iIiDEah~~~~~~~-~~~~~---~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (395)
T 3pey_A          143 LQKIKIFVLDEADNMLDQQG-LGDQC---IRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIK  218 (395)
T ss_dssp             CTTCCEEEEETHHHHHHSTT-HHHHH---HHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGGGCSCTTEE
T ss_pred             cccCCEEEEEChhhhcCccc-cHHHH---HHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEcccccccccccc
Confidence            67899999999999876321 44433   344555666789999999999877766655543222222222222233333


Q ss_pred             EEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcC
Q psy7952         270 YDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRG  339 (444)
Q Consensus       270 ~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g  339 (444)
                      ...........    ....+..++...  .++++||||+++++++.+++.|...          ++..+|..+++.|++|
T Consensus       219 ~~~~~~~~~~~----~~~~l~~~~~~~--~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g  292 (395)
T 3pey_A          219 QLYMDCKNEAD----KFDVLTELYGLM--TIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREG  292 (395)
T ss_dssp             EEEEECSSHHH----HHHHHHHHHTTT--TSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTT
T ss_pred             EEEEEcCchHH----HHHHHHHHHHhc--cCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCC
Confidence            33333322222    233444444433  5689999999999999999999876          8899999999999999


Q ss_pred             CccEEEEcCccccccccCCccEEEEeCCCC------CHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         340 EINVITATISFGMGIDRQNVRFVVHWGMPS------SIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       340 ~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~------s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      +.+|||||+++++|+|+|++++||++++|.      |...|+||+||+||.|+.|.+++++.+.+...+...++
T Consensus       293 ~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~  366 (395)
T 3pey_A          293 RSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQ  366 (395)
T ss_dssp             SCCEEEECGGGSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHH
T ss_pred             CCCEEEECChhhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechHHHHHHHHHH
Confidence            999999999999999999999999999998      99999999999999999999999998765544433333

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=100.00  E-value=1.1e-43  Score=343.17  Aligned_cols=330  Identities=18%  Similarity=0.287  Sum_probs=248.0

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ...+.+++++ +|+.. |+++|.++++.++++++++++.+|||+|||++        +.+++ +..+. .+...+++|++
T Consensus        14 ~~~~~~~l~~-~g~~~-~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~--------~~~~~-~~~~~-~~~~~~~lil~   81 (367)
T 1hv8_A           14 SDNILNAIRN-KGFEK-PTDIQMKVIPLFLNDEYNIVAQARTGSGKTAS--------FAIPL-IELVN-ENNGIEAIILT   81 (367)
T ss_dssp             CHHHHHHHHH-HTCCS-CCHHHHHHHHHHHHTCSEEEEECCSSSSHHHH--------HHHHH-HHHSC-SSSSCCEEEEC
T ss_pred             CHHHHHHHHH-cCCCC-CCHHHHHHHHHHhCCCCCEEEECCCCChHHHH--------HHHHH-HHHhc-ccCCCcEEEEc
Confidence            5677888887 59987 66999999999998867999999999999999        44444 22222 22345779999


Q ss_pred             chhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhh
Q psy7952         113 PILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRY  190 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~  190 (444)
                      |+++|+     .+..+.+  ..+...+.+..+.|+..........       .+++|+|+||+++.    ..+......+
T Consensus        82 P~~~L~-----~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~-------~~~~iiv~T~~~l~----~~~~~~~~~~  145 (367)
T 1hv8_A           82 PTRELA-----IQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL-------KNANIVVGTPGRIL----DHINRGTLNL  145 (367)
T ss_dssp             SCHHHH-----HHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH-------HTCSEEEECHHHHH----HHHHTTCSCT
T ss_pred             CCHHHH-----HHHHHHHHHHhCCCCceEEEEECCcchHHHHhhc-------CCCCEEEecHHHHH----HHHHcCCccc
Confidence            999999     4444444  1122237888888887765443333       26799999999974    3333333446


Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceE
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFY  270 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  270 (444)
                      .++++||+||+|++.+++  +..   .+..++...+.+.+++++|||+++...+.+..+++  ....+.  .....++..
T Consensus       146 ~~~~~iIiDEah~~~~~~--~~~---~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~--~~~~~~--~~~~~~~~~  216 (367)
T 1hv8_A          146 KNVKYFILDEADEMLNMG--FIK---DVEKILNACNKDKRILLFSATMPREILNLAKKYMG--DYSFIK--AKINANIEQ  216 (367)
T ss_dssp             TSCCEEEEETHHHHHTTT--THH---HHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCC--SEEEEE--CCSSSSSEE
T ss_pred             ccCCEEEEeCchHhhhhc--hHH---HHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcC--CCeEEE--ecCCCCceE
Confidence            789999999999997766  443   34445556666789999999999887776666543  222222  222233333


Q ss_pred             EEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCC
Q psy7952         271 DVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGE  340 (444)
Q Consensus       271 ~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~  340 (444)
                      ...... ...+.    ..+...+.   ..+.++||||+++++++.+++.|.+.          ++..+|..+++.|++|+
T Consensus       217 ~~~~~~-~~~~~----~~l~~~l~---~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~  288 (367)
T 1hv8_A          217 SYVEVN-ENERF----EALCRLLK---NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKK  288 (367)
T ss_dssp             EEEECC-GGGHH----HHHHHHHC---STTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTS
T ss_pred             EEEEeC-hHHHH----HHHHHHHh---cCCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCC
Confidence            333222 12222    33333333   25789999999999999999999875          78999999999999999


Q ss_pred             ccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         341 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       341 ~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      .+|||||+++++|+|+|++++||++++|.|...|+||+||+||.|+.|.+++++++.+...+..+.+
T Consensus       289 ~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~  355 (367)
T 1hv8_A          289 IRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIER  355 (367)
T ss_dssp             SSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHH
T ss_pred             CeEEEECChhhcCCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEEEEcHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999998888777754

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=100.00  E-value=3.3e-46  Score=364.51  Aligned_cols=337  Identities=17%  Similarity=0.263  Sum_probs=139.7

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      .+..+.+++.. +|+.. |+++|.++++.++.+ +++++.+|||+|||++        |.+|+ +..+......+++||+
T Consensus        28 l~~~l~~~l~~-~g~~~-~~~~Q~~~i~~i~~~-~~~lv~~~TGsGKT~~--------~~~~~-~~~l~~~~~~~~~lil   95 (394)
T 1fuu_A           28 LDENLLRGVFG-YGFEE-PSAIQQRAIMPIIEG-HDVLAQAQSGTGKTGT--------FSIAA-LQRIDTSVKAPQALML   95 (394)
T ss_dssp             CCHHHHHHHHH-HTCCS-CCHHHHHHHHHHHHT-CCEEECCCSSHHHHHH--------HHHHH-HHHCCTTCCSCCEEEE
T ss_pred             CCHHHHHHHHH-cCCCC-CCHHHHHHHHHHhCC-CCEEEECCCCChHHHH--------HHHHH-HHHhhccCCCCCEEEE
Confidence            35678888887 69987 669999999999999 9999999999999999        55555 3334444445678999


Q ss_pred             cchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         112 SPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      +|+++|+  .|+.+.+..+. ....+.+..++|+.........+.       +++|+|+||+++.    ..+........
T Consensus        96 ~P~~~L~--~q~~~~~~~~~-~~~~~~~~~~~g~~~~~~~~~~~~-------~~~i~v~T~~~l~----~~~~~~~~~~~  161 (394)
T 1fuu_A           96 APTRELA--LQIQKVVMALA-FHMDIKVHACIGGTSFVEDAEGLR-------DAQIVVGTPGRVF----DNIQRRRFRTD  161 (394)
T ss_dssp             CSSHHHH--HHHHHHHHHHT-TTSCCCEEEECSSCCHHHHHHHHH-------HCSEEEECHHHHH----HHHHTTSSCCT
T ss_pred             cCCHHHH--HHHHHHHHHHh-ccCCeeEEEEeCCCchHHHHhhcC-------CCCEEEECHHHHH----HHHHhCCcchh
Confidence            9999999  22233333331 112388888998887655443332       5789999999974    33333334456


Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCC--CCCCce
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST--FRSNLF  269 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~--~~~~~~  269 (444)
                      ++++||+||+|++.+++  +...+.   .+....+...+++++|||+++...+....++.  .+..+.....  ..+.+.
T Consensus       162 ~~~~vIiDEah~~~~~~--~~~~~~---~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~  234 (394)
T 1fuu_A          162 KIKMFILDEADEMLSSG--FKEQIY---QIFTLLPPTTQVVLLSATMPNDVLEVTTKFMR--NPVRILVKKDELTLEGIK  234 (394)
T ss_dssp             TCCEEEEETHHHHHHTT--CHHHHH---HHHHHSCTTCEEEEECSSCCHHHHHHHHHHCC--SCEEEEECC---------
T ss_pred             hCcEEEEEChHHhhCCC--cHHHHH---HHHHhCCCCceEEEEEEecCHHHHHHHHHhcC--CCeEEEecCccccCCCce
Confidence            89999999999987766  554444   44455666789999999999877766665543  4443333221  112222


Q ss_pred             EEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcC
Q psy7952         270 YDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRG  339 (444)
Q Consensus       270 ~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g  339 (444)
                      ............    ...+..++...  ..+++||||+++++++.+++.|...          ++..+|..+++.|++|
T Consensus       235 ~~~~~~~~~~~~----~~~l~~~~~~~--~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~  308 (394)
T 1fuu_A          235 QFYVNVEEEEYK----YECLTDLYDSI--SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSG  308 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEEEcCchhhH----HHHHHHHHhcC--CCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCC
Confidence            111111111112    22233333222  4679999999999999999999765          7789999999999999


Q ss_pred             CccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         340 EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       340 ~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      +.+|||||+++++|+|+|++++||++++|.|...|+||+||+||.|+.|.+++++++.+...+..+.+
T Consensus       309 ~~~vlv~T~~~~~Gldi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~  376 (394)
T 1fuu_A          309 SSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEK  376 (394)
T ss_dssp             --------------------------------------------------------------------
T ss_pred             CCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHcCcccCCCCCceEEEEEchhHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999988777666643

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=100.00  E-value=5.1e-44  Score=341.52  Aligned_cols=321  Identities=17%  Similarity=0.229  Sum_probs=240.6

Q ss_pred             HHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcc
Q psy7952          34 QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISP  113 (444)
Q Consensus        34 ~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P  113 (444)
                      +.+.+++++ +|+.. ++++|.++++.++++ +++++.+|||+|||++        +.+++    +..+   .+++|++|
T Consensus         3 ~~i~~~l~~-~g~~~-l~~~Q~~~i~~i~~~-~~~lv~~~TGsGKT~~--------~~~~~----~~~~---~~~liv~P   64 (337)
T 2z0m_A            3 EKIEQAIRE-MGFKN-FTEVQSKTIPLMLQG-KNVVVRAKTGSGKTAA--------YAIPI----LELG---MKSLVVTP   64 (337)
T ss_dssp             HHHHHHHHH-TTCCS-CCHHHHHHHHHHHTT-CCEEEECCTTSSHHHH--------HHHHH----HHHT---CCEEEECS
T ss_pred             HHHHHHHHH-cCCCC-CCHHHHHHHHHHhcC-CCEEEEcCCCCcHHHH--------HHHHH----Hhhc---CCEEEEeC
Confidence            567888887 69998 569999999999999 8999999999999999        66666    3333   34599999


Q ss_pred             hhhhhcccCccchHhhh-cC-CCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         114 ILSSFYLRFRDDKTSIV-TG-RSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       114 ~~~L~~~~q~~~~~~~l-~~-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      +++|+     .|+.+.+ .. ....+.+..++|+..........       ..++|+|+||+++.    ..+......+.
T Consensus        65 ~~~L~-----~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~i~v~T~~~l~----~~~~~~~~~~~  128 (337)
T 2z0m_A           65 TRELT-----RQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRV-------RNADIVVATPGRLL----DLWSKGVIDLS  128 (337)
T ss_dssp             SHHHH-----HHHHHHHHHHTTTSCCCEEEECTTSCHHHHHHHH-------TTCSEEEECHHHHH----HHHHTTSCCGG
T ss_pred             CHHHH-----HHHHHHHHHHhhhcCCcEEEEECCcchHHHHhhc-------CCCCEEEECHHHHH----HHHHcCCcchh
Confidence            99999     4554444 11 12237888888887765443322       35899999999974    22222333467


Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEE
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYD  271 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~  271 (444)
                      ++++||+||+|++.+++  +...   +..++...+...+++++|||+++...+.+..++.  .+..+ ......+++...
T Consensus       129 ~~~~iViDEah~~~~~~--~~~~---~~~~~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~--~~~~~-~~~~~~~~~~~~  200 (337)
T 2z0m_A          129 SFEIVIIDEADLMFEMG--FIDD---IKIILAQTSNRKITGLFSATIPEEIRKVVKDFIT--NYEEI-EACIGLANVEHK  200 (337)
T ss_dssp             GCSEEEEESHHHHHHTT--CHHH---HHHHHHHCTTCSEEEEEESCCCHHHHHHHHHHSC--SCEEE-ECSGGGGGEEEE
T ss_pred             hCcEEEEEChHHhhccc--cHHH---HHHHHhhCCcccEEEEEeCcCCHHHHHHHHHhcC--Cceee-ecccccCCceEE
Confidence            88999999999998776  4433   3444555666688899999999987777766653  33222 222333344443


Q ss_pred             EEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------cCHHHHHHHHHHHhcCCccEEE
Q psy7952         272 VIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------VNKHERSRVQESFMRGEINVIT  345 (444)
Q Consensus       272 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------~~~~~r~~~~~~f~~g~~~vLv  345 (444)
                      .......   .......    +..  ..++++||||+++++++.+++.|...      ++..+|..+++.|++|+.++||
T Consensus       201 ~~~~~~~---~~~~~~~----~~~--~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv  271 (337)
T 2z0m_A          201 FVHVKDD---WRSKVQA----LRE--NKDKGVIVFVRTRNRVAKLVRLFDNAIELRGDLPQSVRNRNIDAFREGEYDMLI  271 (337)
T ss_dssp             EEECSSS---SHHHHHH----HHT--CCCSSEEEECSCHHHHHHHHTTCTTEEEECTTSCHHHHHHHHHHHHTTSCSEEE
T ss_pred             EEEeChH---HHHHHHH----HHh--CCCCcEEEEEcCHHHHHHHHHHhhhhhhhcCCCCHHHHHHHHHHHHcCCCcEEE
Confidence            3333221   1111122    222  25789999999999999999988754      8899999999999999999999


Q ss_pred             EcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHH
Q psy7952         346 ATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI  406 (444)
Q Consensus       346 aT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  406 (444)
                      ||+++++|+|+|++++||++++|.|...|+||+||+||.|+.|.+++++. .+...++.+.
T Consensus       272 ~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~gR~g~~g~~~~~~~-~~~~~~~~i~  331 (337)
T 2z0m_A          272 TTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFIL-NEYWLEKEVK  331 (337)
T ss_dssp             ECHHHHTTCCCCCBSEEEESSCCSSHHHHHHHHTTBCGGGCCEEEEEEES-SCHHHHHHHC
T ss_pred             EcCccccCCCccCCCEEEEecCCCCHHHhhHhcCccccCCCCceEEEEEe-CcHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999 6665555553

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=100.00  E-value=3.4e-45  Score=366.40  Aligned_cols=329  Identities=17%  Similarity=0.217  Sum_probs=135.0

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHcc-CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLR-THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~-~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      ...+.+++.+ +|+.. |+++|.++++.++.+ .+++++++|||+|||++        |.+|+ +..+...+..+++||+
T Consensus       100 ~~~l~~~l~~-~g~~~-p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~--------~~l~i-l~~l~~~~~~~~~lil  168 (479)
T 3fmp_B          100 KPQLLQGVYA-MGFNR-PSKIQENALPLMLAEPPQNLIAQSQSGTGKTAA--------FVLAM-LSQVEPANKYPQCLCL  168 (479)
T ss_dssp             CHHHHHHHHH-TTCCS-CCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHH--------HHHHH-HTTCCTTSCSCCEEEE
T ss_pred             CHHHHHHHHH-cCCCC-CCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHH--------HHHHH-HHHHhhcCCCCcEEEE
Confidence            5667788887 69998 789999999999986 48999999999999999        66666 4445555555678999


Q ss_pred             cchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH--HHh
Q psy7952         112 SPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH--LVR  189 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~--~~~  189 (444)
                      +|+++|+  .|+.+.++.+......+.+....++......         .....+|+|+||+++.    . .+..  ...
T Consensus       169 ~Pt~~La--~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~Ivv~Tp~~l~----~-~l~~~~~~~  232 (479)
T 3fmp_B          169 SPTYELA--LQTGKVIEQMGKFYPELKLAYAVRGNKLERG---------QKISEQIVIGTPGTVL----D-WCSKLKFID  232 (479)
T ss_dssp             CSSHHHH--HHHHHHHHHHHTTSTTCCEEEESTTCCCCTT---------CCCCCSEEEECHHHHH----H-HHTTSCCCC
T ss_pred             eChHHHH--HHHHHHHHHHHhhCCCceEEEEeCCcccccc---------ccCCCCEEEECchHHH----H-HHHhcCCcC
Confidence            9999999  2234445555222223666666665543211         1245789999999974    1 2212  334


Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCC--CCCC
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTST--FRSN  267 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~--~~~~  267 (444)
                      +.++++||+||+|++.+... +...   +..+....+.+.+++++|||++..........+  +.+..+.....  ....
T Consensus       233 ~~~~~~iViDEah~~~~~~~-~~~~---~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~--~~~~~i~~~~~~~~~~~  306 (479)
T 3fmp_B          233 PKKIKVFVLDEADVMIATQG-HQDQ---SIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVV--PDPNVIKLKREEETLDT  306 (479)
T ss_dssp             GGGCCEEEECCHHHHHTSTT-HHHH---HHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHS--SSEEEEEEC--------
T ss_pred             cccCCEEEEECHHHHhhcCC-cHHH---HHHHHhhCCccceEEEEeCCCCHHHHHHHHHHc--CCCeEEeccccccCcCC
Confidence            57899999999999875321 4433   334555667779999999999988776655543  44433332221  1112


Q ss_pred             ceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHh
Q psy7952         268 LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFM  337 (444)
Q Consensus       268 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~  337 (444)
                      +...+..........    ..+..++...  ...++||||++++.++.++..|...          ++..+|..+++.|+
T Consensus       307 ~~~~~~~~~~~~~~~----~~l~~~~~~~--~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~  380 (479)
T 3fmp_B          307 IKQYYVLCSSRDEKF----QALCNLYGAI--TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFR  380 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ceEEEEEeCCHHHHH----HHHHHHHhhc--cCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHH
Confidence            221222211111222    2222222222  4678999999999999999999765          78899999999999


Q ss_pred             cCCccEEEEcCccccccccCCccEEEEeCCC------CCHHHHHHHhccCCCCCCceeEEEEecccchh
Q psy7952         338 RGEINVITATISFGMGIDRQNVRFVVHWGMP------SSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK  400 (444)
Q Consensus       338 ~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p------~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~  400 (444)
                      +|+.+|||||+++++|+|+|++++||++|+|      .+...|+||+||+||.|+.|.+++++++.+..
T Consensus       381 ~g~~~iLv~T~~~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~~~  449 (479)
T 3fmp_B          381 EGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSM  449 (479)
T ss_dssp             ---------------------------------------------------------------------
T ss_pred             cCCCcEEEEccccccCCccccCCEEEEecCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcchH
Confidence            9999999999999999999999999999999      46789999999999999999999999876533

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=100.00  E-value=4.5e-43  Score=344.64  Aligned_cols=316  Identities=16%  Similarity=0.238  Sum_probs=227.9

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      -+++.+.+++.+|++  |+++|.++++.++++ +++++.+|||+|||++        |++++ +...   ...++++|++
T Consensus         7 ~~~~~~~l~~~~~~~--~~~~Q~~~i~~i~~~-~~~lv~apTGsGKT~~--------~l~~~-~~~~---~~~~~~lil~   71 (414)
T 3oiy_A            7 YEDFRSFFKKKFGKD--LTGYQRLWAKRIVQG-KSFTMVAPTGVGKTTF--------GMMTA-LWLA---RKGKKSALVF   71 (414)
T ss_dssp             HHHHHHHHHHHHSSC--CCHHHHHHHHHHTTT-CCEECCSCSSSSHHHH--------HHHHH-HHHH---TTTCCEEEEE
T ss_pred             HHHHHHHHHHhcCCC--CCHHHHHHHHHHhcC-CCEEEEeCCCCCHHHH--------HHHHH-HHHh---cCCCEEEEEE
Confidence            456778899989996  468999999999999 8999999999999998        55655 2222   3345669999


Q ss_pred             chhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         113 PILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      |+++|+     .|+.+.+ .+...++++..++|+....++......+.  .+.++|+|+||+++...     +. .....
T Consensus        72 Pt~~L~-----~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~--~~~~~Iiv~Tp~~l~~~-----l~-~~~~~  138 (414)
T 3oiy_A           72 PTVTLV-----KQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFE--EDDYHILVFSTQFVSKN-----RE-KLSQK  138 (414)
T ss_dssp             SSHHHH-----HHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHH--HTCCSEEEEEHHHHHHC-----HH-HHTTC
T ss_pred             CCHHHH-----HHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhh--cCCCCEEEECHHHHHHH-----HH-Hhccc
Confidence            999999     5555555 21113389999999998866555555543  24589999999998521     22 25567


Q ss_pred             CccEEEEeccccccccC---------CCcHHHHHHHHHHHHhhC-----------CCCcEEEEecc-CCcchHHHH-HHH
Q psy7952         192 KLAYIVVDEAHCVSEWG---------HDFRPTYRRLGELRQFTG-----------NSIPIIALTAT-AEPSVKQDI-ISV  249 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~---------~~~~~~~~~l~~~~~~~~-----------~~~~~v~lSAT-~~~~~~~~~-~~~  249 (444)
                      ++++||+||+|++.+++         ..|.+.+  +..++..++           .+.+++++||| ++......+ ...
T Consensus       139 ~~~~iViDEaH~~~~~~~~~d~~l~~~~~~~~~--~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~  216 (414)
T 3oiy_A          139 RFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEI--IRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDL  216 (414)
T ss_dssp             CCSEEEESCHHHHHHCHHHHHHHHHHTTCCHHH--HHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHH
T ss_pred             cccEEEEeChHhhhhccchhhhHHhhcCCcHHH--HHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHh
Confidence            89999999999987644         2244431  233333333           56899999999 444443233 233


Q ss_pred             hcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------
Q psy7952         250 LKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------  323 (444)
Q Consensus       250 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------  323 (444)
                      +.....    .......++...+...    .+...+.+++..       .++++||||+++++++.++..|...      
T Consensus       217 ~~~~~~----~~~~~~~~i~~~~~~~----~~~~~l~~~l~~-------~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~  281 (414)
T 3oiy_A          217 LNFTVG----RLVSVARNITHVRISS----RSKEKLVELLEI-------FRDGILIFAQTEEEGKELYEYLKRFKFNVGE  281 (414)
T ss_dssp             HSCCSS----CCCCCCCSEEEEEESS----CCHHHHHHHHHH-------HCSSEEEEESSHHHHHHHHHHHHHTTCCEEE
T ss_pred             hccCcC----ccccccccchheeecc----CHHHHHHHHHHH-------cCCCEEEEECCHHHHHHHHHHHHHcCCceeh
Confidence            321111    1122233333333322    233444455544       2588999999999999999999875      


Q ss_pred             -cCHHHHHHHHHHHhcCCccEEEE----cCccccccccCC-ccEEEEeCCC--CCHHHHHHHhccCCCCC----CceeEE
Q psy7952         324 -VNKHERSRVQESFMRGEINVITA----TISFGMGIDRQN-VRFVVHWGMP--SSIPAYYQESGRAGRDG----LQSYCR  391 (444)
Q Consensus       324 -~~~~~r~~~~~~f~~g~~~vLva----T~~~~~Gidi~~-~~~Vi~~~~p--~s~~~~~Qr~GR~~R~g----~~g~~~  391 (444)
                       +....|.  ++.|++|+.+||||    |+++++|+|+|+ +++||++|+|  .|...|+||+||+||.|    ..|.++
T Consensus       282 ~~h~~~r~--~~~f~~g~~~vLvat~s~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i  359 (414)
T 3oiy_A          282 TWSEFEKN--FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSV  359 (414)
T ss_dssp             SSSCHHHH--HHHHHTTSCSEEEEECCTTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEE
T ss_pred             hhcCcchH--HHHHhCCCCeEEEEecCcCchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEE
Confidence             2333444  99999999999999    999999999999 9999999999  99999999999999987    479999


Q ss_pred             EEec
Q psy7952         392 IYHS  395 (444)
Q Consensus       392 ~~~~  395 (444)
                      +++.
T Consensus       360 ~~~~  363 (414)
T 3oiy_A          360 IFEE  363 (414)
T ss_dssp             EECC
T ss_pred             EEEc
Confidence            9883

>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=100.00  E-value=2.2e-39  Score=330.54  Aligned_cols=320  Identities=13%  Similarity=0.162  Sum_probs=175.4

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC--ccceeEEEcchhhhhcccCccchH
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN--VRSRNGWISPILSSFYLRFRDDKT  127 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~--~~~~vlil~P~~~L~~~~q~~~~~  127 (444)
                      |+++|.++++.++.+ +++++.+|||+|||++        |.+|+ ++.+....  ..+++||++|+++|+  .|+.+.+
T Consensus         8 ~~~~Q~~~i~~~~~~-~~~l~~~~tGsGKT~~--------~~~~~-~~~~~~~~~~~~~~~lil~P~~~L~--~q~~~~~   75 (556)
T 4a2p_A            8 ARSYQIELAQPAING-KNALICAPTGSGKTFV--------SILIC-EHHFQNMPAGRKAKVVFLATKVPVY--EQQKNVF   75 (556)
T ss_dssp             CCHHHHHHHHHHHTT-CCEEEECCTTSCHHHH--------HHHHH-HHHHHTCCSSCCCCEEEECSSHHHH--HHHHHHH
T ss_pred             CCHHHHHHHHHHHcC-CCEEEEcCCCChHHHH--------HHHHH-HHHHHhCcccCCCeEEEEeCCHHHH--HHHHHHH
Confidence            568999999999999 9999999999999999        55555 33333322  145779999999999  2223333


Q ss_pred             hhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH-hhCCccEEEEeccccc
Q psy7952         128 SIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV-RYNKLAYIVVDEAHCV  204 (444)
Q Consensus       128 ~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~-~~~~~~~iViDE~H~~  204 (444)
                      ..+  ..+   +.+..++|+..........      ..+++|+|+||+++.    ..+..... .+.++++||+||||++
T Consensus        76 ~~~~~~~~---~~~~~~~g~~~~~~~~~~~------~~~~~i~v~T~~~l~----~~~~~~~~~~~~~~~~vViDEah~~  142 (556)
T 4a2p_A           76 KHHFERQG---YSVQGISGENFSNVSVEKV------IEDSDIIVVTPQILV----NSFEDGTLTSLSIFTLMIFDECHNT  142 (556)
T ss_dssp             HHHHGGGT---CCEEECCCC-----CHHHH------HHHCSEEEECHHHHH----HHHHSSSCCCSTTCSEEEEETGGGC
T ss_pred             HHHhcccC---ceEEEEeCCCCcchhHHHh------hCCCCEEEECHHHHH----HHHHhCcccccccCCEEEEECCccc
Confidence            333  235   8899999988654433222      135899999999974    22222223 4678999999999999


Q ss_pred             cccCCCcHHHHHHHH-HHHHhhCCCCcEEEEeccCCcchH-------H---HHHHHhcCCCCeEEEecC---------CC
Q psy7952         205 SEWGHDFRPTYRRLG-ELRQFTGNSIPIIALTATAEPSVK-------Q---DIISVLKFNKPYKVFKTS---------TF  264 (444)
Q Consensus       205 ~~~~~~~~~~~~~l~-~~~~~~~~~~~~v~lSAT~~~~~~-------~---~~~~~l~~~~~~~~~~~~---------~~  264 (444)
                      .+++. +...+..+. .......+..++++|||||.....       +   .+...++..   .+....         ..
T Consensus       143 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~i~~l~~~l~~~---~~~~~~~~~~~~~~~~~  218 (556)
T 4a2p_A          143 TGNHP-YNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQ---AISTVRENIQELQRFMN  218 (556)
T ss_dssp             STTSH-HHHHHHHHHHHHHCC---CCEEEEEESCCCCTTCSSHHHHHHHHHHHHHHHTCS---EEECCCTTHHHHHHHTC
T ss_pred             CCcch-HHHHHHHHHHhhhcccCCCCeEEEEeCCcccCchhhHHHHHHHHHHHHHhcCCe---EecchhcchHHHHhcCC
Confidence            87653 332221211 111111344889999999965321       1   112222211   011000         01


Q ss_pred             CCCceEEEEEccc-------------------------------------------------------------------
Q psy7952         265 RSNLFYDVIFDDL-------------------------------------------------------------------  277 (444)
Q Consensus       265 ~~~~~~~~~~~~~-------------------------------------------------------------------  277 (444)
                      ++...+.......                                                                   
T Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  298 (556)
T 4a2p_A          219 KPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRIC  298 (556)
T ss_dssp             CCCEEEEECCCCSCCHHHHHHHHHHHHHHHHHHHHCC---------CCCSSHHHHHHHHHHHHHHHHC---CHHHHHHHH
T ss_pred             CCceEEEEcCCCcCChHHHHHHHHHHHHHHHHHHHhhhhhhhcccccccchhhHHHHHHHHHHHHHhhcccccchhHHHH
Confidence            1111111100000                                                                   


Q ss_pred             -----------------------------------------------------------------------chhhHHHHH
Q psy7952         278 -----------------------------------------------------------------------LKDSYAHVK  286 (444)
Q Consensus       278 -----------------------------------------------------------------------~~~~~~~~~  286 (444)
                                                                                             ...+...+.
T Consensus       299 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~K~~~L~  378 (556)
T 4a2p_A          299 RALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELV  378 (556)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTHHHHHHHHHCSSSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhhHHHHhhhhccCCCCCChHHHHHH
Confidence                                                                                   001111122


Q ss_pred             HHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------------------cCHHHHHHHHHHHhc-CCccE
Q psy7952         287 EFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------------------VNKHERSRVQESFMR-GEINV  343 (444)
Q Consensus       287 ~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------------------~~~~~r~~~~~~f~~-g~~~v  343 (444)
                      +.+.+....  ..+.++||||+++.+++.+++.|...                      ++..+|..+++.|++ |+.+|
T Consensus       379 ~~l~~~~~~--~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~v  456 (556)
T 4a2p_A          379 CILDDAYRY--NPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRL  456 (556)
T ss_dssp             HHHHHHHHH--CTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC------------------------------CCE
T ss_pred             HHHHHHhcC--CCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCceEE
Confidence            222222111  25789999999999999999999653                      778899999999999 99999


Q ss_pred             EEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhH
Q psy7952         344 ITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL  402 (444)
Q Consensus       344 LvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~  402 (444)
                      ||||+++++|+|+|++++||+||+|+|+..|+||+|| ||. +.|.+++++.+.+....
T Consensus       457 LvaT~~~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~~  513 (556)
T 4a2p_A          457 LIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVEN  513 (556)
T ss_dssp             EEEEC-----------CEEEEETCCSCHHHHHHC----------CCEEEEESCHHHHHH
T ss_pred             EEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCcchHHH
Confidence            9999999999999999999999999999999999999 999 88999999987765433

>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=100.00  E-value=2.5e-39  Score=337.94  Aligned_cols=321  Identities=19%  Similarity=0.286  Sum_probs=227.9

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      +..+.+.++. +|+.. ++++|.++++.+.++ +++++++|||+|||.+        +.+++ ++.+..+   .+++|++
T Consensus        11 ~~~~~~~l~~-~g~~~-l~~~Q~~~i~~i~~~-~~~lv~apTGsGKT~~--------~~l~i-l~~~~~~---~~~l~i~   75 (702)
T 2p6r_A           11 SSYAVGILKE-EGIEE-LFPPQAEAVEKVFSG-KNLLLAMPTAAGKTLL--------AEMAM-VREAIKG---GKSLYVV   75 (702)
T ss_dssp             HHHHHHHHHC-C---C-CCCCCHHHHHHHTTC-SCEEEECSSHHHHHHH--------HHHHH-HHHHHTT---CCEEEEE
T ss_pred             CHHHHHHHHh-CCCCC-CCHHHHHHHHHHhCC-CcEEEEcCCccHHHHH--------HHHHH-HHHHHhC---CcEEEEe
Confidence            4556677766 69987 558999999998888 9999999999999999        44444 2223333   3569999


Q ss_pred             chhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH-Hhh
Q psy7952         113 PILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL-VRY  190 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~-~~~  190 (444)
                      |+++|+     .++.+.+ .+...++++..++|+......         ..++++|+|+||+++.     .++... ..+
T Consensus        76 P~r~La-----~q~~~~~~~~~~~g~~v~~~~G~~~~~~~---------~~~~~~Iiv~Tpe~l~-----~~l~~~~~~l  136 (702)
T 2p6r_A           76 PLRALA-----GEKYESFKKWEKIGLRIGISTGDYESRDE---------HLGDCDIIVTTSEKAD-----SLIRNRASWI  136 (702)
T ss_dssp             SSHHHH-----HHHHHHHTTTTTTTCCEEEECSSCBCCSS---------CSTTCSEEEEEHHHHH-----HHHHTTCSGG
T ss_pred             CcHHHH-----HHHHHHHHHHHhcCCEEEEEeCCCCcchh---------hccCCCEEEECHHHHH-----HHHHcChhHH
Confidence            999999     6666666 222223889999998765432         1247899999999974     233332 236


Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCC-Cce
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRS-NLF  269 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~-~~~  269 (444)
                      .++++||+||+|.+.+++  ....+..+...+....++.++|+||||+++  .+.+.++++.+    .+... .++ ++.
T Consensus       137 ~~~~~vIiDE~H~l~~~~--r~~~~~~ll~~l~~~~~~~~ii~lSATl~n--~~~~~~~l~~~----~~~~~-~r~~~l~  207 (702)
T 2p6r_A          137 KAVSCLVVDEIHLLDSEK--RGATLEILVTKMRRMNKALRVIGLSATAPN--VTEIAEWLDAD----YYVSD-WRPVPLV  207 (702)
T ss_dssp             GGCCEEEETTGGGGGCTT--THHHHHHHHHHHHHHCTTCEEEEEECCCTT--HHHHHHHTTCE----EEECC-CCSSCEE
T ss_pred             hhcCEEEEeeeeecCCCC--cccHHHHHHHHHHhcCcCceEEEECCCcCC--HHHHHHHhCCC----cccCC-CCCccce
Confidence            789999999999998755  445555555545455667999999999986  45677777521    11111 121 111


Q ss_pred             EEEEEccc---chh-----hHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHh-------------------
Q psy7952         270 YDVIFDDL---LKD-----SYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR-------------------  322 (444)
Q Consensus       270 ~~~~~~~~---~~~-----~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~-------------------  322 (444)
                      ..+.....   ...     ........+.+.+.    .++++||||+++++++.++..|..                   
T Consensus       208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~  283 (702)
T 2p6r_A          208 EGVLCEGTLELFDGAFSTSRRVKFEELVEECVA----ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEEN  283 (702)
T ss_dssp             EEEECSSEEEEEETTEEEEEECCHHHHHHHHHH----TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTC
T ss_pred             EEEeeCCeeeccCcchhhhhhhhHHHHHHHHHh----cCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhc
Confidence            11110000   000     00002333333332    478999999999999999888763                   


Q ss_pred             --------------h-------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEE----eC---CCCCHHHH
Q psy7952         323 --------------K-------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVH----WG---MPSSIPAY  374 (444)
Q Consensus       323 --------------~-------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~----~~---~p~s~~~~  374 (444)
                                    .       +++++|..+++.|++|.++|||||+++++|+|+|++++||+    ||   .|.|..+|
T Consensus       284 ~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~  363 (702)
T 2p6r_A          284 EGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEY  363 (702)
T ss_dssp             CSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHH
T ss_pred             cccccHHHHHHHhcCeEEecCCCCHHHHHHHHHHHHCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHH
Confidence                          0       78999999999999999999999999999999999999998    66   68899999


Q ss_pred             HHHhccCCCCC--CceeEEEEecccchh
Q psy7952         375 YQESGRAGRDG--LQSYCRIYHSEHSKK  400 (444)
Q Consensus       375 ~Qr~GR~~R~g--~~g~~~~~~~~~~~~  400 (444)
                      .||+||+||.|  ..|.|++++.+.+..
T Consensus       364 ~Qr~GRaGR~g~~~~G~~~~l~~~~~~~  391 (702)
T 2p6r_A          364 KQMAGRAGRPGMDERGEAIIIVGKRDRE  391 (702)
T ss_dssp             HHHHTTBSCTTTCSCEEEEEECCGGGHH
T ss_pred             HHHhhhcCCCCCCCCceEEEEecCccHH
Confidence            99999999988  479999999887744

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=100.00  E-value=1.4e-38  Score=342.29  Aligned_cols=289  Identities=16%  Similarity=0.213  Sum_probs=203.0

Q ss_pred             HHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcc
Q psy7952          34 QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISP  113 (444)
Q Consensus        34 ~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P  113 (444)
                      .++.+.++..+|++  ||++|.++++.++.| ++++++||||+|||++        ++.++ +..+   ...+++||++|
T Consensus        65 ~~~~~~~~~~~gf~--pt~iQ~~ai~~il~g-~dvlv~ApTGSGKTl~--------~l~~i-l~~~---~~~~~~Lil~P  129 (1104)
T 4ddu_A           65 EDFRSFFKKKFGKD--LTGYQRLWAKRIVQG-KSFTMVAPTGVGKTTF--------GMMTA-LWLA---RKGKKSALVFP  129 (1104)
T ss_dssp             HHHHHHHHHHSSSC--CCHHHHHHHHHHTTT-CCEEECCSTTCCHHHH--------HHHHH-HHHH---TTTCCEEEEES
T ss_pred             HHHHHHHHHhcCCC--CCHHHHHHHHHHHcC-CCEEEEeCCCCcHHHH--------HHHHH-HHHH---hcCCeEEEEec
Confidence            34556777778996  679999999999999 9999999999999998        55554 3323   23346699999


Q ss_pred             hhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCC
Q psy7952         114 ILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK  192 (444)
Q Consensus       114 ~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~  192 (444)
                      |++|+     .|+.+.+ .++..++++..++|+....++......+.  .+.++|+|+||+++..     .+. ...+.+
T Consensus       130 treLa-----~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~--~g~~~IlV~Tp~rL~~-----~l~-~l~~~~  196 (1104)
T 4ddu_A          130 TVTLV-----KQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFE--EDDYHILVFSTQFVSK-----NRE-KLSQKR  196 (1104)
T ss_dssp             SHHHH-----HHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHH--TSCCSEEEEEHHHHHH-----SHH-HHHTSC
T ss_pred             hHHHH-----HHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHh--CCCCCEEEECHHHHHH-----HHH-hhcccC
Confidence            99999     5666665 32333489999999998866555555544  2458999999999842     122 256779


Q ss_pred             ccEEEEeccccccccC---------CCcHHHHHHHHHHHHhhC-----------CCCcEEEEeccC-CcchHHHH-HHHh
Q psy7952         193 LAYIVVDEAHCVSEWG---------HDFRPTYRRLGELRQFTG-----------NSIPIIALTATA-EPSVKQDI-ISVL  250 (444)
Q Consensus       193 ~~~iViDE~H~~~~~~---------~~~~~~~~~l~~~~~~~~-----------~~~~~v~lSAT~-~~~~~~~~-~~~l  250 (444)
                      +++||+||+|++...+         .+|...  .+..++..++           .+.|++++|||+ +......+ ...+
T Consensus       197 l~~lViDEaH~l~~~~r~~Dr~L~~~gf~~~--~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l  274 (1104)
T 4ddu_A          197 FDFVFVDDVDAVLKASRNIDTLLMMVGIPEE--IIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLL  274 (1104)
T ss_dssp             CSEEEESCHHHHTTSSHHHHHHHHTSSCCHH--HHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHT
T ss_pred             cCEEEEeCCCccccccccchhhhHhcCCCHH--HHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhcce
Confidence            9999999999876522         113333  1333333333           568999999995 44333222 3332


Q ss_pred             cCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-------
Q psy7952         251 KFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-------  323 (444)
Q Consensus       251 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-------  323 (444)
                      .+    .+........++...+...    .+...+.+++..       .++++||||++++.++.++..|...       
T Consensus       275 ~i----~v~~~~~~~~~i~~~~~~~----~k~~~L~~ll~~-------~~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~  339 (1104)
T 4ddu_A          275 NF----TVGRLVSVARNITHVRISS----RSKEKLVELLEI-------FRDGILIFAQTEEEGKELYEYLKRFKFNVGET  339 (1104)
T ss_dssp             CC----CCCBCCCCCCCEEEEEESC----CCHHHHHHHHHH-------HCSSEEEEESSSHHHHHHHHHHHHTTCCEEES
T ss_pred             eE----EeccCCCCcCCceeEEEec----CHHHHHHHHHHh-------cCCCEEEEECcHHHHHHHHHHHHhCCCCeeeE
Confidence            21    1122223334444444332    234444555554       2589999999999999999999876       


Q ss_pred             cCHHHHHHHHHHHhcCCccEEEE----cCccccccccCC-ccEEEEeCCCC
Q psy7952         324 VNKHERSRVQESFMRGEINVITA----TISFGMGIDRQN-VRFVVHWGMPS  369 (444)
Q Consensus       324 ~~~~~r~~~~~~f~~g~~~vLva----T~~~~~Gidi~~-~~~Vi~~~~p~  369 (444)
                      +.. +|.. ++.|++|+.+||||    |+++++|+|+|+ +++||++|+|.
T Consensus       340 lhg-~rr~-l~~F~~G~~~VLVatas~TdvlarGIDip~~V~~VI~~d~P~  388 (1104)
T 4ddu_A          340 WSE-FEKN-FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPS  388 (1104)
T ss_dssp             SSS-HHHH-HHHHHHTSCSEEEEETTTHHHHCCSCCCTTTCCEEEEESCCE
T ss_pred             ecC-cHHH-HHHHHCCCCCEEEEecCCCCeeEecCcCCCCCCEEEEECCCC
Confidence            122 3555 99999999999999    999999999999 99999999998

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=100.00  E-value=9.1e-39  Score=325.81  Aligned_cols=320  Identities=13%  Similarity=0.142  Sum_probs=201.3

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC--ccceeEEEcchhhhhcccCccchH
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN--VRSRNGWISPILSSFYLRFRDDKT  127 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~--~~~~vlil~P~~~L~~~~q~~~~~  127 (444)
                      |+++|.++++.++.+ +++++.+|||+|||++        |.+|+ ++.+....  ..+++||++|+++|+  .|+.+.+
T Consensus         5 ~~~~Q~~~i~~~~~~-~~~l~~~~tGsGKT~~--------~~~~~-~~~~~~~~~~~~~~~lil~P~~~L~--~q~~~~~   72 (555)
T 3tbk_A            5 PRNYQLELALPAKKG-KNTIICAPTGCGKTFV--------SLLIC-EHHLKKFPCGQKGKVVFFANQIPVY--EQQATVF   72 (555)
T ss_dssp             CCHHHHHHHHHHHTT-CCEEEECCTTSCHHHH--------HHHHH-HHHHHTCCSSCCCCEEEECSSHHHH--HHHHHHH
T ss_pred             CcHHHHHHHHHHhCC-CCEEEEeCCCChHHHH--------HHHHH-HHHHHhcccCCCCEEEEEeCCHHHH--HHHHHHH
Confidence            568999999999999 9999999999999999        55555 33333322  145779999999999  2223333


Q ss_pred             hhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH-hhCCccEEEEeccccc
Q psy7952         128 SIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV-RYNKLAYIVVDEAHCV  204 (444)
Q Consensus       128 ~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~-~~~~~~~iViDE~H~~  204 (444)
                      ..+  ..+   +.+..++|+...........      .+++|+|+||+++.    ..+..... .+.++++||+||||++
T Consensus        73 ~~~~~~~~---~~~~~~~g~~~~~~~~~~~~------~~~~i~v~T~~~l~----~~~~~~~~~~~~~~~~vViDEah~~  139 (555)
T 3tbk_A           73 SRYFERLG---YNIASISGATSDSVSVQHII------EDNDIIILTPQILV----NNLNNGAIPSLSVFTLMIFDECHNT  139 (555)
T ss_dssp             HHHHHTTT---CCEEEECTTTGGGSCHHHHH------HHCSEEEECHHHHH----HHHHTSSSCCGGGCSEEEETTGGGC
T ss_pred             HHHhccCC---cEEEEEcCCCcchhhHHHHh------cCCCEEEECHHHHH----HHHhcCcccccccCCEEEEECcccc
Confidence            333  235   88999999986654433221      35899999999974    22222222 4667899999999999


Q ss_pred             cccCCCcHHHHHHHHHHHHhh-----CCCCcEEEEeccCCcch-------HHHHHHHhcCCCCeEEEecC---------C
Q psy7952         205 SEWGHDFRPTYRRLGELRQFT-----GNSIPIIALTATAEPSV-------KQDIISVLKFNKPYKVFKTS---------T  263 (444)
Q Consensus       205 ~~~~~~~~~~~~~l~~~~~~~-----~~~~~~v~lSAT~~~~~-------~~~~~~~l~~~~~~~~~~~~---------~  263 (444)
                      .+.+. +...+   ...+...     ...++++++||||....       .+.+......-....+....         .
T Consensus       140 ~~~~~-~~~~~---~~~~~~~~~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~l~~~~  215 (555)
T 3tbk_A          140 SKNHP-YNQIM---FRYLDHKLGESRDPLPQVVGLTASVGVGDAKTAEEAMQHICKLCAALDASVIATVRDNVAELEQVV  215 (555)
T ss_dssp             STTCH-HHHHH---HHHHHHHTSSCCSCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHTTCSEEECCCSCHHHHHTTC
T ss_pred             CCcch-HHHHH---HHHHHhhhccccCCCCeEEEEecCcccCccccHHHHHHHHHHHHHhcCCeeeeccccCHHHHHhhc
Confidence            76542 33322   2222221     23478999999997632       12221111111110111100         0


Q ss_pred             CCCCceEEEEEccc------------------------------------------------------------------
Q psy7952         264 FRSNLFYDVIFDDL------------------------------------------------------------------  277 (444)
Q Consensus       264 ~~~~~~~~~~~~~~------------------------------------------------------------------  277 (444)
                      .++...+.......                                                                  
T Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  295 (555)
T 3tbk_A          216 YKPQKISRKVASRTSNTFKCIISQLMKETEKLAKDVSEELGKLFQIQNREFGTQKYEQWIVGVHKACSVFQMADKEEESR  295 (555)
T ss_dssp             CCCCEEEEECCCCSCCHHHHHHHHHHHHHHHHHHTSCHHHHGGGGCCSCCSSSHHHHHHHHHHHHHHHTCCCSSHHHHHH
T ss_pred             CCCceEEEEecCcccChHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccccccchhhhHHHHHHHHHhhhhhccchhhHHH
Confidence            11111111111000                                                                  


Q ss_pred             -------------------------------------------------------------------------chhhHHH
Q psy7952         278 -------------------------------------------------------------------------LKDSYAH  284 (444)
Q Consensus       278 -------------------------------------------------------------------------~~~~~~~  284 (444)
                                                                                               ...+...
T Consensus       296 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~  375 (555)
T 3tbk_A          296 VCKALFLYTSHLRKYNDALIISEDAQMTDALNYLKAFFHDVREAAFDETERELTRRFEEKLEELEKVSRDPSNENPKLRD  375 (555)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHCC-----HHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhccCCCcCCHHHHH
Confidence                                                                                     0111122


Q ss_pred             HHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------------------cCHHHHHHHHHHHhc-CCc
Q psy7952         285 VKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------------------VNKHERSRVQESFMR-GEI  341 (444)
Q Consensus       285 ~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------------------~~~~~r~~~~~~f~~-g~~  341 (444)
                      +.+.+.......  .+.++||||+++.+++.+++.|...                      ++..+|..+++.|++ |+.
T Consensus       376 l~~~l~~~~~~~--~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~  453 (555)
T 3tbk_A          376 LYLVLQEEYHLK--PETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDN  453 (555)
T ss_dssp             HHHHHHHHHHHC--TTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC--------------------------CC
T ss_pred             HHHHHHHHhccC--CCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCe
Confidence            222333322222  4689999999999999999999752                      677899999999998 999


Q ss_pred             cEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhH
Q psy7952         342 NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL  402 (444)
Q Consensus       342 ~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~  402 (444)
                      +|||||+++++|+|+|++++||++|+|+|+..|+||+|| ||. ++|.+++++.+.+....
T Consensus       454 ~vLvaT~~~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~~  512 (555)
T 3tbk_A          454 NILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSADVIEK  512 (555)
T ss_dssp             SEEEECCCTTCCEETTSCSEEEEESCCSSCCCEECSSCC-CTT-TSCEEEEEESCHHHHHH
T ss_pred             eEEEEcchhhcCCccccCCEEEEeCCCCCHHHHHHhcCc-CcC-CCceEEEEEcCCCHHHH
Confidence            999999999999999999999999999999999999999 898 89999999987766544

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=100.00  E-value=3.2e-38  Score=330.47  Aligned_cols=317  Identities=18%  Similarity=0.247  Sum_probs=221.7

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHH-HHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRH-ILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~-~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      +..+.+.++. +|+.. ++++|.++++. +.++ +++++++|||+|||.+        +.+++ ++.+...  ..+++|+
T Consensus        16 ~~~~~~~l~~-~g~~~-l~~~Q~~~i~~~~~~~-~~~lv~apTGsGKT~~--------~~l~i-l~~~~~~--~~~il~i   81 (715)
T 2va8_A           16 PSNVIEIIKK-RGIKK-LNPPQTEAVKKGLLEG-NRLLLTSPTGSGKTLI--------AEMGI-ISFLLKN--GGKAIYV   81 (715)
T ss_dssp             CHHHHHHHHT-TSCCB-CCHHHHHHHHTTTTTT-CCEEEECCTTSCHHHH--------HHHHH-HHHHHHS--CSEEEEE
T ss_pred             CHHHHHHHHh-CCCCC-CCHHHHHHHHHHhcCC-CcEEEEcCCCCcHHHH--------HHHHH-HHHHHHC--CCeEEEE
Confidence            4567788887 69987 56899999999 5566 9999999999999999        44444 2223312  2467999


Q ss_pred             cchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhh
Q psy7952         112 SPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRY  190 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~  190 (444)
                      +|+++|+     .++.+.+ .....++++..++|+.......         ..+++|+|+||+++.    ..+......+
T Consensus        82 ~P~r~La-----~q~~~~~~~~~~~g~~v~~~~G~~~~~~~~---------~~~~~Iiv~Tpe~l~----~~~~~~~~~l  143 (715)
T 2va8_A           82 TPLRALT-----NEKYLTFKDWELIGFKVAMTSGDYDTDDAW---------LKNYDIIITTYEKLD----SLWRHRPEWL  143 (715)
T ss_dssp             CSCHHHH-----HHHHHHHGGGGGGTCCEEECCSCSSSCCGG---------GGGCSEEEECHHHHH----HHHHHCCGGG
T ss_pred             eCcHHHH-----HHHHHHHHHhhcCCCEEEEEeCCCCCchhh---------cCCCCEEEEcHHHHH----HHHhCChhHh
Confidence            9999999     5666655 2211128899999887654320         136899999999974    2222333336


Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCC-ce
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSN-LF  269 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~-~~  269 (444)
                      .++++||+||+|.+.+.+  +...+..+...+.    +.++|+||||+++  .+.+.++++.+    .+.. ..++. +.
T Consensus       144 ~~~~~vIiDE~H~l~~~~--~~~~l~~i~~~~~----~~~ii~lSATl~n--~~~~~~~l~~~----~~~~-~~r~~~l~  210 (715)
T 2va8_A          144 NEVNYFVLDELHYLNDPE--RGPVVESVTIRAK----RRNLLALSATISN--YKQIAKWLGAE----PVAT-NWRPVPLI  210 (715)
T ss_dssp             GGEEEEEECSGGGGGCTT--THHHHHHHHHHHH----TSEEEEEESCCTT--HHHHHHHHTCE----EEEC-CCCSSCEE
T ss_pred             hccCEEEEechhhcCCcc--cchHHHHHHHhcc----cCcEEEEcCCCCC--HHHHHHHhCCC----ccCC-CCCCCCce
Confidence            789999999999987654  4444554443322    4899999999976  35677777531    1111 11111 11


Q ss_pred             E------------EEEEcccchh---hHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----------
Q psy7952         270 Y------------DVIFDDLLKD---SYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----------  323 (444)
Q Consensus       270 ~------------~~~~~~~~~~---~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----------  323 (444)
                      .            ..........   ........+.+.+.    .++++||||+++++++.++..|.+.           
T Consensus       211 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~  286 (715)
T 2va8_A          211 EGVIYPERKKKEYNVIFKDNTTKKVHGDDAIIAYTLDSLS----KNGQVLVFRNSRKMAESTALKIANYMNFVSLDENAL  286 (715)
T ss_dssp             EEEEEECSSTTEEEEEETTSCEEEEESSSHHHHHHHHHHT----TTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHH
T ss_pred             EEEEecCCcccceeeecCcchhhhcccchHHHHHHHHHHh----cCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHH
Confidence            1            1111110000   01233444444432    4789999999999999999888631           


Q ss_pred             -----------------------------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEE----
Q psy7952         324 -----------------------------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVH----  364 (444)
Q Consensus       324 -----------------------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~----  364 (444)
                                                         ++.++|..+++.|++|.++|||||+++++|+|+|++++||+    
T Consensus       287 ~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~  366 (715)
T 2va8_A          287 SEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYR  366 (715)
T ss_dssp             HHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--
T ss_pred             HHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCCHHHHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCee
Confidence                                               77899999999999999999999999999999999999998    


Q ss_pred             eC-------CCCCHHHHHHHhccCCCCC--CceeEEEEecccc
Q psy7952         365 WG-------MPSSIPAYYQESGRAGRDG--LQSYCRIYHSEHS  398 (444)
Q Consensus       365 ~~-------~p~s~~~~~Qr~GR~~R~g--~~g~~~~~~~~~~  398 (444)
                      |+       .|.|..+|.||+||+||.|  ..|.|++++.+.+
T Consensus       367 ~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  409 (715)
T 2va8_A          367 FNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKE  409 (715)
T ss_dssp             ------------CHHHHHHHHTTBCCTTTCSCEEEEEECSCGG
T ss_pred             ccccCCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEeCCch
Confidence            88       7999999999999999987  4799999998765

>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=100.00  E-value=2.3e-38  Score=331.51  Aligned_cols=320  Identities=19%  Similarity=0.259  Sum_probs=225.8

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHH-HHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRH-ILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~-~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      +..+.+.++. +|+.. ++++|.++++. +.++ +++++++|||+|||.+        +.+++ ++.+...  ..+++|+
T Consensus         9 ~~~~~~~l~~-~g~~~-l~~~Q~~~i~~~~~~~-~~~lv~apTGsGKT~~--------~~l~i-l~~~~~~--~~~~l~i   74 (720)
T 2zj8_A            9 DERIKSTLKE-RGIES-FYPPQAEALKSGILEG-KNALISIPTASGKTLI--------AEIAM-VHRILTQ--GGKAVYI   74 (720)
T ss_dssp             CHHHHHHHHH-TTCCB-CCHHHHHHHTTTGGGT-CEEEEECCGGGCHHHH--------HHHHH-HHHHHHH--CSEEEEE
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhcCC-CcEEEEcCCccHHHHH--------HHHHH-HHHHHhC--CCEEEEE
Confidence            4567788887 69987 56899999998 6676 9999999999999999        44454 2223311  2466999


Q ss_pred             cchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhh
Q psy7952         112 SPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRY  190 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~  190 (444)
                      +|+++|+     .++.+.+ .+...++++..++|+.......         .++++|+|+||+++.    ..+......+
T Consensus        75 ~P~raLa-----~q~~~~~~~l~~~g~~v~~~~G~~~~~~~~---------~~~~~Iiv~Tpe~l~----~~~~~~~~~l  136 (720)
T 2zj8_A           75 VPLKALA-----EEKFQEFQDWEKIGLRVAMATGDYDSKDEW---------LGKYDIIIATAEKFD----SLLRHGSSWI  136 (720)
T ss_dssp             CSSGGGH-----HHHHHHTGGGGGGTCCEEEECSCSSCCCGG---------GGGCSEEEECHHHHH----HHHHHTCTTG
T ss_pred             cCcHHHH-----HHHHHHHHHHHhcCCEEEEecCCCCccccc---------cCCCCEEEECHHHHH----HHHHcChhhh
Confidence            9999999     6666665 2211128899999976654321         247899999999974    2222222336


Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCC-ce
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSN-LF  269 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~-~~  269 (444)
                      .++++||+||+|++.+++  ....+..+...+   +++.++|+||||+++  ...+.++++..    .+.. ..++. ..
T Consensus       137 ~~~~~vIiDE~H~l~~~~--r~~~~~~ll~~l---~~~~~ii~lSATl~n--~~~~~~~l~~~----~~~~-~~rp~~l~  204 (720)
T 2zj8_A          137 KDVKILVADEIHLIGSRD--RGATLEVILAHM---LGKAQIIGLSATIGN--PEELAEWLNAE----LIVS-DWRPVKLR  204 (720)
T ss_dssp             GGEEEEEEETGGGGGCTT--THHHHHHHHHHH---BTTBEEEEEECCCSC--HHHHHHHTTEE----EEEC-CCCSSEEE
T ss_pred             hcCCEEEEECCcccCCCc--ccHHHHHHHHHh---hcCCeEEEEcCCcCC--HHHHHHHhCCc----ccCC-CCCCCcce
Confidence            789999999999987654  444444443333   235899999999976  35677776521    1111 11221 11


Q ss_pred             EEEE------EcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh--------------------
Q psy7952         270 YDVI------FDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK--------------------  323 (444)
Q Consensus       270 ~~~~------~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~--------------------  323 (444)
                      ..+.      ...............+.+.+.    .++++||||+++++++.++..|.+.                    
T Consensus       205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i  280 (720)
T 2zj8_A          205 RGVFYQGFVTWEDGSIDRFSSWEELVYDAIR----KKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSL  280 (720)
T ss_dssp             EEEEETTEEEETTSCEEECSSTTHHHHHHHH----TTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTS
T ss_pred             EEEEeCCeeeccccchhhhhHHHHHHHHHHh----CCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHH
Confidence            1111      111000001112233333322    4689999999999999998888631                    


Q ss_pred             -----------------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEE----eC----CCCCHH
Q psy7952         324 -----------------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVH----WG----MPSSIP  372 (444)
Q Consensus       324 -----------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~----~~----~p~s~~  372 (444)
                                             +++++|..+++.|++|.++|||||+++++|+|+|++++||+    ||    .|.|..
T Consensus       281 ~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~  360 (720)
T 2zj8_A          281 EENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPII  360 (720)
T ss_dssp             CSCHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHH
T ss_pred             hcccchHHHHHHHhcCeeeecCCCCHHHHHHHHHHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHH
Confidence                                   78899999999999999999999999999999999999998    55    589999


Q ss_pred             HHHHHhccCCCCC--CceeEEEEecccchh
Q psy7952         373 AYYQESGRAGRDG--LQSYCRIYHSEHSKK  400 (444)
Q Consensus       373 ~~~Qr~GR~~R~g--~~g~~~~~~~~~~~~  400 (444)
                      +|.||+||+||.|  ..|.|++++.+.+..
T Consensus       361 ~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~~  390 (720)
T 2zj8_A          361 EVHQMLGRAGRPKYDEVGEGIIVSTSDDPR  390 (720)
T ss_dssp             HHHHHHTTBCCTTTCSEEEEEEECSSSCHH
T ss_pred             HHHHHHhhcCCCCCCCCceEEEEecCccHH
Confidence            9999999999987  478999999877743

>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=100.00  E-value=1.6e-38  Score=341.94  Aligned_cols=319  Identities=18%  Similarity=0.175  Sum_probs=222.7

Q ss_pred             HHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcc
Q psy7952          41 KALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYL  120 (444)
Q Consensus        41 ~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~  120 (444)
                      ...++|.  ++++|.++++.+..| ++++++||||+|||++        |.+++ +..+..+   .+++|++|+++|+  
T Consensus       178 ~~~~~f~--ltp~Q~~AI~~i~~g-~dvLV~ApTGSGKTlv--------a~l~i-~~~l~~g---~rvlvl~PtraLa--  240 (1108)
T 3l9o_A          178 ARTYPFT--LDPFQDTAISCIDRG-ESVLVSAHTSAGKTVV--------AEYAI-AQSLKNK---QRVIYTSPIKALS--  240 (1108)
T ss_dssp             SSCCSSC--CCHHHHHHHHHHTTT-CCEEEECCSSSHHHHH--------HHHHH-HHHHHTT---CEEEEEESSHHHH--
T ss_pred             HHhCCCC--CCHHHHHHHHHHHcC-CCEEEECCCCCChHHH--------HHHHH-HHHHhcC---CeEEEEcCcHHHH--
Confidence            3444555  468999999999998 9999999999999999        55555 3333333   3569999999999  


Q ss_pred             cCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEe
Q psy7952         121 RFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVD  199 (444)
Q Consensus       121 ~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViD  199 (444)
                         .|+.+.+ ...   -.+..++|+...             .++++|+|+||++|.    ..+......+.++++||+|
T Consensus       241 ---~Q~~~~l~~~~---~~VglltGd~~~-------------~~~~~IlV~Tpe~L~----~~L~~~~~~l~~l~lVVID  297 (1108)
T 3l9o_A          241 ---NQKYRELLAEF---GDVGLMTGDITI-------------NPDAGCLVMTTEILR----SMLYRGSEVMREVAWVIFD  297 (1108)
T ss_dssp             ---HHHHHHHHHHT---SSEEEECSSCBC-------------CCSCSEEEEEHHHHH----HHHHHCSSHHHHEEEEEEE
T ss_pred             ---HHHHHHHHHHh---CCccEEeCcccc-------------CCCCCEEEeChHHHH----HHHHcCccccccCCEEEEh
Confidence               6777777 333   257778887764             357899999999985    3344444446789999999


Q ss_pred             ccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhc--CCCCeEEEecCCCCCCceEEEEEccc
Q psy7952         200 EAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLK--FNKPYKVFKTSTFRSNLFYDVIFDDL  277 (444)
Q Consensus       200 E~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~--~~~~~~~~~~~~~~~~~~~~~~~~~~  277 (444)
                      |||++.+++  +...+..+   +..++...++|+||||+++..  .+..+++  ...+..+........+....+.....
T Consensus       298 EaH~l~d~~--rg~~~e~i---i~~l~~~~qvl~lSATipn~~--e~a~~l~~~~~~~~~vi~~~~rp~pl~~~~~~~~~  370 (1108)
T 3l9o_A          298 EVHYMRDKE--RGVVWEET---IILLPDKVRYVFLSATIPNAM--EFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAHG  370 (1108)
T ss_dssp             TGGGTTSHH--HHHHHHHH---HHHSCTTSEEEEEECSCSSCH--HHHHHHHHHTCSCEEEEEECCCSSCEEEEEEETTS
T ss_pred             hhhhccccc--hHHHHHHH---HHhcCCCceEEEEcCCCCCHH--HHHHHHHhhcCCCeEEEecCCCcccceEEEeecCC
Confidence            999998765  45444443   445677799999999987652  2233322  22333443333222222221111000


Q ss_pred             ----------ch---h--------------------------------------hHHHHHHHHHHHhccCCCCCceEEEE
Q psy7952         278 ----------LK---D--------------------------------------SYAHVKEFIEKCLGKDNKANNCGIIY  306 (444)
Q Consensus       278 ----------~~---~--------------------------------------~~~~~~~~l~~~l~~~~~~~~~~iVf  306 (444)
                                ..   .                                      ....+..++..+...   ...++|||
T Consensus       371 ~~~~~~vd~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~l~~~---~~~~vIVF  447 (1108)
T 3l9o_A          371 DGIYLVVDEKSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKK---KYNPVIVF  447 (1108)
T ss_dssp             SCCEEEEETTTEECHHHHHHHHTTC-----------------------------CHHHHHHHHHHHHHT---TCCCEEEE
T ss_pred             cceeeeeccccchhhhhHHHHHHHHHhhhcccccccccccccccccccccccccchhHHHHHHHHHHhc---CCCCEEEE
Confidence                      00   0                                      012222333333222   46799999


Q ss_pred             ecccchHHHHHHHHHhh-------------------------------------------------cCHHHHHHHHHHHh
Q psy7952         307 CRTREHTTDLADALRRK-------------------------------------------------VNKHERSRVQESFM  337 (444)
Q Consensus       307 ~~s~~~~~~l~~~L~~~-------------------------------------------------~~~~~r~~~~~~f~  337 (444)
                      |+++..|+.++..|...                                                 +++.+|..+++.|+
T Consensus       448 ~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~~R~~v~~~F~  527 (1108)
T 3l9o_A          448 SFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQ  527 (1108)
T ss_dssp             ESCHHHHHHHHHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHHHHHHHHHHHH
T ss_pred             eCcHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHHHHHHHHHHHh
Confidence            99999999999886530                                                 78999999999999


Q ss_pred             cCCccEEEEcCccccccccCCccEEEEeCC--------CCCHHHHHHHhccCCCCC--CceeEEEEeccc-chhhHHHHH
Q psy7952         338 RGEINVITATISFGMGIDRQNVRFVVHWGM--------PSSIPAYYQESGRAGRDG--LQSYCRIYHSEH-SKKSLEYVI  406 (444)
Q Consensus       338 ~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~--------p~s~~~~~Qr~GR~~R~g--~~g~~~~~~~~~-~~~~~~~~~  406 (444)
                      +|.++|||||+++++|||+|++++||+++.        |.|..+|+||+||+||.|  ..|++++++.+. +...+..++
T Consensus       528 ~G~ikVLVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~ill~~~~~~~~~~~~l~  607 (1108)
T 3l9o_A          528 EGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMV  607 (1108)
T ss_dssp             HTCCCEEEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEEEEECCCCCHHHHHHHH
T ss_pred             CCCCeEEEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCCceEEEEEecCCcCHHHHHHHh
Confidence            999999999999999999999999996654        347889999999999999  689999988765 555566666


Q ss_pred             hhc
Q psy7952         407 KTD  409 (444)
Q Consensus       407 ~~~  409 (444)
                      ...
T Consensus       608 ~~~  610 (1108)
T 3l9o_A          608 KGQ  610 (1108)
T ss_dssp             HCC
T ss_pred             cCC
Confidence            544

>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=100.00  E-value=4.5e-37  Score=332.61  Aligned_cols=314  Identities=20%  Similarity=0.180  Sum_probs=225.7

Q ss_pred             HHHHHHHHHHhCCcccCchHHHHHHHHHHc----cC-CcEEEEccCCCcccccccccccceEEeCCCccccccCCcccee
Q psy7952          34 QELTAKLKALFGFDSFKCELQKKAIRHILL----RT-HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRN  108 (444)
Q Consensus        34 ~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~----~~-~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~v  108 (444)
                      ....+.+...||++.  |++|.++++.++.    +. .++++++|||+|||.+|+.        ++ ...+..+   +++
T Consensus       590 ~~~~~~~~~~f~~~~--t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~--------aa-~~~~~~g---~~v  655 (1151)
T 2eyq_A          590 REQYQLFCDSFPFET--TPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMR--------AA-FLAVDNH---KQV  655 (1151)
T ss_dssp             HHHHHHHHHTCCSCC--CHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHH--------HH-HHHHTTT---CEE
T ss_pred             HHHHHHHHHhCCCCC--CHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHH--------HH-HHHHHhC---CeE
Confidence            344566777789984  7899999999987    42 3899999999999998433        32 1112222   367


Q ss_pred             EEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         109 GWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       109 lil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      +|++||++|+     .|+.+.+  .+....+++..+++..+..+....+..+.  .+.++|+|+||+.+         ..
T Consensus       656 lvlvPt~~La-----~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~--~g~~dIvV~T~~ll---------~~  719 (1151)
T 2eyq_A          656 AVLVPTTLLA-----QQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVA--EGKIDILIGTHKLL---------QS  719 (1151)
T ss_dssp             EEECSSHHHH-----HHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHH--TTCCSEEEECTHHH---------HS
T ss_pred             EEEechHHHH-----HHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHh--cCCCCEEEECHHHH---------hC
Confidence            9999999999     5566555  22222388999998888777766666654  35799999998764         33


Q ss_pred             HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCC
Q psy7952         187 LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRS  266 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  266 (444)
                      ...+.++++||+||+|++   +....   ..    +..+..+.++++|||||.+........  ++.+...+......+.
T Consensus       720 ~~~~~~l~lvIiDEaH~~---g~~~~---~~----l~~l~~~~~vl~lSATp~p~~l~~~~~--~~~~~~~i~~~~~~r~  787 (1151)
T 2eyq_A          720 DVKFKDLGLLIVDEEHRF---GVRHK---ER----IKAMRANVDILTLTATPIPRTLNMAMS--GMRDLSIIATPPARRL  787 (1151)
T ss_dssp             CCCCSSEEEEEEESGGGS---CHHHH---HH----HHHHHTTSEEEEEESSCCCHHHHHHHT--TTSEEEECCCCCCBCB
T ss_pred             CccccccceEEEechHhc---ChHHH---HH----HHHhcCCCCEEEEcCCCChhhHHHHHh--cCCCceEEecCCCCcc
Confidence            345788999999999995   31111   22    222334588999999998876554332  2333222222222233


Q ss_pred             CceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------------cCHHHHHHHHH
Q psy7952         267 NLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------VNKHERSRVQE  334 (444)
Q Consensus       267 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------------~~~~~r~~~~~  334 (444)
                      .+...+....    . ..+.+.+...+    ..+++++|||+++++++.+++.|.+.            ++..+|..+++
T Consensus       788 ~i~~~~~~~~----~-~~i~~~il~~l----~~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~  858 (1151)
T 2eyq_A          788 AVKTFVREYD----S-MVVREAILREI----LRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMN  858 (1151)
T ss_dssp             CEEEEEEECC----H-HHHHHHHHHHH----TTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHH
T ss_pred             ccEEEEecCC----H-HHHHHHHHHHH----hcCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHH
Confidence            3332222211    1 12222222222    24789999999999999999999875            88999999999


Q ss_pred             HHhcCCccEEEEcCccccccccCCccEEEEeCC-CCCHHHHHHHhccCCCCCCceeEEEEecccc
Q psy7952         335 SFMRGEINVITATISFGMGIDRQNVRFVVHWGM-PSSIPAYYQESGRAGRDGLQSYCRIYHSEHS  398 (444)
Q Consensus       335 ~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~-p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~  398 (444)
                      .|++|+.+|||||+++++|+|+|++++||+++. +.+...|+||+||+||.|+.|+|++++++.+
T Consensus       859 ~F~~g~~~VLVaT~v~e~GiDip~v~~VIi~~~~~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~~~  923 (1151)
T 2eyq_A          859 DFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPK  923 (1151)
T ss_dssp             HHHTTSCCEEEESSTTGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCGG
T ss_pred             HHHcCCCcEEEECCcceeeecccCCcEEEEeCCCCCCHHHHHHHHhccCcCCCceEEEEEECCcc
Confidence            999999999999999999999999999999888 5689999999999999999999999987653

>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=100.00  E-value=1.1e-38  Score=354.56  Aligned_cols=349  Identities=16%  Similarity=0.194  Sum_probs=239.2

Q ss_pred             HHHHHh-CCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhh
Q psy7952          39 KLKALF-GFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSS  117 (444)
Q Consensus        39 ~l~~~~-g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L  117 (444)
                      ..+..| |++. ++++|.++++.++.+++|++++||||+|||++|.++++..+.-.. ...-.......++||++|+++|
T Consensus        69 ~~~~~f~g~~~-ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~-~~~~~~~~~~~k~lyiaP~kAL  146 (1724)
T 4f92_B           69 YAQAGFEGFKT-LNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHI-NMDGTINVDDFKIIYIAPMRSL  146 (1724)
T ss_dssp             GGSTTCTTCSB-CCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGC-CTTSSCCTTSCEEEEECSSHHH
T ss_pred             HHHHhcCCCCC-CCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhc-cccccccCCCCEEEEECCHHHH
Confidence            344445 7887 558999999999987699999999999999997666543111000 0000001123478999999999


Q ss_pred             hcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH---HhhCC
Q psy7952         118 FYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL---VRYNK  192 (444)
Q Consensus       118 ~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~---~~~~~  192 (444)
                      +     .|..+.+  .++..++++..++|+.......         ..+++|+|+|||++     +.+++..   ..+.+
T Consensus       147 a-----~e~~~~l~~~~~~~gi~V~~~tGd~~~~~~~---------~~~~~IlVtTpEkl-----d~llr~~~~~~~l~~  207 (1724)
T 4f92_B          147 V-----QEMVGSFGKRLATYGITVAELTGDHQLCKEE---------ISATQIIVCTPEKW-----DIITRKGGERTYTQL  207 (1724)
T ss_dssp             H-----HHHHHHHHHHHTTTTCCEEECCSSCSSCCTT---------GGGCSEEEECHHHH-----HHHTTSSTTHHHHTT
T ss_pred             H-----HHHHHHHHHHHhhCCCEEEEEECCCCCCccc---------cCCCCEEEECHHHH-----HHHHcCCccchhhcC
Confidence            9     6777766  2333338999999987654321         24689999999996     3333322   23578


Q ss_pred             ccEEEEecccccccc-CCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCe-EEEecCCCCCC-ce
Q psy7952         193 LAYIVVDEAHCVSEW-GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPY-KVFKTSTFRSN-LF  269 (444)
Q Consensus       193 ~~~iViDE~H~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~-~~~~~~~~~~~-~~  269 (444)
                      +++||+||+|.+.+. |......+..+.+.....+.+.|+|+||||+++  .+++.++++...+. ........||. +.
T Consensus       208 v~~vIiDEvH~l~d~RG~~lE~~l~rl~~~~~~~~~~~riI~LSATl~N--~~dvA~wL~~~~~~~~~~~~~~~RPvpL~  285 (1724)
T 4f92_B          208 VRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPN--YEDVATFLRVDPAKGLFYFDNSFRPVPLE  285 (1724)
T ss_dssp             EEEEEETTGGGGGSTTHHHHHHHHHHHHHHHHHHTCCCEEEEEECSCTT--HHHHHHHTTCCHHHHEEECCGGGCSSCEE
T ss_pred             cCEEEEecchhcCCccHHHHHHHHHHHHHHHHhCCCCCcEEEEecccCC--HHHHHHHhCCCCCCCeEEECCCCccCccE
Confidence            999999999988652 211222223333334456677999999999976  45678888643221 12223333442 22


Q ss_pred             EEEEE--cccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------------------------
Q psy7952         270 YDVIF--DDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------------------  323 (444)
Q Consensus       270 ~~~~~--~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------------------------  323 (444)
                      ..+..  ..............+...+.... .++++||||+|++.|+.++..|.+.                        
T Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~-~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  364 (1724)
T 4f92_B          286 QTYVGITEKKAIKRFQIMNEIVYEKIMEHA-GKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTE  364 (1724)
T ss_dssp             EECCEECCCCHHHHHHHHHHHHHHHHTTCC-SSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHT
T ss_pred             EEEeccCCcchhhhhHHHHHHHHHHHHHHh-cCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhh
Confidence            21111  11111222233333333333322 5679999999999999998888642                        


Q ss_pred             -----------------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEE----eC------CCCC
Q psy7952         324 -----------------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVH----WG------MPSS  370 (444)
Q Consensus       324 -----------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~----~~------~p~s  370 (444)
                                             +++++|..+++.|++|.++|||||++++.|||+|..++||.    ++      .|.|
T Consensus       365 ~~~~~~~~l~~~l~~Gva~HHagL~~~~R~~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls  444 (1724)
T 4f92_B          365 AEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELG  444 (1724)
T ss_dssp             TSCCSTHHHHHHTTTTEEEECSSSCTHHHHHHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECC
T ss_pred             hcccccHHHHHHhhcCEEEEcCCCCHHHHHHHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCC
Confidence                                   78999999999999999999999999999999999998884    33      3568


Q ss_pred             HHHHHHHhccCCCCCC--ceeEEEEecccchhhHHHHHhhccc
Q psy7952         371 IPAYYQESGRAGRDGL--QSYCRIYHSEHSKKSLEYVIKTDTS  411 (444)
Q Consensus       371 ~~~~~Qr~GR~~R~g~--~g~~~~~~~~~~~~~~~~~~~~~~~  411 (444)
                      ..+|.||+|||||.|.  .|.++++..+.+...+..++....+
T Consensus       445 ~~~~~Qm~GRAGR~g~d~~G~~ii~~~~~~~~~~~~ll~~~~p  487 (1724)
T 4f92_B          445 ALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLP  487 (1724)
T ss_dssp             HHHHHHHHTTBSCTTTCSCEEEEEEEESTTCCHHHHHTTTCSC
T ss_pred             HHHHHHhhhhccCCCCCCccEEEEEecchhHHHHHHHHcCCCc
Confidence            9999999999999864  6999999999888888888766544

