Psyllid ID: psy12977

---

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------
Protein Sequence
MKNILTIALGIFTIGFVISIIVTTLAVVSNSIFKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR
Secondary Structure (PSIPRED)
ccccccccccccHHHHHccccHHHHHHHHHcccccccccHHHHHcccccccEEEEcccccHHHHHHHHHHHHHcccccccccEEEEEcccHHHHHHHHHHHHHHHcccccEEEEEEccccHHHHHcccccccccEEEEcccHHHHHHHHcccccccccccEEEEEcccccccccccccHHHHHHHHHHcccccccEEEEEccccHHHHHHHHHHccccEEEEEccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccHHccccHHHHHHHHHcccccccHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHHHHcccccccEEEEEccHHHHHHHHHHHHHHHHHHccccEEEEEcccccHHHHHHHHHcccEEEEEcccHHHHHHHHccccEcccEEEEEEEcHHHHHHHcccccccHHHHHHHHccccccccEEEEEccccHHHHHHHHHHHcccEEEEEccc
Coil and Loop (DISEMBL)
MKNILTIALGIFTIGFVISIIVTTLAVVSNsifkhfephftitylsplgrqifacaptgsgktaaFLIPIihslrgpknlgfravivcptrelaKQTYNETVRLSEGLGLRAHVIGKIQQAAekfgprsaqkfDVLITTPNKLVYLLqmdppalnlanVEWLIVDESDKLFEAGVRGFRDQLAVIYAAcsgpnlkrgmfsatHTEDVAKWCRRKLKRRVQINVGLR
Flexible Loop (DISEMBL)
MKNILTIALGIFTIGFVISIIVTTLAVVSNSIFKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHslrgpknlgFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAekfgprsaqkFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACsgpnlkrgmfsaTHTEDVAKWcrrklkrrvqinvglr
Low Complexity Region (SEG)
MKNILTIALGIFTIGFVISIIVTTLAVVSNSIFKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR
Disordered region (IsUnstruct)
***ILTIALGIFTIGFVISIIVTTLAVVSNSIFKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN****
Disordered Region (DISOPRED)
****LTIALGIFTIGFVISIIVTTLAVVSNSIFKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQA********AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR
Disordered Region (DISEMBL)
MKNILTIALGIFTIGFVISIIVTTLAVVSNSIFKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR
Disordered Region (DISPRO)
******IALGIFTIGFVISIIVTTLAVVSNSIFKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL*
Transmembrane Helix (TMHMM)
iiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MKNILTIALGIFTIGFVISIIVTTLAVVSNSIFKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR
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	226	2.2.26 [Sep-21-2011]
A5D7C1	596	Probable ATP-dependent RN	yes	N/A	0.787	0.298	0.589	1e-59
Q8K301	598	Probable ATP-dependent RN	yes	N/A	0.787	0.297	0.567	1e-59
Q9Y2R4	599	Probable ATP-dependent RN	yes	N/A	0.787	0.297	0.567	5e-59
Q99PT0	598	Probable ATP-dependent RN	yes	N/A	0.787	0.297	0.561	7e-59
Q86IZ9	668	Probable ATP-dependent RN	yes	N/A	0.734	0.248	0.421	3e-30
Q5K5B6	540	DEAD-box ATP-dependent RN	yes	N/A	0.743	0.311	0.414	9e-28
Q6FN65	565	ATP-dependent RNA helicas	yes	N/A	0.845	0.338	0.371	5e-27
Q09775	481	ATP-dependent RNA helicas	yes	N/A	0.756	0.355	0.378	2e-26
Q6BP45	550	ATP-dependent RNA helicas	yes	N/A	0.747	0.307	0.357	1e-25
A5DIX5	537	ATP-dependent RNA helicas	N/A	N/A	0.769	0.324	0.395	2e-25

>sp|A5D7C1|DDX52_BOVIN Probable ATP-dependent RNA helicase DDX52 OS=Bos taurus GN=DDX52 PE=2 SV=1

 Score =  229 bits (584), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 105/178 (58%), Positives = 134/178 (75%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR++ A APTGSGKT AF IPI+  L+ P N GFRA+I+ PTRELA Q + E V+LSEG 
Sbjct: 200 GRELLASAPTGSGKTLAFSIPILMHLKQPTNKGFRALIISPTRELASQIHRELVKLSEGT 259

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
           G R H+I K   AA+KFGP+S++KFD+L+TTPN+L+YLL+ DPP ++L +VEWL+VDESD
Sbjct: 260 GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLTSVEWLVVDESD 319

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           KLFE G  GFRDQLA I+ AC+   +KR MFSAT   DV +WCR  L   + ++VG R
Sbjct: 320 KLFEDGKTGFRDQLASIFLACTSHKVKRAMFSATFAYDVEQWCRLNLDSVITVSVGAR 377

Bos taurus (taxid: 9913)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q8K301|DDX52_MOUSE Probable ATP-dependent RNA helicase DDX52 OS=Mus musculus GN=Ddx52 PE=2 SV=2

 Score =  229 bits (583), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 101/178 (56%), Positives = 135/178 (75%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR++ A APTGSGKT AF IPI+  L+ P N GFRA+++ PTRELA Q + E +++SEG 
Sbjct: 203 GRELLASAPTGSGKTLAFSIPILMQLKQPTNKGFRALVISPTRELASQIHRELIKISEGT 262

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
           G R H+I K   AA+KFGP+S++KFD+L+TTPN+L+YLL+ DPP ++L NVEWL+VDESD
Sbjct: 263 GFRIHMIHKAAIAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLTNVEWLVVDESD 322

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           KLFE G  GFR+QLA I+ AC+ P ++R MFSAT   DV +WC+  L   V +++G R
Sbjct: 323 KLFEDGKTGFREQLASIFLACTSPKVRRAMFSATFAYDVEQWCKLNLDNVVSVSIGAR 380

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9Y2R4|DDX52_HUMAN Probable ATP-dependent RNA helicase DDX52 OS=Homo sapiens GN=DDX52 PE=1 SV=3

 Score =  227 bits (579), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 101/178 (56%), Positives = 135/178 (75%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR++ A APTGSGKT AF IPI+  L+ P N GFRA+I+ PTRELA Q + E +++SEG 
Sbjct: 202 GRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGT 261

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
           G R H+I K   AA+KFGP+S++KFD+L+TTPN+L+YLL+ DPP ++LA+VEWL+VDESD
Sbjct: 262 GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESD 321

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           KLFE G  GFRDQLA I+ AC+   ++R MFSAT   DV +WC+  L   + +++G R
Sbjct: 322 KLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR 379

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q99PT0|DDX52_RAT Probable ATP-dependent RNA helicase DDX52 OS=Rattus norvegicus GN=Ddx52 PE=2 SV=1

 Score =  227 bits (578), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 100/178 (56%), Positives = 135/178 (75%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR++ A APTGSGKT AF IPI+  L+ P N GFRA+++ PTRELA Q + E +++SEG 
Sbjct: 203 GRELLASAPTGSGKTLAFSIPILMQLKQPTNKGFRALVISPTRELASQIHRELIKISEGT 262

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
           G R H+I K   AA+KFGP+S++KFD+L+TTPN+L+YLL+ +PP ++L +VEWL+VDESD
Sbjct: 263 GFRIHMIHKAAIAAKKFGPKSSKKFDILVTTPNRLIYLLKQEPPGIDLTSVEWLVVDESD 322

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           KLFE G  GFRDQLA I+ AC+ P ++R MFSAT   DV +WC+  L   V +++G R
Sbjct: 323 KLFEDGKTGFRDQLASIFLACTSPKVRRAMFSATFAYDVEQWCKLNLDNIVSVSIGAR 380

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q86IZ9|DDX52_DICDI Probable ATP-dependent RNA helicase ddx52 OS=Dictyostelium discoideum GN=ddx52 PE=3 SV=1

 Score =  131 bits (330), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 75/178 (42%), Positives = 110/178 (61%), Gaps = 12/178 (6%)

Query: 50  RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG 109
           R++ A APTGSGKTA+F IPI+ +L  PK  GFR+VI+ PTRELA+Q Y     LS+G  
Sbjct: 237 REVVAIAPTGSGKTASFSIPILQALYEPKKEGFRSVIIAPTRELAQQIYRNFRLLSKGKP 296

Query: 110 LRAHVIGK---IQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE 166
            R  V+ K    Q   E       + +D+LITTP +LVYL++ +   L+L  VE+L+ DE
Sbjct: 297 FRICVLSKNLHNQSTNENL----IKNYDILITTPLRLVYLIKEN--LLSLNKVEYLVFDE 350

Query: 167 SDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG 224
           +DKLF+   + F++Q+ ++  AC  P LK  +FSAT  + V +     +K  ++I +G
Sbjct: 351 ADKLFD---KNFQEQVDIVVTACQNPKLKICLFSATMNQQVEELGHSIMKNPIKIIIG 405

ATP-binding RNA helicase which may be involved in the ribosome biogenesis.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5K5B6|RH57_ORYSJ DEAD-box ATP-dependent RNA helicase 57 OS=Oryza sativa subsp. japonica GN=Os07g0647900 PE=2 SV=2

 Score =  123 bits (309), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 73/176 (41%), Positives = 105/176 (59%), Gaps = 8/176 (4%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR+ FACAPTGSGKT AFL PI+  ++     G +AVI+CPTRELA QT  E  +L++G 
Sbjct: 183 GRECFACAPTGSGKTLAFLFPILMKIKPGSKEGVKAVILCPTRELAAQTTRECKKLAKG- 241

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             R   I  + +   K G       D+LI+TP +L + +Q     L+L+ VE+L++DESD
Sbjct: 242 --RKFYIKLMTKDLSKSGNFKDMHCDILISTPLRLDHAVQKRD--LDLSRVEYLVLDESD 297

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG 224
           KLFE    GF + +  +  ACS P++ R +FSAT  + +    R  +   V++ VG
Sbjct: 298 KLFEL---GFVEVIDSVVKACSNPSIIRSLFSATLPDSIETLARTIMHDAVRVIVG 350

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6FN65|ROK1_CANGA ATP-dependent RNA helicase ROK1 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=ROK1 PE=3 SV=1

 Score =  121 bits (303), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 77/207 (37%), Positives = 123/207 (59%), Gaps = 16/207 (7%)

Query: 7   IALGIFTIGFVISIIVTTLAVVSNSIFKHF-EPHFTITYLSPL---GRQIFACAPTGSGK 62
           I L I +   +IS       +++N I  HF EP        PL   GR + ACAPTGSGK
Sbjct: 115 IPLPIGSFEDLISRFSLDKRLLNNLIENHFTEPTPIQCEAIPLCLNGRDLLACAPTGSGK 174

Query: 63  TAAFLIPIIHSLRGPKNL-GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQA 121
           T AFLIP++  +   KN  G + +I+ PT+ELA Q +NE V+LS+ + L      ++   
Sbjct: 175 TLAFLIPLLQQIIEEKNFSGVKGLIISPTKELATQIFNECVKLSKRIYLDKKRPLQVAIL 234

Query: 122 AEKFGPR------SAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGV 175
           ++  G +      S +K+D++I+TP +L+ +++ +  AL+L+NV+ LI DE+DKLF+   
Sbjct: 235 SKSLGAKLRNKVISDKKYDLIISTPLRLIDVVKNE--ALDLSNVKHLIFDEADKLFD--- 289

Query: 176 RGFRDQLAVIYAACSGPNLKRGMFSAT 202
           + F +Q   I  +C+ P++++ MFSAT
Sbjct: 290 KTFIEQTDDILNSCTDPSMRKSMFSAT 316

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (taxid: 284593)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q09775|ROK1_SCHPO ATP-dependent RNA helicase rok1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rok1 PE=3 SV=1

 Score =  119 bits (298), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 67/177 (37%), Positives = 104/177 (58%), Gaps = 6/177 (3%)

Query: 50  RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG 109
           R + ACAPTGSGKT A+L PI+  L+     G+RA+IV PTREL +Q Y +  +LS G  
Sbjct: 84  RDLLACAPTGSGKTIAYLFPILQKLQLHVPGGYRAIIVAPTRELCEQIYRQAEKLSFGTS 143

Query: 110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK 169
           L+   + K  +  ++  P+  +K+D+ I TP +LV  +Q     L+   VE+ ++DE+D+
Sbjct: 144 LKIIELSKSNEKIQEKAPKLREKYDMCIGTPMRLVQAIQT---GLSFEKVEFFVMDEADR 200

Query: 170 LFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           LFE    GF +Q   I +AC+  N+ + +FSAT    V +  +      ++I VGL+
Sbjct: 201 LFEP---GFIEQTDHILSACTSSNICKSLFSATIPSRVEELAKVVTVDPIRIIVGLK 254

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6BP45|ROK1_DEBHA ATP-dependent RNA helicase ROK1 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=ROK1 PE=3 SV=2

 Score =  116 bits (291), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 65/182 (35%), Positives = 112/182 (61%), Gaps = 13/182 (7%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSL--RGP--KNLGFRAVIVCPTRELAKQTYNETVRL 104
           GR + ACAPTGSGKT AFLIP++ ++    P  KN G R +I+ PT ELA Q + E   +
Sbjct: 151 GRDLIACAPTGSGKTLAFLIPLVQTILQSNPNVKNYGIRGLIISPTNELAVQIFQELNTM 210

Query: 105 SEGLGLRAHVIGKIQQAAEKFGPR--SAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL 162
           ++G  ++  ++ K  Q A K   +  ++ K+D+L++TP +L+  ++ +   ++L+ VE L
Sbjct: 211 TKGKKMKIGILSK--QLANKINNKIINSSKYDILVSTPLRLIDSIKNE--TISLSKVEQL 266

Query: 163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN 222
           ++DE+DKLF+   +GF +Q   I + C+   L++ MFSAT    V +  +  +K  +++ 
Sbjct: 267 VIDETDKLFD---QGFVEQTDEILSNCTNTKLRKSMFSATIPSGVEEMAQSIMKDPIRVI 323

Query: 223 VG 224
           +G
Sbjct: 324 IG 325

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) (taxid: 284592)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5DIX5|ROK1_PICGU ATP-dependent RNA helicase ROK1 OS=Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) GN=ROK1 PE=3 SV=2

 Score =  115 bits (288), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 72/182 (39%), Positives = 103/182 (56%), Gaps = 8/182 (4%)

Query: 46  SPLGRQIFACAPTGSGKTAAFLIPIIHSL-RGP--KNLGFRAVIVCPTRELAKQTYNETV 102
           S  GR + ACAPTGSGKT A+LIP+  +L   P  KN G R V++ PT ELA Q Y    
Sbjct: 140 SAEGRDLIACAPTGSGKTLAYLIPMAQALISSPKTKNYGIRGVVIAPTNELAIQIYQTLA 199

Query: 103 RLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL 162
            +  G  L   ++ K   +       SA KFDVLI TP +L+ L++ +   ++L+ VE L
Sbjct: 200 PMCRGSNLNVTLLSKQVASKISSSIISANKFDVLICTPLRLIDLVKKE--QVDLSKVEHL 257

Query: 163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN 222
           ++DE+DKLF+    GF +Q   I + C+ P  +  MFSAT    V +     +K +++I 
Sbjct: 258 VIDEADKLFD---HGFVEQTDEILSHCTLPTRRTSMFSATIPSGVEEMANSIMKDQIRII 314

Query: 223 VG 224
           VG
Sbjct: 315 VG 316

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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	226
307167458	498	Probable ATP-dependent RNA helicase DDX5	0.787	0.357	0.679	2e-68
322780454	377	hypothetical protein SINV_14078 [Solenop	0.787	0.472	0.674	1e-67
345480251	643	PREDICTED: probable ATP-dependent RNA he	0.787	0.276	0.651	2e-66
193632062	528	PREDICTED: probable ATP-dependent RNA he	0.778	0.333	0.683	2e-66
332020434	558	Putative ATP-dependent RNA helicase DDX5	0.787	0.318	0.651	1e-64
383855221	589	PREDICTED: probable ATP-dependent RNA he	0.787	0.302	0.646	2e-64
380019489	512	PREDICTED: probable ATP-dependent RNA he	0.787	0.347	0.646	6e-64
307198933	452	Probable ATP-dependent RNA helicase DDX5	0.787	0.393	0.657	1e-63
242005744	1130	predicted protein [Pediculus humanus cor	0.783	0.156	0.646	2e-63
291242221	681	PREDICTED: probable ATP-dependent RNA he	0.783	0.259	0.615	3e-63

>gi|307167458|gb|EFN61031.1| Probable ATP-dependent RNA helicase DDX52 [Camponotus floridanus]

 Score =  264 bits (674), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 121/178 (67%), Positives = 144/178 (80%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GRQI ACAPTGSGKTAAFL+PIIHSLRGP+  GFRAVI+ PTRELAKQTY E ++LS+G 
Sbjct: 108 GRQILACAPTGSGKTAAFLVPIIHSLRGPQKKGFRAVILSPTRELAKQTYRECLKLSDGY 167

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             R H+IGKI QA  K+GP S+QKFD+LITTP +LV+LL  DPPA++L NVEWLIVDE+D
Sbjct: 168 DFRIHIIGKINQALTKYGPSSSQKFDILITTPKRLVFLLNQDPPAISLNNVEWLIVDEAD 227

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           KLFE G+RGFR+QL  I  AC+  NL RGMFSAT+T  V+KWCRR +K  + + VG R
Sbjct: 228 KLFEEGIRGFREQLDEITRACTNTNLHRGMFSATNTPAVSKWCRRNMKGLITVTVGHR 285

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322780454|gb|EFZ09942.1| hypothetical protein SINV_14078 [Solenopsis invicta]

 Score =  261 bits (668), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 120/178 (67%), Positives = 142/178 (79%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GRQI ACAPTGSGKTAAFL+PIIHSLRGP+  GFRAVI+ PTRELAKQTY E +RLS+G 
Sbjct: 170 GRQILACAPTGSGKTAAFLLPIIHSLRGPQKKGFRAVILSPTRELAKQTYRECLRLSDGC 229

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             R H+I K+ QA  K+GP S+QKFD+LITTP +LV+LL  DPPA++L NVEWLIVDE+D
Sbjct: 230 DFRIHIISKVNQALNKYGPSSSQKFDILITTPKRLVFLLNQDPPAISLNNVEWLIVDEAD 289

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           KLFE G+RGFR+QL  I  AC   NL RGMFSAT+T  V+KWCRR +K  + + VG R
Sbjct: 290 KLFEEGIRGFREQLDEITRACVNTNLHRGMFSATNTPAVSKWCRRNMKGLITVTVGQR 347

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345480251|ref|XP_001607535.2| PREDICTED: probable ATP-dependent RNA helicase DDX52-like [Nasonia vitripennis]

 Score =  257 bits (657), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 116/178 (65%), Positives = 141/178 (79%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GRQI ACAPTGSGKTA+FL+PIIH L GP+  GFRA+I+ PTRELAKQTY E +RLSEG 
Sbjct: 175 GRQILACAPTGSGKTASFLLPIIHQLNGPRKKGFRAIILSPTRELAKQTYRECIRLSEGR 234

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
           G R H+I KI QA  K+GP+S+QKFD+LITTP +LV+LL  +PPA++L NVEWLIVDE+D
Sbjct: 235 GFRVHIISKINQALTKYGPKSSQKFDILITTPKRLVFLLNQEPPAISLNNVEWLIVDEAD 294

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           KLFE G RGF++QL  I  AC+  N++RGMFSAT+T  V KWCR  LK  V + +G R
Sbjct: 295 KLFEEGTRGFKNQLEEISKACTNENIRRGMFSATNTPAVTKWCRHNLKGLVTVTIGQR 352

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193632062|ref|XP_001950933.1| PREDICTED: probable ATP-dependent RNA helicase DDX52-like [Acyrthosiphon pisum]

 Score =  257 bits (657), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 121/177 (68%), Positives = 140/177 (79%), Gaps = 1/177 (0%)

Query: 50  RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG 109
           RQIFACAPTGSGKTAAFL+PIIH L  P N GFRA+IV PTRELAKQT  E  RL EG+G
Sbjct: 92  RQIFACAPTGSGKTAAFLVPIIHHLNKPLNKGFRALIVSPTRELAKQTLRECTRLCEGIG 151

Query: 110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK 169
           LRAH   KI +  EKF P+ AQKFD+LI TPN+LV+LLQ +PPA+ L N+EWLI+DESDK
Sbjct: 152 LRAHTFTKINKDKEKFNPKLAQKFDILIATPNRLVFLLQQEPPAVELNNIEWLIIDESDK 211

Query: 170 LFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           LFE GVRGFRDQLA+IY AC GPN KR MFSAT+T +VAKW ++ L   + + VG R
Sbjct: 212 LFETGVRGFRDQLAIIYKAC-GPNAKRAMFSATYTVEVAKWSKKNLDGLIAVTVGNR 267

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332020434|gb|EGI60854.1| Putative ATP-dependent RNA helicase DDX52 [Acromyrmex echinatior]

 Score =  251 bits (642), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 116/178 (65%), Positives = 140/178 (78%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GRQI ACAPTGSGKTAAFL+PIIHSLR P+  GFRAVI+ PTRELAKQTY E ++LS+G 
Sbjct: 169 GRQILACAPTGSGKTAAFLLPIIHSLREPQKKGFRAVILNPTRELAKQTYRECLKLSDGC 228

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             R H+I K+ QA  K+GP S+QKFD+LITTP +LV+LL  DPPA++L NVEWLIVDE+D
Sbjct: 229 DFRIHIISKVNQALTKYGPSSSQKFDILITTPKRLVFLLNQDPPAISLNNVEWLIVDEAD 288

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           KLFE G+RGFR+QL  I  AC   NL+  MFSAT+T  V+KWCRR +K  + + VG R
Sbjct: 289 KLFEEGIRGFREQLEEITKACVSTNLRCSMFSATNTPAVSKWCRRNMKGLITVTVGQR 346

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383855221|ref|XP_003703115.1| PREDICTED: probable ATP-dependent RNA helicase DDX52-like [Megachile rotundata]

 Score =  251 bits (640), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 115/178 (64%), Positives = 136/178 (76%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
            RQ+ ACAPTGSGKTAAFL+PIIH L GP+  GFRAVI+CPTRELAKQTY E +RLSEG 
Sbjct: 175 SRQVLACAPTGSGKTAAFLLPIIHHLGGPQKKGFRAVILCPTRELAKQTYRECLRLSEGY 234

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             R H+I KI QA   +GP+S+QKFD+LITTP ++++LL  DPPA++  NVEWLIVDE+D
Sbjct: 235 DFRVHIISKINQALTAYGPKSSQKFDILITTPRRIIFLLSQDPPAISFKNVEWLIVDEAD 294

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           KLFE G R FRDQ+  I  AC+  NL+R MFSAT+T  V KWCR  LK  V I VG R
Sbjct: 295 KLFEDGTRCFRDQMETISKACTNENLRRAMFSATNTPVVTKWCRHNLKGLVTITVGHR 352

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380019489|ref|XP_003693637.1| PREDICTED: probable ATP-dependent RNA helicase DDX52-like, partial [Apis florea]

 Score =  249 bits (636), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 115/178 (64%), Positives = 136/178 (76%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GRQI ACAPTGSGKTAAFL+PIIH L GP+  GFRAVI+ PTRELAKQTY E +RLSEG 
Sbjct: 117 GRQILACAPTGSGKTAAFLLPIIHHLGGPEKKGFRAVILSPTRELAKQTYRECLRLSEGY 176

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             R H+I KI QA  K+GP+S+QKFD+LITTP +++YLL  DPPA++  NVEWLIVDE D
Sbjct: 177 NFRIHIISKINQALNKYGPKSSQKFDILITTPKRIIYLLNQDPPAISFNNVEWLIVDEVD 236

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           KLFE G+R FRDQL  I  +C+   L + MFSAT+T  V KWCRR LK  + + VG R
Sbjct: 237 KLFENGIRCFRDQLEKISKSCTSEKLHKAMFSATNTPIVTKWCRRNLKGLITVTVGHR 294

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307198933|gb|EFN79685.1| Probable ATP-dependent RNA helicase DDX52 [Harpegnathos saltator]

 Score =  248 bits (633), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 117/178 (65%), Positives = 137/178 (76%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR I ACAPTGSGKTAAFL+PII SL+ P+N GFRAVI+ PTRELAKQTY E + LS+G 
Sbjct: 63  GRNILACAPTGSGKTAAFLLPIICSLQKPQNKGFRAVILSPTRELAKQTYRECLSLSDGY 122

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             R H+I K  QA  K+GP S+QKFD+LITTP +LV+LL  DPPA++L NVEWLIVDE+D
Sbjct: 123 DFRIHIINKTNQALTKYGPSSSQKFDILITTPKRLVFLLNQDPPAISLKNVEWLIVDEAD 182

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           KLFE G+RGFR QL  I  AC+  NL  GMFSAT+T  V KWCRR +KR V + VG R
Sbjct: 183 KLFEDGIRGFRQQLDEITKACTNDNLHCGMFSATNTPVVTKWCRRNMKRLVTVTVGQR 240

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242005744|ref|XP_002423722.1| predicted protein [Pediculus humanus corporis] gi|212506907|gb|EEB10984.1| predicted protein [Pediculus humanus corporis]

 Score =  248 bits (632), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 115/178 (64%), Positives = 140/178 (78%), Gaps = 1/178 (0%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GRQ+ ACAPTGSGKTAAFL+PI + L+GP   G+R VIVCPTRELA+QTY E +RLSEG 
Sbjct: 789 GRQVLACAPTGSGKTAAFLVPIFYHLKGPTKKGYRCVIVCPTRELARQTYRECLRLSEGT 848

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
            L+ ++I K+    E +   +++KFD+LITTPN+LVYLL+ +PP +NL +VEWLIVDESD
Sbjct: 849 RLKINIIKKVTLDKENYS-NTSKKFDILITTPNRLVYLLKQEPPKVNLKSVEWLIVDESD 907

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           KLFEAG+RGFRDQLAVIY AC    +KR MFSAT T  + KWCRR LK  V INVG+R
Sbjct: 908 KLFEAGIRGFRDQLAVIYNACDSSVIKRAMFSATQTPHLTKWCRRNLKNLVLINVGVR 965

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|291242221|ref|XP_002741008.1| PREDICTED: probable ATP-dependent RNA helicase DDX52-like [Saccoglossus kowalevskii]

 Score =  247 bits (630), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 109/177 (61%), Positives = 136/177 (76%)

Query: 50  RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG 109
           R++ ACAPTGSGKTAAF+IP++H L+ P+  GFRAV+V PTRELA+QTY E  RL+EG  
Sbjct: 207 REVLACAPTGSGKTAAFIIPVLHHLKEPRKQGFRAVVVSPTRELAQQTYREFCRLAEGRS 266

Query: 110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK 169
            R H+I K  QAA+KFGP+S+QKFD+L+TTPN+LVY+L   PPALNL NVEWLIVDESDK
Sbjct: 267 FRIHIIDKTSQAAKKFGPQSSQKFDILVTTPNRLVYMLNQHPPALNLTNVEWLIVDESDK 326

Query: 170 LFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           LFE G +GFR+QLA+IY AC    ++R MFSAT   DV +WC+  L     + +G R
Sbjct: 327 LFEEGKQGFREQLALIYKACDSMQVRRAMFSATFAYDVEQWCKLNLDNVASVTIGQR 383

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

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	226
ZFIN|ZDB-GENE-060623-1	606	ddx52 "DEAD (Asp-Glu-Ala-Asp)	0.783	0.292	0.593	3.6e-57
MGI|MGI:1925644	598	Ddx52 "DEAD (Asp-Glu-Ala-Asp)	0.787	0.297	0.567	1.3e-54
UNIPROTKB|A5D7C1	596	DDX52 "Probable ATP-dependent	0.787	0.298	0.589	2.1e-54
UNIPROTKB|A8MTP9	491	DDX52 "Probable ATP-dependent	0.787	0.362	0.567	4.3e-54
UNIPROTKB|Q9Y2R4	599	DDX52 "Probable ATP-dependent	0.787	0.297	0.567	4.3e-54
RGD|621743	598	Ddx52 "DEAD (Asp-Glu-Ala-Asp)	0.787	0.297	0.561	4.3e-54
UNIPROTKB|F1NQA6	603	DDX52 "Uncharacterized protein	0.787	0.295	0.573	5.5e-54
UNIPROTKB|I3LJA0	507	DDX52 "Uncharacterized protein	0.787	0.351	0.567	7e-54
UNIPROTKB|E2RB54	601	DDX52 "Uncharacterized protein	0.787	0.296	0.567	1.1e-53
UNIPROTKB|E1C4M1	604	DDX52 "Uncharacterized protein	0.787	0.294	0.569	4.9e-53

ZFIN|ZDB-GENE-060623-1 ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Danio rerio (taxid:7955)]

 Score = 588 (212.0 bits), Expect = 3.6e-57, P = 3.6e-57
 Identities = 105/177 (59%), Positives = 139/177 (78%)

Query:    50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG 109
             R+I ACAPTGSGKT AF +P++  LR P N GFRA+I+ PTRELA QT+ E ++LSEG+G
Sbjct:   205 REILACAPTGSGKTMAFCLPLLAHLRQPLNKGFRALIISPTRELATQTHRELLKLSEGVG 264

Query:   110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK 169
              R H+I K  +A +K+GP+SA+KFD+L+TTPN+L+YLL  DPPA+NL++VEWL+VDESDK
Sbjct:   265 FRVHMINKGVEAVKKYGPKSAKKFDILVTTPNRLIYLLNQDPPAINLSSVEWLVVDESDK 324

Query:   170 LFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
             LFE G  GFR+QLA I+ ACS PN++R +FSAT   DV +WC+  L   V +++G R
Sbjct:   325 LFEDGKTGFREQLATIFLACSSPNVRRVLFSATFATDVERWCKLNLDNLVSVSIGAR 381

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

MGI|MGI:1925644 Ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Mus musculus (taxid:10090)]

 Score = 564 (203.6 bits), Expect = 1.3e-54, P = 1.3e-54
 Identities = 101/178 (56%), Positives = 135/178 (75%)

Query:    49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
             GR++ A APTGSGKT AF IPI+  L+ P N GFRA+++ PTRELA Q + E +++SEG 
Sbjct:   203 GRELLASAPTGSGKTLAFSIPILMQLKQPTNKGFRALVISPTRELASQIHRELIKISEGT 262

Query:   109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             G R H+I K   AA+KFGP+S++KFD+L+TTPN+L+YLL+ DPP ++L NVEWL+VDESD
Sbjct:   263 GFRIHMIHKAAIAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLTNVEWLVVDESD 322

Query:   169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
             KLFE G  GFR+QLA I+ AC+ P ++R MFSAT   DV +WC+  L   V +++G R
Sbjct:   323 KLFEDGKTGFREQLASIFLACTSPKVRRAMFSATFAYDVEQWCKLNLDNVVSVSIGAR 380

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

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

GO:0008150 "biological_process" evidence=ND

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|A5D7C1 DDX52 "Probable ATP-dependent RNA helicase DDX52" [Bos taurus (taxid:9913)]

 Score = 562 (202.9 bits), Expect = 2.1e-54, P = 2.1e-54
 Identities = 105/178 (58%), Positives = 134/178 (75%)

Query:    49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
             GR++ A APTGSGKT AF IPI+  L+ P N GFRA+I+ PTRELA Q + E V+LSEG 
Sbjct:   200 GRELLASAPTGSGKTLAFSIPILMHLKQPTNKGFRALIISPTRELASQIHRELVKLSEGT 259

Query:   109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             G R H+I K   AA+KFGP+S++KFD+L+TTPN+L+YLL+ DPP ++L +VEWL+VDESD
Sbjct:   260 GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLTSVEWLVVDESD 319

Query:   169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
             KLFE G  GFRDQLA I+ AC+   +KR MFSAT   DV +WCR  L   + ++VG R
Sbjct:   320 KLFEDGKTGFRDQLASIFLACTSHKVKRAMFSATFAYDVEQWCRLNLDSVITVSVGAR 377

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|A8MTP9 DDX52 "Probable ATP-dependent RNA helicase DDX52" [Homo sapiens (taxid:9606)]

 Score = 559 (201.8 bits), Expect = 4.3e-54, P = 4.3e-54
 Identities = 101/178 (56%), Positives = 135/178 (75%)

Query:    49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
             GR++ A APTGSGKT AF IPI+  L+ P N GFRA+I+ PTRELA Q + E +++SEG 
Sbjct:    94 GRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGT 153

Query:   109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             G R H+I K   AA+KFGP+S++KFD+L+TTPN+L+YLL+ DPP ++LA+VEWL+VDESD
Sbjct:   154 GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESD 213

Query:   169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
             KLFE G  GFRDQLA I+ AC+   ++R MFSAT   DV +WC+  L   + +++G R
Sbjct:   214 KLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR 271

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q9Y2R4 DDX52 "Probable ATP-dependent RNA helicase DDX52" [Homo sapiens (taxid:9606)]

 Score = 559 (201.8 bits), Expect = 4.3e-54, P = 4.3e-54
 Identities = 101/178 (56%), Positives = 135/178 (75%)

Query:    49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
             GR++ A APTGSGKT AF IPI+  L+ P N GFRA+I+ PTRELA Q + E +++SEG 
Sbjct:   202 GRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGT 261

Query:   109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             G R H+I K   AA+KFGP+S++KFD+L+TTPN+L+YLL+ DPP ++LA+VEWL+VDESD
Sbjct:   262 GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESD 321

Query:   169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
             KLFE G  GFRDQLA I+ AC+   ++R MFSAT   DV +WC+  L   + +++G R
Sbjct:   322 KLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR 379

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

RGD|621743 Ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Rattus norvegicus (taxid:10116)]

 Score = 559 (201.8 bits), Expect = 4.3e-54, P = 4.3e-54
 Identities = 100/178 (56%), Positives = 135/178 (75%)

Query:    49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
             GR++ A APTGSGKT AF IPI+  L+ P N GFRA+++ PTRELA Q + E +++SEG 
Sbjct:   203 GRELLASAPTGSGKTLAFSIPILMQLKQPTNKGFRALVISPTRELASQIHRELIKISEGT 262

Query:   109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             G R H+I K   AA+KFGP+S++KFD+L+TTPN+L+YLL+ +PP ++L +VEWL+VDESD
Sbjct:   263 GFRIHMIHKAAIAAKKFGPKSSKKFDILVTTPNRLIYLLKQEPPGIDLTSVEWLVVDESD 322

Query:   169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
             KLFE G  GFRDQLA I+ AC+ P ++R MFSAT   DV +WC+  L   V +++G R
Sbjct:   323 KLFEDGKTGFRDQLASIFLACTSPKVRRAMFSATFAYDVEQWCKLNLDNIVSVSIGAR 380

GO:0003723 "RNA binding" evidence=IEA

GO:0003724 "RNA helicase activity" evidence=NAS

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005730 "nucleolus" evidence=IEA

GO:0006364 "rRNA processing" evidence=TAS

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

UNIPROTKB|F1NQA6 DDX52 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 558 (201.5 bits), Expect = 5.5e-54, P = 5.5e-54
 Identities = 102/178 (57%), Positives = 136/178 (76%)

Query:    49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
             GR++ A APTGSGKT AF IP++  L+ P N GFRA+I+ PTRELA QT+ E V+L++G 
Sbjct:   196 GRELLASAPTGSGKTLAFCIPLLTHLKQPMNKGFRALIISPTRELASQTHRELVKLADGT 255

Query:   109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             G R H+I K  +AA+KFGP+S++KFD+L+TTPN+L+YLL+ DPPA++L +VEWL+VDESD
Sbjct:   256 GFRIHMIQKASEAAKKFGPKSSRKFDILVTTPNRLIYLLKQDPPAIDLTSVEWLVVDESD 315

Query:   169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
             KLFE G  GFRDQLA I+ AC+   ++R  FSAT   DV +WC+  L   V ++VG R
Sbjct:   316 KLFEDGKSGFRDQLASIFLACTSHVVRRAFFSATFAHDVEEWCKLNLDSIVLVSVGAR 373

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|I3LJA0 DDX52 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 557 (201.1 bits), Expect = 7.0e-54, P = 7.0e-54
 Identities = 101/178 (56%), Positives = 134/178 (75%)

Query:    49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
             GR++ A APTGSGKT AF IPI+  L+ P N GFRA+++ PTRELA Q + E V++SEG 
Sbjct:   110 GRELLASAPTGSGKTLAFSIPILMQLKQPTNKGFRALVISPTRELASQIHRELVKISEGT 169

Query:   109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             G R H+I K   AA+KFGP+S++KFD+L+TTPN+L+YLL+ DPP ++L +VEWL+VDESD
Sbjct:   170 GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLTSVEWLVVDESD 229

Query:   169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
             KLFE G  GFRDQLA I+ AC+   +KR MFSAT   DV +WC+  L   + +++G R
Sbjct:   230 KLFEDGKTGFRDQLASIFLACTSHKVKRAMFSATFAYDVEQWCKLNLDNVITVSIGAR 287

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|E2RB54 DDX52 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 555 (200.4 bits), Expect = 1.1e-53, P = 1.1e-53
 Identities = 101/178 (56%), Positives = 134/178 (75%)

Query:    49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
             GR++ A APTGSGKT AF IPI+  L+ P N GFRA+I+ PTRELA Q + E V++SEG 
Sbjct:   204 GRELLASAPTGSGKTLAFSIPILMQLKQPTNKGFRALIISPTRELANQIHRELVKISEGT 263

Query:   109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             G R H+I K   AA+KFGP+S++KFD+L+TTPN+L+YLL+ DPP ++L +VEWL+VDESD
Sbjct:   264 GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLTSVEWLVVDESD 323

Query:   169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
             KLFE G  GFRDQLA I+ AC+   ++R MFSAT   DV +WC+  L   + +++G R
Sbjct:   324 KLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVITVSIGAR 381

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|E1C4M1 DDX52 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 549 (198.3 bits), Expect = 4.9e-53, P = 4.9e-53
 Identities = 102/179 (56%), Positives = 136/179 (75%)

Query:    49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
             GR++ A APTGSGKT AF IP++  L+ P N GFRA+I+ PTRELA QT+ E V+L++G 
Sbjct:   196 GRELLASAPTGSGKTLAFCIPLLTHLKQPMNKGFRALIISPTRELASQTHRELVKLADGT 255

Query:   109 GLRAHVIGKIQQAAEKFGPRSAQKF-DVLITTPNKLVYLLQMDPPALNLANVEWLIVDES 167
             G R H+I K  +AA+KFGP+S++KF D+L+TTPN+L+YLL+ DPPA++L +VEWL+VDES
Sbjct:   256 GFRIHMIQKASEAAKKFGPKSSRKFVDILVTTPNRLIYLLKQDPPAIDLTSVEWLVVDES 315

Query:   168 DKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
             DKLFE G  GFRDQLA I+ AC+   ++R  FSAT   DV +WC+  L   V ++VG R
Sbjct:   316 DKLFEDGKSGFRDQLASIFLACTSHVVRRAFFSATFAHDVEEWCKLNLDSIVLVSVGAR 374

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
A5D7C1	DDX52_BOVIN	3, ., 6, ., 4, ., 1, 3	0.5898	0.7876	0.2986	yes	N/A
Q9Y2R4	DDX52_HUMAN	3, ., 6, ., 4, ., 1, 3	0.5674	0.7876	0.2971	yes	N/A
Q8K301	DDX52_MOUSE	3, ., 6, ., 4, ., 1, 3	0.5674	0.7876	0.2976	yes	N/A
Q99PT0	DDX52_RAT	3, ., 6, ., 4, ., 1, 3	0.5617	0.7876	0.2976	yes	N/A

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	226
cd00268	203	cd00268, DEADc, DEAD-box helicases	7e-38
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	3e-35
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	6e-35
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	3e-29
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	7e-25
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	3e-21
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-17
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	5e-17
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	5e-17
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	5e-16
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	1e-14
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	3e-13
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	9e-13
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	1e-12
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	3e-11
COG1205	851	COG1205, COG1205, Distinct helicase family with a	1e-10
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	7e-10
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	6e-09
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	5e-07
PRK13767	876	PRK13767, PRK13767, ATP-dependent helicase; Provis	5e-06
PRK14701	1638	PRK14701, PRK14701, reverse gyrase; Provisional	2e-05
PRK01172	674	PRK01172, PRK01172, ski2-like helicase; Provisiona	2e-05
PRK00254	720	PRK00254, PRK00254, ski2-like helicase; Provisiona	3e-05
COG1110	1187	COG1110, COG1110, Reverse gyrase [DNA replication,	1e-04
COG1199	654	COG1199, DinG, Rad3-related DNA helicases [Transcr	3e-04
TIGR01054	1171	TIGR01054, rgy, reverse gyrase	3e-04
cd09710	353	cd09710, Cas3_I-D, CRISPR/Cas system-associated pr	7e-04
TIGR03158	357	TIGR03158, cas3_cyano, CRISPR-associated helicase	0.001
TIGR01407	850	TIGR01407, dinG_rel, DnaQ family exonuclease/DinG	0.002
COG1203	733	COG1203, COG1203, CRISPR-associated helicase Cas3	0.002
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	0.004

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

 Score =  130 bits (329), Expect = 7e-38
 Identities = 62/178 (34%), Positives = 97/178 (54%), Gaps = 14/178 (7%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSL-RGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           GR +   A TGSGKTAAFLIPI+  L   PK  G +A+I+ PTRELA Q      +L + 
Sbjct: 36  GRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKH 95

Query: 108 LGLRAHVI--GK-IQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIV 164
             L+  VI  G  I +   K      +   +++ TP +L+ LL+     L+L+ V++L++
Sbjct: 96  TNLKVVVIYGGTSIDKQIRKL----KRGPHIVVATPGRLLDLLERG--KLDLSKVKYLVL 149

Query: 165 DESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN 222
           DE+D++ +    GF DQ+  I       + +  +FSAT  ++V    R+ L+  V+I 
Sbjct: 150 DEADRMLD---MGFEDQIREILKLLP-KDRQTLLFSATMPKEVRDLARKFLRNPVRIL 203

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

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

 Score =  129 bits (327), Expect = 3e-35
 Identities = 61/184 (33%), Positives = 101/184 (54%), Gaps = 17/184 (9%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSL-RGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           GR +   A TG+GKTAAFL+P++  + +  +     A+I+ PTRELA Q   E  +L + 
Sbjct: 66  GRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKN 125

Query: 108 L-GLRAHVI---GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLI 163
           L GLR  V+     I++  E       +  D+++ TP +L+ L++     L+L+ VE L+
Sbjct: 126 LGGLRVAVVYGGVSIRKQIEAL----KRGVDIVVATPGRLLDLIKRG--KLDLSGVETLV 179

Query: 164 VDESDKLFEAGVRGFRDQLAVIYAACSGPNLKR-GMFSATHTEDVAKWCRRKLKRRVQIN 222
           +DE+D++ +    GF D +  I  A   P  ++  +FSAT  +D+ +  RR L   V+I 
Sbjct: 180 LDEADRMLD---MGFIDDIEKILKAL--PPDRQTLLFSATMPDDIRELARRYLNDPVEIE 234

Query: 223 VGLR 226
           V + 
Sbjct: 235 VSVE 238

Length = 513

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

 Score =  121 bits (307), Expect = 6e-35
 Identities = 57/161 (35%), Positives = 90/161 (55%), Gaps = 6/161 (3%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G+ +   APTGSGKT AFL+PI+ +L  PK  G +A+++ PTRELA+Q Y E  +L + L
Sbjct: 14  GKDVLVQAPTGSGKTLAFLLPILQAL-LPKKGGPQALVLAPTRELAEQIYEELKKLFKIL 72

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
           GLR  ++       E+       K D+L+ TP +L+ LL+       L N++ L++DE+ 
Sbjct: 73  GLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRR-GKLKLLKNLKLLVLDEAH 131

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAK 209
           +L +    GF D L  I +    P+ +  + SAT   ++  
Sbjct: 132 RLLD---MGFGDDLEEILSRLP-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|214692 smart00487, DEXDc, DEAD-like helicases superfamily

 Score =  107 bits (270), Expect = 3e-29
 Identities = 63/184 (34%), Positives = 98/184 (53%), Gaps = 8/184 (4%)

Query: 41  TITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE 100
            I  L    R +   APTGSGKT A L+P + +L+  +  G R +++ PTRELA+Q   E
Sbjct: 16  AIEALLSGLRDVILAAPTGSGKTLAALLPALEALK--RGKGGRVLVLVPTRELAEQWAEE 73

Query: 101 TVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVE 160
             +L   LGL+   +       E+     + K D+L+TTP +L+ LL+ D   L+L+NV+
Sbjct: 74  LKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDK--LSLSNVD 131

Query: 161 WLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQ 220
            +I+DE+ +L +    GF DQL  +       N++  + SAT  E++       L   V 
Sbjct: 132 LVILDEAHRLLD---GGFGDQLEKLLKLL-PKNVQLLLLSATPPEEIENLLELFLNDPVF 187

Query: 221 INVG 224
           I+VG
Sbjct: 188 IDVG 191

Length = 201

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

 Score = 95.1 bits (237), Expect = 7e-25
 Identities = 43/151 (28%), Positives = 73/151 (48%), Gaps = 10/151 (6%)

Query: 52  IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR 111
           +   APTGSGKT A L+PI+  L   K  G + +++ PTRELA Q     ++   G G++
Sbjct: 3   VLLAAPTGSGKTLAALLPILELLDSLK--GGQVLVLAPTRELANQVAER-LKELFGEGIK 59

Query: 112 AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLF 171
              +       ++    S  K D+++ TP +L+  L+     L+L  ++ LI+DE+ +L 
Sbjct: 60  VGYLIGGTSIKQQEKLLS-GKTDIVVGTPGRLLDELERLK--LSLKKLDLLILDEAHRLL 116

Query: 172 EAGVRGFRDQLAVIYAACSGPNLKRGMFSAT 202
             G       L +        + +  + SAT
Sbjct: 117 NQG----FGLLGLKILLKLPKDRQVLLLSAT 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|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase; Provisional

 Score = 91.0 bits (226), Expect = 3e-21
 Identities = 65/192 (33%), Positives = 97/192 (50%), Gaps = 34/192 (17%)

Query: 49  GRQIFACAPTGSGKTAAFLIPII------HSLRGPKNLGFRAVIVCPTRELAKQTYNETV 102
           GR +   A TGSGKTA+FL+PII       S    +     A+++ PTREL  Q  ++  
Sbjct: 158 GRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAK 217

Query: 103 RLSEGLGLR-AHVIG---------KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPP 152
            L +GL  + A V+G         +IQQ  E           +++ TP +L+ LL     
Sbjct: 218 VLGKGLPFKTALVVGGDAMPQQLYRIQQGVE-----------LIVGTPGRLIDLLSKH-- 264

Query: 153 ALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCR 212
            + L NV  L++DE D + E   RGFRDQ+  I+ A S P +   +FSAT + +V K+  
Sbjct: 265 DIELDNVSVLVLDEVDCMLE---RGFRDQVMQIFQALSQPQVL--LFSATVSPEVEKFAS 319

Query: 213 RKLKRRVQINVG 224
              K  + I++G
Sbjct: 320 SLAKDIILISIG 331

Length = 518

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

 Score = 80.8 bits (200), Expect = 1e-17
 Identities = 59/184 (32%), Positives = 92/184 (50%), Gaps = 21/184 (11%)

Query: 49  GRQIFACAPTGSGKTAAFLIPII-HSLRGP-KNLGF-RAVIVCPTRELAKQTYNETVRLS 105
           GR +   APTG+GKTAAFL+P + H L  P +  G  R +I+ PTRELA Q  ++   L+
Sbjct: 38  GRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVADQARELA 97

Query: 106 EGLGLRAHVI-GKI--QQAAEKFGPRSAQKFDVLITTPNKLV-YLLQMDPPALNLANVEW 161
           +   L    I G +     AE F    ++  D+++ TP +L+ Y+        +   VE 
Sbjct: 98  KHTHLDIATITGGVAYMNHAEVF----SENQDIVVATPGRLLQYI---KEENFDCRAVET 150

Query: 162 LIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGM-FSAT-HTEDVAKWCRRKLKRRV 219
           LI+DE+D++ +    GF   +  I A       K+ + FSAT   + V  +  R L   V
Sbjct: 151 LILDEADRMLDM---GFAQDIETIAAETRWR--KQTLLFSATLEGDAVQDFAERLLNDPV 205

Query: 220 QINV 223
           ++  
Sbjct: 206 EVEA 209

Length = 434

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

 Score = 78.7 bits (194), Expect = 5e-17
 Identities = 66/188 (35%), Positives = 99/188 (52%), Gaps = 22/188 (11%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSL--RGPKNLG---FRAVIVCPTRELAKQTYNETVR 103
           GR + A A TG+GKTA F +P++  L  R P   G    RA+I+ PTRELA Q   E VR
Sbjct: 38  GRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQI-GENVR 96

Query: 104 -LSEGLGLRAHVI-GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEW 161
             S+ L +R+ V+ G +    +    R     DVL+ TP +L+ L   +  A+ L  VE 
Sbjct: 97  DYSKYLNIRSLVVFGGVSINPQMMKLRGG--VDVLVATPGRLLDLEHQN--AVKLDQVEI 152

Query: 162 LIVDESDKLFEAG-VRGFRDQLAVIYAACSGPNLKRG--MFSATHTEDVAKWCRRKLKRR 218
           L++DE+D++ + G +   R  LA + A       KR   +FSAT ++D+     + L   
Sbjct: 153 LVLDEADRMLDMGFIHDIRRVLAKLPA-------KRQNLLFSATFSDDIKALAEKLLHNP 205

Query: 219 VQINVGLR 226
           ++I V  R
Sbjct: 206 LEIEVARR 213

Length = 456

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

 Score = 78.7 bits (195), Expect = 5e-17
 Identities = 54/183 (29%), Positives = 91/183 (49%), Gaps = 23/183 (12%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG- 107
           G+ + A A TGSGKTAAF + ++  L   K    +A+++CPTRELA Q   E  RL+   
Sbjct: 41  GKDVIAQAKTGSGKTAAFGLGLLQKLD-VKRFRVQALVLCPTRELADQVAKEIRRLARFI 99

Query: 108 -----LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL 162
                L L   V    Q  + + G        +++ TP +++  L+     L+L  +  L
Sbjct: 100 PNIKVLTLCGGVPMGPQIDSLEHGAH------IIVGTPGRILDHLRKG--TLDLDALNTL 151

Query: 163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRG--MFSATHTEDVAKWCRRKLKRRVQ 220
           ++DE+D++ +    GF+D +  I         +R   +FSAT+ E +A   +R  +  V+
Sbjct: 152 VLDEADRMLDM---GFQDAIDAIIRQAPA---RRQTLLFSATYPEGIAAISQRFQRDPVE 205

Query: 221 INV 223
           + V
Sbjct: 206 VKV 208

Length = 460

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

 Score = 76.0 bits (187), Expect = 5e-16
 Identities = 60/195 (30%), Positives = 91/195 (46%), Gaps = 40/195 (20%)

Query: 49  GRQIFACAPTGSGKTAAFLIP-IIH-----SLR---GPKNLGFRAVIVCPTRELAKQTYN 99
           GR +   A TGSGKT AFL+P I+H      LR   GP  L     ++ PTRELA+Q   
Sbjct: 167 GRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVL-----VLAPTRELAEQIRE 221

Query: 100 ETVRLSEGLGLRAHVI-----GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPAL 154
           +  +      +R  V       + Q  A + G       ++LI  P +L+  L+ +    
Sbjct: 222 QCNKFGASSKIRNTVAYGGVPKRGQIYALRRG------VEILIACPGRLIDFLESN--VT 273

Query: 155 NLANVEWLIVDESDKL----FEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKW 210
           NL  V +L++DE+D++    FE  +R    Q+         P+ +  M+SAT  ++V   
Sbjct: 274 NLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIR--------PDRQTLMWSATWPKEVQSL 325

Query: 211 CRRKLKRR-VQINVG 224
            R   K   V +NVG
Sbjct: 326 ARDLCKEEPVHVNVG 340

Length = 545

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

 Score = 72.3 bits (177), Expect = 1e-14
 Identities = 55/170 (32%), Positives = 90/170 (52%), Gaps = 20/170 (11%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSL--------RGPKNLGFRAVIVCPTRELAKQTYNE 100
           G  +   A TG+GKT AFL+ +++ L        R P++   RA+I+ PTRELA Q + +
Sbjct: 46  GGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDP--RALILAPTRELAIQIHKD 103

Query: 101 TVRLSEGLGLR-AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLV-YLLQMDPPALNLAN 158
            V+    LGLR A V G +    ++   +  Q  DV+I TP +L+ Y+ Q     ++L  
Sbjct: 104 AVKFGADLGLRFALVYGGVDYDKQRELLQ--QGVDVIIATPGRLIDYVKQHK--VVSLHA 159

Query: 159 VEWLIVDESDKLFEAG-VRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV 207
            E  ++DE+D++F+ G ++  R  L  +    +   L   +FSAT +  V
Sbjct: 160 CEICVLDEADRMFDLGFIKDIRFLLRRMPERGTRQTL---LFSATLSHRV 206

Length = 572

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

 Score = 67.6 bits (165), Expect = 3e-13
 Identities = 53/167 (31%), Positives = 82/167 (49%), Gaps = 14/167 (8%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRG--PKNLGF----RAVIVCPTRELAKQTYNETV 102
           G      A TG+GKTAAFLI II+ L    P    +    RA+I+ PTREL  Q   +  
Sbjct: 124 GHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAA 183

Query: 103 RLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL 162
            L++  GL            ++     A+  D+L+ TP +L+   Q     L++  VE +
Sbjct: 184 ALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDM--VEVM 241

Query: 163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRG--MFSATHTEDV 207
           ++DE+D++ +    GF  Q+  I    +    +R   +FSAT T+DV
Sbjct: 242 VLDEADRMLDM---GFIPQVRQIIRQ-TPRKEERQTLLFSATFTDDV 284

Length = 475

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

 Score = 66.4 bits (162), Expect = 9e-13
 Identities = 58/192 (30%), Positives = 96/192 (50%), Gaps = 31/192 (16%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIH----SLRGPKNLGFRAVIVCPTRELAKQTYNETVRL 104
           GR +   A TGSGKTAAF +P++H     L+ P+ L     ++ PTRELA Q        
Sbjct: 43  GRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQIL-----VLAPTRELAVQVAEAMTDF 97

Query: 105 SE---GLGLRAHVIGK---IQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLAN 158
           S+   G+ + A   G+   +Q  A + GP+      +++ TP +L  L  +    L+L+ 
Sbjct: 98  SKHMRGVNVVALYGGQRYDVQLRALRQGPQ------IVVGTPGRL--LDHLKRGTLDLSK 149

Query: 159 VEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKR- 217
           +  L++DE+D++      GF + +  I A     + +  +FSAT  E + +  RR +K  
Sbjct: 150 LSGLVLDEADEMLRM---GFIEDVETIMAQIPEGH-QTALFSATMPEAIRRITRRFMKEP 205

Query: 218 ---RVQINVGLR 226
              R+Q +V  R
Sbjct: 206 QEVRIQSSVTTR 217

Length = 629

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

 Score = 66.3 bits (162), Expect = 1e-12
 Identities = 37/119 (31%), Positives = 59/119 (49%), Gaps = 12/119 (10%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
              +   APTGSGKT   L+ I+ +L      G + V + P + LA++ Y E  RL E L
Sbjct: 47  DENVLISAPTGSGKTLIALLAILSTL---LEGGGKVVYIVPLKALAEEKYEEFSRL-EEL 102

Query: 109 GLR-AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE 166
           G+R     G      E+       ++DV++TTP KL  L +  P  +   ++  +++DE
Sbjct: 103 GIRVGISTGDYDLDDERLA-----RYDVIVTTPEKLDSLTRKRPSWIEEVDL--VVIDE 154

Length = 766

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

 Score = 61.9 bits (151), Expect = 3e-11
 Identities = 51/167 (30%), Positives = 79/167 (47%), Gaps = 25/167 (14%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSL------RGPKNLGFRAVIVCPTRELAKQTYNETV 102
           GR +   A TG+GKT AFL    H L         K    RA+I+ PTRELA Q + +  
Sbjct: 45  GRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAE 104

Query: 103 RLSEGLGLRAHVI--GK---IQQAAEKFGPRSAQKFDVLITTPNKLV-YLLQMDPPALNL 156
            L++  GL+  +   G     Q    + G       D+LI T  +L+ Y  Q     +NL
Sbjct: 105 PLAQATGLKLGLAYGGDGYDKQLKVLESGV------DILIGTTGRLIDYAKQ---NHINL 155

Query: 157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGM-FSAT 202
             ++ +++DE+D++F+    GF   +  ++      N +  M FSAT
Sbjct: 156 GAIQVVVLDEADRMFDL---GFIKDIRWLFRRMPPANQRLNMLFSAT 199

Length = 423

>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 = 60.1 bits (146), Expect = 1e-10
 Identities = 40/124 (32%), Positives = 57/124 (45%), Gaps = 11/124 (8%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHS-LRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           GR +     TGSGKT +FL+PI+   LR P     RA+++ PT  LA         L   
Sbjct: 85  GRNVVVTTGTGSGKTESFLLPILDHLLRDPS---ARALLLYPTNALANDQAERLRELISD 141

Query: 108 LGLRAHVI---GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALN--LANVEWL 162
           L  +       G      E+         D+L+T P+ L YLL  +  A    L N+++L
Sbjct: 142 LPGKVTFGRYTGDTPP--EERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYL 199

Query: 163 IVDE 166
           +VDE
Sbjct: 200 VVDE 203

Length = 851

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

 Score = 57.9 bits (140), Expect = 7e-10
 Identities = 43/162 (26%), Positives = 82/162 (50%), Gaps = 14/162 (8%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G      A +G+GKTA F+I  +  +        +A+I+ PTRELA+Q     + L + L
Sbjct: 65  GYDTIGQAQSGTGKTATFVIAALQLI-DYDLNACQALILAPTRELAQQIQKVVLALGDYL 123

Query: 109 GLRAHV-IG--KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVD 165
            +R H  +G   ++    K          +++ TP + VY + +D   L + +++  I+D
Sbjct: 124 KVRCHACVGGTVVRDDINKL----KAGVHMVVGTPGR-VYDM-IDKRHLRVDDLKLFILD 177

Query: 166 ESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV 207
           E+D++     RGF+ Q+  ++     P+++  +FSAT   ++
Sbjct: 178 EADEMLS---RGFKGQIYDVFKKLP-PDVQVALFSATMPNEI 215

Length = 401

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

 Score = 55.3 bits (134), Expect = 6e-09
 Identities = 66/222 (29%), Positives = 89/222 (40%), Gaps = 60/222 (27%)

Query: 29  SNSIFKHFEPH----FTITYLSPLGRQIFAC------------APTGSGKTAAFLIPIIH 72
              IF   +P     F   + S    Q +A             APTGSGKT A  +P+I+
Sbjct: 1   DEEIFNILDPRVREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVIN 60

Query: 73  SL----RGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHV-IGKIQQAAEKFGP 127
            L    +G    G  A+ + P + L              LG+   V  G   Q +EK   
Sbjct: 61  ELLSLGKGKLEDGIYALYISPLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQ-SEK--- 116

Query: 128 RSAQKF-----DVLITTPNKLVYLLQMDPPAL--NLANVEWLIVDESDKLFEAGVRGFRD 180
              QK       +LITTP  L  LL  + P     L +V ++IVDE   L E+  RG   
Sbjct: 117 ---QKMLKNPPHILITTPESLAILL--NSPKFRELLRDVRYVIVDEIHALAESK-RG--V 168

Query: 181 QLAVIYAACSGPNLKR-----GMF-----SAT--HTEDVAKW 210
           QLA+        +L+R     G F     SAT    E+VAK+
Sbjct: 169 QLAL--------SLERLRELAGDFQRIGLSATVGPPEEVAKF 202

Length = 814

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

 Score = 49.5 bits (119), Expect = 5e-07
 Identities = 53/169 (31%), Positives = 71/169 (42%), Gaps = 22/169 (13%)

Query: 56  APTGSGKT-AAFLIPIIHSLRGPKNL-GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAH 113
           APTGSGKT A FL  +I      K   G   + + P R LA           E LGL   
Sbjct: 35  APTGSGKTLAGFLPSLIDLAGPEKPKKGLHTLYITPLRALAVDIARNLQAPIEELGLPIR 94

Query: 114 V---IGKIQQAAEKFGPRSAQKF---DVLITTPNKLVYLL-QMDPPALNLANVEWLIVDE 166
           V    G    +      R+ Q+    D+L+TTP  L  LL   D   L   ++  ++VDE
Sbjct: 95  VETRTGDTSSSE-----RARQRKKPPDILLTTPESLALLLSYPDAARL-FKDLRCVVVDE 148

Query: 167 SDKLFEAGVRGFRDQLAVIYA--ACSGPNLKRGMFSAT--HTEDVAKWC 211
             +L     RG  DQL +  A      P L+R   SAT  + E+  +  
Sbjct: 149 WHELA-GSKRG--DQLELALARLRRLAPGLRRWGLSATIGNLEEARRVL 194

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

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

 Score = 46.4 bits (111), Expect = 5e-06
 Identities = 46/148 (31%), Positives = 61/148 (41%), Gaps = 44/148 (29%)

Query: 49  GRQIFACAPTGSGKT-AAFLIPIIHSL--RGPKNL---GFRAVIVCPTRELAKQTY-NET 101
           G+ +   +PTGSGKT AAFL  II  L   G +         + V P R L    + N  
Sbjct: 47  GKNVLISSPTGSGKTLAAFLA-IIDELFRLGREGELEDKVYCLYVSPLRALNNDIHRNLE 105

Query: 102 VRLSEGLGLRAHVIGKIQQAAEKFGP-----RSA-----------QKF-----DVLITTP 140
             L+E           I++ A++ G      R A           QK       +LITTP
Sbjct: 106 EPLTE-----------IREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTP 154

Query: 141 NKLVYLLQMDPPALN--LANVEWLIVDE 166
             L  LL  + P     L  V+W+IVDE
Sbjct: 155 ESLAILL--NSPKFREKLRTVKWVIVDE 180

Length = 876

>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional

 Score = 44.9 bits (106), Expect = 2e-05
 Identities = 32/131 (24%), Positives = 53/131 (40%), Gaps = 15/131 (11%)

Query: 49  GRQIFACAPTGSGKTA-AFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           G+     APTG GK+     I +  +L+G K       I+ PT  L KQT  +     E 
Sbjct: 94  GKSFSIVAPTGMGKSTFGAFIALFLALKGKK-----CYIILPTTLLVKQTVEKIESFCEK 148

Query: 108 LGLRAHVIG-----KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL 162
             L   ++      + ++  E         FD+L+TT       L  + P +     +++
Sbjct: 149 ANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQ----FLARNFPEMKHLKFDFI 204

Query: 163 IVDESDKLFEA 173
            VD+ D   +A
Sbjct: 205 FVDDVDAFLKA 215

Length = 1638

>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional

 Score = 44.5 bits (105), Expect = 2e-05
 Identities = 34/119 (28%), Positives = 53/119 (44%), Gaps = 13/119 (10%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  +    PT +GKT      I  +       G +++ + P R LA + Y E  RL   L
Sbjct: 37  GENVIVSVPTAAGKTLIAYSAIYETFLA----GLKSIYIVPLRSLAMEKYEELSRLRS-L 91

Query: 109 GLRAHV-IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE 166
           G+R  + IG          P   +++DV+I T  K   L+  DP  +N  +V  ++ DE
Sbjct: 92  GMRVKISIGDYDDP-----PDFIKRYDVVILTSEKADSLIHHDPYIIN--DVGLIVADE 143

Length = 674

>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional

 Score = 44.0 bits (104), Expect = 3e-05
 Identities = 49/173 (28%), Positives = 78/173 (45%), Gaps = 24/173 (13%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G+ +    PT SGKT    I +++ L      G +AV + P + LA++ Y E  +  E L
Sbjct: 39  GKNLVLAIPTASGKTLVAEIVMVNKLL---REGGKAVYLVPLKALAEEKYRE-FKDWEKL 94

Query: 109 GLR-AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES 167
           GLR A   G      E  G     K+D++I T  K   LL+     +   +V+ ++ DE 
Sbjct: 95  GLRVAMTTGDYDSTDEWLG-----KYDIIIATAEKFDSLLRHGSSWIK--DVKLVVADEI 147

Query: 168 DKLFEAGVRGFRDQ---LAVIYAACSGPNLKRGMFSAT--HTEDVAKWCRRKL 215
             +      G  D+   L +I     G     G+ SAT  + E++A+W   +L
Sbjct: 148 HLI------GSYDRGATLEMILTHMLGRAQILGL-SATVGNAEELAEWLNAEL 193

Length = 720

>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination, and repair]

 Score = 42.4 bits (100), Expect = 1e-04
 Identities = 43/183 (23%), Positives = 69/183 (37%), Gaps = 35/183 (19%)

Query: 56  APTGSGKT------AAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE--- 106
           APTG GKT      + +L             G R  I+ PT  L +Q Y    + +E   
Sbjct: 104 APTGVGKTTFGLLMSLYL----------AKKGKRVYIIVPTTTLVRQVYERLKKFAEDAG 153

Query: 107 GLGLRAHVIGKI-QQAAEKFGPRSAQ-KFDVLITTPNKLVYLLQMDPPALNLANVEWLIV 164
            L +       +  +  E+   R     FD+LITT   L          L+    +++ V
Sbjct: 154 SLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRF----EELSKLKFDFIFV 209

Query: 165 DESDKLFEAG--------VRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLK 216
           D+ D + +A         + GF +   VI +A     L+R ++     E V +  R   +
Sbjct: 210 DDVDAILKASKNVDRLLRLLGFSE--EVIESAYELIKLRRKLYGEKRAERVREELREVER 267

Query: 217 RRV 219
            R 
Sbjct: 268 ERE 270

Length = 1187

>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

 Score = 41.3 bits (97), Expect = 3e-04
 Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 3/52 (5%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE 100
           G  +   APTG+GKT A+L+P +   R     G + +I   T+ L +Q   E
Sbjct: 34  GEGLLIEAPTGTGKTLAYLLPALAYAR---EEGKKVIISTRTKALQEQLLEE 82

Length = 654

>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase

 Score = 41.3 bits (97), Expect = 3e-04
 Identities = 37/139 (26%), Positives = 49/139 (35%), Gaps = 27/139 (19%)

Query: 48  LGRQIFACAPTGSGKT------AAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET 101
            G      APTG GKT      + FL             G R  I+ PT  L  Q   + 
Sbjct: 92  RGDSFAIIAPTGVGKTTFGLAMSLFL----------AKKGKRCYIILPTTLLVIQVAEKI 141

Query: 102 VRLSEGLGLRAHVIGKIQ-----QAAEKFGPRSAQ-KFDVLITTPNKLVYLLQMDPPALN 155
             L+E  G+    IG        +  ++F  R     FD+LITT   L        P  +
Sbjct: 142 SSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELGPKFD 201

Query: 156 LANVEWLIVDESDKLFEAG 174
                   VD+ D L +A 
Sbjct: 202 FI-----FVDDVDALLKAS 215

This model describes reverse gyrase, found in both archaeal and bacterial thermophiles. This enzyme, a fusion of a type I topoisomerase domain and a helicase domain, introduces positive supercoiling to increase the melting temperature of DNA double strands. 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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 1171

>gnl|CDD|187841 cd09710, Cas3_I-D, CRISPR/Cas system-associated protein Cas3; Distinct diverged subfamily of Cas3 helicase domain

 Score = 39.5 bits (92), Expect = 7e-04
 Identities = 29/140 (20%), Positives = 49/140 (35%), Gaps = 32/140 (22%)

Query: 52  IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR 111
           IF  APTG+GKT A+L P++H          +A+ + PT  L +          +    R
Sbjct: 17  IFNTAPTGAGKTLAWLTPLLHG-------ENKAIALYPTNALIEDQTEAIKEFVDDANPR 69

Query: 112 --AHVIG----KIQQAAEKFGPRSAQKF-------------DVLITTPN------KLVYL 146
                +      +    +  G    +K               +L+T P+      +  Y+
Sbjct: 70  HQVKSLSASDITLWPNDKNVGSSKGEKLYNLLRNDIGTSTPIILLTNPDIFVYLTRFAYI 129

Query: 147 LQMDPPALNLANVEWLIVDE 166
            + D  A        +I DE
Sbjct: 130 DRGDIAAGFYTKFSTVIFDE 149

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Diverged DNA helicase Cas3'; signature gene for Type I and subtype I-D. Length = 353

>gnl|CDD|234127 TIGR03158, cas3_cyano, CRISPR-associated helicase Cas3, subtype CYANO

 Score = 38.7 bits (90), Expect = 0.001
 Identities = 32/145 (22%), Positives = 52/145 (35%), Gaps = 38/145 (26%)

Query: 52  IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYN------ETVRLS 105
           IF  APTG+GKT A+L P++H            + + PT  L +          +  +  
Sbjct: 17  IFNTAPTGAGKTLAWLTPLLHG-------ENDTIALYPTNALIEDQTEAIKEFVDVFKPE 69

Query: 106 EGLGLRAHVIGKIQQ-----AAEKFGPRSAQKF-------------DVLITTPN------ 141
             + L  HV     +     A +K G    +K               +L+T P+      
Sbjct: 70  RDVNLL-HVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLT 128

Query: 142 KLVYLLQMDPPALNLANVEWLIVDE 166
           +  Y+ + D  A        +I DE
Sbjct: 129 RFAYIDRGDIAAGFYTKFSTVIFDE 153

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano 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 [Mobile and extrachromosomal element functions, Other]. Length = 357

>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase, putative

 Score = 38.6 bits (90), Expect = 0.002
 Identities = 27/102 (26%), Positives = 43/102 (42%), Gaps = 21/102 (20%)

Query: 56  APTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETV-RLSEGLG--LRA 112
           APTG+GKT  +L+P ++     K +    VI   T+ L  Q   + +  L+E L   + A
Sbjct: 271 APTGTGKTLGYLLPALYYAITEKPV----VISTNTKVLQSQLLEKDIPLLNEILNFKINA 326

Query: 113 HVIGKIQQAAEKFGPR---SAQKFDVLIT--TPNKLVYLLQM 149
            +I          G     S  KF  ++   T N    + +M
Sbjct: 327 ALIK---------GKSNYLSLGKFSQILKDNTDNYEFNIFKM 359

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 850

>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 24/107 (22%), Positives = 36/107 (33%), Gaps = 4/107 (3%)

Query: 42  ITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET 101
           I  L      +   APTG GKT A LI  +  L     L  R + V P R + +  Y   
Sbjct: 207 ILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRA 266

Query: 102 VRLSEGLGLRAHV-IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLL 147
             +     +         ++          Q   + +TT +    LL
Sbjct: 267 KEIFGLFSVIGKSLHSSSKEPLLLE---PDQDILLTLTTNDSYKKLL 310

Length = 733

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

 Score = 37.4 bits (87), Expect = 0.004
 Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 11/54 (20%)

Query: 49  GRQIFACAPTGSGKT--AAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE 100
            R+     PTG+GKT  AA  I           L    +++ PT+EL  Q    
Sbjct: 55  ERRGVIVLPTGAGKTVVAAEAI---------AELKRSTLVLVPTKELLDQWAEA 99

Length = 442

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	226
KOG0331|consensus	519		100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0345|consensus	567		100.0
KOG0330|consensus	476		100.0
KOG0338|consensus	691		100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PTZ00110	545	helicase; Provisional	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
KOG0342|consensus	543		100.0
KOG0328|consensus	400		100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0326|consensus	459		100.0
KOG0343|consensus	758		100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
KOG0336|consensus	629		100.0
KOG0346|consensus	569		100.0
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	100.0
KOG0348|consensus	708		99.98
PTZ00424	401	helicase 45; Provisional	99.98
KOG0339|consensus	731		99.97
KOG0335|consensus	482		99.97
KOG0337|consensus	529		99.97
KOG0334|consensus	997		99.96
KOG0333|consensus	673		99.96
KOG0347|consensus	731		99.96
KOG0329|consensus	387		99.96
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.96
KOG0327|consensus	397		99.96
KOG0340|consensus	442		99.96
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.96
KOG4284|consensus	980		99.95
KOG0332|consensus	477		99.95
KOG0341|consensus	610		99.95
PRK02362	737	ski2-like helicase; Provisional	99.95
PRK00254	720	ski2-like helicase; Provisional	99.94
KOG0350|consensus	620		99.94
KOG0344|consensus	593		99.93
PRK13767	876	ATP-dependent helicase; Provisional	99.93
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.93
PRK01172	674	ski2-like helicase; Provisional	99.92
COG1204	766	Superfamily II helicase [General function predicti	99.91
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.91
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.91
PRK09401	1176	reverse gyrase; Reviewed	99.9
COG1205	851	Distinct helicase family with a unique C-terminal	99.89
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.89
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.88
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.88
PRK14701	1638	reverse gyrase; Provisional	99.88
KOG0952|consensus	1230		99.88
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.88
PRK10689	1147	transcription-repair coupling factor; Provisional	99.88
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.88
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.87
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.87
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.86
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.86
PHA02653	675	RNA helicase NPH-II; Provisional	99.86
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.85
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.84
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.84
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.84
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.81
PHA02558	501	uvsW UvsW helicase; Provisional	99.81
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.81
KOG0354|consensus	746		99.8
COG1202	830	Superfamily II helicase, archaea-specific [General	99.79
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.79
PRK13766	773	Hef nuclease; Provisional	99.79
PRK05580	679	primosome assembly protein PriA; Validated	99.76
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.75
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.73
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.71
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.71
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.7
KOG0951|consensus	1674		99.7
PRK09694	878	helicase Cas3; Provisional	99.69
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.68
KOG0349|consensus	725		99.68
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.68
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.68
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.67
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.66
KOG0947|consensus	1248		99.62
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.58
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.57
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.56
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.55
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.54
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.52
KOG0948|consensus	1041		99.52
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.51
KOG0353|consensus	695		99.5
KOG0351|consensus	941		99.5
KOG0352|consensus	641		99.49
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.49
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.48
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.44
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.44
KOG0949|consensus	1330		99.42
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.41
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.41
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.38
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.36
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.36
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.32
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.29
KOG0950|consensus	1008		99.28
COG4096	875	HsdR Type I site-specific restriction-modification	99.28
KOG0920|consensus	924		99.23
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.23
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.23
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.21
KOG0922|consensus	674		99.21
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.15
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.14
PRK04914	956	ATP-dependent helicase HepA; Validated	99.13
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.11
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	99.11
KOG0951|consensus	1674		99.11
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.08
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.05
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.05
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	99.04
PRK15483	986	type III restriction-modification system StyLTI en	98.97
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	98.95
PRK14873	665	primosome assembly protein PriA; Provisional	98.92
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	98.92
COG0610	962	Type I site-specific restriction-modification syst	98.85
KOG0952|consensus	1230		98.85
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.84
COG3587	985	Restriction endonuclease [Defense mechanisms]	98.76
KOG0926|consensus	1172		98.73
KOG0923|consensus	902		98.72
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.7
KOG0924|consensus	1042		98.68
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.67
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.67
KOG0925|consensus	699		98.65
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	98.59
KOG0385|consensus	971		98.47
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	98.45
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.4
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.38
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.35
KOG1123|consensus	776		98.3
PF13245	76	AAA_19: Part of AAA domain	98.27
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.27
PRK10536	262	hypothetical protein; Provisional	98.24
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	98.2
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	98.19
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	98.15
KOG0387|consensus	923		98.15
PRK06526	254	transposase; Provisional	98.13
KOG0390|consensus	776		98.13
PRK08181	269	transposase; Validated	98.13
KOG0989|consensus	346		98.04
KOG1803|consensus	649		98.02
KOG1132|consensus	945		98.0
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.99
KOG0389|consensus	941		97.99
COG4889	1518	Predicted helicase [General function prediction on	97.96
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.95
KOG1802|consensus	935		97.95
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.93
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.93
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.92
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	97.89
PRK08727	233	hypothetical protein; Validated	97.88
PRK08116	268	hypothetical protein; Validated	97.88
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.84
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.83
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.83
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.82
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.82
KOG4439|consensus	901		97.78
KOG1000|consensus	689		97.78
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.77
PRK12422	445	chromosomal replication initiation protein; Provis	97.74
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.72
PRK06893	229	DNA replication initiation factor; Validated	97.67
PRK06835	329	DNA replication protein DnaC; Validated	97.64
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.63
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	97.62
KOG1002|consensus	791		97.62
PRK08084	235	DNA replication initiation factor; Provisional	97.61
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	97.6
PRK05642	234	DNA replication initiation factor; Validated	97.6
KOG0391|consensus	1958		97.59
PRK06921	266	hypothetical protein; Provisional	97.57
PRK04296	190	thymidine kinase; Provisional	97.56
KOG2340|consensus	698		97.56
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.55
smart00382	148	AAA ATPases associated with a variety of cellular	97.52
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.52
PRK12377	248	putative replication protein; Provisional	97.51
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.51
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	97.49
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.49
KOG0991|consensus	333		97.48
CHL00181	287	cbbX CbbX; Provisional	97.48
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.46
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.46
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.44
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.44
PLN03025	319	replication factor C subunit; Provisional	97.43
PRK07952	244	DNA replication protein DnaC; Validated	97.43
PRK09183	259	transposase/IS protein; Provisional	97.41
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	97.41
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.36
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.36
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.36
PRK14974	336	cell division protein FtsY; Provisional	97.36
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.34
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.34
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.34
KOG1131|consensus	755		97.34
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.33
KOG0921|consensus	1282		97.31
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.31
PF05729	166	NACHT: NACHT domain	97.3
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	97.29
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	97.27
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.24
KOG0734|consensus	752		97.23
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.22
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.21
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.21
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	97.2
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.17
PTZ00112	1164	origin recognition complex 1 protein; Provisional	97.17
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.16
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	97.15
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.15
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	97.14
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.14
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.12
PHA03333	752	putative ATPase subunit of terminase; Provisional	97.11
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.09
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	97.09
PRK04328	249	hypothetical protein; Provisional	97.08
PF13173	128	AAA_14: AAA domain	97.08
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	97.08
TIGR00376	637	DNA helicase, putative. The gene product may repre	97.07
PHA03368	738	DNA packaging terminase subunit 1; Provisional	97.07
KOG0739|consensus	439		97.07
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.07
KOG0392|consensus	1549		97.07
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.06
PRK08939	306	primosomal protein DnaI; Reviewed	97.06
PF00004	132	AAA: ATPase family associated with various cellula	97.04
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	97.04
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.03
KOG0953|consensus	700		97.02
PRK12402	337	replication factor C small subunit 2; Reviewed	97.02
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	97.01
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	96.99
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	96.97
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	96.96
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	96.96
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	96.96
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.95
PRK13826	1102	Dtr system oriT relaxase; Provisional	96.94
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	96.93
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	96.93
KOG0388|consensus	1185		96.92
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	96.92
PHA02544	316	44 clamp loader, small subunit; Provisional	96.91
PRK11054	684	helD DNA helicase IV; Provisional	96.87
COG2256	436	MGS1 ATPase related to the helicase subunit of the	96.87
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	96.85
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	96.85
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	96.82
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	96.81
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	96.79
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.78
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.78
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	96.77
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	96.75
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.75
KOG0386|consensus	1157		96.74
PRK00440	319	rfc replication factor C small subunit; Reviewed	96.73
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.72
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	96.72
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	96.7
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.7
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	96.69
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	96.69
KOG1805|consensus	1100		96.69
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.68
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	96.67
KOG0738|consensus	491		96.67
PRK13342	413	recombination factor protein RarA; Reviewed	96.66
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	96.63
PRK13341	725	recombination factor protein RarA/unknown domain f	96.62
KOG0384|consensus	1373		96.61
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.6
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	96.6
PRK11823	446	DNA repair protein RadA; Provisional	96.6
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.6
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.55
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.55
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	96.5
PRK05973	237	replicative DNA helicase; Provisional	96.49
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	96.48
PRK04195	482	replication factor C large subunit; Provisional	96.48
PRK06067	234	flagellar accessory protein FlaH; Validated	96.48
PRK09112	351	DNA polymerase III subunit delta'; Validated	96.45
KOG0737|consensus	386		96.42
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.41
PRK07940	394	DNA polymerase III subunit delta'; Validated	96.41
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	96.4
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	96.39
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	96.38
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	96.38
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.37
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	96.33
KOG4150|consensus	1034		96.33
PHA02533	534	17 large terminase protein; Provisional	96.33
PRK07471	365	DNA polymerase III subunit delta'; Validated	96.32
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.32
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	96.32
KOG0058|consensus	716		96.23
PHA03372	668	DNA packaging terminase subunit 1; Provisional	96.2
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.19
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	96.18
KOG0742|consensus	630		96.18
KOG0741|consensus	744		96.17
PRK05707	328	DNA polymerase III subunit delta'; Validated	96.16
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	96.12
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.11
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.1
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.1
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.09
PHA00729	226	NTP-binding motif containing protein	96.08
COG3973	747	Superfamily I DNA and RNA helicases [General funct	96.05
KOG2028|consensus	554		96.04
TIGR00959	428	ffh signal recognition particle protein. This mode	96.04
PRK10263	1355	DNA translocase FtsK; Provisional	95.99
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	95.99
PRK09087	226	hypothetical protein; Validated	95.98
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	95.96
KOG1001|consensus	674		95.94
KOG1015|consensus	1567		95.93
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	95.92
COG4626	546	Phage terminase-like protein, large subunit [Gener	95.89
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.89
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	95.88
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	95.83
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	95.83
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	95.82
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	95.81
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	95.78
COG1485	367	Predicted ATPase [General function prediction only	95.78
KOG0298|consensus	1394		95.78
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	95.77
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	95.76
KOG0733|consensus	802		95.76
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	95.76
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	95.75
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	95.74
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.73
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	95.72
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	95.72
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.72
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	95.72
PRK06871	325	DNA polymerase III subunit delta'; Validated	95.72
PRK10867	433	signal recognition particle protein; Provisional	95.71
KOG0740|consensus	428		95.7
PRK10865	857	protein disaggregation chaperone; Provisional	95.69
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.67
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	95.6
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	95.6
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	95.59
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	95.55
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	95.54
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.54
COG1674	858	FtsK DNA segregation ATPase FtsK/SpoIIIE and relat	95.5
PRK06090	319	DNA polymerase III subunit delta'; Validated	95.49
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.47
PRK13851	344	type IV secretion system protein VirB11; Provision	95.45
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	95.42
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	95.4
PRK08058	329	DNA polymerase III subunit delta'; Validated	95.34
CHL00095	821	clpC Clp protease ATP binding subunit	95.34
cd00983	325	recA RecA is a bacterial enzyme which has roles in	95.32
PHA00350	399	putative assembly protein	95.32
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	95.32
PRK07399	314	DNA polymerase III subunit delta'; Validated	95.29
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.29
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	95.19
PRK09354	349	recA recombinase A; Provisional	95.18
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	95.18
CHL00176	638	ftsH cell division protein; Validated	95.14
PRK07993	334	DNA polymerase III subunit delta'; Validated	95.14
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	95.1
CHL00195	489	ycf46 Ycf46; Provisional	95.09
PF05872	502	DUF853: Bacterial protein of unknown function (DUF	95.09
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.06
PRK06964	342	DNA polymerase III subunit delta'; Validated	94.99
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	94.96
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	94.93
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	94.93
PRK08769	319	DNA polymerase III subunit delta'; Validated	94.93
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	94.85
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	94.83
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	94.83
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	94.79
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	94.76
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	94.76
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	94.74
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	94.74
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	94.73
PHA00012	361	I assembly protein	94.64
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	94.63
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	94.61
PRK10416	318	signal recognition particle-docking protein FtsY;	94.6
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	94.59
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	94.56
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	94.56
PRK05748	448	replicative DNA helicase; Provisional	94.56
PRK08699	325	DNA polymerase III subunit delta'; Validated	94.51
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	94.51
PRK06904	472	replicative DNA helicase; Validated	94.47
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	94.45
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	94.41
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	94.38
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	94.33
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	94.32
TIGR00665	434	DnaB replicative DNA helicase. This model describe	94.29
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	94.28
PRK13657	588	cyclic beta-1,2-glucan ABC transporter; Provisiona	94.25
KOG0733|consensus	802		94.25
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	94.25
KOG0652|consensus	424		94.23
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	94.21
PRK05564	313	DNA polymerase III subunit delta'; Validated	94.2
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	94.17
PRK05917	290	DNA polymerase III subunit delta'; Validated	94.14
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	94.11
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	94.11
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	94.09
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	94.05
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	94.04
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	94.0
PF12846	304	AAA_10: AAA-like domain	93.97
COG1221	403	PspF Transcriptional regulators containing an AAA-	93.96
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	93.96
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	93.87
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	93.86
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	93.85
KOG2170|consensus	344		93.79
PRK08506	472	replicative DNA helicase; Provisional	93.76
cd01128	249	rho_factor Transcription termination factor rho is	93.75
KOG2228|consensus	408		93.74
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	93.72
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	93.66
TIGR02857	529	CydD thiol reductant ABC exporter, CydD subunit. U	93.65
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	93.6
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	93.56
PRK10790	592	putative multidrug transporter membrane\ATP-bindin	93.55
PRK09302	509	circadian clock protein KaiC; Reviewed	93.5
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	93.43
PRK08760	476	replicative DNA helicase; Provisional	93.41
PRK11160	574	cysteine/glutathione ABC transporter membrane/ATP-	93.4
COG3972	660	Superfamily I DNA and RNA helicases [General funct	93.4
PRK13897	606	type IV secretion system component VirD4; Provisio	93.39
cd03239	178	ABC_SMC_head The structural maintenance of chromos	93.37
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	93.35
PLN03232	1495	ABC transporter C family member; Provisional	93.31
PRK09165	497	replicative DNA helicase; Provisional	93.3
cd03246	173	ABCC_Protease_Secretion This family represents the	93.27
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	93.24
TIGR02204	576	MsbA_rel ABC transporter, permease/ATP-binding pro	93.24
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	93.21
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	93.2
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	93.19
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	93.19
TIGR01193	708	bacteriocin_ABC ABC-type bacteriocin transporter.	93.14
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	93.1
KOG0055|consensus	1228		92.93
KOG0057|consensus	591		92.91
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	92.9
PF07088	484	GvpD: GvpD gas vesicle protein; InterPro: IPR00978	92.88
PRK07004	460	replicative DNA helicase; Provisional	92.8
cd03240	204	ABC_Rad50 The catalytic domains of Rad50 are simil	92.77
COG1702	348	PhoH Phosphate starvation-inducible protein PhoH,	92.76
KOG0331|consensus	519		92.75
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	92.73
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	92.64
KOG2035|consensus	351		92.59
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	92.53
PRK04841	903	transcriptional regulator MalT; Provisional	92.49
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	92.45
KOG0741|consensus	744		92.42
PRK04301	317	radA DNA repair and recombination protein RadA; Va	92.38

>KOG0331|consensus

Probab=100.00  E-value=1.2e-37  Score=267.04  Aligned_cols=201  Identities=30%  Similarity=0.466  Sum_probs=182.0

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcC-----CCCCCceEEEEcccH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRG-----PKNLGFRAVIVCPTR   91 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~-----~~~~~~~~iil~Pt~   91 (226)
                      +++..+.+.++...+|..|+|+|.+.| .+++|+|++..|.||||||++|++|++..+..     ....+|+++|++|||
T Consensus        96 ~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTR  175 (519)
T KOG0331|consen   96 LGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTR  175 (519)
T ss_pred             ccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcH
Confidence            556678888899999999999998887 88999999999999999999999999988864     244579999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccc
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLF  171 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~  171 (226)
                      |||.|+...+.+++...+.+..+++|+...... .+.+..+.+|+|+||+++.+++..  +.++++++.++|+||||+|+
T Consensus       176 ELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q-~~~l~~gvdiviaTPGRl~d~le~--g~~~l~~v~ylVLDEADrMl  252 (519)
T KOG0331|consen  176 ELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQ-LRDLERGVDVVIATPGRLIDLLEE--GSLNLSRVTYLVLDEADRML  252 (519)
T ss_pred             HHHHHHHHHHHHHcCCCCccEEEEeCCCCccHH-HHHHhcCCcEEEeCChHHHHHHHc--CCccccceeEEEeccHHhhh
Confidence            999999999999999988888888887654333 355778899999999999999999  89999999999999999999


Q ss_pred             ccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        172 EAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       172 ~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      ++   +|..++..|+..++++..|++++|||+|.+++.++..|+.+|+.+++.
T Consensus       253 dm---GFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig  302 (519)
T KOG0331|consen  253 DM---GFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVG  302 (519)
T ss_pred             cc---ccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEec
Confidence            99   799999999999977777999999999999999999999999999875

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

Probab=100.00  E-value=1.2e-36  Score=267.90  Aligned_cols=200  Identities=32%  Similarity=0.487  Sum_probs=177.2

Q ss_pred             HHHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCce-EEEEcccHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFR-AVIVCPTRELAK   95 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~-~iil~Pt~~L~~   95 (226)
                      +.+.+.+++.+.+.+|..++|+|.++ |.++.|+|++..|+||||||++|++|+++.+......... ++|++||||||.
T Consensus        34 l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PTRELA~  113 (513)
T COG0513          34 LGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAV  113 (513)
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCCHHHHH
Confidence            34678999999999999999999777 5889999999999999999999999999998632122112 999999999999


Q ss_pred             HHHHHHHHHhhcC-CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccC
Q psy12977         96 QTYNETVRLSEGL-GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG  174 (226)
Q Consensus        96 q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~  174 (226)
                      |+++.++.+..+. +.++..+.|+....... ..+..++||+|+||+++.+++.+  +.++++.++++|+||||+|++. 
T Consensus       114 Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~-~~l~~~~~ivVaTPGRllD~i~~--~~l~l~~v~~lVlDEADrmLd~-  189 (513)
T COG0513         114 QIAEELRKLGKNLGGLRVAVVYGGVSIRKQI-EALKRGVDIVVATPGRLLDLIKR--GKLDLSGVETLVLDEADRMLDM-  189 (513)
T ss_pred             HHHHHHHHHHhhcCCccEEEEECCCCHHHHH-HHHhcCCCEEEECccHHHHHHHc--CCcchhhcCEEEeccHhhhhcC-
Confidence            9999999999998 78888888876655555 44445799999999999999998  6899999999999999999999 


Q ss_pred             ccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        175 VRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       175 ~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                        +|.+.+..++..+ ++..|+++||||+|+.+.++.++++++|+.+++.
T Consensus       190 --Gf~~~i~~I~~~~-p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~  236 (513)
T COG0513         190 --GFIDDIEKILKAL-PPDRQTLLFSATMPDDIRELARRYLNDPVEIEVS  236 (513)
T ss_pred             --CCHHHHHHHHHhC-CcccEEEEEecCCCHHHHHHHHHHccCCcEEEEc
Confidence              7999999999999 4589999999999999999999999999999886

>KOG0345|consensus

Probab=100.00  E-value=8e-37  Score=254.33  Aligned_cols=203  Identities=28%  Similarity=0.412  Sum_probs=181.5

Q ss_pred             HHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC--CCCC--ceEEEEcccHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP--KNLG--FRAVIVCPTREL   93 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~--~~~~--~~~iil~Pt~~L   93 (226)
                      ++.+.++..+..+||+.+||+|..+ |.+++++|+++.++||||||++|++|+++.+...  +.+.  .-++|++|||||
T Consensus        12 ~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTREL   91 (567)
T KOG0345|consen   12 PLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTREL   91 (567)
T ss_pred             CccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEEecCcHHH
Confidence            4668999999999999999999666 6889999999999999999999999999998322  2222  368999999999


Q ss_pred             HHHHHHHHHHHhhc-CCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccc
Q psy12977         94 AKQTYNETVRLSEG-LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFE  172 (226)
Q Consensus        94 ~~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~  172 (226)
                      |.|+.++...+... .+....++.|+....++......++++|+||||+++.+++++....+++.+++++|+||||++++
T Consensus        92 a~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDEADrLld  171 (567)
T KOG0345|consen   92 ARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDEADRLLD  171 (567)
T ss_pred             HHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEecchHhHhc
Confidence            99999999999887 56788888888887777777778999999999999999999866777788999999999999999


Q ss_pred             cCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        173 AGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       173 ~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      .   +|...++.|+..+ +...++-+||||..+++.++....+.||+.++|..
T Consensus       172 m---gFe~~~n~ILs~L-PKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~  220 (567)
T KOG0345|consen  172 M---GFEASVNTILSFL-PKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKE  220 (567)
T ss_pred             c---cHHHHHHHHHHhc-ccccccccccchhhHHHHHHHHhhccCceeeeecc
Confidence            9   7999999999999 67888999999999999999999999999999864

>KOG0330|consensus

Probab=100.00  E-value=1.9e-36  Score=247.09  Aligned_cols=201  Identities=28%  Similarity=0.383  Sum_probs=181.2

Q ss_pred             HHHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      +.+.+..+.+.++.++..|+++|+++ |..+.|+|++..|.||||||.+|++|+++.+.+ .+..++++|++||||||.|
T Consensus        66 Lgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~-~p~~~~~lVLtPtRELA~Q  144 (476)
T KOG0330|consen   66 LGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQ-EPKLFFALVLTPTRELAQQ  144 (476)
T ss_pred             cCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHc-CCCCceEEEecCcHHHHHH
Confidence            56788999999999999999999777 688999999999999999999999999999985 4445899999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +.++++.++...|.++..+.|+..- ......+.+.+||+|+||+++.+++.+- +.+++..++++|+||||+++++   
T Consensus       145 I~e~fe~Lg~~iglr~~~lvGG~~m-~~q~~~L~kkPhilVaTPGrL~dhl~~T-kgf~le~lk~LVlDEADrlLd~---  219 (476)
T KOG0330|consen  145 IAEQFEALGSGIGLRVAVLVGGMDM-MLQANQLSKKPHILVATPGRLWDHLENT-KGFSLEQLKFLVLDEADRLLDM---  219 (476)
T ss_pred             HHHHHHHhccccCeEEEEEecCchH-HHHHHHhhcCCCEEEeCcHHHHHHHHhc-cCccHHHhHHHhhchHHhhhhh---
Confidence            9999999999999999988887543 3333456788999999999999999732 7889999999999999999999   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      .|...+..|++.+ +...|.++||||+|+.+.++....+++|+.+.+..
T Consensus       220 dF~~~ld~ILk~i-p~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~  267 (476)
T KOG0330|consen  220 DFEEELDYILKVI-PRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSS  267 (476)
T ss_pred             hhHHHHHHHHHhc-CccceEEEEEeecchhhHHHHhhccCCCeEEeccc
Confidence            7999999999999 68999999999999999999999999999998754

>KOG0338|consensus

Probab=100.00  E-value=1.4e-35  Score=249.00  Aligned_cols=202  Identities=33%  Similarity=0.442  Sum_probs=180.2

Q ss_pred             HHHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC--CCCCceEEEEcccHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP--KNLGFRAVIVCPTRELA   94 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~--~~~~~~~iil~Pt~~L~   94 (226)
                      +.|...+|.++...||..|+|+|... |..+.|+|+..+|.||||||.+|++|++.++.-.  ....-|++|++|||+|+
T Consensus       186 mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTRELa  265 (691)
T KOG0338|consen  186 MNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLVPTRELA  265 (691)
T ss_pred             cccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEeccHHHH
Confidence            67788899999999999999999666 6788999999999999999999999999987422  22345899999999999


Q ss_pred             HHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccC
Q psy12977         95 KQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG  174 (226)
Q Consensus        95 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~  174 (226)
                      -|++.+.+++..+..+.++...|+-... .+...+..+|||+|+||+++.+++.+. ..++++++..+|+||||+|++. 
T Consensus       266 iQv~sV~~qlaqFt~I~~~L~vGGL~lk-~QE~~LRs~PDIVIATPGRlIDHlrNs-~sf~ldsiEVLvlDEADRMLee-  342 (691)
T KOG0338|consen  266 IQVHSVTKQLAQFTDITVGLAVGGLDLK-AQEAVLRSRPDIVIATPGRLIDHLRNS-PSFNLDSIEVLVLDEADRMLEE-  342 (691)
T ss_pred             HHHHHHHHHHHhhccceeeeeecCccHH-HHHHHHhhCCCEEEecchhHHHHhccC-CCccccceeEEEechHHHHHHH-
Confidence            9999999999999999999888875433 333457789999999999999999764 6788999999999999999999 


Q ss_pred             ccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        175 VRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       175 ~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                        +|.+.++.|++.. +.+.|.++||||+.+++++++.--++.|+.|.+++
T Consensus       343 --gFademnEii~lc-pk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~  390 (691)
T KOG0338|consen  343 --GFADEMNEIIRLC-PKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDP  390 (691)
T ss_pred             --HHHHHHHHHHHhc-cccccceeehhhhHHHHHHHHHhhcCCCeEEEeCC
Confidence              7999999999999 67999999999999999999999999999999875

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=4.2e-34  Score=247.64  Aligned_cols=202  Identities=24%  Similarity=0.335  Sum_probs=172.2

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCC------CCCceEEEEccc
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK------NLGFRAVIVCPT   90 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~------~~~~~~iil~Pt   90 (226)
                      +.+.+.+++.+.+++|..++|+|+.+. .+++|+|++++||||||||++|++|+++.+....      ..+++++|++||
T Consensus        13 ~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~lil~Pt   92 (423)
T PRK04837         13 FALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPT   92 (423)
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEEECCc
Confidence            346788999999999999999997774 7889999999999999999999999998874321      235799999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccc
Q psy12977         91 RELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKL  170 (226)
Q Consensus        91 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l  170 (226)
                      ++||.|+.+.+..+.+..+.++..+.++....... ..+..+++|+|+||+++.+++..  ..+.+++++++|+||||++
T Consensus        93 reLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~-~~l~~~~~IlV~TP~~l~~~l~~--~~~~l~~v~~lViDEad~l  169 (423)
T PRK04837         93 RELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQL-KVLESGVDILIGTTGRLIDYAKQ--NHINLGAIQVVVLDEADRM  169 (423)
T ss_pred             HHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHH-HHhcCCCCEEEECHHHHHHHHHc--CCcccccccEEEEecHHHH
Confidence            99999999999999998898888777664433222 23456789999999999999987  6788999999999999999


Q ss_pred             cccCccchHHHHHHHHHhcCC-CCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        171 FEAGVRGFRDQLAVIYAACSG-PNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       171 ~~~~~~~~~~~i~~i~~~~~~-~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      ++.   ++...+..+++.+++ ...|.+++|||++..+.+++..++.+|..+.+.+
T Consensus       170 ~~~---~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~  222 (423)
T PRK04837        170 FDL---GFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEP  222 (423)
T ss_pred             hhc---ccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcC
Confidence            998   688999999988854 3567899999999999999999999999988753

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=3e-34  Score=254.65  Aligned_cols=199  Identities=29%  Similarity=0.416  Sum_probs=170.8

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC----CCCCceEEEEcccHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP----KNLGFRAVIVCPTREL   93 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~----~~~~~~~iil~Pt~~L   93 (226)
                      ++.+.+++.+++.+|.+|+|+|.+++ .+++|+|+++.||||||||++|++|++..+...    ...++++||++||++|
T Consensus       136 ~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreL  215 (545)
T PTZ00110        136 SFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTREL  215 (545)
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHH
Confidence            45678999999999999999997775 888999999999999999999999998776432    2346799999999999


Q ss_pred             HHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977         94 AKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus        94 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      |.|+.+.++.+....+.+.....++....... ..+..+++|+|+||++|.+++..  ...+++++++||+||||++++.
T Consensus       216 a~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~-~~l~~~~~IlVaTPgrL~d~l~~--~~~~l~~v~~lViDEAd~mld~  292 (545)
T PTZ00110        216 AEQIREQCNKFGASSKIRNTVAYGGVPKRGQI-YALRRGVEILIACPGRLIDFLES--NVTNLRRVTYLVLDEADRMLDM  292 (545)
T ss_pred             HHHHHHHHHHHhcccCccEEEEeCCCCHHHHH-HHHHcCCCEEEECHHHHHHHHHc--CCCChhhCcEEEeehHHhhhhc
Confidence            99999999999988888887777665433322 23456789999999999999987  6778999999999999999998


Q ss_pred             CccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcC-CCeEEecC
Q psy12977        174 GVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLK-RRVQINVG  224 (226)
Q Consensus       174 ~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~-~p~~i~~~  224 (226)
                         +|...+..++..+ ++..|++++|||+|+++..+++.++. +|+.+.+.
T Consensus       293 ---gf~~~i~~il~~~-~~~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg  340 (545)
T PTZ00110        293 ---GFEPQIRKIVSQI-RPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVG  340 (545)
T ss_pred             ---chHHHHHHHHHhC-CCCCeEEEEEeCCCHHHHHHHHHHhccCCEEEEEC
Confidence               6999999999888 67899999999999999999998885 68887654

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=5.7e-34  Score=249.28  Aligned_cols=199  Identities=26%  Similarity=0.393  Sum_probs=172.0

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      ++.+++++.+.+.+|.+++|+|+++. .+++|+|++++||||||||++|++|+++.+.. ...+++++|++||++|+.|+
T Consensus        10 ~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~-~~~~~~~lil~PtreLa~Q~   88 (460)
T PRK11776         10 PLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDV-KRFRVQALVLCPTRELADQV   88 (460)
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhh-ccCCceEEEEeCCHHHHHHH
Confidence            46789999999999999999998885 77899999999999999999999999998863 33356899999999999999


Q ss_pred             HHHHHHHhhcC-CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         98 YNETVRLSEGL-GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        98 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      .+.++.+.... +.++..+.|+....... ..+..+++|+|+||+++.+++.+  +.+.+++++++|+||||++++.   
T Consensus        89 ~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~-~~l~~~~~IvV~Tp~rl~~~l~~--~~~~l~~l~~lViDEad~~l~~---  162 (460)
T PRK11776         89 AKEIRRLARFIPNIKVLTLCGGVPMGPQI-DSLEHGAHIIVGTPGRILDHLRK--GTLDLDALNTLVLDEADRMLDM---  162 (460)
T ss_pred             HHHHHHHHhhCCCcEEEEEECCCChHHHH-HHhcCCCCEEEEChHHHHHHHHc--CCccHHHCCEEEEECHHHHhCc---
Confidence            99999988765 57777777665443332 23447899999999999999987  6788999999999999999998   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      +|...+..++..+ ++..|++++|||+|+.+..++..++.+|..+.+..
T Consensus       163 g~~~~l~~i~~~~-~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~  210 (460)
T PRK11776        163 GFQDAIDAIIRQA-PARRQTLLFSATYPEGIAAISQRFQRDPVEVKVES  210 (460)
T ss_pred             CcHHHHHHHHHhC-CcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECc
Confidence            6999999999888 67889999999999999999999999999887653

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=7.6e-34  Score=247.97  Aligned_cols=200  Identities=28%  Similarity=0.402  Sum_probs=171.1

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCC-----CCCceEEEEcccHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK-----NLGFRAVIVCPTRE   92 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~-----~~~~~~iil~Pt~~   92 (226)
                      ++.+.+++.+.+.+|..++|+|.++. .+++++|+++++|||+|||++|++|+++.+....     ....++||++||++
T Consensus         7 ~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil~Ptre   86 (456)
T PRK10590          7 GLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRE   86 (456)
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEEeCcHH
Confidence            46788999999999999999997775 7788999999999999999999999999885322     12358999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccc
Q psy12977         93 LAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFE  172 (226)
Q Consensus        93 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~  172 (226)
                      ||.|+.+.++.+.+..+.+...+.++....... ..+..+++|+|+||+++.++...  ....++++++||+||||++++
T Consensus        87 La~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~-~~l~~~~~IiV~TP~rL~~~~~~--~~~~l~~v~~lViDEah~ll~  163 (456)
T PRK10590         87 LAAQIGENVRDYSKYLNIRSLVVFGGVSINPQM-MKLRGGVDVLVATPGRLLDLEHQ--NAVKLDQVEILVLDEADRMLD  163 (456)
T ss_pred             HHHHHHHHHHHHhccCCCEEEEEECCcCHHHHH-HHHcCCCcEEEEChHHHHHHHHc--CCcccccceEEEeecHHHHhc
Confidence            999999999999988888877766665433322 23456789999999999998876  677899999999999999999


Q ss_pred             cCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        173 AGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       173 ~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      .   ++...+..++..+ +...|++++|||+++++.+++..++.+|..+.+.+
T Consensus       164 ~---~~~~~i~~il~~l-~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~  212 (456)
T PRK10590        164 M---GFIHDIRRVLAKL-PAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVAR  212 (456)
T ss_pred             c---ccHHHHHHHHHhC-CccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEec
Confidence            8   6889999999888 56789999999999999999999999998887653

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

Probab=100.00  E-value=1.2e-33  Score=249.96  Aligned_cols=198  Identities=29%  Similarity=0.428  Sum_probs=169.4

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcC------CCCCCceEEEEcccH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRG------PKNLGFRAVIVCPTR   91 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~------~~~~~~~~iil~Pt~   91 (226)
                      ++.+.+++.+.+.+|..++|+|.+++ .+++|+|+++.+|||||||++|++|++..+..      ....+++++|++||+
T Consensus       127 ~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTr  206 (518)
T PLN00206        127 GLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTR  206 (518)
T ss_pred             CCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCH
Confidence            46788999999999999999998775 77899999999999999999999999987632      123568999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccc
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLF  171 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~  171 (226)
                      +||.|+.+.++.+.+..+.+.....++....... ..+..+++|+|+||+++.+++..  ....++++++||+||||+++
T Consensus       207 eLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~-~~l~~~~~IiV~TPgrL~~~l~~--~~~~l~~v~~lViDEad~ml  283 (518)
T PLN00206        207 ELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQL-YRIQQGVELIVGTPGRLIDLLSK--HDIELDNVSVLVLDEVDCML  283 (518)
T ss_pred             HHHHHHHHHHHHHhCCCCceEEEEECCcchHHHH-HHhcCCCCEEEECHHHHHHHHHc--CCccchheeEEEeecHHHHh
Confidence            9999999999999888887776666554333322 23456789999999999999987  57889999999999999999


Q ss_pred             ccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        172 EAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       172 ~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      +.   +|...+..++..+  +..|++++|||+|+++..++..++.+++.+.+.
T Consensus       284 ~~---gf~~~i~~i~~~l--~~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~  331 (518)
T PLN00206        284 ER---GFRDQVMQIFQAL--SQPQVLLFSATVSPEVEKFASSLAKDIILISIG  331 (518)
T ss_pred             hc---chHHHHHHHHHhC--CCCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeC
Confidence            98   6888999998888  568999999999999999999999999988765

>KOG0342|consensus

Probab=100.00  E-value=8.4e-34  Score=237.44  Aligned_cols=202  Identities=30%  Similarity=0.404  Sum_probs=175.1

Q ss_pred             HHHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcC---CCCCCceEEEEcccHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRG---PKNLGFRAVIVCPTREL   93 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~---~~~~~~~~iil~Pt~~L   93 (226)
                      .++.+.++.++++++|.++|++|+.. +.++.|+|++..|.||+|||++|++|+.+.+..   ....+..++|+||||+|
T Consensus        87 ~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTREL  166 (543)
T KOG0342|consen   87 GSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTREL  166 (543)
T ss_pred             cccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEEecccHHH
Confidence            56788999999999999999999666 588899999999999999999999999988732   23356789999999999


Q ss_pred             HHHHHHHHHHHhhcC-CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccc
Q psy12977         94 AKQTYNETVRLSEGL-GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFE  172 (226)
Q Consensus        94 ~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~  172 (226)
                      |.|++.+.+++..+. +..+..+.|+........ .+..+++|+|+||++|.+++++. ...-...++++|+||||++++
T Consensus       167 A~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~-kl~k~~niliATPGRLlDHlqNt-~~f~~r~~k~lvlDEADrlLd  244 (543)
T KOG0342|consen  167 AMQIFAEAKELLKYHESITVGIVIGGNNFSVEAD-KLVKGCNILIATPGRLLDHLQNT-SGFLFRNLKCLVLDEADRLLD  244 (543)
T ss_pred             HHHHHHHHHHHHhhCCCcceEEEeCCccchHHHH-HhhccccEEEeCCchHHhHhhcC-CcchhhccceeEeecchhhhh
Confidence            999999999999988 788888877765544443 34459999999999999999875 345577789999999999999


Q ss_pred             cCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcC-CCeEEecCC
Q psy12977        173 AGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLK-RRVQINVGL  225 (226)
Q Consensus       173 ~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~-~p~~i~~~~  225 (226)
                      .   +|.+.+.+|.+.+ +...|.++||||.|++++++++--++ +|+++++.+
T Consensus       245 ~---GF~~di~~Ii~~l-pk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d  294 (543)
T KOG0342|consen  245 I---GFEEDVEQIIKIL-PKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDD  294 (543)
T ss_pred             c---ccHHHHHHHHHhc-cccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCC
Confidence            9   7999999999999 58999999999999999999988765 699998754

>KOG0328|consensus

Probab=100.00  E-value=3.2e-34  Score=225.79  Aligned_cols=200  Identities=24%  Similarity=0.303  Sum_probs=177.8

Q ss_pred             HHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      ++--+.|+++.+.+|+.|+.+|+.+ ++++.|+|++.++.+|+|||.+|.+.+++.+.- ..+.-++++++|||||+.|+
T Consensus        33 gl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~-~~r~tQ~lilsPTRELa~Qi  111 (400)
T KOG0328|consen   33 GLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDI-SVRETQALILSPTRELAVQI  111 (400)
T ss_pred             CchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeeccc-ccceeeEEEecChHHHHHHH
Confidence            4566899999999999999999776 599999999999999999999999998888753 33456899999999999999


Q ss_pred             HHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccc
Q psy12977         98 YNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG  177 (226)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~  177 (226)
                      .+.+..++.+.++.+..+.|+.+.-+.. .....+.+++.+||+++.+++++  +.+....++++|+||+|.+++.   +
T Consensus       112 ~~vi~alg~~mnvq~hacigg~n~gedi-kkld~G~hvVsGtPGrv~dmikr--~~L~tr~vkmlVLDEaDemL~k---g  185 (400)
T KOG0328|consen  112 QKVILALGDYMNVQCHACIGGKNLGEDI-KKLDYGQHVVSGTPGRVLDMIKR--RSLRTRAVKMLVLDEADEMLNK---G  185 (400)
T ss_pred             HHHHHHhcccccceEEEEecCCccchhh-hhhcccceEeeCCCchHHHHHHh--ccccccceeEEEeccHHHHHHh---h
Confidence            9999999999999988777665533332 22448899999999999999998  8899999999999999999998   7


Q ss_pred             hHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCCC
Q psy12977        178 FRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       178 ~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      +-.++..+++++ ++.+|++++|||+|+++.+..++|+.||+.|.++|.
T Consensus       186 fk~Qiydiyr~l-p~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrd  233 (400)
T KOG0328|consen  186 FKEQIYDIYRYL-PPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRD  233 (400)
T ss_pred             HHHHHHHHHHhC-CCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecC
Confidence            999999999999 789999999999999999999999999999998863

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=1.6e-33  Score=252.74  Aligned_cols=198  Identities=25%  Similarity=0.380  Sum_probs=171.3

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      .+.+++++++.+.+|.+++|+|.++. .++.++|++++||||+|||++|++|+++.+.. ...++++||++||++||.|+
T Consensus        12 ~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~-~~~~~~~LIL~PTreLa~Qv   90 (629)
T PRK11634         12 GLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDP-ELKAPQILVLAPTRELAVQV   90 (629)
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhh-ccCCCeEEEEeCcHHHHHHH
Confidence            46789999999999999999997774 77889999999999999999999999988853 33467999999999999999


Q ss_pred             HHHHHHHhhcC-CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         98 YNETVRLSEGL-GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        98 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      ++.++.+.+.. +..+..+.++....... ..+..+++|+|+||+++.+++.+  ..+++++++++|+||||.+++.   
T Consensus        91 ~~~l~~~~~~~~~i~v~~~~gG~~~~~q~-~~l~~~~~IVVgTPgrl~d~l~r--~~l~l~~l~~lVlDEAd~ml~~---  164 (629)
T PRK11634         91 AEAMTDFSKHMRGVNVVALYGGQRYDVQL-RALRQGPQIVVGTPGRLLDHLKR--GTLDLSKLSGLVLDEADEMLRM---  164 (629)
T ss_pred             HHHHHHHHhhcCCceEEEEECCcCHHHHH-HHhcCCCCEEEECHHHHHHHHHc--CCcchhhceEEEeccHHHHhhc---
Confidence            99999998765 57777766665433222 23456789999999999999987  6788999999999999999998   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      +|...+..++..+ +...|+++||||+|+.+..+.++|+.+|..+.+.
T Consensus       165 gf~~di~~Il~~l-p~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~  211 (629)
T PRK11634        165 GFIEDVETIMAQI-PEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQ  211 (629)
T ss_pred             ccHHHHHHHHHhC-CCCCeEEEEEccCChhHHHHHHHHcCCCeEEEcc
Confidence            6999999999988 6789999999999999999999999999988765

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=8.5e-33  Score=242.66  Aligned_cols=201  Identities=26%  Similarity=0.349  Sum_probs=170.6

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCC------CCceEEEEcccH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKN------LGFRAVIVCPTR   91 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~------~~~~~iil~Pt~   91 (226)
                      .+-+++++++.+.+|..++++|.+++ .+.+|+|+++.+|||||||++|++|+++.+.....      ..++++|++||+
T Consensus        93 ~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~Ptr  172 (475)
T PRK01297         93 NLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTR  172 (475)
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCcH
Confidence            46789999999999999999998775 78899999999999999999999999988754321      247999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccc
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLF  171 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~  171 (226)
                      +|+.|+.+.++.+.+..+..+..+.++..............++|+|+||+++..+...  +...+++++++|+||+|.++
T Consensus       173 eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~--~~~~l~~l~~lViDEah~l~  250 (475)
T PRK01297        173 ELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQR--GEVHLDMVEVMVLDEADRML  250 (475)
T ss_pred             HHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHc--CCcccccCceEEechHHHHH
Confidence            9999999999999988888888777764333332233346789999999999998876  66778999999999999999


Q ss_pred             ccCccchHHHHHHHHHhcCC-CCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        172 EAGVRGFRDQLAVIYAACSG-PNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       172 ~~~~~~~~~~i~~i~~~~~~-~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      +.   ++...+..+++..+. ...|++++|||++.++.++++.++.+|..+.+.
T Consensus       251 ~~---~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  301 (475)
T PRK01297        251 DM---GFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIE  301 (475)
T ss_pred             hc---ccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEec
Confidence            88   688889999888743 357999999999999999999999999887764

>KOG0326|consensus

Probab=100.00  E-value=2e-33  Score=224.61  Aligned_cols=197  Identities=28%  Similarity=0.390  Sum_probs=179.6

Q ss_pred             HHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      .+-++.|..+.+.+|+.|+|+|+.. |..+.|+|++..|..|+|||.+|.+|+++.+. .+....++++++||||||.|+
T Consensus        91 ~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid-~~~~~IQ~~ilVPtrelALQt  169 (459)
T KOG0326|consen   91 CLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKID-PKKNVIQAIILVPTRELALQT  169 (459)
T ss_pred             hhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcC-ccccceeEEEEeecchhhHHH
Confidence            3467899999999999999999655 68899999999999999999999999999997 455678999999999999999


Q ss_pred             HHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccc
Q psy12977         98 YNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG  177 (226)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~  177 (226)
                      ...++++.+..++++....|++.-..+. .++....+++|+||+++++++..  +...++...++|+||||.+++.   .
T Consensus       170 Sqvc~~lskh~~i~vmvttGGT~lrDDI-~Rl~~~VH~~vgTPGRIlDL~~K--gVa~ls~c~~lV~DEADKlLs~---~  243 (459)
T KOG0326|consen  170 SQVCKELSKHLGIKVMVTTGGTSLRDDI-MRLNQTVHLVVGTPGRILDLAKK--GVADLSDCVILVMDEADKLLSV---D  243 (459)
T ss_pred             HHHHHHHhcccCeEEEEecCCcccccce-eeecCceEEEEcCChhHHHHHhc--ccccchhceEEEechhhhhhch---h
Confidence            9999999999999999888887665554 34678899999999999999998  8888999999999999999998   6


Q ss_pred             hHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEec
Q psy12977        178 FRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       178 ~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~  223 (226)
                      |...+..++..+ ++..|++++|||+|-.++.|..+++++|-.|++
T Consensus       244 F~~~~e~li~~l-P~~rQillySATFP~tVk~Fm~~~l~kPy~INL  288 (459)
T KOG0326|consen  244 FQPIVEKLISFL-PKERQILLYSATFPLTVKGFMDRHLKKPYEINL  288 (459)
T ss_pred             hhhHHHHHHHhC-CccceeeEEecccchhHHHHHHHhccCcceeeh
Confidence            999999999988 789999999999999999999999999999986

>KOG0343|consensus

Probab=100.00  E-value=1.4e-33  Score=238.93  Aligned_cols=200  Identities=29%  Similarity=0.451  Sum_probs=179.0

Q ss_pred             HHHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHh---cCCCCCCceEEEEcccHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSL---RGPKNLGFRAVIVCPTREL   93 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~---~~~~~~~~~~iil~Pt~~L   93 (226)
                      +++.--++.++++..|-.++++|... +..+.|+|++-.|.||||||++|++|+++.+   .+....|..+||++|||+|
T Consensus        74 lpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIISPTREL  153 (758)
T KOG0343|consen   74 LPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALIISPTREL  153 (758)
T ss_pred             CCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeEEecchHHH
Confidence            56677899999999999999999776 5889999999999999999999999999887   3455567889999999999


Q ss_pred             HHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977         94 AKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus        94 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      |.|+++.+...+++.....+.+.|+..  ..++....+..+|+||||++|++++... ..++.+++.++|+||||+++++
T Consensus       154 A~QtFevL~kvgk~h~fSaGLiiGG~~--~k~E~eRi~~mNILVCTPGRLLQHmde~-~~f~t~~lQmLvLDEADR~LDM  230 (758)
T KOG0343|consen  154 ALQTFEVLNKVGKHHDFSAGLIIGGKD--VKFELERISQMNILVCTPGRLLQHMDEN-PNFSTSNLQMLVLDEADRMLDM  230 (758)
T ss_pred             HHHHHHHHHHHhhccccccceeecCch--hHHHHHhhhcCCeEEechHHHHHHhhhc-CCCCCCcceEEEeccHHHHHHH
Confidence            999999999999999999888887765  3333445678899999999999999875 6778999999999999999999


Q ss_pred             CccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        174 GVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       174 ~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                         +|...+..|+..+ ++..|+++||||....+.++++-.++||++|.+-
T Consensus       231 ---GFk~tL~~Ii~~l-P~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvh  277 (758)
T KOG0343|consen  231 ---GFKKTLNAIIENL-PKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVH  277 (758)
T ss_pred             ---hHHHHHHHHHHhC-ChhheeeeeecccchhHHHHHHhhcCCCcEEEEe
Confidence               7999999999999 6899999999999999999999999999999764

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1e-32  Score=245.88  Aligned_cols=201  Identities=26%  Similarity=0.380  Sum_probs=169.9

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC------CCCCceEEEEcccH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP------KNLGFRAVIVCPTR   91 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~------~~~~~~~iil~Pt~   91 (226)
                      .+-+++++.+.+.+|..++|+|+++. .+++|+|+++++|||||||++|++|+++.+...      ....+++||++||+
T Consensus        15 ~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PTr   94 (572)
T PRK04537         15 DLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTR   94 (572)
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCcH
Confidence            46789999999999999999997774 888999999999999999999999999887432      12247999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccc
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLF  171 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~  171 (226)
                      +|+.|+++.++.+....++++..+.++....... ..+..+++|+|+||++|.+++.+. ..+.+..+++||+||+|.++
T Consensus        95 eLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~-~~l~~~~dIiV~TP~rL~~~l~~~-~~~~l~~v~~lViDEAh~ll  172 (572)
T PRK04537         95 ELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQR-ELLQQGVDVIIATPGRLIDYVKQH-KVVSLHACEICVLDEADRMF  172 (572)
T ss_pred             HHHHHHHHHHHHHhccCCceEEEEECCCCHHHHH-HHHhCCCCEEEECHHHHHHHHHhc-cccchhheeeeEecCHHHHh
Confidence            9999999999999998888888777765433222 234567899999999999988753 35678899999999999999


Q ss_pred             ccCccchHHHHHHHHHhcCCC-CceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        172 EAGVRGFRDQLAVIYAACSGP-NLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       172 ~~~~~~~~~~i~~i~~~~~~~-~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      +.   +|...+..+++.++.. ..|+++||||+++.+.++...++.+|..+.+.
T Consensus       173 d~---gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~  223 (572)
T PRK04537        173 DL---GFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVE  223 (572)
T ss_pred             hc---chHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEec
Confidence            88   6899999999888432 67999999999999999999999988776553

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=3.5e-32  Score=236.48  Aligned_cols=200  Identities=26%  Similarity=0.346  Sum_probs=170.4

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC---CCCCceEEEEcccHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP---KNLGFRAVIVCPTRELA   94 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~---~~~~~~~iil~Pt~~L~   94 (226)
                      .+-+.+++.+.+++|.+++++|+++. .++.|+|+++++|||+|||++|++|+++.+...   ...+++++|++||++|+
T Consensus         7 ~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eLa   86 (434)
T PRK11192          7 ELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELA   86 (434)
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHHH
Confidence            35678999999999999999997775 778899999999999999999999999887432   22346999999999999


Q ss_pred             HHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccC
Q psy12977         95 KQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG  174 (226)
Q Consensus        95 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~  174 (226)
                      .|+.+.+..+.+..+.++..+.|+....... ..+.++++|+|+||+++.+++..  +.+++.++++||+||||++++. 
T Consensus        87 ~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~-~~l~~~~~IlV~Tp~rl~~~~~~--~~~~~~~v~~lViDEah~~l~~-  162 (434)
T PRK11192         87 MQVADQARELAKHTHLDIATITGGVAYMNHA-EVFSENQDIVVATPGRLLQYIKE--ENFDCRAVETLILDEADRMLDM-  162 (434)
T ss_pred             HHHHHHHHHHHccCCcEEEEEECCCCHHHHH-HHhcCCCCEEEEChHHHHHHHHc--CCcCcccCCEEEEECHHHHhCC-
Confidence            9999999999999899988887765443332 23456789999999999999987  6778899999999999999998 


Q ss_pred             ccchHHHHHHHHHhcCCCCceEEEEeeeCch-hHHHHHHHhcCCCeEEecCC
Q psy12977        175 VRGFRDQLAVIYAACSGPNLKRGMFSATHTE-DVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       175 ~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~-~~~~~~~~~~~~p~~i~~~~  225 (226)
                        ++...+..+.... +...|+++||||++. .+.++...++.+|+.+++..
T Consensus       163 --~~~~~~~~i~~~~-~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~  211 (434)
T PRK11192        163 --GFAQDIETIAAET-RWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEP  211 (434)
T ss_pred             --CcHHHHHHHHHhC-ccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecC
Confidence              6889999988887 567899999999985 57888888899999887653

>KOG0336|consensus

Probab=100.00  E-value=7.6e-33  Score=227.64  Aligned_cols=197  Identities=27%  Similarity=0.393  Sum_probs=170.3

Q ss_pred             HHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcC-----CCCCCceEEEEcccHHH
Q psy12977         20 IIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRG-----PKNLGFRAVIVCPTREL   93 (226)
Q Consensus        20 ~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~-----~~~~~~~~iil~Pt~~L   93 (226)
                      --|++|..+++.+|++|+|+|+|+| ++++|+|++..|+||+|||++|+.|.+..+..     ....++.+++++||++|
T Consensus       227 ~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreL  306 (629)
T KOG0336|consen  227 CYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTREL  306 (629)
T ss_pred             hhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHH
Confidence            3579999999999999999999997 78999999999999999999999997766632     23347899999999999


Q ss_pred             HHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977         94 AKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus        94 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      +.|+.-+.+... +-+.+..+++|+++..+.. ..+..+.+|+++||++|.++...  +.+++.++.++|+||||+|+|+
T Consensus       307 alqie~e~~kys-yng~ksvc~ygggnR~eqi-e~lkrgveiiiatPgrlndL~~~--n~i~l~siTYlVlDEADrMLDM  382 (629)
T KOG0336|consen  307 ALQIEGEVKKYS-YNGLKSVCVYGGGNRNEQI-EDLKRGVEIIIATPGRLNDLQMD--NVINLASITYLVLDEADRMLDM  382 (629)
T ss_pred             HHHHHhHHhHhh-hcCcceEEEecCCCchhHH-HHHhcCceEEeeCCchHhhhhhc--CeeeeeeeEEEEecchhhhhcc
Confidence            999977665553 3366666777776555444 34678899999999999999887  8999999999999999999999


Q ss_pred             CccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        174 GVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       174 ~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                         +|..+|.+++-.+ .|..|+++.|||+|+.+..++..|+++|+.+-+.
T Consensus       383 ---gFEpqIrkilldi-RPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vG  429 (629)
T KOG0336|consen  383 ---GFEPQIRKILLDI-RPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVG  429 (629)
T ss_pred             ---cccHHHHHHhhhc-CCcceeeeecccCchHHHHHHHHhhhCceEEEec
Confidence               7999999999998 7899999999999999999999999999987653

>KOG0346|consensus

Probab=100.00  E-value=7.2e-33  Score=229.25  Aligned_cols=200  Identities=27%  Similarity=0.317  Sum_probs=170.1

Q ss_pred             HHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcC-----CCCCCceEEEEcccHHH
Q psy12977         20 IIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRG-----PKNLGFRAVIVCPTREL   93 (226)
Q Consensus        20 ~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~-----~~~~~~~~iil~Pt~~L   93 (226)
                      +=+-+++++.+.+|+.+|-+|+.+ ++++.|+|++..|.||||||.+|++|+++.+..     ....++.++|++||+||
T Consensus        26 LD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTkEL  105 (569)
T KOG0346|consen   26 LDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTKEL  105 (569)
T ss_pred             CCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEEEechHHH
Confidence            445789999999999999999665 688999999999999999999999999988732     34457899999999999


Q ss_pred             HHHHHHHHHHHhhcCCCeEEEEe--cchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccc
Q psy12977         94 AKQTYNETVRLSEGLGLRAHVIG--KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLF  171 (226)
Q Consensus        94 ~~q~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~  171 (226)
                      |.|+++.+.++..+.+..+..++  ++.++... ...+...+||+|+||+++..++..+ ....+..++++|+||||.++
T Consensus       106 ~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~-~~~L~d~pdIvV~TP~~ll~~~~~~-~~~~~~~l~~LVvDEADLll  183 (569)
T KOG0346|consen  106 AQQVYKVIEKLVEYCSKDLRAINLASSMSDSVN-SVALMDLPDIVVATPAKLLRHLAAG-VLEYLDSLSFLVVDEADLLL  183 (569)
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhhhhcccchHHH-HHHHccCCCeEEeChHHHHHHHhhc-cchhhhheeeEEechhhhhh
Confidence            99999999999887764443332  22223222 2567789999999999999999873 22778899999999999999


Q ss_pred             ccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        172 EAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       172 ~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      +.   +|.++++.+.+.+ ++.+|-++||||+.+++..+-+.++++|+.+.+.+
T Consensus       184 sf---GYeedlk~l~~~L-Pr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e  233 (569)
T KOG0346|consen  184 SF---GYEEDLKKLRSHL-PRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTE  233 (569)
T ss_pred             hc---ccHHHHHHHHHhC-CchhhheeehhhhhhHHHHHHHHhccCCeEEEecc
Confidence            98   7999999999999 68999999999999999999999999999998764

>cd00268 DEADc DEAD-box helicases

Probab=100.00  E-value=1.8e-31  Score=209.41  Aligned_cols=196  Identities=31%  Similarity=0.419  Sum_probs=164.9

Q ss_pred             HHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCC-CCCceEEEEcccHHHHHHH
Q psy12977         20 IIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK-NLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        20 ~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~-~~~~~~iil~Pt~~L~~q~   97 (226)
                      +.+.+.+.+.+.++..+++.|..++ .+.+++|+++.+|||+|||++|++++++.+.... ..+++++|++|+++|+.|+
T Consensus         6 ~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~q~   85 (203)
T cd00268           6 LSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQI   85 (203)
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHHHH
Confidence            3456788899999999999998776 6667999999999999999999999998886531 3567999999999999999


Q ss_pred             HHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccc
Q psy12977         98 YNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG  177 (226)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~  177 (226)
                      .+.++++....+..+....++....... ....++++|+|+||+++.+++..  ....+.+++++|+||+|.+.+.   +
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~iiv~T~~~l~~~l~~--~~~~~~~l~~lIvDE~h~~~~~---~  159 (203)
T cd00268          86 AEVARKLGKHTNLKVVVIYGGTSIDKQI-RKLKRGPHIVVATPGRLLDLLER--GKLDLSKVKYLVLDEADRMLDM---G  159 (203)
T ss_pred             HHHHHHHhccCCceEEEEECCCCHHHHH-HHhcCCCCEEEEChHHHHHHHHc--CCCChhhCCEEEEeChHHhhcc---C
Confidence            9999999887777777776655433222 22336789999999999998887  4577889999999999998866   5


Q ss_pred             hHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEe
Q psy12977        178 FRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN  222 (226)
Q Consensus       178 ~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~  222 (226)
                      +...+..+.+.+ +..+|++++|||+++++.+++.+++.+|+.++
T Consensus       160 ~~~~~~~~~~~l-~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~  203 (203)
T cd00268         160 FEDQIREILKLL-PKDRQTLLFSATMPKEVRDLARKFLRNPVRIL  203 (203)
T ss_pred             hHHHHHHHHHhC-CcccEEEEEeccCCHHHHHHHHHHCCCCEEeC
Confidence            888888888887 56899999999999999999999999999874

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.