>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=100.00  E-value=6.3e-38  Score=331.35  Aligned_cols=322  Identities=13%  Similarity=0.190  Sum_probs=181.8

Q ss_pred             HhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC--ccceeEEEcchhhhhcc
Q psy7952          43 LFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN--VRSRNGWISPILSSFYL  120 (444)
Q Consensus        43 ~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~--~~~~vlil~P~~~L~~~  120 (444)
                      .+|+.. |+++|.++++.++.| +++++++|||+|||++        |.+|+ +..+....  ...++||++|+++|+  
T Consensus       243 ~~g~~~-l~~~Q~~~i~~~l~~-~~~ll~~~TGsGKTl~--------~~~~i-~~~l~~~~~~~~~~~Lvl~Pt~~L~--  309 (797)
T 4a2q_A          243 VYETKK-ARSYQIELAQPAING-KNALICAPTGSGKTFV--------SILIC-EHHFQNMPAGRKAKVVFLATKVPVY--  309 (797)
T ss_dssp             -----C-CCHHHHHHHHHHHTT-CCEEEECCTTSCHHHH--------HHHHH-HHHHHTCCSSCCCCEEEECSSHHHH--
T ss_pred             hcCCCC-CCHHHHHHHHHHHhC-CCEEEEeCCCChHHHH--------HHHHH-HHHHHhccccCCCeEEEEeCCHHHH--
Confidence            457777 669999999999999 9999999999999999        55555 33333321  145779999999999  


Q ss_pred             cCccchHhhh-----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH-hhCCcc
Q psy7952         121 RFRDDKTSIV-----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV-RYNKLA  194 (444)
Q Consensus       121 ~q~~~~~~~l-----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~-~~~~~~  194 (444)
                         .|+...+     ..+   +++..++|+..........      ..+++|+|+||+++.    ..+..... .+.+++
T Consensus       310 ---~Q~~~~~~~~~~~~~---~~v~~~~g~~~~~~~~~~~------~~~~~Ivv~Tp~~l~----~~l~~~~~~~~~~~~  373 (797)
T 4a2q_A          310 ---EQQKNVFKHHFERQG---YSVQGISGENFSNVSVEKV------IEDSDIIVVTPQILV----NSFEDGTLTSLSIFT  373 (797)
T ss_dssp             ---HHHHHHHHHHHGGGT---CCEEEECCC-----CHHHH------HHTCSEEEECHHHHH----HHHHSSSCCCGGGCS
T ss_pred             ---HHHHHHHHHhcccCC---ceEEEEeCCcchhhhHHHh------hCCCCEEEEchHHHH----HHHHhccccccccCC
Confidence               4554444     225   8999999988655433222      237899999999974    22222222 456789


Q ss_pred             EEEEeccccccccCCCcHHHHHHHHHH-HHhhCCCCcEEEEeccCCcch-------HHH---HHHHhcCCCCeEEEecC-
Q psy7952         195 YIVVDEAHCVSEWGHDFRPTYRRLGEL-RQFTGNSIPIIALTATAEPSV-------KQD---IISVLKFNKPYKVFKTS-  262 (444)
Q Consensus       195 ~iViDE~H~~~~~~~~~~~~~~~l~~~-~~~~~~~~~~v~lSAT~~~~~-------~~~---~~~~l~~~~~~~~~~~~-  262 (444)
                      +||+||||++.+.+. +...+..+... .....+.++++++||||....       .+.   +...++..   .+.... 
T Consensus       374 ~iViDEaH~~~~~~~-~~~i~~~~~~~~~~~~~~~~~~l~lSATp~~~~~~~~~~~~~~i~~l~~~L~~~---~i~~~~~  449 (797)
T 4a2q_A          374 LMIFDECHNTTGNHP-YNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQ---AISTVRE  449 (797)
T ss_dssp             EEEETTGGGCSTTSH-HHHHHHHHHHHHHTTCCCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCS---EEECCCT
T ss_pred             EEEEECccccCCCcc-HHHHHHHHHHHhhccCCCCCeEEEEcCCccccccccHHHHHHHHHHHHHhcCCc---EEecccc
Confidence            999999999876442 33322222111 111144588999999996421       111   22222210   011000 


Q ss_pred             --------CCCCCceEEEEEc------------------------------------cc---------------------
Q psy7952         263 --------TFRSNLFYDVIFD------------------------------------DL---------------------  277 (444)
Q Consensus       263 --------~~~~~~~~~~~~~------------------------------------~~---------------------  277 (444)
                              ..++...+.....                                    ..                     
T Consensus       450 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~l~~l~~~~~~~~g~~~~~~~~~~~~~~~~~~~~  529 (797)
T 4a2q_A          450 NIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQL  529 (797)
T ss_dssp             THHHHHHHSCCCCCEEEECCCCSCCHHHHHHHHHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCC
T ss_pred             cHHHHHHhcCCCceEEEecCCCCCcHHHHHHHHHHHHHHHHHHHHHhhHHhhhhccccccchhHHHHHHHHHHHHHHhcc
Confidence                    0111111110000                                    00                     


Q ss_pred             --------------------------------------------------------------------------------
Q psy7952         278 --------------------------------------------------------------------------------  277 (444)
Q Consensus       278 --------------------------------------------------------------------------------  277 (444)
                                                                                                      
T Consensus       530 ~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~  609 (797)
T 4a2q_A          530 EDKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDET  609 (797)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHTTHHHHHHHHHCTT
T ss_pred             cccchhhHHHHHHHHHHHHHHHHHHHHhhhccccHHHHHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHhhcCCC
Confidence                                                                                            


Q ss_pred             -chhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------------------cCHHHHHHHHH
Q psy7952         278 -LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------------------VNKHERSRVQE  334 (444)
Q Consensus       278 -~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------------------~~~~~r~~~~~  334 (444)
                       ...+...+.+.+.+....  ..+.++||||+++.+++.+++.|...                      ++..+|..+++
T Consensus       610 ~~~~K~~~L~~lL~~~~~~--~~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~  687 (797)
T 4a2q_A          610 NENPKLEELVCILDDAYRY--NPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLD  687 (797)
T ss_dssp             CCCHHHHHHHHHHHHHHHH--CSSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC----------------------
T ss_pred             CCChHHHHHHHHHHHHhcc--CCCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHH
Confidence             000111111222221111  25689999999999999999999652                      77889999999


Q ss_pred             HHhc-CCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhh
Q psy7952         335 SFMR-GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKS  401 (444)
Q Consensus       335 ~f~~-g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~  401 (444)
                      .|++ |+.+|||||+++++|||+|++++||+||+|+|+..|+||+|| ||. +.|.+++++.+.+...
T Consensus       688 ~F~~~g~~~vLVaT~~~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~~ee  753 (797)
T 4a2q_A          688 AFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVE  753 (797)
T ss_dssp             ------CCSEEEEECC-------CCCSEEEEESCCSCHHHHHTC---------CCCEEEEECCHHHHH
T ss_pred             HhhccCCceEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCCcHHH
Confidence            9998 999999999999999999999999999999999999999999 999 8899999998776543

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=100.00  E-value=1.7e-38  Score=332.30  Aligned_cols=332  Identities=14%  Similarity=0.154  Sum_probs=187.7

Q ss_pred             HHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC--ccceeEEEcchhh
Q psy7952          39 KLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN--VRSRNGWISPILS  116 (444)
Q Consensus        39 ~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~--~~~~vlil~P~~~  116 (444)
                      ++.. +|+.. |+++|.++++.++.| +++++++|||+|||++        +.+++ ++.+....  ...++||++|+++
T Consensus         5 ~l~~-~g~~~-lr~~Q~~~i~~~l~g-~~~iv~~~TGsGKTl~--------~~~~i-~~~l~~~~~~~~~~~lvl~Pt~~   72 (696)
T 2ykg_A            5 DTNL-YSPFK-PRNYQLELALPAMKG-KNTIICAPTGCGKTFV--------SLLIC-EHHLKKFPQGQKGKVVFFANQIP   72 (696)
T ss_dssp             --CT-TC--C-CCHHHHHHHHHHHTT-CCEEEECCTTSSHHHH--------HHHHH-HHHHHHSCTTCCCCEEEECSSHH
T ss_pred             cccc-cCCCC-ccHHHHHHHHHHHcC-CCEEEEcCCCchHHHH--------HHHHH-HHHHHhCccCCCCeEEEEECCHH
Confidence            4444 69888 569999999999999 9999999999999999        55555 33233221  2246799999999


Q ss_pred             hhcccCccchHhhh-c-CCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH-hhCCc
Q psy7952         117 SFYLRFRDDKTSIV-T-GRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV-RYNKL  193 (444)
Q Consensus       117 L~~~~q~~~~~~~l-~-~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~-~~~~~  193 (444)
                      |+     .|+.+.+ . ....++++..++|+..........      ..+++|+|+||++|.    ..+..... .+.++
T Consensus        73 L~-----~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~------~~~~~Iiv~Tp~~L~----~~l~~~~~~~l~~~  137 (696)
T 2ykg_A           73 VY-----EQNKSVFSKYFERHGYRVTGISGATAENVPVEQI------VENNDIIILTPQILV----NNLKKGTIPSLSIF  137 (696)
T ss_dssp             HH-----HHHHHHHHHHTTTTTCCEEEECSSSCSSSCHHHH------HHTCSEEEECHHHHH----HHHHTTSSCCGGGC
T ss_pred             HH-----HHHHHHHHHHhccCCceEEEEeCCccccccHHHh------ccCCCEEEECHHHHH----HHHhcCcccccccc
Confidence            99     5555555 1 111238899999987654333222      136899999999985    22222222 46778


Q ss_pred             cEEEEeccccccccCCCcHHHHHHHHH-HH-HhhCCCCcEEEEeccCC-------cchHHHHHHHhcCCC----------
Q psy7952         194 AYIVVDEAHCVSEWGHDFRPTYRRLGE-LR-QFTGNSIPIIALTATAE-------PSVKQDIISVLKFNK----------  254 (444)
Q Consensus       194 ~~iViDE~H~~~~~~~~~~~~~~~l~~-~~-~~~~~~~~~v~lSAT~~-------~~~~~~~~~~l~~~~----------  254 (444)
                      ++||+||||++.+.. .+...+..... .+ ...+..+++++|||||.       ....+.+...+...+          
T Consensus       138 ~~vViDEaH~~~~~~-~~~~i~~~~l~~~~~~~~~~~~~il~LTATp~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~~~  216 (696)
T 2ykg_A          138 TLMIFDECHNTSKQH-PYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKTTDEALDYICKLCASLDASVIATVKHN  216 (696)
T ss_dssp             SEEEEETGGGCSTTC-HHHHHHHHHHHHHHTTCCSCCCEEEEEESCCCCSSCCSHHHHHHHHHHHHHHTTCCEEECCCTT
T ss_pred             cEEEEeCCCcccCcc-cHHHHHHHHHHHhhcccCCCCCeEEEEeCccccCccccHHHHHHHHHHHHHhcCCceEeecccc
Confidence            999999999987543 23322221111 11 11234588999999997       222333333321100          


Q ss_pred             ----------CeEEEecCCCCCCceE----------------------------------------------------EE
Q psy7952         255 ----------PYKVFKTSTFRSNLFY----------------------------------------------------DV  272 (444)
Q Consensus       255 ----------~~~~~~~~~~~~~~~~----------------------------------------------------~~  272 (444)
                                +.........+....+                                                    ..
T Consensus       217 ~~~l~~~~~~p~~~~~~~~~~~~~~fs~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  296 (696)
T 2ykg_A          217 LEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQM  296 (696)
T ss_dssp             HHHHHHHSCCCEEEEEECCCCSCCHHHHHHHHHHHHHHHHHHHHSTTGGGSSSCCSCCSSSHHHHHHHHHHHHTSCC---
T ss_pred             hHHHHhhcCCCceeEEecCcccCChHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHHHHHHhhc
Confidence                      1000000000000000                                                    00


Q ss_pred             EEc----------------------------------------------------------------------------c
Q psy7952         273 IFD----------------------------------------------------------------------------D  276 (444)
Q Consensus       273 ~~~----------------------------------------------------------------------------~  276 (444)
                      ...                                                                            .
T Consensus       297 ~~~~~~~~~~~~l~~~~~~l~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  376 (696)
T 2ykg_A          297 PDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPS  376 (696)
T ss_dssp             ---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTHHHHHHHHHCGG
T ss_pred             ccchhhhHHHHHHHHHHHHHHHHhHHHhccchhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            000                                                                            0


Q ss_pred             cchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHh----------------------hcCHHHHHHHHH
Q psy7952         277 LLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR----------------------KVNKHERSRVQE  334 (444)
Q Consensus       277 ~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~----------------------~~~~~~r~~~~~  334 (444)
                      ....+...+.+++.....  ...+.++||||+++.+++.+++.|..                      .++..+|..+++
T Consensus       377 ~~~~k~~~L~~ll~~~~~--~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~  454 (696)
T 2ykg_A          377 NENPKLEDLCFILQEEYH--LNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILD  454 (696)
T ss_dssp             GCCHHHHHHHHHHHHHHT--TCTTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------
T ss_pred             CCCHHHHHHHHHHHHHhc--cCCCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHH
Confidence            001112222233332221  12567999999999999999999975                      266789999999


Q ss_pred             HHhc-CCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhH
Q psy7952         335 SFMR-GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL  402 (444)
Q Consensus       335 ~f~~-g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~  402 (444)
                      +|++ |+.+|||||+++++|||+|++++||+||+|.|...|+||+|| ||. ++|.++.+++..+....
T Consensus       455 ~F~~~g~~~vLVaT~v~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~~~~~  521 (696)
T 2ykg_A          455 AFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNAGVIEK  521 (696)
T ss_dssp             ------CCSCSEEEESSCCC---CCCSEEEEESCC--CCCC-----------CCCEEEEEESCHHHHHH
T ss_pred             HHHhcCCccEEEEechhhcCCcCccCCEEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCCCHHHH
Confidence            9998 999999999999999999999999999999999999999999 998 78999999988776443

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2e-37  Score=330.68  Aligned_cols=319  Identities=19%  Similarity=0.205  Sum_probs=224.4

Q ss_pred             HHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcc
Q psy7952          41 KALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYL  120 (444)
Q Consensus        41 ~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~  120 (444)
                      ...|+|+  ++++|.++++.+.++ +++++++|||+|||++        +.+++ +..+..+   .+++|++|+++|+  
T Consensus        80 ~~~~~f~--L~~~Q~eai~~l~~g-~~vLV~apTGSGKTlv--------a~lai-~~~l~~g---~rvL~l~PtkaLa--  142 (1010)
T 2xgj_A           80 ARTYPFT--LDPFQDTAISCIDRG-ESVLVSAHTSAGKTVV--------AEYAI-AQSLKNK---QRVIYTSPIKALS--  142 (1010)
T ss_dssp             SCCCSSC--CCHHHHHHHHHHHHT-CEEEEECCTTSCHHHH--------HHHHH-HHHHHTT---CEEEEEESSHHHH--
T ss_pred             HHhCCCC--CCHHHHHHHHHHHcC-CCEEEECCCCCChHHH--------HHHHH-HHHhccC---CeEEEECChHHHH--
Confidence            3446777  468999999999998 9999999999999999        44444 2223222   4669999999999  


Q ss_pred             cCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEe
Q psy7952         121 RFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVD  199 (444)
Q Consensus       121 ~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViD  199 (444)
                         .|+.+.+ ...   -.+..++|+....             .+++|+|+||+++.    ..+......+.++++||+|
T Consensus       143 ---~Q~~~~l~~~~---~~vglltGd~~~~-------------~~~~IvV~Tpe~L~----~~L~~~~~~l~~l~lVViD  199 (1010)
T 2xgj_A          143 ---NQKYRELLAEF---GDVGLMTGDITIN-------------PDAGCLVMTTEILR----SMLYRGSEVMREVAWVIFD  199 (1010)
T ss_dssp             ---HHHHHHHHHHH---SCEEEECSSCEEC-------------TTCSEEEEEHHHHH----HHHHHTCTTGGGEEEEEEE
T ss_pred             ---HHHHHHHHHHh---CCEEEEeCCCccC-------------CCCCEEEEcHHHHH----HHHHcCcchhhcCCEEEEe
Confidence               6777777 322   1577788877643             46799999999975    3333444556789999999


Q ss_pred             ccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhc--CCCCeEEEecCCCCCCceEEEEEcc-
Q psy7952         200 EAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLK--FNKPYKVFKTSTFRSNLFYDVIFDD-  276 (444)
Q Consensus       200 E~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~--~~~~~~~~~~~~~~~~~~~~~~~~~-  276 (444)
                      |+|++.+++  +...+..   ++..++.+.++|+||||+++..  .+..+++  ...+..+........++...+.... 
T Consensus       200 EaH~l~d~~--rg~~~e~---il~~l~~~~~il~LSATi~n~~--e~a~~l~~~~~~~~~vi~~~~rp~pl~~~~~~~~~  272 (1010)
T 2xgj_A          200 EVHYMRDKE--RGVVWEE---TIILLPDKVRYVFLSATIPNAM--EFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAHG  272 (1010)
T ss_dssp             TGGGGGCTT--THHHHHH---HHHHSCTTCEEEEEECCCTTHH--HHHHHHHHHHTSCEEEEEECCCSSCEEEEEEETTS
T ss_pred             chhhhcccc--hhHHHHH---HHHhcCCCCeEEEEcCCCCCHH--HHHHHHHhhcCCCeEEEecCCCcccceEEEEecCC
Confidence            999998765  3333333   3345667799999999987642  2334432  1233344333322222222211100 


Q ss_pred             ---------cc---hh------------------------------h--------HHHHHHHHHHHhccCCCCCceEEEE
Q psy7952         277 ---------LL---KD------------------------------S--------YAHVKEFIEKCLGKDNKANNCGIIY  306 (444)
Q Consensus       277 ---------~~---~~------------------------------~--------~~~~~~~l~~~l~~~~~~~~~~iVf  306 (444)
                               ..   ..                              +        ...+..++..+...   ...++|||
T Consensus       273 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~g~~~~~~k~~~~~~~~~~~l~~l~~~l~~~---~~~~~IVF  349 (1010)
T 2xgj_A          273 DGIYLVVDEKSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKK---KYNPVIVF  349 (1010)
T ss_dssp             SCCEEEECTTCCBCHHHHHHHHHTCC------------------------------CHHHHHHHHHHHH---TCCSEEEE
T ss_pred             cceeeeeccccccchHHHHHHHHHHhhhhcccccccccccccccccccccccccchHHHHHHHHHHHhc---CCCCEEEE
Confidence                     00   00                              0        11111222222211   35689999


Q ss_pred             ecccchHHHHHHHHHhh-------------------------------------------------cCHHHHHHHHHHHh
Q psy7952         307 CRTREHTTDLADALRRK-------------------------------------------------VNKHERSRVQESFM  337 (444)
Q Consensus       307 ~~s~~~~~~l~~~L~~~-------------------------------------------------~~~~~r~~~~~~f~  337 (444)
                      |+++..|+.++..|...                                                 +++.+|..+++.|+
T Consensus       350 ~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR~~ve~~F~  429 (1010)
T 2xgj_A          350 SFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQ  429 (1010)
T ss_dssp             ESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHHHHHHHHHH
T ss_pred             ECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHHHHHHHHHh
Confidence            99999999998877540                                                 77889999999999


Q ss_pred             cCCccEEEEcCccccccccCCccEEEE----eCC----CCCHHHHHHHhccCCCCCC--ceeEEEEeccc-chhhHHHHH
Q psy7952         338 RGEINVITATISFGMGIDRQNVRFVVH----WGM----PSSIPAYYQESGRAGRDGL--QSYCRIYHSEH-SKKSLEYVI  406 (444)
Q Consensus       338 ~g~~~vLvaT~~~~~Gidi~~~~~Vi~----~~~----p~s~~~~~Qr~GR~~R~g~--~g~~~~~~~~~-~~~~~~~~~  406 (444)
                      +|.++|||||+++++|||+|++++||+    ||.    |.|..+|+||+||+||.|.  .|.+++++.+. +...+..+.
T Consensus       430 ~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~~e~~~~~~l~  509 (1010)
T 2xgj_A          430 EGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMV  509 (1010)
T ss_dssp             TTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSCCCHHHHHHHH
T ss_pred             cCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCCCceEEEEEECCCCCHHHHHHHH
Confidence            999999999999999999999999999    998    8899999999999999986  59999999865 556667765


Q ss_pred             hhc
Q psy7952         407 KTD  409 (444)
Q Consensus       407 ~~~  409 (444)
                      ...
T Consensus       510 ~~~  512 (1010)
T 2xgj_A          510 KGQ  512 (1010)
T ss_dssp             SCC
T ss_pred             hCC
Confidence            433

>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=100.00  E-value=1e-38  Score=330.53  Aligned_cols=344  Identities=18%  Similarity=0.224  Sum_probs=235.0

Q ss_pred             HHHHHHHHHhCCcccCchHHHHHHHHHHcc-----CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeE
Q psy7952          35 ELTAKLKALFGFDSFKCELQKKAIRHILLR-----THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNG  109 (444)
Q Consensus        35 ~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~-----~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vl  109 (444)
                      ++.+.+.+.+||+  +|++|.++++.++.+     ..++++++|||+|||++        +.+++ +..+..+   .+++
T Consensus       356 ~~~~~~~~~lpf~--lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlv--------all~i-l~~l~~g---~qvl  421 (780)
T 1gm5_A          356 KLAEEFIKSLPFK--LTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVV--------AQLAI-LDNYEAG---FQTA  421 (780)
T ss_dssp             HHHHHHHHHSSSC--CCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHH--------HHHHH-HHHHHHT---SCEE
T ss_pred             HHHHHHHHhCCCC--CCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHH--------HHHHH-HHHHHcC---CeEE
Confidence            4555565668994  679999999998874     14899999999999999        55555 3323333   3569


Q ss_pred             EEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH
Q psy7952         110 WISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL  187 (444)
Q Consensus       110 il~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~  187 (444)
                      |++||++|+     .|+.+.+  .....++++..++|+....++...+..+.  .+.++|+|+||+.+         ...
T Consensus       422 vlaPtr~La-----~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~--~g~~~IvVgT~~ll---------~~~  485 (780)
T 1gm5_A          422 FMVPTSILA-----IQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLR--NGQIDVVIGTHALI---------QED  485 (780)
T ss_dssp             EECSCHHHH-----HHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHH--SSCCCEEEECTTHH---------HHC
T ss_pred             EEeCcHHHH-----HHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHh--cCCCCEEEECHHHH---------hhh
Confidence            999999999     5555554  11112289999999998887776666654  35699999999874         234


Q ss_pred             HhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEec-CCCCC
Q psy7952         188 VRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT-STFRS  266 (444)
Q Consensus       188 ~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~-~~~~~  266 (444)
                      ..+.++++||+||+|++...   .+       ..+.....++++++|||||.+.....  ...+..+ ..+... ...+.
T Consensus       486 ~~~~~l~lVVIDEaHr~g~~---qr-------~~l~~~~~~~~vL~mSATp~p~tl~~--~~~g~~~-~s~i~~~p~~r~  552 (780)
T 1gm5_A          486 VHFKNLGLVIIDEQHRFGVK---QR-------EALMNKGKMVDTLVMSATPIPRSMAL--AFYGDLD-VTVIDEMPPGRK  552 (780)
T ss_dssp             CCCSCCCEEEEESCCCC---------------CCCCSSSSCCCEEEEESSCCCHHHHH--HHTCCSS-CEEECCCCSSCC
T ss_pred             hhccCCceEEecccchhhHH---HH-------HHHHHhCCCCCEEEEeCCCCHHHHHH--HHhCCcc-eeeeeccCCCCc
Confidence            56789999999999996321   11       01112233588999999998765442  2222212 122211 12222


Q ss_pred             CceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccc--------hHHHHHHHHHh-h------------cC
Q psy7952         267 NLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTRE--------HTTDLADALRR-K------------VN  325 (444)
Q Consensus       267 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~--------~~~~l~~~L~~-~------------~~  325 (444)
                      ++...+.    .......+.+.+.+.+    ..+++++|||++.+        .++.+++.|.+ .            ++
T Consensus       553 ~i~~~~~----~~~~~~~l~~~i~~~l----~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~  624 (780)
T 1gm5_A          553 EVQTMLV----PMDRVNEVYEFVRQEV----MRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLS  624 (780)
T ss_dssp             CCEECCC----CSSTHHHHHHHHHHHT----TTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSC
T ss_pred             ceEEEEe----ccchHHHHHHHHHHHH----hcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCC
Confidence            3222111    1222334444444433    25778999999764        46778888877 2            78


Q ss_pred             HHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCC-CHHHHHHHhccCCCCCCceeEEEEecccch---hh
Q psy7952         326 KHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQSYCRIYHSEHSK---KS  401 (444)
Q Consensus       326 ~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~-s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~---~~  401 (444)
                      +.+|..+++.|++|+.+|||||+++++|+|+|++++||+++.|. +...|.||+||+||.|+.|+|++++.+.+.   ..
T Consensus       625 ~~eR~~v~~~F~~G~~~ILVaT~vie~GIDiP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~~~~~~~~r  704 (780)
T 1gm5_A          625 QEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMER  704 (780)
T ss_dssp             CSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCeEEEECCCCCccccCCCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECCCChHHHHH
Confidence            89999999999999999999999999999999999999999986 789999999999999999999999974333   34


Q ss_pred             HHHHHhhccchhHHHHHHHHhhHHHHHH
Q psy7952         402 LEYVIKTDTSTKREQLELKFKNYLSMLE  429 (444)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~  429 (444)
                      +..+..........+.+.++++..++..
T Consensus       705 l~~l~~~~dgf~iae~dL~~Rg~gd~lG  732 (780)
T 1gm5_A          705 LRFFTLNTDGFKIAEYDLKTRGPGEFFG  732 (780)
T ss_dssp             HHHHHTCCCSHHHHHHHHHSSCCCC---
T ss_pred             HHHHHhhhccchhhHhhHhccCcchhhh
Confidence            5555554445554455555554444443

>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=100.00  E-value=1.8e-37  Score=310.87  Aligned_cols=311  Identities=18%  Similarity=0.189  Sum_probs=212.4

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhh
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      ++++|.+++..++.+  ++++.+|||+|||++++        .++ ...+.  +...++||++|+++|+     .++.+.
T Consensus        10 l~~~Q~~~i~~~~~~--~~ll~~~tG~GKT~~~~--------~~~-~~~~~--~~~~~~liv~P~~~L~-----~q~~~~   71 (494)
T 1wp9_A           10 PRIYQEVIYAKCKET--NCLIVLPTGLGKTLIAM--------MIA-EYRLT--KYGGKVLMLAPTKPLV-----LQHAES   71 (494)
T ss_dssp             CCHHHHHHHHHGGGS--CEEEECCTTSCHHHHHH--------HHH-HHHHH--HSCSCEEEECSSHHHH-----HHHHHH
T ss_pred             ccHHHHHHHHHHhhC--CEEEEcCCCCCHHHHHH--------HHH-HHHHh--cCCCeEEEEECCHHHH-----HHHHHH
Confidence            348999999999998  89999999999999943        333 11121  2234669999999999     566666


Q ss_pred             h--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccccc
Q psy7952         130 V--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEW  207 (444)
Q Consensus       130 l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~  207 (444)
                      +  ..+.+...+..++|+..........       .+++|+|+||+.+.    ..+........++++||+||||++.+.
T Consensus        72 ~~~~~~~~~~~v~~~~g~~~~~~~~~~~-------~~~~ivv~T~~~l~----~~~~~~~~~~~~~~~vIiDEaH~~~~~  140 (494)
T 1wp9_A           72 FRRLFNLPPEKIVALTGEKSPEERSKAW-------ARAKVIVATPQTIE----NDLLAGRISLEDVSLIVFDEAHRAVGN  140 (494)
T ss_dssp             HHHHBCSCGGGEEEECSCSCHHHHHHHH-------HHCSEEEECHHHHH----HHHHTTSCCTTSCSEEEEETGGGCSTT
T ss_pred             HHHHhCcchhheEEeeCCcchhhhhhhc-------cCCCEEEecHHHHH----HHHhcCCcchhhceEEEEECCcccCCC
Confidence            6  2342335889999988766544333       25799999999975    222333345678999999999998653


Q ss_pred             CCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcch--HHHHHHHhcCCCCeEEEecCCCCC---------CceEEEEEcc
Q psy7952         208 GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSV--KQDIISVLKFNKPYKVFKTSTFRS---------NLFYDVIFDD  276 (444)
Q Consensus       208 ~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~--~~~~~~~l~~~~~~~~~~~~~~~~---------~~~~~~~~~~  276 (444)
                      .. +    ..+...+....+..++++|||||....  ...+...++....   .......+         ...+......
T Consensus       141 ~~-~----~~~~~~~~~~~~~~~~l~lTaTp~~~~~~~~~l~~~l~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~  212 (494)
T 1wp9_A          141 YA-Y----VFIAREYKRQAKNPLVIGLTASPGSTPEKIMEVINNLGIEHI---EYRSENSPDVRPYVKGIRFEWVRVDLP  212 (494)
T ss_dssp             CH-H----HHHHHHHHHHCSSCCEEEEESCSCSSHHHHHHHHHHTTCCEE---EECCTTSTTTGGGCCCCCEEEEEECCC
T ss_pred             Cc-H----HHHHHHHHhcCCCCeEEEEecCCCCCcHHHHHHHHhcChhee---eccCCCcHHHHHhcCCCceeEEecCCc
Confidence            21 2    233333334455689999999998432  2223333332211   11110000         0000000000


Q ss_pred             --------------------------------------------------------------------------------
Q psy7952         277 --------------------------------------------------------------------------------  276 (444)
Q Consensus       277 --------------------------------------------------------------------------------  276 (444)
                                                                                                      
T Consensus       213 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  292 (494)
T 1wp9_A          213 EIYKEVRKLLREMLRDALKPLAETGLLESSSPDIPKKEVLRAGQIINEEMAKGNHDLRGLLLYHAMALKLHHAIELLETQ  292 (494)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTSSSCCCTTSCHHHHHHHHHHHHHHHTTTCCSTTTHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhccccccCCCcchhHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHHHhh
Confidence                                                                                            


Q ss_pred             -----------------------------------------------cchhhHHHHHHHHHHHhccCCCCCceEEEEecc
Q psy7952         277 -----------------------------------------------LLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRT  309 (444)
Q Consensus       277 -----------------------------------------------~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s  309 (444)
                                                                     ....+...+.+.+......  ..+.++||||++
T Consensus       293 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~--~~~~k~lVF~~~  370 (494)
T 1wp9_A          293 GLSALRAYIKKLYEEAKAGSTKASKEIFSDKRMKKAISLLVQAKEIGLDHPKMDKLKEIIREQLQR--KQNSKIIVFTNY  370 (494)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCCHHHHHHHTSHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHHHH--CTTCCEEEECSC
T ss_pred             cHHHHHHHHHHHHHhhccccchhhhhhhhhHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhcc--CCCCeEEEEEcc
Confidence                                                           0001111222222222211  258899999999


Q ss_pred             cchHHHHHHHHHhh------------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCH
Q psy7952         310 REHTTDLADALRRK------------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSI  371 (444)
Q Consensus       310 ~~~~~~l~~~L~~~------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~  371 (444)
                      +..++.+++.|...                  ++..+|..+++.|++|+.+|||||+++++|+|+|++++||++++|+|.
T Consensus       371 ~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~  450 (494)
T 1wp9_A          371 RETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSA  450 (494)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHH
T ss_pred             HHHHHHHHHHHHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCCceEEEECCccccCCCchhCCEEEEeCCCCCH
Confidence            99999999999864                  356789999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhccCCCCCCceeEEEEecccchh
Q psy7952         372 PAYYQESGRAGRDGLQSYCRIYHSEHSKK  400 (444)
Q Consensus       372 ~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~  400 (444)
                      ..|+||+||+||.|+ |.++.++.+++.+
T Consensus       451 ~~~~Qr~GR~~R~g~-g~~~~l~~~~t~e  478 (494)
T 1wp9_A          451 IRSIQRRGRTGRHMP-GRVIILMAKGTRD  478 (494)
T ss_dssp             HHHHHHHTTSCSCCC-SEEEEEEETTSHH
T ss_pred             HHHHHHHhhccCCCC-ceEEEEEecCCHH
Confidence            999999999999998 9999999877654

>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=100.00  E-value=2.4e-37  Score=343.72  Aligned_cols=366  Identities=15%  Similarity=0.195  Sum_probs=250.3

Q ss_pred             HHHHHh--CCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhh
Q psy7952          39 KLKALF--GFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILS  116 (444)
Q Consensus        39 ~l~~~~--g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~  116 (444)
                      .++.+|  +|+. .+++|.++++.++.++++++++||||+|||++|.+        ++ ++.+... ...+++|++|+++
T Consensus       915 ~~e~l~~~~f~~-fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliael--------ai-l~~l~~~-~~~kavyi~P~ra  983 (1724)
T 4f92_B          915 AFESLYQDKFPF-FNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEF--------AI-LRMLLQS-SEGRCVYITPMEA  983 (1724)
T ss_dssp             HHHTTTTTTCSB-CCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHH--------HH-HHHHHHC-TTCCEEEECSCHH
T ss_pred             HHHHHHHhcCCC-CCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHH--------HH-HHHHHhC-CCCEEEEEcChHH
Confidence            445444  6777 56999999999998878999999999999999544        43 2223322 2346799999999


Q ss_pred             hhcccCccchHhhh--cCC-CCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH---Hhh
Q psy7952         117 SFYLRFRDDKTSIV--TGR-SDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL---VRY  190 (444)
Q Consensus       117 L~~~~q~~~~~~~l--~~~-~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~---~~~  190 (444)
                      |+     .|.++.+  .++ ..++++..++|+......  ..       .+++|+|+|||++     +.+.+..   ..+
T Consensus       984 La-----~q~~~~~~~~f~~~~g~~V~~ltGd~~~~~~--~~-------~~~~IiV~TPEkl-----d~llr~~~~~~~l 1044 (1724)
T 4f92_B          984 LA-----EQVYMDWYEKFQDRLNKKVVLLTGETSTDLK--LL-------GKGNIIISTPEKW-----DILSRRWKQRKNV 1044 (1724)
T ss_dssp             HH-----HHHHHHHHHHHTTTSCCCEEECCSCHHHHHH--HH-------HHCSEEEECHHHH-----HHHHTTTTTCHHH
T ss_pred             HH-----HHHHHHHHHHhchhcCCEEEEEECCCCcchh--hc-------CCCCEEEECHHHH-----HHHHhCccccccc
Confidence            99     6666666  222 123889999987654322  11       2579999999996     3334332   235


Q ss_pred             CCccEEEEeccccccccC-CCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCc-
Q psy7952         191 NKLAYIVVDEAHCVSEWG-HDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNL-  268 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~-  268 (444)
                      .++++||+||+|.+.+.. ..+...+..+..+....+++.|+|+||||+++  .+++.+|++.............||.. 
T Consensus      1045 ~~v~lvViDE~H~l~d~rg~~le~il~rl~~i~~~~~~~~riI~lSATl~N--~~dla~WL~~~~~~~~~~~~~~RPvpL 1122 (1724)
T 4f92_B         1045 QNINLFVVDEVHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSN--AKDVAHWLGCSATSTFNFHPNVRPVPL 1122 (1724)
T ss_dssp             HSCSEEEECCGGGGGSTTHHHHHHHHHHHHHHHHTTSSCCEEEEEESCBTT--HHHHHHHHTCCSTTEEECCGGGCSSCE
T ss_pred             ceeeEEEeechhhcCCCCCccHHHHHHHHHHHHhhcCCCceEEEEeCCCCC--HHHHHHHhCCCCCCeEEeCCCCCCCCe
Confidence            689999999999986532 11222233333444455667999999999976  46788999876554444444455542 


Q ss_pred             eEEEEEcccchh--hHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----------------------
Q psy7952         269 FYDVIFDDLLKD--SYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----------------------  323 (444)
Q Consensus       269 ~~~~~~~~~~~~--~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----------------------  323 (444)
                      ...+........  ........+...+... ..++++||||+|+..|+.++..|...                       
T Consensus      1123 ~~~i~~~~~~~~~~~~~~~~~~~~~~i~~~-~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~ 1201 (1724)
T 4f92_B         1123 ELHIQGFNISHTQTRLLSMAKPVYHAITKH-SPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLE 1201 (1724)
T ss_dssp             EEEEEEECCCSHHHHHHTTHHHHHHHHHHH-CSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHT
T ss_pred             EEEEEeccCCCchhhhhhhcchHHHHHHHh-cCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHh
Confidence            222222221111  1111111111112111 25789999999999999988776432                       


Q ss_pred             ---------------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEE----eC------CCCCHH
Q psy7952         324 ---------------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVH----WG------MPSSIP  372 (444)
Q Consensus       324 ---------------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~----~~------~p~s~~  372 (444)
                                           +++.+|..+++.|++|.++|||||+++++|||+|...+||.    |+      .|.+..
T Consensus      1202 ~~~d~~L~~~l~~GIa~hHagL~~~~R~~VE~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~ 1281 (1724)
T 4f92_B         1202 KLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIY 1281 (1724)
T ss_dssp             TCCCHHHHHHHHTTEEEECTTSCHHHHHHHHHHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHH
T ss_pred             hcccHHHHHHHhCCEEEECCCCCHHHHHHHHHHHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHH
Confidence                                 88999999999999999999999999999999999888883    22      356899


Q ss_pred             HHHHHhccCCCCCC--ceeEEEEecccchhhHHHHHhhccchhHH-----------HHHH-HHhhHHHHHHHhhhceee
Q psy7952         373 AYYQESGRAGRDGL--QSYCRIYHSEHSKKSLEYVIKTDTSTKRE-----------QLEL-KFKNYLSMLEYCEQGYFL  437 (444)
Q Consensus       373 ~~~Qr~GR~~R~g~--~g~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~-~~~~~~~~~~~~~~~~~~  437 (444)
                      +|.||+|||||.|.  .|.+++++.+.+...+++++..+.+.+..           ++-. .+.+..+.++|....|+.
T Consensus      1282 ~~~Qm~GRAGR~g~d~~G~avll~~~~~~~~~~~ll~~~~pveS~L~~~l~~~l~~eI~~~~i~~~~d~~~~l~~Tfl~ 1360 (1724)
T 4f92_B         1282 DVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTFLY 1360 (1724)
T ss_dssp             HHHHHHTTBCCTTTCSCEEEEEEEEGGGHHHHHHHTTSCBCCCCCGGGSCHHHHHHHHHTTSCCBHHHHHHHHTTSSHH
T ss_pred             HHHHhhccccCCCCCCceEEEEEecchHHHHHHHHhCCCCceeeecccchHHHHHHHHHhcccCCHHHHHHHHHhhHHH
Confidence            99999999999986  69999999999999999998776654311           1111 134556666776666553

>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=100.00  E-value=4.7e-38  Score=329.17  Aligned_cols=324  Identities=15%  Similarity=0.155  Sum_probs=200.2

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC---CccceeEEEcchhhhhcccCccch
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG---NVRSRNGWISPILSSFYLRFRDDK  126 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~---~~~~~vlil~P~~~L~~~~q~~~~  126 (444)
                      ++++|.++++.+++| +++++.+|||+|||++        |.+|+ +..+...   +...++||++|+++|+     .|+
T Consensus         8 l~~~Q~~~i~~il~g-~~~ll~~~TGsGKTl~--------~~~~i-~~~l~~~~~~~~~~~vlvl~P~~~L~-----~Q~   72 (699)
T 4gl2_A            8 LRPYQMEVAQPALEG-KNIIICLPTGCGKTRV--------AVYIA-KDHLDKKKKASEPGKVIVLVNKVLLV-----EQL   72 (699)
T ss_dssp             CCHHHHHHHHHHHSS-CCEEECCCTTSCHHHH--------HHHHH-HHHHHHHHHHTCCCCBCCEESCSHHH-----HHH
T ss_pred             ccHHHHHHHHHHHhC-CCEEEEcCCCCcHHHH--------HHHHH-HHHHHhccccCCCCeEEEEECCHHHH-----HHH
Confidence            458999999999998 8999999999999999        66665 3323222   1224679999999999     566


Q ss_pred             -Hhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHH--HHHHHhhCCccEEEEeccc
Q psy7952         127 -TSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYL--LQHLVRYNKLAYIVVDEAH  202 (444)
Q Consensus       127 -~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~--~~~~~~~~~~~~iViDE~H  202 (444)
                       .+.+ ......+.+..++|+...........      +.++|+|+||++|........  ......+.++++||+||||
T Consensus        73 ~~~~l~~~~~~~~~v~~~~g~~~~~~~~~~~~------~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH  146 (699)
T 4gl2_A           73 FRKEFQPFLKKWYRVIGLSGDTQLKISFPEVV------KSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECH  146 (699)
T ss_dssp             HHHTHHHHHTTTSCEEEEC----CCCCHHHHH------HSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGG
T ss_pred             HHHHHHHHcCcCceEEEEeCCcchhhHHHhhh------cCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECcc
Confidence             5555 22222378999999876554333221      478999999999852111000  1222356789999999999


Q ss_pred             cccccCCCcHHHHHHHHH-HHHhhC---------CCCcEEEEeccCCcc-------hHHHHHHHhcCCCCeEEEecC---
Q psy7952         203 CVSEWGHDFRPTYRRLGE-LRQFTG---------NSIPIIALTATAEPS-------VKQDIISVLKFNKPYKVFKTS---  262 (444)
Q Consensus       203 ~~~~~~~~~~~~~~~l~~-~~~~~~---------~~~~~v~lSAT~~~~-------~~~~~~~~l~~~~~~~~~~~~---  262 (444)
                      ++...+ .+......+.. .+....         +.+++++|||||...       ..+.+......-+...+....   
T Consensus       147 ~~~~~~-~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~il~lTATp~~~~~~~~~~~~~~i~~l~~~l~~~~i~~~~~~~  225 (699)
T 4gl2_A          147 HTNKEA-VYNNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENL  225 (699)
T ss_dssp             GCBTTB-SSCSHHHHHHHHHHHHHHHHC----CCCCCEEEEECSCCCCCSCCSHHHHHHHHHHHHHHHTCSCCCCCCTTH
T ss_pred             ccCccc-hHHHHHHHHHHhhhcccccccccccCCCCCEEEEecccccccccccHHHHHHHHHHHHhhcCCCEEEeecCch
Confidence            985422 23333332211 111111         447899999999974       223333222111110000000   


Q ss_pred             ------CCCCCceEEEEEcccc----------------------------------------------------------
Q psy7952         263 ------TFRSNLFYDVIFDDLL----------------------------------------------------------  278 (444)
Q Consensus       263 ------~~~~~~~~~~~~~~~~----------------------------------------------------------  278 (444)
                            ..++...+........                                                          
T Consensus       226 ~~l~~~~~~p~~~~~~~~~~~~~~~~~~l~~l~~~i~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  305 (699)
T 4gl2_A          226 DQLKNQIQEPCKKFAIADATREDPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQMEKKAAKEGNRKERVCAEHLR  305 (699)
T ss_dssp             HHHHHHSCCCEEEEEEEC-----CHHHHHHHHHHHHHHHHTCCCCSCSSSHHHHHHHHHHHHHHHHHTCTTTHHHHHHHH
T ss_pred             HHHhhhcCCCceEEEEcccccCChHHHHHHHHHHHHHHHhccCcchhccchHHHHHHHHHHHHHHHhhhhhhHHHHHHHH
Confidence                  0112222221110000                                                          


Q ss_pred             --------------------------------------------------------------------------hhhHHH
Q psy7952         279 --------------------------------------------------------------------------KDSYAH  284 (444)
Q Consensus       279 --------------------------------------------------------------------------~~~~~~  284 (444)
                                                                                                ..+...
T Consensus       306 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~k~~~  385 (699)
T 4gl2_A          306 KYNEALQINDTIRMIDAYTHLETFYNEEKDKKFAVIEDDLKKPLKLDETDRFLMTLFFENNKMLKRLAENPEYENEKLTK  385 (699)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHC------------CCHHHHHHHHHHHHHHHHHHHHHTCCC----CSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccchhHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHH
Confidence                                                                                      000001


Q ss_pred             HHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------------------------cCHHHHHHHHHHHhcCC
Q psy7952         285 VKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------------------VNKHERSRVQESFMRGE  340 (444)
Q Consensus       285 ~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------------------------~~~~~r~~~~~~f~~g~  340 (444)
                      +.+.+....... ..+.++||||+++++++.+++.|...                        ++..+|..+++.|++|+
T Consensus       386 L~~~L~~~~~~~-~~~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~  464 (699)
T 4gl2_A          386 LRNTIMEQYTRT-EESARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGK  464 (699)
T ss_dssp             SHHHHHHHHHHS-SSCCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC--
T ss_pred             HHHHHHHHHhcC-CCCCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCC
Confidence            111222211111 01789999999999999999999864                        78899999999999999


Q ss_pred             ccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccc
Q psy7952         341 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS  398 (444)
Q Consensus       341 ~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~  398 (444)
                      .+|||||+++++|||+|++++||++|+|+|...|+||+|||||.|  +.++++...++
T Consensus       465 ~~VLVaT~~~~~GIDip~v~~VI~~d~p~s~~~~~Qr~GRArr~g--~~~~l~~~~~~  520 (699)
T 4gl2_A          465 INLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADE--STYVLVAHSGS  520 (699)
T ss_dssp             -CCSEEECSCCTTSCCCSCCCCEEESCCCCHHHHHHHHTTSCSSS--CEEEEEEESSS
T ss_pred             CcEEEEccccccCCccccCCEEEEeCCCCCHHHHHHHcCCCCCCC--ceEEEEEeCCc
Confidence            999999999999999999999999999999999999999987665  44444444443

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=100.00  E-value=7.1e-37  Score=326.47  Aligned_cols=326  Identities=20%  Similarity=0.201  Sum_probs=224.9

Q ss_pred             HHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcc
Q psy7952          34 QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISP  113 (444)
Q Consensus        34 ~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P  113 (444)
                      .++...+...|+|+.  +++|.++++.+++| +++++.+|||+|||++        |.+++ ...+..+   .+++|++|
T Consensus        26 ~~l~~~~~~~~~f~l--~~~Q~~aI~~il~g-~~vlv~apTGsGKTlv--------~~~~i-~~~~~~g---~~vlvl~P   90 (997)
T 4a4z_A           26 DELIPNPARSWPFEL--DTFQKEAVYHLEQG-DSVFVAAHTSAGKTVV--------AEYAI-AMAHRNM---TKTIYTSP   90 (997)
T ss_dssp             HHHCSSCSCCCSSCC--CHHHHHHHHHHHTT-CEEEEECCTTSCSHHH--------HHHHH-HHHHHTT---CEEEEEES
T ss_pred             hhhhHhHHHhCCCCC--CHHHHHHHHHHHcC-CCEEEEECCCCcHHHH--------HHHHH-HHHHhcC---CeEEEEeC
Confidence            333344555678873  68999999999999 9999999999999998        44444 2222222   35699999


Q ss_pred             hhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCc
Q psy7952         114 ILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKL  193 (444)
Q Consensus       114 ~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~  193 (444)
                      +++|+     .|+++.+...+..+.+..++|+...             ...++|+|+||+++.    ..+......+.++
T Consensus        91 traLa-----~Q~~~~l~~~~~~~~v~~l~G~~~~-------------~~~~~IlV~Tpe~L~----~~l~~~~~~l~~l  148 (997)
T 4a4z_A           91 IKALS-----NQKFRDFKETFDDVNIGLITGDVQI-------------NPDANCLIMTTEILR----SMLYRGADLIRDV  148 (997)
T ss_dssp             CGGGH-----HHHHHHHHTTC--CCEEEECSSCEE-------------CTTSSEEEEEHHHHH----HHHHHTCSGGGGE
T ss_pred             CHHHH-----HHHHHHHHHHcCCCeEEEEeCCCcc-------------CCCCCEEEECHHHHH----HHHHhCchhhcCC
Confidence            99999     7778877332223789999998754             356899999999985    3333444456789


Q ss_pred             cEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcC--CCCeEEEecCCCCCCceEE
Q psy7952         194 AYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKF--NKPYKVFKTSTFRSNLFYD  271 (444)
Q Consensus       194 ~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~~~~~  271 (444)
                      ++||+||+|++.+++.  ...+..+   ...++.+.++|++|||+++..  .+.++++.  .....+........++.+.
T Consensus       149 ~lvViDEaH~l~d~~~--g~~~e~i---i~~l~~~v~iIlLSAT~~n~~--ef~~~l~~~~~~~~~vi~~~~r~~pl~~~  221 (997)
T 4a4z_A          149 EFVIFDEVHYVNDQDR--GVVWEEV---IIMLPQHVKFILLSATVPNTY--EFANWIGRTKQKNIYVISTPKRPVPLEIN  221 (997)
T ss_dssp             EEEEECCTTCCCTTCT--TCCHHHH---HHHSCTTCEEEEEECCCTTHH--HHHHHHHHHHTCCEEEEECSSCSSCEEEE
T ss_pred             CEEEEECcccccccch--HHHHHHH---HHhcccCCCEEEEcCCCCChH--HHHHHHhcccCCceEEEecCCCCccceEE
Confidence            9999999999988763  3333333   334666799999999997643  45566542  1333333333322232222


Q ss_pred             EEEcccc-----------hhh-----------------------------------------------------------
Q psy7952         272 VIFDDLL-----------KDS-----------------------------------------------------------  281 (444)
Q Consensus       272 ~~~~~~~-----------~~~-----------------------------------------------------------  281 (444)
                      +......           ...                                                           
T Consensus       222 v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rg~~~~~~~~~~g~~~~~~~~  301 (997)
T 4a4z_A          222 IWAKKELIPVINQNSEFLEANFRKHKEILNGESAKGAPSKTDNGRGGSTARGGRGGSNTRDGRGGRGNSTRGGANRGGSR  301 (997)
T ss_dssp             EEETTEEEEEECTTCCBCHHHHHHHHHHHC--------------------------------------------------
T ss_pred             EecCCcchhcccchhhhhHHHHHHHHHHhhcccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            2110000           000                                                           


Q ss_pred             ------------------HHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHh---------------------
Q psy7952         282 ------------------YAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR---------------------  322 (444)
Q Consensus       282 ------------------~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~---------------------  322 (444)
                                        .......+...+...  ...++||||++++.|+.++..|..                     
T Consensus       302 ~~~~~~~~~~~~~~~~~~~~~~~~~li~~l~~~--~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~  379 (997)
T 4a4z_A          302 GAGAIGSNKRKFFTQDGPSKKTWPEIVNYLRKR--ELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSIT  379 (997)
T ss_dssp             ---------------CCCCTTHHHHHHHHHHHT--TCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHT
T ss_pred             ccccccccccccccccccchhHHHHHHHHHHhC--CCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHH
Confidence                              000111222223222  457999999999999999988843                     


Q ss_pred             ---------------------h-------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCC-----
Q psy7952         323 ---------------------K-------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPS-----  369 (444)
Q Consensus       323 ---------------------~-------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~-----  369 (444)
                                           .       +++.+|..+++.|++|.++|||||+++++|+|+|+ ..||+++.|+     
T Consensus       380 ~l~~~d~~l~~~~~l~~~l~~gi~~~H~gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~  458 (997)
T 4a4z_A          380 RLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNG  458 (997)
T ss_dssp             TSCHHHHTCHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCC-SEEEESCSEEEETTE
T ss_pred             hcchhhhcchhHHHHHHHhhcCeeeecCCCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCC-ceEEEeccccccCcc
Confidence                                 0       78999999999999999999999999999999999 6666666655     


Q ss_pred             ----CHHHHHHHhccCCCCC--CceeEEEEec--ccchhhHHHHH
Q psy7952         370 ----SIPAYYQESGRAGRDG--LQSYCRIYHS--EHSKKSLEYVI  406 (444)
Q Consensus       370 ----s~~~~~Qr~GR~~R~g--~~g~~~~~~~--~~~~~~~~~~~  406 (444)
                          |..+|+||+||+||.|  ..|.+++++.  ..+...+..++
T Consensus       459 ~~~~s~~~y~Qr~GRAGR~G~~~~G~vi~l~~~~~~~~~~~~~~i  503 (997)
T 4a4z_A          459 LRELTPGEFTQMAGRAGRRGLDSTGTVIVMAYNSPLSIATFKEVT  503 (997)
T ss_dssp             EEECCHHHHHHHHGGGCCTTTCSSEEEEEECCSSCCCHHHHHHHH
T ss_pred             CCCCCHHHHhHHhcccccCCCCcceEEEEecCCCcchHHHHHHHh
Confidence                9999999999999998  5688888773  33555555553

>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=100.00  E-value=1.2e-36  Score=324.80  Aligned_cols=322  Identities=14%  Similarity=0.179  Sum_probs=181.0

Q ss_pred             hCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC--ccceeEEEcchhhhhccc
Q psy7952          44 FGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN--VRSRNGWISPILSSFYLR  121 (444)
Q Consensus        44 ~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~--~~~~vlil~P~~~L~~~~  121 (444)
                      +|+.. |+++|.++++.++.| +++++.+|||+|||++        +.+|+ +..+....  ...++||++|+++|+   
T Consensus       244 ~~~~~-~r~~Q~~ai~~il~g-~~~ll~a~TGsGKTl~--------~~~~i-~~~l~~~~~~~~~~vLvl~Pt~~L~---  309 (936)
T 4a2w_A          244 YETKK-ARSYQIELAQPAING-KNALICAPTGSGKTFV--------SILIC-EHHFQNMPAGRKAKVVFLATKVPVY---  309 (936)
T ss_dssp             ----C-CCHHHHHHHHHHHTT-CCEEEECCTTSCHHHH--------HHHHH-HTTTTTCCSSCCCCEEEECSSHHHH---
T ss_pred             cCCCC-CCHHHHHHHHHHHcC-CCEEEEeCCCchHHHH--------HHHHH-HHHHHhccccCCCeEEEEeCCHHHH---
Confidence            45666 569999999999999 9999999999999999        55555 33333321  145679999999999   


Q ss_pred             CccchHhhh-----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH-hhCCccE
Q psy7952         122 FRDDKTSIV-----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV-RYNKLAY  195 (444)
Q Consensus       122 q~~~~~~~l-----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~-~~~~~~~  195 (444)
                        .|+...+     ..+   +++..++|+.........+      ..+++|+|+||+++.    ..+..... .+.++++
T Consensus       310 --~Q~~~~~~~~~~~~~---~~v~~~~G~~~~~~~~~~~------~~~~~IvI~Tp~~L~----~~l~~~~~~~l~~~~l  374 (936)
T 4a2w_A          310 --EQQKNVFKHHFERQG---YSVQGISGENFSNVSVEKV------IEDSDIIVVTPQILV----NSFEDGTLTSLSIFTL  374 (936)
T ss_dssp             --HHHHHHHHHHHHTTT---CCEEEECCC-----CCHHH------HHHCSEEEECHHHHH----HHHHSSSCCCGGGCSE
T ss_pred             --HHHHHHHHHHhcccC---ceEEEEECCcchhhHHHHh------ccCCCEEEecHHHHH----HHHHcCccccccCCCE
Confidence              4555444     235   8999999988654432222      135799999999974    22222222 3567899


Q ss_pred             EEEeccccccccCCCcHHHHHHHHHH-HHhhCCCCcEEEEeccCCcch-------HHHH---HHHhcCCCCeEEEecC--
Q psy7952         196 IVVDEAHCVSEWGHDFRPTYRRLGEL-RQFTGNSIPIIALTATAEPSV-------KQDI---ISVLKFNKPYKVFKTS--  262 (444)
Q Consensus       196 iViDE~H~~~~~~~~~~~~~~~l~~~-~~~~~~~~~~v~lSAT~~~~~-------~~~~---~~~l~~~~~~~~~~~~--  262 (444)
                      ||+||||++...+. +...+..+... ........+++++||||....       .+.+   ...++..   .+....  
T Consensus       375 iViDEaH~~~~~~~-~~~i~~~~~~~~~~~~~~~~~~l~LSATp~~~~~~~l~~~~~~i~~L~~~L~~~---~i~~~~~~  450 (936)
T 4a2w_A          375 MIFDECHNTTGNHP-YNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQ---AISTVREN  450 (936)
T ss_dssp             EEEETGGGCSTTCH-HHHHHHHHHHHHHTTCSCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCS---EEECCCSS
T ss_pred             EEEECccccCCCcc-HHHHHHHHHHHhhccCCCcCeEEEecCCcccccchhHHHHHHHHHHHHHhcCCc---eeeccccc
Confidence            99999999876542 33333222211 111144578999999996421       1111   2222110   011000  


Q ss_pred             -------CCCCCceEEEEEc------------------------------------ccchh-------------------
Q psy7952         263 -------TFRSNLFYDVIFD------------------------------------DLLKD-------------------  280 (444)
Q Consensus       263 -------~~~~~~~~~~~~~------------------------------------~~~~~-------------------  280 (444)
                             ..++...+.....                                    .....                   
T Consensus       451 ~~~l~~~~~~p~~~~~~~~~~~~~~~~~~l~~l~~~i~~~~~~~l~~~~l~~~~~~~~g~~~y~~~l~~l~k~~~~~~l~  530 (936)
T 4a2w_A          451 IQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTIAYVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLE  530 (936)
T ss_dssp             HHHHHHHSCCCCEEEEECCCCSCCHHHHHHHHHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCS
T ss_pred             HHHHHHhccCCcceEEecccccCcHHHHHHHHHHHHHHHHHHHHHhhhhhhhccccccchHHHHHHHHHHHHHHHHhccc
Confidence                   0111111110000                                    00000                   


Q ss_pred             ------------------------------------h-------------------------------------------
Q psy7952         281 ------------------------------------S-------------------------------------------  281 (444)
Q Consensus       281 ------------------------------------~-------------------------------------------  281 (444)
                                                          .                                           
T Consensus       531 ~~~~~~~~~~~l~~~~~~l~~~~~al~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~e~~l~~~~~~~~~~l~~~~~~~~~  610 (936)
T 4a2w_A          531 DKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETN  610 (936)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTSTTC
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHHhhhcchhHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHhhhccCC
Confidence                                                0                                           


Q ss_pred             HHHHHHHHHHHhccC--CCCCceEEEEecccchHHHHHHHHHhh----------------------cCHHHHHHHHHHHh
Q psy7952         282 YAHVKEFIEKCLGKD--NKANNCGIIYCRTREHTTDLADALRRK----------------------VNKHERSRVQESFM  337 (444)
Q Consensus       282 ~~~~~~~l~~~l~~~--~~~~~~~iVf~~s~~~~~~l~~~L~~~----------------------~~~~~r~~~~~~f~  337 (444)
                      .......+.+++...  ...+.++||||+++.+++.+++.|...                      ++..+|..++++|+
T Consensus       611 ~~~K~~~L~~lL~~~~~~~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr  690 (936)
T 4a2w_A          611 ENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFK  690 (936)
T ss_dssp             CCHHHHHHHHHHHHTTTSCTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC-------------------------
T ss_pred             CCHHHHHHHHHHHHHhccCCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhh
Confidence            000111122222221  135789999999999999999999864                      78889999999999


Q ss_pred             c-CCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchh
Q psy7952         338 R-GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK  400 (444)
Q Consensus       338 ~-g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~  400 (444)
                      + |+.+|||||+++++|||+|++++||+||+|+|...|+||+|| ||. ..|.++.++...+..
T Consensus       691 ~~g~~~VLVaT~~~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t~e  752 (936)
T 4a2w_A          691 TSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  752 (936)
T ss_dssp             ---CCSEEEEECC------CCCCSEEEEESCCSCSHHHHCC---------CCCEEEEESCHHHH
T ss_pred             ccCCeeEEEEeCchhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCCEEEEEEeCCCHH
Confidence            8 999999999999999999999999999999999999999999 999 778889998876554

>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=100.00  E-value=6.2e-38  Score=337.50  Aligned_cols=325  Identities=19%  Similarity=0.224  Sum_probs=216.4

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ..++.+.+.+.+|+.  | ++|.++++.+++| +++++.+|||+|||+.         .+|+ +..+..  ..++++|++
T Consensus        43 ~~~~~~~~~~~~g~~--p-~iQ~~ai~~il~g-~dvlv~apTGSGKTl~---------~lp~-l~~~~~--~~~~~lil~  106 (1054)
T 1gku_B           43 LKEFVEFFRKCVGEP--R-AIQKMWAKRILRK-ESFAATAPTGVGKTSF---------GLAM-SLFLAL--KGKRCYVIF  106 (1054)
T ss_dssp             HHHHHHHHHTTTCSC--C-HHHHHHHHHHHTT-CCEECCCCBTSCSHHH---------HHHH-HHHHHT--TSCCEEEEE
T ss_pred             hHHHHHHHHHhcCCC--H-HHHHHHHHHHHhC-CCEEEEcCCCCCHHHH---------HHHH-HHHHhh--cCCeEEEEe
Confidence            345667777778999  5 8999999999999 9999999999999953         3344 221222  234669999


Q ss_pred             chhhhhcccCccchHhhh--cCCCCce----eEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         113 PILSSFYLRFRDDKTSIV--TGRSDLY----QLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l--~~~~~~i----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      ||++|+  .|+.+.++.+  ..+   +    .+..++|+.....+......+   .. ++|+|+||++|..        .
T Consensus       107 PtreLa--~Q~~~~l~~l~~~~~---i~~~~~v~~~~Gg~~~~~~~~~~~~l---~~-~~IlV~TP~~L~~--------~  169 (1054)
T 1gku_B          107 PTSLLV--IQAAETIRKYAEKAG---VGTENLIGYYHGRIPKREKENFMQNL---RN-FKIVITTTQFLSK--------H  169 (1054)
T ss_dssp             SCHHHH--HHHHHHHHHHHTTTC---CSGGGSEEECCSSCCSHHHHHHHHSG---GG-CSEEEEEHHHHHH--------C
T ss_pred             ccHHHH--HHHHHHHHHHHhhcC---CCccceEEEEeCCCChhhHHHHHhhc---cC-CCEEEEcHHHHHH--------H
Confidence            999999  3334444444  223   6    789999998877654444333   23 8999999999742        2


Q ss_pred             HHhhCCccEEEEeccccccccCCCcHHHHHHHHH----HHHhhCCCCcEEEEeccCCcchHH----HHHHHhcCCCCeEE
Q psy7952         187 LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGE----LRQFTGNSIPIIALTATAEPSVKQ----DIISVLKFNKPYKV  258 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~----~~~~~~~~~~~v~lSAT~~~~~~~----~~~~~l~~~~~~~~  258 (444)
                      ...+.++++||+||+|++.++++.++..+..+..    .....+...+++++|||+++. ..    .+.......    +
T Consensus       170 l~~L~~l~~lViDEah~~l~~~~~~~~i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~----v  244 (1054)
T 1gku_B          170 YRELGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFD----I  244 (1054)
T ss_dssp             STTSCCCSEEEESCHHHHHTSTHHHHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCC----C
T ss_pred             HHHhccCCEEEEeChhhhhhccccHHHHHHHhCcchhhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEE----c
Confidence            2226689999999999998876444433332210    001113457899999999876 31    222222211    1


Q ss_pred             EecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----cCHHHHHHHHH
Q psy7952         259 FKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----VNKHERSRVQE  334 (444)
Q Consensus       259 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----~~~~~r~~~~~  334 (444)
                      ........++...+..    ..+...+.+++.    .   .++++||||++++.|+.++..|...    .-...+..+++
T Consensus       245 ~~~~~~~~~i~~~~~~----~~k~~~L~~ll~----~---~~~~~LVF~~t~~~a~~l~~~L~~~~~v~~lhg~~~~~l~  313 (1054)
T 1gku_B          245 GSSRITVRNVEDVAVN----DESISTLSSILE----K---LGTGGIIYARTGEEAEEIYESLKNKFRIGIVTATKKGDYE  313 (1054)
T ss_dssp             SCCEECCCCEEEEEES----CCCTTTTHHHHT----T---SCSCEEEEESSHHHHHHHHHTTTTSSCEEECTTSSSHHHH
T ss_pred             cCcccCcCCceEEEec----hhHHHHHHHHHh----h---cCCCEEEEEcCHHHHHHHHHHHhhccCeeEEeccHHHHHH
Confidence            1111122333333331    222223333332    2   2578999999999999999999864    11123468899


Q ss_pred             HHhcCCccEEEE----cCccccccccCCc-cEEEEeCCC-----------------------------------------
Q psy7952         335 SFMRGEINVITA----TISFGMGIDRQNV-RFVVHWGMP-----------------------------------------  368 (444)
Q Consensus       335 ~f~~g~~~vLva----T~~~~~Gidi~~~-~~Vi~~~~p-----------------------------------------  368 (444)
                      .|++|+.+||||    |+++++|+|+|+| ++||++|.|                                         
T Consensus       314 ~F~~G~~~VLVaTas~Tdv~~rGIDip~VI~~VI~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  393 (1054)
T 1gku_B          314 KFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHI  393 (1054)
T ss_dssp             HHHHTSCSEEEEECC------CCSCCTTTCCEEEEESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCH
T ss_pred             HHHcCCCcEEEEecCCCCeeEeccccCCcccEEEEeCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence            999999999999    9999999999995 999999999                                         


Q ss_pred             ------------------------------CCHHHHHHHhccCCCCCCce--eEEEEecccchhhHHHHH
Q psy7952         369 ------------------------------SSIPAYYQESGRAGRDGLQS--YCRIYHSEHSKKSLEYVI  406 (444)
Q Consensus       369 ------------------------------~s~~~~~Qr~GR~~R~g~~g--~~~~~~~~~~~~~~~~~~  406 (444)
                                                    .|..+|+||+||+||.|.+|  .+++++..++...+..+.
T Consensus       394 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~yiQr~GRagR~g~~g~~~g~~~~~~~d~~~~~~l~  463 (1054)
T 1gku_B          394 DEVREILKKVMGKERPQAKDVVVREGEVIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSELLSAFI  463 (1054)
T ss_dssp             HHHHHHHHHHHTTSCCSCSSSEEETTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEECSCHHHHHHHH
T ss_pred             HHHHHHHHHHhccccccccceeEeecceecCcHHHHhhhhchhhhccCCCCceEEEEEEecCHHHHHHHH
Confidence                                          79999999999999987765  367776666665554443

>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=100.00  E-value=8e-36  Score=303.37  Aligned_cols=316  Identities=15%  Similarity=0.138  Sum_probs=214.2

Q ss_pred             HHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          39 KLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        39 ~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      +.++.+|+ . ||++|..+++.+++| +  +..++||+|||++        |.+|+++..+ .   .+.++|++||++|+
T Consensus        75 a~~r~lG~-~-pt~VQ~~~ip~ll~G-~--Iaea~TGeGKTla--------f~LP~~l~aL-~---g~~vlVltptreLA  137 (844)
T 1tf5_A           75 ASRRVTGM-F-PFKVQLMGGVALHDG-N--IAEMKTGEGKTLT--------STLPVYLNAL-T---GKGVHVVTVNEYLA  137 (844)
T ss_dssp             HHHHHHSC-C-CCHHHHHHHHHHHTT-S--EEECCTTSCHHHH--------HHHHHHHHHT-T---SSCEEEEESSHHHH
T ss_pred             HHHHHcCC-C-CcHHHHHhhHHHhCC-C--EEEccCCcHHHHH--------HHHHHHHHHH-c---CCCEEEEeCCHHHH
Confidence            44456799 4 789999999999999 5  8999999999999        7788722222 2   23569999999999


Q ss_pred             cccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH------Hhh
Q psy7952         119 YLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL------VRY  190 (444)
Q Consensus       119 ~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~------~~~  190 (444)
                        .|+.+.+..+  ..+   +++..+.|+.+...+...+        +++|+|+||+.|.   |+.+..+.      ...
T Consensus       138 --~qd~e~~~~l~~~lg---l~v~~i~gg~~~~~r~~~~--------~~dIv~gTpgrlg---fD~L~D~m~~~~~~l~l  201 (844)
T 1tf5_A          138 --SRDAEQMGKIFEFLG---LTVGLNLNSMSKDEKREAY--------AADITYSTNNELG---FDYLRDNMVLYKEQMVQ  201 (844)
T ss_dssp             --HHHHHHHHHHHHHTT---CCEEECCTTSCHHHHHHHH--------HSSEEEEEHHHHH---HHHHHHTTCSSGGGCCC
T ss_pred             --HHHHHHHHHHHhhcC---CeEEEEeCCCCHHHHHHhc--------CCCEEEECchhhh---HHHHHHhhhcchhhhcc
Confidence              4556667776  567   9999999998765443322        5799999999984   34444443      234


Q ss_pred             CCccEEEEecccccc-ccCCC----------cHHHHHHHHHHHHhhC---------CCCcEE-----------------E
Q psy7952         191 NKLAYIVVDEAHCVS-EWGHD----------FRPTYRRLGELRQFTG---------NSIPII-----------------A  233 (444)
Q Consensus       191 ~~~~~iViDE~H~~~-~~~~~----------~~~~~~~l~~~~~~~~---------~~~~~v-----------------~  233 (444)
                      ..+.++|+||||.++ +.+..          -...+..+..+...++         +..+++                 +
T Consensus       202 r~~~~lVlDEaD~mLiDea~tplIisg~~~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~L  281 (844)
T 1tf5_A          202 RPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNL  281 (844)
T ss_dssp             CCCCEEEEETHHHHHTTTTTCEEEEEEEEECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCT
T ss_pred             cCCCEEEECchhhhhhhccccchhhcCCcccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCcccc
Confidence            688999999999986 54311          0123334444444443         123443                 5


Q ss_pred             EeccCC--------------------------------------------------------------------------
Q psy7952         234 LTATAE--------------------------------------------------------------------------  239 (444)
Q Consensus       234 lSAT~~--------------------------------------------------------------------------  239 (444)
                      +|||.+                                                                          
T Consensus       282 fsat~~~~~~~i~~al~A~~l~~~d~dYiv~dg~v~ivDe~tgr~m~grr~sdGLhqaieake~v~I~~e~~t~a~It~q  361 (844)
T 1tf5_A          282 FDVKHVALNHHINQALKAHVAMQKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQ  361 (844)
T ss_dssp             TSGGGHHHHHHHHHHHHHHHTCCBTTTEEEETTEEEEBCTTTCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEEEHH
T ss_pred             CCCccchhHHHHHHHHHHHHHhhcCCceEEecCeeEEeecccccccCCCccchhhHHHHhhcccceecccccccceeeHH
Confidence            555533                                                                          


Q ss_pred             -----------------cchHHHHHHHhcCCCCeEEEecCCCCCCceEE---EEEcccchhhHHHHHHHHHHHhccCCCC
Q psy7952         240 -----------------PSVKQDIISVLKFNKPYKVFKTSTFRSNLFYD---VIFDDLLKDSYAHVKEFIEKCLGKDNKA  299 (444)
Q Consensus       240 -----------------~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~l~~~l~~~~~~  299 (444)
                                       .. ...+.+..++.   .+. -+..++.+...   .... ....+...+.+.+.....    .
T Consensus       362 ~~fr~y~kl~GmTGTa~te-~~e~~~iY~l~---vv~-IPtn~p~~r~d~~d~v~~-~~~~K~~al~~~i~~~~~----~  431 (844)
T 1tf5_A          362 NYFRMYEKLAGMTGTAKTE-EEEFRNIYNMQ---VVT-IPTNRPVVRDDRPDLIYR-TMEGKFKAVAEDVAQRYM----T  431 (844)
T ss_dssp             HHHTTSSEEEEEESCCGGG-HHHHHHHHCCC---EEE-CCCSSCCCCEECCCEEES-SHHHHHHHHHHHHHHHHH----H
T ss_pred             HHHHHHhhhccCCcccchh-HHHHHHHhCCc---eEE-ecCCCCcccccCCcEEEe-CHHHHHHHHHHHHHHHHh----c
Confidence                             21 11222222211   111 12233333221   1222 233445555555543211    3


Q ss_pred             CceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccC--------CccE
Q psy7952         300 NNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQ--------NVRF  361 (444)
Q Consensus       300 ~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~--------~~~~  361 (444)
                      +.++||||+|++.++.++..|.+.          +...++..+.+.++.  ..|+|||+++++|+||+        ++.+
T Consensus       432 ~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~~ag~~--g~VlIATdmAgRG~DI~l~~~V~~~ggl~  509 (844)
T 1tf5_A          432 GQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQK--GAVTIATNMAGRGTDIKLGEGVKELGGLA  509 (844)
T ss_dssp             TCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTST--TCEEEEETTSSTTCCCCCCTTSGGGTSEE
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHHHHHHHHcCCC--CeEEEeCCccccCcCccccchhhhcCCcE
Confidence            678999999999999999999887          334444444444443  57999999999999999        7889


Q ss_pred             EEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         362 VVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       362 Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                      ||+++.|.|.+.|.||+||+||.|.+|.++.|++.+|.
T Consensus       510 VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD~  547 (844)
T 1tf5_A          510 VVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDE  547 (844)
T ss_dssp             EEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSS
T ss_pred             EEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHHH
Confidence            99999999999999999999999999999999987663

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=100.00  E-value=2e-35  Score=297.87  Aligned_cols=297  Identities=15%  Similarity=0.111  Sum_probs=203.6

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhh
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      ++++|.++++.++.+ +++++++|||+|||++        ++.++ ...+...+  .++||++|+++|+     .|+.+.
T Consensus       114 l~~~Q~~ai~~~~~~-~~~ll~~~tGsGKT~~--------~~~~~-~~~~~~~~--~~vlvl~P~~~L~-----~Q~~~~  176 (510)
T 2oca_A          114 PHWYQKDAVFEGLVN-RRRILNLPTSAGRSLI--------QALLA-RYYLENYE--GKILIIVPTTALT-----TQMADD  176 (510)
T ss_dssp             CCHHHHHHHHHHHHH-SEEEEECCSTTTHHHH--------HHHHH-HHHHHHCS--SEEEEEESSHHHH-----HHHHHH
T ss_pred             CCHHHHHHHHHHHhc-CCcEEEeCCCCCHHHH--------HHHHH-HHHHhCCC--CeEEEEECcHHHH-----HHHHHH
Confidence            568999999999998 8999999999999999        43333 22222221  2679999999999     566666


Q ss_pred             h-cC-CCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccccc
Q psy7952         130 V-TG-RSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEW  207 (444)
Q Consensus       130 l-~~-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~  207 (444)
                      + .+ ..+.+.+..++++......         .....+|+|+||+.+...       ....+.++++||+||+|++.. 
T Consensus       177 ~~~~~~~~~~~v~~~~~~~~~~~~---------~~~~~~I~i~T~~~l~~~-------~~~~~~~~~liIiDE~H~~~~-  239 (510)
T 2oca_A          177 FVDYRLFSHAMIKKIGGGASKDDK---------YKNDAPVVVGTWQTVVKQ-------PKEWFSQFGMMMNDECHLATG-  239 (510)
T ss_dssp             HHHTTSSCGGGEEECGGGCCTTGG---------GCTTCSEEEEEHHHHTTS-------CGGGGGGEEEEEEETGGGCCH-
T ss_pred             HHHhhcCCccceEEEecCCccccc---------cccCCcEEEEeHHHHhhc-------hhhhhhcCCEEEEECCcCCCc-
Confidence            6 32 2233678888887665432         246789999999987532       123456799999999999753 


Q ss_pred             CCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHH--HHHHhcCCCCeEEEecC------CCCCCceEEEEEcccc-
Q psy7952         208 GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQD--IISVLKFNKPYKVFKTS------TFRSNLFYDVIFDDLL-  278 (444)
Q Consensus       208 ~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~--~~~~l~~~~~~~~~~~~------~~~~~~~~~~~~~~~~-  278 (444)
                              ..+..++..+.+..++++|||||++.....  ....++   +.......      ...+...+........ 
T Consensus       240 --------~~~~~il~~~~~~~~~l~lSATp~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  308 (510)
T 2oca_A          240 --------KSISSIISGLNNCMFKFGLSGSLRDGKANIMQYVGMFG---EIFKPVTTSKLMEDGQVTELKINSIFLRYPD  308 (510)
T ss_dssp             --------HHHHHHGGGCTTCCEEEEEESCGGGCSSCHHHHHHHHC---SEECCCCCC---------CCEEEEEEEECCH
T ss_pred             --------ccHHHHHHhcccCcEEEEEEeCCCCCcccHHHhHHhhC---CeEEeeCHHHHhhCCcCCCceEEEEeecCCh
Confidence                    233445556666689999999997654321  122222   11111000      0111111111111000 


Q ss_pred             -----------hh----------hHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHH
Q psy7952         279 -----------KD----------SYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKH  327 (444)
Q Consensus       279 -----------~~----------~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~  327 (444)
                                 ..          +...+.+.+.....   ..+.++||||+ .++++.+++.|.+.          ++..
T Consensus       309 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~---~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~  384 (510)
T 2oca_A          309 EFTTKLKGKTYQEEIKIITGLSKRNKWIAKLAIKLAQ---KDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTE  384 (510)
T ss_dssp             HHHHHHTTCCHHHHHHHHHTCHHHHHHHHHHHHHHHT---TTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHH
T ss_pred             HHhccccccchHHHHHHHhccHHHHHHHHHHHHHHHh---cCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHH
Confidence                       00          11122333333322   13556666666 88999999999874          8889