>KOG0348|consensus

Probab=99.98  E-value=1.3e-32  Score=232.29  Aligned_cols=200  Identities=28%  Similarity=0.386  Sum_probs=167.5

Q ss_pred             HHHHHHHHh-hccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcC-----CCCCCceEEEEcccHHH
Q psy12977         21 IVTTLAVVS-NSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRG-----PKNLGFRAVIVCPTREL   93 (226)
Q Consensus        21 ~~~~l~~~~-~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~-----~~~~~~~~iil~Pt~~L   93 (226)
                      -|...+.+. .+.+..+|.+|+++ |.+++|+|++|.++||||||++|++|+.+.+..     ....|+.++|++|||||
T Consensus       144 ~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTREL  223 (708)
T KOG0348|consen  144 HPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTREL  223 (708)
T ss_pred             CHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCceEEEEechHHH
Confidence            344444443 57889999999777 588899999999999999999999999998843     23347899999999999


Q ss_pred             HHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977         94 AKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus        94 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      |.|+++.++.+.+.+.+-+-+...+++.......++.++++|+|+||+++.+.+.+- ..+.+++++++|+||+|++++.
T Consensus       224 ~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT-~~i~~s~LRwlVlDEaDrlleL  302 (708)
T KOG0348|consen  224 ALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNT-KSIKFSRLRWLVLDEADRLLEL  302 (708)
T ss_pred             HHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhcc-chheeeeeeEEEecchhHHHhc
Confidence            999999999999887777765555555555555678899999999999999998753 6788999999999999999999


Q ss_pred             CccchHHHHHHHHHhc---C---------CCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        174 GVRGFRDQLAVIYAAC---S---------GPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       174 ~~~~~~~~i~~i~~~~---~---------~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                         +|...|..|++.+   +         ++..|.+++|||+.+.+.++...-++||+.|.++
T Consensus       303 ---Gfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld  362 (708)
T KOG0348|consen  303 ---GFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLD  362 (708)
T ss_pred             ---cchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeecc
Confidence               6888888888877   1         1246779999999999999999999999999843

>PTZ00424 helicase 45; Provisional

Probab=99.98  E-value=3.5e-31  Score=227.95  Aligned_cols=198  Identities=21%  Similarity=0.311  Sum_probs=166.6

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      ++.++.++.+.+.+|..|+|+|..+. .+.+++|+++++|||+|||++|++|++..+.. ...+.+++|++|+++|+.|+
T Consensus        34 ~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~-~~~~~~~lil~Pt~~L~~Q~  112 (401)
T PTZ00424         34 KLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDY-DLNACQALILAPTRELAQQI  112 (401)
T ss_pred             CCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcC-CCCCceEEEECCCHHHHHHH
Confidence            45678899999999999999998875 77889999999999999999999999988753 33467899999999999999


Q ss_pred             HHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccc
Q psy12977         98 YNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG  177 (226)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~  177 (226)
                      .+.+..++...+.......++....... .....+++|+|+||+++.+.+.+  ....+++++++|+||+|++.+.   +
T Consensus       113 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~Ivv~Tp~~l~~~l~~--~~~~l~~i~lvViDEah~~~~~---~  186 (401)
T PTZ00424        113 QKVVLALGDYLKVRCHACVGGTVVRDDI-NKLKAGVHMVVGTPGRVYDMIDK--RHLRVDDLKLFILDEADEMLSR---G  186 (401)
T ss_pred             HHHHHHHhhhcCceEEEEECCcCHHHHH-HHHcCCCCEEEECcHHHHHHHHh--CCcccccccEEEEecHHHHHhc---c
Confidence            9999999887777766665554332222 22345689999999999998886  5677999999999999999887   5


Q ss_pred             hHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        178 FRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       178 ~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      +...+..+++.+ ++..|++++|||+|+++.++..+++.+|..+.+.
T Consensus       187 ~~~~~~~i~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  232 (401)
T PTZ00424        187 FKGQIYDVFKKL-PPDVQVALFSATMPNEILELTTKFMRDPKRILVK  232 (401)
T ss_pred             hHHHHHHHHhhC-CCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeC
Confidence            777888888887 6789999999999999999999999988876554

>KOG0339|consensus

Probab=99.97  E-value=4.2e-31  Score=222.13  Aligned_cols=195  Identities=29%  Similarity=0.450  Sum_probs=177.2

Q ss_pred             HHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC----CCCCceEEEEcccHHHHHH
Q psy12977         22 VTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP----KNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        22 ~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~----~~~~~~~iil~Pt~~L~~q   96 (226)
                      -..+.+++..-|..++|+|.++ +..++|++++-.|-||||||.+|+.|++..++.+    ...+|.++|++||++||.|
T Consensus       232 kqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~Q  311 (731)
T KOG0339|consen  232 KQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELASQ  311 (731)
T ss_pred             HHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCCeEEEEeccHHHHHH
Confidence            3567889999999999999776 5889999999999999999999999999888643    3457899999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      ++.+++.+++.+++++.+++++....+.... +..+++|+||||+++.+++..  ...++.++.+||+||+|+|.+.   
T Consensus       312 i~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~-Lk~g~EivVaTPgRlid~Vkm--Katn~~rvS~LV~DEadrmfdm---  385 (731)
T KOG0339|consen  312 IFSEAKKFGKAYGLRVVAVYGGGSKWEQSKE-LKEGAEIVVATPGRLIDMVKM--KATNLSRVSYLVLDEADRMFDM---  385 (731)
T ss_pred             HHHHHHHhhhhccceEEEeecCCcHHHHHHh-hhcCCeEEEechHHHHHHHHh--hcccceeeeEEEEechhhhhcc---
Confidence            9999999999999999999888877665544 458999999999999999998  8999999999999999999999   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEec
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~  223 (226)
                      +|..+++.|...+ .+..|.++||||++..++.+++.++.+|+.+..
T Consensus       386 Gfe~qVrSI~~hi-rpdrQtllFsaTf~~kIe~lard~L~dpVrvVq  431 (731)
T KOG0339|consen  386 GFEPQVRSIKQHI-RPDRQTLLFSATFKKKIEKLARDILSDPVRVVQ  431 (731)
T ss_pred             ccHHHHHHHHhhc-CCcceEEEeeccchHHHHHHHHHHhcCCeeEEE
Confidence            7999999999999 789999999999999999999999999998754

>KOG0335|consensus

Probab=99.97  E-value=1.6e-31  Score=226.21  Aligned_cols=197  Identities=31%  Similarity=0.438  Sum_probs=168.3

Q ss_pred             HHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCC---------CCceEEEEcccH
Q psy12977         22 VTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKN---------LGFRAVIVCPTR   91 (226)
Q Consensus        22 ~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~---------~~~~~iil~Pt~   91 (226)
                      -.....+...+|..++|+|+.. +.+..|++++++|+||+|||.+|++|++..+.....         .+|+++|++|||
T Consensus        83 ~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTR  162 (482)
T KOG0335|consen   83 EALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTR  162 (482)
T ss_pred             HHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcH
Confidence            3455668899999999999887 488889999999999999999999999998854322         368999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccc
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLF  171 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~  171 (226)
                      |||.|++++.+++.-..+.+....+++. +.....+....+|||+|+||++|.+++.+  +.+.+++++++|+||||.|+
T Consensus       163 eL~~Qi~nea~k~~~~s~~~~~~~ygg~-~~~~q~~~~~~gcdIlvaTpGrL~d~~e~--g~i~l~~~k~~vLDEADrMl  239 (482)
T KOG0335|consen  163 ELVDQIYNEARKFSYLSGMKSVVVYGGT-DLGAQLRFIKRGCDILVATPGRLKDLIER--GKISLDNCKFLVLDEADRML  239 (482)
T ss_pred             HHhhHHHHHHHhhcccccceeeeeeCCc-chhhhhhhhccCccEEEecCchhhhhhhc--ceeehhhCcEEEecchHHhh
Confidence            9999999999999877778887777773 33444566789999999999999999998  89999999999999999999


Q ss_pred             c-cCccchHHHHHHHHHhcC---CCCceEEEEeeeCchhHHHHHHHhcCC-CeEEecC
Q psy12977        172 E-AGVRGFRDQLAVIYAACS---GPNLKRGMFSATHTEDVAKWCRRKLKR-RVQINVG  224 (226)
Q Consensus       172 ~-~~~~~~~~~i~~i~~~~~---~~~~q~v~~SAT~~~~~~~~~~~~~~~-p~~i~~~  224 (226)
                      | .   +|..+|..++....   ....|.++||||+|+++..++..++.+ ++.+.|.
T Consensus       240 D~m---gF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~  294 (482)
T KOG0335|consen  240 DEM---GFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVG  294 (482)
T ss_pred             hhc---cccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEe
Confidence            9 6   78899999988773   257899999999999999988777765 7776654

>KOG0337|consensus

Probab=99.97  E-value=8.5e-31  Score=215.96  Aligned_cols=200  Identities=34%  Similarity=0.479  Sum_probs=179.0

Q ss_pred             HHHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      .++-|..++++.+.+|+.++|+|.-. +.++++++++-.+-||||||.||++|++..+......+.|++++.||++|+.|
T Consensus        26 mgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~RalilsptreLa~q  105 (529)
T KOG0337|consen   26 MGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTRELALQ  105 (529)
T ss_pred             cCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCcHHHHHH
Confidence            56789999999999999999999665 68899999999999999999999999999998777778899999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +.+..+++++..+.+..+..++....+++ ..+..++|||++||+++..+.-.  -.+.++.+.++|+||+|.+.++   
T Consensus       106 tlkvvkdlgrgt~lr~s~~~ggD~~eeqf-~~l~~npDii~ATpgr~~h~~ve--m~l~l~sveyVVfdEadrlfem---  179 (529)
T KOG0337|consen  106 TLKVVKDLGRGTKLRQSLLVGGDSIEEQF-ILLNENPDIIIATPGRLLHLGVE--MTLTLSSVEYVVFDEADRLFEM---  179 (529)
T ss_pred             HHHHHHHhccccchhhhhhcccchHHHHH-HHhccCCCEEEecCceeeeeehh--eeccccceeeeeehhhhHHHhh---
Confidence            99999999999888888776665444443 45678999999999999887765  5588999999999999999999   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      +|..++.+++..+ +...|.++||||+|+.+.++.++-+.+|+.+.++
T Consensus       180 gfqeql~e~l~rl-~~~~QTllfSatlp~~lv~fakaGl~~p~lVRld  226 (529)
T KOG0337|consen  180 GFQEQLHEILSRL-PESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLD  226 (529)
T ss_pred             hhHHHHHHHHHhC-CCcceEEEEeccCchhhHHHHHccCCCCceEEee
Confidence            7999999999999 5667999999999999999999999999988743

>KOG0334|consensus

Probab=99.96  E-value=5.2e-30  Score=230.85  Aligned_cols=205  Identities=28%  Similarity=0.435  Sum_probs=179.1

Q ss_pred             hHHHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC----CCCCceEEEEcccH
Q psy12977         17 VISIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP----KNLGFRAVIVCPTR   91 (226)
Q Consensus        17 ~~~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~----~~~~~~~iil~Pt~   91 (226)
                      +.++.+++|..++.++|..++++|.++ |.+++|+|+|..|-||||||++|++|++..++..    ...||-++|++||+
T Consensus       369 q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtr  448 (997)
T KOG0334|consen  369 QCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTR  448 (997)
T ss_pred             hCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEcCCH
Confidence            467889999999999999999999877 5889999999999999999999999999777433    23489999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcC-CCCCCCCCccEEEEcccccc
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMD-PPALNLANVEWLIVDESDKL  170 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~-~~~~~~~~~~~lViDE~h~l  170 (226)
                      +|+.|+.+.++.+.+.+++++.+++|+....... .++..+++|+||||+++.+.+..+ +...++.++.++|+||+|++
T Consensus       449 ela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qi-aelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~deaDrm  527 (997)
T KOG0334|consen  449 ELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQI-AELKRGAEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEADRM  527 (997)
T ss_pred             HHHHHHHHHHHHHHhhcCceEEEecCCccHHHHH-HHHhcCCceEEeccchhhhhHhhcCCccccccccceeeechhhhh
Confidence            9999999999999999999999998886654443 445566999999999999987543 34556788889999999999


Q ss_pred             cccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCCC
Q psy12977        171 FEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       171 ~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      ++.   +|..++..|++.+ .+..|.+++|||+|..++.++.+.++.|+.+.+..|
T Consensus       528 fdm---gfePq~~~Ii~nl-rpdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~  579 (997)
T KOG0334|consen  528 FDM---GFEPQITRILQNL-RPDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGR  579 (997)
T ss_pred             hee---ccCcccchHHhhc-chhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccc
Confidence            988   6888888899999 789999999999999999999999999999888754

>KOG0333|consensus

Probab=99.96  E-value=2.3e-29  Score=212.33  Aligned_cols=200  Identities=30%  Similarity=0.425  Sum_probs=173.9

Q ss_pred             HHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcC--------CCCCCceEEEEcc
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRG--------PKNLGFRAVIVCP   89 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~--------~~~~~~~~iil~P   89 (226)
                      ++..+.++.+..-+|..++|+|.++ ++.++.+|+|..+.||||||++|++|++..+..        +...+|+++++.|
T Consensus       251 ~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilap  330 (673)
T KOG0333|consen  251 GFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAP  330 (673)
T ss_pred             CCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhcccCceeeeech
Confidence            3466788999999999999999777 588889999999999999999999999877632        2345899999999


Q ss_pred             cHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccc
Q psy12977         90 TRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK  169 (226)
Q Consensus        90 t~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~  169 (226)
                      ||+|+.|+.+.-..+.+.++.++..+.|+..-.+. ...+..+|+|+|+||++|.+.+.+  ..+.+..+.++|+||||.
T Consensus       331 tReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq-~fqls~gceiviatPgrLid~Len--r~lvl~qctyvvldeadr  407 (673)
T KOG0333|consen  331 TRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQ-GFQLSMGCEIVIATPGRLIDSLEN--RYLVLNQCTYVVLDEADR  407 (673)
T ss_pred             HHHHHHHHHHHHHHhcccccceEEEEecccchhhh-hhhhhccceeeecCchHHHHHHHH--HHHHhccCceEeccchhh
Confidence            99999999999999999999988877777554433 234678999999999999998887  677789999999999999


Q ss_pred             ccccCccchHHHHHHHHHhcCCC------------------------CceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        170 LFEAGVRGFRDQLAVIYAACSGP------------------------NLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       170 l~~~~~~~~~~~i~~i~~~~~~~------------------------~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      |.|.   +|..++..++.++|..                        ..|.++||||.|+.+..+++.|+++|+.+.++
T Consensus       408 miDm---gfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~pv~vtig  483 (673)
T KOG0333|consen  408 MIDM---GFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVTIG  483 (673)
T ss_pred             hhcc---cccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCCeEEEec
Confidence            9999   7999999999988621                        17899999999999999999999999999875

>KOG0347|consensus

Probab=99.96  E-value=6.3e-30  Score=216.77  Aligned_cols=183  Identities=29%  Similarity=0.339  Sum_probs=152.6

Q ss_pred             HHHHHHHHHHhhccccCCCCccccc-ccCCCC-CeEEEECCCCchHhHHHHHHHHHHhcCC----------CCCCce--E
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLG-RQIFACAPTGSGKTAAFLIPIIHSLRGP----------KNLGFR--A   84 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~-~~~li~apTGsGKT~~~~~~~~~~~~~~----------~~~~~~--~   84 (226)
                      ++.+++|+++++.+|.+|+|+|+.. +.+..| .|++-.|.||||||++|.+|+++.+...          ...+++  +
T Consensus       187 ~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k~~k~~~  266 (731)
T KOG0347|consen  187 FLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTSAKYVKPIA  266 (731)
T ss_pred             CCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhHHhccCccee
Confidence            7899999999999999999999666 455566 7999999999999999999999855321          112344  9


Q ss_pred             EEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCC-CCCCCCccEEE
Q psy12977         85 VIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPP-ALNLANVEWLI  163 (226)
Q Consensus        85 iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~-~~~~~~~~~lV  163 (226)
                      +|++||||||.|+.+.+....+..++++..+.|+-.. .++.+.+...++|+|+||++|+.++..++. .-++++++++|
T Consensus       267 LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLav-qKQqRlL~~~p~IVVATPGRlweli~e~n~~l~~~k~vkcLV  345 (731)
T KOG0347|consen  267 LVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAV-QKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGNFKKVKCLV  345 (731)
T ss_pred             EEecChHHHHHHHHHHHHHhccccCeEEEEeechhHH-HHHHHHHhcCCCEEEecchHHHHHHHhhhhhhhhhhhceEEE
Confidence            9999999999999999999999999999988887543 444566777999999999999999987554 34588999999


Q ss_pred             EcccccccccCccchHHHHHHHHHhcC----CCCceEEEEeeeCch
Q psy12977        164 VDESDKLFEAGVRGFRDQLAVIYAACS----GPNLKRGMFSATHTE  205 (226)
Q Consensus       164 iDE~h~l~~~~~~~~~~~i~~i~~~~~----~~~~q~v~~SAT~~~  205 (226)
                      +||+|+|++.   ++...+..+++.+.    ++..|.+.||||+.-
T Consensus       346 lDEaDRmvek---ghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~  388 (731)
T KOG0347|consen  346 LDEADRMVEK---GHFEELSKLLKHLNEEQKNRQRQTLVFSATLTL  388 (731)
T ss_pred             EccHHHHhhh---ccHHHHHHHHHHhhhhhcccccceEEEEEEeeh
Confidence            9999999998   56677777766663    467899999999763

>KOG0329|consensus

Probab=99.96  E-value=2.2e-29  Score=196.18  Aligned_cols=213  Identities=23%  Similarity=0.297  Sum_probs=181.7

Q ss_pred             eeeechhhhhhhHHH-HHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCce
Q psy12977          6 TIALGIFTIGFVISI-IVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFR   83 (226)
Q Consensus         6 ~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~   83 (226)
                      .+-+||-..||=..+ -|+.++++-+.||+.++++|... |...-|-|++++|.+|.|||..|.++-++.+.. ......
T Consensus        34 gsyv~ihssgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiep-v~g~vs  112 (387)
T KOG0329|consen   34 GSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEP-VDGQVS  112 (387)
T ss_pred             CcEEEEeccchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCC-CCCeEE
Confidence            456778888887554 58999999999999999999544 677889999999999999999999999999873 444678


Q ss_pred             EEEEcccHHHHHHHHHHHHHHhhcCC-CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEE
Q psy12977         84 AVIVCPTRELAKQTYNETVRLSEGLG-LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL  162 (226)
Q Consensus        84 ~iil~Pt~~L~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~l  162 (226)
                      ++++|.||+||-|+.++..++.++.. .++..+.|+..-.... ..+.+.++|+|+||+++..+.++  +.+++++++.+
T Consensus       113 vlvmchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkde-e~lk~~PhivVgTPGrilALvr~--k~l~lk~vkhF  189 (387)
T KOG0329|consen  113 VLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDE-ELLKNCPHIVVGTPGRILALVRN--RSLNLKNVKHF  189 (387)
T ss_pred             EEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccH-HHHhCCCeEEEcCcHHHHHHHHh--ccCchhhccee
Confidence            99999999999999999999999876 6777777664332222 23445889999999999999998  89999999999


Q ss_pred             EEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       163 ViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      |+||||.+++.-  .-+..+.++.+.. ++..|+++||||+++++...++++++||+.|-+++
T Consensus       190 vlDEcdkmle~l--DMrRDvQEifr~t-p~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDd  249 (387)
T KOG0329|consen  190 VLDECDKMLEQL--DMRRDVQEIFRMT-PHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDD  249 (387)
T ss_pred             ehhhHHHHHHHH--HHHHHHHHHhhcC-cccceeeeeeeecchhhHHHHHhhhcCchhhhccc
Confidence            999999998874  6788899999887 67899999999999999999999999999987764

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

Probab=99.96  E-value=8.6e-29  Score=188.43  Aligned_cols=166  Identities=27%  Similarity=0.424  Sum_probs=132.4

Q ss_pred             CCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEE
Q psy12977         37 EPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVI  115 (226)
Q Consensus        37 ~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  115 (226)
                      ||.|...+ .+.+++++++.+|||+|||+++..+++..+.+.  ...++++++|+++|++|+.+.+..++...+.++...
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~--~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~   78 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG--KDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLL   78 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT--SSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEE
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC--CCceEEEEeecccccccccccccccccccccccccc
Confidence            46776665 455889999999999999999999999988754  334999999999999999999999998877788777


Q ss_pred             ecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCC-CCc
Q psy12977        116 GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSG-PNL  194 (226)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~-~~~  194 (226)
                      .++..........+.++++|+|+||+++.+.+..  +..++.+++++|+||+|.+.+.   .+...+..+.+.+.. .+.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~--~~~~~~~~~~iViDE~h~l~~~---~~~~~~~~i~~~~~~~~~~  153 (169)
T PF00270_consen   79 HGGQSISEDQREVLSNQADILVTTPEQLLDLISN--GKINISRLSLIVIDEAHHLSDE---TFRAMLKSILRRLKRFKNI  153 (169)
T ss_dssp             STTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHT--TSSTGTTESEEEEETHHHHHHT---THHHHHHHHHHHSHTTTTS
T ss_pred             cccccccccccccccccccccccCcchhhccccc--cccccccceeeccCcccccccc---cHHHHHHHHHHHhcCCCCC
Confidence            6655432122222346799999999999999987  3347778999999999999887   467777777777632 368


Q ss_pred             eEEEEeeeCchhHHH
Q psy12977        195 KRGMFSATHTEDVAK  209 (226)
Q Consensus       195 q~v~~SAT~~~~~~~  209 (226)
                      |++++|||+++++++
T Consensus       154 ~~i~~SAT~~~~~~~  168 (169)
T PF00270_consen  154 QIILLSATLPSNVEK  168 (169)
T ss_dssp             EEEEEESSSTHHHHH
T ss_pred             cEEEEeeCCChhHhh
Confidence            999999999977765

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 ....

>KOG0327|consensus

Probab=99.96  E-value=6.1e-29  Score=203.09  Aligned_cols=200  Identities=24%  Similarity=0.320  Sum_probs=178.6

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      .+-.+.|+++...||++|+-+|+.+. +...|+|+++++++|+|||.+|..++++.+. -+....++++++|+++|+.|+
T Consensus        32 ~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD-~~~ke~qalilaPtreLa~qi  110 (397)
T KOG0327|consen   32 NLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQID-MSVKETQALILAPTRELAQQI  110 (397)
T ss_pred             CCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcC-cchHHHHHHHhcchHHHHHHH
Confidence            35568899999999999999997774 8899999999999999999999999999985 345567899999999999999


Q ss_pred             HHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccc
Q psy12977         98 YNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG  177 (226)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~  177 (226)
                      .+....++...+.++..+.++..-..+........++|+|+||+++...++.  ..+..+.++++|+||+|.+++.   +
T Consensus       111 ~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~--~~l~~~~iKmfvlDEaDEmLs~---g  185 (397)
T KOG0327|consen  111 QKVVRALGDHMDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNR--GSLSTDGIKMFVLDEADEMLSR---G  185 (397)
T ss_pred             HHHHHhhhcccceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhcc--ccccccceeEEeecchHhhhcc---c
Confidence            9999999999999988777766555454455667799999999999999987  6788888999999999999998   7


Q ss_pred             hHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        178 FRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       178 ~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      +.+.+..+++.+ +++.|++++|||.|+++....++++.+|+.|.++.
T Consensus       186 fkdqI~~if~~l-p~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk  232 (397)
T KOG0327|consen  186 FKDQIYDIFQEL-PSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKK  232 (397)
T ss_pred             hHHHHHHHHHHc-CcchhheeecccCcHHHHHHHHHhccCceEEEecc
Confidence            999999999999 78999999999999999999999999999998864

>KOG0340|consensus

Probab=99.96  E-value=2.7e-28  Score=197.47  Aligned_cols=189  Identities=26%  Similarity=0.325  Sum_probs=165.3

Q ss_pred             HHHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      +++.+-....++.++.+.+||+|+.. |.++.|+|.+-+|.||||||.+|.+|+++++.. .+.+..++|++|||+|+-|
T Consensus        12 LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLse-dP~giFalvlTPTrELA~Q   90 (442)
T KOG0340|consen   12 LGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSE-DPYGIFALVLTPTRELALQ   90 (442)
T ss_pred             cCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhcc-CCCcceEEEecchHHHHHH
Confidence            56677888899999999999999666 689999999999999999999999999999974 4557899999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCC--CCCCCccEEEEcccccccccC
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPA--LNLANVEWLIVDESDKLFEAG  174 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~--~~~~~~~~lViDE~h~l~~~~  174 (226)
                      +.+++..+++..+.++..++|+... ......+..++|++|+||+++..++..+.+.  ..+++++++|+||||.+++. 
T Consensus        91 iaEQF~alGk~l~lK~~vivGG~d~-i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEADrvL~~-  168 (442)
T KOG0340|consen   91 IAEQFIALGKLLNLKVSVIVGGTDM-IMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEADRVLAG-  168 (442)
T ss_pred             HHHHHHHhcccccceEEEEEccHHH-hhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecchhhhhcc-
Confidence            9999999999999999999988644 4445678899999999999999998765333  23888999999999999998 


Q ss_pred             ccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHH
Q psy12977        175 VRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCR  212 (226)
Q Consensus       175 ~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~  212 (226)
                        .|.+.+.-+.+-+ +...|.++||||+.+.+.++..
T Consensus       169 --~f~d~L~~i~e~l-P~~RQtLlfSATitd~i~ql~~  203 (442)
T KOG0340|consen  169 --CFPDILEGIEECL-PKPRQTLLFSATITDTIKQLFG  203 (442)
T ss_pred             --chhhHHhhhhccC-CCccceEEEEeehhhHHHHhhc
Confidence              7999999999988 4558999999999888776653

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

Probab=99.96  E-value=8.2e-28  Score=219.65  Aligned_cols=195  Identities=19%  Similarity=0.178  Sum_probs=147.5

Q ss_pred             HHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHH
Q psy12977         20 IIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTY   98 (226)
Q Consensus        20 ~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~   98 (226)
                      +.+.+.+.+++.+|++++++|..+. .+.+|+|+++.+|||||||++|++|+++.+.+.  .+.+++|++||++|+.|+.
T Consensus        21 l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~--~~~~aL~l~PtraLa~q~~   98 (742)
T TIGR03817        21 AHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD--PRATALYLAPTKALAADQL   98 (742)
T ss_pred             CCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC--CCcEEEEEcChHHHHHHHH
Confidence            4578899999999999999997775 778999999999999999999999999998643  3569999999999999999


Q ss_pred             HHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCC--CCCCCCCccEEEEcccccccccCcc
Q psy12977         99 NETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDP--PALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~--~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +.++.+. ..+.++....|+.....+  ..+..+++|+|+||+++...+...+  ....+++++++|+||+|.+.+..+.
T Consensus        99 ~~l~~l~-~~~i~v~~~~Gdt~~~~r--~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g~fg~  175 (742)
T TIGR03817        99 RAVRELT-LRGVRPATYDGDTPTEER--RWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRGVFGS  175 (742)
T ss_pred             HHHHHhc-cCCeEEEEEeCCCCHHHH--HHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccCccHH
Confidence            9999987 346777777777654433  2344668999999999875432211  1123789999999999998654111


Q ss_pred             chHHHHH---HHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEE
Q psy12977        177 GFRDQLA---VIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQI  221 (226)
Q Consensus       177 ~~~~~i~---~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i  221 (226)
                      .....+.   ++.... +.++|++++|||+++..+ .+++++..|+.+
T Consensus       176 ~~~~il~rL~ri~~~~-g~~~q~i~~SATi~n~~~-~~~~l~g~~~~~  221 (742)
T TIGR03817       176 HVALVLRRLRRLCARY-GASPVFVLASATTADPAA-AASRLIGAPVVA  221 (742)
T ss_pred             HHHHHHHHHHHHHHhc-CCCCEEEEEecCCCCHHH-HHHHHcCCCeEE
Confidence            2222222   222223 457899999999987754 677788877654

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.

>KOG4284|consensus

Probab=99.95  E-value=3e-28  Score=209.95  Aligned_cols=201  Identities=20%  Similarity=0.293  Sum_probs=175.3

Q ss_pred             HHHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      +.+--+.|.+++..+|..++++|..+ |.+..+-|+|+++.+|+|||+.|...+++.+.. ....++.+|++|||+++-|
T Consensus        30 l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~-~~~~~q~~Iv~PTREiaVQ  108 (980)
T KOG4284|consen   30 LALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDS-RSSHIQKVIVTPTREIAVQ  108 (980)
T ss_pred             HHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCc-ccCcceeEEEecchhhhhH
Confidence            66778899999999999999999655 688899999999999999999998888888863 4556899999999999999


Q ss_pred             HHHHHHHHhhcC-CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCc
Q psy12977         97 TYNETVRLSEGL-GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGV  175 (226)
Q Consensus        97 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~  175 (226)
                      +.+.+..++..+ +.++..+.|++.....  ....+.++|+|+||+++..++..  +.++.+.++++|+||||.+++.. 
T Consensus       109 I~~tv~~v~~sf~g~~csvfIGGT~~~~d--~~rlk~~rIvIGtPGRi~qL~el--~~~n~s~vrlfVLDEADkL~~t~-  183 (980)
T KOG4284|consen  109 IKETVRKVAPSFTGARCSVFIGGTAHKLD--LIRLKQTRIVIGTPGRIAQLVEL--GAMNMSHVRLFVLDEADKLMDTE-  183 (980)
T ss_pred             HHHHHHHhcccccCcceEEEecCchhhhh--hhhhhhceEEecCchHHHHHHHh--cCCCccceeEEEeccHHhhhchh-
Confidence            999999998744 5777766666543332  23456788999999999999998  89999999999999999999964 


Q ss_pred             cchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCCC
Q psy12977        176 RGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       176 ~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                       .|.+++..|+..+ +...|++.+|||.|+.+.+.+.+||+||..+..+.|
T Consensus       184 -sfq~~In~ii~sl-P~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~  232 (980)
T KOG4284|consen  184 -SFQDDINIIINSL-PQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNAD  232 (980)
T ss_pred             -hHHHHHHHHHHhc-chhheeeEEeccCchhHHHHHHHHhcccceeecccC
Confidence             7999999999999 678999999999999999999999999999987754

>KOG0332|consensus

Probab=99.95  E-value=2.8e-28  Score=198.53  Aligned_cols=206  Identities=22%  Similarity=0.260  Sum_probs=174.9

Q ss_pred             hhhhhh--HHHHHHHHHHHhhccccCCCCccccc-ccCCC--CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEE
Q psy12977         12 FTIGFV--ISIIVTTLAVVSNSIFKHFEPHFTIT-YLSPL--GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVI   86 (226)
Q Consensus        12 ~~~~~~--~~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~--~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~ii   86 (226)
                      |..+-|  +.+-|..|.++..|+|+.++.+|+.+ |.++.  .+|++.++.+|+|||.+|.+.++.++. .....|+++.
T Consensus        87 yS~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd-~~~~~PQ~iC  165 (477)
T KOG0332|consen   87 YSAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVD-PDVVVPQCIC  165 (477)
T ss_pred             cccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcC-ccccCCCcee
Confidence            444445  67889999999999999999999766 44444  488999999999999999999999997 4556789999


Q ss_pred             EcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcc
Q psy12977         87 VCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE  166 (226)
Q Consensus        87 l~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE  166 (226)
                      ++|+++||.|+.+.+.+++++.++...+...+.    +..+-..-..+|+|+||+.+.+++... ..+++..++.+|+||
T Consensus       166 LaPtrELA~Q~~eVv~eMGKf~~ita~yair~s----k~~rG~~i~eqIviGTPGtv~Dlm~kl-k~id~~kikvfVlDE  240 (477)
T KOG0332|consen  166 LAPTRELAPQTGEVVEEMGKFTELTASYAIRGS----KAKRGNKLTEQIVIGTPGTVLDLMLKL-KCIDLEKIKVFVLDE  240 (477)
T ss_pred             eCchHHHHHHHHHHHHHhcCceeeeEEEEecCc----ccccCCcchhheeeCCCccHHHHHHHH-HhhChhhceEEEecc
Confidence            999999999999999999999877776655443    222222344689999999999998764 678899999999999


Q ss_pred             cccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCCC
Q psy12977        167 SDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       167 ~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      ||.+++..  +|.++-.++++.+ ++++|+++||||+.+.++.|+.+..++|..+.++++
T Consensus       241 AD~Mi~tq--G~~D~S~rI~~~l-P~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~e  297 (477)
T KOG0332|consen  241 ADVMIDTQ--GFQDQSIRIMRSL-PRNQQLLLFSATFVEKVAAFALKIVPNANVIILKRE  297 (477)
T ss_pred             hhhhhhcc--cccccchhhhhhc-CCcceEEeeechhHHHHHHHHHHhcCCCceeeeehh
Confidence            99999874  7899999999999 579999999999999999999999999999988764

>KOG0341|consensus

Probab=99.95  E-value=8.1e-29  Score=202.83  Aligned_cols=198  Identities=25%  Similarity=0.374  Sum_probs=166.1

Q ss_pred             HHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcC-------CCCCCceEEEEcccHH
Q psy12977         21 IVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRG-------PKNLGFRAVIVCPTRE   92 (226)
Q Consensus        21 ~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~-------~~~~~~~~iil~Pt~~   92 (226)
                      ...+|+.+++.+...+||+|.|- |..++|+|.+-.|-||||||+.|.+|++.....       ..+.+|..+|+||+|+
T Consensus       178 P~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRE  257 (610)
T KOG0341|consen  178 PKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRE  257 (610)
T ss_pred             CHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcCcHH
Confidence            34678999999999999999555 688999999999999999999999997765421       2345789999999999


Q ss_pred             HHHHHHHHHHHHhhcCC------CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcc
Q psy12977         93 LAKQTYNETVRLSEGLG------LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE  166 (226)
Q Consensus        93 L~~q~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE  166 (226)
                      ||.|.++.+.++...+.      .+...+.|+-.- .........+.+|+|+||+++.+++..  ..++++-.+++.+||
T Consensus       258 LArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v-~eql~~v~~GvHivVATPGRL~DmL~K--K~~sLd~CRyL~lDE  334 (610)
T KOG0341|consen  258 LARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPV-REQLDVVRRGVHIVVATPGRLMDMLAK--KIMSLDACRYLTLDE  334 (610)
T ss_pred             HHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccH-HHHHHHHhcCeeEEEcCcchHHHHHHH--hhccHHHHHHhhhhh
Confidence            99999999888865542      333333333222 222234567899999999999999988  788899999999999


Q ss_pred             cccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        167 SDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       167 ~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      ||++.|.   +|.++++.++..+ ....|.++||||+|..+..|++.-+-.|+.++|.|
T Consensus       335 ADRmiDm---GFEddir~iF~~F-K~QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVGR  389 (610)
T KOG0341|consen  335 ADRMIDM---GFEDDIRTIFSFF-KGQRQTLLFSATMPKKIQNFAKSALVKPVTVNVGR  389 (610)
T ss_pred             HHHHhhc---cchhhHHHHHHHH-hhhhheeeeeccccHHHHHHHHhhcccceEEeccc
Confidence            9999999   7999999999888 67899999999999999999999999999999976

>PRK02362 ski2-like helicase; Provisional

Probab=99.95  E-value=6.1e-27  Score=215.03  Aligned_cols=181  Identities=23%  Similarity=0.305  Sum_probs=142.8

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc--cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY--LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~--~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      ++.+..++.+.+.++.+++|.|+++.  .+.+|+|+++++|||+|||++|.+++++.+..    +.+++|++|+++||.|
T Consensus         7 ~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~----~~kal~i~P~raLa~q   82 (737)
T PRK02362          7 PLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIAR----GGKALYIVPLRALASE   82 (737)
T ss_pred             CCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhc----CCcEEEEeChHHHHHH
Confidence            35678889999999999999998875  36789999999999999999999999998852    5689999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      .++.++.+.+ .+.++....|+.....    .....++|+|+||+++..++++  +...+.+++++|+||+|.+.+.   
T Consensus        83 ~~~~~~~~~~-~g~~v~~~tGd~~~~~----~~l~~~~IiV~Tpek~~~llr~--~~~~l~~v~lvViDE~H~l~d~---  152 (737)
T PRK02362         83 KFEEFERFEE-LGVRVGISTGDYDSRD----EWLGDNDIIVATSEKVDSLLRN--GAPWLDDITCVVVDEVHLIDSA---  152 (737)
T ss_pred             HHHHHHHhhc-CCCEEEEEeCCcCccc----cccCCCCEEEECHHHHHHHHhc--ChhhhhhcCEEEEECccccCCC---
Confidence            9999997654 4788877776643222    1235689999999999998876  4456789999999999998875   


Q ss_pred             chHHHHHHHHHhc--CCCCceEEEEeeeCc--hhHHHHHHH
Q psy12977        177 GFRDQLAVIYAAC--SGPNLKRGMFSATHT--EDVAKWCRR  213 (226)
Q Consensus       177 ~~~~~i~~i~~~~--~~~~~q~v~~SAT~~--~~~~~~~~~  213 (226)
                      ++...+..++..+  .++..|++++|||++  +++.+|+..
T Consensus       153 ~rg~~le~il~rl~~~~~~~qii~lSATl~n~~~la~wl~~  193 (737)
T PRK02362        153 NRGPTLEVTLAKLRRLNPDLQVVALSATIGNADELADWLDA  193 (737)
T ss_pred             cchHHHHHHHHHHHhcCCCCcEEEEcccCCCHHHHHHHhCC
Confidence            3444444333332  146789999999986  467777653

>PRK00254 ski2-like helicase; Provisional

Probab=99.94  E-value=3e-26  Score=210.01  Aligned_cols=178  Identities=23%  Similarity=0.263  Sum_probs=145.5

Q ss_pred             HHHHHHHHHhhccccCCCCcccccc--cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         20 IIVTTLAVVSNSIFKHFEPHFTITY--LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        20 ~~~~~l~~~~~~~~~~~~~~Q~~~~--~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      +.+.+.+.+++.++++++|+|+++.  ...+|+|+++++|||+|||++|.+++++.+...   +.++||++|+++|+.|+
T Consensus         8 l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~---~~~~l~l~P~~aLa~q~   84 (720)
T PRK00254          8 VDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE---GGKAVYLVPLKALAEEK   84 (720)
T ss_pred             CCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc---CCeEEEEeChHHHHHHH
Confidence            4578889999999999999998886  468899999999999999999999999887532   45899999999999999


Q ss_pred             HHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccc
Q psy12977         98 YNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG  177 (226)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~  177 (226)
                      ++.++.+. ..+.++....|+......    ...+++|+|+||+++..++.+  ....+++++++|+||+|.+.+.   +
T Consensus        85 ~~~~~~~~-~~g~~v~~~~Gd~~~~~~----~~~~~~IiV~Tpe~~~~ll~~--~~~~l~~l~lvViDE~H~l~~~---~  154 (720)
T PRK00254         85 YREFKDWE-KLGLRVAMTTGDYDSTDE----WLGKYDIIIATAEKFDSLLRH--GSSWIKDVKLVVADEIHLIGSY---D  154 (720)
T ss_pred             HHHHHHHh-hcCCEEEEEeCCCCCchh----hhccCCEEEEcHHHHHHHHhC--CchhhhcCCEEEEcCcCccCCc---c
Confidence            99998764 457888877776543221    235689999999999988875  4456889999999999999876   4


Q ss_pred             hHHHHHHHHHhcCCCCceEEEEeeeCc--hhHHHHH
Q psy12977        178 FRDQLAVIYAACSGPNLKRGMFSATHT--EDVAKWC  211 (226)
Q Consensus       178 ~~~~i~~i~~~~~~~~~q~v~~SAT~~--~~~~~~~  211 (226)
                      ....+..++..+ ..+.|++++|||++  +++.+|+
T Consensus       155 rg~~le~il~~l-~~~~qiI~lSATl~n~~~la~wl  189 (720)
T PRK00254        155 RGATLEMILTHM-LGRAQILGLSATVGNAEELAEWL  189 (720)
T ss_pred             chHHHHHHHHhc-CcCCcEEEEEccCCCHHHHHHHh
Confidence            667777787777 56789999999986  4455554

>KOG0350|consensus

Probab=99.94  E-value=1e-26  Score=195.46  Aligned_cols=198  Identities=28%  Similarity=0.401  Sum_probs=152.0

Q ss_pred             HHHHHHHhhccccCCCCccccc-ccC---------CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         22 VTTLAVVSNSIFKHFEPHFTIT-YLS---------PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        22 ~~~l~~~~~~~~~~~~~~Q~~~-~~~---------~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      -.+.+++..++..+.-|+|.+. +++         ...+|+.+.||||||||++|.+|+.+.+....-+..|++|++|++
T Consensus       146 a~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr  225 (620)
T KOG0350|consen  146 ATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTR  225 (620)
T ss_pred             HHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCccceEEEEEeeHH
Confidence            3566888999999999999443 121         336899999999999999999999999977666678999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc----CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccc
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS----AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES  167 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~  167 (226)
                      +|+.|+++.+..++...+..++...|-..-........    ....||+|+||++|.++++.. ..++++.++++|||||
T Consensus       226 ~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~-k~f~Lk~LrfLVIDEA  304 (620)
T KOG0350|consen  226 ELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNT-KSFDLKHLRFLVIDEA  304 (620)
T ss_pred             HHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccCC-CCcchhhceEEEechH
Confidence            99999999999999999988877766543322222212    234599999999999999863 7899999999999999


Q ss_pred             ccccccCccchHHHHHHHHHhc-------------C-----------------CCCceEEEEeeeCchhHHHHHHHhcCC
Q psy12977        168 DKLFEAGVRGFRDQLAVIYAAC-------------S-----------------GPNLKRGMFSATHTEDVAKWCRRKLKR  217 (226)
Q Consensus       168 h~l~~~~~~~~~~~i~~i~~~~-------------~-----------------~~~~q~v~~SAT~~~~~~~~~~~~~~~  217 (226)
                      |++++..+.++...+....+-.             .                 .+..+.+++|||+..+...+..--++.
T Consensus       305 DRll~qsfQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~~satLsqdP~Kl~~l~l~~  384 (620)
T KOG0350|consen  305 DRLLDQSFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLVFSATLSQDPSKLKDLTLHI  384 (620)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHhhhcchhhhcChHHHhhhhcCC
Confidence            9999885555555544433221             0                 123457788999887777777777777


Q ss_pred             CeE
Q psy12977        218 RVQ  220 (226)
Q Consensus       218 p~~  220 (226)
                      |..
T Consensus       385 Prl  387 (620)
T KOG0350|consen  385 PRL  387 (620)
T ss_pred             Cce
Confidence            743

>KOG0344|consensus

Probab=99.93  E-value=2.4e-26  Score=196.54  Aligned_cols=204  Identities=40%  Similarity=0.597  Sum_probs=172.4

Q ss_pred             HHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCC----CCCceEEEEcccHHHHH
Q psy12977         21 IVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK----NLGFRAVIVCPTRELAK   95 (226)
Q Consensus        21 ~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~----~~~~~~iil~Pt~~L~~   95 (226)
                      -+-.++.+.+.+|..++|.|.++ |.++.+++++.++|||+|||++|.+|+++.+....    ..+.+++|+.|+++|+.
T Consensus       144 ~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~  223 (593)
T KOG0344|consen  144 NKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRELAA  223 (593)
T ss_pred             cHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhcccCccceEEEEecchHHHHH
Confidence            44568899999999999999777 58888999999999999999999999999986655    56789999999999999


Q ss_pred             HHHHHHHHHh--hcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977         96 QTYNETVRLS--EGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus        96 q~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      |++.++.++.  +..+.+............+........++|+|+||.++...+....-.++++.+.++|+||+|.+.+.
T Consensus       224 Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~lfe~  303 (593)
T KOG0344|consen  224 QIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADLLFEP  303 (593)
T ss_pred             HHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccchhheeeeEeechHHhhhCh
Confidence            9999999998  54445544444333333333334456689999999999999988656689999999999999999987


Q ss_pred             CccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCCC
Q psy12977        174 GVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       174 ~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                        ..|..++..++....++...+-+||||.+.++++|++..+.+++.+-+..|
T Consensus       304 --~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~  354 (593)
T KOG0344|consen  304 --EFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRVIVGLR  354 (593)
T ss_pred             --hhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeEEEecc
Confidence              369999999999998899999999999999999999999999998877654

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.93  E-value=7.8e-26  Score=210.21  Aligned_cols=193  Identities=26%  Similarity=0.293  Sum_probs=137.5

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCC-----CCCceEEEEcccHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK-----NLGFRAVIVCPTRE   92 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~-----~~~~~~iil~Pt~~   92 (226)
                      ..++..++.+-..+|++++|+|+.++ .+.+|+|++++||||||||++|.+|+++.+....     ..+.+++|++|+++
T Consensus        16 ~~l~~~v~~~~~~~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtra   95 (876)
T PRK13767         16 DLLRPYVREWFKEKFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRA   95 (876)
T ss_pred             hhcCHHHHHHHHHccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHH
Confidence            34445555555568999999998885 7788999999999999999999999998774311     34678999999999


Q ss_pred             HHHHHHHHHHH-------Hh----hcC-CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCcc
Q psy12977         93 LAKQTYNETVR-------LS----EGL-GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVE  160 (226)
Q Consensus        93 L~~q~~~~~~~-------~~----~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~  160 (226)
                      |+.|+++.+.+       +.    ... +.++....|+.....+. ......++|+|+||+++..++........+++++
T Consensus        96 La~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~-~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~  174 (876)
T PRK13767         96 LNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQ-KMLKKPPHILITTPESLAILLNSPKFREKLRTVK  174 (876)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHH-HHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCC
Confidence            99999886553       22    122 45667777765544332 2244678999999999988775421222478999


Q ss_pred             EEEEcccccccccCcc-chHHHHHHHHHhcCCCCceEEEEeeeCch--hHHHHHHH
Q psy12977        161 WLIVDESDKLFEAGVR-GFRDQLAVIYAACSGPNLKRGMFSATHTE--DVAKWCRR  213 (226)
Q Consensus       161 ~lViDE~h~l~~~~~~-~~~~~i~~i~~~~~~~~~q~v~~SAT~~~--~~~~~~~~  213 (226)
                      ++|+||+|.+.+.... .+...+.++.... .+..|++++|||+++  ++.+|+..
T Consensus       175 ~VVIDE~H~l~~~~RG~~l~~~L~rL~~l~-~~~~q~IglSATl~~~~~va~~L~~  229 (876)
T PRK13767        175 WVIVDEIHSLAENKRGVHLSLSLERLEELA-GGEFVRIGLSATIEPLEEVAKFLVG  229 (876)
T ss_pred             EEEEechhhhccCccHHHHHHHHHHHHHhc-CCCCeEEEEecccCCHHHHHHHhcC
Confidence            9999999999865311 1223344444333 467899999999874  56666544

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

Probab=99.93  E-value=3.4e-25  Score=199.92  Aligned_cols=191  Identities=26%  Similarity=0.279  Sum_probs=151.8

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC----CCCCceEEEEcccHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP----KNLGFRAVIVCPTREL   93 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~----~~~~~~~iil~Pt~~L   93 (226)
                      .+-|-+...+++. |.++||.|.+++ .+.+|+|+++.||||||||.++.+|+++.+...    ...+..++|++|.++|
T Consensus         7 ~l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkAL   85 (814)
T COG1201           7 ILDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKAL   85 (814)
T ss_pred             hcCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHH
Confidence            3445556666666 999999998885 788999999999999999999999999888544    2345799999999999


Q ss_pred             HHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977         94 AKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus        94 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      .+++...+..+.+..|..+....|++.+.++. ....+.+||+|+||+++.-++......-.+.+++++|+||.|.+.+.
T Consensus        86 n~Di~~rL~~~~~~~G~~v~vRhGDT~~~er~-r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~s  164 (814)
T COG1201          86 NNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQ-KMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAES  164 (814)
T ss_pred             HHHHHHHHHHHHHHcCCccceecCCCChHHhh-hccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhcc
Confidence            99999999999999999998888887766554 44678899999999999988865333445899999999999998765


Q ss_pred             C-ccchHHHHHHHHHhcCCCCceEEEEeeeCc--hhHHHHHHH
Q psy12977        174 G-VRGFRDQLAVIYAACSGPNLKRGMFSATHT--EDVAKWCRR  213 (226)
Q Consensus       174 ~-~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~--~~~~~~~~~  213 (226)
                      . +......+.++.... . ..|.+++|||..  +++.+|+-.
T Consensus       165 KRG~~Lsl~LeRL~~l~-~-~~qRIGLSATV~~~~~varfL~g  205 (814)
T COG1201         165 KRGVQLALSLERLRELA-G-DFQRIGLSATVGPPEEVAKFLVG  205 (814)
T ss_pred             ccchhhhhhHHHHHhhC-c-ccEEEeehhccCCHHHHHHHhcC
Confidence            3 223444555555444 3 899999999954  556666533

>PRK01172 ski2-like helicase; Provisional

Probab=99.92  E-value=7.8e-25  Score=199.65  Aligned_cols=173  Identities=20%  Similarity=0.275  Sum_probs=134.3

Q ss_pred             HHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHH
Q psy12977         20 IIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTY   98 (226)
Q Consensus        20 ~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~   98 (226)
                      +.+..++.+.+.+|+ +++.|.++. .+.+++|+++++|||+|||+++.+++++.+..    +.++||++|+++||.|++
T Consensus         8 l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~----~~k~v~i~P~raLa~q~~   82 (674)
T PRK01172          8 YDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA----GLKSIYIVPLRSLAMEKY   82 (674)
T ss_pred             CCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh----CCcEEEEechHHHHHHHH
Confidence            567888999999987 999998875 66888999999999999999999999888763    458999999999999999


Q ss_pred             HHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccch
Q psy12977         99 NETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGF  178 (226)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~  178 (226)
                      +.++++. ..+.++....|+......    ....++|+|+||+++..++.+  ....+.+++++|+||+|.+.+..+...
T Consensus        83 ~~~~~l~-~~g~~v~~~~G~~~~~~~----~~~~~dIiv~Tpek~~~l~~~--~~~~l~~v~lvViDEaH~l~d~~rg~~  155 (674)
T PRK01172         83 EELSRLR-SLGMRVKISIGDYDDPPD----FIKRYDVVILTSEKADSLIHH--DPYIINDVGLIVADEIHIIGDEDRGPT  155 (674)
T ss_pred             HHHHHHh-hcCCeEEEEeCCCCCChh----hhccCCEEEECHHHHHHHHhC--ChhHHhhcCEEEEecchhccCCCccHH
Confidence            9998864 457777766665432221    224679999999999998876  345578999999999999877532223


Q ss_pred             HHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        179 RDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       179 ~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      ...+...++.. ++..|++++|||++.
T Consensus       156 le~ll~~~~~~-~~~~riI~lSATl~n  181 (674)
T PRK01172        156 LETVLSSARYV-NPDARILALSATVSN  181 (674)
T ss_pred             HHHHHHHHHhc-CcCCcEEEEeCccCC
Confidence            33333333344 567899999999864

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.91  E-value=4.9e-24  Score=193.85  Aligned_cols=183  Identities=23%  Similarity=0.288  Sum_probs=139.9

Q ss_pred             HHHHHHHHHhhccccCCCC-cccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         20 IIVTTLAVVSNSIFKHFEP-HFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        20 ~~~~~l~~~~~~~~~~~~~-~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      +.......++..++.++.+ +|+..+ ...+++|+++++|||+|||+.+.+.+++.+.+.   +.++||++|+++||.+.
T Consensus        16 ~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~---~~k~vYivPlkALa~Ek   92 (766)
T COG1204          16 LDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG---GGKVVYIVPLKALAEEK   92 (766)
T ss_pred             ccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc---CCcEEEEeChHHHHHHH
Confidence            3445566677777754444 454444 555689999999999999999999999998753   56899999999999999


Q ss_pred             HHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccc
Q psy12977         98 YNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG  177 (226)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~  177 (226)
                      ++.++ ..+.+|.++....|+.....    ....+++|+|+||+++....++.  ......++++|+||+|.+.+..+..
T Consensus        93 ~~~~~-~~~~~GirV~~~TgD~~~~~----~~l~~~~ViVtT~EK~Dsl~R~~--~~~~~~V~lvViDEiH~l~d~~RG~  165 (766)
T COG1204          93 YEEFS-RLEELGIRVGISTGDYDLDD----ERLARYDVIVTTPEKLDSLTRKR--PSWIEEVDLVVIDEIHLLGDRTRGP  165 (766)
T ss_pred             HHHhh-hHHhcCCEEEEecCCcccch----hhhccCCEEEEchHHhhHhhhcC--cchhhcccEEEEeeeeecCCcccCc
Confidence            99999 55667999999988854332    23467899999999999999874  4488899999999999888773223


Q ss_pred             hHHHHHHHHHhcCCCCceEEEEeeeCc--hhHHHHHHH
Q psy12977        178 FRDQLAVIYAACSGPNLKRGMFSATHT--EDVAKWCRR  213 (226)
Q Consensus       178 ~~~~i~~i~~~~~~~~~q~v~~SAT~~--~~~~~~~~~  213 (226)
                      ....+..-+... ++.+|++++|||+|  .++-+|++.
T Consensus       166 ~lE~iv~r~~~~-~~~~rivgLSATlpN~~evA~wL~a  202 (766)
T COG1204         166 VLESIVARMRRL-NELIRIVGLSATLPNAEEVADWLNA  202 (766)
T ss_pred             eehhHHHHHHhh-CcceEEEEEeeecCCHHHHHHHhCC
Confidence            444444444344 45689999999998  466666654

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

Probab=99.91  E-value=1.2e-23  Score=190.94  Aligned_cols=186  Identities=18%  Similarity=0.114  Sum_probs=132.5

Q ss_pred             ccccCCCCcccccc-cCCCCC-eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcC
Q psy12977         31 SIFKHFEPHFTITY-LSPLGR-QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL  108 (226)
Q Consensus        31 ~~~~~~~~~Q~~~~-~~~~~~-~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~  108 (226)
                      .+|+ ++|+|.+.. .+..|+ ++++++|||||||.++..+++.. ........+.|+++|+|+|+.|+++.++.+.+.+
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l   89 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERL   89 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc-cccccccceEEEeCchHHHHHHHHHHHHHHHHHh
Confidence            4666 999997764 667887 68889999999999765444422 2122222355557799999999999999998765


Q ss_pred             -----------------------CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHh-cC------CCCC---C
Q psy12977        109 -----------------------GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQ-MD------PPAL---N  155 (226)
Q Consensus       109 -----------------------~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~-~~------~~~~---~  155 (226)
                                             ++++..+.|+...... ...+..+++|+|+|++.+.+-.- +.      ...+   .
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q-~~~l~~~p~IIVgT~D~i~sr~L~~gYg~~~~~~pi~ag~  168 (844)
T TIGR02621        90 PDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDE-WMLDPHRPAVIVGTVDMIGSRLLFSGYGCGFKSRPLHAGF  168 (844)
T ss_pred             cccchhhhhhhhhhccccccccCCeEEEEEECCCChHHH-HHhcCCCCcEEEECHHHHcCCccccccccccccccchhhh
Confidence                                   3566777777544333 34566789999999655433111 00      0001   2


Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhc--CCC--CceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC--SGP--NLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~--~~~--~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      +.+++++|+||||  ++.   +|...+..|++.+  ++.  ..|+++||||+|.++.+....++.++..+.+.
T Consensus       169 L~~v~~LVLDEAD--Ld~---gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~  236 (844)
T TIGR02621       169 LGQDALIVHDEAH--LEP---AFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVL  236 (844)
T ss_pred             hccceEEEEehhh--hcc---ccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeecc
Confidence            6889999999999  556   6999999999864  221  26999999999999988888888888776664

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.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.91  E-value=3.5e-24  Score=187.82  Aligned_cols=172  Identities=22%  Similarity=0.272  Sum_probs=127.0

Q ss_pred             hhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         29 SNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        29 ~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      +-++|..|+|.|..+. .+++|+|+++.+|||+|||++|++|++..       +..+||++|+++|+.|+.+.++.+   
T Consensus         5 ~~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~-------~~~~lVi~P~~~L~~dq~~~l~~~---   74 (470)
T TIGR00614         5 TVFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS-------DGITLVISPLISLMEDQVLQLKAS---   74 (470)
T ss_pred             hhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc-------CCcEEEEecHHHHHHHHHHHHHHc---
Confidence            4578999999997775 77889999999999999999999998752       347899999999999998888754   


Q ss_pred             CCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCC-CCCCccEEEEcccccccccCccchHHHH-
Q psy12977        108 LGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPAL-NLANVEWLIVDESDKLFEAGVRGFRDQL-  182 (226)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~-~~~~~~~lViDE~h~l~~~~~~~~~~~i-  182 (226)
                       +.....++++.......   ........+|+++||+++....... ..+ ...+++++|+||||+++++++ .|.... 
T Consensus        75 -gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~-~~l~~~~~i~~iViDEaH~i~~~g~-~fr~~~~  151 (470)
T TIGR00614        75 -GIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLL-QTLEERKGITLIAVDEAHCISQWGH-DFRPDYK  151 (470)
T ss_pred             -CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHH-HHHHhcCCcCEEEEeCCcccCcccc-ccHHHHH
Confidence             66666666654433111   1123456899999999976422110 111 467899999999999998753 344443 


Q ss_pred             --HHHHHhcCCCCceEEEEeeeCchhHHHHHHHhc
Q psy12977        183 --AVIYAACSGPNLKRGMFSATHTEDVAKWCRRKL  215 (226)
Q Consensus       183 --~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~  215 (226)
                        ..+...+  +..|++++|||+++.+.+.+.+.+
T Consensus       152 ~l~~l~~~~--~~~~~l~lTAT~~~~~~~di~~~l  184 (470)
T TIGR00614       152 ALGSLKQKF--PNVPIMALTATASPSVREDILRQL  184 (470)
T ss_pred             HHHHHHHHc--CCCceEEEecCCCHHHHHHHHHHc
Confidence              3344444  678999999999998876666654

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

>PRK09401 reverse gyrase; Reviewed

Probab=99.90  E-value=7e-23  Score=193.72  Aligned_cols=164  Identities=22%  Similarity=0.223  Sum_probs=121.6

Q ss_pred             CCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEE
Q psy12977         35 HFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAH  113 (226)
Q Consensus        35 ~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~  113 (226)
                      +++++|..+ +.++.|+|++++||||+|||. +.+++...+..   .+.+++|++||++|+.|+.+.++.+....+..+.
T Consensus        80 ~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~---~g~~alIL~PTreLa~Qi~~~l~~l~~~~~~~~~  155 (1176)
T PRK09401         80 KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK---KGKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGVK  155 (1176)
T ss_pred             CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh---cCCeEEEEeccHHHHHHHHHHHHHHhhhcCceEE
Confidence            789999666 478899999999999999996 44454444432   3679999999999999999999999998887776


Q ss_pred             EEecchhh----hh-hhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCc--------cchH-
Q psy12977        114 VIGKIQQA----AE-KFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGV--------RGFR-  179 (226)
Q Consensus       114 ~~~~~~~~----~~-~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~--------~~~~-  179 (226)
                      ...++...    .. .......+.++|+|+||+++.+.+.    .+...+++++|+||||++++++.        .+|. 
T Consensus       156 ~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~----~l~~~~~~~lVvDEaD~~L~~~k~id~~l~~lGF~~  231 (1176)
T PRK09401        156 ILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD----ELPKKKFDFVFVDDVDAVLKSSKNIDKLLYLLGFSE  231 (1176)
T ss_pred             EEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH----hccccccCEEEEEChHHhhhcccchhhHHHhCCCCH
Confidence            66554321    11 1111123568999999999998765    34456799999999999997421        1453 


Q ss_pred             HHHHHHHHhcCC-----------------------CCceEEEEeeeCchh
Q psy12977        180 DQLAVIYAACSG-----------------------PNLKRGMFSATHTED  206 (226)
Q Consensus       180 ~~i~~i~~~~~~-----------------------~~~q~v~~SAT~~~~  206 (226)
                      +.+..+++.++.                       ...|++++|||.++.
T Consensus       232 ~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~  281 (1176)
T PRK09401        232 EDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPR  281 (1176)
T ss_pred             HHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCcc
Confidence            566666666532                       168999999999864

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

Probab=99.89  E-value=3.7e-22  Score=183.84  Aligned_cols=193  Identities=23%  Similarity=0.264  Sum_probs=146.0

Q ss_pred             HHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHH
Q psy12977         25 LAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVR  103 (226)
Q Consensus        25 l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~  103 (226)
                      ...+.+.+...+..+|..++ .+.+|+|++|++|||||||.+|++|+++.+..+...  ++|++-||++|++.+.+.+.+
T Consensus        60 ~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a--~AL~lYPtnALa~DQ~~rl~~  137 (851)
T COG1205          60 KSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA--RALLLYPTNALANDQAERLRE  137 (851)
T ss_pred             HHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCc--cEEEEechhhhHhhHHHHHHH
Confidence            66677888888999998887 778899999999999999999999999999765444  899999999999999999999


Q ss_pred             HhhcCC--CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCC--CCCCCCCccEEEEcccccccccCccchH
Q psy12977        104 LSEGLG--LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDP--PALNLANVEWLIVDESDKLFEAGVRGFR  179 (226)
Q Consensus       104 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~--~~~~~~~~~~lViDE~h~l~~~~~~~~~  179 (226)
                      +....+  +.....+|+....++. ....+.++|++|||.++..++.+..  ....++++++||+||+|..-+..+.+..
T Consensus       138 ~~~~~~~~v~~~~y~Gdt~~~~r~-~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrGv~GS~vA  216 (851)
T COG1205         138 LISDLPGKVTFGRYTGDTPPEERR-AIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVA  216 (851)
T ss_pred             HHHhCCCcceeeeecCCCChHHHH-HHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccccchhHHH
Confidence            998888  5566666665554432 3456889999999999998554321  2334777999999999977655333444


Q ss_pred             HHHHHHHHhcC--CCCceEEEEeeeCchhHHHHHHHhcCCCeEE
Q psy12977        180 DQLAVIYAACS--GPNLKRGMFSATHTEDVAKWCRRKLKRRVQI  221 (226)
Q Consensus       180 ~~i~~i~~~~~--~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i  221 (226)
                      ..++++++.+.  +...|+++.|||... ..+++..+.+.....
T Consensus       217 ~llRRL~~~~~~~~~~~q~i~~SAT~~n-p~e~~~~l~~~~f~~  259 (851)
T COG1205         217 LLLRRLLRRLRRYGSPLQIICTSATLAN-PGEFAEELFGRDFEV  259 (851)
T ss_pred             HHHHHHHHHHhccCCCceEEEEeccccC-hHHHHHHhcCCccee
Confidence            44445444441  457899999999753 344555555544433

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

Probab=99.89  E-value=9.9e-23  Score=188.07  Aligned_cols=173  Identities=20%  Similarity=0.250  Sum_probs=124.3

Q ss_pred             hhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         29 SNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        29 ~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      .-++++.|+|.|..+. .++.|+|+++.+|||+|||++|++|++..       +..+||++|+++|+.++...+...   
T Consensus       454 ~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~-------~GiTLVISPLiSLmqDQV~~L~~~---  523 (1195)
T PLN03137        454 KVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC-------PGITLVISPLVSLIQDQIMNLLQA---  523 (1195)
T ss_pred             HHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc-------CCcEEEEeCHHHHHHHHHHHHHhC---
Confidence            3467889999997775 78899999999999999999999998753       247999999999998766655543   


Q ss_pred             CCCeEEEEecchhhhhhhC--CC---cCCCCCEEEECchHHHH---hHhcCCCCCCCCCccEEEEcccccccccCccchH
Q psy12977        108 LGLRAHVIGKIQQAAEKFG--PR---SAQKFDVLITTPNKLVY---LLQMDPPALNLANVEWLIVDESDKLFEAGVRGFR  179 (226)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~--~~---~~~~~~IiV~Tp~~l~~---~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~  179 (226)
                       ++....+.++....+...  ..   ....++|+++||+++..   ++...........+.+|||||||+++++++ .|.
T Consensus       524 -GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDEAHcVSqWGh-DFR  601 (1195)
T PLN03137        524 -NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEAHCVSQWGH-DFR  601 (1195)
T ss_pred             -CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccCcchhhhhccc-chH
Confidence             777777766543322211  11   12568999999999863   222111112234588999999999999863 355


Q ss_pred             HHHHH---HHHhcCCCCceEEEEeeeCchhHHHHHHHhc
Q psy12977        180 DQLAV---IYAACSGPNLKRGMFSATHTEDVAKWCRRKL  215 (226)
Q Consensus       180 ~~i~~---i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~  215 (226)
                      .....   +.+.+  +..|++++|||.++.+.+.+.+.+
T Consensus       602 pdYr~L~~Lr~~f--p~vPilALTATAT~~V~eDI~~~L  638 (1195)
T PLN03137        602 PDYQGLGILKQKF--PNIPVLALTATATASVKEDVVQAL  638 (1195)
T ss_pred             HHHHHHHHHHHhC--CCCCeEEEEecCCHHHHHHHHHHc
Confidence            54443   34444  578999999999998887666655

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.88  E-value=2.2e-22  Score=181.07  Aligned_cols=172  Identities=20%  Similarity=0.280  Sum_probs=128.8

Q ss_pred             hhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         29 SNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        29 ~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      +.++|.+|+|.|..+. .+++|+|+++.+|||+|||++|++|++..       +..++|++|+++|+.|+.+.++.+   
T Consensus         7 ~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~-------~g~~lVisPl~sL~~dq~~~l~~~---   76 (591)
T TIGR01389         7 RTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL-------KGLTVVISPLISLMKDQVDQLRAA---   76 (591)
T ss_pred             HhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc-------CCcEEEEcCCHHHHHHHHHHHHHc---
Confidence            3489999999998775 77889999999999999999999998742       236899999999999999988775   


Q ss_pred             CCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHH---H
Q psy12977        108 LGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRD---Q  181 (226)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~---~  181 (226)
                       ++.+..++++....+..   .....+..+|+++||+++......  ..+...+++++|+||||++.++++ .|..   .
T Consensus        77 -gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~--~~l~~~~l~~iViDEaH~i~~~g~-~frp~y~~  152 (591)
T TIGR01389        77 -GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFL--NMLQRIPIALVAVDEAHCVSQWGH-DFRPEYQR  152 (591)
T ss_pred             -CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHH--HHHhcCCCCEEEEeCCcccccccC-ccHHHHHH
Confidence             66666666554332211   122346789999999998753332  344567899999999999988753 3444   4


Q ss_pred             HHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcC
Q psy12977        182 LAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLK  216 (226)
Q Consensus       182 i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~  216 (226)
                      +..+...+  +..+++++|||.++.+.+.+...+.
T Consensus       153 l~~l~~~~--~~~~vi~lTAT~~~~~~~~i~~~l~  185 (591)
T TIGR01389       153 LGSLAERF--PQVPRIALTATADAETRQDIRELLR  185 (591)
T ss_pred             HHHHHHhC--CCCCEEEEEeCCCHHHHHHHHHHcC
Confidence            44445555  4556999999999988777776653

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.

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.88  E-value=1.8e-21  Score=150.56  Aligned_cols=186  Identities=34%  Similarity=0.483  Sum_probs=143.5

Q ss_pred             hccccCCCCcccccc-cCCCC-CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         30 NSIFKHFEPHFTITY-LSPLG-RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        30 ~~~~~~~~~~Q~~~~-~~~~~-~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      ..++.++++.|.... ....+ ++.++.+|||+|||.++..++++.+....  ..++++++|+++++.|+.+.+..+...
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~--~~~~l~~~p~~~~~~~~~~~~~~~~~~   80 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK--GKRVLVLVPTRELAEQWAEELKKLGPS   80 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC--CCcEEEEeCCHHHHHHHHHHHHHHhcc
Confidence            456778899997775 44555 89999999999999999888888876532  358999999999999999999988765


Q ss_pred             CC-CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHH
Q psy12977        108 LG-LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIY  186 (226)
Q Consensus       108 ~~-~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~  186 (226)
                      .. .......+.. .............+++++|++.+.+....  .......++++|+||+|.+.+.   .+...+..++
T Consensus        81 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~v~~~t~~~l~~~~~~--~~~~~~~~~~iIiDE~h~~~~~---~~~~~~~~~~  154 (201)
T smart00487       81 LGLKVVGLYGGDS-KREQLRKLESGKTDILVTTPGRLLDLLEN--DLLELSNVDLVILDEAHRLLDG---GFGDQLEKLL  154 (201)
T ss_pred             CCeEEEEEeCCcc-hHHHHHHHhcCCCCEEEeChHHHHHHHHc--CCcCHhHCCEEEEECHHHHhcC---CcHHHHHHHH
Confidence            54 3333333322 11221112223339999999999999887  3466788999999999999874   4777888888


Q ss_pred             HhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        187 AACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       187 ~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      ..+ ++..+++++|||+++...+....++.+.+.+..+
T Consensus       155 ~~~-~~~~~~v~~saT~~~~~~~~~~~~~~~~~~~~~~  191 (201)
T smart00487      155 KLL-PKNVQLLLLSATPPEEIENLLELFLNDPVFIDVG  191 (201)
T ss_pred             HhC-CccceEEEEecCCchhHHHHHHHhcCCCEEEeCC
Confidence            777 6789999999999999999999999888887665

>PRK14701 reverse gyrase; Provisional

Probab=99.88  E-value=6.7e-22  Score=190.97  Aligned_cols=194  Identities=21%  Similarity=0.174  Sum_probs=133.5

Q ss_pred             HHHHHHHHHhh-ccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         20 IIVTTLAVVSN-SIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        20 ~~~~~l~~~~~-~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      ...+..+.+++ .+| +|+++|..+ +.+++|+|+++.||||+|||++++.+++....    .+.+++|++||++|+.|+
T Consensus        64 ~~~~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~----~g~~aLVl~PTreLa~Qi  138 (1638)
T PRK14701         64 EVEEFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLAL----KGKKCYIILPTTLLVKQT  138 (1638)
T ss_pred             HHHHHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHh----cCCeEEEEECHHHHHHHH
Confidence            34455566665 788 699999666 48889999999999999999966665554332    356899999999999999


Q ss_pred             HHHHHHHhhcCC--CeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccc
Q psy12977         98 YNETVRLSEGLG--LRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFE  172 (226)
Q Consensus        98 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~  172 (226)
                      .+.++.+.+..+  ..+...+++....++.   .....+.++|+|+||+.+.+.+..   .. ..+++++|+||||++++
T Consensus       139 ~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~---l~-~~~i~~iVVDEAD~ml~  214 (1638)
T PRK14701        139 VEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPE---MK-HLKFDFIFVDDVDAFLK  214 (1638)
T ss_pred             HHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHH---Hh-hCCCCEEEEECceeccc
Confidence            999999988765  4455555554433321   112234689999999999877653   12 26799999999999987


Q ss_pred             cCc--------cchHHHHHH----HHH----------------------hcCCCCce-EEEEeeeCchhHHHHHHHhcCC
Q psy12977        173 AGV--------RGFRDQLAV----IYA----------------------ACSGPNLK-RGMFSATHTEDVAKWCRRKLKR  217 (226)
Q Consensus       173 ~~~--------~~~~~~i~~----i~~----------------------~~~~~~~q-~v~~SAT~~~~~~~~~~~~~~~  217 (226)
                      +++        .+|...+..    +++                      .+ +...| .+++|||.++..  ...+++++
T Consensus       215 ~~knid~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~ll~~SAT~~~r~--~~~~l~~~  291 (1638)
T PRK14701        215 ASKNIDRSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKI-GNKIGCLIVASATGKAKG--DRVKLYRE  291 (1638)
T ss_pred             cccccchhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhc-CCCccEEEEEecCCCchh--HHHHHhhc
Confidence            543        256665543    321                      12 23344 678999988531  11234466


Q ss_pred             CeEEecCC
Q psy12977        218 RVQINVGL  225 (226)
Q Consensus       218 p~~i~~~~  225 (226)
                      ++.+++..
T Consensus       292 ~l~f~v~~  299 (1638)
T PRK14701        292 LLGFEVGS  299 (1638)
T ss_pred             CeEEEecC
Confidence            66666543

>KOG0952|consensus

Probab=99.88  E-value=7.9e-23  Score=184.24  Aligned_cols=181  Identities=22%  Similarity=0.271  Sum_probs=138.8

Q ss_pred             hhccccCCCCcccccc--cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCC------CCCceEEEEcccHHHHHHHHHH
Q psy12977         29 SNSIFKHFEPHFTITY--LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK------NLGFRAVIVCPTRELAKQTYNE  100 (226)
Q Consensus        29 ~~~~~~~~~~~Q~~~~--~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~------~~~~~~iil~Pt~~L~~q~~~~  100 (226)
                      .-+.|+++|.+|+..+  ...++.|.+|+||||+|||..+++.+++.+.+..      ....++||++|+++||..+.+.
T Consensus       104 ~~f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~  183 (1230)
T KOG0952|consen  104 GFFSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDK  183 (1230)
T ss_pred             hcccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHH
Confidence            3467789999998886  5567789999999999999999999999987421      2357999999999999999999


Q ss_pred             HHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCC-CCCCCCccEEEEcccccccccCccchH
Q psy12977        101 TVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPP-ALNLANVEWLIVDESDKLFEAGVRGFR  179 (226)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~-~~~~~~~~~lViDE~h~l~~~~~~~~~  179 (226)
                      +.+....+|.++....|+.......    ...++|+|+||+++--.-+++.+ .--++.++++|+||+|.+-+..+....
T Consensus       184 ~~kkl~~~gi~v~ELTGD~ql~~te----i~~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd~RGpvlE  259 (1230)
T KOG0952|consen  184 FSKKLAPLGISVRELTGDTQLTKTE----IADTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHDDRGPVLE  259 (1230)
T ss_pred             HhhhcccccceEEEecCcchhhHHH----HHhcCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhhcCcccchHH
Confidence            9999888899999999886544332    46789999999997554443222 223677899999999988877544444


Q ss_pred             HHHHHHHHhc--CCCCceEEEEeeeCc--hhHHHHHHH
Q psy12977        180 DQLAVIYAAC--SGPNLKRGMFSATHT--EDVAKWCRR  213 (226)
Q Consensus       180 ~~i~~i~~~~--~~~~~q~v~~SAT~~--~~~~~~~~~  213 (226)
                      .-+.+.++..  .....+++++|||+|  .++..|++-
T Consensus       260 tiVaRtlr~vessqs~IRivgLSATlPN~eDvA~fL~v  297 (1230)
T KOG0952|consen  260 TIVARTLRLVESSQSMIRIVGLSATLPNYEDVARFLRV  297 (1230)
T ss_pred             HHHHHHHHHHHhhhhheEEEEeeccCCCHHHHHHHhcC
Confidence            4444555433  134678999999999  466666654

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.88  E-value=5.3e-22  Score=183.93  Aligned_cols=181  Identities=17%  Similarity=0.181  Sum_probs=131.9

Q ss_pred             HHHHHHhh-ccccCCCCcccccc-cCCC------CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHH
Q psy12977         23 TTLAVVSN-SIFKHFEPHFTITY-LSPL------GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELA   94 (226)
Q Consensus        23 ~~l~~~~~-~~~~~~~~~Q~~~~-~~~~------~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~   94 (226)
                      +..+.+.+ ..| ++||.|..+. .+.+      ..|.+++||||+|||.+++.+++..+..    +.+++|++||++||
T Consensus       439 ~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~----g~qvlvLvPT~~LA  513 (926)
T TIGR00580       439 EWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD----GKQVAVLVPTTLLA  513 (926)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh----CCeEEEEeCcHHHH
Confidence            33444444 567 5899997764 3333      3689999999999999999999988764    46899999999999


Q ss_pred             HHHHHHHHHHhhcCCCeEEEEecchhhhhh---hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccc
Q psy12977         95 KQTYNETVRLSEGLGLRAHVIGKIQQAAEK---FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLF  171 (226)
Q Consensus        95 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~  171 (226)
                      .|+++.++++++..+.++..+.+.....+.   ......+.++|+|+||..+    .   ....+++++++|+||+|++.
T Consensus       514 ~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll----~---~~v~f~~L~llVIDEahrfg  586 (926)
T TIGR00580       514 QQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLL----Q---KDVKFKDLGLLIIDEEQRFG  586 (926)
T ss_pred             HHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHh----h---CCCCcccCCEEEeecccccc
Confidence            999999999998888888777665432221   1122235689999999532    2   45668899999999999863


Q ss_pred             ccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        172 EAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       172 ~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      ..    .    ...++.+ .+++|+++||||+.+...........++..|...
T Consensus       587 v~----~----~~~L~~~-~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~  630 (926)
T TIGR00580       587 VK----Q----KEKLKEL-RTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATP  630 (926)
T ss_pred             hh----H----HHHHHhc-CCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecC
Confidence            22    2    2333444 4678999999998776666665666777776643

All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.88  E-value=6e-22  Score=187.06  Aligned_cols=179  Identities=18%  Similarity=0.189  Sum_probs=134.6

Q ss_pred             HHHHhhccccCCCCcccccc-cCCCC------CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         25 LAVVSNSIFKHFEPHFTITY-LSPLG------RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        25 l~~~~~~~~~~~~~~Q~~~~-~~~~~------~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      -+..+++.| ++|+.|..+. .+..+      .|.+++|+||+|||.+++.+++..+.    .+.+++|++||++||.|+
T Consensus       591 ~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~----~g~qvlvLvPT~eLA~Q~  665 (1147)
T PRK10689        591 QLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE----NHKQVAVLVPTTLLAQQH  665 (1147)
T ss_pred             HHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH----cCCeEEEEeCcHHHHHHH
Confidence            344566677 7999997774 44443      78999999999999999888777664    267899999999999999


Q ss_pred             HHHHHHHhhcCCCeEEEEecchhhhhhhC---CCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccC
Q psy12977         98 YNETVRLSEGLGLRAHVIGKIQQAAEKFG---PRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG  174 (226)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~  174 (226)
                      ++.+++.+...+.++....+.....++..   ....+.++|+|+||+.+    .   ..+.+++++++|+||+|++... 
T Consensus       666 ~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL----~---~~v~~~~L~lLVIDEahrfG~~-  737 (1147)
T PRK10689        666 YDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL----Q---SDVKWKDLGLLIVDEEHRFGVR-  737 (1147)
T ss_pred             HHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH----h---CCCCHhhCCEEEEechhhcchh-
Confidence            99999988777777776665544333221   11235789999999643    2   3455789999999999997221 


Q ss_pred             ccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        175 VRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       175 ~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                         .    ...++.+ ++++|++++|||+.+....+....+.++..|...
T Consensus       738 ---~----~e~lk~l-~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~  779 (1147)
T PRK10689        738 ---H----KERIKAM-RADVDILTLTATPIPRTLNMAMSGMRDLSIIATP  779 (1147)
T ss_pred             ---H----HHHHHhc-CCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecC
Confidence               2    2334455 5689999999998888888888888899888754

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.88  E-value=4.1e-22  Score=179.43  Aligned_cols=174  Identities=21%  Similarity=0.277  Sum_probs=126.2

Q ss_pred             hccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcC
Q psy12977         30 NSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL  108 (226)
Q Consensus        30 ~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~  108 (226)
                      -++|+.|+|.|..+. .+++|+|+++.+|||+|||++|++|++..       ...+||++|+++|+.|+.+.++..    
T Consensus        20 ~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~-------~g~tlVisPl~sL~~dqv~~l~~~----   88 (607)
T PRK11057         20 TFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL-------DGLTLVVSPLISLMKDQVDQLLAN----   88 (607)
T ss_pred             HcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc-------CCCEEEEecHHHHHHHHHHHHHHc----
Confidence            379999999997775 77899999999999999999999998753       236899999999999999888765    


Q ss_pred             CCeEEEEecchhhhhh---hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchH---HHH
Q psy12977        109 GLRAHVIGKIQQAAEK---FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFR---DQL  182 (226)
Q Consensus       109 ~~~~~~~~~~~~~~~~---~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~---~~i  182 (226)
                      +.......+.......   .........+++++||+++......  ..+...+++++|+||||++.++++ .|.   ..+
T Consensus        89 gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~--~~l~~~~l~~iVIDEaH~i~~~G~-~fr~~y~~L  165 (607)
T PRK11057         89 GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFL--EHLAHWNPALLAVDEAHCISQWGH-DFRPEYAAL  165 (607)
T ss_pred             CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHH--HHHhhCCCCEEEEeCccccccccC-cccHHHHHH
Confidence            6666666555433221   1122345678999999998742211  223345789999999999998753 243   344


Q ss_pred             HHHHHhcCCCCceEEEEeeeCchhHHHHHHHhc--CCCe
Q psy12977        183 AVIYAACSGPNLKRGMFSATHTEDVAKWCRRKL--KRRV  219 (226)
Q Consensus       183 ~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~--~~p~  219 (226)
                      ..+.+.+  +..+++++|||.++.....+...+  .+|.
T Consensus       166 ~~l~~~~--p~~~~v~lTAT~~~~~~~di~~~l~l~~~~  202 (607)
T PRK11057        166 GQLRQRF--PTLPFMALTATADDTTRQDIVRLLGLNDPL  202 (607)
T ss_pred             HHHHHhC--CCCcEEEEecCCChhHHHHHHHHhCCCCeE
Confidence            4455554  678999999999988765554433  3554

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.87  E-value=1.4e-21  Score=186.34  Aligned_cols=149  Identities=25%  Similarity=0.227  Sum_probs=113.3

Q ss_pred             EECCCCchHhHHHHHHHHHHhcCCC---------CCCceEEEEcccHHHHHHHHHHHHHHhh------------cCCCeE
Q psy12977         54 ACAPTGSGKTAAFLIPIIHSLRGPK---------NLGFRAVIVCPTRELAKQTYNETVRLSE------------GLGLRA  112 (226)
Q Consensus        54 i~apTGsGKT~~~~~~~~~~~~~~~---------~~~~~~iil~Pt~~L~~q~~~~~~~~~~------------~~~~~~  112 (226)
                      |++|||||||++|.+|+++.+....         ..+.++||++|+++|+.|+.+.++....            ..++++
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V   80 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRV   80 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEE
Confidence            5799999999999999998875321         2357999999999999999998875221            235777


Q ss_pred             EEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccC-ccchHHHHHHHHHhcCC
Q psy12977        113 HVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG-VRGFRDQLAVIYAACSG  191 (226)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~-~~~~~~~i~~i~~~~~~  191 (226)
                      ....|+....++. ....+.+||+|+||+++..++.+. ....++++++||+||+|.+.+.. +..+...+.++...+ +
T Consensus        81 ~vrtGDt~~~eR~-rll~~ppdILVTTPEsL~~LLtsk-~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~-~  157 (1490)
T PRK09751         81 GIRTGDTPAQERS-KLTRNPPDILITTPESLYLMLTSR-ARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALL-H  157 (1490)
T ss_pred             EEEECCCCHHHHH-HHhcCCCCEEEecHHHHHHHHhhh-hhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhC-C
Confidence            7788876554432 123467899999999999987652 34568999999999999998652 223455666666655 5


Q ss_pred             CCceEEEEeeeCch
Q psy12977        192 PNLKRGMFSATHTE  205 (226)
Q Consensus       192 ~~~q~v~~SAT~~~  205 (226)
                      .+.|++++|||+++
T Consensus       158 ~~~QrIgLSATI~n  171 (1490)
T PRK09751        158 TSAQRIGLSATVRS  171 (1490)
T ss_pred             CCCeEEEEEeeCCC
Confidence            67899999999876

>TIGR01054 rgy reverse gyrase

Probab=99.87  E-value=9.2e-22  Score=186.34  Aligned_cols=143  Identities=24%  Similarity=0.207  Sum_probs=105.7

Q ss_pred             HHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHH
Q psy12977         22 VTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE  100 (226)
Q Consensus        22 ~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~  100 (226)
                      -+..+.+.+....+|+++|..+ +.++.|+|++++||||+|||. |.+++...+..   .+++++|++||++|+.|+.+.
T Consensus        65 ~~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~---~g~~vLIL~PTreLa~Qi~~~  140 (1171)
T TIGR01054        65 KEFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK---KGKRCYIILPTTLLVIQVAEK  140 (1171)
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh---cCCeEEEEeCHHHHHHHHHHH
Confidence            3445555555556899999666 578899999999999999997 55666555432   267999999999999999999


Q ss_pred             HHHHhhcCCCeEE---EEecchhhhhh---hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977        101 TVRLSEGLGLRAH---VIGKIQQAAEK---FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus       101 ~~~~~~~~~~~~~---~~~~~~~~~~~---~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      ++.+.+..+....   ..+|+.....+   ......++++|+|+||+++.+.+...    .. .++++|+||||++++.
T Consensus       141 l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l----~~-~~~~iVvDEaD~~L~~  214 (1171)
T TIGR01054       141 ISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDEL----GP-KFDFIFVDDVDALLKA  214 (1171)
T ss_pred             HHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHh----cC-CCCEEEEeChHhhhhc
Confidence            9999987775543   23444322221   11122356999999999999877652    11 8999999999999984

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.

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.86  E-value=1.9e-21  Score=175.83  Aligned_cols=164  Identities=16%  Similarity=0.224  Sum_probs=121.0

Q ss_pred             HHHHhhccccCCCCcccccc-cCCCC------CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         25 LAVVSNSIFKHFEPHFTITY-LSPLG------RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        25 l~~~~~~~~~~~~~~Q~~~~-~~~~~------~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      ...+++..| ++++.|..+. .+.++      .+.+++||||||||.+|+++++..+..    +.+++|++||++||.|+
T Consensus       226 ~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~----g~qvlilaPT~~LA~Q~  300 (630)
T TIGR00643       226 TKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA----GYQVALMAPTEILAEQH  300 (630)
T ss_pred             HHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc----CCcEEEECCHHHHHHHH
Confidence            345667777 6999996663 33332      368999999999999999999988763    56899999999999999


Q ss_pred             HHHHHHHhhcCCCeEEEEecchhhhhh---hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccC
Q psy12977         98 YNETVRLSEGLGLRAHVIGKIQQAAEK---FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG  174 (226)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~  174 (226)
                      ++.++++++..+.++..+.|+.....+   ......+.++|+|+||+.+.+       ...+.+++++|+||+|++... 
T Consensus       301 ~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-------~~~~~~l~lvVIDEaH~fg~~-  372 (630)
T TIGR00643       301 YNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-------KVEFKRLALVIIDEQHRFGVE-  372 (630)
T ss_pred             HHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-------cccccccceEEEechhhccHH-
Confidence            999999999888999888877544332   222334678999999987643       345789999999999986432 


Q ss_pred             ccchHHHHHHHHHhcCC-CCceEEEEeeeCchhH
Q psy12977        175 VRGFRDQLAVIYAACSG-PNLKRGMFSATHTEDV  207 (226)
Q Consensus       175 ~~~~~~~i~~i~~~~~~-~~~q~v~~SAT~~~~~  207 (226)
                         ....   +...... ..+++++||||+.+..
T Consensus       373 ---qr~~---l~~~~~~~~~~~~l~~SATp~prt  400 (630)
T TIGR00643       373 ---QRKK---LREKGQGGFTPHVLVMSATPIPRT  400 (630)
T ss_pred             ---HHHH---HHHhcccCCCCCEEEEeCCCCcHH
Confidence               2222   2222211 2689999999975543

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.86  E-value=6.2e-21  Score=173.68  Aligned_cols=161  Identities=20%  Similarity=0.244  Sum_probs=120.0

Q ss_pred             hhccccCCCCcccccc-cCCCC------CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHH
Q psy12977         29 SNSIFKHFEPHFTITY-LSPLG------RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET  101 (226)
Q Consensus        29 ~~~~~~~~~~~Q~~~~-~~~~~------~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~  101 (226)
                      +...| ++++.|..+. .+.++      .+.+++||||||||.+|+++++..+..    +.+++|++||++||.|+++.+
T Consensus       256 ~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~----g~q~lilaPT~~LA~Q~~~~l  330 (681)
T PRK10917        256 ASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA----GYQAALMAPTEILAEQHYENL  330 (681)
T ss_pred             HhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc----CCeEEEEeccHHHHHHHHHHH
Confidence            34455 5999997774 33333      479999999999999999999988753    668999999999999999999


Q ss_pred             HHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccch
Q psy12977        102 VRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGF  178 (226)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~  178 (226)
                      +++.+..+.++..+.|+.....+.   .....+.++|+|+||+.+.       ....+++++++|+||+|++...    .
T Consensus       331 ~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~-------~~v~~~~l~lvVIDE~Hrfg~~----q  399 (681)
T PRK10917        331 KKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQ-------DDVEFHNLGLVIIDEQHRFGVE----Q  399 (681)
T ss_pred             HHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhc-------ccchhcccceEEEechhhhhHH----H
Confidence            999998899998888876533221   1223456999999998763       2345789999999999987432    2


Q ss_pred             HHHHHHHHHhcCCCCceEEEEeeeCchhHHHH
Q psy12977        179 RDQLAVIYAACSGPNLKRGMFSATHTEDVAKW  210 (226)
Q Consensus       179 ~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~  210 (226)
                      ..    .+... ...+++++||||+.+....+
T Consensus       400 r~----~l~~~-~~~~~iL~~SATp~prtl~~  426 (681)
T PRK10917        400 RL----ALREK-GENPHVLVMTATPIPRTLAM  426 (681)
T ss_pred             HH----HHHhc-CCCCCEEEEeCCCCHHHHHH
Confidence            22    22222 34689999999976554433

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.86  E-value=5.2e-21  Score=172.13  Aligned_cols=166  Identities=13%  Similarity=0.083  Sum_probs=116.6

Q ss_pred             ccCCCCCeEEEECCCCchHhHH---------HHHHHHHHhcC--CCCCCceEEEEcccHHHHHHHHHHHHHHhhc---CC
Q psy12977         44 YLSPLGRQIFACAPTGSGKTAA---------FLIPIIHSLRG--PKNLGFRAVIVCPTRELAKQTYNETVRLSEG---LG  109 (226)
Q Consensus        44 ~~~~~~~~~li~apTGsGKT~~---------~~~~~~~~~~~--~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~---~~  109 (226)
                      +.+.++++++++|+||||||.+         |+++.+..+..  ....+.++++++|+++||.|+.+.+.+..++   .+
T Consensus       174 ~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~vg~~~~~g  253 (675)
T PHA02653        174 EAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKSLGFDEIDG  253 (675)
T ss_pred             HHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHHhCccccCC
Confidence            4667899999999999999987         33444444321  1223568999999999999999988776544   24


Q ss_pred             CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      ..+....|+..+.  .........+|+++|++.         ....+++++++|+||||.+...+     +.+..+++..
T Consensus       254 ~~v~v~~Gg~~~~--~~~t~~k~~~Ilv~T~~L---------~l~~L~~v~~VVIDEaHEr~~~~-----DllL~llk~~  317 (675)
T PHA02653        254 SPISLKYGSIPDE--LINTNPKPYGLVFSTHKL---------TLNKLFDYGTVIIDEVHEHDQIG-----DIIIAVARKH  317 (675)
T ss_pred             ceEEEEECCcchH--HhhcccCCCCEEEEeCcc---------cccccccCCEEEccccccCccch-----hHHHHHHHHh
Confidence            4455555554321  111122367899999752         12247889999999999987652     3344445444


Q ss_pred             CCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCCC
Q psy12977        190 SGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       190 ~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      .+...|+++||||+|++++.+ .+|+++|..+++.+|
T Consensus       318 ~~~~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~gr  353 (675)
T PHA02653        318 IDKIRSLFLMTATLEDDRDRI-KEFFPNPAFVHIPGG  353 (675)
T ss_pred             hhhcCEEEEEccCCcHhHHHH-HHHhcCCcEEEeCCC
Confidence            334459999999999988776 689999999988764

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.85  E-value=5.3e-21  Score=162.48  Aligned_cols=158  Identities=19%  Similarity=0.162  Sum_probs=108.5

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhh--------
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAA--------  122 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~--------  122 (226)
                      ++++.+|||+|||.+++.+++..+..  ..+.+++|++|+++|+.|+.+.++.++..   .+....+.....        
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~--~~~~~ii~v~P~~~L~~q~~~~l~~~f~~---~~~~~~~~~~~~~~~~~~~~   75 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKS--QKADRVIIALPTRATINAMYRRAKELFGS---NLGLLHSSSSFKRIKEMGDS   75 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhh--CCCCeEEEEeehHHHHHHHHHHHHHHhCc---ccEEeeccHHHHHHhccCCc
Confidence            57999999999999999999988753  33569999999999999999999998642   222222211100        


Q ss_pred             ---hh------hCCCcCCCCCEEEECchHHHHhHhcCCCC--CCCC--CccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        123 ---EK------FGPRSAQKFDVLITTPNKLVYLLQMDPPA--LNLA--NVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       123 ---~~------~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~--~~~~--~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                         ..      ........++|+|+||+++...+......  ..+.  ..+++|+||+|.+.+..    ...+..+++.+
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~----~~~l~~~l~~l  151 (358)
T TIGR01587        76 EEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYT----LALILAVLEVL  151 (358)
T ss_pred             hhHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHH----HHHHHHHHHHH
Confidence               00      00001134679999999998876641111  1111  23799999999998752    22255555555


Q ss_pred             CCCCceEEEEeeeCchhHHHHHHHhcCC
Q psy12977        190 SGPNLKRGMFSATHTEDVAKWCRRKLKR  217 (226)
Q Consensus       190 ~~~~~q~v~~SAT~~~~~~~~~~~~~~~  217 (226)
                      ...+.|++++|||+|+.+.+++..+...
T Consensus       152 ~~~~~~~i~~SATlp~~l~~~~~~~~~~  179 (358)
T TIGR01587       152 KDNDVPILLMSATLPKFLKEYAEKIGYV  179 (358)
T ss_pred             HHcCCCEEEEecCchHHHHHHHhcCCCc
Confidence            4567899999999999888888776543

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.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.84  E-value=1e-19  Score=167.32  Aligned_cols=160  Identities=21%  Similarity=0.190  Sum_probs=117.4

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHH-HHhhcCCCeEEEEecchhhhhhh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETV-RLSEGLGLRAHVIGKIQQAAEKF  125 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  125 (226)
                      .++++++++||||||||.+|..++++....    +.+++++.|+|++|.|+++.+. .+....+..+....++..     
T Consensus        18 ~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~----~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~vr~~~-----   88 (812)
T PRK11664         18 KTAPQVLLKAPTGAGKSTWLPLQLLQHGGI----NGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYRMRAES-----   88 (812)
T ss_pred             HhCCCEEEEcCCCCCHHHHHHHHHHHcCCc----CCeEEEECChHHHHHHHHHHHHHHhCcccCceEEEEecCcc-----
Confidence            456899999999999999999998876432    3489999999999999999874 445555666655444321     


Q ss_pred             CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccc-ccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        126 GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK-LFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       126 ~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~-l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                        ......+|+|+||+++.+++..+   ..+++++++|+||+|. .++.+  -....+..+.+.+ ++..|+++||||++
T Consensus        89 --~~~~~t~I~v~T~G~Llr~l~~d---~~L~~v~~IIlDEaHER~l~~D--l~L~ll~~i~~~l-r~~lqlilmSATl~  160 (812)
T PRK11664         89 --KVGPNTRLEVVTEGILTRMIQRD---PELSGVGLVILDEFHERSLQAD--LALALLLDVQQGL-RDDLKLLIMSATLD  160 (812)
T ss_pred             --ccCCCCcEEEEChhHHHHHHhhC---CCcCcCcEEEEcCCCccccccc--hHHHHHHHHHHhC-CccceEEEEecCCC
Confidence              12345679999999999988753   4689999999999996 34431  1122334455555 57889999999998


Q ss_pred             hhHHHHHHHhcCCCeEEecCCC
Q psy12977        205 EDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       205 ~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      .+.   +.+|+.++..+.+.+|
T Consensus       161 ~~~---l~~~~~~~~~I~~~gr  179 (812)
T PRK11664        161 NDR---LQQLLPDAPVIVSEGR  179 (812)
T ss_pred             HHH---HHHhcCCCCEEEecCc
Confidence            653   4678887777777654

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.84  E-value=1e-19  Score=167.20  Aligned_cols=159  Identities=20%  Similarity=0.221  Sum_probs=119.1

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHH-HHhhcCCCeEEEEecchhhhhhh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETV-RLSEGLGLRAHVIGKIQQAAEKF  125 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  125 (226)
                      .++.+++++|+||||||.++..++++...    .+.+++++.|+|++|.|+++.+. .+....+..+.......      
T Consensus        15 ~~~~~vIi~a~TGSGKTT~vpl~lL~~~~----~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~vr~~------   84 (819)
T TIGR01970        15 AAHPQVVLEAPPGAGKSTAVPLALLDAPG----IGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRVRGE------   84 (819)
T ss_pred             HcCCcEEEECCCCCCHHHHHHHHHHHhhc----cCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEEccc------
Confidence            45689999999999999999999988763    24589999999999999999874 44444555555443321      


Q ss_pred             CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccc-ccccCccchHHH-HHHHHHhcCCCCceEEEEeeeC
Q psy12977        126 GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK-LFEAGVRGFRDQ-LAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       126 ~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~-l~~~~~~~~~~~-i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                       .....+.+|+|+||+.+.+.+..+   ..++++++||+||+|. .++.   ++... +..+.+.+ ++..|+++||||+
T Consensus        85 -~~~s~~t~I~v~T~G~Llr~l~~d---~~L~~v~~VIiDEaHER~L~~---Dl~L~ll~~i~~~l-r~dlqlIlmSATl  156 (819)
T TIGR01970        85 -NKVSRRTRLEVVTEGILTRMIQDD---PELDGVGALIFDEFHERSLDA---DLGLALALDVQSSL-REDLKILAMSATL  156 (819)
T ss_pred             -cccCCCCcEEEECCcHHHHHHhhC---cccccCCEEEEeccchhhhcc---chHHHHHHHHHHhc-CCCceEEEEeCCC
Confidence             123456789999999999988753   4689999999999994 6665   34333 33444445 5789999999999


Q ss_pred             chhHHHHHHHhcCCCeEEecCCC
Q psy12977        204 TEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       204 ~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      +.+.   +.+|+.++..|.+.+|
T Consensus       157 ~~~~---l~~~l~~~~vI~~~gr  176 (819)
T TIGR01970       157 DGER---LSSLLPDAPVVESEGR  176 (819)
T ss_pred             CHHH---HHHHcCCCcEEEecCc
Confidence            9664   4678877777776654

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.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.84  E-value=9.5e-20  Score=154.51  Aligned_cols=172  Identities=20%  Similarity=0.239  Sum_probs=112.8

Q ss_pred             ccccc-cCCCCC--eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcC----CCeE
Q psy12977         40 FTITY-LSPLGR--QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL----GLRA  112 (226)
Q Consensus        40 Q~~~~-~~~~~~--~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~----~~~~  112 (226)
                      |.+++ .+.++.  ++++.+|||+|||.+++++++..       +.+++|++|+++|++|+.+.++++....    +..+
T Consensus         2 Q~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~-------~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~~v   74 (357)
T TIGR03158         2 QVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHG-------ENDTIALYPTNALIEDQTEAIKEFVDVFKPERDVNL   74 (357)
T ss_pred             HHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHc-------CCCEEEEeChHHHHHHHHHHHHHHHHhcCCCCCceE
Confidence            55554 333333  47899999999999999988742       2368999999999999999999987543    3444


Q ss_pred             EEEecchhhhh-hhC------------------CCcCCCCCEEEECchHHHHhHhcCC---CCC---CCCCccEEEEccc
Q psy12977        113 HVIGKIQQAAE-KFG------------------PRSAQKFDVLITTPNKLVYLLQMDP---PAL---NLANVEWLIVDES  167 (226)
Q Consensus       113 ~~~~~~~~~~~-~~~------------------~~~~~~~~IiV~Tp~~l~~~~~~~~---~~~---~~~~~~~lViDE~  167 (226)
                      ....+...... ...                  ......++|+++||+.+..++....   ...   .+.+++++|+||+
T Consensus        75 ~~~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~~iV~DE~  154 (357)
T TIGR03158        75 LHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDEF  154 (357)
T ss_pred             EEecCCchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCCEEEEecc
Confidence            44444422110 000                  0013468999999999987665321   111   2578999999999


Q ss_pred             ccccccCccc--hHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHh--cCCCe
Q psy12977        168 DKLFEAGVRG--FRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRK--LKRRV  219 (226)
Q Consensus       168 h~l~~~~~~~--~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~--~~~p~  219 (226)
                      |.+.......  +......+++.. ....+++++|||+|+.+.+.+...  +.+|+
T Consensus       155 H~~~~~~~~~~~~~l~~~~~~~~~-~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~  209 (357)
T TIGR03158       155 HLYDAKQLVGMLFLLAYMQLIRFF-ECRRKFVFLSATPDPALILRLQNAKQAGVKI  209 (357)
T ss_pred             cccCcccchhhhhhhHHHHHHHhh-hcCCcEEEEecCCCHHHHHHHHhccccCcee
Confidence            9876542111  112333333333 235799999999999988888765  44443

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.

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

Probab=99.81  E-value=3e-19  Score=151.32  Aligned_cols=165  Identities=18%  Similarity=0.147  Sum_probs=129.3

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCC
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGP  127 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (226)
                      -.+|.++..|||-|||+.+++.+...+.+.  .+ ++|+++||+.|+.|.++.+.+...-....+..+.|.....++.. 
T Consensus        28 l~~NtLvvlPTGLGKT~IA~~V~~~~l~~~--~~-kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~~ltGev~p~~R~~-  103 (542)
T COG1111          28 LFKNTLVVLPTGLGKTFIAAMVIANRLRWF--GG-KVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAALTGEVRPEEREE-  103 (542)
T ss_pred             hhcCeEEEecCCccHHHHHHHHHHHHHHhc--CC-eEEEecCCchHHHHHHHHHHHHhCCChhheeeecCCCChHHHHH-
Confidence            346999999999999999998888888753  23 89999999999999999999998776777777777766554432 


Q ss_pred             CcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch--
Q psy12977        128 RSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE--  205 (226)
Q Consensus       128 ~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~--  205 (226)
                       ...+.+|+|+||+.+.+.+..  +.+++.++.++|+||||+..+.-  .|..-.+..++.-  .++.++++|||+-.  
T Consensus       104 -~w~~~kVfvaTPQvveNDl~~--Grid~~dv~~lifDEAHRAvGny--AYv~Va~~y~~~~--k~~~ilgLTASPGs~~  176 (542)
T COG1111         104 -LWAKKKVFVATPQVVENDLKA--GRIDLDDVSLLIFDEAHRAVGNY--AYVFVAKEYLRSA--KNPLILGLTASPGSDL  176 (542)
T ss_pred             -HHhhCCEEEeccHHHHhHHhc--CccChHHceEEEechhhhccCcc--hHHHHHHHHHHhc--cCceEEEEecCCCCCH
Confidence             345677999999999999998  89999999999999999987752  3555555555543  67899999999774  


Q ss_pred             -hHHHHHHHhcCCCeEEec
Q psy12977        206 -DVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       206 -~~~~~~~~~~~~p~~i~~  223 (226)
                       .+.+.++...-+.+.+..
T Consensus       177 ekI~eV~~nLgIe~vevrT  195 (542)
T COG1111         177 EKIQEVVENLGIEKVEVRT  195 (542)
T ss_pred             HHHHHHHHhCCcceEEEec
Confidence             455555554445554443

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.81  E-value=1.4e-19  Score=159.80  Aligned_cols=149  Identities=15%  Similarity=0.035  Sum_probs=105.3

Q ss_pred             cCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeE
Q psy12977         34 KHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRA  112 (226)
Q Consensus        34 ~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~  112 (226)
                      ..+.+.|..+ ...+.+++.++++|||+|||..+...+...+..   ...+++|++||++|+.|+.+.++++.......+
T Consensus       113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~---~~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~  189 (501)
T PHA02558        113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLEN---YEGKVLIIVPTTSLVTQMIDDFVDYRLFPREAM  189 (501)
T ss_pred             CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhc---CCCeEEEEECcHHHHHHHHHHHHHhccccccce
Confidence            4677788765 455677889999999999998764432222222   233899999999999999999998875444444


Q ss_pred             EEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCC
Q psy12977        113 HVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGP  192 (226)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~  192 (226)
                      ..+.++...        ....+|+|+|++++.+...     ..+++++++|+||||++.+.   .    +..++..+ ++
T Consensus       190 ~~i~~g~~~--------~~~~~I~VaT~qsl~~~~~-----~~~~~~~~iIvDEaH~~~~~---~----~~~il~~~-~~  248 (501)
T PHA02558        190 HKIYSGTAK--------DTDAPIVVSTWQSAVKQPK-----EWFDQFGMVIVDECHLFTGK---S----LTSIITKL-DN  248 (501)
T ss_pred             eEEecCccc--------CCCCCEEEeeHHHHhhchh-----hhccccCEEEEEchhcccch---h----HHHHHHhh-hc
Confidence            344443211        1347899999999876432     23678999999999998764   2    34455555 34


Q ss_pred             CceEEEEeeeCchh
Q psy12977        193 NLKRGMFSATHTED  206 (226)
Q Consensus       193 ~~q~v~~SAT~~~~  206 (226)
                      ..+++++|||+++.
T Consensus       249 ~~~~lGLTATp~~~  262 (501)
T PHA02558        249 CKFKFGLTGSLRDG  262 (501)
T ss_pred             cceEEEEeccCCCc
Confidence            67899999998753

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.81  E-value=1.4e-19  Score=164.51  Aligned_cols=143  Identities=16%  Similarity=0.131  Sum_probs=113.8

Q ss_pred             HHHHHHHHh-----hccccCC---CCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         21 IVTTLAVVS-----NSIFKHF---EPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        21 ~~~~l~~~~-----~~~~~~~---~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      .......+.     .++|+.+   +|.|.+. +.+..+++++..++||+|||++|++|++..+...    ..++|++||+
T Consensus        70 ~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g----~~v~IVTpTr  145 (970)
T PRK12899         70 VKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTG----KPVHLVTVND  145 (970)
T ss_pred             CHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhc----CCeEEEeCCH
Confidence            344444444     5677776   8998666 4777889999999999999999999999777532    2489999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHH-HHhHhcCCCCCCCC-------CccEEE
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKL-VYLLQMDPPALNLA-------NVEWLI  163 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l-~~~~~~~~~~~~~~-------~~~~lV  163 (226)
                      +||.|..+.+..+.++++.++..+.++.....+...   .++||+|+||+++ +++++.  +.+.++       .+.++|
T Consensus       146 ELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~---y~~DIVygTPgRLgfDyLrd--~~~~~~~~~~vqr~~~~~I  220 (970)
T PRK12899        146 YLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEI---YQCDVVYGTASEFGFDYLRD--NSIATRKEEQVGRGFYFAI  220 (970)
T ss_pred             HHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHH---cCCCEEEECCChhHHHHhhC--CCCCcCHHHhhcccccEEE
Confidence            999999999999999999999888777655544322   3699999999999 999886  444444       458999


Q ss_pred             Ecccccccc
Q psy12977        164 VDESDKLFE  172 (226)
Q Consensus       164 iDE~h~l~~  172 (226)
                      +||||.++-
T Consensus       221 IDEADsmLi  229 (970)
T PRK12899        221 IDEVDSILI  229 (970)
T ss_pred             Eechhhhhh
Confidence            999998863

>KOG0354|consensus

Probab=99.80  E-value=4.7e-19  Score=157.44  Aligned_cols=155  Identities=15%  Similarity=0.098  Sum_probs=114.5

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhh
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEK  124 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (226)
                      ..+ |+|+++++|||+|||+.++..+++.+++.+.  .++|+++|++.|+.|+...++.++..  ..+....++......
T Consensus        73 ~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~--~KiVF~aP~~pLv~QQ~a~~~~~~~~--~~~T~~l~~~~~~~~  147 (746)
T KOG0354|consen   73 PAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK--GKVVFLAPTRPLVNQQIACFSIYLIP--YSVTGQLGDTVPRSN  147 (746)
T ss_pred             Hhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCc--ceEEEeeCCchHHHHHHHHHhhccCc--ccceeeccCccCCCc
Confidence            445 9999999999999999999999999987655  59999999999999999777666543  333333343222222


Q ss_pred             hCCCcCCCCCEEEECchHHHHhHhcCCCCCC-CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        125 FGPRSAQKFDVLITTPNKLVYLLQMDPPALN-LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       125 ~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~-~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      . ..+....+|+++||+.+.+.+..  +..+ ++++.++|+||||+-....  .|..-+...+ .......|++++|||+
T Consensus       148 r-~~i~~s~~vff~TpQil~ndL~~--~~~~~ls~fs~iv~DE~Hra~kn~--~Y~~Vmr~~l-~~k~~~~qILgLTASp  221 (746)
T KOG0354|consen  148 R-GEIVASKRVFFRTPQILENDLKS--GLHDELSDFSLIVFDECHRTSKNH--PYNNIMREYL-DLKNQGNQILGLTASP  221 (746)
T ss_pred             h-hhhhcccceEEeChHhhhhhccc--ccccccceEEEEEEcccccccccc--cHHHHHHHHH-HhhhccccEEEEecCC
Confidence            1 24556789999999999999887  3333 6999999999999987762  3444443443 3334556999999998


Q ss_pred             chhHHHH
Q psy12977        204 TEDVAKW  210 (226)
Q Consensus       204 ~~~~~~~  210 (226)
                      .....+.
T Consensus       222 G~~~~~v  228 (746)
T KOG0354|consen  222 GSKLEQV  228 (746)
T ss_pred             CccHHHH
Confidence            8554433

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

Probab=99.79  E-value=2.4e-18  Score=147.73  Aligned_cols=177  Identities=19%  Similarity=0.154  Sum_probs=136.2

Q ss_pred             HHHHHHHHhhccccCCCCcccccc--cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHH
Q psy12977         21 IVTTLAVVSNSIFKHFEPHFTITY--LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTY   98 (226)
Q Consensus        21 ~~~~l~~~~~~~~~~~~~~Q~~~~--~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~   98 (226)
                      ....-+-+..++++++.|+|..+.  =++.|+|.++.++|+||||+..-++-+..+..   .+.+.++++|..+||+|-+
T Consensus       202 pe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~---~g~KmlfLvPLVALANQKy  278 (830)
T COG1202         202 PEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLS---GGKKMLFLVPLVALANQKY  278 (830)
T ss_pred             cHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHh---CCCeEEEEehhHHhhcchH
Confidence            445556678899999999997774  66899999999999999999988876666543   3568999999999999999


Q ss_pred             HHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCc
Q psy12977         99 NETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGV  175 (226)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~  175 (226)
                      +.+++-...++.++..-.|..--....   ......++||||+|.+-+-.+++.  + -.+.++..+||||+|.+-+...
T Consensus       279 ~dF~~rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRt--g-~~lgdiGtVVIDEiHtL~deER  355 (830)
T COG1202         279 EDFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRT--G-KDLGDIGTVVIDEIHTLEDEER  355 (830)
T ss_pred             HHHHHHhhcccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHc--C-CcccccceEEeeeeeeccchhc
Confidence            999999999998887666553222221   123356789999999999888886  3 6689999999999998876432


Q ss_pred             cchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        176 RGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       176 ~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      ..-.+.+..-++.+ -+..|++.+|||.-
T Consensus       356 G~RLdGLI~RLr~l-~~~AQ~i~LSATVg  383 (830)
T COG1202         356 GPRLDGLIGRLRYL-FPGAQFIYLSATVG  383 (830)
T ss_pred             ccchhhHHHHHHHh-CCCCeEEEEEeecC
Confidence            23344444444444 36899999999953

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.79  E-value=6.7e-18  Score=123.37  Aligned_cols=144  Identities=30%  Similarity=0.377  Sum_probs=104.6

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      +++++.+|||+|||..++..+......  ....++++++|++.++.|+.+.+...... +..+....+........ ...
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~--~~~~~~lv~~p~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~-~~~   76 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDS--LKGGQVLVLAPTRELANQVAERLKELFGE-GIKVGYLIGGTSIKQQE-KLL   76 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhc--ccCCCEEEEcCcHHHHHHHHHHHHHHhhC-CcEEEEEecCcchhHHH-HHh
Confidence            468999999999999988888777754  23459999999999999999988888765 55555555543322221 223


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      ....+|+++|++.+.+....  ........+++|+||+|.+....   ......... .......+++++|||+
T Consensus        77 ~~~~~i~i~t~~~~~~~~~~--~~~~~~~~~~iiiDE~h~~~~~~---~~~~~~~~~-~~~~~~~~~i~~saTp  144 (144)
T cd00046          77 SGKTDIVVGTPGRLLDELER--LKLSLKKLDLLILDEAHRLLNQG---FGLLGLKIL-LKLPKDRQVLLLSATP  144 (144)
T ss_pred             cCCCCEEEECcHHHHHHHHc--CCcchhcCCEEEEeCHHHHhhcc---hHHHHHHHH-hhCCccceEEEEeccC
Confidence            46789999999999988876  33446678999999999887662   222211112 2225788999999995

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

>PRK13766 Hef nuclease; Provisional

Probab=99.79  E-value=2.2e-18  Score=159.81  Aligned_cols=168  Identities=20%  Similarity=0.182  Sum_probs=118.5

Q ss_pred             CCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEE
Q psy12977         36 FEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVI  115 (226)
Q Consensus        36 ~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  115 (226)
                      +.+.|.........+|.++++|||+|||.+++.++...+..   .+.+++|++|+++|+.|+.+.++.+....+..+..+
T Consensus        16 ~r~yQ~~~~~~~l~~n~lv~~ptG~GKT~~a~~~i~~~l~~---~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~   92 (773)
T PRK13766         16 ARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAERLHK---KGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVF   92 (773)
T ss_pred             ccHHHHHHHHHHhcCCeEEEcCCCccHHHHHHHHHHHHHHh---CCCeEEEEeCcHHHHHHHHHHHHHHhCCCCceEEEE
Confidence            44456554422233499999999999999998888877742   345999999999999999999998875444566666


Q ss_pred             ecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCce
Q psy12977        116 GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLK  195 (226)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q  195 (226)
                      .|+.....+.  ....+++|+|+||+.+...+..  +.+++.+++++|+||||++.+.   .....+...+... ++.++
T Consensus        93 ~g~~~~~~r~--~~~~~~~iiv~T~~~l~~~l~~--~~~~~~~~~liVvDEaH~~~~~---~~~~~i~~~~~~~-~~~~~  164 (773)
T PRK13766         93 TGEVSPEKRA--ELWEKAKVIVATPQVIENDLIA--GRISLEDVSLLIFDEAHRAVGN---YAYVYIAERYHED-AKNPL  164 (773)
T ss_pred             eCCCCHHHHH--HHHhCCCEEEECHHHHHHHHHc--CCCChhhCcEEEEECCcccccc---ccHHHHHHHHHhc-CCCCE
Confidence            6654332221  2234678999999999887766  6778899999999999998765   2333333333333 35678


Q ss_pred             EEEEeeeCch---hHHHHHHHh
Q psy12977        196 RGMFSATHTE---DVAKWCRRK  214 (226)
Q Consensus       196 ~v~~SAT~~~---~~~~~~~~~  214 (226)
                      ++++|||+..   .+.+.++..
T Consensus       165 il~lTaTP~~~~~~i~~~~~~L  186 (773)
T PRK13766        165 VLGLTASPGSDEEKIKEVCENL  186 (773)
T ss_pred             EEEEEcCCCCCHHHHHHHHHhC
Confidence            9999999743   344444443

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.76  E-value=1.5e-17  Score=151.32  Aligned_cols=159  Identities=23%  Similarity=0.207  Sum_probs=111.6

Q ss_pred             CCCCcccccc-cCCC---CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCC
Q psy12977         35 HFEPHFTITY-LSPL---GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGL  110 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~---~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~  110 (226)
                      ++++.|..+. .+.+   +++.++.++||+|||.+|+.++...+..    +.++++++|+++|+.|+.+.+++.+   +.
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~----g~~vLvLvPt~~L~~Q~~~~l~~~f---g~  216 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ----GKQALVLVPEIALTPQMLARFRARF---GA  216 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHc----CCeEEEEeCcHHHHHHHHHHHHHHh---CC
Confidence            4677776554 2233   4789999999999999998887777653    5689999999999999999988754   55


Q ss_pred             eEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccc---hHHHHHH
Q psy12977        111 RAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG---FRDQLAV  184 (226)
Q Consensus       111 ~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~---~~~~i~~  184 (226)
                      .+..+.++....++.   .....+.++|+|+|++.+.         .++++++++|+||+|.......+.   ....+..
T Consensus       217 ~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~---------~p~~~l~liVvDEeh~~s~~~~~~p~y~~r~va~  287 (679)
T PRK05580        217 PVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF---------LPFKNLGLIIVDEEHDSSYKQQEGPRYHARDLAV  287 (679)
T ss_pred             CEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc---------ccccCCCEEEEECCCccccccCcCCCCcHHHHHH
Confidence            666666654433222   1223456899999998753         347889999999999765432111   1233433


Q ss_pred             HHHhcCCCCceEEEEeeeCchhHHHHH
Q psy12977        185 IYAACSGPNLKRGMFSATHTEDVAKWC  211 (226)
Q Consensus       185 i~~~~~~~~~q~v~~SAT~~~~~~~~~  211 (226)
                      ....  ..+.|++++|||++.+....+
T Consensus       288 ~ra~--~~~~~~il~SATps~~s~~~~  312 (679)
T PRK05580        288 VRAK--LENIPVVLGSATPSLESLANA  312 (679)
T ss_pred             HHhh--ccCCCEEEEcCCCCHHHHHHH
Confidence            3322  368899999999886665554

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

Probab=99.75  E-value=1.2e-17  Score=153.72  Aligned_cols=175  Identities=21%  Similarity=0.307  Sum_probs=133.7

Q ss_pred             HhhccccCCCCcc-cccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhh
Q psy12977         28 VSNSIFKHFEPHF-TITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE  106 (226)
Q Consensus        28 ~~~~~~~~~~~~Q-~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~  106 (226)
                      .++.+|+ +-+.| +....+..+++++++||||+|||+..-+++...+.+    +.+++|.+|.++|.+|.+..+...+.
T Consensus       113 ~~~~~F~-LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~----~qrviYTsPIKALsNQKyrdl~~~fg  187 (1041)
T COG4581         113 AREYPFE-LDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRD----GQRVIYTSPIKALSNQKYRDLLAKFG  187 (1041)
T ss_pred             HHhCCCC-cCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHc----CCceEeccchhhhhhhHHHHHHHHhh
Confidence            3444444 34555 445688889999999999999999988888777764    44699999999999999999888876


Q ss_pred             cCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHH
Q psy12977        107 GLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIY  186 (226)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~  186 (226)
                      +....+....|+.        .+..++.++|.|.+.|.+++.+  +...+..+..||+||+|.+.+..   -.-.+...+
T Consensus       188 dv~~~vGL~TGDv--------~IN~~A~clvMTTEILRnMlyr--g~~~~~~i~~ViFDEvHyi~D~e---RG~VWEE~I  254 (1041)
T COG4581         188 DVADMVGLMTGDV--------SINPDAPCLVMTTEILRNMLYR--GSESLRDIEWVVFDEVHYIGDRE---RGVVWEEVI  254 (1041)
T ss_pred             hhhhhccceecce--------eeCCCCceEEeeHHHHHHHhcc--CcccccccceEEEEeeeeccccc---cchhHHHHH
Confidence            5522334444442        2446788999999999999988  67789999999999999998873   444555566


Q ss_pred             HhcCCCCceEEEEeeeCc--hhHHHHHHHhcCCCeEE
Q psy12977        187 AACSGPNLKRGMFSATHT--EDVAKWCRRKLKRRVQI  221 (226)
Q Consensus       187 ~~~~~~~~q~v~~SAT~~--~~~~~~~~~~~~~p~~i  221 (226)
                      -.+ +...+++++|||.|  .+...|+.+.-..|.++
T Consensus       255 i~l-P~~v~~v~LSATv~N~~EF~~Wi~~~~~~~~~v  290 (1041)
T COG4581         255 ILL-PDHVRFVFLSATVPNAEEFAEWIQRVHSQPIHV  290 (1041)
T ss_pred             Hhc-CCCCcEEEEeCCCCCHHHHHHHHHhccCCCeEE
Confidence            566 66789999999977  56788888765555443

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

Probab=99.73  E-value=1.1e-17  Score=146.69  Aligned_cols=171  Identities=21%  Similarity=0.260  Sum_probs=133.0

Q ss_pred             hccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcC
Q psy12977         30 NSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL  108 (226)
Q Consensus        30 ~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~  108 (226)
                      -+||..|.+-|.... ..++|+|+++..|||.||++||.+|++-.       ..-+||++|..+|+..+.+.++..    
T Consensus        12 ~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~-------~G~TLVVSPLiSLM~DQV~~l~~~----   80 (590)
T COG0514          12 VFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL-------EGLTLVVSPLISLMKDQVDQLEAA----   80 (590)
T ss_pred             HhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc-------CCCEEEECchHHHHHHHHHHHHHc----
Confidence            467999999996664 88899999999999999999999998664       126899999999999999988877    


Q ss_pred             CCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccC--ccchHHHHH
Q psy12977        109 GLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG--VRGFRDQLA  183 (226)
Q Consensus       109 ~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~--~~~~~~~i~  183 (226)
                      |+....+++.....+..   .....+..+++.-+|+++..-...  ..+.-..+.+++|||||+++.|+  +|.-...+.
T Consensus        81 Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~--~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~~lg  158 (590)
T COG0514          81 GIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFL--ELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLG  158 (590)
T ss_pred             CceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHH--HHHHhCCCceEEechHHHHhhcCCccCHhHHHHH
Confidence            77777777664333332   223345679999999999764333  34446678899999999999997  444455556


Q ss_pred             HHHHhcCCCCceEEEEeeeCchhHHHHHHHhc
Q psy12977        184 VIYAACSGPNLKRGMFSATHTEDVAKWCRRKL  215 (226)
Q Consensus       184 ~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~  215 (226)
                      .+...+  ++.+++++|||-++.+.+.+.+.+
T Consensus       159 ~l~~~~--~~~p~~AlTATA~~~v~~DI~~~L  188 (590)
T COG0514         159 RLRAGL--PNPPVLALTATATPRVRDDIREQL  188 (590)
T ss_pred             HHHhhC--CCCCEEEEeCCCChHHHHHHHHHh
Confidence            666666  488999999999988877777754

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.71  E-value=3.7e-17  Score=147.54  Aligned_cols=151  Identities=23%  Similarity=0.165  Sum_probs=107.1

Q ss_pred             hHHHHHHHHHHHhhcccc----CCCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH
Q psy12977         17 VISIIVTTLAVVSNSIFK----HFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE   92 (226)
Q Consensus        17 ~~~~~~~~l~~~~~~~~~----~~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~   92 (226)
                      +..+.|+..+.+++..+.    .+.++|....+.+. +..++.++||+|||++|.+|++.....    +..++|++|+++
T Consensus        48 ld~~l~eafA~vrEa~~R~lglrpydVQlig~l~l~-~G~Iaem~TGeGKTLta~Lpa~l~aL~----g~~V~VVTpn~y  122 (762)
T TIGR03714        48 LDDILPEAYAVVREADKRVLGMFPYDVQVLGAIVLH-QGNIAEMKTGEGKTLTATMPLYLNALT----GKGAMLVTTNDY  122 (762)
T ss_pred             hHHHHHHHHHHHHHHHHhhcCCCccHHHHHHHHHhc-CCceeEecCCcchHHHHHHHHHHHhhc----CCceEEeCCCHH
Confidence            345566777777766655    34445544443322 336999999999999999998765543    457999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCeEEEEecchhh--hhhhCCCcCCCCCEEEECchHH-HHhHhc----CCCCCCCCCccEEEEc
Q psy12977         93 LAKQTYNETVRLSEGLGLRAHVIGKIQQA--AEKFGPRSAQKFDVLITTPNKL-VYLLQM----DPPALNLANVEWLIVD  165 (226)
Q Consensus        93 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~IiV~Tp~~l-~~~~~~----~~~~~~~~~~~~lViD  165 (226)
                      ||.|..+++..+.+.+|.++....++...  .....+...++++|+++||+.+ .+++..    ......+..+.++|+|
T Consensus       123 LA~Rdae~m~~l~~~LGLsv~~~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVD  202 (762)
T TIGR03714       123 LAKRDAEEMGPVYEWLGLTVSLGVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVD  202 (762)
T ss_pred             HHHHHHHHHHHHHhhcCCcEEEEECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEe
Confidence            99999999999999999998876554111  1111122346799999999999 444432    1233457789999999


Q ss_pred             ccccccc
Q psy12977        166 ESDKLFE  172 (226)
Q Consensus       166 E~h~l~~  172 (226)
                      |||.++-
T Consensus       203 EaDsILi  209 (762)
T TIGR03714       203 EVDSVLL  209 (762)
T ss_pred             cHhhHhh
Confidence            9998853

Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.71  E-value=7.3e-17  Score=144.91  Aligned_cols=146  Identities=21%  Similarity=0.143  Sum_probs=111.6

Q ss_pred             HHHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH
Q psy12977         18 ISIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE   92 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~   92 (226)
                      ..+.++-.+.+++..+.    .++++|.... .+..|+  +..++||+|||+++.+|++.....    +.++.+++||++
T Consensus        35 ~~~l~eafA~vrEa~~R~lg~~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~----G~~V~VvTpt~~  108 (745)
T TIGR00963        35 DDLLPEAFAVVREASKRVLGMRPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALT----GKGVHVVTVNDY  108 (745)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHh----CCCEEEEcCCHH
Confidence            44556666666655554    5677786665 444444  999999999999999998543332    447999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHH-HHhHhcCC----CCCCCCCccEEEEccc
Q psy12977         93 LAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKL-VYLLQMDP----PALNLANVEWLIVDES  167 (226)
Q Consensus        93 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l-~~~~~~~~----~~~~~~~~~~lViDE~  167 (226)
                      ||.|.++++..+.+.+++++..+.++.....+.   ....++|+++||+.+ +++++...    ....+..+.++|+||+
T Consensus       109 LA~qdae~~~~l~~~LGLsv~~i~g~~~~~~r~---~~y~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEa  185 (745)
T TIGR00963       109 LAQRDAEWMGQVYRFLGLSVGLILSGMSPEERR---EAYACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEV  185 (745)
T ss_pred             HHHHHHHHHHHHhccCCCeEEEEeCCCCHHHHH---HhcCCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecH
Confidence            999999999999999999999888775544332   334689999999999 77776521    1356889999999999


Q ss_pred             ccccc
Q psy12977        168 DKLFE  172 (226)
Q Consensus       168 h~l~~  172 (226)
                      |.++-
T Consensus       186 Ds~LI  190 (745)
T TIGR00963       186 DSILI  190 (745)
T ss_pred             HHHhH
Confidence            98864

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.

>TIGR00595 priA primosomal protein N'

Probab=99.70  E-value=3.5e-16  Score=137.87  Aligned_cols=141  Identities=24%  Similarity=0.176  Sum_probs=98.6

Q ss_pred             EEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhh---hCCCc
Q psy12977         53 FACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEK---FGPRS  129 (226)
Q Consensus        53 li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~  129 (226)
                      ++.||||+|||.+|+..+...+..    +.+++|++|+++|+.|+.+.+++.+   +..+..+.++....++   .....
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~----g~~vLvlvP~i~L~~Q~~~~l~~~f---~~~v~vlhs~~~~~er~~~~~~~~   73 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLAL----GKSVLVLVPEIALTPQMIQRFKYRF---GSQVAVLHSGLSDSEKLQAWRKVK   73 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHc----CCeEEEEeCcHHHHHHHHHHHHHHh---CCcEEEEECCCCHHHHHHHHHHHH
Confidence            478999999999997766555543    5589999999999999999998765   4556556554433222   22223


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc---chHHHHHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR---GFRDQLAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~---~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                      .+.++|+|+|+..+.         .++.+++++|+||.|.......+   .....+.......  .+.+++++|||++.+
T Consensus        74 ~g~~~IVVGTrsalf---------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra~~--~~~~vil~SATPsle  142 (505)
T TIGR00595        74 NGEILVVIGTRSALF---------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKK--FNCPVVLGSATPSLE  142 (505)
T ss_pred             cCCCCEEECChHHHc---------CcccCCCEEEEECCCccccccccCCCCcHHHHHHHHHHh--cCCCEEEEeCCCCHH
Confidence            456899999998663         34778999999999987643211   1233444444443  688999999997765


Q ss_pred             HHHHH
Q psy12977        207 VAKWC  211 (226)
Q Consensus       207 ~~~~~  211 (226)
                      ....+
T Consensus       143 s~~~~  147 (505)
T TIGR00595       143 SYHNA  147 (505)
T ss_pred             HHHHH
Confidence            54444

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).

>KOG0951|consensus

Probab=99.70  E-value=5.8e-17  Score=148.79  Aligned_cols=176  Identities=20%  Similarity=0.250  Sum_probs=129.5

Q ss_pred             cccCCCCcccccc--cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCC-------CCceEEEEcccHHHHHHHHHHHH
Q psy12977         32 IFKHFEPHFTITY--LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKN-------LGFRAVIVCPTRELAKQTYNETV  102 (226)
Q Consensus        32 ~~~~~~~~Q~~~~--~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~-------~~~~~iil~Pt~~L~~q~~~~~~  102 (226)
                      +.+.++.+|+...  .+-...|++++||||+|||-.+++.+++.+..+..       ...+++|++|.++|+..+...+.
T Consensus       306 g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~VgsfS  385 (1674)
T KOG0951|consen  306 GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSFS  385 (1674)
T ss_pred             cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHHH
Confidence            4456888886554  44455789999999999999999999999865433       24589999999999999999999


Q ss_pred             HHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHH
Q psy12977        103 RLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQL  182 (226)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i  182 (226)
                      +....+|+++....|+......    -....+|+||||++.--.-+..+..--.+-++++|+||.|.+-|..+.....-+
T Consensus       386 kRla~~GI~V~ElTgD~~l~~~----qieeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLLhDdRGpvLESIV  461 (1674)
T KOG0951|consen  386 KRLAPLGITVLELTGDSQLGKE----QIEETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLLHDDRGPVLESIV  461 (1674)
T ss_pred             hhccccCcEEEEecccccchhh----hhhcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhcccccchHHHHHH
Confidence            9999999999988887542222    235678999999997555444333333556899999999987666433333344


Q ss_pred             HHHHHhc--CCCCceEEEEeeeCch--hHHHHH
Q psy12977        183 AVIYAAC--SGPNLKRGMFSATHTE--DVAKWC  211 (226)
Q Consensus       183 ~~i~~~~--~~~~~q~v~~SAT~~~--~~~~~~  211 (226)
                      .+..+..  ....+.++++|||+|.  ++..|+
T Consensus       462 aRt~r~ses~~e~~RlVGLSATLPNy~DV~~Fl  494 (1674)
T KOG0951|consen  462 ARTFRRSESTEEGSRLVGLSATLPNYEDVASFL  494 (1674)
T ss_pred             HHHHHHhhhcccCceeeeecccCCchhhhHHHh
Confidence            4444333  2357899999999994  555554

>PRK09694 helicase Cas3; Provisional

Probab=99.69  E-value=2.6e-16  Score=145.19  Aligned_cols=171  Identities=17%  Similarity=0.049  Sum_probs=111.1

Q ss_pred             CCCCcccccccC-CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcC--CCe
Q psy12977         35 HFEPHFTITYLS-PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL--GLR  111 (226)
Q Consensus        35 ~~~~~Q~~~~~~-~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~--~~~  111 (226)
                      .++|.|+..... .....+++.+|||+|||.+++..+......  ....+++|.+||+++++|+++.+.++.+..  ...
T Consensus       286 ~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~--~~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~~  363 (878)
T PRK09694        286 QPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQ--GLADSIIFALPTQATANAMLSRLEALASKLFPSPN  363 (878)
T ss_pred             CChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHh--CCCCeEEEECcHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            678888766422 345678999999999999987765544432  224589999999999999999988754322  234


Q ss_pred             EEEEecchhhhhhh--------------------------CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC----CccE
Q psy12977        112 AHVIGKIQQAAEKF--------------------------GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA----NVEW  161 (226)
Q Consensus       112 ~~~~~~~~~~~~~~--------------------------~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~----~~~~  161 (226)
                      +....+.......+                          .+...--++|+|||..+++...... +...+.    .-++
T Consensus       364 v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~-kh~~lR~~~La~sv  442 (878)
T PRK09694        364 LILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPV-KHRFIRGFGLGRSV  442 (878)
T ss_pred             eEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHcc-chHHHHHHhhccCe
Confidence            44444433211100                          0011122799999999998654331 111111    2359


Q ss_pred             EEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHH
Q psy12977        162 LIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCR  212 (226)
Q Consensus       162 lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~  212 (226)
                      ||+||+|..-.    .....+...++.+......+++||||+|+...+.+.
T Consensus       443 vIiDEVHAyD~----ym~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~L~  489 (878)
T PRK09694        443 LIVDEVHAYDA----YMYGLLEAVLKAQAQAGGSVILLSATLPATLKQKLL  489 (878)
T ss_pred             EEEechhhCCH----HHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHH
Confidence            99999997632    244456666666655678899999999988765443

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.68  E-value=1.7e-16  Score=144.33  Aligned_cols=145  Identities=23%  Similarity=0.201  Sum_probs=110.7

Q ss_pred             HHHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH
Q psy12977         18 ISIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE   92 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~   92 (226)
                      ..+.++..+.+++..+.    .++++|.... .+..|+  +..+.||+|||+++.+|++.....    |.++.+++||++
T Consensus        57 ~~~~~eafA~vrea~~R~~g~~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~----G~~v~VvTpt~~  130 (790)
T PRK09200         57 DDILPEAFAVVREAAKRVLGMRPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALE----GKGVHLITVNDY  130 (790)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHc----CCCeEEEeCCHH
Confidence            44566777777765554    6667776554 444555  999999999999999998855443    668999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCeEEEEecchh-hhhhhCCCcCCCCCEEEECchHH-HHhHhc----CCCCCCCCCccEEEEcc
Q psy12977         93 LAKQTYNETVRLSEGLGLRAHVIGKIQQ-AAEKFGPRSAQKFDVLITTPNKL-VYLLQM----DPPALNLANVEWLIVDE  166 (226)
Q Consensus        93 L~~q~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~IiV~Tp~~l-~~~~~~----~~~~~~~~~~~~lViDE  166 (226)
                      ||.|.++.+..+.+.+++++..+.++.. ...+.   ...++||+++||+.+ .+++..    .........++++|+||
T Consensus       131 LA~qd~e~~~~l~~~lGl~v~~i~g~~~~~~~r~---~~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDE  207 (790)
T PRK09200        131 LAKRDAEEMGQVYEFLGLTVGLNFSDIDDASEKK---AIYEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDE  207 (790)
T ss_pred             HHHHHHHHHHHHHhhcCCeEEEEeCCCCcHHHHH---HhcCCCEEEECCccccchhHHhccccchhhhcccccceEEEec
Confidence            9999999999999999999998887765 33332   346799999999999 444432    11223567899999999


Q ss_pred             ccccc
Q psy12977        167 SDKLF  171 (226)
Q Consensus       167 ~h~l~  171 (226)
                      +|.++
T Consensus       208 aDsiL  212 (790)
T PRK09200        208 IDSIL  212 (790)
T ss_pred             cccce
Confidence            99875

>KOG0349|consensus

Probab=99.68  E-value=1.1e-16  Score=133.57  Aligned_cols=139  Identities=22%  Similarity=0.260  Sum_probs=110.2

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCC---CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLG---LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      .++++|+-|+++|++|+.+.++++..+..   .+.....++...... -..+..+.+|+|+||+++.+.+..  +.+.+.
T Consensus       286 ap~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q-~~ql~~g~~ivvGtpgRl~~~is~--g~~~lt  362 (725)
T KOG0349|consen  286 APEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQ-CKQLKDGTHIVVGTPGRLLQPISK--GLVTLT  362 (725)
T ss_pred             CcceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHH-HHHhhcCceeeecCchhhhhhhhc--cceeee
Confidence            36899999999999999998888865542   232233333222222 233567899999999999999998  888899


Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCC-----CCceEEEEeeeCc-hhHHHHHHHhcCCCeEEecCC
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSG-----PNLKRGMFSATHT-EDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~-----~~~q~v~~SAT~~-~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      .++++|+||+|.++..   ++.+.|.++..+++.     .+.|.+++|||+. =+++...++.|+.|+.+.+++
T Consensus       363 ~crFlvlDead~lL~q---gy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkg  433 (725)
T KOG0349|consen  363 HCRFLVLDEADLLLGQ---GYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKG  433 (725)
T ss_pred             eeEEEEecchhhhhhc---ccHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEeccc
Confidence            9999999999999998   688888888887742     4689999999987 477888889999999998764

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.68  E-value=7.7e-16  Score=145.41  Aligned_cols=156  Identities=24%  Similarity=0.254  Sum_probs=100.3

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHH-HHHHhcCCCCCCceEEEEcc----cHHHHHHHHHHHHH-HhhcCCCeEEEEecc
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIP-IIHSLRGPKNLGFRAVIVCP----TRELAKQTYNETVR-LSEGLGLRAHVIGKI  118 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~-~~~~~~~~~~~~~~~iil~P----t~~L~~q~~~~~~~-~~~~~~~~~~~~~~~  118 (226)
                      .+.++..++++|+||||||..  +| ++.....  .....+++..|    ++++|.|+.+++.. ++...|..+      
T Consensus        85 ai~~~~VviI~GeTGSGKTTq--lPq~lle~g~--g~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VGY~v------  154 (1294)
T PRK11131         85 AIRDHQVVIVAGETGSGKTTQ--LPKICLELGR--GVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYKV------  154 (1294)
T ss_pred             HHHhCCeEEEECCCCCCHHHH--HHHHHHHcCC--CCCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceeceee------
Confidence            444566788999999999984  66 3332221  11123444456    56888888887754 333223221      


Q ss_pred             hhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccc-cccccCccchHH-HHHHHHHhcCCCCceE
Q psy12977        119 QQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD-KLFEAGVRGFRD-QLAVIYAACSGPNLKR  196 (226)
Q Consensus       119 ~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h-~l~~~~~~~~~~-~i~~i~~~~~~~~~q~  196 (226)
                           .+......+++|+++||+.+.+.+..+   ..+++++++|+|||| ++++.   ++.. .++.++..  .+..|+
T Consensus       155 -----rf~~~~s~~t~I~v~TpG~LL~~l~~d---~~Ls~~~~IIIDEAHERsLn~---DfLLg~Lk~lL~~--rpdlKv  221 (1294)
T PRK11131        155 -----RFNDQVSDNTMVKLMTDGILLAEIQQD---RLLMQYDTIIIDEAHERSLNI---DFILGYLKELLPR--RPDLKV  221 (1294)
T ss_pred             -----cCccccCCCCCEEEEChHHHHHHHhcC---CccccCcEEEecCcccccccc---chHHHHHHHhhhc--CCCceE
Confidence                 222233467899999999999998863   338999999999999 57776   4543 34444332  256899


Q ss_pred             EEEeeeCchhHHHHHHHhcCCCeEEecCCC
Q psy12977        197 GMFSATHTEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       197 v~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      ++||||++.  +.+.+.+.+.| .+++.+|
T Consensus       222 ILmSATid~--e~fs~~F~~ap-vI~V~Gr  248 (1294)
T PRK11131        222 IITSATIDP--ERFSRHFNNAP-IIEVSGR  248 (1294)
T ss_pred             EEeeCCCCH--HHHHHHcCCCC-EEEEcCc
Confidence            999999975  35554444445 5777654

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.68  E-value=3.3e-16  Score=139.77  Aligned_cols=146  Identities=24%  Similarity=0.242  Sum_probs=111.8

Q ss_pred             hHHHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         17 VISIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        17 ~~~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      ...+.++-.+.+++..+.    .++++|.... .++.|+  +..+.||+|||+++.+|++.....    +++++|++||+
T Consensus        81 ~~~~l~eafA~~rEa~~R~lg~~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~----G~~v~VvTptr  154 (656)
T PRK12898         81 RDALLAEAFALVREASGRVLGQRHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALA----GLPVHVITVND  154 (656)
T ss_pred             hHHHHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhc----CCeEEEEcCcH
Confidence            345566666666665554    6778996664 667777  999999999999999999987653    67999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHH-HhHhcC--------------------
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLV-YLLQMD--------------------  150 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~-~~~~~~--------------------  150 (226)
                      +||.|.++.+..+.+.+++++.++.++.....   +....++||+++|...+- +++...                    
T Consensus       155 eLA~qdae~~~~l~~~lGlsv~~i~gg~~~~~---r~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~  231 (656)
T PRK12898        155 YLAERDAELMRPLYEALGLTVGCVVEDQSPDE---RRAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGR  231 (656)
T ss_pred             HHHHHHHHHHHHHHhhcCCEEEEEeCCCCHHH---HHHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccc
Confidence            99999999999999999999998888754332   234578999999999884 343221                    


Q ss_pred             ---CCCCCCCCccEEEEccccccc
Q psy12977        151 ---PPALNLANVEWLIVDESDKLF  171 (226)
Q Consensus       151 ---~~~~~~~~~~~lViDE~h~l~  171 (226)
                         ........+.+.|+||+|.++
T Consensus       232 ~~~~~~~v~r~~~~aIvDEvDSiL  255 (656)
T PRK12898        232 SSRSTQLLLRGLHFAIVDEADSVL  255 (656)
T ss_pred             cCchhhhcccccceeEeeccccee
Confidence               011224567899999999775

>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=99.67  E-value=2.6e-16  Score=120.85  Aligned_cols=141  Identities=23%  Similarity=0.171  Sum_probs=90.2

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEE----------ecc
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVI----------GKI  118 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~----------~~~  118 (226)
                      +++.++.+|||+|||..++..+.....       ++++++|+..|++|+.+.+..+...........          ...
T Consensus        25 ~~~~ll~~~tGsGKT~~~~~~~~~l~~-------~~l~~~p~~~l~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (184)
T PF04851_consen   25 ERRVLLNAPTGSGKTIIALALILELAR-------KVLIVAPNISLLEQWYDEFDDFGSEKYNFFEKSIKPAYDSKEFISI   97 (184)
T ss_dssp             CSEEEEEESTTSSHHHHHHHHHHHHHC-------EEEEEESSHHHHHHHHHHHHHHSTTSEEEEE--GGGCCE-SEEETT
T ss_pred             CCCEEEEECCCCCcChhhhhhhhcccc-------ceeEecCHHHHHHHHHHHHHHhhhhhhhhccccccccccccccccc
Confidence            588999999999999988755554443       899999999999999999966654321111100          000


Q ss_pred             hhhhhhhCCCcCCCCCEEEECchHHHHhHhcCC---------CCCCCCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        119 QQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDP---------PALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       119 ~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~---------~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      ...............+++++|.+.+........         ........+++|+||||+..+.   .-   ...++.  
T Consensus        98 ~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEaH~~~~~---~~---~~~i~~--  169 (184)
T PF04851_consen   98 QDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEAHHYPSD---SS---YREIIE--  169 (184)
T ss_dssp             TTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETGGCTHHH---HH---HHHHHH--
T ss_pred             ccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehhhhcCCH---HH---HHHHHc--
Confidence            000011011224567899999999998765411         1123456789999999998765   21   333333  


Q ss_pred             CCCCceEEEEeeeCch
Q psy12977        190 SGPNLKRGMFSATHTE  205 (226)
Q Consensus       190 ~~~~~q~v~~SAT~~~  205 (226)
                       .+...+++||||+++
T Consensus       170 -~~~~~~l~lTATp~r  184 (184)
T PF04851_consen  170 -FKAAFILGLTATPFR  184 (184)
T ss_dssp             -SSCCEEEEEESS-S-
T ss_pred             -CCCCeEEEEEeCccC
Confidence             367789999999863

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 ....

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.66  E-value=6.3e-16  Score=140.89  Aligned_cols=144  Identities=26%  Similarity=0.231  Sum_probs=109.0

Q ss_pred             HHHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH
Q psy12977         18 ISIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE   92 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~   92 (226)
                      ..+.|.-.+.+++....    .+..+|-... .+..|+  +..++||+|||+++.+|++.....    +..+.|++||++
T Consensus        61 d~~l~eafA~vrEa~~R~lg~~~ydvQliGg~~Lh~G~--Iaem~TGeGKTL~a~Lpa~~~al~----G~~V~VvTpn~y  134 (896)
T PRK13104         61 DELLAEAFATVREVSLRTLGLRHFDVQLIGGMVLHEGN--IAEMRTGEGKTLVATLPAYLNAIS----GRGVHIVTVNDY  134 (896)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCcchHHHhhhhhhccCc--cccccCCCCchHHHHHHHHHHHhc----CCCEEEEcCCHH
Confidence            44556666666665555    3444565444 333344  789999999999999999976643    346999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHH-HHhHhcCCCCCCC-----CCccEEEEcc
Q psy12977         93 LAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKL-VYLLQMDPPALNL-----ANVEWLIVDE  166 (226)
Q Consensus        93 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l-~~~~~~~~~~~~~-----~~~~~lViDE  166 (226)
                      ||.|.++++..+.+.++.++.++.++.....+.   ....+||+++||+.+ +++++.. -..++     ..+.++|+||
T Consensus       135 LA~qd~e~m~~l~~~lGLtv~~i~gg~~~~~r~---~~y~~dIvygT~grlgfDyLrd~-~~~~~~~~v~r~l~~~IvDE  210 (896)
T PRK13104        135 LAKRDSQWMKPIYEFLGLTVGVIYPDMSHKEKQ---EAYKADIVYGTNNEYGFDYLRDN-MAFSLTDKVQRELNFAIVDE  210 (896)
T ss_pred             HHHHHHHHHHHHhcccCceEEEEeCCCCHHHHH---HHhCCCEEEECChhhhHHHHhcC-CccchHhhhccccceEEecc
Confidence            999999999999999999999888775544432   335789999999999 8888752 12333     5899999999


Q ss_pred             ccccc
Q psy12977        167 SDKLF  171 (226)
Q Consensus       167 ~h~l~  171 (226)
                      +|.++
T Consensus       211 aDsiL  215 (896)
T PRK13104        211 VDSIL  215 (896)
T ss_pred             Hhhhh
Confidence            99875

>KOG0947|consensus

Probab=99.62  E-value=1.8e-15  Score=136.11  Aligned_cols=165  Identities=19%  Similarity=0.216  Sum_probs=126.0

Q ss_pred             CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEE
Q psy12977         35 HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAH  113 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~  113 (226)
                      ++.+.|+++. .+..|..+.+.|+|.+|||..+.+++...-.    .+.|+||.+|-++|.+|-++.+++-+.+.|    
T Consensus       297 elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~----h~TR~iYTSPIKALSNQKfRDFk~tF~Dvg----  368 (1248)
T KOG0947|consen  297 ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQK----HMTRTIYTSPIKALSNQKFRDFKETFGDVG----  368 (1248)
T ss_pred             CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHh----hccceEecchhhhhccchHHHHHHhccccc----
Confidence            3445687774 7888999999999999999987666544332    245899999999999999999999887766    


Q ss_pred             EEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCC
Q psy12977        114 VIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPN  193 (226)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~  193 (226)
                      .+.|+..        +...+.++|.|.+.|.+++.+  +.--..+++++|+||+|-+.|..   -.-.+.+++-.+ +..
T Consensus       369 LlTGDvq--------inPeAsCLIMTTEILRsMLYr--gadliRDvE~VIFDEVHYiND~e---RGvVWEEViIMl-P~H  434 (1248)
T KOG0947|consen  369 LLTGDVQ--------INPEASCLIMTTEILRSMLYR--GADLIRDVEFVIFDEVHYINDVE---RGVVWEEVIIML-PRH  434 (1248)
T ss_pred             eeeccee--------eCCCcceEeehHHHHHHHHhc--ccchhhccceEEEeeeeeccccc---ccccceeeeeec-ccc
Confidence            4444421        334567999999999999988  56667889999999999988763   333444555455 678


Q ss_pred             ceEEEEeeeCch--hHHHHHHHhcCCCeEE
Q psy12977        194 LKRGMFSATHTE--DVAKWCRRKLKRRVQI  221 (226)
Q Consensus       194 ~q~v~~SAT~~~--~~~~~~~~~~~~p~~i  221 (226)
                      .+++++|||.|.  +..+|+.+.-+..+++
T Consensus       435 V~~IlLSATVPN~~EFA~WIGRtK~K~IyV  464 (1248)
T KOG0947|consen  435 VNFILLSATVPNTLEFADWIGRTKQKTIYV  464 (1248)
T ss_pred             ceEEEEeccCCChHHHHHHhhhccCceEEE
Confidence            999999999884  6688888876555444

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.58  E-value=4.8e-14  Score=133.72  Aligned_cols=177  Identities=20%  Similarity=0.153  Sum_probs=110.2

Q ss_pred             hccccCCCCccccc----ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         30 NSIFKHFEPHFTIT----YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        30 ~~~~~~~~~~Q~~~----~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      ...|..-.|+....    ..+.++..++++|+||||||..  +|.+-.-. ......++++..|.|--|..+++.+.+- 
T Consensus        59 ~~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTTq--lPq~lle~-~~~~~~~I~~tQPRRlAA~svA~RvA~e-  134 (1283)
T TIGR01967        59 EIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQ--LPKICLEL-GRGSHGLIGHTQPRRLAARTVAQRIAEE-  134 (1283)
T ss_pred             cccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHHH--HHHHHHHc-CCCCCceEecCCccHHHHHHHHHHHHHH-
Confidence            34455556665332    2444567789999999999984  45332211 1122235666778777666665543332 


Q ss_pred             hcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccc-cccccCccchHHH-HH
Q psy12977        106 EGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD-KLFEAGVRGFRDQ-LA  183 (226)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h-~l~~~~~~~~~~~-i~  183 (226)
                        .+..+....|+.   ..+......++.|.++|++.|.+.+..++   .+++++++|+||+| +.++.   ++... ++
T Consensus       135 --lg~~lG~~VGY~---vR~~~~~s~~T~I~~~TdGiLLr~l~~d~---~L~~~~~IIIDEaHERsL~~---D~LL~lLk  203 (1283)
T TIGR01967       135 --LGTPLGEKVGYK---VRFHDQVSSNTLVKLMTDGILLAETQQDR---FLSRYDTIIIDEAHERSLNI---DFLLGYLK  203 (1283)
T ss_pred             --hCCCcceEEeeE---EcCCcccCCCceeeeccccHHHHHhhhCc---ccccCcEEEEcCcchhhccc---hhHHHHHH
Confidence              233333333332   22223345678899999999999987643   48899999999999 57776   45543 55


Q ss_pred             HHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCCC
Q psy12977        184 VIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       184 ~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      .++...  +..|+++||||++.  ..+. +++.+.-.+++.+|
T Consensus       204 ~il~~r--pdLKlIlmSATld~--~~fa-~~F~~apvI~V~Gr  241 (1283)
T TIGR01967       204 QLLPRR--PDLKIIITSATIDP--ERFS-RHFNNAPIIEVSGR  241 (1283)
T ss_pred             HHHhhC--CCCeEEEEeCCcCH--HHHH-HHhcCCCEEEECCC
Confidence            565443  67899999999974  3444 44544445666654

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.

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

Probab=99.57  E-value=1.1e-14  Score=126.69  Aligned_cols=146  Identities=21%  Similarity=0.194  Sum_probs=93.8

Q ss_pred             CCCCcccccc--cCCC---CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCC
Q psy12977         35 HFEPHFTITY--LSPL---GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG  109 (226)
Q Consensus        35 ~~~~~Q~~~~--~~~~---~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~  109 (226)
                      .+.+.|.++.  +...   ++..++++|||+|||..++..+.....       +++|++|+++|+.|+.+.+....... 
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~~-------~~Lvlv~~~~L~~Qw~~~~~~~~~~~-  107 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKR-------STLVLVPTKELLDQWAEALKKFLLLN-  107 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhcC-------CEEEEECcHHHHHHHHHHHHHhcCCc-
Confidence            4667776663  2222   788999999999999987665544322       39999999999999987776665432 


Q ss_pred             CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      ......+++.....       . ..|.|+|-+.+...-..  ........+++|+||||++.+.   .+.. +.......
T Consensus       108 ~~~g~~~~~~~~~~-------~-~~i~vat~qtl~~~~~l--~~~~~~~~~liI~DE~Hh~~a~---~~~~-~~~~~~~~  173 (442)
T COG1061         108 DEIGIYGGGEKELE-------P-AKVTVATVQTLARRQLL--DEFLGNEFGLIIFDEVHHLPAP---SYRR-ILELLSAA  173 (442)
T ss_pred             cccceecCceeccC-------C-CcEEEEEhHHHhhhhhh--hhhcccccCEEEEEccccCCcH---HHHH-HHHhhhcc
Confidence            22333333321100       1 46999999988774211  1222337899999999999876   2322 22222211


Q ss_pred             CCCCceEEEEeeeCchh
Q psy12977        190 SGPNLKRGMFSATHTED  206 (226)
Q Consensus       190 ~~~~~q~v~~SAT~~~~  206 (226)
                          ..++++|||++..
T Consensus       174 ----~~~LGLTATp~R~  186 (442)
T COG1061         174 ----YPRLGLTATPERE  186 (442)
T ss_pred             ----cceeeeccCceee
Confidence                1289999998843

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.56  E-value=2.7e-14  Score=129.03  Aligned_cols=149  Identities=13%  Similarity=0.054  Sum_probs=96.8

Q ss_pred             CCCCcccccc--cCCCC--CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCC
Q psy12977         35 HFEPHFTITY--LSPLG--RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGL  110 (226)
Q Consensus        35 ~~~~~Q~~~~--~~~~~--~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~  110 (226)
                      .+.|.|..+.  ++.++  +.-++++|||+|||+..+..+.. +      +.++||+||+..|++||.+.+.++......
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~-l------~k~tLILvps~~Lv~QW~~ef~~~~~l~~~  327 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACT-V------KKSCLVLCTSAVSVEQWKQQFKMWSTIDDS  327 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHH-h------CCCEEEEeCcHHHHHHHHHHHHHhcCCCCc
Confidence            3455665542  33334  46799999999999987655443 2      236999999999999999999988654444


Q ss_pred             eEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCC------CCCCCCCccEEEEcccccccccCccchHHHHHH
Q psy12977        111 RAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDP------PALNLANVEWLIVDESDKLFEAGVRGFRDQLAV  184 (226)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~------~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~  184 (226)
                      .+....++...      ......+|+|+|.+.+.....+..      ..+.-..++++|+||||++.+.       ...+
T Consensus       328 ~I~~~tg~~k~------~~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA~-------~fr~  394 (732)
T TIGR00603       328 QICRFTSDAKE------RFHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAA-------MFRR  394 (732)
T ss_pred             eEEEEecCccc------ccccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccHH-------HHHH
Confidence            55544443211      112346899999987754322210      1122346789999999998654       2333


Q ss_pred             HHHhcCCCCceEEEEeeeCch
Q psy12977        185 IYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       185 i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      ++..+  .....+++|||+..
T Consensus       395 il~~l--~a~~RLGLTATP~R  413 (732)
T TIGR00603       395 VLTIV--QAHCKLGLTATLVR  413 (732)
T ss_pred             HHHhc--CcCcEEEEeecCcc
Confidence            44444  34467899999874

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).

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

Probab=99.55  E-value=2e-14  Score=104.51  Aligned_cols=141  Identities=18%  Similarity=0.173  Sum_probs=84.2

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCC
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGP  127 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (226)
                      .|+-.++...||+|||.-.+.-++....+   .+.|++++.|||.+++.+.+.++..    +.++......        .
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~---~~~rvLvL~PTRvva~em~~aL~~~----~~~~~t~~~~--------~   67 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIK---RRLRVLVLAPTRVVAEEMYEALKGL----PVRFHTNARM--------R   67 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHH---TT--EEEEESSHHHHHHHHHHTTTS----SEEEESTTSS---------
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHH---ccCeEEEecccHHHHHHHHHHHhcC----CcccCceeee--------c
Confidence            45567899999999998766555543322   2568999999999999988877543    3322211110        1


Q ss_pred             CcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        128 RSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       128 ~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                      ...++.-|-|.|...+.+++..   .....+++++|+||||. .|.   ........+........+.++++|||+|...
T Consensus        68 ~~~g~~~i~vMc~at~~~~~~~---p~~~~~yd~II~DEcH~-~Dp---~sIA~rg~l~~~~~~g~~~~i~mTATPPG~~  140 (148)
T PF07652_consen   68 THFGSSIIDVMCHATYGHFLLN---PCRLKNYDVIIMDECHF-TDP---TSIAARGYLRELAESGEAKVIFMTATPPGSE  140 (148)
T ss_dssp             ---SSSSEEEEEHHHHHHHHHT---SSCTTS-SEEEECTTT---SH---HHHHHHHHHHHHHHTTS-EEEEEESS-TT--
T ss_pred             cccCCCcccccccHHHHHHhcC---cccccCccEEEEecccc-CCH---HHHhhheeHHHhhhccCeeEEEEeCCCCCCC
Confidence            1235566889999998887765   33367999999999996 443   2333333333333234578999999999766


Q ss_pred             HHH
Q psy12977        208 AKW  210 (226)
Q Consensus       208 ~~~  210 (226)
                      ..|
T Consensus       141 ~~f  143 (148)
T PF07652_consen  141 DEF  143 (148)
T ss_dssp             -SS
T ss_pred             CCC
Confidence            443

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 ....

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.54  E-value=4e-14  Score=128.93  Aligned_cols=145  Identities=25%  Similarity=0.204  Sum_probs=110.3

Q ss_pred             hHHHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHH-HHhcCCCCCCceEEEEccc
Q psy12977         17 VISIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPII-HSLRGPKNLGFRAVIVCPT   90 (226)
Q Consensus        17 ~~~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~-~~~~~~~~~~~~~iil~Pt   90 (226)
                      ...+.++..+.+++....    .+..+|-... .+..|+  +..++||+|||+++.+|++ ..+.     +..+-+++||
T Consensus        59 ld~~l~eafA~vrEa~~R~lg~~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~-----G~~V~IvTpn  131 (830)
T PRK12904         59 LDDLLPEAFAVVREASKRVLGMRHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALT-----GKGVHVVTVN  131 (830)
T ss_pred             hhHHHHHHHHHHHHHHHHHhCCCCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHc-----CCCEEEEecC
Confidence            345667777777766654    4556675554 444444  8999999999999999986 5553     3357799999


Q ss_pred             HHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHH-HHhHhcCCC----CCCCCCccEEEEc
Q psy12977         91 RELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKL-VYLLQMDPP----ALNLANVEWLIVD  165 (226)
Q Consensus        91 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l-~~~~~~~~~----~~~~~~~~~lViD  165 (226)
                      .+||.|.++.+..+.+.+|+++.++.++.....+..   ...+||+++||+.+ +++++....    ......+.++|+|
T Consensus       132 ~yLA~rd~e~~~~l~~~LGlsv~~i~~~~~~~er~~---~y~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvD  208 (830)
T PRK12904        132 DYLAKRDAEWMGPLYEFLGLSVGVILSGMSPEERRE---AYAADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVD  208 (830)
T ss_pred             HHHHHHHHHHHHHHHhhcCCeEEEEcCCCCHHHHHH---hcCCCeEEECCcchhhhhhhcccccchhhhcccccceEEEe
Confidence            999999999999999999999998888765544432   24599999999999 778764211    1346788999999


Q ss_pred             cccccc
Q psy12977        166 ESDKLF  171 (226)
Q Consensus       166 E~h~l~  171 (226)
                      |+|.++
T Consensus       209 EaDsiL  214 (830)
T PRK12904        209 EVDSIL  214 (830)
T ss_pred             chhhhe
Confidence            999875

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

Probab=99.52  E-value=2.3e-13  Score=129.06  Aligned_cols=163  Identities=15%  Similarity=0.119  Sum_probs=100.4

Q ss_pred             CCCcccccc-----cC-CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCC
Q psy12977         36 FEPHFTITY-----LS-PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG  109 (226)
Q Consensus        36 ~~~~Q~~~~-----~~-~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~  109 (226)
                      +.+.|..+.     .+ ...++.++++|||||||...+..+...+..  ....++++++|+++|+.|..+.++.......
T Consensus       414 lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li~~L~~~--~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~~  491 (1123)
T PRK11448        414 LRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALMYRLLKA--KRFRRILFLVDRSALGEQAEDAFKDTKIEGD  491 (1123)
T ss_pred             CCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHHHHHHhc--CccCeEEEEecHHHHHHHHHHHHHhcccccc
Confidence            566775542     11 234679999999999998754443333332  2345999999999999999999888743222


Q ss_pred             CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCC---CCCCCCCccEEEEccccccccc------C---cc-
Q psy12977        110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDP---PALNLANVEWLIVDESDKLFEA------G---VR-  176 (226)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~---~~~~~~~~~~lViDE~h~l~~~------~---~~-  176 (226)
                      .....+.+.......   .......|+|+|.+++.+.+....   ....+..++++|+||||+....      +   ++ 
T Consensus       492 ~~~~~i~~i~~L~~~---~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~~~~~~~~~  568 (1123)
T PRK11448        492 QTFASIYDIKGLEDK---FPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMSEGELQFRD  568 (1123)
T ss_pred             cchhhhhchhhhhhh---cccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccccchhccch
Confidence            111111111100011   123457899999999877643211   2245778899999999986320      0   00 


Q ss_pred             --chHHHHHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        177 --GFRDQLAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       177 --~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                        .+...+..++..+   +...++||||+...
T Consensus       569 ~~~~~~~yr~iL~yF---dA~~IGLTATP~r~  597 (1123)
T PRK11448        569 QLDYVSKYRRVLDYF---DAVKIGLTATPALH  597 (1123)
T ss_pred             hhhHHHHHHHHHhhc---CccEEEEecCCccc
Confidence              1234566666654   35679999998643

>KOG0948|consensus

Probab=99.52  E-value=4.9e-14  Score=124.42  Aligned_cols=165  Identities=21%  Similarity=0.260  Sum_probs=125.3

Q ss_pred             CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEE
Q psy12977         35 HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAH  113 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~  113 (226)
                      ++.|.|+.+. -+..+..++++|.|.+|||..+-+++...++.    +.|+||.+|-++|.+|-++.+..=+++.|.-.+
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~----kQRVIYTSPIKALSNQKYREl~~EF~DVGLMTG  204 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLRE----KQRVIYTSPIKALSNQKYRELLEEFKDVGLMTG  204 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHh----cCeEEeeChhhhhcchhHHHHHHHhcccceeec
Confidence            3455666665 34557899999999999999999998888874    458999999999999999988777766554332


Q ss_pred             EEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCC
Q psy12977        114 VIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPN  193 (226)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~  193 (226)
                      -+.            +..++..+|.|.+.|.+++.+  +.--...+..+|+||+|-|-|..   -.-.|.+.+-.+ +.+
T Consensus       205 DVT------------InP~ASCLVMTTEILRsMLYR--GSEvmrEVaWVIFDEIHYMRDkE---RGVVWEETIIll-P~~  266 (1041)
T KOG0948|consen  205 DVT------------INPDASCLVMTTEILRSMLYR--GSEVMREVAWVIFDEIHYMRDKE---RGVVWEETIILL-PDN  266 (1041)
T ss_pred             cee------------eCCCCceeeeHHHHHHHHHhc--cchHhheeeeEEeeeehhccccc---cceeeeeeEEec-ccc
Confidence            111            234567999999999999988  55567789999999999988763   333344444344 678


Q ss_pred             ceEEEEeeeCch--hHHHHHHHhcCCCeEE
Q psy12977        194 LKRGMFSATHTE--DVAKWCRRKLKRRVQI  221 (226)
Q Consensus       194 ~q~v~~SAT~~~--~~~~~~~~~~~~p~~i  221 (226)
                      .+.+++|||+|.  +..+|+-..-+.|.++
T Consensus       267 vr~VFLSATiPNA~qFAeWI~~ihkQPcHV  296 (1041)
T KOG0948|consen  267 VRFVFLSATIPNARQFAEWICHIHKQPCHV  296 (1041)
T ss_pred             ceEEEEeccCCCHHHHHHHHHHHhcCCceE
Confidence            999999999995  4577887766677655

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.51  E-value=1e-13  Score=126.42  Aligned_cols=147  Identities=20%  Similarity=0.191  Sum_probs=110.5

Q ss_pred             hHHHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         17 VISIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        17 ~~~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      +..+.|.-.+.+++....    .+..+|-... .+..|+  +..++||.|||+++.+|++.....    +..+.|++|+.
T Consensus        60 l~~~l~eafA~vrEaa~R~lgm~~ydVQliGgl~L~~G~--IaEm~TGEGKTL~a~lp~~l~al~----g~~VhIvT~nd  133 (908)
T PRK13107         60 LDDIMAEAFATVREASKRVFEMRHFDVQLLGGMVLDSNR--IAEMRTGEGKTLTATLPAYLNALT----GKGVHVITVND  133 (908)
T ss_pred             hHHHHHHHHHHHHHHHHHHhCCCcCchHHhcchHhcCCc--cccccCCCCchHHHHHHHHHHHhc----CCCEEEEeCCH
Confidence            344556666666665554    4455665554 333444  789999999999999999876653    44599999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHH-HHhHhcCCCCCC-----CCCccEEEEc
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKL-VYLLQMDPPALN-----LANVEWLIVD  165 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l-~~~~~~~~~~~~-----~~~~~~lViD  165 (226)
                      +||.|..+++..+.+.+|.++.++.++.....+   ....++||+++||+.+ +++++.. -...     ...+.+.|+|
T Consensus       134 yLA~RD~e~m~~l~~~lGlsv~~i~~~~~~~~r---~~~Y~~dI~YgT~~e~gfDyLrdn-m~~~~~~~vqr~~~~aIvD  209 (908)
T PRK13107        134 YLARRDAENNRPLFEFLGLTVGINVAGLGQQEK---KAAYNADITYGTNNEFGFDYLRDN-MAFSPQERVQRPLHYALID  209 (908)
T ss_pred             HHHHHHHHHHHHHHHhcCCeEEEecCCCCHHHH---HhcCCCCeEEeCCCcccchhhhcc-Cccchhhhhccccceeeec
Confidence            999999999999999999999988776554332   3457899999999999 7777642 1222     3778999999


Q ss_pred             cccccccc
Q psy12977        166 ESDKLFEA  173 (226)
Q Consensus       166 E~h~l~~~  173 (226)
                      |+|.++-+
T Consensus       210 EvDsiLiD  217 (908)
T PRK13107        210 EVDSILID  217 (908)
T ss_pred             chhhhccc
Confidence            99988643

>KOG0353|consensus

Probab=99.50  E-value=9.2e-14  Score=114.74  Aligned_cols=171  Identities=19%  Similarity=0.261  Sum_probs=126.0

Q ss_pred             hccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcC
Q psy12977         30 NSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL  108 (226)
Q Consensus        30 ~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~  108 (226)
                      .+.++.|.|.|..+. ..+.|+++++..|||.||++||.+|++-.       ...++++||..+|++...-+++++    
T Consensus        89 ~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~a-------dg~alvi~plislmedqil~lkql----  157 (695)
T KOG0353|consen   89 QFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCA-------DGFALVICPLISLMEDQILQLKQL----  157 (695)
T ss_pred             HhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhc-------CCceEeechhHHHHHHHHHHHHHh----
Confidence            466779999997775 77899999999999999999999997542       337899999999999988888887    


Q ss_pred             CCeEEEEecchhhhhhh-----CCCcCCCCCEEEECchHHHH---hHhcCCCCCCCCCccEEEEcccccccccCc--cch
Q psy12977        109 GLRAHVIGKIQQAAEKF-----GPRSAQKFDVLITTPNKLVY---LLQMDPPALNLANVEWLIVDESDKLFEAGV--RGF  178 (226)
Q Consensus       109 ~~~~~~~~~~~~~~~~~-----~~~~~~~~~IiV~Tp~~l~~---~~~~~~~~~~~~~~~~lViDE~h~l~~~~~--~~~  178 (226)
                      |+...+.+.....++..     .........++..||+++..   ++++....+....+.++.+||+|+-..+++  |.-
T Consensus       158 gi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~iaidevhccsqwghdfr~d  237 (695)
T KOG0353|consen  158 GIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHCCSQWGHDFRPD  237 (695)
T ss_pred             CcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEeecceeehhhhCcccCcc
Confidence            55554444433322211     11223456799999999975   444444567788899999999999988863  334


Q ss_pred             HHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHH
Q psy12977        179 RDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRR  213 (226)
Q Consensus       179 ~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~  213 (226)
                      ...+.-+.+++  ++..+++++||-..++.+.++.
T Consensus       238 y~~l~ilkrqf--~~~~iigltatatn~vl~d~k~  270 (695)
T KOG0353|consen  238 YKALGILKRQF--KGAPIIGLTATATNHVLDDAKD  270 (695)
T ss_pred             hHHHHHHHHhC--CCCceeeeehhhhcchhhHHHH
Confidence            44555666676  7889999999977666555443

>KOG0351|consensus

Probab=99.50  E-value=1.8e-14  Score=133.14  Aligned_cols=176  Identities=23%  Similarity=0.302  Sum_probs=126.0

Q ss_pred             HHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         27 VVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        27 ~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      +-..++.+.|.+.|.++. ..++|+|.++.+|||.||++||.+|++-.       +.-+|+|.|..+|++.+...+... 
T Consensus       256 l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~-------~gitvVISPL~SLm~DQv~~L~~~-  327 (941)
T KOG0351|consen  256 LKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL-------GGVTVVISPLISLMQDQVTHLSKK-  327 (941)
T ss_pred             HHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc-------CCceEEeccHHHHHHHHHHhhhhc-
Confidence            344678889999997665 77899999999999999999999997542       337899999999999877766333 


Q ss_pred             hcCCCeEEEEecchhhhhhh---CCCcC--CCCCEEEECchHHHHhHhcCCCCCCCCC---ccEEEEcccccccccCc--
Q psy12977        106 EGLGLRAHVIGKIQQAAEKF---GPRSA--QKFDVLITTPNKLVYLLQMDPPALNLAN---VEWLIVDESDKLFEAGV--  175 (226)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~---~~~~~--~~~~IiV~Tp~~l~~~~~~~~~~~~~~~---~~~lViDE~h~l~~~~~--  175 (226)
                         ++....+.+++...+..   .....  ...+|+..||+++...-........+..   +.++|+||||+...|++  
T Consensus       328 ---~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdF  404 (941)
T KOG0351|consen  328 ---GIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDF  404 (941)
T ss_pred             ---CcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhcccc
Confidence               67777776666553221   11112  3579999999998764322112223334   88999999999999874  


Q ss_pred             cchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhc
Q psy12977        176 RGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKL  215 (226)
Q Consensus       176 ~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~  215 (226)
                      |.....+..+....  +...++++|||-...+.+.+-+.+
T Consensus       405 Rp~Yk~l~~l~~~~--~~vP~iALTATAT~~v~~DIi~~L  442 (941)
T KOG0351|consen  405 RPSYKRLGLLRIRF--PGVPFIALTATATERVREDVIRSL  442 (941)
T ss_pred             cHHHHHHHHHHhhC--CCCCeEEeehhccHHHHHHHHHHh
Confidence            33344444555555  458999999999888876666644

>KOG0352|consensus

Probab=99.49  E-value=7.7e-14  Score=116.58  Aligned_cols=177  Identities=19%  Similarity=0.265  Sum_probs=117.4

Q ss_pred             ccccCC-CCcccccc--cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         31 SIFKHF-EPHFTITY--LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        31 ~~~~~~-~~~Q~~~~--~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      +|+..| ++.|+++.  .....+|+.+++|||+||++||.+|.+-.       +.-+|++.|..+|...+.+.+..+   
T Consensus        15 FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~-------~gITIV~SPLiALIkDQiDHL~~L---   84 (641)
T KOG0352|consen   15 FGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH-------GGITIVISPLIALIKDQIDHLKRL---   84 (641)
T ss_pred             hCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh-------CCeEEEehHHHHHHHHHHHHHHhc---
Confidence            445444 45687764  55667899999999999999999998653       237899999999999998888777   


Q ss_pred             CCCeEEEEecchhhh---hhhCC--CcCCCCCEEEECchHHHHhHhc--CCCCCCCCCccEEEEcccccccccCccchHH
Q psy12977        108 LGLRAHVIGKIQQAA---EKFGP--RSAQKFDVLITTPNKLVYLLQM--DPPALNLANVEWLIVDESDKLFEAGVRGFRD  180 (226)
Q Consensus       108 ~~~~~~~~~~~~~~~---~~~~~--~~~~~~~IiV~Tp~~l~~~~~~--~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~  180 (226)
                       .+.+...++.-+..   +...+  ....+..++.-||+.......+  .+...+=..+.++|+||+|+...|++. |..
T Consensus        85 -KVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQWGHD-FRP  162 (641)
T KOG0352|consen   85 -KVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQWGHD-FRP  162 (641)
T ss_pred             -CCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHhhhccc-cCc
Confidence             33333322221111   11111  2234567999999986542211  002333456789999999999998753 444


Q ss_pred             HHH---HHHHhcCCCCceEEEEeeeCchhHHHHHHH--hcCCCeEE
Q psy12977        181 QLA---VIYAACSGPNLKRGMFSATHTEDVAKWCRR--KLKRRVQI  221 (226)
Q Consensus       181 ~i~---~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~--~~~~p~~i  221 (226)
                      +..   .+...+  +....+.++||-.+++++.+..  -+++||-+
T Consensus       163 DYL~LG~LRS~~--~~vpwvALTATA~~~VqEDi~~qL~L~~PVAi  206 (641)
T KOG0352|consen  163 DYLTLGSLRSVC--PGVPWVALTATANAKVQEDIAFQLKLRNPVAI  206 (641)
T ss_pred             chhhhhhHHhhC--CCCceEEeecccChhHHHHHHHHHhhcCcHHh
Confidence            333   333333  6789999999998888776654  44577654

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

Probab=99.49  E-value=4.9e-13  Score=109.03  Aligned_cols=152  Identities=16%  Similarity=0.158  Sum_probs=108.1

Q ss_pred             CCCCcccccc-----cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCC
Q psy12977         35 HFEPHFTITY-----LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG  109 (226)
Q Consensus        35 ~~~~~Q~~~~-----~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~  109 (226)
                      +++|-|+-+.     .+.+.++.+++|-||+|||... +..++...+   .|.++.+.+|..+.|..++..+++.+.  +
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMi-f~~i~~al~---~G~~vciASPRvDVclEl~~Rlk~aF~--~  170 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMI-FQGIEQALN---QGGRVCIASPRVDVCLELYPRLKQAFS--N  170 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhh-HHHHHHHHh---cCCeEEEecCcccchHHHHHHHHHhhc--c
Confidence            5666663331     3455789999999999999864 444444332   377899999999999999999999887  4


Q ss_pred             CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      ..+...+++..+.-        .++++|+|..+++++.+         .+|++|+||+|.+.-..    ...+....++.
T Consensus       171 ~~I~~Lyg~S~~~f--------r~plvVaTtHQLlrFk~---------aFD~liIDEVDAFP~~~----d~~L~~Av~~a  229 (441)
T COG4098         171 CDIDLLYGDSDSYF--------RAPLVVATTHQLLRFKQ---------AFDLLIIDEVDAFPFSD----DQSLQYAVKKA  229 (441)
T ss_pred             CCeeeEecCCchhc--------cccEEEEehHHHHHHHh---------hccEEEEeccccccccC----CHHHHHHHHHh
Confidence            55555665543322        26799999999988755         57899999999885442    12333334444


Q ss_pred             CCCCceEEEEeeeCchhHHHHHHH
Q psy12977        190 SGPNLKRGMFSATHTEDVAKWCRR  213 (226)
Q Consensus       190 ~~~~~q~v~~SAT~~~~~~~~~~~  213 (226)
                      ..+...++.+|||.+++++.-+..
T Consensus       230 rk~~g~~IylTATp~k~l~r~~~~  253 (441)
T COG4098         230 RKKEGATIYLTATPTKKLERKILK  253 (441)
T ss_pred             hcccCceEEEecCChHHHHHHhhh
Confidence            356778899999999887665543

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

Probab=99.48  E-value=2.3e-13  Score=123.95  Aligned_cols=140  Identities=22%  Similarity=0.168  Sum_probs=88.4

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPR  128 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (226)
                      ++..+++.+||||||...+..+...+.  ....+++++++|+.+|..|+.+.+..+....   .........-...   .
T Consensus       263 ~~~gli~~~TGsGKT~t~~~la~~l~~--~~~~~~vl~lvdR~~L~~Q~~~~f~~~~~~~---~~~~~s~~~L~~~---l  334 (667)
T TIGR00348       263 ERGGLIWHTQGSGKTLTMLFAARKALE--LLKNPKVFFVVDRRELDYQLMKEFQSLQKDC---AERIESIAELKRL---L  334 (667)
T ss_pred             CceeEEEEecCCCccHHHHHHHHHHHh--hcCCCeEEEEECcHHHHHHHHHHHHhhCCCC---CcccCCHHHHHHH---H
Confidence            357899999999999887655544442  2345799999999999999999998885321   1111111100011   1


Q ss_pred             cCCCCCEEEECchHHHHhHhcCCCCCCCCCc-cEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        129 SAQKFDVLITTPNKLVYLLQMDPPALNLANV-EWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       129 ~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~-~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      ......|+|+|.+++...+..........+- .++|+||||+....   .+...+.   +.+  ++...++||||+-
T Consensus       335 ~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~~---~~~~~l~---~~~--p~a~~lGfTaTP~  403 (667)
T TIGR00348       335 EKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQYG---ELAKNLK---KAL--KNASFFGFTGTPI  403 (667)
T ss_pred             hCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccch---HHHHHHH---hhC--CCCcEEEEeCCCc
Confidence            1234689999999998644331111221111 28999999986443   2333332   344  5678999999975

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

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

Probab=99.44  E-value=9.2e-13  Score=116.30  Aligned_cols=137  Identities=20%  Similarity=0.340  Sum_probs=105.2

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhh---hhCC
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAE---KFGP  127 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~  127 (226)
                      +=+++|.-|||||..++++++..+..    |.++...+||.-||+|.++.+.++.+.+++++....|......   ....
T Consensus       285 ~RLlQGDVGSGKTvVA~laml~ai~~----G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~  360 (677)
T COG1200         285 NRLLQGDVGSGKTVVALLAMLAAIEA----GYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQ  360 (677)
T ss_pred             HHHhccCcCCCHHHHHHHHHHHHHHc----CCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHH
Confidence            34899999999999999999999875    7789999999999999999999999999999988876643332   2234


Q ss_pred             CcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCC-CceEEEEeee-Cch
Q psy12977        128 RSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGP-NLKRGMFSAT-HTE  205 (226)
Q Consensus       128 ~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~-~~q~v~~SAT-~~~  205 (226)
                      ...+..+|+|+|+.-+.       ....+.++.++|+||=|++.-.      + -..+..+  .. .+-+++|||| .|+
T Consensus       361 l~~G~~~ivVGTHALiQ-------d~V~F~~LgLVIiDEQHRFGV~------Q-R~~L~~K--G~~~Ph~LvMTATPIPR  424 (677)
T COG1200         361 LASGEIDIVVGTHALIQ-------DKVEFHNLGLVIIDEQHRFGVH------Q-RLALREK--GEQNPHVLVMTATPIPR  424 (677)
T ss_pred             HhCCCCCEEEEcchhhh-------cceeecceeEEEEeccccccHH------H-HHHHHHh--CCCCCcEEEEeCCCchH
Confidence            44667999999987443       4566889999999999987322      2 2222222  23 5788899999 454


Q ss_pred             hH
Q psy12977        206 DV  207 (226)
Q Consensus       206 ~~  207 (226)
                      .+
T Consensus       425 TL  426 (677)
T COG1200         425 TL  426 (677)
T ss_pred             HH
Confidence            43

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

Probab=99.44  E-value=1.2e-12  Score=117.26  Aligned_cols=57  Identities=30%  Similarity=0.337  Sum_probs=49.4

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      .+++.+++.||||+|||++|++|++..+...  .+.+++|++||++|.+|+.+.+..+.
T Consensus        14 ~~~~~lliEA~TGtGKTlAYLlpal~~~~~~--~~~rvlIstpT~~Lq~Ql~~~l~~l~   70 (636)
T TIGR03117        14 RQKRIGMLEASTGVGKTLAMIMAALTMLKER--PDQKIAIAVPTLALMGQLWSELERLT   70 (636)
T ss_pred             hcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc--cCceEEEECCcHHHHHHHHHHHHHHH
Confidence            4678899999999999999999998876522  24699999999999999999888887

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.

>KOG0949|consensus

Probab=99.42  E-value=1.1e-12  Score=118.85  Aligned_cols=193  Identities=19%  Similarity=0.147  Sum_probs=124.3

Q ss_pred             echhhhhhhHHHHHHHHHHHh----hccccCCCC--cc-cccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCC
Q psy12977          9 LGIFTIGFVISIIVTTLAVVS----NSIFKHFEP--HF-TITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLG   81 (226)
Q Consensus         9 ~~~~~~~~~~~~~~~~l~~~~----~~~~~~~~~--~Q-~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~   81 (226)
                      +|++++-|++-..-+-+...-    +--++.+-|  -| +.....-.+..+++.|||.+|||+.--+.+=..++..  ..
T Consensus       479 ~g~~~~~fQLqy~Ge~l~rsv~~~kD~RV~dF~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~iEKVLRes--D~  556 (1330)
T KOG0949|consen  479 MGIAGLVFQLQYHGEYLLRSVSSKKDPRVHDFCPDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAIEKVLRES--DS  556 (1330)
T ss_pred             CCccceehhhhhccchhhhccccCCCcchhccCCcHHHHHHhhhhhcccceEEEeeccCCceeccHHHHHHHHhhc--CC
Confidence            567777777666555553322    222221211  23 3334555578899999999999987545544444432  34


Q ss_pred             ceEEEEcccHHHHHHHHHHHHHHhhcCCCe--EEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhc-CCCCCCCCC
Q psy12977         82 FRAVIVCPTRELAKQTYNETVRLSEGLGLR--AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQM-DPPALNLAN  158 (226)
Q Consensus        82 ~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~-~~~~~~~~~  158 (226)
                      .-+|+++|+++|+.|+...+...+......  +..++.-+    +..+...-+|+|+|+.|+.+.+++.. ....-+.++
T Consensus       557 ~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~rg~sl~g~lt----qEYsinp~nCQVLITvPecleslLlspp~~q~~cer  632 (1330)
T KOG0949|consen  557 DVVIYVAPTKALVNQVSANVYARFDTKTFLRGVSLLGDLT----QEYSINPWNCQVLITVPECLESLLLSPPHHQKFCER  632 (1330)
T ss_pred             CEEEEecchHHHhhhhhHHHHHhhccCccccchhhHhhhh----HHhcCCchhceEEEEchHHHHHHhcCchhhhhhhhc
Confidence            489999999999999988877776433222  22222221    11112234799999999999998876 224566889


Q ss_pred             ccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC--chhHHHHHHH
Q psy12977        159 VEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH--TEDVAKWCRR  213 (226)
Q Consensus       159 ~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~--~~~~~~~~~~  213 (226)
                      ++++|+||+|.+....   -..-+.+++..   -.|.++++|||.  |.....|+++
T Consensus       633 IRyiIfDEVH~iG~~e---d~l~~Eqll~l---i~CP~L~LSATigN~~l~qkWlnq  683 (1330)
T KOG0949|consen  633 IRYIIFDEVHLIGNEE---DGLLWEQLLLL---IPCPFLVLSATIGNPNLFQKWLNQ  683 (1330)
T ss_pred             ceEEEechhhhccccc---cchHHHHHHHh---cCCCeeEEecccCCHHHHHHHHHH
Confidence            9999999999987653   22333334333   388999999994  4566778774

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

Probab=99.41  E-value=5.9e-12  Score=115.44  Aligned_cols=162  Identities=20%  Similarity=0.189  Sum_probs=108.5

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHH-HHHhhcCCCeEEEEecchhhhh
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET-VRLSEGLGLRAHVIGKIQQAAE  123 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~-~~~~~~~~~~~~~~~~~~~~~~  123 (226)
                      .+.++..+++.||||+|||...-..+++...   ..+.++.+.-|.|-=|..+++.+ +++....|..+++.       .
T Consensus        61 ai~~~~vvii~getGsGKTTqlP~~lle~g~---~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY~-------i  130 (845)
T COG1643          61 AIEQNQVVIIVGETGSGKTTQLPQFLLEEGL---GIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGYS-------I  130 (845)
T ss_pred             HHHhCCEEEEeCCCCCChHHHHHHHHHhhhc---ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeEE-------E
Confidence            3445677899999999999876555665544   22347778888885555555533 33333344344332       2


Q ss_pred             hhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccc-cccCccchHH-HHHHHHHhcCCCCceEEEEee
Q psy12977        124 KFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKL-FEAGVRGFRD-QLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       124 ~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l-~~~~~~~~~~-~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      ++......+..|-+.|.+.|.+.+..++.   ++.++++|+||+|.= ++.   .+.- .++.++... ++..+++.|||
T Consensus       131 Rfe~~~s~~Trik~mTdGiLlrei~~D~~---Ls~ys~vIiDEaHERSl~t---DilLgllk~~~~~r-r~DLKiIimSA  203 (845)
T COG1643         131 RFESKVSPRTRIKVMTDGILLREIQNDPL---LSGYSVVIIDEAHERSLNT---DILLGLLKDLLARR-RDDLKLIIMSA  203 (845)
T ss_pred             EeeccCCCCceeEEeccHHHHHHHhhCcc---cccCCEEEEcchhhhhHHH---HHHHHHHHHHHhhc-CCCceEEEEec
Confidence            33333456678999999999999997544   999999999999943 333   2333 333334444 45689999999


Q ss_pred             eCchhHHHHHHHhcCCCeEEecCCC
Q psy12977        202 THTEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       202 T~~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      |+..+   .+.+|+.+.-.+++++|
T Consensus       204 Tld~~---rfs~~f~~apvi~i~GR  225 (845)
T COG1643         204 TLDAE---RFSAYFGNAPVIEIEGR  225 (845)
T ss_pred             ccCHH---HHHHHcCCCCEEEecCC
Confidence            98743   36688887777887776

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

Probab=99.41  E-value=2.3e-12  Score=120.60  Aligned_cols=142  Identities=23%  Similarity=0.261  Sum_probs=93.8

Q ss_pred             HHHHhhccccCCCCccccc-----ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHH
Q psy12977         25 LAVVSNSIFKHFEPHFTIT-----YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYN   99 (226)
Q Consensus        25 l~~~~~~~~~~~~~~Q~~~-----~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~   99 (226)
                      ...+.+.+|+ +.|.|...     ..+..++++++.||||+|||++|++|++....    .+.+++|.+||++|.+|+..
T Consensus       236 ~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~----~~~~vvi~t~t~~Lq~Ql~~  310 (850)
T TIGR01407       236 SKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI----TEKPVVISTNTKVLQSQLLE  310 (850)
T ss_pred             HHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc----CCCeEEEEeCcHHHHHHHHH
Confidence            3445556666 56777432     25567899999999999999999999887665    24489999999999999855


Q ss_pred             -HHHHHhhcCC--CeEEEEecch-------------------------------------hhhhhh--------------
Q psy12977        100 -ETVRLSEGLG--LRAHVIGKIQ-------------------------------------QAAEKF--------------  125 (226)
Q Consensus       100 -~~~~~~~~~~--~~~~~~~~~~-------------------------------------~~~~~~--------------  125 (226)
                       .+..+.+.++  .++..+.|..                                     .+....              
T Consensus       311 ~~~~~l~~~~~~~~~~~~~kG~~~ylcl~k~~~~l~~~~~~~~~~~~~~~~~~wl~~T~tGD~~el~~~~~~~~~~~~i~  390 (850)
T TIGR01407       311 KDIPLLNEILNFKINAALIKGKSNYLSLGKFSQILKDNTDNYEFNIFKMQVLVWLTETETGDLDELNLKGGNKMFFAQVR  390 (850)
T ss_pred             HHHHHHHHHcCCCceEEEEEcchhhccHHHHHHHHhcCCCcHHHHHHHHHHHHHhccCCccCHhhccCCCcchhhHHHhh
Confidence             4555544433  3222222111                                     000000              


Q ss_pred             -------------------CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977        126 -------------------GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus       126 -------------------~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                                         .+.....+||+|+....+...+....  ..+...+++|+||||++.+.
T Consensus       391 ~~~~l~~~c~~~~~Cf~~~ar~~a~~AdivItNHa~L~~~~~~~~--~ilp~~~~lIiDEAH~L~d~  455 (850)
T TIGR01407       391 HDGNLSKKDLFYEVDFYNRAQKNAEQAQILITNHAYLITRLVDNP--ELFPSFRDLIIDEAHHLPDI  455 (850)
T ss_pred             cCCCCCCCCCCccccHHHHHHHHHhcCCEEEecHHHHHHHhhccc--ccCCCCCEEEEECcchHHHH
Confidence                               00114568999999999988775422  22455689999999999764

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.

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.38  E-value=2.9e-12  Score=117.95  Aligned_cols=168  Identities=17%  Similarity=0.176  Sum_probs=111.2

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEE-EEecchhhhhhhCC--
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAH-VIGKIQQAAEKFGP--  127 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~--  127 (226)
                      .+++.||||.|||.+.+.++............|++++.|++.+.+++++.++......+.... ..............  
T Consensus       216 ~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~~~~~~~~h~~~~~~~~~~~~~~  295 (733)
T COG1203         216 LVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLFSVIGKSLHSSSKEPLLLEPDQD  295 (733)
T ss_pred             cEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhcccccccccccccccchhhhccccc
Confidence            789999999999999998888777652225679999999999999999999988766554443 22221111111110  


Q ss_pred             ----------CcCCCCCEEEECchHHHHhHhcCCCCCC-C--CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCc
Q psy12977        128 ----------RSAQKFDVLITTPNKLVYLLQMDPPALN-L--ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNL  194 (226)
Q Consensus       128 ----------~~~~~~~IiV~Tp~~l~~~~~~~~~~~~-~--~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~  194 (226)
                                ....-..+.++||.+........ .... +  -..+.+|+||+|.+-+.   .....+..++..+..-+.
T Consensus       296 ~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~S~vIlDE~h~~~~~---~~~~~l~~~i~~l~~~g~  371 (733)
T COG1203         296 ILLTLTTNDSYKKLLLALIVVTPIQILIFSVKG-FKFEFLALLLTSLVILDEVHLYADE---TMLAALLALLEALAEAGV  371 (733)
T ss_pred             cceeEEecccccceeccccccCHhHhhhhhccc-cchHHHHHHHhhchhhccHHhhccc---chHHHHHHHHHHHHhCCC
Confidence                      00122355666666655532211 1111 1  23469999999977665   245555555555545689


Q ss_pred             eEEEEeeeCchhHHHHHHHhcCCCeEEe
Q psy12977        195 KRGMFSATHTEDVAKWCRRKLKRRVQIN  222 (226)
Q Consensus       195 q~v~~SAT~~~~~~~~~~~~~~~p~~i~  222 (226)
                      .++++|||+|+..++.+..+..+...+.
T Consensus       372 ~ill~SATlP~~~~~~l~~~~~~~~~~~  399 (733)
T COG1203         372 PVLLMSATLPPFLKEKLKKALGKGREVV  399 (733)
T ss_pred             CEEEEecCCCHHHHHHHHHHHhccccee
Confidence            9999999999999999988776555443

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

Probab=99.36  E-value=4.8e-12  Score=114.44  Aligned_cols=155  Identities=22%  Similarity=0.184  Sum_probs=112.1

Q ss_pred             CCCCcccccc-cC-CC---CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCC
Q psy12977         35 HFEPHFTITY-LS-PL---GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG  109 (226)
Q Consensus        35 ~~~~~Q~~~~-~~-~~---~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~  109 (226)
                      .+++.|+.+. .+ .+   -+..++.+.||||||..|+-.+...+.+    |.++|+++|-.+|..|+.+.++..+.   
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~----GkqvLvLVPEI~Ltpq~~~rf~~rFg---  270 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQ----GKQVLVLVPEIALTPQLLARFKARFG---  270 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHc----CCEEEEEeccccchHHHHHHHHHHhC---
Confidence            4555665553 22 11   2678999999999999998887777764    67899999999999999999988875   


Q ss_pred             CeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccc---cCccchHHHHH
Q psy12977        110 LRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFE---AGVRGFRDQLA  183 (226)
Q Consensus       110 ~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~---~~~~~~~~~i~  183 (226)
                      .++...+++-++.++.   .....+...|+|+|-..+         ..+++++.++|+||-|.-.-   ++.+....++.
T Consensus       271 ~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAl---------F~Pf~~LGLIIvDEEHD~sYKq~~~prYhARdvA  341 (730)
T COG1198         271 AKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSAL---------FLPFKNLGLIIVDEEHDSSYKQEDGPRYHARDVA  341 (730)
T ss_pred             CChhhhcccCChHHHHHHHHHHhcCCceEEEEechhh---------cCchhhccEEEEeccccccccCCcCCCcCHHHHH
Confidence            4544444443333332   233457789999996543         55688999999999996642   22345677777


Q ss_pred             HHHHhcCCCCceEEEEeeeCchhH
Q psy12977        184 VIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       184 ~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                      ......  .++++++-|||++=+.
T Consensus       342 ~~Ra~~--~~~pvvLgSATPSLES  363 (730)
T COG1198         342 VLRAKK--ENAPVVLGSATPSLES  363 (730)
T ss_pred             HHHHHH--hCCCEEEecCCCCHHH
Confidence            666665  7999999999966433

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

Probab=99.36  E-value=4.9e-12  Score=117.43  Aligned_cols=121  Identities=25%  Similarity=0.307  Sum_probs=86.5

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH-HHHHHHHhhcCCCeEEEEecchh---
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT-YNETVRLSEGLGLRAHVIGKIQQ---  120 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~-~~~~~~~~~~~~~~~~~~~~~~~---  120 (226)
                      .+..++.+++.|+||+|||++|++|++....     +.++||++||++|++|+ .+.+..+.+..+.++..+.|+..   
T Consensus       260 ~l~~~~~~~~eA~tGtGKT~ayllp~l~~~~-----~~~vvI~t~T~~Lq~Ql~~~~i~~l~~~~~~~~~~~kg~~~ylc  334 (820)
T PRK07246        260 DFHDGPASFIEAQTGIGKTYGYLLPLLAQSD-----QRQIIVSVPTKILQDQIMAEEVKAIQEVFHIDCHSLKGPQNYLK  334 (820)
T ss_pred             HHhCCCcEEEECCCCCcHHHHHHHHHHHhcC-----CCcEEEEeCcHHHHHHHHHHHHHHHHHhcCCcEEEEECCccccc
Confidence            4556788999999999999999999887542     45899999999999999 46777777766655543332110   


Q ss_pred             ----------------------------------hhhhhC---------------------------------CCcCCCC
Q psy12977        121 ----------------------------------AAEKFG---------------------------------PRSAQKF  133 (226)
Q Consensus       121 ----------------------------------~~~~~~---------------------------------~~~~~~~  133 (226)
                                                        +.....                                 +.....+
T Consensus       335 l~k~~~~l~~~~~~~~~~~~~~~il~Wl~~T~tGD~~El~~~~~~~~~w~~i~~~~~~~~~cp~~~~cf~~~ar~~a~~A  414 (820)
T PRK07246        335 LDAFYDSLQQNDDNRLVNRYKMQLLVWLTETETGDLDEIKQKQRYAAYFDQLKHDGNLSQSSLFYDYDFWKRSYEKAKTA  414 (820)
T ss_pred             HHHHHHHhhccCcchHHHHHHHHHHHHHhcCCCCCHhhccCCccccHHHHHhhccCCCCCCCCcchhhHHHHHHHHHHhC
Confidence                                              000000                                 0003558


Q ss_pred             CEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977        134 DVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus       134 ~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      ||+|+.+..|...+...+   .+...+++|+||||++.+.
T Consensus       415 divItNHall~~~~~~~~---~~p~~~~lIiDEAH~l~~~  451 (820)
T PRK07246        415 RLLITNHAYFLTRVQDDK---DFARNKVLVFDEAQKLMLQ  451 (820)
T ss_pred             CEEEEchHHHHHHHhhcc---CCCCCCEEEEECcchhHHH
Confidence            999999998888765432   2578999999999998753

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

Probab=99.32  E-value=1.7e-11  Score=111.88  Aligned_cols=142  Identities=23%  Similarity=0.273  Sum_probs=100.2

Q ss_pred             HHHHhhccccCCCCcc-cccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHH
Q psy12977         25 LAVVSNSIFKHFEPHF-TITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVR  103 (226)
Q Consensus        25 l~~~~~~~~~~~~~~Q-~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~  103 (226)
                      -+.+++....++...| .++--+..|++.-+.||||.|||...++..+-...    .+.++.+++||..|+.|+.+.++.
T Consensus        72 ~~fF~k~~G~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~----kgkr~yii~PT~~Lv~Q~~~kl~~  147 (1187)
T COG1110          72 EEFFKKATGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAK----KGKRVYIIVPTTTLVRQVYERLKK  147 (1187)
T ss_pred             HHHHHHhhCCCchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHh----cCCeEEEEecCHHHHHHHHHHHHH
Confidence            3444444444777788 44457789999999999999999754443333222    256999999999999999999999


Q ss_pred             HhhcCC-CeEEEEec----chhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccC
Q psy12977        104 LSEGLG-LRAHVIGK----IQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG  174 (226)
Q Consensus       104 ~~~~~~-~~~~~~~~----~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~  174 (226)
                      +.+..+ ..+.+.+-    .....+...+...++.||+|+|.+.+...+...    .-.+++++++|++|.++..+
T Consensus       148 ~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~L----~~~kFdfifVDDVDA~Lkas  219 (1187)
T COG1110         148 FAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEEL----SKLKFDFIFVDDVDAILKAS  219 (1187)
T ss_pred             HHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHHh----cccCCCEEEEccHHHHHhcc
Confidence            988776 44333211    122233334455678999999998887766542    12478999999999887653

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

Probab=99.29  E-value=2.7e-11  Score=112.65  Aligned_cols=152  Identities=21%  Similarity=0.306  Sum_probs=114.4

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhh---hhhCC
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAA---EKFGP  127 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~  127 (226)
                      |=++||.-|-|||..++=+++..+.+    |+++.+++||.-||+|.++.+++.+..+++++.....-....   .....
T Consensus       617 DRLiCGDVGFGKTEVAmRAAFkAV~~----GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~  692 (1139)
T COG1197         617 DRLICGDVGFGKTEVAMRAAFKAVMD----GKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKG  692 (1139)
T ss_pred             hheeecCcCCcHHHHHHHHHHHHhcC----CCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHH
Confidence            45899999999999998888888875    679999999999999999999999999999988776544333   33334


Q ss_pred             CcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        128 RSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       128 ~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                      ...+..||+|+|+.-|    .   ..+.++++.++||||-|++.=.    .-+.++.+.     .+.-++-+|||+=+..
T Consensus       693 la~G~vDIvIGTHrLL----~---kdv~FkdLGLlIIDEEqRFGVk----~KEkLK~Lr-----~~VDvLTLSATPIPRT  756 (1139)
T COG1197         693 LAEGKVDIVIGTHRLL----S---KDVKFKDLGLLIIDEEQRFGVK----HKEKLKELR-----ANVDVLTLSATPIPRT  756 (1139)
T ss_pred             HhcCCccEEEechHhh----C---CCcEEecCCeEEEechhhcCcc----HHHHHHHHh-----ccCcEEEeeCCCCcch
Confidence            5578899999998533    2   4666899999999999987433    445555554     5668999999954444


Q ss_pred             HHHHHHhcCCCeEEe
Q psy12977        208 AKWCRRKLKRRVQIN  222 (226)
Q Consensus       208 ~~~~~~~~~~p~~i~  222 (226)
                      .++.-.-++|--.|+
T Consensus       757 L~Msm~GiRdlSvI~  771 (1139)
T COG1197         757 LNMSLSGIRDLSVIA  771 (1139)
T ss_pred             HHHHHhcchhhhhcc
Confidence            444434444444433

>KOG0950|consensus

Probab=99.28  E-value=1.7e-11  Score=111.16  Aligned_cols=174  Identities=15%  Similarity=0.088  Sum_probs=126.5

Q ss_pred             hccccCCCCccccc---ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhh
Q psy12977         30 NSIFKHFEPHFTIT---YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE  106 (226)
Q Consensus        30 ~~~~~~~~~~Q~~~---~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~  106 (226)
                      ..+...+..-|..+   +....++|.+..+||+.|||++.-+-++..+..   .+..++.+.|..+.+..-...+..+..
T Consensus       218 ~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~---~rr~~llilp~vsiv~Ek~~~l~~~~~  294 (1008)
T KOG0950|consen  218 DKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLC---RRRNVLLILPYVSIVQEKISALSPFSI  294 (1008)
T ss_pred             hhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHH---HhhceeEecceeehhHHHHhhhhhhcc
Confidence            44444455555333   344578999999999999999988888777643   244689999999999999999999999


Q ss_pred             cCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHH
Q psy12977        107 GLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIY  186 (226)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~  186 (226)
                      ..|..+....|......     ..+.-++.|||-++-..++++.-..-.++.+.++|+||.|.+.+.+   -...+..++
T Consensus       295 ~~G~~ve~y~g~~~p~~-----~~k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~---rg~~lE~~l  366 (1008)
T KOG0950|consen  295 DLGFPVEEYAGRFPPEK-----RRKRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKG---RGAILELLL  366 (1008)
T ss_pred             ccCCcchhhcccCCCCC-----cccceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccc---cchHHHHHH
Confidence            99998877765433322     3355689999999998888765455568889999999999888764   223333333


Q ss_pred             Hhc----CCCCceEEEEeeeCc--hhHHHHHHHh
Q psy12977        187 AAC----SGPNLKRGMFSATHT--EDVAKWCRRK  214 (226)
Q Consensus       187 ~~~----~~~~~q~v~~SAT~~--~~~~~~~~~~  214 (226)
                      .++    .....|+|+||||+|  +.+..|++..
T Consensus       367 ~k~~y~~~~~~~~iIGMSATi~N~~lL~~~L~A~  400 (1008)
T KOG0950|consen  367 AKILYENLETSVQIIGMSATIPNNSLLQDWLDAF  400 (1008)
T ss_pred             HHHHHhccccceeEeeeecccCChHHHHHHhhhh
Confidence            322    234468999999988  4577777763

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

Probab=99.28  E-value=8.9e-12  Score=111.84  Aligned_cols=149  Identities=14%  Similarity=0.144  Sum_probs=103.3

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      +.+++++.||+|||..+ +.++.++.+ .+.-.|+++++.+++|++|.+..+..+.++. ..+..+.+..         .
T Consensus       186 ~raLlvMATGTGKTrTA-iaii~rL~r-~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~-~~~n~i~~~~---------~  253 (875)
T COG4096         186 NRALLVMATGTGKTRTA-IAIIDRLIK-SGWVKRVLFLADRNALVDQAYGAFEDFLPFG-TKMNKIEDKK---------G  253 (875)
T ss_pred             ceEEEEEecCCCcceeH-HHHHHHHHh-cchhheeeEEechHHHHHHHHHHHHHhCCCc-cceeeeeccc---------C
Confidence            45999999999999865 555666652 4455699999999999999999988887653 2222222211         1


Q ss_pred             CCCCCEEEECchHHHHhHhcC---CCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        130 AQKFDVLITTPNKLVYLLQMD---PPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~---~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                      ...++|.++|-..+..-....   ...+...-++++|+||||+-       .......++.++  .. -.++++||+.++
T Consensus       254 ~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRg-------i~~~~~~I~dYF--dA-~~~gLTATP~~~  323 (875)
T COG4096         254 DTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRG-------IYSEWSSILDYF--DA-ATQGLTATPKET  323 (875)
T ss_pred             CcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhh-------HHhhhHHHHHHH--HH-HHHhhccCcccc
Confidence            125789999999998876542   23455566899999999974       444555666666  22 233349999887


Q ss_pred             HHHHHHHhc-CCCeE
Q psy12977        207 VAKWCRRKL-KRRVQ  220 (226)
Q Consensus       207 ~~~~~~~~~-~~p~~  220 (226)
                      +..---.|+ .+|+.
T Consensus       324 ~d~~T~~~F~g~Pt~  338 (875)
T COG4096         324 IDRSTYGFFNGEPTY  338 (875)
T ss_pred             cccccccccCCCcce
Confidence            766666666 66664

>KOG0920|consensus

Probab=99.23  E-value=2.9e-10  Score=104.48  Aligned_cols=165  Identities=21%  Similarity=0.153  Sum_probs=113.0

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHH-HHHhhcCCCeEEEEecchhhhh
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET-VRLSEGLGLRAHVIGKIQQAAE  123 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~-~~~~~~~~~~~~~~~~~~~~~~  123 (226)
                      .+.++..+++.|.||+|||.-..-.+++...... ...++++-.|.|-=|-.+++.. .+.+...+..++......    
T Consensus       184 ~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~-~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g~~VGYqvrl~----  258 (924)
T KOG0920|consen  184 AIEENQVVVISGETGCGKTTQVPQFILDEAIESG-AACNIICTQPRRISAISVAERVAKERGESLGEEVGYQVRLE----  258 (924)
T ss_pred             HHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcC-CCCeEEecCCchHHHHHHHHHHHHHhccccCCeeeEEEeee----
Confidence            4455678899999999999876655666553333 5567888889876666665533 333444454444333221    


Q ss_pred             hhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        124 KFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       124 ~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                         ........++.||.+.+++.+..   .-.+..+.++|+||+|.=.-..  ++...+.+.+-.. ++..++++||||+
T Consensus       259 ---~~~s~~t~L~fcTtGvLLr~L~~---~~~l~~vthiivDEVHER~i~~--DflLi~lk~lL~~-~p~LkvILMSAT~  329 (924)
T KOG0920|consen  259 ---SKRSRETRLLFCTTGVLLRRLQS---DPTLSGVTHIIVDEVHERSINT--DFLLILLKDLLPR-NPDLKVILMSATL  329 (924)
T ss_pred             ---cccCCceeEEEecHHHHHHHhcc---CcccccCceeeeeeEEEccCCc--ccHHHHHHHHhhh-CCCceEEEeeeec
Confidence               22233467999999999999885   4458899999999999543221  3444444443333 5899999999998


Q ss_pred             chhHHHHHHHhcCCCeEEecCCC
Q psy12977        204 TEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       204 ~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      .   .+....|+...-.+++.+|
T Consensus       330 d---ae~fs~YF~~~pvi~i~gr  349 (924)
T KOG0920|consen  330 D---AELFSDYFGGCPVITIPGR  349 (924)
T ss_pred             c---hHHHHHHhCCCceEeecCC
Confidence            8   5567788988888888776

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.23  E-value=3e-11  Score=99.67  Aligned_cols=60  Identities=22%  Similarity=0.254  Sum_probs=48.0

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCC--CCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKN--LGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~--~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      .+..|+++++.+|||+|||++++.|++..+.....  .+.+++|.++|.++.+|....+++.
T Consensus        23 ~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489       23 VLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             HHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            45678899999999999999999999866543222  2348999999999999987777665

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.23  E-value=3e-11  Score=99.67  Aligned_cols=60  Identities=22%  Similarity=0.254  Sum_probs=48.0

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCC--CCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKN--LGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~--~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      .+..|+++++.+|||+|||++++.|++..+.....  .+.+++|.++|.++.+|....+++.
T Consensus        23 ~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488       23 VLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             HHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            45678899999999999999999999866543222  2348999999999999987777665

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.21  E-value=6e-11  Score=108.68  Aligned_cols=145  Identities=21%  Similarity=0.171  Sum_probs=104.0

Q ss_pred             HHHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH
Q psy12977         18 ISIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE   92 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~   92 (226)
                      ..+.|.-.+.+++....    .+..+|-... .+..|+  +....||+|||+++.+|++-....    |..+.+++|+..
T Consensus        61 d~~l~eafA~vrEa~~R~lGm~~ydVQliGg~~Lh~G~--iaEM~TGEGKTLvA~l~a~l~al~----G~~VhvvT~ndy  134 (913)
T PRK13103         61 DQLLPEAFAVAREAGKRVMGMRHFDVQLIGGMTLHEGK--IAEMRTGEGKTLVGTLAVYLNALS----GKGVHVVTVNDY  134 (913)
T ss_pred             hHHHHHHHHHHHHHHHHHhCCCcchhHHHhhhHhccCc--cccccCCCCChHHHHHHHHHHHHc----CCCEEEEeCCHH
Confidence            34455555556555444    4445665444 333444  789999999999999888765543    668899999999


Q ss_pred             HHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHH-HHhHhc----CCCCCCCCCccEEEEccc
Q psy12977         93 LAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKL-VYLLQM----DPPALNLANVEWLIVDES  167 (226)
Q Consensus        93 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l-~~~~~~----~~~~~~~~~~~~lViDE~  167 (226)
                      ||.|-++++..+.+.+|+++.++.+.....++.   ....+||+++|..-+ +++++.    .........+.+.||||+
T Consensus       135 LA~RD~e~m~~l~~~lGl~v~~i~~~~~~~err---~~Y~~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEv  211 (913)
T PRK13103        135 LARRDANWMRPLYEFLGLSVGIVTPFQPPEEKR---AAYAADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEV  211 (913)
T ss_pred             HHHHHHHHHHHHhcccCCEEEEECCCCCHHHHH---HHhcCCEEEEcccccccchhhccceechhhhcccccceeEechh
Confidence            999999999999999999999887765444332   345699999999887 223321    112223478899999999


Q ss_pred             cccc
Q psy12977        168 DKLF  171 (226)
Q Consensus       168 h~l~  171 (226)
                      |.++
T Consensus       212 DsiL  215 (913)
T PRK13103        212 DSIL  215 (913)
T ss_pred             hhee
Confidence            9775

>KOG0922|consensus

Probab=99.21  E-value=2.8e-10  Score=100.08  Aligned_cols=162  Identities=18%  Similarity=0.140  Sum_probs=106.7

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHH-HHHHHhhcCCCeEEEEecchhhhh
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYN-ETVRLSEGLGLRAHVIGKIQQAAE  123 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~-~~~~~~~~~~~~~~~~~~~~~~~~  123 (226)
                      ...+++-+++.|+||||||.-.--.+.+.-..   ...++.+..|.|--|..+++ +..++...+|..+++..       
T Consensus        62 ~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~---~~g~I~~TQPRRVAavslA~RVAeE~~~~lG~~VGY~I-------  131 (674)
T KOG0922|consen   62 AVEDNQVLIVIGETGSGKSTQIPQYLAEAGFA---SSGKIACTQPRRVAAVSLAKRVAEEMGCQLGEEVGYTI-------  131 (674)
T ss_pred             HHHHCCEEEEEcCCCCCccccHhHHHHhcccc---cCCcEEeecCchHHHHHHHHHHHHHhCCCcCceeeeEE-------
Confidence            33456779999999999997543334343322   22347778888866655544 34455555565555433       


Q ss_pred             hhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccc-cccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        124 KFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKL-FEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       124 ~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l-~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      ++...-.....|...|-+.|++-+..++   .+++.+++|+||||.= +..+  -..-.++.+++..  +..+++++|||
T Consensus       132 RFed~ts~~TrikymTDG~LLRE~l~Dp---~LskYsvIIlDEAHERsl~TD--iLlGlLKki~~~R--~~LklIimSAT  204 (674)
T KOG0922|consen  132 RFEDSTSKDTRIKYMTDGMLLREILKDP---LLSKYSVIILDEAHERSLHTD--ILLGLLKKILKKR--PDLKLIIMSAT  204 (674)
T ss_pred             EecccCCCceeEEEecchHHHHHHhcCC---ccccccEEEEechhhhhhHHH--HHHHHHHHHHhcC--CCceEEEEeee
Confidence            2223334567799999999999888643   4899999999999943 2211  1333344444433  56799999999


Q ss_pred             CchhHHHHHHHhcCCCeEEecCCC
Q psy12977        203 HTEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       203 ~~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      +.   .+....|+.+.-.+.|.+|
T Consensus       205 ld---a~kfS~yF~~a~i~~i~GR  225 (674)
T KOG0922|consen  205 LD---AEKFSEYFNNAPILTIPGR  225 (674)
T ss_pred             ec---HHHHHHHhcCCceEeecCC
Confidence            98   4447788888777787776

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

Probab=99.15  E-value=1.9e-10  Score=108.55  Aligned_cols=52  Identities=25%  Similarity=0.213  Sum_probs=43.4

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHH
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYN   99 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~   99 (226)
                      .+.+++.+++.||||+|||++|++|++.....   .+.+++|.++|+.|-+|+.+
T Consensus       272 ~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~---~~~~vvIsT~T~~LQ~Ql~~  323 (928)
T PRK08074        272 ALRDSEHALIEAGTGTGKSLAYLLPAAYFAKK---KEEPVVISTYTIQLQQQLLE  323 (928)
T ss_pred             HHhcCCCEEEECCCCCchhHHHHHHHHHHhhc---cCCeEEEEcCCHHHHHHHHH
Confidence            44567889999999999999999998765542   24689999999999999865

>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=99.14  E-value=1.7e-09  Score=89.34  Aligned_cols=145  Identities=21%  Similarity=0.148  Sum_probs=86.9

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCC-CCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKN-LGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF  125 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~-~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (226)
                      ...+..++....|+|||...+..+......... ....++|++|. .+..|+.+++..+......++....+... ....
T Consensus        23 ~~~~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~~~~v~~~~~~~~-~~~~  100 (299)
T PF00176_consen   23 SPPRGGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPDSLRVIIYDGDSE-RRRL  100 (299)
T ss_dssp             TTT-EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT-TS-EEEESSSCH-HHHT
T ss_pred             cCCCCEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeecc-chhhhhhhhhccccccccccccccccccc-cccc
Confidence            345788999999999998765544332222111 11259999999 88899999999998654556666655541 1222


Q ss_pred             CCCcCCCCCEEEECchHHH-----HhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        126 GPRSAQKFDVLITTPNKLV-----YLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       126 ~~~~~~~~~IiV~Tp~~l~-----~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ........+++|+|.+.+.     ....    .+.-.+.+++|+||+|.+-+.     .......+..+  ....++++|
T Consensus       101 ~~~~~~~~~vvi~ty~~~~~~~~~~~~~----~l~~~~~~~vIvDEaH~~k~~-----~s~~~~~l~~l--~~~~~~lLS  169 (299)
T PF00176_consen  101 SKNQLPKYDVVITTYETLRKARKKKDKE----DLKQIKWDRVIVDEAHRLKNK-----DSKRYKALRKL--RARYRWLLS  169 (299)
T ss_dssp             TSSSCCCSSEEEEEHHHHH--TSTHTTH----HHHTSEEEEEEETTGGGGTTT-----TSHHHHHHHCC--CECEEEEE-
T ss_pred             cccccccceeeecccccccccccccccc----ccccccceeEEEecccccccc-----ccccccccccc--ccceEEeec
Confidence            3344567899999999988     2111    111234889999999998433     22333344445  366788899


Q ss_pred             eeCc
Q psy12977        201 ATHT  204 (226)
Q Consensus       201 AT~~  204 (226)
                      ||+-
T Consensus       170 gTP~  173 (299)
T PF00176_consen  170 GTPI  173 (299)
T ss_dssp             SS-S
T ss_pred             cccc
Confidence            9943

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.

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.13  E-value=5.5e-10  Score=104.49  Aligned_cols=162  Identities=18%  Similarity=0.092  Sum_probs=96.0

Q ss_pred             CCCCcccccc-cCC--CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCe
Q psy12977         35 HFEPHFTITY-LSP--LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR  111 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~--~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~  111 (226)
                      .+.|.|.... ...  ....+++....|.|||.-....+...+...  ...+++|+||. .|..||..++.+.+   +..
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g--~~~rvLIVvP~-sL~~QW~~El~~kF---~l~  225 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTG--RAERVLILVPE-TLQHQWLVEMLRRF---NLR  225 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcC--CCCcEEEEcCH-HHHHHHHHHHHHHh---CCC
Confidence            3667775443 222  235689999999999988766555544432  23489999998 79999999886654   444


Q ss_pred             EEEEecchhhhhhhC-CCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcC
Q psy12977        112 AHVIGKIQQAAEKFG-PRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACS  190 (226)
Q Consensus       112 ~~~~~~~~~~~~~~~-~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~  190 (226)
                      ...+.+......... .......+++|++.+.+...-... ..+.-..++++|+||||++-.......  ...+.++.+.
T Consensus       226 ~~i~~~~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~-~~l~~~~wdlvIvDEAH~lk~~~~~~s--~~y~~v~~La  302 (956)
T PRK04914        226 FSLFDEERYAEAQHDADNPFETEQLVICSLDFLRRNKQRL-EQALAAEWDLLVVDEAHHLVWSEEAPS--REYQVVEQLA  302 (956)
T ss_pred             eEEEcCcchhhhcccccCccccCcEEEEEHHHhhhCHHHH-HHHhhcCCCEEEEechhhhccCCCCcC--HHHHHHHHHh
Confidence            444443321111100 011234689999988776522110 122234789999999999863210011  1122333332


Q ss_pred             CCCceEEEEeeeCch
Q psy12977        191 GPNLKRGMFSATHTE  205 (226)
Q Consensus       191 ~~~~q~v~~SAT~~~  205 (226)
                      .....++++|||+..
T Consensus       303 ~~~~~~LLLTATP~q  317 (956)
T PRK04914        303 EVIPGVLLLTATPEQ  317 (956)
T ss_pred             hccCCEEEEEcCccc
Confidence            344578999999763

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.11  E-value=2e-10  Score=104.78  Aligned_cols=146  Identities=22%  Similarity=0.204  Sum_probs=108.0

Q ss_pred             hHHHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         17 VISIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        17 ~~~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      ...+.|...+.+++....    .+.++|-... .+..|+  +....||+|||+...+|++.....    |..+-+++||.
T Consensus        58 ld~~l~eafA~vrEa~~R~~g~~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~----G~~v~vvT~ne  131 (796)
T PRK12906         58 LDDLLPEAFAVAREGAKRVLGLRPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALT----GKGVHVVTVNE  131 (796)
T ss_pred             hhhHHHHHHHHHHHHHHHHhCCCCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHc----CCCeEEEeccH
Confidence            345566777777766555    4556675554 444455  899999999999999888877654    66889999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCC-----CCCCCCCccEEEEcc
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDP-----PALNLANVEWLIVDE  166 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~-----~~~~~~~~~~lViDE  166 (226)
                      .||.|-++.+..+.+.+|+++.+..++.....+   .....+||+.+|...+--.+-+++     .........+.|+||
T Consensus       132 yLA~Rd~e~~~~~~~~LGl~vg~i~~~~~~~~r---~~~y~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDE  208 (796)
T PRK12906        132 YLSSRDATEMGELYRWLGLTVGLNLNSMSPDEK---RAAYNCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDE  208 (796)
T ss_pred             HHHHhhHHHHHHHHHhcCCeEEEeCCCCCHHHH---HHHhcCCCeecCCccccccchhhccccchhhhhccCcceeeecc
Confidence            999999999999999999999988776544433   345688999999888754332221     122245678999999


Q ss_pred             ccccc
Q psy12977        167 SDKLF  171 (226)
Q Consensus       167 ~h~l~  171 (226)
                      +|.++
T Consensus       209 vDSiL  213 (796)
T PRK12906        209 VDSIL  213 (796)
T ss_pred             chhee
Confidence            99775

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=99.11  E-value=7.7e-10  Score=101.15  Aligned_cols=146  Identities=19%  Similarity=0.186  Sum_probs=107.8

Q ss_pred             hHHHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         17 VISIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        17 ~~~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      ...+.+.-.+.+++....    .+..+|-... .+..|+  +..+.||.|||+++.+|++-....    |..+-|++++.
T Consensus        63 ld~~l~eafA~vREa~~R~lG~r~ydVQliGgl~Lh~G~--IAEM~TGEGKTL~atlpaylnAL~----GkgVhVVTvNd  136 (939)
T PRK12902         63 LDELLPEAFAVVREASKRVLGMRHFDVQLIGGMVLHEGQ--IAEMKTGEGKTLVATLPSYLNALT----GKGVHVVTVND  136 (939)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCcchhHHHhhhhhcCCc--eeeecCCCChhHHHHHHHHHHhhc----CCCeEEEeCCH
Confidence            445566777777766555    4455665544 334444  789999999999999887754432    66789999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHH-----HHhHhcCCCCCCCCCccEEEEcc
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKL-----VYLLQMDPPALNLANVEWLIVDE  166 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l-----~~~~~~~~~~~~~~~~~~lViDE  166 (226)
                      .||.+-++++..+.+.+|..+.++.++.....+   .....|||+.+|+..+     .+.+...........+.+.||||
T Consensus       137 YLA~RDae~m~~vy~~LGLtvg~i~~~~~~~er---r~aY~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDE  213 (939)
T PRK12902        137 YLARRDAEWMGQVHRFLGLSVGLIQQDMSPEER---KKNYACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDE  213 (939)
T ss_pred             HHHHhHHHHHHHHHHHhCCeEEEECCCCChHHH---HHhcCCCeEEecCCcccccchhhhhcccccccccCccceEEEec
Confidence            999999999999999999999988765544333   3568899999999888     33333222334467789999999


Q ss_pred             ccccc
Q psy12977        167 SDKLF  171 (226)
Q Consensus       167 ~h~l~  171 (226)
                      +|.++
T Consensus       214 vDSIL  218 (939)
T PRK12902        214 VDSIL  218 (939)
T ss_pred             cccee
Confidence            99775

>KOG0951|consensus

Probab=99.11  E-value=4.8e-10  Score=104.21  Aligned_cols=156  Identities=25%  Similarity=0.319  Sum_probs=112.3

Q ss_pred             ccccCCCCcccccc--cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc-
Q psy12977         31 SIFKHFEPHFTITY--LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG-  107 (226)
Q Consensus        31 ~~~~~~~~~Q~~~~--~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~-  107 (226)
                      ..|..++|+|++.+  ....+.++++.+|+|||||++.-+.++.     .....+++++.|..+.+..++..+...++. 
T Consensus      1139 ~lf~~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~-----~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~ 1213 (1674)
T KOG0951|consen 1139 TLFQDFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR-----PDTIGRAVYIAPLEEIADEQYRDWEKKFSKL 1213 (1674)
T ss_pred             hhccccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC-----CccceEEEEecchHHHHHHHHHHHHHhhccc
Confidence            34556699999887  5566788999999999999998777655     334559999999999999988877666544 


Q ss_pred             CCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc---chHHHHHH
Q psy12977        108 LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR---GFRDQLAV  184 (226)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~---~~~~~i~~  184 (226)
                      .|..+...+|.....    -.+....+|+|+||+++..+ +      ....+++.|.||.|.+.+..+.   -.+. +..
T Consensus      1214 ~G~~~~~l~ge~s~~----lkl~~~~~vii~tpe~~d~l-q------~iQ~v~l~i~d~lh~igg~~g~v~evi~S-~r~ 1281 (1674)
T KOG0951|consen 1214 LGLRIVKLTGETSLD----LKLLQKGQVIISTPEQWDLL-Q------SIQQVDLFIVDELHLIGGVYGAVYEVICS-MRY 1281 (1674)
T ss_pred             cCceEEecCCccccc----hHHhhhcceEEechhHHHHH-h------hhhhcceEeeehhhhhcccCCceEEEEee-HHH
Confidence            455555555553322    23456789999999998766 2      3678999999999988754321   1223 455


Q ss_pred             HHHhcCCCCceEEEEeeeCc
Q psy12977        185 IYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       185 i~~~~~~~~~q~v~~SAT~~  204 (226)
                      +-.++ -++.+++.+|..+.
T Consensus      1282 ia~q~-~k~ir~v~ls~~la 1300 (1674)
T KOG0951|consen 1282 IASQL-EKKIRVVALSSSLA 1300 (1674)
T ss_pred             HHHHH-HhheeEEEeehhhc
Confidence            55555 45678888877654

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.08  E-value=9.9e-10  Score=98.71  Aligned_cols=146  Identities=23%  Similarity=0.164  Sum_probs=106.8

Q ss_pred             hHHHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         17 VISIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        17 ~~~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      ...+.++..+.+++..+.    .+..+|-... .++.|+  +....||.|||+...+|++.....    |..+.+++|+.
T Consensus        56 ~d~~l~eafAvvREa~~R~lg~r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~----G~~VhvvT~Nd  129 (764)
T PRK12326         56 DSDDLAEFLAIAREAAERTLGLRPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQ----GRRVHVITVND  129 (764)
T ss_pred             hhhHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHc----CCCeEEEcCCH
Confidence            445567777777766665    4445664443 444554  679999999999998888766553    66899999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcC-----CCCCCCCCccEEEEcc
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMD-----PPALNLANVEWLIVDE  166 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~-----~~~~~~~~~~~lViDE  166 (226)
                      .||.|-++++..+.+.+|+++..+.+.....++   .....|||+.+|...+--.+.++     ........+.+.|+||
T Consensus       130 yLA~RDae~m~~ly~~LGLsvg~i~~~~~~~er---r~aY~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDE  206 (764)
T PRK12326        130 YLARRDAEWMGPLYEALGLTVGWITEESTPEER---RAAYACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDE  206 (764)
T ss_pred             HHHHHHHHHHHHHHHhcCCEEEEECCCCCHHHH---HHHHcCCCEEcCCcccccccchhhhccChHhhcCCccceeeecc
Confidence            999999999999999999999988776544333   34467999999988764322221     1222345688999999


Q ss_pred             ccccc
Q psy12977        167 SDKLF  171 (226)
Q Consensus       167 ~h~l~  171 (226)
                      +|.++
T Consensus       207 vDSiL  211 (764)
T PRK12326        207 ADSVL  211 (764)
T ss_pred             hhhhe
Confidence            99775

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.05  E-value=1.9e-09  Score=98.94  Aligned_cols=48  Identities=33%  Similarity=0.346  Sum_probs=40.1

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYN   99 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~   99 (226)
                      ++.+++.||||+|||++|++|++.....   .+.++||-+.|+.|=+|..+
T Consensus        49 ~~~lviEAgTGtGKTlaYLlPai~~A~~---~~k~vVIST~T~~LQeQL~~   96 (697)
T PRK11747         49 GRILVIEAGTGVGKTLSYLLAGIPIARA---EKKKLVISTATVALQEQLVS   96 (697)
T ss_pred             cceEEEECCCCcchhHHHHHHHHHHHHH---cCCeEEEEcCCHHHHHHHHh
Confidence            4678999999999999999998765442   24589999999999999854

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.05  E-value=9.1e-10  Score=100.62  Aligned_cols=146  Identities=22%  Similarity=0.178  Sum_probs=104.8

Q ss_pred             HHHHHHHHHHHhhcccc----CCCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHH
Q psy12977         18 ISIIVTTLAVVSNSIFK----HFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTREL   93 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~----~~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L   93 (226)
                      ..+.++..+.+++..+.    .+..+|-.....+. +.-+..+.||.|||+++.+|++-...    .|..+.|++++..|
T Consensus        55 d~il~eafAvvrEa~~R~lG~r~ydvQlig~l~L~-~G~IaEm~TGEGKTL~a~l~ayl~aL----~G~~VhVvT~NdyL  129 (870)
T CHL00122         55 NKIIPESFALTREASFRTLGLRHFDVQLIGGLVLN-DGKIAEMKTGEGKTLVATLPAYLNAL----TGKGVHIVTVNDYL  129 (870)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCchHhhhhHhhc-CCccccccCCCCchHHHHHHHHHHHh----cCCceEEEeCCHHH
Confidence            44566666666665554    34556655543332 44589999999999999988864333    25679999999999


Q ss_pred             HHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcC-----CCCCCCCCccEEEEcccc
Q psy12977         94 AKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMD-----PPALNLANVEWLIVDESD  168 (226)
Q Consensus        94 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~-----~~~~~~~~~~~lViDE~h  168 (226)
                      |.+-++++..+.+.+|..+.++.++.....+   .....+||+.+|...+--.+-++     ........+.+.|+||+|
T Consensus       130 A~RD~e~m~pvy~~LGLsvg~i~~~~~~~er---r~aY~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvD  206 (870)
T CHL00122        130 AKRDQEWMGQIYRFLGLTVGLIQEGMSSEER---KKNYLKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVD  206 (870)
T ss_pred             HHHHHHHHHHHHHHcCCceeeeCCCCChHHH---HHhcCCCCEecCCccccccchhhccCcChHHhhccccceeeeecch
Confidence            9999999999999999999988766544443   34578999999987664322221     122235668899999999


Q ss_pred             ccc
Q psy12977        169 KLF  171 (226)
Q Consensus       169 ~l~  171 (226)
                      .++
T Consensus       207 SiL  209 (870)
T CHL00122        207 SIL  209 (870)
T ss_pred             hhe
Confidence            775

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

Probab=99.04  E-value=7.9e-10  Score=89.52  Aligned_cols=144  Identities=23%  Similarity=0.215  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHH
Q psy12977         19 SIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTREL   93 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L   93 (226)
                      .+.++.+..+++....    .+.++|-... .+..|+  +++..||-|||+...++++-....    |..+-|++.+..|
T Consensus        57 ~~l~e~~Al~rea~~r~~g~~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~----G~~V~vvT~NdyL  130 (266)
T PF07517_consen   57 DILPEAFALVREAARRTLGLRPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQ----GKGVHVVTSNDYL  130 (266)
T ss_dssp             HHHHHHHHHHHHHHHHHTS----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTT----SS-EEEEESSHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCcccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHh----cCCcEEEeccHHH
Confidence            3455555555544433    5556675554 333344  899999999999988776655443    5689999999999


Q ss_pred             HHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcC-----CCCCCCCCccEEEEcccc
Q psy12977         94 AKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMD-----PPALNLANVEWLIVDESD  168 (226)
Q Consensus        94 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~-----~~~~~~~~~~~lViDE~h  168 (226)
                      |.+=++++..+.+.+|+.+.....+.....+.   ....++|+.+|...+...+-++     .........+++|+||+|
T Consensus       131 A~RD~~~~~~~y~~LGlsv~~~~~~~~~~~r~---~~Y~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvD  207 (266)
T PF07517_consen  131 AKRDAEEMRPFYEFLGLSVGIITSDMSSEERR---EAYAADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVD  207 (266)
T ss_dssp             HHHHHHHHHHHHHHTT--EEEEETTTEHHHHH---HHHHSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHH
T ss_pred             hhccHHHHHHHHHHhhhccccCccccCHHHHH---HHHhCcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccc
Confidence            99999999999999999999988776543321   2356789999999887533221     111225678999999999


Q ss_pred             ccc
Q psy12977        169 KLF  171 (226)
Q Consensus       169 ~l~  171 (226)
                      .++
T Consensus       208 s~L  210 (266)
T PF07517_consen  208 SIL  210 (266)
T ss_dssp             HHT
T ss_pred             eEE
Confidence            775

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 ....

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=98.97  E-value=7.4e-09  Score=96.12  Aligned_cols=147  Identities=21%  Similarity=0.197  Sum_probs=87.7

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHH-----HHhhc-C-CCeEE--EEecch
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETV-----RLSEG-L-GLRAH--VIGKIQ  119 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~-----~~~~~-~-~~~~~--~~~~~~  119 (226)
                      ..++.+.++||+|||.+|+-.++.......  ..++||+||+.++-+.+.+.++     +.+.. + +..+.  ...+..
T Consensus        59 ~~n~~~~M~TGtGKT~~~~~~i~~l~~~~~--~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~~S~k  136 (986)
T PRK15483         59 KANIDIKMETGTGKTYVYTRLMYELHQKYG--LFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVINAGD  136 (986)
T ss_pred             cceEEEEeCCCCCHHHHHHHHHHHHHHHcC--CcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEEecCc
Confidence            358999999999999999888877765432  3589999999999998876654     22221 1 22233  222221


Q ss_pred             ----------hhhhhhCC---CcCCCCCEEEECchHHHHhHh--cC------CCC-CCCCCc----cEEEEccccccccc
Q psy12977        120 ----------QAAEKFGP---RSAQKFDVLITTPNKLVYLLQ--MD------PPA-LNLANV----EWLIVDESDKLFEA  173 (226)
Q Consensus       120 ----------~~~~~~~~---~~~~~~~IiV~Tp~~l~~~~~--~~------~~~-~~~~~~----~~lViDE~h~l~~~  173 (226)
                                .....+..   .-.+..+|+|.|.+.+..-..  ..      .+. .+...+    -.+|+||+|++...
T Consensus       137 ~~k~gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niqa~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIiDEPh~~~~~  216 (986)
T PRK15483        137 KKKSGRKNFPAQLSNFVKASRQNSNTIHVLLINAGMLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVIIDEPHRFPRD  216 (986)
T ss_pred             ccccccccChHHHHHHHhccccCCCceEEEEEehHHhcccccccchhhhhhccCCCChHHHHHhCCCEEEEECCCCCCcc
Confidence                      01111111   112357899999998876321  10      011 222222    28999999998543


Q ss_pred             CccchHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        174 GVRGFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       174 ~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      +  ..+   ..+ ..+ +|.+ ++.+|||+++
T Consensus       217 ~--k~~---~~i-~~l-npl~-~lrysAT~~~  240 (986)
T PRK15483        217 N--KFY---QAI-EAL-KPQM-IIRFGATFPD  240 (986)
T ss_pred             h--HHH---HHH-Hhc-Cccc-EEEEeeecCC
Confidence            1  233   333 344 2333 4669999986

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=98.95  E-value=7.9e-09  Score=97.32  Aligned_cols=143  Identities=19%  Similarity=0.145  Sum_probs=91.3

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh-
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF-  125 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  125 (226)
                      ..|.+.++....|.|||+..+.. +..+.........+|||||. ++..||.+.+..++..  ..+..+.|........ 
T Consensus       186 ~~g~gGILADEMGLGKTlQaIal-L~~L~~~~~~~gp~LIVvP~-SlL~nW~~Ei~kw~p~--l~v~~~~G~~~eR~~~~  261 (1033)
T PLN03142        186 ENGINGILADEMGLGKTLQTISL-LGYLHEYRGITGPHMVVAPK-STLGNWMNEIRRFCPV--LRAVKFHGNPEERAHQR  261 (1033)
T ss_pred             hcCCCEEEEeCCCccHHHHHHHH-HHHHHHhcCCCCCEEEEeCh-HHHHHHHHHHHHHCCC--CceEEEeCCHHHHHHHH
Confidence            35678899999999999865433 33332222223468999996 5778999999998753  4444555543322211 


Q ss_pred             -CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        126 -GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       126 -~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                       ........+|+|+|.+.+......    +.--.++++|+||+|.+-..     ...+.+.++.+  .....+++|+|+-
T Consensus       262 ~~~~~~~~~dVvITSYe~l~~e~~~----L~k~~W~~VIvDEAHrIKN~-----~Sklskalr~L--~a~~RLLLTGTPl  330 (1033)
T PLN03142        262 EELLVAGKFDVCVTSFEMAIKEKTA----LKRFSWRYIIIDEAHRIKNE-----NSLLSKTMRLF--STNYRLLITGTPL  330 (1033)
T ss_pred             HHHhcccCCCcceecHHHHHHHHHH----hccCCCCEEEEcCccccCCH-----HHHHHHHHHHh--hcCcEEEEecCCC
Confidence             112235689999999988764332    22335789999999998543     23344555555  2445678899954

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.92  E-value=6.1e-09  Score=94.59  Aligned_cols=142  Identities=12%  Similarity=0.043  Sum_probs=99.6

Q ss_pred             EEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCc
Q psy12977         53 FACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRS  129 (226)
Q Consensus        53 li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~  129 (226)
                      +..+.+|||||..|+-.+-..+..    |.++|+++|..+|+.|+.+.++..+.  +..+..+++.-.+.++.   ....
T Consensus       164 i~~~~~GSGKTevyl~~i~~~l~~----Gk~vLvLvPEi~lt~q~~~rl~~~f~--~~~v~~lhS~l~~~~R~~~w~~~~  237 (665)
T PRK14873        164 VWQALPGEDWARRLAAAAAATLRA----GRGALVVVPDQRDVDRLEAALRALLG--AGDVAVLSAGLGPADRYRRWLAVL  237 (665)
T ss_pred             HhhcCCCCcHHHHHHHHHHHHHHc----CCeEEEEecchhhHHHHHHHHHHHcC--CCcEEEECCCCCHHHHHHHHHHHh
Confidence            444446999999998877776654    66899999999999999999988774  24455555544333332   2334


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccC---ccchHHHHHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG---VRGFRDQLAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~---~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                      .+...|+|+|-..         -..+++++.++|+||-|.-.-..   .+....++.......  .++.+++.|||++-+
T Consensus       238 ~G~~~IViGtRSA---------vFaP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~--~~~~lvLgSaTPSle  306 (665)
T PRK14873        238 RGQARVVVGTRSA---------VFAPVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQ--HGCALLIGGHARTAE  306 (665)
T ss_pred             CCCCcEEEEccee---------EEeccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHHH--cCCcEEEECCCCCHH
Confidence            5668999999754         35668899999999999554322   123445555555444  789999999998866


Q ss_pred             HHHHH
Q psy12977        207 VAKWC  211 (226)
Q Consensus       207 ~~~~~  211 (226)
                      ...++
T Consensus       307 s~~~~  311 (665)
T PRK14873        307 AQALV  311 (665)
T ss_pred             HHHHH
Confidence            55443

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=98.92  E-value=1.1e-08  Score=95.18  Aligned_cols=157  Identities=21%  Similarity=0.044  Sum_probs=98.8

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---  125 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---  125 (226)
                      |-=++=.|.||+|||++-+=.|+. +. +...|.|..|..-.|.|..|.-+.+++...-......+..|+....+-+   
T Consensus       431 GfF~vNMASTGcGKT~aNARImya-Ls-d~~~g~RfsiALGLRTLTLQTGda~r~rL~L~~ddLAVlIGs~Av~~L~e~~  508 (1110)
T TIGR02562       431 GAFGVNMASTGCGKTLANARAMYA-LR-DDKQGARFAIALGLRSLTLQTGHALKTRLNLSDDDLAVLIGGTAVQTLFDLS  508 (1110)
T ss_pred             CeEEEEecCCCcchHHHHHHHHHH-hC-CCCCCceEEEEccccceeccchHHHHHhcCCCccceEEEECHHHHHHHHHHH
Confidence            334677899999999986443333 22 4556779999999999999998888876544333333333332111000   


Q ss_pred             ------------------C--CC-------------------c--------CCCCCEEEECchHHHHhHhcCCC-CCC--
Q psy12977        126 ------------------G--PR-------------------S--------AQKFDVLITTPNKLVYLLQMDPP-ALN--  155 (226)
Q Consensus       126 ------------------~--~~-------------------~--------~~~~~IiV~Tp~~l~~~~~~~~~-~~~--  155 (226)
                                        .  ..                   +        .-.+.++|||+.+++.......+ ...  
T Consensus       509 ~~~~~~~~~~GSeS~e~l~~e~~~~~~~~~~g~l~~~~l~~~l~~~~k~~rll~apv~V~TIDQlL~a~~~~r~~~~~l~  588 (1110)
T TIGR02562       509 KEKIEQVDEDGSESAPIFLAEGQDCNLPDWDGPLDTIELLGRLSLDDKEKTLLAAPVLVCTIDHLIPATESHRGGHHIAP  588 (1110)
T ss_pred             hhhccccccCCCccchhhhcccCcCCeeeccCCccchhhhhhhccChhhhhhhcCCeEEecHHHHHHHhhhcccchhHHH
Confidence                              0  00                   0        12268999999999987732111 111  


Q ss_pred             CCC--ccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHH
Q psy12977        156 LAN--VEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWC  211 (226)
Q Consensus       156 ~~~--~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~  211 (226)
                      +-+  -+.||+||+|..-..    -...+.++++.+...+..++++|||+|+...+.+
T Consensus       589 ll~La~svlVlDEVHaYD~~----~~~~L~rlL~w~~~lG~~VlLmSATLP~~l~~~L  642 (1110)
T TIGR02562       589 MLRLMSSDLILDEPDDYEPE----DLPALLRLVQLAGLLGSRVLLSSATLPPALVKTL  642 (1110)
T ss_pred             HHHhcCCCEEEECCccCCHH----HHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHH
Confidence            112  358999999976443    3345566665443468899999999998764443

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.

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=98.85  E-value=3.6e-08  Score=93.19  Aligned_cols=142  Identities=18%  Similarity=0.093  Sum_probs=93.2

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCC
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGP  127 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (226)
                      .++.-+||--+|||||++....+-.....  ...+.+++++..++|-.|..+.++.+........ ...+......... 
T Consensus       272 ~~~~G~IWHtqGSGKTlTm~~~A~~l~~~--~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~-~~~s~~~Lk~~l~-  347 (962)
T COG0610         272 DGKGGYIWHTQGSGKTLTMFKLARLLLEL--PKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP-KAESTSELKELLE-  347 (962)
T ss_pred             cCCceEEEeecCCchHHHHHHHHHHHHhc--cCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc-cccCHHHHHHHHh-
Confidence            34568999999999999865554444433  5577999999999999999999999976544433 2222222112211 


Q ss_pred             CcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        128 RSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       128 ~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                        .....|+|||-++|............-.+--.+|+||||+.-..   .....+   ...+  ++...++||.|+
T Consensus       348 --~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRSQ~G---~~~~~~---~~~~--~~a~~~gFTGTP  413 (962)
T COG0610         348 --DGKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRSQYG---ELAKLL---KKAL--KKAIFIGFTGTP  413 (962)
T ss_pred             --cCCCcEEEEEecccchhhhcccccccCCCcEEEEEechhhcccc---HHHHHH---HHHh--ccceEEEeeCCc
Confidence              12457999999999887765311112222338999999986432   233333   3333  458899999994

>KOG0952|consensus

Probab=98.85  E-value=2.5e-09  Score=98.18  Aligned_cols=138  Identities=24%  Similarity=0.298  Sum_probs=109.0

Q ss_pred             hccccCCCCcccccccC--CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         30 NSIFKHFEPHFTITYLS--PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        30 ~~~~~~~~~~Q~~~~~~--~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      +..++.++|.|.+.+.-  .-..++++-+|||+|||.++...+.......  ++.+++|++|.++|+..-.+.+......
T Consensus       922 e~~~~~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~--p~~kvvyIap~kalvker~~Dw~~r~~~  999 (1230)
T KOG0952|consen  922 EALYKYFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYY--PGSKVVYIAPDKALVKERSDDWSKRDEL  999 (1230)
T ss_pred             HHhhcccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccC--CCccEEEEcCCchhhcccccchhhhccc
Confidence            45566889999888743  3457789999999999999999888777644  3469999999999999988877777666


Q ss_pred             CCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977        108 LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      .|.++....++......    ....++++|+||+++....++|...-=+.+++.+|+||.|.+.+.
T Consensus      1000 ~g~k~ie~tgd~~pd~~----~v~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~ 1061 (1230)
T KOG0952|consen 1000 PGIKVIELTGDVTPDVK----AVREADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGED 1061 (1230)
T ss_pred             CCceeEeccCccCCChh----heecCceEEcccccccCccccccchhhhccccceeecccccccCC
Confidence            68888777776544322    235678999999999888887666666889999999999987665

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.84  E-value=1.2e-08  Score=94.03  Aligned_cols=72  Identities=18%  Similarity=0.178  Sum_probs=55.6

Q ss_pred             ccCCCCccccc----c-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         33 FKHFEPHFTIT----Y-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        33 ~~~~~~~Q~~~----~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      |+.+.|.|...    . .+..++++++.+|||+|||++.+.+++...... ...++++|.+.|..-..|+.++++...
T Consensus         8 y~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~-~~~~kIiy~sRThsQl~q~i~Elk~~~   84 (705)
T TIGR00604         8 YEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEK-PEVRKIIYASRTHSQLEQATEELRKLM   84 (705)
T ss_pred             CCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhc-cccccEEEEcccchHHHHHHHHHHhhh
Confidence            44556677333    2 556788999999999999999999988766432 223589999999999999999988853

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).