Q ss_pred             HHHHHHHHHhcCCccEEEEc-CccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEec
Q psy7952         328 ERSRVQESFMRGEINVITAT-ISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHS  395 (444)
Q Consensus       328 ~r~~~~~~f~~g~~~vLvaT-~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~  395 (444)
                      +|..+++.|++|+.+||||| +++++|+|+|++++||++++|.|...|+|++||+||.|+++.++++++
T Consensus       385 ~r~~i~~~f~~g~~~vLv~T~~~~~~GiDip~v~~vi~~~~~~s~~~~~Q~~GR~gR~g~~~~~v~i~~  453 (510)
T 2oca_A          385 TRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVWD  453 (510)
T ss_dssp             HHHHHHHHHHHCCSCEEEEEHHHHHHSCCCCSEEEEEESSCCCSCCHHHHHHHHHHTTTCCCCCCEEEE
T ss_pred             HHHHHHHHHhCCCCCEEEEEcChhhcccccccCcEEEEeCCCCCHHHHHHHHhcccccCCCCceEEEEE
Confidence            99999999999999999999 999999999999999999999999999999999999998875555554

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=100.00  E-value=1.2e-34  Score=297.02  Aligned_cols=304  Identities=16%  Similarity=0.130  Sum_probs=184.0

Q ss_pred             CchHHHHHHHHHHc----cCCcEEEEccCCCcccccccccccceEEeCCCccccccCC-------ccceeEEEcchhhhh
Q psy7952          50 KCELQKKAIRHILL----RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN-------VRSRNGWISPILSSF  118 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~----~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~-------~~~~vlil~P~~~L~  118 (444)
                      ++++|.++++.+++    +.+++++++|||+|||++|+.++          ..+...+       ..+++||++|+++|+
T Consensus       179 lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~----------~~l~~~~~~~~~~~~~~~vlil~P~~~L~  248 (590)
T 3h1t_A          179 PRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQIS----------WKLWSARWNRTGDYRKPRILFLADRNVLV  248 (590)
T ss_dssp             CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHH----------HHHHHTTCCSSCSSSCCCEEEEEC-----
T ss_pred             chHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHH----------HHHHhcccccccccCCCeEEEEeCCHHHH
Confidence            46899999998886    54679999999999999843221          1232222       556889999999999


Q ss_pred             cccCccchH-hhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEE
Q psy7952         119 YLRFRDDKT-SIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYI  196 (444)
Q Consensus       119 ~~~q~~~~~-~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~i  196 (444)
                           .|.. +.+ .++   ..+..+.++.              ...+.+|+|+||+++.................+++|
T Consensus       249 -----~Q~~~~~~~~~~---~~~~~~~~~~--------------~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lv  306 (590)
T 3h1t_A          249 -----DDPKDKTFTPFG---DARHKIEGGK--------------VVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLI  306 (590)
T ss_dssp             -----------CCTTTC---SSEEECCC----------------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEE
T ss_pred             -----HHHHHHHHHhcc---hhhhhhhccC--------------CCCCCcEEEEEhhhhccccccccccccCCCCccCEE
Confidence                 4444 444 444   3334443322              135789999999998631100000112234568999


Q ss_pred             EEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEec------CCCCCCceE
Q psy7952         197 VVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT------STFRSNLFY  270 (444)
Q Consensus       197 ViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~------~~~~~~~~~  270 (444)
                      |+||||++...+   .   ..+..++..++. .++++|||||...........++.  ++.....      ....+...+
T Consensus       307 IiDEaH~~~~~~---~---~~~~~il~~~~~-~~~l~lTATP~~~~~~~~~~~f~~--~~~~~~~~~~i~~~~l~~~~~~  377 (590)
T 3h1t_A          307 IIDECHRGSARD---N---SNWREILEYFEP-AFQIGMTATPLREDNRDTYRYFGN--PIYTYSLRQGIDDGFLAPYRVH  377 (590)
T ss_dssp             EESCCC---------------CHHHHHHSTT-SEEEEEESSCSCTTTHHHHHHSCS--CSEEECHHHHHHHTSSCCEEEE
T ss_pred             EEECCccccccc---h---HHHHHHHHhCCc-ceEEEeccccccccchhHHHHcCC--ceEecCHHHHhhCCccCCcEEE
Confidence            999999986532   0   122233344554 789999999987766665655542  2111100      000111111


Q ss_pred             EEEEcc--------------------------c-------chhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHH
Q psy7952         271 DVIFDD--------------------------L-------LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLA  317 (444)
Q Consensus       271 ~~~~~~--------------------------~-------~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~  317 (444)
                      .+....                          .       .......+.+.+.+++... ...+++||||+++++|+.++
T Consensus       378 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~i~~~l~~~l~~~-~~~~k~lVF~~~~~~a~~l~  456 (590)
T 3h1t_A          378 RVISEVDAAGWRPSKGDVDRFGREIPDGEYQTKDFERVIALKARTDAFAKHLTDFMKRT-DRFAKTIVFCVDQEHADEMR  456 (590)
T ss_dssp             EEEETTCC-----------------------CCSHHHHHHHHHTHHHHHHHHHHHHHHH-CTTSEEEEEESSHHHHHHHH
T ss_pred             EeeeeeeccccccccccccccccccccccCCHHHhhhHhcChHHHHHHHHHHHHHHHhc-CCCccEEEEECCHHHHHHHH
Confidence            111000                          0       0011122233343333332 25689999999999999999


Q ss_pred             HHHHhh-----------------cCHHHHHHHHHHHhcCCcc---EEEEcCccccccccCCccEEEEeCCCCCHHHHHHH
Q psy7952         318 DALRRK-----------------VNKHERSRVQESFMRGEIN---VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQE  377 (444)
Q Consensus       318 ~~L~~~-----------------~~~~~r~~~~~~f~~g~~~---vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr  377 (444)
                      +.|.+.                 ..+++|..+++.|++|+.+   |||||+++++|+|+|++++||++++|.|...|+||
T Consensus       457 ~~L~~~~~~~~~~~~~~~~~i~g~~~~~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~  536 (590)
T 3h1t_A          457 RALNNLNSDLSRKHPDYVARVTSEEGKIGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTCKNVVLARVVNSMSEFKQI  536 (590)
T ss_dssp             HHHHHHTHHHHTTCTTSEEECSSTTHHHHHHHHHHHHCTTCCCCCEEEESSTTTTTCCCTTEEEEEEESCCCCHHHHHHH
T ss_pred             HHHHHhhhhhhccCCCeEEEEeCCChHHHHHHHHHHhCCCCCCCEEEEECChhhcCccchheeEEEEEecCCChHHHHHH
Confidence            999764                 2234599999999998766   89999999999999999999999999999999999


Q ss_pred             hccCCCCCC--ceeEEEEec
Q psy7952         378 SGRAGRDGL--QSYCRIYHS  395 (444)
Q Consensus       378 ~GR~~R~g~--~g~~~~~~~  395 (444)
                      +||+||.+.  ++..+++++
T Consensus       537 iGR~~R~~~~~~k~~~~I~D  556 (590)
T 3h1t_A          537 VGRGTRLREDYGKLWFNIID  556 (590)
T ss_dssp             HTTSCCCBGGGTBSCEEEEE
T ss_pred             HhhhcccCccCCCCEEEEEe
Confidence            999999875  444444554

>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=100.00  E-value=1.2e-35  Score=293.63  Aligned_cols=282  Identities=13%  Similarity=0.054  Sum_probs=190.8

Q ss_pred             CCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCcc
Q psy7952          45 GFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRD  124 (444)
Q Consensus        45 g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~  124 (444)
                      |+.. |+++|+ +++.++++++.+++.+|||+|||++        |++|+ +..+...+  .+++|++||++|+     .
T Consensus         1 G~~q-~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~--------~~~~~-l~~~~~~~--~~~lvl~Ptr~La-----~   62 (451)
T 2jlq_A            1 GSAM-GEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKR--------ILPSI-VREALLRR--LRTLILAPTRVVA-----A   62 (451)
T ss_dssp             CCCC-CSCCCC-CCGGGGSTTCEEEECCCTTSSCCTT--------HHHHH-HHHHHHTT--CCEEEEESSHHHH-----H
T ss_pred             CCCC-CCCcHH-HHHHHHhcCCeEEEECCCCCCHhhH--------HHHHH-HHHHHhcC--CcEEEECCCHHHH-----H
Confidence            4554 677875 7999999844459999999999998        66666 22222222  4569999999999     5


Q ss_pred             chHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccc
Q psy7952         125 DKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCV  204 (444)
Q Consensus       125 ~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~  204 (444)
                      |..+.+. +   ..+..-.......           ..++..|.++|++.+.    +. +.....+.++++||+||+|++
T Consensus        63 Q~~~~l~-g---~~v~~~~~~~~~~-----------~~~~~~i~~~t~~~l~----~~-l~~~~~l~~~~~iViDEah~~  122 (451)
T 2jlq_A           63 EMEEALR-G---LPIRYQTPAVKSD-----------HTGREIVDLMCHATFT----TR-LLSSTRVPNYNLIVMDEAHFT  122 (451)
T ss_dssp             HHHHHTT-T---SCEEECCTTCSCC-----------CCSSCCEEEEEHHHHH----HH-HHHCSCCCCCSEEEEETTTCC
T ss_pred             HHHHHhc-C---ceeeeeecccccc-----------CCCCceEEEEChHHHH----HH-hhCcccccCCCEEEEeCCccC
Confidence            6666552 2   2222212111110           1345678899988763    22 223344678999999999986


Q ss_pred             cccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHH
Q psy7952         205 SEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAH  284 (444)
Q Consensus       205 ~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  284 (444)
                       +.+  +......+..  .....+.++++||||+++.....    . ...+..+.... ..+...+            ..
T Consensus       123 -~~~--~~~~~~~~~~--~~~~~~~~~i~~SAT~~~~~~~~----~-~~~~~~~~~~~-~~p~~~~------------~~  179 (451)
T 2jlq_A          123 -DPC--SVAARGYIST--RVEMGEAAAIFMTATPPGSTDPF----P-QSNSPIEDIER-EIPERSW------------NT  179 (451)
T ss_dssp             -SHH--HHHHHHHHHH--HHHTTSCEEEEECSSCTTCCCSS----C-CCSSCEEEEEC-CCCSSCC------------SS
T ss_pred             -Ccc--hHHHHHHHHH--hhcCCCceEEEEccCCCccchhh----h-cCCCceEecCc-cCCchhh------------HH
Confidence             221  2222222211  12344589999999998754331    1 11222221111 1111000            11


Q ss_pred             HHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCC
Q psy7952         285 VKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------VNKHERSRVQESFMRGEINVITATISFGMGIDRQN  358 (444)
Q Consensus       285 ~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~  358 (444)
                      +...+.+       ..+++||||+++++++.++..|.+.      ++...+..+++.|++|+.+|||||+++++|+|+|+
T Consensus       180 ~~~~l~~-------~~~~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~~~~~f~~g~~~vLVaT~v~~~GiDip~  252 (451)
T 2jlq_A          180 GFDWITD-------YQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFRA  252 (451)
T ss_dssp             SCHHHHH-------CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECTTTHHHHGGGGGSSCCSEEEECGGGGSSCCCCC
T ss_pred             HHHHHHh-------CCCCEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHHHHHHHHhhccCCceEEEECCHHHhCcCCCC
Confidence            1122222       3668999999999999999999876      66677789999999999999999999999999999


Q ss_pred             ccEEEEeC--------------------CCCCHHHHHHHhccCCCCCC-ceeEEEEec
Q psy7952         359 VRFVVHWG--------------------MPSSIPAYYQESGRAGRDGL-QSYCRIYHS  395 (444)
Q Consensus       359 ~~~Vi~~~--------------------~p~s~~~~~Qr~GR~~R~g~-~g~~~~~~~  395 (444)
                       ++||++|                    .|.|..+|+||+||+||.|. +|.+++++.
T Consensus       253 -~~VI~~~~~~~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~  309 (451)
T 2jlq_A          253 -GRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSG  309 (451)
T ss_dssp             -SEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECS
T ss_pred             -CEEEECCCcccccccccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeC
Confidence             9999998                    99999999999999999998 788888874

>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=100.00  E-value=3.4e-35  Score=293.35  Aligned_cols=286  Identities=17%  Similarity=0.112  Sum_probs=196.1

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhh
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      ++++|.++++.++.+ +++++++|||+|||++        ++.++    ...+   .++||++|+++|+     .|..+.
T Consensus        94 l~~~Q~~ai~~i~~~-~~~ll~~~TGsGKT~~--------~l~~i----~~~~---~~~Lvl~P~~~L~-----~Q~~~~  152 (472)
T 2fwr_A           94 LRDYQEKALERWLVD-KRGCIVLPTGSGKTHV--------AMAAI----NELS---TPTLIVVPTLALA-----EQWKER  152 (472)
T ss_dssp             BCHHHHHHHHHHTTT-TEEEEECCTTSCHHHH--------HHHHH----HHHC---SCEEEEESSHHHH-----HHHHHH
T ss_pred             cCHHHHHHHHHHHhc-CCEEEEeCCCCCHHHH--------HHHHH----HHcC---CCEEEEECCHHHH-----HHHHHH
Confidence            468999999999998 7899999999999999        44443    2222   3569999999999     666666


Q ss_pred             h-cCCCCcee-EEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh-hCCccEEEEeccccccc
Q psy7952         130 V-TGRSDLYQ-LELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR-YNKLAYIVVDEAHCVSE  206 (444)
Q Consensus       130 l-~~~~~~i~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~-~~~~~~iViDE~H~~~~  206 (444)
                      + .++   +. +..++|+..               ...+|+|+||+.+..        .... ..++++||+||+|++.+
T Consensus       153 ~~~~~---~~~v~~~~g~~~---------------~~~~Ivv~T~~~l~~--------~~~~~~~~~~liIvDEaH~~~~  206 (472)
T 2fwr_A          153 LGIFG---EEYVGEFSGRIK---------------ELKPLTVSTYDSAYV--------NAEKLGNRFMLLIFDEVHHLPA  206 (472)
T ss_dssp             GGGGC---GGGEEEBSSSCB---------------CCCSEEEEEHHHHHH--------THHHHTTTCSEEEEETGGGTTS
T ss_pred             HHhCC---CcceEEECCCcC---------------CcCCEEEEEcHHHHH--------HHHHhcCCCCEEEEECCcCCCC
Confidence            6 555   77 888888764               356899999988642        1112 24699999999999876


Q ss_pred             cCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHH--HHHHHhcCCCCeEEEec-----CCCCCCceEEEEEcccc-
Q psy7952         207 WGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQ--DIISVLKFNKPYKVFKT-----STFRSNLFYDVIFDDLL-  278 (444)
Q Consensus       207 ~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~--~~~~~l~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~-  278 (444)
                      .+  +..    +   ...++ ..+++++||||.+....  .+...++   +......     ....+...+........ 
T Consensus       207 ~~--~~~----~---~~~~~-~~~~l~lSATp~~~~~~~~~l~~~~~---~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~  273 (472)
T 2fwr_A          207 ES--YVQ----I---AQMSI-APFRLGLTATFEREDGRHEILKEVVG---GKVFELFPDSLAGKHLAKYTIKRIFVPLAE  273 (472)
T ss_dssp             TT--THH----H---HHTCC-CSEEEEEESCCCCTTSGGGSHHHHTC---CEEEECCHHHHTSCCCCSEEECCEEECCCH
T ss_pred             hH--HHH----H---HHhcC-CCeEEEEecCccCCCCHHHHHHHHhC---CeEeecCHHHHhcCcCCCeEEEEEEcCCCH
Confidence            54  432    2   22333 37899999999742211  1111111   0000000     00000000000000000 


Q ss_pred             h--------------------------------------------------------hhHHHHHHHHHHHhccCCCCCce
Q psy7952         279 K--------------------------------------------------------DSYAHVKEFIEKCLGKDNKANNC  302 (444)
Q Consensus       279 ~--------------------------------------------------------~~~~~~~~~l~~~l~~~~~~~~~  302 (444)
                      .                                                        .........+.+++...  .+++
T Consensus       274 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~--~~~k  351 (472)
T 2fwr_A          274 DERVEYEKREKVYKQFLRARGITLRRAEDFNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERH--RKDK  351 (472)
T ss_dssp             HHHHHTTTTTHHHHSCSSSCCCTTTCCSSSTTTTTTTCCSSSSSTTTHHHHHHHHHHHSCSHHHHHHHHHHHHT--SSSC
T ss_pred             HHHHHHHHHHHHHHHHHHhcCccccchhhHHHHHHHhccCHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHhC--CCCc
Confidence            0                                                        00011223344444442  5789


Q ss_pred             EEEEecccchHHHHHHHHHhh-----cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHH
Q psy7952         303 GIIYCRTREHTTDLADALRRK-----VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQE  377 (444)
Q Consensus       303 ~iVf~~s~~~~~~l~~~L~~~-----~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr  377 (444)
                      +||||++++.++.+++.|...     ++..+|..+++.|++|+.+|||||+++++|+|+|++++||+++.|+|...|+||
T Consensus       352 ~lvF~~~~~~~~~l~~~l~~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~  431 (472)
T 2fwr_A          352 IIIFTRHNELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQR  431 (472)
T ss_dssp             BCCBCSCHHHHHHHHHHTTCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHH
T ss_pred             EEEEECCHHHHHHHHHHhCcceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcCcccccCcEEEEECCCCCHHHHHHH
Confidence            999999999999999988543     788999999999999999999999999999999999999999999999999999


Q ss_pred             hccCCCCCCc-eeEE--EEeccc
Q psy7952         378 SGRAGRDGLQ-SYCR--IYHSEH  397 (444)
Q Consensus       378 ~GR~~R~g~~-g~~~--~~~~~~  397 (444)
                      +||+||.|++ +.++  .++..+
T Consensus       432 ~GR~~R~g~~k~~~~i~~lv~~~  454 (472)
T 2fwr_A          432 LGRILRPSKGKKEAVLYELISRG  454 (472)
T ss_dssp             HHHSBCCCTTTCCEEEEEEEECS
T ss_pred             HhhccCCCCCCceEEEEEEEeCC
Confidence            9999999865 4443  455543

>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=100.00  E-value=1.3e-33  Score=286.48  Aligned_cols=318  Identities=16%  Similarity=0.139  Sum_probs=203.5

Q ss_pred             HHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhh
Q psy7952          38 AKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSS  117 (444)
Q Consensus        38 ~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L  117 (444)
                      ++-++.+|..  |+++|..++..+++| +  +..++||+|||++        |.+|+++. ...   .+.++|++||++|
T Consensus        65 ea~~R~lg~~--p~~VQ~~~i~~ll~G-~--Iaem~TGsGKTla--------f~LP~l~~-~l~---g~~vlVltPTreL  127 (853)
T 2fsf_A           65 EASKRVFGMR--HFDVQLLGGMVLNER-C--IAEMRTGEGKTLT--------ATLPAYLN-ALT---GKGVHVVTVNDYL  127 (853)
T ss_dssp             HHHHHHHSCC--CCHHHHHHHHHHHSS-E--EEECCTTSCHHHH--------HHHHHHHH-HTT---SSCCEEEESSHHH
T ss_pred             HHHHHHcCCC--CChHHHhhcccccCC-e--eeeecCCchHHHH--------HHHHHHHH-HHc---CCcEEEEcCCHHH
Confidence            5556667875  578999999999999 4  8999999999999        77777222 122   2356999999999


Q ss_pred             hcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH------Hh
Q psy7952         118 FYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL------VR  189 (444)
Q Consensus       118 ~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~------~~  189 (444)
                      +  .|+.+.+..+  ..+   +++..+.|+.+...+...+        +++|+||||+.|.   |+++..+.      ..
T Consensus       128 A--~Q~~e~~~~l~~~lg---l~v~~i~GG~~~~~r~~~~--------~~dIvvgTpgrl~---fDyLrd~~~~~~~~~~  191 (853)
T 2fsf_A          128 A--QRDAENNRPLFEFLG---LTVGINLPGMPAPAKREAY--------AADITYGTNNEYG---FDYLRDNMAFSPEERV  191 (853)
T ss_dssp             H--HHHHHHHHHHHHHTT---CCEEECCTTCCHHHHHHHH--------HSSEEEEEHHHHH---HHHHHHTTCSSGGGCC
T ss_pred             H--HHHHHHHHHHHHhcC---CeEEEEeCCCCHHHHHHhc--------CCCEEEECCchhh---HHHHHhhhhccHhHhc
Confidence            9  4556666666  567   9999999998764333222        5899999999974   24444443      33


Q ss_pred             hCCccEEEEecccccc-ccCCC----------cHHHHHHHHHHHHhhCC--------------------CCcEE------
Q psy7952         190 YNKLAYIVVDEAHCVS-EWGHD----------FRPTYRRLGELRQFTGN--------------------SIPII------  232 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~-~~~~~----------~~~~~~~l~~~~~~~~~--------------------~~~~v------  232 (444)
                      ..++.++|+||+|.++ +.+..          -...+..+..+...++.                    ..+++      
T Consensus       192 ~~~l~~lVlDEaD~mLiD~a~tpLIiSg~~~~~~~~y~~i~~iv~~L~~~~~~~~~~~~~~~dy~vdek~rqv~lte~g~  271 (853)
T 2fsf_A          192 QRKLHYALVDEVDSILIDEARTPLIISGPAEDSSEMYKRVNKIIPHLIRQEKEDSETFQGEGHFSVDEKSRQVNLTERGL  271 (853)
T ss_dssp             CCSCCEEEESCHHHHTTTTTTCEEEEEEC---------------------------------------------------
T ss_pred             ccCCcEEEECchHHHHHhcCcccccccCCCccchhHHHHHHHHHHhchhhhccccccccccccceeccccceEEEcHHHH
Confidence            5789999999999987 43210          00111122222222211                    12221      


Q ss_pred             ------------------EEeccCCc---c--------------------------------------------------
Q psy7952         233 ------------------ALTATAEP---S--------------------------------------------------  241 (444)
Q Consensus       233 ------------------~lSAT~~~---~--------------------------------------------------  241 (444)
                                        ++|||.+.   .                                                  
T Consensus       272 ~~~e~~l~~~~l~~~~~~Lfsat~~~~~~~i~~al~A~~l~~~d~dYiV~d~~vviVde~tgR~m~grr~sdGLhQaiea  351 (853)
T 2fsf_A          272 VLIEELLVKEGIMDEGESLYSPANIMLMHHVTAALRAHALFTRDVDYIVKDGEVIIVDEHTGRTMQGRRWSDGLHQAVEA  351 (853)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHhCCcccccccccCcccchHHHHHHHHHHHHHHhhcCccceeecCcEEEEecccCcccCCCccchhhhHHHHh
Confidence                              45555321   0                                                  


Q ss_pred             -------------------------------------hHHHHHHHhcCCCCeEEEecCCCCCCceEEE---EEcccchhh
Q psy7952         242 -------------------------------------VKQDIISVLKFNKPYKVFKTSTFRSNLFYDV---IFDDLLKDS  281 (444)
Q Consensus       242 -------------------------------------~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~  281 (444)
                                                           ....+.+..++    .+..-+..+|......   ... ....+
T Consensus       352 ke~v~I~~e~~tla~It~qnyfr~Y~kl~GmTGTa~te~~ef~~iY~l----~vv~IPtn~p~~R~d~~d~v~~-~~~~K  426 (853)
T 2fsf_A          352 KEGVQIQNENQTLASITFQNYFRLYEKLAGMTGTADTEAFEFSSIYKL----DTVVVPTNRPMIRKDLPDLVYM-TEAEK  426 (853)
T ss_dssp             -----CCCCCEEEEEEEHHHHHTTSSEEEEEECTTCCCHHHHHHHHCC----EEEECCCSSCCCCEECCCEEES-SHHHH
T ss_pred             cccceecccccccceeehHHHHhhhhhhhcCCCCchhHHHHHHHHhCC----cEEEcCCCCCceeecCCcEEEe-CHHHH
Confidence                                                 01111111111    1112223344333221   222 22344


Q ss_pred             HHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccc
Q psy7952         282 YAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFG  351 (444)
Q Consensus       282 ~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~  351 (444)
                      +..+.+.+....    ..+.++||||+|++.++.++..|.+.          ....++..+.+.|+.|  .|+|||++++
T Consensus       427 ~~al~~~i~~~~----~~gqpvLVft~sie~se~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAg  500 (853)
T 2fsf_A          427 IQAIIEDIKERT----AKGQPVLVGTISIEKSELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAG  500 (853)
T ss_dssp             HHHHHHHHHHHH----TTTCCEEEEESSHHHHHHHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCS
T ss_pred             HHHHHHHHHHHh----cCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEeccccc
Confidence            445555444321    24678999999999999999999987          3445555566667766  7999999999


Q ss_pred             cccccCCc-------------------------------------cEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEe
Q psy7952         352 MGIDRQNV-------------------------------------RFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYH  394 (444)
Q Consensus       352 ~Gidi~~~-------------------------------------~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~  394 (444)
                      ||+||+..                                     .+||+++.|.|.+.|.||+||+||.|.+|.++.|+
T Consensus       501 RGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fl  580 (853)
T 2fsf_A          501 RGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYL  580 (853)
T ss_dssp             SCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEE
T ss_pred             CCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEe
Confidence            99999863                                     59999999999999999999999999999999999


Q ss_pred             cccch
Q psy7952         395 SEHSK  399 (444)
Q Consensus       395 ~~~~~  399 (444)
                      +.++.
T Consensus       581 s~eD~  585 (853)
T 2fsf_A          581 SMEDA  585 (853)
T ss_dssp             ETTSG
T ss_pred             cccHH
Confidence            87653

>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=100.00  E-value=8.1e-35  Score=296.20  Aligned_cols=290  Identities=13%  Similarity=0.070  Sum_probs=193.3

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhh
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      ++|+|+.+++.++.+ +++++.+|||||||++        |++|+ ++.+...  ..++||++||++|+     .|+.+.
T Consensus       172 ~lpiq~~~i~~l~~g-~dvlv~a~TGSGKT~~--------~~lpi-l~~l~~~--~~~vLvl~PtreLa-----~Qi~~~  234 (618)
T 2whx_A          172 GEPDYEVDEDIFRKK-RLTIMDLHPGAGKTKR--------ILPSI-VREALKR--RLRTLILAPTRVVA-----AEMEEA  234 (618)
T ss_dssp             CCCCCCCCGGGGSTT-CEEEECCCTTSSTTTT--------HHHHH-HHHHHHT--TCCEEEEESSHHHH-----HHHHHH
T ss_pred             CCCccccCHHHHhcC-CeEEEEcCCCCCHHHH--------HHHHH-HHHHHhC--CCeEEEEcChHHHH-----HHHHHH
Confidence            566777778888888 9999999999999999        77777 3333332  24679999999999     566666


Q ss_pred             hcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCC
Q psy7952         130 VTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGH  209 (444)
Q Consensus       130 l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~  209 (444)
                      +. +   ..+. +.......          ...++..+.++|.+.+.     ..+.....+.++++||+||||++ +.+ 
T Consensus       235 l~-~---~~v~-~~~~~l~~----------~~tp~~~i~~~t~~~l~-----~~l~~~~~l~~~~~iViDEah~~-~~~-  292 (618)
T 2whx_A          235 LR-G---LPIR-YQTPAVKS----------DHTGREIVDLMCHATFT-----TRLLSSTRVPNYNLIVMDEAHFT-DPC-  292 (618)
T ss_dssp             TT-T---SCEE-ECCTTSSC----------CCCSSSCEEEEEHHHHH-----HHHHHCSSCCCCSEEEEESTTCC-SHH-
T ss_pred             hc-C---Ccee-Eeccccee----------ccCCCceEEEEChHHHH-----HHHhccccccCCeEEEEECCCCC-Ccc-
Confidence            52 2   2222 22211000          00122334444433321     11122233688999999999997 322 


Q ss_pred             CcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHH
Q psy7952         210 DFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFI  289 (444)
Q Consensus       210 ~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  289 (444)
                       +...+..+...+.  ..+.|+++||||++.....    +.. ..+..+...... +            ......+...+
T Consensus       293 -~~~~~~~i~~~l~--~~~~q~il~SAT~~~~~~~----~~~-~~~~~~~v~~~~-~------------~~~~~~ll~~l  351 (618)
T 2whx_A          293 -SVAARGYISTRVE--MGEAAAIFMTATPPGSTDP----FPQ-SNSPIEDIEREI-P------------ERSWNTGFDWI  351 (618)
T ss_dssp             -HHHHHHHHHHHHH--HTSCEEEEECSSCTTCCCS----SCC-CSSCEEEEECCC-C------------SSCCSSSCHHH
T ss_pred             -HHHHHHHHHHHhc--ccCccEEEEECCCchhhhh----hhc-cCCceeeecccC-C------------HHHHHHHHHHH
Confidence             4444444444332  1348999999999876432    111 112111111100 0            01111122222


Q ss_pred             HHHhccCCCCCceEEEEecccchHHHHHHHHHhh------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEE-
Q psy7952         290 EKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFV-  362 (444)
Q Consensus       290 ~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~V-  362 (444)
                      .+       ..+++||||+++++++.+++.|.+.      +...+|..+++.|++|+.+|||||+++++|+|+| +++| 
T Consensus       352 ~~-------~~~~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VI  423 (618)
T 2whx_A          352 TD-------YQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVI  423 (618)
T ss_dssp             HH-------CCSCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTTHHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEE
T ss_pred             Hh-------CCCCEEEEECChhHHHHHHHHHHHcCCcEEEEChHHHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEE
Confidence            22       3678999999999999999999886      5567899999999999999999999999999998 8887 


Q ss_pred             -------------------EEeCCCCCHHHHHHHhccCCCCCC-ceeEEEEec---ccchhhHHHHHh
Q psy7952         363 -------------------VHWGMPSSIPAYYQESGRAGRDGL-QSYCRIYHS---EHSKKSLEYVIK  407 (444)
Q Consensus       363 -------------------i~~~~p~s~~~~~Qr~GR~~R~g~-~g~~~~~~~---~~~~~~~~~~~~  407 (444)
                                         |+++.|.|..+|+||+||+||.|. .|.+++++.   +++...+..+..
T Consensus       424 d~g~~~~P~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~~l~~le~  491 (618)
T 2whx_A          424 DPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEA  491 (618)
T ss_dssp             ECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTCHHHHHH
T ss_pred             ECcceecceecccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchhhHHHHHHHHh
Confidence                               777779999999999999999965 899999997   666666555543

>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=100.00  E-value=1.7e-34  Score=284.14  Aligned_cols=273  Identities=15%  Similarity=0.114  Sum_probs=176.7

Q ss_pred             HHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-cCCCCceeE
Q psy7952          61 ILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQL  139 (444)
Q Consensus        61 ~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~  139 (444)
                      +++| +++++++|||||||++        |++|+ +..+...+  .+++|++||++|+     .|+.+.+ ..+   +. 
T Consensus         5 l~~g-~~vlv~a~TGSGKT~~--------~l~~~-l~~~~~~~--~~~lil~Ptr~La-----~Q~~~~l~~~~---v~-   63 (440)
T 1yks_A            5 LKKG-MTTVLDFHPGAGKTRR--------FLPQI-LAECARRR--LRTLVLAPTRVVL-----SEMKEAFHGLD---VK-   63 (440)
T ss_dssp             TSTT-CEEEECCCTTSSTTTT--------HHHHH-HHHHHHTT--CCEEEEESSHHHH-----HHHHHHTTTSC---EE-
T ss_pred             hhCC-CCEEEEcCCCCCHHHH--------HHHHH-HHHHHhcC--CeEEEEcchHHHH-----HHHHHHHhcCC---eE-
Confidence            3456 8999999999999999        65555 33232222  4669999999999     6666666 333   22 


Q ss_pred             EEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH----HHHhhCCccEEEEeccccccccCCCcHHHH
Q psy7952         140 ELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ----HLVRYNKLAYIVVDEAHCVSEWGHDFRPTY  215 (444)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~----~~~~~~~~~~iViDE~H~~~~~~~~~~~~~  215 (444)
                       ...+..                    -.++||+.+........+.    ....+.++++||+||+|++ +.+  +...+
T Consensus        64 -~~~~~~--------------------~~v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~-~~~--~~~~~  119 (440)
T 1yks_A           64 -FHTQAF--------------------SAHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL-DPA--SIAAR  119 (440)
T ss_dssp             -EESSCC--------------------CCCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC-SHH--HHHHH
T ss_pred             -Eecccc--------------------eeccCCccceeeecccchhHhhhCcccccCccEEEEECcccc-Ccc--hHHHH
Confidence             111110                    0388998876432222121    1123678999999999997 222  33333


Q ss_pred             HHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhcc
Q psy7952         216 RRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGK  295 (444)
Q Consensus       216 ~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~  295 (444)
                      ..+..+..  +.+.++++||||+++....    ......+......              .............+.+    
T Consensus       120 ~~~~~~~~--~~~~~~l~~SAT~~~~~~~----~~~~~~~~~~~~~--------------~~~~~~~~~~~~~l~~----  175 (440)
T 1yks_A          120 GWAAHRAR--ANESATILMTATPPGTSDE----FPHSNGEIEDVQT--------------DIPSEPWNTGHDWILA----  175 (440)
T ss_dssp             HHHHHHHH--TTSCEEEEECSSCTTCCCS----SCCCSSCEEEEEC--------------CCCSSCCSSSCHHHHH----
T ss_pred             HHHHHHhc--cCCceEEEEeCCCCchhhh----hhhcCCCeeEeee--------------ccChHHHHHHHHHHHh----
Confidence            33333322  3458999999999876432    1111111111110              0001111111222222    


Q ss_pred             CCCCCceEEEEecccchHHHHHHHHHhh------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEE-----
Q psy7952         296 DNKANNCGIIYCRTREHTTDLADALRRK------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVH-----  364 (444)
Q Consensus       296 ~~~~~~~~iVf~~s~~~~~~l~~~L~~~------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~-----  364 (444)
                         .++++||||++++.++.+++.|.+.      +...+|..+++.|++|+.+|||||+++++|+|+| +++||+     
T Consensus       176 ---~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~  251 (440)
T 1yks_A          176 ---DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAF  251 (440)
T ss_dssp             ---CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEEE
T ss_pred             ---cCCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecchhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCccc
Confidence               3679999999999999999999876      4447889999999999999999999999999999 999986     


Q ss_pred             --------------eCCCCCHHHHHHHhccCCCC-CCceeEEEEe---cccchhhHHHHH
Q psy7952         365 --------------WGMPSSIPAYYQESGRAGRD-GLQSYCRIYH---SEHSKKSLEYVI  406 (444)
Q Consensus       365 --------------~~~p~s~~~~~Qr~GR~~R~-g~~g~~~~~~---~~~~~~~~~~~~  406 (444)
                                    ++.|.+..+|+||+||+||. |+.|.|++++   ++.+...+..+.
T Consensus       252 ~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~~~~~~~~~~l~~l~  311 (440)
T 1yks_A          252 KPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHHVCWLE  311 (440)
T ss_dssp             EEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTBHHHHH
T ss_pred             eeeecccccceeeccccccCHHHHHHhccccCCCCCCCceEEEEeccCChhhhhhhhhhh
Confidence                          88899999999999999997 6899999996   566666655554

>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=100.00  E-value=1.9e-33  Score=285.51  Aligned_cols=323  Identities=17%  Similarity=0.170  Sum_probs=219.4

Q ss_pred             HHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhh
Q psy7952          37 TAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILS  116 (444)
Q Consensus        37 ~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~  116 (444)
                      .++.++.+|+.  |+++|..+++.+++| +  +..++||+|||++        +.+|+++..+ .+   +.++|++||++
T Consensus       101 rEa~~R~lG~r--P~~VQ~~~ip~Ll~G-~--Iaem~TGeGKTLa--------~~LP~~l~aL-~g---~~v~VvTpTre  163 (922)
T 1nkt_A          101 REAAWRVLDQR--PFDVQVMGAAALHLG-N--VAEMKTGEGKTLT--------CVLPAYLNAL-AG---NGVHIVTVNDY  163 (922)
T ss_dssp             HHHHHHHHSCC--CCHHHHHHHHHHHTT-E--EEECCTTSCHHHH--------THHHHHHHHT-TT---SCEEEEESSHH
T ss_pred             HHHHHHHcCCC--CCHHHHHHHHhHhcC-C--EEEecCCCccHHH--------HHHHHHHHHH-hC---CCeEEEeCCHH
Confidence            34666778984  688999999999998 4  9999999999999        6677722222 22   35699999999


Q ss_pred             hhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH------H
Q psy7952         117 SFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL------V  188 (444)
Q Consensus       117 L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~------~  188 (444)
                      |+  .|+.+.+..+  ..+   +++..+.|+.+...+...+        .++|+|+||..|.   |+++..+.      .
T Consensus       164 LA--~Qdae~m~~l~~~lG---Lsv~~i~gg~~~~~r~~~y--------~~DIvygTpgrlg---fDyLrD~m~~~~~~l  227 (922)
T 1nkt_A          164 LA--KRDSEWMGRVHRFLG---LQVGVILATMTPDERRVAY--------NADITYGTNNEFG---FDYLRDNMAHSLDDL  227 (922)
T ss_dssp             HH--HHHHHHHHHHHHHTT---CCEEECCTTCCHHHHHHHH--------HSSEEEEEHHHHH---HHHHHHTTCSSGGGC
T ss_pred             HH--HHHHHHHHHHHhhcC---CeEEEEeCCCCHHHHHHhc--------CCCEEEECchHhh---HHHHHhhhhccHhhh
Confidence            99  4456666666  567   9999999998765443333        5799999999984   35555442      3


Q ss_pred             hhCCccEEEEecccccc-ccCC----------CcHHHHHHHHHHHHhhC---------CCCcEE----------------
Q psy7952         189 RYNKLAYIVVDEAHCVS-EWGH----------DFRPTYRRLGELRQFTG---------NSIPII----------------  232 (444)
Q Consensus       189 ~~~~~~~iViDE~H~~~-~~~~----------~~~~~~~~l~~~~~~~~---------~~~~~v----------------  232 (444)
                      ....+.++|+||+|.++ +.+.          .-...+..+..+...++         +..+++                
T Consensus       228 ~lr~l~~lIVDEaDsmLiDeartPLiiSg~~~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~  307 (922)
T 1nkt_A          228 VQRGHHYAIVDEVDSILIDEARTPLIISGPADGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGID  307 (922)
T ss_dssp             CCCCCCEEEETTHHHHHTTGGGSCEEEEEECCCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCS
T ss_pred             ccCCCCEEEEeChHHHHHhcCccceeecCCCCcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCc
Confidence            35679999999999987 4321          11345566666666665         456676                


Q ss_pred             -EEeccCCc---chHHHHHH--HhcCCCCeEE-------E----------------------------------------
Q psy7952         233 -ALTATAEP---SVKQDIIS--VLKFNKPYKV-------F----------------------------------------  259 (444)
Q Consensus       233 -~lSAT~~~---~~~~~~~~--~l~~~~~~~~-------~----------------------------------------  259 (444)
                       ++|||.+.   .+.+.+..  .+.-...+.+       .                                        
T Consensus       308 ~Lfsat~~~l~~~i~~aL~A~~l~~~d~dYiV~dg~vviVDe~TGR~m~grr~sdGLHQaieaKe~V~I~~e~~TlatIt  387 (922)
T 1nkt_A          308 NLYEAANSPLVSYLNNALKAKELFSRDKDYIVRDGEVLIVDEFTGRVLIGRRYNEGMHQAIEAKEHVEIKAENQTLATIT  387 (922)
T ss_dssp             STTCSTTCCHHHHHHHHHHHHHHCCBTTTEEECSSCEEEBCSSSCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEEC
T ss_pred             cccCCcchhHHHHHHHHHHHHHHhhcccceeeecCceEEEecccCcccCCccccchhhHHHhccccccccccccccceee
Confidence             77888654   11111111  1110100000       0                                        


Q ss_pred             ----------------------------------ecCCCCCCceEE---EEEcccchhhHHHHHHHHHHHhccCCCCCce
Q psy7952         260 ----------------------------------KTSTFRSNLFYD---VIFDDLLKDSYAHVKEFIEKCLGKDNKANNC  302 (444)
Q Consensus       260 ----------------------------------~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~  302 (444)
                                                        .-+..+|.+...   .... ....++..+.+.+....    ..+.+
T Consensus       388 ~Qnyfr~Y~kL~GMTGTa~te~~Ef~~iY~l~vv~IPtn~p~~R~d~~d~v~~-t~~~K~~al~~~i~~~~----~~gqp  462 (922)
T 1nkt_A          388 LQNYFRLYDKLAGMTGTAQTEAAELHEIYKLGVVSIPTNMPMIREDQSDLIYK-TEEAKYIAVVDDVAERY----AKGQP  462 (922)
T ss_dssp             HHHHHTTSSEEEEEESCCGGGHHHHHHHHCCEEEECCCSSCCCCEECCCEEES-CHHHHHHHHHHHHHHHH----HTTCC
T ss_pred             hHHHHHhhhhhhccccCchhHHHHHHHHhCCCeEEeCCCCCcccccCCcEEEe-CHHHHHHHHHHHHHHHH----hcCCc
Confidence                                              000111111110   1111 12234444444443321    24678


Q ss_pred             EEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCc-------------
Q psy7952         303 GIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNV-------------  359 (444)
Q Consensus       303 ~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~-------------  359 (444)
                      +||||+|++.++.++..|.+.          ....++..+.+.|+.|  .|+|||++++||+||+..             
T Consensus       463 vLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~~~~~~~~~~~~~~  540 (922)
T 1nkt_A          463 VLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRG--GVTVATNMAGRGTDIVLGGNVDFLTDQRLRE  540 (922)
T ss_dssp             EEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTT--CEEEEETTCSTTCCCCTTCCHHHHHHHHHHH
T ss_pred             EEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecchhhcCccccCCCCHHHHHHHHHhh
Confidence            999999999999999999987          3344444455556655  799999999999999964             


Q ss_pred             ---------------------------------------cEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         360 ---------------------------------------RFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       360 ---------------------------------------~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                                                             .+||+++.|.|.+.|.||+||+||.|.+|.++.|++.+|.
T Consensus       541 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSleD~  619 (922)
T 1nkt_A          541 RGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDE  619 (922)
T ss_dssp             TTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSH
T ss_pred             ccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEechhHH
Confidence                                                   4999999999999999999999999999999999987664

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=100.00  E-value=2.9e-34  Score=293.89  Aligned_cols=282  Identities=14%  Similarity=0.139  Sum_probs=186.2

Q ss_pred             CchHHH-----HHHHHHH------ccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          50 KCELQK-----KAIRHIL------LRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        50 ~t~~Q~-----~~~~~~~------~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      ||++|+     ++++.++      .+ +++++.+|||+|||++        |++++ +..+...  ..+++|++||++|+
T Consensus       216 pt~IQ~~~r~~~aIp~~l~~~~l~~g-~dvlv~apTGSGKTl~--------~ll~i-l~~l~~~--~~~~lilaPTr~La  283 (673)
T 2wv9_A          216 VSAIVQGERVEEPVPEAYNPEMLKKR-QLTVLDLHPGAGKTRR--------ILPQI-IKDAIQK--RLRTAVLAPTRVVA  283 (673)
T ss_dssp             EEEEECC-------CCCCCGGGGSTT-CEEEECCCTTTTTTTT--------HHHHH-HHHHHHT--TCCEEEEESSHHHH
T ss_pred             cCceeeccccccchHHHhhHHHHhcC-CeEEEEeCCCCCHHHH--------HHHHH-HHHHHhC--CCcEEEEccHHHHH
Confidence            788999     8998887      67 9999999999999999        65555 3222222  24669999999999


Q ss_pred             cccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH-HH---HHhhCCc
Q psy7952         119 YLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL-QH---LVRYNKL  193 (444)
Q Consensus       119 ~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~-~~---~~~~~~~  193 (444)
                           .|+.+.+ ..+   +.  ...+..                    -.++||+.+....-...+ ..   ...+.++
T Consensus       284 -----~Q~~~~l~~~~---i~--~~~~~l--------------------~~v~tp~~ll~~l~~~~l~~~l~~~~~l~~l  333 (673)
T 2wv9_A          284 -----AEMAEALRGLP---VR--YLTPAV--------------------QREHSGNEIVDVMCHATLTHRLMSPLRVPNY  333 (673)
T ss_dssp             -----HHHHHHTTTSC---CE--ECCC-----------------------CCCCSCCCEEEEEHHHHHHHHHSSSCCCCC
T ss_pred             -----HHHHHHHhcCC---ee--eecccc--------------------cccCCHHHHHHHHHhhhhHHHHhcccccccc
Confidence                 6666666 333   22  111000                    016777776432211111 11   1246789


Q ss_pred             cEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEE
Q psy7952         194 AYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVI  273 (444)
Q Consensus       194 ~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  273 (444)
                      ++||+||+|++.. .  +...+..+.....  +.+.++++||||+++....    ......++.....            
T Consensus       334 ~lvViDEaH~~~~-~--~~~~~~~l~~~~~--~~~~~vl~~SAT~~~~i~~----~~~~~~~i~~v~~------------  392 (673)
T 2wv9_A          334 NLFVMDEAHFTDP-A--SIAARGYIATRVE--AGEAAAIFMTATPPGTSDP----FPDTNSPVHDVSS------------  392 (673)
T ss_dssp             SEEEEESTTCCCH-H--HHHHHHHHHHHHH--TTSCEEEEECSSCTTCCCS----SCCCSSCEEEEEC------------
T ss_pred             eEEEEeCCcccCc-c--HHHHHHHHHHhcc--ccCCcEEEEcCCCChhhhh----hcccCCceEEEee------------
Confidence            9999999999721 1  2222233333221  2458999999999876432    1111111111110            


Q ss_pred             EcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------cCHHHHHHHHHHHhcCCccEEEEc
Q psy7952         274 FDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------VNKHERSRVQESFMRGEINVITAT  347 (444)
Q Consensus       274 ~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------~~~~~r~~~~~~f~~g~~~vLvaT  347 (444)
                        .........+...+.+       .++++||||+++++++.++..|...      +...+|..+++.|++|+.+|||||
T Consensus       393 --~~~~~~~~~~l~~l~~-------~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~eR~~v~~~F~~g~~~VLVaT  463 (673)
T 2wv9_A          393 --EIPDRAWSSGFEWITD-------YAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRKSYDTEYPKCKNGDWDFVITT  463 (673)
T ss_dssp             --CCCSSCCSSCCHHHHS-------CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSSSHHHHGGGGGTCCCSEEEEC
T ss_pred             --ecCHHHHHHHHHHHHh-------CCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChHHHHHHHHHHHCCCceEEEEC
Confidence              0000111111122211       4789999999999999999999876      555789999999999999999999


Q ss_pred             CccccccccCCccEEEE--------------------eCCCCCHHHHHHHhccCCCC-CCceeEEEEe---cccchhhHH
Q psy7952         348 ISFGMGIDRQNVRFVVH--------------------WGMPSSIPAYYQESGRAGRD-GLQSYCRIYH---SEHSKKSLE  403 (444)
Q Consensus       348 ~~~~~Gidi~~~~~Vi~--------------------~~~p~s~~~~~Qr~GR~~R~-g~~g~~~~~~---~~~~~~~~~  403 (444)
                      +++++|+|+| +++||+                    ++.|.|..+|+||+||+||. |+.|.+++++   ++.+...+.
T Consensus       464 dv~e~GIDip-v~~VI~~g~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~~~~~~d~~~l~  542 (673)
T 2wv9_A          464 DISEMGANFG-ASRVIDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSEDDTMLAH  542 (673)
T ss_dssp             GGGGTTCCCC-CSEEEECCEECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECSCCCCCCTTBHH
T ss_pred             chhhcceeeC-CcEEEECCCcccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEecCChhHHHHHH
Confidence            9999999999 999998                    56899999999999999999 7899999996   455544333


Q ss_pred             H
Q psy7952         404 Y  404 (444)
Q Consensus       404 ~  404 (444)
                      .
T Consensus       543 ~  543 (673)
T 2wv9_A          543 W  543 (673)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=100.00  E-value=1.2e-33  Score=279.81  Aligned_cols=272  Identities=14%  Similarity=0.118  Sum_probs=173.7

Q ss_pred             HHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhhcCCCCcee
Q psy7952          59 RHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQ  138 (444)
Q Consensus        59 ~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~  138 (444)
                      +.++.+++++++.+|||+|||.+        |.+|+ +..+...  ..++||++||++|+     .|+.+.+. +   ..
T Consensus        15 ~~~l~~~~~vlv~a~TGsGKT~~--------~~l~i-l~~~~~~--~~~~lvl~Ptr~La-----~Q~~~~l~-g---~~   74 (459)
T 2z83_A           15 PNMLRKRQMTVLDLHPGSGKTRK--------ILPQI-IKDAIQQ--RLRTAVLAPTRVVA-----AEMAEALR-G---LP   74 (459)
T ss_dssp             CGGGSTTCEEEECCCTTSCTTTT--------HHHHH-HHHHHHT--TCCEEEEECSHHHH-----HHHHHHTT-T---SC
T ss_pred             HHHHhcCCcEEEECCCCCCHHHH--------HHHHH-HHHHHhC--CCcEEEECchHHHH-----HHHHHHhc-C---ce
Confidence            33444438999999999999999        77776 3323322  24569999999999     66666653 2   22


Q ss_pred             EEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHH
Q psy7952         139 LELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRL  218 (444)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l  218 (444)
                      +....+.....           ..++..+.++|.+.+.    . .+.....+.++++||+||||++...   ....+..+
T Consensus        75 v~~~~~~~~~~-----------~t~~~~i~~~~~~~l~----~-~l~~~~~l~~~~~iViDEaH~~~~~---~~~~~~~~  135 (459)
T 2z83_A           75 VRYQTSAVQRE-----------HQGNEIVDVMCHATLT----H-RLMSPNRVPNYNLFVMDEAHFTDPA---SIAARGYI  135 (459)
T ss_dssp             EEECC-------------------CCCSEEEEEHHHHH----H-HHHSCC-CCCCSEEEESSTTCCSHH---HHHHHHHH
T ss_pred             EeEEecccccC-----------CCCCcEEEEEchHHHH----H-HhhccccccCCcEEEEECCccCCch---hhHHHHHH
Confidence            22211111100           0123345555644432    1 1222234678999999999985210   11111112


Q ss_pred             HHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCC
Q psy7952         219 GELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNK  298 (444)
Q Consensus       219 ~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~  298 (444)
                      ....  ...+.++++||||++.....    ......++......              ............+.+       
T Consensus       136 ~~~~--~~~~~~~il~SAT~~~~~~~----~~~~~~pi~~~~~~--------------~~~~~~~~~~~~l~~-------  188 (459)
T 2z83_A          136 ATKV--ELGEAAAIFMTATPPGTTDP----FPDSNAPIHDLQDE--------------IPDRAWSSGYEWITE-------  188 (459)
T ss_dssp             HHHH--HTTSCEEEEECSSCTTCCCS----SCCCSSCEEEEECC--------------CCSSCCSSCCHHHHH-------
T ss_pred             HHHh--ccCCccEEEEEcCCCcchhh----hccCCCCeEEeccc--------------CCcchhHHHHHHHHh-------
Confidence            2211  22458999999999875422    11112222221110              001111111222333       


Q ss_pred             CCceEEEEecccchHHHHHHHHHhh------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEE--------
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVH--------  364 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~--------  364 (444)
                      .++++||||++++.++.+++.|...      +..++|..+++.|++|+.+|||||+++++|+|+|+ ++||+        
T Consensus       189 ~~~~~LVF~~s~~~~~~l~~~L~~~g~~v~~lh~~~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~~~~  267 (459)
T 2z83_A          189 YAGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNRKSYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSVKPT  267 (459)
T ss_dssp             CCSCEEEECSCHHHHHHHHHHHHHTTCCEEEESTTCCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEECCEE
T ss_pred             cCCCEEEEeCChHHHHHHHHHHHhcCCcEEecCHHHHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCcccccc
Confidence            3679999999999999999999876      66678889999999999999999999999999999 99999        


Q ss_pred             ------------eCCCCCHHHHHHHhccCCCCCC-ceeEEEEeccc
Q psy7952         365 ------------WGMPSSIPAYYQESGRAGRDGL-QSYCRIYHSEH  397 (444)
Q Consensus       365 ------------~~~p~s~~~~~Qr~GR~~R~g~-~g~~~~~~~~~  397 (444)
                                  ++.|.|..+|+||+||+||.|. .|.+++++.+.
T Consensus       268 ~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          268 ILEEGEGRVILGNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             EECSSSCEEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             cccccccccccccCCCCCHHHHHHhccccCCCCCCCCeEEEEEccc
Confidence                        6699999999999999999997 89999999865

>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=99.98  E-value=2.3e-32  Score=284.89  Aligned_cols=317  Identities=14%  Similarity=0.096  Sum_probs=210.8

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCC-ccccccCCccceeEEE
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPG-ADFILNGNVRSRNGWI  111 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~-~~~l~~~~~~~~vlil  111 (444)
                      ...+.+.++.. |  .+|+..|++++..++.+++++++.+|||+|||..          +|.+ .......+...+++++
T Consensus        80 ~~~~~~~l~~r-~--~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTtl----------lp~ll~~~~~~~~~g~~ilvl  146 (773)
T 2xau_A           80 TPKYVDILKIR-R--ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQ----------IPQFVLFDEMPHLENTQVACT  146 (773)
T ss_dssp             CHHHHHHHHHH-T--TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHH----------HHHHHHHHHCGGGGTCEEEEE
T ss_pred             CHHHHHHHHHh-h--cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHHH----------HHHHHHHhccccCCCceEEec
Confidence            45677778775 5  3578899999998887757899999999999974          2221 0001112223467999


Q ss_pred             cchhhhhcccCccchHhhh--cCCCC-ceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHH
Q psy7952         112 SPILSSFYLRFRDDKTSIV--TGRSD-LYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLV  188 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l--~~~~~-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~  188 (444)
                      +|+++|+     .++.+.+  ..+.. ...+..-......            .....+|+++||+++.    . ......
T Consensus       147 ~P~r~La-----~q~~~~l~~~~~~~v~~~vG~~i~~~~~------------~~~~~~I~v~T~G~l~----r-~l~~~~  204 (773)
T 2xau_A          147 QPRRVAA-----MSVAQRVAEEMDVKLGEEVGYSIRFENK------------TSNKTILKYMTDGMLL----R-EAMEDH  204 (773)
T ss_dssp             ESCHHHH-----HHHHHHHHHHTTCCBTTTEEEEETTEEE------------CCTTCSEEEEEHHHHH----H-HHHHST
T ss_pred             CchHHHH-----HHHHHHHHHHhCCchhheecceeccccc------------cCCCCCEEEECHHHHH----H-HHhhCc
Confidence            9999999     5555544  22200 0111111110000            1246789999999974    2 222234


Q ss_pred             hhCCccEEEEecccc-ccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCC
Q psy7952         189 RYNKLAYIVVDEAHC-VSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSN  267 (444)
Q Consensus       189 ~~~~~~~iViDE~H~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  267 (444)
                      .+.++++||+||+|. ..+    ....+..+..+....+ +.++++||||++.   +.+..+++  ....+....... +
T Consensus       205 ~l~~~~~lIlDEah~R~ld----~d~~~~~l~~l~~~~~-~~~iIl~SAT~~~---~~l~~~~~--~~~vi~v~gr~~-p  273 (773)
T 2xau_A          205 DLSRYSCIILDEAHERTLA----TDILMGLLKQVVKRRP-DLKIIIMSATLDA---EKFQRYFN--DAPLLAVPGRTY-P  273 (773)
T ss_dssp             TCTTEEEEEECSGGGCCHH----HHHHHHHHHHHHHHCT-TCEEEEEESCSCC---HHHHHHTT--SCCEEECCCCCC-C
T ss_pred             cccCCCEEEecCccccccc----hHHHHHHHHHHHHhCC-CceEEEEeccccH---HHHHHHhc--CCCcccccCccc-c
Confidence            577899999999996 332    1112233334443333 4899999999964   34555553  222233222211 2


Q ss_pred             ceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHh-----------h----------cCH
Q psy7952         268 LFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR-----------K----------VNK  326 (444)
Q Consensus       268 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~-----------~----------~~~  326 (444)
                      +...+... ............+.......  .++++||||+++++++.++..|.+           .          +++
T Consensus       274 v~~~~~~~-~~~~~~~~~l~~l~~~~~~~--~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~  350 (773)
T 2xau_A          274 VELYYTPE-FQRDYLDSAIRTVLQIHATE--EAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPP  350 (773)
T ss_dssp             EEEECCSS-CCSCHHHHHHHHHHHHHHHS--CSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCH
T ss_pred             eEEEEecC-CchhHHHHHHHHHHHHHHhc--CCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCH
Confidence            22111111 11222233333343333322  478999999999999999999985           1          889


Q ss_pred             HHHHHHHHHHh-----cCCccEEEEcCccccccccCCccEEEEeCC------------------CCCHHHHHHHhccCCC
Q psy7952         327 HERSRVQESFM-----RGEINVITATISFGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGR  383 (444)
Q Consensus       327 ~~r~~~~~~f~-----~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~------------------p~s~~~~~Qr~GR~~R  383 (444)
                      ++|..+++.|+     +|..+|||||+++++|||+|++++||++|.                  |.|..+|+||+||+||
T Consensus       351 ~eR~~v~~~f~~~~~~~g~~kVlVAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR  430 (773)
T 2xau_A          351 HQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGR  430 (773)
T ss_dssp             HHHGGGGSCCCCCSSSSCCEEEEEECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGS
T ss_pred             HHHHHHHhhcccccCCCCceEEEEeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCC
Confidence            99999999999     999999999999999999999999999888                  8899999999999999


Q ss_pred             CCCceeEEEEecccch
Q psy7952         384 DGLQSYCRIYHSEHSK  399 (444)
Q Consensus       384 ~g~~g~~~~~~~~~~~  399 (444)
                      . .+|.|+.++++.+.
T Consensus       431 ~-~~G~~~~l~~~~~~  445 (773)
T 2xau_A          431 T-RPGKCFRLYTEEAF  445 (773)
T ss_dssp             S-SSEEEEESSCHHHH
T ss_pred             C-CCCEEEEEecHHHh
Confidence            9 88999999987655

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.98  E-value=7e-33  Score=272.09  Aligned_cols=263  Identities=13%  Similarity=0.077  Sum_probs=167.4

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCC
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSG  145 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~  145 (444)
                      +++++++|||+|||.+        |++++ ++.+...+  .+++|++||++|+     .|..+.+. +   +.+....+.
T Consensus         3 ~~~lv~a~TGsGKT~~--------~l~~~-l~~~~~~g--~~~lvl~Pt~~La-----~Q~~~~~~-~---~~v~~~~~~   62 (431)
T 2v6i_A            3 ELTVLDLHPGAGKTRR--------VLPQL-VREAVKKR--LRTVILAPTRVVA-----SEMYEALR-G---EPIRYMTPA   62 (431)
T ss_dssp             CEEEEECCTTSCTTTT--------HHHHH-HHHHHHTT--CCEEEEESSHHHH-----HHHHHHTT-T---SCEEEC---
T ss_pred             CEEEEEcCCCCCHHHH--------HHHHH-HHHHHhCC--CCEEEECcHHHHH-----HHHHHHhC-C---CeEEEEecC
Confidence            7999999999999999        54555 22222222  3569999999999     55555443 3   444444443


Q ss_pred             CChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhh
Q psy7952         146 QTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFT  225 (444)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~  225 (444)
                      ....           ..++..+.+.|.+.+.    +.+.. ...+.++++||+||+|++.. +  +......+....  .
T Consensus        63 ~~~~-----------~~~~~~~~~~~~~~l~----~~l~~-~~~~~~l~~vViDEaH~~~~-~--~~~~~~~l~~~~--~  121 (431)
T 2v6i_A           63 VQSE-----------RTGNEIVDFMCHSTFT----MKLLQ-GVRVPNYNLYIMDEAHFLDP-A--SVAARGYIETRV--S  121 (431)
T ss_dssp             -----------------CCCSEEEEEHHHHH----HHHHH-TCCCCCCSEEEEESTTCCSH-H--HHHHHHHHHHHH--H
T ss_pred             cccc-----------CCCCceEEEEchHHHH----HHHhc-CccccCCCEEEEeCCccCCc-c--HHHHHHHHHHHh--h
Confidence            2210           0123345555655442    22222 33477899999999999621 1  222233333322  2


Q ss_pred             CCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEE
Q psy7952         226 GNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGII  305 (444)
Q Consensus       226 ~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iV  305 (444)
                      +.++++++||||+++....    +.....+......              .........+.+.+.+       .++++||
T Consensus       122 ~~~~~~l~~SAT~~~~~~~----~~~~~~~i~~~~~--------------~~~~~~~~~~~~~l~~-------~~~~~lV  176 (431)
T 2v6i_A          122 MGDAGAIFMTATPPGTTEA----FPPSNSPIIDEET--------------RIPDKAWNSGYEWITE-------FDGRTVW  176 (431)
T ss_dssp             TTSCEEEEEESSCTTCCCS----SCCCSSCCEEEEC--------------CCCSSCCSSCCHHHHS-------CSSCEEE
T ss_pred             CCCCcEEEEeCCCCcchhh----hcCCCCceeeccc--------------cCCHHHHHHHHHHHHc-------CCCCEEE
Confidence            3458999999999875321    1100111111100              0001111112222222       3668999


Q ss_pred             EecccchHHHHHHHHHhh------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccE-----------------E
Q psy7952         306 YCRTREHTTDLADALRRK------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRF-----------------V  362 (444)
Q Consensus       306 f~~s~~~~~~l~~~L~~~------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~-----------------V  362 (444)
                      ||+++++++.+++.|.+.      +...+|..+++.|++|+.+|||||+++++|+|+| +.+                 |
T Consensus       177 F~~~~~~~~~l~~~L~~~~~~v~~lhg~~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~~~~v~d~~~~v  255 (431)
T 2v6i_A          177 FVHSIKQGAEIGTCLQKAGKKVLYLNRKTFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPRKTIKPILLDGRVS  255 (431)
T ss_dssp             ECSSHHHHHHHHHHHHHTTCCEEEESTTTHHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECCEEEEEEEETTEEE
T ss_pred             EeCCHHHHHHHHHHHHHcCCeEEEeCCccHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecCccccceeccccee
Confidence            999999999999999876      5556889999999999999999999999999999 544                 6


Q ss_pred             EEeCCCCCHHHHHHHhccCCCCCCceeEEEEec
Q psy7952         363 VHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHS  395 (444)
Q Consensus       363 i~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~  395 (444)
                      |+++.|.+..+|+||+||+||.|..+.+++++.
T Consensus       256 i~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          256 MQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             EEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             ecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence            788899999999999999999986544444443

>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=99.97  E-value=5.8e-33  Score=280.11  Aligned_cols=263  Identities=14%  Similarity=0.104  Sum_probs=177.6

Q ss_pred             HHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh--
Q psy7952          53 LQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV--  130 (444)
Q Consensus        53 ~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l--  130 (444)
                      +|.+++..+..+ +++++.||||+|||.+        +.+++    +..+.   +++|++||++|+     .+..+.+  
T Consensus       221 ~q~~i~~~L~~~-~~vlv~ApTGSGKT~a--------~~l~l----l~~g~---~vLVl~PTReLA-----~Qia~~l~~  279 (666)
T 3o8b_A          221 DNSSPPAVPQSF-QVAHLHAPTGSGKSTK--------VPAAY----AAQGY---KVLVLNPSVAAT-----LGFGAYMSK  279 (666)
T ss_dssp             CCCSCCCCCSSC-EEEEEECCTTSCTTTH--------HHHHH----HHTTC---CEEEEESCHHHH-----HHHHHHHHH
T ss_pred             HHHHHHHHHHcC-CeEEEEeCCchhHHHH--------HHHHH----HHCCC---eEEEEcchHHHH-----HHHHHHHHH
Confidence            555555555555 8999999999999988        55555    33322   569999999999     4444454  


Q ss_pred             cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCC
Q psy7952         131 TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHD  210 (444)
Q Consensus       131 ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~  210 (444)
                      ..+   ..+....|+...             ..+.+|+|+||++|.       ......+.++++||+||+|++.. +  
T Consensus       280 ~~g---~~vg~~vG~~~~-------------~~~~~IlV~TPGrLl-------~~~~l~l~~l~~lVlDEAH~l~~-~--  333 (666)
T 3o8b_A          280 AHG---IDPNIRTGVRTI-------------TTGAPVTYSTYGKFL-------ADGGCSGGAYDIIICDECHSTDS-T--  333 (666)
T ss_dssp             HHS---CCCEEECSSCEE-------------CCCCSEEEEEHHHHH-------HTTSCCTTSCSEEEETTTTCCSH-H--
T ss_pred             HhC---CCeeEEECcEec-------------cCCCCEEEECcHHHH-------hCCCcccCcccEEEEccchhcCc-c--
Confidence            334   445556665432             467899999999962       23334566799999999987532 2  


Q ss_pred             cHHHHHHHHHHHHhhCCCCc--EEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHH
Q psy7952         211 FRPTYRRLGELRQFTGNSIP--IIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEF  288 (444)
Q Consensus       211 ~~~~~~~l~~~~~~~~~~~~--~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  288 (444)
                      +...+..+   ++..+...+  ++++|||+++...        ...+............+.    .... ...       
T Consensus       334 ~~~~l~~I---l~~l~~~~~~llil~SAT~~~~i~--------~~~p~i~~v~~~~~~~i~----~~~~-~~~-------  390 (666)
T 3o8b_A          334 TILGIGTV---LDQAETAGARLVVLATATPPGSVT--------VPHPNIEEVALSNTGEIP----FYGK-AIP-------  390 (666)
T ss_dssp             HHHHHHHH---HHHTTTTTCSEEEEEESSCTTCCC--------CCCTTEEEEECBSCSSEE----ETTE-EEC-------
T ss_pred             HHHHHHHH---HHhhhhcCCceEEEECCCCCcccc--------cCCcceEEEeecccchhH----HHHh-hhh-------
Confidence            44444444   444444344  7888999987421        112111111111111110    0000 000       


Q ss_pred             HHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCC
Q psy7952         289 IEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQN  358 (444)
Q Consensus       289 l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~  358 (444)
                          +.  ...++++||||++++.++.+++.|.+.          +++++       |+++..+|||||+++++|||+| 
T Consensus       391 ----l~--~~~~~~vLVFv~Tr~~ae~la~~L~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVATdVaerGIDId-  456 (666)
T 3o8b_A          391 ----IE--AIRGGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGD-  456 (666)
T ss_dssp             ----GG--GSSSSEEEEECSCHHHHHHHHHHHHTTTCCEEEECTTSCGGG-------SCSSSCEEEEECTTHHHHCCCC-
T ss_pred             ----hh--hccCCcEEEEeCCHHHHHHHHHHHHhCCCcEEEecCCCCHHH-------HHhCCCcEEEECChHHccCCCC-
Confidence                01  115789999999999999999999876          44432       5566779999999999999997 


Q ss_pred             ccEEE----------EeC-----------CCCCHHHHHHHhccCCCCCCceeEEEEecccchhh
Q psy7952         359 VRFVV----------HWG-----------MPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKS  401 (444)
Q Consensus       359 ~~~Vi----------~~~-----------~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~  401 (444)
                      +++||          +||           .|.|..+|+||+||+|| |+.|. +.|+.+.+...
T Consensus       457 V~~VI~~Gl~~~~ViNyDydP~~gl~~~~~P~s~~syiQRiGRtGR-g~~G~-i~lvt~~e~~~  518 (666)
T 3o8b_A          457 FDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR-GRRGI-YRFVTPGERPS  518 (666)
T ss_dssp             BSEEEECCEEEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEE-EEESCCCCBCS
T ss_pred             CcEEEecCcccccccccccccccccccccCcCCHHHHHHHhccCCC-CCCCE-EEEEecchhhc
Confidence            99988          566           89999999999999999 89999 88888776544

>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=99.97  E-value=4.7e-32  Score=289.91  Aligned_cols=314  Identities=15%  Similarity=0.096  Sum_probs=201.5

Q ss_pred             CchHHHHHHHHHHcc-CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHh
Q psy7952          50 KCELQKKAIRHILLR-THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTS  128 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~-~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~  128 (444)
                      +++||.+++..++.. ..++++.++||+|||++|+.++          ..+...+...++||+||+ +|+     .++..
T Consensus       154 LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i----------~~l~~~g~~~rvLIVvP~-sLl-----~Qw~~  217 (968)
T 3dmq_A          154 LIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMIL----------HQQLLSGAAERVLIIVPE-TLQ-----HQWLV  217 (968)
T ss_dssp             CCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHH----------HHHHHTSSCCCEEEECCT-TTH-----HHHHH
T ss_pred             CcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHH----------HHHHHhCCCCeEEEEeCH-HHH-----HHHHH
Confidence            358999999998874 2578999999999999854322          123344555578999999 888     56666


Q ss_pred             hh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccc
Q psy7952         129 IV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSE  206 (444)
Q Consensus       129 ~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~  206 (444)
                      .+  .++   +++..++++....    ...........++|+|+|++.+....   .........++++||+||+|++..
T Consensus       218 E~~~~f~---l~v~v~~~~~~~~----~~~~~~~~~~~~dIvI~T~~~L~~~~---~~~~~l~~~~~dlVIvDEAH~~kn  287 (968)
T 3dmq_A          218 EMLRRFN---LRFALFDDERYAE----AQHDAYNPFDTEQLVICSLDFARRSK---QRLEHLCEAEWDLLVVDEAHHLVW  287 (968)
T ss_dssp             HHHHHSC---CCCEECCHHHHHH----HHHTTCSSSTTCSEEEECHHHHHTST---TTTHHHHTSCCCEEEECCSSCCCC
T ss_pred             HHHHHhC---CCEEEEccchhhh----hhhhcccccccCCEEEEcHHHHhhCH---HHHHHhhhcCCCEEEehhhHhhcC
Confidence            66  445   6666665432211    11111122346799999988874311   001223356899999999999965


Q ss_pred             cCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCC-------------------------------
Q psy7952         207 WGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKP-------------------------------  255 (444)
Q Consensus       207 ~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~-------------------------------  255 (444)
                      .+......+..+..+..   +..++++|||||.++...++...+.+-.+                               
T Consensus       288 ~~~~~s~~~~~l~~L~~---~~~~~L~LTATPi~n~~~el~sll~~L~p~~~~~~~~f~~~~~~~~~i~~~~~~l~~~~~  364 (968)
T 3dmq_A          288 SEDAPSREYQAIEQLAE---HVPGVLLLTATPEQLGMESHFARLRLLDPNRFHDFAQFVEEQKNYCPVADAVAMLLAGNK  364 (968)
T ss_dssp             BTTBCCHHHHHHHHHHT---TCSSEEESCSSCSSSCSSCTHHHHHHHCTTTCSSTHHHHHHHHHHHHHHHHHHTTTTSCC
T ss_pred             CCCcchHHHHHHHHHhh---cCCcEEEEEcCCccCCHHHHHHHHHhcCccccCCHHHHHHHHHhHHHHHHHHHHHhccCC
Confidence            54333333444544322   33669999999964222111111000000                               


Q ss_pred             --------------------------------------------------eEEEecCC----CCCC-ceEEEEEccc---
Q psy7952         256 --------------------------------------------------YKVFKTST----FRSN-LFYDVIFDDL---  277 (444)
Q Consensus       256 --------------------------------------------------~~~~~~~~----~~~~-~~~~~~~~~~---  277 (444)
                                                                        -.......    ..+. ..........   
T Consensus       365 ~~~~~~~~L~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~i~~lld~~g~~~~l~r~~r~~i~~~p~r~~~~~~l~~~~~~  444 (968)
T 3dmq_A          365 LSNDELNMLGEMIGEQDIEPLLQAANSDSEDAQSARQELVSMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIKLPLPTQY  444 (968)
T ss_dssp             CCGGGTTSSTTTTCTTCSSTTGGGTCCCSSCSTTTHHHHHHHHGGGCTTTTTEECCCTTTCCCCCCCCCCEEEECCCHHH
T ss_pred             CCHHHHHHHHHHhcchhhHHHHhcccchhhhhHHHHHHHHHHHHHhhCcchhhhhhhhhhhcccChhheEeeecCCCHHH
Confidence                                                              00000000    0000 0000000000   


Q ss_pred             --------------------------------------chhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHH
Q psy7952         278 --------------------------------------LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADA  319 (444)
Q Consensus       278 --------------------------------------~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~  319 (444)
                                                            ...........+.+++...  .+.++||||+++.+++.++..
T Consensus       445 ~~~~~~~~~~~~~~~~~~~~~~~l~pe~~~~~l~~~~~~~~~~~~K~~~L~~ll~~~--~~~k~iVF~~~~~~~~~l~~~  522 (968)
T 3dmq_A          445 QTAIKVSGIMGARKSAEDRARDMLYPERIYQEFEGDNATWWNFDPRVEWLMGYLTSH--RSQKVLVICAKAATALQLEQV  522 (968)
T ss_dssp             HHHHHHHHHTTCCSSGGGGTHHHHCSGGGTTTTTSSSCCTTTTSHHHHHHHHHHHHT--SSSCCCEECSSTHHHHHHHHH
T ss_pred             HHHHHHHhhhhhhhhhHHHHhhhcChHHHHHHhhhhhhcccCccHHHHHHHHHHHhC--CCCCEEEEeCcHHHHHHHHHH
Confidence                                                  0000112233344444332  688999999999999999999


Q ss_pred             HHhh-----------cCHHHHHHHHHHHhcCC--ccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCC
Q psy7952         320 LRRK-----------VNKHERSRVQESFMRGE--INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGL  386 (444)
Q Consensus       320 L~~~-----------~~~~~r~~~~~~f~~g~--~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~  386 (444)
                      |...           ++..+|..+++.|++|+  .+|||||+++++|+|+|++++||++++|+++..|.||+||+||.|+
T Consensus       523 L~~~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq  602 (968)
T 3dmq_A          523 LREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQ  602 (968)
T ss_dssp             HHTTTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCCTTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSS
T ss_pred             HHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecchhhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCC
Confidence            9953           88899999999999998  9999999999999999999999999999999999999999999999


Q ss_pred             ceeEEEEe
Q psy7952         387 QSYCRIYH  394 (444)
Q Consensus       387 ~g~~~~~~  394 (444)
                      .+.++++.
T Consensus       603 ~~~v~v~~  610 (968)
T 3dmq_A          603 AHDIQIHV  610 (968)
T ss_dssp             CSCCEEEE
T ss_pred             CceEEEEE
Confidence            88765554

>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=99.97  E-value=2.2e-30  Score=260.42  Aligned_cols=305  Identities=15%  Similarity=0.159  Sum_probs=194.1

Q ss_pred             CchHHHHHHHHHH----ccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccc
Q psy7952          50 KCELQKKAIRHIL----LRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDD  125 (444)
Q Consensus        50 ~t~~Q~~~~~~~~----~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~  125 (444)
                      +.+||.+++..+.    .+ +++++..+||+|||++|+.++          ..+...+...++||+|| .+|+  .||.+
T Consensus        38 L~~~Q~~~v~~l~~~~~~~-~~~ilad~~GlGKT~~ai~~i----------~~~~~~~~~~~~LIv~P-~~l~--~qw~~  103 (500)
T 1z63_A           38 LRPYQIKGFSWMRFMNKLG-FGICLADDMGLGKTLQTIAVF----------SDAKKENELTPSLVICP-LSVL--KNWEE  103 (500)
T ss_dssp             CCHHHHHHHHHHHHHHHTT-CCEEECCCTTSCHHHHHHHHH----------HHHHHTTCCSSEEEEEC-STTH--HHHHH
T ss_pred             chHHHHHHHHHHHHHhhCC-CCEEEEeCCCCcHHHHHHHHH----------HHHHhcCCCCCEEEEcc-HHHH--HHHHH
Confidence            4589999998774    34 789999999999998843221          11333344456799999 5577  33444


Q ss_pred             hHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccc
Q psy7952         126 KTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVS  205 (444)
Q Consensus       126 ~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~  205 (444)
                      .++.+...   .++..++++....           ....++|+|+||+.+....       ......+++||+||||++.
T Consensus       104 e~~~~~~~---~~v~~~~g~~~~~-----------~~~~~~ivi~t~~~l~~~~-------~l~~~~~~~vIvDEaH~~k  162 (500)
T 1z63_A          104 ELSKFAPH---LRFAVFHEDRSKI-----------KLEDYDIILTTYAVLLRDT-------RLKEVEWKYIVIDEAQNIK  162 (500)
T ss_dssp             HHHHHCTT---SCEEECSSSTTSC-----------CGGGSSEEEEEHHHHTTCH-------HHHTCCEEEEEEETGGGGS
T ss_pred             HHHHHCCC---ceEEEEecCchhc-----------cccCCcEEEeeHHHHhccc-------hhcCCCcCEEEEeCccccC
Confidence            44444333   6677777665321           1246799999999986432       1334578999999999986