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=98.76  E-value=2.6e-08  Score=90.03  Aligned_cols=150  Identities=20%  Similarity=0.201  Sum_probs=92.2

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcC------CCeEEEEecchhhh
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL------GLRAHVIGKIQQAA  122 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~------~~~~~~~~~~~~~~  122 (226)
                      .-|+-|.+.||+|||.+|+-.++..-++..  -.+.||++||.++-+-++...+...+++      +.+...+..+ ...
T Consensus        74 ~lNiDI~METGTGKTy~YlrtmfeLhk~YG--~~KFIivVPs~AIkeGv~~~s~~~~ehF~k~~Yent~~e~~i~~-~~~  150 (985)
T COG3587          74 KLNIDILMETGTGKTYTYLRTMFELHKKYG--LFKFIIVVPSLAIKEGVFLTSKETTEHFFKSEYENTRLESYIYD-EDI  150 (985)
T ss_pred             cceeeEEEecCCCceeeHHHHHHHHHHHhC--ceeEEEEeccHHHHhhhHHHHHHHHHHHhhhhccCcceeEEeec-hHH
Confidence            357889999999999999988777665433  3489999999999888766655554433      2444444333 222


Q ss_pred             hhhCCCcCCCCCEEEECchHHHHh------Hhc----CCC-----CCC---CCCc-cEEEEcccccccccCccchHHHHH
Q psy12977        123 EKFGPRSAQKFDVLITTPNKLVYL------LQM----DPP-----ALN---LANV-EWLIVDESDKLFEAGVRGFRDQLA  183 (226)
Q Consensus       123 ~~~~~~~~~~~~IiV~Tp~~l~~~------~~~----~~~-----~~~---~~~~-~~lViDE~h~l~~~~~~~~~~~i~  183 (226)
                      ........+.+.+++.|-..+..-      +++    ..+     .-+   +..+ -++|+||.|.+...+  .++..+.
T Consensus       151 ~~~~~~~~~~~~vLl~~~~Afnk~~inan~iN~~s~~~~~~~~~~~spvd~la~~rPIvIvDEPh~f~~~~--k~~~~i~  228 (985)
T COG3587         151 EKFKFKSNNKPCVLLIFVSAFNKEEINANMINSESMENTNLFNGATSPVDALASMRPIVIVDEPHRFLGDD--KTYGAIK  228 (985)
T ss_pred             HHHhhccCCCceEEEEehhhhccccccccccchhhhcccCccccccCHHHHHHhcCCEEEecChhhcccch--HHHHHHH
Confidence            333334456778888876655433      111    001     000   1122 289999999997632  3444444


Q ss_pred             HHHHhcCCCCceEEEEeeeCchhHHH
Q psy12977        184 VIYAACSGPNLKRGMFSATHTEDVAK  209 (226)
Q Consensus       184 ~i~~~~~~~~~q~v~~SAT~~~~~~~  209 (226)
                      .+.      ..-++=+|||++++...
T Consensus       229 ~l~------pl~ilRfgATfkd~y~~  248 (985)
T COG3587         229 QLN------PLLILRFGATFKDEYNN  248 (985)
T ss_pred             hhC------ceEEEEecccchhhhcC
Confidence            332      23356789999987663

>KOG0926|consensus

Probab=98.73  E-value=6.4e-08  Score=87.11  Aligned_cols=144  Identities=19%  Similarity=0.154  Sum_probs=84.2

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCC--CCCCceEEEEcccHHHHHHHHHH-HHHHhhcCCCeEEEEecchhhhhhh
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGP--KNLGFRAVIVCPTRELAKQTYNE-TVRLSEGLGLRAHVIGKIQQAAEKF  125 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~--~~~~~~~iil~Pt~~L~~q~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  125 (226)
                      +--++|+|.||||||.-.---++++-...  ...+.-+-|.-|.|--|..+++. ..++.. ++..+.+..       ++
T Consensus       271 n~vvIIcGeTGsGKTTQvPQFLYEAGf~s~~~~~~gmIGITqPRRVAaiamAkRVa~EL~~-~~~eVsYqI-------Rf  342 (1172)
T KOG0926|consen  271 NPVVIICGETGSGKTTQVPQFLYEAGFASEQSSSPGMIGITQPRRVAAIAMAKRVAFELGV-LGSEVSYQI-------RF  342 (1172)
T ss_pred             CCeEEEecCCCCCccccchHHHHHcccCCccCCCCCeeeecCchHHHHHHHHHHHHHHhcc-CccceeEEE-------Ee
Confidence            44589999999999976433344432211  11222455667877655555443 233333 344443322       22


Q ss_pred             CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccc-ccC-ccchHHHHHHHHHhcC-----CCCceEEE
Q psy12977        126 GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLF-EAG-VRGFRDQLAVIYAACS-----GPNLKRGM  198 (226)
Q Consensus       126 ~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~-~~~-~~~~~~~i~~i~~~~~-----~~~~q~v~  198 (226)
                      ......+..|-+.|.+.|++-+.+   .+.+.+.+.+|+||||.-. ..+ --+....+..+.....     -...+++.
T Consensus       343 d~ti~e~T~IkFMTDGVLLrEi~~---DflL~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~k~~ke~~~~kpLKLII  419 (1172)
T KOG0926|consen  343 DGTIGEDTSIKFMTDGVLLREIEN---DFLLTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQKYYKEQCQIKPLKLII  419 (1172)
T ss_pred             ccccCCCceeEEecchHHHHHHHH---hHhhhhceeEEechhhhccchHHHHHHHHHHHHHHHHHHhhhhcccCceeEEE
Confidence            223456678999999999998885   5568899999999999432 111 0012222223333321     13567899


Q ss_pred             EeeeC
Q psy12977        199 FSATH  203 (226)
Q Consensus       199 ~SAT~  203 (226)
                      ||||+
T Consensus       420 MSATL  424 (1172)
T KOG0926|consen  420 MSATL  424 (1172)
T ss_pred             EeeeE
Confidence            99995

>KOG0923|consensus

Probab=98.72  E-value=2.4e-07  Score=81.94  Aligned_cols=162  Identities=19%  Similarity=0.102  Sum_probs=102.3

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHH-HHHHHhhcCCCeEEEEecchhhhhh
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYN-ETVRLSEGLGLRAHVIGKIQQAAEK  124 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  124 (226)
                      +....-++|.|.||||||.-.--.+.+.-.  ...+.++-+..|.|--|..++. ..+++...+|-.+++.       .+
T Consensus       277 v~e~QVLiI~GeTGSGKTTQiPQyL~EaGy--tk~gk~IgcTQPRRVAAmSVAaRVA~EMgvkLG~eVGYs-------IR  347 (902)
T KOG0923|consen  277 VKEHQVLIIVGETGSGKTTQIPQYLYEAGY--TKGGKKIGCTQPRRVAAMSVAARVAEEMGVKLGHEVGYS-------IR  347 (902)
T ss_pred             HHhCcEEEEEcCCCCCccccccHHHHhccc--ccCCceEeecCcchHHHHHHHHHHHHHhCcccccccceE-------EE
Confidence            344567899999999999763222333222  2234457788898877777644 4555555554444322       22


Q ss_pred             hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccc-cccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        125 FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKL-FEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       125 ~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l-~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      +...-.++.-|=+.|.+.|++-+..   ..++++.+.+||||||.- +..+  -....++.|.+.  .+..+++..|||+
T Consensus       348 FEdcTSekTvlKYMTDGmLlREfL~---epdLasYSViiiDEAHERTL~TD--ILfgLvKDIar~--RpdLKllIsSAT~  420 (902)
T KOG0923|consen  348 FEDCTSEKTVLKYMTDGMLLREFLS---EPDLASYSVIIVDEAHERTLHTD--ILFGLVKDIARF--RPDLKLLISSATM  420 (902)
T ss_pred             eccccCcceeeeeecchhHHHHHhc---cccccceeEEEeehhhhhhhhhh--HHHHHHHHHHhh--CCcceEEeecccc
Confidence            3333445556779999999988774   556999999999999953 2221  122333444433  4789999999998


Q ss_pred             chhHHHHHHHhcCCCeEEecCCC
Q psy12977        204 TEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       204 ~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      ..+   ....|+.+.-+..+.+|
T Consensus       421 DAe---kFS~fFDdapIF~iPGR  440 (902)
T KOG0923|consen  421 DAE---KFSAFFDDAPIFRIPGR  440 (902)
T ss_pred             CHH---HHHHhccCCcEEeccCc
Confidence            733   35567776655555544

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

Probab=98.70  E-value=3.7e-08  Score=90.25  Aligned_cols=71  Identities=27%  Similarity=0.315  Sum_probs=53.3

Q ss_pred             ccccCCCCccccc-----ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         31 SIFKHFEPHFTIT-----YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        31 ~~~~~~~~~Q~~~-----~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      +..-++.+.|...     ..+.+++.+++.||||+|||++|+.|++......   +.+++|.++|+.+-+|..+....+
T Consensus        11 ~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~---~~~viist~t~~lq~q~~~~~~~~   86 (654)
T COG1199          11 FPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREE---GKKVIISTRTKALQEQLLEEDLPI   86 (654)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHc---CCcEEEECCCHHHHHHHHHhhcch
Confidence            3344555556333     2455667799999999999999999998876543   368999999999999998765554

>KOG0924|consensus

Probab=98.68  E-value=2.3e-07  Score=82.35  Aligned_cols=159  Identities=18%  Similarity=0.069  Sum_probs=93.2

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHH-HHHHhhcCCCeEEEEecchhhhhhh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE-TVRLSEGLGLRAHVIGKIQQAAEKF  125 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  125 (226)
                      -.+.-+++.+.||||||.-..-.++..-..   .+.-+-+..|.|.-|..+++. ..++...+|..+.+.       .++
T Consensus       369 r~n~vvvivgETGSGKTTQl~QyL~edGY~---~~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VGYs-------IRF  438 (1042)
T KOG0924|consen  369 RENQVVVIVGETGSGKTTQLAQYLYEDGYA---DNGMIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGYS-------IRF  438 (1042)
T ss_pred             hhCcEEEEEecCCCCchhhhHHHHHhcccc---cCCeeeecCchHHHHHHHHHHHHHHhCCccccccceE-------EEe
Confidence            345678999999999998654444443221   222445566888777776654 334433344443322       222


Q ss_pred             CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcC--CCCceEEEEeeeC
Q psy12977        126 GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACS--GPNLKRGMFSATH  203 (226)
Q Consensus       126 ~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~--~~~~q~v~~SAT~  203 (226)
                      ...-..+..|=..|-+.|++-.-.   .-.+.+.+.+|+||||.-.-.     .+.+..+++...  ....+++.+|||+
T Consensus       439 EdvT~~~T~IkymTDGiLLrEsL~---d~~L~kYSviImDEAHERslN-----tDilfGllk~~larRrdlKliVtSATm  510 (1042)
T KOG0924|consen  439 EDVTSEDTKIKYMTDGILLRESLK---DRDLDKYSVIIMDEAHERSLN-----TDILFGLLKKVLARRRDLKLIVTSATM  510 (1042)
T ss_pred             eecCCCceeEEEeccchHHHHHhh---hhhhhheeEEEechhhhcccc-----hHHHHHHHHHHHHhhccceEEEeeccc
Confidence            233335567889999999886553   344889999999999953211     122222222221  3578999999998


Q ss_pred             chhHHHHHHHhcCCCeEEecCCC
Q psy12977        204 TEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       204 ~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      ..  .. ...|+.+-=..++.+|
T Consensus       511 ~a--~k-f~nfFgn~p~f~IpGR  530 (1042)
T KOG0924|consen  511 DA--QK-FSNFFGNCPQFTIPGR  530 (1042)
T ss_pred             cH--HH-HHHHhCCCceeeecCC
Confidence            63  22 3355553333444443

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.67  E-value=1.1e-07  Score=87.17  Aligned_cols=145  Identities=21%  Similarity=0.200  Sum_probs=104.3

Q ss_pred             HHHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH
Q psy12977         18 ISIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE   92 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~   92 (226)
                      ..+.+...+.+++....    .+..+|-... .+..|+  +....||-|||++..+|++-....    |..+-|++.+-.
T Consensus        57 d~~l~eafAvvREA~~R~lG~r~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL~----GkgVhVVTvNdY  130 (925)
T PRK12903         57 EDIRVEAFAVAREATKRVLGKRPYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLNALT----GKGVIVSTVNEY  130 (925)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCcCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHHHhc----CCceEEEecchh
Confidence            44566666666666555    4555675554 334443  799999999999988887643332    567899999999


Q ss_pred             HHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCC-----CCCCCCCccEEEEccc
Q psy12977         93 LAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDP-----PALNLANVEWLIVDES  167 (226)
Q Consensus        93 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~-----~~~~~~~~~~lViDE~  167 (226)
                      ||..=.+++..+...+|..+.+...+.....+   .....|||+.+|...|--.+-+++     .......+.+.|+||+
T Consensus       131 LA~RDae~mg~vy~fLGLsvG~i~~~~~~~~r---r~aY~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEV  207 (925)
T PRK12903        131 LAERDAEEMGKVFNFLGLSVGINKANMDPNLK---REAYACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEV  207 (925)
T ss_pred             hhhhhHHHHHHHHHHhCCceeeeCCCCChHHH---HHhccCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccc
Confidence            99999999999999999999988765443333   345789999999888754332221     1223567889999999


Q ss_pred             cccc
Q psy12977        168 DKLF  171 (226)
Q Consensus       168 h~l~  171 (226)
                      |.++
T Consensus       208 DSIL  211 (925)
T PRK12903        208 DSIL  211 (925)
T ss_pred             hhee
Confidence            9775

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

Probab=98.67  E-value=4.6e-08  Score=77.65  Aligned_cols=68  Identities=15%  Similarity=0.225  Sum_probs=44.9

Q ss_pred             CCCcccccc-cCCCCCe-EEEECCCCchHhHHHHHHHHHHhc----CCCCCCceEEEEcccHHHHHHHHHHHHH
Q psy12977         36 FEPHFTITY-LSPLGRQ-IFACAPTGSGKTAAFLIPIIHSLR----GPKNLGFRAVIVCPTRELAKQTYNETVR  103 (226)
Q Consensus        36 ~~~~Q~~~~-~~~~~~~-~li~apTGsGKT~~~~~~~~~~~~----~~~~~~~~~iil~Pt~~L~~q~~~~~~~  103 (226)
                      +++-|..+. ..++... .+|+||+|||||......+...+.    .....+.++++++|+++-+.++.+.+.+
T Consensus         2 ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    2 LNESQREAIQSALSSNGITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             --HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            456676664 4556666 899999999999654433333311    1134566999999999999999998877

>KOG0925|consensus

Probab=98.65  E-value=8.7e-08  Score=82.04  Aligned_cols=161  Identities=19%  Similarity=0.101  Sum_probs=93.3

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHH-HHHHhhcCCCeEEEEecchhhhh
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE-TVRLSEGLGLRAHVIGKIQQAAE  123 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~-~~~~~~~~~~~~~~~~~~~~~~~  123 (226)
                      .+.++..+++.|.||||||.-.--..+.......   ..+....|.|--|-+++.. ..++--.+|-.++    ..   .
T Consensus        58 ~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~---~~v~CTQprrvaamsva~RVadEMDv~lG~EVG----ys---I  127 (699)
T KOG0925|consen   58 LLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHL---TGVACTQPRRVAAMSVAQRVADEMDVTLGEEVG----YS---I  127 (699)
T ss_pred             HHhcCceEEEEecCCCCccccCcHHHHHHHHhhc---cceeecCchHHHHHHHHHHHHHHhccccchhcc----cc---c
Confidence            4456778999999999999753333333332211   3567777888777776553 2233222222221    11   2


Q ss_pred             hhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccc-cccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        124 KFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKL-FEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       124 ~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l-~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      ++++....+.-.-.+|.+.+.+-...   ...+.+...+|+||+|.- ++.+  -..-.++.....-  +..+++.+|||
T Consensus       128 rfEdC~~~~T~Lky~tDgmLlrEams---~p~l~~y~viiLDeahERtlATD--iLmGllk~v~~~r--pdLk~vvmSat  200 (699)
T KOG0925|consen  128 RFEDCTSPNTLLKYCTDGMLLREAMS---DPLLGRYGVIILDEAHERTLATD--ILMGLLKEVVRNR--PDLKLVVMSAT  200 (699)
T ss_pred             cccccCChhHHHHHhcchHHHHHHhh---CcccccccEEEechhhhhhHHHH--HHHHHHHHHHhhC--CCceEEEeecc
Confidence            22221111111223444444444443   334889999999999943 3321  2444455555444  68999999999


Q ss_pred             CchhHHHHHHHhcCCCeEEecCC
Q psy12977        203 HTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       203 ~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      +.   ...+++|+.|+=.++|.+
T Consensus       201 l~---a~Kfq~yf~n~Pll~vpg  220 (699)
T KOG0925|consen  201 LD---AEKFQRYFGNAPLLAVPG  220 (699)
T ss_pred             cc---hHHHHHHhCCCCeeecCC
Confidence            87   444778998888887764

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=98.59  E-value=1.3e-06  Score=79.64  Aligned_cols=157  Identities=15%  Similarity=0.152  Sum_probs=99.3

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      .-.++.+|-|||||.+..-++-+.+.   .+..++++++..++|+.+..+.++...-. +. +......  + ..   ..
T Consensus        50 ~V~vVRSpMGTGKTtaLi~wLk~~l~---~~~~~VLvVShRrSL~~sL~~rf~~~~l~-gF-v~Y~d~~--~-~~---i~  118 (824)
T PF02399_consen   50 GVLVVRSPMGTGKTTALIRWLKDALK---NPDKSVLVVSHRRSLTKSLAERFKKAGLS-GF-VNYLDSD--D-YI---ID  118 (824)
T ss_pred             CeEEEECCCCCCcHHHHHHHHHHhcc---CCCCeEEEEEhHHHHHHHHHHHHhhcCCC-cc-eeeeccc--c-cc---cc
Confidence            44689999999999877555544443   23558999999999999999988765211 11 1111111  0 00   00


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHH---HHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQ---LAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~---i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                      ....+-+++..+.+.+...     -.+.+.++||+||+...+..-+......   ...++..+-.....++++-|++.+.
T Consensus       119 ~~~~~rLivqIdSL~R~~~-----~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~  193 (824)
T PF02399_consen  119 GRPYDRLIVQIDSLHRLDG-----SLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQ  193 (824)
T ss_pred             ccccCeEEEEehhhhhccc-----ccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHH
Confidence            1234577777777766532     2366789999999997766522112222   2222223325677889999999999


Q ss_pred             HHHHHHHhcC-CCeEEe
Q psy12977        207 VAKWCRRKLK-RRVQIN  222 (226)
Q Consensus       207 ~~~~~~~~~~-~p~~i~  222 (226)
                      ..+++..+.+ +++.+-
T Consensus       194 tvdFl~~~Rp~~~i~vI  210 (824)
T PF02399_consen  194 TVDFLASCRPDENIHVI  210 (824)
T ss_pred             HHHHHHHhCCCCcEEEE
Confidence            9999988764 444443

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

>KOG0385|consensus

Probab=98.47  E-value=2e-06  Score=77.34  Aligned_cols=155  Identities=20%  Similarity=0.223  Sum_probs=101.2

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF  125 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (226)
                      ..+|-|.|+...-|-|||+-. ++++..+....+...-.+|++|-..| ..+.+.++++++  ++.+....|+.......
T Consensus       183 ~engingILaDEMGLGKTlQt-Is~l~yl~~~~~~~GPfLVi~P~StL-~NW~~Ef~rf~P--~l~~~~~~Gdk~eR~~~  258 (971)
T KOG0385|consen  183 YENGINGILADEMGLGKTLQT-ISLLGYLKGRKGIPGPFLVIAPKSTL-DNWMNEFKRFTP--SLNVVVYHGDKEERAAL  258 (971)
T ss_pred             HhcCcccEeehhcccchHHHH-HHHHHHHHHhcCCCCCeEEEeeHhhH-HHHHHHHHHhCC--CcceEEEeCCHHHHHHH
Confidence            355778899999999999754 33333332212222246888998665 668888888887  56677777776655544


Q ss_pred             CCC--cCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        126 GPR--SAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       126 ~~~--~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      .+.  .....+|+|+|.+.....-    ..+.--.++++||||+|++-..     ...+.++++.+  ...-.+++|.|+
T Consensus       259 ~r~~~~~~~fdV~iTsYEi~i~dk----~~lk~~~W~ylvIDEaHRiKN~-----~s~L~~~lr~f--~~~nrLLlTGTP  327 (971)
T KOG0385|consen  259 RRDIMLPGRFDVCITSYEIAIKDK----SFLKKFNWRYLVIDEAHRIKNE-----KSKLSKILREF--KTDNRLLLTGTP  327 (971)
T ss_pred             HHHhhccCCCceEeehHHHHHhhH----HHHhcCCceEEEechhhhhcch-----hhHHHHHHHHh--cccceeEeeCCc
Confidence            332  2457899999999877642    2333346789999999999654     34555777777  344566778884


Q ss_pred             c----hhHHHHHHHhc
Q psy12977        204 T----EDVAKWCRRKL  215 (226)
Q Consensus       204 ~----~~~~~~~~~~~  215 (226)
                      =    .+++.+++-.+
T Consensus       328 LQNNL~ELWaLLnFll  343 (971)
T KOG0385|consen  328 LQNNLHELWALLNFLL  343 (971)
T ss_pred             ccccHHHHHHHHHhhc
Confidence            4    34455554443

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=98.45  E-value=3.9e-07  Score=84.65  Aligned_cols=126  Identities=23%  Similarity=0.204  Sum_probs=92.2

Q ss_pred             CCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEE
Q psy12977         37 EPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVI  115 (226)
Q Consensus        37 ~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  115 (226)
                      ..+|-.-. .+..|+  +..+.||-|||++..+|++-....    |..+-+++.+-.||..=.+++..+...+|..+.++
T Consensus       140 ydVQLiGgivLh~G~--IAEM~TGEGKTLvatlp~yLnAL~----G~gVHvVTvNDYLA~RDaewm~p~y~flGLtVg~i  213 (1025)
T PRK12900        140 YDVQLIGGIVLHSGK--ISEMATGEGKTLVSTLPTFLNALT----GRGVHVVTVNDYLAQRDKEWMNPVFEFHGLSVGVI  213 (1025)
T ss_pred             cchHHhhhHHhhcCC--ccccCCCCCcchHhHHHHHHHHHc----CCCcEEEeechHhhhhhHHHHHHHHHHhCCeeeee
Confidence            34554443 334444  789999999999999887654442    55688999999999999999999999999999988


Q ss_pred             ecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcC-----CCCCCCCCccEEEEccccccc
Q psy12977        116 GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMD-----PPALNLANVEWLIVDESDKLF  171 (226)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~-----~~~~~~~~~~~lViDE~h~l~  171 (226)
                      ........+   .....|||..+|..-|--.+-++     +.........+.||||+|.++
T Consensus       214 ~~~~~~~~R---r~aY~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDSvL  271 (1025)
T PRK12900        214 LNTMRPEER---REQYLCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDSVL  271 (1025)
T ss_pred             CCCCCHHHH---HHhCCCcceecCCCccccccchhccccchhhhhccCCceEEEechhhhh
Confidence            665443333   46689999999987764322221     122335677899999999775

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=98.40  E-value=1.3e-06  Score=74.37  Aligned_cols=112  Identities=18%  Similarity=0.213  Sum_probs=69.2

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      +-++|.|.+|||||+..+.-+ ..+ .....+.++++++++.++.....+.+.....  +                    
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~-~~l-~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~--~--------------------   57 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLA-KEL-QNSEEGKKVLYLCGNHPLRNKLREQLAKKYN--P--------------------   57 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHH-HHh-hccccCCceEEEEecchHHHHHHHHHhhhcc--c--------------------
Confidence            357899999999998664433 333 1223456899999999999988877655430  0                    


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc----chHHHHHHHHHh
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR----GFRDQLAVIYAA  188 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~----~~~~~i~~i~~~  188 (226)
                       ......+..+..+......  ........+++|+||||++......    .....+..+++.
T Consensus        58 -~~~~~~~~~~~~~i~~~~~--~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   58 -KLKKSDFRKPTSFINNYSE--SDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             -chhhhhhhhhHHHHhhccc--ccccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence             0001223344444333321  3345778899999999999874211    234566666654

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>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=98.38  E-value=2.1e-07  Score=72.59  Aligned_cols=143  Identities=15%  Similarity=0.121  Sum_probs=68.4

Q ss_pred             CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEE
Q psy12977         35 HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAH  113 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~  113 (226)
                      ..|+-|..+. .+.+...+++.||.|||||+..+..+++.+.+  ....+.++.-|..+..+.+-    -+......+..
T Consensus         4 p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~--g~~~kiii~Rp~v~~~~~lG----flpG~~~eK~~   77 (205)
T PF02562_consen    4 PKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKE--GEYDKIIITRPPVEAGEDLG----FLPGDLEEKME   77 (205)
T ss_dssp             --SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT--TS-SEEEEEE-S--TT--------SS---------
T ss_pred             CCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHh--CCCcEEEEEecCCCCccccc----cCCCCHHHHHH
Confidence            3455665553 44466778999999999999998888888875  33458999988876532221    11111011100


Q ss_pred             EEecchhhhhhhCC--------CcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHH
Q psy12977        114 VIGKIQQAAEKFGP--------RSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVI  185 (226)
Q Consensus       114 ~~~~~~~~~~~~~~--------~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i  185 (226)
                      .....  -......        .......|-+..++.+        +...++ -.++|+|||+.+       ....++.+
T Consensus        78 p~~~p--~~d~l~~~~~~~~~~~~~~~~~Ie~~~~~~i--------RGrt~~-~~~iIvDEaQN~-------t~~~~k~i  139 (205)
T PF02562_consen   78 PYLRP--IYDALEELFGKEKLEELIQNGKIEIEPLAFI--------RGRTFD-NAFIIVDEAQNL-------TPEELKMI  139 (205)
T ss_dssp             TTTHH--HHHHHTTTS-TTCHHHHHHTTSEEEEEGGGG--------TT--B--SEEEEE-SGGG---------HHHHHHH
T ss_pred             HHHHH--HHHHHHHHhChHhHHHHhhcCeEEEEehhhh--------cCcccc-ceEEEEecccCC-------CHHHHHHH
Confidence            00000  0000000        0112334555554432        122233 279999999986       44578888


Q ss_pred             HHhcCCCCceEEEEeee
Q psy12977        186 YAACSGPNLKRGMFSAT  202 (226)
Q Consensus       186 ~~~~~~~~~q~v~~SAT  202 (226)
                      +..+ ..+++++++.-.
T Consensus       140 lTR~-g~~skii~~GD~  155 (205)
T PF02562_consen  140 LTRI-GEGSKIIITGDP  155 (205)
T ss_dssp             HTTB--TT-EEEEEE--
T ss_pred             Hccc-CCCcEEEEecCc
Confidence            8888 678888887655

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.35  E-value=7.4e-07  Score=83.01  Aligned_cols=127  Identities=27%  Similarity=0.239  Sum_probs=91.0

Q ss_pred             CCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEE
Q psy12977         36 FEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHV  114 (226)
Q Consensus        36 ~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~  114 (226)
                      +..+|-.-. .+..|+  +..+.||-|||++..+|++-....    |..+-+++.+-.||..=.+++..+..++|..+.+
T Consensus       170 ~yDVQliGgivLh~G~--IAEM~TGEGKTLvAtlp~yLnAL~----GkgVHvVTVNDYLA~RDaewmgply~fLGLsvg~  243 (1112)
T PRK12901        170 HYDVQLIGGVVLHQGK--IAEMATGEGKTLVATLPVYLNALT----GNGVHVVTVNDYLAKRDSEWMGPLYEFHGLSVDC  243 (1112)
T ss_pred             ccchHHhhhhhhcCCc--eeeecCCCCchhHHHHHHHHHHHc----CCCcEEEEechhhhhccHHHHHHHHHHhCCceee
Confidence            334454443 333444  789999999999999887755443    5567899999999999999999999999999998


Q ss_pred             Eecch-hhhhhhCCCcCCCCCEEEECchHHHHhHhcC-----CCCCCCCCccEEEEccccccc
Q psy12977        115 IGKIQ-QAAEKFGPRSAQKFDVLITTPNKLVYLLQMD-----PPALNLANVEWLIVDESDKLF  171 (226)
Q Consensus       115 ~~~~~-~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~-----~~~~~~~~~~~lViDE~h~l~  171 (226)
                      +.... ....   +.....|||..+|..-|--.+-++     ..........+.|+||+|.++
T Consensus       244 i~~~~~~~~~---rr~aY~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDSIL  303 (1112)
T PRK12901        244 IDKHQPNSEA---RRKAYNADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDSVL  303 (1112)
T ss_pred             cCCCCCCHHH---HHHhCCCcceecCCCccccccchhccccchHhhhCcCCceeEeechhhhh
Confidence            86532 2222   345688999999987764322221     122335668899999999775

>KOG1123|consensus

Probab=98.30  E-value=3.6e-07  Score=78.62  Aligned_cols=135  Identities=19%  Similarity=0.137  Sum_probs=90.7

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      +.-+|..|-|+|||+.-+-+++ .+      +.+++++|.+---++||..+++.+.--....++.+..+..+      ..
T Consensus       321 RSGiIVLPCGAGKtLVGvTAa~-ti------kK~clvLcts~VSVeQWkqQfk~wsti~d~~i~rFTsd~Ke------~~  387 (776)
T KOG1123|consen  321 RSGIIVLPCGAGKTLVGVTAAC-TI------KKSCLVLCTSAVSVEQWKQQFKQWSTIQDDQICRFTSDAKE------RF  387 (776)
T ss_pred             cCceEEEecCCCCceeeeeeee-ee------cccEEEEecCccCHHHHHHHHHhhcccCccceEEeeccccc------cC
Confidence            5678999999999987644432 22      34799999999999999999999976666666666655432      24


Q ss_pred             CCCCCEEEECchHHHHhHhcCC------CCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDP------PALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~------~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      ..++.|+|+|-..+..--++..      ..+.-..+.++++||+|.+.+.   -|...+ .+...    . -.++++||+
T Consensus       388 ~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA~---MFRRVl-siv~a----H-cKLGLTATL  458 (776)
T KOG1123|consen  388 PSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPAK---MFRRVL-SIVQA----H-CKLGLTATL  458 (776)
T ss_pred             CCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchHH---HHHHHH-HHHHH----H-hhccceeEE
Confidence            4678899999876654222110      1122456789999999988776   233333 33322    2 345779997


Q ss_pred             chh
Q psy12977        204 TED  206 (226)
Q Consensus       204 ~~~  206 (226)
                      -++
T Consensus       459 vRE  461 (776)
T KOG1123|consen  459 VRE  461 (776)
T ss_pred             eec
Confidence            643

>PF13245 AAA_19: Part of AAA domain

Probab=98.27  E-value=4.1e-06  Score=54.99  Aligned_cols=53  Identities=25%  Similarity=0.379  Sum_probs=39.3

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET  101 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~  101 (226)
                      ++-+++.+|+|||||...+-.+...+......+.++++++|++..+.++.+.+
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence            34466799999999976665555555321122669999999999999988877

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=98.27  E-value=3e-06  Score=66.10  Aligned_cols=124  Identities=23%  Similarity=0.292  Sum_probs=67.4

Q ss_pred             CCCcccccc-cC-CCC-CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeE
Q psy12977         36 FEPHFTITY-LS-PLG-RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRA  112 (226)
Q Consensus        36 ~~~~Q~~~~-~~-~~~-~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~  112 (226)
                      +++-|..+. .+ .++ +-.+++||+|+|||... ..+...+..   .+.++++++||..-+....+..       +...
T Consensus         2 L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l-~~~~~~~~~---~g~~v~~~apT~~Aa~~L~~~~-------~~~a   70 (196)
T PF13604_consen    2 LNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLL-KALAEALEA---AGKRVIGLAPTNKAAKELREKT-------GIEA   70 (196)
T ss_dssp             S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHH-HHHHHHHHH---TT--EEEEESSHHHHHHHHHHH-------TS-E
T ss_pred             CCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHH-HHHHHHHHh---CCCeEEEECCcHHHHHHHHHhh-------Ccch
Confidence            445564443 22 233 45789999999999753 335555543   2468999999998888766642       2221


Q ss_pred             EEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcC--CCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcC
Q psy12977        113 HVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMD--PPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACS  190 (226)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~--~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~  190 (226)
                      .                         |-.+++......  .......+.+++||||+-.+...       .+..+++...
T Consensus        71 ~-------------------------Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~~~-------~~~~ll~~~~  118 (196)
T PF13604_consen   71 Q-------------------------TIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVDSR-------QLARLLRLAK  118 (196)
T ss_dssp             E-------------------------EHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-BHH-------HHHHHHHHS-
T ss_pred             h-------------------------hHHHHHhcCCcccccccccCCcccEEEEecccccCHH-------HHHHHHHHHH
Confidence            1                         211111111100  00111556679999999976433       5666666665


Q ss_pred             CCCceEEEEeee
Q psy12977        191 GPNLKRGMFSAT  202 (226)
Q Consensus       191 ~~~~q~v~~SAT  202 (226)
                      ..+.+++++.-+
T Consensus       119 ~~~~klilvGD~  130 (196)
T PF13604_consen  119 KSGAKLILVGDP  130 (196)
T ss_dssp             T-T-EEEEEE-T
T ss_pred             hcCCEEEEECCc
Confidence            557888887665

>PRK10536 hypothetical protein; Provisional

Probab=98.24  E-value=5.5e-06  Score=66.67  Aligned_cols=142  Identities=14%  Similarity=0.022  Sum_probs=76.6

Q ss_pred             CCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHH-----------HHHHHHH
Q psy12977         35 HFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAK-----------QTYNETV  102 (226)
Q Consensus        35 ~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~-----------q~~~~~~  102 (226)
                      ..+..|... ..+.++..+++.||+|+|||+......++.+.+..  ..++++.-|+.+..+           -....+.
T Consensus        59 p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~--~~kIiI~RP~v~~ge~LGfLPG~~~eK~~p~~~  136 (262)
T PRK10536         59 ARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHKD--VDRIIVTRPVLQADEDLGFLPGDIAEKFAPYFR  136 (262)
T ss_pred             CCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCC--eeEEEEeCCCCCchhhhCcCCCCHHHHHHHHHH
Confidence            334445433 35556678899999999999987777776664322  446777767654322           1222222


Q ss_pred             HHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHH
Q psy12977        103 RLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQL  182 (226)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i  182 (226)
                      .+...+...    .+... .....  ......|-|...+.    ++    ...+ +-+++|+||++.+.       ...+
T Consensus       137 pi~D~L~~~----~~~~~-~~~~~--~~~~~~Iei~~l~y----mR----Grtl-~~~~vIvDEaqn~~-------~~~~  193 (262)
T PRK10536        137 PVYDVLVRR----LGASF-MQYCL--RPEIGKVEIAPFAY----MR----GRTF-ENAVVILDEAQNVT-------AAQM  193 (262)
T ss_pred             HHHHHHHHH----hChHH-HHHHH--HhccCcEEEecHHH----hc----CCcc-cCCEEEEechhcCC-------HHHH
Confidence            222211110    01100 01100  01122355554432    22    2223 33799999999863       3577


Q ss_pred             HHHHHhcCCCCceEEEEeee
Q psy12977        183 AVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       183 ~~i~~~~~~~~~q~v~~SAT  202 (226)
                      +.++..+ ..+++++++.-.
T Consensus       194 k~~ltR~-g~~sk~v~~GD~  212 (262)
T PRK10536        194 KMFLTRL-GENVTVIVNGDI  212 (262)
T ss_pred             HHHHhhc-CCCCEEEEeCCh
Confidence            7788887 678888876544

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=98.20  E-value=1.7e-05  Score=64.95  Aligned_cols=151  Identities=18%  Similarity=0.082  Sum_probs=97.6

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPR  128 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (226)
                      +.-.++--.||.||--...-.+++.+.+.   ..|.|.++.+..|-....+.++.++.. .+.+..+..-..  .   ..
T Consensus        62 R~Gf~lGDGtGvGKGR~iAgiI~~n~l~G---r~r~vwvS~s~dL~~Da~RDl~DIG~~-~i~v~~l~~~~~--~---~~  132 (303)
T PF13872_consen   62 RAGFFLGDGTGVGKGRQIAGIILENWLRG---RKRAVWVSVSNDLKYDAERDLRDIGAD-NIPVHPLNKFKY--G---DI  132 (303)
T ss_pred             CcEEEeccCCCcCccchhHHHHHHHHHcC---CCceEEEECChhhhhHHHHHHHHhCCC-cccceechhhcc--C---cC
Confidence            45688999999999977666667666542   347999999999999999999988654 333322222110  0   11


Q ss_pred             cCCCCCEEEECchHHHHhHhcCC-CCCC---------CCCccEEEEcccccccccCc-----cchHHHHHHHHHhcCCCC
Q psy12977        129 SAQKFDVLITTPNKLVYLLQMDP-PALN---------LANVEWLIVDESDKLFEAGV-----RGFRDQLAVIYAACSGPN  193 (226)
Q Consensus       129 ~~~~~~IiV~Tp~~l~~~~~~~~-~~~~---------~~~~~~lViDE~h~l~~~~~-----~~~~~~i~~i~~~~~~~~  193 (226)
                      ...+-.|+.+|-..|........ ....         -+.-.++|+||||..-....     ......+..+.+.+  |+
T Consensus       133 ~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~sk~g~avl~LQ~~L--P~  210 (303)
T PF13872_consen  133 IRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHKAKNLSSGSKKPSKTGIAVLELQNRL--PN  210 (303)
T ss_pred             CCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchhcCCCCccCccccHHHHHHHHHHHhC--CC
Confidence            12234599999888877643210 1111         11224999999998755421     12445666777777  67


Q ss_pred             ceEEEEeeeCchhHHHH
Q psy12977        194 LKRGMFSATHTEDVAKW  210 (226)
Q Consensus       194 ~q~v~~SAT~~~~~~~~  210 (226)
                      .+++.+|||--.+.+++
T Consensus       211 ARvvY~SATgasep~Nm  227 (303)
T PF13872_consen  211 ARVVYASATGASEPRNM  227 (303)
T ss_pred             CcEEEecccccCCCcee
Confidence            77999999976665554

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=98.19  E-value=7.9e-05  Score=63.91  Aligned_cols=135  Identities=15%  Similarity=0.109  Sum_probs=74.4

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEE-EEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAV-IVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGP  127 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~i-il~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (226)
                      .+.+++.||||+|||....--+..........+.++. +-+.+...+.  .++++.+.+..+..+..             
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa--~eQL~~~a~~lgvpv~~-------------  238 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGA--KKQIQTYGDIMGIPVKA-------------  238 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHH--HHHHHHHhhcCCcceEe-------------
Confidence            4678999999999998765433322221111222333 4344322211  12355565555554321             


Q ss_pred             CcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc-hh
Q psy12977        128 RSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT-ED  206 (226)
Q Consensus       128 ~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~-~~  206 (226)
                               +-++..+...+..      ..+.+++++|++.+.....  .....+..++....++.--.+.+|||-. .+
T Consensus       239 ---------~~~~~~l~~~L~~------~~~~DlVLIDTaGr~~~~~--~~l~el~~~l~~~~~~~e~~LVlsat~~~~~  301 (388)
T PRK12723        239 ---------IESFKDLKEEITQ------SKDFDLVLVDTIGKSPKDF--MKLAEMKELLNACGRDAEFHLAVSSTTKTSD  301 (388)
T ss_pred             ---------eCcHHHHHHHHHH------hCCCCEEEEcCCCCCccCH--HHHHHHHHHHHhcCCCCeEEEEEcCCCCHHH
Confidence                     1234445444443      4578999999999775321  2345566666555323235577789865 56


Q ss_pred             HHHHHHHhc
Q psy12977        207 VAKWCRRKL  215 (226)
Q Consensus       207 ~~~~~~~~~  215 (226)
                      +.+.+++|-
T Consensus       302 ~~~~~~~~~  310 (388)
T PRK12723        302 VKEIFHQFS  310 (388)
T ss_pred             HHHHHHHhc
Confidence            677777773

>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=98.15  E-value=2.9e-05  Score=67.23  Aligned_cols=137  Identities=15%  Similarity=0.169  Sum_probs=90.4

Q ss_pred             CCCCCceEEEEcccHHHHHHHHHHHHHHhhcC-CC--------eEE------------------------EEecchhhhh
Q psy12977         77 PKNLGFRAVIVCPTRELAKQTYNETVRLSEGL-GL--------RAH------------------------VIGKIQQAAE  123 (226)
Q Consensus        77 ~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~-~~--------~~~------------------------~~~~~~~~~~  123 (226)
                      +.-..|+++|++|+|.-|.++.+.+.++.... ..        ...                        .+.|...+.-
T Consensus        33 QGftRPkVLIL~P~R~~A~~~V~~Li~l~~~~~~~~nk~RF~~efg~~~~~~~~~~~~~~~~~kP~D~~~~F~GN~DD~F  112 (442)
T PF06862_consen   33 QGFTRPKVLILLPFRNSALRIVETLISLLPPGKQVENKKRFEEEFGLPEDEDDDEEPPEFKKSKPEDFKALFSGNNDDCF  112 (442)
T ss_pred             cCCCCceEEEEcccHHHHHHHHHHHHHHcCccchHHHHHHHHHHcCCCccccchhhhccccCCCchhHHHhcCCCccceE
Confidence            34446899999999999999999888876541 00        000                        0000000000


Q ss_pred             hhC----------CCcCCCCCEEEECchHHHHhHhc----CCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        124 KFG----------PRSAQKFDVLITTPNKLVYLLQM----DPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       124 ~~~----------~~~~~~~~IiV~Tp~~l~~~~~~----~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      +.-          ...-.++|||||+|=-|...+..    ....--++++.++|+|.+|.++-.    .|+.+..+++.+
T Consensus       113 rlGik~trk~ikLys~Fy~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQ----NW~Hv~~v~~~l  188 (442)
T PF06862_consen  113 RLGIKFTRKSIKLYSDFYSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQ----NWEHVLHVFEHL  188 (442)
T ss_pred             EEeEEEecCeeeeecccccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHh----hHHHHHHHHHHh
Confidence            000          00036699999999988877763    222333899999999999976543    566666666655


Q ss_pred             C-----------------------CCCceEEEEeeeCchhHHHHHHHhcCC
Q psy12977        190 S-----------------------GPNLKRGMFSATHTEDVAKWCRRKLKR  217 (226)
Q Consensus       190 ~-----------------------~~~~q~v~~SAT~~~~~~~~~~~~~~~  217 (226)
                      .                       ..-.|++++|+...+++..+.++.+.|
T Consensus       189 N~~P~~~~~~DfsRVR~w~Ldg~a~~~RQtii~S~~~~pe~~slf~~~~~N  239 (442)
T PF06862_consen  189 NLQPKKSHDTDFSRVRPWYLDGQAKYYRQTIIFSSFQTPEINSLFNRHCQN  239 (442)
T ss_pred             ccCCCCCCCCCHHHHHHHHHcCcchheeEeEEecCCCCHHHHHHHHhhCcC
Confidence            2                       124799999999999999999986654

; GO: 0005634 nucleus

>KOG0387|consensus

Probab=98.15  E-value=1.7e-05  Score=71.85  Aligned_cols=143  Identities=17%  Similarity=0.177  Sum_probs=87.8

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhh-----
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQA-----  121 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~-----  121 (226)
                      .+++-=|+--.=|-|||.-.+.- +..+.........++|+||.. +..||.+++..++..+.+  ....+....     
T Consensus       222 ~q~~GGILgDeMGLGKTIQiisF-LaaL~~S~k~~~paLIVCP~T-ii~qW~~E~~~w~p~~rv--~ilh~t~s~~r~~~  297 (923)
T KOG0387|consen  222 CQRAGGILGDEMGLGKTIQIISF-LAALHHSGKLTKPALIVCPAT-IIHQWMKEFQTWWPPFRV--FILHGTGSGARYDA  297 (923)
T ss_pred             hccCCCeecccccCccchhHHHH-HHHHhhcccccCceEEEccHH-HHHHHHHHHHHhCcceEE--EEEecCCccccccc
Confidence            44555678888999999653222 222211111225799999984 889999999999875443  333333221     


Q ss_pred             -------hhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCc
Q psy12977        122 -------AEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNL  194 (226)
Q Consensus       122 -------~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~  194 (226)
                             .....+......+|+++|-..+.-    ....+.--.++++|+||.|.+-..+     ..+...++++  ...
T Consensus       298 ~~~~~~~~~~L~r~~~~~~~ilitty~~~r~----~~d~l~~~~W~y~ILDEGH~IrNpn-----s~islackki--~T~  366 (923)
T KOG0387|consen  298 SHSSHKKDKLLIRKVATDGGILITTYDGFRI----QGDDLLGILWDYVILDEGHRIRNPN-----SKISLACKKI--RTV  366 (923)
T ss_pred             chhhhhhhhhheeeecccCcEEEEehhhhcc----cCcccccccccEEEecCcccccCCc-----cHHHHHHHhc--ccc
Confidence                   011112334556899999775532    2234555677899999999986552     3444555566  466


Q ss_pred             eEEEEeeeCc
Q psy12977        195 KRGMFSATHT  204 (226)
Q Consensus       195 q~v~~SAT~~  204 (226)
                      +.+.+|.|+=
T Consensus       367 ~RiILSGTPi  376 (923)
T KOG0387|consen  367 HRIILSGTPI  376 (923)
T ss_pred             ceEEeeCccc
Confidence            7777788843

>PRK06526 transposase; Provisional

Probab=98.13  E-value=3.5e-05  Score=62.51  Aligned_cols=129  Identities=15%  Similarity=0.075  Sum_probs=69.5

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhh
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEK  124 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (226)
                      ++..++++++.||+|+|||.............    +.++++. ...++.++....    ..                  
T Consensus        94 fi~~~~nlll~Gp~GtGKThLa~al~~~a~~~----g~~v~f~-t~~~l~~~l~~~----~~------------------  146 (254)
T PRK06526         94 FVTGKENVVFLGPPGTGKTHLAIGLGIRACQA----GHRVLFA-TAAQWVARLAAA----HH------------------  146 (254)
T ss_pred             hhhcCceEEEEeCCCCchHHHHHHHHHHHHHC----CCchhhh-hHHHHHHHHHHH----Hh------------------
Confidence            34557899999999999997654433333332    3345443 333344443211    00                  


Q ss_pred             hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        125 FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       125 ~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                                  -.+   +...+..      +.+.++||+||+|......  .....+..++.... .+..+++.|...+
T Consensus       147 ------------~~~---~~~~l~~------l~~~dlLIIDD~g~~~~~~--~~~~~L~~li~~r~-~~~s~IitSn~~~  202 (254)
T PRK06526        147 ------------AGR---LQAELVK------LGRYPLLIVDEVGYIPFEP--EAANLFFQLVSSRY-ERASLIVTSNKPF  202 (254)
T ss_pred             ------------cCc---HHHHHHH------hccCCEEEEcccccCCCCH--HHHHHHHHHHHHHH-hcCCEEEEcCCCH
Confidence                        001   1111221      3457899999999764321  23344555554432 2345888888776


Q ss_pred             hhHHH----------HHHHhcCCCeEEecC
Q psy12977        205 EDVAK----------WCRRKLKRRVQINVG  224 (226)
Q Consensus       205 ~~~~~----------~~~~~~~~p~~i~~~  224 (226)
                      .+..+          .+.+..+....++++
T Consensus       203 ~~w~~~~~d~~~a~ai~dRl~~~~~~i~~~  232 (254)
T PRK06526        203 GRWGEVFGDDVVAAAMIDRLVHHAEVISLK  232 (254)
T ss_pred             HHHHHHcCChHHHHHHHHHHhcCceEEeec
Confidence            65433          245555555555544

>KOG0390|consensus

Probab=98.13  E-value=4.8e-05  Score=69.64  Aligned_cols=152  Identities=16%  Similarity=0.111  Sum_probs=91.8

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCC---CCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhh---
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKN---LGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAE---  123 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~---~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---  123 (226)
                      .-.++.-.+|+|||+-...-+-..++..+.   .-.+.+|++|. .|+..|.+++..+.....+....+.+......   
T Consensus       264 ~GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~-sLv~nWkkEF~KWl~~~~i~~l~~~~~~~~~w~~~  342 (776)
T KOG0390|consen  264 GGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPS-SLVNNWKKEFGKWLGNHRINPLDFYSTKKSSWIKL  342 (776)
T ss_pred             CceEeeCCCCcchHHHHHHHHHHHHHhCcCccccccccEEEccH-HHHHHHHHHHHHhccccccceeeeecccchhhhhh
Confidence            346788889999998654333333333222   11589999997 59999999999997654444444444433200   


Q ss_pred             ---hhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        124 ---KFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       124 ---~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                         ....-......+++-+-+.+.+++.    .+....++++|+||.|.+-.     ....+...+..+  ...+.|++|
T Consensus       343 ~sil~~~~~~~~~~vli~sye~~~~~~~----~il~~~~glLVcDEGHrlkN-----~~s~~~kaL~~l--~t~rRVLLS  411 (776)
T KOG0390|consen  343 KSILFLGYKQFTTPVLIISYETASDYCR----KILLIRPGLLVCDEGHRLKN-----SDSLTLKALSSL--KTPRRVLLT  411 (776)
T ss_pred             HHHHHhhhhheeEEEEeccHHHHHHHHH----HHhcCCCCeEEECCCCCccc-----hhhHHHHHHHhc--CCCceEEee
Confidence               0000011223466667777665554    33466889999999998743     333444455555  455678889


Q ss_pred             eeC-chhHHHHHHH
Q psy12977        201 ATH-TEDVAKWCRR  213 (226)
Q Consensus       201 AT~-~~~~~~~~~~  213 (226)
                      .|+ -.++.++.+-
T Consensus       412 GTp~QNdl~EyFnl  425 (776)
T KOG0390|consen  412 GTPIQNDLKEYFNL  425 (776)
T ss_pred             CCcccccHHHHHHH
Confidence            994 3455555443

>PRK08181 transposase; Validated

Probab=98.13  E-value=3.2e-05  Score=63.17  Aligned_cols=129  Identities=14%  Similarity=0.142  Sum_probs=72.6

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhh
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEK  124 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (226)
                      +...++++++.||+|+|||..... +...+...   +.+++++ +..+|..+.....    ..                 
T Consensus       102 ~~~~~~nlll~Gp~GtGKTHLa~A-ia~~a~~~---g~~v~f~-~~~~L~~~l~~a~----~~-----------------  155 (269)
T PRK08181        102 WLAKGANLLLFGPPGGGKSHLAAA-IGLALIEN---GWRVLFT-RTTDLVQKLQVAR----RE-----------------  155 (269)
T ss_pred             HHhcCceEEEEecCCCcHHHHHHH-HHHHHHHc---CCceeee-eHHHHHHHHHHHH----hC-----------------
Confidence            344678999999999999965433 33333221   3345554 4555665543210    00                 


Q ss_pred             hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        125 FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       125 ~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                                   .+...   .+..      +.+.++||+||.+......  .....+..++.... .+..+++.|...+
T Consensus       156 -------------~~~~~---~l~~------l~~~dLLIIDDlg~~~~~~--~~~~~Lf~lin~R~-~~~s~IiTSN~~~  210 (269)
T PRK08181        156 -------------LQLES---AIAK------LDKFDLLILDDLAYVTKDQ--AETSVLFELISARY-ERRSILITANQPF  210 (269)
T ss_pred             -------------CcHHH---HHHH------HhcCCEEEEeccccccCCH--HHHHHHHHHHHHHH-hCCCEEEEcCCCH
Confidence                         01112   2222      4467899999999764431  33456666666552 2457777777766


Q ss_pred             hhHHHH----------HHHhcCCCeEEecC
Q psy12977        205 EDVAKW----------CRRKLKRRVQINVG  224 (226)
Q Consensus       205 ~~~~~~----------~~~~~~~p~~i~~~  224 (226)
                      ++..+.          +.+.++....++++
T Consensus       211 ~~w~~~~~D~~~a~aildRL~h~~~~i~~~  240 (269)
T PRK08181        211 GEWNRVFPDPAMTLAAVDRLVHHATIFEMN  240 (269)
T ss_pred             HHHHHhcCCccchhhHHHhhhcCceEEecC
Confidence            665443          35555555555554

>KOG0989|consensus

Probab=98.04  E-value=3e-05  Score=63.37  Aligned_cols=58  Identities=10%  Similarity=0.142  Sum_probs=42.6

Q ss_pred             CCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc---hhHHHHHHHh
Q psy12977        152 PALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT---EDVAKWCRRK  214 (226)
Q Consensus       152 ~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~---~~~~~~~~~~  214 (226)
                      ...+.+..+.+|+||||.|...    .+..+.+.++.. +..+.+++.+..+.   +.+..-+.+|
T Consensus       123 ~~~~~~~fKiiIlDEcdsmtsd----aq~aLrr~mE~~-s~~trFiLIcnylsrii~pi~SRC~Kf  183 (346)
T KOG0989|consen  123 DGYPCPPFKIIILDECDSMTSD----AQAALRRTMEDF-SRTTRFILICNYLSRIIRPLVSRCQKF  183 (346)
T ss_pred             cCCCCCcceEEEEechhhhhHH----HHHHHHHHHhcc-ccceEEEEEcCChhhCChHHHhhHHHh
Confidence            4455777899999999999876    888899999886 56778888777643   4444444444

>KOG1803|consensus

Probab=98.02  E-value=1.1e-05  Score=71.14  Aligned_cols=68  Identities=13%  Similarity=0.198  Sum_probs=49.2

Q ss_pred             ccccCCCCcccccc-cCCCC-CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHH
Q psy12977         31 SIFKHFEPHFTITY-LSPLG-RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETV  102 (226)
Q Consensus        31 ~~~~~~~~~Q~~~~-~~~~~-~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~  102 (226)
                      ..-+.+++.|..+- ...+. .-.+++||||+|||.....-+.+.+.+    +.++++..||+.-+..+.+.+.
T Consensus       181 ~~~~~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~----~k~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  181 FFNKNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQ----KKRVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             cCCccccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHc----CCeEEEEcCchHHHHHHHHHhc
Confidence            33445666676664 33333 457899999999999876666666654    5689999999999888888543

>KOG1132|consensus

Probab=98.00  E-value=4.1e-05  Score=70.13  Aligned_cols=42  Identities=19%  Similarity=0.256  Sum_probs=31.8

Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccc
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFE  172 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~  172 (226)
                      ...+|||.|-.+.+.+-.-+....+++.+ ..||+||||.+-+
T Consensus       220 ~edAdIIF~PYnYLiDp~iR~~~~v~Lkn-sIVIfDEAHNiEd  261 (945)
T KOG1132|consen  220 KEDADIIFCPYNYLIDPKIRRSHKVDLKN-SIVIFDEAHNIED  261 (945)
T ss_pred             cccCcEEEechhhhcCHhhhccccccccc-cEEEEeccccHHH
Confidence            57789999999998887666434455544 4999999998754

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.99  E-value=4.6e-05  Score=69.04  Aligned_cols=142  Identities=16%  Similarity=0.137  Sum_probs=80.6

Q ss_pred             Ccccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEe
Q psy12977         38 PHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIG  116 (226)
Q Consensus        38 ~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~  116 (226)
                      +-|+.+. ....++-.++.|++|+|||....--+............++.+.+||..=|..+.+.+.......+..     
T Consensus       155 d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~~~-----  229 (615)
T PRK10875        155 DWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGKALRQLPLT-----  229 (615)
T ss_pred             HHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhhccccc-----
Confidence            4566554 5566778999999999999764322222111112233578889999998888888776554333211     


Q ss_pred             cchhhhhhhCCCcCCCCCEEEECchHHHHhHhcC----CCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCC
Q psy12977        117 KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMD----PPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGP  192 (226)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~----~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~  192 (226)
                          +...      .....-..|-.+++......    ....+....+++|+||+-++ +.      ..+..+++.+ ++
T Consensus       230 ----~~~~------~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMv-d~------~lm~~ll~al-~~  291 (615)
T PRK10875        230 ----DEQK------KRIPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMV-DL------PMMARLIDAL-PP  291 (615)
T ss_pred             ----hhhh------hcCCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhcc-cH------HHHHHHHHhc-cc
Confidence                0000      00001122333333221110    01123445689999999854 32      3556667777 57


Q ss_pred             CceEEEEeee
Q psy12977        193 NLKRGMFSAT  202 (226)
Q Consensus       193 ~~q~v~~SAT  202 (226)
                      .++++++.-.
T Consensus       292 ~~rlIlvGD~  301 (615)
T PRK10875        292 HARVIFLGDR  301 (615)
T ss_pred             CCEEEEecch
Confidence            8899988766

>KOG0389|consensus

Probab=97.99  E-value=2.1e-05  Score=71.15  Aligned_cols=150  Identities=19%  Similarity=0.206  Sum_probs=90.1

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPR  128 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (226)
                      +-+-|+.-.=|-|||.-. ++.+..+.+....|| -+|+||+..| +.|.+++..||+  ..++...+|.+.........
T Consensus       418 ~l~gILADEMGLGKTiQv-IaFlayLkq~g~~gp-HLVVvPsSTl-eNWlrEf~kwCP--sl~Ve~YyGSq~ER~~lR~~  492 (941)
T KOG0389|consen  418 KLNGILADEMGLGKTIQV-IAFLAYLKQIGNPGP-HLVVVPSSTL-ENWLREFAKWCP--SLKVEPYYGSQDERRELRER  492 (941)
T ss_pred             cccceehhhccCcchhHH-HHHHHHHHHcCCCCC-cEEEecchhH-HHHHHHHHHhCC--ceEEEeccCcHHHHHHHHHH
Confidence            345689999999999654 333333333333343 4677898765 667777888876  56777777776544333222


Q ss_pred             c---CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC-c
Q psy12977        129 S---AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH-T  204 (226)
Q Consensus       129 ~---~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~-~  204 (226)
                      +   ....+|+++|-+.+..-- .+...+.-.+++++|+||.|.+-..    .....+.++. +  +.-+.+++|.|+ .
T Consensus       493 i~~~~~~ydVllTTY~la~~~k-dDRsflk~~~~n~viyDEgHmLKN~----~SeRy~~LM~-I--~An~RlLLTGTPLQ  564 (941)
T KOG0389|consen  493 IKKNKDDYDVLLTTYNLAASSK-DDRSFLKNQKFNYVIYDEGHMLKNR----TSERYKHLMS-I--NANFRLLLTGTPLQ  564 (941)
T ss_pred             HhccCCCccEEEEEeecccCCh-HHHHHHHhccccEEEecchhhhhcc----chHHHHHhcc-c--cccceEEeeCCccc
Confidence            2   236899999987654211 1112233457889999999977665    2223333332 2  345677778884 3


Q ss_pred             hhHHHHH
Q psy12977        205 EDVAKWC  211 (226)
Q Consensus       205 ~~~~~~~  211 (226)
                      .++.+++
T Consensus       565 NNL~ELi  571 (941)
T KOG0389|consen  565 NNLKELI  571 (941)
T ss_pred             ccHHHHH
Confidence            4444444

>COG4889 Predicted helicase [General function prediction only]

Probab=97.96  E-value=2.1e-05  Score=72.19  Aligned_cols=130  Identities=22%  Similarity=0.199  Sum_probs=75.8

Q ss_pred             cCCCCcccccc-----cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcC
Q psy12977         34 KHFEPHFTITY-----LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL  108 (226)
Q Consensus        34 ~~~~~~Q~~~~-----~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~  108 (226)
                      +++.|.|+.+.     .+..+..-=+.+..|+|||+..+- +.+++.     ..++++++|+.+|..|..+.+..-.+. 
T Consensus       160 kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsLk-isEala-----~~~iL~LvPSIsLLsQTlrew~~~~~l-  232 (1518)
T COG4889         160 KKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSLK-ISEALA-----AARILFLVPSISLLSQTLREWTAQKEL-  232 (1518)
T ss_pred             CCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHHH-HHHHHh-----hhheEeecchHHHHHHHHHHHhhccCc-
Confidence            46677775552     111122222445689999987643 344443     258999999999999998876554322 


Q ss_pred             CCeEEEEecchhhh------------------------hhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEE
Q psy12977        109 GLRAHVIGKIQQAA------------------------EKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIV  164 (226)
Q Consensus       109 ~~~~~~~~~~~~~~------------------------~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lVi  164 (226)
                      ......+.++....                        ....+....+--|+.+|-+.+...-.-  ....+..++++|.
T Consensus       233 ~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~~i~eA--Qe~G~~~fDliic  310 (1518)
T COG4889         233 DFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLPRIKEA--QEAGLDEFDLIIC  310 (1518)
T ss_pred             cceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchHHHHHH--HHcCCCCccEEEe
Confidence            22222222111100                        011112234456778887777655433  3445788999999


Q ss_pred             cccccccc
Q psy12977        165 DESDKLFE  172 (226)
Q Consensus       165 DE~h~l~~  172 (226)
                      ||||+-.+
T Consensus       311 DEAHRTtG  318 (1518)
T COG4889         311 DEAHRTTG  318 (1518)
T ss_pred             cchhcccc
Confidence            99998754

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.95  E-value=7.1e-05  Score=67.62  Aligned_cols=140  Identities=18%  Similarity=0.155  Sum_probs=78.2

Q ss_pred             cccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcC-C-CCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEE
Q psy12977         39 HFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRG-P-KNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVI  115 (226)
Q Consensus        39 ~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~-~-~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  115 (226)
                      .|+.+. ..+.++-.+++|++|||||..... ++..+.. . ...+.++++.+||..=+..+.+.+......+...    
T Consensus       149 ~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~-ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~~~~~l~~~----  223 (586)
T TIGR01447       149 WQKVAVALALKSNFSLITGGPGTGKTTTVAR-LLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRKAVKNLAAA----  223 (586)
T ss_pred             HHHHHHHHHhhCCeEEEEcCCCCCHHHHHHH-HHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHhhhcccccc----
Confidence            454443 556678899999999999986432 2222211 1 1113579999999988888777665543322211    


Q ss_pred             ecchhhhhhhCCCcCCCCCEEEECchHHHHhHhc----CCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCC
Q psy12977        116 GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQM----DPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSG  191 (226)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~----~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~  191 (226)
                          .. ..      ....+-..|-.+++.....    .....+...+++||+||+-++. .      ..+..+++.+ +
T Consensus       224 ----~~-~~------~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMvd-~------~l~~~ll~al-~  284 (586)
T TIGR01447       224 ----EA-LI------AALPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMVD-L------PLMAKLLKAL-P  284 (586)
T ss_pred             ----hh-hh------hccccccchhhhhhcccCCcchhhhcccCCCcccEEEEcccccCC-H------HHHHHHHHhc-C
Confidence                00 00      0001113333333322110    0011224468999999998552 2      3566667777 5


Q ss_pred             CCceEEEEeee
Q psy12977        192 PNLKRGMFSAT  202 (226)
Q Consensus       192 ~~~q~v~~SAT  202 (226)
                      +..++|++.-.
T Consensus       285 ~~~rlIlvGD~  295 (586)
T TIGR01447       285 PNTKLILLGDK  295 (586)
T ss_pred             CCCEEEEECCh
Confidence            78889887665

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.

>KOG1802|consensus

Probab=97.95  E-value=3.3e-05  Score=68.90  Aligned_cols=76  Identities=13%  Similarity=0.083  Sum_probs=58.6

Q ss_pred             HHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         27 VVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        27 ~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      .+...++.+++.-|+.+. ..+++.-.+++||+|+|||....--+++.++.   ....+++.+|+.--+.|.++.+.+-+
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~---~~~~VLvcApSNiAVDqLaeKIh~tg  478 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ---HAGPVLVCAPSNIAVDQLAEKIHKTG  478 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHh---cCCceEEEcccchhHHHHHHHHHhcC
Confidence            344566777788887775 55666678999999999998876666776664   24479999999999999998877663

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.93  E-value=0.00016  Score=63.64  Aligned_cols=111  Identities=15%  Similarity=0.156  Sum_probs=61.9

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      ..+++.||+|+|||... ..+...+... ..+.+++++ +..++..+....++.-                         
T Consensus       149 ~~l~l~G~~G~GKThL~-~ai~~~~~~~-~~~~~v~yi-~~~~~~~~~~~~~~~~-------------------------  200 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLL-HAIGNYILEK-NPNAKVVYV-TSEKFTNDFVNALRNN-------------------------  200 (450)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHHh-CCCCeEEEE-EHHHHHHHHHHHHHcC-------------------------
Confidence            45899999999999754 3444444322 123456665 5455555443332110                         


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHH
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVA  208 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~  208 (226)
                               +.+.+.+.         +.+.++|++||+|.+....  .....+..++..+...+.++++.|...|.++.
T Consensus       201 ---------~~~~~~~~---------~~~~dlLiiDDi~~l~~~~--~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~  259 (450)
T PRK00149        201 ---------TMEEFKEK---------YRSVDVLLIDDIQFLAGKE--RTQEEFFHTFNALHEAGKQIVLTSDRPPKELP  259 (450)
T ss_pred             ---------cHHHHHHH---------HhcCCEEEEehhhhhcCCH--HHHHHHHHHHHHHHHCCCcEEEECCCCHHHHH
Confidence                     11122221         2357799999999875541  23445555555553445677775555665543

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=97.93  E-value=0.00025  Score=51.39  Aligned_cols=26  Identities=27%  Similarity=0.447  Sum_probs=18.7

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      .++.+++.||+|+|||... -.+...+
T Consensus        18 ~~~~v~i~G~~G~GKT~l~-~~i~~~~   43 (151)
T cd00009          18 PPKNLLLYGPPGTGKTTLA-RAIANEL   43 (151)
T ss_pred             CCCeEEEECCCCCCHHHHH-HHHHHHh
Confidence            4678999999999999743 3333333

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.92  E-value=1.9e-05  Score=57.08  Aligned_cols=22  Identities=32%  Similarity=0.377  Sum_probs=14.1

Q ss_pred             CCCeEEEECCCCchHhHHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIP   69 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~   69 (226)
                      +++.+++.||+|+|||......
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~   24 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRL   24 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHH
Confidence            3567899999999999875443

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=97.89  E-value=0.00097  Score=56.91  Aligned_cols=136  Identities=18%  Similarity=0.165  Sum_probs=87.3

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPR  128 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (226)
                      ++.+.+.||||.|||...+--+..... ......-+||-+.|...+-.  ++++.+++-++..+                
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~-~~~~~kVaiITtDtYRIGA~--EQLk~Ya~im~vp~----------------  263 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVM-LKKKKKVAIITTDTYRIGAV--EQLKTYADIMGVPL----------------  263 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHh-hccCcceEEEEeccchhhHH--HHHHHHHHHhCCce----------------
Confidence            788999999999999875543333331 12234467888888777654  66777776666654                


Q ss_pred             cCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee-CchhH
Q psy12977        129 SAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT-HTEDV  207 (226)
Q Consensus       129 ~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT-~~~~~  207 (226)
                            .++-+|.-|...+..      +.+.+++.+|=+-+-..+.  .....+..+..... +---.+.+||| -.+++
T Consensus       264 ------~vv~~~~el~~ai~~------l~~~d~ILVDTaGrs~~D~--~~i~el~~~~~~~~-~i~~~Lvlsat~K~~dl  328 (407)
T COG1419         264 ------EVVYSPKELAEAIEA------LRDCDVILVDTAGRSQYDK--EKIEELKELIDVSH-SIEVYLVLSATTKYEDL  328 (407)
T ss_pred             ------EEecCHHHHHHHHHH------hhcCCEEEEeCCCCCccCH--HHHHHHHHHHhccc-cceEEEEEecCcchHHH
Confidence                  455677777776664      5667899988887543221  35556666655542 22233556787 44677


Q ss_pred             HHHHHHhcCCC
Q psy12977        208 AKWCRRKLKRR  218 (226)
Q Consensus       208 ~~~~~~~~~~p  218 (226)
                      ++.+.+|-.-|
T Consensus       329 kei~~~f~~~~  339 (407)
T COG1419         329 KEIIKQFSLFP  339 (407)
T ss_pred             HHHHHHhccCC
Confidence            88888876544

>PRK08727 hypothetical protein; Validated

Probab=97.88  E-value=0.00024  Score=56.92  Aligned_cols=49  Identities=4%  Similarity=-0.053  Sum_probs=30.4

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                      .+.++||+||+|.+....  .....+..++......+.++++.|...|.+.
T Consensus        92 ~~~dlLiIDDi~~l~~~~--~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l  140 (233)
T PRK08727         92 EGRSLVALDGLESIAGQR--EDEVALFDFHNRARAAGITLLYTARQMPDGL  140 (233)
T ss_pred             hcCCEEEEeCcccccCCh--HHHHHHHHHHHHHHHcCCeEEEECCCChhhh
Confidence            355799999999886542  2334455555544334556777666666655

>PRK08116 hypothetical protein; Validated

Probab=97.88  E-value=0.00026  Score=57.93  Aligned_cols=113  Identities=19%  Similarity=0.207  Sum_probs=62.6

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      ..+++.|++|+|||... .++.+.+...   +..++++ +..++..++...+..-    .              .     
T Consensus       115 ~gl~l~G~~GtGKThLa-~aia~~l~~~---~~~v~~~-~~~~ll~~i~~~~~~~----~--------------~-----  166 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLA-ACIANELIEK---GVPVIFV-NFPQLLNRIKSTYKSS----G--------------K-----  166 (268)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHHHc---CCeEEEE-EHHHHHHHHHHHHhcc----c--------------c-----
Confidence            45999999999999754 3455555432   2344444 5555555443322100    0              0     


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHH
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAK  209 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~  209 (226)
                              .+...+   +..      +.+.++||+||++.-....  .....+..++........++++.|...|.++.+
T Consensus       167 --------~~~~~~---~~~------l~~~dlLviDDlg~e~~t~--~~~~~l~~iin~r~~~~~~~IiTsN~~~~eL~~  227 (268)
T PRK08116        167 --------EDENEI---IRS------LVNADLLILDDLGAERDTE--WAREKVYNIIDSRYRKGLPTIVTTNLSLEELKN  227 (268)
T ss_pred             --------ccHHHH---HHH------hcCCCEEEEecccCCCCCH--HHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHH
Confidence                    011112   221      4467899999996432211  244556666665544567788888777766543

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.84  E-value=0.00017  Score=63.29  Aligned_cols=112  Identities=13%  Similarity=0.139  Sum_probs=66.7

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      ..+++.|++|+|||... ..+.+.+.. ...+.+++|+.+ .++..+....+....                        
T Consensus       142 npl~i~G~~G~GKTHLl-~Ai~~~l~~-~~~~~~v~yv~~-~~f~~~~~~~l~~~~------------------------  194 (450)
T PRK14087        142 NPLFIYGESGMGKTHLL-KAAKNYIES-NFSDLKVSYMSG-DEFARKAVDILQKTH------------------------  194 (450)
T ss_pred             CceEEECCCCCcHHHHH-HHHHHHHHH-hCCCCeEEEEEH-HHHHHHHHHHHHHhh------------------------
Confidence            45889999999999543 455555432 123446666544 566666555442210                        


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                                 +.+.+....      +.+.++||+||+|.+....  .....+..++..+...+.|+++.|-..|.+.
T Consensus       195 -----------~~~~~~~~~------~~~~dvLiIDDiq~l~~k~--~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l  253 (450)
T PRK14087        195 -----------KEIEQFKNE------ICQNDVLIIDDVQFLSYKE--KTNEIFFTIFNNFIENDKQLFFSSDKSPELL  253 (450)
T ss_pred             -----------hHHHHHHHH------hccCCEEEEeccccccCCH--HHHHHHHHHHHHHHHcCCcEEEECCCCHHHH
Confidence                       111222222      3467899999999875431  3455666666666455668888766666555

>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=97.83  E-value=4e-05  Score=60.84  Aligned_cols=110  Identities=17%  Similarity=0.237  Sum_probs=66.9

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      ..+.+.||+|+|||- .+.++.+.+.+. .++.+++|+ +..+......+.+++-                         
T Consensus        35 ~~l~l~G~~G~GKTH-LL~Ai~~~~~~~-~~~~~v~y~-~~~~f~~~~~~~~~~~-------------------------   86 (219)
T PF00308_consen   35 NPLFLYGPSGLGKTH-LLQAIANEAQKQ-HPGKRVVYL-SAEEFIREFADALRDG-------------------------   86 (219)
T ss_dssp             SEEEEEESTTSSHHH-HHHHHHHHHHHH-CTTS-EEEE-EHHHHHHHHHHHHHTT-------------------------
T ss_pred             CceEEECCCCCCHHH-HHHHHHHHHHhc-cccccceee-cHHHHHHHHHHHHHcc-------------------------
Confidence            458999999999997 345555555321 124466666 3334554443332210                         


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                               ..+.+.   ..      +.+.+++++|++|.+.+..  .....+..++..+...+.++++.|...|.++
T Consensus        87 ---------~~~~~~---~~------~~~~DlL~iDDi~~l~~~~--~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l  144 (219)
T PF00308_consen   87 ---------EIEEFK---DR------LRSADLLIIDDIQFLAGKQ--RTQEELFHLFNRLIESGKQLILTSDRPPSEL  144 (219)
T ss_dssp             ---------SHHHHH---HH------HCTSSEEEEETGGGGTTHH--HHHHHHHHHHHHHHHTTSEEEEEESS-TTTT
T ss_pred             ---------cchhhh---hh------hhcCCEEEEecchhhcCch--HHHHHHHHHHHHHHhhCCeEEEEeCCCCccc
Confidence                     111222   22      4478899999999886542  3566777777777566778888887877654

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.

>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=97.83  E-value=3.8e-05  Score=63.67  Aligned_cols=70  Identities=21%  Similarity=0.105  Sum_probs=51.7

Q ss_pred             CCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         37 EPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        37 ~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      ++-|...... .+++++|.|++|||||.+.+.-+...+........+.+++++|+..+..+.+.+......
T Consensus         2 ~~eQ~~~i~~-~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l~~   71 (315)
T PF00580_consen    2 TDEQRRIIRS-TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIRELLEE   71 (315)
T ss_dssp             -HHHHHHHHS--SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHhC-CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHhcCc
Confidence            3445444433 678999999999999998777666666554455668999999999999999988887554

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 ....

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.82  E-value=0.00028  Score=61.85  Aligned_cols=116  Identities=14%  Similarity=0.222  Sum_probs=63.5

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      ..+++.||+|+|||... ..+.+.+... ..+.+++|+. ..++..+....++.     +                    
T Consensus       131 n~l~lyG~~G~GKTHLl-~ai~~~l~~~-~~~~~v~yi~-~~~f~~~~~~~~~~-----~--------------------  182 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLL-QSIGNYVVQN-EPDLRVMYIT-SEKFLNDLVDSMKE-----G--------------------  182 (440)
T ss_pred             CeEEEEcCCCCcHHHHH-HHHHHHHHHh-CCCCeEEEEE-HHHHHHHHHHHHhc-----c--------------------
Confidence            35899999999999754 4444544322 2234677764 33444433332210     0                    


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHH
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAK  209 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~  209 (226)
                               +.+.+...+.        .+.+++++||+|.+.+..  .....+..++..+...+.++++.|...|.++..
T Consensus       183 ---------~~~~f~~~~~--------~~~dvLlIDDi~~l~~~~--~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~  243 (440)
T PRK14088        183 ---------KLNEFREKYR--------KKVDVLLIDDVQFLIGKT--GVQTELFHTFNELHDSGKQIVICSDREPQKLSE  243 (440)
T ss_pred             ---------cHHHHHHHHH--------hcCCEEEEechhhhcCcH--HHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHH
Confidence                     0112222111        246799999999886542  233445555555534456777766666666555


Q ss_pred             HHH
Q psy12977        210 WCR  212 (226)
Q Consensus       210 ~~~  212 (226)
                      +..
T Consensus       244 l~~  246 (440)
T PRK14088        244 FQD  246 (440)
T ss_pred             HHH
Confidence            433

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.82  E-value=0.00047  Score=58.81  Aligned_cols=135  Identities=16%  Similarity=0.164  Sum_probs=71.0

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEc-ccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhh
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVC-PTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEK  124 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~-Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (226)
                      ...++.+++.||||+|||....--+........  ..++.++. .+...  --.++++.+.+..+..+..          
T Consensus       134 ~~~g~ii~lvGptGvGKTTtiakLA~~~~~~~G--~~~V~lit~D~~R~--ga~EqL~~~a~~~gv~~~~----------  199 (374)
T PRK14722        134 MERGGVFALMGPTGVGKTTTTAKLAARCVMRFG--ASKVALLTTDSYRI--GGHEQLRIFGKILGVPVHA----------  199 (374)
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHHHHhcC--CCeEEEEecccccc--cHHHHHHHHHHHcCCceEe----------
Confidence            445788999999999999876544433332211  12333333 23211  2234555555555544322          


Q ss_pred             hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        125 FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       125 ~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                                  +-++..+...+..      +.+.++++||++-......  ...+.+..+.. ...+...++.+|||-.
T Consensus       200 ------------~~~~~~l~~~l~~------l~~~DlVLIDTaG~~~~d~--~l~e~La~L~~-~~~~~~~lLVLsAts~  258 (374)
T PRK14722        200 ------------VKDGGDLQLALAE------LRNKHMVLIDTIGMSQRDR--TVSDQIAMLHG-ADTPVQRLLLLNATSH  258 (374)
T ss_pred             ------------cCCcccHHHHHHH------hcCCCEEEEcCCCCCcccH--HHHHHHHHHhc-cCCCCeEEEEecCccC
Confidence                        3344444444443      4456899999997543221  23333433322 2123344677899864


Q ss_pred             -hhHHHHHHHhc
Q psy12977        205 -EDVAKWCRRKL  215 (226)
Q Consensus       205 -~~~~~~~~~~~  215 (226)
                       +.+.+.+++|.
T Consensus       259 ~~~l~evi~~f~  270 (374)
T PRK14722        259 GDTLNEVVQAYR  270 (374)
T ss_pred             hHHHHHHHHHHH
Confidence             45566666664

>KOG4439|consensus

Probab=97.78  E-value=7e-05  Score=67.15  Aligned_cols=119  Identities=24%  Similarity=0.317  Sum_probs=77.8

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHh-----cC--CCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhh
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSL-----RG--PKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAE  123 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~-----~~--~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (226)
                      --|+...-|-|||++.+..+++.-     ++  ..... .++|+||.. |..||..++......-..++.+++|...  .
T Consensus       347 GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~-~TLII~PaS-li~qW~~Ev~~rl~~n~LsV~~~HG~n~--r  422 (901)
T KOG4439|consen  347 GGILADDMGLGKTLSMISLILHQKAARKAREKKGESAS-KTLIICPAS-LIHQWEAEVARRLEQNALSVYLYHGPNK--R  422 (901)
T ss_pred             CcccccccccccchHHHHHHHHHHHHHHhhcccccccC-CeEEeCcHH-HHHHHHHHHHHHHhhcceEEEEecCCcc--c
Confidence            357788889999997554444332     11  11122 599999985 8999999988888777788888877653  2


Q ss_pred             hhCCCcCCCCCEEEECchHHHH----hHhcCCCCCCCC--CccEEEEccccccccc
Q psy12977        124 KFGPRSAQKFDVLITTPNKLVY----LLQMDPPALNLA--NVEWLIVDESDKLFEA  173 (226)
Q Consensus       124 ~~~~~~~~~~~IiV~Tp~~l~~----~~~~~~~~~~~~--~~~~lViDE~h~l~~~  173 (226)
                      ..........||+|+|..-+..    -.......-.+.  .+..+|+||||.+-+.
T Consensus       423 ~i~~~~L~~YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~IrN~  478 (901)
T KOG4439|consen  423 EISAKELRKYDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNIRNS  478 (901)
T ss_pred             cCCHHHHhhcceEEEeeeccccCCchhhhcccCccHHHHhhHHHhhhhhhhhhccc
Confidence            2223345678999999876655    111111112233  3468999999988655

>KOG1000|consensus

Probab=97.78  E-value=0.00025  Score=61.43  Aligned_cols=151  Identities=20%  Similarity=0.188  Sum_probs=88.5

Q ss_pred             ccCCCCccccc--ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCC
Q psy12977         33 FKHFEPHFTIT--YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGL  110 (226)
Q Consensus        33 ~~~~~~~Q~~~--~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~  110 (226)
                      +..+.|.|..-  +.+..|..+++...-|-|||.-++. +...++..    .-.+|+||.. +-..+.+.+..+.+...-
T Consensus       196 vs~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAla-IA~yyraE----wplliVcPAs-vrftWa~al~r~lps~~p  269 (689)
T KOG1000|consen  196 VSRLLPFQREGVIFALERGGRILLADEMGLGKTIQALA-IARYYRAE----WPLLIVCPAS-VRFTWAKALNRFLPSIHP  269 (689)
T ss_pred             HHhhCchhhhhHHHHHhcCCeEEEecccccchHHHHHH-HHHHHhhc----CcEEEEecHH-HhHHHHHHHHHhcccccc
Confidence            34456666443  3556788899999999999986543 33333322    2368889974 667788888888765433


Q ss_pred             eEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcC
Q psy12977        111 RAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACS  190 (226)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~  190 (226)
                       +..+.++.    +..........|.|.+.+.+..+-.    .+.....+.+|+||+|.+-+..    ....+.++..+ 
T Consensus       270 -i~vv~~~~----D~~~~~~t~~~v~ivSye~ls~l~~----~l~~~~~~vvI~DEsH~Lk~sk----tkr~Ka~~dll-  335 (689)
T KOG1000|consen  270 -IFVVDKSS----DPLPDVCTSNTVAIVSYEQLSLLHD----ILKKEKYRVVIFDESHMLKDSK----TKRTKAATDLL-  335 (689)
T ss_pred             -eEEEeccc----CCccccccCCeEEEEEHHHHHHHHH----HHhcccceEEEEechhhhhccc----hhhhhhhhhHH-
Confidence             22222221    1111122334577877776655432    3334568899999999886542    11122222222 


Q ss_pred             CCCceEEEEeeeC
Q psy12977        191 GPNLKRGMFSATH  203 (226)
Q Consensus       191 ~~~~q~v~~SAT~  203 (226)
                      ..-..++++|.|+
T Consensus       336 k~akhvILLSGTP  348 (689)
T KOG1000|consen  336 KVAKHVILLSGTP  348 (689)
T ss_pred             HHhhheEEecCCc
Confidence            2234678889884

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.77  E-value=0.00032  Score=60.86  Aligned_cols=112  Identities=14%  Similarity=0.163  Sum_probs=60.5

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      ..+++.||+|+|||... ..+.+.+... ..+.+++++. ..++..+....+..                          
T Consensus       137 n~l~l~G~~G~GKThL~-~ai~~~l~~~-~~~~~v~yi~-~~~~~~~~~~~~~~--------------------------  187 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLL-HAIGNEILEN-NPNAKVVYVS-SEKFTNDFVNALRN--------------------------  187 (405)
T ss_pred             CeEEEECCCCCcHHHHH-HHHHHHHHHh-CCCCcEEEEE-HHHHHHHHHHHHHc--------------------------
Confidence            35789999999999754 4445554322 2244677763 33444433222110                          


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHH
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAK  209 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~  209 (226)
                        +      +.+.+.+.         +.+.++|++||+|.+.+..  .....+..++..+...+.++++.|...|.++..
T Consensus       188 --~------~~~~~~~~---------~~~~dlLiiDDi~~l~~~~--~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~  248 (405)
T TIGR00362       188 --N------KMEEFKEK---------YRSVDLLLIDDIQFLAGKE--RTQEEFFHTFNALHENGKQIVLTSDRPPKELPG  248 (405)
T ss_pred             --C------CHHHHHHH---------HHhCCEEEEehhhhhcCCH--HHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhh
Confidence              0      11122222         2246799999999876541  233445555554434456777655555655543

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).

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.74  E-value=0.00044  Score=60.61  Aligned_cols=109  Identities=17%  Similarity=0.248  Sum_probs=61.8

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      ..+++.||+|+|||... ..+.+.+...   +.+++++. ...+..+....+..              +           
T Consensus       142 npl~L~G~~G~GKTHLl-~Ai~~~l~~~---~~~v~yi~-~~~f~~~~~~~l~~--------------~-----------  191 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLM-QAAVHALRES---GGKILYVR-SELFTEHLVSAIRS--------------G-----------  191 (445)
T ss_pred             ceEEEEcCCCCCHHHHH-HHHHHHHHHc---CCCEEEee-HHHHHHHHHHHHhc--------------c-----------
Confidence            45899999999999743 3455554432   44667664 34444433322210              0           


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHH
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVA  208 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~  208 (226)
                               ..+.+...         ..+.+++++||+|.+.+..  .....+..++..+...+.|+++.|.+.|.++.
T Consensus       192 ---------~~~~f~~~---------~~~~dvLiIDDiq~l~~k~--~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~  250 (445)
T PRK12422        192 ---------EMQRFRQF---------YRNVDALFIEDIEVFSGKG--ATQEEFFHTFNSLHTEGKLIVISSTCAPQDLK  250 (445)
T ss_pred             ---------hHHHHHHH---------cccCCEEEEcchhhhcCCh--hhHHHHHHHHHHHHHCCCcEEEecCCCHHHHh
Confidence                     00111111         2367899999999876542  24445555555443456677776666676654

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.72  E-value=0.00041  Score=62.54  Aligned_cols=125  Identities=17%  Similarity=0.206  Sum_probs=70.3

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcC
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSA  130 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  130 (226)
                      .+++.|++|+|||... ..+.+.+.. ...+.+++|+ +..+++++....+..-                          
T Consensus       316 pL~LyG~sGsGKTHLL-~AIa~~a~~-~~~g~~V~Yi-taeef~~el~~al~~~--------------------------  366 (617)
T PRK14086        316 PLFIYGESGLGKTHLL-HAIGHYARR-LYPGTRVRYV-SSEEFTNEFINSIRDG--------------------------  366 (617)
T ss_pred             cEEEECCCCCCHHHHH-HHHHHHHHH-hCCCCeEEEe-eHHHHHHHHHHHHHhc--------------------------
Confidence            4899999999999743 344454432 1123466665 4455555443322110                          


Q ss_pred             CCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHH--
Q psy12977        131 QKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVA--  208 (226)
Q Consensus       131 ~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~--  208 (226)
                              ..+.+.   .+      +.++++|+|||+|.+....  .....+..++..+...+.++++.|-..|.++.  
T Consensus       367 --------~~~~f~---~~------y~~~DLLlIDDIq~l~gke--~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l  427 (617)
T PRK14086        367 --------KGDSFR---RR------YREMDILLVDDIQFLEDKE--STQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTL  427 (617)
T ss_pred             --------cHHHHH---HH------hhcCCEEEEehhccccCCH--HHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhc
Confidence                    001111   11      3457899999999886542  34456666776665556788887666666543  


Q ss_pred             -HHHHHhcCCCeEEec
Q psy12977        209 -KWCRRKLKRRVQINV  223 (226)
Q Consensus       209 -~~~~~~~~~p~~i~~  223 (226)
                       +.+..-+...+.+++
T Consensus       428 ~~rL~SRf~~GLvv~I  443 (617)
T PRK14086        428 EDRLRNRFEWGLITDV  443 (617)
T ss_pred             cHHHHhhhhcCceEEc
Confidence             223334444444444

>PRK06893 DNA replication initiation factor; Validated

Probab=97.67  E-value=0.00027  Score=56.46  Aligned_cols=46  Identities=7%  Similarity=0.092  Sum_probs=30.0

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      .+.+++++||+|.+....  .+...+..++......+.+++++|++.+
T Consensus        90 ~~~dlLilDDi~~~~~~~--~~~~~l~~l~n~~~~~~~~illits~~~  135 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNE--EWELAIFDLFNRIKEQGKTLLLISADCS  135 (229)
T ss_pred             ccCCEEEEeChhhhcCCh--HHHHHHHHHHHHHHHcCCcEEEEeCCCC
Confidence            466899999999876442  3444566666655344556767777643

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.64  E-value=0.00081  Score=56.62  Aligned_cols=129  Identities=17%  Similarity=0.092  Sum_probs=71.8

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCC
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGP  127 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (226)
                      .++++++.||||+|||.... .+...+...   +..++++ +..++..+....-  + .  .        .    .    
T Consensus       182 ~~~~Lll~G~~GtGKThLa~-aIa~~l~~~---g~~V~y~-t~~~l~~~l~~~~--~-~--~--------~----~----  235 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLSN-CIAKELLDR---GKSVIYR-TADELIEILREIR--F-N--N--------D----K----  235 (329)
T ss_pred             cCCcEEEECCCCCcHHHHHH-HHHHHHHHC---CCeEEEE-EHHHHHHHHHHHH--h-c--c--------c----h----
Confidence            35889999999999997543 444444322   3355554 5555655443210  0 0  0        0    0    


Q ss_pred             CcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        128 RSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       128 ~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                                    .....+..      +.++++||+|+.+......  .....+..++......+.++++.|.-.|+++
T Consensus       236 --------------~~~~~~~~------l~~~DLLIIDDlG~e~~t~--~~~~~Lf~iin~R~~~~k~tIiTSNl~~~el  293 (329)
T PRK06835        236 --------------ELEEVYDL------LINCDLLIIDDLGTEKITE--FSKSELFNLINKRLLRQKKMIISTNLSLEEL  293 (329)
T ss_pred             --------------hHHHHHHH------hccCCEEEEeccCCCCCCH--HHHHHHHHHHHHHHHCCCCEEEECCCCHHHH
Confidence                          00001121      4467899999998664331  2445666666665444567777666666665


Q ss_pred             HH-----HHHHhcCCCeEEecC
Q psy12977        208 AK-----WCRRKLKRRVQINVG  224 (226)
Q Consensus       208 ~~-----~~~~~~~~p~~i~~~  224 (226)
                      .+     ...+.......+.+.
T Consensus       294 ~~~~~eri~SRL~~~~~~i~~~  315 (329)
T PRK06835        294 LKTYSERISSRLLGNFTLLKFY  315 (329)
T ss_pred             HHHHhHHHHHHHHcCCEEEEec
Confidence            33     445555555555543

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.63  E-value=0.00058  Score=63.39  Aligned_cols=127  Identities=20%  Similarity=0.121  Sum_probs=72.7

Q ss_pred             cCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeE
Q psy12977         34 KHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRA  112 (226)
Q Consensus        34 ~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~  112 (226)
                      ..+++-|..+. ....++-.+++|++|+|||... -.++..+... .....+++++||..-+.++.+..       +...
T Consensus       322 ~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~-~~~~~v~l~ApTg~AA~~L~e~~-------g~~a  392 (720)
T TIGR01448       322 KGLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEEL-GGLLPVGLAAPTGRAAKRLGEVT-------GLTA  392 (720)
T ss_pred             CCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHc-CCCceEEEEeCchHHHHHHHHhc-------CCcc
Confidence            35677776664 4455678999999999999754 3334444322 11146888899987776544321       2111


Q ss_pred             EEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcC---CCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        113 HVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMD---PPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~---~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                                               .|-.+++......   ...-.....+++|+||++++...       .+..+++.+
T Consensus       393 -------------------------~Tih~lL~~~~~~~~~~~~~~~~~~~llIvDEaSMvd~~-------~~~~Ll~~~  440 (720)
T TIGR01448       393 -------------------------STIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMMDTW-------LALSLLAAL  440 (720)
T ss_pred             -------------------------ccHHHHhhccCCccchhhhhccccCCEEEEeccccCCHH-------HHHHHHHhC
Confidence                                     1111221110000   00011345789999999976332       445566666


Q ss_pred             CCCCceEEEEeee
Q psy12977        190 SGPNLKRGMFSAT  202 (226)
Q Consensus       190 ~~~~~q~v~~SAT  202 (226)
                       +...+++++.-.
T Consensus       441 -~~~~rlilvGD~  452 (720)
T TIGR01448       441 -PDHARLLLVGDT  452 (720)
T ss_pred             -CCCCEEEEECcc
Confidence             467889887665

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.

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=97.62  E-value=0.00019  Score=66.21  Aligned_cols=125  Identities=26%  Similarity=0.171  Sum_probs=90.7

Q ss_pred             cccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecc
Q psy12977         39 HFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKI  118 (226)
Q Consensus        39 ~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~  118 (226)
                      +|......+. ..-+....||-|||+...+|+.-...    .|..+.+++-+-.||..-.+++..+.+.+|..+.....+
T Consensus        84 VQliG~i~lh-~g~iaEM~TGEGKTL~atlp~ylnaL----~gkgVhvVTvNdYLA~RDae~m~~l~~~LGlsvG~~~~~  158 (822)
T COG0653          84 VQLLGGIVLH-LGDIAEMRTGEGKTLVATLPAYLNAL----AGKGVHVVTVNDYLARRDAEWMGPLYEFLGLSVGVILAG  158 (822)
T ss_pred             HHHhhhhhhc-CCceeeeecCCchHHHHHHHHHHHhc----CCCCcEEeeehHHhhhhCHHHHHHHHHHcCCceeeccCC
Confidence            5555543322 33478999999999999888765433    255789999999999999999999999999999887776


Q ss_pred             hhhhhhhCCCcCCCCCEEEECchHHHHhHhcCC-----CCCCCCCccEEEEccccccc
Q psy12977        119 QQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDP-----PALNLANVEWLIVDESDKLF  171 (226)
Q Consensus       119 ~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~-----~~~~~~~~~~lViDE~h~l~  171 (226)
                      ....++   .....|||..+|...+-..+.+++     .........+-|+||+|.++
T Consensus       159 m~~~ek---~~aY~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSIL  213 (822)
T COG0653         159 MSPEEK---RAAYACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSIL  213 (822)
T ss_pred             CChHHH---HHHHhcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhhee
Confidence            644433   345889999999877643222211     22234467899999999775

>KOG1002|consensus

Probab=97.62  E-value=0.0003  Score=61.02  Aligned_cols=135  Identities=19%  Similarity=0.195  Sum_probs=83.6

Q ss_pred             EEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCC
Q psy12977         53 FACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQK  132 (226)
Q Consensus        53 li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (226)
                      ++...-|.|||.-.+.-++....     +...++++|+.+| .|+.+++.+.... ..++-...|..   .........+
T Consensus       208 iLADEMGMGKTIQtIaLllae~~-----ra~tLVvaP~VAl-mQW~nEI~~~T~g-slkv~~YhG~~---R~~nikel~~  277 (791)
T KOG1002|consen  208 ILADEMGMGKTIQTIALLLAEVD-----RAPTLVVAPTVAL-MQWKNEIERHTSG-SLKVYIYHGAK---RDKNIKELMN  277 (791)
T ss_pred             eehhhhccchHHHHHHHHHhccc-----cCCeeEEccHHHH-HHHHHHHHHhccC-ceEEEEEeccc---ccCCHHHhhc
Confidence            67788999999876555555443     3358999999988 5788888888762 23333333322   1222223467


Q ss_pred             CCEEEECchHHHHhHhcCCCC-----------CCCCC--ccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEE
Q psy12977        133 FDVLITTPNKLVYLLQMDPPA-----------LNLAN--VEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMF  199 (226)
Q Consensus       133 ~~IiV~Tp~~l~~~~~~~~~~-----------~~~~~--~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~  199 (226)
                      .|++.+|...+.+-++.....           ..+.+  +--+|+||||.+-+... +....+..+.      ......+
T Consensus       278 YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~IK~R~s-nTArAV~~L~------tt~rw~L  350 (791)
T KOG1002|consen  278 YDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNIKDRQS-NTARAVFALE------TTYRWCL  350 (791)
T ss_pred             CcEEEEecHHHHHHHHhccccccccCCcccccchhhhceeeeeehhhhcccccccc-cHHHHHHhhH------hhhhhhc
Confidence            899999999888777541111           11233  34799999999876532 3444443332      3345567


Q ss_pred             eeeCc
Q psy12977        200 SATHT  204 (226)
Q Consensus       200 SAT~~  204 (226)
                      |.|+=
T Consensus       351 SGTPL  355 (791)
T KOG1002|consen  351 SGTPL  355 (791)
T ss_pred             cCCcc
Confidence            88844

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.61  E-value=0.00061  Score=54.67  Aligned_cols=46  Identities=4%  Similarity=0.025  Sum_probs=27.9

Q ss_pred             ccEEEEcccccccccCccchHHHHHHHHHhcCCC-CceEEEEeeeCchh
Q psy12977        159 VEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGP-NLKRGMFSATHTED  206 (226)
Q Consensus       159 ~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~-~~q~v~~SAT~~~~  206 (226)
                      .+++++||+|.+....  .....+..++...... +.++++.|...|.+
T Consensus        98 ~dlliiDdi~~~~~~~--~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~  144 (235)
T PRK08084         98 LSLVCIDNIECIAGDE--LWEMAIFDLYNRILESGRTRLLITGDRPPRQ  144 (235)
T ss_pred             CCEEEEeChhhhcCCH--HHHHHHHHHHHHHHHcCCCeEEEeCCCChHH
Confidence            4799999999886442  3445555555554222 34677755555544

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=97.60  E-value=0.0004  Score=61.56  Aligned_cols=137  Identities=18%  Similarity=0.129  Sum_probs=81.6

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      +.+++.-|-|.|||......++..+.-....+..+++.+++++-|..+++.++.+................        .
T Consensus        23 ~~~~l~v~RkNGKS~l~a~i~ly~l~~~g~~~~~i~~~A~~~~QA~~~f~~~~~~i~~~~~l~~~~~~~~~--------~   94 (477)
T PF03354_consen   23 REVYLEVPRKNGKSTLAAAIALYMLFLDGEPGAEIYCAANTRDQAKIVFDEAKKMIEASPELRKRKKPKII--------K   94 (477)
T ss_pred             EEEEEEEcCccCccHHHHHHHHHHHhcCCccCceEEEEeCCHHHHHHHHHHHHHHHHhChhhccchhhhhh--------h
Confidence            45788889999999765444333332234456789999999999999999999887663322111100000        0


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEE
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMF  199 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~  199 (226)
                      ...-.|.....+.....+.......+=.+.+++|+||+|...+.   .....+..-+...  ++++++..
T Consensus        95 ~~~~~i~~~~~~s~~~~~s~~~~~~dG~~~~~~i~DE~h~~~~~---~~~~~l~~g~~~r--~~pl~~~I  159 (477)
T PF03354_consen   95 SNKKEIEFPKTGSFFKALSSDADSLDGLNPSLAIFDELHAHKDD---ELYDALESGMGAR--PNPLIIII  159 (477)
T ss_pred             hhceEEEEcCCCcEEEEEecCCCCccCCCCceEEEeCCCCCCCH---HHHHHHHhhhccC--CCceEEEE
Confidence            01112333222333333333334555556789999999988664   4666666666554  45565554

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK05642 DNA replication initiation factor; Validated

Probab=97.60  E-value=0.0005  Score=55.11  Aligned_cols=47  Identities=9%  Similarity=0.181  Sum_probs=30.4

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                      +.+++++|++|.+....  .+...+..++..+...+.++++.|-+.|++
T Consensus        97 ~~d~LiiDDi~~~~~~~--~~~~~Lf~l~n~~~~~g~~ilits~~~p~~  143 (234)
T PRK05642         97 QYELVCLDDLDVIAGKA--DWEEALFHLFNRLRDSGRRLLLAASKSPRE  143 (234)
T ss_pred             hCCEEEEechhhhcCCh--HHHHHHHHHHHHHHhcCCEEEEeCCCCHHH
Confidence            55799999999775442  345667777776644556666655445543

>KOG0391|consensus

Probab=97.59  E-value=0.00027  Score=66.76  Aligned_cols=164  Identities=18%  Similarity=0.157  Sum_probs=96.2

Q ss_pred             HHHHHHHHHhhccccCCCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHH
Q psy12977         20 IIVTTLAVVSNSIFKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYN   99 (226)
Q Consensus        20 ~~~~~l~~~~~~~~~~~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~   99 (226)
                      +++-.|+-++.-|+..+-.      +...+-|-|+...-|-|||.-.+.-+.+..-+..+.|+..| ++||- ....|.=
T Consensus       611 LLrGqLReYQkiGLdWLat------LYeknlNGILADEmGLGKTIQtISllAhLACeegnWGPHLI-VVpTs-viLnWEM  682 (1958)
T KOG0391|consen  611 LLRGQLREYQKIGLDWLAT------LYEKNLNGILADEMGLGKTIQTISLLAHLACEEGNWGPHLI-VVPTS-VILNWEM  682 (1958)
T ss_pred             HHHHHHHHHHHhhHHHHHH------HHHhcccceehhhhcccchhHHHHHHHHHHhcccCCCCceE-Eeech-hhhhhhH
Confidence            4444454455444443311      12234466889999999998654433344444455566655 55764 3445666


Q ss_pred             HHHHHhhcCCCeEEEEecchhhh-hhh-CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccc
Q psy12977        100 ETVRLSEGLGLRAHVIGKIQQAA-EKF-GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG  177 (226)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~-~~~-~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~  177 (226)
                      ++++++.  +.++....|..... .+. .+...+..|+-|++...+.+....    +.-.++.|+|+||+|++-..    
T Consensus       683 ElKRwcP--glKILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~~A----FkrkrWqyLvLDEaqnIKnf----  752 (1958)
T KOG0391|consen  683 ELKRWCP--GLKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDLTA----FKRKRWQYLVLDEAQNIKNF----  752 (1958)
T ss_pred             HHhhhCC--cceEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHHHH----HHhhccceeehhhhhhhcch----
Confidence            7888887  56666555553322 222 233445568888887776665432    22457889999999998665    


Q ss_pred             hHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        178 FRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       178 ~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      -...+..++. +  ...+.++++.|+=
T Consensus       753 ksqrWQAlln-f--nsqrRLLLtgTPL  776 (1958)
T KOG0391|consen  753 KSQRWQALLN-F--NSQRRLLLTGTPL  776 (1958)
T ss_pred             hHHHHHHHhc-c--chhheeeecCCch
Confidence            2334444442 2  3456677788843

>PRK06921 hypothetical protein; Provisional

Probab=97.57  E-value=0.0012  Score=54.01  Aligned_cols=45  Identities=22%  Similarity=0.132  Sum_probs=27.7

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      .+.++++.|++|+|||... ..+...+....  +..++++. ..++..+
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~~~~--g~~v~y~~-~~~l~~~  160 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELMRKK--GVPVLYFP-FVEGFGD  160 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHhhhc--CceEEEEE-HHHHHHH
Confidence            3578999999999999754 34444443211  34566654 4444444

>PRK04296 thymidine kinase; Provisional

Probab=97.56  E-value=0.00032  Score=54.40  Aligned_cols=37  Identities=19%  Similarity=0.330  Sum_probs=24.2

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcc
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCP   89 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~P   89 (226)
                      |.-.++.||+|+|||...+--+.....    .+.+++++-|
T Consensus         2 g~i~litG~~GsGKTT~~l~~~~~~~~----~g~~v~i~k~   38 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQRAYNYEE----RGMKVLVFKP   38 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHHHHH----cCCeEEEEec
Confidence            345689999999999765443333322    2457787755

>KOG2340|consensus

Probab=97.56  E-value=8.1e-05  Score=64.83  Aligned_cols=181  Identities=17%  Similarity=0.155  Sum_probs=108.6

Q ss_pred             ccCCCCcccccc-cCCCCCeEEEE-CCCCchH--hHHHHHHHHHHhcC---------------------------CCCCC
Q psy12977         33 FKHFEPHFTITY-LSPLGRQIFAC-APTGSGK--TAAFLIPIIHSLRG---------------------------PKNLG   81 (226)
Q Consensus        33 ~~~~~~~Q~~~~-~~~~~~~~li~-apTGsGK--T~~~~~~~~~~~~~---------------------------~~~~~   81 (226)
                      -..+++.|...+ ...+-+|++.. ..-+.|+  +-.|++-+++.+.+                           +.-..
T Consensus       214 s~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tR  293 (698)
T KOG2340|consen  214 SEPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTR  293 (698)
T ss_pred             cCcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCC
Confidence            346777786665 44555776532 2223444  23355555555410                           11125


Q ss_pred             ceEEEEcccHHHHHHHHHHHHHHhhcCCC-eEEEE---------ecchhhh-------hhhC------------------
Q psy12977         82 FRAVIVCPTRELAKQTYNETVRLSEGLGL-RAHVI---------GKIQQAA-------EKFG------------------  126 (226)
Q Consensus        82 ~~~iil~Pt~~L~~q~~~~~~~~~~~~~~-~~~~~---------~~~~~~~-------~~~~------------------  126 (226)
                      |+++|+||+|+-|-.+.+.+..+...... +....         .+.+...       ..+.                  
T Consensus       294 pkVLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~ft  373 (698)
T KOG2340|consen  294 PKVLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAFT  373 (698)
T ss_pred             ceEEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHHH
Confidence            89999999999999999988888332211 11111         1100000       0000                  


Q ss_pred             ------CCcCCCCCEEEECchHHHHhHhc---C-CCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcC---C--
Q psy12977        127 ------PRSAQKFDVLITTPNKLVYLLQM---D-PPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACS---G--  191 (226)
Q Consensus       127 ------~~~~~~~~IiV~Tp~~l~~~~~~---~-~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~---~--  191 (226)
                            .....++||+||+|--|.-.+..   . ...--++++.++|||.+|.++..    .|..+.-++..+.   .  
T Consensus       374 kKtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~Q----NwEhl~~ifdHLn~~P~k~  449 (698)
T KOG2340|consen  374 KKTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQ----NWEHLLHIFDHLNLQPSKQ  449 (698)
T ss_pred             HHHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHh----hHHHHHHHHHHhhcCcccc
Confidence                  00046799999999887766652   1 12233888999999999988765    6777777766652   1  


Q ss_pred             ------------------CCceEEEEeeeCchhHHHHHHHhcCC
Q psy12977        192 ------------------PNLKRGMFSATHTEDVAKWCRRKLKR  217 (226)
Q Consensus       192 ------------------~~~q~v~~SAT~~~~~~~~~~~~~~~  217 (226)
                                        --.|+++||+--.+....+.+.|+++
T Consensus       450 h~~DfSRVR~wyL~~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N  493 (698)
T KOG2340|consen  450 HDVDFSRVRMWYLDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQN  493 (698)
T ss_pred             cCCChhheehheeccHHHHHHHHHHHHhhccHHHHHHHHHhhhh
Confidence                              12577888888777888888777654

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.55  E-value=0.0037  Score=54.54  Aligned_cols=135  Identities=16%  Similarity=0.195  Sum_probs=71.6

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHh-cCCCCCCceEEEE-cccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSL-RGPKNLGFRAVIV-CPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEK  124 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~-~~~~~~~~~~iil-~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (226)
                      ..++.+.+.||||+|||.....-+.... ..   .+.++.++ +.+...+.  .++++.+....+..+            
T Consensus       219 ~~~~~i~~vGptGvGKTTt~~kLA~~~~~~~---~g~~V~li~~D~~r~~a--~eqL~~~a~~~~vp~------------  281 (424)
T PRK05703        219 KQGGVVALVGPTGVGKTTTLAKLAARYALLY---GKKKVALITLDTYRIGA--VEQLKTYAKIMGIPV------------  281 (424)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHHHhc---CCCeEEEEECCccHHHH--HHHHHHHHHHhCCce------------
Confidence            3467889999999999976554333332 11   12344444 33322111  234444443334322            


Q ss_pred             hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        125 FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       125 ~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                                ..+.++..+...+..      +.+.++++||.+-......  .....+..++.....+....+++|||..
T Consensus       282 ----------~~~~~~~~l~~~l~~------~~~~DlVlIDt~G~~~~d~--~~~~~L~~ll~~~~~~~~~~LVl~a~~~  343 (424)
T PRK05703        282 ----------EVVYDPKELAKALEQ------LRDCDVILIDTAGRSQRDK--RLIEELKALIEFSGEPIDVYLVLSATTK  343 (424)
T ss_pred             ----------EccCCHHhHHHHHHH------hCCCCEEEEeCCCCCCCCH--HHHHHHHHHHhccCCCCeEEEEEECCCC
Confidence                      112344455555543      3467899999986543221  3445566665522123344667788865


Q ss_pred             -hhHHHHHHHhcC
Q psy12977        205 -EDVAKWCRRKLK  216 (226)
Q Consensus       205 -~~~~~~~~~~~~  216 (226)
                       .++.+.+..|-.
T Consensus       344 ~~~l~~~~~~f~~  356 (424)
T PRK05703        344 YEDLKDIYKHFSR  356 (424)
T ss_pred             HHHHHHHHHHhCC
Confidence             466666666553

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.52  E-value=0.00069  Score=48.53  Aligned_cols=42  Identities=29%  Similarity=0.342  Sum_probs=26.1

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELA   94 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~   94 (226)
                      +..+++.||+|+|||.....- +..+...   +..++++.+.....
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l-~~~~~~~---~~~~~~~~~~~~~~   43 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARAL-ARELGPP---GGGVIYIDGEDILE   43 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHH-HhccCCC---CCCEEEECCEEccc
Confidence            567899999999999865333 3333221   12467766665433

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.

>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=97.52  E-value=0.0002  Score=54.98  Aligned_cols=48  Identities=21%  Similarity=0.214  Sum_probs=32.4

Q ss_pred             EEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        52 ~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      +++.||||+|||...+--+...+..    +.+++|++ +.+-..++.+.+..+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~----g~~v~~~s-~e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLAR----GEPGLYVT-LEESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHC----CCcEEEEE-CCCCHHHHHHHHHHc
Confidence            6899999999998655444554432    45677775 445667766666555

A related protein is found in archaea.

>PRK12377 putative replication protein; Provisional

Probab=97.51  E-value=0.0018  Score=52.38  Aligned_cols=111  Identities=18%  Similarity=0.190  Sum_probs=62.9

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPR  128 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (226)
                      ..++++.||+|+|||... ..+...+...   +..+++ .+..++..++...+..     +             .     
T Consensus       101 ~~~l~l~G~~GtGKThLa-~AIa~~l~~~---g~~v~~-i~~~~l~~~l~~~~~~-----~-------------~-----  152 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLA-AAIGNRLLAK---GRSVIV-VTVPDVMSRLHESYDN-----G-------------Q-----  152 (248)
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHHHHc---CCCeEE-EEHHHHHHHHHHHHhc-----c-------------c-----
Confidence            367999999999999744 3444444322   334444 4555666655442210     0             0     


Q ss_pred             cCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHH
Q psy12977        129 SAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVA  208 (226)
Q Consensus       129 ~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~  208 (226)
                                +   ....+..      +.++++||+||++......  .....+..++........++++.|.--++++.
T Consensus       153 ----------~---~~~~l~~------l~~~dLLiIDDlg~~~~s~--~~~~~l~~ii~~R~~~~~ptiitSNl~~~~l~  211 (248)
T PRK12377        153 ----------S---GEKFLQE------LCKVDLLVLDEIGIQRETK--NEQVVLNQIIDRRTASMRSVGMLTNLNHEAMS  211 (248)
T ss_pred             ----------h---HHHHHHH------hcCCCEEEEcCCCCCCCCH--HHHHHHHHHHHHHHhcCCCEEEEcCCCHHHHH
Confidence                      0   0112222      5678999999997543331  24446666666654556778887775555443

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.51  E-value=0.0031  Score=54.09  Aligned_cols=134  Identities=15%  Similarity=0.182  Sum_probs=73.1

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceE-EEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRA-VIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGP  127 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~-iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (226)
                      .+.+.+.||+|+|||.....-+......    +.++ ++-+.+...+  ..++++.+....+..+               
T Consensus       241 ~~vI~LVGptGvGKTTTiaKLA~~L~~~----GkkVglI~aDt~Ria--AvEQLk~yae~lgipv---------------  299 (436)
T PRK11889        241 VQTIALIGPTGVGKTTTLAKMAWQFHGK----KKTVGFITTDHSRIG--TVQQLQDYVKTIGFEV---------------  299 (436)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHHc----CCcEEEEecCCcchH--HHHHHHHHhhhcCCcE---------------
Confidence            3678999999999998755444333221    2234 4444333211  1222333333223221               


Q ss_pred             CcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee-Cchh
Q psy12977        128 RSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT-HTED  206 (226)
Q Consensus       128 ~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT-~~~~  206 (226)
                             +.+.+|..+.+.+.....   ..+.++++||-+=+.....  .....+..+++.. .+..-++.+||| -+++
T Consensus       300 -------~v~~d~~~L~~aL~~lk~---~~~~DvVLIDTaGRs~kd~--~lm~EL~~~lk~~-~PdevlLVLsATtk~~d  366 (436)
T PRK11889        300 -------IAVRDEAAMTRALTYFKE---EARVDYILIDTAGKNYRAS--ETVEEMIETMGQV-EPDYICLTLSASMKSKD  366 (436)
T ss_pred             -------EecCCHHHHHHHHHHHHh---ccCCCEEEEeCccccCcCH--HHHHHHHHHHhhc-CCCeEEEEECCccChHH
Confidence                   223466676665543111   1257899999987654331  3556666666555 233334558887 4467


Q ss_pred             HHHHHHHhcC
Q psy12977        207 VAKWCRRKLK  216 (226)
Q Consensus       207 ~~~~~~~~~~  216 (226)
                      +.+.+++|-.
T Consensus       367 ~~~i~~~F~~  376 (436)
T PRK11889        367 MIEIITNFKD  376 (436)
T ss_pred             HHHHHHHhcC
Confidence            7788877654

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=97.49  E-value=0.0014  Score=51.85  Aligned_cols=21  Identities=24%  Similarity=0.362  Sum_probs=17.2

Q ss_pred             CCCeEEEECCCCchHhHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~   68 (226)
                      .+.++++.||+|+|||.....
T Consensus        37 ~~~~lll~G~~G~GKT~la~~   57 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQA   57 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHHH
Confidence            457899999999999976543

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.49  E-value=0.0016  Score=53.04  Aligned_cols=21  Identities=24%  Similarity=0.205  Sum_probs=16.8

Q ss_pred             CCCeEEEECCCCchHhHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~   68 (226)
                      ...++++.||+|+|||...-.
T Consensus        41 ~~~~vll~GppGtGKTtlA~~   61 (261)
T TIGR02881        41 QVLHMIFKGNPGTGKTTVARI   61 (261)
T ss_pred             CcceEEEEcCCCCCHHHHHHH
Confidence            346899999999999976533

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.

>KOG0991|consensus

Probab=97.48  E-value=0.0003  Score=55.65  Aligned_cols=48  Identities=13%  Similarity=0.138  Sum_probs=34.1

Q ss_pred             CCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        152 PALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       152 ~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      ..++.-+-+.+|+||||.|.+.    ..+.+.+.++-. ++.+++.+...+..
T Consensus       107 v~lp~grhKIiILDEADSMT~g----AQQAlRRtMEiy-S~ttRFalaCN~s~  154 (333)
T KOG0991|consen  107 VTLPPGRHKIIILDEADSMTAG----AQQALRRTMEIY-SNTTRFALACNQSE  154 (333)
T ss_pred             ccCCCCceeEEEeeccchhhhH----HHHHHHHHHHHH-cccchhhhhhcchh
Confidence            3444567789999999999764    777888888777 55666665555533

>CHL00181 cbbX CbbX; Provisional

Probab=97.48  E-value=0.0031  Score=52.15  Aligned_cols=22  Identities=27%  Similarity=0.297  Sum_probs=17.7

Q ss_pred             CCCeEEEECCCCchHhHHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIP   69 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~   69 (226)
                      .+.++++.||||+|||..+-..
T Consensus        58 ~~~~ill~G~pGtGKT~lAr~l   79 (287)
T CHL00181         58 PGLHMSFTGSPGTGKTTVALKM   79 (287)
T ss_pred             CCceEEEECCCCCCHHHHHHHH
Confidence            4677999999999999865443

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.46  E-value=0.0018  Score=47.98  Aligned_cols=49  Identities=12%  Similarity=0.102  Sum_probs=29.3

Q ss_pred             CCCccEEEEcccccccccCc-------cchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        156 LANVEWLIVDESDKLFEAGV-------RGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~-------~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      ..+.+++|+||++.+.+...       ......+..+.......+..+++.+-+..
T Consensus        83 ~~~~~~lviDe~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~vv~~~~~~~  138 (165)
T cd01120          83 RGGDDLIILDELTRLVRALREIREGYPGELDEELRELLERARKGGVTVIFTLQVPS  138 (165)
T ss_pred             CCCCEEEEEEcHHHHHHHHHHHHhcCChHHHHHHHHHHHHHhcCCceEEEEEecCC
Confidence            34677999999998754311       12345566666555334566666555543

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.

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=97.46  E-value=0.0036  Score=53.88  Aligned_cols=65  Identities=11%  Similarity=0.175  Sum_probs=45.0

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHH---HHHHHhcCCCeEEecC
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVA---KWCRRKLKRRVQINVG  224 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~---~~~~~~~~~p~~i~~~  224 (226)
                      +++++++|+++.+....  .....+..++..+...+.|+++.|...|.++.   +-+...+.-.+.+++.
T Consensus       175 ~~dlllIDDiq~l~gk~--~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~  242 (408)
T COG0593         175 SLDLLLIDDIQFLAGKE--RTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIE  242 (408)
T ss_pred             ccCeeeechHhHhcCCh--hHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeC
Confidence            78899999999887653  45667777777775666799998888887754   3333344444555443

>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=97.44  E-value=0.0026  Score=49.61  Aligned_cols=132  Identities=17%  Similarity=0.153  Sum_probs=71.2

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcC
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSA  130 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  130 (226)
                      -+++.||||+|||....--+.....+   ...-+++-+.+...+  ..++++.+.+.+++.+.......           
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~---~~~v~lis~D~~R~g--a~eQL~~~a~~l~vp~~~~~~~~-----------   66 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLK---GKKVALISADTYRIG--AVEQLKTYAEILGVPFYVARTES-----------   66 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT---T--EEEEEESTSSTH--HHHHHHHHHHHHTEEEEESSTTS-----------
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhc---cccceeecCCCCCcc--HHHHHHHHHHHhccccchhhcch-----------
Confidence            46899999999998765444333332   222344444443322  23556666666566543322110           


Q ss_pred             CCCCEEEECchHHH-HhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHH
Q psy12977        131 QKFDVLITTPNKLV-YLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAK  209 (226)
Q Consensus       131 ~~~~IiV~Tp~~l~-~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~  209 (226)
                              .|..+. +.+..    ...++.++++||-+-+.....  .....+..+.+.. .+..-.+.+|||...+..+
T Consensus        67 --------~~~~~~~~~l~~----~~~~~~D~vlIDT~Gr~~~d~--~~~~el~~~~~~~-~~~~~~LVlsa~~~~~~~~  131 (196)
T PF00448_consen   67 --------DPAEIAREALEK----FRKKGYDLVLIDTAGRSPRDE--ELLEELKKLLEAL-NPDEVHLVLSATMGQEDLE  131 (196)
T ss_dssp             --------CHHHHHHHHHHH----HHHTTSSEEEEEE-SSSSTHH--HHHHHHHHHHHHH-SSSEEEEEEEGGGGGHHHH
T ss_pred             --------hhHHHHHHHHHH----HhhcCCCEEEEecCCcchhhH--HHHHHHHHHhhhc-CCccceEEEecccChHHHH
Confidence                    122222 22221    113467899999997654321  4667777777777 4445556678997655433


Q ss_pred             HHHH
Q psy12977        210 WCRR  213 (226)
Q Consensus       210 ~~~~  213 (226)
                      .+.+
T Consensus       132 ~~~~  135 (196)
T PF00448_consen  132 QALA  135 (196)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4433

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 ....

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.44  E-value=0.0019  Score=51.42  Aligned_cols=44  Identities=14%  Similarity=0.154  Sum_probs=25.8

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      ..+++++||+|.+...    ....+..++.........+++++++.++
T Consensus        90 ~~~~liiDdi~~l~~~----~~~~L~~~~~~~~~~~~~~vl~~~~~~~  133 (227)
T PRK08903         90 EAELYAVDDVERLDDA----QQIALFNLFNRVRAHGQGALLVAGPAAP  133 (227)
T ss_pred             cCCEEEEeChhhcCch----HHHHHHHHHHHHHHcCCcEEEEeCCCCH
Confidence            4568999999987543    3445555555442233334666666543

>PLN03025 replication factor C subunit; Provisional

Probab=97.43  E-value=0.0022  Score=53.83  Aligned_cols=41  Identities=15%  Similarity=0.181  Sum_probs=27.4

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      .+.+++|+||+|.+...    ....+.++++.. +..+.+++.+..
T Consensus        98 ~~~kviiiDE~d~lt~~----aq~aL~~~lE~~-~~~t~~il~~n~  138 (319)
T PLN03025         98 GRHKIVILDEADSMTSG----AQQALRRTMEIY-SNTTRFALACNT  138 (319)
T ss_pred             CCeEEEEEechhhcCHH----HHHHHHHHHhcc-cCCceEEEEeCC
Confidence            35789999999998765    455666666654 455666664433

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.43  E-value=0.0027  Score=51.21  Aligned_cols=53  Identities=25%  Similarity=0.304  Sum_probs=34.3

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHH
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKW  210 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~  210 (226)
                      +.++++|||||++......  .-...+..++..-...+..+++.|.--++++.+.
T Consensus       160 l~~~dlLvIDDig~~~~s~--~~~~~l~~Ii~~Ry~~~~~tiitSNl~~~~l~~~  212 (244)
T PRK07952        160 LSNVDLLVIDEIGVQTESR--YEKVIINQIVDRRSSSKRPTGMLTNSNMEEMTKL  212 (244)
T ss_pred             hccCCEEEEeCCCCCCCCH--HHHHHHHHHHHHHHhCCCCEEEeCCCCHHHHHHH
Confidence            4578899999999765431  1223555566554345678888887766665443

>PRK09183 transposase/IS protein; Provisional

Probab=97.41  E-value=0.0057  Score=49.81  Aligned_cols=46  Identities=22%  Similarity=0.281  Sum_probs=27.9

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      +..+.++++.||+|+|||.....-......    .+.++.++ +..++..+
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al~~~a~~----~G~~v~~~-~~~~l~~~  144 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIALGYEAVR----AGIKVRFT-TAADLLLQ  144 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHHHHHHHH----cCCeEEEE-eHHHHHHH
Confidence            566789999999999999654433222222    13355554 43445443

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=97.41  E-value=0.001  Score=53.39  Aligned_cols=54  Identities=17%  Similarity=0.186  Sum_probs=37.6

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      ..|..+++.||+|+|||...+-.+...+.+    +.+++|++ +.+-..|+.+.+..+.
T Consensus        19 ~~gs~~lI~G~pGsGKT~la~~~l~~~~~~----ge~~lyvs-~ee~~~~i~~~~~~~g   72 (237)
T TIGR03877        19 PERNVVLLSGGPGTGKSIFSQQFLWNGLQM----GEPGIYVA-LEEHPVQVRRNMAQFG   72 (237)
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHHHHHc----CCcEEEEE-eeCCHHHHHHHHHHhC
Confidence            456889999999999998655545555532    55778876 4556667777666553

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.

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.36  E-value=0.0014  Score=61.21  Aligned_cols=123  Identities=15%  Similarity=0.164  Sum_probs=71.4

Q ss_pred             CCCCcccccc-cCCC-CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeE
Q psy12977         35 HFEPHFTITY-LSPL-GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRA  112 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~-~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~  112 (226)
                      .+++-|..+. .+.. ++-.++.|++|+|||... -.+...+..   .+.+++.++||..-+..+.+.       .+...
T Consensus       352 ~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll-~~i~~~~~~---~g~~V~~~ApTg~Aa~~L~~~-------~g~~a  420 (744)
T TIGR02768       352 RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWEA---AGYRVIGAALSGKAAEGLQAE-------SGIES  420 (744)
T ss_pred             CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHHh---CCCeEEEEeCcHHHHHHHHhc-------cCCce
Confidence            4677776664 3333 467899999999999753 334444433   256899999998666554321       12211


Q ss_pred             EEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCC
Q psy12977        113 HVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGP  192 (226)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~  192 (226)
                                               .|-.++...+..  ....+...+++|+||+-.+...       .+..+++.....
T Consensus       421 -------------------------~Ti~~~~~~~~~--~~~~~~~~~llIvDEasMv~~~-------~~~~Ll~~~~~~  466 (744)
T TIGR02768       421 -------------------------RTLASLEYAWAN--GRDLLSDKDVLVIDEAGMVGSR-------QMARVLKEAEEA  466 (744)
T ss_pred             -------------------------eeHHHHHhhhcc--CcccCCCCcEEEEECcccCCHH-------HHHHHHHHHHhc
Confidence                                     122222111111  2333567899999999966433       233444433245


Q ss_pred             CceEEEEeee
Q psy12977        193 NLKRGMFSAT  202 (226)
Q Consensus       193 ~~q~v~~SAT  202 (226)
                      ..+++++.=+
T Consensus       467 ~~kliLVGD~  476 (744)
T TIGR02768       467 GAKVVLVGDP  476 (744)
T ss_pred             CCEEEEECCh
Confidence            7788887643

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.

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=97.36  E-value=0.00029  Score=56.72  Aligned_cols=88  Identities=18%  Similarity=0.166  Sum_probs=60.1

Q ss_pred             CCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCC
Q psy12977         79 NLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLAN  158 (226)
Q Consensus        79 ~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~  158 (226)
                      ...|.+||++.+--.|-.+.+.++.+..........+.-.-.-.+..........+|.||||+++..++..  +.+.+++
T Consensus       124 ~gsP~~lvvs~SalRa~dl~R~l~~~~~k~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~--~~L~l~~  201 (252)
T PF14617_consen  124 KGSPHVLVVSSSALRAADLIRALRSFKGKDCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLEN--GALSLSN  201 (252)
T ss_pred             CCCCEEEEEcchHHHHHHHHHHHHhhccCCchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHc--CCCCccc
Confidence            34689999999988888888888877421111111111111111222222335788999999999999987  8999999


Q ss_pred             ccEEEEcccc
Q psy12977        159 VEWLIVDESD  168 (226)
Q Consensus       159 ~~~lViDE~h  168 (226)
                      +.++|+|--|
T Consensus       202 l~~ivlD~s~  211 (252)
T PF14617_consen  202 LKRIVLDWSY  211 (252)
T ss_pred             CeEEEEcCCc
Confidence            9999999865

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=97.36  E-value=0.00026  Score=54.38  Aligned_cols=48  Identities=19%  Similarity=0.374  Sum_probs=28.1

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      ++.+++++++.||+|+|||......+...+..    +..+++ .+..+|..++
T Consensus        43 ~~~~~~~l~l~G~~G~GKThLa~ai~~~~~~~----g~~v~f-~~~~~L~~~l   90 (178)
T PF01695_consen   43 FIENGENLILYGPPGTGKTHLAVAIANEAIRK----GYSVLF-ITASDLLDEL   90 (178)
T ss_dssp             S-SC--EEEEEESTTSSHHHHHHHHHHHHHHT----T--EEE-EEHHHHHHHH
T ss_pred             CcccCeEEEEEhhHhHHHHHHHHHHHHHhccC----CcceeE-eecCceeccc
Confidence            45678899999999999997654433344432    334555 4555666553

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.

>PRK14974 cell division protein FtsY; Provisional

Probab=97.36  E-value=0.0043  Score=52.35  Aligned_cols=131  Identities=18%  Similarity=0.190  Sum_probs=72.4

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEccc---HHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPT---RELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG  126 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt---~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (226)
                      .-+++.|++|+|||....-.+ ..+..   .+.+++++...   ..-.+|+    +.+....+..+.....+.       
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA-~~l~~---~g~~V~li~~Dt~R~~a~eqL----~~~a~~lgv~v~~~~~g~-------  205 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLA-YYLKK---NGFSVVIAAGDTFRAGAIEQL----EEHAERLGVKVIKHKYGA-------  205 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHH-HHHHH---cCCeEEEecCCcCcHHHHHHH----HHHHHHcCCceecccCCC-------
Confidence            457899999999998654333 23322   13355555432   2333443    334443454432111110       


Q ss_pred             CCcCCCCCEEEECchH-HHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        127 PRSAQKFDVLITTPNK-LVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       127 ~~~~~~~~IiV~Tp~~-l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                                  .|.. +.+.+..    ....+.+++++|.+.++....  .....+..+.+.. ++..-++.++|+...
T Consensus       206 ------------dp~~v~~~ai~~----~~~~~~DvVLIDTaGr~~~~~--~lm~eL~~i~~~~-~pd~~iLVl~a~~g~  266 (336)
T PRK14974        206 ------------DPAAVAYDAIEH----AKARGIDVVLIDTAGRMHTDA--NLMDELKKIVRVT-KPDLVIFVGDALAGN  266 (336)
T ss_pred             ------------CHHHHHHHHHHH----HHhCCCCEEEEECCCccCCcH--HHHHHHHHHHHhh-CCceEEEeeccccch
Confidence                        1222 1222221    012356799999999875332  5777888887766 566667888998776


Q ss_pred             hHHHHHHHh
Q psy12977        206 DVAKWCRRK  214 (226)
Q Consensus       206 ~~~~~~~~~  214 (226)
                      +..+.++.+
T Consensus       267 d~~~~a~~f  275 (336)
T PRK14974        267 DAVEQAREF  275 (336)
T ss_pred             hHHHHHHHH
Confidence            666555554

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.34  E-value=0.0013  Score=62.57  Aligned_cols=123  Identities=16%  Similarity=0.093  Sum_probs=74.5

Q ss_pred             CCCCcccccc-cCCCCC-eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeE
Q psy12977         35 HFEPHFTITY-LSPLGR-QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRA  112 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~~~-~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~  112 (226)
                      .+++-|..+. .+..++ -++++|+.|+|||.. +-.+...+..   .+.+++.++||-.-+....+       ..+...
T Consensus       346 ~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~---~G~~V~~~ApTGkAA~~L~e-------~tGi~a  414 (988)
T PRK13889        346 VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEA---AGYEVRGAALSGIAAENLEG-------GSGIAS  414 (988)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHH---cCCeEEEecCcHHHHHHHhh-------ccCcch
Confidence            5788887775 445544 578999999999985 3344444443   25689999999866654432       112210


Q ss_pred             EEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCC
Q psy12977        113 HVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGP  192 (226)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~  192 (226)
                                               .|-.++..-+..  +...+...++|||||+-.+...       .+..+++.....
T Consensus       415 -------------------------~TI~sll~~~~~--~~~~l~~~~vlIVDEASMv~~~-------~m~~LL~~a~~~  460 (988)
T PRK13889        415 -------------------------RTIASLEHGWGQ--GRDLLTSRDVLVIDEAGMVGTR-------QLERVLSHAADA  460 (988)
T ss_pred             -------------------------hhHHHHHhhhcc--cccccccCcEEEEECcccCCHH-------HHHHHHHhhhhC
Confidence                                     122233221111  2334667789999999965333       444555544456


Q ss_pred             CceEEEEeee
Q psy12977        193 NLKRGMFSAT  202 (226)
Q Consensus       193 ~~q~v~~SAT  202 (226)
                      .+++|++.=+
T Consensus       461 garvVLVGD~  470 (988)
T PRK13889        461 GAKVVLVGDP  470 (988)
T ss_pred             CCEEEEECCH
Confidence            7889888766

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.34  E-value=0.0046  Score=51.06  Aligned_cols=19  Identities=21%  Similarity=0.195  Sum_probs=16.3

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .+.++++.||+|+|||..+
T Consensus        57 ~~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        57 PTLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CCceEEEEcCCCCCHHHHH
Confidence            3568999999999999765

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.