Q ss_pred             ccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCC--------------------------------
Q psy7952         206 EWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFN--------------------------------  253 (444)
Q Consensus       206 ~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~--------------------------------  253 (444)
                      +.+.   ..+..+    ..++. .+.+++||||..+...++...+.+-                                
T Consensus       163 n~~~---~~~~~l----~~l~~-~~~l~LTaTP~~n~~~el~~ll~~l~p~~~~~~~~f~~~~~~~~~~~~~~~~~~l~~  234 (500)
T 1z63_A          163 NPQT---KIFKAV----KELKS-KYRIALTGTPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMAKEELKA  234 (500)
T ss_dssp             CTTS---HHHHHH----HTSCE-EEEEEECSSCSTTCHHHHHHHHHHHSTTTTCCHHHHHTTTHHHHHTTCHHHHHHHHH
T ss_pred             CHhH---HHHHHH----Hhhcc-CcEEEEecCCCCCCHHHHHHHHHHhCCCcCCCHHHHHHHhccccccccHHHHHHHHH
Confidence            5432   112222    22333 6789999999776544443322110                                


Q ss_pred             --CCeEEEecC------CCCCCceEEEEEcccchhh---HH---------------------------------------
Q psy7952         254 --KPYKVFKTS------TFRSNLFYDVIFDDLLKDS---YA---------------------------------------  283 (444)
Q Consensus       254 --~~~~~~~~~------~~~~~~~~~~~~~~~~~~~---~~---------------------------------------  283 (444)
                        .++.+.+..      ...|...............   +.                                       
T Consensus       235 ~l~~~~lrr~k~~~~~~~~lp~~~~~~v~~~l~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lr~~~~~p~l~  314 (500)
T 1z63_A          235 IISPFILRRTKYDKAIINDLPDKIETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIVDHPALL  314 (500)
T ss_dssp             HHTTTEECCCTTCHHHHTTSCSEEEEEEEECCCHHHHHHHHHHHHHHTTTTTTCCTHHHHHHHHHHHHHHHHHTTCTHHH
T ss_pred             HHhhHeeeecccccchhhcCCCCeEEEEEcCCCHHHHHHHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhCCHHHh
Confidence              122222111      1122222222221111100   00                                       


Q ss_pred             ----------HHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----------cCHHHHHHHHHHHhcC-Cc
Q psy7952         284 ----------HVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----------VNKHERSRVQESFMRG-EI  341 (444)
Q Consensus       284 ----------~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----------~~~~~r~~~~~~f~~g-~~  341 (444)
                                .....+.+.+......+.++||||++...++.++..|...           ++..+|..+++.|++| ..
T Consensus       315 ~~~~~~~~~s~K~~~l~~~l~~~~~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~  394 (500)
T 1z63_A          315 KGGEQSVRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSV  394 (500)
T ss_dssp             HCSCCCSTTCHHHHHHHHHHHHHHTTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTC
T ss_pred             cCccchhhcchhHHHHHHHHHHHHccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCC
Confidence                      0111112222222235789999999999999999999763           7889999999999988 55


Q ss_pred             c-EEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEE--EEeccc
Q psy7952         342 N-VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCR--IYHSEH  397 (444)
Q Consensus       342 ~-vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~--~~~~~~  397 (444)
                      + +|++|+++++|+|+|.+++||++|+|+|+..|.|++||++|.|+.+.+.  .++..+
T Consensus       395 ~vil~st~~~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~  453 (500)
T 1z63_A          395 KFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  453 (500)
T ss_dssp             CCCEEECCCC-CCCCCTTCSEEEESSCCSCC---CHHHHTTTTTTTTSCEEEEEEEETT
T ss_pred             CEEEEecccccCCCchhhCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCC
Confidence            5 7999999999999999999999999999999999999999999876653  344444

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.97  E-value=8.1e-30  Score=260.25  Aligned_cols=282  Identities=14%  Similarity=0.136  Sum_probs=190.7

Q ss_pred             HHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-c
Q psy7952          53 LQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-T  131 (444)
Q Consensus        53 ~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~  131 (444)
                      .|.......+++ ++++++||||+|||..|             +..+...+..   +|++|+++|+     .|..+.+ .
T Consensus       144 ~~~~p~ar~l~r-k~vlv~apTGSGKT~~a-------------l~~l~~~~~g---l~l~PtR~LA-----~Qi~~~l~~  201 (677)
T 3rc3_A          144 PNWYPDARAMQR-KIIFHSGPTNSGKTYHA-------------IQKYFSAKSG---VYCGPLKLLA-----HEIFEKSNA  201 (677)
T ss_dssp             GGGCHHHHTSCC-EEEEEECCTTSSHHHHH-------------HHHHHHSSSE---EEEESSHHHH-----HHHHHHHHH
T ss_pred             hhhCHHHHhcCC-CEEEEEcCCCCCHHHHH-------------HHHHHhcCCe---EEEeCHHHHH-----HHHHHHHHh
Confidence            333333455566 89999999999999752             2224444444   9999999999     6777777 6


Q ss_pred             CCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCc
Q psy7952         132 GRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDF  211 (444)
Q Consensus       132 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~  211 (444)
                      .+   +.+..++|+.......        .....+++++|++.+.            ....++++|+||+|++.+.+  +
T Consensus       202 ~g---~~v~lltG~~~~iv~T--------pGr~~~il~~T~e~~~------------l~~~v~lvVIDEaH~l~d~~--~  256 (677)
T 3rc3_A          202 AG---VPCDLVTGEERVTVQP--------NGKQASHVSCTVEMCS------------VTTPYEVAVIDEIQMIRDPA--R  256 (677)
T ss_dssp             TT---CCEEEECSSCEECCST--------TCCCCSEEEEEGGGCC------------SSSCEEEEEECSGGGGGCTT--T
T ss_pred             cC---CcEEEEECCeeEEecC--------CCcccceeEecHhHhh------------hcccCCEEEEecceecCCcc--c
Confidence            67   8888888876541000        0013678888887753            13567999999999997655  4


Q ss_pred             HHHHHHHHHHHHhhC-CCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHH
Q psy7952         212 RPTYRRLGELRQFTG-NSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIE  290 (444)
Q Consensus       212 ~~~~~~l~~~~~~~~-~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  290 (444)
                      ...+..+   +...+ ...+++++|||.+  ....+....+  ....+...  .+... ...  ......          
T Consensus       257 g~~~~~~---l~~l~~~~i~il~~SAT~~--~i~~l~~~~~--~~~~v~~~--~r~~~-l~~--~~~~l~----------  314 (677)
T 3rc3_A          257 GWAWTRA---LLGLCAEEVHLCGEPAAID--LVMELMYTTG--EEVEVRDY--KRLTP-ISV--LDHALE----------  314 (677)
T ss_dssp             HHHHHHH---HHHCCEEEEEEEECGGGHH--HHHHHHHHHT--CCEEEEEC--CCSSC-EEE--CSSCCC----------
T ss_pred             hHHHHHH---HHccCccceEEEeccchHH--HHHHHHHhcC--CceEEEEe--eecch-HHH--HHHHHH----------
Confidence            4433332   22333 4578999999942  2333333322  23222211  11110 000  000000          


Q ss_pred             HHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhc--CCccEEEEcCccccccccCC
Q psy7952         291 KCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMR--GEINVITATISFGMGIDRQN  358 (444)
Q Consensus       291 ~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~--g~~~vLvaT~~~~~Gidi~~  358 (444)
                       .+..   .....+|||+++++++.++..|.+.          +++++|..+++.|++  |..+|||||+++++|+|+ +
T Consensus       315 -~l~~---~~~g~iIf~~s~~~ie~la~~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~  389 (677)
T 3rc3_A          315 -SLDN---LRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-S  389 (677)
T ss_dssp             -SGGG---CCTTEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-C
T ss_pred             -HHHh---cCCCCEEEEcCHHHHHHHHHHHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-C
Confidence             0001   1334589999999999999999876          899999999999998  889999999999999999 8


Q ss_pred             ccEEEEeCC--------------CCCHHHHHHHhccCCCCCCc---eeEEEEecccchhhHHHHHhhc
Q psy7952         359 VRFVVHWGM--------------PSSIPAYYQESGRAGRDGLQ---SYCRIYHSEHSKKSLEYVIKTD  409 (444)
Q Consensus       359 ~~~Vi~~~~--------------p~s~~~~~Qr~GR~~R~g~~---g~~~~~~~~~~~~~~~~~~~~~  409 (444)
                      +++||++|.              |.|..+|+||+||+||.|..   |.|+.+. +++...+..+....
T Consensus       390 v~~VI~~~~~k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l~-~~d~~~~~~~~~~~  456 (677)
T 3rc3_A          390 IRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMN-HEDLSLLKEILKRP  456 (677)
T ss_dssp             BSEEEESCSBC-----------CBCCHHHHHHHHTTBTCTTSSCSSEEEEESS-TTHHHHHHHHHHSC
T ss_pred             ccEEEECCccccccccCCccccccCCHHHHHHHhcCCCCCCCCCCCEEEEEEe-cchHHHHHHHHhcC
Confidence            999999998              77999999999999999864   6655544 44555666666544

>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=99.95  E-value=1.9e-27  Score=252.53  Aligned_cols=323  Identities=13%  Similarity=0.074  Sum_probs=194.6

Q ss_pred             CCHHHHHHHHHHHhCC-----cccCchHHHHHHHHHHcc-------------CCcEEEEccCCCcccccccccccceEEe
Q psy7952          31 VSEQELTAKLKALFGF-----DSFKCELQKKAIRHILLR-------------THDIFVSMPTGAVSLVGSVVSARSRVRI   92 (444)
Q Consensus        31 ~~~~~~~~~l~~~~g~-----~~~~t~~Q~~~~~~~~~~-------------~~~~ii~apTGsGKT~~a~~~~~~~~~~   92 (444)
                      +....+.+.+....-+     ...|+++|.+|++.++..             .++.+++++||||||+++         +
T Consensus       248 ~~~~~ll~~l~~f~~~~~~~~~~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~---------~  318 (1038)
T 2w00_A          248 FQKHTLLNVLVNYSVFDSSQTLLVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS---------F  318 (1038)
T ss_dssp             TSHHHHHHHHHHSEEECTTCCEEECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH---------H
T ss_pred             hchHHHHHHHHhheeeccccccccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH---------H
Confidence            3455666666553211     112568999999998761             267999999999999993         2


Q ss_pred             CCCccccccCCccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEEC
Q psy7952          93 PPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVT  171 (444)
Q Consensus        93 ~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~T  171 (444)
                      ++ +..+...+...++||++|+++|+     .|..+.+ .+...     .+.+..+.....   ..+.  ..+.+|+|+|
T Consensus       319 ~l-~~ll~~~~~~~rvLvlvpr~eL~-----~Q~~~~f~~f~~~-----~v~~~~s~~~l~---~~L~--~~~~~IiVtT  382 (1038)
T 2w00_A          319 KA-ARLATELDFIDKVFFVVDRKDLD-----YQTMKEYQRFSPD-----SVNGSENTAGLK---RNLD--KDDNKIIVTT  382 (1038)
T ss_dssp             HH-HHHHTTCTTCCEEEEEECGGGCC-----HHHHHHHHTTSTT-----CSSSSCCCHHHH---HHHH--CSSCCEEEEE
T ss_pred             HH-HHHHHhcCCCceEEEEeCcHHHH-----HHHHHHHHHhccc-----ccccccCHHHHH---HHhc--CCCCCEEEEE
Confidence            22 22232223335889999999999     4444444 33211     112222222222   2221  3578999999


Q ss_pred             CCccccccHHHHHHH---HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchH----H
Q psy7952         172 PERAVTESFHYLLQH---LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVK----Q  244 (444)
Q Consensus       172 pe~l~~~~~~~~~~~---~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~----~  244 (444)
                      |++|..     ....   ...+....+||+||||++..     ...+   ..+...+++ .++++|||||.....    .
T Consensus       383 iqkl~~-----~l~~~~~~~~~~~~~lvIiDEAHrs~~-----~~~~---~~I~~~~p~-a~~lgfTATP~~~~~~~~~~  448 (1038)
T 2w00_A          383 IQKLNN-----LMKAESDLPVYNQQVVFIFDECHRSQF-----GEAQ---KNLKKKFKR-YYQFGFTGTPIFPENALGSE  448 (1038)
T ss_dssp             HHHHHH-----HHHHCCCCGGGGSCEEEEEESCCTTHH-----HHHH---HHHHHHCSS-EEEEEEESSCCCSTTCTTSC
T ss_pred             HHHHHH-----HHhcccchhccccccEEEEEccchhcc-----hHHH---HHHHHhCCc-ccEEEEeCCccccccchhhh
Confidence            999742     2221   12345778999999999642     1222   234455665 789999999986431    1


Q ss_pred             HHHHHhcCCCCeEEEec-----CCCCCCceEEEEE--cc----------------------cchhhHHHHHHHHHHHh-c
Q psy7952         245 DIISVLKFNKPYKVFKT-----STFRSNLFYDVIF--DD----------------------LLKDSYAHVKEFIEKCL-G  294 (444)
Q Consensus       245 ~~~~~l~~~~~~~~~~~-----~~~~~~~~~~~~~--~~----------------------~~~~~~~~~~~~l~~~l-~  294 (444)
                      .....++  .++....-     .....++.+.+..  ..                      ........+...+.... .
T Consensus       449 ~t~~~FG--~~i~~Y~l~~AI~dg~l~p~~v~y~~v~~~~~~~~~e~d~~~~~~i~~~~~l~~~~ri~~I~~~Il~~~~~  526 (1038)
T 2w00_A          449 TTASVFG--RELHSYVITDAIRDEKVLKFKVDYNDVRPQFKSLETETDEKKLSAAENQQAFLHPMRIQEITQYILNNFRQ  526 (1038)
T ss_dssp             CHHHHHC--SEEEEECHHHHHHHTSSCCEEEEECCCCGGGHHHHTCCCHHHHHHTCSTTTTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhC--CeeEeecHHHHHhCCCcCCeEEEEEeccchhhhccccccHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHH
Confidence            2233333  11111100     0000111110100  00                      00111122222222221 1


Q ss_pred             cC-----CCCCceEEEEecccchHHHHHHHHHhh-------------------cC------------------------H
Q psy7952         295 KD-----NKANNCGIIYCRTREHTTDLADALRRK-------------------VN------------------------K  326 (444)
Q Consensus       295 ~~-----~~~~~~~iVf~~s~~~~~~l~~~L~~~-------------------~~------------------------~  326 (444)
                      ..     ...+.++||||+|+.+|..+++.|.+.                   ++                        +
T Consensus       527 ~~~~~~~~~~g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~  606 (1038)
T 2w00_A          527 KTHRTFPGSKGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDS  606 (1038)
T ss_dssp             HTTCSSSSCCCCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEECCCCC------CCCCCCCCSCGGGSCH
T ss_pred             hhhhhcccCCCCcEEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEEEeCCCccccccccccccccccccccch
Confidence            11     013468999999999999999888542                   11                        1


Q ss_pred             -----------------------------HHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHH
Q psy7952         327 -----------------------------HERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQE  377 (444)
Q Consensus       327 -----------------------------~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr  377 (444)
                                                   ..|..++++|++|++++||+|+++.+|+|+|.+ .++.+|.|.+...|+|+
T Consensus       607 ~~r~~l~~~I~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd~lltGfDiP~l-~tlylDkpl~~~~liQa  685 (1038)
T 2w00_A          607 SAKEFLDAAIREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQA  685 (1038)
T ss_dssp             HHHHHHHHHHHHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcchHHhCcCcccc-cEEEEccCCCccceeeh
Confidence                                         137788999999999999999999999999999 66778999999999999


Q ss_pred             hccCCCCCCc----eeEEEEec
Q psy7952         378 SGRAGRDGLQ----SYCRIYHS  395 (444)
Q Consensus       378 ~GR~~R~g~~----g~~~~~~~  395 (444)
                      +||++|.+.+    |.++.|..
T Consensus       686 IGRtnR~~~~~K~~G~IVdf~~  707 (1038)
T 2w00_A          686 FSRTNRIYDATKTFGNIVTFRD  707 (1038)
T ss_dssp             HHTTCCCCCTTCCSEEEEESSC
T ss_pred             hhccCcCCCCCCCcEEEEEccc
Confidence            9999998653    66665554

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.95  E-value=3.7e-28  Score=256.14  Aligned_cols=316  Identities=16%  Similarity=0.120  Sum_probs=199.6

Q ss_pred             hHHHHHHHHHH----ccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchH
Q psy7952          52 ELQKKAIRHIL----LRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKT  127 (444)
Q Consensus        52 ~~Q~~~~~~~~----~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~  127 (444)
                      +||.+++..+.    .+ +++++..+||+|||+.++.++.         ..+...+...++||||| .+|+  .|+.+.+
T Consensus       239 ~yQ~egv~~l~~~~~~~-~~~ILademGlGKT~~ai~~i~---------~l~~~~~~~~~~LIV~P-~sll--~qW~~E~  305 (800)
T 3mwy_W          239 DFQLTGINWMAFLWSKG-DNGILADEMGLGKTVQTVAFIS---------WLIFARRQNGPHIIVVP-LSTM--PAWLDTF  305 (800)
T ss_dssp             THHHHHHHHHHHHHTTT-CCEEECCCTTSSTTHHHHHHHH---------HHHHHHSCCSCEEEECC-TTTH--HHHHHHH
T ss_pred             HHHHHHHHHHHHHhhcC-CCEEEEeCCCcchHHHHHHHHH---------HHHHhcCCCCCEEEEEC-chHH--HHHHHHH
Confidence            79999998776    45 8899999999999988433211         11112222334599999 5566  2334444


Q ss_pred             hhhcCCCCceeEEEEeCCCChhhHHHHHHHH------HhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecc
Q psy7952         128 SIVTGRSDLYQLELIVSGQTKTENKAILEEL------RLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEA  201 (444)
Q Consensus       128 ~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~  201 (444)
                      ..+...   +++..++|+.............      ......++|+|+|++.+...      ........+++||+|||
T Consensus       306 ~~~~p~---~~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~------~~~l~~~~w~~vIvDEa  376 (800)
T 3mwy_W          306 EKWAPD---LNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKD------RAELGSIKWQFMAVDEA  376 (800)
T ss_dssp             HHHSTT---CCEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHT------HHHHHTSEEEEEEETTG
T ss_pred             HHHCCC---ceEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhh------HHHHhcCCcceeehhhh
Confidence            444434   7788888776543322211100      01235688999999997521      12223346899999999


Q ss_pred             ccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCC----------------------------
Q psy7952         202 HCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFN----------------------------  253 (444)
Q Consensus       202 H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~----------------------------  253 (444)
                      |++-....   ..+..+    ..+.. ...+++||||..+....+...+.+-                            
T Consensus       377 H~lkn~~s---~~~~~l----~~l~~-~~rl~LTgTPiqN~l~el~~ll~fL~p~~~~~~~~~~~~~~~~~~~~~~~~L~  448 (800)
T 3mwy_W          377 HRLKNAES---SLYESL----NSFKV-ANRMLITGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLH  448 (800)
T ss_dssp             GGGCCSSS---HHHHHH----TTSEE-EEEEEECSCCCSSCSHHHHHHHHHHCSCCC---------CCTTHHHHHHHHHH
T ss_pred             hhhcCchh---HHHHHH----HHhhh-ccEEEeeCCcCCCCHHHHHHHHHHhCccccCchhhhcccccchhHHHHHHHHH
Confidence            99855332   112222    22322 5678999999765555444433321                            


Q ss_pred             ---CCeEEEecCC----CCCCceEEEEEcccchhh---------------------------------------------
Q psy7952         254 ---KPYKVFKTST----FRSNLFYDVIFDDLLKDS---------------------------------------------  281 (444)
Q Consensus       254 ---~~~~~~~~~~----~~~~~~~~~~~~~~~~~~---------------------------------------------  281 (444)
                         .++.+.+...    ..|...............                                             
T Consensus       449 ~~l~p~~lRR~k~dv~~~LP~k~~~~v~v~ls~~q~~~Y~~i~~~~~~~l~~~~~~~~~~~l~~l~~Lrk~~~hp~l~~~  528 (800)
T 3mwy_W          449 RRIQPFILRRLKKDVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDN  528 (800)
T ss_dssp             HTTGGGEEECCGGGGTTTSCCEEEEEEEECCCHHHHHHHHHHHHHCCC----------CTHHHHHHHHHHHHHCGGGSSS
T ss_pred             HHHhHHHhhhhHHhhhhccCCcEEEEEEeCCCHHHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHhcChhhhcc
Confidence               1112211110    011111111111110000                                             


Q ss_pred             -------------------------HHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCH
Q psy7952         282 -------------------------YAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNK  326 (444)
Q Consensus       282 -------------------------~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~  326 (444)
                                               .......+.+++......++++||||.....+..+.+.|...          ++.
T Consensus       529 ~~~~~~~~~~~~~~~~~~~~~~l~~~s~K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~  608 (800)
T 3mwy_W          529 AEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPS  608 (800)
T ss_dssp             HHHHHCCCC----CCSHHHHHHHHHTCHHHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCH
T ss_pred             hHHHHHHhcccccccHHHHHHHhhhcChHHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCH
Confidence                                     001122333344433446789999999999999999999866          889


Q ss_pred             HHHHHHHHHHhcCCc---cEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEE--EEeccc
Q psy7952         327 HERSRVQESFMRGEI---NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCR--IYHSEH  397 (444)
Q Consensus       327 ~~r~~~~~~f~~g~~---~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~--~~~~~~  397 (444)
                      .+|..+++.|+++..   .+|++|.++++|+|++.+++||++|+|+|+..+.|++||+.|.|+...+.  .++..+
T Consensus       609 ~eR~~~i~~F~~~~~~~~v~LlSt~agg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~  684 (800)
T 3mwy_W          609 AQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKD  684 (800)
T ss_dssp             HHHHHHHHTTSSTTCSCCCEEEEHHHHTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETT
T ss_pred             HHHHHHHHHhhCCCCCceEEEEecccccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCC
Confidence            999999999998654   48999999999999999999999999999999999999999999875554  345544

>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=99.95  E-value=1.2e-26  Score=230.96  Aligned_cols=320  Identities=19%  Similarity=0.141  Sum_probs=210.5

Q ss_pred             HHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhh
Q psy7952          37 TAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILS  116 (444)
Q Consensus        37 ~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~  116 (444)
                      .++-++.+|..+  .+.|.-..-.+.+| +  +..+.||.|||++        +.+|+.+..+. +.   .|.|++|+..
T Consensus        65 REAa~R~lg~r~--~dvQligg~~L~~G-~--iaEM~TGEGKTLv--------a~lp~~lnAL~-G~---~vhVvT~ndy  127 (822)
T 3jux_A           65 REAARRTLGMRP--FDVQVMGGIALHEG-K--VAEMKTGEGKTLA--------ATMPIYLNALI-GK---GVHLVTVNDY  127 (822)
T ss_dssp             HHHHHHHTSCCC--CHHHHHHHHHHHTT-C--EEECCTTSCHHHH--------THHHHHHHHTT-SS---CEEEEESSHH
T ss_pred             HHHHHHHhCCCC--cHHHHHHHHHHhCC-C--hhhccCCCCccHH--------HHHHHHHHHhc-CC---ceEEEeccHH
Confidence            356677778886  35898888888887 3  8999999999999        55555223232 33   3489999999


Q ss_pred             hhcccCccchHhhh--cCCCCceeEEEEeC--------------------------------------------------
Q psy7952         117 SFYLRFRDDKTSIV--TGRSDLYQLELIVS--------------------------------------------------  144 (444)
Q Consensus       117 L~~~~q~~~~~~~l--~~~~~~i~~~~~~~--------------------------------------------------  144 (444)
                      ||.  |-.+.+..+  .+|   +.+..+.+                                                  
T Consensus       128 LA~--rdae~m~~l~~~Lg---lsvg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~  202 (822)
T 3jux_A          128 LAR--RDALWMGPVYLFLG---LRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQV  202 (822)
T ss_dssp             HHH--HHHHHHHHHHHHTT---CCEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCE
T ss_pred             HHH--hHHHHHHHHHHHhC---CEEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccc
Confidence            992  113344444  667   88888887                                                  


Q ss_pred             CCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh------hCCccEEEEecccccc-ccC---------
Q psy7952         145 GQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR------YNKLAYIVVDEAHCVS-EWG---------  208 (444)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~------~~~~~~iViDE~H~~~-~~~---------  208 (444)
                      +.+..++...+        .+||+++|..-+.   |+++..++..      ...+.+.||||+|.++ +..         
T Consensus       203 ~~~~~err~aY--------~~DItYgTn~Efg---FDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiLIDeArtPLiISg~  271 (822)
T 3jux_A          203 ELKEITRKEAY--------LCDVTYGTNNEFG---FDYLRDNLVLDYNDKVQRGHFYAIVDEADSVLIDEARTPLIISGP  271 (822)
T ss_dssp             ECCBCCHHHHH--------HSSEEEEEHHHHH---HHHHHHTSCSSTTSCCCCCCCEEEEETHHHHHTTGGGSCEEEECC
T ss_pred             cCCHHHHHHHh--------cCCCEEccCcchh---hHhHHhhccCCHHHhccCCCCeEEEecccceeecCCCCCceeeCC
Confidence            23334444444        4799999977765   5666655422      2468999999999762 211         


Q ss_pred             ---------------------CCc---------------------------------HHHHHHHHHHHH-----------
Q psy7952         209 ---------------------HDF---------------------------------RPTYRRLGELRQ-----------  223 (444)
Q Consensus       209 ---------------------~~~---------------------------------~~~~~~l~~~~~-----------  223 (444)
                                           .+|                                 ...+..+...++           
T Consensus       272 ~~~~~~~y~~~~~~v~~l~~~~dy~vdek~~~v~lTe~G~~~~E~~l~i~nly~~~n~~l~~~i~~AL~A~~l~~~d~dY  351 (822)
T 3jux_A          272 SKESPSVYRRFAQIAKKFVKDKDFTVDEKARTIILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDY  351 (822)
T ss_dssp             CCSCHHHHHHHHHHTTSSCBTTTEEECCSSSCEEECHHHHHHHHHHHTCSCTTSGGGHHHHHHHHHHHHHHHHSTTTSSE
T ss_pred             CCCccHHHHHHHHHHHhcCcCCcEEEEcccCeEEECHHHHHHHHHHhCCccccchhhhHHHHHHHHHHHHHHHHcCCCcE
Confidence                                 000                                 001111110000           


Q ss_pred             -----------------------------------------------------hhCCCCcEEEEeccCCcchHHHHHHHh
Q psy7952         224 -----------------------------------------------------FTGNSIPIIALTATAEPSVKQDIISVL  250 (444)
Q Consensus       224 -----------------------------------------------------~~~~~~~~v~lSAT~~~~~~~~~~~~l  250 (444)
                                                                           .|.-..++.+||||.... ...+.+..
T Consensus       352 iV~dg~V~iVDe~TGR~m~grr~s~GLHQaiEaKEgv~i~~e~~tla~IT~Qn~Fr~Y~kL~GMTGTa~te-~~Ef~~iY  430 (822)
T 3jux_A          352 VVMNGEVIIVDEFTGRLLPGRRYSGGLHQAIEAKEGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTE-ESEFVQVY  430 (822)
T ss_dssp             EEETTEEEECSSSSCSCCCSCCCGGGHHHHHHHHHSSCCCCCCCEEEEECHHHHHTTSSEEEEEESSCGGG-HHHHHHHS
T ss_pred             EEECCEEEEEECCCCcCCCCCcCchHHHHHHHHHcCCCCCCCcchhHHHHHHHHHHHhhHHeEECCCCchH-HHHHHHHh
Confidence                                                                 011223469999999764 45555555


Q ss_pred             cCCCCeEEEecCCCCCCceEEE--EEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----
Q psy7952         251 KFNKPYKVFKTSTFRSNLFYDV--IFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----  323 (444)
Q Consensus       251 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----  323 (444)
                      ++.   .+.. +..+|......  ........+...+.+.+.....    .+.++||||+|++.++.++..|.+.     
T Consensus       431 ~l~---vv~I-Ptnkp~~R~d~~d~vy~t~~eK~~al~~~I~~~~~----~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~  502 (822)
T 3jux_A          431 GME---VVVI-PTHKPMIRKDHDDLVFRTQKEKYEKIVEEIEKRYK----KGQPVLVGTTSIEKSELLSSMLKKKGIPHQ  502 (822)
T ss_dssp             CCC---EEEC-CCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHH----HTCCEEEEESSHHHHHHHHHHHHTTTCCCE
T ss_pred             CCe---EEEE-CCCCCcceeecCcEEEecHHHHHHHHHHHHHHHhh----CCCCEEEEECCHHHHHHHHHHHHHCCCCEE
Confidence            432   2222 33344333322  1222234555555555554321    3678999999999999999999887     


Q ss_pred             ---cCHHHHHHHHHHHhcCCccEEEEcCccccccccC--------CccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEE
Q psy7952         324 ---VNKHERSRVQESFMRGEINVITATISFGMGIDRQ--------NVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRI  392 (444)
Q Consensus       324 ---~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~--------~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~  392 (444)
                         -...+|...+-.+.-+...|+|||+++++|+||+        +..+||+++.|.|.+.|.||+||+||.|.+|.++.
T Consensus       503 vLhgkq~~rE~~ii~~ag~~g~VtVATdmAgRGtDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~  582 (822)
T 3jux_A          503 VLNAKYHEKEAEIVAKAGQKGMVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIF  582 (822)
T ss_dssp             EECSCHHHHHHHHHHHHHSTTCEEEEETTTTTTCCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEE
T ss_pred             EeeCCchHHHHHHHHhCCCCCeEEEEcchhhCCcCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEE
Confidence               2334444444333333457999999999999998        56699999999999999999999999999999999


Q ss_pred             Eecccc
Q psy7952         393 YHSEHS  398 (444)
Q Consensus       393 ~~~~~~  398 (444)
                      |++.+|
T Consensus       583 fvsleD  588 (822)
T 3jux_A          583 FLSLED  588 (822)
T ss_dssp             EEETTS
T ss_pred             EechhH
Confidence            998776

>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=99.95  E-value=1.9e-26  Score=237.32  Aligned_cols=99  Identities=15%  Similarity=0.179  Sum_probs=88.2

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCcc---EEEEcCccccccccCCccEEEEe
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEIN---VITATISFGMGIDRQNVRFVVHW  365 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~---vLvaT~~~~~Gidi~~~~~Vi~~  365 (444)
                      .+.++||||+....++.+...|...          ++..+|..+++.|++|...   +|++|+++++|+|++++++||++
T Consensus       415 ~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~g~Glnl~~a~~Vi~~  494 (644)
T 1z3i_X          415 TSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMF  494 (644)
T ss_dssp             CCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEEC
T ss_pred             CCCEEEEEEccHHHHHHHHHHHHHCCCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecccccCCcccccCCEEEEE
Confidence            4789999999999999999999766          8899999999999988654   79999999999999999999999


Q ss_pred             CCCCCHHHHHHHhccCCCCCCceeEEE--Eeccc
Q psy7952         366 GMPSSIPAYYQESGRAGRDGLQSYCRI--YHSEH  397 (444)
Q Consensus       366 ~~p~s~~~~~Qr~GR~~R~g~~g~~~~--~~~~~  397 (444)
                      |+|+|+..+.|++||++|.|+...+.+  ++..+
T Consensus       495 d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv~~~  528 (644)
T 1z3i_X          495 DPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTG  528 (644)
T ss_dssp             SCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETT
T ss_pred             CCCCCccHHHHHHHhhhhcCCCCceEEEEEEECC
Confidence            999999999999999999998765443  44444

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=99.94  E-value=2e-26  Score=208.93  Aligned_cols=195  Identities=17%  Similarity=0.164  Sum_probs=146.8

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc-----CCccce
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN-----GNVRSR  107 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~-----~~~~~~  107 (444)
                      +..+.+++++ +|+.. |+++|.++++.+++| +++++.+|||+|||++        |.+|+ +..+..     .+..++
T Consensus        37 ~~~l~~~l~~-~g~~~-~~~~Q~~~i~~~~~g-~~~l~~apTGsGKT~~--------~~l~~-l~~l~~~~~~~~~~~~~  104 (242)
T 3fe2_A           37 PANVMDVIAR-QNFTE-PTAIQAQGWPVALSG-LDMVGVAQTGSGKTLS--------YLLPA-IVHINHQPFLERGDGPI  104 (242)
T ss_dssp             CHHHHHHHHT-TTCCS-CCHHHHHHHHHHHHT-CCEEEEECTTSCHHHH--------HHHHH-HHHHHTSCCCCTTCCCS
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CCEEEECCCcCHHHHH--------HHHHH-HHHHHhccccccCCCCE
Confidence            5677888887 69997 779999999999999 9999999999999999        66666 332322     234457


Q ss_pred             eEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH
Q psy7952         108 NGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ  185 (444)
Q Consensus       108 vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~  185 (444)
                      +||++|+++|+  .|+.+.++.+  ..+   +.+..++|+.........+.      .+++|+|+||+++.    ..+..
T Consensus       105 ~lil~Pt~~L~--~Q~~~~~~~~~~~~~---~~~~~~~g~~~~~~~~~~~~------~~~~I~v~Tp~~l~----~~l~~  169 (242)
T 3fe2_A          105 CLVLAPTRELA--QQVQQVAAEYCRACR---LKSTCIYGGAPKGPQIRDLE------RGVEICIATPGRLI----DFLEC  169 (242)
T ss_dssp             EEEECSSHHHH--HHHHHHHHHHHHHTT---CCEEEECTTSCHHHHHHHHH------HCCSEEEECHHHHH----HHHHH
T ss_pred             EEEEeCcHHHH--HHHHHHHHHHHhhcC---ceEEEEECCCChHHHHHHhc------CCCCEEEECHHHHH----HHHHc
Confidence            89999999999  3334445555  445   88889999887765544442      36899999999985    33444


Q ss_pred             HHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEec
Q psy7952         186 HLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT  261 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~  261 (444)
                      ....+.+++++|+||||++.+++  |...+..   +++.++++.|++++|||+++...+.+..++  .++..+...
T Consensus       170 ~~~~~~~~~~lViDEah~l~~~~--~~~~~~~---i~~~~~~~~q~~~~SAT~~~~~~~~~~~~l--~~~~~i~~~  238 (242)
T 3fe2_A          170 GKTNLRRTTYLVLDEADRMLDMG--FEPQIRK---IVDQIRPDRQTLMWSATWPKEVRQLAEDFL--KDYIHINIG  238 (242)
T ss_dssp             TSCCCTTCCEEEETTHHHHHHTT--CHHHHHH---HHTTSCSSCEEEEEESCCCHHHHHHHHHHC--SSCEEEEEC
T ss_pred             CCCCcccccEEEEeCHHHHhhhC--cHHHHHH---HHHhCCccceEEEEEeecCHHHHHHHHHHC--CCCEEEEec
Confidence            44567789999999999998877  6655554   455666779999999999998887777665  466555443

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=99.93  E-value=2.2e-26  Score=203.51  Aligned_cols=193  Identities=18%  Similarity=0.182  Sum_probs=140.2

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ..++.++++. +|+.. |+++|.++++.++++ +++++.+|||+|||++        |.+|+ +..+......++++|++
T Consensus        11 ~~~l~~~l~~-~g~~~-~~~~Q~~~i~~~~~~-~~~lv~apTGsGKT~~--------~~~~~-~~~~~~~~~~~~~lil~   78 (206)
T 1vec_A           11 KRELLMGIFE-MGWEK-PSPIQEESIPIALSG-RDILARAKNGTGKSGA--------YLIPL-LERLDLKKDNIQAMVIV   78 (206)
T ss_dssp             CHHHHHHHHT-TTCCS-CCHHHHHHHHHHHTT-CCEEEECCSSSTTHHH--------HHHHH-HHHCCTTSCSCCEEEEC
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHccC-CCEEEECCCCCchHHH--------HHHHH-HHHhcccCCCeeEEEEe
Confidence            5678888887 69987 669999999999999 9999999999999999        66665 33343344446789999


Q ss_pred             chhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCC
Q psy7952         113 PILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK  192 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~  192 (444)
                      |+++|+  .|+.+.+..+....+.+.+..+.|+........      ....+++|+|+||+++.    ..+......+.+
T Consensus        79 Pt~~L~--~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~------~~~~~~~i~v~T~~~l~----~~~~~~~~~~~~  146 (206)
T 1vec_A           79 PTRELA--LQVSQICIQVSKHMGGAKVMATTGGTNLRDDIM------RLDDTVHVVIATPGRIL----DLIKKGVAKVDH  146 (206)
T ss_dssp             SCHHHH--HHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHH------HTTSCCSEEEECHHHHH----HHHHTTCSCCTT
T ss_pred             CcHHHH--HHHHHHHHHHHhhcCCceEEEEeCCccHHHHHH------hcCCCCCEEEeCHHHHH----HHHHcCCcCccc
Confidence            999999  222334444422222378888888877654322      23467899999999974    333333345678


Q ss_pred             ccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCe
Q psy7952         193 LAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPY  256 (444)
Q Consensus       193 ~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~  256 (444)
                      ++++|+||+|++.+.+  +...+.   .+...++++.+++++|||+++...+.+..++  .+++
T Consensus       147 ~~~lViDEah~~~~~~--~~~~l~---~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l--~~p~  203 (206)
T 1vec_A          147 VQMIVLDEADKLLSQD--FVQIME---DIILTLPKNRQILLYSATFPLSVQKFMNSHL--EKPY  203 (206)
T ss_dssp             CCEEEEETHHHHTSTT--THHHHH---HHHHHSCTTCEEEEEESCCCHHHHHHHHHHC--SSCE
T ss_pred             CCEEEEEChHHhHhhC--cHHHHH---HHHHhCCccceEEEEEeeCCHHHHHHHHHHc--CCCe
Confidence            9999999999987755  554444   4455666679999999999998877777665  3554

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=99.93  E-value=1.2e-26  Score=208.88  Aligned_cols=195  Identities=16%  Similarity=0.167  Sum_probs=140.3

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ...+.+++++ +|+.. |+++|.++++.+++| +++++.+|||+|||++        |.+|+ +..+...+..+++||++
T Consensus        32 ~~~l~~~l~~-~g~~~-~~~~Q~~~i~~~~~~-~~~l~~a~TGsGKT~~--------~~l~~-l~~l~~~~~~~~~lil~   99 (230)
T 2oxc_A           32 SRPVLEGLRA-AGFER-PSPVQLKAIPLGRCG-LDLIVQAKSGTGKTCV--------FSTIA-LDSLVLENLSTQILILA   99 (230)
T ss_dssp             CHHHHHHHHH-TTCCS-CCHHHHHHHHHHHTT-CCEEEECCTTSSHHHH--------HHHHH-HHHCCTTSCSCCEEEEC
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CCEEEECCCCCcHHHH--------HHHHH-HHHHHhcCCCceEEEEe
Confidence            5678888887 69997 669999999999999 9999999999999999        66666 44444444556789999


Q ss_pred             chhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCC
Q psy7952         113 PILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK  192 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~  192 (444)
                      |+++|+  .|+.+.++.+......+++..++|+..........       .+++|+|+||+++.    ..+......+.+
T Consensus       100 Pt~~L~--~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-------~~~~Iiv~Tp~~l~----~~~~~~~~~~~~  166 (230)
T 2oxc_A          100 PTREIA--VQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-------KKCHIAVGSPGRIK----QLIELDYLNPGS  166 (230)
T ss_dssp             SSHHHH--HHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-------TSCSEEEECHHHHH----HHHHTTSSCGGG
T ss_pred             CCHHHH--HHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-------cCCCEEEECHHHHH----HHHhcCCccccc
Confidence            999999  22334444442222248889999988765443322       47899999999974    222223334567


Q ss_pred             ccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEE
Q psy7952         193 LAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKV  258 (444)
Q Consensus       193 ~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~  258 (444)
                      ++++|+||+|++.+++. +...+.   .+++.++...|++++|||+++...+.+..+  +.++..+
T Consensus       167 ~~~lViDEah~~~~~~~-~~~~~~---~i~~~~~~~~~~l~lSAT~~~~~~~~~~~~--~~~p~~i  226 (230)
T 2oxc_A          167 IRLFILDEADKLLEEGS-FQEQIN---WIYSSLPASKQMLAVSATYPEFLANALTKY--MRDPTFV  226 (230)
T ss_dssp             CCEEEESSHHHHHSTTS-SHHHHH---HHHHHSCSSCEEEEEESCCCHHHHHHHTTT--CSSCEEE
T ss_pred             CCEEEeCCchHhhcCcc-hHHHHH---HHHHhCCCCCeEEEEEeccCHHHHHHHHHH--cCCCeEE
Confidence            89999999999987652 555444   445566667899999999988766655444  3455433

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=99.93  E-value=9.4e-27  Score=209.29  Aligned_cols=193  Identities=18%  Similarity=0.189  Sum_probs=134.9

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc------CCccc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN------GNVRS  106 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~------~~~~~  106 (444)
                      ..++.+++++ +|+.. |+++|.++++.+++| +++++.+|||+|||++        |++|+ +..+..      ....+
T Consensus        28 ~~~l~~~l~~-~g~~~-~~~~Q~~~i~~~~~~-~~~l~~apTGsGKT~~--------~~l~~-~~~l~~~~~~~~~~~~~   95 (228)
T 3iuy_A           28 YPDLLKSIIR-VGILK-PTPIQSQAWPIILQG-IDLIVVAQTGTGKTLS--------YLMPG-FIHLDSQPISREQRNGP   95 (228)
T ss_dssp             CHHHHHHHHH-HTCCS-CCHHHHHHHHHHHTT-CCEEEECCTTSCHHHH--------HHHHH-HHHHC---------CCC
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CCEEEECCCCChHHHH--------HHHHH-HHHHHhccchhhccCCC
Confidence            3567888888 59987 779999999999999 9999999999999999        55555 222221      12445


Q ss_pred             eeEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         107 RNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       107 ~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      +++|++|+++|+  .|+.+.++.+  ....+.+..+.|+.........+      ..+++|+|+||+++.    ..+...
T Consensus        96 ~~lil~Pt~~L~--~q~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~------~~~~~iiv~Tp~~l~----~~~~~~  161 (228)
T 3iuy_A           96 GMLVLTPTRELA--LHVEAECSKY--SYKGLKSICIYGGRNRNGQIEDI------SKGVDIIIATPGRLN----DLQMNN  161 (228)
T ss_dssp             SEEEECSSHHHH--HHHHHHHHHH--CCTTCCEEEECC------CHHHH------HSCCSEEEECHHHHH----HHHHTT
T ss_pred             cEEEEeCCHHHH--HHHHHHHHHh--cccCceEEEEECCCChHHHHHHh------cCCCCEEEECHHHHH----HHHHcC
Confidence            789999999999  2234444444  22338888888877655443332      357899999999985    333333


Q ss_pred             HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEE
Q psy7952         187 LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKV  258 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~  258 (444)
                      ...+.++++||+||||++.+++  +...+..+   +...+.+.|++++|||+++...+.+..++  .++..+
T Consensus       162 ~~~~~~~~~lViDEah~~~~~~--~~~~~~~i---~~~~~~~~~~l~~SAT~~~~~~~~~~~~l--~~p~~i  226 (228)
T 3iuy_A          162 SVNLRSITYLVIDEADKMLDME--FEPQIRKI---LLDVRPDRQTVMTSATWPDTVRQLALSYL--KDPMIV  226 (228)
T ss_dssp             CCCCTTCCEEEECCHHHHHHTT--CHHHHHHH---HHHSCSSCEEEEEESCCCHHHHHHHHTTC--SSCEEE
T ss_pred             CcCcccceEEEEECHHHHhccc--hHHHHHHH---HHhCCcCCeEEEEEeeCCHHHHHHHHHHC--CCCEEE
Confidence            4456789999999999998876  66555544   44566679999999999998877665543  455443

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=99.93  E-value=7.3e-26  Score=205.90  Aligned_cols=193  Identities=19%  Similarity=0.200  Sum_probs=141.9

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ...+.++++. +|+.. |+++|.++++.++++ +++++.+|||+|||++        |.+++ +..+.......++||++
T Consensus        51 ~~~l~~~l~~-~g~~~-~~~~Q~~~i~~i~~~-~~~lv~a~TGsGKT~~--------~~~~i-l~~l~~~~~~~~~lil~  118 (249)
T 3ber_A           51 TDVLCEACDQ-LGWTK-PTKIQIEAIPLALQG-RDIIGLAETGSGKTGA--------FALPI-LNALLETPQRLFALVLT  118 (249)
T ss_dssp             CHHHHHHHHH-TTCCS-CCHHHHHHHHHHHTT-CCEEEECCTTSCHHHH--------HHHHH-HHHHHHSCCSSCEEEEC
T ss_pred             CHHHHHHHHH-cCCCC-CCHHHHHHHHHHhCC-CCEEEEcCCCCCchhH--------hHHHH-HHHHhcCCCCceEEEEe
Confidence            4577888887 69987 669999999999999 9999999999999999        66666 44444444455789999


Q ss_pred             chhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH-HHHh
Q psy7952         113 PILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ-HLVR  189 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~-~~~~  189 (444)
                      |+++|+  .|+.+.++.+  ..+   +.+..+.|+..........      ..+++|+|+||+++.    ..+.. ....
T Consensus       119 Ptr~L~--~q~~~~~~~~~~~~~---~~~~~~~g~~~~~~~~~~~------~~~~~I~v~Tp~~l~----~~l~~~~~~~  183 (249)
T 3ber_A          119 PTRELA--FQISEQFEALGSSIG---VQSAVIVGGIDSMSQSLAL------AKKPHIIIATPGRLI----DHLENTKGFN  183 (249)
T ss_dssp             SSHHHH--HHHHHHHHHHHGGGT---CCEEEECTTSCHHHHHHHH------HTCCSEEEECHHHHH----HHHHHSTTCC
T ss_pred             CCHHHH--HHHHHHHHHHhccCC---eeEEEEECCCChHHHHHHh------cCCCCEEEECHHHHH----HHHHcCCCcC
Confidence            999999  3334444444  335   7888899887765443332      357899999999974    22222 2234


Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEE
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVF  259 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~  259 (444)
                      +.++++||+||||++.+++  +...+..   ++..++.+.+++++|||+++...+.+..++  .++..+.
T Consensus       184 l~~~~~lViDEah~l~~~~--~~~~l~~---i~~~~~~~~~~l~~SAT~~~~v~~~~~~~l--~~p~~i~  246 (249)
T 3ber_A          184 LRALKYLVMDEADRILNMD--FETEVDK---ILKVIPRDRKTFLFSATMTKKVQKLQRAAL--KNPVKCA  246 (249)
T ss_dssp             CTTCCEEEECSHHHHHHTT--CHHHHHH---HHHSSCSSSEEEEEESSCCHHHHHHHHHHC--SSCEEEE
T ss_pred             ccccCEEEEcChhhhhccC--hHHHHHH---HHHhCCCCCeEEEEeccCCHHHHHHHHHHC--CCCEEEE
Confidence            6789999999999998776  6655444   445666678999999999998877666554  4665443

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=99.93  E-value=1.2e-25  Score=200.95  Aligned_cols=197  Identities=14%  Similarity=0.166  Sum_probs=139.6

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      ...++.+++++ +|+.. |+++|.++++.++++ +++++.+|||+|||++        |.+++ +..+.......+++|+
T Consensus        21 l~~~l~~~l~~-~g~~~-~~~~Q~~~i~~~~~~-~~~li~~~TGsGKT~~--------~~~~~-~~~~~~~~~~~~~lil   88 (220)
T 1t6n_A           21 LKPELLRAIVD-CGFEH-PSEVQHECIPQAILG-MDVLCQAKSGMGKTAV--------FVLAT-LQQLEPVTGQVSVLVM   88 (220)
T ss_dssp             CCHHHHHHHHH-TTCCC-CCHHHHHHHHHHHTT-CCEEEECCTTSCHHHH--------HHHHH-HHHCCCCTTCCCEEEE
T ss_pred             CCHHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CCEEEECCCCCchhhh--------hhHHH-HHhhhccCCCEEEEEE
Confidence            35678888887 69997 669999999999999 8999999999999999        55555 3333333334578999


Q ss_pred             cchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         112 SPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      +|+++|+  .|+.+.++.+....+.+++..++|+.........+.     .+.++|+|+||+++.    ..+......+.
T Consensus        89 ~Pt~~L~--~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~-----~~~~~i~v~T~~~l~----~~~~~~~~~~~  157 (220)
T 1t6n_A           89 CHTRELA--FQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLK-----KNCPHIVVGTPGRIL----ALARNKSLNLK  157 (220)
T ss_dssp             CSCHHHH--HHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHH-----HSCCSEEEECHHHHH----HHHHTTSSCCT
T ss_pred             eCCHHHH--HHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHh-----cCCCCEEEeCHHHHH----HHHHhCCCCcc
Confidence            9999999  223444444422222388999999887665544432     245799999999974    22233334467


Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeE
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYK  257 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~  257 (444)
                      +++++|+||||++.++. .+.   ..+..++...+.+.+++++|||+++...+....++  .++..
T Consensus       158 ~~~~lViDEah~~~~~~-~~~---~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~--~~p~~  217 (220)
T 1t6n_A          158 HIKHFILDECDKMLEQL-DMR---RDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFM--QDPME  217 (220)
T ss_dssp             TCCEEEEESHHHHHSSH-HHH---HHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTC--SSCEE
T ss_pred             cCCEEEEcCHHHHhccc-CcH---HHHHHHHHhCCCcCeEEEEEeecCHHHHHHHHHHc--CCCeE
Confidence            89999999999987531 144   33445555667678999999999998777555443  45543

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.93  E-value=2.2e-26  Score=205.47  Aligned_cols=196  Identities=16%  Similarity=0.196  Sum_probs=140.5

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ...+.+++++ +|+.. |+++|.++++.++++ +++++.+|||+|||++        |.+|+ +..+...+...+++|++
T Consensus        12 ~~~l~~~l~~-~g~~~-~~~~Q~~~i~~~~~~-~~~lv~a~TGsGKT~~--------~~~~~-l~~l~~~~~~~~~lil~   79 (219)
T 1q0u_A           12 QPFIIEAIKT-LRFYK-PTEIQERIIPGALRG-ESMVGQSQTGTGKTHA--------YLLPI-MEKIKPERAEVQAVITA   79 (219)
T ss_dssp             CHHHHHHHHH-TTCCS-CCHHHHHHHHHHHHT-CCEEEECCSSHHHHHH--------HHHHH-HHHCCTTSCSCCEEEEC
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CCEEEECCCCChHHHH--------HHHHH-HHHHHhCcCCceEEEEc
Confidence            4578888887 69998 679999999999999 9999999999999999        66666 44444444456789999


Q ss_pred             chhhhhcccCccchHhhhcCCC---CceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh
Q psy7952         113 PILSSFYLRFRDDKTSIVTGRS---DLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR  189 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l~~~~---~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~  189 (444)
                      |+++|+  .|+.+.+..+....   ..+.+..+.|+......      ......+++|+|+||+++.    ..+......
T Consensus        80 Pt~~L~--~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~------~~~~~~~~~Iiv~Tp~~l~----~~l~~~~~~  147 (219)
T 1q0u_A           80 PTRELA--TQIYHETLKITKFCPKDRMIVARCLIGGTDKQKA------LEKLNVQPHIVIGTPGRIN----DFIREQALD  147 (219)
T ss_dssp             SSHHHH--HHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHT------TCCCSSCCSEEEECHHHHH----HHHHTTCCC
T ss_pred             CcHHHH--HHHHHHHHHHhhhcccccceEEEEEeCCCCHHHH------HHHcCCCCCEEEeCHHHHH----HHHHcCCCC
Confidence            999999  22344444441111   03778888887654322      1222357899999999974    222333344


Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEE
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVF  259 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~  259 (444)
                      +.+++++|+||||++.+++  +..   .+..++..++.+.+++++|||+++...+.+..++  .+|..+.
T Consensus       148 ~~~~~~lViDEah~~~~~~--~~~---~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~--~~p~~~~  210 (219)
T 1q0u_A          148 VHTAHILVVDEADLMLDMG--FIT---DVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYM--ENPTFVH  210 (219)
T ss_dssp             GGGCCEEEECSHHHHHHTT--CHH---HHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHC--SSCEEEE
T ss_pred             cCcceEEEEcCchHHhhhC--hHH---HHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHc--CCCeEEE
Confidence            6788999999999998776  543   3445555677678999999999998887776664  4665443

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=99.92  E-value=1e-25  Score=206.47  Aligned_cols=187  Identities=20%  Similarity=0.294  Sum_probs=136.9

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC----Cccce
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG----NVRSR  107 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~----~~~~~  107 (444)
                      ....+.++++. +|+.. ++++|.++++.++.+ +++++++|||+|||++        |++|+ +..+...    ....+
T Consensus        61 l~~~l~~~l~~-~g~~~-~~~~Q~~~i~~~~~~-~~~lv~a~TGsGKT~~--------~~l~~-l~~l~~~~~~~~~~~~  128 (262)
T 3ly5_A           61 VNENTLKAIKE-MGFTN-MTEIQHKSIRPLLEG-RDLLAAAKTGSGKTLA--------FLIPA-VELIVKLRFMPRNGTG  128 (262)
T ss_dssp             CCHHHHHHHHH-TTCCB-CCHHHHHHHHHHHHT-CCCEECCCTTSCHHHH--------HHHHH-HHHHHHTTCCGGGCCC
T ss_pred             cCHHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CcEEEEccCCCCchHH--------HHHHH-HHHHHhccccccCCce
Confidence            46778888988 69998 679999999999999 9999999999999999        66665 3323221    23346


Q ss_pred             eEEEcchhhhhcccCccchHhhh-c-CCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH
Q psy7952         108 NGWISPILSSFYLRFRDDKTSIV-T-GRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ  185 (444)
Q Consensus       108 vlil~P~~~L~~~~q~~~~~~~l-~-~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~  185 (444)
                      ++|++||++|+     .|+.+.+ . .....+.+..+.|+.........+      ..+++|+|+||+++.    ..+..
T Consensus       129 ~lil~Pt~~La-----~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~------~~~~~Iiv~Tp~~l~----~~~~~  193 (262)
T 3ly5_A          129 VLILSPTRELA-----MQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKL------GNGINIIVATPGRLL----DHMQN  193 (262)
T ss_dssp             EEEECSSHHHH-----HHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHH------HHCCSEEEECHHHHH----HHHHH
T ss_pred             EEEEeCCHHHH-----HHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHh------cCCCCEEEEcHHHHH----HHHHc
Confidence            79999999999     5555544 1 112227788888887765443333      236899999999974    22222


Q ss_pred             H-HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHh
Q psy7952         186 H-LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVL  250 (444)
Q Consensus       186 ~-~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l  250 (444)
                      . ...+.++++||+||||++.+++  +...+..+   +..++...|+++||||+++...+.....+
T Consensus       194 ~~~~~~~~l~~lViDEah~l~~~~--~~~~l~~i---~~~~~~~~q~l~~SAT~~~~v~~~~~~~l  254 (262)
T 3ly5_A          194 TPGFMYKNLQCLVIDEADRILDVG--FEEELKQI---IKLLPTRRQTMLFSATQTRKVEDLARISL  254 (262)
T ss_dssp             CTTCCCTTCCEEEECSHHHHHHTT--CHHHHHHH---HHHSCSSSEEEEECSSCCHHHHHHHHHHC
T ss_pred             cCCcccccCCEEEEcChHHHhhhh--HHHHHHHH---HHhCCCCCeEEEEEecCCHHHHHHHHHHc
Confidence            2 2346789999999999998877  66555544   45667778999999999998877665554

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=99.92  E-value=4.5e-26  Score=204.27  Aligned_cols=192  Identities=16%  Similarity=0.229  Sum_probs=135.0

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ...+.+.++. +|+.. ++++|.++++.++++ +++++.+|||+|||++        |.+++ ++.+......++++|++
T Consensus        22 ~~~l~~~l~~-~g~~~-~~~~Q~~~i~~~~~~-~~~lv~~pTGsGKT~~--------~~~~~-l~~l~~~~~~~~~lil~   89 (224)
T 1qde_A           22 DENLLRGVFG-YGFEE-PSAIQQRAIMPIIEG-HDVLAQAQSGTGKTGT--------FSIAA-LQRIDTSVKAPQALMLA   89 (224)
T ss_dssp             CHHHHHHHHH-HTCCS-CCHHHHHHHHHHHTT-CCEEEECCTTSSHHHH--------HHHHH-HHHCCTTCCSCCEEEEC
T ss_pred             CHHHHHHHHH-CCCCC-CcHHHHHHHHHHhcC-CCEEEECCCCCcHHHH--------HHHHH-HHHHhccCCCceEEEEE
Confidence            5678888887 59987 669999999999999 9999999999999999        66666 44444444456789999


Q ss_pred             chhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhh
Q psy7952         113 PILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRY  190 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~  190 (444)
                      |+++|+  .|+.+.+..+  ..+   +.+..++|+.........       ...++|+|+||+++.    ..+......+
T Consensus        90 Pt~~L~--~q~~~~~~~~~~~~~---~~~~~~~g~~~~~~~~~~-------~~~~~iiv~Tp~~l~----~~~~~~~~~~  153 (224)
T 1qde_A           90 PTRELA--LQIQKVVMALAFHMD---IKVHACIGGTSFVEDAEG-------LRDAQIVVGTPGRVF----DNIQRRRFRT  153 (224)
T ss_dssp             SSHHHH--HHHHHHHHHHTTTSC---CCEEEECC-----------------CTTCSEEEECHHHHH----HHHHTTSSCC
T ss_pred             CCHHHH--HHHHHHHHHHhcccC---ceEEEEeCCcchHHHHhc-------CCCCCEEEECHHHHH----HHHHhCCcch
Confidence            999999  2234444444  234   788888887665433221       134899999999974    3333334446


Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEE
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVF  259 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~  259 (444)
                      .++++||+||||++.+++  +...+.   .+....+.+.+++++|||+++...+.+..++  .++..+.
T Consensus       154 ~~~~~iViDEah~~~~~~--~~~~l~---~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~--~~p~~i~  215 (224)
T 1qde_A          154 DKIKMFILDEADEMLSSG--FKEQIY---QIFTLLPPTTQVVLLSATMPNDVLEVTTKFM--RNPVRIL  215 (224)
T ss_dssp             TTCCEEEEETHHHHHHTT--CHHHHH---HHHHHSCTTCEEEEEESSCCHHHHHHHHHHC--SSCEEEC
T ss_pred             hhCcEEEEcChhHHhhhh--hHHHHH---HHHHhCCccCeEEEEEeecCHHHHHHHHHHC--CCCEEEE
Confidence            789999999999998766  554444   4445566678999999999998877776664  4554443

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=99.92  E-value=8.6e-26  Score=210.83  Aligned_cols=194  Identities=15%  Similarity=0.183  Sum_probs=142.4

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHcc-CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLR-THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~-~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      ...+.+++.. +||.. ||++|.++++.++.+ .+++++++|||+|||++        |++|+ +..+...+..+++||+
T Consensus       100 ~~~l~~~l~~-~g~~~-pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a--------~~lp~-l~~l~~~~~~~~~lil  168 (300)
T 3fmo_B          100 KPQLLQGVYA-MGFNR-PSKIQENALPLMLAEPPQNLIAQSQSGTGKTAA--------FVLAM-LSQVEPANKYPQCLCL  168 (300)
T ss_dssp             CHHHHHHHHH-TTCCS-CCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHH--------HHHHH-HHHCCTTSCSCCEEEE
T ss_pred             CHHHHHHHHH-cCCCC-CCHHHHHHHHHHHcCCCCeEEEECCCCCCccHH--------HHHHH-HHhhhccCCCceEEEE
Confidence            5678888887 69998 889999999999986 48999999999999999        77777 5555555666688999


Q ss_pred             cchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH-HHHhh
Q psy7952         112 SPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ-HLVRY  190 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~-~~~~~  190 (444)
                      +||++|+  .|+.+.+..+......+.+....++......         ....++|+|+||+++.    ..+.. ....+
T Consensus       169 ~PtreLa--~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~---------~~~~~~IlV~TP~~l~----~~l~~~~~~~l  233 (300)
T 3fmo_B          169 SPTYELA--LQTGKVIEQMGKFYPELKLAYAVRGNKLERG---------QKISEQIVIGTPGTVL----DWCSKLKFIDP  233 (300)
T ss_dssp             CSSHHHH--HHHHHHHHHHTTTSTTCCEEEESTTCCCCTT---------CCCCCSEEEECHHHHH----HHHTTTCCCCG
T ss_pred             cCcHHHH--HHHHHHHHHHHhhCCCcEEEEEeCCccHhhh---------hcCCCCEEEECHHHHH----HHHHhcCCCCh
Confidence            9999999  3334455555322233778888877654321         1356799999999974    22212 23346


Q ss_pred             CCccEEEEeccccccc-cCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEE
Q psy7952         191 NKLAYIVVDEAHCVSE-WGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVF  259 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~  259 (444)
                      .++++||+||+|++.+ .+  +...+.   .+...++.++|++++|||+++...+....++  .++..+.
T Consensus       234 ~~l~~lVlDEad~l~~~~~--~~~~~~---~i~~~~~~~~q~i~~SAT~~~~v~~~a~~~l--~~p~~i~  296 (300)
T 3fmo_B          234 KKIKVFVLDEADVMIATQG--HQDQSI---RIQRMLPRNCQMLLFSATFEDSVWKFAQKVV--PDPNVIK  296 (300)
T ss_dssp             GGCSEEEETTHHHHHHSTT--HHHHHH---HHHTTSCTTCEEEEEESCCCHHHHHHHHHHS--SSCEEEE
T ss_pred             hhceEEEEeCHHHHhhccC--cHHHHH---HHHHhCCCCCEEEEEeccCCHHHHHHHHHHC--CCCeEEE
Confidence            7899999999999986 44  554444   4455667779999999999998887666654  4665443

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=99.92  E-value=2.7e-25  Score=196.59  Aligned_cols=189  Identities=20%  Similarity=0.223  Sum_probs=137.8

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc---CCccceeE
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN---GNVRSRNG  109 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~---~~~~~~vl  109 (444)
                      .+++.+++++ +|+.. |+++|.++++.++++ +++++.+|||+|||++        |.+++ +..+..   .+..++++
T Consensus         9 ~~~l~~~l~~-~~~~~-~~~~Q~~~i~~~~~~-~~~li~~~TGsGKT~~--------~~~~~-~~~l~~~~~~~~~~~~l   76 (207)
T 2gxq_A            9 KPEILEALHG-RGLTT-PTPIQAAALPLALEG-KDLIGQARTGTGKTLA--------FALPI-AERLAPSQERGRKPRAL   76 (207)
T ss_dssp             CHHHHHHHHH-TTCCS-CCHHHHHHHHHHHTT-CCEEEECCTTSCHHHH--------HHHHH-HHHCCCCCCTTCCCSEE
T ss_pred             CHHHHHHHHH-cCCCC-CCHHHHHHHHHHcCC-CCEEEECCCCChHHHH--------HHHHH-HHHHhhccccCCCCcEE
Confidence            4677888887 69987 679999999999999 9999999999999999        44544 222322   23446789


Q ss_pred             EEcchhhhhcccCccchHhhh---cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         110 WISPILSSFYLRFRDDKTSIV---TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       110 il~P~~~L~~~~q~~~~~~~l---~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      |++|+++|+     .+..+.+   ...   +++..++|+..........      ..+++|+|+||+++.    ..+...
T Consensus        77 il~P~~~L~-----~q~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~------~~~~~i~v~T~~~l~----~~~~~~  138 (207)
T 2gxq_A           77 VLTPTRELA-----LQVASELTAVAPH---LKVVAVYGGTGYGKQKEAL------LRGADAVVATPGRAL----DYLRQG  138 (207)
T ss_dssp             EECSSHHHH-----HHHHHHHHHHCTT---SCEEEECSSSCSHHHHHHH------HHCCSEEEECHHHHH----HHHHHT
T ss_pred             EEECCHHHH-----HHHHHHHHHHhhc---ceEEEEECCCChHHHHHHh------hCCCCEEEECHHHHH----HHHHcC
Confidence            999999999     5555555   333   7788888887665443333      237899999999974    333333


Q ss_pred             HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEE
Q psy7952         187 LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKV  258 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~  258 (444)
                      ...+.+++++|+||||++.+++  +...+.   .++...+.+.+++++|||+++...+....++  .++..+
T Consensus       139 ~~~~~~~~~iViDEah~~~~~~--~~~~~~---~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~--~~p~~i  203 (207)
T 2gxq_A          139 VLDLSRVEVAVLDEADEMLSMG--FEEEVE---ALLSATPPSRQTLLFSATLPSWAKRLAERYM--KNPVLI  203 (207)
T ss_dssp             SSCCTTCSEEEEESHHHHHHTT--CHHHHH---HHHHTSCTTSEEEEECSSCCHHHHHHHHHHC--SSCEEE
T ss_pred             CcchhhceEEEEEChhHhhccc--hHHHHH---HHHHhCCccCeEEEEEEecCHHHHHHHHHHc--CCCeEE
Confidence            4456789999999999987766  554444   4455666678999999999988776665554  455443

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=99.92  E-value=6.9e-26  Score=204.75  Aligned_cols=195  Identities=16%  Similarity=0.178  Sum_probs=133.3

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ...+.++++. +|+.. |+++|.++++.++++ +++++.+|||+|||++        |.+++ +..+.......++||++
T Consensus        38 ~~~l~~~l~~-~g~~~-~~~~Q~~ai~~i~~~-~~~li~apTGsGKT~~--------~~l~~-l~~l~~~~~~~~~lil~  105 (237)
T 3bor_A           38 KESLLRGIYA-YGFEK-PSAIQQRAIIPCIKG-YDVIAQAQSGTGKTAT--------FAISI-LQQLEIEFKETQALVLA  105 (237)
T ss_dssp             CHHHHHHHHH-HTCCS-CCHHHHHHHHHHHTT-CCEEECCCSSHHHHHH--------HHHHH-HHHCCTTSCSCCEEEEC
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CCEEEECCCCCcHHHH--------HHHHH-HHHHHhcCCCceEEEEE
Confidence            5677788876 69997 679999999999999 9999999999999999        66666 43343333445789999


Q ss_pred             chhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCC
Q psy7952         113 PILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK  192 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~  192 (444)
                      |+++|+  .|+.+.++.+.. ...+.+..+.|+.........+.     .+.++|+|+||+++.    ..+......+.+
T Consensus       106 Pt~~L~--~q~~~~~~~~~~-~~~~~~~~~~g~~~~~~~~~~l~-----~~~~~Ilv~Tp~~l~----~~l~~~~~~~~~  173 (237)
T 3bor_A          106 PTRELA--QQIQKVILALGD-YMGATCHACIGGTNVRNEMQKLQ-----AEAPHIVVGTPGRVF----DMLNRRYLSPKW  173 (237)
T ss_dssp             SSHHHH--HHHHHHHHHHTT-TTTCCEEEECC------------------CCCSEEEECHHHHH----HHHHTTSSCSTT
T ss_pred             CcHHHH--HHHHHHHHHHhh-hcCceEEEEECCCchHHHHHHHh-----cCCCCEEEECHHHHH----HHHHhCCcCccc
Confidence            999999  222333443311 11267777777765433222111     234899999999974    333333345678


Q ss_pred             ccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEE
Q psy7952         193 LAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKV  258 (444)
Q Consensus       193 ~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~  258 (444)
                      +++||+||||++.+++  +...+   ..+++.++...+++++|||+++...+.+..++  .++..+
T Consensus       174 ~~~lViDEah~~~~~~--~~~~l---~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~l--~~p~~i  232 (237)
T 3bor_A          174 IKMFVLDEADEMLSRG--FKDQI---YEIFQKLNTSIQVVLLSATMPTDVLEVTKKFM--RDPIRI  232 (237)
T ss_dssp             CCEEEEESHHHHHHTT--CHHHH---HHHHHHSCTTCEEEEECSSCCHHHHHHHHHHC--SSCEEE
T ss_pred             CcEEEECCchHhhccC--cHHHH---HHHHHhCCCCCeEEEEEEecCHHHHHHHHHHC--CCCEEE
Confidence            9999999999998766  55444   34455566678999999999998887776665  355544

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.91  E-value=4e-25  Score=199.68  Aligned_cols=193  Identities=19%  Similarity=0.224  Sum_probs=136.0

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc----CCccce
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN----GNVRSR  107 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~----~~~~~~  107 (444)
                      ....+.+++++ +|+.. |+++|.++++.++++ +++++.+|||+|||++        |.+|+ +..+..    ....++
T Consensus        32 l~~~l~~~l~~-~~~~~-~~~~Q~~~i~~~~~~-~~~li~a~TGsGKT~~--------~~~~~-l~~l~~~~~~~~~~~~   99 (236)
T 2pl3_A           32 LSKKTLKGLQE-AQYRL-VTEIQKQTIGLALQG-KDVLGAAKTGSGKTLA--------FLVPV-LEALYRLQWTSTDGLG   99 (236)
T ss_dssp             CCHHHHHHHHH-TTCCB-CCHHHHHHHHHHHTT-CCEEEECCTTSCHHHH--------HHHHH-HHHHHHTTCCGGGCCC
T ss_pred             CCHHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CCEEEEeCCCCcHHHH--------HHHHH-HHHHHhhcccccCCce
Confidence            35677888887 59998 679999999999999 9999999999999999        66665 333322    123457


Q ss_pred             eEEEcchhhhhcccCccchHhhh-cC-CCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH
Q psy7952         108 NGWISPILSSFYLRFRDDKTSIV-TG-RSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ  185 (444)
Q Consensus       108 vlil~P~~~L~~~~q~~~~~~~l-~~-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~  185 (444)
                      ++|++|+++|+     .|+.+.+ .. ....+.+..++|+..........       .+++|+|+||+++.    ..+..
T Consensus       100 ~lil~Pt~~L~-----~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-------~~~~iiv~Tp~~l~----~~l~~  163 (236)
T 2pl3_A          100 VLIISPTRELA-----YQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-------NNINILVCTPGRLL----QHMDE  163 (236)
T ss_dssp             EEEECSSHHHH-----HHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-------TTCSEEEECHHHHH----HHHHH
T ss_pred             EEEEeCCHHHH-----HHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-------CCCCEEEECHHHHH----HHHHh
Confidence            89999999999     4444444 11 11227888888887655433322       47899999999974    22222


Q ss_pred             H-HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEE
Q psy7952         186 H-LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVF  259 (444)
Q Consensus       186 ~-~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~  259 (444)
                      . .....+++++|+||+|++.+++  +...   +..++..++.+.+++++|||+++...+....+  +.++..+.
T Consensus       164 ~~~~~~~~~~~lViDEah~~~~~~--~~~~---~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~--~~~p~~i~  231 (236)
T 2pl3_A          164 TVSFHATDLQMLVLDEADRILDMG--FADT---MNAVIENLPKKRQTLLFSATQTKSVKDLARLS--LKNPEYVW  231 (236)
T ss_dssp             CSSCCCTTCCEEEETTHHHHHHTT--THHH---HHHHHHTSCTTSEEEEEESSCCHHHHHHHHHS--CSSCEEEE
T ss_pred             cCCcccccccEEEEeChHHHhcCC--cHHH---HHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHh--CCCCEEEE
Confidence            1 2345688999999999998876  5544   44455567777899999999998876644443  45665554

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=99.91  E-value=2.4e-25  Score=203.31  Aligned_cols=197  Identities=18%  Similarity=0.205  Sum_probs=136.3

Q ss_pred             HHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC---------Cc
Q psy7952          34 QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG---------NV  104 (444)
Q Consensus        34 ~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~---------~~  104 (444)
                      ..+.++++. +|+.. |+++|.++++.++++ +++++.+|||+|||++        |++|+ +..+...         ..
T Consensus        32 ~~l~~~l~~-~g~~~-~~~~Q~~~i~~i~~~-~~~l~~a~TGsGKT~~--------~~~~~-l~~l~~~~~~~~~~~~~~   99 (253)
T 1wrb_A           32 PTIRNNILL-ASYQR-PTPIQKNAIPAILEH-RDIMACAQTGSGKTAA--------FLIPI-INHLVCQDLNQQRYSKTA   99 (253)
T ss_dssp             CSTTTTTTT-TTCCS-CCHHHHHHHHHHHTT-CCEEEECCTTSSHHHH--------HHHHH-HHHHHTTCC------CCB
T ss_pred             HHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CCEEEECCCCChHHHH--------HHHHH-HHHHHhhccccccccccC
Confidence            345566665 59987 679999999999999 9999999999999999        56655 3333221         22


Q ss_pred             cceeEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         105 RSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       105 ~~~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .+++||++|+++|+  .|+.+.+..+.. ...+.+..+.|+.........      +..+++|+|+||+++.    ..+.
T Consensus       100 ~~~~lil~Pt~~L~--~q~~~~~~~~~~-~~~~~~~~~~g~~~~~~~~~~------~~~~~~Ivv~Tp~~l~----~~l~  166 (253)
T 1wrb_A          100 YPKCLILAPTRELA--IQILSESQKFSL-NTPLRSCVVYGGADTHSQIRE------VQMGCHLLVATPGRLV----DFIE  166 (253)
T ss_dssp             CCSEEEECSSHHHH--HHHHHHHHHHHT-TSSCCEEEECSSSCSHHHHHH------HSSCCSEEEECHHHHH----HHHH
T ss_pred             CceEEEEECCHHHH--HHHHHHHHHHhc-cCCceEEEEECCCCHHHHHHH------hCCCCCEEEECHHHHH----HHHH
Confidence            35789999999999  222344444411 112778888888765543322      2467899999999974    3333


Q ss_pred             HHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCC--CCcEEEEeccCCcchHHHHHHHhcCCCCeEEEe
Q psy7952         185 QHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGN--SIPIIALTATAEPSVKQDIISVLKFNKPYKVFK  260 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~--~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~  260 (444)
                      .....+.+++++|+||||++.+++  +...+..+...+. .+.  +.|++++|||+++...+....++  .++..+..
T Consensus       167 ~~~~~~~~~~~lViDEah~~~~~~--~~~~~~~i~~~~~-~~~~~~~q~l~~SAT~~~~~~~~~~~~l--~~~~~i~~  239 (253)
T 1wrb_A          167 KNKISLEFCKYIVLDEADRMLDMG--FEPQIRKIIEESN-MPSGINRQTLMFSATFPKEIQKLAADFL--YNYIFMTV  239 (253)
T ss_dssp             TTSBCCTTCCEEEEETHHHHHHTT--CHHHHHHHHHSSC-CCCGGGCEEEEEESSCCHHHHHHHHHHC--SSCEEEEE
T ss_pred             cCCCChhhCCEEEEeCHHHHHhCc--hHHHHHHHHhhcc-CCCCCCcEEEEEEEeCCHHHHHHHHHHc--CCCEEEEE
Confidence            333456788999999999998876  6666555543211 232  47899999999998777666654  35554443

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=99.91  E-value=2.1e-25  Score=202.69  Aligned_cols=199  Identities=20%  Similarity=0.205  Sum_probs=132.5

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc-CCccceeEEE
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN-GNVRSRNGWI  111 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~-~~~~~~vlil  111 (444)
                      ...+.+++.+ +|+.. |+++|.++++.+++| +++++.+|||+|||++        |.+|+ +..+.. .+...+++|+
T Consensus        37 ~~~l~~~l~~-~g~~~-~~~~Q~~~i~~~~~~-~~~l~~a~TGsGKT~~--------~~l~~-l~~l~~~~~~~~~~lil  104 (245)
T 3dkp_A           37 NSRLLQNILD-AGFQM-PTPIQMQAIPVMLHG-RELLASAPTGSGKTLA--------FSIPI-LMQLKQPANKGFRALII  104 (245)
T ss_dssp             CHHHHHHHHH-TTCCS-CCHHHHHHHHHHHTT-CCEEEECCTTSCHHHH--------HHHHH-HHHHCSCCSSSCCEEEE
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHhCC-CCEEEECCCCCcHHHH--------HHHHH-HHHHhhcccCCceEEEE
Confidence            4567788887 59997 679999999999999 9999999999999999        66666 333332 2344578999


Q ss_pred             cchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH---HH
Q psy7952         112 SPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH---LV  188 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~---~~  188 (444)
                      +|+++|+  .|+.+.+..+.. ...+.+..++++.......     ......+++|+|+||+++.    . .+..   ..
T Consensus       105 ~Pt~~L~--~q~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~I~v~Tp~~l~----~-~l~~~~~~~  171 (245)
T 3dkp_A          105 SPTRELA--SQIHRELIKISE-GTGFRIHMIHKAAVAAKKF-----GPKSSKKFDILVTTPNRLI----Y-LLKQDPPGI  171 (245)
T ss_dssp             CSSHHHH--HHHHHHHHHHTT-TSCCCEECCCHHHHHHTTT-----STTSCCCCCEEEECHHHHH----H-HHHSSSCSC
T ss_pred             eCCHHHH--HHHHHHHHHHhc-ccCceEEEEecCccHHHHh-----hhhhcCCCCEEEECHHHHH----H-HHHhCCCCc
Confidence            9999999  222333333311 1125665555432211100     0112457899999999974    2 2322   23