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.34  E-value=0.0021  Score=59.30  Aligned_cols=39  Identities=15%  Similarity=0.125  Sum_probs=25.5

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      .+.+++||||+|.|...    ....+.++++.- ++.+.+++.|
T Consensus       118 gr~KVIIIDEah~LT~~----A~NALLKtLEEP-P~~v~FILaT  156 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNH----AFNAMLKTLEEP-PPHVKFILAT  156 (830)
T ss_pred             CCceEEEEeChhhCCHH----HHHHHHHHHHhc-CCCeEEEEEE
Confidence            46789999999988765    344455566554 3455666543

>KOG1131|consensus

Probab=97.34  E-value=0.0014  Score=57.37  Aligned_cols=61  Identities=20%  Similarity=0.151  Sum_probs=38.1

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      -.+.+.++..|+|+|||.+.+..+...-...+....+.||-.-|..=.+....+++.+..+
T Consensus        33 DakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~l~~y   93 (755)
T KOG1131|consen   33 DAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKRLMDY   93 (755)
T ss_pred             ccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHHHHHH
Confidence            4557789999999999987654433332222323457777776665555555555555433

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.33  E-value=0.0026  Score=54.80  Aligned_cols=36  Identities=19%  Similarity=0.332  Sum_probs=22.6

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEE
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIV   87 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil   87 (226)
                      .++++.||+|+|||...-. ++..+.... .+..++++
T Consensus        56 ~~~lI~G~~GtGKT~l~~~-v~~~l~~~~-~~~~~v~i   91 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTVKK-VFEELEEIA-VKVVYVYI   91 (394)
T ss_pred             CeEEEECCCCCCHHHHHHH-HHHHHHHhc-CCcEEEEE
Confidence            6799999999999986543 344443221 23345555

>KOG0921|consensus

Probab=97.31  E-value=0.0011  Score=61.21  Aligned_cols=158  Identities=16%  Similarity=0.120  Sum_probs=92.1

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCc-eEEEEcccHHHHHHHHHH-HHHHhhcCCCeEEEEecchhhhhhhC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGF-RAVIVCPTRELAKQTYNE-TVRLSEGLGLRAHVIGKIQQAAEKFG  126 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~-~~iil~Pt~~L~~q~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (226)
                      +.-+++.+.||+|||.-+.--+++.+..++.... -+.+--|++..+.-+.+. +++-++..+..+..-..-      .+
T Consensus       393 n~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisiaerva~er~e~~g~tvgy~vRf------~S  466 (1282)
T KOG0921|consen  393 NRVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERVANERGEEVGETCGYNVRF------DS  466 (1282)
T ss_pred             CceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccchHHHHHHHHHhhHHhhcccccccccc------cc
Confidence            4557899999999999988888888866555433 345555666655555443 333333333332221110      00


Q ss_pred             CCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        127 PRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       127 ~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                      .....---|+.||-+-+.+.+...     +..+.++++||.|..--..  .|...+.+-+... .+...++++|||..  
T Consensus       467 a~prpyg~i~fctvgvllr~~e~g-----lrg~sh~i~deiherdv~~--dfll~~lr~m~~t-y~dl~v~lmsatId--  536 (1282)
T KOG0921|consen  467 ATPRPYGSIMFCTVGVLLRMMENG-----LRGISHVIIDEIHERDVDT--DFVLIVLREMIST-YRDLRVVLMSATID--  536 (1282)
T ss_pred             cccccccceeeeccchhhhhhhhc-----ccccccccchhhhhhccch--HHHHHHHHhhhcc-chhhhhhhhhcccc--
Confidence            001111259999999999988763     5578899999999553221  3444444444333 34566677777765  


Q ss_pred             HHHHHHHhcCCCeEEec
Q psy12977        207 VAKWCRRKLKRRVQINV  223 (226)
Q Consensus       207 ~~~~~~~~~~~p~~i~~  223 (226)
                       .+++..|+.+-..+++
T Consensus       537 -Td~f~~~f~~~p~~~~  552 (1282)
T KOG0921|consen  537 -TDLFTNFFSSIPDVTV  552 (1282)
T ss_pred             -hhhhhhhhccccceee
Confidence             3334445544444333

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.31  E-value=0.0018  Score=56.92  Aligned_cols=20  Identities=30%  Similarity=0.341  Sum_probs=16.0

Q ss_pred             CeEEEECCCCchHhHHHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFLIP   69 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~   69 (226)
                      +.++++||+|+|||..+..-
T Consensus        41 ha~Lf~GP~GtGKTTlAriL   60 (484)
T PRK14956         41 HAYIFFGPRGVGKTTIARIL   60 (484)
T ss_pred             eEEEEECCCCCCHHHHHHHH
Confidence            44799999999999876443

>PF05729 NACHT: NACHT domain

Probab=97.30  E-value=0.0057  Score=45.54  Aligned_cols=61  Identities=25%  Similarity=0.293  Sum_probs=33.7

Q ss_pred             EEEEcccccccccCcc----chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        161 WLIVDESDKLFEAGVR----GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       161 ~lViDE~h~l~~~~~~----~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      ++|+|-+|.+.+....    .....+..++..-..++.++++.|.+-  ...+ +.+.+.....++++
T Consensus        84 llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~--~~~~-~~~~~~~~~~~~l~  148 (166)
T PF05729_consen   84 LLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPR--AFPD-LRRRLKQAQILELE  148 (166)
T ss_pred             EEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCC--hHHH-HHHhcCCCcEEEEC
Confidence            5999999998774311    233445555555224677777765542  2222 44555555444443

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=97.29  E-value=0.00044  Score=64.36  Aligned_cols=72  Identities=15%  Similarity=0.122  Sum_probs=54.8

Q ss_pred             ccCCCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         33 FKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        33 ~~~~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      +..+|+.|..+... ...+++|.|.+|||||.....-+...+........++++++-|+.-|..+.+.+..+.
T Consensus         7 l~~Ln~~Q~~av~~-~~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~   78 (721)
T PRK11773          7 LDSLNDKQREAVAA-PLGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLL   78 (721)
T ss_pred             HHhcCHHHHHHHhC-CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHh
Confidence            34578888776543 3468899999999999887666666664333344589999999999999999887775

>TIGR01075 uvrD DNA helicase II

Probab=97.27  E-value=0.00055  Score=63.67  Aligned_cols=72  Identities=17%  Similarity=0.075  Sum_probs=55.1

Q ss_pred             ccCCCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         33 FKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        33 ~~~~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      +..+++.|..+... .+.+++|.|.+|||||.+...-+...+........++++++.|+.-|..+.+.+.++.
T Consensus         2 l~~Ln~~Q~~av~~-~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~   73 (715)
T TIGR01075         2 LDGLNDKQREAVAA-PPGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALL   73 (715)
T ss_pred             ccccCHHHHHHHcC-CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHh
Confidence            34678888666543 3468999999999999987766666665333345589999999999999999887775

Designed to identify uvrD members of the uvrD/rep subfamily.

>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=97.24  E-value=0.0064  Score=45.88  Aligned_cols=44  Identities=20%  Similarity=0.181  Sum_probs=31.4

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      ....+++|+||+|.|...    ....+.++++.- +.++.++++|....
T Consensus       100 ~~~~KviiI~~ad~l~~~----a~NaLLK~LEep-p~~~~fiL~t~~~~  143 (162)
T PF13177_consen  100 EGKYKVIIIDEADKLTEE----AQNALLKTLEEP-PENTYFILITNNPS  143 (162)
T ss_dssp             TSSSEEEEEETGGGS-HH----HHHHHHHHHHST-TTTEEEEEEES-GG
T ss_pred             cCCceEEEeehHhhhhHH----HHHHHHHHhcCC-CCCEEEEEEECChH
Confidence            357899999999998776    667777777775 56777777655443

...

>KOG0734|consensus

Probab=97.23  E-value=0.0018  Score=57.02  Aligned_cols=67  Identities=16%  Similarity=0.035  Sum_probs=42.6

Q ss_pred             CccEEEEcccccccccCcc----chHHHHHHHHHhc--CCCCceEEEEeee-CchhHHHHHHHhcCCCeEEecC
Q psy12977        158 NVEWLIVDESDKLFEAGVR----GFRDQLAVIYAAC--SGPNLKRGMFSAT-HTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~----~~~~~i~~i~~~~--~~~~~q~v~~SAT-~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      .-..+.|||.|.+.+....    ...+.+.+++-.+  ...+--++.+.|| +|+.+.+.+-+=-+.-.+|.|.
T Consensus       396 APcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe~LD~AL~RPGRFD~~v~Vp  469 (752)
T KOG0734|consen  396 APCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFPEALDKALTRPGRFDRHVTVP  469 (752)
T ss_pred             CCeEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCChhhhhHHhcCCCccceeEecC
Confidence            4568899999988754311    2233455555444  2455678888999 7777777776655555566553

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.22  E-value=0.0056  Score=54.19  Aligned_cols=40  Identities=18%  Similarity=0.149  Sum_probs=25.6

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ..+.+++||||+|.+...    ....+.+.++.- ++.+.+++.+
T Consensus       114 ~~~~KVvIIDEah~Ls~~----A~NaLLK~LEeP-p~~v~fIlat  153 (491)
T PRK14964        114 SSKFKVYIIDEVHMLSNS----AFNALLKTLEEP-APHVKFILAT  153 (491)
T ss_pred             cCCceEEEEeChHhCCHH----HHHHHHHHHhCC-CCCeEEEEEe
Confidence            357889999999988664    334455555543 4455666543

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=97.21  E-value=0.00077  Score=56.60  Aligned_cols=45  Identities=16%  Similarity=0.194  Sum_probs=33.8

Q ss_pred             EEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        52 ~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      +.+.|+-|||||+.++.+.+..... .....+.|+.-|+..+.+.+
T Consensus       248 V~L~G~AGtGKTlLALaAgleqv~e-~~~y~KiiVtRp~vpvG~dI  292 (436)
T COG1875         248 VSLGGKAGTGKTLLALAAGLEQVLE-RKRYRKIIVTRPTVPVGEDI  292 (436)
T ss_pred             EEeeccCCccHhHHHHHHHHHHHHH-HhhhceEEEecCCcCccccc
Confidence            6789999999998888777766643 23355889988988776543

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.21  E-value=0.004  Score=55.57  Aligned_cols=39  Identities=13%  Similarity=0.037  Sum_probs=27.0

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      .+.+++||||+|.+...    ....+.++++.- ++.+.+++.+
T Consensus       118 ~~~kV~iIDE~~~ls~~----a~naLLk~LEep-p~~~~fIlat  156 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGH----SFNALLKTLEEP-PSHVKFILAT  156 (509)
T ss_pred             CCcEEEEEEChHhcCHH----HHHHHHHHHhcc-CCCeEEEEEE
Confidence            46789999999988765    344555666664 4566777654

>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase

Probab=97.20  E-value=0.00022  Score=54.48  Aligned_cols=124  Identities=20%  Similarity=0.254  Sum_probs=53.0

Q ss_pred             EEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCC
Q psy12977         53 FACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQK  132 (226)
Q Consensus        53 li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (226)
                      ++.|+-|-|||.+.-+.+...+...   ..++++.+|+.+-++..++.+..-.+..+.+.......    .........+
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~~---~~~I~vtAP~~~~~~~lf~~~~~~l~~~~~~~~~~~~~----~~~~~~~~~~   73 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQKG---KIRILVTAPSPENVQTLFEFAEKGLKALGYKEEKKKRI----GQIIKLRFNK   73 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS--------EEEE-SS--S-HHHHHCC------------------------------C
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHhc---CceEEEecCCHHHHHHHHHHHHhhcccccccccccccc----cccccccccc
Confidence            5789999999987655544433321   24799999999998888886655555444433100000    0000011224


Q ss_pred             CCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        133 FDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       133 ~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      ..|-...|+.+...         ....+++|||||=.+.-.       .+.+++     .....++||.|..
T Consensus        74 ~~i~f~~Pd~l~~~---------~~~~DlliVDEAAaIp~p-------~L~~ll-----~~~~~vv~stTi~  124 (177)
T PF05127_consen   74 QRIEFVAPDELLAE---------KPQADLLIVDEAAAIPLP-------LLKQLL-----RRFPRVVFSTTIH  124 (177)
T ss_dssp             CC--B--HHHHCCT-------------SCEEECTGGGS-HH-------HHHHHH-----CCSSEEEEEEEBS
T ss_pred             ceEEEECCHHHHhC---------cCCCCEEEEechhcCCHH-------HHHHHH-----hhCCEEEEEeecc
Confidence            45666666654322         123489999999866332       444444     2334666777854

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.

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.17  E-value=0.0038  Score=58.72  Aligned_cols=44  Identities=18%  Similarity=0.100  Sum_probs=29.4

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      ..+.+++||||+|.|...    ....+.++++.. +..+.+|+.+ |-++
T Consensus       118 ~~~~KV~IIDEad~lt~~----a~NaLLK~LEEp-P~~~~fIl~t-t~~~  161 (824)
T PRK07764        118 ESRYKIFIIDEAHMVTPQ----GFNALLKIVEEP-PEHLKFIFAT-TEPD  161 (824)
T ss_pred             cCCceEEEEechhhcCHH----HHHHHHHHHhCC-CCCeEEEEEe-CChh
Confidence            356789999999999765    445566666665 4556666654 4333

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=97.17  E-value=0.009  Score=56.09  Aligned_cols=42  Identities=26%  Similarity=0.267  Sum_probs=24.9

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      ..+.+||+||+|.+...    ....+..+++.......++++...+
T Consensus       868 r~v~IIILDEID~L~kK----~QDVLYnLFR~~~~s~SKLiLIGIS  909 (1164)
T PTZ00112        868 RNVSILIIDEIDYLITK----TQKVLFTLFDWPTKINSKLVLIAIS  909 (1164)
T ss_pred             ccceEEEeehHhhhCcc----HHHHHHHHHHHhhccCCeEEEEEec
Confidence            45679999999998764    2234444554432334555554444

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.16  E-value=0.0041  Score=56.65  Aligned_cols=39  Identities=13%  Similarity=0.025  Sum_probs=26.1

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      .+.+++||||+|.+...    ....+.++++.- ++...+++.+
T Consensus       117 gk~KV~IIDEVh~LS~~----A~NALLKtLEEP-P~~v~FILaT  155 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTH----SFNALLKTLEEP-PEHVKFLFAT  155 (702)
T ss_pred             CCcEEEEEechHhcCHH----HHHHHHHHHhcC-CCCcEEEEEE
Confidence            45789999999988655    445566666654 4456666643

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=97.15  E-value=0.0049  Score=53.26  Aligned_cols=137  Identities=13%  Similarity=0.068  Sum_probs=77.5

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH-HHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE-LAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~-L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      -.++.|..|||||.....-++..+... ..+.+++++-++.. +..-+...++.....++.....-...    ....-..
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~-~~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~g~~~~~~~~~----~~~~i~~   77 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAIN-KKQQNILAARKVQNSIRDSVFKDIENLLSIEGINYEFKKSK----SSMEIKI   77 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhc-CCCcEEEEEehhhhHHHHHHHHHHHHHHHHcCChhheeecC----CccEEEe
Confidence            457899999999998877766666543 12458898988887 77777888887777666532211111    0000001


Q ss_pred             CC-CCCEEEECc-hHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        130 AQ-KFDVLITTP-NKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       130 ~~-~~~IiV~Tp-~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      .. +..|++..- +...+       ......++++.+||+..+...    ....+...++. + .....+++|.+++.
T Consensus        78 ~~~g~~i~f~g~~d~~~~-------ik~~~~~~~~~idEa~~~~~~----~~~~l~~rlr~-~-~~~~~i~~t~NP~~  142 (396)
T TIGR01547        78 LNTGKKFIFKGLNDKPNK-------LKSGAGIAIIWFEEASQLTFE----DIKELIPRLRE-T-GGKKFIIFSSNPES  142 (396)
T ss_pred             cCCCeEEEeecccCChhH-------hhCcceeeeehhhhhhhcCHH----HHHHHHHHhhc-c-CCccEEEEEcCcCC
Confidence            12 344555443 21111       111334689999999988543    44444333322 1 12224667777654

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.

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.15  E-value=0.0032  Score=57.20  Aligned_cols=42  Identities=10%  Similarity=0.032  Sum_probs=27.7

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      ..+.+++||||+|.|...    ....+.++++.- +.++.+++.|.-
T Consensus       122 ~gr~KViIIDEah~Ls~~----AaNALLKTLEEP-P~~v~FILaTte  163 (700)
T PRK12323        122 AGRFKVYMIDEVHMLTNH----AFNAMLKTLEEP-PEHVKFILATTD  163 (700)
T ss_pred             cCCceEEEEEChHhcCHH----HHHHHHHhhccC-CCCceEEEEeCC
Confidence            346789999999998765    333444455543 456777776543

>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=97.14  E-value=0.00048  Score=54.53  Aligned_cols=123  Identities=18%  Similarity=0.229  Sum_probs=72.1

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcC-CCeEEEEe--cchhh--
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL-GLRAHVIG--KIQQA--  121 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~--~~~~~--  121 (226)
                      .+|+|.+.+.-.|.|||.+ +.|++.....+..  .-+.+++| ++|.+|..+.+....... +-++..+.  .....  
T Consensus        39 ~~~~n~v~QlnMGeGKTsV-I~Pmla~~LAdg~--~LvrviVp-k~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~  114 (229)
T PF12340_consen   39 PSGKNSVMQLNMGEGKTSV-IVPMLALALADGS--RLVRVIVP-KALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTP  114 (229)
T ss_pred             CCCCCeEeeecccCCccch-HHHHHHHHHcCCC--cEEEEEcC-HHHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCH
Confidence            3578999999999999975 4666666554322  25555555 579999998887775443 33322221  11100  


Q ss_pred             -----hhhhCCCcCCCCCEEEECchHHHHhHhcCC-----CC-----------CCCCCccEEEEccccccccc
Q psy12977        122 -----AEKFGPRSAQKFDVLITTPNKLVYLLQMDP-----PA-----------LNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus       122 -----~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~-----~~-----------~~~~~~~~lViDE~h~l~~~  173 (226)
                           .............|+++||+.+.++.-..-     +.           ..+.+...=|+||+|..++.
T Consensus       115 ~~~~~~~~l~~~~~~~~gill~~PEhilSf~L~~le~l~~~~~~~~~~l~~~q~~l~~~~rdilDEsDe~L~~  187 (229)
T PF12340_consen  115 ETLEKIRQLLEECMRSGGILLATPEHILSFKLKGLERLQDGKPEEARELLKIQKWLDEHSRDILDESDEILSV  187 (229)
T ss_pred             HHHHHHHHHHHHHHHcCCEEEeChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhcCCeEeECchhccCc
Confidence                 010001122445699999999987542210     11           11334445699999987754

There are two conserved sequence motifs: LLE and NMG.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=97.14  E-value=0.00089  Score=57.28  Aligned_cols=47  Identities=30%  Similarity=0.444  Sum_probs=32.7

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      ..+.++.+.|+-|+|||..+ -.+.+.++.   .+..+++++||-.=|..+
T Consensus        20 ~~~~~~fv~G~~GtGKs~l~-~~i~~~~~~---~~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen   20 EEGLNFFVTGPAGTGKSFLI-KAIIDYLRS---RGKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             cCCcEEEEEcCCCCChhHHH-HHHHHHhcc---ccceEEEecchHHHHHhc
Confidence            46688999999999999754 333444433   345788888887655544

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.12  E-value=0.008  Score=53.53  Aligned_cols=20  Identities=25%  Similarity=0.199  Sum_probs=16.4

Q ss_pred             CeEEEECCCCchHhHHHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFLIP   69 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~   69 (226)
                      +.++++||+|+|||..+..-
T Consensus        44 ~a~Lf~Gp~G~GKTT~Aril   63 (507)
T PRK06645         44 GGYLLTGIRGVGKTTSARII   63 (507)
T ss_pred             ceEEEECCCCCCHHHHHHHH
Confidence            56899999999999876443

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=97.11  E-value=0.01  Score=54.04  Aligned_cols=137  Identities=17%  Similarity=0.125  Sum_probs=79.8

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCC--------eEEEEecch
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGL--------RAHVIGKIQ  119 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~--------~~~~~~~~~  119 (226)
                      ..+-.++.+|-|.|||++..+.+...+..   .+.+++|.+|...-+.++++.++...+..+.        .+....++.
T Consensus       186 kq~~tV~taPRqrGKS~iVgi~l~~La~f---~Gi~IlvTAH~~~ts~evF~rv~~~le~lg~~~~fp~~~~iv~vkgg~  262 (752)
T PHA03333        186 GKCYTAATVPRRCGKTTIMAIILAAMISF---LEIDIVVQAQRKTMCLTLYNRVETVVHAYQHKPWFPEEFKIVTLKGTD  262 (752)
T ss_pred             hhcceEEEeccCCCcHHHHHHHHHHHHHh---cCCeEEEECCChhhHHHHHHHHHHHHHHhccccccCCCceEEEeeCCe
Confidence            34667899999999999866554444321   2568999999999999999988888774431        111122111


Q ss_pred             hhhh-hhCCCcC-CCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEE
Q psy12977        120 QAAE-KFGPRSA-QKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRG  197 (226)
Q Consensus       120 ~~~~-~~~~~~~-~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v  197 (226)
                      +... ....... +++.|..++..         +....-.+.+++|+|||..+...    ....+.-++..   ...+.+
T Consensus       263 E~I~f~~p~gak~G~sti~F~Ars---------~~s~RG~~~DLLIVDEAAfI~~~----~l~aIlP~l~~---~~~k~I  326 (752)
T PHA03333        263 ENLEYISDPAAKEGKTTAHFLASS---------PNAARGQNPDLVIVDEAAFVNPG----ALLSVLPLMAV---KGTKQI  326 (752)
T ss_pred             eEEEEecCcccccCcceeEEeccc---------CCCcCCCCCCEEEEECcccCCHH----HHHHHHHHHcc---CCCceE
Confidence            1000 0000001 11233333222         12223335689999999987664    44445444432   466777


Q ss_pred             EEeeeC
Q psy12977        198 MFSATH  203 (226)
Q Consensus       198 ~~SAT~  203 (226)
                      ++|.+.
T Consensus       327 iISS~~  332 (752)
T PHA03333        327 HISSPV  332 (752)
T ss_pred             EEeCCC
Confidence            778885

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.09  E-value=0.026  Score=49.43  Aligned_cols=132  Identities=17%  Similarity=0.150  Sum_probs=68.7

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEc-ccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCC
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVC-PTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPR  128 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~-Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (226)
                      ..+++.|++|+|||....--+. .+...   +.++.++. .+..-  ...++++.+....+..+......          
T Consensus        96 ~vI~lvG~~GsGKTTtaakLA~-~L~~~---g~kV~lV~~D~~R~--aa~eQL~~la~~~gvp~~~~~~~----------  159 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTAAKLAR-YFKKK---GLKVGLVAADTYRP--AAYDQLKQLAEKIGVPFYGDPDN----------  159 (437)
T ss_pred             eEEEEECCCCCcHHHHHHHHHH-HHHHc---CCeEEEecCCCCCH--HHHHHHHHHHHHcCCcEEecCCc----------
Confidence            4688999999999987544333 33321   23444443 33211  12344445544444432111000          


Q ss_pred             cCCCCCEEEECchH-HHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        129 SAQKFDVLITTPNK-LVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       129 ~~~~~~IiV~Tp~~-l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                               ..|.. +.+.+..      ....+++|+|.+-+.....  .....+..+.... .+..-++.++|+...+.
T Consensus       160 ---------~d~~~i~~~al~~------~~~~DvVIIDTAGr~~~d~--~lm~El~~l~~~~-~pdevlLVvda~~gq~a  221 (437)
T PRK00771        160 ---------KDAVEIAKEGLEK------FKKADVIIVDTAGRHALEE--DLIEEMKEIKEAV-KPDEVLLVIDATIGQQA  221 (437)
T ss_pred             ---------cCHHHHHHHHHHH------hhcCCEEEEECCCcccchH--HHHHHHHHHHHHh-cccceeEEEeccccHHH
Confidence                     01112 2233333      1223899999995443221  3666666766655 45556677788877666


Q ss_pred             HHHHHHhc
Q psy12977        208 AKWCRRKL  215 (226)
Q Consensus       208 ~~~~~~~~  215 (226)
                      .+.++.+.
T Consensus       222 v~~a~~F~  229 (437)
T PRK00771        222 KNQAKAFH  229 (437)
T ss_pred             HHHHHHHH
Confidence            66666643

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.09  E-value=0.0031  Score=56.13  Aligned_cols=147  Identities=15%  Similarity=0.129  Sum_probs=81.1

Q ss_pred             EECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh----------hcC--CCeEEEEecchhh
Q psy12977         54 ACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS----------EGL--GLRAHVIGKIQQA  121 (226)
Q Consensus        54 i~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~----------~~~--~~~~~~~~~~~~~  121 (226)
                      ..+.||||||+..+.-+++....+   ....++.+....+.+.....+..-.          ...  .+.+..+.     
T Consensus         2 f~matgsgkt~~ma~lil~~y~kg---yr~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkvn-----   73 (812)
T COG3421           2 FEMATGSGKTLVMAGLILECYKKG---YRNFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKVN-----   73 (812)
T ss_pred             cccccCCChhhHHHHHHHHHHHhc---hhhEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeeec-----
Confidence            357899999998766666666542   3467888877666665544322111          000  11111111     


Q ss_pred             hhhhCCCcCCCCCEEEECchHHHHhHhcC-CCCCCCCCc---c-EEEEcccccccccC----------ccchHHHHHHHH
Q psy12977        122 AEKFGPRSAQKFDVLITTPNKLVYLLQMD-PPALNLANV---E-WLIVDESDKLFEAG----------VRGFRDQLAVIY  186 (226)
Q Consensus       122 ~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~-~~~~~~~~~---~-~lViDE~h~l~~~~----------~~~~~~~i~~i~  186 (226)
                        .++ ....+.+|..+|.+.+...+.+- ...+.+.++   . .++-||+|++....          .+.+...+...+
T Consensus        74 --~fs-ehnd~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~  150 (812)
T COG3421          74 --NFS-EHNDAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLAL  150 (812)
T ss_pred             --ccC-ccCCceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHH
Confidence              111 14466789999999999877542 123333333   3 56679999986431          112222222222


Q ss_pred             HhcCCCCceEEEEeeeCchhHHHHHHHh
Q psy12977        187 AACSGPNLKRGMFSATHTEDVAKWCRRK  214 (226)
Q Consensus       187 ~~~~~~~~q~v~~SAT~~~~~~~~~~~~  214 (226)
                      +.  ++..-++.+|||.|++ +....+|
T Consensus       151 ~~--nkd~~~lef~at~~k~-k~v~~ky  175 (812)
T COG3421         151 EQ--NKDNLLLEFSATIPKE-KSVEDKY  175 (812)
T ss_pred             hc--CCCceeehhhhcCCcc-ccHHHHh
Confidence            22  3555667899998833 3334344

>PRK04328 hypothetical protein; Provisional

Probab=97.08  E-value=0.0066  Score=49.14  Aligned_cols=54  Identities=19%  Similarity=0.175  Sum_probs=36.0

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      ..|..+++.|++|+|||...+-.+...+.+    +.+++|+. +.+-..++.+.++.+.
T Consensus        21 p~gs~ili~G~pGsGKT~l~~~fl~~~~~~----ge~~lyis-~ee~~~~i~~~~~~~g   74 (249)
T PRK04328         21 PERNVVLLSGGPGTGKSIFSQQFLWNGLQM----GEPGVYVA-LEEHPVQVRRNMRQFG   74 (249)
T ss_pred             cCCcEEEEEcCCCCCHHHHHHHHHHHHHhc----CCcEEEEE-eeCCHHHHHHHHHHcC
Confidence            356789999999999997655545555543    44567765 5455556666666553

>PF13173 AAA_14: AAA domain

Probab=97.08  E-value=0.0091  Score=43.03  Aligned_cols=39  Identities=21%  Similarity=0.358  Sum_probs=28.1

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      .-.++++||+|.+.     ++...++.+...-  ++.++++.+...
T Consensus        61 ~~~~i~iDEiq~~~-----~~~~~lk~l~d~~--~~~~ii~tgS~~   99 (128)
T PF13173_consen   61 GKKYIFIDEIQYLP-----DWEDALKFLVDNG--PNIKIILTGSSS   99 (128)
T ss_pred             CCcEEEEehhhhhc-----cHHHHHHHHHHhc--cCceEEEEccch
Confidence            45689999999873     4677777777654  567888765553

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=97.08  E-value=0.0021  Score=54.78  Aligned_cols=18  Identities=39%  Similarity=0.562  Sum_probs=15.5

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      .++++.||+|+|||....
T Consensus        41 ~~i~I~G~~GtGKT~l~~   58 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVTK   58 (365)
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            679999999999997643

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.

>TIGR00376 DNA helicase, putative

Probab=97.07  E-value=0.0012  Score=60.45  Aligned_cols=65  Identities=14%  Similarity=0.248  Sum_probs=46.5

Q ss_pred             CCCCcccccc-cCCC-CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHH
Q psy12977         35 HFEPHFTITY-LSPL-GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVR  103 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~-~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~  103 (226)
                      .+++-|..+. ..+. ....+++||+|+|||....-.+.+.+..    +.++++++||..-+.++.+.+..
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~~----g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKR----GLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHHc----CCCEEEEcCcHHHHHHHHHHHHh
Confidence            4455665553 2233 3678999999999997655444454442    45899999999999999888766

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.

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=97.07  E-value=0.011  Score=53.64  Aligned_cols=143  Identities=14%  Similarity=0.115  Sum_probs=86.7

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcC--CCeEEEEecchhhhhhh
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL--GLRAHVIGKIQQAAEKF  125 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~  125 (226)
                      ..+-.++..|--.|||+... +++..+.. ...+.++++.+|.+..++.+++++....+..  +..+....+.     ..
T Consensus       253 kqk~tVflVPRR~GKTwivv-~iI~~ll~-s~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkGe-----~I  325 (738)
T PHA03368        253 RQRATVFLVPRRHGKTWFLV-PLIALALA-TFRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKGE-----TI  325 (738)
T ss_pred             hccceEEEecccCCchhhHH-HHHHHHHH-hCCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecCc-----EE
Confidence            45677889999999999655 54443321 2236799999999999999999998886643  1112222221     11


Q ss_pred             CCCcCCC--CCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        126 GPRSAQK--FDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       126 ~~~~~~~--~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      .....++  +.|...+.        +..+...=.+++++|+|||+.+.+.    ....+.-.+.   ..+++.+++|.|.
T Consensus       326 ~i~f~nG~kstI~FaSa--------rntNsiRGqtfDLLIVDEAqFIk~~----al~~ilp~l~---~~n~k~I~ISS~N  390 (738)
T PHA03368        326 SFSFPDGSRSTIVFASS--------HNTNGIRGQDFNLLFVDEANFIRPD----AVQTIMGFLN---QTNCKIIFVSSTN  390 (738)
T ss_pred             EEEecCCCccEEEEEec--------cCCCCccCCcccEEEEechhhCCHH----HHHHHHHHHh---ccCccEEEEecCC
Confidence            0011112  24555422        1112333458999999999988765    3444433332   3589999999996


Q ss_pred             ch-hHHHHHH
Q psy12977        204 TE-DVAKWCR  212 (226)
Q Consensus       204 ~~-~~~~~~~  212 (226)
                      .. ...-|+.
T Consensus       391 s~~~sTSFL~  400 (738)
T PHA03368        391 TGKASTSFLY  400 (738)
T ss_pred             CCccchHHHH
Confidence            64 3344443

>KOG0739|consensus

Probab=97.07  E-value=0.014  Score=48.16  Aligned_cols=124  Identities=19%  Similarity=0.215  Sum_probs=76.6

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      +-+++-+|+|+||+..+-..+-+     .+   -+.+-+.+..|+..+.-.-..+-+                       
T Consensus       167 rgiLLyGPPGTGKSYLAKAVATE-----An---STFFSvSSSDLvSKWmGESEkLVk-----------------------  215 (439)
T KOG0739|consen  167 RGILLYGPPGTGKSYLAKAVATE-----AN---STFFSVSSSDLVSKWMGESEKLVK-----------------------  215 (439)
T ss_pred             eeEEEeCCCCCcHHHHHHHHHhh-----cC---CceEEeehHHHHHHHhccHHHHHH-----------------------
Confidence            34899999999999643322211     11   356777777888765543333311                       


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhc-------CCCCceEEEEeee
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC-------SGPNLKRGMFSAT  202 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~-------~~~~~q~v~~SAT  202 (226)
                                  .|+.+.+.       ..-+++.|||+|.+......+-.+.-.+|...+       -+.+--++.+.||
T Consensus       216 ------------nLFemARe-------~kPSIIFiDEiDslcg~r~enEseasRRIKTEfLVQMqGVG~d~~gvLVLgAT  276 (439)
T KOG0739|consen  216 ------------NLFEMARE-------NKPSIIFIDEIDSLCGSRSENESEASRRIKTEFLVQMQGVGNDNDGVLVLGAT  276 (439)
T ss_pred             ------------HHHHHHHh-------cCCcEEEeehhhhhccCCCCCchHHHHHHHHHHHHhhhccccCCCceEEEecC
Confidence                        23333332       244689999999887655444455555554443       2455677888999


Q ss_pred             -CchhHHHHHHHhcCCCeEEec
Q psy12977        203 -HTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       203 -~~~~~~~~~~~~~~~p~~i~~  223 (226)
                       .|=.+...+++.+...++|-+
T Consensus       277 NiPw~LDsAIRRRFekRIYIPL  298 (439)
T KOG0739|consen  277 NIPWVLDSAIRRRFEKRIYIPL  298 (439)
T ss_pred             CCchhHHHHHHHHhhcceeccC
Confidence             565677778887777777644

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=97.07  E-value=0.0022  Score=52.90  Aligned_cols=97  Identities=14%  Similarity=0.136  Sum_probs=50.5

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhc---CCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLR---GPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG  126 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~---~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (226)
                      .++++.|+|+.|||...--..-..-.   .....-|-+.+-+|...-....+..+-...   +..........   ..  
T Consensus        62 p~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~l---gaP~~~~~~~~---~~--  133 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEAL---GAPYRPRDRVA---KL--  133 (302)
T ss_pred             CceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHh---CcccCCCCCHH---HH--
Confidence            57999999999999854221111111   011112455666677766666665543332   22211000000   00  


Q ss_pred             CCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccC
Q psy12977        127 PRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG  174 (226)
Q Consensus       127 ~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~  174 (226)
                                   -.+..+++.       .-+++++||||+|.++...
T Consensus       134 -------------~~~~~~llr-------~~~vrmLIIDE~H~lLaGs  161 (302)
T PF05621_consen  134 -------------EQQVLRLLR-------RLGVRMLIIDEFHNLLAGS  161 (302)
T ss_pred             -------------HHHHHHHHH-------HcCCcEEEeechHHHhccc
Confidence                         012223333       3478899999999987653

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>KOG0392|consensus

Probab=97.07  E-value=0.0058  Score=58.42  Aligned_cols=141  Identities=16%  Similarity=0.170  Sum_probs=85.6

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCC-----CCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhh
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKN-----LGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAE  123 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~-----~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (226)
                      +-+=|++-.=|-|||+-.+..+.....+...     ...-.+|+||+ .|+--|..++.++++.+  ++....|.. .+.
T Consensus       994 ~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPs-TLtGHW~~E~~kf~pfL--~v~~yvg~p-~~r 1069 (1549)
T KOG0392|consen  994 KLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPS-TLTGHWKSEVKKFFPFL--KVLQYVGPP-AER 1069 (1549)
T ss_pred             cccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCc-hhhhHHHHHHHHhcchh--hhhhhcCCh-HHH
Confidence            4466899999999998766554443322211     11227999998 48899999999998873  333223222 222


Q ss_pred             hhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        124 KFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       124 ~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      ...+.-.++++|+|+..+.+.+.+..    +.-.++.|.|+||-|.+-..     ...+....+++ ..+ ..+.+|.|+
T Consensus      1070 ~~lR~q~~~~~iiVtSYDv~RnD~d~----l~~~~wNYcVLDEGHVikN~-----ktkl~kavkqL-~a~-hRLILSGTP 1138 (1549)
T KOG0392|consen 1070 RELRDQYKNANIIVTSYDVVRNDVDY----LIKIDWNYCVLDEGHVIKNS-----KTKLTKAVKQL-RAN-HRLILSGTP 1138 (1549)
T ss_pred             HHHHhhccccceEEeeHHHHHHHHHH----HHhcccceEEecCcceecch-----HHHHHHHHHHH-hhc-ceEEeeCCC
Confidence            22344457789999998887754321    11235679999999977432     22333333333 123 345568994


Q ss_pred             c
Q psy12977        204 T  204 (226)
Q Consensus       204 ~  204 (226)
                      =
T Consensus      1139 I 1139 (1549)
T KOG0392|consen 1139 I 1139 (1549)
T ss_pred             c
Confidence            3

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=97.06  E-value=0.006  Score=49.54  Aligned_cols=52  Identities=19%  Similarity=0.240  Sum_probs=34.5

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHH
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET  101 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~  101 (226)
                      ++..+.++++.||+|+|||..+..- ...+...   +.+ ++.+++.+++.++...+
T Consensus       101 ~~~~~~nl~l~G~~G~GKThLa~Ai-~~~l~~~---g~s-v~f~~~~el~~~Lk~~~  152 (254)
T COG1484         101 FFERGENLVLLGPPGVGKTHLAIAI-GNELLKA---GIS-VLFITAPDLLSKLKAAF  152 (254)
T ss_pred             HhccCCcEEEECCCCCcHHHHHHHH-HHHHHHc---CCe-EEEEEHHHHHHHHHHHH
Confidence            3347889999999999999765443 3333321   333 55567888888766644

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.06  E-value=0.0086  Score=49.97  Aligned_cols=54  Identities=15%  Similarity=0.114  Sum_probs=31.7

Q ss_pred             CCCccEEEEcccccccccCccchHHHH-HHHHHhcCCCCceEEEEeeeCchhHHHHH
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQL-AVIYAACSGPNLKRGMFSATHTEDVAKWC  211 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i-~~i~~~~~~~~~q~v~~SAT~~~~~~~~~  211 (226)
                      +.++++||+||...-.-..  -..+.+ ..++.........+++.|.-.++++.+.+
T Consensus       215 l~~~dlLiIDDiG~e~~s~--~~~~~ll~~Il~~R~~~~~~ti~TSNl~~~el~~~~  269 (306)
T PRK08939        215 VKEAPVLMLDDIGAEQMSS--WVRDEVLGVILQYRMQEELPTFFTSNFDFDELEHHL  269 (306)
T ss_pred             hcCCCEEEEecCCCccccH--HHHHHHHHHHHHHHHHCCCeEEEECCCCHHHHHHHH
Confidence            5578899999998543221  122233 44544432356778887776666655443

>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=97.04  E-value=0.0034  Score=44.93  Aligned_cols=63  Identities=19%  Similarity=0.159  Sum_probs=33.2

Q ss_pred             ccEEEEcccccccccC-------ccchHHHHHHHHHhcCCC--CceEEEEeeeCchhHHHHHHHhcCCCeEEec
Q psy12977        159 VEWLIVDESDKLFEAG-------VRGFRDQLAVIYAACSGP--NLKRGMFSATHTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       159 ~~~lViDE~h~l~~~~-------~~~~~~~i~~i~~~~~~~--~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~  223 (226)
                      -.++++||+|.+....       .......+...+......  +..+++.|.+ ++.+...+.+ -.....+++
T Consensus        59 ~~vl~iDe~d~l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~-~~~i~~~l~~-~rf~~~i~~  130 (132)
T PF00004_consen   59 PCVLFIDEIDKLFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNS-PDKIDPALLR-SRFDRRIEF  130 (132)
T ss_dssp             SEEEEEETGGGTSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESS-GGGSCHHHHS-TTSEEEEEE
T ss_pred             ceeeeeccchhcccccccccccccccccceeeecccccccccccceeEEeeCC-hhhCCHhHHh-CCCcEEEEc
Confidence            4799999999987663       011234444445444332  2344444444 5555555553 333444443

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 ....

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=97.04  E-value=0.0071  Score=50.48  Aligned_cols=46  Identities=20%  Similarity=0.205  Sum_probs=30.2

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                      ....+++++||+|.|...    ....+.+.++.- +.++.+++.+. -|..+
T Consensus       107 ~~~~kviiidead~mt~~----A~nallk~lEep-~~~~~~il~~n-~~~~i  152 (325)
T COG0470         107 EGGYKVVIIDEADKLTED----AANALLKTLEEP-PKNTRFILITN-DPSKI  152 (325)
T ss_pred             CCCceEEEeCcHHHHhHH----HHHHHHHHhccC-CCCeEEEEEcC-Chhhc
Confidence            467899999999999775    455565666544 45566666544 34333

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

Probab=97.03  E-value=0.002  Score=56.58  Aligned_cols=55  Identities=22%  Similarity=0.242  Sum_probs=42.7

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCe
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR  111 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~  111 (226)
                      +.-.+-|.||||||+...-.+ ....      .-++|++|++.||-|.+..++++++.-.+.
T Consensus        33 ~~QtLLGvTGSGKTfT~AnVI-~~~~------rPtLV~AhNKTLAaQLy~Efk~fFP~NaVE   87 (663)
T COG0556          33 KHQTLLGVTGSGKTFTMANVI-AKVQ------RPTLVLAHNKTLAAQLYSEFKEFFPENAVE   87 (663)
T ss_pred             eeeEEeeeccCCchhHHHHHH-HHhC------CCeEEEecchhHHHHHHHHHHHhCcCcceE
Confidence            567889999999998754433 3222      247999999999999999999999764443

>KOG0953|consensus

Probab=97.02  E-value=0.0022  Score=56.46  Aligned_cols=100  Identities=20%  Similarity=0.245  Sum_probs=67.0

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPR  128 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (226)
                      ++-++=+|||.||||..+    ++++..    ...++|.-|.|-||..+++.+...    |+.+....|.......   .
T Consensus       191 RkIi~H~GPTNSGKTy~A----Lqrl~~----aksGvycGPLrLLA~EV~~r~na~----gipCdL~TGeE~~~~~---~  255 (700)
T KOG0953|consen  191 RKIIMHVGPTNSGKTYRA----LQRLKS----AKSGVYCGPLRLLAHEVYDRLNAL----GIPCDLLTGEERRFVL---D  255 (700)
T ss_pred             heEEEEeCCCCCchhHHH----HHHHhh----hccceecchHHHHHHHHHHHhhhc----CCCccccccceeeecC---C
Confidence            455677899999999764    555543    235699999999999999998887    6666555554211111   1


Q ss_pred             cCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977        129 SAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus       129 ~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      ....++.+=||-++..          .-..++..|+||.+.|-|.
T Consensus       256 ~~~~a~hvScTVEM~s----------v~~~yeVAViDEIQmm~Dp  290 (700)
T KOG0953|consen  256 NGNPAQHVSCTVEMVS----------VNTPYEVAVIDEIQMMRDP  290 (700)
T ss_pred             CCCcccceEEEEEEee----------cCCceEEEEehhHHhhcCc
Confidence            1234567777766431          1335679999999987665

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.02  E-value=0.0044  Score=52.10  Aligned_cols=40  Identities=15%  Similarity=0.174  Sum_probs=26.5

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      ...+++|+||+|.+.+.    ....+..+++.. ++.+.+++.+.
T Consensus       124 ~~~~vlilDe~~~l~~~----~~~~L~~~le~~-~~~~~~Il~~~  163 (337)
T PRK12402        124 ADYKTILLDNAEALRED----AQQALRRIMEQY-SRTCRFIIATR  163 (337)
T ss_pred             CCCcEEEEeCcccCCHH----HHHHHHHHHHhc-cCCCeEEEEeC
Confidence            45679999999987543    445666666655 34566666443

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.01  E-value=0.014  Score=54.29  Aligned_cols=133  Identities=13%  Similarity=0.170  Sum_probs=72.5

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceE-EEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRA-VIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG  126 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~-iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (226)
                      .++-+.+.||||+|||.....-+....... . +.++ ++-+.+...+  ..++++.+.+..++.+              
T Consensus       184 ~g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~-G-~kkV~lit~Dt~Rig--A~eQL~~~a~~~gvpv--------------  245 (767)
T PRK14723        184 QGGVLALVGPTGVGKTTTTAKLAARCVARE-G-ADQLALLTTDSFRIG--ALEQLRIYGRILGVPV--------------  245 (767)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHhhHHHHc-C-CCeEEEecCcccchH--HHHHHHHHHHhCCCCc--------------
Confidence            356788999999999987654433322111 1 1233 3333333221  1344555555444432              


Q ss_pred             CCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc-h
Q psy12977        127 PRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT-E  205 (226)
Q Consensus       127 ~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~-~  205 (226)
                              ..+.+|..+.+.+..      +.+.++++||=+=+.....  .....+..+.... .+..-++.+|||.. +
T Consensus       246 --------~~~~~~~~l~~al~~------~~~~D~VLIDTAGRs~~d~--~l~eel~~l~~~~-~p~e~~LVLsAt~~~~  308 (767)
T PRK14723        246 --------HAVKDAADLRFALAA------LGDKHLVLIDTVGMSQRDR--NVSEQIAMLCGVG-RPVRRLLLLNAASHGD  308 (767)
T ss_pred             --------cccCCHHHHHHHHHH------hcCCCEEEEeCCCCCccCH--HHHHHHHHHhccC-CCCeEEEEECCCCcHH
Confidence                    123366666666654      4456789998887654321  3444555544433 34445667788754 5


Q ss_pred             hHHHHHHHhc
Q psy12977        206 DVAKWCRRKL  215 (226)
Q Consensus       206 ~~~~~~~~~~  215 (226)
                      ++.+.+++|-
T Consensus       309 ~l~~i~~~f~  318 (767)
T PRK14723        309 TLNEVVHAYR  318 (767)
T ss_pred             HHHHHHHHHh
Confidence            5666666663

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=96.99  E-value=0.0018  Score=59.70  Aligned_cols=89  Identities=16%  Similarity=0.057  Sum_probs=62.7

Q ss_pred             CCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEE
Q psy12977         36 FEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVI  115 (226)
Q Consensus        36 ~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  115 (226)
                      +++.|..+... .+.+++|.|.+|||||.....-+...+........++++++.|+.-+.++.+.+.+..+..       
T Consensus         2 Ln~~Q~~av~~-~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l~~~-------   73 (664)
T TIGR01074         2 LNPQQQEAVEY-VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTLGKG-------   73 (664)
T ss_pred             CCHHHHHHHhC-CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhCcc-------
Confidence            56777665433 3568999999999999987766666664322334588999999999999988887664310       


Q ss_pred             ecchhhhhhhCCCcCCCCCEEEECchHHHHhH
Q psy12977        116 GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLL  147 (226)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~  147 (226)
                                     ....+-|+|..++...+
T Consensus        74 ---------------~~~~v~v~TfHs~a~~i   90 (664)
T TIGR01074        74 ---------------EARGLTISTFHTLGLDI   90 (664)
T ss_pred             ---------------ccCCeEEEeHHHHHHHH
Confidence                           11247788888886544

Designed to identify rep members of the uvrD/rep subfamily.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=96.97  E-value=0.015  Score=44.81  Aligned_cols=40  Identities=15%  Similarity=0.181  Sum_probs=26.2

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ....+++|+||+|.+...    ....+...++.- ++.+-+++.+
T Consensus        94 ~~~~kviiide~~~l~~~----~~~~Ll~~le~~-~~~~~~il~~  133 (188)
T TIGR00678        94 ESGRRVVIIEDAERMNEA----AANALLKTLEEP-PPNTLFILIT  133 (188)
T ss_pred             cCCeEEEEEechhhhCHH----HHHHHHHHhcCC-CCCeEEEEEE
Confidence            456789999999998764    344555555553 4455666554

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.96  E-value=0.012  Score=50.44  Aligned_cols=39  Identities=13%  Similarity=0.055  Sum_probs=24.8

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      .+.+++|+||+|.+...    ....+.+.++.- ++.+.+++.+
T Consensus       118 ~~~kviIIDEa~~l~~~----a~naLLk~lEe~-~~~~~fIl~t  156 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRH----SFNALLKTLEEP-PQHIKFILAT  156 (363)
T ss_pred             CCceEEEEEChhhcCHH----HHHHHHHHHhcC-CCCeEEEEEc
Confidence            45689999999988654    333445555443 4456666644

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=96.96  E-value=0.011  Score=54.25  Aligned_cols=39  Identities=13%  Similarity=0.060  Sum_probs=26.1

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      .+.+++||||+|.+...    ....+.++++.- +..+.+|+.+
T Consensus       118 gk~KVIIIDEad~Ls~~----A~NALLKtLEEP-p~~v~fILaT  156 (709)
T PRK08691        118 GKYKVYIIDEVHMLSKS----AFNAMLKTLEEP-PEHVKFILAT  156 (709)
T ss_pred             CCcEEEEEECccccCHH----HHHHHHHHHHhC-CCCcEEEEEe
Confidence            46789999999987654    334555555554 4566777654

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=96.96  E-value=0.0032  Score=58.95  Aligned_cols=83  Identities=16%  Similarity=0.102  Sum_probs=64.3

Q ss_pred             CCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch-----
Q psy12977        131 QKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE-----  205 (226)
Q Consensus       131 ~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~-----  205 (226)
                      ....|+++||..+...+-.  +.+++..+..+|+||||++.+.   .....+.++++.- ++..-+.+|||.+..     
T Consensus         6 ~~ggi~~~T~rIl~~DlL~--~ri~~~~itgiiv~~Ahr~~~~---~~eaFI~rlyr~~-n~~gfIkafSdsP~~~~~g~   79 (814)
T TIGR00596         6 LEGGIFSITSRILVVDLLT--GIIPPELITGILVLRADRIIES---SQEAFILRLYRQK-NKTGFIKAFSDNPEAFTMGF   79 (814)
T ss_pred             hcCCEEEEechhhHhHHhc--CCCCHHHccEEEEeeccccccc---ccHHHHHHHHHHh-CCCcceEEecCCCcccccch
Confidence            3456999999999988877  8999999999999999999877   4555666777666 567789999999774     


Q ss_pred             -hHHHHHHHhcCCCe
Q psy12977        206 -DVAKWCRRKLKRRV  219 (226)
Q Consensus       206 -~~~~~~~~~~~~p~  219 (226)
                       .+.+.++...-..+
T Consensus        80 ~~l~~vmk~L~i~~v   94 (814)
T TIGR00596        80 SPLETKMRNLFLRHV   94 (814)
T ss_pred             HHHHHHHHHhCcCeE
Confidence             45666655443333

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

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.95  E-value=0.0055  Score=48.98  Aligned_cols=53  Identities=17%  Similarity=0.201  Sum_probs=34.3

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      ..|..+++.+++|+|||......+...+.+    +.++++++.. +-..+..+.+..+
T Consensus        22 ~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~----g~~~~yi~~e-~~~~~~~~~~~~~   74 (230)
T PRK08533         22 PAGSLILIEGDESTGKSILSQRLAYGFLQN----GYSVSYVSTQ-LTTTEFIKQMMSL   74 (230)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHhC----CCcEEEEeCC-CCHHHHHHHHHHh
Confidence            457789999999999998654444444432    4577888743 3335555555444

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=96.94  E-value=0.0076  Score=58.06  Aligned_cols=123  Identities=15%  Similarity=0.139  Sum_probs=74.3

Q ss_pred             CCCCcccccc-cC-CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeE
Q psy12977         35 HFEPHFTITY-LS-PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRA  112 (226)
Q Consensus        35 ~~~~~Q~~~~-~~-~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~  112 (226)
                      .+++-|..+. .+ ..++-.+++|+.|+|||... -.+...+..   .+.+++-++||-.-+....+       ..+...
T Consensus       381 ~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l-~~~~~~~e~---~G~~V~g~ApTgkAA~~L~e-------~~Gi~a  449 (1102)
T PRK13826        381 RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMM-KAAREAWEA---AGYRVVGGALAGKAAEGLEK-------EAGIQS  449 (1102)
T ss_pred             CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHH-HHHHHHHHH---cCCeEEEEcCcHHHHHHHHH-------hhCCCe
Confidence            5778786664 23 34566899999999999754 334444432   25689999999766655433       123322


Q ss_pred             EEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCC
Q psy12977        113 HVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGP  192 (226)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~  192 (226)
                      .                         |-.++.....  .+...+..-++|||||+..+...       .+..+++.....
T Consensus       450 ~-------------------------TIas~ll~~~--~~~~~l~~~~vlVIDEAsMv~~~-------~m~~Ll~~~~~~  495 (1102)
T PRK13826        450 R-------------------------TLSSWELRWN--QGRDQLDNKTVFVLDEAGMVASR-------QMALFVEAVTRA  495 (1102)
T ss_pred             e-------------------------eHHHHHhhhc--cCccCCCCCcEEEEECcccCCHH-------HHHHHHHHHHhc
Confidence            1                         2222211111  12334666789999999965332       444556655456


Q ss_pred             CceEEEEeee
Q psy12977        193 NLKRGMFSAT  202 (226)
Q Consensus       193 ~~q~v~~SAT  202 (226)
                      .++++++.=+
T Consensus       496 garvVLVGD~  505 (1102)
T PRK13826        496 GAKLVLVGDP  505 (1102)
T ss_pred             CCEEEEECCH
Confidence            7899988766

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.93  E-value=0.032  Score=45.69  Aligned_cols=132  Identities=16%  Similarity=0.161  Sum_probs=72.0

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH--HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR--ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG  126 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~--~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (226)
                      +..+.+.+|+|+|||..+..-+......   ...-.++-+.+.  ....|+    +...+..+..               
T Consensus        75 ~~~i~~~G~~g~GKTtl~~~l~~~l~~~---~~~v~~i~~D~~ri~~~~ql----~~~~~~~~~~---------------  132 (270)
T PRK06731         75 VQTIALIGPTGVGKTTTLAKMAWQFHGK---KKTVGFITTDHSRIGTVQQL----QDYVKTIGFE---------------  132 (270)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEecCCCCHHHHHHH----HHHhhhcCce---------------
Confidence            3678999999999998765443332221   122333444332  233333    3333322322               


Q ss_pred             CCcCCCCCEEE-ECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC-c
Q psy12977        127 PRSAQKFDVLI-TTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH-T  204 (226)
Q Consensus       127 ~~~~~~~~IiV-~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~-~  204 (226)
                              +.. .++..+.+.+...   -...+.+++++|.+=+.....  .....+..+.+.. .+..-.+.+|||. +
T Consensus       133 --------~~~~~~~~~l~~~l~~l---~~~~~~D~ViIDt~Gr~~~~~--~~l~el~~~~~~~-~~~~~~LVl~a~~~~  198 (270)
T PRK06731        133 --------VIAVRDEAAMTRALTYF---KEEARVDYILIDTAGKNYRAS--ETVEEMIETMGQV-EPDYICLTLSASMKS  198 (270)
T ss_pred             --------EEecCCHHHHHHHHHHH---HhcCCCCEEEEECCCCCcCCH--HHHHHHHHHHhhh-CCCeEEEEEcCccCH
Confidence                    222 2455555444321   112467899999997653221  3555666666555 3333456689884 5


Q ss_pred             hhHHHHHHHhcC
Q psy12977        205 EDVAKWCRRKLK  216 (226)
Q Consensus       205 ~~~~~~~~~~~~  216 (226)
                      .+..+.+++|-.
T Consensus       199 ~d~~~~~~~f~~  210 (270)
T PRK06731        199 KDMIEIITNFKD  210 (270)
T ss_pred             HHHHHHHHHhCC
Confidence            678888887753

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=96.93  E-value=0.0088  Score=54.38  Aligned_cols=40  Identities=23%  Similarity=0.120  Sum_probs=27.4

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ..+.+++||||+|.+...    ....+.+.++.- ++.+.+|+.+
T Consensus       130 ~a~~KVvIIDEad~Ls~~----a~naLLKtLEeP-p~~~~fIl~t  169 (598)
T PRK09111        130 SARYKVYIIDEVHMLSTA----AFNALLKTLEEP-PPHVKFIFAT  169 (598)
T ss_pred             cCCcEEEEEEChHhCCHH----HHHHHHHHHHhC-CCCeEEEEEe
Confidence            456789999999988754    344555555554 4566777754

>KOG0388|consensus

Probab=96.92  E-value=0.0029  Score=57.37  Aligned_cols=143  Identities=19%  Similarity=0.208  Sum_probs=86.5

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhh---
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAE---  123 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---  123 (226)
                      .+|-|-++...-|-|||.-.+..+.+..+.....|| .+|++|...| +.+.+++.++++.  .++.-.-|+..+..   
T Consensus       584 dqGiNGILADeMGLGKTVQsisvlAhLaE~~nIwGP-FLVVtpaStL-~NWaqEisrFlP~--~k~lpywGs~~eRkiLr  659 (1185)
T KOG0388|consen  584 DQGINGILADEMGLGKTVQSISVLAHLAETHNIWGP-FLVVTPASTL-HNWAQEISRFLPS--FKVLPYWGSPSERKILR  659 (1185)
T ss_pred             HccccceehhhhccchhHHHHHHHHHHHHhccCCCc-eEEeehHHHH-hHHHHHHHHhCcc--ceeecCcCChhhhHHHH
Confidence            456677899999999998775555555554444454 5677787655 6677777777663  33333333332221   


Q ss_pred             hhC-----CCcCCCCCEEEECchHHHH---hHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCce
Q psy12977        124 KFG-----PRSAQKFDVLITTPNKLVY---LLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLK  195 (226)
Q Consensus       124 ~~~-----~~~~~~~~IiV~Tp~~l~~---~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q  195 (226)
                      ++.     .....+.||+|++.+.+..   ++++       -++.+.|+|||+.+-+.    ....++.++..   ...-
T Consensus       660 Kfw~rKnmY~rna~fhVviTSYQlvVtDeky~qk-------vKWQYMILDEAQAIKSS----sS~RWKtLLsF---~cRN  725 (1185)
T KOG0388|consen  660 KFWNRKNMYRRNAPFHVVITSYQLVVTDEKYLQK-------VKWQYMILDEAQAIKSS----SSSRWKTLLSF---KCRN  725 (1185)
T ss_pred             HhcchhhhhccCCCceEEEEeeeeeechHHHHHh-------hhhhheehhHHHHhhhh----hhhHHHHHhhh---hccc
Confidence            111     1245678999998776643   3322       24569999999988655    34455555432   1234


Q ss_pred             EEEEeeeCchhH
Q psy12977        196 RGMFSATHTEDV  207 (226)
Q Consensus       196 ~v~~SAT~~~~~  207 (226)
                      .++++.|+=.+-
T Consensus       726 RLLLTGTPIQNs  737 (1185)
T KOG0388|consen  726 RLLLTGTPIQNS  737 (1185)
T ss_pred             eeeecCCccchH
Confidence            567788865443

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=96.92  E-value=0.014  Score=50.02  Aligned_cols=45  Identities=18%  Similarity=0.237  Sum_probs=27.6

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      ....-++|+||+|.+.+...    ..+..+.+.......++.+..-+..
T Consensus       121 ~~~~~IvvLDEid~L~~~~~----~~LY~L~r~~~~~~~~v~vi~i~n~  165 (366)
T COG1474         121 KGKTVIVILDEVDALVDKDG----EVLYSLLRAPGENKVKVSIIAVSND  165 (366)
T ss_pred             cCCeEEEEEcchhhhccccc----hHHHHHHhhccccceeEEEEEEecc
Confidence            34556999999999988742    5555555554333455555444433

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.91  E-value=0.01  Score=49.52  Aligned_cols=40  Identities=23%  Similarity=0.150  Sum_probs=26.5

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      ..+++|+||+|.+...   .....+..+++.. +.++++++.|.
T Consensus       100 ~~~vliiDe~d~l~~~---~~~~~L~~~le~~-~~~~~~Ilt~n  139 (316)
T PHA02544        100 GGKVIIIDEFDRLGLA---DAQRHLRSFMEAY-SKNCSFIITAN  139 (316)
T ss_pred             CCeEEEEECcccccCH---HHHHHHHHHHHhc-CCCceEEEEcC
Confidence            4579999999988333   2455666666665 45667776543

>PRK11054 helD DNA helicase IV; Provisional

Probab=96.87  E-value=0.002  Score=59.49  Aligned_cols=72  Identities=14%  Similarity=0.115  Sum_probs=53.7

Q ss_pred             cCCCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhh
Q psy12977         34 KHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE  106 (226)
Q Consensus        34 ~~~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~  106 (226)
                      ..+++.|..+.... ..+++|.|.+|||||.....-+...+......+.++++++.|+..|..+.+.+.....
T Consensus       195 ~~L~~~Q~~av~~~-~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~lg  266 (684)
T PRK11054        195 SPLNPSQARAVVNG-EDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERLG  266 (684)
T ss_pred             CCCCHHHHHHHhCC-CCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhcC
Confidence            35677776665433 3568999999999998876665555544444456899999999999999988877654

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=96.87  E-value=0.0055  Score=52.22  Aligned_cols=19  Identities=26%  Similarity=0.499  Sum_probs=15.8

Q ss_pred             CeEEEECCCCchHhHHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~   68 (226)
                      .+.|++||+|+|||..+-+
T Consensus        49 ~SmIl~GPPG~GKTTlA~l   67 (436)
T COG2256          49 HSMILWGPPGTGKTTLARL   67 (436)
T ss_pred             ceeEEECCCCCCHHHHHHH
Confidence            5799999999999976443

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.85  E-value=0.0092  Score=56.12  Aligned_cols=44  Identities=14%  Similarity=0.082  Sum_probs=28.3

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                      .+.+++||||+|.|...    ....+.++++.- +..+.+++. .|-+..
T Consensus       118 gk~KViIIDEAh~LT~e----AqNALLKtLEEP-P~~vrFILa-TTe~~k  161 (944)
T PRK14949        118 GRFKVYLIDEVHMLSRS----SFNALLKTLEEP-PEHVKFLLA-TTDPQK  161 (944)
T ss_pred             CCcEEEEEechHhcCHH----HHHHHHHHHhcc-CCCeEEEEE-CCCchh
Confidence            46789999999998654    455666666554 345566664 444443

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=96.85  E-value=0.0016  Score=60.75  Aligned_cols=71  Identities=18%  Similarity=0.221  Sum_probs=53.8

Q ss_pred             cCCCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         34 KHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        34 ~~~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      ..++|.|..+... ...+++|.|.+|||||.....-+...+........+++.++-|+.-|..+.+.+.++.
T Consensus         3 ~~Ln~~Q~~av~~-~~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~~   73 (726)
T TIGR01073         3 AHLNPEQREAVKT-TEGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLL   73 (726)
T ss_pred             cccCHHHHHHHhC-CCCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHHh
Confidence            4578888666543 3578999999999999987776666665333334589999999999999888887764

Designed to identify pcrA members of the uvrD/rep subfamily.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.82  E-value=0.017  Score=51.10  Aligned_cols=19  Identities=32%  Similarity=0.482  Sum_probs=15.3

Q ss_pred             CeEEEECCCCchHhHHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~   68 (226)
                      +.++++||+|+|||..+..
T Consensus        37 ~~~Lf~GPpGtGKTTlA~~   55 (472)
T PRK14962         37 HAYIFAGPRGTGKTTVARI   55 (472)
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            3479999999999986544

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.81  E-value=0.014  Score=53.27  Aligned_cols=42  Identities=14%  Similarity=0.094  Sum_probs=26.1

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      .+.+++||||+|.+...    ....+.+.++.- +..+.+++.+ |-+
T Consensus       123 g~~KV~IIDEvh~Ls~~----a~NaLLKtLEEP-P~~~~fIL~T-td~  164 (618)
T PRK14951        123 GRFKVFMIDEVHMLTNT----AFNAMLKTLEEP-PEYLKFVLAT-TDP  164 (618)
T ss_pred             CCceEEEEEChhhCCHH----HHHHHHHhcccC-CCCeEEEEEE-CCc
Confidence            46889999999998765    233444444443 3455666543 543

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=96.79  E-value=0.014  Score=49.18  Aligned_cols=44  Identities=23%  Similarity=0.237  Sum_probs=27.4

Q ss_pred             CccEEEEccccccccc-------CccchHHHHHHHHHhc----CCCCceEEEEeeeC
Q psy12977        158 NVEWLIVDESDKLFEA-------GVRGFRDQLAVIYAAC----SGPNLKRGMFSATH  203 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~-------~~~~~~~~i~~i~~~~----~~~~~q~v~~SAT~  203 (226)
                      .-+.+.|||.|.+...       +.+.....+.+++.++    +..+.++++  ||.
T Consensus       244 aPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~nvKVI~--ATN  298 (406)
T COG1222         244 APSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIM--ATN  298 (406)
T ss_pred             CCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCCCCeEEEE--ecC
Confidence            4568999999988543       2334555666666665    234556665  773

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.78  E-value=0.015  Score=46.18  Aligned_cols=53  Identities=23%  Similarity=0.277  Sum_probs=32.7

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      ..|..+++.+++|+|||......+...+.+    +..++++.. .+-.+++.+..+.+
T Consensus        18 ~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~----g~~~~~is~-e~~~~~i~~~~~~~   70 (229)
T TIGR03881        18 PRGFFVAVTGEPGTGKTIFCLHFAYKGLRD----GDPVIYVTT-EESRESIIRQAAQF   70 (229)
T ss_pred             cCCeEEEEECCCCCChHHHHHHHHHHHHhc----CCeEEEEEc-cCCHHHHHHHHHHh
Confidence            457889999999999997554434444432    346777754 33445554444443

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.78  E-value=0.004  Score=50.69  Aligned_cols=39  Identities=15%  Similarity=0.084  Sum_probs=27.4

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCP   89 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~P   89 (226)
                      ..|.-+++.|++|+|||...+--+.+.+.+    +.+++|++-
T Consensus        34 p~gs~~lI~G~pGtGKT~l~~qf~~~~a~~----Ge~vlyis~   72 (259)
T TIGR03878        34 PAYSVINITGVSDTGKSLMVEQFAVTQASR----GNPVLFVTV   72 (259)
T ss_pred             ECCcEEEEEcCCCCCHHHHHHHHHHHHHhC----CCcEEEEEe
Confidence            356778999999999997655545554432    457788763

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=96.77  E-value=0.012  Score=50.34  Aligned_cols=112  Identities=17%  Similarity=0.104  Sum_probs=69.3

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCC
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGP  127 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (226)
                      ..+.+.++|+.|.|||+.. =..++.+..  ..+.|+    .-.+-+.++.+.+.++..           ..   .    
T Consensus        61 ~~~GlYl~G~vG~GKT~Lm-d~f~~~lp~--~~k~R~----HFh~Fm~~vh~~l~~~~~-----------~~---~----  115 (362)
T PF03969_consen   61 PPKGLYLWGPVGRGKTMLM-DLFYDSLPI--KRKRRV----HFHEFMLDVHSRLHQLRG-----------QD---D----  115 (362)
T ss_pred             CCceEEEECCCCCchhHHH-HHHHHhCCc--cccccc----cccHHHHHHHHHHHHHhC-----------CC---c----
Confidence            4578999999999999742 222333321  112222    446777777777766640           00   0    


Q ss_pred             CcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        128 RSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       128 ~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                                 .-..+.+.+        .....+|.+||+| +.|-   +-.-.+.++++.+...+.-+|.+|.+.|+++
T Consensus       116 -----------~l~~va~~l--------~~~~~lLcfDEF~-V~Di---aDAmil~rLf~~l~~~gvvlVaTSN~~P~~L  172 (362)
T PF03969_consen  116 -----------PLPQVADEL--------AKESRLLCFDEFQ-VTDI---ADAMILKRLFEALFKRGVVLVATSNRPPEDL  172 (362)
T ss_pred             -----------cHHHHHHHH--------HhcCCEEEEeeee-ccch---hHHHHHHHHHHHHHHCCCEEEecCCCChHHH
Confidence                       001222222        2355699999999 4444   3455666777777778999999999999753

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

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

Probab=96.75  E-value=0.0048  Score=58.40  Aligned_cols=145  Identities=22%  Similarity=0.168  Sum_probs=85.6

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhh----hhh
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQA----AEK  124 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~----~~~  124 (226)
                      +.+-++...-|.|||...+..+.......+...+.+++++|+. +..++.+.+..+...... +....|....    ...
T Consensus       358 ~~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~s-~~~nw~~e~~k~~~~~~~-~~~~~g~~~~~~~~~~~  435 (866)
T COG0553         358 LLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPAS-LLSNWKREFEKFAPDLRL-VLVYHGEKSELDKKREA  435 (866)
T ss_pred             cCCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecHH-HHHHHHHHHhhhCccccc-eeeeeCCcccccHHHHH
Confidence            4555677999999998765554443332222245788988984 778888888777765553 4444443321    122


Q ss_pred             hCCCcCC----CCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        125 FGPRSAQ----KFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       125 ~~~~~~~----~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      .......    ..+++++|-+.+.+.. .+...+.-...+.+|+||+|.+-.... .-...+..+..     . -.+.+|
T Consensus       436 ~~~~~~~~~~~~~~v~itty~~l~~~~-~~~~~l~~~~~~~~v~DEa~~ikn~~s-~~~~~l~~~~~-----~-~~~~Lt  507 (866)
T COG0553         436 LRDLLKLHLVIIFDVVITTYELLRRFL-VDHGGLKKIEWDRVVLDEAHRIKNDQS-SEGKALQFLKA-----L-NRLDLT  507 (866)
T ss_pred             HHHHhhhcccceeeEEechHHHHHHhh-hhHHHHhhceeeeeehhhHHHHhhhhh-HHHHHHHHHhh-----c-ceeeCC
Confidence            2111221    2789999998887742 122445566788999999999755421 23333332221     1 226778


Q ss_pred             eeC
Q psy12977        201 ATH  203 (226)
Q Consensus       201 AT~  203 (226)
                      .|+
T Consensus       508 gTP  510 (866)
T COG0553         508 GTP  510 (866)
T ss_pred             CCh
Confidence            886

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.75  E-value=0.024  Score=50.81  Aligned_cols=40  Identities=18%  Similarity=0.119  Sum_probs=28.5

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ..+.+++|+||+|.+...    ....+.+.++.- ++.+.+++.+
T Consensus       115 ~~~~KVvIIDEad~Lt~~----A~NALLK~LEEp-p~~t~FIL~t  154 (535)
T PRK08451        115 MARFKIFIIDEVHMLTKE----AFNALLKTLEEP-PSYVKFILAT  154 (535)
T ss_pred             cCCeEEEEEECcccCCHH----HHHHHHHHHhhc-CCceEEEEEE
Confidence            357789999999988765    455666666665 5567777754

>KOG0386|consensus

Probab=96.74  E-value=0.0023  Score=59.83  Aligned_cols=152  Identities=18%  Similarity=0.164  Sum_probs=84.1

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEE--ecchhhhhhh
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVI--GKIQQAAEKF  125 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~  125 (226)
                      ++-|=++.-.+|-|||.....-+...++.....|| .+|++|+-.|.+ +...+..+    ...+..+  .|.......+
T Consensus       412 NnLNGILADEMGLGKTIQtIsLitYLmE~K~~~GP-~LvivPlstL~N-W~~Ef~kW----aPSv~~i~YkGtp~~R~~l  485 (1157)
T KOG0386|consen  412 NNLNGILADEMGLGKTIQTISLITYLMEHKQMQGP-FLIIVPLSTLVN-WSSEFPKW----APSVQKIQYKGTPQQRSGL  485 (1157)
T ss_pred             CCcccccchhcccchHHHHHHHHHHHHHHcccCCC-eEEeccccccCC-chhhcccc----ccceeeeeeeCCHHHHhhH
Confidence            34567899999999998754433333332333344 466689877754 33333333    2233322  2222211111


Q ss_pred             -CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        126 -GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       126 -~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                       ......+.+|+++|-+.+..    ++..+.--++.++||||-|+|-..     ...+...+.-. -.....+++|.|+-
T Consensus       486 ~~qir~gKFnVLlTtyEyiik----dk~lLsKI~W~yMIIDEGHRmKNa-----~~KLt~~L~t~-y~~q~RLLLTGTPL  555 (1157)
T KOG0386|consen  486 TKQQRHGKFNVLLTTYEYIIK----DKALLSKISWKYMIIDEGHRMKNA-----ICKLTDTLNTH-YRAQRRLLLTGTPL  555 (1157)
T ss_pred             HHHHhcccceeeeeeHHHhcC----CHHHHhccCCcceeecccccccch-----hhHHHHHhhcc-ccchhhhhhcCChh
Confidence             12334889999999887654    334455566789999999998643     23333333211 12334566788844


Q ss_pred             ----hhHHHHHHHhc
Q psy12977        205 ----EDVAKWCRRKL  215 (226)
Q Consensus       205 ----~~~~~~~~~~~  215 (226)
                          ++.+.+++..+
T Consensus       556 QN~LpELWaLLNFlL  570 (1157)
T KOG0386|consen  556 QNNLPELWALLNFLL  570 (1157)
T ss_pred             hhccHHHHHHHHHhc
Confidence                34555554433

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=96.73  E-value=0.029  Score=46.69  Aligned_cols=39  Identities=15%  Similarity=0.152  Sum_probs=26.0

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      ..+++++||+|.+...    ....+..+++.. ++.+.+++.+.
T Consensus       102 ~~~vviiDe~~~l~~~----~~~~L~~~le~~-~~~~~lIl~~~  140 (319)
T PRK00440        102 PFKIIFLDEADNLTSD----AQQALRRTMEMY-SQNTRFILSCN  140 (319)
T ss_pred             CceEEEEeCcccCCHH----HHHHHHHHHhcC-CCCCeEEEEeC
Confidence            4579999999988654    345566666654 45667776543

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.72  E-value=0.05  Score=48.59  Aligned_cols=135  Identities=19%  Similarity=0.178  Sum_probs=66.0

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEE-cccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhh
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIV-CPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAE  123 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil-~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (226)
                      ++..|+.+.+.||+|+|||.....-+.......  .+.++.++ ..+...+.  .++++.+....+..+..         
T Consensus       346 ~l~~G~vIaLVGPtGvGKTTtaakLAa~la~~~--~gkkVaLIdtDtyRigA--~EQLk~ya~iLgv~v~~---------  412 (559)
T PRK12727        346 PLERGGVIALVGPTGAGKTTTIAKLAQRFAAQH--APRDVALVTTDTQRVGG--REQLHSYGRQLGIAVHE---------  412 (559)
T ss_pred             cccCCCEEEEECCCCCCHHHHHHHHHHHHHHhc--CCCceEEEecccccccH--HHHHHHhhcccCceeEe---------
Confidence            345678899999999999987544333322221  12234333 33322211  13333443333332211         


Q ss_pred             hhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        124 KFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       124 ~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                                   +-++..+...+..      +.+.++|+||.+=......  .....+..+....  ...-+++++++.
T Consensus       413 -------------a~d~~~L~~aL~~------l~~~DLVLIDTaG~s~~D~--~l~eeL~~L~aa~--~~a~lLVLpAts  469 (559)
T PRK12727        413 -------------ADSAESLLDLLER------LRDYKLVLIDTAGMGQRDR--ALAAQLNWLRAAR--QVTSLLVLPANA  469 (559)
T ss_pred             -------------cCcHHHHHHHHHH------hccCCEEEecCCCcchhhH--HHHHHHHHHHHhh--cCCcEEEEECCC
Confidence                         1133445555543      3457899999886542221  2233333332222  223455666665


Q ss_pred             c-hhHHHHHHHhc
Q psy12977        204 T-EDVAKWCRRKL  215 (226)
Q Consensus       204 ~-~~~~~~~~~~~  215 (226)
                      . .++.+.+++|-
T Consensus       470 s~~Dl~eii~~f~  482 (559)
T PRK12727        470 HFSDLDEVVRRFA  482 (559)
T ss_pred             ChhHHHHHHHHHH
Confidence            4 45666666554

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.72  E-value=0.022  Score=51.23  Aligned_cols=40  Identities=13%  Similarity=0.046  Sum_probs=26.4

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ..+.+++||||+|.+...    ....+.+.++.- +..+.+++.|
T Consensus       117 ~~~~kVvIIDEad~ls~~----a~naLLK~LEep-p~~~~fIL~t  156 (527)
T PRK14969        117 RGRFKVYIIDEVHMLSKS----AFNAMLKTLEEP-PEHVKFILAT  156 (527)
T ss_pred             cCCceEEEEcCcccCCHH----HHHHHHHHHhCC-CCCEEEEEEe
Confidence            346789999999988765    334455555553 4566777654

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=96.70  E-value=0.0032  Score=58.16  Aligned_cols=70  Identities=20%  Similarity=0.149  Sum_probs=52.9

Q ss_pred             CCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhh
Q psy12977         36 FEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE  106 (226)
Q Consensus        36 ~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~  106 (226)
                      +++.|..+... .+.+++|.|++|||||.....-+...+........++++++.|+.-|.++.+.+..+..
T Consensus         3 Ln~~Q~~av~~-~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~l~   72 (672)
T PRK10919          3 LNPGQQQAVEF-VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTLG   72 (672)
T ss_pred             CCHHHHHHHhC-CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHhC
Confidence            57777666533 34678899999999999877766666653333345899999999999999988877653

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.70  E-value=0.054  Score=47.13  Aligned_cols=136  Identities=14%  Similarity=0.105  Sum_probs=70.2

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG  126 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (226)
                      ..++.+.+.||||+|||.....-+........ ...-.++...+...+  ..+++..+++.++..+..            
T Consensus       189 ~~g~vi~lvGpnG~GKTTtlakLA~~~~~~~~-~~~v~~i~~d~~rig--alEQL~~~a~ilGvp~~~------------  253 (420)
T PRK14721        189 EQGGVYALIGPTGVGKTTTTAKLAARAVIRHG-ADKVALLTTDSYRIG--GHEQLRIYGKLLGVSVRS------------  253 (420)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHHhcC-CCeEEEEecCCcchh--HHHHHHHHHHHcCCceec------------
Confidence            45677899999999999875543332222111 112355556654432  234455555544544322            


Q ss_pred             CCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC-ch
Q psy12977        127 PRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH-TE  205 (226)
Q Consensus       127 ~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~-~~  205 (226)
                                +.++..+...+..      +.+.+.+.+|.+=+.-..  ......+..+.... .+.-.++.+|||. .+
T Consensus       254 ----------v~~~~dl~~al~~------l~~~d~VLIDTaGrsqrd--~~~~~~l~~l~~~~-~~~~~~LVl~at~~~~  314 (420)
T PRK14721        254 ----------IKDIADLQLMLHE------LRGKHMVLIDTVGMSQRD--QMLAEQIAMLSQCG-TQVKHLLLLNATSSGD  314 (420)
T ss_pred             ----------CCCHHHHHHHHHH------hcCCCEEEecCCCCCcch--HHHHHHHHHHhccC-CCceEEEEEcCCCCHH
Confidence                      2233333333332      556688999986322111  02334444432211 2333556788885 46


Q ss_pred             hHHHHHHHhcC
Q psy12977        206 DVAKWCRRKLK  216 (226)
Q Consensus       206 ~~~~~~~~~~~  216 (226)
                      ++.+.+..|-.
T Consensus       315 ~~~~~~~~f~~  325 (420)
T PRK14721        315 TLDEVISAYQG  325 (420)
T ss_pred             HHHHHHHHhcC
Confidence            67777777653

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.69  E-value=0.017  Score=52.31  Aligned_cols=45  Identities=22%  Similarity=0.096  Sum_probs=28.6

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                      ..+.+++||||+|.+...    ....+..+++.- ++.+-+++.+ |-++.
T Consensus       116 ~~~~KVvIIDEah~Lt~~----A~NALLK~LEEp-p~~~~fIL~t-te~~k  160 (584)
T PRK14952        116 QSRYRIFIVDEAHMVTTA----GFNALLKIVEEP-PEHLIFIFAT-TEPEK  160 (584)
T ss_pred             cCCceEEEEECCCcCCHH----HHHHHHHHHhcC-CCCeEEEEEe-CChHh
Confidence            356789999999988755    444555556554 4455666654 54433

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=96.69  E-value=0.013  Score=53.63  Aligned_cols=42  Identities=14%  Similarity=0.054  Sum_probs=26.4

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      .+.+++||||+|.|...    ....+.++++.- ++.+.+++. .|-+
T Consensus       118 g~~KV~IIDEah~Ls~~----a~NALLKtLEEP-p~~v~FIL~-Tt~~  159 (647)
T PRK07994        118 GRFKVYLIDEVHMLSRH----SFNALLKTLEEP-PEHVKFLLA-TTDP  159 (647)
T ss_pred             CCCEEEEEechHhCCHH----HHHHHHHHHHcC-CCCeEEEEe-cCCc
Confidence            46789999999988765    344555555553 344555554 4433

>KOG1805|consensus

Probab=96.69  E-value=0.0033  Score=58.70  Aligned_cols=128  Identities=12%  Similarity=0.107  Sum_probs=75.9

Q ss_pred             cccCCCCcccccc--cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCC
Q psy12977         32 IFKHFEPHFTITY--LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG  109 (226)
Q Consensus        32 ~~~~~~~~Q~~~~--~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~  109 (226)
                      .+..+|..|.++.  .+......+|.|=||+|||......+-..+.    .+.+++..+-|..=+..+.-.++...    
T Consensus       666 ~~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~LIkiL~~----~gkkVLLtsyThsAVDNILiKL~~~~----  737 (1100)
T KOG1805|consen  666 ILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVA----LGKKVLLTSYTHSAVDNILIKLKGFG----  737 (1100)
T ss_pred             HHhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHHHHHHHHH----cCCeEEEEehhhHHHHHHHHHHhccC----
Confidence            4557788887774  3334455799999999999764333222222    25689999999988777766665552    


Q ss_pred             CeEEEEecch----------------hhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977        110 LRAHVIGKIQ----------------QAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus       110 ~~~~~~~~~~----------------~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      +...-.+...                .+....-....+.+.|+.||---+.+.+      +....+|+.|+|||-++...
T Consensus       738 i~~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~pl------f~~R~FD~cIiDEASQI~lP  811 (1100)
T KOG1805|consen  738 IYILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINHPL------FVNRQFDYCIIDEASQILLP  811 (1100)
T ss_pred             cceeecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCchh------hhccccCEEEEccccccccc
Confidence            2211111110                0000000123466788888854443332      22456899999999987643

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.68  E-value=0.024  Score=51.25  Aligned_cols=44  Identities=16%  Similarity=0.027  Sum_probs=25.7

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      ....+++||||+|.+...    ....+.+.++.- ++.+.+++. +|-+.
T Consensus       117 ~~~~kViIIDE~~~Lt~~----a~naLLKtLEep-p~~~ifIla-tt~~~  160 (559)
T PRK05563        117 EAKYKVYIIDEVHMLSTG----AFNALLKTLEEP-PAHVIFILA-TTEPH  160 (559)
T ss_pred             cCCeEEEEEECcccCCHH----HHHHHHHHhcCC-CCCeEEEEE-eCChh
Confidence            456789999999988654    333444455443 334444443 44443

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.67  E-value=0.025  Score=48.96  Aligned_cols=40  Identities=15%  Similarity=-0.009  Sum_probs=23.9

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ..+.+++|+||+|.+...    ....+...++.- ++.+.+++.+
T Consensus       125 ~~~~kvvIIdea~~l~~~----~~~~LLk~LEep-~~~t~~Il~t  164 (397)
T PRK14955        125 KGRYRVYIIDEVHMLSIA----AFNAFLKTLEEP-PPHAIFIFAT  164 (397)
T ss_pred             cCCeEEEEEeChhhCCHH----HHHHHHHHHhcC-CCCeEEEEEe
Confidence            456789999999998654    233444444433 3344555543

>KOG0738|consensus

Probab=96.67  E-value=0.02  Score=48.73  Aligned_cols=67  Identities=18%  Similarity=0.171  Sum_probs=41.0

Q ss_pred             CCccEEEEcccccccccCcc-chHHHHHHHHHhc-------C---CCCceEEEEeee-CchhHHHHHHHhcCCCeEEec
Q psy12977        157 ANVEWLIVDESDKLFEAGVR-GFRDQLAVIYAAC-------S---GPNLKRGMFSAT-HTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~-~~~~~i~~i~~~~-------~---~~~~q~v~~SAT-~~~~~~~~~~~~~~~p~~i~~  223 (226)
                      -.-..+.|||+|.+.+..+. +-.+.-++....+       .   ....-++.+.|| +|=++.+.+.+.+...++|-+
T Consensus       303 yAPStIFiDEIDslcs~RG~s~EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLAATN~PWdiDEAlrRRlEKRIyIPL  381 (491)
T KOG0738|consen  303 YAPSTIFIDEIDSLCSQRGGSSEHEASRRVKSELLVQMDGVQGTLENSKVVMVLAATNFPWDIDEALRRRLEKRIYIPL  381 (491)
T ss_pred             hCCceeehhhHHHHHhcCCCccchhHHHHHHHHHHHHhhccccccccceeEEEEeccCCCcchHHHHHHHHhhheeeeC
Confidence            34568999999998764322 2222222222222       1   122336677888 888888888888877777754

>PRK13342 recombination factor protein RarA; Reviewed

Probab=96.66  E-value=0.022  Score=49.61  Aligned_cols=18  Identities=28%  Similarity=0.460  Sum_probs=15.2

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      .++++.||+|+|||....
T Consensus        37 ~~ilL~GppGtGKTtLA~   54 (413)
T PRK13342         37 SSMILWGPPGTGKTTLAR   54 (413)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            478999999999997643

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.63  E-value=0.02  Score=51.41  Aligned_cols=40  Identities=13%  Similarity=0.005  Sum_probs=26.3

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ..+.+++||||+|.+...    ....+...++.- +..+.+++.+
T Consensus       117 ~g~~kViIIDEa~~ls~~----a~naLLK~LEep-p~~v~fIL~T  156 (546)
T PRK14957        117 QGRYKVYLIDEVHMLSKQ----SFNALLKTLEEP-PEYVKFILAT  156 (546)
T ss_pred             cCCcEEEEEechhhccHH----HHHHHHHHHhcC-CCCceEEEEE
Confidence            346689999999998765    444555566553 4455666644

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=96.62  E-value=0.017  Score=53.69  Aligned_cols=39  Identities=23%  Similarity=0.211  Sum_probs=24.2

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      +..++++||+|.+...    ....+...+     ...++++.++|-+.
T Consensus       109 ~~~IL~IDEIh~Ln~~----qQdaLL~~l-----E~g~IiLI~aTTen  147 (725)
T PRK13341        109 KRTILFIDEVHRFNKA----QQDALLPWV-----ENGTITLIGATTEN  147 (725)
T ss_pred             CceEEEEeChhhCCHH----HHHHHHHHh-----cCceEEEEEecCCC
Confidence            3468999999988644    233333322     34567777777543

>KOG0384|consensus

Probab=96.61  E-value=0.014  Score=55.98  Aligned_cols=146  Identities=19%  Similarity=0.191  Sum_probs=83.4

Q ss_pred             CCCCeEEEECCCCchHhHH---HHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhh
Q psy12977         47 PLGRQIFACAPTGSGKTAA---FLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAE  123 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~---~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (226)
                      ..+.+.|+.-.-|-|||.-   |+..+++...-   .| -.|+++|...+ ..+.+.+..+.   ..++.+..|......
T Consensus       387 ~~~~n~ILADEmgLgktvqti~fl~~l~~~~~~---~g-pflvvvplst~-~~W~~ef~~w~---~mn~i~y~g~~~sr~  458 (1373)
T KOG0384|consen  387 YKRNNCILADEMGLGKTVQTITFLSYLFHSLQI---HG-PFLVVVPLSTI-TAWEREFETWT---DMNVIVYHGNLESRQ  458 (1373)
T ss_pred             HhcccceehhhcCCCcchHHHHHHHHHHHhhhc---cC-CeEEEeehhhh-HHHHHHHHHHh---hhceeeeecchhHHH
Confidence            4578899999999999954   44445444422   23 35677787544 44666676666   333333333332221


Q ss_pred             ---hhCCCc-----CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCce
Q psy12977        124 ---KFGPRS-----AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLK  195 (226)
Q Consensus       124 ---~~~~~~-----~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q  195 (226)
                         ....-.     .-+.+++++|.+.++....    .+.--...++++||||++-...     ..+...+..+ . .-.
T Consensus       459 ~i~~ye~~~~~~~~~lkf~~lltTye~~LkDk~----~L~~i~w~~~~vDeahrLkN~~-----~~l~~~l~~f-~-~~~  527 (1373)
T KOG0384|consen  459 LIRQYEFYHSSNTKKLKFNALLTTYEIVLKDKA----ELSKIPWRYLLVDEAHRLKNDE-----SKLYESLNQF-K-MNH  527 (1373)
T ss_pred             HHHHHHheecCCccccccceeehhhHHHhccHh----hhccCCcceeeecHHhhcCchH-----HHHHHHHHHh-c-ccc
Confidence               111111     1258999999998766443    3334456799999999996441     2222224344 2 233


Q ss_pred             EEEEeeeCc-hhHHHHH
Q psy12977        196 RGMFSATHT-EDVAKWC  211 (226)
Q Consensus       196 ~v~~SAT~~-~~~~~~~  211 (226)
                      .++.|.|+= ..++++.
T Consensus       528 rllitgTPlQNsikEL~  544 (1373)
T KOG0384|consen  528 RLLITGTPLQNSLKELW  544 (1373)
T ss_pred             eeeecCCCccccHHHHH
Confidence            455678854 3444443

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.60  E-value=0.028  Score=51.09  Aligned_cols=44  Identities=18%  Similarity=0.126  Sum_probs=28.4

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      ..+.+++||||+|.+...    ....+.++++.- ++.+.+++.+ |-++
T Consensus       117 ~~~~KVvIIdev~~Lt~~----a~naLLk~LEep-p~~~~fIl~t-~~~~  160 (576)
T PRK14965        117 RSRYKIFIIDEVHMLSTN----AFNALLKTLEEP-PPHVKFIFAT-TEPH  160 (576)
T ss_pred             cCCceEEEEEChhhCCHH----HHHHHHHHHHcC-CCCeEEEEEe-CChh
Confidence            457789999999988754    344555666553 4455666544 5443

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=96.60  E-value=0.015  Score=46.16  Aligned_cols=17  Identities=29%  Similarity=0.485  Sum_probs=14.2

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      .+++++||+|+|||..+
T Consensus        51 ~h~lf~GPPG~GKTTLA   67 (233)
T PF05496_consen   51 DHMLFYGPPGLGKTTLA   67 (233)
T ss_dssp             -EEEEESSTTSSHHHHH
T ss_pred             ceEEEECCCccchhHHH
Confidence            46899999999999754

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.

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.60  E-value=0.026  Score=49.64  Aligned_cols=51  Identities=24%  Similarity=0.232  Sum_probs=32.3

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      |.-+++.+++|+|||...+..+.....    .+.+++|+.- .+-.+|+......+
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~----~g~~vlYvs~-Ees~~qi~~ra~rl  130 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLAA----AGGKVLYVSG-EESASQIKLRAERL  130 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHh----cCCeEEEEEc-cccHHHHHHHHHHc
Confidence            466899999999999855443333332    2457888764 44556665555444

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=96.60  E-value=0.0041  Score=49.37  Aligned_cols=137  Identities=15%  Similarity=0.185  Sum_probs=66.4

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCC-----CeEEEEecchhh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG-----LRAHVIGKIQQA  121 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~-----~~~~~~~~~~~~  121 (226)
                      ..|..+++.||+|+|||...+-.+.+.+.+.   +.+++|++- .+-.+++.+.++.+.-+..     ............
T Consensus        17 p~gs~~li~G~~GsGKT~l~~q~l~~~~~~~---ge~vlyvs~-ee~~~~l~~~~~s~g~d~~~~~~~g~l~~~d~~~~~   92 (226)
T PF06745_consen   17 PKGSVVLISGPPGSGKTTLALQFLYNGLKNF---GEKVLYVSF-EEPPEELIENMKSFGWDLEEYEDSGKLKIIDAFPER   92 (226)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHHH---T--EEEEES-SS-HHHHHHHHHTTTS-HHHHHHTTSEEEEESSGGG
T ss_pred             CCCcEEEEEeCCCCCcHHHHHHHHHHhhhhc---CCcEEEEEe-cCCHHHHHHHHHHcCCcHHHHhhcCCEEEEeccccc
Confidence            4567899999999999976555555555420   336777763 4444666665555532110     012222111110


Q ss_pred             hhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccc-cCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        122 AEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFE-AGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       122 ~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~-~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ...        .   -..++.+...+..   .+.-.+.+.+|+|-...+.. .....+...+..+...+ .....+++++
T Consensus        93 ~~~--------~---~~~~~~l~~~i~~---~i~~~~~~~vVIDsls~l~~~~~~~~~r~~l~~l~~~l-~~~~~t~llt  157 (226)
T PF06745_consen   93 IGW--------S---PNDLEELLSKIRE---AIEELKPDRVVIDSLSALLLYDDPEELRRFLRALIKFL-KSRGVTTLLT  157 (226)
T ss_dssp             ST---------T---SCCHHHHHHHHHH---HHHHHTSSEEEEETHHHHTTSSSGGGHHHHHHHHHHHH-HHTTEEEEEE
T ss_pred             ccc--------c---ccCHHHHHHHHHH---HHHhcCCCEEEEECHHHHhhcCCHHHHHHHHHHHHHHH-HHCCCEEEEE
Confidence            000        0   1123333333321   11112338999999998722 22224555566666665 2333444555


Q ss_pred             ee
Q psy12977        201 AT  202 (226)
Q Consensus       201 AT  202 (226)
                      +.
T Consensus       158 ~~  159 (226)
T PF06745_consen  158 SE  159 (226)
T ss_dssp             EE
T ss_pred             Ec
Confidence            55

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 ....

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.55  E-value=0.013  Score=48.30  Aligned_cols=21  Identities=38%  Similarity=0.499  Sum_probs=17.1

Q ss_pred             CCCeEEEECCCCchHhHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~   68 (226)
                      .++.+.+.||||+|||....-
T Consensus       193 ~~~vi~~vGptGvGKTTt~~k  213 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAK  213 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            456888999999999976543

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.55  E-value=0.048  Score=46.78  Aligned_cols=134  Identities=18%  Similarity=0.164  Sum_probs=65.5

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceE-EEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRA-VIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF  125 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~-iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (226)
                      ..++.+.+.||+|+|||....--+.....+    +.++ ++-+.+...+  ..++++.+.+..+..+.            
T Consensus       204 ~~~~ii~lvGptGvGKTTt~akLA~~l~~~----g~~V~lItaDtyR~g--AveQLk~yae~lgvpv~------------  265 (407)
T PRK12726        204 SNHRIISLIGQTGVGKTTTLVKLGWQLLKQ----NRTVGFITTDTFRSG--AVEQFQGYADKLDVELI------------  265 (407)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHHc----CCeEEEEeCCccCcc--HHHHHHHHhhcCCCCEE------------
Confidence            346778999999999997655444333332    2234 4444443221  12334445444343321            


Q ss_pred             CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc-
Q psy12977        126 GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT-  204 (226)
Q Consensus       126 ~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~-  204 (226)
                                ...+|..+...+...   ....+.+++++|=+=+....  ......+..+.... .+..-.+.+||+.. 
T Consensus       266 ----------~~~dp~dL~~al~~l---~~~~~~D~VLIDTAGr~~~d--~~~l~EL~~l~~~~-~p~~~~LVLsag~~~  329 (407)
T PRK12726        266 ----------VATSPAELEEAVQYM---TYVNCVDHILIDTVGRNYLA--EESVSEISAYTDVV-HPDLTCFTFSSGMKS  329 (407)
T ss_pred             ----------ecCCHHHHHHHHHHH---HhcCCCCEEEEECCCCCccC--HHHHHHHHHHhhcc-CCceEEEECCCcccH
Confidence                      123455554443321   01234677777777554221  13445555555444 23333445566433 


Q ss_pred             hhHHHHHHHh
Q psy12977        205 EDVAKWCRRK  214 (226)
Q Consensus       205 ~~~~~~~~~~  214 (226)
                      .++.+.+++|
T Consensus       330 ~d~~~i~~~f  339 (407)
T PRK12726        330 ADVMTILPKL  339 (407)
T ss_pred             HHHHHHHHhc
Confidence            4555555544

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.50  E-value=0.026  Score=50.37  Aligned_cols=19  Identities=26%  Similarity=0.436  Sum_probs=15.4

Q ss_pred             CeEEEECCCCchHhHHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~   68 (226)
                      +-+++.||+|+|||.....
T Consensus        37 ha~Lf~GppGtGKTTlA~~   55 (504)
T PRK14963         37 HAYLFSGPRGVGKTTTARL   55 (504)
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4469999999999987543

>PRK05973 replicative DNA helicase; Provisional

Probab=96.49  E-value=0.023  Score=45.57  Aligned_cols=72  Identities=15%  Similarity=0.126  Sum_probs=44.8

Q ss_pred             HhhccccCCCCccccc----------ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         28 VSNSIFKHFEPHFTIT----------YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        28 ~~~~~~~~~~~~Q~~~----------~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      -.++||..++-+...+          --+..|.-++|.|+||+|||...+-.+.+...+    +.+++|++ ..+-.+|+
T Consensus        33 a~~~g~~~w~~~~~~~~~~~p~~~l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~----Ge~vlyfS-lEes~~~i  107 (237)
T PRK05973         33 AAEEGFSSWSLLAAKAAATTPAEELFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKS----GRTGVFFT-LEYTEQDV  107 (237)
T ss_pred             HHHhccchHHHHHHhccCCCCHHHhcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhc----CCeEEEEE-EeCCHHHH
Confidence            3467777665554222          123445678999999999998666555555542    44677774 33345666


Q ss_pred             HHHHHHH
Q psy12977         98 YNETVRL  104 (226)
Q Consensus        98 ~~~~~~~  104 (226)
                      .+.+..+
T Consensus       108 ~~R~~s~  114 (237)
T PRK05973        108 RDRLRAL  114 (237)
T ss_pred             HHHHHHc
Confidence            6666655

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.48  E-value=0.027  Score=51.24  Aligned_cols=21  Identities=24%  Similarity=0.176  Sum_probs=16.7

Q ss_pred             CeEEEECCCCchHhHHHHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFLIPI   70 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~   70 (226)
                      +.+++.||.|+|||.....-+
T Consensus        39 ha~Lf~GPpG~GKTtiArilA   59 (624)
T PRK14959         39 PAYLFSGTRGVGKTTIARIFA   59 (624)
T ss_pred             ceEEEECCCCCCHHHHHHHHH
Confidence            567899999999998765443

>PRK04195 replication factor C large subunit; Provisional

Probab=96.48  E-value=0.02  Score=50.88  Aligned_cols=42  Identities=12%  Similarity=0.111  Sum_probs=25.5

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      .-++||+||+|.+.....++....+..+++   ..+..+++.+..
T Consensus        98 ~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~---~~~~~iIli~n~  139 (482)
T PRK04195         98 RRKLILLDEVDGIHGNEDRGGARAILELIK---KAKQPIILTAND  139 (482)
T ss_pred             CCeEEEEecCcccccccchhHHHHHHHHHH---cCCCCEEEeccC
Confidence            456999999999876432234445555544   345566665433

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=96.48  E-value=0.019  Score=45.89  Aligned_cols=53  Identities=15%  Similarity=0.239  Sum_probs=34.0

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      ..|.-+++.|++|+|||.....-+...+.+    +.+++|+.-.. -..++.+.+..+
T Consensus        23 ~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~----g~~~~y~~~e~-~~~~~~~~~~~~   75 (234)
T PRK06067         23 PFPSLILIEGDHGTGKSVLSQQFVYGALKQ----GKKVYVITTEN-TSKSYLKQMESV   75 (234)
T ss_pred             cCCcEEEEECCCCCChHHHHHHHHHHHHhC----CCEEEEEEcCC-CHHHHHHHHHHC
Confidence            346778999999999997655544554442    45777776543 334555555554

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=96.45  E-value=0.05  Score=46.36  Aligned_cols=40  Identities=13%  Similarity=0.042  Sum_probs=27.9

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ....+++||||+|.+...    ....+.++++.- +.++.++++|
T Consensus       139 ~g~~rVviIDeAd~l~~~----aanaLLk~LEEp-p~~~~fiLit  178 (351)
T PRK09112        139 DGNWRIVIIDPADDMNRN----AANAILKTLEEP-PARALFILIS  178 (351)
T ss_pred             cCCceEEEEEchhhcCHH----HHHHHHHHHhcC-CCCceEEEEE
Confidence            456789999999998765    455566666663 4556666654

>KOG0737|consensus

Probab=96.42  E-value=0.036  Score=46.77  Aligned_cols=65  Identities=18%  Similarity=0.224  Sum_probs=43.5

Q ss_pred             cEEEEcccccccccCccchHHHHHHHHHhc--------CCCCceEEEEeeeC-chhHHHHHHHhcCCCeEEecC
Q psy12977        160 EWLIVDESDKLFEAGVRGFRDQLAVIYAAC--------SGPNLKRGMFSATH-TEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       160 ~~lViDE~h~l~~~~~~~~~~~i~~i~~~~--------~~~~~q~v~~SAT~-~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      ..+.|||+|.++.....+-.+....+..++        .+.+.+++++.||. |.++.+.+-+.+....+|.+.
T Consensus       188 ~iIFIDEvds~L~~R~s~dHEa~a~mK~eFM~~WDGl~s~~~~rVlVlgATNRP~DlDeAiiRR~p~rf~V~lP  261 (386)
T KOG0737|consen  188 SIIFIDEVDSFLGQRRSTDHEATAMMKNEFMALWDGLSSKDSERVLVLGATNRPFDLDEAIIRRLPRRFHVGLP  261 (386)
T ss_pred             ceeehhhHHHHHhhcccchHHHHHHHHHHHHHHhccccCCCCceEEEEeCCCCCccHHHHHHHhCcceeeeCCC
Confidence            488999999888654222333444444433        34567899999994 567888887888777766654

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=96.41  E-value=0.037  Score=45.12  Aligned_cols=52  Identities=23%  Similarity=0.174  Sum_probs=31.1

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHH
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET  101 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~  101 (226)
                      +..|.-+++.|+||+|||......+.+....   .+.+++|+.- .+-..++...+
T Consensus        27 ~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~---~g~~vl~iS~-E~~~~~~~~r~   78 (271)
T cd01122          27 LRKGELIILTAGTGVGKTTFLREYALDLITQ---HGVRVGTISL-EEPVVRTARRL   78 (271)
T ss_pred             EcCCcEEEEEcCCCCCHHHHHHHHHHHHHHh---cCceEEEEEc-ccCHHHHHHHH
Confidence            3556788999999999997554444443332   1446777653 22334444444

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=96.41  E-value=0.051  Score=47.03  Aligned_cols=46  Identities=20%  Similarity=0.231  Sum_probs=27.7

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                      ....+++||||+|.+...    ....+.++++.- ++++.+++ ++|-+..+
T Consensus       115 ~~~~kViiIDead~m~~~----aanaLLk~LEep-~~~~~fIL-~a~~~~~l  160 (394)
T PRK07940        115 TGRWRIVVIEDADRLTER----AANALLKAVEEP-PPRTVWLL-CAPSPEDV  160 (394)
T ss_pred             cCCcEEEEEechhhcCHH----HHHHHHHHhhcC-CCCCeEEE-EECChHHC
Confidence            346789999999999765    334555555543 34444444 44434433

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=96.40  E-value=0.059  Score=49.88  Aligned_cols=126  Identities=22%  Similarity=0.272  Sum_probs=75.9

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      +-+++.|.-|-|||.+.-+.+........  +.+++|.+|+.+-++.+++-+.+-.+.+|.+.............   ..
T Consensus       232 ~~~vlTAdRGRGKSA~lGi~~~~~~~~~~--~~~iiVTAP~~~nv~~Lf~fa~~~l~~lg~~~~v~~d~~g~~~~---~~  306 (758)
T COG1444         232 RALVLTADRGRGKSAALGIALAAAARLAG--SVRIIVTAPTPANVQTLFEFAGKGLEFLGYKRKVAPDALGEIRE---VS  306 (758)
T ss_pred             ceEEEEcCCCCcHhHHHhHHHHHHHHhcC--CceEEEeCCCHHHHHHHHHHHHHhHHHhCCccccccccccceee---ec
Confidence            46889999999999987766643333221  45899999999999999888777777777653222211100000   01


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      .....|=...|....            ..-+++|+|||=.+.=       ..+.++...+     +.++||.|..
T Consensus       307 ~~~~~i~y~~P~~a~------------~~~DllvVDEAAaIpl-------plL~~l~~~~-----~rv~~sTTIh  357 (758)
T COG1444         307 GDGFRIEYVPPDDAQ------------EEADLLVVDEAAAIPL-------PLLHKLLRRF-----PRVLFSTTIH  357 (758)
T ss_pred             CCceeEEeeCcchhc------------ccCCEEEEehhhcCCh-------HHHHHHHhhc-----CceEEEeeec
Confidence            122234455554321            1167999999976532       2344444322     5667777755

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=96.39  E-value=0.061  Score=45.60  Aligned_cols=24  Identities=25%  Similarity=0.372  Sum_probs=17.2

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      +..++.||+|+|||... ..+...+
T Consensus        37 ~~~Ll~G~~G~GKt~~a-~~la~~l   60 (355)
T TIGR02397        37 HAYLFSGPRGTGKTSIA-RIFAKAL   60 (355)
T ss_pred             eEEEEECCCCCCHHHHH-HHHHHHh
Confidence            45799999999999754 3334444

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.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=96.38  E-value=0.012  Score=47.07  Aligned_cols=39  Identities=23%  Similarity=0.154  Sum_probs=26.8

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVC   88 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~   88 (226)
                      ..|.-+++.|+||+|||...+--+.+...+.   +..++|++
T Consensus        11 ~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~---g~~vly~s   49 (242)
T cd00984          11 QPGDLIIIAARPSMGKTAFALNIAENIAKKQ---GKPVLFFS   49 (242)
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHhC---CCceEEEe
Confidence            3567789999999999976554455554421   44677776

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.

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.38  E-value=0.053  Score=49.44  Aligned_cols=39  Identities=23%  Similarity=0.102  Sum_probs=23.5

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEE
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMF  199 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~  199 (226)
                      ..+.+++||||+|.+...    ....+...++.- ++.+.+++.
T Consensus       118 ~~~~kVvIIDEa~~L~~~----a~naLLk~LEep-p~~tv~Il~  156 (585)
T PRK14950        118 LARYKVYIIDEVHMLSTA----AFNALLKTLEEP-PPHAIFILA  156 (585)
T ss_pred             cCCeEEEEEeChHhCCHH----HHHHHHHHHhcC-CCCeEEEEE
Confidence            456789999999988654    333444444443 334444443

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=96.37  E-value=0.032  Score=48.75  Aligned_cols=23  Identities=26%  Similarity=0.316  Sum_probs=19.1

Q ss_pred             cCCCCCeEEEECCCCchHhHHHH
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~   67 (226)
                      .+..++++++.||+|+|||..+.
T Consensus       190 ~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        190 RLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             HHhcCCCEEEECCCCCCHHHHHH
Confidence            44568999999999999997654

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=96.33  E-value=0.039  Score=50.04  Aligned_cols=45  Identities=13%  Similarity=0.057  Sum_probs=26.4

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                      ...+++|+||+|.+...    ....+...++.- ++.+-+++++ +-+..+
T Consensus       118 ~~~KVIIIDEad~Lt~~----A~NaLLKtLEEP-p~~tvfIL~T-t~~~KL  162 (605)
T PRK05896        118 FKYKVYIIDEAHMLSTS----AWNALLKTLEEP-PKHVVFIFAT-TEFQKI  162 (605)
T ss_pred             CCcEEEEEechHhCCHH----HHHHHHHHHHhC-CCcEEEEEEC-CChHhh
Confidence            35679999999988654    344555555543 3344455543 444333

>KOG4150|consensus

Probab=96.33  E-value=0.0014  Score=57.91  Aligned_cols=179  Identities=7%  Similarity=-0.109  Sum_probs=108.9

Q ss_pred             hhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhh-
Q psy12977         29 SNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE-  106 (226)
Q Consensus        29 ~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~-  106 (226)
                      +.+--+.+..+|..+. .+.+|++.++...+.+||+++|............  ....++..|+.+++....+.+.-..+ 
T Consensus       280 ~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~--~s~~~~~~~~~~~~~~~~~~~~V~~~~  357 (1034)
T KOG4150|consen  280 NKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCH--ATNSLLPSEMVEHLRNGSKGQVVHVEV  357 (1034)
T ss_pred             hcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCc--ccceecchhHHHHhhccCCceEEEEEe
Confidence            3444445556665554 5677899999999999999999887766653322  23578999999998865442211111 


Q ss_pred             --cCC-CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHh--cCCCCCCCCCccEEEEcccccccccCccchHHH
Q psy12977        107 --GLG-LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQ--MDPPALNLANVEWLIVDESDKLFEAGVRGFRDQ  181 (226)
Q Consensus       107 --~~~-~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~--~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~  181 (226)
                        ..+ .-+.+..+..+...  ......+..++.+.|........  +......+-...+.+.||+|......+......
T Consensus       358 I~~~K~A~V~~~D~~sE~~~--~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~  435 (1034)
T KOG4150|consen  358 IKARKSAYVEMSDKLSETTK--SALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALAQDQ  435 (1034)
T ss_pred             hhhhhcceeecccCCCchhH--HHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecchhhHHHHH
Confidence              011 11223333332222  23345778899999998876542  222334455567899999997765432233344


Q ss_pred             HHHHHHhc----CCCCceEEEEeeeCchhHHHHH
Q psy12977        182 LAVIYAAC----SGPNLKRGMFSATHTEDVAKWC  211 (226)
Q Consensus       182 i~~i~~~~----~~~~~q~v~~SAT~~~~~~~~~  211 (226)
                      +.++.+..    .+.+.|++-.|||+.+.+...-
T Consensus       436 ~R~L~~L~~~F~~~~~~~~~~~~~~~K~~~~~~~  469 (1034)
T KOG4150|consen  436 LRALSDLIKGFEASINMGVYDGDTPYKDRTRLRS  469 (1034)
T ss_pred             HHHHHHHHHHHHhhcCcceEeCCCCcCCHHHHHH
Confidence            44444333    3567899999999876654443

>PHA02533 17 large terminase protein; Provisional

Probab=96.33  E-value=0.034  Score=49.95  Aligned_cols=122  Identities=13%  Similarity=-0.018  Sum_probs=69.8

Q ss_pred             CCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEE-
Q psy12977         36 FEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAH-  113 (226)
Q Consensus        36 ~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~-  113 (226)
                      +.|-|.... .+..++-.++..+-..|||......++......  .+..+.+++|+.+-|..+++.++.+.+..+.... 
T Consensus        60 L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~--~~~~v~i~A~~~~QA~~vF~~ik~~ie~~P~l~~~  137 (534)
T PHA02533         60 MRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFN--KDKNVGILAHKASMAAEVLDRTKQAIELLPDFLQP  137 (534)
T ss_pred             CcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhC--CCCEEEEEeCCHHHHHHHHHHHHHHHHhCHHHhhc
Confidence            344554443 222355567889999999988664443332212  2458999999999999999988877654332110 


Q ss_pred             EEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccc
Q psy12977        114 VIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFE  172 (226)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~  172 (226)
                      .....    ....-.+.+++.|.+.|.+.         ....=.+.+++++||+|.+.+
T Consensus       138 ~i~~~----~~~~I~l~NGS~I~~lss~~---------~t~rG~~~~~liiDE~a~~~~  183 (534)
T PHA02533        138 GIVEW----NKGSIELENGSKIGAYASSP---------DAVRGNSFAMIYIDECAFIPN  183 (534)
T ss_pred             ceeec----CccEEEeCCCCEEEEEeCCC---------CccCCCCCceEEEeccccCCC
Confidence            00000    01111124566666655431         112223567899999997643

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=96.32  E-value=0.074  Score=45.55  Aligned_cols=42  Identities=14%  Similarity=0.048  Sum_probs=27.2

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      ....+.+||||+|.+...    ....+.+.++.- ++.+.++++|..
T Consensus       139 ~~~~kVviIDead~m~~~----aanaLLK~LEep-p~~~~~IL~t~~  180 (365)
T PRK07471        139 EGGWRVVIVDTADEMNAN----AANALLKVLEEP-PARSLFLLVSHA  180 (365)
T ss_pred             cCCCEEEEEechHhcCHH----HHHHHHHHHhcC-CCCeEEEEEECC
Confidence            456789999999988654    555566666553 345555554443

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.32  E-value=0.038  Score=43.20  Aligned_cols=40  Identities=28%  Similarity=0.376  Sum_probs=27.6

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEccc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPT   90 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt   90 (226)
                      ..|.-+.+.||+|+|||...+..+.+....    +.+++|+.-.
T Consensus        10 ~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~----g~~v~yi~~e   49 (209)
T TIGR02237        10 ERGTITQIYGPPGSGKTNICMILAVNAARQ----GKKVVYIDTE   49 (209)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhC----CCeEEEEECC
Confidence            345678899999999998665555444432    4477777654

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.32  E-value=0.049  Score=49.90  Aligned_cols=20  Identities=30%  Similarity=0.419  Sum_probs=16.3

Q ss_pred             CeEEEECCCCchHhHHHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFLIP   69 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~   69 (226)
                      +.+++.||.|+|||......
T Consensus        39 ~a~Lf~Gp~G~GKttlA~~l   58 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSARIL   58 (620)
T ss_pred             ceEEEECCCCCChHHHHHHH
Confidence            56799999999999865443

>KOG0058|consensus

Probab=96.23  E-value=0.022  Score=51.99  Aligned_cols=129  Identities=16%  Similarity=0.138  Sum_probs=69.6

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhh
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEK  124 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (226)
                      -+..|+.+-+.||+|+|||.+  ..++.+++++...    =|+..-..+-+--...+.+.....+..-..+.++-.+.. 
T Consensus       490 ti~pGe~vALVGPSGsGKSTi--asLL~rfY~PtsG----~IllDG~~i~~~~~~~lr~~Ig~V~QEPvLFs~sI~eNI-  562 (716)
T KOG0058|consen  490 TIRPGEVVALVGPSGSGKSTI--ASLLLRFYDPTSG----RILLDGVPISDINHKYLRRKIGLVGQEPVLFSGSIRENI-  562 (716)
T ss_pred             eeCCCCEEEEECCCCCCHHHH--HHHHHHhcCCCCC----eEEECCeehhhcCHHHHHHHeeeeeccceeecccHHHHH-
Confidence            345578899999999999976  5667777654333    344455444443334444433333333233332211111 


Q ss_pred             hCCCcCCCCCEEEECchHHHH---------hHhcCCCCC------------------------CCCCccEEEEccccccc
Q psy12977        125 FGPRSAQKFDVLITTPNKLVY---------LLQMDPPAL------------------------NLANVEWLIVDESDKLF  171 (226)
Q Consensus       125 ~~~~~~~~~~IiV~Tp~~l~~---------~~~~~~~~~------------------------~~~~~~~lViDE~h~l~  171 (226)
                           ..+.+  -+|.+.+.+         ++...+...                        -+.+-+.+|+|||-..+
T Consensus       563 -----~YG~~--~~t~e~i~~AAk~ANah~FI~~~p~gY~T~VGEkG~qLSGGQKQRIAIARALlr~P~VLILDEATSAL  635 (716)
T KOG0058|consen  563 -----AYGLD--NATDEEIEAAAKMANAHEFITNFPDGYNTVVGEKGSQLSGGQKQRIAIARALLRNPRVLILDEATSAL  635 (716)
T ss_pred             -----hcCCC--CCCHHHHHHHHHHhChHHHHHhCccccccccCCccccccchHHHHHHHHHHHhcCCCEEEEechhhhc
Confidence                 11111  222222221         111111111                        16677899999999999


Q ss_pred             ccCccchHHHHHHHHHhcC
Q psy12977        172 EAGVRGFRDQLAVIYAACS  190 (226)
Q Consensus       172 ~~~~~~~~~~i~~i~~~~~  190 (226)
                      |.   .....+++.+..+.
T Consensus       636 Da---eSE~lVq~aL~~~~  651 (716)
T KOG0058|consen  636 DA---ESEYLVQEALDRLM  651 (716)
T ss_pred             ch---hhHHHHHHHHHHhh
Confidence            98   67777887777663

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=96.20  E-value=0.051  Score=48.94  Aligned_cols=134  Identities=18%  Similarity=0.164  Sum_probs=81.7

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc-CCCeEEEEecchhhhhhhC
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG-LGLRAHVIGKIQQAAEKFG  126 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  126 (226)
                      ..+-.+.--|--.|||| ++.|++..+.. .-.+.++.|++.-+..++-+++++...... ++.+.....          
T Consensus       201 KQkaTVFLVPRRHGKTW-f~VpiIsllL~-s~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~~~~vi~~----------  268 (668)
T PHA03372        201 KQKATVFLVPRRHGKTW-FIIPIISFLLK-NIIGISIGYVAHQKHVSQFVLKEVEFRCRRMFPRKHTIEN----------  268 (668)
T ss_pred             hccceEEEecccCCcee-hHHHHHHHHHH-hhcCceEEEEeeHHHHHHHHHHHHHHHHhhhcCccceeee----------
Confidence            34556677788999998 56777666653 345779999999999998888776544332 122211111          


Q ss_pred             CCcCCCCCEEEECchHHHH---hHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        127 PRSAQKFDVLITTPNKLVY---LLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       127 ~~~~~~~~IiV~Tp~~l~~---~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                          ++--|.+.-|+.=..   ....+...+.-.+.+++++||||-+-..       .+..++-.+.-.++++++.|.|.
T Consensus       269 ----k~~tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI~~~-------a~~tilgfm~q~~~KiIfISS~N  337 (668)
T PHA03372        269 ----KDNVISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFIKKD-------AFNTILGFLAQNTTKIIFISSTN  337 (668)
T ss_pred             ----cCcEEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhccCHH-------HHHHhhhhhcccCceEEEEeCCC
Confidence                111233333321100   1112224566778899999999976443       44455555556789999999985


Q ss_pred             c
Q psy12977        204 T  204 (226)
Q Consensus       204 ~  204 (226)
                      .
T Consensus       338 s  338 (668)
T PHA03372        338 T  338 (668)
T ss_pred             C
Confidence            4

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.19  E-value=0.052  Score=47.84  Aligned_cols=40  Identities=15%  Similarity=0.055  Sum_probs=25.1

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ..+.+++|+||+|.+...    ....+.+.++.- ++.+.+++.+
T Consensus       119 ~~~~kvvIIdead~lt~~----~~n~LLk~lEep-~~~~~~Il~t  158 (451)
T PRK06305        119 KSRYKIYIIDEVHMLTKE----AFNSLLKTLEEP-PQHVKFFLAT  158 (451)
T ss_pred             cCCCEEEEEecHHhhCHH----HHHHHHHHhhcC-CCCceEEEEe
Confidence            356789999999988654    334455555543 3455555544

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.18  E-value=0.08  Score=48.46  Aligned_cols=40  Identities=15%  Similarity=0.012  Sum_probs=24.2

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ..+-+++||||+|.+...    ....+...++.- ++.+-+++.+
T Consensus       125 ~~~~KVvIIdEad~Lt~~----a~naLLK~LEeP-p~~tv~IL~t  164 (620)
T PRK14954        125 KGRYRVYIIDEVHMLSTA----AFNAFLKTLEEP-PPHAIFIFAT  164 (620)
T ss_pred             cCCCEEEEEeChhhcCHH----HHHHHHHHHhCC-CCCeEEEEEe
Confidence            456789999999998654    234444444443 2344455544

>KOG0742|consensus

Probab=96.18  E-value=0.011  Score=50.63  Aligned_cols=17  Identities=41%  Similarity=0.626  Sum_probs=15.3

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +|++..+|+|+|||...
T Consensus       385 RNilfyGPPGTGKTm~A  401 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMFA  401 (630)
T ss_pred             hheeeeCCCCCCchHHH
Confidence            78999999999999853

>KOG0741|consensus

Probab=96.17  E-value=0.06  Score=47.76  Aligned_cols=50  Identities=20%  Similarity=0.254  Sum_probs=30.8

Q ss_pred             CccEEEEcccccccccC---cc---chHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        158 NVEWLIVDESDKLFEAG---VR---GFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~---~~---~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                      .+.++|+|+..+++|+-   .|   ...+.+..+++..|+...+++.+.-|=..++
T Consensus       598 ~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~v  653 (744)
T KOG0741|consen  598 PLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREV  653 (744)
T ss_pred             cceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHH
Confidence            56799999999998863   11   2334555556666555566666655544444

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=96.16  E-value=0.047  Score=46.05  Aligned_cols=40  Identities=8%  Similarity=0.063  Sum_probs=27.2

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ....+.+||||+|.|...    ....+.++++.- ++++.+++.|
T Consensus       104 ~~~~kv~iI~~a~~m~~~----aaNaLLK~LEEP-p~~~~fiL~t  143 (328)
T PRK05707        104 LGGRKVVLIEPAEAMNRN----AANALLKSLEEP-SGDTVLLLIS  143 (328)
T ss_pred             cCCCeEEEECChhhCCHH----HHHHHHHHHhCC-CCCeEEEEEE
Confidence            456789999999999776    555555666663 4455555544

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=96.12  E-value=0.046  Score=45.36  Aligned_cols=17  Identities=29%  Similarity=0.512  Sum_probs=14.6

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      .++++.||+|+|||...
T Consensus        31 ~~~ll~Gp~G~GKT~la   47 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLA   47 (305)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            56899999999999754

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.11  E-value=0.33  Score=39.86  Aligned_cols=23  Identities=22%  Similarity=0.161  Sum_probs=17.0

Q ss_pred             CCeEEEECCCCchHhHHHHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPII   71 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~   71 (226)
                      .+-+.+.+|+|+|||....--+.
T Consensus        72 ~~vi~l~G~~G~GKTTt~akLA~   94 (272)
T TIGR00064        72 PNVILFVGVNGVGKTTTIAKLAN   94 (272)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHH
Confidence            35677889999999986554443

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.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.10  E-value=0.093  Score=48.07  Aligned_cols=40  Identities=13%  Similarity=0.014  Sum_probs=26.3

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ....+++||||+|.+...    ....+..+++.- +..+-+++.+
T Consensus       119 ~~~~KVvIIdea~~Ls~~----a~naLLK~LEep-p~~tifIL~t  158 (614)
T PRK14971        119 IGKYKIYIIDEVHMLSQA----AFNAFLKTLEEP-PSYAIFILAT  158 (614)
T ss_pred             cCCcEEEEEECcccCCHH----HHHHHHHHHhCC-CCCeEEEEEe
Confidence            457889999999998664    445566666654 3444455533

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.10  E-value=0.25  Score=43.80  Aligned_cols=62  Identities=16%  Similarity=0.127  Sum_probs=33.2

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeE
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRA  112 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~  112 (226)
                      .++-+.+.||||+|||.....-+....... ....-+++-+.+..++  ..+.++.+.+..+..+
T Consensus       255 ~g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~-G~~kV~LI~~Dt~Rig--A~EQLr~~AeilGVpv  316 (484)
T PRK06995        255 RGGVFALMGPTGVGKTTTTAKLAARCVMRH-GASKVALLTTDSYRIG--GHEQLRIYGKILGVPV  316 (484)
T ss_pred             CCcEEEEECCCCccHHHHHHHHHHHHHHhc-CCCeEEEEeCCccchh--HHHHHHHHHHHhCCCe
Confidence            456788999999999987554333322211 1111234444442222  2455566665555544

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.09  E-value=0.2  Score=43.79  Aligned_cols=54  Identities=13%  Similarity=0.143  Sum_probs=29.4

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHh
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRK  214 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~  214 (226)
                      ..+++++|=+-+.-..  ......+..+.+.. .+..-++.++|+...+..+.++.|
T Consensus       182 ~~DvViIDTaGr~~~d--~~lm~El~~i~~~~-~p~e~lLVlda~~Gq~a~~~a~~F  235 (429)
T TIGR01425       182 NFDIIIVDTSGRHKQE--DSLFEEMLQVAEAI-QPDNIIFVMDGSIGQAAEAQAKAF  235 (429)
T ss_pred             CCCEEEEECCCCCcch--HHHHHHHHHHhhhc-CCcEEEEEeccccChhHHHHHHHH
Confidence            4567777777544322  13555555555444 344455666777665555555444

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.

>PHA00729 NTP-binding motif containing protein

Probab=96.08  E-value=0.063  Score=42.68  Aligned_cols=75  Identities=17%  Similarity=0.133  Sum_probs=38.3

Q ss_pred             EEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHH-----HHHHHHHhcCCCCceEEEEeeeCchhHHH
Q psy12977        135 VLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRD-----QLAVIYAACSGPNLKRGMFSATHTEDVAK  209 (226)
Q Consensus       135 IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~-----~i~~i~~~~~~~~~q~v~~SAT~~~~~~~  209 (226)
                      .++.+.+.+.+.+..  ..-...+.+++|+||+-.....   ..+.     ....+...+ ...++++.+...-|+++..
T Consensus        61 ~~fid~~~Ll~~L~~--a~~~~~~~dlLIIDd~G~~~~~---~~wh~~~~~~yf~L~~aL-rSR~~l~il~~ls~edL~~  134 (226)
T PHA00729         61 SYFFELPDALEKIQD--AIDNDYRIPLIIFDDAGIWLSK---YVWYEDYMKTFYKIYALI-RTRVSAVIFTTPSPEDLAF  134 (226)
T ss_pred             EEEEEHHHHHHHHHH--HHhcCCCCCEEEEeCCchhhcc---cchhhhccchHHHHHHHH-HhhCcEEEEecCCHHHHHH
Confidence            344444445544432  1111235678999995433332   1111     112222222 2456777777777788877


Q ss_pred             HHHHhc
Q psy12977        210 WCRRKL  215 (226)
Q Consensus       210 ~~~~~~  215 (226)
                      .++..-
T Consensus       135 ~Lr~Rg  140 (226)
T PHA00729        135 YLREKG  140 (226)
T ss_pred             HHHhCC
Confidence            776643

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=96.05  E-value=0.014  Score=52.28  Aligned_cols=62  Identities=19%  Similarity=0.163  Sum_probs=46.7

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHHHHHhcC--CCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPIIHSLRG--PKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~~~~~~~--~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      ...++-++|+|..|||||.+++.-+...+..  .......++++.|++-..+-+...+-+++..
T Consensus       223 ~ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~vFleYis~VLPeLGe~  286 (747)
T COG3973         223 FEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVFLEYISRVLPELGEE  286 (747)
T ss_pred             ccCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcHHHHHHHHHhchhhccC
Confidence            3456779999999999999887655444422  2222344999999999999999998888654

>KOG2028|consensus

Probab=96.04  E-value=0.026  Score=47.83  Aligned_cols=50  Identities=18%  Similarity=0.218  Sum_probs=33.0

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      .+++++|+|+|||..+-+-+..    .+..+-+.|=+..|.+-+..+...+++.
T Consensus       164 SmIlWGppG~GKTtlArlia~t----sk~~SyrfvelSAt~a~t~dvR~ife~a  213 (554)
T KOG2028|consen  164 SMILWGPPGTGKTTLARLIAST----SKKHSYRFVELSATNAKTNDVRDIFEQA  213 (554)
T ss_pred             ceEEecCCCCchHHHHHHHHhh----cCCCceEEEEEeccccchHHHHHHHHHH
Confidence            5899999999999754332211    2223457777888877777766655444

>TIGR00959 ffh signal recognition particle protein

Probab=96.04  E-value=0.24  Score=43.38  Aligned_cols=22  Identities=27%  Similarity=0.169  Sum_probs=16.7

Q ss_pred             eEEEECCCCchHhHHHHHHHHH
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIH   72 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~   72 (226)
                      .+++.|++|+|||....--+..
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~  122 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYY  122 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHH
Confidence            5789999999999875544433

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.