Q ss_pred             hhCCccEEEEeccccccccC-CCcHHHHHHHHHHHHhh-CCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEec
Q psy7952         189 RYNKLAYIVVDEAHCVSEWG-HDFRPTYRRLGELRQFT-GNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT  261 (444)
Q Consensus       189 ~~~~~~~iViDE~H~~~~~~-~~~~~~~~~l~~~~~~~-~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~  261 (444)
                      .+.++++||+||||++.+++ ..+...+..+   +... +.+.++++||||+++...+.....+  .++..+...
T Consensus       172 ~~~~~~~lViDEah~~~~~~~~~~~~~~~~i---~~~~~~~~~~~~~~SAT~~~~v~~~~~~~l--~~p~~i~~~  241 (245)
T 3dkp_A          172 DLASVEWLVVDESDKLFEDGKTGFRDQLASI---FLACTSHKVRRAMFSATFAYDVEQWCKLNL--DNVISVSIG  241 (245)
T ss_dssp             CCTTCCEEEESSHHHHHHHC--CHHHHHHHH---HHHCCCTTCEEEEEESSCCHHHHHHHHHHS--SSCEEEEEC
T ss_pred             ccccCcEEEEeChHHhcccccccHHHHHHHH---HHhcCCCCcEEEEEeccCCHHHHHHHHHhC--CCCEEEEeC
Confidence            46789999999999998754 2355544444   3333 3458999999999988777666554  466655543

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=99.90  E-value=2.5e-22  Score=206.50  Aligned_cols=106  Identities=16%  Similarity=0.207  Sum_probs=96.5

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCC-
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGM-  367 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~-  367 (444)
                      .+.++||||+|+..++.+++.|...          +++.+|..+++.|+.|+.+|||||+++++|+|+|++++||+++. 
T Consensus       438 ~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~lVI~~d~d  517 (664)
T 1c4o_A          438 RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDAD  517 (664)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTT
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCEEEEeCCc
Confidence            4679999999999999999999876          88999999999999999999999999999999999999999997 


Q ss_pred             ----CCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHH
Q psy7952         368 ----PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV  405 (444)
Q Consensus       368 ----p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~  405 (444)
                          |.|...|+||+||+||.+ .|.+++++++.+....+.+
T Consensus       518 ~~G~p~s~~~~iQr~GRagR~~-~G~~i~~~~~~~~~~~~~i  558 (664)
T 1c4o_A          518 KEGFLRSERSLIQTIGRAARNA-RGEVWLYADRVSEAMQRAI  558 (664)
T ss_dssp             SCSGGGSHHHHHHHHGGGTTST-TCEEEEECSSCCHHHHHHH
T ss_pred             ccCCCCCHHHHHHHHCccCcCC-CCEEEEEEcCCCHHHHHHH
Confidence                899999999999999994 7999999988766544444

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.90  E-value=3.4e-22  Score=202.70  Aligned_cols=137  Identities=16%  Similarity=0.166  Sum_probs=103.5

Q ss_pred             HHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchh
Q psy7952          36 LTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPIL  115 (444)
Q Consensus        36 ~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~  115 (444)
                      +.++-++.+|+.  |+++|..+++.+++| +  +..++||+|||++        +.+|+++..+ .+   ..++|++||+
T Consensus        68 vREAs~R~lG~~--Pt~VQ~~~ip~LlqG-~--IaeakTGeGKTLv--------f~Lp~~L~aL-~G---~qv~VvTPTr  130 (997)
T 2ipc_A           68 TRESAKRYLGMR--HFDVQLIGGAVLHEG-K--IAEMKTGEGKTLV--------ATLAVALNAL-TG---KGVHVVTVND  130 (997)
T ss_dssp             HHHHHHHHTCCC--CCHHHHHHHHHHHTT-S--EEECCSTHHHHHH--------HHHHHHHHHT-TC---SCCEEEESSH
T ss_pred             HHHHHHHHhCCC--CcHHHHhhcccccCC-c--eeeccCCCchHHH--------HHHHHHHHHH-hC---CCEEEEeCCH
Confidence            456777788994  688999999999999 5  8999999999999        6666622222 22   3469999999


Q ss_pred             hhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH------
Q psy7952         116 SSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL------  187 (444)
Q Consensus       116 ~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~------  187 (444)
                      .|+  .|..+.+..+  ..+   +++..+.|+.+...+...+        .++|+|+||..|.   |+.+..+.      
T Consensus       131 eLA--~Qdae~m~~l~~~lG---Lsv~~i~Gg~~~~~r~~ay--------~~DIvyGTpgrlg---fDyLrd~m~~~~~~  194 (997)
T 2ipc_A          131 YLA--RRDAEWMGPVYRGLG---LSVGVIQHASTPAERRKAY--------LADVTYVTNSELG---FDYLRDNMAISPDQ  194 (997)
T ss_dssp             HHH--HHHHHHHHHHHHTTT---CCEEECCTTCCHHHHHHHH--------TSSEEEEEHHHHH---HHHHHHTSCSSTTT
T ss_pred             HHH--HHHHHHHHHHHHhcC---CeEEEEeCCCCHHHHHHHc--------CCCEEEECchhhh---hHHHHHhhhcchhh
Confidence            999  4446666666  567   9999999998765444433        5899999999974   35555443      


Q ss_pred             HhhC---CccEEEEecccccc
Q psy7952         188 VRYN---KLAYIVVDEAHCVS  205 (444)
Q Consensus       188 ~~~~---~~~~iViDE~H~~~  205 (444)
                      ..+.   ++.++|+||+|.++
T Consensus       195 l~~r~d~~l~~lIIDEaDsmL  215 (997)
T 2ipc_A          195 LVLRHDHPLHYAIIDEVDSIL  215 (997)
T ss_dssp             CCSCSSSSSCEEEETTHHHHT
T ss_pred             cccccCCCcceEEEechHHHH
Confidence            2356   89999999999985

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.88  E-value=1.1e-21  Score=166.26  Aligned_cols=137  Identities=26%  Similarity=0.432  Sum_probs=116.1

Q ss_pred             CCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHH
Q psy7952         264 FRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQ  333 (444)
Q Consensus       264 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~  333 (444)
                      ..+++...+.... ...+...+.+++...      .++++||||+++++++.++..|...          +++.+|..++
T Consensus         6 ~~~~i~~~~~~~~-~~~K~~~L~~ll~~~------~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~   78 (163)
T 2hjv_A            6 TTRNIEHAVIQVR-EENKFSLLKDVLMTE------NPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVM   78 (163)
T ss_dssp             CCCCEEEEEEECC-GGGHHHHHHHHHHHH------CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             CcccceEEEEECC-hHHHHHHHHHHHHhc------CCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHH
Confidence            3455555555543 244555555555442      4679999999999999999999876          8899999999


Q ss_pred             HHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         334 ESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       334 ~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      +.|++|+.++||||+++++|+|+|++++||++++|.+...|+||+||+||.|+.|.+++++.+.+...+..+.+
T Consensus        79 ~~f~~g~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~  152 (163)
T 2hjv_A           79 NEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADIEE  152 (163)
T ss_dssp             HHHHTTSCSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGGGHHHHHHHHH
T ss_pred             HHHHcCCCeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999888877776644

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=99.87  E-value=1.4e-21  Score=167.72  Aligned_cols=136  Identities=23%  Similarity=0.343  Sum_probs=109.4

Q ss_pred             CCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHH
Q psy7952         266 SNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQES  335 (444)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~  335 (444)
                      +++...+...+....+.    ..+..++...  ..+++||||+++.+++.++..|...          +++.+|..+++.
T Consensus         6 ~~i~q~~~~~~~~~~K~----~~L~~ll~~~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~   79 (175)
T 2rb4_A            6 NNIRQYYVLCEHRKDKY----QALCNIYGSI--TIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQR   79 (175)
T ss_dssp             CCEEEEEEECSSHHHHH----HHHHHHHTTS--CCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHH
T ss_pred             CCceEEEEEcCChHhHH----HHHHHHHHhC--CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHH
Confidence            34455555444333333    3344444433  4679999999999999999999876          889999999999


Q ss_pred             HhcCCccEEEEcCccccccccCCccEEEEeCCC------CCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         336 FMRGEINVITATISFGMGIDRQNVRFVVHWGMP------SSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       336 f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p------~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      |++|+.++||||+++++|+|+|++++||++|+|      .+...|+||+||+||.|+.|.+++++.+.+...+..+.+
T Consensus        80 f~~g~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~  157 (175)
T 2rb4_A           80 FRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQD  157 (175)
T ss_dssp             HHTTSCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGGHHHHHHHHH
T ss_pred             HHcCCCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccchHHHHHHHHH
Confidence            999999999999999999999999999999999      999999999999999999999999999888776666643

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.87  E-value=1.6e-21  Score=165.68  Aligned_cols=121  Identities=22%  Similarity=0.453  Sum_probs=102.9

Q ss_pred             hHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCcc
Q psy7952         281 SYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISF  350 (444)
Q Consensus       281 ~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~  350 (444)
                      +...+.+++..    .  .++++||||++++.++.++..|...          ++..+|..+++.|++|+.++||||+++
T Consensus        17 K~~~l~~ll~~----~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~   90 (165)
T 1fuk_A           17 KYECLTDLYDS----I--SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLL   90 (165)
T ss_dssp             HHHHHHHHHHH----T--TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGG
T ss_pred             HHHHHHHHHHh----C--CCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcChh
Confidence            55555554444    2  4689999999999999999999875          889999999999999999999999999


Q ss_pred             ccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         351 GMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       351 ~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      ++|+|+|++++||++|+|.+...|+||+||+||.|+.|.+++++.+.+...+..+.+
T Consensus        91 ~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~  147 (165)
T 1fuk_A           91 ARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEK  147 (165)
T ss_dssp             TTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHH
T ss_pred             hcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcchHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999888777666643

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=99.86  E-value=4.7e-21  Score=169.49  Aligned_cols=123  Identities=26%  Similarity=0.474  Sum_probs=106.9

Q ss_pred             hhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcC
Q psy7952         279 KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATI  348 (444)
Q Consensus       279 ~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~  348 (444)
                      ..+...+.+++...      .++++||||+++.+++.++..|...          +++.+|..+++.|++|..+|||||+
T Consensus        16 ~~k~~~l~~ll~~~------~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~   89 (212)
T 3eaq_A           16 RGRLEVLSDLLYVA------SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD   89 (212)
T ss_dssp             TSHHHHHHHHHHHH------CCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECT
T ss_pred             HHHHHHHHHHHHhC------CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecC
Confidence            34444454544432      4789999999999999999999876          8899999999999999999999999


Q ss_pred             ccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         349 SFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       349 ~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      ++++|+|+|++++||++|+|.|...|+||+||+||.|+.|.+++++++.+...+..+.+
T Consensus        90 ~~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~  148 (212)
T 3eaq_A           90 VAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALER  148 (212)
T ss_dssp             TTTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGGGHHHHHHHHH
T ss_pred             hhhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchhHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999988777766643

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.86  E-value=4.2e-21  Score=166.66  Aligned_cols=133  Identities=20%  Similarity=0.376  Sum_probs=105.6

Q ss_pred             CCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHH
Q psy7952         265 RSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQE  334 (444)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~  334 (444)
                      ..++...+..... ..+.    ..+.+++..   .++++||||+++..++.++..|...          +++.+|..+++
T Consensus        27 ~~~i~q~~~~~~~-~~K~----~~L~~~l~~---~~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~   98 (191)
T 2p6n_A           27 SLDVIQEVEYVKE-EAKM----VYLLECLQK---TPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIE   98 (191)
T ss_dssp             -CCSEEEEEECCG-GGHH----HHHHHHHTT---SCSCEEEECSCHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHH
T ss_pred             CcCceEEEEEcCh-HHHH----HHHHHHHHh---CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHH
Confidence            4455555554432 2333    334444443   2568999999999999999999865          88999999999


Q ss_pred             HHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEeccc-chhhHHHH
Q psy7952         335 SFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEH-SKKSLEYV  405 (444)
Q Consensus       335 ~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~~  405 (444)
                      .|++|+.+|||||+++++|+|+|++++||++|+|.+...|+||+||+||.|+.|.+++++.+. +...+..+
T Consensus        99 ~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~~l  170 (191)
T 2p6n_A           99 AFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLMDL  170 (191)
T ss_dssp             HHHHTSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSCHHHHHHH
T ss_pred             HHhcCCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchhHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999876 44444443

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=99.86  E-value=6.5e-21  Score=164.74  Aligned_cols=138  Identities=20%  Similarity=0.383  Sum_probs=104.6

Q ss_pred             CCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHH
Q psy7952         264 FRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQ  333 (444)
Q Consensus       264 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~  333 (444)
                      ..+++...+..... ..+...+.+++..    . ..+.++||||+++..++.++..|...          ++..+|..++
T Consensus        16 ~~~~i~q~~~~v~~-~~K~~~L~~ll~~----~-~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~   89 (185)
T 2jgn_A           16 TSENITQKVVWVEE-SDKRSFLLDLLNA----T-GKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEAL   89 (185)
T ss_dssp             CCTTEEEEEEECCG-GGHHHHHHHHHHH----C--CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHH
T ss_pred             CCCCceEEEEEeCc-HHHHHHHHHHHHh----c-CCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHH
Confidence            34566655555442 3444444444443    2 15789999999999999999999876          7889999999


Q ss_pred             HHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         334 ESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       334 ~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      +.|++|+.+|||||+++++|+|+|++++||++|+|+|...|+||+||+||.|+.|.+++++.+.+...++.+.+
T Consensus        90 ~~f~~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~  163 (185)
T 2jgn_A           90 HQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLD  163 (185)
T ss_dssp             HHHHHTSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGGGGHHHHHH
T ss_pred             HHHHcCCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999888877776654

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=99.86  E-value=1.5e-21  Score=166.73  Aligned_cols=121  Identities=22%  Similarity=0.353  Sum_probs=104.4

Q ss_pred             hhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcC
Q psy7952         279 KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATI  348 (444)
Q Consensus       279 ~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~  348 (444)
                      ..+...+.+++..    .  .+.++||||+++.+++.++..|...          +++.+|..+++.|++|+.++||||+
T Consensus        16 ~~K~~~L~~ll~~----~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~   89 (172)
T 1t5i_A           16 NEKNRKLFDLLDV----L--EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN   89 (172)
T ss_dssp             GGHHHHHHHHHHH----S--CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESS
T ss_pred             HHHHHHHHHHHHh----C--CCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECC
Confidence            3444444444443    2  4679999999999999999999875          8899999999999999999999999


Q ss_pred             ccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccc-hhhHHHH
Q psy7952         349 SFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS-KKSLEYV  405 (444)
Q Consensus       349 ~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~-~~~~~~~  405 (444)
                      ++++|+|+|++++||++|+|+|...|+||+||+||.|+.|.+++++.+.+ ...++.+
T Consensus        90 ~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~l  147 (172)
T 1t5i_A           90 LFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDV  147 (172)
T ss_dssp             CCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHH
T ss_pred             chhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChhHHHHHHHH
Confidence            99999999999999999999999999999999999999999999998754 3444444

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.84  E-value=1.3e-20  Score=189.84  Aligned_cols=110  Identities=15%  Similarity=0.133  Sum_probs=69.9

Q ss_pred             HHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----cCHHHHHHHHHHHhcCCccEEE--EcCccccccc
Q psy7952         283 AHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----VNKHERSRVQESFMRGEINVIT--ATISFGMGID  355 (444)
Q Consensus       283 ~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----~~~~~r~~~~~~f~~g~~~vLv--aT~~~~~Gid  355 (444)
                      ..+.+.+..++..   ..+.++||++|...++.+++.+...     -....+..+++.|+.+. .||+  +|+.+++|||
T Consensus       370 ~~~~~~l~~~~~~---~~g~~lvff~S~~~~~~v~~~l~~~~~~~q~~~~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD  445 (540)
T 2vl7_A          370 PIYSILLKRIYEN---SSKSVLVFFPSYEMLESVRIHLSGIPVIEENKKTRHEEVLELMKTGK-YLVMLVMRAKESEGVE  445 (540)
T ss_dssp             HHHHHHHHHHHHT---CSSEEEEEESCHHHHHHHHTTCTTSCEEESTTTCCHHHHHHHHHTSC-CEEEEEC---------
T ss_pred             HHHHHHHHHHHHh---CCCCEEEEeCCHHHHHHHHHHhccCceEecCCCCcHHHHHHHHhcCC-eEEEEEecCceeccee
Confidence            4455556665543   4678999999999999999888653     11247889999998864 5666  8899999999


Q ss_pred             cCC----ccEEEEeCCCCC------------------------------HHHHHHHhccCCCCCCceeEEEEecc
Q psy7952         356 RQN----VRFVVHWGMPSS------------------------------IPAYYQESGRAGRDGLQSYCRIYHSE  396 (444)
Q Consensus       356 i~~----~~~Vi~~~~p~s------------------------------~~~~~Qr~GR~~R~g~~g~~~~~~~~  396 (444)
                      +|+    +++||+++.|..                              ...+.|.+||+-|...+--+++++++
T Consensus       446 ~~~~~~~~~~Vii~~lPf~~~~d~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~Q~~GR~iR~~~D~g~v~llD~  520 (540)
T 2vl7_A          446 FREKENLFESLVLAGLPYPNVSDDMVRKRIERLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCDS  520 (540)
T ss_dssp             ------CEEEEEEESCCCCCTTSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCCSTTCCCEEEEESG
T ss_pred             cCCCcccccEEEEECCCCCCCCCHHHHHHHHHHHHhhCCChhHHHHHHHHHHHHHHhCCcccCCCccEEEEEEcc
Confidence            997    889999998852                              13357999999998544334555554

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.83  E-value=5.9e-20  Score=170.08  Aligned_cols=121  Identities=27%  Similarity=0.473  Sum_probs=102.9

Q ss_pred             hhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCc
Q psy7952         280 DSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATIS  349 (444)
Q Consensus       280 ~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~  349 (444)
                      .+...+.+++...      .++++||||+++++++.++..|...          +++.+|..+++.|++|..+|||||++
T Consensus        14 ~K~~~L~~ll~~~------~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~v   87 (300)
T 3i32_A           14 GRLEVLSDLLYVA------SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDV   87 (300)
T ss_dssp             SHHHHHHHHHHHH------CCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECST
T ss_pred             HHHHHHHHHHHhc------CCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEech
Confidence            4444455544442      4789999999999999999999876          88999999999999999999999999


Q ss_pred             cccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHH
Q psy7952         350 FGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI  406 (444)
Q Consensus       350 ~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  406 (444)
                      +++|+|+|++++||++|.|.|...|+||+||+||.|+.|.|++++++.+...+..+.
T Consensus        88 a~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~~~~~~ie  144 (300)
T 3i32_A           88 AARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALE  144 (300)
T ss_dssp             TTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSSTHHHHHHHH
T ss_pred             hhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999998877666654

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}

Probab=99.71  E-value=6.6e-22  Score=168.86  Aligned_cols=109  Identities=28%  Similarity=0.397  Sum_probs=100.8

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCC
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMP  368 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p  368 (444)
                      .++++||||+++.+++.++..|...          +++.+|..+++.|++|+.++||||+++++|+|+|++++||++|+|
T Consensus        29 ~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi~~~~p  108 (170)
T 2yjt_D           29 EATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMP  108 (170)
Confidence            4679999999999999999999765          778999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         369 SSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       369 ~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      .|...|+||+||+||.|+.|.+++++.+.+...+..+.+
T Consensus       109 ~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  147 (170)
T 2yjt_D          109 RSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGR  147 (170)
Confidence            999999999999999999999999999888777666643

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=99.81  E-value=8.9e-19  Score=179.97  Aligned_cols=105  Identities=21%  Similarity=0.253  Sum_probs=96.3

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCC-
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGM-  367 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~-  367 (444)
                      .+.++||||+|+..++.+++.|...          +++.+|..+++.|++|+.+|||||+++++|+|+|++++||+++. 
T Consensus       444 ~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d  523 (661)
T 2d7d_A          444 RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDAD  523 (661)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEEETTTT
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEEEeCcc
Confidence            4679999999999999999999876          78999999999999999999999999999999999999999997 


Q ss_pred             ----CCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHH
Q psy7952         368 ----PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEY  404 (444)
Q Consensus       368 ----p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~  404 (444)
                          |.|...|+||+||+||. ..|.+++++++.+....+.
T Consensus       524 ~~G~p~s~~~~iQr~GRagR~-~~G~~i~~~~~~~~~~~~~  563 (661)
T 2d7d_A          524 KEGFLRSERSLIQTIGRAARN-AEGRVIMYADKITKSMEIA  563 (661)
T ss_dssp             CCTTTTSHHHHHHHHHTTTTS-TTCEEEEECSSCCHHHHHH
T ss_pred             cccCCCCHHHHHHHhCcccCC-CCCEEEEEEeCCCHHHHHH
Confidence                99999999999999998 7899999998876544433

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.79  E-value=5.2e-19  Score=178.86  Aligned_cols=321  Identities=12%  Similarity=0.122  Sum_probs=192.3

Q ss_pred             CCcccCchHHHHHHHHHH----ccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcc
Q psy7952          45 GFDSFKCELQKKAIRHIL----LRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYL  120 (444)
Q Consensus        45 g~~~~~t~~Q~~~~~~~~----~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~  120 (444)
                      |++. + ++|.+++..+.    .| +++++.+|||+|||++        |++|+    +..   .++++|++||++|+  
T Consensus         1 ~~~~-r-~~Q~~~~~~v~~~l~~~-~~~~~~a~TGtGKT~~--------~l~p~----l~~---~~~v~i~~pt~~l~--   60 (551)
T 3crv_A            1 MVKL-R-DWQEKLKDKVIEGLRNN-FLVALNAPTGSGKTLF--------SLLVS----LEV---KPKVLFVVRTHNEF--   60 (551)
T ss_dssp             CCSC-C-HHHHHHHHHHHHHHHTT-CEEEEECCTTSSHHHH--------HHHHH----HHH---CSEEEEEESSGGGH--
T ss_pred             CCCC-C-HHHHHHHHHHHHHHHcC-CcEEEECCCCccHHHH--------HHHHH----HhC---CCeEEEEcCCHHHH--
Confidence            4553 4 79999877544    46 8999999999999999        88888    443   34669999999999  


Q ss_pred             cCccchHhhhcCCCCceeEEEEeCCCChh------------------------------hHHHHHHH-------------
Q psy7952         121 RFRDDKTSIVTGRSDLYQLELIVSGQTKT------------------------------ENKAILEE-------------  157 (444)
Q Consensus       121 ~q~~~~~~~l~~~~~~i~~~~~~~~~~~~------------------------------~~~~~~~~-------------  157 (444)
                      .|+.+.+..+... ..+++..+.|.....                              ........             
T Consensus        61 ~q~~~~~~~l~~~-~~~~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy  139 (551)
T 3crv_A           61 YPIYRDLTKIREK-RNITFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPY  139 (551)
T ss_dssp             HHHHHHHTTCCCS-SCCCEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHH
T ss_pred             HHHHHHHHHHhhh-cCccEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCcc
Confidence            2333333333111 127777776632110                              00111111             


Q ss_pred             --HHhcCCCeeEEEECCCccccccHHHHHHHHHh-hCCccEEEEeccccccccCCCc-----------------------
Q psy7952         158 --LRLVKPRIKLLYVTPERAVTESFHYLLQHLVR-YNKLAYIVVDEAHCVSEWGHDF-----------------------  211 (444)
Q Consensus       158 --~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~-~~~~~~iViDE~H~~~~~~~~~-----------------------  211 (444)
                        .+.....++|+|+|+..+...    ....... .....++||||||++.+ ...+                       
T Consensus       140 ~~ar~~~~~adIVV~~~~~l~~~----~~~~~~~~~~~~~~vIiDEAHnl~d-~~~~~s~~ls~~~l~~~~~~l~~~~~~  214 (551)
T 3crv_A          140 YSLLNSLYKADVIALTYPYFFID----RYREFIDIDLREYMIVIDEAHNLDK-VNELEERSLSEITIQMAIKQSKSEESR  214 (551)
T ss_dssp             HHHHHHGGGCSEEEEETHHHHCH----HHHTTSCCCSTTEEEEETTGGGGGG-GGGGGCEEEEHHHHHHHHHHCSCHHHH
T ss_pred             HHHHhhhhcCCEEEeCchHhcCH----HHHHhcCCCcCCeEEEEecccchHH-HHHhhceecCHHHHHHHHHHHHHHHHH
Confidence              122345789999999998642    2222111 23567899999999876 2100                       


Q ss_pred             ------------------------------HHHHH-------------------------HHHHHH--------------
Q psy7952         212 ------------------------------RPTYR-------------------------RLGELR--------------  222 (444)
Q Consensus       212 ------------------------------~~~~~-------------------------~l~~~~--------------  222 (444)
                                                    ...+.                         .+..++              
T Consensus       215 ~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~~~  294 (551)
T 3crv_A          215 RILSKLLNQLREVVLPDEKYIKVENVPKLSKEELEILADDYEDIRKDSLKQGKVNKIHIGSILRFFSLLSIGSFIPFSYS  294 (551)
T ss_dssp             HHHHHHHHHHTTSCCSCSSCEECSCCCCCCHHHHHHHHHHHHHHHHHHHHTTCBCCCHHHHHHHHHHHHHHSSCEEEEET
T ss_pred             HHHHHHHHHHHHHhhccccccccccChHHHHHHHHHHHHHHHHHHHhhhhcCCcccchHHHHHHHHHHHhccCCeEeccC
Confidence                                          00000                         010000              


Q ss_pred             --------------HhhCCC-CcEEEEeccCCcchHHHHHHHhcCCCCeEE-----EecCCCCCCceEEEEEccc----c
Q psy7952         223 --------------QFTGNS-IPIIALTATAEPSVKQDIISVLKFNKPYKV-----FKTSTFRSNLFYDVIFDDL----L  278 (444)
Q Consensus       223 --------------~~~~~~-~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~-----~~~~~~~~~~~~~~~~~~~----~  278 (444)
                                    +.+.+. ..+|++|||+.+  .+.+...+|++.+...     ...+....+... +.....    .
T Consensus       295 ~~l~~~pl~~~~~l~~~~~~~~svIltSaTL~~--~~~~~~~lGl~~~~~~~~~~~~~~spf~~~~~l-~v~~~~~~~~~  371 (551)
T 3crv_A          295 KRLVIKNPEISYYLNLLNDNELSIILMSGTLPP--REYMEKVWGIKRNMLYLDVEREIQKRVSGSYEC-YIGVDVTSKYD  371 (551)
T ss_dssp             TEEEEECCCTHHHHGGGGCTTCEEEEEESSCCC--HHHHHHTSCCCSCEEEEEHHHHTTSCCSCEEEE-EEECSCCCCTT
T ss_pred             CEEEEEECCHHHHHHHHhccCceEEEEeeCCCc--HHHHHHHhCCCCccccccceeecCCcCCCceEE-EEeCCCCCccc
Confidence                          012233 579999999987  5677788887644321     011111122211 111111    0


Q ss_pred             ---hhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh--c--CHHHHHHHHHHHhcCCccEEEEc--Cc
Q psy7952         279 ---KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK--V--NKHERSRVQESFMRGEINVITAT--IS  349 (444)
Q Consensus       279 ---~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~--~--~~~~r~~~~~~f~~g~~~vLvaT--~~  349 (444)
                         ......+.+.+.++...   .++.++||++|....+++++.+...  .  ....+...++.|+.+...||+|+  ..
T Consensus       372 ~r~~~~~~~l~~~i~~l~~~---~~g~~lvlF~Sy~~l~~v~~~~~~~v~~q~~~~~~~~~~~~~~~~~~~vl~~v~gg~  448 (551)
T 3crv_A          372 MRSDNMWKRYADYLLKIYFQ---AKANVLVVFPSYEIMDRVMSRISLPKYVESEDSSVEDLYSAISANNKVLIGSVGKGK  448 (551)
T ss_dssp             TCCHHHHHHHHHHHHHHHHH---CSSEEEEEESCHHHHHHHHTTCCSSEEECCSSCCHHHHHHHTTSSSSCEEEEESSCC
T ss_pred             cCCHHHHHHHHHHHHHHHHh---CCCCEEEEecCHHHHHHHHHhcCCcEEEcCCCCCHHHHHHHHHhcCCeEEEEEecce
Confidence               12245566666666544   3679999999999999988743222  1  11135667888864445899998  69


Q ss_pred             cccccccC-----CccEEEEeCCCCC------------------------------HHHHHHHhccCCCCCCceeEEEEe
Q psy7952         350 FGMGIDRQ-----NVRFVVHWGMPSS------------------------------IPAYYQESGRAGRDGLQSYCRIYH  394 (444)
Q Consensus       350 ~~~Gidi~-----~~~~Vi~~~~p~s------------------------------~~~~~Qr~GR~~R~g~~g~~~~~~  394 (444)
                      +++|||+|     .++.||..+.|..                              ...+.|.+||+-|..++--+++++
T Consensus       449 ~~EGiD~~d~~g~~l~~viI~~lPfp~~dp~~~ar~~~~~~~~g~~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~ll  528 (551)
T 3crv_A          449 LAEGIELRNNDRSLISDVVIVGIPYPPPDDYLKILAQRVSLKMNRENEEFLFKIPALVTIKQAIGRAIRDVNDKCNVWLL  528 (551)
T ss_dssp             SCCSSCCEETTEESEEEEEEESCCCCCCSHHHHHHHHHTTCCSSTTTHHHHTHHHHHHHHHHHHHTTCCSTTCEEEEEEE
T ss_pred             ecccccccccCCcceeEEEEEcCCCCCCCHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHhccCccCCCccEEEEEe
Confidence            99999999     3788998887651                              112359999999985554455566


Q ss_pred             ccc
Q psy7952         395 SEH  397 (444)
Q Consensus       395 ~~~  397 (444)
                      ++.
T Consensus       529 D~R  531 (551)
T 3crv_A          529 DKR  531 (551)
T ss_dssp             SGG
T ss_pred             ehh
Confidence            544

>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=99.78  E-value=3.3e-20  Score=164.81  Aligned_cols=177  Identities=13%  Similarity=0.083  Sum_probs=102.3

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc---CCcccee
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN---GNVRSRN  108 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~---~~~~~~v  108 (444)
                      .++.+........++.  ++++|.++++.++++ +++++.+|||+|||++        +..++ ...+..   .+...++
T Consensus        18 ~~~~~~~~~~~~~~~~--l~~~Q~~~i~~~~~~-~~~li~~~tGsGKT~~--------~~~~~-~~~~~~~~~~~~~~~~   85 (216)
T 3b6e_A           18 DEENVAARASPEPELQ--LRPYQMEVAQPALEG-KNIIICLPTGSGKTRV--------AVYIA-KDHLDKKKKASEPGKV   85 (216)
T ss_dssp             CHHHHHHHTCCSCCCC--CCHHHHHHHHHHHTT-CCEEEECSCHHHHHHH--------HHHHH-HHHHHHHHHTTCCCCE
T ss_pred             CchhhhcccCccCCCC--chHHHHHHHHHHhcC-CCEEEEcCCCCCHHHH--------HHHHH-HHHHhhcccccCCCcE
Confidence            3444444433322333  458999999999998 8999999999999999        44333 221211   1223567


Q ss_pred             EEEcchhhhhcccC-ccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         109 GWISPILSSFYLRF-RDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       109 lil~P~~~L~~~~q-~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      +|++|+++|+  .| +.+.+..+ ..+   +.+..+.|+...........      ..++|+|+||+.+..     .+..
T Consensus        86 lil~p~~~L~--~q~~~~~~~~~~~~~---~~v~~~~g~~~~~~~~~~~~------~~~~i~v~T~~~l~~-----~~~~  149 (216)
T 3b6e_A           86 IVLVNKVLLV--EQLFRKEFQPFLKKW---YRVIGLSGDTQLKISFPEVV------KSCDIIISTAQILEN-----SLLN  149 (216)
T ss_dssp             EEEESSHHHH--HHHHHHTHHHHHTTT---SCEEECCC---CCCCHHHHH------HHCSEEEEEHHHHHH-----HHHC
T ss_pred             EEEECHHHHH--HHHHHHHHHHHhccC---ceEEEEeCCcccchhHHhhc------cCCCEEEECHHHHHH-----HHhc
Confidence            9999999999  21 22333444 334   77888887765433222221      257999999999742     2222


Q ss_pred             H-------HhhCCccEEEEeccccccccCCCcHHHHHHHHHH-HHhh---------CCCCcEEEEecc
Q psy7952         187 L-------VRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGEL-RQFT---------GNSIPIIALTAT  237 (444)
Q Consensus       187 ~-------~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~-~~~~---------~~~~~~v~lSAT  237 (444)
                      .       ..+.++++||+||||++.+.+. +...+..+... ....         .+.+++++||||
T Consensus       150 ~~~~~~~~~~~~~~~~iIiDEah~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          150 LENGEDAGVQLSDFSLIIIDECHHTNKEAV-YNNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             -------CCCGGGCSEEEETTC-------C-HHHHHHHHHHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             cCcccccccchhcccEEEEECchhhccCCc-HHHHHHHHHHHhcccccccccccCCCCcceEEEeecC
Confidence            1       3356789999999999875432 33333332211 1111         145889999998

>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=99.73  E-value=1e-18  Score=161.89  Aligned_cols=151  Identities=15%  Similarity=0.114  Sum_probs=103.2

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhh
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      ++++|.++++.++.+ ++.++++|||+|||.+++        .++ ...+..++  .++||++|+++|+     .+..+.
T Consensus       114 l~~~Q~~ai~~~l~~-~~~ll~~~tGsGKT~~~~--------~~~-~~~~~~~~--~~~lil~Pt~~L~-----~q~~~~  176 (282)
T 1rif_A          114 PHWYQKDAVFEGLVN-RRRILNLPTSAGRSLIQA--------LLA-RYYLENYE--GKILIIVPTTALT-----TQMADD  176 (282)
T ss_dssp             CCHHHHHHHHHHHHH-SEEEECCCTTSCHHHHHH--------HHH-HHHHHHCS--SEEEEECSSHHHH-----HHHHHH
T ss_pred             ccHHHHHHHHHHHhc-CCeEEEcCCCCCcHHHHH--------HHH-HHHHHcCC--CeEEEEECCHHHH-----HHHHHH
Confidence            468999999999988 788999999999999943        222 11122111  2569999999999     455555


Q ss_pred             h-cCC-CCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccccc
Q psy7952         130 V-TGR-SDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEW  207 (444)
Q Consensus       130 l-~~~-~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~  207 (444)
                      + .++ .....+..+.++.....         ......+|+|+||+.+...       ......++++||+||||++.+ 
T Consensus       177 l~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~I~v~T~~~l~~~-------~~~~~~~~~~vIiDEaH~~~~-  239 (282)
T 1rif_A          177 FVDYRLFSHAMIKKIGGGASKDD---------KYKNDAPVVVGTWQTVVKQ-------PKEWFSQFGMMMNDECHLATG-  239 (282)
T ss_dssp             HHHHTSCCGGGEEECSTTCSSTT---------CCCTTCSEEEECHHHHTTS-------CGGGGGGEEEEEEETGGGCCH-
T ss_pred             HHHhcccccceEEEEeCCCcchh---------hhccCCcEEEEchHHHHhh-------HHHHHhhCCEEEEECCccCCc-
Confidence            5 222 22256666666654321         1135789999999987532       112356789999999999753 


Q ss_pred             CCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcch
Q psy7952         208 GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSV  242 (444)
Q Consensus       208 ~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~  242 (444)
                              ..+..++..+....+++++||||++..
T Consensus       240 --------~~~~~il~~~~~~~~~l~lSATp~~~~  266 (282)
T 1rif_A          240 --------KSISSIISGLNNCMFKFGLSGSLRDGK  266 (282)
T ss_dssp             --------HHHHHHTTTCTTCCEEEEECSSCCTTS
T ss_pred             --------ccHHHHHHHhhcCCeEEEEeCCCCCcc
Confidence                    233445555555689999999998754

>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=99.69  E-value=1.8e-17  Score=149.02  Aligned_cols=137  Identities=16%  Similarity=0.095  Sum_probs=96.0

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhh
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      ++++|.+++..++++ +++++++|||+|||.+|+.        ++    ...+   .+++|++|+++|+     .+..+.
T Consensus        94 l~~~Q~~ai~~~~~~-~~~ll~~~tG~GKT~~a~~--------~~----~~~~---~~~liv~P~~~L~-----~q~~~~  152 (237)
T 2fz4_A           94 LRDYQEKALERWLVD-KRGCIVLPTGSGKTHVAMA--------AI----NELS---TPTLIVVPTLALA-----EQWKER  152 (237)
T ss_dssp             CCHHHHHHHHHHTTT-SEEEEEESSSTTHHHHHHH--------HH----HHSC---SCEEEEESSHHHH-----HHHHHH
T ss_pred             cCHHHHHHHHHHHhC-CCEEEEeCCCCCHHHHHHH--------HH----HHcC---CCEEEEeCCHHHH-----HHHHHH
Confidence            468999999999998 7899999999999998432        22    1112   3559999999999     555666


Q ss_pred             h-cCCCCcee-EEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccccc
Q psy7952         130 V-TGRSDLYQ-LELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEW  207 (444)
Q Consensus       130 l-~~~~~~i~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~  207 (444)
                      + .++   +. +..+.++..               ...+|+|+|++.+...     ..  ....++++||+||+|++.+.
T Consensus       153 ~~~~~---~~~v~~~~g~~~---------------~~~~i~v~T~~~l~~~-----~~--~~~~~~~llIiDEaH~l~~~  207 (237)
T 2fz4_A          153 LGIFG---EEYVGEFSGRIK---------------ELKPLTVSTYDSAYVN-----AE--KLGNRFMLLIFDEVHHLPAE  207 (237)
T ss_dssp             HGGGC---GGGEEEESSSCB---------------CCCSEEEEEHHHHHHT-----HH--HHTTTCSEEEEECSSCCCTT
T ss_pred             HHhCC---CCeEEEEeCCCC---------------CcCCEEEEeHHHHHhh-----HH--HhcccCCEEEEECCccCCCh
Confidence            6 445   66 777777653               2568999999886421     11  11246999999999998654


Q ss_pred             CCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcch
Q psy7952         208 GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSV  242 (444)
Q Consensus       208 ~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~  242 (444)
                      .  ++    .+   ...++ ..+++++||||.+..
T Consensus       208 ~--~~----~i---~~~~~-~~~~l~LSATp~r~D  232 (237)
T 2fz4_A          208 S--YV----QI---AQMSI-APFRLGLTATFERED  232 (237)
T ss_dssp             T--HH----HH---HHTCC-CSEEEEEEESCC---
T ss_pred             H--HH----HH---HHhcc-CCEEEEEecCCCCCC
Confidence            3  32    22   22333 378999999998753

>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=99.69  E-value=4.3e-17  Score=146.65  Aligned_cols=160  Identities=14%  Similarity=0.100  Sum_probs=100.8

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC--ccceeEEEcchhhhhcccCccchHh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN--VRSRNGWISPILSSFYLRFRDDKTS  128 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~--~~~~vlil~P~~~L~~~~q~~~~~~  128 (444)
                      +++|.++++.+..| +++++.||||+|||..        +..+. +......+  ...++++++|+++++     .+..+
T Consensus        63 ~~~q~~~i~~i~~g-~~~~i~g~TGsGKTt~--------~~~~~-~~~~~~~~~~~~~~~l~~~p~~~la-----~q~~~  127 (235)
T 3llm_A           63 KKFESEILEAISQN-SVVIIRGATGCGKTTQ--------VPQFI-LDDFIQNDRAAECNIVVTQPRRISA-----VSVAE  127 (235)
T ss_dssp             GGGHHHHHHHHHHC-SEEEEECCTTSSHHHH--------HHHHH-HHHHHHTTCGGGCEEEEEESSHHHH-----HHHHH
T ss_pred             HHHHHHHHHHHhcC-CEEEEEeCCCCCcHHh--------HHHHH-hcchhhcCCCCceEEEEeccchHHH-----HHHHH
Confidence            47999999999999 9999999999999976        34433 22222222  234789999999999     44444


Q ss_pred             hh--cCCCC-ceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccc-
Q psy7952         129 IV--TGRSD-LYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCV-  204 (444)
Q Consensus       129 ~l--~~~~~-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~-  204 (444)
                      .+  ..+.. ...+..-.......           ...+++|+|+||+++..    . +..  .+.++++||+||+|.+ 
T Consensus       128 ~~~~~~~~~~~~~~g~~~~~~~~~-----------~~~~~~Ivv~Tpg~l~~----~-l~~--~l~~~~~lVlDEah~~~  189 (235)
T 3llm_A          128 RVAFERGEEPGKSCGYSVRFESIL-----------PRPHASIMFCTVGVLLR----K-LEA--GIRGISHVIVDEIHERD  189 (235)
T ss_dssp             HHHHTTTCCTTSSEEEEETTEEEC-----------CCSSSEEEEEEHHHHHH----H-HHH--CCTTCCEEEECCTTSCC
T ss_pred             HHHHHhccccCceEEEeechhhcc-----------CCCCCeEEEECHHHHHH----H-HHh--hhcCCcEEEEECCccCC
Confidence            44  11100 02222111111000           02468899999999752    2 222  4789999999999985 


Q ss_pred             cccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhc
Q psy7952         205 SEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLK  251 (444)
Q Consensus       205 ~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~  251 (444)
                      .+.+  +.  ...+..+....+ +.+++++|||++...   +.++++
T Consensus       190 ~~~~--~~--~~~l~~i~~~~~-~~~~il~SAT~~~~~---~~~~~~  228 (235)
T 3llm_A          190 INTD--FL--LVVLRDVVQAYP-EVRIVLMSATIDTSM---FCEYFF  228 (235)
T ss_dssp             HHHH--HH--HHHHHHHHHHCT-TSEEEEEECSSCCHH---HHHHTT
T ss_pred             cchH--HH--HHHHHHHHhhCC-CCeEEEEecCCCHHH---HHHHcC
Confidence            3222  21  233444444444 489999999998765   555553

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.67  E-value=6.3e-16  Score=157.52  Aligned_cols=161  Identities=16%  Similarity=0.165  Sum_probs=99.1

Q ss_pred             cEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCC-CCCceEEEEEc------ccchhhHHHHHHHHHHHhccCCCCCce
Q psy7952         230 PIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTF-RSNLFYDVIFD------DLLKDSYAHVKEFIEKCLGKDNKANNC  302 (444)
Q Consensus       230 ~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~------~~~~~~~~~~~~~l~~~l~~~~~~~~~  302 (444)
                      .+|++|||+.+  .+.+.+.+|+. .......+.. ..+....+...      .........+.+.+.+++..   .++.
T Consensus       377 ~~il~SaTL~p--~~~~~~~lGl~-~~~~~~~spf~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~i~~l~~~---~~g~  450 (620)
T 4a15_A          377 KTIHMSGTLDP--FDFYSDITGFE-IPFKKIGEIFPPENRYIAYYDGVSSKYDTLDEKELDRMATVIEDIILK---VKKN  450 (620)
T ss_dssp             EEEEEESSCCS--HHHHHHHHCCC-CCEEECCCCSCGGGEEEEEECCC-------CHHHHHHHHHHHHHHHHH---HCSC
T ss_pred             eEEEEccCCCc--HHHHHHHhCCC-ceeeecCCCCCHHHeEEEEeCCCCCcCCCCCHHHHHHHHHHHHHHHHh---CCCC
Confidence            35899999987  56778888886 4333333222 22222211110      01112234455555565544   3677


Q ss_pred             EEEEecccchHHHHHHHHHhh-------cCHHHHHHHHHHHhcCCccEEEEc--CccccccccCC--ccEEEEeCCCCC-
Q psy7952         303 GIIYCRTREHTTDLADALRRK-------VNKHERSRVQESFMRGEINVITAT--ISFGMGIDRQN--VRFVVHWGMPSS-  370 (444)
Q Consensus       303 ~iVf~~s~~~~~~l~~~L~~~-------~~~~~r~~~~~~f~~g~~~vLvaT--~~~~~Gidi~~--~~~Vi~~~~p~s-  370 (444)
                      ++||++|....+++++.+...       ++...+..++++|+ ++..||+++  ..+++|||+|+  ++.||..+.|.. 
T Consensus       451 ~lvlF~Sy~~l~~v~~~l~~~~~~~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~l~~viI~~lPfp~  529 (620)
T 4a15_A          451 TIVYFPSYSLMDRVENRVSFEHMKEYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNELEMIILAGLPFPR  529 (620)
T ss_dssp             EEEEESCHHHHHHHTSSCCSCCEECCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CCCCEEEESSCCCCC
T ss_pred             EEEEeCCHHHHHHHHHHHHhcchhccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCceEEEEEEcCCCCC
Confidence            999999999999998877511       23567899999999 888999997  48999999985  778999998752 


Q ss_pred             ----------------------------HHHHHHHhccCCCCCCceeEEEEeccc
Q psy7952         371 ----------------------------IPAYYQESGRAGRDGLQSYCRIYHSEH  397 (444)
Q Consensus       371 ----------------------------~~~~~Qr~GR~~R~g~~g~~~~~~~~~  397 (444)
                                                  ...+.|.+||+-|...+--+++++++.
T Consensus       530 ~~p~~~ar~~~~~~~~g~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~R  584 (620)
T 4a15_A          530 PDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDKR  584 (620)
T ss_dssp             CCHHHHHHHHHHHHHHSCHHHHHTHHHHHHHHHHHHHTTCCSTTCCEEEEEECGG
T ss_pred             CCHHHHHHHHHHHHhhCCCchHHhHHHHHHHHHHHhCccccCCCceEEEEEEccc
Confidence                                        122369999999985544455566543

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.56  E-value=5.2e-15  Score=135.20  Aligned_cols=115  Identities=17%  Similarity=0.211  Sum_probs=83.7

Q ss_pred             hhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----------cCHHHHHHHHHHHhcC-Ccc-EEE
Q psy7952         279 KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----------VNKHERSRVQESFMRG-EIN-VIT  345 (444)
Q Consensus       279 ~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----------~~~~~r~~~~~~f~~g-~~~-vLv  345 (444)
                      ..+...+.+++.....    .+.++||||++...++.+...|...           ++..+|..+++.|++| ..+ +|+
T Consensus        95 s~K~~~L~~ll~~~~~----~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~  170 (271)
T 1z5z_A           95 SGKMIRTMEIIEEALD----EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVL  170 (271)
T ss_dssp             CHHHHHHHHHHHHHHH----TTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEE
T ss_pred             CHHHHHHHHHHHHHHh----CCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEE
Confidence            3455556666655433    4789999999999999999999763           7889999999999988 677 699


Q ss_pred             EcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeE--EEEeccc
Q psy7952         346 ATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYC--RIYHSEH  397 (444)
Q Consensus       346 aT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~--~~~~~~~  397 (444)
                      +|+++++|+|++.+++||++|+|+++..|.||+||++|.|+.+.+  +.++..+
T Consensus       171 st~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~  224 (271)
T 1z5z_A          171 SVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  224 (271)
T ss_dssp             ECCTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETT
T ss_pred             ehhhhcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeCC
Confidence            999999999999999999999999999999999999999987765  3445544

>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=98.51  E-value=6.2e-08  Score=98.58  Aligned_cols=77  Identities=21%  Similarity=0.185  Sum_probs=55.1

Q ss_pred             CCCHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc--CCccce
Q psy7952          30 KVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN--GNVRSR  107 (444)
Q Consensus        30 ~~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~--~~~~~~  107 (444)
                      .+++.++...+...|+... .+++|..++..++.+ +.+++.+|+|||||.++.      +.++.    +..  .+...+
T Consensus       131 ~~~~~~~~~~l~~~~~~~~-~~~~Q~~Ai~~~l~~-~~~vi~G~pGTGKTt~l~------~ll~~----l~~~~~~~~~~  198 (608)
T 1w36_D          131 EVDEALLAQTLDKLFPVSD-EINWQKVAAAVALTR-RISVISGGPGTGKTTTVA------KLLAA----LIQMADGERCR  198 (608)
T ss_dssp             CCCHHHHHHHHHTTCCCTT-SCCHHHHHHHHHHTB-SEEEEECCTTSTHHHHHH------HHHHH----HHHTCSSCCCC
T ss_pred             CCCHHHHHHHHHHHhccCC-CCHHHHHHHHHHhcC-CCEEEEeCCCCCHHHHHH------HHHHH----HHHhhhcCCCe
Confidence            3557778888887765332 257999999999988 899999999999995511      22222    221  123347


Q ss_pred             eEEEcchhhhh
Q psy7952         108 NGWISPILSSF  118 (444)
Q Consensus       108 vlil~P~~~L~  118 (444)
                      +++++||..++
T Consensus       199 vll~APTg~AA  209 (608)
T 1w36_D          199 IRLAAPTGKAA  209 (608)
T ss_dssp             EEEEBSSHHHH
T ss_pred             EEEEeCChhHH
Confidence            79999999999

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.03  E-value=1.8e-06  Score=88.85  Aligned_cols=66  Identities=14%  Similarity=0.021  Sum_probs=47.8

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      ++-|.+|+..++..+.-.+|+||+|||||.+.+         .+ +..+...  ..+||+++||...+     .+.++++
T Consensus       191 N~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~---------~~-I~~l~~~--~~~ILv~a~TN~Av-----D~i~erL  253 (646)
T 4b3f_X          191 DTSQKEAVLFALSQKELAIIHGPPGTGKTTTVV---------EI-ILQAVKQ--GLKVLCCAPSNIAV-----DNLVERL  253 (646)
T ss_dssp             CHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHH---------HH-HHHHHHT--TCCEEEEESSHHHH-----HHHHHHH
T ss_pred             CHHHHHHHHHHhcCCCceEEECCCCCCHHHHHH---------HH-HHHHHhC--CCeEEEEcCchHHH-----HHHHHHH
Confidence            478999999998762457999999999998721         11 1112222  24679999999999     7888877


Q ss_pred             -cCC
Q psy7952         131 -TGR  133 (444)
Q Consensus       131 -~~~  133 (444)
                       ..+
T Consensus       254 ~~~~  257 (646)
T 4b3f_X          254 ALCK  257 (646)
T ss_dssp             HHTT
T ss_pred             HhcC
Confidence             444

>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=97.86  E-value=1.4e-05  Score=81.76  Aligned_cols=66  Identities=17%  Similarity=0.071  Sum_probs=47.2

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      ++.|.+|+..++.+ ...+|.||+|||||.++.         .. +..+... ...++++++||...+     .+..+++
T Consensus       182 n~~Q~~av~~~l~~-~~~li~GppGTGKT~~~~---------~~-i~~l~~~-~~~~ilv~a~tn~A~-----~~l~~~l  244 (624)
T 2gk6_A          182 NHSQVYAVKTVLQR-PLSLIQGPPGTGKTVTSA---------TI-VYHLARQ-GNGPVLVCAPSNIAV-----DQLTEKI  244 (624)
T ss_dssp             CHHHHHHHHHHHTC-SEEEEECCTTSCHHHHHH---------HH-HHHHHTS-SSCCEEEEESSHHHH-----HHHHHHH
T ss_pred             CHHHHHHHHHHhcC-CCeEEECCCCCCHHHHHH---------HH-HHHHHHc-CCCeEEEEeCcHHHH-----HHHHHHH
Confidence            57899999999876 778999999999997721         11 1112221 234679999999998     6666766


Q ss_pred             -cCC
Q psy7952         131 -TGR  133 (444)
Q Consensus       131 -~~~  133 (444)
                       ..+
T Consensus       245 ~~~~  248 (624)
T 2gk6_A          245 HQTG  248 (624)
T ss_dssp             HTTT
T ss_pred             HhcC
Confidence             444

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=97.71  E-value=2.5e-05  Score=81.70  Aligned_cols=66  Identities=18%  Similarity=0.108  Sum_probs=47.5

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      ++.|.+|+..++.+ ...+|.||+|||||.++.-         . +..+... ...++++++||...+     .+..+++
T Consensus       362 n~~Q~~Av~~~l~~-~~~lI~GppGTGKT~~i~~---------~-i~~l~~~-~~~~ILv~a~tn~A~-----d~l~~rL  424 (802)
T 2xzl_A          362 NSSQSNAVSHVLQR-PLSLIQGPPGTGKTVTSAT---------I-VYHLSKI-HKDRILVCAPSNVAV-----DHLAAKL  424 (802)
T ss_dssp             CHHHHHHHHHHTTC-SEEEEECSTTSSHHHHHHH---------H-HHHHHHH-HCCCEEEEESSHHHH-----HHHHHHH
T ss_pred             CHHHHHHHHHHhcC-CCEEEECCCCCCHHHHHHH---------H-HHHHHhC-CCCeEEEEcCcHHHH-----HHHHHHH
Confidence            57999999999876 6789999999999977211         1 1112211 234679999999999     7777776


Q ss_pred             -cCC
Q psy7952         131 -TGR  133 (444)
Q Consensus       131 -~~~  133 (444)
                       ..+
T Consensus       425 ~~~g  428 (802)
T 2xzl_A          425 RDLG  428 (802)
T ss_dssp             HHTT
T ss_pred             HhhC
Confidence             444

>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=97.68  E-value=2.3e-05  Score=81.87  Aligned_cols=66  Identities=17%  Similarity=0.071  Sum_probs=47.4

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      ++.|.+|+..++.+ ...+|.||+|||||.++.         .. +..+... ...++++++||...+     .+..+++
T Consensus       358 n~~Q~~Av~~~l~~-~~~lI~GppGTGKT~ti~---------~~-i~~l~~~-~~~~ilv~a~tn~A~-----~~l~~~l  420 (800)
T 2wjy_A          358 NHSQVYAVKTVLQR-PLSLIQGPPGTGKTVTSA---------TI-VYHLARQ-GNGPVLVCAPSNIAV-----DQLTEKI  420 (800)
T ss_dssp             CHHHHHHHHHHHTS-SEEEEECCTTSCHHHHHH---------HH-HHHHHTT-CSSCEEEEESSHHHH-----HHHHHHH
T ss_pred             CHHHHHHHHHhccC-CeEEEEcCCCCCHHHHHH---------HH-HHHHHHc-CCCcEEEEcCcHHHH-----HHHHHHH
Confidence            57899999999887 778999999999997721         11 1122221 234679999999998     6666766


Q ss_pred             -cCC
Q psy7952         131 -TGR  133 (444)
Q Consensus       131 -~~~  133 (444)
                       ..+
T Consensus       421 ~~~g  424 (800)
T 2wjy_A          421 HQTG  424 (800)
T ss_dssp             HTTT
T ss_pred             HHhC
Confidence             444

>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=97.60  E-value=8.1e-05  Score=73.13  Aligned_cols=62  Identities=16%  Similarity=0.149  Sum_probs=43.3

Q ss_pred             CCcccCchHHHHHHHHHHcc----CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          45 GFDSFKCELQKKAIRHILLR----THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        45 g~~~~~t~~Q~~~~~~~~~~----~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      .+.. .++-|++++..++..    +..++|.|++|||||.++          ..++..+...+. .++++++||...+
T Consensus        22 ~~~~-Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll----------~~~~~~l~~~~~-~~il~~a~T~~Aa   87 (459)
T 3upu_A           22 TFDD-LTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT----------KFIIEALISTGE-TGIILAAPTHAAK   87 (459)
T ss_dssp             CSSC-CCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH----------HHHHHHHHHTTC-CCEEEEESSHHHH
T ss_pred             cccc-CCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH----------HHHHHHHHhcCC-ceEEEecCcHHHH
Confidence            5566 458999999977542    358999999999999772          111222333333 3568999999887

>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=97.55  E-value=4.8e-05  Score=76.59  Aligned_cols=55  Identities=13%  Similarity=0.042  Sum_probs=40.9

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      ++.|.+++..++.+ +.+++.+|+|||||.++.          .++..+...+  .++++++||...+
T Consensus       191 ~~~Q~~Av~~~~~~-~~~~I~G~pGTGKTt~i~----------~l~~~l~~~g--~~Vl~~ApT~~Aa  245 (574)
T 3e1s_A          191 SEEQASVLDQLAGH-RLVVLTGGPGTGKSTTTK----------AVADLAESLG--LEVGLCAPTGKAA  245 (574)
T ss_dssp             CHHHHHHHHHHTTC-SEEEEECCTTSCHHHHHH----------HHHHHHHHTT--CCEEEEESSHHHH
T ss_pred             CHHHHHHHHHHHhC-CEEEEEcCCCCCHHHHHH----------HHHHHHHhcC--CeEEEecCcHHHH
Confidence            58999999999987 889999999999997611          1111122222  4568999999888

>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=97.18  E-value=0.0054  Score=62.91  Aligned_cols=77  Identities=9%  Similarity=-0.060  Sum_probs=49.1

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC-ccceeEEEcchhhhhcccCccchHhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN-VRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~-~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      ++-|.+++..  .+ .+++|.|++|||||.++         +..+...+...+ ...+++++++|+..+     .+..++
T Consensus        11 n~~Q~~av~~--~~-~~~lV~a~aGsGKT~~l---------~~ri~~l~~~~~~~~~~iL~ltft~~aa-----~e~~~r   73 (647)
T 3lfu_A           11 NDKQREAVAA--PR-SNLLVLAGAGSGKTRVL---------VHRIAWLMSVENCSPYSIMAVTFTNKAA-----AEMRHR   73 (647)
T ss_dssp             CHHHHHHHTC--CS-SCEEEEECTTSCHHHHH---------HHHHHHHHHTSCCCGGGEEEEESSHHHH-----HHHHHH
T ss_pred             CHHHHHHHhC--CC-CCEEEEECCCCCHHHHH---------HHHHHHHHHhCCCChhhEEEEeccHHHH-----HHHHHH
Confidence            4789999983  23 68999999999999881         111122222223 234789999999998     666666


Q ss_pred             h-c---CCCCceeEEEEeC
Q psy7952         130 V-T---GRSDLYQLELIVS  144 (444)
Q Consensus       130 l-~---~~~~~i~~~~~~~  144 (444)
                      + .   .....+.+..+++
T Consensus        74 l~~~~~~~~~~~~v~Tfhs   92 (647)
T 3lfu_A           74 IGQLMGTSQGGMWVGTFHG   92 (647)
T ss_dssp             HHHHHCSCCTTCEEEEHHH
T ss_pred             HHHHhccccCCcEEEcHHH
Confidence            5 1   1112355666554

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=96.53  E-value=0.018  Score=53.04  Aligned_cols=16  Identities=0%  Similarity=0.061  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .++++.||||+|||.+
T Consensus        46 ~~lli~GpPGTGKT~~   61 (318)
T 3te6_A           46 KLFYITNADDSTKFQL   61 (318)
T ss_dssp             CEEEEECCCSHHHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            6799999999999977

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=96.50  E-value=0.022  Score=52.31  Aligned_cols=16  Identities=6%  Similarity=-0.103  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .++++.+|+|+|||..
T Consensus        68 ~~vll~G~~GtGKT~l   83 (309)
T 3syl_A           68 LHMSFTGNPGTGKTTV   83 (309)
T ss_dssp             CEEEEEECTTSSHHHH
T ss_pred             ceEEEECCCCCCHHHH
Confidence            4699999999999977

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=96.49  E-value=0.0036  Score=60.13  Aligned_cols=42  Identities=10%  Similarity=-0.035  Sum_probs=29.6

Q ss_pred             cEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh
Q psy7952          67 DIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        67 ~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      -.++.|++|+|||..        +     .+ +....   +.++++||++++     .+..+.+
T Consensus       163 v~~I~G~aGsGKTt~--------I-----~~-~~~~~---~~lVlTpT~~aa-----~~l~~kl  204 (446)
T 3vkw_A          163 VVLVDGVPGCGKTKE--------I-----LS-RVNFE---EDLILVPGRQAA-----EMIRRRA  204 (446)
T ss_dssp             EEEEEECTTSCHHHH--------H-----HH-HCCTT---TCEEEESCHHHH-----HHHHHHH
T ss_pred             EEEEEcCCCCCHHHH--------H-----HH-HhccC---CeEEEeCCHHHH-----HHHHHHh
Confidence            468999999999977        1     11 12223   449999999999     5555555

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=96.26  E-value=0.033  Score=44.73  Aligned_cols=19  Identities=21%  Similarity=0.198  Sum_probs=16.4

Q ss_pred             ccCCcEEEEccCCCccccc
Q psy7952          63 LRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        63 ~~~~~~ii~apTGsGKT~~   81 (444)
                      ....++++.+|+|+|||..
T Consensus        25 ~~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           25 KRTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             TCSSCEEEEEETTCCHHHH
T ss_pred             CCCCcEEEECCCCccHHHH
Confidence            3448899999999999977

>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=96.04  E-value=0.0068  Score=50.89  Aligned_cols=29  Identities=14%  Similarity=-0.042  Sum_probs=21.8

Q ss_pred             hHHHHHHHHHH---------ccCCcEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHIL---------LRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~---------~~~~~~ii~apTGsGKT~~   81 (444)
                      +.|.+++..+.         .+ +.+++.+|+|+|||..
T Consensus        17 ~~~~~~~~~~~~~~~~~~~~~g-~~~~l~G~~G~GKTtL   54 (180)
T 3ec2_A           17 VSQNRALLTIRVFVHNFNPEEG-KGLTFVGSPGVGKTHL   54 (180)
T ss_dssp             HHHHHHHHHHHHHHHSCCGGGC-CEEEECCSSSSSHHHH
T ss_pred             HHHHHHHHHHHHHHHhccccCC-CEEEEECCCCCCHHHH
Confidence            45666665554         24 7899999999999977

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=96.01  E-value=0.048  Score=49.90  Aligned_cols=117  Identities=8%  Similarity=-0.085  Sum_probs=74.3

Q ss_pred             HHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh---------cCHHHHHHHHHHHhcCCccEEEEcCccccccc--
Q psy7952         287 EFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK---------VNKHERSRVQESFMRGEINVITATISFGMGID--  355 (444)
Q Consensus       287 ~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~---------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gid--  355 (444)
                      .++.+++......+++++||++.....+-+.+.+...         .....+    .+-..+...+-+.|...+-|+|  
T Consensus       112 ~~L~~LL~~l~~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~~----~k~~~~~~~i~Lltsag~~gin~~  187 (328)
T 3hgt_A          112 SVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSA----AAANDFSCTVHLFSSEGINFTKYP  187 (328)
T ss_dssp             HHHHHHHHHHTTSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC-----------CCSEEEEEEESSCCCTTTSC
T ss_pred             HHHHHHHHHHHhCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhhh----hhcccCCceEEEEECCCCCCcCcc
Confidence            3444444444446899999999999998888888766         111111    1112445556444666666776  


Q ss_pred             ---cCCccEEEEeCCCCCHHHH-HHHhccCCCCC----CceeEEEEecccchhhHHHHHh
Q psy7952         356 ---RQNVRFVVHWGMPSSIPAY-YQESGRAGRDG----LQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       356 ---i~~~~~Vi~~~~p~s~~~~-~Qr~GR~~R~g----~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                         ....++||.||..+++..- +|.+-|+.|.|    +.-.++-++.....++..--..
T Consensus       188 ~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~TiEh~~l~~~  247 (328)
T 3hgt_A          188 IKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSIDHCRLFFG  247 (328)
T ss_dssp             CCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETTSHHHHHHHHH
T ss_pred             cccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCCCHHHHHHHcc
Confidence               6789999999999998885 89888888763    3445666777776666554443

>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=95.75  E-value=0.013  Score=54.43  Aligned_cols=16  Identities=19%  Similarity=0.125  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.||+|+|||..
T Consensus        38 ~~lll~G~~GtGKT~l   53 (324)
T 1l8q_A           38 NPIFIYGSVGTGKTHL   53 (324)
T ss_dssp             SSEEEECSSSSSHHHH
T ss_pred             CeEEEECCCCCcHHHH
Confidence            5899999999999977

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.54  E-value=0.043  Score=51.99  Aligned_cols=16  Identities=13%  Similarity=0.189  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus       183 rGvLL~GPPGTGKTll  198 (405)
T 4b4t_J          183 KGVILYGPPGTGKTLL  198 (405)
T ss_dssp             CCEEEESCSSSSHHHH
T ss_pred             CceEEeCCCCCCHHHH
Confidence            7899999999999977

>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=95.52  E-value=0.13  Score=48.53  Aligned_cols=58  Identities=7%  Similarity=-0.049  Sum_probs=39.5

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      +++||...+..+... +-+++..+-+.|||.++...++.        ..+.  ....+++++.|+..-+
T Consensus       164 L~p~Qk~il~~l~~~-R~~vi~~sRq~GKT~l~a~~~l~--------~a~~--~~g~~v~~vA~t~~qA  221 (385)
T 2o0j_A          164 LRDYQRDMLKIMSSK-RMTVCNLSRQLGKTTVVAIFLAH--------FVCF--NKDKAVGILAHKGSMS  221 (385)
T ss_dssp             CCHHHHHHHHHHHHS-SEEEEEECSSSCHHHHHHHHHHH--------HHHS--SSSCEEEEEESSHHHH
T ss_pred             CCHHHHHHHHhhccC-cEEEEEEcCcCChhHHHHHHHHH--------HHHh--CCCCeEEEEeCCHHHH
Confidence            368999999877544 66899999999999873322111        0011  2233569999999887

>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=95.51  E-value=0.019  Score=51.44  Aligned_cols=23  Identities=9%  Similarity=0.053  Sum_probs=17.8

Q ss_pred             HHHHccCCcEEEEccCCCccccc
Q psy7952          59 RHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        59 ~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      ..+.....++++.+|+|+|||..
T Consensus        23 ~~~~~~~~~vll~G~~GtGKt~l   45 (265)
T 2bjv_A           23 SHLAPLDKPVLIIGERGTGKELI   45 (265)
T ss_dssp             HHHTTSCSCEEEECCTTSCHHHH
T ss_pred             HHHhCCCCCEEEECCCCCcHHHH
Confidence            33334447899999999999977

>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=95.09  E-value=0.059  Score=52.24  Aligned_cols=16  Identities=13%  Similarity=0.021  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +++++.||+|+|||..
T Consensus       131 ~~lll~Gp~G~GKTtL  146 (440)
T 2z4s_A          131 NPLFIYGGVGLGKTHL  146 (440)
T ss_dssp             CCEEEECSSSSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            5799999999999977

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.03  E-value=0.054  Score=52.09  Aligned_cols=16  Identities=13%  Similarity=0.210  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++++|+|+|||..
T Consensus       216 rGvLL~GPPGtGKTll  231 (437)
T 4b4t_L          216 KGVLLYGPPGTGKTLL  231 (437)
T ss_dssp             CEEEEESCTTSSHHHH
T ss_pred             CeEEEECCCCCcHHHH
Confidence            7899999999999977

>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=94.83  E-value=0.038  Score=48.35  Aligned_cols=16  Identities=13%  Similarity=0.031  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus        53 ~~~ll~G~~G~GKT~l   68 (242)
T 3bos_A           53 QAIYLWGPVKSGRTHL   68 (242)
T ss_dssp             SEEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            7899999999999977

>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=94.79  E-value=0.061  Score=49.75  Aligned_cols=16  Identities=19%  Similarity=0.135  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus        52 ~~vLl~GppGtGKT~l   67 (322)
T 3eie_A           52 SGILLYGPPGTGKSYL   67 (322)
T ss_dssp             CEEEEECSSSSCHHHH
T ss_pred             CeEEEECCCCCcHHHH
Confidence            5799999999999977

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=94.76  E-value=0.014  Score=54.20  Aligned_cols=165  Identities=12%  Similarity=0.014  Sum_probs=78.8

Q ss_pred             CcccCchHHHHHHHHHHcc---CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcch---hhhhc
Q psy7952          46 FDSFKCELQKKAIRHILLR---THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPI---LSSFY  119 (444)
Q Consensus        46 ~~~~~t~~Q~~~~~~~~~~---~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~---~~L~~  119 (444)
                      ...+||.+.  .+..+..|   ..-+++.|++|+|||..|+..+.         .....+.   +|+|++.-   ..++ 
T Consensus        26 ~~gi~TG~~--~LD~~~gGl~~G~LiiIaG~pG~GKTt~al~ia~---------~~a~~g~---~Vl~fSlEms~~ql~-   90 (338)
T 4a1f_A           26 VTGIPTGFV--QLDNYTSGFNKGSLVIIGARPSMGKTSLMMNMVL---------SALNDDR---GVAVFSLEMSAEQLA-   90 (338)
T ss_dssp             CCSBCCSCH--HHHHHHCSBCTTCEEEEEECTTSCHHHHHHHHHH---------HHHHTTC---EEEEEESSSCHHHHH-
T ss_pred             cCcccCCCh--HHHHHhcCCCCCcEEEEEeCCCCCHHHHHHHHHH---------HHHHcCC---eEEEEeCCCCHHHHH-
Confidence            344555443  55555543   15589999999999976332111         1112222   34777642   2333 


Q ss_pred             ccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEE-CCCccccccHHHHHHHHHhhC-CccEE
Q psy7952         120 LRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYV-TPERAVTESFHYLLQHLVRYN-KLAYI  196 (444)
Q Consensus       120 ~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~-Tpe~l~~~~~~~~~~~~~~~~-~~~~i  196 (444)
                          ...+... ......+    ..+..+..++..+......+. ...+.|- +|.. .-.............. .+++|
T Consensus        91 ----~Rlls~~~~v~~~~l----~~g~Ls~~e~~~l~~a~~~l~-~~~l~I~d~~~~-si~~i~~~ir~l~~~~gg~~lI  160 (338)
T 4a1f_A           91 ----LRALSDLTSINMHDL----ESGRLDDDQWENLAKCFDHLS-QKKLFFYDKSYV-RIEQIRLQLRKLKSQHKELGIA  160 (338)
T ss_dssp             ----HHHHHHHHCCCHHHH----HHTCCCHHHHHHHHHHHHHHH-HSCEEEECCTTC-CHHHHHHHHHHHHHHCTTEEEE
T ss_pred             ----HHHHHHhhCCCHHHH----hcCCCCHHHHHHHHHHHHHHh-cCCeEEeCCCCC-cHHHHHHHHHHHHHhcCCCCEE
Confidence                2222211 1110001    123344444433332222222 2345553 3431 1111222333333344 79999


Q ss_pred             EEeccccccccC------CCcHHHHHHHHHHHHhhCCCCcEEEEecc
Q psy7952         197 VVDEAHCVSEWG------HDFRPTYRRLGELRQFTGNSIPIIALTAT  237 (444)
Q Consensus       197 ViDE~H~~~~~~------~~~~~~~~~l~~~~~~~~~~~~~v~lSAT  237 (444)
                      |||-.+.+...+      .........|+.+.+.+.  ++++++|-.
T Consensus       161 VIDyLqlm~~~~~~~~r~~ei~~isr~LK~lAkel~--vpVi~lsQl  205 (338)
T 4a1f_A          161 FIDYLQLMSGSKATKERHEQIAEISRELKTLARELE--IPIIALVQL  205 (338)
T ss_dssp             EEEEEECCCTHHHHHHCCCCHHHHHHHHHHHHHHHT--SCEEEEEEC
T ss_pred             EEechHHhcCCCCCCChHHHHHHHHHHHHHHHHHcC--CeEEEEEec
Confidence            999999885311      234455555666555554  778887754

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=94.68  E-value=0.033  Score=54.14  Aligned_cols=129  Identities=9%  Similarity=-0.004  Sum_probs=60.0

Q ss_pred             HHHHHHcc---CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcch---hhhhcccCccchHhhh
Q psy7952          57 AIRHILLR---THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPI---LSSFYLRFRDDKTSIV  130 (444)
Q Consensus        57 ~~~~~~~~---~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~---~~L~~~~q~~~~~~~l  130 (444)
                      .+..++.|   ..-+++.|++|+|||..|+..+.         ......+  .+|+++...   ..+.     .......
T Consensus       189 ~LD~~lgGl~~G~l~ii~G~pg~GKT~lal~ia~---------~~a~~~g--~~vl~~slE~~~~~l~-----~R~~~~~  252 (444)
T 2q6t_A          189 ELDQLIGTLGPGSLNIIAARPAMGKTAFALTIAQ---------NAALKEG--VGVGIYSLEMPAAQLT-----LRMMCSE  252 (444)
T ss_dssp             HHHHHHCCCCTTCEEEEEECTTSCHHHHHHHHHH---------HHHHTTC--CCEEEEESSSCHHHHH-----HHHHHHH
T ss_pred             hhhhhcCCcCCCcEEEEEeCCCCCHHHHHHHHHH---------HHHHhCC--CeEEEEECCCCHHHHH-----HHHHHHH
Confidence            45555532   15589999999999976332111         1111112  234776542   2333     2222111


Q ss_pred             -cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccc
Q psy7952         131 -TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSE  206 (444)
Q Consensus       131 -~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~  206 (444)
                       ......+.    .+.....++......+..+. ...+.+-.+..+....+............+++||||..+.+..
T Consensus       253 ~~i~~~~l~----~g~l~~~~~~~~~~a~~~l~-~~~l~i~d~~~~s~~~l~~~~~~l~~~~~~~lIvID~l~~~~~  324 (444)
T 2q6t_A          253 ARIDMNRVR----LGQLTDRDFSRLVDVASRLS-EAPIYIDDTPDLTLMEVRARARRLVSQNQVGLIIIDYLQLMSG  324 (444)
T ss_dssp             TTCCTTTCC----GGGCCHHHHHHHHHHHHHHH-TSCEEEECCTTCBHHHHHHHHHHHHHHSCCCEEEEECGGGCBC
T ss_pred             cCCCHHHHh----CCCCCHHHHHHHHHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEcChhhcCC
Confidence             11111111    23344444433333332222 2345554433222111222333344445799999999999864

>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=94.64  E-value=0.029  Score=52.22  Aligned_cols=31  Identities=6%  Similarity=0.079  Sum_probs=23.1

Q ss_pred             hHHHHHHHHHHc----cC--CcEEEEccCCCcccccc
Q psy7952          52 ELQKKAIRHILL----RT--HDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        52 ~~Q~~~~~~~~~----~~--~~~ii~apTGsGKT~~a   82 (444)
                      |||.+++..+..    |+  +.+++.||+|+|||..|
T Consensus         5 pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a   41 (334)
T 1a5t_A            5 PWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALI   41 (334)
T ss_dssp             GGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHH
T ss_pred             CchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHH
Confidence            588887766553    32  34899999999999773

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=94.61  E-value=0.048  Score=49.34  Aligned_cols=16  Identities=19%  Similarity=0.229  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus        52 ~~~ll~G~~GtGKT~l   67 (285)
T 3h4m_A           52 KGILLYGPPGTGKTLL   67 (285)
T ss_dssp             SEEEEESSSSSSHHHH
T ss_pred             CeEEEECCCCCcHHHH
Confidence            7899999999999977

>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=94.54  E-value=0.018  Score=50.10  Aligned_cols=16  Identities=19%  Similarity=-0.002  Sum_probs=13.9

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .-+++.+|+|+|||..
T Consensus        13 ~i~litG~mGsGKTT~   28 (223)
T 2b8t_A           13 WIEFITGPMFAGKTAE   28 (223)
T ss_dssp             EEEEEECSTTSCHHHH
T ss_pred             EEEEEECCCCCcHHHH
Confidence            4578899999999987

>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=94.50  E-value=0.27  Score=41.90  Aligned_cols=40  Identities=18%  Similarity=0.134  Sum_probs=24.3

Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEecc
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTAT  237 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT  237 (444)
                      .-.+||+||+|.+...      ....+..++...+.+..+|+.|..
T Consensus       102 ~~~vliiDe~~~l~~~------~~~~l~~~l~~~~~~~~~i~~~~~  141 (226)
T 2chg_A          102 PFKIIFLDEADALTAD------AQAALRRTMEMYSKSCRFILSCNY  141 (226)
T ss_dssp             SCEEEEEETGGGSCHH------HHHHHHHHHHHTTTTEEEEEEESC
T ss_pred             CceEEEEeChhhcCHH------HHHHHHHHHHhcCCCCeEEEEeCC
Confidence            4679999999997432      234455555555554556655543

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.41  E-value=0.11  Score=49.48  Aligned_cols=16  Identities=6%  Similarity=0.038  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus       217 rGvLLyGPPGTGKTlL  232 (437)
T 4b4t_I          217 KGVILYGAPGTGKTLL  232 (437)
T ss_dssp             SEEEEESSTTTTHHHH
T ss_pred             CCCceECCCCchHHHH
Confidence            6799999999999977

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.37  E-value=0.048  Score=52.41  Aligned_cols=16  Identities=13%  Similarity=0.125  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.++++||+|+|||..
T Consensus       216 rGvLLyGPPGTGKTll  231 (434)
T 4b4t_M          216 KGALMYGPPGTGKTLL  231 (434)
T ss_dssp             CEEEEESCTTSSHHHH
T ss_pred             CeeEEECcCCCCHHHH
Confidence            6899999999999977

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=94.23  E-value=0.068  Score=43.20  Aligned_cols=18  Identities=22%  Similarity=-0.068  Sum_probs=15.8

Q ss_pred             ccCCcEEEEccCCCccccc
Q psy7952          63 LRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        63 ~~~~~~ii~apTGsGKT~~   81 (444)
                      .+ +.+.+.+|+|+|||..
T Consensus        35 ~g-~~~~l~G~~G~GKTtL   52 (149)
T 2kjq_A           35 HG-QFIYVWGEEGAGKSHL   52 (149)
T ss_dssp             CC-SEEEEESSSTTTTCHH
T ss_pred             CC-CEEEEECCCCCCHHHH
Confidence            45 7899999999999966