>PRK10263 DNA translocase FtsK; Provisional

Probab=95.99  E-value=0.039  Score=53.77  Aligned_cols=65  Identities=11%  Similarity=0.144  Sum_probs=40.5

Q ss_pred             cEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch-hHHHHHHHhcCCCeEEecC
Q psy12977        160 EWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE-DVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       160 ~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~-~~~~~~~~~~~~p~~i~~~  224 (226)
                      -+|||||+..++..........+.++.+.-..-...+++.|..+.. .+...++..+...+...+.
T Consensus      1142 IVVIIDE~AdLm~~~~kevE~lI~rLAqkGRAaGIHLILATQRPsvDVItg~IKAN~ptRIAfrVs 1207 (1355)
T PRK10263       1142 IVVLVDEFADLMMTVGKKVEELIARLAQKARAAGIHLVLATQRPSVDVITGLIKANIPTRIAFTVS 1207 (1355)
T ss_pred             EEEEEcChHHHHhhhhHHHHHHHHHHHHHhhhcCeEEEEEecCcccccchHHHHhhccceEEEEcC
Confidence            3899999987765432334455666665554556677776666553 3455677777666655543

>TIGR03689 pup_AAA proteasome ATPase

Probab=95.99  E-value=0.099  Score=46.68  Aligned_cols=18  Identities=28%  Similarity=0.490  Sum_probs=15.5

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||...
T Consensus       216 p~GILLyGPPGTGKT~LA  233 (512)
T TIGR03689       216 PKGVLLYGPPGCGKTLIA  233 (512)
T ss_pred             CcceEEECCCCCcHHHHH
Confidence            467999999999999854

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>PRK09087 hypothetical protein; Validated

Probab=95.98  E-value=0.047  Score=43.52  Aligned_cols=60  Identities=12%  Similarity=0.003  Sum_probs=34.1

Q ss_pred             cEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHH---HHHHhcCCCeEEecC
Q psy12977        160 EWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAK---WCRRKLKRRVQINVG  224 (226)
Q Consensus       160 ~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~---~~~~~~~~p~~i~~~  224 (226)
                      +++++||+|.+..     ....+..++..+...+.++++.|.+.|++...   -+...+.....++++
T Consensus        89 ~~l~iDDi~~~~~-----~~~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~  151 (226)
T PRK09087         89 GPVLIEDIDAGGF-----DETGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIG  151 (226)
T ss_pred             CeEEEECCCCCCC-----CHHHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHHHHhCCceeecC
Confidence            3899999997632     23445666655544567777766666654322   233444444555443

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=95.96  E-value=0.1  Score=47.28  Aligned_cols=44  Identities=16%  Similarity=0.081  Sum_probs=25.7

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      ..+.+++|+||+|.+...    ....+...++.- ++.+-+++ .+|-+.
T Consensus       117 ~~~~KVvIIDEa~~Ls~~----a~naLLK~LEep-p~~~vfI~-~tte~~  160 (563)
T PRK06647        117 SSRYRVYIIDEVHMLSNS----AFNALLKTIEEP-PPYIVFIF-ATTEVH  160 (563)
T ss_pred             cCCCEEEEEEChhhcCHH----HHHHHHHhhccC-CCCEEEEE-ecCChH
Confidence            457789999999988654    334444445442 33444444 334333

>KOG1001|consensus

Probab=95.94  E-value=0.091  Score=48.45  Aligned_cols=111  Identities=23%  Similarity=0.260  Sum_probs=68.7

Q ss_pred             eEEEECCCCchHhHHHHHHHHH-HhcCC----CCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIH-SLRGP----KNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF  125 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~-~~~~~----~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (226)
                      --|+.-.-|-|||...+..++. .....    .......+++||+ ++..|+..++.+..+.....+...+| ...    
T Consensus       154 ggIladd~glgkt~~ti~l~l~~~~~~~~~~~~~~~kttLivcp~-s~~~qW~~elek~~~~~~l~v~v~~g-r~k----  227 (674)
T KOG1001|consen  154 GGILADDMGLGKTVKTIALILKQKLKSKEEDRQKEFKTTLIVCPT-SLLTQWKTELEKVTEEDKLSIYVYHG-RTK----  227 (674)
T ss_pred             cceEeeccccchHHHHHHHHHhcccCCcchhhccccCceeEecch-HHHHHHHHHHhccCCccceEEEEecc-ccc----
Confidence            3577888899999876544333 23221    1234567888887 47788888775555544455555555 111    


Q ss_pred             CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977        126 GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus       126 ~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      ........+++++|++.+...     . +..-..-.+|+||+|.+...
T Consensus       228 d~~el~~~dVVltTy~il~~~-----~-l~~i~w~Riildea~~ikn~  269 (674)
T KOG1001|consen  228 DKSELNSYDVVLTTYDILKNS-----P-LVKIKWLRIVLDEAHTIKNK  269 (674)
T ss_pred             ccchhcCCceEEeeHHHhhcc-----c-ccceeEEEEEeccccccCCc
Confidence            112335677999999887641     1 11234558999999988765

>KOG1015|consensus

Probab=95.93  E-value=0.044  Score=51.60  Aligned_cols=146  Identities=21%  Similarity=0.216  Sum_probs=77.3

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCC----CeEEEEecchhhhhh
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG----LRAHVIGKIQQAAEK  124 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~----~~~~~~~~~~~~~~~  124 (226)
                      |.-.|+.---|-|||+-.+..+.-.+......-.+++|++|-. .+..|++.|..+...+.    +.+..+........+
T Consensus       696 GsGcILAHcMGLGKTlQVvtflhTvL~c~klg~ktaLvV~PlN-t~~NW~~EFekWm~~~e~~~~leV~eL~~vkr~e~R  774 (1567)
T KOG1015|consen  696 GSGCILAHCMGLGKTLQVVTFLHTVLLCDKLGFKTALVVCPLN-TALNWMNEFEKWMEGLEDDEKLEVSELATVKRPEER  774 (1567)
T ss_pred             CcchHHHHhhcccceehhhHHHHHHHHhhccCCceEEEEcchH-HHHHHHHHHHHhcccccccccceeehhhhccChHHH
Confidence            3445666667889997643332222333334456899999986 56789999999987532    333333322221111


Q ss_pred             ---hCCCcCCCCCEEEECchHHHHhHhcCC-----------CCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcC
Q psy12977        125 ---FGPRSAQKFDVLITTPNKLVYLLQMDP-----------PALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACS  190 (226)
Q Consensus       125 ---~~~~~~~~~~IiV~Tp~~l~~~~~~~~-----------~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~  190 (226)
                         +..+...+ .|.|.-...+..+.....           ..+.-..-++||.||+|.+-... .....++..+...  
T Consensus       775 ~~~L~~W~~~g-gVmIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvdpGPD~vVCDE~HiLKNek-sa~Skam~~irtk--  850 (1567)
T KOG1015|consen  775 SYMLQRWQEDG-GVMIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILKNEK-SAVSKAMNSIRTK--  850 (1567)
T ss_pred             HHHHHHHHhcC-CEEEEehHHHHHHhcccchhhhHHHHHHHHhccCCCCCeEEecchhhhccch-HHHHHHHHHHHhh--
Confidence               11122233 344444444433332110           11223456899999999775432 1344555555532  


Q ss_pred             CCCceEEEEeeeC
Q psy12977        191 GPNLKRGMFSATH  203 (226)
Q Consensus       191 ~~~~q~v~~SAT~  203 (226)
                          +.|.+|.|+
T Consensus       851 ----RRI~LTGTP  859 (1567)
T KOG1015|consen  851 ----RRIILTGTP  859 (1567)
T ss_pred             ----eeEEeecCc
Confidence                345557773

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=95.92  E-value=0.12  Score=49.25  Aligned_cols=19  Identities=26%  Similarity=0.212  Sum_probs=16.0

Q ss_pred             CCeEEEECCCCchHhHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~   67 (226)
                      ..+.++.||+|+|||...-
T Consensus       194 ~~n~lL~G~pGvGKT~l~~  212 (852)
T TIGR03346       194 KNNPVLIGEPGVGKTAIVE  212 (852)
T ss_pred             CCceEEEcCCCCCHHHHHH
Confidence            3689999999999997654

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.

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=95.89  E-value=0.08  Score=47.09  Aligned_cols=134  Identities=15%  Similarity=0.136  Sum_probs=78.1

Q ss_pred             eEEEECCCCchHhHHHH-HHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         51 QIFACAPTGSGKTAAFL-IPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~-~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      .++|..|-+-|||.... +.+...+.. ...+.+..+++|+.+-+.+.+..++.+..... ..          ....+..
T Consensus        88 e~fI~v~RkngKt~l~A~i~~~~~l~~-~~~~~~~~i~A~s~~qa~~~F~~ar~mv~~~~-~l----------~~~~~~q  155 (546)
T COG4626          88 EAFIFIPRKNGKSTLAAGIMMTALLLN-WRSGAGIYILAPSVEQAANSFNPARDMVKRDD-DL----------RDLCNVQ  155 (546)
T ss_pred             EEEEEEecCCchHHHHHHHHHHHHHhh-hhcCCcEEEEeccHHHHHHhhHHHHHHHHhCc-ch----------hhhhccc
Confidence            47899999999996544 444444432 24566899999999999999998888866544 00          0000000


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhc-CCCCceEEEEee
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC-SGPNLKRGMFSA  201 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~-~~~~~q~v~~SA  201 (226)
                      .....|...-.......+.......+-.+..+.|+||.|.....   +  ..+..+...+ ..++.+++..|-
T Consensus       156 ~~s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~~---~--~~~~~~~~g~~ar~~~l~~~ITT  223 (546)
T COG4626         156 THSRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGKQ---E--DMYSEAKGGLGARPEGLVVYITT  223 (546)
T ss_pred             cceeEEEecccceeeeeeccCCCcccCCCcceEEEehhhhhcCH---H--HHHHHHHhhhccCcCceEEEEec
Confidence            01111222222333333344445566667789999999977654   1  3344343333 235666666543

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=95.89  E-value=0.073  Score=40.27  Aligned_cols=18  Identities=28%  Similarity=0.265  Sum_probs=14.3

Q ss_pred             EEEECCCCchHhHHHHHH
Q psy12977         52 IFACAPTGSGKTAAFLIP   69 (226)
Q Consensus        52 ~li~apTGsGKT~~~~~~   69 (226)
                      +++.|++|+|||.....-
T Consensus         3 ~~~~G~~G~GKTt~~~~l   20 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKL   20 (173)
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            578999999999865433

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.

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=95.88  E-value=0.037  Score=55.33  Aligned_cols=127  Identities=17%  Similarity=0.123  Sum_probs=71.4

Q ss_pred             cCCCCcccccc-cCC--CCCeEEEECCCCchHhHHHH--HHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcC
Q psy12977         34 KHFEPHFTITY-LSP--LGRQIFACAPTGSGKTAAFL--IPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL  108 (226)
Q Consensus        34 ~~~~~~Q~~~~-~~~--~~~~~li~apTGsGKT~~~~--~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~  108 (226)
                      ..+++-|..+. .++  .++-++++|..|+|||...-  ..++..+.  ...+.+++.++||..-+....+    .    
T Consensus       834 ~~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~--e~~g~~V~glAPTgkAa~~L~e----~----  903 (1623)
T PRK14712        834 EKLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLP--ESERPRVVGLGPTHRAVGEMRS----A----  903 (1623)
T ss_pred             cccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHh--hccCceEEEEechHHHHHHHHH----h----
Confidence            46888887774 333  34678999999999997632  22233221  2234578889999876665432    1    


Q ss_pred             CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHh--cCCCCCCCCCccEEEEcccccccccCccchHHHHHHHH
Q psy12977        109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQ--MDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIY  186 (226)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~--~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~  186 (226)
                      ++...                         |-.+|+....  ...........+++||||+-.+...       .+..++
T Consensus       904 Gi~A~-------------------------TIasfL~~~~~~~~~~~~~~~~~~llIVDEASMV~~~-------~m~~ll  951 (1623)
T PRK14712        904 GVDAQ-------------------------TLASFLHDTQLQQRSGETPDFSNTLFLLDESSMVGNT-------DMARAY  951 (1623)
T ss_pred             CchHh-------------------------hHHHHhccccchhhcccCCCCCCcEEEEEccccccHH-------HHHHHH
Confidence            22110                         1111111000  0001122234689999999865433       444455


Q ss_pred             HhcCCCCceEEEEeee
Q psy12977        187 AACSGPNLKRGMFSAT  202 (226)
Q Consensus       187 ~~~~~~~~q~v~~SAT  202 (226)
                      +.+.....+++++.-+
T Consensus       952 ~~~~~~garvVLVGD~  967 (1623)
T PRK14712        952 ALIAAGGGRAVASGDT  967 (1623)
T ss_pred             HhhhhCCCEEEEEcch
Confidence            5553456888888766

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=95.83  E-value=0.054  Score=50.69  Aligned_cols=20  Identities=25%  Similarity=0.160  Sum_probs=16.4

Q ss_pred             CCeEEEECCCCchHhHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~   68 (226)
                      ..++++.||+|+|||.....
T Consensus       207 ~~n~LLvGppGvGKT~lae~  226 (758)
T PRK11034        207 KNNPLLVGESGVGKTAIAEG  226 (758)
T ss_pred             CCCeEEECCCCCCHHHHHHH
Confidence            45899999999999986433

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=95.83  E-value=0.049  Score=43.14  Aligned_cols=52  Identities=21%  Similarity=0.238  Sum_probs=34.5

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      .|.-+++.|++|+|||...+..+...+.+    +.+++|+.. .+-.+++.+.+..+
T Consensus        15 ~g~~~li~G~~G~GKt~~~~~~~~~~~~~----g~~~~y~s~-e~~~~~l~~~~~~~   66 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSLQFLYQGLKN----GEKAMYISL-EEREERILGYAKSK   66 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC----CCeEEEEEC-CCCHHHHHHHHHHc
Confidence            46778999999999997554445554442    446777654 44566666666555

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.

>TIGR02012 tigrfam_recA protein RecA

Probab=95.82  E-value=0.075  Score=44.60  Aligned_cols=43  Identities=30%  Similarity=0.351  Sum_probs=28.8

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAK   95 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~   95 (226)
                      |+-+.+.+|+|+|||...+..+.+....    +.+++|+-.-..+-.
T Consensus        55 G~iteI~G~~GsGKTtLaL~~~~~~~~~----g~~v~yId~E~~~~~   97 (321)
T TIGR02012        55 GRIIEIYGPESSGKTTLALHAIAEAQKA----GGTAAFIDAEHALDP   97 (321)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc----CCcEEEEcccchhHH
Confidence            4668899999999998665555554432    457777755444433

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=95.81  E-value=0.15  Score=46.25  Aligned_cols=32  Identities=19%  Similarity=0.174  Sum_probs=25.3

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcC
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACS  190 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~  190 (226)
                      +.+-+++|+||+-.-+|.   .....+...+..+.
T Consensus       481 l~~~~ILILDEaTSalD~---~tE~~I~~~l~~l~  512 (567)
T COG1132         481 LRNPPILILDEATSALDT---ETEALIQDALKKLL  512 (567)
T ss_pred             hcCCCEEEEeccccccCH---HhHHHHHHHHHHHh
Confidence            556689999999999988   57777777776663

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=95.78  E-value=0.1  Score=44.86  Aligned_cols=51  Identities=24%  Similarity=0.236  Sum_probs=31.3

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      |.-+++.+++|+|||...+..+.....    .+.+++|+.-. +-..|+.....++
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~a~----~g~~VlYvs~E-Es~~qi~~Ra~rl  132 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARLAK----RGGKVLYVSGE-ESPEQIKLRADRL  132 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHh----cCCeEEEEECC-cCHHHHHHHHHHc
Confidence            566899999999999865444333332    23477887643 3445555444443

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.

>COG1485 Predicted ATPase [General function prediction only]

Probab=95.78  E-value=0.085  Score=44.43  Aligned_cols=110  Identities=19%  Similarity=0.137  Sum_probs=70.3

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      +-+-++|+-|.|||+. +=..++.+.-+.  +    .-++..+-+.++.+.+..+-+.   .                  
T Consensus        66 ~GlYl~GgVGrGKT~L-MD~Fy~~lp~~~--k----~R~HFh~FM~~vH~~l~~l~g~---~------------------  117 (367)
T COG1485          66 RGLYLWGGVGRGKTML-MDLFYESLPGER--K----RRLHFHRFMARVHQRLHTLQGQ---T------------------  117 (367)
T ss_pred             ceEEEECCCCccHHHH-HHHHHhhCCccc--c----ccccHHHHHHHHHHHHHHHcCC---C------------------
Confidence            6789999999999974 223344443211  1    1246677888888877776411   0                  


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                          |.+   +....++         ..+.+.|.+||++ +.|-   +-.--+.++++.+.+.++.++..|.|.|+++
T Consensus       118 ----dpl---~~iA~~~---------~~~~~vLCfDEF~-VtDI---~DAMiL~rL~~~Lf~~GV~lvaTSN~~P~~L  175 (367)
T COG1485         118 ----DPL---PPIADEL---------AAETRVLCFDEFE-VTDI---ADAMILGRLLEALFARGVVLVATSNTAPDNL  175 (367)
T ss_pred             ----Ccc---HHHHHHH---------HhcCCEEEeeeee-ecCh---HHHHHHHHHHHHHHHCCcEEEEeCCCChHHh
Confidence                000   1111122         3356799999999 4443   3444666778888788999999999999764

>KOG0298|consensus

Probab=95.78  E-value=0.058  Score=52.09  Aligned_cols=150  Identities=19%  Similarity=0.174  Sum_probs=89.6

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcC--------------CCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCC
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRG--------------PKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGL  110 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~--------------~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~  110 (226)
                      ....|+++++.-.-|.|||..-+...+.....              +.....-++|++|. ++-.||++++..-.... .
T Consensus       370 ~~~~g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P~-aIl~QW~~EI~kH~~~~-l  447 (1394)
T KOG0298|consen  370 DKKHGKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICPN-AILMQWFEEIHKHISSL-L  447 (1394)
T ss_pred             CccCCcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECcH-HHHHHHHHHHHHhcccc-c
Confidence            34557888999999999998866554433211              11113468999998 67799999988877654 5


Q ss_pred             eEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCC------------CCCC----CCCcc--EEEEcccccccc
Q psy12977        111 RAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDP------------PALN----LANVE--WLIVDESDKLFE  172 (226)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~------------~~~~----~~~~~--~lViDE~h~l~~  172 (226)
                      ++...-|..+..... ......+|||+||-..+..-+....            +..+    +..+.  -+++|||+.+-.
T Consensus       448 Kv~~Y~Girk~~~~~-~~el~~yDIVlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWRIclDEaQMves  526 (1394)
T KOG0298|consen  448 KVLLYFGIRKTFWLS-PFELLQYDIVLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWRICLDEAQMVES  526 (1394)
T ss_pred             eEEEEechhhhcccC-chhhhccCEEEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHHHhhhHHHhhcc
Confidence            555554443222111 2344678999999999887653320            1111    11111  579999996543


Q ss_pred             cCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        173 AGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       173 ~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      .     ..+..++...+  +..-.=.+|.|+=
T Consensus       527 s-----sS~~a~M~~rL--~~in~W~VTGTPi  551 (1394)
T KOG0298|consen  527 S-----SSAAAEMVRRL--HAINRWCVTGTPI  551 (1394)
T ss_pred             h-----HHHHHHHHHHh--hhhceeeecCCch
Confidence            2     23333444444  3444556778843

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=95.77  E-value=0.084  Score=54.44  Aligned_cols=135  Identities=17%  Similarity=0.110  Sum_probs=73.7

Q ss_pred             CCCCcccccc--cCCC-CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCe
Q psy12977         35 HFEPHFTITY--LSPL-GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR  111 (226)
Q Consensus        35 ~~~~~Q~~~~--~~~~-~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~  111 (226)
                      .+++-|..+.  .+.+ .+-.+++|+.|+|||... -.+...+..   .+.+++.++||..-+.+..+..       +..
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l-~~l~~~~~~---~G~~V~~lAPTgrAA~~L~e~~-------g~~  497 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIA-QLLLHLASE---QGYEIQIITAGSLSAQELRQKI-------PRL  497 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHH-HHHHHHHHh---cCCeEEEEeCCHHHHHHHHHHh-------cch
Confidence            3556665553  2223 366899999999999753 334444433   3568999999987666655432       111


Q ss_pred             EEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCC
Q psy12977        112 AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSG  191 (226)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~  191 (226)
                      ...+.      ..... .. .. .-..|...+.   .   ...++..-++|||||+-.+...       .+..+++....
T Consensus       498 A~Ti~------~~l~~-l~-~~-~~~~tv~~fl---~---~~~~l~~~~vlIVDEAsMl~~~-------~~~~Ll~~a~~  555 (1960)
T TIGR02760       498 ASTFI------TWVKN-LF-ND-DQDHTVQGLL---D---KSSPFSNKDIFVVDEANKLSNN-------ELLKLIDKAEQ  555 (1960)
T ss_pred             hhhHH------HHHHh-hc-cc-ccchhHHHhh---c---ccCCCCCCCEEEEECCCCCCHH-------HHHHHHHHHhh
Confidence            00000      00000 00 00 0011222222   1   2233567789999999965333       45555555545


Q ss_pred             CCceEEEEeee
Q psy12977        192 PNLKRGMFSAT  202 (226)
Q Consensus       192 ~~~q~v~~SAT  202 (226)
                      .+.+++++.=+
T Consensus       556 ~garvVlvGD~  566 (1960)
T TIGR02760       556 HNSKLILLNDS  566 (1960)
T ss_pred             cCCEEEEEcCh
Confidence            67899988766

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.

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=95.76  E-value=0.049  Score=42.14  Aligned_cols=148  Identities=12%  Similarity=0.010  Sum_probs=79.7

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHH-HHHHHHHHHhhcCCCeEEEEecchhhhhhh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAK-QTYNETVRLSEGLGLRAHVIGKIQQAAEKF  125 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~-q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (226)
                      ..+.++.+..++|.|||.+.+--++..+..    +.+++++-=.+--.. --...++.+   .++.......+-.    +
T Consensus        20 ~~~g~v~v~~g~GkGKtt~a~g~a~ra~g~----G~~V~ivQFlKg~~~~GE~~~l~~l---~~v~~~~~g~~~~----~   88 (191)
T PRK05986         20 EEKGLLIVHTGNGKGKSTAAFGMALRAVGH----GKKVGVVQFIKGAWSTGERNLLEFG---GGVEFHVMGTGFT----W   88 (191)
T ss_pred             ccCCeEEEECCCCCChHHHHHHHHHHHHHC----CCeEEEEEEecCCCccCHHHHHhcC---CCcEEEECCCCCc----c
Confidence            355789999999999999887777776653    557777754443211 111222221   1232222221100    0


Q ss_pred             CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        126 GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       126 ~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      .   ....+--.......++...   ..+.-...++||+||+-..++.+.- ..+.+..+++.. ++..-+|+..-..|+
T Consensus        89 ~---~~~~~e~~~~~~~~~~~a~---~~l~~~~ydlvVLDEi~~Al~~gli-~~eevi~~L~~r-p~~~evVlTGR~~p~  160 (191)
T PRK05986         89 E---TQDRERDIAAAREGWEEAK---RMLADESYDLVVLDELTYALKYGYL-DVEEVLEALNAR-PGMQHVVITGRGAPR  160 (191)
T ss_pred             c---CCCcHHHHHHHHHHHHHHH---HHHhCCCCCEEEEehhhHHHHCCCc-cHHHHHHHHHcC-CCCCEEEEECCCCCH
Confidence            0   0000000001111122222   2344567899999999988776432 344566666654 567778887777888


Q ss_pred             hHHHHHHH
Q psy12977        206 DVAKWCRR  213 (226)
Q Consensus       206 ~~~~~~~~  213 (226)
                      ++.+.+..
T Consensus       161 ~Lie~ADl  168 (191)
T PRK05986        161 ELIEAADL  168 (191)
T ss_pred             HHHHhCch
Confidence            88777644

>KOG0733|consensus

Probab=95.76  E-value=0.04  Score=49.56  Aligned_cols=52  Identities=13%  Similarity=0.058  Sum_probs=32.4

Q ss_pred             CCCccEEEEcccccccccCc----cchHHHHHHHHHhcC--CCCceEEEEeeeCchhH
Q psy12977        156 LANVEWLIVDESDKLFEAGV----RGFRDQLAVIYAACS--GPNLKRGMFSATHTEDV  207 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~----~~~~~~i~~i~~~~~--~~~~q~v~~SAT~~~~~  207 (226)
                      .+.-..+.+||+|.+.....    ......+.+++..+-  ..+.++..+.||.-+++
T Consensus       602 ~saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDi  659 (802)
T KOG0733|consen  602 ASAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDI  659 (802)
T ss_pred             cCCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcc
Confidence            44556889999998864321    123445555555551  35678888889955443

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=95.76  E-value=0.053  Score=48.69  Aligned_cols=64  Identities=20%  Similarity=0.309  Sum_probs=34.4

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEec
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGK  117 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~  117 (226)
                      ..|+-+.+.||+|+|||..  +-++..+..+...    =|.....++.+- .+.+++...+...+...+.+
T Consensus       359 ~~G~~vaIvG~SGsGKSTL--l~lL~g~~~p~~G----~I~i~g~~i~~~-~~~lr~~i~~V~Q~~~lF~~  422 (529)
T TIGR02868       359 PPGERVAILGPSGSGKSTL--LMLLTGLLDPLQG----EVTLDGVSVSSL-QDELRRRISVFAQDAHLFDT  422 (529)
T ss_pred             cCCCEEEEECCCCCCHHHH--HHHHhcCCCCCCc----EEEECCEEhhhH-HHHHHhheEEEccCcccccc
Confidence            4578899999999999964  3333344322221    233455555443 44455444444444333333

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=95.75  E-value=0.21  Score=37.93  Aligned_cols=116  Identities=16%  Similarity=0.091  Sum_probs=64.5

Q ss_pred             EEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCC
Q psy12977         52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQ  131 (226)
Q Consensus        52 ~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (226)
                      +++.|++|||||....--+..       .+.+++|+......-..+.+.+...-+.-+...                   
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~-------~~~~~~y~at~~~~d~em~~rI~~H~~~R~~~w-------------------   55 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE-------LGGPVTYIATAEAFDDEMAERIARHRKRRPAHW-------------------   55 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh-------cCCCeEEEEccCcCCHHHHHHHHHHHHhCCCCc-------------------
Confidence            578999999999754433322       234788998887776666665554322111111                   


Q ss_pred             CCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCc--------cchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        132 KFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGV--------RGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       132 ~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~--------~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                         ..+-.|..+.+.+...      +.-+.+++|=...+.....        ......+..+++.+.....-+++.|.-
T Consensus        56 ---~t~E~~~~l~~~l~~~------~~~~~VLIDclt~~~~n~l~~~~~~~~~~~~~~i~~l~~~l~~~~~~~viVsnE  125 (169)
T cd00544          56 ---RTIETPRDLVSALKEL------DPGDVVLIDCLTLWVTNLLFADLEEWEAAIADEIDALLAAVRNKPGTLILVSNE  125 (169)
T ss_pred             ---eEeecHHHHHHHHHhc------CCCCEEEEEcHhHHHHHhCCCccccchhHHHHHHHHHHHHHHcCCCcEEEEECC
Confidence               2234455555554331      1344677777665443210        012345555666664556667777765

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=95.74  E-value=0.085  Score=42.83  Aligned_cols=19  Identities=26%  Similarity=0.326  Sum_probs=15.5

Q ss_pred             CCeEEEECCCCchHhHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~   67 (226)
                      +..+++.||+|+|||....
T Consensus        43 ~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHH
Confidence            3468999999999998654

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.73  E-value=0.062  Score=47.83  Aligned_cols=54  Identities=20%  Similarity=0.146  Sum_probs=38.5

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      ..|.-+++.+|||+|||...+.-+...+.+    +.+++|++ ..|-..|+...++.+.
T Consensus       261 ~~gs~~li~G~~G~GKt~l~~~f~~~~~~~----ge~~~y~s-~eEs~~~i~~~~~~lg  314 (484)
T TIGR02655       261 FKDSIILATGATGTGKTLLVSKFLENACAN----KERAILFA-YEESRAQLLRNAYSWG  314 (484)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHHHC----CCeEEEEE-eeCCHHHHHHHHHHcC
Confidence            345779999999999998665555555542    45778865 6667777777776663

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.

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=95.72  E-value=0.071  Score=49.94  Aligned_cols=20  Identities=25%  Similarity=0.137  Sum_probs=16.4

Q ss_pred             CCeEEEECCCCchHhHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~   68 (226)
                      ..|+++.||+|+|||...-.
T Consensus       203 ~~n~lL~G~pG~GKT~l~~~  222 (731)
T TIGR02639       203 KNNPLLVGEPGVGKTAIAEG  222 (731)
T ss_pred             CCceEEECCCCCCHHHHHHH
Confidence            45899999999999986533

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=95.72  E-value=0.072  Score=53.95  Aligned_cols=128  Identities=17%  Similarity=0.128  Sum_probs=71.9

Q ss_pred             cCCCCcccccc-cCCC--CCeEEEECCCCchHhHHHHHHHHHHhcC-CCCCCceEEEEcccHHHHHHHHHHHHHHhhcCC
Q psy12977         34 KHFEPHFTITY-LSPL--GRQIFACAPTGSGKTAAFLIPIIHSLRG-PKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG  109 (226)
Q Consensus        34 ~~~~~~Q~~~~-~~~~--~~~~li~apTGsGKT~~~~~~~~~~~~~-~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~  109 (226)
                      ..+++-|..+. .++.  ++-++++|..|+|||... -.+...+.. ....+.+++.++||..-+.++.+        .+
T Consensus       966 ~~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l~~~~~~~V~glAPTgrAAk~L~e--------~G 1036 (1747)
T PRK13709        966 EGLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTLPESERPRVVGLGPTHRAVGEMRS--------AG 1036 (1747)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHhhcccCceEEEECCcHHHHHHHHh--------cC
Confidence            46788887664 3333  467899999999999763 223333321 12234578889999876665432        12


Q ss_pred             CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHh--cCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHH
Q psy12977        110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQ--MDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYA  187 (226)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~--~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~  187 (226)
                      ...                         .|-.+++....  ...+......-+++||||+-.+...       .+..+++
T Consensus      1037 i~A-------------------------~TI~s~L~~~~~~~~~~~~~~~~~~llIVDEaSMv~~~-------~m~~Ll~ 1084 (1747)
T PRK13709       1037 VDA-------------------------QTLASFLHDTQLQQRSGETPDFSNTLFLLDESSMVGNT-------DMARAYA 1084 (1747)
T ss_pred             cch-------------------------hhHHHHhcccccccccccCCCCCCcEEEEEccccccHH-------HHHHHHH
Confidence            221                         12222211100  0001112234589999999865333       4555555


Q ss_pred             hcCCCCceEEEEeee
Q psy12977        188 ACSGPNLKRGMFSAT  202 (226)
Q Consensus       188 ~~~~~~~q~v~~SAT  202 (226)
                      ......+++|++.=+
T Consensus      1085 ~~~~~garvVLVGD~ 1099 (1747)
T PRK13709       1085 LIAAGGGRAVSSGDT 1099 (1747)
T ss_pred             hhhcCCCEEEEecch
Confidence            554457889988766

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.72  E-value=0.35  Score=42.12  Aligned_cols=57  Identities=9%  Similarity=0.045  Sum_probs=32.7

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCC--CCceEEEEeeeCch-hHHHHHHHhc
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSG--PNLKRGMFSATHTE-DVAKWCRRKL  215 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~--~~~q~v~~SAT~~~-~~~~~~~~~~  215 (226)
                      .+.++++||=+-......  .....+..+.+....  +.--++.+|||... ++.+.++.|-
T Consensus       298 ~~~D~VLIDTaGr~~rd~--~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~~~~f~  357 (432)
T PRK12724        298 DGSELILIDTAGYSHRNL--EQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTVLKAYE  357 (432)
T ss_pred             CCCCEEEEeCCCCCccCH--HHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHHHHHhc
Confidence            356889999765442211  355555555554411  22345677888665 6666666653

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.72  E-value=0.015  Score=47.97  Aligned_cols=29  Identities=31%  Similarity=0.520  Sum_probs=21.5

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCC
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKN   79 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~   79 (226)
                      .=++|.||||||||... .++++.+.+...
T Consensus       126 GLILVTGpTGSGKSTTl-AamId~iN~~~~  154 (353)
T COG2805         126 GLILVTGPTGSGKSTTL-AAMIDYINKHKA  154 (353)
T ss_pred             ceEEEeCCCCCcHHHHH-HHHHHHHhccCC
Confidence            34899999999999853 567777765433

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=95.72  E-value=0.18  Score=42.40  Aligned_cols=41  Identities=15%  Similarity=0.122  Sum_probs=28.4

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      ....+.+||||+|.|...    ....+.++++. |++++.+++.|.
T Consensus       105 ~g~~KV~iI~~a~~m~~~----AaNaLLKtLEE-Pp~~~~fiL~t~  145 (325)
T PRK06871        105 QGGNKVVYIQGAERLTEA----AANALLKTLEE-PRPNTYFLLQAD  145 (325)
T ss_pred             cCCceEEEEechhhhCHH----HHHHHHHHhcC-CCCCeEEEEEEC
Confidence            456789999999999865    55566666666 355555555543

>PRK10867 signal recognition particle protein; Provisional

Probab=95.71  E-value=0.28  Score=43.00  Aligned_cols=22  Identities=23%  Similarity=0.132  Sum_probs=16.6

Q ss_pred             CeEEEECCCCchHhHHHHHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFLIPII   71 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~   71 (226)
                      .-+++.|++|+|||....--+.
T Consensus       101 ~vI~~vG~~GsGKTTtaakLA~  122 (433)
T PRK10867        101 TVIMMVGLQGAGKTTTAGKLAK  122 (433)
T ss_pred             EEEEEECCCCCcHHHHHHHHHH
Confidence            3578999999999987554433

>KOG0740|consensus

Probab=95.70  E-value=0.04  Score=47.73  Aligned_cols=66  Identities=20%  Similarity=0.272  Sum_probs=41.6

Q ss_pred             CccEEEEcccccccccC----ccchHH-HHHHHHHhc---CCCCceEEEEeee-CchhHHHHHHHhcCCCeEEec
Q psy12977        158 NVEWLIVDESDKLFEAG----VRGFRD-QLAVIYAAC---SGPNLKRGMFSAT-HTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~----~~~~~~-~i~~i~~~~---~~~~~q~v~~SAT-~~~~~~~~~~~~~~~p~~i~~  223 (226)
                      ...+++|||+|.++...    ++.... ..+.++...   ..+..++++++|| .|.++.+-+.+.+...++|-.
T Consensus       245 qPsvifidEidslls~Rs~~e~e~srr~ktefLiq~~~~~s~~~drvlvigaTN~P~e~Dea~~Rrf~kr~yipl  319 (428)
T KOG0740|consen  245 QPSVIFIDEIDSLLSKRSDNEHESSRRLKTEFLLQFDGKNSAPDDRVLVIGATNRPWELDEAARRRFVKRLYIPL  319 (428)
T ss_pred             CCeEEEechhHHHHhhcCCcccccchhhhhHHHhhhccccCCCCCeEEEEecCCCchHHHHHHHHHhhceeeecC
Confidence            44577799999887542    111211 222222221   2456689999999 888999988888877766543

>PRK10865 protein disaggregation chaperone; Provisional

Probab=95.69  E-value=0.13  Score=49.00  Aligned_cols=20  Identities=25%  Similarity=0.127  Sum_probs=16.3

Q ss_pred             CCeEEEECCCCchHhHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~   68 (226)
                      ..++++.||+|+|||.....
T Consensus       199 ~~n~lL~G~pGvGKT~l~~~  218 (857)
T PRK10865        199 KNNPVLIGEPGVGKTAIVEG  218 (857)
T ss_pred             cCceEEECCCCCCHHHHHHH
Confidence            35899999999999986543

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=95.67  E-value=0.099  Score=39.29  Aligned_cols=138  Identities=16%  Similarity=0.176  Sum_probs=75.4

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH---HHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCC
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE---LAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGP  127 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~---L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (226)
                      -+.+-.++|.|||.+.+--++..+..    +.+++++-=.+.   -.+  ...++.+.   ++.......+.    .+..
T Consensus         4 ~i~vy~g~G~Gkt~~a~g~~~ra~~~----g~~v~~vQFlKg~~~~gE--~~~l~~l~---~v~~~~~g~~~----~~~~   70 (159)
T cd00561           4 LIQVYTGNGKGKTTAALGLALRALGH----GYRVGVVQFLKGGWKYGE--LKALERLP---NIEIHRMGRGF----FWTT   70 (159)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC----CCeEEEEEEeCCCCccCH--HHHHHhCC---CcEEEECCCCC----ccCC
Confidence            35677888999999887777766653    557777443332   112  12233331   33332222110    0000


Q ss_pred             CcCCCCCEEEECch---HHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        128 RSAQKFDVLITTPN---KLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       128 ~~~~~~~IiV~Tp~---~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                         .  +    .++   .....+......+.....+++|+||+=..++.+. --.+.+..+++.. ++..-+|+.+-..|
T Consensus        71 ---~--~----~~~~~~~a~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gl-i~~~~v~~ll~~r-p~~~evIlTGr~~p  139 (159)
T cd00561          71 ---E--N----DEEDIAAAAEGWAFAKEAIASGEYDLVILDEINYALGYGL-LDVEEVVDLLKAK-PEDLELVLTGRNAP  139 (159)
T ss_pred             ---C--C----hHHHHHHHHHHHHHHHHHHhcCCCCEEEEechHhHhhCCC-CCHHHHHHHHHcC-CCCCEEEEECCCCC
Confidence               0  0    111   1111111111233456789999999987766532 2455666777666 56778888777788


Q ss_pred             hhHHHHHH
Q psy12977        205 EDVAKWCR  212 (226)
Q Consensus       205 ~~~~~~~~  212 (226)
                      +++.+.+.
T Consensus       140 ~~l~e~AD  147 (159)
T cd00561         140 KELIEAAD  147 (159)
T ss_pred             HHHHHhCc
Confidence            88877764

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=95.60  E-value=0.24  Score=39.09  Aligned_cols=45  Identities=24%  Similarity=0.184  Sum_probs=28.0

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCC--CCCCceEEEEcccH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGP--KNLGFRAVIVCPTR   91 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~--~~~~~~~iil~Pt~   91 (226)
                      ..|+-+.+.||+|+|||...+..+.......  .....+++|+....
T Consensus        17 ~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~   63 (226)
T cd01393          17 PTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEG   63 (226)
T ss_pred             cCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCC
Confidence            4567789999999999986554444433321  01124678877643

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.60  E-value=0.13  Score=44.07  Aligned_cols=24  Identities=29%  Similarity=0.656  Sum_probs=17.5

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      +.+++.||+|+|||..... +...+
T Consensus        40 ~~~L~~G~~G~GKt~~a~~-la~~l   63 (367)
T PRK14970         40 QALLFCGPRGVGKTTCARI-LARKI   63 (367)
T ss_pred             eEEEEECCCCCCHHHHHHH-HHHHh
Confidence            5788999999999975433 34444

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=95.59  E-value=0.088  Score=48.81  Aligned_cols=46  Identities=13%  Similarity=0.063  Sum_probs=27.5

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                      ..+.+++|+||+|.+...    ....+...++.- ++.+.+++. +|-++.+
T Consensus       116 ~g~~KV~IIDEa~~LT~~----A~NALLKtLEEP-P~~tifILa-Tte~~KL  161 (725)
T PRK07133        116 QSKYKIYIIDEVHMLSKS----AFNALLKTLEEP-PKHVIFILA-TTEVHKI  161 (725)
T ss_pred             cCCCEEEEEEChhhCCHH----HHHHHHHHhhcC-CCceEEEEE-cCChhhh
Confidence            457789999999988654    344555555543 344555554 3444333

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=95.55  E-value=0.073  Score=42.16  Aligned_cols=40  Identities=23%  Similarity=0.323  Sum_probs=27.0

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEccc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPT   90 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt   90 (226)
                      ..|.-+.+.|++|+|||...+..+.+....    +.+++|+.--
T Consensus        21 ~~g~i~~i~G~~GsGKT~l~~~la~~~~~~----~~~v~yi~~e   60 (225)
T PRK09361         21 ERGTITQIYGPPGSGKTNICLQLAVEAAKN----GKKVIYIDTE   60 (225)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHC----CCeEEEEECC
Confidence            346778999999999997655544444432    4467776543

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=95.54  E-value=0.078  Score=40.39  Aligned_cols=144  Identities=13%  Similarity=0.063  Sum_probs=75.4

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHH-HHHHHHHHHhhcCCCeEEEEecchhhhhhhCCC
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAK-QTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPR  128 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~-q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (226)
                      .-+.+..++|.|||.+.+--++..+..    +.+++++-=.+.-.. --.+.+..+    +..+.....+-.    +.  
T Consensus         6 Gli~v~~g~GkGKtt~a~g~a~ra~~~----g~~v~ivQFlKg~~~~GE~~~l~~~----~~~~~~~g~g~~----~~--   71 (173)
T TIGR00708         6 GIIIVHTGNGKGKTTAAFGMALRALGH----GKKVGVIQFIKGAWPNGERAAFEPH----GVEFQVMGTGFT----WE--   71 (173)
T ss_pred             cEEEEECCCCCChHHHHHHHHHHHHHC----CCeEEEEEEecCCcccChHHHHHhc----CcEEEECCCCCe----ec--
Confidence            346788889999999887766666643    557776643332100 001112221    333222221100    00  


Q ss_pred             cCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHH
Q psy12977        129 SAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVA  208 (226)
Q Consensus       129 ~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~  208 (226)
                       ..+.+   -......+.+..-...+.-...++||+||+-..++.+.- ..+.+..+++.. ++..-+|+..-..|+++.
T Consensus        72 -~~~~~---~~~~~~~~~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli-~~~~v~~lL~~r-p~~~evVlTGR~~p~~l~  145 (173)
T TIGR00708        72 -TQNRE---ADTAIAKAAWQHAKEMLADPELDLVLLDELTYALKYGYL-DVEEVVEALQER-PGHQHVIITGRGCPQDLL  145 (173)
T ss_pred             -CCCcH---HHHHHHHHHHHHHHHHHhcCCCCEEEehhhHHHHHCCCc-CHHHHHHHHHhC-CCCCEEEEECCCCCHHHH
Confidence             00000   000111122221112333467899999999877776432 334566666665 567788887777888887


Q ss_pred             HHHHH
Q psy12977        209 KWCRR  213 (226)
Q Consensus       209 ~~~~~  213 (226)
                      +++..
T Consensus       146 e~AD~  150 (173)
T TIGR00708       146 ELADL  150 (173)
T ss_pred             HhCce
Confidence            77643

Alternate name: corrinoid adenosyltransferase.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.54  E-value=0.024  Score=47.61  Aligned_cols=48  Identities=27%  Similarity=0.215  Sum_probs=33.2

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHH
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELA   94 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~   94 (226)
                      ....+++++++|+||||||.. +..++..+... ..+.+++.+-.+.||.
T Consensus       140 ~v~~~~nilI~G~tGSGKTTl-l~aL~~~i~~~-~~~~rivtiEd~~El~  187 (323)
T PRK13833        140 AIDSRLNIVISGGTGSGKTTL-ANAVIAEIVAS-APEDRLVILEDTAEIQ  187 (323)
T ss_pred             HHHcCCeEEEECCCCCCHHHH-HHHHHHHHhcC-CCCceEEEecCCcccc
Confidence            445578999999999999974 35566665321 2234788887777763

>COG1674 FtsK DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]

Probab=95.50  E-value=0.13  Score=49.09  Aligned_cols=64  Identities=13%  Similarity=0.190  Sum_probs=45.2

Q ss_pred             cEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEec
Q psy12977        160 EWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       160 ~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~  223 (226)
                      -++|+||++.+....+......+.++.+.-......+++.|.-+..++..-++..++..+...+
T Consensus       641 iviiiDe~adlm~~~~k~ve~~i~rLa~~ara~GIHlilatqRps~dVit~ikanipsrIaf~v  704 (858)
T COG1674         641 IVIIIDEYADLMMVAGKELEELIARLAQKGRAAGIHLILATQRPSVDVITGIKANIPTRIALRL  704 (858)
T ss_pred             EEEEEcchHHHhhhhhHHHHHHHHHHHHhhhhcceEEEEecCCCCcchhHHHHhCCcceEEEEE
Confidence            4899999998887654456777888877766667788886655666565557777766555444

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=95.49  E-value=0.21  Score=41.94  Aligned_cols=42  Identities=14%  Similarity=0.225  Sum_probs=28.8

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      ....+++|||++|.|...    ....+.+++++ |++++.+++.|..
T Consensus       106 ~~~~kV~iI~~ae~m~~~----AaNaLLKtLEE-Pp~~t~fiL~t~~  147 (319)
T PRK06090        106 LNGYRLFVIEPADAMNES----ASNALLKTLEE-PAPNCLFLLVTHN  147 (319)
T ss_pred             cCCceEEEecchhhhCHH----HHHHHHHHhcC-CCCCeEEEEEECC
Confidence            456889999999999765    55566666666 3455556655443

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.47  E-value=0.034  Score=46.28  Aligned_cols=48  Identities=29%  Similarity=0.326  Sum_probs=33.6

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHH
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELA   94 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~   94 (226)
                      ....+++++++|+||||||.. +..++..+... ....+++.+-.+.|+.
T Consensus       128 ~v~~~~~ilI~G~tGSGKTTl-l~al~~~i~~~-~~~~ri~tiEd~~El~  175 (299)
T TIGR02782       128 AVLARKNILVVGGTGSGKTTL-ANALLAEIAKN-DPTDRVVIIEDTRELQ  175 (299)
T ss_pred             HHHcCCeEEEECCCCCCHHHH-HHHHHHHhhcc-CCCceEEEECCchhhc
Confidence            344678999999999999974 35566665431 2244788888887763

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.

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=95.45  E-value=0.018  Score=48.80  Aligned_cols=45  Identities=29%  Similarity=0.349  Sum_probs=31.6

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHH
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELA   94 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~   94 (226)
                      ....++++++.||||||||.. +..++..+..    ..+.+.+-.+.|+.
T Consensus       158 ~v~~~~nilI~G~tGSGKTTl-l~aLl~~i~~----~~rivtiEd~~El~  202 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTTM-SKTLISAIPP----QERLITIEDTLELV  202 (344)
T ss_pred             HHHcCCeEEEECCCCccHHHH-HHHHHcccCC----CCCEEEECCCcccc
Confidence            335679999999999999974 3555555532    34677777777664

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=95.42  E-value=0.055  Score=55.69  Aligned_cols=126  Identities=15%  Similarity=0.140  Sum_probs=70.6

Q ss_pred             cCCCCcccccc-cCCC--CCeEEEECCCCchHhHHHH---HHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         34 KHFEPHFTITY-LSPL--GRQIFACAPTGSGKTAAFL---IPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        34 ~~~~~~Q~~~~-~~~~--~~~~li~apTGsGKT~~~~---~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      ..+++-|..+. .++.  ++-++++|+.|+|||....   -++...+..   .+.+++.++||..-+.+..+        
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~---~g~~v~glApT~~Aa~~L~~-------- 1086 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES---EQLQVIGLAPTHEAVGELKS-------- 1086 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh---cCCeEEEEeChHHHHHHHHh--------
Confidence            46788887774 3333  4567899999999997652   223333332   25578889999766655432        


Q ss_pred             CCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHH
Q psy12977        108 LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYA  187 (226)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~  187 (226)
                      .+....                         |-.+++.........-.....+++|+||+-.+..       ..+..+++
T Consensus      1087 ~g~~a~-------------------------Ti~s~l~~~~~~~~~~~~~~~~v~ivDEasMv~~-------~~~~~l~~ 1134 (1960)
T TIGR02760      1087 AGVQAQ-------------------------TLDSFLTDISLYRNSGGDFRNTLFILDESSMVSN-------FQLTHATE 1134 (1960)
T ss_pred             cCCchH-------------------------hHHHHhcCcccccccCCCCcccEEEEEccccccH-------HHHHHHHH
Confidence            122210                         1111111000000111244568999999985533       34555555


Q ss_pred             hcCCCCceEEEEeee
Q psy12977        188 ACSGPNLKRGMFSAT  202 (226)
Q Consensus       188 ~~~~~~~q~v~~SAT  202 (226)
                      .......+++++.-+
T Consensus      1135 ~~~~~~ak~vlvGD~ 1149 (1960)
T TIGR02760      1135 LVQKSGSRAVSLGDI 1149 (1960)
T ss_pred             hccCCCCEEEEeCCh
Confidence            544556788877655

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.

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []

Probab=95.40  E-value=0.6  Score=39.29  Aligned_cols=147  Identities=15%  Similarity=0.077  Sum_probs=62.8

Q ss_pred             EEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHH---HHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         53 FACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTY---NETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        53 li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      ++.++.|+|||......++..+..... ...+++...+.++...+.   ..+..+... ...........   ..  ...
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~-~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~---~~--~~~   73 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPP-GRRVIIASTYRQARDIFGRFWKGIIELLPS-WFEIKFNEWND---RK--IIL   73 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS---EEEEEESSHHHHHHHHHHHHHHHHTS-T-TTS--EEEE-S---SE--EEE
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCC-CcEEEEecCHHHHHHHHHHhHHHHHHHHHH-hcCcccccCCC---Cc--EEe
Confidence            467899999999877766666543322 235666644444444432   333344333 12222110000   00  011


Q ss_pred             CCCCCEEEECchHH--HHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee--Cch
Q psy12977        130 AQKFDVLITTPNKL--VYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT--HTE  205 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l--~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT--~~~  205 (226)
                      .+++.|.+.+-+.-  ..-+.       =...+++++||+-.+.+.   .+...+.......  .....++.|.+  ...
T Consensus        74 ~nG~~i~~~~~~~~~~~~~~~-------G~~~~~i~iDE~~~~~~~---~~~~~~~~~~~~~--~~~~~~~~s~p~~~~~  141 (384)
T PF03237_consen   74 PNGSRIQFRGADSPDSGDNIR-------GFEYDLIIIDEAAKVPDD---AFSELIRRLRATW--GGSIRMYISTPPNPGG  141 (384)
T ss_dssp             TTS-EEEEES-----SHHHHH-------TS--SEEEEESGGGSTTH---HHHHHHHHHHHCS--TT--EEEEEE---SSS
T ss_pred             cCceEEEEecccccccccccc-------ccccceeeeeecccCchH---HHHHHHHhhhhcc--cCcceEEeecCCCCCC
Confidence            35555666664321  11111       156789999999877655   2444443333222  22222244443  223


Q ss_pred             hHHHHHHHhcCCC
Q psy12977        206 DVAKWCRRKLKRR  218 (226)
Q Consensus       206 ~~~~~~~~~~~~p  218 (226)
                      ...++..+...+.
T Consensus       142 ~~~~~~~~~~~~~  154 (384)
T PF03237_consen  142 WFYEIFQRNLDDD  154 (384)
T ss_dssp             HHHHHHHHHHCTS
T ss_pred             ceeeeeehhhcCC
Confidence            4555555555443

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=95.34  E-value=0.16  Score=42.82  Aligned_cols=41  Identities=12%  Similarity=0.145  Sum_probs=28.1

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      ....+++||||+|.+...    ....+...++.- ++.+.+++.|.
T Consensus       108 ~~~~kvviI~~a~~~~~~----a~NaLLK~LEEP-p~~~~~Il~t~  148 (329)
T PRK08058        108 ESNKKVYIIEHADKMTAS----AANSLLKFLEEP-SGGTTAILLTE  148 (329)
T ss_pred             ccCceEEEeehHhhhCHH----HHHHHHHHhcCC-CCCceEEEEeC
Confidence            456789999999998765    455566666653 55666666443

>CHL00095 clpC Clp protease ATP binding subunit

Probab=95.34  E-value=0.085  Score=50.06  Aligned_cols=20  Identities=25%  Similarity=0.102  Sum_probs=16.6

Q ss_pred             CCeEEEECCCCchHhHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~   68 (226)
                      ..++++.||+|+|||...-.
T Consensus       200 ~~n~lL~G~pGvGKTal~~~  219 (821)
T CHL00095        200 KNNPILIGEPGVGKTAIAEG  219 (821)
T ss_pred             cCCeEEECCCCCCHHHHHHH
Confidence            35899999999999986543

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=95.32  E-value=0.13  Score=43.27  Aligned_cols=43  Identities=28%  Similarity=0.295  Sum_probs=29.7

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAK   95 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~   95 (226)
                      |+-+.+.+|+|+|||...+..+.+....    +.+++|+.+-..+-.
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~~~----g~~~vyId~E~~~~~   97 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQKL----GGTVAFIDAEHALDP   97 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc----CCCEEEECccccHHH
Confidence            4567899999999997665555554432    457888876555543

RecA couples ATP hydrolysis to DNA strand exchange.

>PHA00350 putative assembly protein

Probab=95.32  E-value=0.29  Score=42.32  Aligned_cols=25  Identities=24%  Similarity=0.262  Sum_probs=18.2

Q ss_pred             EEEECCCCchHhHHHHH-HHHHHhcC
Q psy12977         52 IFACAPTGSGKTAAFLI-PIIHSLRG   76 (226)
Q Consensus        52 ~li~apTGsGKT~~~~~-~~~~~~~~   76 (226)
                      .++.|.+|||||...+- -++..++.
T Consensus         4 ~l~tG~pGSGKT~~aV~~~i~palk~   29 (399)
T PHA00350          4 YAIVGRPGSYKSYEAVVYHIIPALKD   29 (399)
T ss_pred             EEEecCCCCchhHHHHHHHHHHHHHC
Confidence            47899999999987664 35555543

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=95.32  E-value=0.21  Score=47.54  Aligned_cols=18  Identities=28%  Similarity=0.298  Sum_probs=15.5

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      .+.++.||+|+|||...-
T Consensus       209 ~n~lLvG~pGvGKTal~~  226 (852)
T TIGR03345       209 NNPILTGEAGVGKTAVVE  226 (852)
T ss_pred             CceeEECCCCCCHHHHHH
Confidence            579999999999998653

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.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=95.29  E-value=0.18  Score=42.30  Aligned_cols=41  Identities=15%  Similarity=0.172  Sum_probs=28.4

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      ....+++||||+|.|...    ....+.++++.- + ++.+++.|..
T Consensus       122 ~~~~kVvII~~ae~m~~~----aaNaLLK~LEEP-p-~~~fILi~~~  162 (314)
T PRK07399        122 EAPRKVVVIEDAETMNEA----AANALLKTLEEP-G-NGTLILIAPS  162 (314)
T ss_pred             cCCceEEEEEchhhcCHH----HHHHHHHHHhCC-C-CCeEEEEECC
Confidence            357889999999998765    556666677664 3 5556665543

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.29  E-value=0.38  Score=45.16  Aligned_cols=20  Identities=25%  Similarity=0.411  Sum_probs=16.5

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..++.+++.||+|+|||...
T Consensus       210 ~~~~giLL~GppGtGKT~la  229 (733)
T TIGR01243       210 EPPKGVLLYGPPGTGKTLLA  229 (733)
T ss_pred             CCCceEEEECCCCCChHHHH
Confidence            34578999999999999753

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.

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=95.19  E-value=0.048  Score=53.96  Aligned_cols=124  Identities=17%  Similarity=0.133  Sum_probs=73.1

Q ss_pred             CCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEE
Q psy12977         36 FEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVI  115 (226)
Q Consensus        36 ~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  115 (226)
                      +|+-|..+.. ..+++++|.|..|||||....--++..+... ..-.++++++-|+.-+..+.+.+.+.....-..    
T Consensus         2 ~t~~Q~~ai~-~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~-~~~~~il~~tFt~~aa~e~~~ri~~~l~~~~~~----   75 (1232)
T TIGR02785         2 WTDEQWQAIY-TRGQNILVSASAGSGKTAVLVERIIKKILRG-VDIDRLLVVTFTNAAAREMKERIEEALQKALQQ----   75 (1232)
T ss_pred             CCHHHHHHHh-CCCCCEEEEecCCCcHHHHHHHHHHHHHhcC-CCHhhEEEEeccHHHHHHHHHHHHHHHHHHHhc----
Confidence            4666655554 4678999999999999998766666666433 222479999999999998888777664321110    


Q ss_pred             ecchhhhhhhCCCcCCCCCEEEECchHHHHhHhc-CCCCCCCCCccEEEEccccc
Q psy12977        116 GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQM-DPPALNLANVEWLIVDESDK  169 (226)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~-~~~~~~~~~~~~lViDE~h~  169 (226)
                      ..   ......+.+..-...-|+|-..+...+-+ ....+++ +-.+=|.||...
T Consensus        76 ~p---~~~~L~~q~~~~~~~~i~Tihsf~~~~~~~~~~~l~l-dP~F~i~de~e~  126 (1232)
T TIGR02785        76 EP---NSKHLRRQLALLNTANISTLHSFCLKVIRKHYYLLDL-DPSFRILTDTEQ  126 (1232)
T ss_pred             Cc---hhHHHHHHHhhccCCeEeeHHHHHHHHHHHhhhhcCC-CCCceeCCHHHH
Confidence            00   00111111122234568888887654433 2122221 123456887774

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.

>PRK09354 recA recombinase A; Provisional

Probab=95.18  E-value=0.16  Score=43.05  Aligned_cols=43  Identities=28%  Similarity=0.344  Sum_probs=30.6

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAK   95 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~   95 (226)
                      |+-+.+.+|+|+|||...+..+.+....    +.+++|+-.-.++-.
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~~----G~~~~yId~E~s~~~  102 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQKA----GGTAAFIDAEHALDP  102 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc----CCcEEEECCccchHH
Confidence            4567899999999998766555555432    557888876665554

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.18  E-value=0.45  Score=42.43  Aligned_cols=19  Identities=32%  Similarity=0.415  Sum_probs=15.0

Q ss_pred             eEEEECCCCchHhHHHHHH
Q psy12977         51 QIFACAPTGSGKTAAFLIP   69 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~   69 (226)
                      -.++.||+|+|||....+-
T Consensus        40 ayLf~Gp~G~GKTtlAr~l   58 (486)
T PRK14953         40 AYIFAGPRGTGKTTIARIL   58 (486)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3578999999999765543

>CHL00176 ftsH cell division protein; Validated

Probab=95.14  E-value=0.51  Score=43.48  Aligned_cols=18  Identities=28%  Similarity=0.508  Sum_probs=15.3

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      +.+++.||+|+|||...-
T Consensus       217 ~gVLL~GPpGTGKT~LAr  234 (638)
T CHL00176        217 KGVLLVGPPGTGKTLLAK  234 (638)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            469999999999997643

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=95.14  E-value=0.2  Score=42.42  Aligned_cols=41  Identities=12%  Similarity=0.015  Sum_probs=28.6

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      ....+.+|||++|.|...    ....+.++++. |++++-+++.|.
T Consensus       106 ~g~~kV~iI~~ae~m~~~----AaNaLLKtLEE-Pp~~t~fiL~t~  146 (334)
T PRK07993        106 LGGAKVVWLPDAALLTDA----AANALLKTLEE-PPENTWFFLACR  146 (334)
T ss_pred             cCCceEEEEcchHhhCHH----HHHHHHHHhcC-CCCCeEEEEEEC
Confidence            457889999999999876    55566666665 455556666554

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=95.10  E-value=0.14  Score=43.21  Aligned_cols=18  Identities=28%  Similarity=0.434  Sum_probs=15.5

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      .++++.||+|+|||....
T Consensus        52 ~~~ll~GppG~GKT~la~   69 (328)
T PRK00080         52 DHVLLYGPPGLGKTTLAN   69 (328)
T ss_pred             CcEEEECCCCccHHHHHH
Confidence            579999999999998654

>CHL00195 ycf46 Ycf46; Provisional

Probab=95.09  E-value=0.16  Score=45.24  Aligned_cols=19  Identities=21%  Similarity=0.331  Sum_probs=16.0

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      ..+.+++.||+|+|||...
T Consensus       258 ~pkGILL~GPpGTGKTllA  276 (489)
T CHL00195        258 TPRGLLLVGIQGTGKSLTA  276 (489)
T ss_pred             CCceEEEECCCCCcHHHHH
Confidence            3477999999999999754

>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold

Probab=95.09  E-value=0.061  Score=46.82  Aligned_cols=59  Identities=15%  Similarity=0.235  Sum_probs=47.9

Q ss_pred             hHhcCCCCCCCCCccE-EEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        146 LLQMDPPALNLANVEW-LIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       146 ~~~~~~~~~~~~~~~~-lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      ++...++.=++++-++ +.+||||.+++.....+.+.+.++.+.+.++.+-++++|.++.
T Consensus       242 Lfe~LPEvGD~dkPklVfFfDEAHLLF~da~kall~~ieqvvrLIRSKGVGv~fvTQ~P~  301 (502)
T PF05872_consen  242 LFEQLPEVGDLDKPKLVFFFDEAHLLFNDAPKALLDKIEQVVRLIRSKGVGVYFVTQNPT  301 (502)
T ss_pred             HHHhCccCCCCCCceEEEEEechhhhhcCCCHHHHHHHHHHHHHhhccCceEEEEeCCCC
Confidence            3345566666777776 5599999999887778999999999999889999999998843

This family is restricted to bacterial proteins, none of which have currently been characterised.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.06  E-value=0.031  Score=47.18  Aligned_cols=43  Identities=21%  Similarity=0.206  Sum_probs=30.3

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELA   94 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~   94 (226)
                      ..+++++++|+||||||.. +-.++..+..    ..+++.+-.+.|+.
T Consensus       158 ~~~~nili~G~tgSGKTTl-l~aL~~~ip~----~~ri~tiEd~~El~  200 (332)
T PRK13900        158 ISKKNIIISGGTSTGKTTF-TNAALREIPA----IERLITVEDAREIV  200 (332)
T ss_pred             HcCCcEEEECCCCCCHHHH-HHHHHhhCCC----CCeEEEecCCCccc
Confidence            4578999999999999974 4556666542    34677765665553

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=94.99  E-value=0.29  Score=41.51  Aligned_cols=42  Identities=14%  Similarity=0.065  Sum_probs=28.2

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      ....+++|||++|.|...    ....+.++++. |++++-+++.|..
T Consensus       130 ~~~~kV~iI~~ae~m~~~----AaNaLLKtLEE-Pp~~t~fiL~t~~  171 (342)
T PRK06964        130 RGGARVVVLYPAEALNVA----AANALLKTLEE-PPPGTVFLLVSAR  171 (342)
T ss_pred             cCCceEEEEechhhcCHH----HHHHHHHHhcC-CCcCcEEEEEECC
Confidence            456789999999999776    55556666665 3455555555433

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=94.96  E-value=0.62  Score=36.71  Aligned_cols=64  Identities=11%  Similarity=-0.003  Sum_probs=37.2

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee---CchhHHHHHHHhcCCCeE
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT---HTEDVAKWCRRKLKRRVQ  220 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT---~~~~~~~~~~~~~~~p~~  220 (226)
                      ..+-+.+|+|-...+.-.+......+....++.+ ...-+++++|+.   +++++.-.++....-.+.
T Consensus       121 ~~~~dViIIDSls~~~~~~~~~~vl~fm~~~r~l-~d~gKvIilTvhp~~l~e~~~~rirs~~d~~l~  187 (235)
T COG2874         121 RWEKDVIIIDSLSAFATYDSEDAVLNFMTFLRKL-SDLGKVIILTVHPSALDEDVLTRIRSACDVYLR  187 (235)
T ss_pred             hhcCCEEEEecccHHhhcccHHHHHHHHHHHHHH-HhCCCEEEEEeChhhcCHHHHHHHHHhhheeEE
Confidence            5677899999999776553111222222333334 346688888887   456665555554433333

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=94.93  E-value=0.14  Score=40.75  Aligned_cols=44  Identities=20%  Similarity=0.042  Sum_probs=27.4

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCC--CCCCceEEEEccc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGP--KNLGFRAVIVCPT   90 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~--~~~~~~~iil~Pt   90 (226)
                      ..|.-+.+.||+|+|||...+..+.......  ...+.+++++..-
T Consensus        17 ~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e   62 (235)
T cd01123          17 ETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTE   62 (235)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCC
Confidence            3567789999999999976554444433211  1113478887643

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=94.93  E-value=0.92  Score=36.27  Aligned_cols=56  Identities=14%  Similarity=0.102  Sum_probs=31.0

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhc--------CCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLR--------GPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~--------~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      -.++.||+|+|||...+--++....        .....+.+++|+.- .+=..++.+.+..+...
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~~-Ed~~~~i~~Rl~~i~~~   66 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSA-EDPREEIHRRLEAILQH   66 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEEC-CCCHHHHHHHHHHHHhh
Confidence            3579999999999865544443321        11223457788762 22223444455555443

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.

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=94.93  E-value=0.35  Score=40.63  Aligned_cols=42  Identities=21%  Similarity=0.156  Sum_probs=29.6

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      ....+++||||+|.|...    ....+.++++.= ++++.+++.|..
T Consensus       111 ~g~~kV~iI~~ae~m~~~----AaNaLLKtLEEP-p~~~~fiL~~~~  152 (319)
T PRK08769        111 YGIAQVVIVDPADAINRA----ACNALLKTLEEP-SPGRYLWLISAQ  152 (319)
T ss_pred             cCCcEEEEeccHhhhCHH----HHHHHHHHhhCC-CCCCeEEEEECC
Confidence            346789999999999765    555666677663 556667766543

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=94.85  E-value=0.093  Score=39.39  Aligned_cols=30  Identities=17%  Similarity=0.336  Sum_probs=21.1

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHH
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYA  187 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~  187 (226)
                      ..-|++|+||.--|--. .+.|...+..++.
T Consensus        99 ~~aDvIIIDEIGpMElk-s~~f~~~ve~vl~  128 (179)
T COG1618          99 EEADVIIIDEIGPMELK-SKKFREAVEEVLK  128 (179)
T ss_pred             hcCCEEEEecccchhhc-cHHHHHHHHHHhc
Confidence            34689999999866321 1268888888874

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=94.83  E-value=0.44  Score=37.24  Aligned_cols=59  Identities=12%  Similarity=0.125  Sum_probs=32.9

Q ss_pred             CchHHHHhHhcCCCCCCCCCccEEEEccccccc-cc-CccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        139 TPNKLVYLLQMDPPALNLANVEWLIVDESDKLF-EA-GVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       139 Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~-~~-~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      +...+.+.+......      -++|+||+|.+. .. ....+...+..+...........++++++-
T Consensus       105 ~l~~~~~~l~~~~~~------~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~v~~~S~  165 (234)
T PF01637_consen  105 ALERLLEKLKKKGKK------VIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNVSIVITGSS  165 (234)
T ss_dssp             -HHHHHHHHHHCHCC------EEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTEEEEEEESS
T ss_pred             HHHHHHHHHHhcCCc------EEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCceEEEECCc
Confidence            445555555542121      599999999998 21 123567777777777434444444456664

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=94.83  E-value=0.026  Score=47.36  Aligned_cols=61  Identities=23%  Similarity=0.117  Sum_probs=39.2

Q ss_pred             ccccCCCCccccc-ccCCCC-CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         31 SIFKHFEPHFTIT-YLSPLG-RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        31 ~~~~~~~~~Q~~~-~~~~~~-~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      -.|+.+++-|... +.+..+ .|++++|.||||||.. +..+...+.    ...|+|.+-.|-||-.+
T Consensus       153 i~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl-LNal~~~i~----~~eRvItiEDtaELql~  215 (355)
T COG4962         153 IIFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL-LNALSGFID----SDERVITIEDTAELQLA  215 (355)
T ss_pred             HHcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH-HHHHHhcCC----CcccEEEEeehhhhccC
Confidence            3566777766333 444444 5999999999999974 233333333    23388998888777544

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=94.79  E-value=0.09  Score=48.50  Aligned_cols=51  Identities=25%  Similarity=0.315  Sum_probs=39.6

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      ++.++.|.||||||+.... ++...      +..++|++|++.+|.|.++.++.+.+.
T Consensus        30 ~~~~l~Gvtgs~kt~~~a~-~~~~~------~~p~Lvi~~n~~~A~ql~~el~~f~p~   80 (655)
T TIGR00631        30 KHQTLLGVTGSGKTFTMAN-VIAQV------NRPTLVIAHNKTLAAQLYNEFKEFFPE   80 (655)
T ss_pred             CcEEEECCCCcHHHHHHHH-HHHHh------CCCEEEEECCHHHHHHHHHHHHHhCCC
Confidence            3567999999999986543 33322      235899999999999999999999753

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

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=94.76  E-value=0.077  Score=48.04  Aligned_cols=111  Identities=18%  Similarity=0.148  Sum_probs=65.6

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHH-HHHHHHhhcCCCeEEEEec---chhhhhhh
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTY-NETVRLSEGLGLRAHVIGK---IQQAAEKF  125 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~-~~~~~~~~~~~~~~~~~~~---~~~~~~~~  125 (226)
                      +.+.+..++-+|||...+..+...+...+   .-++++.||.+.+.+.. +.+..+.+....--..+..   ........
T Consensus        34 ~~Vv~~k~aQ~GkT~~~~n~~g~~i~~~P---~~~l~v~Pt~~~a~~~~~~rl~Pmi~~sp~l~~~~~~~~~~~~~~t~~  110 (557)
T PF05876_consen   34 REVVVMKSAQVGKTELLLNWIGYSIDQDP---GPMLYVQPTDDAAKDFSKERLDPMIRASPVLRRKLSPSKSRDSGNTIL  110 (557)
T ss_pred             cEEEEEEcchhhHhHHHHhhceEEEEeCC---CCEEEEEEcHHHHHHHHHHHHHHHHHhCHHHHHHhCchhhcccCCchh
Confidence            57899999999999966555545554332   25899999999999976 4566665543321111111   11111111


Q ss_pred             CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccc
Q psy12977        126 GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFE  172 (226)
Q Consensus       126 ~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~  172 (226)
                      ..... +..+.++..+.        +..+.-..++++++||+|...+
T Consensus       111 ~k~f~-gg~l~~~ga~S--------~~~l~s~~~r~~~~DEvD~~p~  148 (557)
T PF05876_consen  111 YKRFP-GGFLYLVGANS--------PSNLRSRPARYLLLDEVDRYPD  148 (557)
T ss_pred             heecC-CCEEEEEeCCC--------CcccccCCcCEEEEechhhccc
Confidence            11122 34455544332        1344455788999999998854

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 [].

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=94.76  E-value=0.23  Score=40.81  Aligned_cols=40  Identities=25%  Similarity=0.311  Sum_probs=26.1

Q ss_pred             chHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        140 PNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       140 p~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      |+-+..++..      +..=|.+.+||.|++...    ..+.+.-.++.+
T Consensus        91 ~gDlaaiLt~------Le~~DVLFIDEIHrl~~~----vEE~LYpaMEDf  130 (332)
T COG2255          91 PGDLAAILTN------LEEGDVLFIDEIHRLSPA----VEEVLYPAMEDF  130 (332)
T ss_pred             hhhHHHHHhc------CCcCCeEEEehhhhcChh----HHHHhhhhhhhe
Confidence            4555555554      666789999999998654    444555555544

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=94.74  E-value=0.051  Score=45.67  Aligned_cols=46  Identities=30%  Similarity=0.354  Sum_probs=31.2

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHH
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTREL   93 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L   93 (226)
                      ...++++++.|+||||||. ++-.++..+.. .....+++++-.+.|+
T Consensus       145 v~~~~~ilI~G~tGSGKTT-ll~aL~~~~~~-~~~~~rivtIEd~~El  190 (319)
T PRK13894        145 VRAHRNILVIGGTGSGKTT-LVNAIINEMVI-QDPTERVFIIEDTGEI  190 (319)
T ss_pred             HHcCCeEEEECCCCCCHHH-HHHHHHHhhhh-cCCCceEEEEcCCCcc
Confidence            3467899999999999995 44555554321 1123477887777766

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=94.74  E-value=0.49  Score=36.65  Aligned_cols=106  Identities=17%  Similarity=0.138  Sum_probs=61.8

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPR  128 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (226)
                      ++=.++.+|=.||||...+-.+..    ....+.++++..|...---+            ...+....|.          
T Consensus         4 g~l~~i~gpM~SGKT~eLl~r~~~----~~~~g~~v~vfkp~iD~R~~------------~~~V~Sr~G~----------   57 (201)
T COG1435           4 GWLEFIYGPMFSGKTEELLRRARR----YKEAGMKVLVFKPAIDTRYG------------VGKVSSRIGL----------   57 (201)
T ss_pred             EEEEEEEccCcCcchHHHHHHHHH----HHHcCCeEEEEecccccccc------------cceeeeccCC----------
Confidence            344678999999999864443333    23346688888876432110            1111111111          


Q ss_pred             cCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        129 SAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       129 ~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                        +..-++|-.+..+...+...+.   ...++++.||||+-+.+.    ....+.++...+
T Consensus        58 --~~~A~~i~~~~~i~~~i~~~~~---~~~~~~v~IDEaQF~~~~----~v~~l~~lad~l  109 (201)
T COG1435          58 --SSEAVVIPSDTDIFDEIAALHE---KPPVDCVLIDEAQFFDEE----LVYVLNELADRL  109 (201)
T ss_pred             --cccceecCChHHHHHHHHhccc---CCCcCEEEEehhHhCCHH----HHHHHHHHHhhc
Confidence              1223666677777777765322   223899999999965443    666666666543

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=94.73  E-value=0.024  Score=44.95  Aligned_cols=15  Identities=33%  Similarity=0.494  Sum_probs=12.8

Q ss_pred             EEEECCCCchHhHHH
Q psy12977         52 IFACAPTGSGKTAAF   66 (226)
Q Consensus        52 ~li~apTGsGKT~~~   66 (226)
                      ++|.|++|+|||...
T Consensus         1 ~vv~G~pGsGKSt~i   15 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLI   15 (234)
T ss_pred             CEEEcCCCCCHHHHH
Confidence            478999999999854

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

>PHA00012 I assembly protein

Probab=94.64  E-value=0.28  Score=41.15  Aligned_cols=61  Identities=13%  Similarity=0.092  Sum_probs=35.6

Q ss_pred             CCCCccEEEEcccccccccCc--cchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcC
Q psy12977        155 NLANVEWLIVDESDKLFEAGV--RGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLK  216 (226)
Q Consensus       155 ~~~~~~~lViDE~h~l~~~~~--~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~  216 (226)
                      +...-.++|+||||..+....  ......+...+......+.=++++|..+ ..+...+++.+.
T Consensus        78 dep~gsLlVlDEaq~~fp~R~~~sk~p~~vie~l~~hRh~G~DvilITQ~p-s~VDs~IR~ll~  140 (361)
T PHA00012         78 DESKNGLLVLDECGTWFNSRSWNDKERQPVIDWFLHARKLGWDIIFIIQDI-SIMDKQAREALA  140 (361)
T ss_pred             CCCCCcEEEEECcccccCCCCcCcCCcHHHHHHHHHhccCCceEEEEcCCH-HHHhHHHHHhhh
Confidence            345667999999999876421  0122334444444434566677766553 466666655443

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=94.63  E-value=0.18  Score=44.06  Aligned_cols=39  Identities=21%  Similarity=0.051  Sum_probs=25.0

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVC   88 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~   88 (226)
                      ..|.-+++.|+||+|||...+--+.+....   .+..+++++
T Consensus       192 ~~g~liviag~pg~GKT~~al~ia~~~a~~---~g~~v~~fS  230 (421)
T TIGR03600       192 VKGDLIVIGARPSMGKTTLALNIAENVALR---EGKPVLFFS  230 (421)
T ss_pred             CCCceEEEEeCCCCCHHHHHHHHHHHHHHh---CCCcEEEEE
Confidence            345668899999999998655444444322   133566665

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=94.61  E-value=0.042  Score=44.83  Aligned_cols=42  Identities=29%  Similarity=0.361  Sum_probs=30.1

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTREL   93 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L   93 (226)
                      .+.++++.|+||||||... ..++..+...   ..+++.+-.+.|+
T Consensus       126 ~~~~ili~G~tGSGKTT~l-~all~~i~~~---~~~iv~iEd~~E~  167 (270)
T PF00437_consen  126 GRGNILISGPTGSGKTTLL-NALLEEIPPE---DERIVTIEDPPEL  167 (270)
T ss_dssp             TTEEEEEEESTTSSHHHHH-HHHHHHCHTT---TSEEEEEESSS-S
T ss_pred             cceEEEEECCCccccchHH-HHHhhhcccc---ccceEEeccccce
Confidence            4789999999999999854 5566666532   3477777766655

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 ....

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.60  E-value=2.2  Score=35.88  Aligned_cols=57  Identities=16%  Similarity=0.218  Sum_probs=32.5

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhc----C-CCCceEEEEeeeCchhHHHHHHHhc
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC----S-GPNLKRGMFSATHTEDVAKWCRRKL  215 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~----~-~~~~q~v~~SAT~~~~~~~~~~~~~  215 (226)
                      .+.+++++|=+-++....  .....+..+.+..    + .+..-++.++||...+....+..+.
T Consensus       195 ~~~D~ViIDTaGr~~~~~--~l~~eL~~~~~v~~~~~~~~p~~~~LVl~a~~g~~~~~~a~~f~  256 (318)
T PRK10416        195 RGIDVLIIDTAGRLHNKT--NLMEELKKIKRVIKKADPDAPHEVLLVLDATTGQNALSQAKAFH  256 (318)
T ss_pred             CCCCEEEEeCCCCCcCCH--HHHHHHHHHHHHHhhhcCCCCceEEEEEECCCChHHHHHHHHHH
Confidence            467899999887664321  3555666655432    1 1333467778886554433444443

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=94.59  E-value=0.24  Score=44.21  Aligned_cols=56  Identities=16%  Similarity=0.105  Sum_probs=31.3

Q ss_pred             CccEEEEcccccccccCccch----HHHHHHHHHhcC--CCCceEEEEeee-CchhHHHHHHH
Q psy12977        158 NVEWLIVDESDKLFEAGVRGF----RDQLAVIYAACS--GPNLKRGMFSAT-HTEDVAKWCRR  213 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~----~~~i~~i~~~~~--~~~~q~v~~SAT-~~~~~~~~~~~  213 (226)
                      .-..+.+||+|.+......+.    ...+..++..+.  .....++++.|| .|..+...+.+
T Consensus       335 ~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR  397 (494)
T COG0464         335 APSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLR  397 (494)
T ss_pred             CCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcc
Confidence            446899999998876532111    244445544441  334456666777 44444544444

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=94.56  E-value=0.52  Score=42.10  Aligned_cols=17  Identities=29%  Similarity=0.579  Sum_probs=15.0

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +.+++.||+|+|||...
T Consensus        89 ~giLL~GppGtGKT~la  105 (495)
T TIGR01241        89 KGVLLVGPPGTGKTLLA  105 (495)
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            57999999999999764

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.

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.56  E-value=0.017  Score=48.02  Aligned_cols=21  Identities=38%  Similarity=0.384  Sum_probs=17.7

Q ss_pred             CCCCeEEEECCCCchHhHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~   67 (226)
                      ++..|+++.+|||||||+.+.
T Consensus        95 L~KSNILLiGPTGsGKTlLAq  115 (408)
T COG1219          95 LSKSNILLIGPTGSGKTLLAQ  115 (408)
T ss_pred             eeeccEEEECCCCCcHHHHHH
Confidence            456789999999999998654

>PRK05748 replicative DNA helicase; Provisional

Probab=94.56  E-value=0.18  Score=44.40  Aligned_cols=50  Identities=18%  Similarity=-0.006  Sum_probs=29.0

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET  101 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~  101 (226)
                      .|.-+++.|+||+|||...+--+.+....   .+..++++ ....-..|+...+
T Consensus       202 ~G~livIaarpg~GKT~~al~ia~~~a~~---~g~~v~~f-SlEms~~~l~~R~  251 (448)
T PRK05748        202 PNDLIIVAARPSVGKTAFALNIAQNVATK---TDKNVAIF-SLEMGAESLVMRM  251 (448)
T ss_pred             CCceEEEEeCCCCCchHHHHHHHHHHHHh---CCCeEEEE-eCCCCHHHHHHHH
Confidence            34568899999999998655444443322   13345555 3334444554444

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=94.51  E-value=0.65  Score=39.18  Aligned_cols=40  Identities=8%  Similarity=0.105  Sum_probs=27.4

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ....+.+|+|++|.+...    ....+.+.++.. +..+.+++.|
T Consensus       111 ~~~~kV~iiEp~~~Ld~~----a~naLLk~LEep-~~~~~~Ilvt  150 (325)
T PRK08699        111 RGGLRVILIHPAESMNLQ----AANSLLKVLEEP-PPQVVFLLVS  150 (325)
T ss_pred             cCCceEEEEechhhCCHH----HHHHHHHHHHhC-cCCCEEEEEe
Confidence            356789999999988655    666666777776 3445555543

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=94.51  E-value=0.12  Score=46.73  Aligned_cols=31  Identities=16%  Similarity=0.215  Sum_probs=24.4

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      +.+-+.+++||+-.-+|.   .....+.+.+...
T Consensus       485 l~~~~illLDEpts~LD~---~~~~~i~~~L~~~  515 (571)
T TIGR02203       485 LKDAPILILDEATSALDN---ESERLVQAALERL  515 (571)
T ss_pred             hcCCCEEEEeCccccCCH---HHHHHHHHHHHHH
Confidence            556689999999988887   5777777766666

This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.

>PRK06904 replicative DNA helicase; Validated

Probab=94.47  E-value=0.19  Score=44.58  Aligned_cols=147  Identities=15%  Similarity=0.002  Sum_probs=66.4

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEec---chhhhhh
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGK---IQQAAEK  124 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~---~~~~~~~  124 (226)
                      .|.=+++.|.||.|||...+-.+.+....   .+..+++++ ...=.+|+...+-........... ..+   ......+
T Consensus       220 ~G~LiiIaarPg~GKTafalnia~~~a~~---~g~~Vl~fS-lEMs~~ql~~Rlla~~s~v~~~~i-~~g~~l~~~e~~~  294 (472)
T PRK06904        220 PSDLIIVAARPSMGKTTFAMNLCENAAMA---SEKPVLVFS-LEMPAEQIMMRMLASLSRVDQTKI-RTGQNLDQQDWAK  294 (472)
T ss_pred             CCcEEEEEeCCCCChHHHHHHHHHHHHHh---cCCeEEEEe-ccCCHHHHHHHHHHhhCCCCHHHh-ccCCCCCHHHHHH
Confidence            34557899999999998554333333322   133455553 333444554443333221111100 011   0000000


Q ss_pred             ---hCCCcCCCCCEEEE-----CchHHHHhHhcCCCCCCCCCccEEEEcccccccccCc-cchHHHHHHHHHhc----CC
Q psy12977        125 ---FGPRSAQKFDVLIT-----TPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGV-RGFRDQLAVIYAAC----SG  191 (226)
Q Consensus       125 ---~~~~~~~~~~IiV~-----Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~-~~~~~~i~~i~~~~----~~  191 (226)
                         ....+...+++.|-     |+..+....++...  ....++++|||-.+.+...+. .+....+..+.+.+    ..
T Consensus       295 ~~~a~~~l~~~~~l~I~d~~~~t~~~i~~~~r~~~~--~~~~~~lvvIDYLqli~~~~~~~~r~~ei~~isr~LK~lAke  372 (472)
T PRK06904        295 ISSTVGMFKQKPNLYIDDSSGLTPTELRSRARRVYR--ENGGLSLIMVDYLQLMRAPGFEDNRTLEIAEISRSLKALAKE  372 (472)
T ss_pred             HHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHH--hCCCCCEEEEecHHhcCCCCCCCcHHHHHHHHHHHHHHHHHH
Confidence               00111223445552     44555443332101  112578999999997753321 12222333333322    12


Q ss_pred             CCceEEEEee
Q psy12977        192 PNLKRGMFSA  201 (226)
Q Consensus       192 ~~~q~v~~SA  201 (226)
                      .++.++++|.
T Consensus       373 l~ipVi~lsQ  382 (472)
T PRK06904        373 LKVPVVALSQ  382 (472)
T ss_pred             hCCeEEEEEe
Confidence            4788888863

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=94.45  E-value=0.038  Score=47.60  Aligned_cols=56  Identities=29%  Similarity=0.390  Sum_probs=39.9

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEe
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIG  116 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~  116 (226)
                      ++++.||||+|||.++++|-+...      +..+|++=|--++........+..    |.++..++
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~------~~s~vv~D~Kge~~~~t~~~r~~~----G~~V~v~n   56 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTW------PGSVVVLDPKGENFELTSEHRRAL----GRKVFVFD   56 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcC------CCCEEEEccchhHHHHHHHHHHHc----CCeEEEEc
Confidence            478999999999999888855432      236888889989988776655443    44444443

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.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=94.41  E-value=0.21  Score=46.62  Aligned_cols=46  Identities=13%  Similarity=0.234  Sum_probs=37.4

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      ..+--++|+|+.|.+.+.   .....+.++++.. +++...++.|=+-|+
T Consensus       127 ~~~pl~LVlDDyHli~~~---~l~~~l~fLl~~~-P~~l~lvv~SR~rP~  172 (894)
T COG2909         127 YEGPLYLVLDDYHLISDP---ALHEALRFLLKHA-PENLTLVVTSRSRPQ  172 (894)
T ss_pred             hcCceEEEeccccccCcc---cHHHHHHHHHHhC-CCCeEEEEEeccCCC
Confidence            334469999999999888   6888999999888 678888888877553

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=94.38  E-value=0.055  Score=46.18  Aligned_cols=17  Identities=18%  Similarity=0.110  Sum_probs=14.4

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +-+++.+|+|+|||+..
T Consensus       149 lgllL~GPPGcGKTllA  165 (413)
T PLN00020        149 LILGIWGGKGQGKSFQC  165 (413)
T ss_pred             eEEEeeCCCCCCHHHHH
Confidence            45789999999999864

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=94.33  E-value=0.38  Score=36.64  Aligned_cols=136  Identities=16%  Similarity=0.142  Sum_probs=66.3

Q ss_pred             EEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH-HHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcC
Q psy12977         52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE-LAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSA  130 (226)
Q Consensus        52 ~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~-L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  130 (226)
                      +.+-...|-|||.+++--++..+-.    +.+++++-=.+. ...--...++.+.   +........+            
T Consensus         6 i~vytG~GKGKTTAAlGlalRA~G~----G~rV~ivQFlKg~~~~GE~~~l~~l~---~~~~~~~g~~------------   66 (172)
T PF02572_consen    6 IQVYTGDGKGKTTAALGLALRAAGH----GMRVLIVQFLKGGRYSGELKALKKLP---NVEIERFGKG------------   66 (172)
T ss_dssp             EEEEESSSS-HHHHHHHHHHHHHCT----T--EEEEESS--SS--HHHHHHGGGT-----EEEE--TT------------
T ss_pred             EEEEeCCCCCchHHHHHHHHHHHhC----CCEEEEEEEecCCCCcCHHHHHHhCC---eEEEEEcCCc------------
Confidence            5567778999999887777776643    668888876665 2121122222221   2222221110            


Q ss_pred             CCCCEEEEC------chHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        131 QKFDVLITT------PNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       131 ~~~~IiV~T------p~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                          .+...      .....+.+......+.-...++||+||+-..++.+. -..+.+..+++.- ++..-+|+..-..|
T Consensus        67 ----f~~~~~~~~~~~~~~~~~~~~a~~~i~~~~~dlvILDEi~~a~~~gl-l~~~~v~~~l~~r-p~~~evVlTGR~~~  140 (172)
T PF02572_consen   67 ----FVWRMNEEEEDRAAAREGLEEAKEAISSGEYDLVILDEINYAVDYGL-LSEEEVLDLLENR-PESLEVVLTGRNAP  140 (172)
T ss_dssp             --------GGGHHHHHHHHHHHHHHHHHHTT-TT-SEEEEETHHHHHHTTS-S-HHHHHHHHHTS--TT-EEEEE-SS--
T ss_pred             ----ccccCCCcHHHHHHHHHHHHHHHHHHhCCCCCEEEEcchHHHhHCCC-ccHHHHHHHHHcC-CCCeEEEEECCCCC
Confidence                11111      112222222222344456899999999988777643 2445666666654 56778888777788


Q ss_pred             hhHHHHHH
Q psy12977        205 EDVAKWCR  212 (226)
Q Consensus       205 ~~~~~~~~  212 (226)
                      +++.+.+.
T Consensus       141 ~~l~e~AD  148 (172)
T PF02572_consen  141 EELIEAAD  148 (172)
T ss_dssp             HHHHHH-S
T ss_pred             HHHHHhCC
Confidence            88877663

5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins []. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [, ]. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1G64_A 1G5T_A 1G5R_A.

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=94.32  E-value=0.068  Score=47.25  Aligned_cols=57  Identities=30%  Similarity=0.531  Sum_probs=40.8

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEe
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIG  116 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~  116 (226)
                      .++++.||||||||.++++|.+-...     + -+|+.=|-.++........++.    +.++..+.
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~~~-----~-s~iV~D~KgEl~~~t~~~r~~~----G~~V~vld  101 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLNYP-----G-SMIVTDPKGELYEKTAGYRKKR----GYKVYVLD  101 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHhcc-----C-CEEEEECCCcHHHHHHHHHHHC----CCEEEEee
Confidence            47999999999999999988664321     1 5788888888887776655554    44554444

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

>TIGR00665 DnaB replicative DNA helicase

Probab=94.29  E-value=0.16  Score=44.51  Aligned_cols=51  Identities=20%  Similarity=0.031  Sum_probs=29.5

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETV  102 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~  102 (226)
                      .|.-+++.|+||+|||...+-.+.+.....   +..+++++ ...=..|+.+.+.
T Consensus       194 ~G~l~vi~g~pg~GKT~~~l~~a~~~a~~~---g~~vl~~S-lEm~~~~i~~R~~  244 (434)
T TIGR00665       194 PSDLIILAARPSMGKTAFALNIAENAAIKE---GKPVAFFS-LEMSAEQLAMRML  244 (434)
T ss_pred             CCeEEEEEeCCCCChHHHHHHHHHHHHHhC---CCeEEEEe-CcCCHHHHHHHHH
Confidence            345678999999999986554444444321   33455554 3334444444443

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.

>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=94.28  E-value=0.023  Score=43.22  Aligned_cols=44  Identities=23%  Similarity=0.209  Sum_probs=29.1

Q ss_pred             cCCCCCEEEECchHHHHhHhcCCC-CCCCCCccEEEEccccccccc
Q psy12977        129 SAQKFDVLITTPNKLVYLLQMDPP-ALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus       129 ~~~~~~IiV~Tp~~l~~~~~~~~~-~~~~~~~~~lViDE~h~l~~~  173 (226)
                      ....+||+|++...+++....... .+. .+-.+||+||||.+.+.
T Consensus       116 ~~~~adivi~~y~yl~~~~~~~~~~~~~-~~~~ivI~DEAHNL~~~  160 (174)
T PF06733_consen  116 LAKNADIVICNYNYLFDPSIRKSLFGID-LKDNIVIFDEAHNLEDA  160 (174)
T ss_dssp             CGGG-SEEEEETHHHHSHHHHHHHCT---CCCEEEEETTGGGCGGG
T ss_pred             hcccCCEEEeCHHHHhhHHHHhhhcccc-ccCcEEEEecccchHHH
Confidence            456789999999988865432111 122 34469999999999765

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.

>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional

Probab=94.25  E-value=0.096  Score=47.73  Aligned_cols=31  Identities=16%  Similarity=0.239  Sum_probs=24.4

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      +++-+++|+||+-.-+|.   .....+.+.+...
T Consensus       487 l~~~~iliLDEpts~LD~---~t~~~i~~~l~~~  517 (588)
T PRK13657        487 LKDPPILILDEATSALDV---ETEAKVKAALDEL  517 (588)
T ss_pred             hcCCCEEEEeCCccCCCH---HHHHHHHHHHHHH
Confidence            667789999999988887   5777777666665

>KOG0733|consensus

Probab=94.25  E-value=0.34  Score=43.87  Aligned_cols=56  Identities=20%  Similarity=0.112  Sum_probs=31.3

Q ss_pred             ccEEEEcccccccccCccchHHHHHHHHHhc-------CCC---CceEEEEeeeC-chhHHHHHHHh
Q psy12977        159 VEWLIVDESDKLFEAGVRGFRDQLAVIYAAC-------SGP---NLKRGMFSATH-TEDVAKWCRRK  214 (226)
Q Consensus       159 ~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~-------~~~---~~q~v~~SAT~-~~~~~~~~~~~  214 (226)
                      -.+++|||.|.+.........+.-++|..++       ..+   +..++...||- |+.+..-+++-
T Consensus       283 PcivFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g~~VlVIgATnRPDslDpaLRRa  349 (802)
T KOG0733|consen  283 PCIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEKTKGDPVLVIGATNRPDSLDPALRRA  349 (802)
T ss_pred             CeEEEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccccCCCCeEEEecCCCCcccCHHHhcc
Confidence            3589999999886542112222333333332       122   35688888994 44555555553

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=94.25  E-value=0.99  Score=34.79  Aligned_cols=145  Identities=16%  Similarity=0.105  Sum_probs=75.1

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHH-HHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTY-NETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      =+++...+|-|||.+.+-.++..+-.    |.++.|+.=.+-=-..=. ..+..+    +..+....-+..-.....   
T Consensus        30 li~V~TG~GKGKTTAAlG~alRa~Gh----G~rv~vvQFiKg~~~~GE~~~~~~~----~~~v~~~~~~~g~tw~~~---   98 (198)
T COG2109          30 LIIVFTGNGKGKTTAALGLALRALGH----GLRVGVVQFIKGGWKYGEEAALEKF----GLGVEFHGMGEGFTWETQ---   98 (198)
T ss_pred             eEEEEecCCCChhHHHHHHHHHHhcC----CCEEEEEEEeecCcchhHHHHHHhh----ccceeEEecCCceeCCCc---
Confidence            37788999999999887777776643    557777754332211111 122222    222222211100000000   


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHH
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAK  209 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~  209 (226)
                      ....|+  ......+....   ..+.-.+++++|+||.--.+..+.- -.+.+..+++.- ++..-+|+..-..|+++.+
T Consensus        99 ~~~~d~--~aa~~~w~~a~---~~l~~~~ydlviLDEl~~al~~g~l-~~eeV~~~l~~k-P~~~~vIiTGr~ap~~lie  171 (198)
T COG2109          99 DREADI--AAAKAGWEHAK---EALADGKYDLVILDELNYALRYGLL-PLEEVVALLKAR-PEHTHVIITGRGAPPELIE  171 (198)
T ss_pred             CcHHHH--HHHHHHHHHHH---HHHhCCCCCEEEEehhhHHHHcCCC-CHHHHHHHHhcC-CCCcEEEEECCCCCHHHHH
Confidence            000122  22222232222   2333447999999999977776432 345666666554 4556666655557777777


Q ss_pred             HHHH
Q psy12977        210 WCRR  213 (226)
Q Consensus       210 ~~~~  213 (226)
                      .+..
T Consensus       172 ~ADl  175 (198)
T COG2109         172 LADL  175 (198)
T ss_pred             HHHH
Confidence            6654

>KOG0652|consensus

Probab=94.23  E-value=0.25  Score=40.19  Aligned_cols=46  Identities=15%  Similarity=0.187  Sum_probs=28.2

Q ss_pred             CccEEEEccccccccc-------CccchHHHHHHHHHhc--CCCCceEEEEeeeC
Q psy12977        158 NVEWLIVDESDKLFEA-------GVRGFRDQLAVIYAAC--SGPNLKRGMFSATH  203 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~-------~~~~~~~~i~~i~~~~--~~~~~q~v~~SAT~  203 (226)
                      .-..+.+||.|.+...       +.+.....+..++.++  .++..++-...||.
T Consensus       264 aP~IIFIDElDAIGtKRfDSek~GDREVQRTMLELLNQLDGFss~~~vKviAATN  318 (424)
T KOG0652|consen  264 APTIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSDDRVKVIAATN  318 (424)
T ss_pred             CCeEEEEechhhhccccccccccccHHHHHHHHHHHHhhcCCCCccceEEEeecc
Confidence            4458899999987532       2445566666666665  23445555556773

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=94.21  E-value=0.57  Score=37.30  Aligned_cols=54  Identities=17%  Similarity=0.265  Sum_probs=39.9

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHH
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRR  213 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~  213 (226)
                      ..+-++++-||.=.-+|.   .....+..+++.+....-+.+++ +|..+++...+.+
T Consensus       158 ~~~P~iilADEPTgnLD~---~t~~~V~~ll~~~~~~~g~tii~-VTHd~~lA~~~dr  211 (226)
T COG1136         158 INNPKIILADEPTGNLDS---KTAKEVLELLRELNKERGKTIIM-VTHDPELAKYADR  211 (226)
T ss_pred             hcCCCeEEeeCccccCCh---HHHHHHHHHHHHHHHhcCCEEEE-EcCCHHHHHhCCE
Confidence            445679999999988887   57888888888874444456655 8888888776655

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=94.20  E-value=0.71  Score=38.58  Aligned_cols=40  Identities=10%  Similarity=0.065  Sum_probs=26.7

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ...-+++||||+|.+...    ....+...++.- ++.+.+++.+
T Consensus        91 ~~~~kv~iI~~ad~m~~~----a~naLLK~LEep-p~~t~~il~~  130 (313)
T PRK05564         91 EGDKKVIIIYNSEKMTEQ----AQNAFLKTIEEP-PKGVFIILLC  130 (313)
T ss_pred             cCCceEEEEechhhcCHH----HHHHHHHHhcCC-CCCeEEEEEe
Confidence            357789999999988665    455666666553 4555566544

>TIGR00602 rad24 checkpoint protein rad24

Probab=94.17  E-value=0.49  Score=43.50  Aligned_cols=20  Identities=30%  Similarity=0.615  Sum_probs=15.7

Q ss_pred             CCeEEEECCCCchHhHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~   68 (226)
                      ++-+++.||+|+|||..+-+
T Consensus       110 ~~illL~GP~GsGKTTl~~~  129 (637)
T TIGR00602       110 KRILLITGPSGCGKSTTIKI  129 (637)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            34489999999999986433

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

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=94.14  E-value=0.93  Score=37.54  Aligned_cols=42  Identities=12%  Similarity=0.021  Sum_probs=31.0

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      -...+++|||++|.|...    ....+.++++. |++++-+++.|..
T Consensus        93 e~~~kv~ii~~ad~mt~~----AaNaLLK~LEE-Pp~~~~fiL~~~~  134 (290)
T PRK05917         93 ESPYKIYIIHEADRMTLD----AISAFLKVLED-PPQHGVIILTSAK  134 (290)
T ss_pred             CCCceEEEEechhhcCHH----HHHHHHHHhhc-CCCCeEEEEEeCC
Confidence            456889999999999776    56667777766 4566777776555

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=94.11  E-value=0.13  Score=41.73  Aligned_cols=56  Identities=23%  Similarity=0.315  Sum_probs=39.1

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      ..|+.+++.|++|+|||....-.+...+..    +.+++++ .+.+-..++.+.+.++..+
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~----ge~vlyv-s~~e~~~~l~~~~~~~g~d   76 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYEGARE----GEPVLYV-STEESPEELLENARSFGWD   76 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHHHHhc----CCcEEEE-EecCCHHHHHHHHHHcCCC
Confidence            567889999999999998655555555543    4456665 5556777777777666433

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=94.11  E-value=0.082  Score=48.15  Aligned_cols=31  Identities=19%  Similarity=0.246  Sum_probs=24.8

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      +++-+.+++||+-.-+|.   .....+...+..+
T Consensus       501 l~~~~IliLDE~TSaLD~---~te~~i~~~l~~~  531 (588)
T PRK11174        501 LQPCQLLLLDEPTASLDA---HSEQLVMQALNAA  531 (588)
T ss_pred             hcCCCEEEEeCCccCCCH---HHHHHHHHHHHHH
Confidence            556789999999998888   5777777777666

>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=94.09  E-value=0.053  Score=43.99  Aligned_cols=145  Identities=14%  Similarity=0.075  Sum_probs=68.7

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcc---cHHHHHHHHHHHHHHhhcCCCeEEEEecc--hhhh
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCP---TRELAKQTYNETVRLSEGLGLRAHVIGKI--QQAA  122 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~P---t~~L~~q~~~~~~~~~~~~~~~~~~~~~~--~~~~  122 (226)
                      .|.=+++.|+||.|||...+-.+.+.....   +..++|++.   ..+++..+.......    ...-. ..+.  ..+.
T Consensus        18 ~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~---~~~vly~SlEm~~~~l~~R~la~~s~v----~~~~i-~~g~l~~~e~   89 (259)
T PF03796_consen   18 PGELTVIAARPGVGKTAFALQIALNAALNG---GYPVLYFSLEMSEEELAARLLARLSGV----PYNKI-RSGDLSDEEF   89 (259)
T ss_dssp             TT-EEEEEESTTSSHHHHHHHHHHHHHHTT---SSEEEEEESSS-HHHHHHHHHHHHHTS----THHHH-HCCGCHHHHH
T ss_pred             cCcEEEEEecccCCchHHHHHHHHHHHHhc---CCeEEEEcCCCCHHHHHHHHHHHhhcc----hhhhh-hccccCHHHH
Confidence            345678999999999987766666666532   346777764   234444333322111    10000 0000  0000


Q ss_pred             hhh---CCCcCCCCCEEEE----CchHHHHhHhcCCCCCCCCCccEEEEccccccccc-CccchHHHHHHHHHhc----C
Q psy12977        123 EKF---GPRSAQKFDVLIT----TPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA-GVRGFRDQLAVIYAAC----S  190 (226)
Q Consensus       123 ~~~---~~~~~~~~~IiV~----Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~-~~~~~~~~i~~i~~~~----~  190 (226)
                      ...   ...+....-.+..    |++.+.+.+...  ......++++|||-.|.+... ...+....+..+.+.+    .
T Consensus        90 ~~~~~~~~~l~~~~l~i~~~~~~~~~~i~~~i~~~--~~~~~~~~~v~IDyl~ll~~~~~~~~~~~~~~~i~~~Lk~lA~  167 (259)
T PF03796_consen   90 ERLQAAAEKLSDLPLYIEDTPSLTIDDIESKIRRL--KREGKKVDVVFIDYLQLLKSEDSSDNRRQEIGEISRELKALAK  167 (259)
T ss_dssp             HHHHHHHHHHHTSEEEEEESSS-BHHHHHHHHHHH--HHHSTTEEEEEEEEGGGSBTSCSSSCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhCcEEEECCCCCCHHHHHHHHHHH--HhhccCCCEEEechHHHhcCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            000   0001111112223    344555544431  111267899999999988653 2222333333332222    1


Q ss_pred             CCCceEEEEeee
Q psy12977        191 GPNLKRGMFSAT  202 (226)
Q Consensus       191 ~~~~q~v~~SAT  202 (226)
                      ..++.++++|..
T Consensus       168 ~~~i~vi~~sQl  179 (259)
T PF03796_consen  168 ELNIPVIALSQL  179 (259)
T ss_dssp             HHTSEEEEEEEB
T ss_pred             HcCCeEEEcccc
Confidence            236778877665

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 ....

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=94.05  E-value=0.14  Score=45.65  Aligned_cols=21  Identities=24%  Similarity=0.194  Sum_probs=16.3

Q ss_pred             CCCCCCccEEEEccccccccc
Q psy12977        153 ALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus       153 ~~~~~~~~~lViDE~h~l~~~  173 (226)
                      .-...+.+..||||+|.+.-.
T Consensus       114 ~P~~~ryKVyiIDEvHMLS~~  134 (515)
T COG2812         114 APSEGRYKVYIIDEVHMLSKQ  134 (515)
T ss_pred             CCccccceEEEEecHHhhhHH
Confidence            334678899999999977655

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=94.04  E-value=0.43  Score=40.01  Aligned_cols=54  Identities=6%  Similarity=-0.163  Sum_probs=30.3

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcC--CCCCCceEEEEcccHHH-HHHHHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRG--PKNLGFRAVIVCPTREL-AKQTYNETV  102 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~--~~~~~~~~iil~Pt~~L-~~q~~~~~~  102 (226)
                      |.-+.+.||+|+|||...+..++.....  ....+.+++|+.--... .+++.+..+
T Consensus        96 G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~~a~  152 (313)
T TIGR02238        96 MSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRAIAE  152 (313)
T ss_pred             CeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHHHHH
Confidence            4567899999999996544333332211  11234588888754322 344444333

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>TIGR00416 sms DNA repair protein RadA

Probab=94.00  E-value=0.47  Score=41.91  Aligned_cols=52  Identities=21%  Similarity=0.269  Sum_probs=32.9

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      .|.-+++.|++|+|||...+..+......    +.+++|+.. .+-..|+.....++
T Consensus        93 ~GsvilI~G~pGsGKTTL~lq~a~~~a~~----g~kvlYvs~-EEs~~qi~~ra~rl  144 (454)
T TIGR00416        93 PGSLILIGGDPGIGKSTLLLQVACQLAKN----QMKVLYVSG-EESLQQIKMRAIRL  144 (454)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHhc----CCcEEEEEC-cCCHHHHHHHHHHc
Confidence            35678999999999998655444443321    346888764 34456665544443

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>PF12846 AAA_10: AAA-like domain

Probab=93.97  E-value=0.11  Score=42.56  Aligned_cols=45  Identities=7%  Similarity=0.070  Sum_probs=31.3

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      ..-.++++||+|.+....  .....+..+.+...+.+.-+++.|.++
T Consensus       219 ~~~~~i~iDEa~~~~~~~--~~~~~~~~~~~~~Rk~g~~~~l~tQ~~  263 (304)
T PF12846_consen  219 GRPKIIVIDEAHNFLSNP--SGAEFLDELLREGRKYGVGLILATQSP  263 (304)
T ss_pred             CceEEEEeCCcccccccc--chhhhhhHHHHHHHhcCCEEEEeeCCH
Confidence            445688999999998764  455566666666655567777766664

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=93.96  E-value=0.64  Score=40.24  Aligned_cols=43  Identities=23%  Similarity=0.362  Sum_probs=27.0

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcc
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCP   89 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~P   89 (226)
                      ...++.++++.|+||+||++.+..  ++........+|.+-+-|-
T Consensus        97 ~ap~~~~vLi~GetGtGKel~A~~--iH~~s~r~~~~PFI~~NCa  139 (403)
T COG1221          97 YAPSGLPVLIIGETGTGKELFARL--IHALSARRAEAPFIAFNCA  139 (403)
T ss_pred             hCCCCCcEEEecCCCccHHHHHHH--HHHhhhcccCCCEEEEEHH
Confidence            335689999999999999986433  2233222134556655543

>PRK11176 lipid transporter ATP-binding/permease protein; Provisional

Probab=93.96  E-value=0.15  Score=46.32  Aligned_cols=41  Identities=15%  Similarity=0.175  Sum_probs=28.1

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      +.+-+++++||+-.-+|.   .....+.+.+..+ ..++-+++.|
T Consensus       496 l~~~~ililDEptsaLD~---~t~~~i~~~l~~~-~~~~tvI~Vt  536 (582)
T PRK11176        496 LRDSPILILDEATSALDT---ESERAIQAALDEL-QKNRTSLVIA  536 (582)
T ss_pred             HhCCCEEEEECccccCCH---HHHHHHHHHHHHH-hCCCEEEEEe
Confidence            556689999999998887   5666676666665 2344444443

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=93.87  E-value=0.14  Score=43.51  Aligned_cols=43  Identities=21%  Similarity=0.284  Sum_probs=27.8

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTREL   93 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L   93 (226)
                      .+..++++||||||||... ..++..+...  .+.+++.+-...|.
T Consensus       121 ~~g~ili~G~tGSGKTT~l-~al~~~i~~~--~~~~i~tiEdp~E~  163 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL-ASMIDYINKN--AAGHIITIEDPIEY  163 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH-HHHHHhhCcC--CCCEEEEEcCChhh
Confidence            4578999999999999854 4455555422  23356666555444

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=93.86  E-value=0.064  Score=47.22  Aligned_cols=26  Identities=38%  Similarity=0.574  Sum_probs=20.3

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcC
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRG   76 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~   76 (226)
                      .=+++.||||||||.. ++.++..+..
T Consensus       259 GliLvTGPTGSGKTTT-LY~~L~~ln~  284 (500)
T COG2804         259 GLILVTGPTGSGKTTT-LYAALSELNT  284 (500)
T ss_pred             eEEEEeCCCCCCHHHH-HHHHHHHhcC
Confidence            4578999999999985 4677777654

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=93.85  E-value=0.12  Score=48.04  Aligned_cols=31  Identities=13%  Similarity=0.183  Sum_probs=24.6

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      +.+-+++++||+=.-+|.   .....+.+.+..+
T Consensus       617 l~~p~iliLDE~Ts~LD~---~te~~i~~~l~~~  647 (694)
T TIGR03375       617 LRDPPILLLDEPTSAMDN---RSEERFKDRLKRW  647 (694)
T ss_pred             hcCCCEEEEeCCCCCCCH---HHHHHHHHHHHHH
Confidence            567789999999988887   5777777777666

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>KOG2170|consensus

Probab=93.79  E-value=0.17  Score=41.78  Aligned_cols=53  Identities=21%  Similarity=0.148  Sum_probs=39.1

Q ss_pred             ccEEEEcccccccccCccchHHHHHHHHHhcC------CCCceEEEEeeeCchhHHHHHHHhc
Q psy12977        159 VEWLIVDESDKLFEAGVRGFRDQLAVIYAACS------GPNLKRGMFSATHTEDVAKWCRRKL  215 (226)
Q Consensus       159 ~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~------~~~~q~v~~SAT~~~~~~~~~~~~~  215 (226)
                      =.++|+||+|.|..    +..+.++-.+.+.+      ..+.-++++|.+-.+++.+.+....
T Consensus       179 rslFIFDE~DKmp~----gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg~eI~~~aL~~~  237 (344)
T KOG2170|consen  179 RSLFIFDEVDKLPP----GLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGGSEIARIALENA  237 (344)
T ss_pred             CceEEechhhhcCH----hHHHHHhhhhccccccccccccceEEEEEcCCcchHHHHHHHHHH
Confidence            35999999998865    48888888887642      2456789999887777766655544

>PRK08506 replicative DNA helicase; Provisional

Probab=93.76  E-value=0.38  Score=42.70  Aligned_cols=49  Identities=20%  Similarity=0.126  Sum_probs=29.6

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET  101 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~  101 (226)
                      .|.-+++.|+||.|||...+-.+.+....    +..+++++ ...=..|+...+
T Consensus       191 ~G~LivIaarpg~GKT~fal~ia~~~~~~----g~~V~~fS-lEMs~~ql~~Rl  239 (472)
T PRK08506        191 KGDLIIIAARPSMGKTTLCLNMALKALNQ----DKGVAFFS-LEMPAEQLMLRM  239 (472)
T ss_pred             CCceEEEEcCCCCChHHHHHHHHHHHHhc----CCcEEEEe-CcCCHHHHHHHH
Confidence            34567899999999998665555554432    33566654 333444444443

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=93.75  E-value=0.19  Score=40.65  Aligned_cols=29  Identities=28%  Similarity=0.383  Sum_probs=21.1

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHHHHHhc
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPIIHSLR   75 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~~~~~~   75 (226)
                      +-.|..+++.||.|+|||.. +-.+++.+.
T Consensus        13 i~~Gqr~~I~G~~G~GKTTL-lr~I~n~l~   41 (249)
T cd01128          13 IGKGQRGLIVAPPKAGKTTL-LQSIANAIT   41 (249)
T ss_pred             cCCCCEEEEECCCCCCHHHH-HHHHHhccc
Confidence            46789999999999999963 233444443

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.

>KOG2228|consensus

Probab=93.74  E-value=0.89  Score=38.37  Aligned_cols=19  Identities=32%  Similarity=0.497  Sum_probs=15.8

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .+..+++.||-|+|||.-.
T Consensus        48 EsnsviiigprgsgkT~li   66 (408)
T KOG2228|consen   48 ESNSVIIIGPRGSGKTILI   66 (408)
T ss_pred             CCCceEEEccCCCCceEee
Confidence            3577999999999999653

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=93.72  E-value=0.064  Score=44.93  Aligned_cols=56  Identities=25%  Similarity=0.361  Sum_probs=38.5

Q ss_pred             ccCCCCcc-cccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHH
Q psy12977         33 FKHFEPHF-TITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTREL   93 (226)
Q Consensus        33 ~~~~~~~Q-~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L   93 (226)
                      ++.+++.| .+.+ .+..+++++++++||||||. ++.+++..+..    ..|.+.+-.+.++
T Consensus       125 ~gt~~~~~~ayL~~~ie~~~siii~G~t~sGKTt-~lnall~~Ip~----~~rivtIEdt~E~  182 (312)
T COG0630         125 YGTISPEQAAYLWLAIEARKSIIICGGTASGKTT-LLNALLDFIPP----EERIVTIEDTPEL  182 (312)
T ss_pred             cCCCCHHHHHHHHHHHHcCCcEEEECCCCCCHHH-HHHHHHHhCCc----hhcEEEEeccccc
Confidence            45556665 3334 66778999999999999997 45666666642    3367777666655

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=93.66  E-value=0.25  Score=41.96  Aligned_cols=42  Identities=14%  Similarity=-0.078  Sum_probs=25.4

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHH-hcC-CCCCCceEEEEccc
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHS-LRG-PKNLGFRAVIVCPT   90 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~-~~~-~~~~~~~~iil~Pt   90 (226)
                      |.-+.+.|++|+|||...+-.++.. +.. ....+.+++|+..-
T Consensus       126 G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE  169 (344)
T PLN03187        126 RCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTE  169 (344)
T ss_pred             CeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcC
Confidence            4557799999999996443333322 211 12223588888763

>TIGR02857 CydD thiol reductant ABC exporter, CydD subunit

Probab=93.65  E-value=0.17  Score=45.55  Aligned_cols=31  Identities=19%  Similarity=0.239  Sum_probs=23.7

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      +.+-+.+++||+-.-+|.   .....+.+.+..+
T Consensus       474 ~~~~~ililDE~ts~lD~---~~~~~i~~~l~~~  504 (529)
T TIGR02857       474 LRDAPLLLLDEPTAHLDA---ETEALVTEALRAL  504 (529)
T ss_pred             hcCCCEEEEeCcccccCH---HHHHHHHHHHHHh
Confidence            556789999999988887   5666776666666

Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=93.60  E-value=0.48  Score=34.81  Aligned_cols=48  Identities=13%  Similarity=0.084  Sum_probs=30.7

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHH
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKW  210 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~  210 (226)
                      ..+-+++++||.-.-+|.   .....+...++.+   +. .++++..-++.+..+
T Consensus        86 ~~~p~illlDEP~~~LD~---~~~~~l~~~l~~~---~~-til~~th~~~~~~~~  133 (144)
T cd03221          86 LENPNLLLLDEPTNHLDL---ESIEALEEALKEY---PG-TVILVSHDRYFLDQV  133 (144)
T ss_pred             hcCCCEEEEeCCccCCCH---HHHHHHHHHHHHc---CC-EEEEEECCHHHHHHh
Confidence            345679999999988877   4667777777666   22 455544444444443

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=93.56  E-value=0.15  Score=43.63  Aligned_cols=27  Identities=33%  Similarity=0.495  Sum_probs=20.4

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhc
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLR   75 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~   75 (226)
                      .+..++++||||||||... ..++..+.
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i~  159 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIRELA  159 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            4678999999999999754 45555553

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=93.55  E-value=0.12  Score=47.05  Aligned_cols=31  Identities=23%  Similarity=0.339  Sum_probs=24.2

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      +.+-+++++||+-.-+|.   .....+.+.++.+
T Consensus       492 l~~~~illlDEpts~LD~---~t~~~i~~~l~~~  522 (592)
T PRK10790        492 VQTPQILILDEATANIDS---GTEQAIQQALAAV  522 (592)
T ss_pred             HhCCCEEEEeCCcccCCH---HHHHHHHHHHHHH
Confidence            456689999999988887   5677777777666

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=93.50  E-value=0.28  Score=44.00  Aligned_cols=53  Identities=23%  Similarity=0.156  Sum_probs=35.0

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      ..|..+++.+++|+|||......+.+.+..    +.+++|++- .+-..++.+.+..+
T Consensus       271 ~~g~~~li~G~~G~GKT~l~~~~~~~~~~~----g~~~~yis~-e~~~~~i~~~~~~~  323 (509)
T PRK09302        271 FRGSIILVSGATGTGKTLLASKFAEAACRR----GERCLLFAF-EESRAQLIRNARSW  323 (509)
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHHHHhC----CCcEEEEEe-cCCHHHHHHHHHHc
Confidence            345778899999999998655545555442    446777754 34466666666555

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=93.43  E-value=1.4  Score=33.45  Aligned_cols=119  Identities=13%  Similarity=0.082  Sum_probs=61.8

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      ..+++.|++|||||.....- ....      +...+++......-.++.+.+......-+..                  
T Consensus         2 ~~ili~G~~~sGKS~~a~~l-~~~~------~~~~~~iat~~~~~~e~~~ri~~h~~~R~~~------------------   56 (170)
T PRK05800          2 MLILVTGGARSGKSRFAERL-AAQS------GLQVLYIATAQPFDDEMAARIAHHRQRRPAH------------------   56 (170)
T ss_pred             CEEEEECCCCccHHHHHHHH-HHHc------CCCcEeCcCCCCChHHHHHHHHHHHhcCCCC------------------
Confidence            35789999999999754332 2222      1245676665544444444443332111111                  


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccC---c--cchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG---V--RGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~---~--~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                          =..+-.|..+...+...     .+.-+.+++|-...+....   .  ..+...+..+.+.+......+++.|..
T Consensus        57 ----w~t~E~~~~l~~~i~~~-----~~~~~~VlID~Lt~~~~n~l~~~~~~~~~~~l~~li~~L~~~~~tvVlVs~E  125 (170)
T PRK05800         57 ----WQTVEEPLDLAELLRAD-----AAPGRCVLVDCLTTWVTNLLFEEGEEAIAAEIDALLAALQQLPAKIILVTNE  125 (170)
T ss_pred             ----CeEecccccHHHHHHhh-----cCCCCEEEehhHHHHHHHHhcccchHHHHHHHHHHHHHHHcCCCCEEEEEcC
Confidence                12334454455544320     1234478888777664321   0  123345555666664556677887776

>PRK08760 replicative DNA helicase; Provisional

Probab=93.41  E-value=0.46  Score=42.28  Aligned_cols=52  Identities=15%  Similarity=-0.042  Sum_probs=29.4

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVR  103 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~  103 (226)
                      .|.=+++.|+||.|||...+-.+.+.....   +..++|++ ...=..|+...+..
T Consensus       228 ~G~LivIaarPg~GKTafal~iA~~~a~~~---g~~V~~fS-lEMs~~ql~~Rl~a  279 (476)
T PRK08760        228 PTDLIILAARPAMGKTTFALNIAEYAAIKS---KKGVAVFS-MEMSASQLAMRLIS  279 (476)
T ss_pred             CCceEEEEeCCCCChhHHHHHHHHHHHHhc---CCceEEEe-ccCCHHHHHHHHHH
Confidence            345578999999999986655444443221   23455553 22333455444433

>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=93.40  E-value=0.38  Score=43.77  Aligned_cols=46  Identities=17%  Similarity=0.210  Sum_probs=31.5

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                      +.+-+++++||+-.-+|.   .....+.+.+..+. + .+.+++.+.-++.
T Consensus       491 l~~~~ililDE~ts~lD~---~t~~~i~~~l~~~~-~-~~tviiitHr~~~  536 (574)
T PRK11160        491 LHDAPLLLLDEPTEGLDA---ETERQILELLAEHA-Q-NKTVLMITHRLTG  536 (574)
T ss_pred             hcCCCEEEEeCCcccCCH---HHHHHHHHHHHHHc-C-CCEEEEEecChhH
Confidence            566789999999988887   57777777777662 2 3445444554433

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=93.40  E-value=0.43  Score=42.14  Aligned_cols=66  Identities=21%  Similarity=0.128  Sum_probs=47.6

Q ss_pred             CCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         37 EPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        37 ~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      ...|+.+ ...-.|+- .+.|-.|||||...+.-+......  ++..+.++.+-|+.|+.++.....+++
T Consensus       164 D~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~Kaa~lh~k--nPd~~I~~Tfftk~L~s~~r~lv~~F~  230 (660)
T COG3972         164 DTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAHKAAELHSK--NPDSRIAFTFFTKILASTMRTLVPEFF  230 (660)
T ss_pred             cchhheeeeecCCchh-hhhcccCCCchhHHHHHHHHHhcC--CCCceEEEEeehHHHHHHHHHHHHHHH
Confidence            4445433 34445554 688999999998776665555543  445599999999999999988877776

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=93.39  E-value=0.15  Score=46.61  Aligned_cols=59  Identities=25%  Similarity=0.207  Sum_probs=44.0

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEec
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGK  117 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~  117 (226)
                      ..++++.||||||||.++++|-+....      .-+||+=|--|+........++.    |.++..+.-
T Consensus       158 ~~hvLviapTgSGKg~g~VIPnLL~~~------~S~VV~DpKGEl~~~Ta~~R~~~----G~~V~vfdP  216 (606)
T PRK13897        158 FQHALLFAPTGSGKGVGFVIPNLLFWE------DSVVVHDIKLENYELTSGWREKQ----GQKVFVWEP  216 (606)
T ss_pred             CceEEEEcCCCCCcceEEehhhHHhCC------CCEEEEeCcHHHHHHHHHHHHHC----CCeEEEEeC
Confidence            357899999999999999999766542      24788889999988877666554    555555543

>cd03239 ABC_SMC_head The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms

Probab=93.37  E-value=0.26  Score=37.73  Aligned_cols=41  Identities=10%  Similarity=0.146  Sum_probs=28.0

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      .+-+++++||...-+|.   .....+...+..+...+.++++.|
T Consensus       115 ~~p~llilDEp~~~LD~---~~~~~i~~~L~~~~~~g~tiIiiS  155 (178)
T cd03239         115 KPSPFYVLDEIDAALDP---TNRRRVSDMIKEMAKHTSQFIVIT  155 (178)
T ss_pred             CCCCEEEEECCCCCCCH---HHHHHHHHHHHHHHhCCCEEEEEE
Confidence            56689999999988887   455666666665533345666643

SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=93.35  E-value=0.15  Score=39.70  Aligned_cols=39  Identities=21%  Similarity=0.352  Sum_probs=23.4

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE   92 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~   92 (226)
                      -+++.||||||||... ..++..+...  .+.+++.+....+
T Consensus         3 lilI~GptGSGKTTll-~~ll~~~~~~--~~~~i~t~e~~~E   41 (198)
T cd01131           3 LVLVTGPTGSGKSTTL-AAMIDYINKN--KTHHILTIEDPIE   41 (198)
T ss_pred             EEEEECCCCCCHHHHH-HHHHHHhhhc--CCcEEEEEcCCcc
Confidence            4689999999999864 4445554322  2235555544333

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PLN03232 ABC transporter C family member; Provisional

Probab=93.31  E-value=0.15  Score=51.47  Aligned_cols=31  Identities=13%  Similarity=0.130  Sum_probs=24.7

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      +++-+++|+||+-.-+|.   .....+.+.++..
T Consensus      1387 Lr~~~ILILDEATSaLD~---~Te~~Iq~~L~~~ 1417 (1495)
T PLN03232       1387 LRRSKILVLDEATASVDV---RTDSLIQRTIREE 1417 (1495)
T ss_pred             HhCCCEEEEECCcccCCH---HHHHHHHHHHHHH
Confidence            556689999999988887   5777887777766

>PRK09165 replicative DNA helicase; Provisional

Probab=93.30  E-value=0.72  Score=41.27  Aligned_cols=25  Identities=20%  Similarity=0.116  Sum_probs=18.2

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHS   73 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~   73 (226)
                      |.-+++.|+||+|||...+--+.+.
T Consensus       217 g~livIaarpg~GKT~~al~ia~~~  241 (497)
T PRK09165        217 SDLIILAGRPSMGKTALATNIAFNA  241 (497)
T ss_pred             CceEEEEeCCCCChHHHHHHHHHHH
Confidence            4557899999999998655444443

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=93.27  E-value=0.36  Score=36.55  Aligned_cols=43  Identities=19%  Similarity=0.185  Sum_probs=29.2

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      ..+-+++++||.-.-+|.   .....+..+++.+..... .++++..
T Consensus       112 ~~~p~~lllDEPt~~LD~---~~~~~l~~~l~~~~~~~~-tii~~sh  154 (173)
T cd03246         112 YGNPRILVLDEPNSHLDV---EGERALNQAIAALKAAGA-TRIVIAH  154 (173)
T ss_pred             hcCCCEEEEECCccccCH---HHHHHHHHHHHHHHhCCC-EEEEEeC
Confidence            456789999999988887   567777777777633333 4444333

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=93.24  E-value=1.1  Score=41.61  Aligned_cols=115  Identities=21%  Similarity=0.218  Sum_probs=70.3

Q ss_pred             CCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhh---hhCCCcCCCCCEEEECchHHHHhHhcCCCCCC
Q psy12977         79 NLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAE---KFGPRSAQKFDVLITTPNKLVYLLQMDPPALN  155 (226)
Q Consensus        79 ~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~  155 (226)
                      ..+.+++|.++|+..++.+.+.+.+.    +..+...+++....+   .......+..+|+|||-     .+.   ..++
T Consensus       440 ~~g~~vLIf~~tk~~ae~L~~~L~~~----gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~-----~L~---rGfD  507 (655)
T TIGR00631       440 ARNERVLVTTLTKKMAEDLTDYLKEL----GIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGIN-----LLR---EGLD  507 (655)
T ss_pred             cCCCEEEEEECCHHHHHHHHHHHhhh----ccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcC-----hhc---CCee
Confidence            34668999999999999988877765    666666655422211   11122346688999983     222   6888


Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                      +..++++|+-|++...-..  .....+.++-+...+.....+++--...+.+
T Consensus       508 iP~v~lVvi~DadifG~p~--~~~~~iqriGRagR~~~G~vi~~~~~~~~~~  557 (655)
T TIGR00631       508 LPEVSLVAILDADKEGFLR--SERSLIQTIGRAARNVNGKVIMYADKITDSM  557 (655)
T ss_pred             eCCCcEEEEeCcccccCCC--CHHHHHHHhcCCCCCCCCEEEEEEcCCCHHH
Confidence            9999999998888653221  2334444444444334455555544444433

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

>TIGR02204 MsbA_rel ABC transporter, permease/ATP-binding protein

Probab=93.24  E-value=0.38  Score=43.66  Aligned_cols=31  Identities=16%  Similarity=0.239  Sum_probs=23.7

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      +++-+.+++||+-.-+|.   ...+.+.+.++.+
T Consensus       492 ~~~~~ililDEpts~lD~---~~~~~i~~~l~~~  522 (576)
T TIGR02204       492 LKDAPILLLDEATSALDA---ESEQLVQQALETL  522 (576)
T ss_pred             HhCCCeEEEeCcccccCH---HHHHHHHHHHHHH
Confidence            556789999999988887   4666676666666

This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=93.21  E-value=0.55  Score=35.94  Aligned_cols=146  Identities=9%  Similarity=0.018  Sum_probs=77.5

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      .-+.+--..|-|||.+++--++..+-    .+.+++++-=.+--..+=...+.+..+  ++.....+.+..  -.... .
T Consensus        22 Gli~VYtGdGKGKTTAAlGlalRAaG----~G~rV~iiQFlKg~~~~GE~~~l~~~~--~v~~~~~g~~~~--~~~~~-~   92 (178)
T PRK07414         22 GLVQVFTSSQRNFFTSVMAQALRIAG----QGTPVLIVQFLKGGIQQGPDRPIQLGQ--NLDWVRCDLPRC--LDTPH-L   92 (178)
T ss_pred             CEEEEEeCCCCCchHHHHHHHHHHhc----CCCEEEEEEEecCCCcchHHHHHHhCC--CcEEEECCCCCe--eeCCC-c
Confidence            44667888999999988777776654    366888886555431111111111111  233222211100  00000 0


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHH
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAK  209 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~  209 (226)
                      ..   -   ........+..-...+.-..++++|+||+-...+.+.- -.+.+..+++.. ++..-+|+..-..|+++.+
T Consensus        93 ~~---~---~~~~~~~~~~~a~~~l~~~~~dlvVLDEi~~Al~~gli-~~eeVl~~L~~r-p~~~evILTGR~~p~~Lie  164 (178)
T PRK07414         93 DE---S---EKKALQELWQYTQAVVDEGRYSLVVLDELSLAIQFGLI-PETEVLEFLEKR-PSHVDVILTGPEMPESLLA  164 (178)
T ss_pred             CH---H---HHHHHHHHHHHHHHHHhCCCCCEEEEehhHHHHHCCCc-cHHHHHHHHHhC-CCCCEEEEECCCCCHHHHH
Confidence            00   0   00111122221112344567899999999888776422 344566666665 5677888877778888877


Q ss_pred             HHH
Q psy12977        210 WCR  212 (226)
Q Consensus       210 ~~~  212 (226)
                      .+.
T Consensus       165 ~AD  167 (178)
T PRK07414        165 IAD  167 (178)
T ss_pred             hCC
Confidence            663

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies

Probab=93.20  E-value=0.18  Score=39.27  Aligned_cols=29  Identities=17%  Similarity=0.256  Sum_probs=19.2

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLR   75 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~   75 (226)
                      ....++++.|+||+|||......+...+.
T Consensus        36 ~~~~h~li~G~tgsGKS~~l~~ll~~l~~   64 (205)
T PF01580_consen   36 KKNPHLLIAGATGSGKSTLLRTLLLSLAL   64 (205)
T ss_dssp             GGS-SEEEE--TTSSHHHHHHHHHHHHHT
T ss_pred             CCCceEEEEcCCCCCccHHHHHHHHHHHH
Confidence            34458999999999999876655555554

The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=93.19  E-value=3.1  Score=35.06  Aligned_cols=131  Identities=17%  Similarity=0.176  Sum_probs=73.7

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEc-cc-HHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCC
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVC-PT-RELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPR  128 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~-Pt-~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (226)
                      -+++.|..|+|||.+..--+.. +.+   .+.++++.+ .| |+=|   .++++.+.+..+..+.....++         
T Consensus       141 Vil~vGVNG~GKTTTIaKLA~~-l~~---~g~~VllaA~DTFRAaA---iEQL~~w~er~gv~vI~~~~G~---------  204 (340)
T COG0552         141 VILFVGVNGVGKTTTIAKLAKY-LKQ---QGKSVLLAAGDTFRAAA---IEQLEVWGERLGVPVISGKEGA---------  204 (340)
T ss_pred             EEEEEecCCCchHhHHHHHHHH-HHH---CCCeEEEEecchHHHHH---HHHHHHHHHHhCCeEEccCCCC---------
Confidence            3689999999999875433323 322   244555544 22 2222   3455666666676665432111         


Q ss_pred             cCCCCCEEEECchHHH-HhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCc-----eEEEEeee
Q psy12977        129 SAQKFDVLITTPNKLV-YLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNL-----KRGMFSAT  202 (226)
Q Consensus       129 ~~~~~~IiV~Tp~~l~-~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~-----q~v~~SAT  202 (226)
                                .|..+. +-++.    -...+++++++|=|-++-...  +.+..+..+.+-..+...     -++.+=||
T Consensus       205 ----------DpAaVafDAi~~----Akar~~DvvliDTAGRLhnk~--nLM~EL~KI~rV~~k~~~~ap~e~llvlDAt  268 (340)
T COG0552         205 ----------DPAAVAFDAIQA----AKARGIDVVLIDTAGRLHNKK--NLMDELKKIVRVIKKDDPDAPHEILLVLDAT  268 (340)
T ss_pred             ----------CcHHHHHHHHHH----HHHcCCCEEEEeCcccccCch--hHHHHHHHHHHHhccccCCCCceEEEEEEcc
Confidence                      233322 22221    114578899999999886543  688888888776632221     34444788


Q ss_pred             CchhHHHHHHH
Q psy12977        203 HTEDVAKWCRR  213 (226)
Q Consensus       203 ~~~~~~~~~~~  213 (226)
                      .-.+..+-++.
T Consensus       269 tGqnal~QAk~  279 (340)
T COG0552         269 TGQNALSQAKI  279 (340)
T ss_pred             cChhHHHHHHH
Confidence            77665554533

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=93.19  E-value=1  Score=34.13  Aligned_cols=43  Identities=16%  Similarity=0.189  Sum_probs=29.0

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      ..+-+++++||.-.-+|.   .....+..+++.+. .. ..++++..-
T Consensus       114 ~~~p~~lllDEP~~~LD~---~~~~~l~~~l~~~~-~~-~tii~~sh~  156 (178)
T cd03247         114 LQDAPIVLLDEPTVGLDP---ITERQLLSLIFEVL-KD-KTLIWITHH  156 (178)
T ss_pred             hcCCCEEEEECCcccCCH---HHHHHHHHHHHHHc-CC-CEEEEEecC
Confidence            456689999999988887   56677777777663 33 344443333

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter

Probab=93.14  E-value=0.18  Score=47.06  Aligned_cols=31  Identities=19%  Similarity=0.192  Sum_probs=23.8

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      +++-+++++||+-.-+|.   .....+...+..+
T Consensus       627 l~~p~iliLDE~Ts~LD~---~te~~i~~~L~~~  657 (708)
T TIGR01193       627 LTDSKVLILDESTSNLDT---ITEKKIVNNLLNL  657 (708)
T ss_pred             hhCCCEEEEeCccccCCH---HHHHHHHHHHHHh
Confidence            567789999999988887   5666666666654

This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=93.10  E-value=0.22  Score=37.87  Aligned_cols=53  Identities=9%  Similarity=0.143  Sum_probs=35.4

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHH
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWC  211 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~  211 (226)
                      ..+-+++++||.-.-+|.   .....+..+++.+.......++++..-++.+.+++
T Consensus       116 ~~~p~llilDEP~~~LD~---~~~~~l~~~l~~~~~~~~~tiii~sH~~~~~~~~~  168 (178)
T cd03229         116 AMDPDVLLLDEPTSALDP---ITRREVRALLKSLQAQLGITVVLVTHDLDEAARLA  168 (178)
T ss_pred             HCCCCEEEEeCCcccCCH---HHHHHHHHHHHHHHHhcCCEEEEEeCCHHHHHHhc
Confidence            456689999999988887   57777777777763321345666666555554444

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>KOG0055|consensus

Probab=92.93  E-value=0.32  Score=47.46  Aligned_cols=34  Identities=15%  Similarity=0.171  Sum_probs=28.5

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCC
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGP  192 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~  192 (226)
                      +++-+.|.+|||-..+|.   .....++..++..+..
T Consensus      1142 lRnPkILLLDEATSALDs---eSErvVQeALd~a~~g 1175 (1228)
T KOG0055|consen 1142 LRNPKILLLDEATSALDS---ESERVVQEALDRAMEG 1175 (1228)
T ss_pred             HcCCCeeeeeccchhhhh---hhHHHHHHHHHHhhcC
Confidence            677889999999999998   6888888888887433

>KOG0057|consensus

Probab=92.91  E-value=1.8  Score=38.80  Aligned_cols=64  Identities=13%  Similarity=0.188  Sum_probs=37.7

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEe
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIG  116 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~  116 (226)
                      +..|+.+-+.|++|||||.. +-.++...+ .+..     |.....++-.--.+.+++.....+.....++
T Consensus       375 I~kGekVaIvG~nGsGKSTi-lr~LlrF~d-~sG~-----I~IdG~dik~~~~~SlR~~Ig~VPQd~~LFn  438 (591)
T KOG0057|consen  375 IPKGEKVAIVGSNGSGKSTI-LRLLLRFFD-YSGS-----ILIDGQDIKEVSLESLRQSIGVVPQDSVLFN  438 (591)
T ss_pred             ecCCCEEEEECCCCCCHHHH-HHHHHHHhc-cCCc-----EEECCeeHhhhChHHhhhheeEeCCcccccc
Confidence            35578899999999999974 344455554 3332     3445555555555555555554444433333

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=92.90  E-value=0.47  Score=36.31  Aligned_cols=63  Identities=22%  Similarity=0.194  Sum_probs=36.2

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC------CCCCceEEEEcccHHHHHHHHHHHHHHhhcC
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP------KNLGFRAVIVCPTRELAKQTYNETVRLSEGL  108 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~------~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~  108 (226)
                      .+..|.-.++.||+|+|||...+-.+.......      ...+.+++++..-.. ..++.+.+..+....
T Consensus        28 ~~~~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~~~~   96 (193)
T PF13481_consen   28 LLPRGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALLQDY   96 (193)
T ss_dssp             EE-TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHHTTS
T ss_pred             cccCCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHhccc
Confidence            334567789999999999986554444444311      113456777755444 667777777766433

>PF07088 GvpD: GvpD gas vesicle protein; InterPro: IPR009788 This family consists of several archaeal GvpD gas vesicle proteins

Probab=92.88  E-value=0.38  Score=41.40  Aligned_cols=146  Identities=11%  Similarity=0.122  Sum_probs=68.6

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCe-EEEEecchhhhhh
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR-AHVIGKIQQAAEK  124 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~-~~~~~~~~~~~~~  124 (226)
                      ...|+.++|.|.+|+|||. +.+-+++.+....    -++|+++. .=-..+++.+  +.....+. ...+.-.+   ..
T Consensus         7 ~~~G~TLLIKG~PGTGKTt-faLelL~~l~~~~----~v~YISTR-Vd~d~vy~~y--~~~~~~i~~~~vlDatQ---d~   75 (484)
T PF07088_consen    7 QEPGQTLLIKGEPGTGKTT-FALELLNSLKDHG----NVMYISTR-VDQDTVYEMY--PWIEESIDPTNVLDATQ---DP   75 (484)
T ss_pred             CCCCcEEEEecCCCCCcee-eehhhHHHHhccC----CeEEEEec-cCHHHHHHhh--hhhccccChhhhhhhcc---ch
Confidence            3568899999999999997 4566677765422    24676554 2222233333  11110111 11111110   11


Q ss_pred             hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc-----C-ccchHHHHHHHHHhcCCCCceEEE
Q psy12977        125 FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA-----G-VRGFRDQLAVIYAACSGPNLKRGM  198 (226)
Q Consensus       125 ~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~-----~-~~~~~~~i~~i~~~~~~~~~q~v~  198 (226)
                      +.........+-=.-++.+.+++..-..   ..+--++|+|--+.+.+.     + ...+....+.+.+........+++
T Consensus        76 ~~~~~~~~vp~~~l~~ds~~~f~~~i~~---~~k~~iI~~DSWdaiieyla~~~~~~ed~e~l~~dLv~lard~g~~LIl  152 (484)
T PF07088_consen   76 FELPLDKDVPFERLDIDSFRDFVDKINE---AGKKPIIAFDSWDAIIEYLAEEHDEPEDIETLTNDLVELARDMGINLIL  152 (484)
T ss_pred             hhccccccCcccccCHHHHHHHHHHhhh---cccCcEEEEecHHHHHHHhhhhhcCcHHHHHHHHHHHHHHhhcCceEEE
Confidence            1111111111111236777777763111   245569999994443331     1 011222222222222345778888


Q ss_pred             EeeeCch
Q psy12977        199 FSATHTE  205 (226)
Q Consensus       199 ~SAT~~~  205 (226)
                      .|-+-..
T Consensus       153 VsEsa~~  159 (484)
T PF07088_consen  153 VSESAEN  159 (484)
T ss_pred             EEecCCC
Confidence            8877543

GvpD is thought to be involved in the regulation of gas vesicle formation [,].; GO: 0005524 ATP binding

>PRK07004 replicative DNA helicase; Provisional

Probab=92.80  E-value=0.48  Score=41.95  Aligned_cols=26  Identities=23%  Similarity=0.027  Sum_probs=18.6

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHS   73 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~   73 (226)
                      .|.-+++.|.||+|||...+--+.+.
T Consensus       212 ~g~liviaarpg~GKT~~al~ia~~~  237 (460)
T PRK07004        212 GGELIIVAGRPSMGKTAFSMNIGEYV  237 (460)
T ss_pred             CCceEEEEeCCCCCccHHHHHHHHHH
Confidence            35567899999999998655444443

>cd03240 ABC_Rad50 The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains

Probab=92.77  E-value=1.8  Score=33.72  Aligned_cols=42  Identities=19%  Similarity=0.194  Sum_probs=28.8

Q ss_pred             CCccEEEEcccccccccCccchHH-HHHHHHHhcCCC-CceEEEEee
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRD-QLAVIYAACSGP-NLKRGMFSA  201 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~-~i~~i~~~~~~~-~~q~v~~SA  201 (226)
                      .+.+++++||.-.-+|.   .... .+..++..+... ..++++.|-
T Consensus       138 ~~p~illlDEP~~~LD~---~~~~~~l~~~l~~~~~~~~~~iiiitH  181 (204)
T cd03240         138 SNCGILALDEPTTNLDE---ENIEESLAEIIEERKSQKNFQLIVITH  181 (204)
T ss_pred             cCCCEEEEcCCccccCH---HHHHHHHHHHHHHHHhccCCEEEEEEe
Confidence            56789999999988887   4556 677777666333 456665433

The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.