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=94.16  E-value=0.028  Score=54.81  Aligned_cols=33  Identities=6%  Similarity=0.009  Sum_probs=22.5

Q ss_pred             ccCchHHHHHHHHHHcc---CCcEEEEccCCCcccccc
Q psy7952          48 SFKCELQKKAIRHILLR---THDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        48 ~~~t~~Q~~~~~~~~~~---~~~~ii~apTGsGKT~~a   82 (444)
                      .++|.+.  .++.+..|   ..-+++.|++|+|||..+
T Consensus       185 ~i~tG~~--~LD~~~gGl~~G~liiI~G~pG~GKTtl~  220 (454)
T 2r6a_A          185 GIPTGFT--ELDRMTSGFQRSDLIIVAARPSVGKTAFA  220 (454)
T ss_dssp             SBCCSCH--HHHHHHSSBCTTCEEEEECCTTSCHHHHH
T ss_pred             CCCCCcH--HHHhhcCCCCCCCEEEEECCCCCCHHHHH
Confidence            4455443  56666632   156899999999999773

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.13  E-value=0.11  Score=49.88  Aligned_cols=16  Identities=13%  Similarity=0.206  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.++++||+|+|||..
T Consensus       207 rGiLL~GPPGtGKT~l  222 (428)
T 4b4t_K          207 RGVLLYGPPGTGKTML  222 (428)
T ss_dssp             CEEEEESCTTTTHHHH
T ss_pred             ceEEEECCCCCCHHHH
Confidence            6799999999999977

>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=94.05  E-value=0.2  Score=50.52  Aligned_cols=58  Identities=9%  Similarity=0.006  Sum_probs=39.8

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      ++++|...+..+... +.+++..+-|+|||.++...++         ..+.. ....+++++.|+...+
T Consensus       164 l~p~Q~~i~~~l~~~-r~~~i~~~Rq~GKS~~~a~~~l---------~~~~~-~~~~~i~~va~t~~qA  221 (592)
T 3cpe_A          164 LRDYQRDMLKIMSSK-RMTVCNLSRQLGKTTVVAIFLA---------HFVCF-NKDKAVGILAHKGSMS  221 (592)
T ss_dssp             CCHHHHHHHHHHHHC-SEEEEEECSSSCHHHHHHHHHH---------HHHHT-SSSCEEEEEESSHHHH
T ss_pred             CCHHHHHHHHhhccc-cEEEEEEcCccChHHHHHHHHH---------HHHHh-CCCCeEEEEECCHHHH
Confidence            368999999887444 6789999999999987322111         01111 1233679999999988

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.98  E-value=0.12  Score=49.67  Aligned_cols=17  Identities=18%  Similarity=0.264  Sum_probs=15.3

Q ss_pred             CCcEEEEccCCCccccc
Q psy7952          65 THDIFVSMPTGAVSLVG   81 (444)
Q Consensus        65 ~~~~ii~apTGsGKT~~   81 (444)
                      .+.+++++|+|+|||+.
T Consensus       243 prGILLyGPPGTGKTlL  259 (467)
T 4b4t_H          243 PKGILLYGPPGTGKTLC  259 (467)
T ss_dssp             CSEEEECSCTTSSHHHH
T ss_pred             CCceEeeCCCCCcHHHH
Confidence            37899999999999977

>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=93.82  E-value=0.064  Score=52.68  Aligned_cols=49  Identities=22%  Similarity=0.188  Sum_probs=28.3

Q ss_pred             CccEEEEeccccccccC-----CCcHHHHHHHHHHHHhhCCCCcEEEEeccCCc
Q psy7952         192 KLAYIVVDEAHCVSEWG-----HDFRPTYRRLGELRQFTGNSIPIIALTATAEP  240 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~  240 (444)
                      ...+|++||+|.+....     ..-......+...++.......++.+.||-.+
T Consensus       297 ~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~  350 (489)
T 3hu3_A          297 APAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRP  350 (489)
T ss_dssp             CSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCG
T ss_pred             CCcEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecCCc
Confidence            45799999999885421     10122334455555555554567777777443

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=93.58  E-value=0.11  Score=49.30  Aligned_cols=16  Identities=13%  Similarity=0.162  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +++++.+|+|+|||.+
T Consensus       149 ~~vLL~GppGtGKT~l  164 (389)
T 3vfd_A          149 RGLLLFGPPGNGKTML  164 (389)
T ss_dssp             SEEEEESSTTSCHHHH
T ss_pred             ceEEEECCCCCCHHHH
Confidence            6899999999999977

>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=93.49  E-value=0.094  Score=46.59  Aligned_cols=16  Identities=13%  Similarity=0.123  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++++|+|+|||..
T Consensus        40 ~~vll~G~~GtGKT~l   55 (262)
T 2qz4_A           40 KGALLLGPPGCGKTLL   55 (262)
T ss_dssp             CEEEEESCTTSSHHHH
T ss_pred             ceEEEECCCCCCHHHH
Confidence            6799999999999977

>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=93.38  E-value=0.14  Score=49.25  Aligned_cols=52  Identities=17%  Similarity=0.126  Sum_probs=29.4

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHH
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQ  244 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~  244 (444)
                      ...+++|+|++.+.... . -...+..+..+.....+..-++.++|+......+
T Consensus       178 ~~~DvvIIDTaGr~~~~-~-d~~lm~el~~i~~~~~pd~vlLVlDa~~gq~a~~  229 (433)
T 3kl4_A          178 NKMDIIIVDTAGRHGYG-E-ETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYD  229 (433)
T ss_dssp             TTCSEEEEEECCCSSSC-C-TTHHHHHHHHHHHHHCCSEEEEEEEGGGGGGGHH
T ss_pred             cCCCEEEEECCCCcccc-C-CHHHHHHHHHHHHhhCCcceEEEEeCccchHHHH
Confidence            36889999999764300 0 1223344444444444445567788876554433

>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=93.37  E-value=0.72  Score=37.99  Aligned_cols=120  Identities=8%  Similarity=0.099  Sum_probs=73.1

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||+|+++.-+     ....+.+ ..+   +.+..++|+.+..++......++  .+..+|+|+| +.+.        
T Consensus        32 ~~~lVF~~~~~~~-----~~l~~~L~~~~---~~~~~~hg~~~~~~r~~~~~~f~--~g~~~vLvaT-~~~~--------   92 (172)
T 1t5i_A           32 NQVVIFVKSVQRC-----IALAQLLVEQN---FPAIAIHRGMPQEERLSRYQQFK--DFQRRILVAT-NLFG--------   92 (172)
T ss_dssp             SSEEEECSSHHHH-----HHHHHHHHHTT---CCEEEECTTSCHHHHHHHHHHHH--TTSCSEEEES-SCCS--------
T ss_pred             CcEEEEECCHHHH-----HHHHHHHHhcC---CCEEEEECCCCHHHHHHHHHHHH--CCCCcEEEEC-Cchh--------
Confidence            4679999999998     5666666 667   88999999999988888888776  4788999999 3322        


Q ss_pred             HHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhc
Q psy7952         185 QHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLK  251 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~  251 (444)
                       .-.++..+++||.-+...      ......+.+.+..+......-+++++..-.....+.+.+.++
T Consensus        93 -~Gldi~~~~~Vi~~d~p~------~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~l~~~~~  152 (172)
T 1t5i_A           93 -RGMDIERVNIAFNYDMPE------DSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFE  152 (172)
T ss_dssp             -TTCCGGGCSEEEESSCCS------SHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHC
T ss_pred             -cCcchhhCCEEEEECCCC------CHHHHHHHhcccccCCCCcEEEEEEcChhHHHHHHHHHHHHh
Confidence             223445677777533321      144444555554443333223334433212223344444443

>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=93.37  E-value=0.099  Score=47.78  Aligned_cols=16  Identities=13%  Similarity=0.173  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus        50 ~~vLL~Gp~GtGKT~l   65 (301)
T 3cf0_A           50 KGVLFYGPPGCGKTLL   65 (301)
T ss_dssp             SEEEEECSSSSSHHHH
T ss_pred             ceEEEECCCCcCHHHH
Confidence            6799999999999977

>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=93.34  E-value=0.12  Score=48.59  Aligned_cols=16  Identities=19%  Similarity=0.135  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus        85 ~~iLL~GppGtGKT~l  100 (355)
T 2qp9_X           85 SGILLYGPPGTGKSYL  100 (355)
T ss_dssp             CCEEEECSTTSCHHHH
T ss_pred             ceEEEECCCCCcHHHH
Confidence            5799999999999977

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=93.33  E-value=0.045  Score=46.09  Aligned_cols=16  Identities=6%  Similarity=-0.081  Sum_probs=14.0

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .-.++.+|+|+|||..
T Consensus         4 ~i~vi~G~~gsGKTT~   19 (184)
T 2orw_A            4 KLTVITGPMYSGKTTE   19 (184)
T ss_dssp             CEEEEEESTTSSHHHH
T ss_pred             EEEEEECCCCCCHHHH
Confidence            4578999999999977

>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=93.33  E-value=0.11  Score=47.85  Aligned_cols=40  Identities=15%  Similarity=0.207  Sum_probs=24.7

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEec
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTA  236 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSA  236 (444)
                      ....++|+||+|.+...      ....+.+.+...+.+..+|+.|.
T Consensus       109 ~~~~vliiDe~~~l~~~------~~~~L~~~le~~~~~~~~i~~~~  148 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQD------AQQALRRTMEMFSSNVRFILSCN  148 (327)
T ss_dssp             CSCEEEEEETGGGSCHH------HHHHHHHHHHHTTTTEEEEEEES
T ss_pred             CCCeEEEEeCCCcCCHH------HHHHHHHHHHhcCCCCeEEEEeC
Confidence            35679999999997532      23445555555555555665543

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=93.32  E-value=0.041  Score=50.80  Aligned_cols=33  Identities=0%  Similarity=0.002  Sum_probs=22.4

Q ss_pred             ccCchHHHHHHHHHHcc---CCcEEEEccCCCcccccc
Q psy7952          48 SFKCELQKKAIRHILLR---THDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        48 ~~~t~~Q~~~~~~~~~~---~~~~ii~apTGsGKT~~a   82 (444)
                      .++|.+.  .+..++.|   ..-+++.|++|+|||..|
T Consensus        50 ~i~TG~~--~LD~~lgGl~~G~l~li~G~pG~GKTtl~   85 (315)
T 3bh0_A           50 GVPSGFT--ELDRMTYGYKRRNFVLIAARPSMGKTAFA   85 (315)
T ss_dssp             SBCCSCH--HHHHHHSSBCTTCEEEEECCTTSSHHHHH
T ss_pred             CccCChH--HHHhhcCCCCCCcEEEEEeCCCCCHHHHH
Confidence            4555443  56666632   156899999999999663

>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=93.26  E-value=0.054  Score=55.46  Aligned_cols=60  Identities=15%  Similarity=-0.036  Sum_probs=41.7

Q ss_pred             CchHHHHHHHHHHc----cCCcEEEEccCCCcccccccccccceEEeCCCcccccc-CCccceeEEEcchhhhhcccCcc
Q psy7952          50 KCELQKKAIRHILL----RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN-GNVRSRNGWISPILSSFYLRFRD  124 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~----~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~-~~~~~~vlil~P~~~L~~~~q~~  124 (444)
                      |+.+|..++..+..    |.+...+.+.||+|||+++          ..   .+.. .++   +||++|+..++     .
T Consensus        13 p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~----------a~---~~~~~~~~---~lvv~~~~~~A-----~   71 (661)
T 2d7d_A           13 PQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTV----------SN---LIKEVNKP---TLVIAHNKTLA-----G   71 (661)
T ss_dssp             CCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH----------HH---HHHHHCCC---EEEECSSHHHH-----H
T ss_pred             CCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHH----------HH---HHHHhCCC---EEEEECCHHHH-----H
Confidence            57899988886654    3235778899999999881          11   1111 234   49999999999     5


Q ss_pred             chHhhh
Q psy7952         125 DKTSIV  130 (444)
Q Consensus       125 ~~~~~l  130 (444)
                      +....+
T Consensus        72 ~l~~el   77 (661)
T 2d7d_A           72 QLYSEF   77 (661)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            666666

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=93.26  E-value=0.099  Score=52.85  Aligned_cols=54  Identities=13%  Similarity=0.007  Sum_probs=38.9

Q ss_pred             CchHHHHHHHHHHccC-CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          50 KCELQKKAIRHILLRT-HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~-~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      +|.-|.+++..+.+-. ...++.|+-|.|||.++.+++..          +.  +   +++|.+|+.+-+
T Consensus       176 ~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a~----------~~--~---~~~vtAP~~~a~  230 (671)
T 2zpa_A          176 PQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLISR----------IA--G---RAIVTAPAKAST  230 (671)
T ss_dssp             CCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHHH----------SS--S---CEEEECSSCCSC
T ss_pred             CCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHHH----------HH--h---CcEEECCCHHHH
Confidence            5788999999988731 35799999999999774433221          21  1   348889999887

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=93.19  E-value=0.11  Score=47.93  Aligned_cols=16  Identities=19%  Similarity=0.133  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus        46 ~~iLL~GppGtGKT~l   61 (322)
T 1xwi_A           46 RGILLFGPPGTGKSYL   61 (322)
T ss_dssp             SEEEEESSSSSCHHHH
T ss_pred             ceEEEECCCCccHHHH
Confidence            6799999999999977

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=92.93  E-value=0.45  Score=44.69  Aligned_cols=16  Identities=13%  Similarity=-0.012  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.||+|+|||..
T Consensus        45 ~~vll~G~~G~GKT~l   60 (387)
T 2v1u_A           45 SNALLYGLTGTGKTAV   60 (387)
T ss_dssp             CCEEECBCTTSSHHHH
T ss_pred             CcEEEECCCCCCHHHH
Confidence            6799999999999977

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=92.92  E-value=0.26  Score=47.71  Aligned_cols=16  Identities=19%  Similarity=0.231  Sum_probs=14.5

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .++++++|+|+|||..
T Consensus        51 ~~vLL~GppGtGKTtl   66 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTL   66 (447)
T ss_dssp             CEEEEECSTTSSHHHH
T ss_pred             cEEEEECCCCCcHHHH
Confidence            4699999999999977

>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=92.90  E-value=0.28  Score=50.97  Aligned_cols=46  Identities=24%  Similarity=0.199  Sum_probs=27.4

Q ss_pred             CccEEEEecccccccc-----CCCcHHHHHHHHHHHHhhCCCCcEEEEecc
Q psy7952         192 KLAYIVVDEAHCVSEW-----GHDFRPTYRRLGELRQFTGNSIPIIALTAT  237 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~-----~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT  237 (444)
                      ...+|+|||+|.+...     +..-+.....+...+..+..+.+++.+-||
T Consensus       297 ~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~VIaaT  347 (806)
T 3cf2_A          297 APAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAAT  347 (806)
T ss_dssp             CSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEEEEEEC
T ss_pred             CCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhcccccCCEEEEEec
Confidence            4678999999998531     111233444555555555544566666666

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=92.89  E-value=0.32  Score=44.06  Aligned_cols=16  Identities=13%  Similarity=0.167  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.||+|+|||..
T Consensus        55 ~~vll~Gp~GtGKT~l   70 (297)
T 3b9p_A           55 KGLLLFGPPGNGKTLL   70 (297)
T ss_dssp             SEEEEESSSSSCHHHH
T ss_pred             CeEEEECcCCCCHHHH
Confidence            7899999999999977

>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=92.87  E-value=0.33  Score=46.63  Aligned_cols=15  Identities=7%  Similarity=-0.051  Sum_probs=13.5

Q ss_pred             cEEEEccCCCccccc
Q psy7952          67 DIFVSMPTGAVSLVG   81 (444)
Q Consensus        67 ~~ii~apTGsGKT~~   81 (444)
                      -+++++++|+|||.+
T Consensus       102 vIlivG~~G~GKTTt  116 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTT  116 (443)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECcCCCCHHHH
Confidence            478999999999977

>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=92.52  E-value=0.45  Score=44.82  Aligned_cols=15  Identities=13%  Similarity=-0.062  Sum_probs=14.0

Q ss_pred             cEEEEccCCCccccc
Q psy7952          67 DIFVSMPTGAVSLVG   81 (444)
Q Consensus        67 ~~ii~apTGsGKT~~   81 (444)
                      .+++.||+|+|||..
T Consensus        46 ~~li~G~~G~GKTtl   60 (389)
T 1fnn_A           46 RATLLGRPGTGKTVT   60 (389)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             eEEEECCCCCCHHHH
Confidence            699999999999977

>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=92.50  E-value=0.15  Score=47.78  Aligned_cols=16  Identities=19%  Similarity=0.208  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus       118 ~~vLl~GppGtGKT~l  133 (357)
T 3d8b_A          118 KGILLFGPPGTGKTLI  133 (357)
T ss_dssp             SEEEEESSTTSSHHHH
T ss_pred             ceEEEECCCCCCHHHH
Confidence            6799999999999977

>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=92.48  E-value=0.032  Score=57.91  Aligned_cols=64  Identities=11%  Similarity=-0.034  Sum_probs=42.9

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC-ccceeEEEcchhhhhcccCccchHh
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN-VRSRNGWISPILSSFYLRFRDDKTS  128 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~-~~~~vlil~P~~~L~~~~q~~~~~~  128 (444)
                      .++-|++++..  .+ .+++|.|+.|||||.+        .. ..+...+...+ ...++|+++.|+..+     .+.-+
T Consensus        12 Ln~~Q~~av~~--~~-g~~lV~AgAGSGKT~v--------L~-~ri~~ll~~~~~~p~~IL~vTFTnkAA-----~Em~~   74 (724)
T 1pjr_A           12 LNKEQQEAVRT--TE-GPLLIMAGAGSGKTRV--------LT-HRIAYLMAEKHVAPWNILAITFTNKAA-----REMRE   74 (724)
T ss_dssp             SCHHHHHHHHC--CS-SCEEEEECTTSCHHHH--------HH-HHHHHHHHTTCCCGGGEEEEESSHHHH-----HHHHH
T ss_pred             CCHHHHHHHhC--CC-CCEEEEEcCCCCHHHH--------HH-HHHHHHHHhcCCCHHHeEEEeccHHHH-----HHHHH
Confidence            34789999876  23 6899999999999988        11 11122222233 234789999999888     55555


Q ss_pred             hh
Q psy7952         129 IV  130 (444)
Q Consensus       129 ~l  130 (444)
                      ++
T Consensus        75 Rl   76 (724)
T 1pjr_A           75 RV   76 (724)
T ss_dssp             HH
T ss_pred             HH
Confidence            55

>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=92.28  E-value=0.033  Score=61.35  Aligned_cols=64  Identities=16%  Similarity=-0.013  Sum_probs=44.4

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC---ccceeEEEcchhhhhcccCccch
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN---VRSRNGWISPILSSFYLRFRDDK  126 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~---~~~~vlil~P~~~L~~~~q~~~~  126 (444)
                      .|+-|.+++..-  + ++++|.|+.|||||.+        .. -.++..+..+.   ...+++++++|++.+     .+.
T Consensus        11 ~t~eQ~~~i~~~--~-~~~~v~a~AGSGKT~v--------l~-~ri~~ll~~~~~~~~~~~il~~Tft~~aa-----~e~   73 (1232)
T 3u4q_A           11 WTDDQWNAIVST--G-QDILVAAAAGSGKTAV--------LV-ERMIRKITAEENPIDVDRLLVVTFTNASA-----AEM   73 (1232)
T ss_dssp             CCHHHHHHHHCC--S-SCEEEEECTTCCHHHH--------HH-HHHHHHHSCSSSCCCGGGEEEECSSHHHH-----HHH
T ss_pred             CCHHHHHHHhCC--C-CCEEEEecCCCcHHHH--------HH-HHHHHHHhcCCCCCCccceEEEeccHHHH-----HHH
Confidence            367899998863  5 7999999999999988        21 11122233322   335889999999888     565


Q ss_pred             Hhhh
Q psy7952         127 TSIV  130 (444)
Q Consensus       127 ~~~l  130 (444)
                      .+++
T Consensus        74 ~~ri   77 (1232)
T 3u4q_A           74 KHRI   77 (1232)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5554

>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=92.27  E-value=0.16  Score=49.27  Aligned_cols=16  Identities=19%  Similarity=0.133  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus       168 ~~vLL~GppGtGKT~l  183 (444)
T 2zan_A          168 RGILLFGPPGTGKSYL  183 (444)
T ss_dssp             SEEEEECSTTSSHHHH
T ss_pred             ceEEEECCCCCCHHHH
Confidence            6799999999999977

>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=92.24  E-value=0.023  Score=58.42  Aligned_cols=77  Identities=10%  Similarity=-0.033  Sum_probs=49.2

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC-ccceeEEEcchhhhhcccCccchHhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN-VRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~-~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      |+-|.+++...  + .+++|.|+.|||||.+        .. ..+.+.+...+ ...++++++.|+..+     .+.-++
T Consensus         4 ~~~Q~~av~~~--~-~~~lV~AgaGSGKT~~--------l~-~ri~~ll~~~~~~~~~IL~lTfT~~Aa-----~em~~R   66 (673)
T 1uaa_A            4 NPGQQQAVEFV--T-GPCLVLAGAGSGKTRV--------IT-NKIAHLIRGCGYQARHIAAVTFTNKAA-----REMKER   66 (673)
T ss_dssp             CHHHHHHHHCC--S-SEEEECCCTTSCHHHH--------HH-HHHHHHHHHHCCCGGGEEEEESSHHHH-----HHHHHH
T ss_pred             CHHHHHHHhCC--C-CCEEEEeCCCCChHHH--------HH-HHHHHHHHhcCCCHHHeEEEeccHHHH-----HHHHHH
Confidence            57899999863  3 6899999999999988        11 11122222223 335789999999998     666666


Q ss_pred             h--cCC---CCceeEEEEeC
Q psy7952         130 V--TGR---SDLYQLELIVS  144 (444)
Q Consensus       130 l--~~~---~~~i~~~~~~~  144 (444)
                      +  ..+   ...+.+.++++
T Consensus        67 l~~~l~~~~~~~~~v~Tfhs   86 (673)
T 1uaa_A           67 VGQTLGRKEARGLMISTFHT   86 (673)
T ss_dssp             HHHHSCTTTTTTSEEEEHHH
T ss_pred             HHHHcCcccccCCEEEeHHH
Confidence            5  212   12356666554

>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=92.20  E-value=0.12  Score=43.60  Aligned_cols=16  Identities=6%  Similarity=-0.238  Sum_probs=13.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +-.++.+|+|+|||..
T Consensus         9 ~i~v~~G~mgsGKTT~   24 (191)
T 1xx6_A            9 WVEVIVGPMYSGKSEE   24 (191)
T ss_dssp             EEEEEECSTTSSHHHH
T ss_pred             EEEEEECCCCCcHHHH
Confidence            4578899999999977

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=92.17  E-value=0.068  Score=42.91  Aligned_cols=20  Identities=10%  Similarity=0.152  Sum_probs=16.8

Q ss_pred             HccCCcEEEEccCCCccccc
Q psy7952          62 LLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        62 ~~~~~~~ii~apTGsGKT~~   81 (444)
                      .....++++.+|+|+|||..
T Consensus        21 a~~~~~vll~G~~GtGKt~l   40 (145)
T 3n70_A           21 SETDIAVWLYGAPGTGRMTG   40 (145)
T ss_dssp             TTCCSCEEEESSTTSSHHHH
T ss_pred             hCCCCCEEEECCCCCCHHHH
Confidence            34448999999999999977

>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=91.99  E-value=0.65  Score=42.61  Aligned_cols=41  Identities=20%  Similarity=0.198  Sum_probs=25.0

Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEecc
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTAT  237 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT  237 (444)
                      ..+++|+||+|.+..     ......+...+...+.+.++|+.|..
T Consensus       105 ~~~vliiDEi~~l~~-----~~~~~~L~~~le~~~~~~~iI~~~n~  145 (324)
T 3u61_B          105 RQKVIVIDEFDRSGL-----AESQRHLRSFMEAYSSNCSIIITANN  145 (324)
T ss_dssp             CEEEEEEESCCCGGG-----HHHHHHHHHHHHHHGGGCEEEEEESS
T ss_pred             CCeEEEEECCcccCc-----HHHHHHHHHHHHhCCCCcEEEEEeCC
Confidence            578999999999751     12234455555555555666664443

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=91.91  E-value=0.11  Score=50.37  Aligned_cols=33  Identities=0%  Similarity=0.002  Sum_probs=22.5

Q ss_pred             ccCchHHHHHHHHHHcc---CCcEEEEccCCCcccccc
Q psy7952          48 SFKCELQKKAIRHILLR---THDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        48 ~~~t~~Q~~~~~~~~~~---~~~~ii~apTGsGKT~~a   82 (444)
                      .++|.+.  .++.++.|   ..-+++.|++|+|||..|
T Consensus       179 gi~TG~~--~LD~~lgGl~~G~liiIaG~pG~GKTtla  214 (444)
T 3bgw_A          179 GVPSGFT--ELDRMTYGYKRRNFVLIAARPSMGKTAFA  214 (444)
T ss_dssp             SBCCSCH--HHHHHHSSBCSSCEEEEEECSSSSHHHHH
T ss_pred             CcCCCcH--HHHhhcCCCCCCcEEEEEeCCCCChHHHH
Confidence            4555443  56666532   156899999999999774

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=91.87  E-value=0.88  Score=38.24  Aligned_cols=74  Identities=11%  Similarity=0.104  Sum_probs=56.3

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      +++||+|+++.-+     ....+.+ ..+   +.+..++|+.+..++...+..++.  +..+|+|+|         . ..
T Consensus        55 ~~~lVF~~~~~~~-----~~l~~~L~~~g---~~~~~lhg~~~~~~R~~~l~~F~~--g~~~vLvaT---------~-~~  114 (191)
T 2p6n_A           55 PPVLIFAEKKADV-----DAIHEYLLLKG---VEAVAIHGGKDQEERTKAIEAFRE--GKKDVLVAT---------D-VA  114 (191)
T ss_dssp             SCEEEECSCHHHH-----HHHHHHHHHHT---CCEEEECTTSCHHHHHHHHHHHHH--TSCSEEEEC---------H-HH
T ss_pred             CCEEEEECCHHHH-----HHHHHHHHHcC---CcEEEEeCCCCHHHHHHHHHHHhc--CCCEEEEEc---------C-ch
Confidence            3679999999998     5665666 667   889999999999888888887763  678899999         1 13


Q ss_pred             HHHHhhCCccEEEEe
Q psy7952         185 QHLVRYNKLAYIVVD  199 (444)
Q Consensus       185 ~~~~~~~~~~~iViD  199 (444)
                      ..-.++..+++||.=
T Consensus       115 ~~Gldi~~v~~VI~~  129 (191)
T 2p6n_A          115 SKGLDFPAIQHVINY  129 (191)
T ss_dssp             HTTCCCCCCSEEEES
T ss_pred             hcCCCcccCCEEEEe
Confidence            334456678888763

>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=90.85  E-value=0.27  Score=46.25  Aligned_cols=16  Identities=25%  Similarity=0.248  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.||+|+|||..
T Consensus        46 ~~vli~G~~G~GKTtl   61 (386)
T 2qby_A           46 NNIFIYGLTGTGKTAV   61 (386)
T ss_dssp             CCEEEEECTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            6799999999999977

>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=90.83  E-value=0.081  Score=54.93  Aligned_cols=51  Identities=12%  Similarity=0.131  Sum_probs=28.0

Q ss_pred             CccEEEEecccccccc-C-------CCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcch
Q psy7952         192 KLAYIVVDEAHCVSEW-G-------HDFRPTYRRLGELRQFTGNSIPIIALTATAEPSV  242 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~-~-------~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~  242 (444)
                      ....|+|||+|.+... +       ...+..+..+...+..+.....++.+-||=.+..
T Consensus       570 ~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~~~V~vi~aTN~p~~  628 (806)
T 3cf2_A          570 APCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDI  628 (806)
T ss_dssp             CSEEEECSCGGGCC--------------CHHHHHHHHHHHSSCSSSSEEEECC-CCSSS
T ss_pred             CCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCchh
Confidence            4578999999998531 1       0112233444444444555566888888855443

>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=89.83  E-value=0.81  Score=42.50  Aligned_cols=43  Identities=12%  Similarity=0.227  Sum_probs=26.3

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCC
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAE  239 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~  239 (444)
                      .+..++|+||+|.+...      ....+.+.+...+.+..+|+.|..+.
T Consensus       133 ~~~~vlilDE~~~L~~~------~~~~L~~~le~~~~~~~~Il~t~~~~  175 (354)
T 1sxj_E          133 HRYKCVIINEANSLTKD------AQAALRRTMEKYSKNIRLIMVCDSMS  175 (354)
T ss_dssp             -CCEEEEEECTTSSCHH------HHHHHHHHHHHSTTTEEEEEEESCSC
T ss_pred             CCCeEEEEeCccccCHH------HHHHHHHHHHhhcCCCEEEEEeCCHH
Confidence            35689999999995321      12445555555555566666665544

>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=89.63  E-value=0.42  Score=46.52  Aligned_cols=16  Identities=19%  Similarity=0.248  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus        50 ~gvLL~GppGtGKT~L   65 (476)
T 2ce7_A           50 KGILLVGPPGTGKTLL   65 (476)
T ss_dssp             SEEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            5799999999999977

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=88.78  E-value=1.8  Score=40.97  Aligned_cols=16  Identities=6%  Similarity=-0.137  Sum_probs=13.8

Q ss_pred             CcEEE--EccCCCccccc
Q psy7952          66 HDIFV--SMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii--~apTGsGKT~~   81 (444)
                      ..+++  .+|+|+|||..
T Consensus        51 ~~~li~i~G~~G~GKT~L   68 (412)
T 1w5s_A           51 VNMIYGSIGRVGIGKTTL   68 (412)
T ss_dssp             EEEEEECTTCCSSSHHHH
T ss_pred             CEEEEeCcCcCCCCHHHH
Confidence            46788  89999999977

>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=88.67  E-value=0.89  Score=37.45  Aligned_cols=75  Identities=13%  Similarity=0.098  Sum_probs=56.0

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||+|+++..+     ......+ ..+   +.+..++|+.+..++......++  .+..+|+|+|. .+.        
T Consensus        35 ~~~lVF~~~~~~~-----~~l~~~L~~~~---~~~~~~~g~~~~~~R~~~~~~f~--~g~~~vLvaT~-~~~--------   95 (175)
T 2rb4_A           35 GQAIIFCQTRRNA-----KWLTVEMIQDG---HQVSLLSGELTVEQRASIIQRFR--DGKEKVLITTN-VCA--------   95 (175)
T ss_dssp             SEEEEECSCHHHH-----HHHHHHHHTTT---CCEEEECSSCCHHHHHHHHHHHH--TTSCSEEEECC-SCC--------
T ss_pred             CCEEEEECCHHHH-----HHHHHHHHHcC---CcEEEEeCCCCHHHHHHHHHHHH--cCCCeEEEEec-chh--------
Confidence            4679999999998     5666666 667   88999999999998888888776  46789999992 221        


Q ss_pred             HHHHhhCCccEEEEec
Q psy7952         185 QHLVRYNKLAYIVVDE  200 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE  200 (444)
                       .-.++..+++||.-+
T Consensus        96 -~Gid~~~~~~Vi~~d  110 (175)
T 2rb4_A           96 -RGIDVKQVTIVVNFD  110 (175)
T ss_dssp             -TTTCCTTEEEEEESS
T ss_pred             -cCCCcccCCEEEEeC
Confidence             223455677887533

>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=88.66  E-value=0.26  Score=42.26  Aligned_cols=16  Identities=0%  Similarity=-0.409  Sum_probs=13.0

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .-.++.+|.|+|||..
T Consensus        29 ~l~vitG~MgsGKTT~   44 (214)
T 2j9r_A           29 WIEVICGSMFSGKSEE   44 (214)
T ss_dssp             EEEEEECSTTSCHHHH
T ss_pred             EEEEEECCCCCcHHHH
Confidence            3456899999999977

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=88.37  E-value=0.9  Score=36.93  Aligned_cols=75  Identities=11%  Similarity=0.167  Sum_probs=56.2

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||+|+++.-+     ....+.+ ..+   +.+..++|+.+..++......++  .+..+|+|+| +.+         
T Consensus        36 ~~~lVF~~~~~~~-----~~l~~~L~~~~---~~~~~~hg~~~~~~r~~~~~~f~--~g~~~vlv~T-~~~---------   95 (163)
T 2hjv_A           36 DSCIIFCRTKEHV-----NQLTDELDDLG---YPCDKIHGGMIQEDRFDVMNEFK--RGEYRYLVAT-DVA---------   95 (163)
T ss_dssp             SSEEEECSSHHHH-----HHHHHHHHHTT---CCEEEECTTSCHHHHHHHHHHHH--TTSCSEEEEC-GGG---------
T ss_pred             CcEEEEECCHHHH-----HHHHHHHHHcC---CcEEEEeCCCCHHHHHHHHHHHH--cCCCeEEEEC-Chh---------
Confidence            3669999999998     5666666 667   88999999999988888887776  4678999999 222         


Q ss_pred             HHHHhhCCccEEEEec
Q psy7952         185 QHLVRYNKLAYIVVDE  200 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE  200 (444)
                      ..-.++..+++||.-+
T Consensus        96 ~~Gld~~~~~~Vi~~~  111 (163)
T 2hjv_A           96 ARGIDIENISLVINYD  111 (163)
T ss_dssp             TTTCCCSCCSEEEESS
T ss_pred             hcCCchhcCCEEEEeC
Confidence            2333456678887643

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=88.02  E-value=0.54  Score=40.28  Aligned_cols=16  Identities=0%  Similarity=-0.398  Sum_probs=13.4

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .-.++.+|.|+|||..
T Consensus        29 ~I~vitG~M~sGKTT~   44 (219)
T 3e2i_A           29 WIECITGSMFSGKSEE   44 (219)
T ss_dssp             EEEEEEECTTSCHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            4568899999999976

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=87.09  E-value=1  Score=36.64  Aligned_cols=75  Identities=12%  Similarity=0.235  Sum_probs=55.7

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||+|+++.-+     ......+ ..+   +.+..++|+.+..++.......+  .+...|+|+| +.+         
T Consensus        31 ~~~lVF~~~~~~~-----~~l~~~L~~~~---~~~~~~~~~~~~~~r~~~~~~f~--~g~~~vlv~T-~~~---------   90 (165)
T 1fuk_A           31 TQAVIFCNTRRKV-----EELTTKLRNDK---FTVSAIYSDLPQQERDTIMKEFR--SGSSRILIST-DLL---------   90 (165)
T ss_dssp             SCEEEEESSHHHH-----HHHHHHHHHTT---CCEEEECTTSCHHHHHHHHHHHH--TTSCSEEEEE-GGG---------
T ss_pred             CCEEEEECCHHHH-----HHHHHHHHHcC---CCEEEEECCCCHHHHHHHHHHHH--cCCCEEEEEc-Chh---------
Confidence            4669999999998     5666666 667   88999999999988888888776  4778999999 221         


Q ss_pred             HHHHhhCCccEEEEec
Q psy7952         185 QHLVRYNKLAYIVVDE  200 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE  200 (444)
                      ..-.++..+++||.-+
T Consensus        91 ~~G~d~~~~~~Vi~~~  106 (165)
T 1fuk_A           91 ARGIDVQQVSLVINYD  106 (165)
T ss_dssp             TTTCCCCSCSEEEESS
T ss_pred             hcCCCcccCCEEEEeC
Confidence            2223455677777643

>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=87.01  E-value=0.74  Score=43.00  Aligned_cols=26  Identities=8%  Similarity=-0.082  Sum_probs=20.0

Q ss_pred             HHHHHHc-c----CCcEEEEccCCCcccccc
Q psy7952          57 AIRHILL-R----THDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        57 ~~~~~~~-~----~~~~ii~apTGsGKT~~a   82 (444)
                      .++.++. |    .+-+++.+|+|+|||..|
T Consensus        50 ~LD~~Lg~GGl~~G~ii~I~G~pGsGKTtLa   80 (356)
T 1u94_A           50 SLDIALGAGGLPMGRIVEIYGPESSGKTTLT   80 (356)
T ss_dssp             HHHHHTSSSSEETTSEEEEECSTTSSHHHHH
T ss_pred             HHHHHhccCCccCCeEEEEECCCCCCHHHHH
Confidence            5677775 2    156899999999999774

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=86.94  E-value=0.81  Score=52.19  Aligned_cols=34  Identities=6%  Similarity=-0.059  Sum_probs=24.2

Q ss_pred             cccCchHHHHHHHHHHc-c----CCcEEEEccCCCcccccc
Q psy7952          47 DSFKCELQKKAIRHILL-R----THDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        47 ~~~~t~~Q~~~~~~~~~-~----~~~~ii~apTGsGKT~~a   82 (444)
                      ..++|-..  .+..++. |    .+.+++.+|+|+|||..|
T Consensus      1406 ~~isTG~~--~LD~lLG~GGi~~g~~vll~GppGtGKT~LA 1444 (2050)
T 3cmu_A         1406 ETISTGSL--SLDIALGAGGLPMGRIVEIYGPESSGKTTLT 1444 (2050)
T ss_dssp             CEECCSCH--HHHHHHSSSSEETTSEEEEECCTTSSHHHHH
T ss_pred             ccccCCCH--HHHHhcCCCCccCCeEEEEECCCCCCHHHHH
Confidence            34455444  3777776 2    278999999999999774

>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=86.77  E-value=0.7  Score=40.02  Aligned_cols=16  Identities=6%  Similarity=-0.207  Sum_probs=13.6

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .-.++.+|.|+|||..
T Consensus        20 ~l~v~~G~MgsGKTT~   35 (234)
T 2orv_A           20 QIQVILGPMFSGKSTE   35 (234)
T ss_dssp             EEEEEECCTTSCHHHH
T ss_pred             EEEEEECCCCCcHHHH
Confidence            5578899999999977

>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=86.62  E-value=0.87  Score=38.03  Aligned_cols=75  Identities=11%  Similarity=0.096  Sum_probs=46.4

Q ss_pred             ccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHH
Q psy7952         104 VRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHY  182 (444)
Q Consensus       104 ~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~  182 (444)
                      ...++||+|+++.-+     ....+.+ ..+   +.+..++|+.+..++...+..++.  +...|+|+| +.        
T Consensus        45 ~~~k~lVF~~~~~~~-----~~l~~~L~~~g---~~~~~lhg~~~~~~r~~~~~~f~~--g~~~vLvaT-~~--------  105 (185)
T 2jgn_A           45 KDSLTLVFVETKKGA-----DSLEDFLYHEG---YACTSIHGDRSQRDREEALHQFRS--GKSPILVAT-AV--------  105 (185)
T ss_dssp             CCSCEEEEESCHHHH-----HHHHHHHHHTT---CCEEEEC--------CHHHHHHHH--TSSSEEEEE-C---------
T ss_pred             CCCeEEEEECCHHHH-----HHHHHHHHHcC---CceEEEeCCCCHHHHHHHHHHHHc--CCCeEEEEc-Ch--------
Confidence            345679999999998     5666666 667   889999999988888777777663  678899999 22        


Q ss_pred             HHHHHHhhCCccEEEE
Q psy7952         183 LLQHLVRYNKLAYIVV  198 (444)
Q Consensus       183 ~~~~~~~~~~~~~iVi  198 (444)
                       ...-.++..+++||.
T Consensus       106 -~~~Gldi~~~~~VI~  120 (185)
T 2jgn_A          106 -AARGLDISNVKHVIN  120 (185)
T ss_dssp             ------CCCSBSEEEE
T ss_pred             -hhcCCCcccCCEEEE
Confidence             223345567787775

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=86.37  E-value=1.1  Score=46.48  Aligned_cols=15  Identities=20%  Similarity=0.069  Sum_probs=13.9

Q ss_pred             cEEEEccCCCccccc
Q psy7952          67 DIFVSMPTGAVSLVG   81 (444)
Q Consensus        67 ~~ii~apTGsGKT~~   81 (444)
                      ++++.+|||+|||..
T Consensus       523 ~~Ll~Gp~GtGKT~l  537 (758)
T 3pxi_A          523 SFIFLGPTGVGKTEL  537 (758)
T ss_dssp             EEEEESCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            599999999999977

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=85.83  E-value=1.1  Score=42.06  Aligned_cols=26  Identities=8%  Similarity=-0.138  Sum_probs=19.9

Q ss_pred             HHHHHHc-c----CCcEEEEccCCCcccccc
Q psy7952          57 AIRHILL-R----THDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        57 ~~~~~~~-~----~~~~ii~apTGsGKT~~a   82 (444)
                      .++.++. |    ..-++|.+|+|+|||..|
T Consensus        61 ~LD~~Lg~GGl~~G~li~I~G~pGsGKTtla   91 (366)
T 1xp8_A           61 SLDLALGVGGIPRGRITEIYGPESGGKTTLA   91 (366)
T ss_dssp             HHHHHTSSSSEETTSEEEEEESTTSSHHHHH
T ss_pred             HHHHHhCCCCccCCcEEEEEcCCCCChHHHH
Confidence            5777776 2    156899999999999773

>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=85.76  E-value=0.49  Score=46.62  Aligned_cols=17  Identities=24%  Similarity=0.122  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCcccccc
Q psy7952          66 HDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a   82 (444)
                      .-++|.|++|+|||..|
T Consensus       243 ~l~li~G~pG~GKT~la  259 (503)
T 1q57_A          243 EVIMVTSGSGMVMSTFV  259 (503)
T ss_dssp             CEEEEEESSCHHHHHHH
T ss_pred             eEEEEeecCCCCchHHH
Confidence            56899999999999774

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=85.71  E-value=0.12  Score=45.35  Aligned_cols=51  Identities=16%  Similarity=0.180  Sum_probs=29.6

Q ss_pred             HHHHhhCCccEEEEeccccccc---cCCCcHHHHHHHHHHHHhhCCCCcEEEEecc
Q psy7952         185 QHLVRYNKLAYIVVDEAHCVSE---WGHDFRPTYRRLGELRQFTGNSIPIIALTAT  237 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE~H~~~~---~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT  237 (444)
                      .........+++|+|-...+..   .....+.....+..+.+...  +.+++++-.
T Consensus       128 ~~~~~~~~~~~vviD~~~~l~~~~~~~~~~~~~~~~L~~~a~~~~--i~vi~~~q~  181 (251)
T 2zts_A          128 YRVVKAINAKRLVIDSIPSIALRLEEERKIREVLLKLNTILLEMG--VTTILTTEA  181 (251)
T ss_dssp             HHHHHHTTCSEEEEECHHHHHHHSSSGGGHHHHHHHHHHHHHHHC--CEEEEEECC
T ss_pred             HHHHHhcCCcEEEEEcHHHHhhhccChHHHHHHHHHHHHHHHHcC--CCeEEEEEE
Confidence            3444556789999999987632   11224445555555555543  556665543

>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=85.41  E-value=0.82  Score=42.78  Aligned_cols=16  Identities=25%  Similarity=0.318  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .++++.+|||+|||.+
T Consensus        52 ~~vll~GppGtGKT~l   67 (363)
T 3hws_A           52 SNILLIGPTGSGKTLL   67 (363)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            6899999999999987

>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=85.17  E-value=1.4  Score=37.68  Aligned_cols=73  Identities=11%  Similarity=0.117  Sum_probs=54.7

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||+|+++.-+     ....+.+ ..+   +.+..++|+.+...+.......+  .+..+|+|+|. .+         
T Consensus        32 ~~~lVF~~~~~~~-----~~l~~~L~~~~---~~~~~lhg~~~~~~r~~~~~~f~--~g~~~vlvaT~-~~---------   91 (212)
T 3eaq_A           32 DRAMVFTRTKAET-----EEIAQGLLRLG---HPAQALHGDLSQGERERVLGAFR--QGEVRVLVATD-VA---------   91 (212)
T ss_dssp             SCEEEECSSHHHH-----HHHHHHHHHHT---CCEEEECSSSCHHHHHHHHHHHH--SSSCCEEEECT-TT---------
T ss_pred             CeEEEEeCCHHHH-----HHHHHHHHHcC---CCEEEEECCCCHHHHHHHHHHHH--CCCCeEEEecC-hh---------
Confidence            3669999999988     5666666 667   88999999999998888888776  46789999992 22         


Q ss_pred             HHHHhhCCccEEEE
Q psy7952         185 QHLVRYNKLAYIVV  198 (444)
Q Consensus       185 ~~~~~~~~~~~iVi  198 (444)
                      ..-.+...+++||.
T Consensus        92 ~~Gidi~~v~~Vi~  105 (212)
T 3eaq_A           92 ARGLDIPQVDLVVH  105 (212)
T ss_dssp             TCSSSCCCBSEEEE
T ss_pred             hcCCCCccCcEEEE
Confidence            12334556777773

>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=85.13  E-value=1.3  Score=41.11  Aligned_cols=26  Identities=12%  Similarity=-0.047  Sum_probs=20.1

Q ss_pred             HHHHHHc-c----CCcEEEEccCCCcccccc
Q psy7952          57 AIRHILL-R----THDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        57 ~~~~~~~-~----~~~~ii~apTGsGKT~~a   82 (444)
                      .++.++. |    .+-+++.+|+|+|||..|
T Consensus        48 ~LD~~Lg~GGl~~G~iv~I~G~pGsGKTtLa   78 (349)
T 2zr9_A           48 SLDVALGIGGLPRGRVIEIYGPESSGKTTVA   78 (349)
T ss_dssp             HHHHHTSSSSEETTSEEEEEESTTSSHHHHH
T ss_pred             HHHHHhccCCccCCeEEEEECCCCCCHHHHH
Confidence            5677776 3    156899999999999773

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=84.40  E-value=0.81  Score=39.09  Aligned_cols=31  Identities=23%  Similarity=0.043  Sum_probs=26.3

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCccccc
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      .+.-|..++..+..| .-+.+.+|.|+|||..
T Consensus         8 k~~g~~~~l~~i~~G-e~~~liG~nGsGKSTL   38 (208)
T 3b85_A            8 KTLGQKHYVDAIDTN-TIVFGLGPAGSGKTYL   38 (208)
T ss_dssp             CSHHHHHHHHHHHHC-SEEEEECCTTSSTTHH
T ss_pred             CCHhHHHHHHhccCC-CEEEEECCCCCCHHHH
Confidence            455678889999888 8889999999999976

>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=83.36  E-value=1.2  Score=40.32  Aligned_cols=16  Identities=25%  Similarity=0.231  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .++++.+|+|+|||..
T Consensus        51 ~~vll~G~~GtGKT~l   66 (310)
T 1ofh_A           51 KNILMIGPTGVGKTEI   66 (310)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             ceEEEECCCCCCHHHH
Confidence            7899999999999977

>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=82.83  E-value=2.1  Score=39.30  Aligned_cols=27  Identities=11%  Similarity=-0.162  Sum_probs=20.2

Q ss_pred             HHHHHHcc----CCcEEEEccCCCccccccc
Q psy7952          57 AIRHILLR----THDIFVSMPTGAVSLVGSV   83 (444)
Q Consensus        57 ~~~~~~~~----~~~~ii~apTGsGKT~~a~   83 (444)
                      .++.++.|    ..-+++.+|+|+|||..|.
T Consensus        95 ~LD~~L~GGl~~G~i~~i~G~~GsGKT~la~  125 (324)
T 2z43_A           95 ALDGLLAGGIETRTMTEFFGEFGSGKTQLCH  125 (324)
T ss_dssp             HHHHHTTTSEETTSEEEEEESTTSSHHHHHH
T ss_pred             hHHHhcCCCCCCCcEEEEECCCCCCHhHHHH
Confidence            56677643    1568999999999997743

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=82.47  E-value=0.56  Score=42.78  Aligned_cols=19  Identities=5%  Similarity=0.032  Sum_probs=16.3

Q ss_pred             ccCCcEEEEccCCCccccc
Q psy7952          63 LRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        63 ~~~~~~ii~apTGsGKT~~   81 (444)
                      ....++++.+|||+|||.+
T Consensus        23 ~~~~~vLi~Ge~GtGKt~l   41 (304)
T 1ojl_A           23 PSDATVLIHGDSGTGKELV   41 (304)
T ss_dssp             STTSCEEEESCTTSCHHHH
T ss_pred             CCCCcEEEECCCCchHHHH
Confidence            3447899999999999977

>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=82.26  E-value=1.5  Score=41.09  Aligned_cols=78  Identities=10%  Similarity=0.123  Sum_probs=58.7

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||+|+++.-+     ....+.+ ..+   +.+..++|+....++....+.++  .+..+|+|+|.-          .
T Consensus       244 ~~~lvf~~~~~~~-----~~l~~~l~~~~---~~~~~~~~~~~~~~r~~~~~~f~--~g~~~vlv~T~~----------~  303 (395)
T 3pey_A          244 GSSIIFVATKKTA-----NVLYGKLKSEG---HEVSILHGDLQTQERDRLIDDFR--EGRSKVLITTNV----------L  303 (395)
T ss_dssp             SEEEEECSCHHHH-----HHHHHHHHHTT---CCCEEECTTSCHHHHHHHHHHHH--TTSCCEEEECGG----------G
T ss_pred             CCEEEEeCCHHHH-----HHHHHHHHhcC---CcEEEeCCCCCHHHHHHHHHHHH--CCCCCEEEECCh----------h
Confidence            4779999999998     5666666 667   88999999999998888888776  467889999921          1


Q ss_pred             HHHHhhCCccEEEEecccc
Q psy7952         185 QHLVRYNKLAYIVVDEAHC  203 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE~H~  203 (444)
                      ..-.++..+++||.-+...
T Consensus       304 ~~Gidip~~~~Vi~~~~p~  322 (395)
T 3pey_A          304 ARGIDIPTVSMVVNYDLPT  322 (395)
T ss_dssp             SSSCCCTTEEEEEESSCCB
T ss_pred             hcCCCcccCCEEEEcCCCC
Confidence            2334556788888765544

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=81.89  E-value=3.1  Score=39.32  Aligned_cols=74  Identities=11%  Similarity=0.118  Sum_probs=56.9

Q ss_pred             cceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHH
Q psy7952         105 RSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYL  183 (444)
Q Consensus       105 ~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~  183 (444)
                      ..++||+|+++.-+     ....+.+ ..+   +.+..++|+....++......++.  +..+|+|+|         . .
T Consensus       276 ~~~~lVf~~~~~~~-----~~l~~~L~~~~---~~~~~~h~~~~~~~r~~~~~~f~~--g~~~vlvaT---------~-~  335 (417)
T 2i4i_A          276 DSLTLVFVETKKGA-----DSLEDFLYHEG---YACTSIHGDRSQRDREEALHQFRS--GKSPILVAT---------A-V  335 (417)
T ss_dssp             TCEEEEECSSHHHH-----HHHHHHHHHTT---CCEEEECTTSCHHHHHHHHHHHHH--TSSCEEEEC---------H-H
T ss_pred             CCeEEEEECCHHHH-----HHHHHHHHHCC---CCeeEecCCCCHHHHHHHHHHHHc--CCCCEEEEC---------C-h
Confidence            35689999999999     5656666 667   889999999999888888887763  678899999         2 2


Q ss_pred             HHHHHhhCCccEEEE
Q psy7952         184 LQHLVRYNKLAYIVV  198 (444)
Q Consensus       184 ~~~~~~~~~~~~iVi  198 (444)
                      ...-.++..+++||.
T Consensus       336 ~~~Gidip~v~~Vi~  350 (417)
T 2i4i_A          336 AARGLDISNVKHVIN  350 (417)
T ss_dssp             HHTTSCCCCEEEEEE
T ss_pred             hhcCCCcccCCEEEE
Confidence            344456667787774

>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=81.64  E-value=1.9  Score=40.73  Aligned_cols=75  Identities=11%  Similarity=0.093  Sum_probs=56.7

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||+|+++.-+     ....+.+ ..+   +.+..++|+....++....+.++  .+..+|+|+|.-          .
T Consensus       267 ~~~lvf~~~~~~~-----~~l~~~L~~~~---~~~~~~~~~~~~~~r~~~~~~f~--~g~~~vlv~T~~----------~  326 (412)
T 3fht_A          267 AQAMIFCHTRKTA-----SWLAAELSKEG---HQVALLSGEMMVEQRAAVIERFR--EGKEKVLVTTNV----------C  326 (412)
T ss_dssp             SEEEEECSSHHHH-----HHHHHHHHHTT---CCCEEECTTSCHHHHHHHHHHHH--TTSCSEEEECGG----------G
T ss_pred             CCEEEEeCCHHHH-----HHHHHHHHhCC---CeEEEecCCCCHHHHHHHHHHHH--CCCCcEEEEcCc----------c
Confidence            4789999999998     5666666 667   88999999999999988888876  467889999921          2


Q ss_pred             HHHHhhCCccEEEEec
Q psy7952         185 QHLVRYNKLAYIVVDE  200 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE  200 (444)
                      ..-.++..+++||.-.
T Consensus       327 ~~Gidip~~~~Vi~~~  342 (412)
T 3fht_A          327 ARGIDVEQVSVVINFD  342 (412)
T ss_dssp             TSSCCCTTEEEEEESS
T ss_pred             ccCCCccCCCEEEEEC
Confidence            2334556778887533

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=81.46  E-value=1.6  Score=46.04  Aligned_cols=15  Identities=20%  Similarity=0.091  Sum_probs=14.0

Q ss_pred             cEEEEccCCCccccc
Q psy7952          67 DIFVSMPTGAVSLVG   81 (444)
Q Consensus        67 ~~ii~apTGsGKT~~   81 (444)
                      ++++.+|||+|||.+
T Consensus       590 ~vLl~Gp~GtGKT~l  604 (854)
T 1qvr_A          590 SFLFLGPTGVGKTEL  604 (854)
T ss_dssp             EEEEBSCSSSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            689999999999977

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=81.44  E-value=0.84  Score=37.66  Aligned_cols=16  Identities=6%  Similarity=-0.105  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      ..+++.+|+|+|||..
T Consensus        44 ~~~ll~G~~G~GKT~l   59 (195)
T 1jbk_A           44 NNPVLIGEPGVGKTAI   59 (195)
T ss_dssp             CEEEEECCTTSCHHHH
T ss_pred             CceEEECCCCCCHHHH
Confidence            6799999999999977

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=81.20  E-value=0.61  Score=45.72  Aligned_cols=24  Identities=17%  Similarity=0.231  Sum_probs=19.0

Q ss_pred             HHHHHHccCCcEEEEccCCCccccc
Q psy7952          57 AIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        57 ~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      +...+..+ .++++.||+|+|||..
T Consensus        34 l~~al~~~-~~VLL~GpPGtGKT~L   57 (500)
T 3nbx_X           34 CLLAALSG-ESVFLLGPPGIAKSLI   57 (500)
T ss_dssp             HHHHHHHT-CEEEEECCSSSSHHHH
T ss_pred             HHHHHhcC-CeeEeecCchHHHHHH
Confidence            34444455 8999999999999977

>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=80.93  E-value=0.83  Score=41.71  Aligned_cols=42  Identities=2%  Similarity=-0.073  Sum_probs=24.9

Q ss_pred             cEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhh
Q psy7952          67 DIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSF  118 (444)
Q Consensus        67 ~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~  118 (444)
                      .+.+.+|+|+|||..++.++.         . ....+...+++|+....++.
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~---------~-~~~~g~g~~vlyId~E~s~~   71 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVS---------S-YMRQYPDAVCLFYDSEFGIT   71 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHH---------H-HHHHCTTCEEEEEESSCCCC
T ss_pred             eEEEECCCCCCHHHHHHHHHH---------H-HHhcCCCceEEEEeccchhh
Confidence            478999999999977432111         1 22221123458877666655

>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=80.67  E-value=3  Score=35.02  Aligned_cols=47  Identities=13%  Similarity=0.110  Sum_probs=26.2

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCc
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEP  240 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~  240 (444)
                      ..+++||+||+-.....+-  -+ ...+..++...+....+|+.+--+++
T Consensus       119 ~~yDlvILDEi~~al~~g~--l~-~~ev~~~l~~Rp~~~~vIlTGr~ap~  165 (196)
T 1g5t_A          119 PLLDMVVLDELTYMVAYDY--LP-LEEVISALNARPGHQTVIITGRGCHR  165 (196)
T ss_dssp             TTCSEEEEETHHHHHHTTS--SC-HHHHHHHHHTSCTTCEEEEECSSCCH
T ss_pred             CCCCEEEEeCCCccccCCC--CC-HHHHHHHHHhCcCCCEEEEECCCCcH
Confidence            5799999999966433331  11 13344555555654445444444443

>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=80.50  E-value=2.5  Score=39.12  Aligned_cols=27  Identities=7%  Similarity=-0.330  Sum_probs=20.1

Q ss_pred             HHHHHHccC----CcEEEEccCCCccccccc
Q psy7952          57 AIRHILLRT----HDIFVSMPTGAVSLVGSV   83 (444)
Q Consensus        57 ~~~~~~~~~----~~~ii~apTGsGKT~~a~   83 (444)
                      .+..++.|.    .-+++.+|+|+|||..|.
T Consensus       110 ~LD~~LgGGl~~G~i~~I~G~~GsGKTtla~  140 (343)
T 1v5w_A          110 EFDKLLGGGIESMAITEAFGEFRTGKTQLSH  140 (343)
T ss_dssp             HHHHHTTSSBCSSEEEEEECCTTCTHHHHHH
T ss_pred             hHHHHhcCCCCCCeEEEEECCCCCCHHHHHH
Confidence            467777531    457999999999997743

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=80.31  E-value=0.82  Score=38.57  Aligned_cols=16  Identities=6%  Similarity=0.036  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +++++.+|+|+|||..
T Consensus        55 ~~~~l~G~~GtGKT~l   70 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYL   70 (202)
T ss_dssp             CEEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            6799999999999977

---

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	444
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	1e-19
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	7e-14
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	8e-14
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	1e-13
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	1e-13
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	5e-12
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	3e-11
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	1e-10
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	1e-08
d1gm5a4	206	c.37.1.19 (A:550-755) RecG helicase domain {Thermo	7e-08
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	8e-08
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	1e-07
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	4e-07
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	7e-07
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	2e-06
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	8e-06
d1tf5a4	175	c.37.1.19 (A:396-570) Translocation ATPase SecA, n	1e-05
d2eyqa5	211	c.37.1.19 (A:779-989) Transcription-repair couplin	5e-05
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	9e-04
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	0.004

>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 = 84.7 bits (208), Expect = 1e-19
 Identities = 58/229 (25%), Positives = 100/229 (43%), Gaps = 32/229 (13%)

Query: 33  EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRI 92
           E      L+  FG+  F+   Q++ I  +L    D  V MPTG     G  +  +    +
Sbjct: 10  ESGAKQVLQETFGYQQFR-PGQEEIIDTVLSG-RDCLVVMPTGG----GKSLCYQIPALL 63

Query: 93  PPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENK 152
             G   +++  +      +  + ++       + T     + ++                
Sbjct: 64  LNGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCR----------- 112

Query: 153 AILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFR 212
                      +I+LLY+ PER + ++F       + +     + VDEAHC+S+WGHDFR
Sbjct: 113 ---------TGQIRLLYIAPERLMLDNFL----EHLAHWNPVLLAVDEAHCISQWGHDFR 159

Query: 213 PTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKT 261
           P Y  LG+LRQ     +P +ALTATA+ + +QDI+ +L  N P  +  +
Sbjct: 160 PEYAALGQLRQRFPT-LPFMALTATADDTTRQDIVRLLGLNDP-LIQIS 206

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 299

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

 Score = 69.6 bits (170), Expect = 7e-14
 Identities = 16/121 (13%), Positives = 33/121 (27%), Gaps = 23/121 (19%)

Query: 286 KEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----VNKH-------------- 327
             F  K +  +       +I+C +++   +LA  L       V  +              
Sbjct: 22  IPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDV 81

Query: 328 --ERSRVQESFMRGEIN--VITATISFGM-GIDRQNVRFVVHWGMPSSIPAYYQESGRAG 382
               +    +   G+ +  +   T               +    +P    +  Q  GR G
Sbjct: 82  VVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTG 141

Query: 383 R 383
           R
Sbjct: 142 R 142

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 248

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 68.6 bits (167), Expect = 8e-14
 Identities = 26/128 (20%), Positives = 47/128 (36%), Gaps = 13/128 (10%)

Query: 297 NKANNCGIIYCRTREHTTDLADALRRK----VNKHERSRVQESFMRGEINVITATISFGM 352
            K    GIIY RT E   ++ ++L+ K    +    +    E F+ GEI+ +  T  +  
Sbjct: 22  EKLGTGGIIYARTGEEAEEIYESLKNKFRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYG 81

Query: 353 GIDR-----QNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK 407
            + R     + +RF V  G PS    +            Q    + +   +   +E ++ 
Sbjct: 82  TLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLP 137

Query: 408 TDTSTKRE 415
                  E
Sbjct: 138 AVERHIDE 145

>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 = 69.2 bits (168), Expect = 1e-13
 Identities = 39/233 (16%), Positives = 64/233 (27%), Gaps = 36/233 (15%)

Query: 180 FHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAE 239
           F   L   +R      I++DEAH         R       E+ +        I +TAT  
Sbjct: 88  FTMRLLSPIRVPNYNLIIMDEAHFTDPASIAARGYISTRVEMGE-----AAGIFMTATPP 142

Query: 240 PSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKA 299
            S                 F  S          I +      +  V +F  K +      
Sbjct: 143 GSRDP--------------FPQSNAPIMDEEREIPERSWNSGHEWVTDFKGKTVWFVPSI 188

Query: 300 NNCGIIYCRTREHTTDLADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDR--- 356
                I    R++       L RK    E  + + +     +    + +      +R   
Sbjct: 189 KAGNDIAACLRKNGKK-VIQLSRKTFDSEYIKTRTNDWDFVVTTDISEMGANFKAERVID 247

Query: 357 ------------QNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCR-IYHSE 396
                          R ++   MP +  +  Q  GR GR+      + IY  E
Sbjct: 248 PRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGE 300

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 138

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

 Score = 65.5 bits (159), Expect = 1e-13
 Identities = 21/117 (17%), Positives = 34/117 (29%), Gaps = 6/117 (5%)

Query: 286 KEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKH---ERSRVQESFMRGEIN 342
             F  K +  +       +I+C +++   +LA  L           R             
Sbjct: 21  IPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTNGDV 80

Query: 343 VITATISFGMGIDRQN---VRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 396
           V+ AT +   G        +      G P    +  Q  GR GR     Y  +   E
Sbjct: 81  VVVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRTGRGKPGIYRFVAPGE 137

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 286

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 63.8 bits (154), Expect = 5e-12
 Identities = 25/123 (20%), Positives = 44/123 (35%)

Query: 271 DVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERS 330
           ++I + L +   + +  F           N       + +      +    R +++ E+ 
Sbjct: 150 EIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQK 209

Query: 331 RVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYC 390
            + + F RGE NV+ AT     G+D   V  VV +    S     Q  GR GR       
Sbjct: 210 LILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMPGRVI 269

Query: 391 RIY 393
            + 
Sbjct: 270 ILM 272

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 60.4 bits (145), Expect = 3e-11
 Identities = 52/181 (28%), Positives = 89/181 (49%), Gaps = 21/181 (11%)

Query: 262 STFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDL----- 316
           S  R N+ Y ++           +  ++++      +    GIIYC +R    D      
Sbjct: 1   SFDRPNIRYMLMEKF---KPLDQLMRYVQE------QRGKSGIIYCNSRAKVEDTAARLQ 51

Query: 317 -----ADALRRKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSI 371
                A A    +  + R+ VQE F R ++ ++ AT++FGMGI++ NVRFVVH+ +P +I
Sbjct: 52  SKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNI 111

Query: 372 PAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYC 431
            +YYQE+GRAGRDGL +   +++       L   ++     + + +E    N  +M  + 
Sbjct: 112 ESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQGQLQDIERHKLN--AMGAFA 169

Query: 432 E 432
           E
Sbjct: 170 E 170

>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 = 59.5 bits (143), Expect = 1e-10
 Identities = 30/228 (13%), Positives = 56/228 (24%), Gaps = 33/228 (14%)

Query: 31  VSEQELTAKLKALF--GFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARS 88
             E  L  +    F       +  +QK   + IL R      + PTG       +  +  
Sbjct: 24  FPEDFLLKEFVEFFRKCVGEPR-AIQKMWAKRIL-RKESFAATAPTGVGKTSFGLAMSLF 81

Query: 89  RVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTK 148
                     I   ++            +                      E ++     
Sbjct: 82  LALKGKRCYVIFPTSLLVIQ-----AAETIRKYAEKAGVGT----------ENLIGYYHG 126

Query: 149 TENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWG 208
              K   E         K++  T          +L +H        +I VD+   + +  
Sbjct: 127 RIPKREKENFMQNLRNFKIVITTT--------QFLSKHYRELGHFDFIFVDDVDAILKAS 178

Query: 209 HDFRPTYRRLG------ELRQFTGNSIPIIALTATAEPSVKQDIISVL 250
            +       LG                 ++  TATA+   K ++   L
Sbjct: 179 KNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQL 226

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]} Length = 174

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

 Score = 52.0 bits (124), Expect = 1e-08
 Identities = 20/162 (12%), Positives = 50/162 (30%), Gaps = 31/162 (19%)

Query: 275 DDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRR----------KV 324
            DL++     ++E   +            ++   T     +L   L            ++
Sbjct: 18  LDLME----GIRERAAR--------GERTLVTVLTVRMAEELTSFLVEHGIRARYLHHEL 65

Query: 325 NKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSI-----PAYYQESG 379
           +  +R  +      G  + +        G+D   V  V               +  Q  G
Sbjct: 66  DAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIG 125

Query: 380 RAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKF 421
           RA R+         +++   ++++  I  + + +R  L+  +
Sbjct: 126 RAARNA--RGEVWLYADRVSEAMQRAI--EETNRRRALQEAY 163

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 50.6 bits (120), Expect = 7e-08
 Identities = 23/110 (20%), Positives = 42/110 (38%), Gaps = 1/110 (0%)

Query: 289 IEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERSRVQESFMRGEINVITATI 348
           IE+    + K+      Y             +  ++++ E+ RV   F  G  +++ +T 
Sbjct: 39  IEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTT 98

Query: 349 SFGMGIDRQNVRFVVHWGMPSSIPAYY-QESGRAGRDGLQSYCRIYHSEH 397
              +GID      +V         A   Q  GR GR G ++YC +   + 
Sbjct: 99  VIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDV 148

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 50.3 bits (119), Expect = 8e-08
 Identities = 21/95 (22%), Positives = 34/95 (35%), Gaps = 5/95 (5%)

Query: 296 DNKANNCGIIYCRTREHTTDLAD-----ALRRKVNKHERSRVQESFMRGEINVITATISF 350
           +    +  II+ R  E    ++      A+  + ++ ER  + E F  G    I ++   
Sbjct: 89  ERHRKDKIIIFTRHNELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVL 148

Query: 351 GMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 385
             GID  +    V      S   Y Q  GR  R  
Sbjct: 149 DEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPS 183

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 155

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 48.8 bits (115), Expect = 1e-07
 Identities = 31/126 (24%), Positives = 58/126 (46%), Gaps = 11/126 (8%)

Query: 303 GIIYCRTREHTTDLADALRRKVN----------KHERSRVQESFMRGEINVITATISFGM 352
           G+++C+T+  T +LA  LR              + +R +V   F + +I ++ AT     
Sbjct: 31  GLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSR 90

Query: 353 GIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTST 412
           GID  ++  V+++ +P +  +Y    GR GR G +       +    K L Y I+     
Sbjct: 91  GIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRY-IERAMKL 149

Query: 413 KREQLE 418
           K ++L+
Sbjct: 150 KIKKLK 155

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 162

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.6 bits (112), Expect = 4e-07
 Identities = 26/122 (21%), Positives = 51/122 (41%), Gaps = 10/122 (8%)

Query: 296 DNKANNCGIIYCRTREHTTDLAD----------ALRRKVNKHERSRVQESFMRGEINVIT 345
           D+ +    +I+C TR    +L            A+   + + ER  + + F  G   ++ 
Sbjct: 23  DSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILI 82

Query: 346 ATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV 405
           +T     GID Q V  V+++ +P++   Y    GR GR G +     + +     ++  +
Sbjct: 83  STDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMREL 142

Query: 406 IK 407
            K
Sbjct: 143 EK 144

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]} Length = 181

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

 Score = 47.1 bits (111), Expect = 7e-07
 Identities = 23/152 (15%), Positives = 43/152 (28%), Gaps = 5/152 (3%)

Query: 275 DDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERSRVQE 334
           DDL+ +    V+   E+ L                 +        L  ++   ER  +  
Sbjct: 18  DDLIGEIRERVERN-ERTLV-TTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIR 75

Query: 335 SFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQES--GRAGRDGLQSYCRI 392
               G+ +V+        G+D   V  V             + S     GR    +   +
Sbjct: 76  DLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHV 135

Query: 393 YHSEHSKKSLEYVIKTDTSTKRE-QLELKFKN 423
                +      +   +T  +R  Q E   K+
Sbjct: 136 IMYADTITKSMEIAIQETKRRRAIQEEYNRKH 167

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 201

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 46.1 bits (108), Expect = 2e-06
 Identities = 27/123 (21%), Positives = 51/123 (41%), Gaps = 16/123 (13%)

Query: 296 DNKANNCGIIYCRTREHTTDLADALRRKV-------NKHERSRVQESFMRGEINVITATI 348
           +N+     I+     E +  LA+ +R+            +R  V+++F RG I V+ AT 
Sbjct: 69  ENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATP 128

Query: 349 SFGMGIDRQNVRFVVH-------WGMPSSIPAYYQESGRAGRDGL--QSYCRIYHSEHSK 399
           +   G++    R +V        +     +  Y Q +GRAGR G+  +    I   +  +
Sbjct: 129 TLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDR 188

Query: 400 KSL 402
           +  
Sbjct: 189 EIA 191

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 168

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.8 bits (102), Expect = 8e-06
 Identities = 23/122 (18%), Positives = 47/122 (38%), Gaps = 10/122 (8%)

Query: 296 DNKANNCGIIYCRTREHTTDLADALRRKVNKH----------ERSRVQESFMRGEINVIT 345
           D       +I+C T+     L + +R                ER  + + F  G   V+ 
Sbjct: 30  DTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLI 89

Query: 346 ATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV 405
           +T  +  G+D   V  ++++ +P++   Y    GR+GR G +     +      + L  +
Sbjct: 90  STDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDI 149

Query: 406 IK 407
            +
Sbjct: 150 EQ 151

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]} Length = 175

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

 Score = 43.3 bits (102), Expect = 1e-05
 Identities = 26/141 (18%), Positives = 45/141 (31%), Gaps = 21/141 (14%)

Query: 271 DVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRKVNKHERS 330
           D+I+  + +  +  V E + +            ++     E +  ++  L+ K   H+  
Sbjct: 10  DLIYRTM-EGKFKAVAEDVAQR----YMTGQPVLVGTVAVETSELISKLLKNKGIPHQVL 64

Query: 331 RVQESFMRGEI--------NVITATISFGMGIDRQNVRFVVHWG--------MPSSIPAY 374
             +      +I         V  AT   G G D +    V   G           S    
Sbjct: 65  NAKNHEREAQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRID 124

Query: 375 YQESGRAGRDGLQSYCRIYHS 395
            Q  GR+GR G     + Y S
Sbjct: 125 NQLRGRSGRQGDPGITQFYLS 145

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]} Length = 211

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

 Score = 42.0 bits (98), Expect = 5e-05
 Identities = 20/95 (21%), Positives = 35/95 (36%), Gaps = 7/95 (7%)

Query: 322 RKVNKHERSRVQESFMRGEINVITATISFGMGIDRQNVR-FVVHWGMPSSIPAYYQESGR 380
            ++ + E  RV   F     NV+  T     GID       ++       +   +Q  GR
Sbjct: 65  GQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGR 124

Query: 381 AGRDGLQSYCRI------YHSEHSKKSLEYVIKTD 409
            GR   Q+Y  +        +  ++K LE +   +
Sbjct: 125 VGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLE 159

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 299

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score = 38.8 bits (90), Expect = 9e-04
 Identities = 22/145 (15%), Positives = 45/145 (31%), Gaps = 27/145 (18%)

Query: 304 IIYCRTREHTTDLADALRRK------VNKHERSRVQESFMRGEINVITATISFGMGIDRQ 357
             +  +      +A +LR+       +N+    R   +  + + + I AT    MG +  
Sbjct: 40  AWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPTIKQKKPDFILATDIAEMGAN-L 98

Query: 358 NVRFVVHWGMPSSIPAY-------------------YQESGRAGRDGLQSYC-RIYHSEH 397
            V  V+                               Q  GR GR+  +      Y    
Sbjct: 99  CVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPT 158

Query: 398 SKKSLEYVIKTDTSTKREQLELKFK 422
           S+ +  +V   + S   + +E++  
Sbjct: 159 SENNAHHVCWLEASMLLDNMEVRGG 183

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	444
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.97
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.96
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.96
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.95
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.95
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.94
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.94
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.94
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.94
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.93
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.92
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.92
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.92
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.91
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.91
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.91
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.9
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.89
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.88
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.88
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.85
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.84
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.83
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.77
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.77
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.76
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.76
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.76
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.74
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.71
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.66
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.66
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.66
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.64
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.6
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.58
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.56
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.19
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.18
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.18
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.15
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.14
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.08
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.51
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.48
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.45
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.15
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.89
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.69
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	96.63
d1okkd2	207	GTPase domain of the signal recognition particle r	96.58
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.45
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.43
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	96.42
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	96.37
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	96.22
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.18
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	95.91
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	94.81
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	94.67
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	94.64
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	94.58
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	94.49
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	94.32
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	93.36
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	92.49
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	92.43
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	92.35
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	92.18
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	92.17
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	92.13
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	91.28
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	90.85
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	90.37
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	90.36
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	90.31
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	90.13
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	90.11
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	89.83
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	88.72
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	88.51
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	88.36
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	87.41
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	87.29
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	86.76
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	85.97
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	85.63
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	85.55
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	85.53
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	84.84
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	84.17
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	84.01
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	83.53
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	82.78
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	82.64
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	82.48
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	82.19
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	81.88
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	81.85
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	81.7
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	80.63
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	80.63
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	80.48
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	80.32
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	80.01

>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=99.97  E-value=3.6e-32  Score=253.58  Aligned_cols=265  Identities=15%  Similarity=0.088  Sum_probs=166.3

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeC
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVS  144 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~  144 (444)
                      +++++.||||+|||++        |+.++ +.....  ...+++|++|+++|+     .|..+.+ ..+   +.......
T Consensus        10 ~~~lv~~~TGsGKT~~--------~l~~~-~~~~~~--~~~~~lvi~Ptr~La-----~q~~~~l~~~~---~~~~~~~~   70 (305)
T d2bmfa2          10 RLTIMDLHPGAGKTKR--------YLPAI-VREAIK--RGLRTLILAPTRVVA-----AEMEEALRGLP---IRYQTPAI   70 (305)
T ss_dssp             CEEEECCCTTSSTTTT--------HHHHH-HHHHHH--HTCCEEEEESSHHHH-----HHHHHHTTTSC---CBCCC---
T ss_pred             CcEEEEECCCCCHHHH--------HHHHH-HHHHHh--cCCEEEEEccHHHHH-----HHHHHHHhcCC---cceeeeEE
Confidence            8999999999999988        54344 221222  223569999999999     6666666 333   21111111


Q ss_pred             CCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHh
Q psy7952         145 GQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQF  224 (444)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~  224 (444)
                      ...             ......++++|++.+.     ........+.+++++|+||+|++..++..++..+.   . ...
T Consensus        71 ~~~-------------~~~~~~i~~~t~~~l~-----~~~~~~~~~~~~~~vViDE~H~~~~~~~~~~~~l~---~-~~~  128 (305)
T d2bmfa2          71 RAE-------------HTGREIVDLMCHATFT-----MRLLSPIRVPNYNLIIMDEAHFTDPASIAARGYIS---T-RVE  128 (305)
T ss_dssp             ------------------CCCSEEEEEHHHHH-----HHHTSSSCCCCCSEEEEESTTCCSHHHHHHHHHHH---H-HHH
T ss_pred             eec-------------ccCccccccCCcHHHH-----HHHhcCccccceeEEEeeeeeecchhhHHHHHHHH---H-hhc
Confidence            000             1346789999988753     23333444678999999999998765532222221   1 122


Q ss_pred             hCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEEecCCCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEE
Q psy7952         225 TGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVFKTSTFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGI  304 (444)
Q Consensus       225 ~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~i  304 (444)
                      .+ ..+++++|||++.....    ......+........              ...........+.+       .+++++
T Consensus       129 ~~-~~~~v~~SAT~~~~~~~----~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~-------~~~~~l  182 (305)
T d2bmfa2         129 MG-EAAGIFMTATPPGSRDP----FPQSNAPIMDEEREI--------------PERSWNSGHEWVTD-------FKGKTV  182 (305)
T ss_dssp             HT-SCEEEEECSSCTTCCCS----SCCCSSCEEEEECCC--------------CCSCCSSCCHHHHS-------SCSCEE
T ss_pred             cc-cceEEEeecCCCcceee----ecccCCcceEEEEec--------------cHHHHHHHHHHHHh-------hCCCEE
Confidence            23 37899999998764321    000111111111100              00000000111111       478899


Q ss_pred             EEecccchHHHHHHHHHhh------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEE----------eC--
Q psy7952         305 IYCRTREHTTDLADALRRK------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVH----------WG--  366 (444)
Q Consensus       305 Vf~~s~~~~~~l~~~L~~~------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~----------~~--  366 (444)
                      |||++++++++++..|.+.      +...........|++|..++++||+++++|+|++ ++.||.          ++  
T Consensus       183 vf~~~~~~~~~l~~~L~~~~~~~~~l~~~~~~~~~~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~~~~~~~~~~~~  261 (305)
T d2bmfa2         183 WFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEYIKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRCMKPVILTDGE  261 (305)
T ss_dssp             EECSCHHHHHHHHHHHHHHTCCCEECCTTCHHHHGGGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSS
T ss_pred             EEeccHHHHHHHHHHHHhCCCCEEEeCCcChHHHHhhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCCceeeeEecCCC
Confidence            9999999999999999876      3333344556678899999999999999999995 555442          33  


Q ss_pred             --------CCCCHHHHHHHhccCCCCCCceeEEEEecccc
Q psy7952         367 --------MPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS  398 (444)
Q Consensus       367 --------~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~  398 (444)
                              .|.|..+|+||+||+||.|+++..+.++....
T Consensus       262 ~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~~~  301 (305)
T d2bmfa2         262 ERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGEP  301 (305)
T ss_dssp             CEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEECSCC
T ss_pred             CceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEECCCC
Confidence                    35689999999999999999988887776543

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=2.6e-29  Score=219.04  Aligned_cols=195  Identities=17%  Similarity=0.177  Sum_probs=151.9

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      .+.++.+++++ +||+. ||++|.++++.+++| +|+++.||||+|||++        |++|+ ++.+......++++++
T Consensus        10 L~~~l~~~l~~-~g~~~-pt~iQ~~aip~il~g-~dvl~~a~TGsGKTla--------yllP~-l~~~~~~~~~~~~lil   77 (206)
T d1veca_          10 LKRELLMGIFE-MGWEK-PSPIQEESIPIALSG-RDILARAKNGTGKSGA--------YLIPL-LERLDLKKDNIQAMVI   77 (206)
T ss_dssp             CCHHHHHHHHT-TTCCS-CCHHHHHHHHHHHTT-CCEEEECCSSSTTHHH--------HHHHH-HHHCCTTSCSCCEEEE
T ss_pred             cCHHHHHHHHH-CCCCC-CCHHHHHHHHHHHcC-CCEEeeccCccccccc--------cccch-hhcccccccCcceEEE
Confidence            36788999998 49998 999999999999999 9999999999999999        99998 6666666667789999


Q ss_pred             cchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         112 SPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      +|+++|+  .|+.+.+..+......+......|+.........+      ...++|+|+||+++.    ..+......+.
T Consensus        78 ~pt~el~--~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l------~~~~~ivv~TPgrl~----~~~~~~~~~~~  145 (206)
T d1veca_          78 VPTRELA--LQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRL------DDTVHVVIATPGRIL----DLIKKGVAKVD  145 (206)
T ss_dssp             CSCHHHH--HHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHT------TSCCSEEEECHHHHH----HHHHTTCSCCT
T ss_pred             eecchhh--HHHHHHHHHHhhcccCcccccccCCccHHHHHHHH------HhccCeEEeCCcccc----ccccchhcccc
Confidence            9999999  44455555553333336677777777665443333      568999999999985    44444455677


Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeE
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYK  257 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~  257 (444)
                      +++++|+||||.+.+.+  |...+   ..++..++++.|++++|||+++.+.+....+  +.+|+.
T Consensus       146 ~l~~lVlDEaD~ll~~~--f~~~i---~~I~~~~~~~~Q~~l~SAT~~~~v~~l~~~~--l~~P~~  204 (206)
T d1veca_         146 HVQMIVLDEADKLLSQD--FVQIM---EDIILTLPKNRQILLYSATFPLSVQKFMNSH--LEKPYE  204 (206)
T ss_dssp             TCCEEEEETHHHHTSTT--THHHH---HHHHHHSCTTCEEEEEESCCCHHHHHHHHHH--CSSCEE
T ss_pred             ccceEEEeccccccccc--hHHHH---HHHHHhCCCCCEEEEEEecCCHHHHHHHHHH--CCCCEE
Confidence            89999999999999877  66544   4555677888999999999998877766555  456654

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=1.6e-29  Score=222.05  Aligned_cols=195  Identities=15%  Similarity=0.215  Sum_probs=153.3

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      .+.++.+++++ .||.. ||++|.++++.+++| +|+++.||||||||++        |.+|. ++.+......++++++
T Consensus        24 L~~~l~~~L~~-~g~~~-pt~IQ~~aIp~il~g-~dvi~~a~TGSGKTla--------yllPi-l~~l~~~~~~~~~lil   91 (222)
T d2j0sa1          24 LREDLLRGIYA-YGFEK-PSAIQQRAIKQIIKG-RDVIAQSQSGTGKTAT--------FSISV-LQCLDIQVRETQALIL   91 (222)
T ss_dssp             CCHHHHHHHHH-HTCCS-CCHHHHHHHHHHHTT-CCEEEECCTTSSHHHH--------HHHHH-HHTCCTTSCSCCEEEE
T ss_pred             CCHHHHHHHHH-CCCCC-CCHHHHHHHHHHHCC-CCeEEEcCcchhhhhh--------hcccc-cccccccccCceeEEe
Confidence            36788889998 49998 999999999999999 9999999999999999        99998 6667666677789999


Q ss_pred             cchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         112 SPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      +||++|+  .|+.+.+..+..+ ..+++..+.|+.........+.      .+++|+|+||+++.    +.+......+.
T Consensus        92 ~PtreLa--~Qi~~~~~~l~~~-~~i~~~~~~g~~~~~~~~~~l~------~~~~Ilv~TPgrl~----~~~~~~~~~~~  158 (222)
T d2j0sa1          92 APTRELA--VQIQKGLLALGDY-MNVQCHACIGGTNVGEDIRKLD------YGQHVVAGTPGRVF----DMIRRRSLRTR  158 (222)
T ss_dssp             CSSHHHH--HHHHHHHHHHTTT-TTCCEEEECTTSCHHHHHHHHH------HCCSEEEECHHHHH----HHHHTTSSCCT
T ss_pred             cchHHHH--HHHHHHHHHHhCc-cceeEEEEeecccchhhHHHhc------cCCeEEeCCCCcHH----hcccccccccc
Confidence            9999999  4446666666222 2388999999888766655443      36899999999985    44444555678


Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEE
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKV  258 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~  258 (444)
                      +++++|+||||.+.+.|  |..   .+..+++.++++.|++++|||+++...+....+  +.+|+.+
T Consensus       159 ~l~~lVlDEaD~ll~~~--f~~---~i~~I~~~l~~~~Q~ilfSAT~~~~v~~l~~~~--l~~Pv~I  218 (222)
T d2j0sa1         159 AIKMLVLDEADEMLNKG--FKE---QIYDVYRYLPPATQVVLISATLPHEILEMTNKF--MTDPIRI  218 (222)
T ss_dssp             TCCEEEEETHHHHTSTT--THH---HHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGT--CSSCEEE
T ss_pred             cceeeeecchhHhhhcC--cHH---HHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHH--CCCCEEE
Confidence            89999999999999877  554   455666778888999999999988765543333  4566544

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=9.2e-29  Score=215.65  Aligned_cols=197  Identities=14%  Similarity=0.184  Sum_probs=152.1

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      +.++.+++++ .||+. ||++|.++++.+++| +|+++.||||||||++        |.+|. ++.+......+++++++
T Consensus         9 ~~~l~~~l~~-~g~~~-pt~iQ~~aip~il~g-~dvl~~A~TGsGKTla--------~~lp~-l~~~~~~~~~~~~lil~   76 (207)
T d1t6na_           9 KPELLRAIVD-CGFEH-PSEVQHECIPQAILG-MDVLCQAKSGMGKTAV--------FVLAT-LQQLEPVTGQVSVLVMC   76 (207)
T ss_dssp             CHHHHHHHHH-TTCCC-CCHHHHHHHHHHHTT-CCEEEECCTTSCHHHH--------HHHHH-HHHCCCCTTCCCEEEEC
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHHcC-CCeEEEeccccccccc--------cccce-eeeecccCCCceEEEEe
Confidence            5678899998 49998 999999999999999 9999999999999999        88998 55566666667899999


Q ss_pred             chhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCC
Q psy7952         113 PILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNK  192 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~  192 (444)
                      ||++|+  .|+.+.++.+......+....+.|+.........+.     ...++|+|+||+++.    ..+......+.+
T Consensus        77 PtreL~--~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~-----~~~~~ilI~TP~rl~----~~~~~~~~~l~~  145 (207)
T d1t6na_          77 HTRELA--FQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLK-----KNCPHIVVGTPGRIL----ALARNKSLNLKH  145 (207)
T ss_dssp             SCHHHH--HHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHH-----HSCCSEEEECHHHHH----HHHHTTSSCCTT
T ss_pred             ccchhh--HHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHH-----hcCCCEEEeCcchhh----hhccCCceeccc
Confidence            999999  444666666644334477888888887665544332     357899999999985    334444456789


Q ss_pred             ccEEEEecccccccc-CCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEE
Q psy7952         193 LAYIVVDEAHCVSEW-GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVF  259 (444)
Q Consensus       193 ~~~iViDE~H~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~  259 (444)
                      +.++|+||||.+.+. +  +.   ..+.++.+..+++.|++++|||+++...+....+  +.+|+.+.
T Consensus       146 l~~lVlDEaD~ll~~~~--~~---~~i~~I~~~~~~~~Q~il~SAT~~~~v~~l~~~~--l~~P~~I~  206 (207)
T d1t6na_         146 IKHFILDECDKMLEQLD--MR---RDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKF--MQDPMEIF  206 (207)
T ss_dssp             CCEEEEESHHHHHSSHH--HH---HHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTT--CSSCEEEE
T ss_pred             cceeehhhhhhhhhcCC--cH---HHHHHHHHhCCCCCEEEEEeeeCCHHHHHHHHHH--CCCCEEEe
Confidence            999999999998763 3  44   3455666678888999999999998877755443  56676543

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.95  E-value=3.1e-28  Score=212.80  Aligned_cols=194  Identities=15%  Similarity=0.208  Sum_probs=143.5

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      .++++.+++++ +|++. ||++|.++++.+++| +|+++.+|||+|||++        |++|. ++.+......++++++
T Consensus        17 l~~~l~~~L~~-~g~~~-pt~iQ~~aip~il~g-~dvl~~a~TGsGKT~a--------~~lp~-i~~l~~~~~~~~~lil   84 (212)
T d1qdea_          17 LDENLLRGVFG-YGFEE-PSAIQQRAIMPIIEG-HDVLAQAQSGTGKTGT--------FSIAA-LQRIDTSVKAPQALML   84 (212)
T ss_dssp             CCHHHHHHHHH-HTCCS-CCHHHHHHHHHHHTT-CCEEEECCTTSSHHHH--------HHHHH-HHHCCTTCCSCCEEEE
T ss_pred             CCHHHHHHHHH-CCCCC-CCHHHHHHHHHHHcC-CCEEeecccccchhhh--------hHhhh-HhhhhccCCCcceEEE
Confidence            36788899988 59998 899999999999999 9999999999999999        88998 6666667777899999


Q ss_pred             cchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         112 SPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      +||++|+  .|+.+.+..+... ..+......++.........       ..+++|+|+||+++.    .........+.
T Consensus        85 ~pt~el~--~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~-------~~~~~IvI~TP~~l~----~~~~~~~~~l~  150 (212)
T d1qdea_          85 APTRELA--LQIQKVVMALAFH-MDIKVHACIGGTSFVEDAEG-------LRDAQIVVGTPGRVF----DNIQRRRFRTD  150 (212)
T ss_dssp             CSSHHHH--HHHHHHHHHHTTT-SCCCEEEECC-----------------CTTCSEEEECHHHHH----HHHHTTSSCCT
T ss_pred             cccHHHh--hhhhhhhcccccc-cccceeeEeeccchhHHHHH-------hcCCcEEEECCCccc----cccccCceecC
Confidence            9999999  3334555444221 12566666666554433222       246899999999985    33444455678


Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEE
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKV  258 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~  258 (444)
                      +++++|+||||.+.+.+  |...   +..+++.+++++|++++|||+++...+....+  +.+|+.+
T Consensus       151 ~l~~lVlDEad~lld~~--f~~~---v~~I~~~~~~~~Q~vl~SAT~~~~v~~l~~~~--l~~Pv~i  210 (212)
T d1qdea_         151 KIKMFILDEADEMLSSG--FKEQ---IYQIFTLLPPTTQVVLLSATMPNDVLEVTTKF--MRNPVRI  210 (212)
T ss_dssp             TCCEEEEETHHHHHHTT--CHHH---HHHHHHHSCTTCEEEEEESSCCHHHHHHHHHH--CSSCEEE
T ss_pred             cceEEeehhhhhhcccc--hHHH---HHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHH--CCCCEEE
Confidence            89999999999999877  6544   44555667888999999999998877755555  4566544

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=2.1e-28  Score=214.71  Aligned_cols=197  Identities=15%  Similarity=0.174  Sum_probs=147.3

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      .+.++.+++.+ +||+. ||++|..+++.++.| +|+++.||||||||++        |.+|. ++.+......++++|+
T Consensus        19 L~~~l~~~L~~-~g~~~-pt~iQ~~aip~il~g-~dvl~~a~TGsGKTla--------yllp~-l~~i~~~~~~~~alil   86 (218)
T d2g9na1          19 LSESLLRGIYA-YGFEK-PSAIQQRAILPCIKG-YDVIAQAQSGTGKTAT--------FAISI-LQQIELDLKATQALVL   86 (218)
T ss_dssp             CCHHHHHHHHH-HTCCS-CCHHHHHHHHHHHHT-CCEEEECCTTSSHHHH--------HHHHH-HHHCCTTCCSCCEEEE
T ss_pred             CCHHHHHHHHH-CCCCC-CCHHHHHHHHHHHcC-CCEEEEcccchhhhhh--------hhhhh-hheecccccCccEEEE
Confidence            46678889987 59998 999999999999999 9999999999999999        99998 6666666677789999


Q ss_pred             cchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         112 SPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      +||++|+  .|+.+.+..+..... +....+.++..........     ....++|+|+||+++.    ..+......+.
T Consensus        87 ~Pt~eL~--~Q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-----~~~~~~IvV~TP~rl~----~~l~~~~~~~~  154 (218)
T d2g9na1          87 APTRELA--QQIQKVVMALGDYMG-ASCHACIGGTNVRAEVQKL-----QMEAPHIIVGTPGRVF----DMLNRRYLSPK  154 (218)
T ss_dssp             CSSHHHH--HHHHHHHHHHHTTTT-CCEEEECC--CCCSTTTSS-----SSCCCSEEEECHHHHH----HHHHTTSSCST
T ss_pred             cccchhh--hhHHHHHhhhccccc-eeEEeeecccchhHHHHHH-----hcCCCEEEEeCChhHH----HHHhcCCcccc
Confidence            9999999  444666666622211 5555555544333221111     2357899999999985    44445556678


Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEE
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVF  259 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~  259 (444)
                      +++++|+||||.+.+.+  |...+   ..+++.++++.|++++|||+++...+....++  .+|+.+.
T Consensus       155 ~l~~lVlDEaD~ll~~~--f~~~~---~~Il~~~~~~~Q~il~SAT~~~~v~~~~~~~l--~~pv~i~  215 (218)
T d2g9na1         155 YIKMFVLDEADEMLSRG--FKDQI---YDIFQKLNSNTQVVLLSATMPSDVLEVTKKFM--RDPIRIL  215 (218)
T ss_dssp             TCCEEEEESHHHHHHTT--CHHHH---HHHHHHSCTTCEEEEEESCCCHHHHHHHHHHC--SSCEEEE
T ss_pred             cceEEEeeecchhhcCc--hHHHH---HHHHHhCCCCCeEEEEEecCCHHHHHHHHHHC--CCCEEEE
Confidence            89999999999998877  66444   45566778889999999999998777666554  5676554

>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=99.94  E-value=1.7e-27  Score=208.34  Aligned_cols=192  Identities=34%  Similarity=0.594  Sum_probs=152.2

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ++.+.+.+++.||++.|+ ++|.++++.+++| +|+++.+|||+|||++        |.+|.    +...+..   ++++
T Consensus        10 ~~~~~~~l~~~fg~~~~r-p~Q~~ai~~~l~g-~~vlv~apTGsGKT~~--------~~~~~----~~~~~~~---~~v~   72 (206)
T d1oywa2          10 ESGAKQVLQETFGYQQFR-PGQEEIIDTVLSG-RDCLVVMPTGGGKSLC--------YQIPA----LLLNGLT---VVVS   72 (206)
T ss_dssp             HHHHHHHHHHTTCCSSCC-TTHHHHHHHHHTT-CCEEEECSCHHHHHHH--------HHHHH----HHSSSEE---EEEC
T ss_pred             CHHHHHHHHHhcCCCCCC-HHHHHHHHHHHcC-CCEEEEcCCCCCCcch--------hhhhh----hhccCce---EEec
Confidence            566789999999999866 8999999999999 8999999999999999        77777    5555555   9999


Q ss_pred             chhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         113 PILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      |+++|+     .++.+.+ ..+   .......................  .+..+++++||+.+....    ........
T Consensus        73 P~~~L~-----~q~~~~l~~~~---~~~~~~~~~~~~~~~~~~~~~~~--~~~~~i~~~t~~~~~~~~----~~~~~~~~  138 (206)
T d1oywa2          73 PLISLM-----KDQVDQLQANG---VAAACLNSTQTREQQLEVMTGCR--TGQIRLLYIAPERLMLDN----FLEHLAHW  138 (206)
T ss_dssp             SCHHHH-----HHHHHHHHHTT---CCEEEECTTSCHHHHHHHHHHHH--HTCCSEEEECHHHHTSTT----HHHHHTTS
T ss_pred             cchhhh-----hhHHHHHHhhc---ccccccccccccccchhHHHHHh--cCCceEEEEechhhhchh----hcccchhh
Confidence            999999     7777777 555   45555555555444433333332  367899999998876432    33444567


Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCe
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPY  256 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~  256 (444)
                      +++++|+||+|++.+++..++..+..+..+.+.+++ +|++++|||+++...+++.+.+++.+|+
T Consensus       139 ~v~~lviDEaH~~~~~~~~~~~~~~~~~~l~~~~~~-~~ii~lSATl~~~v~~di~~~L~l~~p~  202 (206)
T d1oywa2         139 NPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPT-LPFMALTATADDTTRQDIVRLLGLNDPL  202 (206)
T ss_dssp             CEEEEEESSGGGGCTTSSCCCHHHHGGGGHHHHCTT-SCEEEEESCCCHHHHHHHHHHHTCCSCE
T ss_pred             eeeeeeeeeeeeeeccccchHHHHHHHHHHHHhCCC-CceEEEEeCCCHHHHHHHHHHcCCCCCc
Confidence            899999999999999888788877777777777765 9999999999998888999999999985

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.94  E-value=2.2e-27  Score=207.29  Aligned_cols=192  Identities=16%  Similarity=0.209  Sum_probs=145.3

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      .+.++.+++++ +||+. ||++|.++++.+++|+.|+++++|||+|||++        |.+|. +.. ...+..++++|+
T Consensus        11 l~~~l~~~l~~-~g~~~-pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~--------~~l~~-~~~-~~~~~~~~~lil   78 (208)
T d1hv8a1          11 LSDNILNAIRN-KGFEK-PTDIQMKVIPLFLNDEYNIVAQARTGSGKTAS--------FAIPL-IEL-VNENNGIEAIIL   78 (208)
T ss_dssp             CCHHHHHHHHH-HTCCS-CCHHHHHHHHHHHHTCSEEEEECCSSSSHHHH--------HHHHH-HHH-SCSSSSCCEEEE
T ss_pred             CCHHHHHHHHH-CCCCC-CCHHHHHHHHHHHcCCCCeeeechhcccccce--------eeccc-ccc-cccccCcceEEE
Confidence            35678888987 59998 89999999999999856999999999999999        66666 222 233455688999


Q ss_pred             cchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh
Q psy7952         112 SPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR  189 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~  189 (444)
                      +||++|+  .|+.+.+..+  ..+   ..+....|+.........+       .+++|+|+||+++.    ..+......
T Consensus        79 ~pt~~l~--~q~~~~~~~~~~~~~---~~v~~~~g~~~~~~~~~~l-------~~~~IlV~TP~~l~----~~l~~~~~~  142 (208)
T d1hv8a1          79 TPTRELA--IQVADEIESLKGNKN---LKIAKIYGGKAIYPQIKAL-------KNANIVVGTPGRIL----DHINRGTLN  142 (208)
T ss_dssp             CSCHHHH--HHHHHHHHHHHCSSC---CCEEEECTTSCHHHHHHHH-------HTCSEEEECHHHHH----HHHHTTCSC
T ss_pred             eeccccc--hhhhhhhhhhcccCC---eEEEEeeCCCChHHHHHhc-------CCCCEEEEChHHHH----HHHHcCCCC
Confidence            9999999  3335555555  334   7888888888766554433       26899999999974    334444556


Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEE
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKV  258 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~  258 (444)
                      +++++++|+||+|++.+.+  +.   ..+.++++..++++|++++|||+++...+...+++  .++..+
T Consensus       143 ~~~l~~lViDEad~l~~~~--~~---~~i~~I~~~~~~~~Q~i~~SAT~~~~v~~~~~~~l--~~~~~I  204 (208)
T d1hv8a1         143 LKNVKYFILDEADEMLNMG--FI---KDVEKILNACNKDKRILLFSATMPREILNLAKKYM--GDYSFI  204 (208)
T ss_dssp             TTSCCEEEEETHHHHHTTT--TH---HHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHC--CSEEEE
T ss_pred             cccCcEEEEEChHHhhcCC--Ch---HHHHHHHHhCCCCCeEEEEEccCCHHHHHHHHHHC--CCCeEE
Confidence            7899999999999987765  44   34556667778889999999999988777666664  455443

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.94  E-value=6.9e-26  Score=194.93  Aligned_cols=159  Identities=32%  Similarity=0.604  Sum_probs=133.0

Q ss_pred             CCCCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHH
Q psy7952         263 TFRSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRV  332 (444)
Q Consensus       263 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~  332 (444)
                      ..|||+.|.+....   .+.+.+..++..    .  .+.++||||+|++.++.++..|...          ++..+|..+
T Consensus         2 ~~RpNi~y~v~~~~---~k~~~L~~~l~~----~--~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~   72 (200)
T d1oywa3           2 FDRPNIRYMLMEKF---KPLDQLMRYVQE----Q--RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADV   72 (200)
T ss_dssp             CCCTTEEEEEEECS---SHHHHHHHHHHH----T--TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHH
T ss_pred             CCCCCcEEEEEcCC---cHHHHHHHHHHh----c--CCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHH
Confidence            46899998886543   234444444443    2  4678999999999999999999887          899999999


Q ss_pred             HHHHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhhccch
Q psy7952         333 QESFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTST  412 (444)
Q Consensus       333 ~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~  412 (444)
                      ++.|++|+.++||||+++++|||+|++++||++|+|.|+.+|+||+||+||.|++|.+++++.+.+...++++++.....
T Consensus        73 ~~~f~~g~~~ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d~~~l~~~i~~~~~~  152 (200)
T d1oywa3          73 QEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQG  152 (200)
T ss_dssp             HHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHHHTSCCS
T ss_pred             HHHHhcccceEEEecchhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHHHHHHHHhhhhccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999998877666


Q ss_pred             hHHHHHHHHhhHHHHHHHhh
Q psy7952         413 KREQLELKFKNYLSMLEYCE  432 (444)
Q Consensus       413 ~~~~~~~~~~~~~~~~~~~~  432 (444)
                      ...+..  ......|..|++
T Consensus       153 ~~~~~~--~~~~~~m~~~~~  170 (200)
T d1oywa3         153 QLQDIE--RHKLNAMGAFAE  170 (200)
T ss_dssp             HHHHHH--HHHHHHHHHHHT
T ss_pred             cchhhh--HHHHHHHHHHHh
Confidence            544333  333455555544

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.93  E-value=3.9e-26  Score=199.18  Aligned_cols=193  Identities=18%  Similarity=0.250  Sum_probs=150.2

Q ss_pred             CHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEE
Q psy7952          32 SEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWI  111 (444)
Q Consensus        32 ~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil  111 (444)
                      .+.++.+++++ .||+. ||++|.++++.+++| +|+++.||||+|||++        |++|. ++.+.......+++++
T Consensus         8 L~~~l~~~L~~-~g~~~-pt~iQ~~aip~il~g-~dvi~~a~tGsGKTla--------y~lp~-i~~~~~~~~~~~~~~~   75 (206)
T d1s2ma1           8 LKRELLMGIFE-AGFEK-PSPIQEEAIPVAITG-RDILARAKNGTGKTAA--------FVIPT-LEKVKPKLNKIQALIM   75 (206)
T ss_dssp             CCHHHHHHHHH-TTCCS-CCHHHHHHHHHHHHT-CCEEEECCTTSCHHHH--------HHHHH-HHHCCTTSCSCCEEEE
T ss_pred             CCHHHHHHHHH-CCCCC-CCHHHHHHHHHHHcC-CCEEEecCCcchhhhh--------hcccc-ccccccccccccceee
Confidence            36778899998 59998 999999999999999 9999999999999999        88888 5555556666788999


Q ss_pred             cchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh
Q psy7952         112 SPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR  189 (444)
Q Consensus       112 ~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~  189 (444)
                      +|+.+++     .+....+  ......+++..+.|+.........+      ...++|+|+||+++.    ..+......
T Consensus        76 ~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l------~~~~~Ili~TP~~l~----~~l~~~~~~  140 (206)
T d1s2ma1          76 VPTRELA-----LQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRL------NETVHILVGTPGRVL----DLASRKVAD  140 (206)
T ss_dssp             CSSHHHH-----HHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHT------TSCCSEEEECHHHHH----HHHHTTCSC
T ss_pred             ccchhhh-----hhhhhhhhhcccccCeeEEeecCccchhhHHHHh------cccceEEEECCcccc----cccccceee
Confidence            9999999     3333333  2222338999999988876554443      568999999999985    334444455


Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEE
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKV  258 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~  258 (444)
                      +.+++++|+||||.+.+.+  |..   .+..+++.+++++|++++|||+++.+.+....++  .+|..+
T Consensus       141 l~~l~~lV~DEaD~l~~~~--f~~---~v~~I~~~l~~~~Q~il~SATl~~~v~~~~~~~l--~~P~~I  202 (206)
T d1s2ma1         141 LSDCSLFIMDEADKMLSRD--FKT---IIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHL--HKPYEI  202 (206)
T ss_dssp             CTTCCEEEEESHHHHSSHH--HHH---HHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHC--SSCEEE
T ss_pred             cccceEEEeechhhhhhhh--hHH---HHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHC--CCCEEE
Confidence            7889999999999998765  554   4556666788889999999999988877666654  566544

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=99.92  E-value=9.9e-27  Score=206.93  Aligned_cols=198  Identities=17%  Similarity=0.218  Sum_probs=144.1

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccC---------C
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNG---------N  103 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~---------~  103 (444)
                      .+++.+++++ .||+. ||++|..+++.+++| +|+++.||||+|||++        |++|. ++.+...         .
T Consensus        29 ~~~l~~~L~~-~g~~~-pt~iQ~~~ip~il~g-~dvvi~a~TGsGKTla--------yllp~-l~~l~~~~~~~~~~~~~   96 (238)
T d1wrba1          29 DPTIRNNILL-ASYQR-PTPIQKNAIPAILEH-RDIMACAQTGSGKTAA--------FLIPI-INHLVCQDLNQQRYSKT   96 (238)
T ss_dssp             CCSTTTTTTT-TTCCS-CCHHHHHHHHHHHTT-CCEEEECCTTSSHHHH--------HHHHH-HHHHHTTCC------CC
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHhhhhhCC-CCEEEECCCCCCccee--------eHHHH-HHHHHhcccccccccCC
Confidence            4456777776 59998 999999999999999 9999999999999999        88888 5444322         2


Q ss_pred             ccceeEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHH
Q psy7952         104 VRSRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYL  183 (444)
Q Consensus       104 ~~~~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~  183 (444)
                      ..++++|++|+++|+  .|+.+.+..+..+ ..+++..+.|+..........      ..+++|+|+||+++.    +.+
T Consensus        97 ~~~~alil~pt~el~--~q~~~~~~~~~~~-~~~~~~~~~g~~~~~~~~~~~------~~~~~ivV~TP~~l~----~~~  163 (238)
T d1wrba1          97 AYPKCLILAPTRELA--IQILSESQKFSLN-TPLRSCVVYGGADTHSQIREV------QMGCHLLVATPGRLV----DFI  163 (238)
T ss_dssp             BCCSEEEECSSHHHH--HHHHHHHHHHHTT-SSCCEEEECSSSCSHHHHHHH------SSCCSEEEECHHHHH----HHH
T ss_pred             CCceEEEeccchhhh--cchheeeeecccC-CCcEEEEEeccchhhHHHhhc------ccCCceeecCHHHHH----hHH
Confidence            346899999999999  3334444444222 228888888887766543332      568999999999985    444


Q ss_pred             HHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHh-hCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEEE
Q psy7952         184 LQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQF-TGNSIPIIALTATAEPSVKQDIISVLKFNKPYKVF  259 (444)
Q Consensus       184 ~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~~  259 (444)
                      ......+.++.++|+||+|.+.+.+  |...+..+.+.... .+.++|++++|||+++...+....+  +.+++.+.
T Consensus       164 ~~~~~~l~~v~~lViDEaD~ll~~~--f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~l~~~~--~~~p~~i~  236 (238)
T d1wrba1         164 EKNKISLEFCKYIVLDEADRMLDMG--FEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADF--LYNYIFMT  236 (238)
T ss_dssp             HTTSBCCTTCCEEEEETHHHHHHTT--CHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHH--CSSCEEEE
T ss_pred             ccCceeccccceeeeehhhhhhhhc--cHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHHHHHHH--CCCCEEEE
Confidence            4455567899999999999998876  66555554332111 1224799999999998887765555  45665543

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=1.9e-24  Score=180.89  Aligned_cols=136  Identities=16%  Similarity=0.323  Sum_probs=119.1

Q ss_pred             CCCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHH
Q psy7952         265 RSNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQE  334 (444)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~  334 (444)
                      ..++...+...+....+...+.+++...      ...++||||++++.++.++..|...          +++.+|..+++
T Consensus         5 l~~i~q~~v~v~~~~~K~~~L~~ll~~~------~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~   78 (168)
T d2j0sa2           5 LEGIKQFFVAVEREEWKFDTLCDLYDTL------TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMK   78 (168)
T ss_dssp             CTTEEEEEEEESSTTHHHHHHHHHHHHH------TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHH
T ss_pred             CCCcEEEEEEecChHHHHHHHHHHHHhC------CCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHH
Confidence            3455555555555556666666666554      5679999999999999999999887          89999999999


Q ss_pred             HHhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHH
Q psy7952         335 SFMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI  406 (444)
Q Consensus       335 ~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  406 (444)
                      .|++|+.++||||+++++|+|+|++++||+||+|.+...|+||+||+||.|+.|.+++++.+.+...++.+.
T Consensus        79 ~fk~g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d~~~~~~i~  150 (168)
T d2j0sa2          79 EFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIE  150 (168)
T ss_dssp             HHHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHH
T ss_pred             HHhcCCccEEeccchhcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999887777664

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.92  E-value=1.3e-24  Score=181.07  Aligned_cols=124  Identities=22%  Similarity=0.438  Sum_probs=105.6

Q ss_pred             chhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEc
Q psy7952         278 LKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITAT  347 (444)
Q Consensus       278 ~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT  347 (444)
                      .+.+...+.+++...      ...++||||+++..++.++..|...          +++.+|..+++.|+.|+.++||||
T Consensus        11 ~e~K~~~L~~ll~~~------~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~T   84 (162)
T d1fuka_          11 EEYKYECLTDLYDSI------SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILIST   84 (162)
T ss_dssp             GGGHHHHHHHHHHHT------TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEE
T ss_pred             cHHHHHHHHHHHHhC------CCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccceeecc
Confidence            344555555555442      5788999999999999999999887          899999999999999999999999


Q ss_pred             CccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         348 ISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       348 ~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      +++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.+++++.+.+...++.+.+
T Consensus        85 dv~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d~~~~~~i~~  144 (162)
T d1fuka_          85 DLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEK  144 (162)
T ss_dssp             GGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHH
T ss_pred             ccccccccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999988877776653

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.91  E-value=2.8e-24  Score=178.13  Aligned_cols=133  Identities=23%  Similarity=0.434  Sum_probs=113.1

Q ss_pred             CCceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHH
Q psy7952         266 SNLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQES  335 (444)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~  335 (444)
                      +++.+.+..... ..+...+.    +++..   .+.++||||+++++|+.++..|...          ++..+|..++++
T Consensus         2 ~nI~~~~i~v~~-~~K~~~L~----~ll~~---~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~   73 (155)
T d1hv8a2           2 ANIEQSYVEVNE-NERFEALC----RLLKN---KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRL   73 (155)
T ss_dssp             SSSEEEEEECCG-GGHHHHHH----HHHCS---TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHH
T ss_pred             CCeEEEEEEeCh-HHHHHHHH----HHHcc---CCCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhh
Confidence            345555555543 34444444    44432   4668999999999999999999887          889999999999


Q ss_pred             HhcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHH
Q psy7952         336 FMRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI  406 (444)
Q Consensus       336 f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  406 (444)
                      |+.|+.++||||+++++|+|+|++++||++|+|+|+..|+||+||+||.|+.|.+++++.+.+...++.+.
T Consensus        74 f~~~~~~ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~d~~~~~~i~  144 (155)
T d1hv8a2          74 FKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIE  144 (155)
T ss_dssp             HHTTSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHH
T ss_pred             hhcccceeeeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEchHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999998887776653

>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=99.91  E-value=1.3e-25  Score=196.67  Aligned_cols=195  Identities=15%  Similarity=0.181  Sum_probs=141.4

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      ++++.+++++ +||+. ||++|.++++.+++| +|++++||||||||++        |++|. ++...........++++
T Consensus         9 ~~~l~~~l~~-~g~~~-pt~iQ~~aip~~l~G-~dvii~a~TGSGKTla--------yllp~-l~~~~~~~~~~~~~~~~   76 (209)
T d1q0ua_           9 QPFIIEAIKT-LRFYK-PTEIQERIIPGALRG-ESMVGQSQTGTGKTHA--------YLLPI-MEKIKPERAEVQAVITA   76 (209)
T ss_dssp             CHHHHHHHHH-TTCCS-CCHHHHHHHHHHHHT-CCEEEECCSSHHHHHH--------HHHHH-HHHCCTTSCSCCEEEEC
T ss_pred             CHHHHHHHHH-CCCCC-CCHHHHHHHHHHHCC-CCeEeeccccccccee--------eeeee-ccccccccccccccccc
Confidence            6778889998 59998 899999999999999 9999999999999999        88888 55566666666779999


Q ss_pred             chhhhhcccCccchHhhh-cCC--CCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh
Q psy7952         113 PILSSFYLRFRDDKTSIV-TGR--SDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR  189 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l-~~~--~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~  189 (444)
                      |+..+.  .+..+++... ...  .....+....+.......      ......+++|+|+||+++.    ..+......
T Consensus        77 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~Ilv~TP~~l~----~~~~~~~~~  144 (209)
T d1q0ua_          77 PTRELA--TQIYHETLKITKFCPKDRMIVARCLIGGTDKQKA------LEKLNVQPHIVIGTPGRIN----DFIREQALD  144 (209)
T ss_dssp             SSHHHH--HHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHT------TCCCSSCCSEEEECHHHHH----HHHHTTCCC
T ss_pred             cccchh--HHHHHHHHhhhccccccccccccccccchhhHHH------HHHhccCceEEEecCchhh----hhhhhhccc
Confidence            999887  2223334333 111  112445555555433221      2223567999999999975    333344455


Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcCCCCeEE
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKFNKPYKV  258 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~~~~~~~  258 (444)
                      ..+++++|+||+|.+.+++  |...+.   .++..++++.|++++|||+++...+.+..+  +++|..+
T Consensus       145 ~~~l~~lViDEad~ll~~~--f~~~v~---~I~~~~~~~~Q~il~SATl~~~v~~l~~~~--l~~p~~i  206 (209)
T d1q0ua_         145 VHTAHILVVDEADLMLDMG--FITDVD---QIAARMPKDLQMLVFSATIPEKLKPFLKKY--MENPTFV  206 (209)
T ss_dssp             GGGCCEEEECSHHHHHHTT--CHHHHH---HHHHTSCTTCEEEEEESCCCGGGHHHHHHH--CSSCEEE
T ss_pred             cccceEEEEeecccccccc--cHHHHH---HHHHHCCCCCEEEEEEccCCHHHHHHHHHH--CCCCEEE
Confidence            6789999999999999887  665544   455567788999999999998887755555  4566544

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.91  E-value=2.3e-23  Score=175.45  Aligned_cols=134  Identities=20%  Similarity=0.331  Sum_probs=115.3

Q ss_pred             CceEEEEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHH
Q psy7952         267 NLFYDVIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESF  336 (444)
Q Consensus       267 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f  336 (444)
                      ++...+...+. ..+...+.+++.+    .  +..++||||+++++++.++..|...          ++..+|..+++.|
T Consensus         6 ~i~q~yi~v~~-~~K~~~L~~ll~~----~--~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f   78 (171)
T d1s2ma2           6 GITQYYAFVEE-RQKLHCLNTLFSK----L--QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEF   78 (171)
T ss_dssp             TEEEEEEECCG-GGHHHHHHHHHHH----S--CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHH
T ss_pred             ceEEEEEEcCH-HHHHHHHHHHHHh----C--CCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhc
Confidence            44444444432 4455555555544    2  5789999999999999999999887          8999999999999


Q ss_pred             hcCCccEEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHh
Q psy7952         337 MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK  407 (444)
Q Consensus       337 ~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  407 (444)
                      +.|..++||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.+++|+.+.+...++.+.+
T Consensus        79 ~~~~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e~~~~~~i~~  149 (171)
T d1s2ma2          79 RQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQ  149 (171)
T ss_dssp             HTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHH
T ss_pred             ccCccccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999998888777653

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=3e-23  Score=173.83  Aligned_cols=115  Identities=21%  Similarity=0.361  Sum_probs=103.0

Q ss_pred             hhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcC
Q psy7952         279 KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATI  348 (444)
Q Consensus       279 ~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~  348 (444)
                      +.+...+.+++...      ...++||||+++++++.+++.|.+.          +++.+|..+++.|++|+.++||||+
T Consensus        12 ~~K~~~L~~ll~~~------~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~   85 (168)
T d1t5ia_          12 NEKNRKLFDLLDVL------EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN   85 (168)
T ss_dssp             GGHHHHHHHHHHHS------CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESS
T ss_pred             HHHHHHHHHHHHhC------CCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccceeeeccc
Confidence            45555555555442      4678999999999999999999877          8999999999999999999999999


Q ss_pred             ccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccch
Q psy7952         349 SFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       349 ~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                      ++++|+|+|.+++||++++|.+...|+||+||+||.|+.|.+++++.+.+.
T Consensus        86 ~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~~~  136 (168)
T d1t5ia_          86 LFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEND  136 (168)
T ss_dssp             CCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHH
T ss_pred             cccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECchHH
Confidence            999999999999999999999999999999999999999999999977543

>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=99.88  E-value=5.6e-24  Score=185.09  Aligned_cols=182  Identities=16%  Similarity=0.178  Sum_probs=124.1

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS  112 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~  112 (444)
                      .+.+...+++ .|++. ++++|.+++.++.+| +++++++|||+|||.+        +.+++ +..+...   +++++++
T Consensus        11 ~~~~~~~l~~-~g~~~-l~~~Q~~ai~~l~~~-~~~il~apTGsGKT~~--------a~l~i-~~~~~~~---~~vl~l~   75 (202)
T d2p6ra3          11 SSYAVGILKE-EGIEE-LFPPQAEAVEKVFSG-KNLLLAMPTAAGKTLL--------AEMAM-VREAIKG---GKSLYVV   75 (202)
T ss_dssp             HHHHHHHHHC-C---C-CCCCCHHHHHHHTTC-SCEEEECSSHHHHHHH--------HHHHH-HHHHHTT---CCEEEEE
T ss_pred             hHHHHHHHHH-cCCCC-CCHHHHHHHHHHHcC-CCEEEEcCCCCchhHH--------HHHHH-HHHhhcc---Ccceeec
Confidence            3455666776 59988 558999999999999 8999999999999998        33443 2223233   3569999


Q ss_pred             chhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhC
Q psy7952         113 PILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYN  191 (444)
Q Consensus       113 P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~  191 (444)
                      |+++|+     .++.+.+ ........+....++......         ....++++++||..+.    ..+......+.
T Consensus        76 P~~~L~-----~q~~~~~~~~~~~~~~v~~~~~~~~~~~~---------~~~~~~ii~~~~~~~~----~~~~~~~~~~~  137 (202)
T d2p6ra3          76 PLRALA-----GEKYESFKKWEKIGLRIGISTGDYESRDE---------HLGDCDIIVTTSEKAD----SLIRNRASWIK  137 (202)
T ss_dssp             SSHHHH-----HHHHHHHTTTTTTTCCEEEECSSCBCCSS---------CSTTCSEEEEEHHHHH----HHHHTTCSGGG
T ss_pred             ccHHHH-----HHHHHHHHHHhhccccceeeccCcccccc---------cccccceeeeccHHHH----HHHhccchhhh
Confidence            999999     6777776 333333566666665443211         1356889999999874    33333344567


Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhc
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLK  251 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~  251 (444)
                      ++++||+||+|.+.+..  ....+..+...++..+++.|+|+||||+++  .+++.++++
T Consensus       138 ~~~~ii~DE~h~~~~~~--r~~~~~~~l~~i~~~~~~~~~l~lSATl~n--~~~~~~~l~  193 (202)
T d2p6ra3         138 AVSCLVVDEIHLLDSEK--RGATLEILVTKMRRMNKALRVIGLSATAPN--VTEIAEWLD  193 (202)
T ss_dssp             GCCEEEETTGGGGGCTT--THHHHHHHHHHHHHHCTTCEEEEEECCCTT--HHHHHHHTT
T ss_pred             hhhhccccHHHHhcccc--cchHHHHHHHHHHhcCCCCcEEEEcCCCCc--HHHHHHHcC
Confidence            88999999999987655  333344444444555666899999999865  366778774

>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=99.88  E-value=1.4e-24  Score=193.96  Aligned_cols=182  Identities=16%  Similarity=0.136  Sum_probs=117.0

Q ss_pred             HHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcc
Q psy7952          34 QELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISP  113 (444)
Q Consensus        34 ~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P  113 (444)
                      .++.+.+++  ++.. |+++|+++++.++.| ++++++||||+|||.+        +.+++ +.....   .++++|++|
T Consensus        31 ~~~~~~~~~--~~~~-p~~~Q~~~i~~~l~g-~~~~i~apTGsGKT~~--------~~~~~-~~~~~~---~~rvliv~P   94 (237)
T d1gkub1          31 KEFVEFFRK--CVGE-PRAIQKMWAKRILRK-ESFAATAPTGVGKTSF--------GLAMS-LFLALK---GKRCYVIFP   94 (237)
T ss_dssp             HHHHHHHHT--TTCS-CCHHHHHHHHHHHTT-CCEECCCCBTSCSHHH--------HHHHH-HHHHTT---SCCEEEEES
T ss_pred             HHHHHHHHh--ccCC-CCHHHHHHHHHHHCC-CCEEEEecCCChHHHH--------HHHHH-HHHHHh---cCeEEEEec
Confidence            344555544  4444 678999999999999 9999999999999988        44444 222222   346699999


Q ss_pred             hhhhhcccCccchHhhh-----cCCC-CceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHH
Q psy7952         114 ILSSFYLRFRDDKTSIV-----TGRS-DLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHL  187 (444)
Q Consensus       114 ~~~L~~~~q~~~~~~~l-----~~~~-~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~  187 (444)
                      +++|+     .|+.+.+     ..+. .........++.........+.    ...+++|+|+||+.+        .++.
T Consensus        95 t~~La-----~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~----~~~~~~Ilv~Tp~~l--------~~~~  157 (237)
T d1gkub1          95 TSLLV-----IQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQ----NLRNFKIVITTTQFL--------SKHY  157 (237)
T ss_dssp             CHHHH-----HHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHH----SGGGCSEEEEEHHHH--------HHCS
T ss_pred             cHHHH-----HHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhc----cccccceeccChHHH--------HHhh
Confidence            99999     4555444     2221 1123444455555444443332    234679999999875        3344


Q ss_pred             HhhCCccEEEEeccccccccCCCcHHHHHHHHHHH----------HhhCCCCcEEEEeccCCcchHHHH-HHHhcC
Q psy7952         188 VRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELR----------QFTGNSIPIIALTATAEPSVKQDI-ISVLKF  252 (444)
Q Consensus       188 ~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~----------~~~~~~~~~v~lSAT~~~~~~~~~-~~~l~~  252 (444)
                      ....++++||+||+|.+.+.+..    ...+..+.          ...+...+++++|||+++.....+ .+.+++
T Consensus       158 ~~~~~~~~vVvDE~d~~l~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~l~r~ll~f  229 (237)
T d1gkub1         158 RELGHFDFIFVDDVDAILKASKN----VDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQLLNF  229 (237)
T ss_dssp             TTSCCCSEEEESCHHHHHTSTHH----HHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTHHHHHHHHCC
T ss_pred             hhcCCCCEEEEEChhhhhhcccc----hhHHHHhcCChHHHHHHHhhCCCCCeEEEEeCCCCcccHHHHHHHHhCC
Confidence            55678999999999998765422    12222221          122344679999999987665544 445543

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=99.85  E-value=8.5e-21  Score=156.81  Aligned_cols=106  Identities=17%  Similarity=0.232  Sum_probs=91.9

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCC
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMP  368 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p  368 (444)
                      .+.++||||+++++|+.++..|.+.          ++..+|..++++|++|++.|||||+++++|+|+|++++||++++|
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~V~~Vi~~~~~  109 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDAD  109 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTT
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCCCcEEEEeccc
Confidence            5789999999999999999999988          999999999999999999999999999999999999999999977


Q ss_pred             C-----CHHHHHHHhccCCCCCCceeEEEEecccchhhHHHHH
Q psy7952         369 S-----SIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI  406 (444)
Q Consensus       369 ~-----s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~  406 (444)
                      +     |...|+||+||+||.|+ |.++++..... ..+.+.+
T Consensus       110 ~~~~~~~~~~~iq~~GR~gR~~~-g~~~~~~~~~~-~~~~~~i  150 (174)
T d1c4oa2         110 KEGFLRSERSLIQTIGRAARNAR-GEVWLYADRVS-EAMQRAI  150 (174)
T ss_dssp             SCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSSCC-HHHHHHH
T ss_pred             cccccchhHHHHHHhhhhhhcCC-CeeEEeecCCC-HHHHHHH
Confidence            6     55889999999999876 55555554433 3444444

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=99.84  E-value=1.9e-20  Score=157.30  Aligned_cols=98  Identities=21%  Similarity=0.289  Sum_probs=88.1

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCCC
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGMP  368 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~p  368 (444)
                      .+.++||||+++.+++.++..|...          +++.+|..+++.|++|+.+|||||+++++|+|+|++++||+||+|
T Consensus        30 ~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDip~v~~VI~~d~p  109 (181)
T d1t5la2          30 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDAD  109 (181)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCCTTEEEEEETTTT
T ss_pred             cCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCCCCCCEEEEecCC
Confidence            3679999999999999999999888          999999999999999999999999999999999999999999999


Q ss_pred             C-----CHHHHHHHhccCCCCCCceeEEEEeccc
Q psy7952         369 S-----SIPAYYQESGRAGRDGLQSYCRIYHSEH  397 (444)
Q Consensus       369 ~-----s~~~~~Qr~GR~~R~g~~g~~~~~~~~~  397 (444)
                      .     |...|+||+||+||.|..+ +.+++...
T Consensus       110 ~~~~~~s~~~yi~R~GRagR~g~~~-~~~~~~~~  142 (181)
T d1t5la2         110 KEGFLRSERSLIQTIGRAARNANGH-VIMYADTI  142 (181)
T ss_dssp             SCSGGGSHHHHHHHHGGGTTSTTCE-EEEECSSC
T ss_pred             cccccccHHHHHHHHHhhccccCce-eEeecchh
Confidence            6     7899999999999998644 34444433

>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=99.83  E-value=6.9e-21  Score=165.16  Aligned_cols=159  Identities=14%  Similarity=0.105  Sum_probs=107.6

Q ss_pred             CchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhh
Q psy7952          50 KCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      |.+||.+++..+..  +++++++|||+|||++++++        + ...+..  ...++++++|+++|+     .|+.+.
T Consensus        10 pr~~Q~~~~~~~~~--~n~lv~~pTGsGKT~i~~~~--------~-~~~~~~--~~~~il~i~P~~~L~-----~q~~~~   71 (200)
T d1wp9a1          10 PRIYQEVIYAKCKE--TNCLIVLPTGLGKTLIAMMI--------A-EYRLTK--YGGKVLMLAPTKPLV-----LQHAES   71 (200)
T ss_dssp             CCHHHHHHHHHGGG--SCEEEECCTTSCHHHHHHHH--------H-HHHHHH--SCSCEEEECSSHHHH-----HHHHHH
T ss_pred             CCHHHHHHHHHHhc--CCeEEEeCCCCcHHHHHHHH--------H-HHHHHh--cCCcEEEEcCchHHH-----HHHHHH
Confidence            45899999999875  57999999999999884332        2 111211  123569999999999     565655


Q ss_pred             h--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccccc
Q psy7952         130 V--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEW  207 (444)
Q Consensus       130 l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~  207 (444)
                      +  ..+....++...+++.....+...+.       .++++++||+.+.    ..+......+.++++||+||||++...
T Consensus        72 ~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-------~~~i~i~t~~~~~----~~~~~~~~~~~~~~~vIiDE~H~~~~~  140 (200)
T d1wp9a1          72 FRRLFNLPPEKIVALTGEKSPEERSKAWA-------RAKVIVATPQTIE----NDLLAGRISLEDVSLIVFDEAHRAVGN  140 (200)
T ss_dssp             HHHHBCSCGGGEEEECSCSCHHHHHHHHH-------HCSEEEECHHHHH----HHHHTTSCCTTSCSEEEEETGGGCSTT
T ss_pred             HHHhhcccccceeeeecccchhHHHHhhh-------cccccccccchhH----HHHhhhhhhccccceEEEEehhhhhcc
Confidence            5  23334477888888777766555442       4689999999975    333444445678999999999997643


Q ss_pred             CCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcch
Q psy7952         208 GHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSV  242 (444)
Q Consensus       208 ~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~  242 (444)
                      .. .    ..+.........++++++|||||....
T Consensus       141 ~~-~----~~~~~~~~~~~~~~~~l~~SATp~~~~  170 (200)
T d1wp9a1         141 YA-Y----VFIAREYKRQAKNPLVIGLTASPGSTP  170 (200)
T ss_dssp             CH-H----HHHHHHHHHHCSSCCEEEEESCSCSSH
T ss_pred             hh-H----HHHHHHHHhcCCCCcEEEEEecCCCcH
Confidence            21 1    222222223344588999999986643

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.77  E-value=4.6e-19  Score=162.19  Aligned_cols=117  Identities=26%  Similarity=0.376  Sum_probs=99.6

Q ss_pred             hHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh------------------cCHHHHHHHHHHHhcCCcc
Q psy7952         281 SYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK------------------VNKHERSRVQESFMRGEIN  342 (444)
Q Consensus       281 ~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~------------------~~~~~r~~~~~~f~~g~~~  342 (444)
                      +...+.+.+.+.+...  .+.++||||+++.+++.+++.|.+.                  ++..+|..+++.|++|+++
T Consensus       144 K~~~l~~~l~~~~~~~--~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~  221 (286)
T d1wp9a2         144 KMDKLKEIIREQLQRK--QNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFN  221 (286)
T ss_dssp             HHHHHHHHHHHHHHHC--TTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCS
T ss_pred             HHHHHHHHHHHHHHhC--CCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCc
Confidence            4455666666665554  5789999999999999999999875                  4445789999999999999


Q ss_pred             EEEEcCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccchh
Q psy7952         343 VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK  400 (444)
Q Consensus       343 vLvaT~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~  400 (444)
                      |||||+++++|+|+|++++||+||+|+|+..|+||+||+||.+ +|.++.++.++..+
T Consensus       222 vLv~T~~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~-~~~~~~l~~~~~~e  278 (286)
T d1wp9a2         222 VLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGTRD  278 (286)
T ss_dssp             EEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCC-CSEEEEEEETTSHH
T ss_pred             EEEEccceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCC-CCEEEEEEeCCCHH
Confidence            9999999999999999999999999999999999999999975 67778888766543

>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=99.77  E-value=1.7e-18  Score=150.34  Aligned_cols=172  Identities=22%  Similarity=0.224  Sum_probs=128.0

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHc----c-CCcEEEEccCCCcccccccccccceEEeCCCccccccCCccce
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILL----R-THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSR  107 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~----~-~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~  107 (444)
                      +.+..+.+...|+|..  |+-|.+++..+.+    + ..+.+++|.||||||.+        |...+ ...+..+.   +
T Consensus        41 ~~~~~~~~~~~lP~~l--t~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V--------~~~a~-~~~~~~g~---q  106 (233)
T d2eyqa3          41 DREQYQLFCDSFPFET--TPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEV--------AMRAA-FLAVDNHK---Q  106 (233)
T ss_dssp             CHHHHHHHHHTCCSCC--CHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHH--------HHHHH-HHHHTTTC---E
T ss_pred             CHHHHHhhhhcccccc--chhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHH--------HHHHH-HHHHHcCC---c
Confidence            4556666666678874  7899999988765    2 24689999999999999        44333 22233333   4


Q ss_pred             eEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH
Q psy7952         108 NGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ  185 (444)
Q Consensus       108 vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~  185 (444)
                      +++++|+..|+     .|.++++  .++..++++..+++..+..++...+..+.  .+..+|+|||         +..+.
T Consensus       107 v~~l~Pt~~La-----~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~--~g~~~iviGt---------hs~l~  170 (233)
T d2eyqa3         107 VAVLVPTTLLA-----QQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVA--EGKIDILIGT---------HKLLQ  170 (233)
T ss_dssp             EEEECSSHHHH-----HHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHH--TTCCSEEEEC---------THHHH
T ss_pred             eEEEccHHHhH-----HHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHh--CCCCCEEEee---------hhhhc
Confidence            59999999999     7777777  33333489999999999999888888876  5788999999         66777


Q ss_pred             HHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHH
Q psy7952         186 HLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQ  244 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~  244 (444)
                      ....+.++++||+||-|++.     ++..    ..+. ....++.++.+||||.+....
T Consensus       171 ~~~~f~~LgLiIiDEeH~fg-----~kQ~----~~l~-~~~~~~~~l~~SATPiprtl~  219 (233)
T d2eyqa3         171 SDVKFKDLGLLIVDEEHRFG-----VRHK----ERIK-AMRANVDILTLTATPIPRTLN  219 (233)
T ss_dssp             SCCCCSSEEEEEEESGGGSC-----HHHH----HHHH-HHHTTSEEEEEESSCCCHHHH
T ss_pred             cCCccccccceeeechhhhh-----hHHH----HHHH-hhCCCCCEEEEecchhHHHHH
Confidence            77788999999999999943     2211    1222 223348899999999997755

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=99.76  E-value=1.5e-17  Score=140.10  Aligned_cols=137  Identities=19%  Similarity=0.231  Sum_probs=123.7

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh------------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeC
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK------------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWG  366 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~------------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~  366 (444)
                      .++++.+.||..+..+.++..+.+.            |++++++.++.+|++|+.+|||||.++++|||+|+++++|..+
T Consensus        30 rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGiDvpnA~~iiI~~  109 (211)
T d2eyqa5          30 RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIER  109 (211)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEETT
T ss_pred             cCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhccCCCCCcEEEEec
Confidence            6899999999999999999999887            9999999999999999999999999999999999999999888


Q ss_pred             CCC-CHHHHHHHhccCCCCCCceeEEEEeccc------chhhHHHHHhhcc---chhHHHHHHHHhhHHHHHHHhhhce
Q psy7952         367 MPS-SIPAYYQESGRAGRDGLQSYCRIYHSEH------SKKSLEYVIKTDT---STKREQLELKFKNYLSMLEYCEQGY  435 (444)
Q Consensus       367 ~p~-s~~~~~Qr~GR~~R~g~~g~~~~~~~~~------~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~  435 (444)
                      ... ....+.|..||+||.+..++|++++++.      ..++++.+.....   ..+..+.+.+++...+++-..++|.
T Consensus       110 a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~~~~~~~~a~~RL~~l~~~~dlg~GF~iA~~DL~iRG~G~llG~~QsG~  188 (211)
T d2eyqa5         110 ADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGS  188 (211)
T ss_dssp             TTSSCHHHHHHHHTTCCBTTBCEEEEEEECCGGGSCHHHHHHHHHHTTCCSBSHHHHHHHHHHHHHHHHHHHCHHHHHH
T ss_pred             chhccccccccccceeeecCccceEEEEecCCcCCCchHHHHHHHHHhcccCCcceeeeHhHHhhcCCccccccccCCc
Confidence            764 8999999999999999999999998643      2456777777777   7788899999999999998887774

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.76  E-value=3.8e-19  Score=142.42  Aligned_cols=94  Identities=19%  Similarity=0.250  Sum_probs=79.1

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeC----CC
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWG----MP  368 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~----~p  368 (444)
                      .++++||||+|+++|+.+++.|.+.      ..   +....+.|++|+.++||||+++++|+| |+++.||+++    +|
T Consensus        34 ~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H---~~~~~~~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~~~~~~P  109 (138)
T d1jr6a_          34 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYY---RGLDVSVIPTNGDVVVVATDALMTGFT-GDFDSVIDCNTSDGKP  109 (138)
T ss_dssp             TTSCEEEECSCHHHHHHHHHHHHHHTCEEEEEC---TTCCSCCCTTSSCEEEEESSSSCSSSC-CCBSEEEECSEETTEE
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHhccccchhhhh---ccchhhhhhhhhcceeehhHHHHhccc-cccceEEEEEecCCCC
Confidence            4779999999999999999999887      11   111134578899999999999999999 9999999865    69


Q ss_pred             CCHHHHHHHhccCCCCCCceeEEEEecccc
Q psy7952         369 SSIPAYYQESGRAGRDGLQSYCRIYHSEHS  398 (444)
Q Consensus       369 ~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~  398 (444)
                      .+..+|+||+||+|| |++|. +.|+.+.+
T Consensus       110 ~~~~~y~qr~GR~gR-g~~G~-~~~i~~~e  137 (138)
T d1jr6a_         110 QDAVSRTQRRGRTGR-GKPGI-YRFVAPGE  137 (138)
T ss_dssp             CCHHHHHHHHTTBCS-SSCEE-EEECCSSC
T ss_pred             CCHHHHHhHhccccC-CCCcE-EEEEcCCC
Confidence            999999999999999 89995 66776654

>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=99.76  E-value=9.3e-19  Score=155.03  Aligned_cols=171  Identities=19%  Similarity=0.202  Sum_probs=125.9

Q ss_pred             HHHHHHHHHHhCCcccCchHHHHHHHHHHc----c-CCcEEEEccCCCcccccccccccceEEeCCCccccccCCcccee
Q psy7952          34 QELTAKLKALFGFDSFKCELQKKAIRHILL----R-THDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRN  108 (444)
Q Consensus        34 ~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~----~-~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~v  108 (444)
                      .++.+.+...+.|+  .|+-|.+++..+..    + ..+.+++|.||||||.+|+.        .+ ...+..+..   +
T Consensus        70 ~~l~~~f~~~LPFe--LT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~--------a~-~~~~~~g~q---~  135 (264)
T d1gm5a3          70 GKLAEEFIKSLPFK--LTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQL--------AI-LDNYEAGFQ---T  135 (264)
T ss_dssp             THHHHHHHHHSSSC--CCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHH--------HH-HHHHHHTSC---E
T ss_pred             hHHHHHHHhhcccc--CCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHH--------HH-HHHHhcccc---e
Confidence            34556666667888  48899999999874    2 24679999999999999443        33 222444444   4


Q ss_pred             EEEcchhhhhcccCccchHhhh--cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHH
Q psy7952         109 GWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQH  186 (444)
Q Consensus       109 lil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~  186 (444)
                      ++++||..|+     .|+++.+  .+...++.+..++|+....++.+.+..+.  .+..+|+|||         +.++..
T Consensus       136 ~~m~Pt~~La-----~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~--~g~~~iiIGT---------hsl~~~  199 (264)
T d1gm5a3         136 AFMVPTSILA-----IQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLR--NGQIDVVIGT---------HALIQE  199 (264)
T ss_dssp             EEECSCHHHH-----HHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHH--SSCCCEEEEC---------TTHHHH
T ss_pred             eEEeehHhhh-----HHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHH--CCCCCEEEee---------hHHhcC
Confidence            9999999999     6777666  33222389999999999999999998886  5889999999         555677


Q ss_pred             HHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHH
Q psy7952         187 LVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQ  244 (444)
Q Consensus       187 ~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~  244 (444)
                      ...+.++++|||||-|++.-.+.          ..+.....++.++.|||||.+....
T Consensus       200 ~~~f~~LglviiDEqH~fgv~Qr----------~~l~~~~~~~~~l~~SATPiprtl~  247 (264)
T d1gm5a3         200 DVHFKNLGLVIIDEQHRFGVKQR----------EALMNKGKMVDTLVMSATPIPRSMA  247 (264)
T ss_dssp             CCCCSCCCEEEEESCCCC---------------CCCCSSSSCCCEEEEESSCCCHHHH
T ss_pred             CCCccccceeeeccccccchhhH----------HHHHHhCcCCCEEEEECCCCHHHHH
Confidence            77788999999999999642221          1112233458899999999987654

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.74  E-value=5.2e-18  Score=145.70  Aligned_cols=110  Identities=26%  Similarity=0.472  Sum_probs=93.8

Q ss_pred             HHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh----------------------------------------cCH
Q psy7952         287 EFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK----------------------------------------VNK  326 (444)
Q Consensus       287 ~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~----------------------------------------~~~  326 (444)
                      +++.+.+.    .++++||||+|++.|+.++..|...                                        +++
T Consensus        31 ~l~~~~i~----~~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~  106 (201)
T d2p6ra4          31 ELVEECVA----ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLN  106 (201)
T ss_dssp             HHHHHHHH----TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCH
T ss_pred             HHHHHHHH----cCCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhh
Confidence            44444443    3678999999999999998887753                                        789


Q ss_pred             HHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEE-------eCCCCCHHHHHHHhccCCCCCC--ceeEEEEeccc
Q psy7952         327 HERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVH-------WGMPSSIPAYYQESGRAGRDGL--QSYCRIYHSEH  397 (444)
Q Consensus       327 ~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~-------~~~p~s~~~~~Qr~GR~~R~g~--~g~~~~~~~~~  397 (444)
                      ++|..+++.|++|.+++||||+++++|||+|...+||+       .+.|.+..+|+||+|||||.|.  .|.++++..+.
T Consensus       107 ~~r~~ie~~f~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~  186 (201)
T d2p6ra4         107 GQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKR  186 (201)
T ss_dssp             HHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGG
T ss_pred             hhHHHHHHHHhCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCCC
Confidence            99999999999999999999999999999998888886       5567899999999999999884  68888887776


Q ss_pred             chh
Q psy7952         398 SKK  400 (444)
Q Consensus       398 ~~~  400 (444)
                      +..
T Consensus       187 ~~~  189 (201)
T d2p6ra4         187 DRE  189 (201)
T ss_dssp             GHH
T ss_pred             ChH
Confidence            543

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.71  E-value=7.9e-19  Score=149.75  Aligned_cols=151  Identities=20%  Similarity=0.317  Sum_probs=115.9

Q ss_pred             HHHHHHHHHHHhccCCCCCceEEEEecccchHHHH--------HHHHHhh-------------cCHHHHHHHHHHHhcCC
Q psy7952         282 YAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDL--------ADALRRK-------------VNKHERSRVQESFMRGE  340 (444)
Q Consensus       282 ~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l--------~~~L~~~-------------~~~~~r~~~~~~f~~g~  340 (444)
                      ...+.+.+.+.+.    .++++.|.||..+..+.+        ++.|.+.             |++++|+.++++|++|+
T Consensus        15 ~~~v~~~I~~el~----~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~   90 (206)
T d1gm5a4          15 VNEVYEFVRQEVM----RGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGR   90 (206)
T ss_dssp             HHHHHHHHHHHTT----TSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTS
T ss_pred             HHHHHHHHHHHHH----cCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCC
Confidence            3445555555443    578889999877665543        2333222             99999999999999999


Q ss_pred             ccEEEEcCccccccccCCccEEEEeCCCC-CHHHHHHHhccCCCCCCceeEEEEecccch---hhHHHHHhhccchhHHH
Q psy7952         341 INVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQSYCRIYHSEHSK---KSLEYVIKTDTSTKREQ  416 (444)
Q Consensus       341 ~~vLvaT~~~~~Gidi~~~~~Vi~~~~p~-s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~---~~~~~~~~~~~~~~~~~  416 (444)
                      ++|||||+++++|||+|++++||+++.|. +...+.|..||+||.|..|+|++++++.+.   +.++.+.......+..+
T Consensus        91 ~~iLVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~~~~~~rl~~~~~~~dGf~ia~  170 (206)
T d1gm5a4          91 YDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERLRFFTLNTDGFKIAE  170 (206)
T ss_dssp             SSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHHHHHHHHTCCCSHHHHH
T ss_pred             EEEEEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeeccccccchhhhhhccccCCCchHHH
Confidence            99999999999999999999999999987 788889999999999999999999976554   45666667888888889


Q ss_pred             HHHHHhhHHHHHHHhhhcee
Q psy7952         417 LELKFKNYLSMLEYCEQGYF  436 (444)
Q Consensus       417 ~~~~~~~~~~~~~~~~~~~~  436 (444)
                      .+++++...++.-..++|..
T Consensus       171 ~Dl~lRG~G~~lG~~QsG~~  190 (206)
T d1gm5a4         171 YDLKTRGPGEFFGVKQHGLS  190 (206)
T ss_dssp             HHHHSSCCCC----CCCSSC
T ss_pred             HHHhccCCccccccccCCCC
Confidence            99999999888877777753

>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=99.66  E-value=2.3e-17  Score=142.82  Aligned_cols=134  Identities=17%  Similarity=0.115  Sum_probs=87.4

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l  130 (444)
                      .+||.+++..+.++ ++.++.+|||+|||++|+..+          .  ...   .++||+||+++|+     .|..+.+
T Consensus        72 r~yQ~eav~~~~~~-~~~ll~~~tG~GKT~~a~~~~----------~--~~~---~~~Liv~p~~~L~-----~q~~~~~  130 (206)
T d2fz4a1          72 RDYQEKALERWLVD-KRGCIVLPTGSGKTHVAMAAI----------N--ELS---TPTLIVVPTLALA-----EQWKERL  130 (206)
T ss_dssp             CHHHHHHHHHHTTT-SEEEEEESSSTTHHHHHHHHH----------H--HSC---SCEEEEESSHHHH-----HHHHHHH
T ss_pred             CHHHHHHHHHHHhC-CCcEEEeCCCCCceehHHhHH----------H--Hhc---CceeEEEcccchH-----HHHHHHH
Confidence            47999999999988 788999999999998833211          0  112   3569999999999     5555555


Q ss_pred             -cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCC
Q psy7952         131 -TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGH  209 (444)
Q Consensus       131 -~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~  209 (444)
                       .++.  ..+....+..               ....+++++|++.+..       .......++++||+||||++.... 
T Consensus       131 ~~~~~--~~~~~~~~~~---------------~~~~~i~i~t~~~~~~-------~~~~~~~~~~lvIiDEaH~~~a~~-  185 (206)
T d2fz4a1         131 GIFGE--EYVGEFSGRI---------------KELKPLTVSTYDSAYV-------NAEKLGNRFMLLIFDEVHHLPAES-  185 (206)
T ss_dssp             GGGCG--GGEEEESSSC---------------BCCCSEEEEEHHHHHH-------THHHHTTTCSEEEEECSSCCCTTT-
T ss_pred             Hhhcc--cchhhccccc---------------ccccccccceehhhhh-------hhHhhCCcCCEEEEECCeeCCcHH-
Confidence             3331  2234444432               2345789999777531       112234679999999999975321 


Q ss_pred             CcHHHHHHHHHHHHhhCCCCcEEEEeccCC
Q psy7952         210 DFRPTYRRLGELRQFTGNSIPIIALTATAE  239 (444)
Q Consensus       210 ~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~  239 (444)
                       +    ..   +...++. ...++||||+.
T Consensus       186 -~----~~---i~~~~~~-~~~lgLTATl~  206 (206)
T d2fz4a1         186 -Y----VQ---IAQMSIA-PFRLGLTATFE  206 (206)
T ss_dssp             -H----HH---HHHTCCC-SEEEEEEESCC
T ss_pred             -H----HH---HHhccCC-CcEEEEecCCC
Confidence             2    22   2233332 56899999983

>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=99.66  E-value=8.2e-18  Score=152.46  Aligned_cols=172  Identities=15%  Similarity=0.142  Sum_probs=108.0

Q ss_pred             CCCCCHHHHHHHHHHHh------CCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCcccccc
Q psy7952          28 GGKVSEQELTAKLKALF------GFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILN  101 (444)
Q Consensus        28 ~~~~~~~~~~~~l~~~~------g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~  101 (444)
                      ...+...++.+.++..-      .++ +| +||.+++..++.+ ++.++.+|||+|||++|...+          ..+..
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~r-dyQ~~av~~~l~~-~~~il~~pTGsGKT~i~~~i~----------~~~~~  154 (282)
T d1rifa_          88 KEELSRKDFDEWLSKLEIYSGNKRIE-PH-WYQKDAVFEGLVN-RRRILNLPTSAGRSLIQALLA----------RYYLE  154 (282)
T ss_dssp             CCCCCHHHHHHHHHTCCCEETTEECC-CC-HHHHHHHHHHHHH-SEEEECCCTTSCHHHHHHHHH----------HHHHH
T ss_pred             cccccchhcccccccccccccCCccc-cc-hHHHHHHHHHHhc-CCceeEEEcccCccHHHHHHH----------HHhhh
Confidence            44556777776666421      233 24 8999999999998 889999999999998843211          11222


Q ss_pred             CCccceeEEEcchhhhhcccCccchHhhh-cCC-CCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCcccccc
Q psy7952         102 GNVRSRNGWISPILSSFYLRFRDDKTSIV-TGR-SDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTES  179 (444)
Q Consensus       102 ~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~-~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~  179 (444)
                      .+ ..++||++|+++|+     .|..+.+ ..+ .....+..+.++......         .....+++++|++.+... 
T Consensus       155 ~~-~~k~Liivp~~~Lv-----~Q~~~~f~~~~~~~~~~~~~~~~g~~~~~~---------~~~~~~i~i~t~qs~~~~-  218 (282)
T d1rifa_         155 NY-EGKILIIVPTTALT-----TQMADDFVDYRLFSHAMIKKIGGGASKDDK---------YKNDAPVVVGTWQTVVKQ-  218 (282)
T ss_dssp             HC-SSEEEEECSSHHHH-----HHHHHHHHHHTSCCGGGEEECSTTCSSTTC---------CCTTCSEEEECHHHHTTS-
T ss_pred             cc-cceEEEEEcCchhH-----HHHHHHHHHhhccccccceeecceeccccc---------ccccceEEEEeeehhhhh-
Confidence            22 23679999999999     5555655 222 122334455554432211         124578999998776421 


Q ss_pred             HHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchH
Q psy7952         180 FHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVK  243 (444)
Q Consensus       180 ~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~  243 (444)
                            ....+.++++||+||||++.+         ..+..++..+.+....++|||||++...
T Consensus       219 ------~~~~~~~f~~VIvDEaH~~~a---------~~~~~il~~~~~~~~rlGlTaT~~~~~~  267 (282)
T d1rifa_         219 ------PKEWFSQFGMMMNDECHLATG---------KSISSIISGLNNCMFKFGLSGSLRDGKA  267 (282)
T ss_dssp             ------CGGGGGGEEEEEEETGGGCCH---------HHHHHHTTTCTTCCEEEEECSSCCTTST
T ss_pred             ------cccccCCCCEEEEECCCCCCc---------hhHHHHHHhccCCCeEEEEEeecCCCCc
Confidence                  112345799999999999642         2233444445443456999999976543

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.66  E-value=2.1e-17  Score=142.54  Aligned_cols=99  Identities=21%  Similarity=0.277  Sum_probs=87.7

Q ss_pred             HHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEE
Q psy7952         288 FIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFV  362 (444)
Q Consensus       288 ~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~V  362 (444)
                      .+.+++...  .+.++||||++.+.++.+++.|...     ++..+|..+++.|++|+.+|||+|+++++|+|+|.+++|
T Consensus        83 ~l~~ll~~~--~~~k~lvf~~~~~~~~~l~~~l~~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gidl~~~~~v  160 (200)
T d2fwra1          83 KLREILERH--RKDKIIIFTRHNELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVG  160 (200)
T ss_dssp             HHHHHHHHT--SSSCBCCBCSCHHHHHHHHHHTTCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEE
T ss_pred             HHHHHHHhC--CCCcEEEEeCcHHHHHHHHhhcCcceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhcccCCCCCCEE
Confidence            334444433  4789999999999999999888655     788999999999999999999999999999999999999


Q ss_pred             EEeCCCCCHHHHHHHhccCCCCCCce
Q psy7952         363 VHWGMPSSIPAYYQESGRAGRDGLQS  388 (444)
Q Consensus       363 i~~~~p~s~~~~~Qr~GR~~R~g~~g  388 (444)
                      |++++|+|...|+||+||++|.|+++
T Consensus       161 i~~~~~~s~~~~~Q~iGR~~R~~~~k  186 (200)
T d2fwra1         161 VIMSGSGSAREYIQRLGRILRPSKGK  186 (200)
T ss_dssp             EEECCSSCCHHHHHHHHHSBCCCTTT
T ss_pred             EEeCCCCCHHHHHHHHHhcCCCCCCC
Confidence            99999999999999999999998754

>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=99.64  E-value=2.1e-17  Score=133.92  Aligned_cols=136  Identities=15%  Similarity=0.073  Sum_probs=80.2

Q ss_pred             HccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh-cCCCCceeEE
Q psy7952          62 LLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLE  140 (444)
Q Consensus        62 ~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~  140 (444)
                      ++..+++++.+|||+|||.+|+.+        . +.....  ...++++++|+++++     .+..+.+ ...   ..+.
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~--------~-~~~~~~--~~~~vli~~p~~~l~-----~q~~~~~~~~~---~~~~   64 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQ--------I-LAECAR--RRLRTLVLAPTRVVL-----SEMKEAFHGLD---VKFH   64 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHH--------H-HHHHHH--TTCCEEEEESSHHHH-----HHHHHHTTTSC---EEEE
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHH--------H-HHHhhh--cCceeeeeecchhHH-----HHHHHHhhhhh---hhhc
Confidence            444489999999999999883221        1 111222  224669999999999     6666655 333   3333


Q ss_pred             EEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHH
Q psy7952         141 LIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGE  220 (444)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~  220 (444)
                      ........             .....+.+.|...+     ...........++++||+||||++...+.    ....+..
T Consensus        65 ~~~~~~~~-------------~~~~~~~~~~~~~l-----~~~~~~~~~~~~~~lvIiDEaH~~~~~~~----~~~~~~~  122 (140)
T d1yksa1          65 TQAFSAHG-------------SGREVIDAMCHATL-----TYRMLEPTRVVNWEVIIMDEAHFLDPASI----AARGWAA  122 (140)
T ss_dssp             SSCCCCCC-------------CSSCCEEEEEHHHH-----HHHHTSSSCCCCCSEEEETTTTCCSHHHH----HHHHHHH
T ss_pred             cccccccc-------------ccccchhhhhHHHH-----HHHHhccccccceeEEEEccccccChhhH----HHHHHHH
Confidence            22222221             13445666665443     22233334467899999999999754321    1122222


Q ss_pred             HHHhhCCCCcEEEEeccCC
Q psy7952         221 LRQFTGNSIPIIALTATAE  239 (444)
Q Consensus       221 ~~~~~~~~~~~v~lSAT~~  239 (444)
                      .+.. .++.++|+||||||
T Consensus       123 ~~~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1         123 HRAR-ANESATILMTATPP  140 (140)
T ss_dssp             HHHH-TTSCEEEEECSSCT
T ss_pred             HHhh-CCCCCEEEEEcCCC
Confidence            2222 34589999999996

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.60  E-value=1.1e-17  Score=149.46  Aligned_cols=105  Identities=24%  Similarity=0.343  Sum_probs=91.2