>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]

Probab=92.76  E-value=0.034  Score=46.51  Aligned_cols=54  Identities=19%  Similarity=0.248  Sum_probs=35.6

Q ss_pred             cCCCCcccccccCCCCCe-EEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcc
Q psy12977         34 KHFEPHFTITYLSPLGRQ-IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCP   89 (226)
Q Consensus        34 ~~~~~~Q~~~~~~~~~~~-~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~P   89 (226)
                      ..-++-|...+.....++ ++-.+|-|+|||+.......+.+....-.  ++|..-|
T Consensus       127 ~~kt~~Q~~y~eai~~~di~fGiGpAGTGKTyLava~av~al~~~~v~--rIiLtRP  181 (348)
T COG1702         127 IPKTPGQNMYPEAIEEHDIVFGIGPAGTGKTYLAVAKAVDALGAGQVR--RIILTRP  181 (348)
T ss_pred             EecChhHHHHHHHHHhcCeeeeecccccCChhhhHHhHhhhhhhcccc--eeeecCc
Confidence            344566766654444455 56889999999998777777777643333  5666556

>KOG0331|consensus

Probab=92.75  E-value=0.62  Score=41.53  Aligned_cols=94  Identities=18%  Similarity=0.177  Sum_probs=64.7

Q ss_pred             CchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC---CCcCCCCCE
Q psy12977         59 GSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG---PRSAQKFDV  135 (226)
Q Consensus        59 GsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~I  135 (226)
                      ...|-. -+..++..+.  ...+.++||.|.|+.-|.++...+...    ++....++|+....++..   ....+++.|
T Consensus       322 ~~~K~~-~l~~lL~~~~--~~~~~KvIIFc~tkr~~~~l~~~l~~~----~~~a~~iHGd~sQ~eR~~~L~~FreG~~~v  394 (519)
T KOG0331|consen  322 ETAKLR-KLGKLLEDIS--SDSEGKVIIFCETKRTCDELARNLRRK----GWPAVAIHGDKSQSERDWVLKGFREGKSPV  394 (519)
T ss_pred             HHHHHH-HHHHHHHHHh--ccCCCcEEEEecchhhHHHHHHHHHhc----CcceeeecccccHHHHHHHHHhcccCCcce
Confidence            444443 2344444444  334569999999999999988877665    577777777765554432   344788999


Q ss_pred             EEECchHHHHhHhcCCCCCCCCCccEEEEccc
Q psy12977        136 LITTPNKLVYLLQMDPPALNLANVEWLIVDES  167 (226)
Q Consensus       136 iV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~  167 (226)
                      +|+|--.      .  +.++..++++||-=+.
T Consensus       395 LVATdVA------a--RGLDi~dV~lVInydf  418 (519)
T KOG0331|consen  395 LVATDVA------A--RGLDVPDVDLVINYDF  418 (519)
T ss_pred             EEEcccc------c--ccCCCccccEEEeCCC
Confidence            9999532      1  7899999999986443

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=92.73  E-value=0.27  Score=39.65  Aligned_cols=45  Identities=27%  Similarity=0.287  Sum_probs=26.9

Q ss_pred             CCCC-eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         47 PLGR-QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        47 ~~~~-~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      ..|+ -+.++|+.|||||...- .+...+..    +..++++.|...+..+
T Consensus        48 ~d~qg~~~vtGevGsGKTv~~R-al~~s~~~----d~~~~v~i~~~~~s~~   93 (269)
T COG3267          48 ADGQGILAVTGEVGSGKTVLRR-ALLASLNE----DQVAVVVIDKPTLSDA   93 (269)
T ss_pred             hcCCceEEEEecCCCchhHHHH-HHHHhcCC----CceEEEEecCcchhHH
Confidence            3344 67899999999998766 44444432    2234444454444443

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=92.64  E-value=0.48  Score=35.12  Aligned_cols=49  Identities=14%  Similarity=0.152  Sum_probs=31.7

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHH
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKW  210 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~  210 (226)
                      +.+++++||...-+|.   .....+..++..+... .+.++++....+.+..+
T Consensus        98 ~~~i~ilDEp~~~lD~---~~~~~l~~~l~~~~~~-~~tii~~sh~~~~~~~~  146 (157)
T cd00267          98 NPDLLLLDEPTSGLDP---ASRERLLELLRELAEE-GRTVIIVTHDPELAELA  146 (157)
T ss_pred             CCCEEEEeCCCcCCCH---HHHHHHHHHHHHHHHC-CCEEEEEeCCHHHHHHh
Confidence            4679999999988876   4666776766665333 34555555555554444

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>KOG2035|consensus

Probab=92.59  E-value=1  Score=37.09  Aligned_cols=53  Identities=11%  Similarity=0.137  Sum_probs=39.3

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHH
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRR  213 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~  213 (226)
                      ...++.+|+-|+|.+..+    ....+.+.++.. ..++++++...+.++-+...=.+
T Consensus       125 qr~fKvvvi~ead~LT~d----AQ~aLRRTMEkY-s~~~RlIl~cns~SriIepIrSR  177 (351)
T KOG2035|consen  125 QRPFKVVVINEADELTRD----AQHALRRTMEKY-SSNCRLILVCNSTSRIIEPIRSR  177 (351)
T ss_pred             ccceEEEEEechHhhhHH----HHHHHHHHHHHH-hcCceEEEEecCcccchhHHhhh
Confidence            446899999999998765    667788888877 57888888777766544444433

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=92.53  E-value=0.16  Score=42.48  Aligned_cols=28  Identities=25%  Similarity=0.400  Sum_probs=20.4

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      ...+.++++.||||||||... -.++..+
T Consensus       141 v~~~~~ili~G~tGsGKTTll-~al~~~~  168 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTFL-KSLVDEI  168 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHHH-HHHHccC
Confidence            446789999999999999753 3344433

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=92.49  E-value=1  Score=43.10  Aligned_cols=43  Identities=12%  Similarity=0.180  Sum_probs=31.8

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      .--++|+|++|.+.+.   .....+..+++.. +++..+++.|-+.|
T Consensus       121 ~~~~lvlDD~h~~~~~---~~~~~l~~l~~~~-~~~~~lv~~sR~~~  163 (903)
T PRK04841        121 QPLYLVIDDYHLITNP---EIHEAMRFFLRHQ-PENLTLVVLSRNLP  163 (903)
T ss_pred             CCEEEEEeCcCcCCCh---HHHHHHHHHHHhC-CCCeEEEEEeCCCC
Confidence            3358999999987544   4666888888777 56778888776644

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=92.45  E-value=1.3  Score=41.75  Aligned_cols=18  Identities=28%  Similarity=0.503  Sum_probs=15.3

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||...
T Consensus       487 ~~giLL~GppGtGKT~la  504 (733)
T TIGR01243       487 PKGVLLFGPPGTGKTLLA  504 (733)
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            366899999999999754

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.

>KOG0741|consensus

Probab=92.42  E-value=0.087  Score=46.79  Aligned_cols=17  Identities=35%  Similarity=0.595  Sum_probs=15.1

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +-+++-+|+|+|||+.+
T Consensus       257 KGiLLyGPPGTGKTLiA  273 (744)
T KOG0741|consen  257 KGILLYGPPGTGKTLIA  273 (744)
T ss_pred             eeEEEECCCCCChhHHH
Confidence            77999999999999854

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=92.38  E-value=0.36  Score=40.49  Aligned_cols=41  Identities=20%  Similarity=0.040  Sum_probs=25.8

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCC--CCCceEEEEcc
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPK--NLGFRAVIVCP   89 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~--~~~~~~iil~P   89 (226)
                      |.-+.+.||+|+|||...+..+.+......  ..+.+++|+.-
T Consensus       102 g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~t  144 (317)
T PRK04301        102 QSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDT  144 (317)
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeC
Confidence            566789999999999755444444432211  12347888764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	226
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		2e-60
3ly5_A	262	Ddx18 Dead-Domain Length = 262		1e-15
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		2e-15
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		3e-15
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		5e-15
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		2e-14
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		6e-13
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		2e-12
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		2e-12
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		2e-12
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		4e-12
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		1e-11
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		3e-11
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		4e-11
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		4e-11
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		2e-10
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		3e-10
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		5e-10
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		3e-09
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		4e-09
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		4e-09
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		5e-09
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		5e-09
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		9e-09
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		9e-09
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		1e-08
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		1e-08
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		6e-08
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		7e-08
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		1e-07
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		2e-07
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		1e-06
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		1e-06
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		2e-06
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		2e-06
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-06
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		3e-06
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		3e-06
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		3e-06
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		3e-06
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		4e-06
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		4e-06
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		7e-06
2zj2_A	720	Archaeal Dna Helicase Hjm Apo State In Form 1 Lengt		4e-05
2va8_A	715	Dna Repair Helicase Hel308 Length = 715		3e-04

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score =  228 bits (580), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 101/178 (56%), Positives = 135/178 (75%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR++ A APTGSGKT AF IPI+  L+ P N GFRA+I+ PTRELA Q + E +++SEG 
Sbjct: 66  GRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGT 125
Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
           G R H+I K   AA+KFGP+S++KFD+L+TTPN+L+YLL+ DPP ++LA+VEWL+VDESD
Sbjct: 126 GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESD 185
Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           KLFE G  GFRDQLA I+ AC+   ++R MFSAT   DV +WC+  L   + +++G R
Sbjct: 186 KLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR 243

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 79.7 bits (195), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 63/179 (35%), Positives = 93/179 (51%), Gaps = 21/179 (11%)
Query: 49  GRQIFACAPTGSGKTAAFLIP---IIHSLR-GPKNLGFRAVIVCPTRELAKQTYNETVRL 104
           GR + A A TGSGKT AFLIP   +I  LR  P+N G   +I+ PTRELA QT+     L
Sbjct: 91  GRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRN-GTGVLILSPTRELAMQTFG---VL 146
Query: 105 SEGLGLRAHVIGKIQQAAEKFGPRSAQKF----DVLITTPNKLVYLLQMDPPALNLANVE 160
            E +    H  G I   + +     AQK     ++++ TP +L+  +Q + P     N++
Sbjct: 147 KELMTHHVHTYGLIMGGSNRSA--EAQKLGNGINIIVATPGRLLDHMQ-NTPGFMYKNLQ 203
Query: 161 WLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGM-FSATHTEDVAKWCRRKLKRR 218
            L++DE+D++ +    GF ++L  I      P  ++ M FSAT T  V    R  LK+ 
Sbjct: 204 CLVIDEADRILDV---GFEEELKQIIKLL--PTRRQTMLFSATQTRKVEDLARISLKKE 257

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 79.3 bits (194), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 59/179 (32%), Positives = 95/179 (53%), Gaps = 18/179 (10%)
Query: 33  FKHF-EPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR 91
           FK+F E       L   G+ +   A TGSGKTAA+ IPI+        LG ++++V PTR
Sbjct: 14  FKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE-------LGMKSLVVTPTR 66
Query: 92  ELAKQTYNETVRLSEGLGLR-AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMD 150
           EL +Q  +    +   +  + A V G +   A+    R+A   D+++ TP +L+ L    
Sbjct: 67  ELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNA---DIVVATPGRLLDLWS-- 121
Query: 151 PPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAK 209
              ++L++ E +I+DE+D +FE    GF D + +I A  S   +  G+FSAT  E++ K
Sbjct: 122 KGVIDLSSFEIVIIDEADLMFEM---GFIDDIKIILAQTSNRKIT-GLFSATIPEEIRK 176

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score = 78.2 bits (191), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 62/187 (33%), Positives = 96/187 (51%), Gaps = 19/187 (10%)
Query: 50  RQIFACAPTGSGKTAAFLIPIIHSL--------RGPKNLGFRAVIVCPTRELAKQTYNET 101
           R I ACA TGSGKTAAFLIPII+ L        R  K    + +I+ PTRELA Q  +E+
Sbjct: 61  RDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSES 120
Query: 102 VRLSEGLGLRAHVIGKIQQAAEKFGPRSAQK-FDVLITTPNKLVYLLQMDPPALNLANVE 160
            + S    LR+ V+        +   R  Q    +L+ TP +LV  ++ +   ++L   +
Sbjct: 121 QKFSLNTPLRSCVVYGGADTHSQI--REVQMGCHLLVATPGRLVDFIEKN--KISLEFCK 176
Query: 161 WLIVDESDKLFEAGVRGFRDQLAVIYAAC---SGPNLKRGMFSATHTEDVAKWCRRKLKR 217
           ++++DE+D++ +    GF  Q+  I       SG N +  MFSAT  +++ K     L  
Sbjct: 177 YIVLDEADRMLDM---GFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYN 233
Query: 218 RVQINVG 224
            + + VG
Sbjct: 234 YIFMTVG 240

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 77.8 bits (190), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 57/183 (31%), Positives = 92/183 (50%), Gaps = 13/183 (7%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHS-LRGPKNLGF---RAVIVCPTRELAKQTYNETVRL 104
           GR + ACA TGSGKTAAFL+PI+   L  P  L     + VIV PTRELA Q +NE  + 
Sbjct: 93  GRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKF 152
Query: 105 SEGLGLRAHVI--GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL 162
           +    L+  ++  G   +   +   R      V+I TP +L+  +  D   +   +  ++
Sbjct: 153 AFESYLKIGIVYGGTSFRHQNECITRGCH---VVIATPGRLLDFV--DRTFITFEDTRFV 207
Query: 163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN 222
           ++DE+D++ + G     D   ++      P  +  MFSAT  E++ +     LK  V + 
Sbjct: 208 VLDEADRMLDMGFS--EDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVA 265
Query: 223 VGL 225
           +G+
Sbjct: 266 IGI 268

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 75.9 bits (185), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 58/177 (32%), Positives = 95/177 (53%), Gaps = 11/177 (6%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHS-LRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           GR I   A TGSGKT AF +PI+++ L  P+ L   A+++ PTRELA Q   +   L   
Sbjct: 80  GRDIIGLAETGSGKTGAFALPILNALLETPQRL--FALVLTPTRELAFQISEQFEALGSS 137
Query: 108 LGLRAHVI-GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE 166
           +G+++ VI G I   ++      A+K  ++I TP +L+  L+ +    NL  +++L++DE
Sbjct: 138 IGVQSAVIVGGIDSMSQSLA--LAKKPHIIIATPGRLIDHLE-NTKGFNLRALKYLVMDE 194
Query: 167 SDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           +D++         D++  +       + K  +FSAT T+ V K  R  LK  V+  V
Sbjct: 195 ADRILNMDFETEVDKILKVIPR----DRKTFLFSATMTKKVQKLQRAALKNPVKCAV 247

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 70.9 bits (172), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 53/176 (30%), Positives = 91/176 (51%), Gaps = 20/176 (11%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHS---LRGPKNLGFRAVIVCPTRELAKQTYNETVRLS 105
           G+ +   A TGSGKT AFL+P++ +   L+     G   +I+ PTRELA QT+    ++ 
Sbjct: 62  GKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVG 121
Query: 106 EGLGLRAHVI--GK-IQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPP-ALNLANVEW 161
           +     A +I  GK ++  AE+         ++L+ TP +L  L  MD   + +  +++ 
Sbjct: 122 KNHDFSAGLIIGGKDLKHEAERIN-----NINILVCTPGRL--LQHMDETVSFHATDLQM 174
Query: 162 LIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRG-MFSATHTEDVAKWCRRKLK 216
           L++DE+D++ +    GF D +  +      P  ++  +FSAT T+ V    R  LK
Sbjct: 175 LVLDEADRILDM---GFADTMNAVIENL--PKKRQTLLFSATQTKSVKDLARLSLK 225

>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 = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/189 (31%), Positives = 92/189 (48%), Gaps = 21/189 (11%)
Query: 45  LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK---NLGFRAVIVCPTRELAKQTYNET 101
           LS     + A A TG+GKT AFLIPI   L   K       +AVIV PTR+LA Q   E 
Sbjct: 56  LSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEV 115
Query: 102 VRLSE-GLGLRAH-----VIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALN 155
            ++ +   GL+ +     V G   +AA      +  + +++I TP +L+ +L+       
Sbjct: 116 KKIHDMNYGLKKYACVSLVGGTDFRAA--MNKMNKLRPNIVIATPGRLIDVLEKYSNKF- 172
Query: 156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYA------ACSGPNLKRGMFSATHTEDVAK 209
              V++ ++DE+D+L E    GFRD L  I        + S  N+K  +FSAT  + V K
Sbjct: 173 FRFVDYKVLDEADRLLEI---GFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQK 229
Query: 210 WCRRKLKRR 218
                + ++
Sbjct: 230 LANNIMNKK 238

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/189 (31%), Positives = 92/189 (48%), Gaps = 21/189 (11%)
Query: 45  LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK---NLGFRAVIVCPTRELAKQTYNET 101
           LS     + A A TG+GKT AFLIPI   L   K       +AVIV PTR+LA Q   E 
Sbjct: 107 LSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEV 166
Query: 102 VRLSE-GLGLRAH-----VIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALN 155
            ++ +   GL+ +     V G   +AA      +  + +++I TP +L+ +L+       
Sbjct: 167 KKIHDMNYGLKKYACVSLVGGTDFRAA--MNKMNKLRPNIVIATPGRLIDVLEKYSNKF- 223
Query: 156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYA------ACSGPNLKRGMFSATHTEDVAK 209
              V++ ++DE+D+L E    GFRD L  I        + S  N+K  +FSAT  + V K
Sbjct: 224 FRFVDYKVLDEADRLLEI---GFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQK 280
Query: 210 WCRRKLKRR 218
                + ++
Sbjct: 281 LANNIMNKK 289

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/189 (31%), Positives = 92/189 (48%), Gaps = 21/189 (11%)
Query: 45  LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK---NLGFRAVIVCPTRELAKQTYNET 101
           LS     + A A TG+GKT AFLIPI   L   K       +AVIV PTR+LA Q   E 
Sbjct: 56  LSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEV 115
Query: 102 VRLSE-GLGLRAH-----VIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALN 155
            ++ +   GL+ +     V G   +AA      +  + +++I TP +L+ +L+       
Sbjct: 116 KKIHDMNYGLKKYACVSLVGGTDFRAA--MNKMNKLRPNIVIATPGRLIDVLEKYSNKF- 172
Query: 156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYA------ACSGPNLKRGMFSATHTEDVAK 209
              V++ ++DE+D+L E    GFRD L  I        + S  N+K  +FSAT  + V K
Sbjct: 173 FRFVDYKVLDEADRLLEI---GFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQK 229
Query: 210 WCRRKLKRR 218
                + ++
Sbjct: 230 LANNIMNKK 238

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 68.2 bits (165), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 52/164 (31%), Positives = 86/164 (52%), Gaps = 12/164 (7%)
Query: 51  QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGL 110
            I A A TGSGKTA+F IP+I  +   +N G  A+I+ PTRELA Q  +E   L     L
Sbjct: 46  NIVAQARTGSGKTASFAIPLIELVN--ENNGIEAIILTPTRELAIQVADEIESLKGNKNL 103
Query: 111 RAHVIGKIQQAAEKFGP-RSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK 169
           +   I KI      +   ++ +  ++++ TP ++  L  ++   LNL NV++ I+DE+D+
Sbjct: 104 K---IAKIYGGKAIYPQIKALKNANIVVGTPGRI--LDHINRGTLNLKNVKYFILDEADE 158
Query: 170 LFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRR 213
                  GF   +  I  AC+  + +  +FSAT   ++    ++
Sbjct: 159 XLNX---GFIKDVEKILNACN-KDKRILLFSATXPREILNLAKK 198

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 66.2 bits (160), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 58/198 (29%), Positives = 96/198 (48%), Gaps = 32/198 (16%)
Query: 50  RQIFACAPTGSGKTAAFLIPII---------HSLRGPKNLGFR--------AVIVCPTRE 92
           R + ACA TGSGKTAAFL+PI+          +LR  K  G          ++++ PTRE
Sbjct: 53  RDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRE 112
Query: 93  LAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQK-FDVLITTPNKLVYLLQMDP 151
           LA Q Y E  + S    +R  V+       ++   R  ++   +L+ TP +LV +++   
Sbjct: 113 LAVQIYEEARKFSYRSRVRPCVVYGGADIGQQI--RDLERGCHLLVATPGRLVDMMERGK 170
Query: 152 PALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRG-----MFSATHTED 206
             L+    ++L++DE+D++ +    GF  Q+  I    + P   +G     MFSAT  ++
Sbjct: 171 IGLDFC--KYLVLDEADRMLDM---GFEPQIRRIVEQDTMP--PKGVRHTMMFSATFPKE 223
Query: 207 VAKWCRRKLKRRVQINVG 224
           +    R  L   + + VG
Sbjct: 224 IQMLARDFLDEYIFLAVG 241

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 65.1 bits (157), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 49/172 (28%), Positives = 87/172 (50%), Gaps = 18/172 (10%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G      + TG+GKT A+L+PI   ++ P+    +AVI  PTRELA Q Y+ET+++++  
Sbjct: 41  GESXVGQSQTGTGKTHAYLLPIXEKIK-PERAEVQAVITAPTRELATQIYHETLKITKFC 99
Query: 109 GLRAHVIGKI-------QQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEW 161
                ++ +        Q+A EK   +      ++I TP ++   ++    AL++     
Sbjct: 100 PKDRXIVARCLIGGTDKQKALEKLNVQP----HIVIGTPGRINDFIREQ--ALDVHTAHI 153
Query: 162 LIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRR 213
           L+VDE+D   + G     DQ+    AA    +L+  +FSAT  E +  + ++
Sbjct: 154 LVVDEADLXLDXGFITDVDQI----AARXPKDLQXLVFSATIPEKLKPFLKK 201

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 64.7 bits (156), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 56/178 (31%), Positives = 90/178 (50%), Gaps = 13/178 (7%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGF--RAVIVCPTRELAKQTYNETVRLSE 106
           G+ +   A TG+GKT AF +PI   L   +  G   RA+++ PTRELA Q  +E   ++ 
Sbjct: 38  GKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAP 97
Query: 107 GLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNK-LVYLLQMDPPALNLANVEWLIVD 165
            L + A   G      ++   R A   D ++ TP + L YL Q     L+L+ VE  ++D
Sbjct: 98  HLKVVAVYGGTGYGKQKEALLRGA---DAVVATPGRALDYLRQG---VLDLSRVEVAVLD 151
Query: 166 ESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           E+D++      GF +++  + +A   P+ +  +FSAT      +   R +K  V INV
Sbjct: 152 EADEMLSM---GFEEEVEALLSATP-PSRQTLLFSATLPSWAKRLAERYMKNPVLINV 205

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 64.7 bits (156), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 56/178 (31%), Positives = 90/178 (50%), Gaps = 13/178 (7%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGF--RAVIVCPTRELAKQTYNETVRLSE 106
           G+ +   A TG+GKT AF +PI   L   +  G   RA+++ PTRELA Q  +E   ++ 
Sbjct: 38  GKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAP 97
Query: 107 GLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNK-LVYLLQMDPPALNLANVEWLIVD 165
            L + A   G      ++   R A   D ++ TP + L YL Q     L+L+ VE  ++D
Sbjct: 98  HLKVVAVYGGTGYGKQKEALLRGA---DAVVATPGRALDYLRQG---VLDLSRVEVAVLD 151
Query: 166 ESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           E+D++      GF +++  + +A   P+ +  +FSAT      +   R +K  V INV
Sbjct: 152 EADEMLSM---GFEEEVEALLSATP-PSRQTLLFSATLPSWAKRLAERYMKNPVLINV 205

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 50/175 (28%), Positives = 84/175 (48%), Gaps = 8/175 (4%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR I A A  G+GKTAAF+IP +  ++ PK    +A+I+ PTRELA QT      L +  
Sbjct: 58  GRDILARAKNGTGKTAAFVIPTLEKVK-PKLNKIQALIMVPTRELALQTSQVVRTLGKHC 116
Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
           G+   V        +    R  +   +L+ TP +++ L        +L++    I+DE+D
Sbjct: 117 GISCMVTTGGTNLRDDI-LRLNETVHILVGTPGRVLDLASR--KVADLSDCSLFIMDEAD 173
Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           K+     +   +Q+         P  +  +FSAT    V ++  + L +  +IN+
Sbjct: 174 KMLSRDFKTIIEQILSFLP----PTHQSLLFSATFPLTVKEFMVKHLHKPYEINL 224

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 61.6 bits (148), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 53/187 (28%), Positives = 88/187 (47%), Gaps = 25/187 (13%)
Query: 49  GRQIFACAPTGSGKTAAFLIP-IIHSLRGP---KNLGFRAVIVCPTRELAKQTYNETVRL 104
           G  +   A TGSGKT ++L+P I+H    P   +  G   +++ PTRELA+Q        
Sbjct: 66  GLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEY 125
Query: 105 SEGLGLRAHVIGKIQQAAEKFGP--RSAQK-FDVLITTPNKLVYLLQMDPPALNLANVEW 161
                L++  I          GP  R  ++  ++ I TP +L+  L+      NL    +
Sbjct: 126 CRACRLKSTCI----YGGAPKGPQIRDLERGVEICIATPGRLIDFLECG--KTNLRRTTY 179
Query: 162 LIVDESDKL----FEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKR 217
           L++DE+D++    FE  +R   DQ+         P+ +  M+SAT  ++V +     LK 
Sbjct: 180 LVLDEADRMLDMGFEPQIRKIVDQIR--------PDRQTLMWSATWPKEVRQLAEDFLKD 231
Query: 218 RVQINVG 224
            + IN+G
Sbjct: 232 YIHINIG 238

>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human Dead-Box Rna Helicase Ddx5 (P68) Length = 253

Iteration: 1
 Score = 61.2 bits (147), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 53/187 (28%), Positives = 88/187 (47%), Gaps = 25/187 (13%)
Query: 49  GRQIFACAPTGSGKTAAFLIP-IIHSLRGP---KNLGFRAVIVCPTRELAKQTYNETVRL 104
           G  +   A TGSGKT ++L+P I+H    P   +  G   +++ PTRELA+Q        
Sbjct: 80  GLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEY 139
Query: 105 SEGLGLRAHVIGKIQQAAEKFGP--RSAQK-FDVLITTPNKLVYLLQMDPPALNLANVEW 161
                L++  I          GP  R  ++  ++ I TP +L+  L+      NL    +
Sbjct: 140 CRACRLKSTCI----YGGAPKGPQIRDLERGVEICIATPGRLIDFLECG--KTNLRRTTY 193
Query: 162 LIVDESDKL----FEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKR 217
           L++DE+D++    FE  +R   DQ+         P+ +  M+SAT  ++V +     LK 
Sbjct: 194 LVLDEADRMLDMGFEPQIRKIVDQIR--------PDRQTLMWSATWPKEVRQLAEDFLKD 245
Query: 218 RVQINVG 224
            + IN+G
Sbjct: 246 YIHINIG 252

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 47/175 (26%), Positives = 88/175 (50%), Gaps = 9/175 (5%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR I A A  G+GK+ A+LIP++  L   K+   +A+++ PTRELA Q     +++S+ +
Sbjct: 40  GRDILARAKNGTGKSGAYLIPLLERLDLKKD-NIQAMVIVPTRELALQVSQICIQVSKHM 98
Query: 109 GLRAHVIGKIQQAAEKFG-PRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES 167
           G  A V+        +    R      V+I TP +++ L++     ++  +V+ +++DE+
Sbjct: 99  G-GAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVD--HVQMIVLDEA 155
Query: 168 DKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN 222
           DKL         + + +        N +  ++SAT    V K+    L++  +IN
Sbjct: 156 DKLLSQDFVQIMEDIILTLPK----NRQILLYSATFPLSVQKFMNSHLEKPYEIN 206

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score = 58.2 bits (139), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 54/176 (30%), Positives = 93/176 (52%), Gaps = 16/176 (9%)
Query: 47  PLGR---QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVR 103
           PLGR    +   A +G+GKT  F    + SL   +NL  + +I+ PTRE+A Q ++    
Sbjct: 56  PLGRCGLDLIVQAKSGTGKTCVFSTIALDSLV-LENLSTQILILAPTREIAVQIHSVITA 114
Query: 104 LSEGL-GLRAHV-IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEW 161
           +   + GL  HV IG    + +K      +K  + + +P ++  L+++D   LN  ++  
Sbjct: 115 IGIKMEGLECHVFIGGTPLSQDK---TRLKKCHIAVGSPGRIKQLIELD--YLNPGSIRL 169
Query: 162 LIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGM-FSATHTEDVAKWCRRKLK 216
            I+DE+DKL E G   F++Q+  IY+  S P  K+ +  SAT+ E +A    + ++
Sbjct: 170 FILDEADKLLEEG--SFQEQINWIYS--SLPASKQMLAVSATYPEFLANALTKYMR 221

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 57.8 bits (138), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 48/179 (26%), Positives = 89/179 (49%), Gaps = 19/179 (10%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  + A A +G+GKTA F I I+  +        +A+++ PTRELA+Q     + L + +
Sbjct: 51  GYDVIAQAQSGTGKTATFAISILQQIELDLK-ATQALVLAPTRELAQQIQKVVMALGDYM 109
Query: 109 GLRAHV-IGKIQQAAEKFGPRSAQKFD-----VLITTPNKLVYLLQMDPPALNLANVEWL 162
           G   H  IG     AE       QK       +++ TP ++  +L  +   L+   ++  
Sbjct: 110 GASCHACIGGTNVRAE------VQKLQMEAPHIIVGTPGRVFDML--NRRYLSPKYIKMF 161
Query: 163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQI 221
           ++DE+D++     RGF+DQ+  I+   +  N +  + SAT   DV +  ++ ++  ++I
Sbjct: 162 VLDEADEMLS---RGFKDQIYDIFQKLNS-NTQVVLLSATMPSDVLEVTKKFMRDPIRI 216

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 57.8 bits (138), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 48/179 (26%), Positives = 89/179 (49%), Gaps = 19/179 (10%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  + A A +G+GKTA F I I+  +        +A+++ PTRELA+Q     + L + +
Sbjct: 77  GYDVIAQAQSGTGKTATFAISILQQIELDLK-ATQALVLAPTRELAQQIQKVVMALGDYM 135
Query: 109 GLRAHV-IGKIQQAAEKFGPRSAQKFD-----VLITTPNKLVYLLQMDPPALNLANVEWL 162
           G   H  IG     AE       QK       +++ TP ++  +L  +   L+   ++  
Sbjct: 136 GASCHACIGGTNVRAE------VQKLQMEAPHIIVGTPGRVFDML--NRRYLSPKYIKMF 187
Query: 163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQI 221
           ++DE+D++     RGF+DQ+  I+   +  N +  + SAT   DV +  ++ ++  ++I
Sbjct: 188 VLDEADEMLS---RGFKDQIYDIFQKLNS-NTQVVLLSATMPSDVLEVTKKFMRDPIRI 242

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score = 57.8 bits (138), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 45/178 (25%), Positives = 90/178 (50%), Gaps = 13/178 (7%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFR---AVIVCPTRELAKQTYNETVRLS 105
           G  + A A +G+GKTA F I I+  L     + F+   A+++ PTRELA+Q     + L 
Sbjct: 67  GYDVIAQAQSGTGKTATFAISILQQLE----IEFKETQALVLAPTRELAQQIQKVILALG 122
Query: 106 EGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVD 165
           + +G   H          +     A+   +++ TP ++  +L  +   L+   ++  ++D
Sbjct: 123 DYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDML--NRRYLSPKWIKMFVLD 180
Query: 166 ESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           E+D++     RGF+DQ+  I+   +  +++  + SAT   DV +  ++ ++  ++I V
Sbjct: 181 EADEMLS---RGFKDQIYEIFQKLN-TSIQVVLLSATMPTDVLEVTKKFMRDPIRILV 234

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 57.0 bits (136), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 93/185 (50%), Gaps = 21/185 (11%)
Query: 48  LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           LG  +   A +G GKTA F++  +  L  P       +++C TRELA Q   E  R S+ 
Sbjct: 43  LGMDVLCQAKSGMGKTAVFVLATLQQLE-PVTGQVSVLVMCHTRELAFQISKEYERFSKY 101
Query: 108 L-GLRAHV------IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVE 160
           +  ++  V      I K ++  +K  P       +++ TP +++ L +    +LNL +++
Sbjct: 102 MPNVKVAVFFGGLSIKKDEEVLKKNCPH------IVVGTPGRILALAR--NKSLNLKHIK 153
Query: 161 WLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKR-GMFSATHTEDVAKWCRRKLKRRV 219
             I+DE+DK+ E      R  +  I+     P+ K+  MFSAT ++++   CR+ ++  +
Sbjct: 154 HFILDEADKMLEQ--LDMRRDVQEIFRMT--PHEKQVMMFSATLSKEIRPVCRKFMQDPM 209
Query: 220 QINVG 224
           +I V 
Sbjct: 210 EIFVD 214

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score = 57.0 bits (136), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 51/184 (27%), Positives = 92/184 (50%), Gaps = 21/184 (11%)
Query: 48  LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           LG  +   A +G GKTA F++  +  L  P       +++C TRELA Q   E  R S+ 
Sbjct: 50  LGMDVLCQAKSGMGKTAVFVLATLQQLE-PVTGQVSVLVMCHTRELAFQISKEYERFSKY 108
Query: 108 L-GLRAHV------IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVE 160
           +  ++  V      I K ++  +K  P       +++ TP +++ L +    +LNL +++
Sbjct: 109 MPNVKVAVFFGGLSIKKDEEVLKKNCPH------IVVGTPGRILALAR--NKSLNLKHIK 160
Query: 161 WLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKR-GMFSATHTEDVAKWCRRKLKRRV 219
             I+DE DK+ E      R  +  I+     P+ K+  MFSAT ++++   CR+ ++  +
Sbjct: 161 HFILDECDKMLEQ--LDMRRDVQEIFRM--TPHEKQVMMFSATLSKEIRPVCRKFMQDPM 216
Query: 220 QINV 223
           +I V
Sbjct: 217 EIFV 220

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 56.2 bits (134), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 92/185 (49%), Gaps = 21/185 (11%)
Query: 48  LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           LG  +   A +G GKTA F++  +  L  P       +++C TRELA Q   E  R S+ 
Sbjct: 44  LGMDVLCQAKSGMGKTAVFVLATLQQLE-PVTGQVSVLVMCHTRELAFQISKEYERFSKY 102
Query: 108 L-GLRAHV------IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVE 160
           +  ++  V      I K ++  +K  P       +++ TP +++ L +    +LNL +++
Sbjct: 103 MPNVKVAVFFGGLSIKKDEEVLKKNCPH------IVVGTPGRILALAR--NKSLNLKHIK 154
Query: 161 WLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKR-GMFSATHTEDVAKWCRRKLKRRV 219
             I+DE DK+ E      R  +  I+     P+ K+  MFSAT ++++   CR+ ++  +
Sbjct: 155 HFILDECDKMLEQ--LDMRRDVQEIFRMT--PHEKQVMMFSATLSKEIRPVCRKFMQDPM 210
Query: 220 QINVG 224
           +I V 
Sbjct: 211 EIFVD 215

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 56.2 bits (134), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 92/185 (49%), Gaps = 21/185 (11%)
Query: 48  LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           LG  +   A +G GKTA F++  +  L  P       +++C TRELA Q   E  R S+ 
Sbjct: 44  LGMDVLCQAKSGMGKTAVFVLATLQQLE-PVTGQVSVLVMCHTRELAFQISKEYERFSKY 102
Query: 108 L-GLRAHV------IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVE 160
           +  ++  V      I K ++  +K  P       +++ TP +++ L +    +LNL +++
Sbjct: 103 MPNVKVAVFFGGLSIKKDEEVLKKNCPH------IVVGTPGRILALAR--NKSLNLKHIK 154
Query: 161 WLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKR-GMFSATHTEDVAKWCRRKLKRRV 219
             I+DE DK+ E      R  +  I+     P+ K+  MFSAT ++++   CR+ ++  +
Sbjct: 155 HFILDECDKMLEQ--LDMRRDVQEIFRMT--PHEKQVMMFSATLSKEIRPVCRKFMQDPM 210
Query: 220 QINVG 224
           +I V 
Sbjct: 211 EIFVD 215

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score = 54.3 bits (129), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 47/180 (26%), Positives = 87/180 (48%), Gaps = 19/180 (10%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIH----SLRGPKNLGFRAVIVCPTRELAKQTYNETVRL 104
           G  + A A +G+GKT  F I  +     S++ P+     A+++ PTRELA Q     + L
Sbjct: 58  GHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQ-----ALMLAPTRELALQIQKVVMAL 112
Query: 105 SEGLGLRAHV-IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLI 163
           +  + ++ H  IG      +  G R AQ   +++ TP ++   +Q          ++  I
Sbjct: 113 AFHMDIKVHACIGGTSFVEDAEGLRDAQ---IVVGTPGRVFDNIQR--RRFRTDKIKMFI 167
Query: 164 VDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           +DE+D++  +   GF++Q+  I+     P  +  + SAT   DV +   + ++  V+I V
Sbjct: 168 LDEADEMLSS---GFKEQIYQIFTLLP-PTTQVVLLSATMPNDVLEVTTKFMRNPVRILV 223

>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation Initiation Factor 4a From Saccharomyces Cerevisiae-The Prototype Of The Dead Box Protein Family Length = 224

Iteration: 1
 Score = 53.9 bits (128), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 47/180 (26%), Positives = 87/180 (48%), Gaps = 19/180 (10%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIH----SLRGPKNLGFRAVIVCPTRELAKQTYNETVRL 104
           G  + A A +G+GKT  F I  +     S++ P+     A+++ PTRELA Q     + L
Sbjct: 51  GHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQ-----ALMLAPTRELALQIQKVVMAL 105
Query: 105 SEGLGLRAHV-IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLI 163
           +  + ++ H  IG      +  G R AQ   +++ TP ++   +Q          ++  I
Sbjct: 106 AFHMDIKVHACIGGTSFVEDAEGLRDAQ---IVVGTPGRVFDNIQR--RRFRTDKIKMFI 160
Query: 164 VDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           +DE+D++  +   GF++Q+  I+     P  +  + SAT   DV +   + ++  V+I V
Sbjct: 161 LDEADEMLSS---GFKEQIYQIFTLLP-PTTQVVLLSATMPNDVLEVTTKFMRNPVRILV 216

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 46/178 (25%), Positives = 86/178 (48%), Gaps = 19/178 (10%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIH----SLRGPKNLGFRAVIVCPTRELAKQTYNETVRL 104
           G  + A A +G+GKT  F I  +     S++ P+     A+++ PTRELA Q     + L
Sbjct: 59  GHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQ-----ALMLAPTRELALQIQKVVMAL 113
Query: 105 SEGLGLRAHV-IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLI 163
           +  + ++ H  IG      +  G R AQ   +++ TP ++   +Q          ++  I
Sbjct: 114 AFHMDIKVHACIGGTSFVEDAEGLRDAQ---IVVGTPGRVFDNIQR--RRFRTDKIKMFI 168
Query: 164 VDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQI 221
           +DE+D++  +   GF++Q+  I+     P  +  + SAT   DV +   + ++  V+I
Sbjct: 169 LDEADEMLSS---GFKEQIYQIFTLLP-PTTQVVLLSATMPNDVLEVTTKFMRNPVRI 222

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 46/176 (26%), Positives = 84/176 (47%), Gaps = 9/176 (5%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  + A A +G+G TA F I I+  +        +A+++ PTRELA+Q     + L + +
Sbjct: 52  GYDVIAQAQSGTGXTATFAISILQQIE-LDLXATQALVLAPTRELAQQIQXVVMALGDYM 110
Query: 109 GLRAHV-IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES 167
           G   H  IG     AE       +   +++ TP ++  +L  +   L+   +   ++DE+
Sbjct: 111 GASCHACIGGTNVRAE-VQXLQMEAPHIIVGTPGRVFDML--NRRYLSPXYIXMFVLDEA 167
Query: 168 DKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           D++     RGF DQ+  I+   +  N +  + SAT   DV +     ++  ++I V
Sbjct: 168 DEMLS---RGFXDQIYDIFQXLNS-NTQVVLLSATMPSDVLEVTXXFMRDPIRILV 219

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 39/164 (23%), Positives = 86/164 (52%), Gaps = 11/164 (6%)
Query: 50  RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG 109
           R + A + +G+GKTAAF + ++  +  P++   +A+ + P+RELA+QT      + +   
Sbjct: 45  RNMIAQSQSGTGKTAAFSLTMLTRV-NPEDASPQAICLAPSRELARQTLEVVQEMGKFTK 103
Query: 110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK 169
           + + +I  +  + EK    +AQ   V++ TP  ++ L++     + L  ++  ++DE+D 
Sbjct: 104 ITSQLI--VPDSFEKNKQINAQ---VIVGTPGTVLDLMRR--KLMQLQKIKIFVLDEADN 156
Query: 170 LFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRR 213
           + +   +G  DQ   +       + +  +FSAT  + V ++ ++
Sbjct: 157 MLDQ--QGLGDQCIRVKRFLP-KDTQLVLFSATFADAVRQYAKK 197

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 39/164 (23%), Positives = 86/164 (52%), Gaps = 11/164 (6%)
Query: 50  RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG 109
           R + A + +G+GKTAAF + ++  +  P++   +A+ + P+RELA+QT      + +   
Sbjct: 45  RNMIAQSQSGTGKTAAFSLTMLTRV-NPEDASPQAICLAPSRELARQTLEVVQEMGKFTK 103
Query: 110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK 169
           + + +I  +  + EK    +AQ   V++ TP  ++ L++     + L  ++  ++DE+D 
Sbjct: 104 ITSQLI--VPDSFEKNKQINAQ---VIVGTPGTVLDLMRR--KLMQLQKIKIFVLDEADN 156
Query: 170 LFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRR 213
           + +   +G  DQ   +       + +  +FSAT  + V ++ ++
Sbjct: 157 MLDQ--QGLGDQCIRVKRFLP-KDTQLVLFSATFADAVRQYAKK 197

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 52/180 (28%), Positives = 87/180 (48%), Gaps = 27/180 (15%)
Query: 49  GRQIFACAPTGSGKTAAFLIP-IIHSLRGP----KNLGFRAVIVCPTRELAKQTYNETVR 103
           G  +   A TG+GKT ++L+P  IH    P    +  G   +++ PTRELA     E  +
Sbjct: 57  GIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSK 116
Query: 104 LSEGLGLRAHVI-------GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNL 156
            S   GL++  I       G+I+  +        +  D++I TP +L   LQM+  ++NL
Sbjct: 117 YSYK-GLKSICIYGGRNRNGQIEDIS--------KGVDIIIATPGRL-NDLQMNN-SVNL 165
Query: 157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLK 216
            ++ +L++DE+DK+ +     F  Q+  I      P+ +  M SAT  + V +     LK
Sbjct: 166 RSITYLVIDEADKMLDM---EFEPQIRKILLDVR-PDRQTVMTSATWPDTVRQLALSYLK 221

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 39/164 (23%), Positives = 86/164 (52%), Gaps = 11/164 (6%)
Query: 50  RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG 109
           R + A + +G+GKTAAF + ++  +  P++   +A+ + P+RELA+QT      + +   
Sbjct: 62  RNMIAQSQSGTGKTAAFSLTMLTRV-NPEDASPQAICLAPSRELARQTLEVVQEMGKFTK 120
Query: 110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK 169
           + + +I  +  + EK    +AQ   V++ TP  ++ L++     + L  ++  ++DE+D 
Sbjct: 121 ITSQLI--VPDSFEKNKQINAQ---VIVGTPGTVLDLMRRK--LMQLQKIKIFVLDEADN 173
Query: 170 LFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRR 213
           + +   +G  DQ   +       + +  +FSAT  + V ++ ++
Sbjct: 174 MLDQ--QGLGDQCIRVKRFLPK-DTQLVLFSATFADAVRQYAKK 214

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 37/145 (25%), Positives = 74/145 (51%), Gaps = 21/145 (14%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFR---AVIVCPTRELAKQTYNETVRLS 105
           GR + A + +G+GKTA F + ++  L    ++  R   A+I+ PTRELA Q     + L 
Sbjct: 38  GRDVIAQSQSGTGKTATFSVSVLQCL----DIQVRETQALILAPTRELAVQVQKGLLALG 93
Query: 106 EGLGLRAHVIGKIQQAAEKFGPRSAQKFD----VLITTPNKLVYLLQMDPPALNLANVEW 161
           + + +++H         E       +K D    V+  TP ++  +++    +L    ++ 
Sbjct: 94  DYMNVQSHACIGGTNVGEDI-----RKLDYGQHVVAGTPGRVFDMIRR--RSLRTRAIKM 146
Query: 162 LIVDESDKLFEAGVRGFRDQLAVIY 186
           L++DE+D++     +GF++Q+  +Y
Sbjct: 147 LVLDEADEMLN---KGFKEQIYDVY 168

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 38/145 (26%), Positives = 73/145 (50%), Gaps = 21/145 (14%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFR---AVIVCPTRELAKQTYNETVRLS 105
           GR + A + +G+GKTA F I ++  L    ++  R   A+I+ PTRELA Q     + L 
Sbjct: 74  GRDVIAQSQSGTGKTATFSISVLQCL----DIQVRETQALILAPTRELAVQIQKGLLALG 129
Query: 106 EGLGLRAHVIGKIQQAAEKFGPRSAQKFD----VLITTPNKLVYLLQMDPPALNLANVEW 161
           + + ++ H         E       +K D    V+  TP ++  +++    +L    ++ 
Sbjct: 130 DYMNVQCHACIGGTNVGEDI-----RKLDYGQHVVAGTPGRVFDMIRR--RSLRTRAIKM 182
Query: 162 LIVDESDKLFEAGVRGFRDQLAVIY 186
           L++DE+D++     +GF++Q+  +Y
Sbjct: 183 LVLDEADEMLN---KGFKEQIYDVY 204

>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 411

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 38/145 (26%), Positives = 73/145 (50%), Gaps = 21/145 (14%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFR---AVIVCPTRELAKQTYNETVRLS 105
           GR + A + +G+GKTA F I ++  L    ++  R   A+I+ PTRELA Q     + L 
Sbjct: 75  GRDVIAQSQSGTGKTATFSISVLQCL----DIQVRETQALILAPTRELAVQIQKGLLALG 130
Query: 106 EGLGLRAHVIGKIQQAAEKFGPRSAQKFD----VLITTPNKLVYLLQMDPPALNLANVEW 161
           + + ++ H         E       +K D    V+  TP ++  +++    +L    ++ 
Sbjct: 131 DYMNVQCHACIGGTNVGEDI-----RKLDYGQHVVAGTPGRVFDMIRR--RSLRTRAIKM 183
Query: 162 LIVDESDKLFEAGVRGFRDQLAVIY 186
           L++DE+D++     +GF++Q+  +Y
Sbjct: 184 LVLDEADEMLN---KGFKEQIYDVY 205

>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 413

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 38/145 (26%), Positives = 73/145 (50%), Gaps = 21/145 (14%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFR---AVIVCPTRELAKQTYNETVRLS 105
           GR + A + +G+GKTA F I ++  L    ++  R   A+I+ PTRELA Q     + L 
Sbjct: 75  GRDVIAQSQSGTGKTATFSISVLQCL----DIQVRETQALILAPTRELAVQIQKGLLALG 130
Query: 106 EGLGLRAHVIGKIQQAAEKFGPRSAQKFD----VLITTPNKLVYLLQMDPPALNLANVEW 161
           + + ++ H         E       +K D    V+  TP ++  +++    +L    ++ 
Sbjct: 131 DYMNVQCHACIGGTNVGEDI-----RKLDYGQHVVAGTPGRVFDMIRR--RSLRTRAIKM 183
Query: 162 LIVDESDKLFEAGVRGFRDQLAVIY 186
           L++DE+D++     +GF++Q+  +Y
Sbjct: 184 LVLDEADEMLN---KGFKEQIYDVY 205

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 38/145 (26%), Positives = 73/145 (50%), Gaps = 21/145 (14%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFR---AVIVCPTRELAKQTYNETVRLS 105
           GR + A + +G+GKTA F I ++  L    ++  R   A+I+ PTRELA Q     + L 
Sbjct: 53  GRDVIAQSQSGTGKTATFSISVLQCL----DIQVRETQALILAPTRELAVQIQKGLLALG 108
Query: 106 EGLGLRAHVIGKIQQAAEKFGPRSAQKFD----VLITTPNKLVYLLQMDPPALNLANVEW 161
           + + ++ H         E       +K D    V+  TP ++  +++    +L    ++ 
Sbjct: 109 DYMNVQCHACIGGTNVGEDI-----RKLDYGQHVVAGTPGRVFDMIRR--RSLRTRAIKM 161
Query: 162 LIVDESDKLFEAGVRGFRDQLAVIY 186
           L++DE+D++     +GF++Q+  +Y
Sbjct: 162 LVLDEADEMLN---KGFKEQIYDVY 183

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 48.1 bits (113), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 37/145 (25%), Positives = 73/145 (50%), Gaps = 21/145 (14%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFR---AVIVCPTRELAKQTYNETVRLS 105
           GR + A + +G+GKTA F + ++  L    ++  R   A+I+ PTRELA Q     + L 
Sbjct: 38  GRDVIAQSQSGTGKTATFSVSVLQCL----DIQVRETQALILAPTRELAVQVQKGLLALG 93
Query: 106 EGLGLRAHVIGKIQQAAEKFGPRSAQKFD----VLITTPNKLVYLLQMDPPALNLANVEW 161
           + + ++ H         E       +K D    V+  TP ++  +++    +L    ++ 
Sbjct: 94  DYMNVQCHACIGGTNVGEDI-----RKLDYGQHVVAGTPGRVFDMIRR--RSLRTRAIKM 146
Query: 162 LIVDESDKLFEAGVRGFRDQLAVIY 186
           L++DE+D++     +GF++Q+  +Y
Sbjct: 147 LVLDEADEMLN---KGFKEQIYDVY 168

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 47.4 bits (111), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 46/178 (25%), Positives = 81/178 (45%), Gaps = 19/178 (10%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIH----SLRGPKNLGFRAVIVCPTRELAKQTYNETVRL 104
           G  + A A +G+GKT  F I  +     S++ P+     A+ + PTRELA Q       L
Sbjct: 58  GHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQ-----ALXLAPTRELALQIQKVVXAL 112
Query: 105 SEGLGLRAHV-IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLI 163
           +    ++ H  IG      +  G R AQ   +++ TP ++   +Q          ++  I
Sbjct: 113 AFHXDIKVHACIGGTSFVEDAEGLRDAQ---IVVGTPGRVFDNIQR--RRFRTDKIKXFI 167
Query: 164 VDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQI 221
           +DE+D+   +   GF++Q+  I+     P  +  + SAT   DV +   +  +  V+I
Sbjct: 168 LDEADEXLSS---GFKEQIYQIFTLLP-PTTQVVLLSATXPNDVLEVTTKFXRNPVRI 221

>pdb|2ZJ2|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 1 Length = 720

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 50/170 (29%), Positives = 77/170 (45%), Gaps = 18/170 (10%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G+      PT SGKT    I ++H +      G +AV + P + LA++ + E  +  E +
Sbjct: 39  GKNALISIPTASGKTLIAEIAMVHRIL---TQGGKAVYIVPLKALAEEKFQE-FQDWEKI 94
Query: 109 GLR-AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES 167
           GLR A   G      E  G     K+D++I T  K   LL+     +   +V+ L+ DE 
Sbjct: 95  GLRVAMATGDYDSKDEWLG-----KYDIIIATAEKFDSLLRHGSSWIK--DVKILVADE- 146
Query: 168 DKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT--HTEDVAKWCRRKL 215
             +   G R     L VI A   G     G+ SAT  + E++A+W   +L
Sbjct: 147 --IHLIGSRDRGATLEVILAHMLGKAQIIGL-SATIGNPEELAEWLNAEL 193

>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308 Length = 715

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 58/120 (48%), Gaps = 14/120 (11%)
Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G ++   +PTGSGKT    + II  L   KN G +A+ V P R L  + Y  T +  E +
Sbjct: 46  GNRLLLTSPTGSGKTLIAEMGIISFLL--KN-GGKAIYVTPLRALTNEKY-LTFKDWELI 101
Query: 109 GLRAHVIGKIQQAAEKFGPRSA--QKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE 166
           G       K+   +  +    A  + +D++ITT  KL  L +  P  LN   V + ++DE
Sbjct: 102 GF------KVAMTSGDYDTDDAWLKNYDIIITTYEKLDSLWRHRPEWLN--EVNYFVLDE 153

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	226
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	4e-74
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	8e-37
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	3e-36
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	5e-34
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	5e-33
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	1e-31
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-30
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	3e-29
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	7e-29
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	7e-27
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	3e-26
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-25
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-24
3bor_A	237	Human initiation factor 4A-II; translation initiat	2e-24
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	2e-24
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	7e-24
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	7e-24
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	2e-23
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	2e-23
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	4e-23
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	5e-23
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	5e-23
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	7e-23
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	2e-22
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	6e-21
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	6e-21
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	3e-20
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-19
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	1e-19
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	2e-19
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	4e-17
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	5e-12
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	9e-12
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	6e-11
3b6e_A	216	Interferon-induced helicase C domain-containing P;	1e-10
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	2e-09
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	7e-09
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	6e-08
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	2e-07
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	2e-07
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	2e-07
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	3e-07
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	4e-07
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	8e-06
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	8e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	8e-05
1yks_A	440	Genome polyprotein [contains: flavivirin protease	1e-04

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens} Length = 245

 Score =  223 bits (572), Expect = 4e-74
 Identities = 101/178 (56%), Positives = 135/178 (75%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR++ A APTGSGKT AF IPI+  L+ P N GFRA+I+ PTRELA Q + E +++SEG 
Sbjct: 66  GRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGT 125

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
           G R H+I K   AA+KFGP+S++KFD+L+TTPN+L+YLL+ DPP ++LA+VEWL+VDESD
Sbjct: 126 GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESD 185

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR 226
           KLFE G  GFRDQLA I+ AC+   ++R MFSAT   DV +WC+  L   + +++G R
Sbjct: 186 KLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR 243

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  132 bits (334), Expect = 8e-37
 Identities = 28/176 (15%), Positives = 68/176 (38%), Gaps = 14/176 (7%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G+     APTG GKT   ++  +   R     G ++ +V PT  L KQT     +L++  
Sbjct: 36  GKSFTMVAPTGVGKTTFGMMTALWLARK----GKKSALVFPTVTLVKQTLERLQKLADEK 91

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQK--FDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE 166
                    +++  ++   +S ++  + +L+ +       +  +   L+    +++ VD+
Sbjct: 92  VKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQ----FVSKNREKLSQKRFDFVFVDD 147

Query: 167 SDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN 222
            D + +A          ++        + R  FS      + +  +      + ++
Sbjct: 148 VDAVLKA---SRNIDTLLMMVGIP-EEIIRKAFSTIKQGKIYERPKNLKPGILVVS 199

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score =  126 bits (319), Expect = 3e-36
 Identities = 50/183 (27%), Positives = 90/183 (49%), Gaps = 20/183 (10%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNL---GFRAVIVCPTRELAKQTYNETVRLS 105
           G+ +   A TGSGKT AFL+P++ +L   +     G   +I+ PTRELA QT+    ++ 
Sbjct: 62  GKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVG 121

Query: 106 EGLGLRAHVI--GK--IQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEW 161
           +     A +I  GK    +A            ++L+ TP +L+  +  +  + +  +++ 
Sbjct: 122 KNHDFSAGLIIGGKDLKHEAERINNI------NILVCTPGRLLQHMD-ETVSFHATDLQM 174

Query: 162 LIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGM-FSATHTEDVAKWCRRKLKRRVQ 220
           L++DE+D++ +    GF D +  +      P  ++ + FSAT T+ V    R  LK    
Sbjct: 175 LVLDEADRILDM---GFADTMNAVIENL--PKKRQTLLFSATQTKSVKDLARLSLKNPEY 229

Query: 221 INV 223
           + V
Sbjct: 230 VWV 232

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens} Length = 262

 Score =  121 bits (306), Expect = 5e-34
 Identities = 55/174 (31%), Positives = 87/174 (50%), Gaps = 13/174 (7%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSL---RGPKNLGFRAVIVCPTRELAKQTYNETVRLS 105
           GR + A A TGSGKT AFLIP +  +   R     G   +I+ PTRELA QT+     L 
Sbjct: 91  GRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELM 150

Query: 106 EGLGLRAH-VIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIV 164
                    ++G   ++AE    +     ++++ TP +L+  +Q + P     N++ L++
Sbjct: 151 THHVHTYGLIMGGSNRSAEAQ--KLGNGINIIVATPGRLLDHMQ-NTPGFMYKNLQCLVI 207

Query: 165 DESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGM-FSATHTEDVAKWCRRKLKR 217
           DE+D++ +    GF ++L  I      P  ++ M FSAT T  V    R  LK+
Sbjct: 208 DEADRILDV---GFEEELKQIIKLL--PTRRQTMLFSATQTRKVEDLARISLKK 256

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens} Length = 249

 Score =  118 bits (298), Expect = 5e-33
 Identities = 58/182 (31%), Positives = 91/182 (50%), Gaps = 21/182 (11%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSL-RGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           GR I   A TGSGKT AF +PI+++L   P+     A+++ PTRELA Q   +   L   
Sbjct: 80  GRDIIGLAETGSGKTGAFALPILNALLETPQ--RLFALVLTPTRELAFQISEQFEALGSS 137

Query: 108 LGLRAHVI-G----KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL 162
           +G+++ VI G      Q  A    P       ++I TP +L+  L+ +    NL  +++L
Sbjct: 138 IGVQSAVIVGGIDSMSQSLALAKKP------HIIIATPGRLIDHLE-NTKGFNLRALKYL 190

Query: 163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGM-FSATHTEDVAKWCRRKLKRRVQI 221
           ++DE+D++       F  ++  I      P  ++   FSAT T+ V K  R  LK  V+ 
Sbjct: 191 VMDEADRILNM---DFETEVDKILKVI--PRDRKTFLFSATMTKKVQKLQRAALKNPVKC 245

Query: 222 NV 223
            V
Sbjct: 246 AV 247

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19 Length = 253

 Score =  114 bits (289), Expect = 1e-31
 Identities = 59/192 (30%), Positives = 95/192 (49%), Gaps = 27/192 (14%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSL--RGPKNLGF------RAVIVCPTRELAKQTYNE 100
            R I ACA TGSGKTAAFLIPII+ L  +      +      + +I+ PTRELA Q  +E
Sbjct: 60  HRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSE 119

Query: 101 TVRLSEGLGLRAHVI----GKIQQAAE-KFGPRSAQKFDVLITTPNKLVYLLQMDPPALN 155
           + + S    LR+ V+        Q  E + G        +L+ TP +LV  ++     ++
Sbjct: 120 SQKFSLNTPLRSCVVYGGADTHSQIREVQMGC------HLLVATPGRLVDFIEK--NKIS 171

Query: 156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKR---GMFSATHTEDVAKWCR 212
           L   +++++DE+D++ +    GF  Q+  I    + P+       MFSAT  +++ K   
Sbjct: 172 LEFCKYIVLDEADRMLDM---GFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAA 228

Query: 213 RKLKRRVQINVG 224
             L   + + VG
Sbjct: 229 DFLYNYIFMTVG 240

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score =  115 bits (291), Expect = 1e-30
 Identities = 56/187 (29%), Positives = 89/187 (47%), Gaps = 23/187 (12%)

Query: 49  GRQIFACAPTGSGKTAAFLIPII-HSLRGPKNLGF---RAVIVCPTRELAKQTYNETVRL 104
           GR + ACA TGSGKTAAFL+PI+   L  P  L     + VIV PTRELA Q +NE  + 
Sbjct: 93  GRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKF 152

Query: 105 SEGLGLRAHVI----GKIQQAAE-KFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANV 159
           +    L+  ++        Q      G        V+I TP +L+  +      +   + 
Sbjct: 153 AFESYLKIGIVYGGTSFRHQNECITRGC------HVVIATPGRLLDFVDR--TFITFEDT 204

Query: 160 EWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKR--GMFSATHTEDVAKWCRRKLKR 217
            ++++DE+D++ +    GF + +  I    +    +    MFSAT  E++ +     LK 
Sbjct: 205 RFVVLDEADRMLDM---GFSEDMRRIMTHVTMRP-EHQTLMFSATFPEEIQRMAGEFLKN 260

Query: 218 RVQINVG 224
            V + +G
Sbjct: 261 YVFVAIG 267

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} Length = 242

 Score =  108 bits (272), Expect = 3e-29
 Identities = 52/185 (28%), Positives = 87/185 (47%), Gaps = 21/185 (11%)

Query: 49  GRQIFACAPTGSGKTAAFLIP-IIHSLRGP---KNLGFRAVIVCPTRELAKQTYNETVRL 104
           G  +   A TGSGKT ++L+P I+H    P   +  G   +++ PTRELA+Q        
Sbjct: 66  GLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEY 125

Query: 105 SEGLGLRAHVI----GKIQQAAE-KFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANV 159
                L++  I     K  Q  + + G       ++ I TP +L+  L+      NL   
Sbjct: 126 CRACRLKSTCIYGGAPKGPQIRDLERGV------EICIATPGRLIDFLECG--KTNLRRT 177

Query: 160 EWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRV 219
            +L++DE+D++ +    GF  Q+  I      P+ +  M+SAT  ++V +     LK  +
Sbjct: 178 TYLVLDEADRMLDM---GFEPQIRKIVDQIR-PDRQTLMWSATWPKEVRQLAEDFLKDYI 233

Query: 220 QINVG 224
            IN+G
Sbjct: 234 HINIG 238

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  110 bits (278), Expect = 7e-29
 Identities = 56/204 (27%), Positives = 89/204 (43%), Gaps = 42/204 (20%)

Query: 49  GRQIFACAPTGSGKTAAFLIPII-HSLRGPKNLGFR----------------AVIVCPTR 91
            R + ACA TGSGKTAAFL+PI+            R                ++++ PTR
Sbjct: 52  KRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTR 111

Query: 92  ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG--PRSAQKF------DVLITTPNKL 143
           ELA Q Y E  + S    +R  V+         +G      Q         +L+ TP +L
Sbjct: 112 ELAVQIYEEARKFSYRSRVRPCVV---------YGGADIGQQIRDLERGCHLLVATPGRL 162

Query: 144 VYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACS-GPNLKR--GMFS 200
           V +++     + L   ++L++DE+D++ +    GF  Q+  I    +  P   R   MFS
Sbjct: 163 VDMMER--GKIGLDFCKYLVLDEADRMLDM---GFEPQIRRIVEQDTMPPKGVRHTMMFS 217

Query: 201 ATHTEDVAKWCRRKLKRRVQINVG 224
           AT  +++    R  L   + + VG
Sbjct: 218 ATFPKEIQMLARDFLDEYIFLAVG 241

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A Length = 400

 Score =  105 bits (264), Expect = 7e-27
 Identities = 52/180 (28%), Positives = 85/180 (47%), Gaps = 18/180 (10%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR I A A  G+GKTAAF+IP +  ++ PK    +A+I+ PTRELA QT      L +  
Sbjct: 58  GRDILARAKNGTGKTAAFVIPTLEKVK-PKLNKIQALIMVPTRELALQTSQVVRTLGKHC 116

Query: 109 GLRAHVI-G----KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLI 163
           G+   V  G    +                 +L+ TP +++ L        +L++    I
Sbjct: 117 GISCMVTTGGTNLRDDILRLNETV------HILVGTPGRVLDLASRK--VADLSDCSLFI 168

Query: 164 VDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           +DE+DK+     R F+  +  I +    P  +  +FSAT    V ++  + L +  +IN+
Sbjct: 169 MDEADKMLS---RDFKTIIEQILSFLP-PTHQSLLFSATFPLTVKEFMVKHLHKPYEINL 224

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens} Length = 228

 Score =  100 bits (251), Expect = 3e-26
 Identities = 51/185 (27%), Positives = 86/185 (46%), Gaps = 23/185 (12%)

Query: 49  GRQIFACAPTGSGKTAAFLIP-IIHSLRGPKNL----GFRAVIVCPTRELAKQTYNETVR 103
           G  +   A TG+GKT ++L+P  IH    P +     G   +++ PTRELA     E  +
Sbjct: 57  GIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSK 116

Query: 104 LSEGLGLRAHVI----GKIQQAAE-KFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLAN 158
            S   GL++  I     +  Q  +   G       D++I TP +L  L   +  ++NL +
Sbjct: 117 YSY-KGLKSICIYGGRNRNGQIEDISKGV------DIIIATPGRLNDLQMNN--SVNLRS 167

Query: 159 VEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRR 218
           + +L++DE+DK+ +     F  Q+  I      P+ +  M SAT  + V +     LK  
Sbjct: 168 ITYLVIDEADKMLDM---EFEPQIRKILLDVR-PDRQTVMTSATWPDTVRQLALSYLKDP 223

Query: 219 VQINV 223
           + + V
Sbjct: 224 MIVYV 228

>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 =  102 bits (257), Expect = 1e-25
 Identities = 53/199 (26%), Positives = 86/199 (43%), Gaps = 29/199 (14%)

Query: 45  LSPLGRQIFACAPTGSGKTAAFLIPIIHSL---RGPKNLGFRAVIVCPTRELAKQTYNET 101
           LS     + A A TG+GKT AFLIPI   L   +       +AVIV PTR+LA Q   E 
Sbjct: 107 LSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEV 166

Query: 102 VRLSEG----LGLRAH-VIG----KIQQAA-EKFGPRSAQKFDVLITTPNKLVYLLQMDP 151
            ++ +            ++G    +       K  P      +++I TP +L+ +L+   
Sbjct: 167 KKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRP------NIVIATPGRLIDVLE-KY 219

Query: 152 PALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAA-----CSGPNLKRGM-FSATHTE 205
                  V++ ++DE+D+L E    GFRD L  I            +  + + FSAT  +
Sbjct: 220 SNKFFRFVDYKVLDEADRLLEI---GFRDDLETISGILNEKNSKSADNIKTLLFSATLDD 276

Query: 206 DVAKWCRRKLKRRVQINVG 224
            V K     + ++  + + 
Sbjct: 277 KVQKLANNIMNKKECLFLD 295

>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 =  100 bits (250), Expect = 1e-24
 Identities = 55/196 (28%), Positives = 86/196 (43%), Gaps = 23/196 (11%)

Query: 45  LSPLGRQIFACAPTGSGKTAAFLIPIIHSL---RGPKNLGFRAVIVCPTRELAKQTYNET 101
           LS     + A A TG+GKT AFLIPI   L   +       +AVIV PTR+LA Q   E 
Sbjct: 56  LSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEV 115

Query: 102 VRLSEG----LGLRAH-VIG--KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPAL 154
            ++ +            ++G    + A  K          ++I TP +L+ +L+      
Sbjct: 116 KKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPN---IVIATPGRLIDVLE-KYSNK 171

Query: 155 NLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRG------MFSATHTEDVA 208
               V++ ++DE+D+L E    GFRD L  I    +  N K        +FSAT  + V 
Sbjct: 172 FFRFVDYKVLDEADRLLEI---GFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQ 228

Query: 209 KWCRRKLKRRVQINVG 224
           K     + ++  + + 
Sbjct: 229 KLANNIMNKKECLFLD 244

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A* Length = 237

 Score = 96.1 bits (240), Expect = 2e-24
 Identities = 46/178 (25%), Positives = 92/178 (51%), Gaps = 13/178 (7%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  + A A +G+GKTA F I I+  L   +    +A+++ PTRELA+Q     + L + +
Sbjct: 67  GYDVIAQAQSGTGKTATFAISILQQLE-IEFKETQALVLAPTRELAQQIQKVILALGDYM 125

Query: 109 GLRAH-VIG--KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVD 165
           G   H  IG   ++   +K    +     +++ TP ++  +L      L+   ++  ++D
Sbjct: 126 GATCHACIGGTNVRNEMQKLQAEAPH---IVVGTPGRVFDMLNRR--YLSPKWIKMFVLD 180

Query: 166 ESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           E+D++     RGF+DQ+  I+   +  +++  + SAT   DV +  ++ ++  ++I V
Sbjct: 181 EADEMLS---RGFKDQIYEIFQKLN-TSIQVVLLSATMPTDVLEVTKKFMRDPIRILV 234

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A* Length = 230

 Score = 95.8 bits (239), Expect = 2e-24
 Identities = 46/181 (25%), Positives = 87/181 (48%), Gaps = 19/181 (10%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  +   A +G+GKT  F    + SL   +NL  + +I+ PTRE+A Q ++    +   +
Sbjct: 61  GLDLIVQAKSGTGKTCVFSTIALDSLV-LENLSTQILILAPTREIAVQIHSVITAIGIKM 119

Query: 109 -GLRAHVI-G----KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL 162
            GL  HV  G       +          +K  + + +P ++  L+++D   LN  ++   
Sbjct: 120 EGLECHVFIGGTPLSQDK-------TRLKKCHIAVGSPGRIKQLIELD--YLNPGSIRLF 170

Query: 163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN 222
           I+DE+DKL E G   F++Q+  IY++    + +    SAT+ E +A    + ++    + 
Sbjct: 171 ILDEADKLLEEG--SFQEQINWIYSSLP-ASKQMLAVSATYPEFLANALTKYMRDPTFVR 227

Query: 223 V 223
           +
Sbjct: 228 L 228

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19 Length = 220

 Score = 93.8 bits (234), Expect = 7e-24
 Identities = 50/183 (27%), Positives = 89/183 (48%), Gaps = 19/183 (10%)

Query: 48  LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           LG  +   A +G GKTA F++  +  L  P       +++C TRELA Q   E  R S+ 
Sbjct: 50  LGMDVLCQAKSGMGKTAVFVLATLQQLE-PVTGQVSVLVMCHTRELAFQISKEYERFSKY 108

Query: 108 L-GLRAHVI-G----KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEW 161
           +  ++  V  G    K  +   K          +++ TP +++ L +    +LNL +++ 
Sbjct: 109 MPNVKVAVFFGGLSIKKDEEVLKKNCP-----HIVVGTPGRILALARNK--SLNLKHIKH 161

Query: 162 LIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKR-GMFSATHTEDVAKWCRRKLKRRVQ 220
            I+DE DK+ E      R  +  I+     P+ K+  MFSAT ++++   CR+ ++  ++
Sbjct: 162 FILDECDKMLEQ--LDMRRDVQEIFRMT--PHEKQVMMFSATLSKEIRPVCRKFMQDPME 217

Query: 221 INV 223
           I V
Sbjct: 218 IFV 220

>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 = 97.3 bits (243), Expect = 7e-24
 Identities = 43/180 (23%), Positives = 87/180 (48%), Gaps = 18/180 (10%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR + A + +G+GKTA F I ++  L   +    +A+I+ PTRELA Q     + L + +
Sbjct: 74  GRDVIAQSQSGTGKTATFSISVLQCLD-IQVRETQALILAPTRELAVQIQKGLLALGDYM 132

Query: 109 GLRAH-VIG----KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLI 163
            ++ H  IG            +G        V+  TP ++  +++    +L    ++ L+
Sbjct: 133 NVQCHACIGGTNVGEDIRKLDYGQ------HVVAGTPGRVFDMIRRR--SLRTRAIKMLV 184

Query: 164 VDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           +DE+D++     +GF++Q+  +Y     P  +  + SAT   ++ +   + +   ++I V
Sbjct: 185 LDEADEMLN---KGFKEQIYDVYRYLP-PATQVVLISATLPHEILEMTNKFMTDPIRILV 240

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A Length = 224

 Score = 93.0 bits (232), Expect = 2e-23
 Identities = 40/175 (22%), Positives = 78/175 (44%), Gaps = 9/175 (5%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  + A A +G+GKT  F I  +  +        +A+++ PTRELA Q     + L+  +
Sbjct: 51  GHDVLAQAQSGTGKTGTFSIAALQRID-TSVKAPQALMLAPTRELALQIQKVVMALAFHM 109

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
            ++ H         E       +   +++ TP ++   +Q          ++  I+DE+D
Sbjct: 110 DIKVHACIGGTSFVEDA--EGLRDAQIVVGTPGRVFDNIQRR--RFRTDKIKMFILDEAD 165

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           ++      GF++Q+  I+     P  +  + SAT   DV +   + ++  V+I V
Sbjct: 166 EMLS---SGFKEQIYQIFTLLP-PTTQVVLLSATMPNDVLEVTTKFMRNPVRILV 216

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score = 91.4 bits (228), Expect = 4e-23
 Identities = 47/180 (26%), Positives = 85/180 (47%), Gaps = 19/180 (10%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR I A A  G+GK+ A+LIP++  L   K    +A+++ PTRELA Q     +++S+ +
Sbjct: 40  GRDILARAKNGTGKSGAYLIPLLERLD-LKKDNIQAMVIVPTRELALQVSQICIQVSKHM 98

Query: 109 -GLRAHVI-G----KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL 162
            G +     G    +                 V+I TP +++ L++       + +V+ +
Sbjct: 99  GGAKVMATTGGTNLRDDIMRLDDTV------HVVIATPGRILDLIKKG--VAKVDHVQMI 150

Query: 163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN 222
           ++DE+DKL     + F   +  I       N +  ++SAT    V K+    L++  +IN
Sbjct: 151 VLDEADKLLS---QDFVQIMEDIILTLP-KNRQILLYSATFPLSVQKFMNSHLEKPYEIN 206

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 91.5 bits (228), Expect = 5e-23
 Identities = 47/185 (25%), Positives = 88/185 (47%), Gaps = 24/185 (12%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  +   + TG+GKT A+L+PI+  ++ P+    +AVI  PTRELA Q Y+ET+++++  
Sbjct: 41  GESMVGQSQTGTGKTHAYLLPIMEKIK-PERAEVQAVITAPTRELATQIYHETLKITKFC 99

Query: 109 GLRAHV----------IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLAN 158
                +            K         P       ++I TP ++   ++    AL++  
Sbjct: 100 PKDRMIVARCLIGGTDKQK-ALEKLNVQP------HIVIGTPGRINDFIREQ--ALDVHT 150

Query: 159 VEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRR 218
              L+VDE+D + +    GF   +  I A     +L+  +FSAT  E +  + ++ ++  
Sbjct: 151 AHILVVDEADLMLD---MGFITDVDQIAARMP-KDLQMLVFSATIPEKLKPFLKKYMENP 206

Query: 219 VQINV 223
             ++V
Sbjct: 207 TFVHV 211

>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 = 94.6 bits (236), Expect = 5e-23
 Identities = 48/180 (26%), Positives = 87/180 (48%), Gaps = 13/180 (7%)

Query: 48  LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           LG  +   A +G GKTA F++  +  L  P       +++C TRELA Q   E  R S+ 
Sbjct: 44  LGMDVLCQAKSGMGKTAVFVLATLQQLE-PVTGQVSVLVMCHTRELAFQISKEYERFSKY 102

Query: 108 L-GLRAHVI--GK-IQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLI 163
           +  ++  V   G  I++  E           +++ TP +++ L +    +LNL +++  I
Sbjct: 103 MPNVKVAVFFGGLSIKKDEEVLKKNCPH---IVVGTPGRILALARNK--SLNLKHIKHFI 157

Query: 164 VDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           +DE DK+ E      R  +  I+        +  MFSAT ++++   CR+ ++  ++I V
Sbjct: 158 LDECDKMLEQ--LDMRRDVQEIFRMTP-HEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 214

>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 = 94.1 bits (235), Expect = 7e-23
 Identities = 40/175 (22%), Positives = 78/175 (44%), Gaps = 9/175 (5%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  + A A +G+GKT  F I  +  +        +A+++ PTRELA Q     + L+  +
Sbjct: 58  GHDVLAQAQSGTGKTGTFSIAALQRID-TSVKAPQALMLAPTRELALQIQKVVMALAFHM 116

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
            ++ H         E       +   +++ TP ++   +Q          ++  I+DE+D
Sbjct: 117 DIKVHACIGGTSFVEDA--EGLRDAQIVVGTPGRVFDNIQRR--RFRTDKIKMFILDEAD 172

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           ++      GF++Q+  I+     P  +  + SAT   DV +   + ++  V+I V
Sbjct: 173 EMLS---SGFKEQIYQIFTLLP-PTTQVVLLSATMPNDVLEVTTKFMRNPVRILV 223

>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 = 93.4 bits (233), Expect = 2e-22
 Identities = 45/181 (24%), Positives = 87/181 (48%), Gaps = 19/181 (10%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  + A A +G+GKTA F I I+  +        +A+++ PTRELA+Q     + L + +
Sbjct: 77  GYDVIAQAQSGTGKTATFAISILQQIE-LDLKATQALVLAPTRELAQQIQKVVMALGDYM 135

Query: 109 GLRAHV------IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL 162
           G   H       +    Q  +   P       +++ TP ++  +L      L+   ++  
Sbjct: 136 GASCHACIGGTNVRAEVQKLQMEAP------HIIVGTPGRVFDMLNRR--YLSPKYIKMF 187

Query: 163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN 222
           ++DE+D++     RGF+DQ+  I+   +  N +  + SAT   DV +  ++ ++  ++I 
Sbjct: 188 VLDEADEMLS---RGFKDQIYDIFQKLN-SNTQVVLLSATMPSDVLEVTKKFMRDPIRIL 243

Query: 223 V 223
           V
Sbjct: 244 V 244

>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 = 88.3 bits (220), Expect = 6e-21
 Identities = 50/183 (27%), Positives = 88/183 (48%), Gaps = 25/183 (13%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G+ +   A TGSGKTAA+ IPI+    G      ++++V PTREL +Q  +    +   +
Sbjct: 31  GKNVVVRAKTGSGKTAAYAIPILE--LGM-----KSLVVTPTRELTRQVASHIRDIGRYM 83

Query: 109 GLRAHVI--GKIQQAAEKFGP--RSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIV 164
             +   +  G        +       +  D+++ TP +L+ L       ++L++ E +I+
Sbjct: 84  DTKVAEVYGG------MPYKAQINRVRNADIVVATPGRLLDLWSKG--VIDLSSFEIVII 135

Query: 165 DESDKLFEAGVRGFRDQLAVIYAACSGPNLKR-GMFSATHTEDVAKWCRRKLKRRVQINV 223
           DE+D +FE    GF D + +I A     N K  G+FSAT  E++ K  +  +    +I  
Sbjct: 136 DEADLMFEM---GFIDDIKIILAQT--SNRKITGLFSATIPEEIRKVVKDFITNYEEIEA 190

Query: 224 GLR 226
            + 
Sbjct: 191 CIG 193

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A Length = 207

 Score = 85.7 bits (213), Expect = 6e-21
 Identities = 54/182 (29%), Positives = 89/182 (48%), Gaps = 21/182 (11%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSL--RGPKNLGFRAVIVCPTRELAKQTYNETVRLSE 106
           G+ +   A TG+GKT AF +PI   L     +    RA+++ PTRELA Q  +E   ++ 
Sbjct: 38  GKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAP 97

Query: 107 GLGLRAHVIG----KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWL 162
            L + A V G      Q+ A   G       D ++ TP + +  L+     L+L+ VE  
Sbjct: 98  HLKVVA-VYGGTGYGKQKEALLRGA------DAVVATPGRALDYLRQG--VLDLSRVEVA 148

Query: 163 IVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGM-FSATHTEDVAKWCRRKLKRRVQI 221
           ++DE+D++      GF +++  + +A   P  ++ + FSAT      +   R +K  V I
Sbjct: 149 VLDEADEMLSM---GFEEEVEALLSAT--PPSRQTLLFSATLPSWAKRLAERYMKNPVLI 203

Query: 222 NV 223
           NV
Sbjct: 204 NV 205

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens} Length = 300

 Score = 85.9 bits (213), Expect = 3e-20
 Identities = 39/182 (21%), Positives = 81/182 (44%), Gaps = 14/182 (7%)

Query: 45  LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL 104
           L+   + + A + +G+GKTAAF++ ++  +  P N   + + + PT ELA QT     ++
Sbjct: 127 LAEPPQNLIAQSQSGTGKTAAFVLAMLSQVE-PANKYPQCLCLSPTYELALQTGKVIEQM 185

Query: 105 SEGL-GLRAHVI--GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEW 161
            +    L+      G   +  +K          ++I TP  ++         ++   ++ 
Sbjct: 186 GKFYPELKLAYAVRGNKLERGQKISE------QIVIGTPGTVLDWCS-KLKFIDPKKIKV 238

Query: 162 LIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQI 221
            ++DE+D +     +G +DQ   I       N +  +FSAT  + V K+ ++ +     I
Sbjct: 239 FVLDEADVMIAT--QGHQDQSIRIQRMLP-RNCQMLLFSATFEDSVWKFAQKVVPDPNVI 295

Query: 222 NV 223
            +
Sbjct: 296 KL 297

>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 = 85.4 bits (212), Expect = 1e-19
 Identities = 40/186 (21%), Positives = 82/186 (44%), Gaps = 22/186 (11%)

Query: 45  LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL 104
           L+   + + A + +G+GKTAAF++ ++  +  P N   + + + PT ELA QT     ++
Sbjct: 127 LAEPPQNLIAQSQSGTGKTAAFVLAMLSQVE-PANKYPQCLCLSPTYELALQTGKVIEQM 185

Query: 105 SEGL-GLRAHVI--GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMD----PPALNLA 157
            +    L+      G   +  +K          ++I TP  +     +D       ++  
Sbjct: 186 GKFYPELKLAYAVRGNKLERGQKISE------QIVIGTPGTV-----LDWCSKLKFIDPK 234

Query: 158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKR 217
            ++  ++DE+D +     +G +DQ   I       N +  +FSAT  + V K+ ++ +  
Sbjct: 235 KIKVFVLDEADVMIAT--QGHQDQSIRIQRMLP-RNCQMLLFSATFEDSVWKFAQKVVPD 291

Query: 218 RVQINV 223
              I +
Sbjct: 292 PNVIKL 297

>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 = 85.3 bits (212), Expect = 1e-19
 Identities = 40/186 (21%), Positives = 82/186 (44%), Gaps = 22/186 (11%)

Query: 45  LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL 104
           L+   + + A + +G+GKTAAF++ ++  +  P N   + + + PT ELA QT     ++
Sbjct: 60  LAEPPQNLIAQSQSGTGKTAAFVLAMLSQVE-PANKYPQCLCLSPTYELALQTGKVIEQM 118

Query: 105 SEGL-GLRAHVI--GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMD----PPALNLA 157
            +    L+      G   +  +K          ++I TP  +     +D       ++  
Sbjct: 119 GKFYPELKLAYAVRGNKLERGQKISE------QIVIGTPGTV-----LDWCSKLKFIDPK 167

Query: 158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKR 217
            ++  ++DE+D +     +G +DQ   I       N +  +FSAT  + V K+ ++ +  
Sbjct: 168 KIKVFVLDEADVMIAT--QGHQDQSIRIQRMLP-RNCQMLLFSATFEDSVWKFAQKVVPD 224

Query: 218 RVQINV 223
              I +
Sbjct: 225 PNVIKL 230

>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 = 84.5 bits (210), Expect = 2e-19
 Identities = 35/180 (19%), Positives = 86/180 (47%), Gaps = 13/180 (7%)

Query: 45  LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL 104
           L    R + A + +G+GKTAAF + ++  +  P++   +A+ + P+RELA+QT      +
Sbjct: 40  LHNPPRNMIAQSQSGTGKTAAFSLTMLTRVN-PEDASPQAICLAPSRELARQTLEVVQEM 98

Query: 105 SEGLGLRAH-VIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLI 163
            +   + +  ++    +  ++          V++ TP  ++ L++     + L  ++  +
Sbjct: 99  GKFTKITSQLIVPDSFEKNKQINA------QVIVGTPGTVLDLMRRK--LMQLQKIKIFV 150

Query: 164 VDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           +DE+D + +   +G  DQ   +       + +  +FSAT  + V ++ ++ +     + +
Sbjct: 151 LDEADNMLDQ--QGLGDQCIRVKRFLP-KDTQLVLFSATFADAVRQYAKKIVPNANTLEL 207

>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 = 78.0 bits (193), Expect = 4e-17
 Identities = 52/174 (29%), Positives = 81/174 (46%), Gaps = 22/174 (12%)

Query: 56  APTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVI 115
           A TGSGKTA+F IP+I  +     +   A+I+ PTRELA Q  +E   L     L+   I
Sbjct: 51  ARTGSGKTASFAIPLIELVNENNGI--EAIILTPTRELAIQVADEIESLKGNKNLKIAKI 108

Query: 116 -G----KIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKL 170
            G      Q  A K         ++++ TP +++  +      LNL NV++ I+DE+D++
Sbjct: 109 YGGKAIYPQIKALKNA-------NIVVGTPGRILDHINRG--TLNLKNVKYFILDEADEM 159

Query: 171 FEAGVRGFRDQLAVIYAACSGPNLKR-GMFSATHTEDVAKWCRRKLKRRVQINV 223
                 GF   +  I  AC     KR  +FSAT   ++    ++ +     I  
Sbjct: 160 LNM---GFIKDVEKILNAC--NKDKRILLFSATMPREILNLAKKYMGDYSFIKA 208

>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 = 63.7 bits (154), Expect = 5e-12
 Identities = 25/178 (14%), Positives = 58/178 (32%), Gaps = 16/178 (8%)

Query: 48  LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
                    PTG GKT   ++   + L        + +++ PT+ L  Q           
Sbjct: 22  KETNCLIVLPTGLGKTLIAMMIAEYRLTKYGG---KVLMLAPTKPLVLQHAES---FRRL 75

Query: 108 LGLRAHVIGKIQ-QAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE 166
             L    I  +  + + +   ++  +  V++ TP  +   L      ++L +V  ++ DE
Sbjct: 76  FNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAG--RISLEDVSLIVFDE 133

Query: 167 SDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH---TEDVAKWCRRKLKRRVQI 221
           + +    G   +             P +     +A+     E + +         ++ 
Sbjct: 134 AHRA--VGNYAYVFIAREYKRQAKNPLV--IGLTASPGSTPEKIMEVINNLGIEHIEY 187

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Length = 720

 Score = 62.9 bits (153), Expect = 9e-12
 Identities = 43/170 (25%), Positives = 74/170 (43%), Gaps = 18/170 (10%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G+      PT SGKT    I ++H +      G +AV + P + LA++ + E     E +
Sbjct: 39  GKNALISIPTASGKTLIAEIAMVHRIL---TQGGKAVYIVPLKALAEEKFQEFQDW-EKI 94

Query: 109 GLR-AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES 167
           GLR A   G               K+D++I T  K   LL+     +   +V+ L+ DE 
Sbjct: 95  GLRVAMATGDYDS-----KDEWLGKYDIIIATAEKFDSLLRHGSSWIK--DVKILVADEI 147

Query: 168 DKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT--HTEDVAKWCRRKL 215
             +     RG   ++ + +       +  G+ SAT  + E++A+W   +L
Sbjct: 148 HLIGSRD-RGATLEVILAHMLGKAQII--GL-SATIGNPEELAEWLNAEL 193

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 60.5 bits (147), Expect = 6e-11
 Identities = 44/167 (26%), Positives = 69/167 (41%), Gaps = 23/167 (13%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G ++   +PTGSGKT    + II  L      G +A+ V P R L  + Y         +
Sbjct: 46  GNRLLLTSPTGSGKTLIAEMGIISFL---LKNGGKAIYVTPLRALTNEKYLTFKDWEL-I 101

Query: 109 GLR-AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES 167
           G + A   G              + +D++ITT  KL  L +  P  LN   V + ++DE 
Sbjct: 102 GFKVAMTSGDYDT-----DDAWLKNYDIIITTYEKLDSLWRHRPEWLNE--VNYFVLDEL 154

Query: 168 DKLFEAGVRGFRDQLAVIYAACSGPNLKR--GMFSAT--HTEDVAKW 210
             L +   RG      V+ +       +    + SAT  + + +AKW
Sbjct: 155 HYLNDPE-RG-----PVVESVTIRAKRRNLLAL-SATISNYKQIAKW 194

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens} Length = 216

 Score = 57.9 bits (140), Expect = 1e-10
 Identities = 25/119 (21%), Positives = 49/119 (41%), Gaps = 7/119 (5%)

Query: 54  ACAPTGSGKT--AAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR 111
            C PTGSGKT  A ++       +   +   + +++     L +Q + +  +       R
Sbjct: 53  ICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYR 112

Query: 112 AHVIGKIQQAAEKFGPRSAQKFDVLITTP----NKLVYLLQMDPPALNLANVEWLIVDE 166
              +    Q    F P   +  D++I+T     N L+ L   +   + L++   +I+DE
Sbjct: 113 VIGLSGDTQLKISF-PEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDE 170

>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 = 56.0 bits (135), Expect = 2e-09
 Identities = 28/119 (23%), Positives = 48/119 (40%), Gaps = 13/119 (10%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G+ +    PT +GKT    + ++         G +++ V P R LA + Y    +  E +
Sbjct: 40  GKNLLLAMPTAAGKTLLAEMAMVREAIK----GGKSLYVVPLRALAGEKYESFKKW-EKI 94

Query: 109 GLR-AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE 166
           GLR     G  +              D+++TT  K   L++     +    V  L+VDE
Sbjct: 95  GLRIGISTGDYE-----SRDEHLGDCDIIVTTSEKADSLIRNRASWIK--AVSCLVVDE 146

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 54.1 bits (129), Expect = 7e-09
 Identities = 27/102 (26%), Positives = 37/102 (36%), Gaps = 2/102 (1%)

Query: 48  LGRQIFACAPTGSGKTAAFLIPIIHSLR-GPKNLGFRAVIVCPTRELAKQTYNETVRLSE 106
            G+    CAPTG GKT   L+   H L+  P     + V       + +Q      R  E
Sbjct: 18  KGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFE 77

Query: 107 GLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQ 148
            LG     I      +        +  D++I TP  LV  L 
Sbjct: 78  RLGYNIASISGATSDSVSVQ-HIIEDNDIIILTPQILVNNLN 118

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B* Length = 1054

 Score = 51.6 bits (124), Expect = 6e-08
 Identities = 37/164 (22%), Positives = 65/164 (39%), Gaps = 29/164 (17%)

Query: 29  SNSIFKHFEPHFTITYLSPLGRQI-----------FA-CAPTGSGKTAAFLIPIIHSLRG 76
            + + K F   F      P   Q            FA  APTG GKT+ F +    SL  
Sbjct: 39  EDFLLKEFVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTS-FGL--AMSLFL 95

Query: 77  PKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVI-----GKIQQAAEKFGPRSAQ 131
               G R  ++ PT  L  Q      + +E  G+    +     G+I +  ++   ++ +
Sbjct: 96  ALK-GKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLR 154

Query: 132 KFDVLITTPNKLVYLLQ-MDPPALNLANVEWLIVDESDKLFEAG 174
            F ++ITT     +L +        L + +++ VD+ D + +A 
Sbjct: 155 NFKIVITTTQ---FLSKHYR----ELGHFDFIFVDDVDAILKAS 191

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos} Length = 797

 Score = 50.4 bits (119), Expect = 2e-07
 Identities = 28/122 (22%), Positives = 46/122 (37%), Gaps = 3/122 (2%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRG-PKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           G+    CAPTGSGKT   ++   H  +  P     + V +     + +Q  N      E 
Sbjct: 263 GKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER 322

Query: 108 LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES 167
            G     I     +      +  +  D+++ TP  LV   + D    +L+    +I DE 
Sbjct: 323 QGYSVQGISGENFSNVSVE-KVIEDSDIIVVTPQILVNSFE-DGTLTSLSIFTLMIFDEC 380

Query: 168 DK 169
             
Sbjct: 381 HN 382

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A* Length = 556

 Score = 49.9 bits (118), Expect = 2e-07
 Identities = 28/119 (23%), Positives = 46/119 (38%), Gaps = 3/119 (2%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLR-GPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           G+    CAPTGSGKT   ++   H  +  P     + V +     + +Q  N      E 
Sbjct: 22  GKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER 81

Query: 108 LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE 166
            G     I     +      +  +  D+++ TP  LV   + D    +L+    +I DE
Sbjct: 82  QGYSVQGISGENFSNVSV-EKVIEDSDIIVVTPQILVNSFE-DGTLTSLSIFTLMIFDE 138

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae} Length = 1108

 Score = 49.8 bits (118), Expect = 2e-07
 Identities = 37/175 (21%), Positives = 62/175 (35%), Gaps = 24/175 (13%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  +   A T +GKT      I  SL+       R +   P + L+ Q Y E +     +
Sbjct: 199 GESVLVSAHTSAGKTVVAEYAIAQSLKN----KQRVIYTSPIKALSNQKYRELLAEFGDV 254

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
           GL   + G I    +            L+ T   L  +L      +    V W+I DE  
Sbjct: 255 GL---MTGDITINPDA---------GCLVMTTEILRSMLYRGSEVMR--EVAWVIFDEVH 300

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT--HTEDVAKWCRRKLKRRVQI 221
            + +   RG   +  +I        ++    SAT  +  + A+W  +   +   I
Sbjct: 301 YMRDKE-RGVVWEETIILLP---DKVRYVFLSATIPNAMEFAEWICKIHSQPCHI 351

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae} Length = 1010

 Score = 49.8 bits (118), Expect = 3e-07
 Identities = 37/175 (21%), Positives = 62/175 (35%), Gaps = 24/175 (13%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  +   A T +GKT      I  SL+       R +   P + L+ Q Y E +     +
Sbjct: 101 GESVLVSAHTSAGKTVVAEYAIAQSLKN----KQRVIYTSPIKALSNQKYRELLAEFGDV 156

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
           GL   + G I    +            L+ T   L  +L      +    V W+I DE  
Sbjct: 157 GL---MTGDITINPDA---------GCLVMTTEILRSMLYRGSEVMR--EVAWVIFDEVH 202

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT--HTEDVAKWCRRKLKRRVQI 221
            + +   RG   +  +I        ++    SAT  +  + A+W  +   +   I
Sbjct: 203 YMRDKE-RGVVWEETIILLP---DKVRYVFLSATIPNAMEFAEWICKIHSQPCHI 253

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 49.2 bits (116), Expect = 4e-07
 Identities = 30/122 (24%), Positives = 47/122 (38%), Gaps = 3/122 (2%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLR-GPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           G+    CAPTG GKT   L+   H L+  P+    + V       + +Q  +   +  E 
Sbjct: 28  GKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFSKYFER 87

Query: 108 LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES 167
            G R   I            +  +  D++I TP  LV  L+      +L+    +I DE 
Sbjct: 88  HGYRVTGISGATAENVPVE-QIVENNDIIILTPQILVNNLKKG-TIPSLSIFTLMIFDEC 145

Query: 168 DK 169
             
Sbjct: 146 HN 147

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos} Length = 936

 Score = 45.3 bits (106), Expect = 8e-06
 Identities = 28/122 (22%), Positives = 44/122 (36%), Gaps = 3/122 (2%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRG-PKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
           G+    CAPTGSGKT   ++   H  +  P     + V +     + +Q  N      E 
Sbjct: 263 GKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER 322

Query: 108 LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES 167
            G     I     +            D+++ TP  LV   + D    +L+    +I DE 
Sbjct: 323 QGYSVQGISGENFSNVSVEKVIEDS-DIIVVTPQILVNSFE-DGTLTSLSIFTLMIFDEC 380

Query: 168 DK 169
             
Sbjct: 381 HN 382

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A* Length = 472

 Score = 44.8 bits (106), Expect = 8e-06
 Identities = 28/120 (23%), Positives = 38/120 (31%), Gaps = 30/120 (25%)

Query: 49  GRQIFACAPTGSGKT--AAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE 106
            R      PTGSGKT  A   I           L    +IV PT  LA+Q         E
Sbjct: 109 KRGCI-VLPTGSGKTHVAMAAI---------NELSTPTLIVVPTLALAEQWKERLGIFGE 158

Query: 107 GLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE 166
                   +G       +F  R  +   + ++T +      +       L     LI DE
Sbjct: 159 ------EYVG-------EFSGRIKELKPLTVSTYDSAYVNAEKLGNRFML-----LIFDE 200

>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 = 44.5 bits (104), Expect = 1e-05
 Identities = 29/210 (13%), Positives = 62/210 (29%), Gaps = 51/210 (24%)

Query: 23  TTLA--VVSNSIFKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNL 80
           T +A  V  +   +     F I +L+ L              +   ++ ++      + L
Sbjct: 164 TWVALDVCLSYKVQCKMD-FKIFWLN-LKNC----------NSPETVLEML------QKL 205

Query: 81  GFRAVIVCPTRELAKQTYNETVRLSEG-LGLRAHVIGKIQQAAEKFGPRS---------- 129
            ++  I       +  + N  +R+      LR  +         K               
Sbjct: 206 LYQ--IDPNWTSRSDHSSNIKLRIHSIQAELRRLL-------KSKPYENCLLVLLNVQNA 256

Query: 130 --AQKFD----VLITTPNKLV--YLLQMDPPALNLANVEW-LIVDESDKLFEAGVRGFRD 180
                F+    +L+TT  K V  +L       ++L +    L  DE   L    +     
Sbjct: 257 KAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ 316

Query: 181 QLAVIYAACSGPNLKRGMFSATHTEDVAKW 210
            L       +    +  + + +  + +A W
Sbjct: 317 DLPR--EVLTTNPRRLSIIAESIRDGLATW 344

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A* Length = 620

 Score = 42.0 bits (99), Expect = 8e-05
 Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 3/64 (4%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
              +   +PTGSGKT   L   +      K    + + +  T    +Q   E   LS  +
Sbjct: 22  SYGVALESPTGSGKTIMALKSALQYSSERKL---KVLYLVRTNSQEEQVIKELRSLSSTM 78

Query: 109 GLRA 112
            +RA
Sbjct: 79  KIRA 82

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A* Length = 440

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 23/118 (19%), Positives = 37/118 (31%), Gaps = 18/118 (15%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G         G+GKT  FL P I  L        R +++ PTR +  +       L    
Sbjct: 8   GMTTVLDFHPGAGKTRRFL-PQI--LAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVKF 64

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDE 166
             +A                 + +  +       L Y +        + N E +I+DE
Sbjct: 65  HTQAFSA------------HGSGREVIDAMCHATLTYRMLEPT---RVVNWEVIIMDE 107

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	226
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	100.0
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	100.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	100.0
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	100.0
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	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,	99.97
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.97
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.97
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.97
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.97
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.97
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.97
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.97
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.97
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.96
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.96
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.96
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.96
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.96
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.94
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.94
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.93
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.93
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.93
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.93
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.92
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.92
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.91
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.91
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.91
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.91
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.91
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.91
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.9
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.9
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.9
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.89
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.89
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.89
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.88
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.88
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.87
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.86
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.86
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.86
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.85
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.85
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.85
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.85
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.83
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.83
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.81
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.8
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.79
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.78
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.78
3h1t_A	590	Type I site-specific restriction-modification syst	99.78
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.78
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.77
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.75
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.7
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.69
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.64
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.59
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.57
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.56
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.4
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.37
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.14
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.93
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.83
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.27
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.26
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.16
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.15
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.04
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	97.99
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.79
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.73
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.63
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.52
2chg_A	226	Replication factor C small subunit; DNA-binding pr	97.42
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.39
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.39
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.38
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.34
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.31
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	97.23
3bos_A	242	Putative DNA replication factor; P-loop containing	97.15
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.13
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	97.11
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	97.1
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.07
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	96.96
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.91
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.91
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	96.9
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	96.88
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	96.88
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	96.82
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.77
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	96.77
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	96.76
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	96.75
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	96.75
3co5_A	143	Putative two-component system transcriptional RES	96.75
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	96.74
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	96.72
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	96.7
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.7
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	96.69
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.68
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	96.67
2qgz_A	308	Helicase loader, putative primosome component; str	96.66
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	96.65
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	96.65
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	96.63
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.58
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	96.54
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	96.52
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	96.5
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	96.49
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	96.48
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	96.46
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	96.43
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	96.4
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	96.29
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	96.28
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.26
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	96.26
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.25
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	96.21
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	96.0
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	95.82
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	95.81
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	95.72
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	95.65
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	95.64
3pvs_A	447	Replication-associated recombination protein A; ma	95.59
2chq_A	319	Replication factor C small subunit; DNA-binding pr	95.58
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	95.24
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	95.14
2r6a_A	454	DNAB helicase, replicative helicase; replication,	95.14
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	95.06
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	94.95
1xp8_A	366	RECA protein, recombinase A; recombination, radior	94.87
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	94.85
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	94.8
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	94.8
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	94.78
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	94.67
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	94.64
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	94.42
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	94.42
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	94.2
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	94.18
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	94.06
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	94.04
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	94.01
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	93.99
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	93.83
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	93.78
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	93.75
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	93.61
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	93.39
2fna_A	357	Conserved hypothetical protein; structural genomic	93.07
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	93.0
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	92.94
4a74_A	231	DNA repair and recombination protein RADA; hydrola	92.54
3io5_A	333	Recombination and repair protein; storage dimer, i	92.42
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	92.31
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	92.21
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	92.12
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	91.93
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	91.8
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	91.63
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	91.22
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	91.17
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	91.1
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	91.02
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	90.81
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	90.58
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	90.58
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	90.31
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	90.28
1tue_A	212	Replication protein E1; helicase, replication, E1E	90.19
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	90.14
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	89.85
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	89.8
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	89.69
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	89.67
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	89.54
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	89.2
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	89.09
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	88.98
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	88.91
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	88.89
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	88.83
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	88.65
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	88.45
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	88.28
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	88.21
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	88.08
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	87.95
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	87.83
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	87.82
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	87.78
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	87.75
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	87.74
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	87.73
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	87.72
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	87.64
2eyu_A	261	Twitching motility protein PILT; pilus retraction	87.56
1p9r_A	418	General secretion pathway protein E; bacterial typ	87.45
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	87.45
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	87.43
2r44_A	331	Uncharacterized protein; putative ATPase, structur	87.42
2cvh_A	220	DNA repair and recombination protein RADB; filamen	87.42
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	87.08
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	86.81
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	86.77
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	86.75
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	86.64
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	86.63
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	86.6
1yks_A	440	Genome polyprotein [contains: flavivirin protease	86.6
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	86.56
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	86.55
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	86.52
2z43_A	324	DNA repair and recombination protein RADA; archaea	86.5
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	86.47
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	86.44
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	86.44
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	86.36
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	86.35
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	86.33
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	86.29
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	85.87
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	85.83
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	85.82
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	85.7
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	85.6
1u94_A	356	RECA protein, recombinase A; homologous recombinat	85.56
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	85.49
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	85.47
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	85.47
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	85.45
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	85.35
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	85.3
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	85.1
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	84.83
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	84.8
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	84.77
2ewv_A	372	Twitching motility protein PILT; pilus retraction	84.74
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	84.6
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	84.57
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	84.39
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	84.35
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	84.24
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	84.24
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	84.22
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	84.13
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	84.13
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	84.08
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	83.89
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	83.71
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	83.65
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	83.65
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	83.63
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	83.62
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	83.55
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	83.54
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	83.51
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	83.39
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	83.15
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	83.13
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	83.12
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	83.1
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	82.93
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	82.82
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	82.78
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	82.69
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	82.61
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	82.32
2l8b_A	189	Protein TRAI, DNA helicase I; RECD, hydrolase; NMR	81.99
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	81.95
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	81.89
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	81.73
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	81.57
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	81.53
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	81.51
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	81.32
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	81.23
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	81.13
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	81.09
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	80.98
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	80.92
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	80.84
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	80.73
1via_A	175	Shikimate kinase; structural genomics, transferase	80.72
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	80.55
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	80.37
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	80.22
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	80.17
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	80.04

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=100.00  E-value=5.4e-39  Score=257.77  Aligned_cols=208  Identities=50%  Similarity=0.864  Sum_probs=182.7

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      .+.+.+++.+.+.+|..+++.|..+. .+.+|+++++.+|||+|||++|++|++..+......+++++|++|+++|+.|+
T Consensus        35 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~lil~Pt~~L~~q~  114 (245)
T 3dkp_A           35 KINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQI  114 (245)
T ss_dssp             CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCCSSSCCEEEECSSHHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcccCCceEEEEeCCHHHHHHH
Confidence            46678999999999999999997775 67789999999999999999999999999876666778999999999999999


Q ss_pred             HHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccc
Q psy12977         98 YNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG  177 (226)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~  177 (226)
                      .+.++++....+..+....++.............+++|+|+||+++.+++........+.+++++|+||||++.+++..+
T Consensus       115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lViDEah~~~~~~~~~  194 (245)
T 3dkp_A          115 HRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTG  194 (245)
T ss_dssp             HHHHHHHTTTSCCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEEESSHHHHHHHC--C
T ss_pred             HHHHHHHhcccCceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEEEeChHHhccccccc
Confidence            99999999888888887777765555555566778999999999999999875556789999999999999999865557


Q ss_pred             hHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCCC
Q psy12977        178 FRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       178 ~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      +...+..++..+.+++.|++++|||+|+++.++++.++++|+.+.+++|
T Consensus       195 ~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  243 (245)
T 3dkp_A          195 FRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR  243 (245)
T ss_dssp             HHHHHHHHHHHCCCTTCEEEEEESSCCHHHHHHHHHHSSSCEEEEECC-
T ss_pred             HHHHHHHHHHhcCCCCcEEEEEeccCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            9999999998887778999999999999999999999999999999875

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=100.00  E-value=1.4e-37  Score=249.38  Aligned_cols=201  Identities=24%  Similarity=0.393  Sum_probs=173.9

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC----CCCCceEEEEcccHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP----KNLGFRAVIVCPTRE   92 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~----~~~~~~~iil~Pt~~   92 (226)
                      +++-+.+++.+.+.+|.+++++|..+. .+.+|+|+++.+|||+|||++|++|++..+...    ...+++++|++|+++
T Consensus        34 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~  113 (242)
T 3fe2_A           34 ANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRE  113 (242)
T ss_dssp             TTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEEeCcHH
Confidence            346778999999999999999997775 677889999999999999999999999887542    234678999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccc
Q psy12977         93 LAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFE  172 (226)
Q Consensus        93 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~  172 (226)
                      |+.|+.+.++.+....+.++....++....... .....+++|+|+||+++.+++..  ....+.+++++|+||||++.+
T Consensus       114 L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~I~v~Tp~~l~~~l~~--~~~~~~~~~~lViDEah~l~~  190 (242)
T 3fe2_A          114 LAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQI-RDLERGVEICIATPGRLIDFLEC--GKTNLRRTTYLVLDEADRMLD  190 (242)
T ss_dssp             HHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHH-HHHHHCCSEEEECHHHHHHHHHH--TSCCCTTCCEEEETTHHHHHH
T ss_pred             HHHHHHHHHHHHHhhcCceEEEEECCCChHHHH-HHhcCCCCEEEECHHHHHHHHHc--CCCCcccccEEEEeCHHHHhh
Confidence            999999999999998888888877765443322 22335689999999999999987  566789999999999999999


Q ss_pred             cCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        173 AGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       173 ~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      .   ++...+..+++.+ ++..|++++|||+|+++.++++.++++|+.|++++
T Consensus       191 ~---~~~~~~~~i~~~~-~~~~q~~~~SAT~~~~~~~~~~~~l~~~~~i~~~~  239 (242)
T 3fe2_A          191 M---GFEPQIRKIVDQI-RPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGA  239 (242)
T ss_dssp             T---TCHHHHHHHHTTS-CSSCEEEEEESCCCHHHHHHHHHHCSSCEEEEECC
T ss_pred             h---CcHHHHHHHHHhC-CccceEEEEEeecCHHHHHHHHHHCCCCEEEEecC
Confidence            8   6899999999888 67899999999999999999999999999999875

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=100.00  E-value=9.4e-37  Score=251.95  Aligned_cols=199  Identities=20%  Similarity=0.197  Sum_probs=169.3

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCC--CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLG--RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELA   94 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~--~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~   94 (226)
                      +.+-+.+++.+.+++|..++++|..+. .++.+  +|+++++|||||||++|++|+++.+.. ...+++++|++||++||
T Consensus        97 l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~-~~~~~~~lil~PtreLa  175 (300)
T 3fmo_B           97 LRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEP-ANKYPQCLCLSPTYELA  175 (300)
T ss_dssp             GTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCT-TSCSCCEEEECSSHHHH
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhc-cCCCceEEEEcCcHHHH
Confidence            456789999999999999999997775 55665  999999999999999999999999864 34567999999999999


Q ss_pred             HHHHHHHHHHhhcC-CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977         95 KQTYNETVRLSEGL-GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus        95 ~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      .|+++.++.+.... +..+....++...    ......+++|+|+||+++.+++.+. +.+++++++++|+||+|++++.
T Consensus       176 ~Q~~~~~~~l~~~~~~~~~~~~~~~~~~----~~~~~~~~~IlV~TP~~l~~~l~~~-~~~~l~~l~~lVlDEad~l~~~  250 (300)
T 3fmo_B          176 LQTGKVIEQMGKFYPELKLAYAVRGNKL----ERGQKISEQIVIGTPGTVLDWCSKL-KFIDPKKIKVFVLDEADVMIAT  250 (300)
T ss_dssp             HHHHHHHHHHTTTSTTCCEEEESTTCCC----CTTCCCCCSEEEECHHHHHHHHTTT-CCCCGGGCSEEEETTHHHHHHS
T ss_pred             HHHHHHHHHHHhhCCCcEEEEEeCCccH----hhhhcCCCCEEEECHHHHHHHHHhc-CCCChhhceEEEEeCHHHHhhc
Confidence            99999999998765 4666666665332    2223567899999999999998653 5677899999999999999983


Q ss_pred             CccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        174 GVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       174 ~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      .  ++...+..+.+.+ ++.+|+++||||+|+++.++++.++++|+.|.+++
T Consensus       251 ~--~~~~~~~~i~~~~-~~~~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~~  299 (300)
T 3fmo_B          251 Q--GHQDQSIRIQRML-PRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR  299 (300)
T ss_dssp             T--THHHHHHHHHTTS-CTTCEEEEEESCCCHHHHHHHHHHSSSCEEEEECC
T ss_pred             c--CcHHHHHHHHHhC-CCCCEEEEEeccCCHHHHHHHHHHCCCCeEEEecC
Confidence            2  6888899998888 67899999999999999999999999999999875

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=100.00  E-value=2.6e-36  Score=241.23  Aligned_cols=200  Identities=23%  Similarity=0.312  Sum_probs=164.0

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      .+-+.+++.+.+.+|..+++.|..+. .+.+++|+++.+|||+|||++|+++++..+.. ...+.+++|++|+++|+.|+
T Consensus        36 ~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~-~~~~~~~lil~Pt~~L~~q~  114 (237)
T 3bor_A           36 NLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEI-EFKETQALVLAPTRELAQQI  114 (237)
T ss_dssp             CCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCT-TSCSCCEEEECSSHHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHh-cCCCceEEEEECcHHHHHHH
Confidence            45678899999999999999997774 67788999999999999999999999998863 23456999999999999999


Q ss_pred             HHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccc
Q psy12977         98 YNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG  177 (226)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~  177 (226)
                      .+.++.+....+..+....++..............++|+|+||+++.+.+.+  +...+.+++++|+||||++.+.   +
T Consensus       115 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~--~~~~~~~~~~lViDEah~~~~~---~  189 (237)
T 3bor_A          115 QKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNR--RYLSPKWIKMFVLDEADEMLSR---G  189 (237)
T ss_dssp             HHHHHHHTTTTTCCEEEECC-------------CCCSEEEECHHHHHHHHHT--TSSCSTTCCEEEEESHHHHHHT---T
T ss_pred             HHHHHHHhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHh--CCcCcccCcEEEECCchHhhcc---C
Confidence            9999999888788877777665443333333344589999999999999887  5677889999999999999887   6


Q ss_pred             hHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        178 FRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       178 ~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      +...+..+++.+ ++..|++++|||+|+++.++++.++++|+.|.+++
T Consensus       190 ~~~~l~~i~~~~-~~~~~~i~~SAT~~~~~~~~~~~~l~~p~~i~v~~  236 (237)
T 3bor_A          190 FKDQIYEIFQKL-NTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKK  236 (237)
T ss_dssp             CHHHHHHHHHHS-CTTCEEEEECSSCCHHHHHHHHHHCSSCEEEC---
T ss_pred             cHHHHHHHHHhC-CCCCeEEEEEEecCHHHHHHHHHHCCCCEEEEecC
Confidence            888888898888 57899999999999999999999999999998875

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=5.4e-36  Score=236.49  Aligned_cols=199  Identities=23%  Similarity=0.318  Sum_probs=169.8

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      ++-+.+++.+++.+|.++++.|..+. .+.+++++++.+|||+|||++|++|++..+.. ...+.+++|++|+++|+.|+
T Consensus        10 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~-~~~~~~~lil~Pt~~L~~q~   88 (219)
T 1q0u_A           10 PFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKP-ERAEVQAVITAPTRELATQI   88 (219)
T ss_dssp             CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCT-TSCSCCEEEECSSHHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHh-CcCCceEEEEcCcHHHHHHH
Confidence            45678999999999999999997775 66788999999999999999999999998864 33467999999999999999