Q ss_pred             CceEEEEecccchHHHHHHHHHhh----cCHHHHHHHHHHHhcCCccEEEEc----CccccccccCC-ccEEEEeCCCCC
Q psy7952         300 NNCGIIYCRTREHTTDLADALRRK----VNKHERSRVQESFMRGEINVITAT----ISFGMGIDRQN-VRFVVHWGMPSS  370 (444)
Q Consensus       300 ~~~~iVf~~s~~~~~~l~~~L~~~----~~~~~r~~~~~~f~~g~~~vLvaT----~~~~~Gidi~~-~~~Vi~~~~p~s  370 (444)
                      +.++||||++++.++.++..|...    ++..+|..++++|++|+++|||||    +++++|+|+|+ +++||+||+|+ 
T Consensus        25 ~~~~iif~~~~~~~~~l~~~l~~~~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v~~rGlDip~~v~~VI~~d~P~-  103 (248)
T d1gkub2          25 GTGGIIYARTGEEAEEIYESLKNKFRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS-  103 (248)
T ss_dssp             CSCEEEEESSHHHHHHHHHTTTTSSCEEECTTSSSHHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEEEESCCE-
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhCCCeEEEEeccccchhhhccCccccccEEEEeCCCc-
Confidence            567999999999999999999777    888999999999999999999999    77899999996 99999999994 


Q ss_pred             HHHHHHHhccCCCCCCceeEEEEecccchhhHHHHHhh
Q psy7952         371 IPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKT  408 (444)
Q Consensus       371 ~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~  408 (444)
                         |.||+||+||.|..|.+++++...+...+..+...
T Consensus       104 ---~~~r~gR~~R~g~~~~~~~~~~~~~~~~~~~l~~~  138 (248)
T d1gkub2         104 ---FRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPA  138 (248)
T ss_dssp             ---EEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTT
T ss_pred             ---chhhhhhhhccCcceEeeeeccHhhHHHHHHHHHH
Confidence               88999999999999999888888777776665543

>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=99.58  E-value=3.2e-16  Score=126.32  Aligned_cols=126  Identities=12%  Similarity=0.038  Sum_probs=75.5

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccchHhhh--cCCCCceeEEEEe
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDDKTSIV--TGRSDLYQLELIV  143 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~~~~~l--~~~~~~i~~~~~~  143 (444)
                      +..++.+|||+|||.++        ....    ...   ..+++|++|+++|+     +|..+.+  ..+   .......
T Consensus         9 ~~~ll~apTGsGKT~~~--------~~~~----~~~---~~~vli~~P~~~l~-----~q~~~~~~~~~~---~~~~~~~   65 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKV--------PAAY----AAQ---GYKVLVLNPSVAAT-----LGFGAYMSKAHG---VDPNIRT   65 (136)
T ss_dssp             EEEEEECCTTSCTTTHH--------HHHH----HTT---TCCEEEEESCHHHH-----HHHHHHHHHHHS---CCCEEEC
T ss_pred             CEEEEEeCCCCCHHHHH--------HHHH----HHc---CCcEEEEcChHHHH-----HHHHHHHHHHhh---ccccccc
Confidence            67899999999999772        1111    222   23569999999999     4554444  222   2222333


Q ss_pred             CCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEeccccccccCCCcHHHHHHHHHHHH
Q psy7952         144 SGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQ  223 (444)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~  223 (444)
                      ++...             .....+.++|.+.+.       ......+.++++||+||+|++....   ...+..+.+..+
T Consensus        66 ~~~~~-------------~~~~~~~~~~~~~~~-------~~~~~~~~~~~~vIiDE~H~~~~~~---~~~~~~~l~~~~  122 (136)
T d1a1va1          66 GVRTI-------------TTGSPITYSTYGKFL-------ADGGCSGGAYDIIICDECHSTDATS---ILGIGTVLDQAE  122 (136)
T ss_dssp             SSCEE-------------CCCCSEEEEEHHHHH-------HTTGGGGCCCSEEEEETTTCCSHHH---HHHHHHHHHHTT
T ss_pred             ccccc-------------ccccceEEEeeeeec-------cccchhhhcCCEEEEecccccCHHH---HHHHHHHHHHHH
Confidence            33222             234567788866542       2333456789999999999964321   122333333333


Q ss_pred             hhCCCCcEEEEeccC
Q psy7952         224 FTGNSIPIIALTATA  238 (444)
Q Consensus       224 ~~~~~~~~v~lSAT~  238 (444)
                      ..+ ..+++++||||
T Consensus       123 ~~~-~~~~l~~TATP  136 (136)
T d1a1va1         123 TAG-ARLVVLATATP  136 (136)
T ss_dssp             TTT-CSEEEEEESSC
T ss_pred             HCC-CCcEEEEeCCC
Confidence            333 36799999997

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.56  E-value=6.6e-16  Score=136.00  Aligned_cols=96  Identities=15%  Similarity=0.225  Sum_probs=79.9

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh----------cCHHHH----------HHHHHHHhcCCccEEEEcCcccc---ccc
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK----------VNKHER----------SRVQESFMRGEINVITATISFGM---GID  355 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r----------~~~~~~f~~g~~~vLvaT~~~~~---Gid  355 (444)
                      .++++||||+|++.|++++..|++.          ++.+.|          ...++.|+.|+.+++|+|+.+.+   |+|
T Consensus        35 kggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giD  114 (299)
T d1a1va2          35 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFS  114 (299)
T ss_dssp             HSSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECC
T ss_pred             cCCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCC
Confidence            3779999999999999999999877          444443          45778899999999999999888   677


Q ss_pred             cCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEec
Q psy7952         356 RQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHS  395 (444)
Q Consensus       356 i~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~  395 (444)
                      ++.+.+|++++.|.|+.+|+||+||+|| |++|....++.
T Consensus       115 id~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~  153 (299)
T d1a1va2         115 LDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAP  153 (299)
T ss_dssp             CSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCS
T ss_pred             CCcceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEec
Confidence            7788899999999999999999999999 88887665553

>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=99.19  E-value=7.2e-12  Score=114.29  Aligned_cols=177  Identities=11%  Similarity=0.099  Sum_probs=97.9

Q ss_pred             cCchHHHHHHHHHHc--------cCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcc
Q psy7952          49 FKCELQKKAIRHILL--------RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYL  120 (444)
Q Consensus        49 ~~t~~Q~~~~~~~~~--------~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~  120 (444)
                      ++ +||.+++..+.+        +...+++.-..|+|||+.|+..+.. + +..   .........++||+||...+.  
T Consensus        56 Lr-~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~-l-~~~---~~~~~~~~~~~LIV~P~sl~~--  127 (298)
T d1z3ix2          56 LR-PHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWT-L-LKQ---SPDCKPEIDKVIVVSPSSLVR--  127 (298)
T ss_dssp             CC-HHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHH-H-HHC---CTTSSCSCSCEEEEECHHHHH--
T ss_pred             cc-HHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHH-H-HHh---cccccCCCCcEEEEccchhhH--
Confidence            45 799999987642        2256899999999999863321110 0 000   000111234679999987443  


Q ss_pred             cCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHh--cCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEE
Q psy7952         121 RFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRL--VKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIV  197 (444)
Q Consensus       121 ~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iV  197 (444)
                       ||.+.+..+ ...   ..+..++++...............  .....+++++|++.+..      ........++++||
T Consensus       128 -qW~~Ei~k~~~~~---~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~------~~~~l~~~~~~~vI  197 (298)
T d1z3ix2         128 -NWYNEVGKWLGGR---VQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRL------HAEVLHKGKVGLVI  197 (298)
T ss_dssp             -HHHHHHHHHHGGG---CCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHH------HTTTTTTSCCCEEE
T ss_pred             -HHHHHHHhhcCCc---eeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeeccccc------chhcccccceeeee
Confidence             334555554 333   455556655433322222222211  12345788888666421      11222234689999


Q ss_pred             EeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhc
Q psy7952         198 VDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLK  251 (444)
Q Consensus       198 iDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~  251 (444)
                      +||+|++...+   ...+..+..    +.. ...+++||||..+...++...+.
T Consensus       198 ~DEaH~ikn~~---s~~~~a~~~----l~~-~~rllLTGTPi~N~~~dl~~ll~  243 (298)
T d1z3ix2         198 CDEGHRLKNSD---NQTYLALNS----MNA-QRRVLISGTPIQNDLLEYFSLVH  243 (298)
T ss_dssp             ETTGGGCCTTC---HHHHHHHHH----HCC-SEEEEECSSCSGGGGGGCHHHHH
T ss_pred             ccccccccccc---chhhhhhhc----ccc-ceeeeecchHHhhhhHHHHHHHH
Confidence            99999986543   122223322    232 56799999998876665555544

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=99.18  E-value=1.1e-11  Score=111.34  Aligned_cols=96  Identities=21%  Similarity=0.176  Sum_probs=72.5

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh------cCHHHHHHHHHHHhcCCccEEEEcCccccccccCCccEEEEeCC-----
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK------VNKHERSRVQESFMRGEINVITATISFGMGIDRQNVRFVVHWGM-----  367 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gidi~~~~~Vi~~~~-----  367 (444)
                      ..++++|||+++.+++.++..|++.      ++........++|++|+.++||||++++.|+|+ ++.+||+.+.     
T Consensus        35 ~~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~~~~~  113 (299)
T d1yksa2          35 DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPTIKQKKPDFILATDIAEMGANL-CVERVLDCRTAFKPV  113 (299)
T ss_dssp             CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC--------CCCSEEEESSSTTCCTTC-CCSEEEECCEEEEEE
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHhhhhcCCcCEEEEechhhhceec-CceEEEecCceecee
Confidence            4788999999999999999999987      222222233456789999999999999999999 5999997664     


Q ss_pred             --------------CCCHHHHHHHhccCCCCCCceeEEEEec
Q psy7952         368 --------------PSSIPAYYQESGRAGRDGLQSYCRIYHS  395 (444)
Q Consensus       368 --------------p~s~~~~~Qr~GR~~R~g~~g~~~~~~~  395 (444)
                                    |.|..+..||.||+||.+...+++.++.
T Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2         114 LVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             EETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             eecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence                          2478899999999999876666666664

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=99.18  E-value=1.2e-10  Score=107.40  Aligned_cols=94  Identities=15%  Similarity=0.185  Sum_probs=84.3

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh----------cCHHHHHHHHHHHhcCCc--c-EEEEcCccccccccCCccEEEEe
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK----------VNKHERSRVQESFMRGEI--N-VITATISFGMGIDRQNVRFVVHW  365 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~----------~~~~~r~~~~~~f~~g~~--~-vLvaT~~~~~Gidi~~~~~Vi~~  365 (444)
                      .+.++|||++.....+.+...|...          ++..+|..+++.|+++..  . +|++|.+++.|+|++.+++||++
T Consensus       117 ~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~agg~GlnL~~a~~vi~~  196 (346)
T d1z3ix1         117 TSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMF  196 (346)
T ss_dssp             CCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEEC
T ss_pred             cCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecchhhhhccccccceEEEEe
Confidence            5789999999999999999988876          788999999999997643  2 68889999999999999999999


Q ss_pred             CCCCCHHHHHHHhccCCCCCCceeEEE
Q psy7952         366 GMPSSIPAYYQESGRAGRDGLQSYCRI  392 (444)
Q Consensus       366 ~~p~s~~~~~Qr~GR~~R~g~~g~~~~  392 (444)
                      |+++++..+.|++||+.|.|+...+.+
T Consensus       197 d~~wnp~~~~Qa~~R~~R~GQ~~~V~v  223 (346)
T d1z3ix1         197 DPDWNPANDEQAMARVWRDGQKKTCYI  223 (346)
T ss_dssp             SCCSSHHHHHHHHTTSSSTTCCSCEEE
T ss_pred             cCCCccchHhHhhhcccccCCCCceEE
Confidence            999999999999999999998866544

>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=99.15  E-value=7.2e-12  Score=109.80  Aligned_cols=161  Identities=15%  Similarity=0.147  Sum_probs=98.8

Q ss_pred             cCchHHHHHHHHHHc---cCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccc
Q psy7952          49 FKCELQKKAIRHILL---RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDD  125 (444)
Q Consensus        49 ~~t~~Q~~~~~~~~~---~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~  125 (444)
                      ++ +||.+++..+..   ....+++..++|+|||+.|+..          +..+...+...++||+||...+.   |+.+
T Consensus        13 L~-~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~----------~~~~~~~~~~~~~LIv~p~~l~~---~W~~   78 (230)
T d1z63a1          13 LR-PYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAV----------FSDAKKENELTPSLVICPLSVLK---NWEE   78 (230)
T ss_dssp             CC-HHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHH----------HHHHHHTTCCSSEEEEECSTTHH---HHHH
T ss_pred             hh-HHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHh----------hhhhhhcccccccceecchhhhh---HHHH
Confidence            45 899999987653   2256899999999999884321          22244445555779999965554   2344


Q ss_pred             hHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHhhCCccEEEEecccccc
Q psy7952         126 KTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVRYNKLAYIVVDEAHCVS  205 (444)
Q Consensus       126 ~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~~~~~~~iViDE~H~~~  205 (444)
                      .+..+...   ..+...........           ..+++|+++|++.+...  .     ......+++||+||+|.+.
T Consensus        79 e~~~~~~~---~~~~~~~~~~~~~~-----------~~~~~vvi~~~~~~~~~--~-----~l~~~~~~~vI~DEah~~k  137 (230)
T d1z63a1          79 ELSKFAPH---LRFAVFHEDRSKIK-----------LEDYDIILTTYAVLLRD--T-----RLKEVEWKYIVIDEAQNIK  137 (230)
T ss_dssp             HHHHHCTT---SCEEECSSSTTSCC-----------GGGSSEEEEEHHHHTTC--H-----HHHTCCEEEEEEETGGGGS
T ss_pred             HHHhhccc---ccceeeccccchhh-----------ccCcCEEEeeHHHHHhH--H-----HHhcccceEEEEEhhhccc
Confidence            44444333   34444333322211           23578999998886531  1     1223468999999999986


Q ss_pred             ccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhcC
Q psy7952         206 EWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLKF  252 (444)
Q Consensus       206 ~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~~  252 (444)
                      ....   .....+.    .+.. ...+++||||..+...++...+.+
T Consensus       138 ~~~s---~~~~~~~----~l~a-~~r~~LTgTPi~n~~~dl~~ll~~  176 (230)
T d1z63a1         138 NPQT---KIFKAVK----ELKS-KYRIALTGTPIENKVDDLWSIMTF  176 (230)
T ss_dssp             CTTS---HHHHHHH----TSCE-EEEEEECSSCSTTCHHHHHHHHHH
T ss_pred             ccch---hhhhhhh----hhcc-ceEEEEecchHHhHHHHHHHHHHh
Confidence            5442   1122222    2222 457899999998888887766654

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=99.14  E-value=1.8e-10  Score=93.23  Aligned_cols=116  Identities=22%  Similarity=0.143  Sum_probs=88.8

Q ss_pred             hhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh--------cCHHHHHHHHHHHhcCCccEEEEcCcc
Q psy7952         279 KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK--------VNKHERSRVQESFMRGEINVITATISF  350 (444)
Q Consensus       279 ~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~--------~~~~~r~~~~~~f~~g~~~vLvaT~~~  350 (444)
                      ..++..+.+.+.+...    .+.++||++.|++.++.++..|.+.        -...+++..+-...-....|.|||+++
T Consensus        17 ~eK~~AIi~eV~~~~~----~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II~~Ag~~g~VtIATNmA   92 (175)
T d1tf5a4          17 EGKFKAVAEDVAQRYM----TGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMA   92 (175)
T ss_dssp             HHHHHHHHHHHHHHHH----HTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTTCEEEEETTS
T ss_pred             HHHHHHHHHHHHHHHh----cCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHHHhccCCCceeehhhHH
Confidence            4555666666655432    5889999999999999999999887        112222322222223345799999999


Q ss_pred             ccccccC--------CccEEEEeCCCCCHHHHHHHhccCCCCCCceeEEEEecccc
Q psy7952         351 GMGIDRQ--------NVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS  398 (444)
Q Consensus       351 ~~Gidi~--------~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~  398 (444)
                      ++|.|+.        +--+||....|.|.....|..||+||.|.+|....|++-+|
T Consensus        93 GRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD  148 (175)
T d1tf5a4          93 GRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  148 (175)
T ss_dssp             STTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             HcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCH
Confidence            9999986        22379999999999999999999999999999999997665

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.08  E-value=2e-10  Score=101.28  Aligned_cols=114  Identities=18%  Similarity=0.196  Sum_probs=78.1

Q ss_pred             hhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh-----------cCHHHHHHHHHHHhcCC-ccEE-EE
Q psy7952         280 DSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK-----------VNKHERSRVQESFMRGE-INVI-TA  346 (444)
Q Consensus       280 ~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~-----------~~~~~r~~~~~~f~~g~-~~vL-va  346 (444)
                      .+...+.+++.+...    .++++||||+.....+.+...+...           ++..+|...++.|.++. ..++ ++
T Consensus        69 ~K~~~l~~~l~~~~~----~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~  144 (244)
T d1z5za1          69 GKMIRTMEIIEEALD----EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLS  144 (244)
T ss_dssp             HHHHHHHHHHHHHHH----TTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEE
T ss_pred             hHHHHHHHHHHhhcc----cccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhcccc
Confidence            355555666655432    5789999999999998888777654           78899999999998664 5665 55


Q ss_pred             cCccccccccCCccEEEEeCCCCCHHHHHHHhccCCCCCCceeEE--EEeccc
Q psy7952         347 TISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCR--IYHSEH  397 (444)
Q Consensus       347 T~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~--~~~~~~  397 (444)
                      +.+.+.|+|++.+++||++++|+|+..+.|+.||+.|.|+...+.  .++..+
T Consensus       145 ~~~~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~~  197 (244)
T d1z5za1         145 VKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  197 (244)
T ss_dssp             CCTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETT
T ss_pred             ccccccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEEEEeeCC
Confidence            688999999999999999999999999999999999998765443  344444

>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=98.51  E-value=2.5e-08  Score=85.77  Aligned_cols=173  Identities=15%  Similarity=0.178  Sum_probs=115.5

Q ss_pred             HHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchh
Q psy7952          36 LTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPIL  115 (444)
Q Consensus        36 ~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~  115 (444)
                      +.++-++.+|..+|  +.|.-.--.+.+|   -+....||-|||++|        .+|+++..+..++.    -+++...
T Consensus        69 VREAakRtlG~Rhy--DVQLiGgi~L~~G---~iaem~TGEGKTL~a--------~l~a~l~al~g~~v----hvvTvNd  131 (273)
T d1tf5a3          69 VREASRRVTGMFPF--KVQLMGGVALHDG---NIAEMKTGEGKTLTS--------TLPVYLNALTGKGV----HVVTVNE  131 (273)
T ss_dssp             HHHHHHHHHSCCCC--HHHHHHHHHHHTT---SEEECCTTSCHHHHH--------HHHHHHHHTTSSCE----EEEESSH
T ss_pred             HHHHHHHhhceEEe--hhHHHHHHHHHhh---hheeecCCCcchhHH--------HHHHHHHHhcCCCc----eEEecCc
Confidence            45677777898863  5888877777776   479999999999994        44553333433333    5667777


Q ss_pred             hhhcccCccchHhhh-----cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHHHHHh-
Q psy7952         116 SSFYLRFRDDKTSIV-----TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQHLVR-  189 (444)
Q Consensus       116 ~L~~~~q~~~~~~~l-----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~~~~~-  189 (444)
                      -|+     ....+.+     .+|   +.+..+.++....++.+.+        .+||+++|...+.   |+++..+... 
T Consensus       132 yLA-----~RDae~m~~iy~~lG---lsvg~~~~~~~~~~r~~~Y--------~~di~Ygt~~e~~---fDyLrd~~~~~  192 (273)
T d1tf5a3         132 YLA-----SRDAEQMGKIFEFLG---LTVGLNLNSMSKDEKREAY--------AADITYSTNNELG---FDYLRDNMVLY  192 (273)
T ss_dssp             HHH-----HHHHHHHHHHHHHTT---CCEEECCTTSCHHHHHHHH--------HSSEEEEEHHHHH---HHHHHHTTCSS
T ss_pred             ccc-----chhhhHHhHHHHHcC---CCccccccccCHHHHHHHh--------hCCceecchhhhh---hhhcchhhhcC
Confidence            787     5666555     677   9999999998888887777        5899999988776   5666555432 


Q ss_pred             -----hCCccEEEEeccccc-cccCC----------CcHH-HHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhc
Q psy7952         190 -----YNKLAYIVVDEAHCV-SEWGH----------DFRP-TYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLK  251 (444)
Q Consensus       190 -----~~~~~~iViDE~H~~-~~~~~----------~~~~-~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~  251 (444)
                           ...+.+.|+||+|.+ .|...          .... .++   .+   +.-..++-+||+|.... ...+.+..+
T Consensus       193 ~~~~~~r~~~~aIvDEvDsiliDeartpliisg~~~~~a~it~q---~~---f~~y~~l~gmtgta~~~-~~e~~~iy~  264 (273)
T d1tf5a3         193 KEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQSMTLATITFQ---NY---FRMYEKLAGMTGTAKTE-EEEFRNIYN  264 (273)
T ss_dssp             GGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEEEEEEEEEHH---HH---HTTSSEEEEEESCCGGG-HHHHHHHHC
T ss_pred             hhhhccCCCCEEEEEcchhhhhhccCCceEeccCccchhhhhHH---HH---HHHHHHHhCCccccHHH-HHHHHhccC
Confidence                 246899999999987 33220          0000 011   22   33335689999997553 444555444

>d1nkta4 c.37.1.19 (A:397-615) Translocation ATPase SecA, nucleotide-binding domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.45  E-value=1.3e-06  Score=71.59  Aligned_cols=116  Identities=22%  Similarity=0.192  Sum_probs=89.7

Q ss_pred             hhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh--------cCHHHHHHHHHHHhcC-CccEEEEcCc
Q psy7952         279 KDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK--------VNKHERSRVQESFMRG-EINVITATIS  349 (444)
Q Consensus       279 ~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~--------~~~~~r~~~~~~f~~g-~~~vLvaT~~  349 (444)
                      ..++..+.+.+.....    .+.|+||.+.|++.++.+...|.+.        -...+|+.-+-. ..| ...|-|||+|
T Consensus        17 ~~K~~Avv~ei~~~h~----~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herEAeIIA-qAG~~GaVTIATNM   91 (219)
T d1nkta4          17 EAKYIAVVDDVAERYA----KGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIA-VAGRRGGVTVATNM   91 (219)
T ss_dssp             HHHHHHHHHHHHHHHH----TTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHH-TTTSTTCEEEEETT
T ss_pred             HHHHHHHHHHHHHHHh----cCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHHHHHHH-hcccCCcEEeeccc
Confidence            4566666666666533    6889999999999999999999988        222333333322 234 4678999999


Q ss_pred             cccccccCC----------------------------------------------------ccEEEEeCCCCCHHHHHHH
Q psy7952         350 FGMGIDRQN----------------------------------------------------VRFVVHWGMPSSIPAYYQE  377 (444)
Q Consensus       350 ~~~Gidi~~----------------------------------------------------~~~Vi~~~~p~s~~~~~Qr  377 (444)
                      +++|.||.=                                                    --+||-.....|..---|-
T Consensus        92 AGRGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRIDnQL  171 (219)
T d1nkta4          92 AGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQL  171 (219)
T ss_dssp             CSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHH
T ss_pred             cCCCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEeccccccccccccc
Confidence            999999931                                                    1268888888999999999


Q ss_pred             hccCCCCCCceeEEEEecccch
Q psy7952         378 SGRAGRDGLQSYCRIYHSEHSK  399 (444)
Q Consensus       378 ~GR~~R~g~~g~~~~~~~~~~~  399 (444)
                      .||+||.|.+|.+..|++-+|.
T Consensus       172 RGRsGRQGDPGsSrFflSLeDd  193 (219)
T d1nkta4         172 RGRSGRQGDPGESRFYLSLGDE  193 (219)
T ss_dssp             HHTSSGGGCCEEEEEEEETTSH
T ss_pred             cccccccCCCccceeEEeccHH
Confidence            9999999999999999987664

>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=98.15  E-value=1e-06  Score=81.00  Aligned_cols=79  Identities=20%  Similarity=0.131  Sum_probs=55.3

Q ss_pred             CCCHHHHHHHHHHHhCCcccCchHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeE
Q psy7952          30 KVSEQELTAKLKALFGFDSFKCELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNG  109 (444)
Q Consensus        30 ~~~~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vl  109 (444)
                      ++....+.+.+.+.|.... .+++|..|+..++.+ +-++|.+|+|||||.+..-      .+.. +... ......+++
T Consensus       130 ~~~~~~~~~~~~~~~~~~~-~~~~Q~~A~~~al~~-~~~vI~G~pGTGKTt~i~~------~l~~-l~~~-~~~~~~~I~  199 (359)
T d1w36d1         130 EVDEALLAQTLDKLFPVSD-EINWQKVAAAVALTR-RISVISGGPGTGKTTTVAK------LLAA-LIQM-ADGERCRIR  199 (359)
T ss_dssp             CCCHHHHHHHHHTTCCCTT-SCCHHHHHHHHHHTB-SEEEEECCTTSTHHHHHHH------HHHH-HHHT-CSSCCCCEE
T ss_pred             CCChHHHHHHHHHhccCcc-cccHHHHHHHHHHcC-CeEEEEcCCCCCceehHHH------HHHH-HHHH-HhccCCeEE
Confidence            4567778888887776555 357999999999988 8899999999999977210      0011 0001 122344779


Q ss_pred             EEcchhhhh
Q psy7952         110 WISPILSSF  118 (444)
Q Consensus       110 il~P~~~L~  118 (444)
                      +++||..-+
T Consensus       200 l~ApTgkAA  208 (359)
T d1w36d1         200 LAAPTGKAA  208 (359)
T ss_dssp             EEBSSHHHH
T ss_pred             EecCcHHHH
Confidence            999999887

>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=96.89  E-value=0.0011  Score=55.08  Aligned_cols=56  Identities=18%  Similarity=0.179  Sum_probs=35.1

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHH
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISV  249 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~  249 (444)
                      ..+.++|+||=+-+...    -...+..+.++....+....++.++|+......+.+..+
T Consensus        90 ~~~~d~vlIDTaGr~~~----d~~~~~el~~~~~~~~~~~~llv~~a~~~~~~~~~~~~f  145 (207)
T d1ls1a2          90 LEARDLILVDTAGRLQI----DEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAF  145 (207)
T ss_dssp             HHTCCEEEEECCCCSSC----CHHHHHHHHHHHHHHCCSEEEEEEEGGGTHHHHHHHHHH
T ss_pred             hccCcceeecccccchh----hhhhHHHHHHHHhhcCCceEEEEeccccchhHHHHHHHH
Confidence            44667788887766432    344556666666666655567788888776666555444

>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=96.69  E-value=0.0026  Score=52.65  Aligned_cols=56  Identities=7%  Similarity=0.089  Sum_probs=32.7

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhC------CCCcEEEEeccCCcchHHHHHHHh
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTG------NSIPIIALTATAEPSVKQDIISVL  250 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~------~~~~~v~lSAT~~~~~~~~~~~~l  250 (444)
                      .+.++|+||=+-+...    -...+.++.++.+...      +...++.++||........+...+
T Consensus        90 ~~~d~ilIDTaGr~~~----d~~~~~el~~l~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~~~~~~  151 (211)
T d2qy9a2          90 RNIDVLIADTAGRLQN----KSHLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVSQAKLFH  151 (211)
T ss_dssp             TTCSEEEECCCCCGGG----HHHHHHHHHHHHHHHTTTCTTCCSEEEEEEEGGGTHHHHHHHHHHH
T ss_pred             cCCCEEEeccCCCccc----cHHHHHHHHHHHHHHhhhcccCcceeeeehhcccCcchHHHHhhhh
Confidence            4678888888766422    2233344444443332      224578899998877666665554

>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=96.63  E-value=0.001  Score=55.74  Aligned_cols=16  Identities=19%  Similarity=0.125  Sum_probs=14.0

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.++++||+|+|||..
T Consensus        37 n~l~l~G~~G~GKTHL   52 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHL   52 (213)
T ss_dssp             SSEEEECSSSSSHHHH
T ss_pred             CcEEEECCCCCcHHHH
Confidence            3489999999999966

>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=96.58  E-value=0.0025  Score=52.67  Aligned_cols=48  Identities=8%  Similarity=-0.015  Sum_probs=29.2

Q ss_pred             CcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEc--chhhhhcccCccchHhhh
Q psy7952          66 HDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWIS--PILSSFYLRFRDDKTSIV  130 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~--P~~~L~~~~q~~~~~~~l  130 (444)
                      +-+++++|||+|||.+        . ... ..++...+  .+|.+++  ..|.-+     .+|++.+
T Consensus         7 ~vi~lvGptGvGKTTT--------i-aKL-A~~~~~~g--~kV~lit~Dt~R~gA-----~eQL~~~   56 (207)
T d1okkd2           7 RVVLVVGVNGVGKTTT--------I-AKL-GRYYQNLG--KKVMFCAGDTFRAAG-----GTQLSEW   56 (207)
T ss_dssp             SEEEEECSTTSSHHHH--------H-HHH-HHHHHTTT--CCEEEECCCCSSTTH-----HHHHHHH
T ss_pred             EEEEEECCCCCCHHHH--------H-HHH-HHHHHHCC--CcEEEEEeccccccc-----hhhHhhc
Confidence            4578899999999988        1 111 22233333  2345444  356666     6888877

>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=96.45  E-value=0.028  Score=46.30  Aligned_cols=60  Identities=10%  Similarity=0.017  Sum_probs=35.7

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCCcchHHHHHHHhc
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAEPSVKQDIISVLK  251 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~~~~~~~~~~~l~  251 (444)
                      ..+.++|+||=+-+....  .....+..+..+.........++.++|+......+.+...+.
T Consensus        92 ~~~~d~IlIDTaGr~~~~--~~~~~~~el~~~~~~~~~~~~~LVl~a~~~~~~~~~~~~~~~  151 (211)
T d1j8yf2          92 SEKMEIIIVDTAGRHGYG--EEAALLEEMKNIYEAIKPDEVTLVIDASIGQKAYDLASKFNQ  151 (211)
T ss_dssp             HTTCSEEEEECCCSCCTT--CHHHHHHHHHHHHHHHCCSEEEEEEEGGGGGGHHHHHHHHHH
T ss_pred             ccCCceEEEecCCcCccc--hhhHHHHHHHHHHhhcCCceEEEEEecccCcchHHHHhhhhc
Confidence            346788888877552111  122334555566666655456788899987766666555543

>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=96.43  E-value=0.0031  Score=52.33  Aligned_cols=57  Identities=9%  Similarity=0.072  Sum_probs=31.9

Q ss_pred             hCCccEEEEeccccccccCCCcHHHHHHHHHHHHhhC------CCCcEEEEeccCCcchHHHHHHHh
Q psy7952         190 YNKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTG------NSIPIIALTATAEPSVKQDIISVL  250 (444)
Q Consensus       190 ~~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~------~~~~~v~lSAT~~~~~~~~~~~~l  250 (444)
                      ..+.++|+||=+-+...    -...+..+..+.+...      +...++.++||........+...+
T Consensus        91 ~~~~d~ilIDTaGr~~~----d~~~~~el~~~~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~~~~~~  153 (213)
T d1vmaa2          91 ARNKDVVIIDTAGRLHT----KKNLMEELRKVHRVVKKKIPDAPHETLLVIDATTGQNGLVQAKIFK  153 (213)
T ss_dssp             HTTCSEEEEEECCCCSC----HHHHHHHHHHHHHHGGGTCTTCCSEEEEEEEGGGHHHHHHHHHHHH
T ss_pred             HcCCCEEEEeccccccc----hHHHHHHHHHHHhhhhhccccccceeEEeeccccCcchhhhhhhhc
Confidence            44677888887766432    2333444444443322      123578889887766655555444

>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=96.42  E-value=0.0034  Score=53.68  Aligned_cols=42  Identities=12%  Similarity=0.230  Sum_probs=25.9

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccC
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATA  238 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~  238 (444)
                      ....++|+||+|.+...      ....+.+.+...+.++.+++.|..+
T Consensus       130 ~~~~iiiide~d~l~~~------~~~~l~~~~e~~~~~~~~Il~tn~~  171 (252)
T d1sxje2         130 HRYKCVIINEANSLTKD------AQAALRRTMEKYSKNIRLIMVCDSM  171 (252)
T ss_dssp             -CCEEEEEECTTSSCHH------HHHHHHHHHHHSTTTEEEEEEESCS
T ss_pred             CCceEEEeccccccccc------cchhhhcccccccccccceeeeccc
Confidence            35679999999997432      2344555555666656666655443

>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=96.37  E-value=0.00028  Score=62.84  Aligned_cols=63  Identities=11%  Similarity=-0.044  Sum_probs=41.3

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC-ccceeEEEcchhhhhcccCccchHhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN-VRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~-~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      ++-|++++..  .. .+++|.|++|||||.+++         -.+...+...+ ...+|+++++|++++     .+...+
T Consensus         3 ~~eQ~~av~~--~~-~~~lI~g~aGTGKTt~l~---------~rv~~ll~~~~~~~~~ILvlt~tn~a~-----~~i~~~   65 (306)
T d1uaaa1           3 NPGQQQAVEF--VT-GPCLVLAGAGSGKTRVIT---------NKIAHLIRGCGYQARHIAAVTFTNKAA-----REMKER   65 (306)
T ss_dssp             CHHHHHHHHC--CS-SEEEECCCTTSCHHHHHH---------HHHHHHHHHHCCCGGGEEEEESSHHHH-----HHHHHH
T ss_pred             CHHHHHHHhC--CC-CCEEEEeeCCccHHHHHH---------HHHHHHHHhcCCChhHEEEEeCcHHHH-----HHHHHH
Confidence            4689999975  23 579999999999998721         11011122222 334789999999998     554444


Q ss_pred             h
Q psy7952         130 V  130 (444)
Q Consensus       130 l  130 (444)
                      +
T Consensus        66 ~   66 (306)
T d1uaaa1          66 V   66 (306)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=96.22  E-value=0.0028  Score=52.65  Aligned_cols=32  Identities=6%  Similarity=0.065  Sum_probs=23.9

Q ss_pred             hHHHHHHHHHHc----cC--CcEEEEccCCCccccccc
Q psy7952          52 ELQKKAIRHILL----RT--HDIFVSMPTGAVSLVGSV   83 (444)
Q Consensus        52 ~~Q~~~~~~~~~----~~--~~~ii~apTGsGKT~~a~   83 (444)
                      |||..+++.+.+    +.  +.+++.||+|+|||..|.
T Consensus         5 Pw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~   42 (207)
T d1a5ta2           5 PWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIY   42 (207)
T ss_dssp             GGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHH
T ss_pred             cccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHH
Confidence            588887776653    32  348999999999998743

>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=96.18  E-value=0.0067  Score=49.82  Aligned_cols=43  Identities=9%  Similarity=0.041  Sum_probs=30.5

Q ss_pred             CCccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCC
Q psy7952         191 NKLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAE  239 (444)
Q Consensus       191 ~~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~  239 (444)
                      +..+++|+||||.|...      ...++.+.+..-+++..++++|..+.
T Consensus        78 ~~~KviIId~ad~l~~~------aqNaLLK~LEEPp~~t~fiLit~~~~  120 (198)
T d2gnoa2          78 YTRKYVIVHDCERMTQQ------AANAFLKALEEPPEYAVIVLNTRRWH  120 (198)
T ss_dssp             SSSEEEEETTGGGBCHH------HHHHTHHHHHSCCTTEEEEEEESCGG
T ss_pred             CCCEEEEEeCccccchh------hhhHHHHHHhCCCCCceeeeccCChh
Confidence            35689999999998542      24566677777777777777766653

>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=95.91  E-value=0.00096  Score=59.61  Aligned_cols=63  Identities=11%  Similarity=-0.047  Sum_probs=41.4

Q ss_pred             chHHHHHHHHHHccCCcEEEEccCCCcccccccccccceEEeCCCccccccCC-ccceeEEEcchhhhhcccCccchHhh
Q psy7952          51 CELQKKAIRHILLRTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGN-VRSRNGWISPILSSFYLRFRDDKTSI  129 (444)
Q Consensus        51 t~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~-~~~~vlil~P~~~L~~~~q~~~~~~~  129 (444)
                      ++-|.+++..  .+ .+++|.|++|||||.++         +..+.+.+...+ ...+++++++++.++     .+....
T Consensus        13 ~~eQ~~~v~~--~~-g~~lV~g~aGSGKTt~l---------~~ri~~ll~~~~~~p~~il~lt~t~~aa-----~~~~~~   75 (318)
T d1pjra1          13 NKEQQEAVRT--TE-GPLLIMAGAGSGKTRVL---------THRIAYLMAEKHVAPWNILAITFTNKAA-----REMRER   75 (318)
T ss_dssp             CHHHHHHHHC--CS-SCEEEEECTTSCHHHHH---------HHHHHHHHHTTCCCGGGEEEEESSHHHH-----HHHHHH
T ss_pred             CHHHHHHHhC--CC-CCEEEEecCCccHHHHH---------HHHHHHHHHcCCCCHHHeEeEeccHHHH-----HHHHHH
Confidence            3679999975  23 57999999999999882         111011222232 224789999999998     554444


Q ss_pred             h
Q psy7952         130 V  130 (444)
Q Consensus       130 l  130 (444)
                      +
T Consensus        76 ~   76 (318)
T d1pjra1          76 V   76 (318)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=94.67  E-value=0.015  Score=49.99  Aligned_cols=25  Identities=16%  Similarity=0.118  Sum_probs=18.4

Q ss_pred             HHHHHHcc-CCcEEEEccCCCccccc
Q psy7952          57 AIRHILLR-THDIFVSMPTGAVSLVG   81 (444)
Q Consensus        57 ~~~~~~~~-~~~~ii~apTGsGKT~~   81 (444)
                      .+..+.+. .+++++++|+|.|||.+
T Consensus        30 l~~iL~r~~k~n~lLVG~~GvGKTal   55 (268)
T d1r6bx2          30 AIQVLCRRRKNNPLLVGESGVGKTAI   55 (268)
T ss_dssp             HHHHHTSSSSCEEEEECCTTSSHHHH
T ss_pred             HHHHHhcCccCCcEEECCCCCcHHHH
Confidence            34444433 37899999999999976

>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=94.64  E-value=0.012  Score=48.18  Aligned_cols=82  Identities=7%  Similarity=0.121  Sum_probs=62.8

Q ss_pred             ceeEEEcchhhhhcccCccchHhhhcCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIVTGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ  185 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~  185 (444)
                      .+|.||||..+-.     .+..+.+...++..++..+||.++..+......+..  .+..+|+|+|.-          +.
T Consensus        32 gQvy~V~p~I~~~-----e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~--~g~~~ILv~Ttv----------IE   94 (211)
T d2eyqa5          32 GQVYYLYNDVENI-----QKAAERLAELVPEARIAIGHGQMRERELERVMNDFH--HQRFNVLVCTTI----------IE   94 (211)
T ss_dssp             CEEEEECCCSSCH-----HHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHH--TTSCCEEEESST----------TG
T ss_pred             CeEEEEEcCccch-----hhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHH--cCCcceEEEehh----------hh
Confidence            4569999988766     455555533334489999999999999988887776  588999999932          34


Q ss_pred             HHHhhCCccEEEEeccccc
Q psy7952         186 HLVRYNKLAYIVVDEAHCV  204 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~~  204 (444)
                      .-.+..+..++||..++++
T Consensus        95 vGiDvpnA~~iiI~~a~rf  113 (211)
T d2eyqa5          95 TGIDIPTANTIIIERADHF  113 (211)
T ss_dssp             GGSCCTTEEEEEETTTTSS
T ss_pred             hccCCCCCcEEEEecchhc
Confidence            4556778899999999994

>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=94.58  E-value=0.025  Score=48.01  Aligned_cols=16  Identities=13%  Similarity=0.140  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus        43 ~giLl~GppGtGKT~l   58 (247)
T d1ixza_          43 KGVLLVGPPGVGKTHL   58 (247)
T ss_dssp             SEEEEECCTTSSHHHH
T ss_pred             ceEEEecCCCCChhHH
Confidence            5699999999999977

>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=94.49  E-value=0.037  Score=47.31  Aligned_cols=16  Identities=19%  Similarity=0.227  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus        39 ~giLL~GppGtGKT~l   54 (258)
T d1e32a2          39 RGILLYGPPGTGKTLI   54 (258)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             ceeEEecCCCCCchHH
Confidence            6799999999999977

>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=94.32  E-value=0.04  Score=43.68  Aligned_cols=78  Identities=12%  Similarity=0.086  Sum_probs=63.1

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||+|+++.-+     .+....| ..|   +++..++|+++..++...+.+++  .+..+|+|+|.-          .
T Consensus        32 ~r~lvfc~t~~~~-----~~l~~~L~~~G---i~a~~~Hg~~~~~eR~~~l~~F~--~G~~~vLVaT~v----------~   91 (174)
T d1c4oa2          32 ERTLVTVLTVRMA-----EELTSFLVEHG---IRARYLHHELDAFKRQALIRDLR--LGHYDCLVGINL----------L   91 (174)
T ss_dssp             CEEEEECSSHHHH-----HHHHHHHHHTT---CCEEEECTTCCHHHHHHHHHHHH--TTSCSEEEESCC----------C
T ss_pred             CcEEEEEcchhHH-----HHHHHHHHhcC---CceEEEecccchHHHHHHHHHHH--CCCeEEEEeeee----------e
Confidence            3569999999999     6666667 888   99999999999999999999987  489999999922          2


Q ss_pred             HHHHhhCCccEEEEecccc
Q psy7952         185 QHLVRYNKLAYIVVDEAHC  203 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE~H~  203 (444)
                      ..-.+..++++||+=.++.
T Consensus        92 ~~GiDip~V~~Vi~~~~~~  110 (174)
T d1c4oa2          92 REGLDIPEVSLVAILDADK  110 (174)
T ss_dssp             CTTCCCTTEEEEEETTTTS
T ss_pred             eeeccCCCCcEEEEecccc
Confidence            2344667888998866665

>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=93.36  E-value=0.024  Score=49.95  Aligned_cols=16  Identities=25%  Similarity=0.231  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +++++++|||+|||..
T Consensus        50 ~~iLl~GPpG~GKT~l   65 (309)
T d1ofha_          50 KNILMIGPTGVGKTEI   65 (309)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             ceEEEECCCCCCHHHH
Confidence            6899999999999987

>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=92.49  E-value=0.075  Score=45.48  Aligned_cols=22  Identities=18%  Similarity=0.282  Sum_probs=15.7

Q ss_pred             HHHHhhCCccEEEEeccccccc
Q psy7952         185 QHLVRYNKLAYIVVDEAHCVSE  206 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE~H~~~~  206 (444)
                      ...........+++||+|.+..
T Consensus       125 ~~~~~~~~~~~~iide~d~l~~  146 (287)
T d1w5sa2         125 DNLYVENHYLLVILDEFQSMLS  146 (287)
T ss_dssp             HHHHHHTCEEEEEEESTHHHHS
T ss_pred             HHHHhccCccccceeEEEEecc
Confidence            3333455677889999999854

>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=92.43  E-value=0.12  Score=41.20  Aligned_cols=77  Identities=14%  Similarity=0.122  Sum_probs=62.5

Q ss_pred             eeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH
Q psy7952         107 RNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ  185 (444)
Q Consensus       107 ~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~  185 (444)
                      +++|+|+++.-+     ......+ ..+   +++..++|+++..++...+.+++.  +..+|+|+|.-.          .
T Consensus        33 ~~iif~~~~~~~-----~~~~~~l~~~g---~~~~~~hg~~~~~eR~~~l~~Fr~--g~~~vLVaTdv~----------~   92 (181)
T d1t5la2          33 RTLVTTLTKKMA-----EDLTDYLKEAG---IKVAYLHSEIKTLERIEIIRDLRL--GKYDVLVGINLL----------R   92 (181)
T ss_dssp             EEEEECSSHHHH-----HHHHHHHHTTT---CCEEEECSSCCHHHHHHHHHHHHH--TSCSEEEESCCC----------S
T ss_pred             eEEEEeehhhhh-----HHHHHHHHhCC---cceeEecCCccHHHHHHHHHHHHC--CCCCEEEehhHH----------H
Confidence            569999999998     5555556 778   999999999999999999998874  889999999222          2


Q ss_pred             HHHhhCCccEEEEecccc
Q psy7952         186 HLVRYNKLAYIVVDEAHC  203 (444)
Q Consensus       186 ~~~~~~~~~~iViDE~H~  203 (444)
                      .-.+..++++||.-++..
T Consensus        93 rGiDip~v~~VI~~d~p~  110 (181)
T d1t5la2          93 EGLDIPEVSLVAILDADK  110 (181)
T ss_dssp             SSCCCTTEEEEEETTTTS
T ss_pred             ccCCCCCCCEEEEecCCc
Confidence            344667899999888876

>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=92.35  E-value=0.13  Score=41.30  Aligned_cols=17  Identities=6%  Similarity=-0.097  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCCccccc
Q psy7952          65 THDIFVSMPTGAVSLVG   81 (444)
Q Consensus        65 ~~~~ii~apTGsGKT~~   81 (444)
                      ..++++++|+|.|||.+
T Consensus        43 k~n~lLvG~pGVGKTal   59 (195)
T d1jbka_          43 KNNPVLIGEPGVGKTAI   59 (195)
T ss_dssp             SCEEEEECCTTSCHHHH
T ss_pred             CCCeEEEecCCcccHHH
Confidence            36899999999999977

>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=92.18  E-value=1  Score=37.04  Aligned_cols=92  Identities=9%  Similarity=0.091  Sum_probs=70.1

Q ss_pred             EEEcccchhhHHHHHHHHHHHhccCCCCCceEEEEecccchHHHHHHHHHhh--------------cCHHHHHHHHHHHh
Q psy7952         272 VIFDDLLKDSYAHVKEFIEKCLGKDNKANNCGIIYCRTREHTTDLADALRRK--------------VNKHERSRVQESFM  337 (444)
Q Consensus       272 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~iVf~~s~~~~~~l~~~L~~~--------------~~~~~r~~~~~~f~  337 (444)
                      .........+.+.....+...+.    .+.++++.+++..-+.+.+..+++.              .+..+|..+++.+.
T Consensus        80 LL~GdvGsGKT~V~~~a~~~~~~----~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~  155 (233)
T d2eyqa3          80 LVCGDVGFGKTEVAMRAAFLAVD----NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVA  155 (233)
T ss_dssp             EEECCCCTTTHHHHHHHHHHHHT----TTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHH
T ss_pred             EEEcCCCCCcHHHHHHHHHHHHH----cCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHh
Confidence            33333344444444444444443    5889999999999999999999875              67889999999999


Q ss_pred             cCCccEEEEcCccc-cccccCCccEEEEeCC
Q psy7952         338 RGEINVITATISFG-MGIDRQNVRFVVHWGM  367 (444)
Q Consensus       338 ~g~~~vLvaT~~~~-~Gidi~~~~~Vi~~~~  367 (444)
                      +|+.+++|+|..+- ..+.++++..||...-
T Consensus       156 ~g~~~iviGths~l~~~~~f~~LgLiIiDEe  186 (233)
T d2eyqa3         156 EGKIDILIGTHKLLQSDVKFKDLGLLIVDEE  186 (233)
T ss_dssp             TTCCSEEEECTHHHHSCCCCSSEEEEEEESG
T ss_pred             CCCCCEEEeehhhhccCCccccccceeeech
Confidence            99999999998754 4688889999886553

>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=92.17  E-value=0.53  Score=39.69  Aligned_cols=79  Identities=13%  Similarity=0.094  Sum_probs=61.0

Q ss_pred             CCceEEEEecccchHHHHHHHHHhh--------------cCHHHHHHHHHHHhcCCccEEEEcCcc-ccccccCCccEEE
Q psy7952         299 ANNCGIIYCRTREHTTDLADALRRK--------------VNKHERSRVQESFMRGEINVITATISF-GMGIDRQNVRFVV  363 (444)
Q Consensus       299 ~~~~~iVf~~s~~~~~~l~~~L~~~--------------~~~~~r~~~~~~f~~g~~~vLvaT~~~-~~Gidi~~~~~Vi  363 (444)
                      .+.++++.+++.--+.+.+..+.+.              ++..+|..++...++|+++++|+|..+ ...+.+.++..||
T Consensus       131 ~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~~Lglvi  210 (264)
T d1gm5a3         131 AGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVI  210 (264)
T ss_dssp             HTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEE
T ss_pred             cccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcCCCCccccceee
Confidence            4789999999999998888888776              778999999999999999999999875 4568888999988


Q ss_pred             EeCCCCCHHHHHHHhc
Q psy7952         364 HWGMPSSIPAYYQESG  379 (444)
Q Consensus       364 ~~~~p~s~~~~~Qr~G  379 (444)
                      ...-.  --.|.||-+
T Consensus       211 iDEqH--~fgv~Qr~~  224 (264)
T d1gm5a3         211 IDEQH--RFGVKQREA  224 (264)
T ss_dssp             EESCC--CC-----CC
T ss_pred             ecccc--ccchhhHHH
Confidence            65533  224667653

>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=92.13  E-value=0.062  Score=49.00  Aligned_cols=61  Identities=13%  Similarity=-0.037  Sum_probs=41.5

Q ss_pred             CchHHHHHHHHHHc----cCCcEEEEccCCCcccccccccccceEEeCCCccccccCCccceeEEEcchhhhhcccCccc
Q psy7952          50 KCELQKKAIRHILL----RTHDIFVSMPTGAVSLVGSVVSARSRVRIPPGADFILNGNVRSRNGWISPILSSFYLRFRDD  125 (444)
Q Consensus        50 ~t~~Q~~~~~~~~~----~~~~~ii~apTGsGKT~~a~~~~~~~~~~~~~~~~l~~~~~~~~vlil~P~~~L~~~~q~~~  125 (444)
                      |+--|=+|+..+.+    |.++.++.+.||||||++          +..    +.... ...+|||+|+..+|     .+
T Consensus        12 p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~----------iA~----l~~~~-~rp~LVVt~n~~~A-----~q   71 (413)
T d1t5la1          12 PQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFT----------ISN----VIAQV-NKPTLVIAHNKTLA-----GQ   71 (413)
T ss_dssp             CCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHH----------HHH----HHHHH-TCCEEEECSSHHHH-----HH
T ss_pred             CCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHH----------HHH----HHHHh-CCCEEEEeCCHHHH-----HH
Confidence            56677777766665    446789999999999977          111    22221 12349999999999     55


Q ss_pred             hHhhh
Q psy7952         126 KTSIV  130 (444)
Q Consensus       126 ~~~~l  130 (444)
                      ..+.+
T Consensus        72 L~~dL   76 (413)
T d1t5la1          72 LYSEL   76 (413)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55555

>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=91.28  E-value=0.027  Score=52.19  Aligned_cols=18  Identities=22%  Similarity=0.189  Sum_probs=15.9

Q ss_pred             CcEEEEccCCCccccccc
Q psy7952          66 HDIFVSMPTGAVSLVGSV   83 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~a~   83 (444)
                      .|+++.+|||+|||+.|=
T Consensus        50 sNILliGPTGvGKTlLAr   67 (443)
T d1g41a_          50 KNILMIGPTGVGKTEIAR   67 (443)
T ss_dssp             CCEEEECCTTSSHHHHHH
T ss_pred             ccEEEECCCCCCHHHHHH
Confidence            689999999999998843

>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=90.85  E-value=0.053  Score=47.86  Aligned_cols=30  Identities=20%  Similarity=0.112  Sum_probs=24.9

Q ss_pred             hHHHHHHHHHHccCCcEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHILLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~~~~ii~apTGsGKT~~   81 (444)
                      +.+...+..+..+.+++++++|||||||..
T Consensus       153 ~~~~~~l~~~v~~~~nili~G~tgSGKTT~  182 (323)
T d1g6oa_         153 EQAISAIKDGIAIGKNVIVCGGTGSGKTTY  182 (323)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEESTTSSHHHH
T ss_pred             HHHHHHHHHHHHhCCCEEEEeeccccchHH
Confidence            456677777777668999999999999976

>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=90.37  E-value=0.34  Score=37.26  Aligned_cols=72  Identities=10%  Similarity=0.181  Sum_probs=56.2

Q ss_pred             eeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHHH
Q psy7952         107 RNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLLQ  185 (444)
Q Consensus       107 ~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~  185 (444)
                      ++||.|+++.-+     .+..+.+ ..+   +.+..++++.+..++...+...+  .+...|+|+|. .         ..
T Consensus        30 k~IIF~~s~~~~-----~~l~~~L~~~g---~~~~~~~~~~~~~~r~~~~~~f~--~~~~~ilv~T~-~---------~~   89 (155)
T d1hv8a2          30 YGLVFCKTKRDT-----KELASMLRDIG---FKAGAIHGDLSQSQREKVIRLFK--QKKIRILIATD-V---------MS   89 (155)
T ss_dssp             CEEEECSSHHHH-----HHHHHHHHHTT---CCEEEECSSSCHHHHHHHHHHHH--TTSSSEEEECT-T---------HH
T ss_pred             CEEEEECchHHH-----HHHHhhhcccc---cccccccccchhhhhhhhhhhhh--cccceeeeehh-H---------Hh
Confidence            569999999988     5555556 777   88999999999999988888876  47789999992 1         33


Q ss_pred             HHHhhCCccEEEE
Q psy7952         186 HLVRYNKLAYIVV  198 (444)
Q Consensus       186 ~~~~~~~~~~iVi  198 (444)
                      .-.++..+++||.
T Consensus        90 ~Gid~~~v~~Vi~  102 (155)
T d1hv8a2          90 RGIDVNDLNCVIN  102 (155)
T ss_dssp             HHCCCSCCSEEEE
T ss_pred             hhhhhccCcEEEE
Confidence            4456777888884

>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=90.36  E-value=0.19  Score=39.23  Aligned_cols=75  Identities=13%  Similarity=0.240  Sum_probs=58.3

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||.|.++.-+     .+..+.+ ..+   +.+..++|+.+...+...++..+  .+...|+|+|.-          .
T Consensus        28 ~k~iIF~~s~~~~-----~~l~~~L~~~~---~~~~~~~~~~~~~~r~~~l~~f~--~~~~~iLv~Tdv----------~   87 (162)
T d1fuka_          28 TQAVIFCNTRRKV-----EELTTKLRNDK---FTVSAIYSDLPQQERDTIMKEFR--SGSSRILISTDL----------L   87 (162)
T ss_dssp             SCEEEEESSHHHH-----HHHHHHHHHTT---CCEEEECTTSCHHHHHHHHHHHH--TTSCSEEEEEGG----------G
T ss_pred             CcEEEEEEEEchH-----HHHHHHHhhcC---ceEEEeccCCchhhHHHHHHHHh--hcccceeecccc----------c
Confidence            4679999999999     6666666 778   89999999999999999888776  478889999932          2


Q ss_pred             HHHHhhCCccEEEEec
Q psy7952         185 QHLVRYNKLAYIVVDE  200 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE  200 (444)
                      ..-.++.++++||.=+
T Consensus        88 ~rGiDi~~v~~VI~~d  103 (162)
T d1fuka_          88 ARGIDVQQVSLVINYD  103 (162)
T ss_dssp             TTTCCCCSCSEEEESS
T ss_pred             cccccCCCceEEEEec
Confidence            2344566788887644

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=90.31  E-value=0.048  Score=49.38  Aligned_cols=28  Identities=11%  Similarity=0.076  Sum_probs=20.4

Q ss_pred             HHHHHHHHHc-cCCcEEEEccCCCccccc
Q psy7952          54 QKKAIRHILL-RTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        54 Q~~~~~~~~~-~~~~~ii~apTGsGKT~~   81 (444)
                      =.+++..+.+ ++.+++++||+|.|||.+
T Consensus        31 i~~~~~~L~r~~k~n~llvG~~GvGKtai   59 (387)
T d1qvra2          31 IRRVIQILLRRTKNNPVLIGEPGVGKTAI   59 (387)
T ss_dssp             HHHHHHHHHCSSCCCCEEEECTTSCHHHH
T ss_pred             HHHHHHHHhcCCCCCCeEECCCCCCHHHH
Confidence            3445555554 336799999999999976

>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=90.13  E-value=0.27  Score=38.52  Aligned_cols=76  Identities=7%  Similarity=0.034  Sum_probs=55.8

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||+|+++.-+     ....+.+ ..+   +++..++|+.+..++...+...+  .+..+|+|+|.-.-         
T Consensus        28 ~k~iIF~~~~~~~-----~~l~~~L~~~~---~~~~~ihg~~~~~~r~~~l~~F~--~g~~~iLv~T~~~~---------   88 (168)
T d1t5ia_          28 NQVVIFVKSVQRC-----IALAQLLVEQN---FPAIAIHRGMPQEERLSRYQQFK--DFQRRILVATNLFG---------   88 (168)
T ss_dssp             SSEEEECSSHHHH-----HHHHHHHHHTT---CCEEEECTTSCHHHHHHHHHHHH--TTSCSEEEESSCCS---------
T ss_pred             CeEEEEEeeeecc-----hhhhhhhcccc---ccccccccccchhhhhhhhhhhc--cccceeeecccccc---------
Confidence            3679999999988     5555555 777   88999999999999998888776  47889999993321         


Q ss_pred             HHHHhhCCccEEEEecc
Q psy7952         185 QHLVRYNKLAYIVVDEA  201 (444)
Q Consensus       185 ~~~~~~~~~~~iViDE~  201 (444)
                       .-.++..++++|.=+.
T Consensus        89 -~Gid~~~~~~vi~~~~  104 (168)
T d1t5ia_          89 -RGMDIERVNIAFNYDM  104 (168)
T ss_dssp             -TTCCGGGCSEEEESSC
T ss_pred             -chhhcccchhhhhhhc
Confidence             2234446677765443

>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=90.11  E-value=0.07  Score=45.46  Aligned_cols=16  Identities=6%  Similarity=-0.022  Sum_probs=14.2

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.||||+|||..
T Consensus        33 ~~ilL~GpPGtGKT~l   48 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSL   48 (273)
T ss_dssp             EEEEEECCTTSCTHHH
T ss_pred             EEEEEECCCCCCHHHH
Confidence            3489999999999977

>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=89.83  E-value=0.042  Score=46.07  Aligned_cols=16  Identities=13%  Similarity=0.200  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .+++++||+|+|||.+
T Consensus        36 ~~~L~~GPpGtGKT~l   51 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTL   51 (238)
T ss_dssp             CCEEEESSTTSSHHHH
T ss_pred             CeEEEECCCCCcHHHH
Confidence            5799999999999977

>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=88.72  E-value=0.5  Score=39.02  Aligned_cols=26  Identities=12%  Similarity=-0.013  Sum_probs=20.2

Q ss_pred             HHHHHHccC----CcEEEEccCCCcccccc
Q psy7952          57 AIRHILLRT----HDIFVSMPTGAVSLVGS   82 (444)
Q Consensus        57 ~~~~~~~~~----~~~ii~apTGsGKT~~a   82 (444)
                      .++.++.|.    .-+++.+|+|+|||..|
T Consensus        14 ~LD~~l~GGi~~gsl~li~G~pGsGKT~l~   43 (242)
T d1tf7a2          14 RLDEMCGGGFFKDSIILATGATGTGKTLLV   43 (242)
T ss_dssp             HHHHHTTSSEESSCEEEEEECTTSSHHHHH
T ss_pred             HHHHhhcCCCcCCeEEEEEeCCCCCHHHHH
Confidence            466777641    56899999999999874

>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=88.51  E-value=0.06  Score=45.13  Aligned_cols=16  Identities=13%  Similarity=0.113  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .+++++||+|+|||..
T Consensus        36 ~~~Ll~GPpG~GKTtl   51 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTL   51 (239)
T ss_dssp             CCEEEECCTTSCHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            5799999999999977

>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=88.36  E-value=0.41  Score=38.61  Aligned_cols=73  Identities=7%  Similarity=0.091  Sum_probs=56.5

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++||.|+|+.-+     ......+ ..+   +.+..++|+.+..++...+..++  .+..+|+|+|.-.          
T Consensus        31 ~~~IIF~~t~~~~-----~~l~~~l~~~~---~~~~~~h~~~~~~~r~~~~~~f~--~g~~~ilvaTd~~----------   90 (200)
T d1oywa3          31 KSGIIYCNSRAKV-----EDTAARLQSKG---ISAAAYHAGLENNVRADVQEKFQ--RDDLQIVVATVAF----------   90 (200)
T ss_dssp             CCEEEECSSHHHH-----HHHHHHHHHTT---CCEEEECTTSCHHHHHHHHHHHH--TTSCSEEEECTTS----------
T ss_pred             CCEEEEEeeehhh-----HHhhhhhccCC---ceeEEecCCCcHHHHHHHHHHHh--cccceEEEecchh----------
Confidence            4569999999999     5566666 778   89999999999999998888876  4788999999432          


Q ss_pred             HHHHhhCCccEEEE
Q psy7952         185 QHLVRYNKLAYIVV  198 (444)
Q Consensus       185 ~~~~~~~~~~~iVi  198 (444)
                      ..-.+..++++||.
T Consensus        91 ~~GiD~p~v~~VI~  104 (200)
T d1oywa3          91 GMGINKPNVRFVVH  104 (200)
T ss_dssp             CTTTCCTTCCEEEE
T ss_pred             hhccCCCCCCEEEE
Confidence            22345567777763

>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=87.41  E-value=0.46  Score=37.17  Aligned_cols=77  Identities=6%  Similarity=0.044  Sum_probs=57.8

Q ss_pred             cceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHH
Q psy7952         105 RSRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYL  183 (444)
Q Consensus       105 ~~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~  183 (444)
                      ..++||+|+++.-+     ......+ ..+   +.+..++|+.+..++...+.+..  .+..+++|+|.-.         
T Consensus        32 ~~k~iVF~~~~~~~-----~~l~~~L~~~g---~~~~~~h~~~~~~~r~~~~~~f~--~~~~~ilv~Td~~---------   92 (171)
T d1s2ma2          32 INQAIIFCNSTNRV-----ELLAKKITDLG---YSCYYSHARMKQQERNKVFHEFR--QGKVRTLVCSDLL---------   92 (171)
T ss_dssp             CSEEEEECSSHHHH-----HHHHHHHHHHT---CCEEEECTTSCHHHHHHHHHHHH--TTSSSEEEESSCS---------
T ss_pred             CCceEEEEeeeehh-----hHhHHhhhccc---ccccccccccchhhhhhhhhhcc--cCccccccchhHh---------
Confidence            34779999999988     5666666 667   88999999999999998888776  4788999999532         


Q ss_pred             HHHHHhhCCccEEEEecc
Q psy7952         184 LQHLVRYNKLAYIVVDEA  201 (444)
Q Consensus       184 ~~~~~~~~~~~~iViDE~  201 (444)
                       ..-.++..+++||.=++
T Consensus        93 -~~Gid~~~v~~VI~~d~  109 (171)
T d1s2ma2          93 -TRGIDIQAVNVVINFDF  109 (171)
T ss_dssp             -SSSCCCTTEEEEEESSC
T ss_pred             -hhccccceeEEEEecCC
Confidence             23334556777774444

>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=86.76  E-value=0.2  Score=45.43  Aligned_cols=30  Identities=23%  Similarity=0.310  Sum_probs=25.0

Q ss_pred             hHHHHHHHHHHccC-CcEEEEccCCCccccc
Q psy7952          52 ELQKKAIRHILLRT-HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        52 ~~Q~~~~~~~~~~~-~~~ii~apTGsGKT~~   81 (444)
                      +.|.+.+..+.... .-+++.+|||||||.+
T Consensus       144 ~~~~~~l~~l~~~~~GliLvtGpTGSGKSTT  174 (401)
T d1p9ra_         144 AHNHDNFRRLIKRPHGIILVTGPTGSGKSTT  174 (401)
T ss_dssp             HHHHHHHHHHHTSSSEEEEEECSTTSCHHHH
T ss_pred             HHHHHHHHHHHhhhhceEEEEcCCCCCccHH
Confidence            58888999888653 3489999999999987

>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=85.97  E-value=0.16  Score=42.93  Aligned_cols=16  Identities=13%  Similarity=-0.080  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .++++.||+|+|||.+
T Consensus        44 ~~lll~GppGtGKT~l   59 (276)
T d1fnna2          44 PRATLLGRPGTGKTVT   59 (276)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             CceEEECCCCCCHHHH
Confidence            5799999999999977

>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=85.63  E-value=0.13  Score=40.53  Aligned_cols=16  Identities=19%  Similarity=0.343  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      ++++|.+|+|+|||..
T Consensus         2 k~v~ItG~~GtGKTtl   17 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTL   17 (189)
T ss_dssp             CCEEEESCCSSCHHHH
T ss_pred             cEEEEECCCCCcHHHH
Confidence            6899999999999976

>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=85.55  E-value=0.2  Score=41.29  Aligned_cols=42  Identities=17%  Similarity=0.186  Sum_probs=25.1

Q ss_pred             CccEEEEeccccccccCCCcHHHHHHHHHHHHhhCCCCcEEEEeccCC
Q psy7952         192 KLAYIVVDEAHCVSEWGHDFRPTYRRLGELRQFTGNSIPIIALTATAE  239 (444)
Q Consensus       192 ~~~~iViDE~H~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~lSAT~~  239 (444)
                      +..++|+||+|.+....      ...+.......+....+++.+....
T Consensus       101 ~~kviiiDe~d~~~~~~------~~~ll~~~e~~~~~~~~i~~~~~~~  142 (224)
T d1sxjb2         101 KHKIVILDEADSMTAGA------QQALRRTMELYSNSTRFAFACNQSN  142 (224)
T ss_dssp             CCEEEEEESGGGSCHHH------HHTTHHHHHHTTTTEEEEEEESCGG
T ss_pred             ceEEEEEecccccchhH------HHHHhhhccccccceeeeeccCchh
Confidence            45699999999976421      2334444445555455666665543

>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=85.53  E-value=0.13  Score=39.70  Aligned_cols=16  Identities=31%  Similarity=0.362  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +++++.||+|+|||.+
T Consensus         3 k~I~l~G~~GsGKSTv   18 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTI   18 (169)
T ss_dssp             CCEEEECCTTSCHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            6899999999999977

>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=84.84  E-value=0.12  Score=46.22  Aligned_cols=16  Identities=25%  Similarity=0.337  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .++++.+|||+|||..
T Consensus        69 ~niLfiGPTGvGKTEl   84 (364)
T d1um8a_          69 SNILLIGPTGSGKTLM   84 (364)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             cceeeeCCCCccHHHH
Confidence            5799999999999988

>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=84.17  E-value=0.86  Score=35.43  Aligned_cols=73  Identities=12%  Similarity=0.155  Sum_probs=56.0

Q ss_pred             ceeEEEcchhhhhcccCccchHhhh-cCCCCceeEEEEeCCCChhhHHHHHHHHHhcCCCeeEEEECCCccccccHHHHH
Q psy7952         106 SRNGWISPILSSFYLRFRDDKTSIV-TGRSDLYQLELIVSGQTKTENKAILEELRLVKPRIKLLYVTPERAVTESFHYLL  184 (444)
Q Consensus       106 ~~vlil~P~~~L~~~~q~~~~~~~l-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~  184 (444)
                      .++|+.|+++.-+     ......+ ..+   +.+..++|+.+...+...+...+  .+..+|+|+|--          .
T Consensus        35 ~k~iiF~~~~~~~-----~~~~~~l~~~~---~~~~~~~~~~~~~~r~~~~~~fk--~g~~~iLv~Td~----------~   94 (168)
T d2j0sa2          35 TQAVIFCNTKRKV-----DWLTEKMREAN---FTVSSMHGDMPQKERESIMKEFR--SGASRVLISTDV----------W   94 (168)
T ss_dssp             SEEEEECSSHHHH-----HHHHHHHHHTT---CCCEEECTTSCHHHHHHHHHHHH--HTSSCEEEECGG----------G
T ss_pred             CceEEEeeeHHHH-----HHHHHHhhhcc---cchhhhhhhhhHHHHHHHHHHHh--cCCccEEeccch----------h
Confidence            4679999999999     5555555 677   88999999999999988888776  367899999932          2


Q ss_pred             HHHHhhCCccEEEE
Q psy7952         185 QHLVRYNKLAYIVV  198 (444)
Q Consensus       185 ~~~~~~~~~~~iVi  198 (444)
                      ..-.++.++++||.
T Consensus        95 ~rGiDi~~v~~VIn  108 (168)
T d2j0sa2          95 ARGLDVPQVSLIIN  108 (168)
T ss_dssp             SSSCCCTTEEEEEE
T ss_pred             cccccccCcceEEE
Confidence            23445667788774

>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=84.01  E-value=0.13  Score=40.01  Aligned_cols=16  Identities=13%  Similarity=0.137  Sum_probs=14.0

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +-+++.||+|+|||.+
T Consensus         3 klI~i~G~~GsGKTTv   18 (176)
T d2bdta1           3 KLYIITGPAGVGKSTT   18 (176)
T ss_dssp             EEEEEECSTTSSHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            3478999999999987

>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=83.53  E-value=0.26  Score=40.73  Aligned_cols=16  Identities=13%  Similarity=0.256  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .++++.||+|+|||.+
T Consensus        46 ~~lll~Gp~G~GKTtl   61 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTA   61 (231)
T ss_dssp             CEEEEESCTTSSHHHH
T ss_pred             CeEEEECCCCCcHHHH
Confidence            5699999999999977

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=82.78  E-value=0.14  Score=43.04  Aligned_cols=16  Identities=6%  Similarity=0.017  Sum_probs=14.4

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus        41 ~~vLL~GppGtGKT~l   56 (246)
T d1d2na_          41 VSVLLEGPPHSGKTAL   56 (246)
T ss_dssp             EEEEEECSTTSSHHHH
T ss_pred             eEEEEECcCCCCHHHH
Confidence            4599999999999977

>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=82.64  E-value=0.3  Score=40.31  Aligned_cols=26  Identities=12%  Similarity=0.192  Sum_probs=18.6

Q ss_pred             HHHHHHHccC--CcEEEEccCCCccccc
Q psy7952          56 KAIRHILLRT--HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        56 ~~~~~~~~~~--~~~ii~apTGsGKT~~   81 (444)
                      +.+..++.+.  .++++.||+|+|||..
T Consensus        22 ~~l~~~i~~~~~~~lll~Gp~G~GKTtl   49 (237)
T d1sxjd2          22 TVLKKTLKSANLPHMLFYGPPGTGKTST   49 (237)
T ss_dssp             HHHHHHTTCTTCCCEEEECSTTSSHHHH
T ss_pred             HHHHHHHHcCCCCeEEEECCCCCChHHH
Confidence            3444444432  4589999999999977

>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=82.48  E-value=0.3  Score=41.58  Aligned_cols=19  Identities=16%  Similarity=-0.097  Sum_probs=15.4

Q ss_pred             HccCCcEEEEccCCCccccc
Q psy7952          62 LLRTHDIFVSMPTGAVSLVG   81 (444)
Q Consensus        62 ~~~~~~~ii~apTGsGKT~~   81 (444)
                      ..| +-+++.|+||+|||..
T Consensus        33 ~~G-~l~vi~G~~G~GKT~~   51 (277)
T d1cr2a_          33 RGG-EVIMVTSGSGMGKSTF   51 (277)
T ss_dssp             CTT-CEEEEECSTTSSHHHH
T ss_pred             CCC-eEEEEEeCCCCCHHHH
Confidence            344 6789999999999965

>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=82.19  E-value=0.21  Score=38.00  Aligned_cols=15  Identities=13%  Similarity=-0.168  Sum_probs=13.2

Q ss_pred             cEEEEccCCCccccc
Q psy7952          67 DIFVSMPTGAVSLVG   81 (444)
Q Consensus        67 ~~ii~apTGsGKT~~   81 (444)
                      -++++||+|||||..
T Consensus         4 lIii~G~pGsGKTTl   18 (152)
T d1ly1a_           4 IILTIGCPGSGKSTW   18 (152)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478899999999976

>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=81.88  E-value=0.52  Score=41.05  Aligned_cols=46  Identities=17%  Similarity=0.086  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHhCCcccCchHHHHHHHHHHc-------c----C---CcEEEEccCCCccccc
Q psy7952          33 EQELTAKLKALFGFDSFKCELQKKAIRHILL-------R----T---HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        33 ~~~~~~~l~~~~g~~~~~t~~Q~~~~~~~~~-------~----~---~~~ii~apTGsGKT~~   81 (444)
                      +.+..+.+++.+.-.- -  .|.+|+..+..       |    +   ..+++++|||+|||..
T Consensus         9 d~~~l~~l~~~L~~~v-i--GQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~l   68 (315)
T d1r6bx3           9 DRDTLKNLGDRLKMLV-F--GQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEV   68 (315)
T ss_dssp             HHHHHHHHHHHHTTTS-C--SCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHH
T ss_pred             HHHHHHHHHHHhCCee-c--ChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHH
Confidence            3444455555444332 2  67777765542       1    1   1489999999999977

>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=81.85  E-value=0.51  Score=35.49  Aligned_cols=15  Identities=20%  Similarity=0.308  Sum_probs=12.7

Q ss_pred             CCccEEEEecccccc
Q psy7952         191 NKLAYIVVDEAHCVS  205 (444)
Q Consensus       191 ~~~~~iViDE~H~~~  205 (444)
                      .+.++|.|||+|-+.
T Consensus        78 ~~~dvI~IDE~QFf~   92 (139)
T d2b8ta1          78 DETKVIGIDEVQFFD   92 (139)
T ss_dssp             TTCCEEEECSGGGSC
T ss_pred             cCcCEEEechhhhcc
Confidence            478999999999853

>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=81.70  E-value=0.39  Score=39.36  Aligned_cols=16  Identities=13%  Similarity=0.150  Sum_probs=14.3

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .+++++||+|+|||.+
T Consensus        36 ~~lLl~Gp~G~GKttl   51 (227)
T d1sxjc2          36 PHLLFYGPPGTGKTST   51 (227)
T ss_dssp             CCEEEECSSSSSHHHH
T ss_pred             CeEEEECCCCCChhHH
Confidence            3699999999999977

>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=80.63  E-value=0.22  Score=41.70  Aligned_cols=16  Identities=13%  Similarity=0.148  Sum_probs=14.5

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.||+|+|||.+
T Consensus        53 ~~lll~GPpG~GKTt~   68 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTA   68 (253)
T ss_dssp             SEEEEECSTTSSHHHH
T ss_pred             ceEEEECCCCCCHHHH
Confidence            4699999999999977

>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=80.63  E-value=0.19  Score=39.62  Aligned_cols=16  Identities=6%  Similarity=-0.155  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.||+|+|||..
T Consensus         8 K~I~i~G~~GsGKTTl   23 (192)
T d1lw7a2           8 KTVAILGGESSGKSVL   23 (192)
T ss_dssp             EEEEEECCTTSHHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            6799999999999977

>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=80.48  E-value=0.24  Score=41.82  Aligned_cols=16  Identities=13%  Similarity=0.225  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      +.+++.+|+|+|||..
T Consensus        46 ~~iLL~GppGtGKT~l   61 (256)
T d1lv7a_          46 KGVLMVGPPGTGKTLL   61 (256)
T ss_dssp             CEEEEECCTTSCHHHH
T ss_pred             CeEEeeCCCCCCccHH
Confidence            6799999999999977

>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=80.32  E-value=0.29  Score=37.94  Aligned_cols=16  Identities=13%  Similarity=0.104  Sum_probs=14.3

Q ss_pred             CcEEEEccCCCccccc
Q psy7952          66 HDIFVSMPTGAVSLVG   81 (444)
Q Consensus        66 ~~~ii~apTGsGKT~~   81 (444)
                      .++++.||+|||||.+
T Consensus         5 ~~I~i~G~pGsGKTTi   20 (173)
T d1rkba_           5 PNILLTGTPGVGKTTL   20 (173)
T ss_dssp             CCEEEECSTTSSHHHH
T ss_pred             CEEEEECCCCCCHHHH
Confidence            4689999999999977

>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=80.01  E-value=0.43  Score=39.39  Aligned_cols=39  Identities=3%  Similarity=-0.271  Sum_probs=27.9

Q ss_pred             hCCcccCchHHHHHHHHHHccC----CcEEEEccCCCcccccccc
Q psy7952          44 FGFDSFKCELQKKAIRHILLRT----HDIFVSMPTGAVSLVGSVV   84 (444)
Q Consensus        44 ~g~~~~~t~~Q~~~~~~~~~~~----~~~ii~apTGsGKT~~a~~   84 (444)
                      .++..+||-+.  .++.++.|.    +-+++.+|+|+|||..|+.
T Consensus        11 ~~~~~i~TGi~--~LD~ll~GGi~~G~~~li~G~pGsGKT~l~lq   53 (251)
T d1szpa2          11 SELICLTTGSK--NLDTLLGGGVETGSITELFGEFRTGKSQLCHT   53 (251)
T ss_dssp             HSSCEECCSCH--HHHHHHTSSEESSSEEEEEESTTSSHHHHHHH
T ss_pred             cCCCeecCCCH--HHHhhhCCCCcCCeEEEEEcCCCCCHHHHHHH
Confidence            35555666433  677777752    5689999999999987544