Q ss_pred             HHHHHHHhhcC----CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977         98 YNETVRLSEGL----GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus        98 ~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      .+.++++....    +..+....++...... ......+++|+|+||+++.+.+..  +...+.+++++|+||||++.+.
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~~~~~lViDEah~~~~~  165 (219)
T 1q0u_A           89 YHETLKITKFCPKDRMIVARCLIGGTDKQKA-LEKLNVQPHIVIGTPGRINDFIRE--QALDVHTAHILVVDEADLMLDM  165 (219)
T ss_dssp             HHHHHHHHTTSCGGGCCCEEEECCCSHHHHT-TCCCSSCCSEEEECHHHHHHHHHT--TCCCGGGCCEEEECSHHHHHHT
T ss_pred             HHHHHHHhhhcccccceEEEEEeCCCCHHHH-HHHcCCCCCEEEeCHHHHHHHHHc--CCCCcCcceEEEEcCchHHhhh
Confidence            99999998776    5666666666544333 334456889999999999999887  5677889999999999999987


Q ss_pred             CccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        174 GVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       174 ~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                         ++...+..+++.+ ++..|++++|||+|+++.+++++++++|+.+.+..
T Consensus       166 ---~~~~~l~~i~~~~-~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~~~~~~  213 (219)
T 1q0u_A          166 ---GFITDVDQIAARM-PKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVLE  213 (219)
T ss_dssp             ---TCHHHHHHHHHTS-CTTCEEEEEESCCCGGGHHHHHHHCSSCEEEECC-
T ss_pred             ---ChHHHHHHHHHhC-CcccEEEEEecCCCHHHHHHHHHHcCCCeEEEeec
Confidence               6888999999888 56889999999999999999999999999998753

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=100.00  E-value=3.3e-36  Score=239.07  Aligned_cols=197  Identities=25%  Similarity=0.334  Sum_probs=162.8

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC-----CCCCceEEEEcccHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP-----KNLGFRAVIVCPTRE   92 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~-----~~~~~~~iil~Pt~~   92 (226)
                      .+.+.+++.+.+.+|.+++++|..+. .+.+|+|+++.+|||+|||++|++|++..+...     ...+++++|++|+++
T Consensus        26 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt~~  105 (228)
T 3iuy_A           26 QQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRE  105 (228)
T ss_dssp             TTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSSHH
T ss_pred             ccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCCHH
Confidence            46689999999999999999997775 677899999999999999999999999877532     235678999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccc
Q psy12977         93 LAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFE  172 (226)
Q Consensus        93 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~  172 (226)
                      |+.|+.+.++.+. ..+..+....++....... .....+++|+|+||+++.+++..  ....+.+++++|+||||++.+
T Consensus       106 L~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-~~~~~~~~iiv~Tp~~l~~~~~~--~~~~~~~~~~lViDEah~~~~  181 (228)
T 3iuy_A          106 LALHVEAECSKYS-YKGLKSICIYGGRNRNGQI-EDISKGVDIIIATPGRLNDLQMN--NSVNLRSITYLVIDEADKMLD  181 (228)
T ss_dssp             HHHHHHHHHHHHC-CTTCCEEEECC------CH-HHHHSCCSEEEECHHHHHHHHHT--TCCCCTTCCEEEECCHHHHHH
T ss_pred             HHHHHHHHHHHhc-ccCceEEEEECCCChHHHH-HHhcCCCCEEEECHHHHHHHHHc--CCcCcccceEEEEECHHHHhc
Confidence            9999999999986 3366666666554322211 12345689999999999998877  667789999999999999998


Q ss_pred             cCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEec
Q psy12977        173 AGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       173 ~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~  223 (226)
                      .   ++...+..+++.+ +++.|++++|||+|+++.++++.++++|+.|.|
T Consensus       182 ~---~~~~~~~~i~~~~-~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i~v  228 (228)
T 3iuy_A          182 M---EFEPQIRKILLDV-RPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV  228 (228)
T ss_dssp             T---TCHHHHHHHHHHS-CSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEC
T ss_pred             c---chHHHHHHHHHhC-CcCCeEEEEEeeCCHHHHHHHHHHCCCCEEEeC
Confidence            8   6889999999888 678999999999999999999999999999865

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=100.00  E-value=1.4e-35  Score=231.61  Aligned_cols=196  Identities=25%  Similarity=0.372  Sum_probs=167.0

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      .+-+.+++.+.+++|.++++.|..+. .+.+++++++.+|||+|||++|++|++..+.. ...+++++|++|+++|+.|+
T Consensus         9 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~-~~~~~~~lil~Pt~~L~~q~   87 (206)
T 1vec_A            9 CLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDL-KKDNIQAMVIVPTRELALQV   87 (206)
T ss_dssp             CCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCT-TSCSCCEEEECSCHHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcc-cCCCeeEEEEeCcHHHHHHH
Confidence            35678999999999999999997775 66788999999999999999999999988753 33457899999999999999


Q ss_pred             HHHHHHHhhcC-CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         98 YNETVRLSEGL-GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        98 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      .+.++++.+.. +..+....++....... .....+++|+|+||+++.+.+.+  +...+.+++++|+||||++.+.   
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~i~v~T~~~l~~~~~~--~~~~~~~~~~lViDEah~~~~~---  161 (206)
T 1vec_A           88 SQICIQVSKHMGGAKVMATTGGTNLRDDI-MRLDDTVHVVIATPGRILDLIKK--GVAKVDHVQMIVLDEADKLLSQ---  161 (206)
T ss_dssp             HHHHHHHTTTSSSCCEEEECSSSCHHHHH-HHTTSCCSEEEECHHHHHHHHHT--TCSCCTTCCEEEEETHHHHTST---
T ss_pred             HHHHHHHHhhcCCceEEEEeCCccHHHHH-HhcCCCCCEEEeCHHHHHHHHHc--CCcCcccCCEEEEEChHHhHhh---
Confidence            99999998876 67777766665433222 22346789999999999998886  5667889999999999999887   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEe
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN  222 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~  222 (226)
                      ++...+..+...+ ++..|++++|||+|+++.++++.++++|+.|+
T Consensus       162 ~~~~~l~~i~~~~-~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i~  206 (206)
T 1vec_A          162 DFVQIMEDIILTL-PKNRQILLYSATFPLSVQKFMNSHLEKPYEIN  206 (206)
T ss_dssp             TTHHHHHHHHHHS-CTTCEEEEEESCCCHHHHHHHHHHCSSCEEEC
T ss_pred             CcHHHHHHHHHhC-CccceEEEEEeeCCHHHHHHHHHHcCCCeEeC
Confidence            6888999999888 56899999999999999999999999999873

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=100.00  E-value=7.7e-36  Score=237.45  Aligned_cols=198  Identities=24%  Similarity=0.326  Sum_probs=167.7

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      .+-+.+++.+++.+|.++++.|..+. .+.+|+|+++.+|||+|||++|++|++..+.. ...+++++|++|+++|+.|+
T Consensus        30 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~-~~~~~~~lil~Pt~~L~~q~  108 (230)
T 2oxc_A           30 LLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVL-ENLSTQILILAPTREIAVQI  108 (230)
T ss_dssp             TCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCT-TSCSCCEEEECSSHHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHh-cCCCceEEEEeCCHHHHHHH
Confidence            45688999999999999999997775 66788999999999999999999999988763 23467999999999999999


Q ss_pred             HHHHHHHhhcC-CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         98 YNETVRLSEGL-GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        98 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      .+.++.+.... +.++....++........  ...+++|+|+||+++.+++..  +...+.+++++|+||||++.+.+  
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~Iiv~Tp~~l~~~~~~--~~~~~~~~~~lViDEah~~~~~~--  182 (230)
T 2oxc_A          109 HSVITAIGIKMEGLECHVFIGGTPLSQDKT--RLKKCHIAVGSPGRIKQLIEL--DYLNPGSIRLFILDEADKLLEEG--  182 (230)
T ss_dssp             HHHHHHHTTTSTTCCEEEECTTSCHHHHHH--HTTSCSEEEECHHHHHHHHHT--TSSCGGGCCEEEESSHHHHHSTT--
T ss_pred             HHHHHHHhcccCCceEEEEeCCCCHHHHHH--hccCCCEEEECHHHHHHHHhc--CCcccccCCEEEeCCchHhhcCc--
Confidence            99999998765 677777776654333221  224689999999999999876  56778899999999999998873  


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      .+...+..+++.+ ++..|++++|||+|+++.+++++++++|++|.++
T Consensus       183 ~~~~~~~~i~~~~-~~~~~~l~lSAT~~~~~~~~~~~~~~~p~~i~~~  229 (230)
T 2oxc_A          183 SFQEQINWIYSSL-PASKQMLAVSATYPEFLANALTKYMRDPTFVRLN  229 (230)
T ss_dssp             SSHHHHHHHHHHS-CSSCEEEEEESCCCHHHHHHHTTTCSSCEEECC-
T ss_pred             chHHHHHHHHHhC-CCCCeEEEEEeccCHHHHHHHHHHcCCCeEEEcC
Confidence            3888999999888 5688999999999999999999999999999876

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=100.00  E-value=1.8e-35  Score=233.94  Aligned_cols=200  Identities=22%  Similarity=0.286  Sum_probs=165.0

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      +++-+.+++.+.+.+|.++++.|..+. .+.+++++++.+|||+|||++|+++++..+.. ...+++++|++|+++|+.|
T Consensus        19 l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~-~~~~~~~lil~Pt~~L~~q   97 (224)
T 1qde_A           19 MELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDT-SVKAPQALMLAPTRELALQ   97 (224)
T ss_dssp             GTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCT-TCCSCCEEEECSSHHHHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhc-cCCCceEEEEECCHHHHHH
Confidence            346788999999999999999997775 67788999999999999999999999998864 3346799999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +.+.++.+....+.++....++........  ...+++|+|+||+++.+.+.+  ....+.+++++|+||||++.+.   
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~iiv~Tp~~l~~~~~~--~~~~~~~~~~iViDEah~~~~~---  170 (224)
T 1qde_A           98 IQKVVMALAFHMDIKVHACIGGTSFVEDAE--GLRDAQIVVGTPGRVFDNIQR--RRFRTDKIKMFILDEADEMLSS---  170 (224)
T ss_dssp             HHHHHHHHTTTSCCCEEEECC------------CTTCSEEEECHHHHHHHHHT--TSSCCTTCCEEEEETHHHHHHT---
T ss_pred             HHHHHHHHhcccCceEEEEeCCcchHHHHh--cCCCCCEEEECHHHHHHHHHh--CCcchhhCcEEEEcChhHHhhh---
Confidence            999999998888888877777654333222  223489999999999998887  5677889999999999999887   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCCC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                      ++...+..++..+ ++..|++++|||+|+++.+++++++++|+.+.++++
T Consensus       171 ~~~~~l~~i~~~~-~~~~~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~~  219 (224)
T 1qde_A          171 GFKEQIYQIFTLL-PPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKD  219 (224)
T ss_dssp             TCHHHHHHHHHHS-CTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC----
T ss_pred             hhHHHHHHHHHhC-CccCeEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            6888888888888 578999999999999999999999999999988753

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=100.00  E-value=8.6e-36  Score=237.80  Aligned_cols=201  Identities=25%  Similarity=0.396  Sum_probs=168.6

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC---CCCCceEEEEcccHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP---KNLGFRAVIVCPTRELA   94 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~---~~~~~~~iil~Pt~~L~   94 (226)
                      ++-+.+++.+++.+|..+++.|..+. .+.+++++++.+|||+|||++|++|++..+...   ...+++++|++|+++|+
T Consensus        31 ~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~Pt~~L~  110 (236)
T 2pl3_A           31 PLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELA  110 (236)
T ss_dssp             CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEEeCCHHHH
Confidence            45678899999999999999997775 777899999999999999999999998876421   23467899999999999


Q ss_pred             HHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccC
Q psy12977         95 KQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG  174 (226)
Q Consensus        95 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~  174 (226)
                      .|+.+.++.+....+..+....++........  ...+++|+|+||+++.+.+... ....+.+++++|+||||++.+. 
T Consensus       111 ~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~iiv~Tp~~l~~~l~~~-~~~~~~~~~~lViDEah~~~~~-  186 (236)
T 2pl3_A          111 YQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAE--RINNINILVCTPGRLLQHMDET-VSFHATDLQMLVLDEADRILDM-  186 (236)
T ss_dssp             HHHHHHHHHHTTTSSCCEEEECCC--CHHHHH--HHTTCSEEEECHHHHHHHHHHC-SSCCCTTCCEEEETTHHHHHHT-
T ss_pred             HHHHHHHHHHhCCCCeeEEEEECCCCHHHHHH--hCCCCCEEEECHHHHHHHHHhc-CCcccccccEEEEeChHHHhcC-
Confidence            99999999998887888877777654332211  1257899999999999988763 3466889999999999999988 


Q ss_pred             ccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCCC
Q psy12977        175 VRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       175 ~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                        ++...+..+++.+ ++..|++++|||+|+++.++++.++.+|+++.+++|
T Consensus       187 --~~~~~~~~i~~~~-~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  235 (236)
T 2pl3_A          187 --GFADTMNAVIENL-PKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHEK  235 (236)
T ss_dssp             --TTHHHHHHHHHTS-CTTSEEEEEESSCCHHHHHHHHHSCSSCEEEECCC-
T ss_pred             --CcHHHHHHHHHhC-CCCCeEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCC
Confidence              6888999999888 568999999999999999999999999999999875

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=100.00  E-value=2.5e-35  Score=237.27  Aligned_cols=201  Identities=28%  Similarity=0.361  Sum_probs=170.9

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      +++-+.+++.+++++|.++++.|..+. .+.+++++++.+|||+|||++|+++++..+... ..+++++|++|+++|+.|
T Consensus        48 l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~-~~~~~~lil~Ptr~L~~q  126 (249)
T 3ber_A           48 LGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLET-PQRLFALVLTPTRELAFQ  126 (249)
T ss_dssp             GTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHS-CCSSCEEEECSSHHHHHH
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcC-CCCceEEEEeCCHHHHHH
Confidence            345678899999999999999997775 677889999999999999999999999887532 335689999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +.+.++.+....+.++....++....... .....+++|+|+||+++.+.+... ....+.+++++|+||||++.+.   
T Consensus       127 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~I~v~Tp~~l~~~l~~~-~~~~l~~~~~lViDEah~l~~~---  201 (249)
T 3ber_A          127 ISEQFEALGSSIGVQSAVIVGGIDSMSQS-LALAKKPHIIIATPGRLIDHLENT-KGFNLRALKYLVMDEADRILNM---  201 (249)
T ss_dssp             HHHHHHHHHGGGTCCEEEECTTSCHHHHH-HHHHTCCSEEEECHHHHHHHHHHS-TTCCCTTCCEEEECSHHHHHHT---
T ss_pred             HHHHHHHHhccCCeeEEEEECCCChHHHH-HHhcCCCCEEEECHHHHHHHHHcC-CCcCccccCEEEEcChhhhhcc---
Confidence            99999999988888888777765432221 223467899999999999988753 3456889999999999999988   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      ++...+..+++.+ ++..|++++|||+++++.++++.++++|+.|.++.
T Consensus       202 ~~~~~l~~i~~~~-~~~~~~l~~SAT~~~~v~~~~~~~l~~p~~i~v~~  249 (249)
T 3ber_A          202 DFETEVDKILKVI-PRDRKTFLFSATMTKKVQKLQRAALKNPVKCAVSS  249 (249)
T ss_dssp             TCHHHHHHHHHSS-CSSSEEEEEESSCCHHHHHHHHHHCSSCEEEECCC
T ss_pred             ChHHHHHHHHHhC-CCCCeEEEEeccCCHHHHHHHHHHCCCCEEEEecC
Confidence            6888999999888 56899999999999999999999999999998863

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=100.00  E-value=2.1e-35  Score=233.12  Aligned_cols=200  Identities=24%  Similarity=0.321  Sum_probs=167.1

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      +++-+.+++.+.+.+|+++++.|..+. .+.+++++++.+|||+|||++|+++++..+.. ...+++++|++|+++|+.|
T Consensus        19 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~-~~~~~~~lil~Pt~~L~~q   97 (220)
T 1t6n_A           19 FLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEP-VTGQVSVLVMCHTRELAFQ   97 (220)
T ss_dssp             SCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCC-CTTCCCEEEECSCHHHHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhc-cCCCEEEEEEeCCHHHHHH
Confidence            346688999999999999999997775 66788999999999999999999999988764 2335689999999999999


Q ss_pred             HHHHHHHHhhcC-CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCc
Q psy12977         97 TYNETVRLSEGL-GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGV  175 (226)
Q Consensus        97 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~  175 (226)
                      +.+.++++.+.. +.++....++..............++|+|+||+++.+.+..  ....+.+++++|+||||++.+.. 
T Consensus        98 ~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~--~~~~~~~~~~lViDEah~~~~~~-  174 (220)
T 1t6n_A           98 ISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN--KSLNLKHIKHFILDECDKMLEQL-  174 (220)
T ss_dssp             HHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT--TSSCCTTCCEEEEESHHHHHSSH-
T ss_pred             HHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHh--CCCCcccCCEEEEcCHHHHhccc-
Confidence            999999998776 67777777665433322222234579999999999999887  56678999999999999998732 


Q ss_pred             cchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEec
Q psy12977        176 RGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       176 ~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~  223 (226)
                       ++...+..+++.+ ++..|++++|||+|+++.+++++++.+|+.|++
T Consensus       175 -~~~~~~~~i~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~v  220 (220)
T 1t6n_A          175 -DMRRDVQEIFRMT-PHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV  220 (220)
T ss_dssp             -HHHHHHHHHHHTS-CSSSEEEEEESCCCTTTHHHHHTTCSSCEEEEC
T ss_pred             -CcHHHHHHHHHhC-CCcCeEEEEEeecCHHHHHHHHHHcCCCeEEeC
Confidence             5788888888877 568999999999999999999999999999875

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=100.00  E-value=2.4e-35  Score=237.61  Aligned_cols=201  Identities=29%  Similarity=0.404  Sum_probs=167.7

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCC--------CCCceEEEEcc
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK--------NLGFRAVIVCP   89 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~--------~~~~~~iil~P   89 (226)
                      .+-+.+++.+.+.+|.++++.|..+. .+.+++|+++.+|||+|||++|++|++..+....        ..+++++|++|
T Consensus        29 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~~lil~P  108 (253)
T 1wrb_A           29 KLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAP  108 (253)
T ss_dssp             SCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECS
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCceEEEEEC
Confidence            34567788889999999999997775 6778899999999999999999999998875332        23469999999


Q ss_pred             cHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccc
Q psy12977         90 TRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK  169 (226)
Q Consensus        90 t~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~  169 (226)
                      +++|+.|+.+.++.+....+..+....++....... .....+++|+|+||+++.+.+..  ....+.+++++|+||||+
T Consensus       109 t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~Ivv~Tp~~l~~~l~~--~~~~~~~~~~lViDEah~  185 (253)
T 1wrb_A          109 TRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQI-REVQMGCHLLVATPGRLVDFIEK--NKISLEFCKYIVLDEADR  185 (253)
T ss_dssp             SHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHH-HHHSSCCSEEEECHHHHHHHHHT--TSBCCTTCCEEEEETHHH
T ss_pred             CHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHH-HHhCCCCCEEEECHHHHHHHHHc--CCCChhhCCEEEEeCHHH
Confidence            999999999999999888788877776665433222 22346789999999999999887  566788999999999999


Q ss_pred             ccccCccchHHHHHHHHHhcCCC---CceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        170 LFEAGVRGFRDQLAVIYAACSGP---NLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       170 l~~~~~~~~~~~i~~i~~~~~~~---~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      +.+.   ++...+..+++.+..+   ..|++++|||+|+++.++++.++.+|+.+.+++
T Consensus       186 ~~~~---~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~  241 (253)
T 1wrb_A          186 MLDM---GFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGR  241 (253)
T ss_dssp             HHHT---TCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC-
T ss_pred             HHhC---chHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECC
Confidence            9988   6888999998854222   689999999999999999999999999998864

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=100.00  E-value=1.4e-34  Score=226.01  Aligned_cols=197  Identities=26%  Similarity=0.350  Sum_probs=164.3

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC--CCCCceEEEEcccHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP--KNLGFRAVIVCPTRELAK   95 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~--~~~~~~~iil~Pt~~L~~   95 (226)
                      ++-+.+++.+++.++.++++.|..+. .+.+++++++.+|||+|||.+|+.+++..+...  ...+++++|++|+++|+.
T Consensus         7 ~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~~   86 (207)
T 2gxq_A            7 PLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELAL   86 (207)
T ss_dssp             CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHHH
T ss_pred             CCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHHH
Confidence            35678899999999999999997775 677889999999999999999999999988532  234678999999999999


Q ss_pred             HHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCc
Q psy12977         96 QTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGV  175 (226)
Q Consensus        96 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~  175 (226)
                      |+.+.++.+...  .++....++....... .....+++|+|+||+++.+.+..  +...+.+++++|+||||++.+.  
T Consensus        87 q~~~~~~~~~~~--~~~~~~~~~~~~~~~~-~~~~~~~~i~v~T~~~l~~~~~~--~~~~~~~~~~iViDEah~~~~~--  159 (207)
T 2gxq_A           87 QVASELTAVAPH--LKVVAVYGGTGYGKQK-EALLRGADAVVATPGRALDYLRQ--GVLDLSRVEVAVLDEADEMLSM--  159 (207)
T ss_dssp             HHHHHHHHHCTT--SCEEEECSSSCSHHHH-HHHHHCCSEEEECHHHHHHHHHH--TSSCCTTCSEEEEESHHHHHHT--
T ss_pred             HHHHHHHHHhhc--ceEEEEECCCChHHHH-HHhhCCCCEEEECHHHHHHHHHc--CCcchhhceEEEEEChhHhhcc--
Confidence            999999999765  4555555543321111 12235689999999999999887  6677899999999999999887  


Q ss_pred             cchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        176 RGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       176 ~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                       ++...+..++..+ ++..|++++|||+|+++.++++.++.+|+.+.++
T Consensus       160 -~~~~~~~~i~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~~~  206 (207)
T 2gxq_A          160 -GFEEEVEALLSAT-PPSRQTLLFSATLPSWAKRLAERYMKNPVLINVI  206 (207)
T ss_dssp             -TCHHHHHHHHHTS-CTTSEEEEECSSCCHHHHHHHHHHCSSCEEEECC
T ss_pred             -chHHHHHHHHHhC-CccCeEEEEEEecCHHHHHHHHHHcCCCeEEEcC
Confidence             6888899888887 5689999999999999999999999999999875

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=100.00  E-value=1.6e-34  Score=234.20  Aligned_cols=196  Identities=27%  Similarity=0.376  Sum_probs=164.7

Q ss_pred             HHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC---CCCCceEEEEcccHHHHH
Q psy12977         20 IIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP---KNLGFRAVIVCPTRELAK   95 (226)
Q Consensus        20 ~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~---~~~~~~~iil~Pt~~L~~   95 (226)
                      +.+.+++.+++++|..++++|..+. .+..++|+++++|||+|||++|++|++..+...   ...+.+++|++|+++|+.
T Consensus        61 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~  140 (262)
T 3ly5_A           61 VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAM  140 (262)
T ss_dssp             CCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHH
T ss_pred             cCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHH
Confidence            5678999999999999999997775 667889999999999999999999999877432   224678999999999999


Q ss_pred             HHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCc
Q psy12977         96 QTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGV  175 (226)
Q Consensus        96 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~  175 (226)
                      |+.+.++++....+..+....++....... .....+++|+|+||+++.+.+... ....+.+++++|+||||++.+.  
T Consensus       141 q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~Iiv~Tp~~l~~~~~~~-~~~~~~~l~~lViDEah~l~~~--  216 (262)
T 3ly5_A          141 QTFGVLKELMTHHVHTYGLIMGGSNRSAEA-QKLGNGINIIVATPGRLLDHMQNT-PGFMYKNLQCLVIDEADRILDV--  216 (262)
T ss_dssp             HHHHHHHHHTTTCCSCEEEECSSSCHHHHH-HHHHHCCSEEEECHHHHHHHHHHC-TTCCCTTCCEEEECSHHHHHHT--
T ss_pred             HHHHHHHHHHhhcCceEEEEECCCCHHHHH-HHhcCCCCEEEEcHHHHHHHHHcc-CCcccccCCEEEEcChHHHhhh--
Confidence            999999999988888888777765443332 123345899999999999988763 3466889999999999999998  


Q ss_pred             cchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcC-CCeEE
Q psy12977        176 RGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLK-RRVQI  221 (226)
Q Consensus       176 ~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~-~p~~i  221 (226)
                       ++...+..+++.+ ++.+|++++|||+|+++.++++.+++ +|+++
T Consensus       217 -~~~~~l~~i~~~~-~~~~q~l~~SAT~~~~v~~~~~~~l~~~~~~v  261 (262)
T 3ly5_A          217 -GFEEELKQIIKLL-PTRRQTMLFSATQTRKVEDLARISLKKEPLYV  261 (262)
T ss_dssp             -TCHHHHHHHHHHS-CSSSEEEEECSSCCHHHHHHHHHHCSSCCEEC
T ss_pred             -hHHHHHHHHHHhC-CCCCeEEEEEecCCHHHHHHHHHHcCCCCeee
Confidence             6889999999888 57899999999999999999999987 45443

>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=4.8e-34  Score=246.91  Aligned_cols=201  Identities=28%  Similarity=0.425  Sum_probs=172.0

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC----CCCCceEEEEcccHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP----KNLGFRAVIVCPTRE   92 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~----~~~~~~~iil~Pt~~   92 (226)
                      +.+-+.+++.+++++|.+++|+|.++. .+++|+|+++++|||||||++|++|++..+...    ...+++++|++||++
T Consensus        61 ~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~Ptre  140 (434)
T 2db3_A           61 ADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRE  140 (434)
T ss_dssp             SCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEECSSHH
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEecCHH
Confidence            346788999999999999999997775 778899999999999999999999999887432    234679999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccc
Q psy12977         93 LAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFE  172 (226)
Q Consensus        93 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~  172 (226)
                      |+.|+++.++++....+.++..+.|+....... .....+++|+|+||+++.+++.+  ....+.+++++|+||||++++
T Consensus       141 La~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~-~~l~~~~~Ivv~Tp~~l~~~l~~--~~~~l~~~~~lVlDEah~~~~  217 (434)
T 2db3_A          141 LAIQIFNEARKFAFESYLKIGIVYGGTSFRHQN-ECITRGCHVVIATPGRLLDFVDR--TFITFEDTRFVVLDEADRMLD  217 (434)
T ss_dssp             HHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHH-HHHTTCCSEEEECHHHHHHHHHT--TSCCCTTCCEEEEETHHHHTS
T ss_pred             HHHHHHHHHHHHhccCCcEEEEEECCCCHHHHH-HHhhcCCCEEEEChHHHHHHHHh--CCcccccCCeEEEccHhhhhc
Confidence            999999999999988888887777765433222 23446799999999999999987  567789999999999999999


Q ss_pred             cCccchHHHHHHHHHhcC-CCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        173 AGVRGFRDQLAVIYAACS-GPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       173 ~~~~~~~~~i~~i~~~~~-~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      .   ++...+..++..+. ++..|++++|||+|+++.+++..++.+|+.+.+.
T Consensus       218 ~---gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~  267 (434)
T 2db3_A          218 M---GFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIG  267 (434)
T ss_dssp             T---TTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEES
T ss_pred             c---CcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEec
Confidence            8   68999999988752 5678999999999999999999999999988765

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=99.97  E-value=1.4e-31  Score=229.15  Aligned_cols=199  Identities=22%  Similarity=0.309  Sum_probs=169.2

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      +.+-+.+++.+++.+|.+++|+|..+. .+.+++++++.+|||+|||++|++|+++.+.. ...+.+++|++|+++|+.|
T Consensus        42 ~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~-~~~~~~~lil~Pt~~L~~q  120 (410)
T 2j0s_A           42 MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI-QVRETQALILAPTRELAVQ  120 (410)
T ss_dssp             GCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCT-TSCSCCEEEECSSHHHHHH
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhh-ccCCceEEEEcCcHHHHHH
Confidence            345688999999999999999997775 67788999999999999999999999988753 3346799999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +.+.++.+....+..+....++....... .....+++|+|+||+++.+.+..  ....+.+++++|+||+|++.+.   
T Consensus       121 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~ivv~Tp~~l~~~l~~--~~~~~~~~~~vViDEah~~~~~---  194 (410)
T 2j0s_A          121 IQKGLLALGDYMNVQCHACIGGTNVGEDI-RKLDYGQHVVAGTPGRVFDMIRR--RSLRTRAIKMLVLDEADEMLNK---  194 (410)
T ss_dssp             HHHHHHHHTTTTTCCEEEECTTSCHHHHH-HHHHHCCSEEEECHHHHHHHHHT--TSSCCTTCCEEEEETHHHHTST---
T ss_pred             HHHHHHHHhccCCeEEEEEECCCCHHHHH-HHhhcCCCEEEcCHHHHHHHHHh--CCccHhheeEEEEccHHHHHhh---
Confidence            99999999988888888777665433322 12335679999999999999887  5677889999999999999887   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      ++...+..+++.+ ++..|++++|||+|+++.+++..++.+|..+.+.
T Consensus       195 ~~~~~~~~i~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  241 (410)
T 2j0s_A          195 GFKEQIYDVYRYL-PPATQVVLISATLPHEILEMTNKFMTDPIRILVK  241 (410)
T ss_dssp             TTHHHHHHHHTTS-CTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCC
T ss_pred             hhHHHHHHHHHhC-ccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEec
Confidence            6888888888877 6789999999999999999999999999988764

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.97  E-value=3.4e-31  Score=226.90  Aligned_cols=200  Identities=26%  Similarity=0.399  Sum_probs=166.5

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC-----------------CCC
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP-----------------KNL   80 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~-----------------~~~   80 (226)
                      .+-+.+++.+...+|.+++|+|..+. .+..++|+++.+|||+|||++|++|+++.+...                 ...
T Consensus        21 ~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (417)
T 2i4i_A           21 EMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQ  100 (417)
T ss_dssp             CCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBTTBSCSB
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccccccccccC
Confidence            45678999999999999999997775 677899999999999999999999998876422                 122


Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCcc
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVE  160 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~  160 (226)
                      +++++|++|+++|+.|+.+.++.+....+.++....++....... .....+++|+|+||+++.+.+..  ....+.+++
T Consensus       101 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~I~v~Tp~~l~~~l~~--~~~~~~~~~  177 (417)
T 2i4i_A          101 YPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQI-RDLERGCHLLVATPGRLVDMMER--GKIGLDFCK  177 (417)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHH-HHHTTCCSEEEECHHHHHHHHHT--TSBCCTTCC
T ss_pred             CccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHH-HHhhCCCCEEEEChHHHHHHHHc--CCcChhhCc
Confidence            468999999999999999999999988888888777765433322 22346789999999999999887  567788999


Q ss_pred             EEEEcccccccccCccchHHHHHHHHHhcC---CCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        161 WLIVDESDKLFEAGVRGFRDQLAVIYAACS---GPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       161 ~lViDE~h~l~~~~~~~~~~~i~~i~~~~~---~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      ++|+||+|.+.+.   ++...+..+.....   ....|++++|||+|+++..++..++.+|..+.+.
T Consensus       178 ~iViDEah~~~~~---~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  241 (417)
T 2i4i_A          178 YLVLDEADRMLDM---GFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVG  241 (417)
T ss_dssp             EEEESSHHHHHHT---TCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC
T ss_pred             EEEEEChhHhhcc---CcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeC
Confidence            9999999999988   68888888887532   1268999999999999999999999999887764

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.97  E-value=3.2e-31  Score=226.71  Aligned_cols=201  Identities=22%  Similarity=0.309  Sum_probs=172.6

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      +++-+..++.+.+.+|..+++.|..+. .+..++++++.+|||+|||++|++++++.+.. ...+.+++|++|+++|+.|
T Consensus        45 ~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q  123 (414)
T 3eiq_A           45 MNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIEL-DLKATQALVLAPTRELAQQ  123 (414)
T ss_dssp             GCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCT-TSCSCCEEEECSSHHHHHH
T ss_pred             CCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhh-cCCceeEEEEeChHHHHHH
Confidence            345678899999999999999997774 77789999999999999999999999998864 3346689999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +.+.++.+....+..+....++.............+++|+|+||+++.+.+..  ....+.+++++|+||+|++.+.   
T Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~--~~~~~~~~~~vViDEah~~~~~---  198 (414)
T 3eiq_A          124 IQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNR--RYLSPKYIKMFVLDEADEMLSR---  198 (414)
T ss_dssp             HHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHH--TSSCSTTCCEEEECSHHHHHHT---
T ss_pred             HHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHc--CCcccccCcEEEEECHHHhhcc---
Confidence            99999999988888888777765554444333447789999999999999887  6677888999999999999887   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      ++...+..++..+ ++..|++++|||+++++.+++..++.+|..+.+..
T Consensus       199 ~~~~~~~~~~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  246 (414)
T 3eiq_A          199 GFKDQIYDIFQKL-NSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKK  246 (414)
T ss_dssp             TTHHHHHHHHTTS-CTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCC
T ss_pred             CcHHHHHHHHHhC-CCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecC
Confidence            6888888898888 67899999999999999999999999998887653

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=99.97  E-value=1.7e-30  Score=227.07  Aligned_cols=199  Identities=20%  Similarity=0.197  Sum_probs=163.7

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCC--CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLG--RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELA   94 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~--~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~   94 (226)
                      +.+.+.+++.+.+++|..++|+|..+. .++.+  +++++.||||||||++|++|++..+.. ...++++||++|+++|+
T Consensus        97 ~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~-~~~~~~~lil~Pt~~La  175 (479)
T 3fmp_B           97 LRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEP-ANKYPQCLCLSPTYELA  175 (479)
T ss_dssp             GTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCT-TSCSCCEEEECSSHHHH
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhh-cCCCCcEEEEeChHHHH
Confidence            456789999999999999999997775 55555  899999999999999999999988864 33456899999999999


Q ss_pred             HHHHHHHHHHhhcC-CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977         95 KQTYNETVRLSEGL-GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus        95 ~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      .|+.+.++++.... +..+....++...    .......++|+|+||+++.+++.+. ..+++.+++++|+||+|.+.+.
T Consensus       176 ~Q~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~Ivv~Tp~~l~~~l~~~-~~~~~~~~~~iViDEah~~~~~  250 (479)
T 3fmp_B          176 LQTGKVIEQMGKFYPELKLAYAVRGNKL----ERGQKISEQIVIGTPGTVLDWCSKL-KFIDPKKIKVFVLDEADVMIAT  250 (479)
T ss_dssp             HHHHHHHHHHHTTSTTCCEEEESTTCCC----CTTCCCCCSEEEECHHHHHHHHTTS-CCCCGGGCCEEEECCHHHHHTS
T ss_pred             HHHHHHHHHHHhhCCCceEEEEeCCccc----cccccCCCCEEEECchHHHHHHHhc-CCcCcccCCEEEEECHHHHhhc
Confidence            99999999998764 3555555554321    2223456799999999999988653 5677899999999999999874


Q ss_pred             CccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        174 GVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       174 ~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      .  ++...+..+.+.+ ++.+|++++|||++.++..++..++.+|..+.+.+
T Consensus       251 ~--~~~~~~~~i~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~  299 (479)
T 3fmp_B          251 Q--GHQDQSIRIQRML-PRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR  299 (479)
T ss_dssp             T--THHHHHHHHHTTS-CTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC-
T ss_pred             C--CcHHHHHHHHhhC-CccceEEEEeCCCCHHHHHHHHHHcCCCeEEeccc
Confidence            3  5777888888777 67899999999999999999999999999887654

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.97  E-value=1.7e-30  Score=220.72  Aligned_cols=201  Identities=23%  Similarity=0.311  Sum_probs=166.5

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      .+-+.+++.+++.+|.+++|.|..+. .+..++++++.+|||+|||++|+++++..+.. ...+.+++|++|+++|+.|+
T Consensus        14 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~-~~~~~~~lil~P~~~L~~q~   92 (391)
T 1xti_A           14 LLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEP-VTGQVSVLVMCHTRELAFQI   92 (391)
T ss_dssp             CCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCC-CTTCCCEEEECSCHHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcc-cCCCeeEEEECCCHHHHHHH
Confidence            45688999999999999999997775 67788999999999999999999999988753 33456899999999999999


Q ss_pred             HHHHHHHhhcC-CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         98 YNETVRLSEGL-GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        98 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      .+.++++.+.. +.++....++..............++|+|+||+++.+.+..  ....+.+++++|+||||.+.+..  
T Consensus        93 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~--~~~~~~~~~~vViDEaH~~~~~~--  168 (391)
T 1xti_A           93 SKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN--KSLNLKHIKHFILDECDKMLEQL--  168 (391)
T ss_dssp             HHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT--TSSCCTTCSEEEECSHHHHTSSH--
T ss_pred             HHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHc--CCccccccCEEEEeCHHHHhhcc--
Confidence            99999998776 67777777665433322222234579999999999998887  56678899999999999998742  


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      ++...+..++... ++..|++++|||++++....+..++.+|..+.+..
T Consensus       169 ~~~~~~~~~~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  216 (391)
T 1xti_A          169 DMRRDVQEIFRMT-PHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDD  216 (391)
T ss_dssp             HHHHHHHHHHHTS-CSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCC
T ss_pred             chHHHHHHHHhhC-CCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecC
Confidence            5777888888777 56899999999999999999999999998887653

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.97  E-value=1.4e-30  Score=221.19  Aligned_cols=199  Identities=22%  Similarity=0.284  Sum_probs=168.4

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      +.+-+.+++.+.+.+|.+++|.|..+. .+..++++++.+|||+|||++|++|++..+.. ...+++++|++|+++|+.|
T Consensus        26 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~-~~~~~~~lil~P~~~L~~q  104 (394)
T 1fuu_A           26 MELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDT-SVKAPQALMLAPTRELALQ  104 (394)
T ss_dssp             GCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCT-TCCSCCEEEECSSHHHHHH
T ss_pred             cCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhc-cCCCCCEEEEcCCHHHHHH
Confidence            356788999999999999999997775 66788999999999999999999999988764 3346799999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +.+.+..+....+.++....++.........  ..+++|+|+||+++.+.+..  ....+.+++++|+||+|.+.+.   
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~--~~~~~i~v~T~~~l~~~~~~--~~~~~~~~~~vIiDEah~~~~~---  177 (394)
T 1fuu_A          105 IQKVVMALAFHMDIKVHACIGGTSFVEDAEG--LRDAQIVVGTPGRVFDNIQR--RRFRTDKIKMFILDEADEMLSS---  177 (394)
T ss_dssp             HHHHHHHHTTTSCCCEEEECSSCCHHHHHHH--HHHCSEEEECHHHHHHHHHT--TSSCCTTCCEEEEETHHHHHHT---
T ss_pred             HHHHHHHHhccCCeeEEEEeCCCchHHHHhh--cCCCCEEEECHHHHHHHHHh--CCcchhhCcEEEEEChHHhhCC---
Confidence            9999999988888888877776543322111  12578999999999998887  5667889999999999999887   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      ++...+..+...+ ++..|++++|||+++.+.++...++.+|..+.+..
T Consensus       178 ~~~~~~~~~~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  225 (394)
T 1fuu_A          178 GFKEQIYQIFTLL-PPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKK  225 (394)
T ss_dssp             TCHHHHHHHHHHS-CTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC
T ss_pred             CcHHHHHHHHHhC-CCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecC
Confidence            5888888888887 67899999999999999999999999999887653

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.97  E-value=5.9e-30  Score=218.58  Aligned_cols=198  Identities=20%  Similarity=0.201  Sum_probs=163.1

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCC--CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLG--RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELA   94 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~--~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~   94 (226)
                      +++-+.+++.+++.+|..++|.|..+. .+..+  +++++.+|||+|||++|++|++..+.. ...+++++|++|+++|+
T Consensus        30 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~  108 (412)
T 3fht_A           30 LRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEP-ANKYPQCLCLSPTYELA  108 (412)
T ss_dssp             GTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCT-TSCSCCEEEECSSHHHH
T ss_pred             CCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhh-cCCCCCEEEECCCHHHH
Confidence            456789999999999999999997775 45555  899999999999999999999988864 34456899999999999


Q ss_pred             HHHHHHHHHHhhcC-CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977         95 KQTYNETVRLSEGL-GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus        95 ~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      .|+.+.++++.... +..+....++...    .......++|+|+||+++.+.+... ....+.+++++|+||+|++.+.
T Consensus       109 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~ivv~T~~~l~~~~~~~-~~~~~~~~~~iViDEah~~~~~  183 (412)
T 3fht_A          109 LQTGKVIEQMGKFYPELKLAYAVRGNKL----ERGQKISEQIVIGTPGTVLDWCSKL-KFIDPKKIKVFVLDEADVMIAT  183 (412)
T ss_dssp             HHHHHHHHHHTTTSTTCCEEEECTTCCC----CTTCCCCCSEEEECHHHHHHHHTTS-CSSCGGGCCEEEEETHHHHHST
T ss_pred             HHHHHHHHHHHhhcccceEEEeecCcch----hhhhcCCCCEEEECchHHHHHHHhc-CCcChhhCcEEEEeCHHHHhhc
Confidence            99999999998765 4566655554322    2223456899999999999988653 5667889999999999999874


Q ss_pred             CccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        174 GVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       174 ~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      .  ++...+..+...+ ++..|++++|||+++.+..++..++.+|..+.+.
T Consensus       184 ~--~~~~~~~~~~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  231 (412)
T 3fht_A          184 Q--GHQDQSIRIQRML-PRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLK  231 (412)
T ss_dssp             T--TTHHHHHHHHHTS-CTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCC
T ss_pred             C--CcHHHHHHHHhhC-CCCceEEEEEeecCHHHHHHHHHhcCCCeEEeec
Confidence            3  5777788888777 6789999999999999999999999999888764

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.97  E-value=4.5e-30  Score=218.94  Aligned_cols=199  Identities=27%  Similarity=0.373  Sum_probs=167.2

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      +.+-+.+++.+.+.+|++++|.|..+. .+.+++++++.+|||+|||++|++|++..+.. ...+.+++|++|+++|+.|
T Consensus        26 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~q  104 (400)
T 1s2m_A           26 FYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKP-KLNKIQALIMVPTRELALQ  104 (400)
T ss_dssp             GCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCT-TSCSCCEEEECSSHHHHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhh-ccCCccEEEEcCCHHHHHH
Confidence            345688999999999999999997775 66788999999999999999999999988763 2345689999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +.+.++.+....+..+....++....... .....+++|+|+||+++.+.+..  ....+.+++++|+||+|++.+.   
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~Ivv~T~~~l~~~~~~--~~~~~~~~~~vIiDEaH~~~~~---  178 (400)
T 1s2m_A          105 TSQVVRTLGKHCGISCMVTTGGTNLRDDI-LRLNETVHILVGTPGRVLDLASR--KVADLSDCSLFIMDEADKMLSR---  178 (400)
T ss_dssp             HHHHHHHHTTTTTCCEEEECSSSCHHHHH-HHTTSCCSEEEECHHHHHHHHHT--TCSCCTTCCEEEEESHHHHSSH---
T ss_pred             HHHHHHHHhcccCceEEEEeCCcchHHHH-HHhcCCCCEEEEchHHHHHHHHh--CCcccccCCEEEEeCchHhhhh---
Confidence            99999999988888887777665433322 12346789999999999998876  5667889999999999999877   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      ++...+..+...+ ++..|++++|||+|+.+.+++..++.+|..+.+.
T Consensus       179 ~~~~~~~~i~~~~-~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~  225 (400)
T 1s2m_A          179 DFKTIIEQILSFL-PPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLM  225 (400)
T ss_dssp             HHHHHHHHHHTTS-CSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCC
T ss_pred             chHHHHHHHHHhC-CcCceEEEEEecCCHHHHHHHHHHcCCCeEEEec
Confidence            5778888888777 5688999999999999999999999998877654

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.97  E-value=7.2e-30  Score=216.58  Aligned_cols=195  Identities=19%  Similarity=0.300  Sum_probs=163.9

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCC--CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLG--RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAK   95 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~--~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~   95 (226)
                      ++-+.+++.+.+.+|.+++|.|..+. .+..+  +++++.+|||+|||++|+.+++..+.. ...+++++|++|+++|+.
T Consensus        11 ~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~-~~~~~~~lil~P~~~L~~   89 (395)
T 3pey_A           11 GLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNP-EDASPQAICLAPSRELAR   89 (395)
T ss_dssp             CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCT-TCCSCCEEEECSSHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhcc-CCCCccEEEECCCHHHHH
Confidence            45678999999999999999997775 55555  899999999999999999999988764 334669999999999999


Q ss_pred             HHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCc
Q psy12977         96 QTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGV  175 (226)
Q Consensus        96 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~  175 (226)
                      |+.+.++++....+.......++....     ....+++|+|+||+++.+.+..  ....+.+++++|+||+|++.+.. 
T Consensus        90 q~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~iiv~T~~~l~~~~~~--~~~~~~~~~~iIiDEah~~~~~~-  161 (395)
T 3pey_A           90 QTLEVVQEMGKFTKITSQLIVPDSFEK-----NKQINAQVIVGTPGTVLDLMRR--KLMQLQKIKIFVLDEADNMLDQQ-  161 (395)
T ss_dssp             HHHHHHHHHTTTSCCCEEEESTTSSCT-----TSCBCCSEEEECHHHHHHHHHT--TCBCCTTCCEEEEETHHHHHHST-
T ss_pred             HHHHHHHHHhcccCeeEEEEecCchhh-----hccCCCCEEEEcHHHHHHHHHc--CCcccccCCEEEEEChhhhcCcc-
Confidence            999999999888787777766553322     2235789999999999999877  66778999999999999998742 


Q ss_pred             cchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        176 RGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       176 ~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                       ++...+..+...+ ++..|++++|||+++.+.++...++.++..+.+.
T Consensus       162 -~~~~~~~~~~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  208 (395)
T 3pey_A          162 -GLGDQCIRVKRFL-PKDTQLVLFSATFADAVRQYAKKIVPNANTLELQ  208 (395)
T ss_dssp             -THHHHHHHHHHTS-CTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCC
T ss_pred             -ccHHHHHHHHHhC-CCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEcc
Confidence             5777888888777 6789999999999999999999999988877654

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.96  E-value=1.6e-29  Score=212.42  Aligned_cols=196  Identities=27%  Similarity=0.372  Sum_probs=164.1

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCC-CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLG-RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~-~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      ++.+.+++.+++.+|.+++|.|..+. .+.++ +++++.+|||+|||++++.+++..+...  .+.+++|++|+++|+.|
T Consensus        12 ~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~--~~~~~lil~P~~~L~~q   89 (367)
T 1hv8_A           12 NLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN--NGIEAIILTPTRELAIQ   89 (367)
T ss_dssp             SCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS--SSCCEEEECSCHHHHHH
T ss_pred             CCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc--CCCcEEEEcCCHHHHHH
Confidence            46788999999999999999997775 44555 7999999999999999999998887543  45689999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +.+.++.+....+..+....++........  ...+++|+|+||+++.+.+..  ....+.+++++|+||+|.+.+.   
T Consensus        90 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~--~~~~~~iiv~T~~~l~~~~~~--~~~~~~~~~~iIiDEah~~~~~---  162 (367)
T 1hv8_A           90 VADEIESLKGNKNLKIAKIYGGKAIYPQIK--ALKNANIVVGTPGRILDHINR--GTLNLKNVKYFILDEADEMLNM---  162 (367)
T ss_dssp             HHHHHHHHHCSSCCCEEEECTTSCHHHHHH--HHHTCSEEEECHHHHHHHHHT--TCSCTTSCCEEEEETHHHHHTT---
T ss_pred             HHHHHHHHhCCCCceEEEEECCcchHHHHh--hcCCCCEEEecHHHHHHHHHc--CCcccccCCEEEEeCchHhhhh---
Confidence            999999998887888877776654332211  113689999999999999887  5667889999999999999887   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      ++...+..++..+ ++..+++++|||++++..+++..++.++..+...
T Consensus       163 ~~~~~~~~~~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  209 (367)
T 1hv8_A          163 GFIKDVEKILNAC-NKDKRILLFSATMPREILNLAKKYMGDYSFIKAK  209 (367)
T ss_dssp             TTHHHHHHHHHTS-CSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECC
T ss_pred             chHHHHHHHHHhC-CCCceEEEEeeccCHHHHHHHHHHcCCCeEEEec
Confidence            6888888888877 6789999999999999999999999988777653

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=99.96  E-value=3.8e-29  Score=208.04  Aligned_cols=186  Identities=28%  Similarity=0.434  Sum_probs=158.1

Q ss_pred             HHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHH
Q psy12977         22 VTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE  100 (226)
Q Consensus        22 ~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~  100 (226)
                      +.+.+.+++++|.+++|.|..+. .+.+++++++.+|||+|||++|+.+++..       +.+++|++|+++|+.|+.+.
T Consensus         3 ~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~-------~~~~liv~P~~~L~~q~~~~   75 (337)
T 2z0m_A            3 EKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL-------GMKSLVVTPTRELTRQVASH   75 (337)
T ss_dssp             HHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH-------TCCEEEECSSHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh-------cCCEEEEeCCHHHHHHHHHH
Confidence            56788999999999999997775 66788999999999999999999998764       45899999999999999999


Q ss_pred             HHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHH
Q psy12977        101 TVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRD  180 (226)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~  180 (226)
                      ++++....+..+....++........  ...+++|+|+||+++.+.+..  ....+.+++++|+||+|++.+.   ++..
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~i~v~T~~~l~~~~~~--~~~~~~~~~~iViDEah~~~~~---~~~~  148 (337)
T 2z0m_A           76 IRDIGRYMDTKVAEVYGGMPYKAQIN--RVRNADIVVATPGRLLDLWSK--GVIDLSSFEIVIIDEADLMFEM---GFID  148 (337)
T ss_dssp             HHHHTTTSCCCEEEECTTSCHHHHHH--HHTTCSEEEECHHHHHHHHHT--TSCCGGGCSEEEEESHHHHHHT---TCHH
T ss_pred             HHHHhhhcCCcEEEEECCcchHHHHh--hcCCCCEEEECHHHHHHHHHc--CCcchhhCcEEEEEChHHhhcc---ccHH
Confidence            99998888888887777654333221  113489999999999998876  5667889999999999999888   6888


Q ss_pred             HHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEe
Q psy12977        181 QLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN  222 (226)
Q Consensus       181 ~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~  222 (226)
                      .+..++... +...+++++|||+|++..+.+..++.++..+.
T Consensus       149 ~~~~~~~~~-~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~  189 (337)
T 2z0m_A          149 DIKIILAQT-SNRKITGLFSATIPEEIRKVVKDFITNYEEIE  189 (337)
T ss_dssp             HHHHHHHHC-TTCSEEEEEESCCCHHHHHHHHHHSCSCEEEE
T ss_pred             HHHHHHhhC-CcccEEEEEeCcCCHHHHHHHHHhcCCceeee
Confidence            888888877 56889999999999999999999998887764

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.96  E-value=6.4e-30  Score=228.39  Aligned_cols=200  Identities=27%  Similarity=0.354  Sum_probs=157.0

Q ss_pred             HHHHHHHHHhhccccCCCCcccccc-cCC--CCCeEEEECCCCchHhHHHHHHHHHHhcCCC---CCCceEEEEcccHHH
Q psy12977         20 IIVTTLAVVSNSIFKHFEPHFTITY-LSP--LGRQIFACAPTGSGKTAAFLIPIIHSLRGPK---NLGFRAVIVCPTREL   93 (226)
Q Consensus        20 ~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~--~~~~~li~apTGsGKT~~~~~~~~~~~~~~~---~~~~~~iil~Pt~~L   93 (226)
                      +-+.+++.+.+++|.+++|+|..+. .++  .++++++.+|||+|||++|++|+++.+....   ..++++||++|+++|
T Consensus        28 l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~L  107 (579)
T 3sqw_A           28 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDL  107 (579)
T ss_dssp             SCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHHH
Confidence            5678999999999999999997775 444  6789999999999999999999998874332   335689999999999


Q ss_pred             HHHHHHHHHHHhhc----CCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccc
Q psy12977         94 AKQTYNETVRLSEG----LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK  169 (226)
Q Consensus        94 ~~q~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~  169 (226)
                      +.|+.+.++.+...    ....+....++.............+++|+|+||+++.+.+... ....++.++++|+||||+
T Consensus       108 a~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~-~~~~~~~~~~lViDEah~  186 (579)
T 3sqw_A          108 ALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKY-SNKFFRFVDYKVLDEADR  186 (579)
T ss_dssp             HHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHH-HHHHCTTCCEEEEETHHH
T ss_pred             HHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhc-cccccccCCEEEEEChHH
Confidence            99999999998643    2345555555544333322222346899999999999888652 234577899999999999


Q ss_pred             ccccCccchHHHHHHHHHhcC------CCCceEEEEeeeCchhHHHHHHHhcCCCeEEec
Q psy12977        170 LFEAGVRGFRDQLAVIYAACS------GPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       170 l~~~~~~~~~~~i~~i~~~~~------~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~  223 (226)
                      ++++   +|...+..+...++      .+.+|++++|||+++.+.+++..++.+|..+.+
T Consensus       187 l~~~---gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~  243 (579)
T 3sqw_A          187 LLEI---GFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFL  243 (579)
T ss_dssp             HTST---TTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEE
T ss_pred             hhcC---CCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEE
Confidence            9998   57777766665542      237799999999999999999999998877654

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.96  E-value=2.1e-29  Score=224.15  Aligned_cols=200  Identities=27%  Similarity=0.354  Sum_probs=155.5

Q ss_pred             HHHHHHHHHhhccccCCCCcccccc-cCC--CCCeEEEECCCCchHhHHHHHHHHHHhcCCC---CCCceEEEEcccHHH
Q psy12977         20 IIVTTLAVVSNSIFKHFEPHFTITY-LSP--LGRQIFACAPTGSGKTAAFLIPIIHSLRGPK---NLGFRAVIVCPTREL   93 (226)
Q Consensus        20 ~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~--~~~~~li~apTGsGKT~~~~~~~~~~~~~~~---~~~~~~iil~Pt~~L   93 (226)
                      +-+.++..+.+++|.+++|+|..+. .++  .++|+++.+|||+|||++|++|+++.+....   ..++++||++|+++|
T Consensus        79 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~L  158 (563)
T 3i5x_A           79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDL  158 (563)
T ss_dssp             SCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHH
Confidence            5678899999999999999997775 444  5789999999999999999999998875332   234689999999999


Q ss_pred             HHHHHHHHHHHhhc----CCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccc
Q psy12977         94 AKQTYNETVRLSEG----LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK  169 (226)
Q Consensus        94 ~~q~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~  169 (226)
                      +.|+.+.++.+...    ....+....++.............+++|+|+||+++.+.+.+. ....++.++++|+||||+
T Consensus       159 a~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~-~~~~~~~~~~lViDEah~  237 (563)
T 3i5x_A          159 ALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKY-SNKFFRFVDYKVLDEADR  237 (563)
T ss_dssp             HHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHH-HHHHCTTCCEEEEETHHH
T ss_pred             HHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhc-cccccccceEEEEeCHHH
Confidence            99999999998543    2344555555544333322222457899999999999888652 123477899999999999


Q ss_pred             ccccCccchHHHHHHHHHhcC------CCCceEEEEeeeCchhHHHHHHHhcCCCeEEec
Q psy12977        170 LFEAGVRGFRDQLAVIYAACS------GPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       170 l~~~~~~~~~~~i~~i~~~~~------~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~  223 (226)
                      ++++   ++...+..+...++      .+.+|++++|||+|+.+.+++..++.++..+.+
T Consensus       238 l~~~---~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~  294 (563)
T 3i5x_A          238 LLEI---GFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFL  294 (563)
T ss_dssp             HTST---TTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEE
T ss_pred             Hhcc---chHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEE
Confidence            9998   46666666655541      347899999999999999999999988776654

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=99.94  E-value=1.3e-25  Score=204.61  Aligned_cols=183  Identities=20%  Similarity=0.219  Sum_probs=138.6

Q ss_pred             HHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHH
Q psy12977         20 IIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTY   98 (226)
Q Consensus        20 ~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~   98 (226)
                      +.+.+.+.+++.+|++++|.|+.+. .+.+++++++++|||+|||.++.+++++.+..    +.+++|++|+++|+.|++
T Consensus        10 l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~----~~~~l~i~P~r~La~q~~   85 (702)
T 2p6r_A           10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK----GGKSLYVVPLRALAGEKY   85 (702)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT----TCCEEEEESSHHHHHHHH
T ss_pred             cCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh----CCcEEEEeCcHHHHHHHH
Confidence            6778889999999999999998775 56789999999999999999999999988763    458999999999999999


Q ss_pred             HHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccch
Q psy12977         99 NETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGF  178 (226)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~  178 (226)
                      +.++.+. ..+.++....|+.....    ....+++|+|+||+++...+.+  ....+++++++|+||+|.+.+..+...
T Consensus        86 ~~~~~~~-~~g~~v~~~~G~~~~~~----~~~~~~~Iiv~Tpe~l~~~l~~--~~~~l~~~~~vIiDE~H~l~~~~r~~~  158 (702)
T 2p6r_A           86 ESFKKWE-KIGLRIGISTGDYESRD----EHLGDCDIIVTTSEKADSLIRN--RASWIKAVSCLVVDEIHLLDSEKRGAT  158 (702)
T ss_dssp             HHHTTTT-TTTCCEEEECSSCBCCS----SCSTTCSEEEEEHHHHHHHHHT--TCSGGGGCCEEEETTGGGGGCTTTHHH
T ss_pred             HHHHHHH-hcCCEEEEEeCCCCcch----hhccCCCEEEECHHHHHHHHHc--ChhHHhhcCEEEEeeeeecCCCCcccH
Confidence            9996443 44788887777643322    2235789999999999998887  445588999999999999987632223


Q ss_pred             HHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcC
Q psy12977        179 RDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLK  216 (226)
Q Consensus       179 ~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~  216 (226)
                      .+.+...++.. .+..|++++|||+++ ..++. .++.
T Consensus       159 ~~~ll~~l~~~-~~~~~ii~lSATl~n-~~~~~-~~l~  193 (702)
T 2p6r_A          159 LEILVTKMRRM-NKALRVIGLSATAPN-VTEIA-EWLD  193 (702)
T ss_dssp             HHHHHHHHHHH-CTTCEEEEEECCCTT-HHHHH-HHTT
T ss_pred             HHHHHHHHHhc-CcCceEEEECCCcCC-HHHHH-HHhC
Confidence            33333333333 468999999999984 33333 4444

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.94  E-value=4.2e-27  Score=201.90  Aligned_cols=178  Identities=16%  Similarity=0.167  Sum_probs=134.3

Q ss_pred             HHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHH
Q psy12977         22 VTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE  100 (226)
Q Consensus        22 ~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~  100 (226)
                      .+..+.+++...-+++|.|..+. .+.+++|+++.+|||+|||++|+.+++....    .+++++|++|+++|+.|+.+.
T Consensus         8 ~~~~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~----~~~~~lil~Pt~~L~~q~~~~   83 (414)
T 3oiy_A            8 EDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR----KGKKSALVFPTVTLVKQTLER   83 (414)
T ss_dssp             HHHHHHHHHHHSSCCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHT----TTCCEEEEESSHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhc----CCCEEEEEECCHHHHHHHHHH
Confidence            34455555544447899997775 6778899999999999999999999887763    366899999999999999999


Q ss_pred             HHHHhhcCCCeEEEEecchhhh---hhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCc--
Q psy12977        101 TVRLSEGLGLRAHVIGKIQQAA---EKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGV--  175 (226)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~--  175 (226)
                      ++.+.+ .+.++..+.|+....   ........+.++|+|+||+++.+.+..    ..+.+++++|+||||++.+++.  
T Consensus        84 ~~~~~~-~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~----~~~~~~~~iViDEaH~~~~~~~~~  158 (414)
T 3oiy_A           84 LQKLAD-EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK----LSQKRFDFVFVDDVDAVLKASRNI  158 (414)
T ss_dssp             HHHHCC-SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH----HTTCCCSEEEESCHHHHHHCHHHH
T ss_pred             HHHHcc-CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH----hccccccEEEEeChHhhhhccchh
Confidence            999887 788888888776542   122122234489999999999887763    4567899999999998765320  


Q ss_pred             ------cchHHH-HHHHHHhcC----------CCCceEEEEeee-CchhHH
Q psy12977        176 ------RGFRDQ-LAVIYAACS----------GPNLKRGMFSAT-HTEDVA  208 (226)
Q Consensus       176 ------~~~~~~-i~~i~~~~~----------~~~~q~v~~SAT-~~~~~~  208 (226)
                            .++... +..++..++          .+..|++++||| .|+.+.
T Consensus       159 d~~l~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~  209 (414)
T 3oiy_A          159 DTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIR  209 (414)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSST
T ss_pred             hhHHhhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhH
Confidence                  145555 666776652          167899999999 666554

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.93  E-value=6.1e-26  Score=202.65  Aligned_cols=187  Identities=19%  Similarity=0.255  Sum_probs=140.5

Q ss_pred             HHHHHHHHHHhh-ccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         19 SIIVTTLAVVSN-SIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        19 ~~~~~~l~~~~~-~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      ++.+...+.+++ ++|..|+|.|..+. .+++|+|+++.+|||+|||++|++|++..       +.++||++|+++|+.|
T Consensus        27 ~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~-------~g~~lVisP~~~L~~q   99 (591)
T 2v1x_A           27 PWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS-------DGFTLVICPLISLMED   99 (591)
T ss_dssp             TTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS-------SSEEEEECSCHHHHHH
T ss_pred             CCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc-------CCcEEEEeCHHHHHHH
Confidence            456778888888 79999999997775 77789999999999999999999998652       3489999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhC--C---CcCCCCCEEEECchHHHH---hHhcCCCCCCCCCccEEEEcccc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFG--P---RSAQKFDVLITTPNKLVY---LLQMDPPALNLANVEWLIVDESD  168 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~---~~~~~~~IiV~Tp~~l~~---~~~~~~~~~~~~~~~~lViDE~h  168 (226)
                      +.+.+..+    +..+..+.++........  .   .....++|+|+||+++..   ++........+.+++++|+||||
T Consensus       100 ~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~~~~i~~iViDEAH  175 (591)
T 2v1x_A          100 QLMVLKQL----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVH  175 (591)
T ss_dssp             HHHHHHHH----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHHHHHTTCEEEEEEETGG
T ss_pred             HHHHHHhc----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHhhhhccCCcEEEEECcc
Confidence            99999887    677777776654332211  0   124678999999998742   22211123346789999999999


Q ss_pred             cccccC--ccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCC
Q psy12977        169 KLFEAG--VRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRR  218 (226)
Q Consensus       169 ~l~~~~--~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p  218 (226)
                      ++.+++  ++.....+..+...+  +..|++++|||+++.+.+.+..++..+
T Consensus       176 ~is~~g~dfr~~~~~l~~l~~~~--~~~~ii~lSAT~~~~v~~~i~~~l~~~  225 (591)
T 2v1x_A          176 CCSQWGHDFRPDYKALGILKRQF--PNASLIGLTATATNHVLTDAQKILCIE  225 (591)
T ss_dssp             GGSTTCTTCCGGGGGGGHHHHHC--TTSEEEEEESSCCHHHHHHHHHHTTCC
T ss_pred             cccccccccHHHHHHHHHHHHhC--CCCcEEEEecCCCHHHHHHHHHHhCCC
Confidence            998875  222233333444444  679999999999999988888877643

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.93  E-value=1.8e-25  Score=204.25  Aligned_cols=173  Identities=23%  Similarity=0.252  Sum_probs=141.1

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-c-CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-L-SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~-~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      ++.+...+.+++.+|.+++|.|+.+. . +.+++++++++|||+|||.++.+++++.+...   +.+++|++|+++|+.|
T Consensus         7 ~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~---~~~~l~i~P~raLa~q   83 (720)
T 2zj8_A            7 RVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ---GGKAVYIVPLKALAEE   83 (720)
T ss_dssp             CSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH---CSEEEEECSSGGGHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC---CCEEEEEcCcHHHHHH
Confidence            35667888999999999999998876 3 57899999999999999999999998877522   5699999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +++.++.+.+ .+.++....|+.....    ....+++|+|+||+++...+..  ....+++++++|+||+|.+.+.   
T Consensus        84 ~~~~~~~l~~-~g~~v~~~~G~~~~~~----~~~~~~~Iiv~Tpe~l~~~~~~--~~~~l~~~~~vIiDE~H~l~~~---  153 (720)
T 2zj8_A           84 KFQEFQDWEK-IGLRVAMATGDYDSKD----EWLGKYDIIIATAEKFDSLLRH--GSSWIKDVKILVADEIHLIGSR---  153 (720)
T ss_dssp             HHHHTGGGGG-GTCCEEEECSCSSCCC----GGGGGCSEEEECHHHHHHHHHH--TCTTGGGEEEEEEETGGGGGCT---
T ss_pred             HHHHHHHHHh-cCCEEEEecCCCCccc----cccCCCCEEEECHHHHHHHHHc--ChhhhhcCCEEEEECCcccCCC---
Confidence            9999965544 4788887777543222    2235789999999999998887  4555889999999999999876   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      +....+..++..+. ...|++++|||+++
T Consensus       154 ~r~~~~~~ll~~l~-~~~~ii~lSATl~n  181 (720)
T 2zj8_A          154 DRGATLEVILAHML-GKAQIIGLSATIGN  181 (720)
T ss_dssp             TTHHHHHHHHHHHB-TTBEEEEEECCCSC
T ss_pred             cccHHHHHHHHHhh-cCCeEEEEcCCcCC
Confidence            46677777777774 38999999999874

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.93  E-value=6e-25  Score=200.62  Aligned_cols=172  Identities=22%  Similarity=0.256  Sum_probs=139.8

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-c-CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-L-SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~-~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      ++.+...+.+++.+|.+++|.|+++. . +.+++++++++|||+|||.++.+++++.+...   +.+++|++|+++|+.|
T Consensus        14 ~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~---~~~il~i~P~r~La~q   90 (715)
T 2va8_A           14 KLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN---GGKAIYVTPLRALTNE   90 (715)
T ss_dssp             SSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS---CSEEEEECSCHHHHHH
T ss_pred             CCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC---CCeEEEEeCcHHHHHH
Confidence            35678888999999999999998886 3 57899999999999999999999999877522   4699999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +++.++.+ ...+.++....|+......    ...+++|+|+||+++...+..  ....+++++++|+||+|.+.+.   
T Consensus        91 ~~~~~~~~-~~~g~~v~~~~G~~~~~~~----~~~~~~Iiv~Tpe~l~~~~~~--~~~~l~~~~~vIiDE~H~l~~~---  160 (715)
T 2va8_A           91 KYLTFKDW-ELIGFKVAMTSGDYDTDDA----WLKNYDIIITTYEKLDSLWRH--RPEWLNEVNYFVLDELHYLNDP---  160 (715)
T ss_dssp             HHHHHGGG-GGGTCCEEECCSCSSSCCG----GGGGCSEEEECHHHHHHHHHH--CCGGGGGEEEEEECSGGGGGCT---
T ss_pred             HHHHHHHh-hcCCCEEEEEeCCCCCchh----hcCCCCEEEEcHHHHHHHHhC--ChhHhhccCEEEEechhhcCCc---
Confidence            99999644 3457888877776433222    224789999999999998887  4455889999999999998765   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      .+...+..++..+  +..|++++|||+++
T Consensus       161 ~~~~~l~~i~~~~--~~~~ii~lSATl~n  187 (715)
T 2va8_A          161 ERGPVVESVTIRA--KRRNLLALSATISN  187 (715)
T ss_dssp             TTHHHHHHHHHHH--HTSEEEEEESCCTT
T ss_pred             ccchHHHHHHHhc--ccCcEEEEcCCCCC
Confidence            4666777777666  38899999999874

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=99.93  E-value=3.5e-25  Score=209.36  Aligned_cols=174  Identities=18%  Similarity=0.194  Sum_probs=144.1

Q ss_pred             HHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         27 VVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        27 ~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      .+...+.-+++|.|..+. .+..|++++++||||+|||++|.++++..+..    +.+++|++|+++|+.|+++.+.+++
T Consensus       176 ~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~----g~rvlvl~PtraLa~Q~~~~l~~~~  251 (1108)
T 3l9o_A          176 NEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN----KQRVIYTSPIKALSNQKYRELLAEF  251 (1108)
T ss_dssp             SCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHT----TCEEEEEESSHHHHHHHHHHHHHHT
T ss_pred             HHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhc----CCeEEEEcCcHHHHHHHHHHHHHHh
Confidence            344556667899997774 77889999999999999999999999988853    5699999999999999999999986


Q ss_pred             hcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHH
Q psy12977        106 EGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVI  185 (226)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i  185 (226)
                      .    .+..+.|+..        ...+++|+|+||+++.+++.+  +...+.++++||+||||++.+.   ++...+..+
T Consensus       252 ~----~VglltGd~~--------~~~~~~IlV~Tpe~L~~~L~~--~~~~l~~l~lVVIDEaH~l~d~---~rg~~~e~i  314 (1108)
T 3l9o_A          252 G----DVGLMTGDIT--------INPDAGCLVMTTEILRSMLYR--GSEVMREVAWVIFDEVHYMRDK---ERGVVWEET  314 (1108)
T ss_dssp             S----SEEEECSSCB--------CCCSCSEEEEEHHHHHHHHHH--CSSHHHHEEEEEEETGGGTTSH---HHHHHHHHH
T ss_pred             C----CccEEeCccc--------cCCCCCEEEeChHHHHHHHHc--CccccccCCEEEEhhhhhcccc---chHHHHHHH
Confidence            5    4555555532        335689999999999999887  5556889999999999999887   577888888


Q ss_pred             HHhcCCCCceEEEEeeeCch--hHHHHHHHhcCCCeEEe
Q psy12977        186 YAACSGPNLKRGMFSATHTE--DVAKWCRRKLKRRVQIN  222 (226)
Q Consensus       186 ~~~~~~~~~q~v~~SAT~~~--~~~~~~~~~~~~p~~i~  222 (226)
                      +..+ ++..|++++|||+|.  ++.+|+.....+|..+.
T Consensus       315 i~~l-~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi  352 (1108)
T 3l9o_A          315 IILL-PDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIV  352 (1108)
T ss_dssp             HHHS-CTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEE
T ss_pred             HHhc-CCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEE
Confidence            8888 678999999999886  46789988887776654

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.92  E-value=4.2e-25  Score=215.46  Aligned_cols=173  Identities=21%  Similarity=0.272  Sum_probs=132.3

Q ss_pred             cccCCCCcccccc--cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC-------CCCCceEEEEcccHHHHHHHHHHHH
Q psy12977         32 IFKHFEPHFTITY--LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP-------KNLGFRAVIVCPTRELAKQTYNETV  102 (226)
Q Consensus        32 ~~~~~~~~Q~~~~--~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~-------~~~~~~~iil~Pt~~L~~q~~~~~~  102 (226)
                      +|+++|++|+..+  .+.+++|++++||||+|||+++.+++++.+.+.       ...+.++||++|+++||.|+++.++
T Consensus        76 g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~  155 (1724)
T 4f92_B           76 GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFG  155 (1724)
T ss_dssp             TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHH
Confidence            6889999998886  456789999999999999999999999988532       2246799999999999999999999


Q ss_pred             HHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccch-HH-
Q psy12977        103 RLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGF-RD-  180 (226)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~-~~-  180 (226)
                      +..+..|+++....|+....    .....+++|+|+||+++..++++......+++++++|+||+|.+.+.  |+. ++ 
T Consensus       156 ~~~~~~gi~V~~~tGd~~~~----~~~~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d~--RG~~lE~  229 (1724)
T 4f92_B          156 KRLATYGITVAELTGDHQLC----KEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHDD--RGPVLEA  229 (1724)
T ss_dssp             HHHTTTTCCEEECCSSCSSC----CTTGGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGST--THHHHHH
T ss_pred             HHHhhCCCEEEEEECCCCCC----ccccCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCCc--cHHHHHH
Confidence            99999999998888775322    12235689999999998777665323334788999999999977653  232 22 


Q ss_pred             HHHHHH---HhcCCCCceEEEEeeeCc--hhHHHHH
Q psy12977        181 QLAVIY---AACSGPNLKRGMFSATHT--EDVAKWC  211 (226)
Q Consensus       181 ~i~~i~---~~~~~~~~q~v~~SAT~~--~~~~~~~  211 (226)
                      .+.+++   +.. ++..|++++|||+|  +++.+|+
T Consensus       230 ~l~rl~~~~~~~-~~~~riI~LSATl~N~~dvA~wL  264 (1724)
T 4f92_B          230 LVARAIRNIEMT-QEDVRLIGLSATLPNYEDVATFL  264 (1724)
T ss_dssp             HHHHHHHHHHHH-TCCCEEEEEECSCTTHHHHHHHT
T ss_pred             HHHHHHHHHHhC-CCCCcEEEEecccCCHHHHHHHh
Confidence            222332   233 57889999999987  4455554

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.92  E-value=2.1e-25  Score=217.60  Aligned_cols=184  Identities=22%  Similarity=0.261  Sum_probs=140.2

Q ss_pred             HHHHHHHhhccccCCCCcccccc--cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHH
Q psy12977         22 VTTLAVVSNSIFKHFEPHFTITY--LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYN   99 (226)
Q Consensus        22 ~~~l~~~~~~~~~~~~~~Q~~~~--~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~   99 (226)
                      +.....+.+..|+.|+|+|++++  ....++|++++||||||||+++.+++++.+.+.  .+.+++|++|+++||.|.++
T Consensus       913 ~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~--~~~kavyi~P~raLa~q~~~  990 (1724)
T 4f92_B          913 NSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQS--SEGRCVYITPMEALAEQVYM  990 (1724)
T ss_dssp             CHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHC--TTCCEEEECSCHHHHHHHHH
T ss_pred             CHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhC--CCCEEEEEcChHHHHHHHHH
Confidence            45667777888999999998886  445678999999999999999999999988643  24589999999999999999


Q ss_pred             HHHHH-hhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccch
Q psy12977        100 ETVRL-SEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGF  178 (226)
Q Consensus       100 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~  178 (226)
                      .+++. .+..+.++....|+.....+    ...+++|+|+||+++..+++++.....+++++++|+||+|.+.+..+..+
T Consensus       991 ~~~~~f~~~~g~~V~~ltGd~~~~~~----~~~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d~rg~~l 1066 (1724)
T 4f92_B          991 DWYEKFQDRLNKKVVLLTGETSTDLK----LLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGENGPVL 1066 (1724)
T ss_dssp             HHHHHHTTTSCCCEEECCSCHHHHHH----HHHHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGSTTHHHH
T ss_pred             HHHHHhchhcCCEEEEEECCCCcchh----hcCCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCCCCCccH
Confidence            98765 45578888888877554332    22457999999999988887755555688999999999998876532112


Q ss_pred             HHHHHH---HHHhcCCCCceEEEEeeeCc--hhHHHHHH
Q psy12977        179 RDQLAV---IYAACSGPNLKRGMFSATHT--EDVAKWCR  212 (226)
Q Consensus       179 ~~~i~~---i~~~~~~~~~q~v~~SAT~~--~~~~~~~~  212 (226)
                      ...+.+   +.... +++.|++++|||++  +++.+|+.
T Consensus      1067 e~il~rl~~i~~~~-~~~~riI~lSATl~N~~dla~WL~ 1104 (1724)
T 4f92_B         1067 EVICSRMRYISSQI-ERPIRIVALSSSLSNAKDVAHWLG 1104 (1724)
T ss_dssp             HHHHHHHHHHHHTT-SSCCEEEEEESCBTTHHHHHHHHT
T ss_pred             HHHHHHHHHHHhhc-CCCceEEEEeCCCCCHHHHHHHhC
Confidence            222222   22233 56899999999987  45566663

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.91  E-value=5.6e-24  Score=199.59  Aligned_cols=171  Identities=19%  Similarity=0.215  Sum_probs=137.2

Q ss_pred             hhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         29 SNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        29 ~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      +...|+ +++.|..+. .+.+++++++++|||+|||++|.++++..+..    +.+++|++|+++|+.|+++.+.+++. 
T Consensus        81 ~~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~----g~rvL~l~PtkaLa~Q~~~~l~~~~~-  154 (1010)
T 2xgj_A           81 RTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN----KQRVIYTSPIKALSNQKYRELLAEFG-  154 (1010)
T ss_dssp             CCCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHT----TCEEEEEESSHHHHHHHHHHHHHHHS-
T ss_pred             HhCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhcc----CCeEEEECChHHHHHHHHHHHHHHhC-
Confidence            344554 899997775 66788999999999999999999999888753    56999999999999999999998875 


Q ss_pred             CCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHH
Q psy12977        108 LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYA  187 (226)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~  187 (226)
                         .+....|+..        ....++|+|+||+++.+++.+  +...+.+++++|+||+|.+.+.   ++...+..++.
T Consensus       155 ---~vglltGd~~--------~~~~~~IvV~Tpe~L~~~L~~--~~~~l~~l~lVViDEaH~l~d~---~rg~~~e~il~  218 (1010)
T 2xgj_A          155 ---DVGLMTGDIT--------INPDAGCLVMTTEILRSMLYR--GSEVMREVAWVIFDEVHYMRDK---ERGVVWEETII  218 (1010)
T ss_dssp             ---CEEEECSSCE--------ECTTCSEEEEEHHHHHHHHHH--TCTTGGGEEEEEEETGGGGGCT---TTHHHHHHHHH
T ss_pred             ---CEEEEeCCCc--------cCCCCCEEEEcHHHHHHHHHc--CcchhhcCCEEEEechhhhccc---chhHHHHHHHH
Confidence               4555665532        124578999999999998877  5667889999999999999887   46666777777


Q ss_pred             hcCCCCceEEEEeeeCchh--HHHHHHHhcCCCeEEe
Q psy12977        188 ACSGPNLKRGMFSATHTED--VAKWCRRKLKRRVQIN  222 (226)
Q Consensus       188 ~~~~~~~q~v~~SAT~~~~--~~~~~~~~~~~p~~i~  222 (226)
                      .+ ++..|++++|||+|..  ..+|+......+..+.
T Consensus       219 ~l-~~~~~il~LSATi~n~~e~a~~l~~~~~~~~~vi  254 (1010)
T 2xgj_A          219 LL-PDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIV  254 (1010)
T ss_dssp             HS-CTTCEEEEEECCCTTHHHHHHHHHHHHTSCEEEE
T ss_pred             hc-CCCCeEEEEcCCCCCHHHHHHHHHhhcCCCeEEE
Confidence            77 6789999999999864  4577777666665543

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.91  E-value=1.2e-24  Score=192.08  Aligned_cols=187  Identities=20%  Similarity=0.225  Sum_probs=137.4

Q ss_pred             HHHHHHHHHHhh-ccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         19 SIIVTTLAVVSN-SIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        19 ~~~~~~l~~~~~-~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      .+-+...+.+++ ++|..++|.|..+. .+++|+|+++.+|||+|||++|++|++..       ..+++|++|+++|+.|
T Consensus         8 ~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~-------~g~~lvi~P~~aL~~q   80 (523)
T 1oyw_A            8 NLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL-------NGLTVVVSPLISLMKD   80 (523)
T ss_dssp             SHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS-------SSEEEEECSCHHHHHH
T ss_pred             CCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh-------CCCEEEECChHHHHHH
Confidence            345678888888 89999999997775 67789999999999999999999998753       2479999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      +.+.++.+    +.....+.++.......   .....+.++|+++||+++......  ..+...+++++|+||||++.++
T Consensus        81 ~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~--~~l~~~~~~~vViDEaH~i~~~  154 (523)
T 1oyw_A           81 QVDQLQAN----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFL--EHLAHWNPVLLAVDEAHCISQW  154 (523)
T ss_dssp             HHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHH--HHHTTSCEEEEEESSGGGGCTT
T ss_pred             HHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHH--HHHhhCCCCEEEEeCccccCcC
Confidence            99998875    66777776654332211   112245689999999998632211  2233478999999999999887


Q ss_pred             Cc--cchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhc--CCCeE
Q psy12977        174 GV--RGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKL--KRRVQ  220 (226)
Q Consensus       174 ~~--~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~--~~p~~  220 (226)
                      ++  +.....+..+.+.+  ++.+++++|||+++.+.+.+.+.+  .+|..
T Consensus       155 g~~fr~~~~~l~~l~~~~--~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~  203 (523)
T 1oyw_A          155 GHDFRPEYAALGQLRQRF--PTLPFMALTATADDTTRQDIVRLLGLNDPLI  203 (523)
T ss_dssp             SSCCCHHHHGGGGHHHHC--TTSCEEEEESCCCHHHHHHHHHHHTCCSCEE
T ss_pred             CCccHHHHHHHHHHHHhC--CCCCEEEEeCCCCHHHHHHHHHHhCCCCCeE
Confidence            52  22234445555555  578999999999988766554444  34443

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.91  E-value=2e-24  Score=190.81  Aligned_cols=166  Identities=20%  Similarity=0.162  Sum_probs=128.7

Q ss_pred             CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCC-CCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeE
Q psy12977         35 HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK-NLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRA  112 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~-~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~  112 (226)
                      +++|.|..+. .++.++++++.+|||+|||++|++|+++.+.... ..+.+++|++|+++|+.|+.+.++.++...+.++
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~   83 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYNI   83 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCCE
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCcEE
Confidence            5678886664 6668899999999999999999999998886432 2266899999999999999999999999888888


Q ss_pred             EEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCC-CCCCccEEEEcccccccccCccchHHHHHHHHHhc--
Q psy12977        113 HVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPAL-NLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC--  189 (226)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~-~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~--  189 (226)
                      ..+.|+....... .....+++|+|+||+++.+.+..  +.. .+.+++++|+||||++.+..  .+...+...+...  
T Consensus        84 ~~~~g~~~~~~~~-~~~~~~~~i~v~T~~~l~~~~~~--~~~~~~~~~~~vViDEah~~~~~~--~~~~~~~~~~~~~~~  158 (555)
T 3tbk_A           84 ASISGATSDSVSV-QHIIEDNDIIILTPQILVNNLNN--GAIPSLSVFTLMIFDECHNTSKNH--PYNQIMFRYLDHKLG  158 (555)
T ss_dssp             EEECTTTGGGSCH-HHHHHHCSEEEECHHHHHHHHHT--SSSCCGGGCSEEEETTGGGCSTTC--HHHHHHHHHHHHHTS
T ss_pred             EEEcCCCcchhhH-HHHhcCCCEEEECHHHHHHHHhc--CcccccccCCEEEEECccccCCcc--hHHHHHHHHHHhhhc
Confidence            8888776433221 11234589999999999999876  445 68899999999999998763  3444443444332  


Q ss_pred             --CCCCceEEEEeeeCch
Q psy12977        190 --SGPNLKRGMFSATHTE  205 (226)
Q Consensus       190 --~~~~~q~v~~SAT~~~  205 (226)
                        ..+.+|++++|||++.
T Consensus       159 ~~~~~~~~~l~lSAT~~~  176 (555)
T 3tbk_A          159 ESRDPLPQVVGLTASVGV  176 (555)
T ss_dssp             SCCSCCCEEEEEESCCCC
T ss_pred             cccCCCCeEEEEecCccc
Confidence              1256899999999853

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.91  E-value=3.2e-24  Score=195.05  Aligned_cols=175  Identities=19%  Similarity=0.135  Sum_probs=131.5

Q ss_pred             HHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCC-CCCceEEEEcccHHHHHHHHHHHH
Q psy12977         25 LAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK-NLGFRAVIVCPTRELAKQTYNETV  102 (226)
Q Consensus        25 l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~-~~~~~~iil~Pt~~L~~q~~~~~~  102 (226)
                      -..+..+++.++++.|.... .++.|+|+++.+|||+|||++|++++++.+.... ..+.+++|++|+++|+.|+.+.++
T Consensus         3 ~~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~   82 (696)
T 2ykg_A            3 VSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFS   82 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHH
T ss_pred             CCcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHH
Confidence            34677899999999997764 6678999999999999999999999998775322 223689999999999999999999


Q ss_pred             HHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCC-CCCCccEEEEcccccccccCccchHHH
Q psy12977        103 RLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPAL-NLANVEWLIVDESDKLFEAGVRGFRDQ  181 (226)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~-~~~~~~~lViDE~h~l~~~~~~~~~~~  181 (226)
                      ++.+..+.++..+.|+....... .....+++|+|+||+++.+.+..  +.+ .+.+++++|+||||++.+..  .+...
T Consensus        83 ~~~~~~~~~v~~~~g~~~~~~~~-~~~~~~~~Iiv~Tp~~L~~~l~~--~~~~~l~~~~~vViDEaH~~~~~~--~~~~i  157 (696)
T 2ykg_A           83 KYFERHGYRVTGISGATAENVPV-EQIVENNDIIILTPQILVNNLKK--GTIPSLSIFTLMIFDECHNTSKQH--PYNMI  157 (696)
T ss_dssp             HHTTTTTCCEEEECSSSCSSSCH-HHHHHTCSEEEECHHHHHHHHHT--TSSCCGGGCSEEEEETGGGCSTTC--HHHHH
T ss_pred             HHhccCCceEEEEeCCccccccH-HHhccCCCEEEECHHHHHHHHhc--CcccccccccEEEEeCCCcccCcc--cHHHH
Confidence            99988788888887765322111 11224689999999999999886  445 68899999999999988653  34444


Q ss_pred             HHHHHHh----cCCCCceEEEEeeeCc
Q psy12977        182 LAVIYAA----CSGPNLKRGMFSATHT  204 (226)
Q Consensus       182 i~~i~~~----~~~~~~q~v~~SAT~~  204 (226)
                      +...+..    ..++.++++++|||+.
T Consensus       158 ~~~~l~~~~~~~~~~~~~il~LTATp~  184 (696)
T 2ykg_A          158 MFNYLDQKLGGSSGPLPQVIGLTASVG  184 (696)
T ss_dssp             HHHHHHHHHTTCCSCCCEEEEEESCCC
T ss_pred             HHHHHHHhhcccCCCCCeEEEEeCccc
Confidence            4333332    2246789999999986

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=99.91  E-value=2.1e-24  Score=190.93  Aligned_cols=168  Identities=17%  Similarity=0.139  Sum_probs=124.4

Q ss_pred             cccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCC-CCCceEEEEcccHHHHHHHHHHHHHHhhcCC
Q psy12977         32 IFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK-NLGFRAVIVCPTRELAKQTYNETVRLSEGLG  109 (226)
Q Consensus        32 ~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~-~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~  109 (226)
                      ..-+++|.|..+. .++.++++++.+|||+|||++|++|+++.+.... ..+.+++|++|+++|+.|+.+.++.++...+
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~   83 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQG   83 (556)
T ss_dssp             ----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGT
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhcccC
Confidence            3457888997774 6668899999999999999999999998886533 2266899999999999999999999998888


Q ss_pred             CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCC-CCCCccEEEEcccccccccCccchHHHHHHHHHh
Q psy12977        110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPAL-NLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAA  188 (226)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~-~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~  188 (226)
                      .++..+.|+....... .....+++|+|+||+++.+.+..  +.. .+.+++++|+||||++.+.+  .+...+...+..
T Consensus        84 ~~~~~~~g~~~~~~~~-~~~~~~~~i~v~T~~~l~~~~~~--~~~~~~~~~~~vViDEah~~~~~~--~~~~~~~~~~~~  158 (556)
T 4a2p_A           84 YSVQGISGENFSNVSV-EKVIEDSDIIVVTPQILVNSFED--GTLTSLSIFTLMIFDECHNTTGNH--PYNVLMTRYLEQ  158 (556)
T ss_dssp             CCEEECCCC-----CH-HHHHHHCSEEEECHHHHHHHHHS--SSCCCSTTCSEEEEETGGGCSTTS--HHHHHHHHHHHH
T ss_pred             ceEEEEeCCCCcchhH-HHhhCCCCEEEECHHHHHHHHHh--CcccccccCCEEEEECCcccCCcc--hHHHHHHHHHHh
Confidence            8888887775332211 11224589999999999999876  455 78999999999999998773  233333333322


Q ss_pred             -cC--CCCceEEEEeeeCc
Q psy12977        189 -CS--GPNLKRGMFSATHT  204 (226)
Q Consensus       189 -~~--~~~~q~v~~SAT~~  204 (226)
                       +.  .+..|++++|||++
T Consensus       159 ~~~~~~~~~~~l~lSAT~~  177 (556)
T 4a2p_A          159 KFNSASQLPQILGLTASVG  177 (556)
T ss_dssp             HHCC---CCEEEEEESCCC
T ss_pred             hhcccCCCCeEEEEeCCcc
Confidence             21  35689999999985

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.91  E-value=1.7e-24  Score=204.57  Aligned_cols=168  Identities=17%  Similarity=0.167  Sum_probs=129.7

Q ss_pred             ccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCC
Q psy12977         31 SIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG  109 (226)
Q Consensus        31 ~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~  109 (226)
                      .+| +++|+|..+. .++.|+|++++||||+|||++++.+++..+.    .+++++|++||++||.|+.+.++.+. ..+
T Consensus        75 ~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~----~~~~~Lil~PtreLa~Q~~~~l~~l~-~~~  148 (1104)
T 4ddu_A           75 FGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR----KGKKSALVFPTVTLVKQTLERLQKLA-DEK  148 (1104)
T ss_dssp             SSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHT----TTCCEEEEESSHHHHHHHHHHHHTTS-CTT
T ss_pred             cCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHh----cCCeEEEEechHHHHHHHHHHHHHhh-CCC
Confidence            455 6999997774 7788999999999999999998888887773    36689999999999999999999977 667


Q ss_pred             CeEEEEecchhh---hhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccC-------c-cch
Q psy12977        110 LRAHVIGKIQQA---AEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG-------V-RGF  178 (226)
Q Consensus       110 ~~~~~~~~~~~~---~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~-------~-~~~  178 (226)
                      .++..+.|+...   .........+.++|+|+||+++.+++..    +.+.+++++|+||||++.+.+       . .+|
T Consensus       149 i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~----l~~~~l~~lViDEaH~l~~~~r~~Dr~L~~~gf  224 (1104)
T 4ddu_A          149 VKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK----LSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGI  224 (1104)
T ss_dssp             SCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH----HHTSCCSEEEESCHHHHTTSSHHHHHHHHTSSC
T ss_pred             CeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh----hcccCcCEEEEeCCCccccccccchhhhHhcCC
Confidence            888888877654   2222222234589999999999887763    456789999999998766521       0 145


Q ss_pred             HHH-HHHHHHhcC----------CCCceEEEEeee-CchhHH
Q psy12977        179 RDQ-LAVIYAACS----------GPNLKRGMFSAT-HTEDVA  208 (226)
Q Consensus       179 ~~~-i~~i~~~~~----------~~~~q~v~~SAT-~~~~~~  208 (226)
                      ... +..+++.++          .+..|++++||| .|+.+.
T Consensus       225 ~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~  266 (1104)
T 4ddu_A          225 PEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIR  266 (1104)
T ss_dssp             CHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSST
T ss_pred             CHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHH
Confidence            555 777777662          167899999999 666554

>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=99.90  E-value=2.3e-23  Score=165.93  Aligned_cols=168  Identities=16%  Similarity=0.121  Sum_probs=120.3

Q ss_pred             CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcC-CCCCCceEEEEcccHHHHHHHHHHHHHHhh-cCCCe
Q psy12977         35 HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRG-PKNLGFRAVIVCPTRELAKQTYNETVRLSE-GLGLR  111 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~-~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~-~~~~~  111 (226)
                      .++++|.... .+..|+++++.||||||||..+..++++.... ....+.+++++.|+++++.|+.+.+..... ..+..
T Consensus        61 p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~~~~  140 (235)
T 3llm_A           61 PVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKS  140 (235)
T ss_dssp             GGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCTTSS
T ss_pred             ChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhccccCce
Confidence            4677786664 66788999999999999999888888776532 222345899999999999999888766543 23333


Q ss_pred             EEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccc-cccCccchH-HHHHHHHHhc
Q psy12977        112 AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKL-FEAGVRGFR-DQLAVIYAAC  189 (226)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l-~~~~~~~~~-~~i~~i~~~~  189 (226)
                      +......    ..  .....+++|+|+||+++.+.+..     .+++++++|+||+|.+ .+.   ++. ..+..+....
T Consensus       141 ~g~~~~~----~~--~~~~~~~~Ivv~Tpg~l~~~l~~-----~l~~~~~lVlDEah~~~~~~---~~~~~~l~~i~~~~  206 (235)
T 3llm_A          141 CGYSVRF----ES--ILPRPHASIMFCTVGVLLRKLEA-----GIRGISHVIVDEIHERDINT---DFLLVVLRDVVQAY  206 (235)
T ss_dssp             EEEEETT----EE--ECCCSSSEEEEEEHHHHHHHHHH-----CCTTCCEEEECCTTSCCHHH---HHHHHHHHHHHHHC
T ss_pred             EEEeech----hh--ccCCCCCeEEEECHHHHHHHHHh-----hhcCCcEEEEECCccCCcch---HHHHHHHHHHHhhC
Confidence            3321111    11  11125688999999999999876     2789999999999985 555   455 4666666665


Q ss_pred             CCCCceEEEEeeeCchhHHHHHHHhcCCCeEE
Q psy12977        190 SGPNLKRGMFSATHTEDVAKWCRRKLKRRVQI  221 (226)
Q Consensus       190 ~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i  221 (226)
                        ++.|++++|||++.+.   +.+|+.+.-.+
T Consensus       207 --~~~~~il~SAT~~~~~---~~~~~~~~pvi  233 (235)
T 3llm_A          207 --PEVRIVLMSATIDTSM---FCEYFFNCPII  233 (235)
T ss_dssp             --TTSEEEEEECSSCCHH---HHHHTTSCCCE
T ss_pred             --CCCeEEEEecCCCHHH---HHHHcCCCCEE
Confidence              5799999999999776   44555544333

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=99.90  E-value=2.4e-23  Score=192.10  Aligned_cols=170  Identities=17%  Similarity=0.126  Sum_probs=127.5

Q ss_pred             hccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCC-CCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         30 NSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK-NLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        30 ~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~-~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      .+++.+++|.|..+. .++.|+++++.+|||+|||++|++|++..+.... ..+.+++|++|+++|+.|+.+.++.++..
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~  322 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER  322 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGG
T ss_pred             hcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhccc
Confidence            456788999997774 6678899999999999999999999998886532 22668999999999999999999999988


Q ss_pred             CCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCC-CCCCccEEEEcccccccccCccchHHHHHHHH
Q psy12977        108 LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPAL-NLANVEWLIVDESDKLFEAGVRGFRDQLAVIY  186 (226)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~-~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~  186 (226)
                      .+.++..+.|+....... .....+++|+|+||+++.+.+..  ..+ .+.+++++|+||||++.+..  .+...+....
T Consensus       323 ~~~~v~~~~g~~~~~~~~-~~~~~~~~Ivv~Tp~~l~~~l~~--~~~~~~~~~~~iViDEaH~~~~~~--~~~~i~~~~~  397 (797)
T 4a2q_A          323 QGYSVQGISGENFSNVSV-EKVIEDSDIIVVTPQILVNSFED--GTLTSLSIFTLMIFDECHNTTGNH--PYNVLMTRYL  397 (797)
T ss_dssp             GTCCEEEECCC-----CH-HHHHHTCSEEEECHHHHHHHHHS--SSCCCGGGCSEEEETTGGGCSTTS--HHHHHHHHHH
T ss_pred             CCceEEEEeCCcchhhhH-HHhhCCCCEEEEchHHHHHHHHh--ccccccccCCEEEEECccccCCCc--cHHHHHHHHH
Confidence            888888888776332211 12235689999999999999876  455 78899999999999998763  2333333333


Q ss_pred             Hhc---CCCCceEEEEeeeCc
Q psy12977        187 AAC---SGPNLKRGMFSATHT  204 (226)
Q Consensus       187 ~~~---~~~~~q~v~~SAT~~  204 (226)
                      ...   ..+.+|++++|||++
T Consensus       398 ~~~~~~~~~~~~~l~lSATp~  418 (797)
T 4a2q_A          398 EQKFNSASQLPQILGLTASVG  418 (797)
T ss_dssp             HHHHTTCCCCCEEEEEESCCC
T ss_pred             HHhhccCCCCCeEEEEcCCcc
Confidence            321   145689999999985

>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=99.90  E-value=2.2e-24  Score=168.75  Aligned_cols=168  Identities=18%  Similarity=0.146  Sum_probs=111.9

Q ss_pred             hccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC--CCCCceEEEEcccHHHHHH-HHHHHHHHh
Q psy12977         30 NSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP--KNLGFRAVIVCPTRELAKQ-TYNETVRLS  105 (226)
Q Consensus        30 ~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~--~~~~~~~iil~Pt~~L~~q-~~~~~~~~~  105 (226)
                      .....++++.|..+. .+..++++++.+|||+|||++++.++...+...  ...+.+++|++|+++|+.| +.+.+..+.
T Consensus        28 ~~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~  107 (216)
T 3b6e_A           28 PEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFL  107 (216)
T ss_dssp             CSCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHH
T ss_pred             ccCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHh
Confidence            344457888997775 566789999999999999999999988766421  1235689999999999999 777888876


Q ss_pred             hcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCC----CCCCCCccEEEEcccccccccCccchHHH
Q psy12977        106 EGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPP----ALNLANVEWLIVDESDKLFEAGVRGFRDQ  181 (226)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~----~~~~~~~~~lViDE~h~l~~~~~~~~~~~  181 (226)
                      .. +..+....++....... .....+++|+|+||+.+.+.+.....    ...+.+++++|+||||++.+.   ++...
T Consensus       108 ~~-~~~v~~~~g~~~~~~~~-~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~---~~~~~  182 (216)
T 3b6e_A          108 KK-WYRVIGLSGDTQLKISF-PEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKE---AVYNN  182 (216)
T ss_dssp             TT-TSCEEECCC---CCCCH-HHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC----------CHHH
T ss_pred             cc-CceEEEEeCCcccchhH-HhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccC---CcHHH
Confidence            65 56666655543211110 01123588999999999998876321    256788999999999999765   34444


Q ss_pred             H-HHHHHhc------------CCCCceEEEEeee
Q psy12977        182 L-AVIYAAC------------SGPNLKRGMFSAT  202 (226)
Q Consensus       182 i-~~i~~~~------------~~~~~q~v~~SAT  202 (226)
                      + ..+....            ..+.++++++|||
T Consensus       183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          183 IMRHYLMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HHHHHHHHhcccccccccccCCCCcceEEEeecC
Confidence            3 2322211            1267899999998

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=99.89  E-value=1.6e-23  Score=189.77  Aligned_cols=184  Identities=19%  Similarity=0.172  Sum_probs=142.4

Q ss_pred             HHHHHHHHHHHh-----hccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         18 ISIIVTTLAVVS-----NSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        18 ~~~~~~~l~~~~-----~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      ..++|..++.++     ..+| .++++|.... .+++|+  +..++||+|||++|.+|++.....    +++++|++||+
T Consensus        62 d~~l~ea~a~vrea~~r~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~----g~~vlVltptr  134 (844)
T 1tf5_A           62 DDLLVEAFAVVREASRRVTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT----GKGVHVVTVNE  134 (844)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT----SSCEEEEESSH
T ss_pred             HHHHHHHHHHHHHHHHHHcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHc----CCCEEEEeCCH
Confidence            445666666555     4788 9999997774 667777  999999999999999999844322    55899999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHH-HHhHhcC----CCCCCCCCccEEEEcc
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKL-VYLLQMD----PPALNLANVEWLIVDE  166 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l-~~~~~~~----~~~~~~~~~~~lViDE  166 (226)
                      +||.|..+++..+...++.++.++.++.....+   ....++||+|+||+++ ++++...    .+...+..+.++|+||
T Consensus       135 eLA~qd~e~~~~l~~~lgl~v~~i~gg~~~~~r---~~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDE  211 (844)
T 1tf5_A          135 YLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEK---REAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDE  211 (844)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEECCTTSCHHHH---HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEET
T ss_pred             HHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHH---HHhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECc
Confidence            999999999999999999999988887654333   2345799999999999 5555432    2346688999999999


Q ss_pred             ccccc-ccCcc------------chHHHHHHHHHhcCC--------CCceEE-----------------EEeeeCc---h
Q psy12977        167 SDKLF-EAGVR------------GFRDQLAVIYAACSG--------PNLKRG-----------------MFSATHT---E  205 (226)
Q Consensus       167 ~h~l~-~~~~~------------~~~~~i~~i~~~~~~--------~~~q~v-----------------~~SAT~~---~  205 (226)
                      ||.++ +.+..            ++...+..+...++.        +..|+.                 ++|||.+   .
T Consensus       212 aD~mLiDea~tplIisg~~~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~~~~  291 (844)
T 1tf5_A          212 VDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNH  291 (844)
T ss_dssp             HHHHHTTTTTCEEEEEEEEECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHHHHH
T ss_pred             hhhhhhhccccchhhcCCcccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCccccCCCccchhHH
Confidence            99988 55311            377889999998853        467887                 8999977   4


Q ss_pred             hHHHHH
Q psy12977        206 DVAKWC  211 (226)
Q Consensus       206 ~~~~~~  211 (226)
                      .+.+.+
T Consensus       292 ~i~~al  297 (844)
T 1tf5_A          292 HINQAL  297 (844)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            555544

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.89  E-value=4.8e-23  Score=193.20  Aligned_cols=161  Identities=20%  Similarity=0.209  Sum_probs=128.1

Q ss_pred             CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEE
Q psy12977         35 HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAH  113 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~  113 (226)
                      ++++.|..+. .+.+|+++++.+|||+|||++|++++......    +.+++|++|+++|+.|+++.+++.+.  +..+.
T Consensus        39 ~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~----g~~vlvl~PtraLa~Q~~~~l~~~~~--~~~v~  112 (997)
T 4a4z_A           39 ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRN----MTKTIYTSPIKALSNQKFRDFKETFD--DVNIG  112 (997)
T ss_dssp             CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHT----TCEEEEEESCGGGHHHHHHHHHTTC----CCEE
T ss_pred             CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhc----CCeEEEEeCCHHHHHHHHHHHHHHcC--CCeEE
Confidence            4788997664 77789999999999999999999988877653    56899999999999999999888754  56677


Q ss_pred             EEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCC
Q psy12977        114 VIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPN  193 (226)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~  193 (226)
                      ...|+..        ....++|+|+||+++.+.+..  ....+.+++++|+||+|++.+++   +...+..++..+ ++.
T Consensus       113 ~l~G~~~--------~~~~~~IlV~Tpe~L~~~l~~--~~~~l~~l~lvViDEaH~l~d~~---~g~~~e~ii~~l-~~~  178 (997)
T 4a4z_A          113 LITGDVQ--------INPDANCLIMTTEILRSMLYR--GADLIRDVEFVIFDEVHYVNDQD---RGVVWEEVIIML-PQH  178 (997)
T ss_dssp             EECSSCE--------ECTTSSEEEEEHHHHHHHHHH--TCSGGGGEEEEEECCTTCCCTTC---TTCCHHHHHHHS-CTT
T ss_pred             EEeCCCc--------cCCCCCEEEECHHHHHHHHHh--CchhhcCCCEEEEECcccccccc---hHHHHHHHHHhc-ccC
Confidence            7766532        224578999999999998876  56668899999999999998883   555566666677 578


Q ss_pred             ceEEEEeeeCch--hHHHHHHHhc
Q psy12977        194 LKRGMFSATHTE--DVAKWCRRKL  215 (226)
Q Consensus       194 ~q~v~~SAT~~~--~~~~~~~~~~  215 (226)
                      .|++++|||+|+  +..+|+....
T Consensus       179 v~iIlLSAT~~n~~ef~~~l~~~~  202 (997)
T 4a4z_A          179 VKFILLSATVPNTYEFANWIGRTK  202 (997)
T ss_dssp             CEEEEEECCCTTHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCChHHHHHHHhccc
Confidence            999999999874  4566665443

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=99.89  E-value=2.3e-24  Score=203.40  Aligned_cols=172  Identities=19%  Similarity=0.158  Sum_probs=130.6

Q ss_pred             HhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhh
Q psy12977         28 VSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE  106 (226)
Q Consensus        28 ~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~  106 (226)
                      .+.++|. + ++|..+. .+++|+|+++.+|||||||+ |.+|++..+..   .+++++|++||++|+.|+.+.++.++.
T Consensus        51 ~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~---~~~~~lil~PtreLa~Q~~~~l~~l~~  124 (1054)
T 1gku_B           51 RKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL---KGKRCYVIFPTSLLVIQAAETIRKYAE  124 (1054)
T ss_dssp             HTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT---TSCCEEEEESCHHHHHHHHHHHHHHHT
T ss_pred             HHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh---cCCeEEEEeccHHHHHHHHHHHHHHHh
Confidence            3458999 8 9997775 67789999999999999998 88888877653   356899999999999999999999998


Q ss_pred             cCCC----eEEEEecchhhhhh--hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHH
Q psy12977        107 GLGL----RAHVIGKIQQAAEK--FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRD  180 (226)
Q Consensus       107 ~~~~----~~~~~~~~~~~~~~--~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~  180 (226)
                      ..+.    ++....|+......  ....+.. ++|+|+||+++.+++.+      +++++++|+||||++++.+     .
T Consensus       125 ~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~------L~~l~~lViDEah~~l~~~-----~  192 (1054)
T 1gku_B          125 KAGVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE------LGHFDFIFVDDVDAILKAS-----K  192 (1054)
T ss_dssp             TTCCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT------SCCCSEEEESCHHHHHTST-----H
T ss_pred             hcCCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH------hccCCEEEEeChhhhhhcc-----c
Confidence            8887    78777776544331  1122333 89999999999987764      6689999999999998742     3


Q ss_pred             HHHHHHHhcC----------CCCceEEEEeeeCchhHHHHHHHhcCCC
Q psy12977        181 QLAVIYAACS----------GPNLKRGMFSATHTEDVAKWCRRKLKRR  218 (226)
Q Consensus       181 ~i~~i~~~~~----------~~~~q~v~~SAT~~~~~~~~~~~~~~~p  218 (226)
                      .+..++..+.          +...|++++|||.+.. ..+...++.++
T Consensus       193 ~~~~i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~  239 (1054)
T 1gku_B          193 NVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQL  239 (1054)
T ss_dssp             HHHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHH
T ss_pred             cHHHHHHHhCcchhhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcc
Confidence            4444444431          3467899999998876 53443443333

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}

Probab=99.88  E-value=1.8e-22  Score=188.78  Aligned_cols=169  Identities=17%  Similarity=0.124  Sum_probs=126.7

Q ss_pred             ccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCC-CCCceEEEEcccHHHHHHHHHHHHHHhhcC
Q psy12977         31 SIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK-NLGFRAVIVCPTRELAKQTYNETVRLSEGL  108 (226)
Q Consensus        31 ~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~-~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~  108 (226)
                      .++.+++|.|..+. .++.|+++++.+|||+|||++|++|++..+.... ..+.+++|++|+++|+.|+.+.++.++...
T Consensus       244 ~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~  323 (936)
T 4a2w_A          244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQ  323 (936)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhccc
Confidence            34678899997764 6678999999999999999999999988876432 125689999999999999999999999888


Q ss_pred             CCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCC-CCCCccEEEEcccccccccCccchHHHHHHHHH
Q psy12977        109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPAL-NLANVEWLIVDESDKLFEAGVRGFRDQLAVIYA  187 (226)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~-~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~  187 (226)
                      +.++..+.|+...... ......+++|+|+||+++.+.+..  ... .+.+++++|+||||++.+..  .+...+..+..
T Consensus       324 ~~~v~~~~G~~~~~~~-~~~~~~~~~IvI~Tp~~L~~~l~~--~~~~~l~~~~liViDEaH~~~~~~--~~~~i~~~~~~  398 (936)
T 4a2w_A          324 GYSVQGISGENFSNVS-VEKVIEDSDIIVVTPQILVNSFED--GTLTSLSIFTLMIFDECHNTTGNH--PYNVLMTRYLE  398 (936)
T ss_dssp             TCCEEEECCC-----C-CHHHHHHCSEEEECHHHHHHHHHS--SSCCCGGGCSEEEEETGGGCSTTC--HHHHHHHHHHH
T ss_pred             CceEEEEECCcchhhH-HHHhccCCCEEEecHHHHHHHHHc--CccccccCCCEEEEECccccCCCc--cHHHHHHHHHH
Confidence            8888888877533221 112234689999999999999886  444 68899999999999988763  24444434433


Q ss_pred             hc---CCCCceEEEEeeeCc
Q psy12977        188 AC---SGPNLKRGMFSATHT  204 (226)
Q Consensus       188 ~~---~~~~~q~v~~SAT~~  204 (226)
                      ..   ..+..|++++|||++
T Consensus       399 ~~~~~~~~~~~~l~LSATp~  418 (936)
T 4a2w_A          399 QKFNSASQLPQILGLTASVG  418 (936)
T ss_dssp             HHHTTCSCCCEEEEEESCCC
T ss_pred             HhhccCCCcCeEEEecCCcc
Confidence            21   145689999999985

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=99.88  E-value=6.1e-22  Score=171.30  Aligned_cols=167  Identities=17%  Similarity=0.145  Sum_probs=124.8

Q ss_pred             CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEE
Q psy12977         35 HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAH  113 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~  113 (226)
                      ++.|.|.... .+..+ ++++.+|||+|||++++.++...+.   ..+.+++|++|+++|+.|+.+.+.++.......+.
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~---~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~   84 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLT---KYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIV   84 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHH---HSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEE
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHh---cCCCeEEEEECCHHHHHHHHHHHHHHhCcchhheE
Confidence            5678886664 45555 9999999999999999999888765   23558999999999999999999998754445777


Q ss_pred             EEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCC
Q psy12977        114 VIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPN  193 (226)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~  193 (226)
                      .+.|+.......  ....+++|+|+||+.+.+.+..  +.....+++++|+||||++.+.   .....+...+... .+.
T Consensus        85 ~~~g~~~~~~~~--~~~~~~~ivv~T~~~l~~~~~~--~~~~~~~~~~vIiDEaH~~~~~---~~~~~~~~~~~~~-~~~  156 (494)
T 1wp9_A           85 ALTGEKSPEERS--KAWARAKVIVATPQTIENDLLA--GRISLEDVSLIVFDEAHRAVGN---YAYVFIAREYKRQ-AKN  156 (494)
T ss_dssp             EECSCSCHHHHH--HHHHHCSEEEECHHHHHHHHHT--TSCCTTSCSEEEEETGGGCSTT---CHHHHHHHHHHHH-CSS
T ss_pred             EeeCCcchhhhh--hhccCCCEEEecHHHHHHHHhc--CCcchhhceEEEEECCcccCCC---CcHHHHHHHHHhc-CCC
Confidence            776665433221  1123578999999999998876  5667889999999999999765   2344444444444 467


Q ss_pred             ceEEEEeeeCch---hHHHHHHH
Q psy12977        194 LKRGMFSATHTE---DVAKWCRR  213 (226)
Q Consensus       194 ~q~v~~SAT~~~---~~~~~~~~  213 (226)
                      .+++++|||++.   ++.+++..
T Consensus       157 ~~~l~lTaTp~~~~~~~~~l~~~  179 (494)
T 1wp9_A          157 PLVIGLTASPGSTPEKIMEVINN  179 (494)
T ss_dssp             CCEEEEESCSCSSHHHHHHHHHH
T ss_pred             CeEEEEecCCCCCcHHHHHHHHh
Confidence            899999999873   34455543

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=99.87  E-value=1.3e-22  Score=165.68  Aligned_cols=153  Identities=14%  Similarity=0.056  Sum_probs=114.1

Q ss_pred             CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEE
Q psy12977         35 HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAH  113 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~  113 (226)
                      ++++.|..+. ....+++.++.+|||+|||.+++.++...+...   +.+++|++|+++|+.|+.+.++++.......+.
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~---~~~~lil~Pt~~L~~q~~~~l~~~~~~~~~~~~  189 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY---EGKILIIVPTTALTTQMADDFVDYRLFSHAMIK  189 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC---SSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEE
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcC---CCeEEEEECCHHHHHHHHHHHHHhcccccceEE
Confidence            6777787765 455567889999999999999988777666421   338999999999999999999998765556666


Q ss_pred             EEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCC
Q psy12977        114 VIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPN  193 (226)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~  193 (226)
                      .+.++.....    ....+++|+|+||+.+.+.     ....+.+++++|+||||++.+.       .+..+++.+ .+.
T Consensus       190 ~~~~~~~~~~----~~~~~~~I~v~T~~~l~~~-----~~~~~~~~~~vIiDEaH~~~~~-------~~~~il~~~-~~~  252 (282)
T 1rif_A          190 KIGGGASKDD----KYKNDAPVVVGTWQTVVKQ-----PKEWFSQFGMMMNDECHLATGK-------SISSIISGL-NNC  252 (282)
T ss_dssp             ECSTTCSSTT----CCCTTCSEEEECHHHHTTS-----CGGGGGGEEEEEEETGGGCCHH-------HHHHHTTTC-TTC
T ss_pred             EEeCCCcchh----hhccCCcEEEEchHHHHhh-----HHHHHhhCCEEEEECCccCCcc-------cHHHHHHHh-hcC
Confidence            6655532221    2336789999999876443     2234678899999999998643       555666666 457


Q ss_pred             ceEEEEeeeCchhH
Q psy12977        194 LKRGMFSATHTEDV  207 (226)
Q Consensus       194 ~q~v~~SAT~~~~~  207 (226)
                      .+++++|||+++..
T Consensus       253 ~~~l~lSATp~~~~  266 (282)
T 1rif_A          253 MFKFGLSGSLRDGK  266 (282)
T ss_dssp             CEEEEECSSCCTTS
T ss_pred             CeEEEEeCCCCCcc
Confidence            99999999998653

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=99.86  E-value=2.8e-22  Score=181.39  Aligned_cols=165  Identities=20%  Similarity=0.144  Sum_probs=119.5

Q ss_pred             hHHHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         17 VISIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        17 ~~~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      +..+.|...+.+++..+.    .++++|.... .++.|+  +..++||+|||++|.+|++.....    +++++|++||+
T Consensus        52 ld~~lpeafA~vrea~~R~lg~~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~----g~~vlVltPTr  125 (853)
T 2fsf_A           52 LENLIPEAFAVVREASKRVFGMRHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALT----GKGVHVVTVND  125 (853)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTT----SSCCEEEESSH
T ss_pred             hhhhhHHHHHHHHHHHHHHcCCCCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHc----CCcEEEEcCCH
Confidence            455677888877776664    8899997774 666776  999999999999999999865432    55899999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHH-HHhHhcCC----CCCCCCCccEEEEcc
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKL-VYLLQMDP----PALNLANVEWLIVDE  166 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l-~~~~~~~~----~~~~~~~~~~lViDE  166 (226)
                      +||.|+++++..+.+.++.++..+.|+.....+   ....+++|+|+||+++ ++++....    +...+++++++|+||
T Consensus       126 eLA~Q~~e~~~~l~~~lgl~v~~i~GG~~~~~r---~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDE  202 (853)
T 2fsf_A          126 YLAQRDAENNRPLFEFLGLTVGINLPGMPAPAK---REAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDE  202 (853)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEECCTTCCHHHH---HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESC
T ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEeCCCCHHHH---HHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECc
Confidence            999999999999999999999988887654322   2345789999999999 67776421    236688999999999


Q ss_pred             ccccc-ccCc------------cchHHHHHHHHHhcC
Q psy12977        167 SDKLF-EAGV------------RGFRDQLAVIYAACS  190 (226)
Q Consensus       167 ~h~l~-~~~~------------~~~~~~i~~i~~~~~  190 (226)
                      ||.++ +.+.            .++...+..+...++
T Consensus       203 aD~mLiD~a~tpLIiSg~~~~~~~~y~~i~~iv~~L~  239 (853)
T 2fsf_A          203 VDSILIDEARTPLIISGPAEDSSEMYKRVNKIIPHLI  239 (853)
T ss_dssp             HHHHTTTTTTCEEEEEEC-------------------
T ss_pred             hHHHHHhcCcccccccCCCccchhHHHHHHHHHHhch
Confidence            99998 4321            135667777777774

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=99.86  E-value=1.2e-21  Score=169.90  Aligned_cols=166  Identities=14%  Similarity=0.085  Sum_probs=116.5

Q ss_pred             cccCCCCcccccccCCCCCeE-EEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCC
Q psy12977         32 IFKHFEPHFTITYLSPLGRQI-FACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGL  110 (226)
Q Consensus        32 ~~~~~~~~Q~~~~~~~~~~~~-li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~  110 (226)
                      |+..++|+|+..+.+++++++ ++++|||||||.+|++|++..+..   .+.+++|++||++|+.|+.+.+.      +.
T Consensus         1 G~~q~~~iq~~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~---~~~~~lvl~Ptr~La~Q~~~~l~------g~   71 (451)
T 2jlq_A            1 GSAMGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALL---RRLRTLILAPTRVVAAEMEEALR------GL   71 (451)
T ss_dssp             CCCCCSCCCCCCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHH---TTCCEEEEESSHHHHHHHHHHTT------TS
T ss_pred             CCCCCCCcHHHHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHh---cCCcEEEECCCHHHHHHHHHHhc------Cc
Confidence            567889999877777777766 999999999999999998876543   25689999999999999999774      22


Q ss_pred             eEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcC
Q psy12977        111 RAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACS  190 (226)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~  190 (226)
                      .+......      .......+..|.++|++.+.+.+.+.   ..+.+++++|+||+|.+ +.   .+...+..+.....
T Consensus        72 ~v~~~~~~------~~~~~~~~~~i~~~t~~~l~~~l~~~---~~l~~~~~iViDEah~~-~~---~~~~~~~~~~~~~~  138 (451)
T 2jlq_A           72 PIRYQTPA------VKSDHTGREIVDLMCHATFTTRLLSS---TRVPNYNLIVMDEAHFT-DP---CSVAARGYISTRVE  138 (451)
T ss_dssp             CEEECCTT------CSCCCCSSCCEEEEEHHHHHHHHHHC---SCCCCCSEEEEETTTCC-SH---HHHHHHHHHHHHHH
T ss_pred             eeeeeecc------ccccCCCCceEEEEChHHHHHHhhCc---ccccCCCEEEEeCCccC-Cc---chHHHHHHHHHhhc
Confidence            22211111      11122345679999999998877653   45789999999999977 33   23333333333333


Q ss_pred             CCCceEEEEeeeCchhHHHHHHHhcCCCeEEe
Q psy12977        191 GPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN  222 (226)
Q Consensus       191 ~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~  222 (226)
                      .++.|+++||||+|.+...+   +..++..+.
T Consensus       139 ~~~~~~i~~SAT~~~~~~~~---~~~~~~~~~  167 (451)
T 2jlq_A          139 MGEAAAIFMTATPPGSTDPF---PQSNSPIED  167 (451)
T ss_dssp             TTSCEEEEECSSCTTCCCSS---CCCSSCEEE
T ss_pred             CCCceEEEEccCCCccchhh---hcCCCceEe
Confidence            56899999999998765433   234454444

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=99.86  E-value=1.1e-21  Score=177.85  Aligned_cols=187  Identities=21%  Similarity=0.194  Sum_probs=143.6

Q ss_pred             hHHHHHHHHHHHhh-----ccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEccc
Q psy12977         17 VISIIVTTLAVVSN-----SIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPT   90 (226)
Q Consensus        17 ~~~~~~~~l~~~~~-----~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt   90 (226)
                      +..+.|...+.+++     .++ .++++|.... .++.|+  +..++||+|||++|.+|++.....    +.+++|++||
T Consensus        89 ld~~lpeafA~vrEa~~R~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~----g~~v~VvTpT  161 (922)
T 1nkt_A           89 LDDLLPEAFAVAREAAWRVLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALA----GNGVHIVTVN  161 (922)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTT----TSCEEEEESS
T ss_pred             HHHHHHHHHHHHHHHHHHHcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHh----CCCeEEEeCC
Confidence            45566776666655     444 8999997774 566776  999999999999999999754332    4589999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHH-HHhHhcC----CCCCCCCCccEEEEc
Q psy12977         91 RELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKL-VYLLQMD----PPALNLANVEWLIVD  165 (226)
Q Consensus        91 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l-~~~~~~~----~~~~~~~~~~~lViD  165 (226)
                      ++||.|..+++..+...+++++.++.++.....+   ....++||+++||++| ++++...    .+...+..+.++|+|
T Consensus       162 reLA~Qdae~m~~l~~~lGLsv~~i~gg~~~~~r---~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVD  238 (922)
T 1nkt_A          162 DYLAKRDSEWMGRVHRFLGLQVGVILATMTPDER---RVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVD  238 (922)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCEEECCTTCCHHHH---HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEET
T ss_pred             HHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHH---HHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEe
Confidence            9999999999999999999999988887654332   2345789999999999 6766542    134668899999999


Q ss_pred             cccccc-ccCc------------cchHHHHHHHHHhcCC--------CCceEE-----------------EEeeeCch--
Q psy12977        166 ESDKLF-EAGV------------RGFRDQLAVIYAACSG--------PNLKRG-----------------MFSATHTE--  205 (226)
Q Consensus       166 E~h~l~-~~~~------------~~~~~~i~~i~~~~~~--------~~~q~v-----------------~~SAT~~~--  205 (226)
                      |||+++ +.+.            .++...+..+...++.        +..|+.                 ++|||.++  
T Consensus       239 EaDsmLiDeartPLiiSg~~~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~l~  318 (922)
T 1nkt_A          239 EVDSILIDEARTPLIISGPADGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPLV  318 (922)
T ss_dssp             THHHHHTTGGGSCEEEEEECCCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCCHH
T ss_pred             ChHHHHHhcCccceeecCCCCcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchhHH
Confidence            999998 4311            2477899999999952        678888                 89999764  


Q ss_pred             -hHHHHHHH
Q psy12977        206 -DVAKWCRR  213 (226)
Q Consensus       206 -~~~~~~~~  213 (226)
                       .+.+.++.
T Consensus       319 ~~i~~aL~A  327 (922)
T 1nkt_A          319 SYLNNALKA  327 (922)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence             55554433

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=99.85  E-value=3.4e-22  Score=179.20  Aligned_cols=188  Identities=14%  Similarity=0.150  Sum_probs=127.0

Q ss_pred             echhhhhhhHHHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEE
Q psy12977          9 LGIFTIGFVISIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIV   87 (226)
Q Consensus         9 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil   87 (226)
                      +|+|..++ +.+.+..++.+... .+.++|+|+.. +.+.+++|+++.+|||||||++|++|+++.+..   .+.+++|+
T Consensus       147 vg~~~~~~-l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~---~~~~vLvl  221 (618)
T 2whx_A          147 IGLYGNGV-VTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALK---RRLRTLIL  221 (618)
T ss_dssp             EEECCC----------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHH---TTCCEEEE
T ss_pred             eccccccc-ccchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHh---CCCeEEEE
Confidence            46666553 12223333333332 47788888655 477889999999999999999999999988754   35689999


Q ss_pred             cccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccc
Q psy12977         88 CPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES  167 (226)
Q Consensus        88 ~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~  167 (226)
                      +||++||.|+.+.++      +..+.. ...     ........+..+.++|.+.+.+.+...   ..+++++++|+|||
T Consensus       222 ~PtreLa~Qi~~~l~------~~~v~~-~~~-----~l~~~~tp~~~i~~~t~~~l~~~l~~~---~~l~~~~~iViDEa  286 (618)
T 2whx_A          222 APTRVVAAEMEEALR------GLPIRY-QTP-----AVKSDHTGREIVDLMCHATFTTRLLSS---TRVPNYNLIVMDEA  286 (618)
T ss_dssp             ESSHHHHHHHHHHTT------TSCEEE-CCT-----TSSCCCCSSSCEEEEEHHHHHHHHHHC---SSCCCCSEEEEEST
T ss_pred             cChHHHHHHHHHHhc------CCceeE-ecc-----cceeccCCCceEEEEChHHHHHHHhcc---ccccCCeEEEEECC
Confidence            999999999998775      222221 111     111122334567788888887766652   45889999999999


Q ss_pred             ccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEec
Q psy12977        168 DKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       168 h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~  223 (226)
                      |++ +.   ++...+..+.+.++.+..|+++||||+|+.+..+..   .++..+.+
T Consensus       287 h~~-~~---~~~~~~~~i~~~l~~~~~q~il~SAT~~~~~~~~~~---~~~~~~~v  335 (618)
T 2whx_A          287 HFT-DP---CSVAARGYISTRVEMGEAAAIFMTATPPGSTDPFPQ---SNSPIEDI  335 (618)
T ss_dssp             TCC-SH---HHHHHHHHHHHHHHHTSCEEEEECSSCTTCCCSSCC---CSSCEEEE
T ss_pred             CCC-Cc---cHHHHHHHHHHHhcccCccEEEEECCCchhhhhhhc---cCCceeee
Confidence            998 44   577777777777644789999999999987654433   24544443

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.85  E-value=5.8e-22  Score=174.18  Aligned_cols=154  Identities=14%  Similarity=0.053  Sum_probs=119.0

Q ss_pred             cCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeE
Q psy12977         34 KHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRA  112 (226)
Q Consensus        34 ~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~  112 (226)
                      .+++|.|..+. .+..+++.++++|||+|||.+++.++...+...   +.+++|++|+++|+.|+.+.++++....+..+
T Consensus       112 ~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~---~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v  188 (510)
T 2oca_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY---EGKILIIVPTTALTTQMADDFVDYRLFSHAMI  188 (510)
T ss_dssp             ECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHC---SSEEEEEESSHHHHHHHHHHHHHTTSSCGGGE
T ss_pred             CCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCC---CCeEEEEECcHHHHHHHHHHHHHhhcCCccce
Confidence            37888897764 556678999999999999999999888777532   34999999999999999999988866555677


Q ss_pred             EEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCC
Q psy12977        113 HVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGP  192 (226)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~  192 (226)
                      ..+.++......    ....++|+|+||+.+...     ....+.+++++|+||+|++.+.       .+..+++.+ .+
T Consensus       189 ~~~~~~~~~~~~----~~~~~~I~i~T~~~l~~~-----~~~~~~~~~liIiDE~H~~~~~-------~~~~il~~~-~~  251 (510)
T 2oca_A          189 KKIGGGASKDDK----YKNDAPVVVGTWQTVVKQ-----PKEWFSQFGMMMNDECHLATGK-------SISSIISGL-NN  251 (510)
T ss_dssp             EECGGGCCTTGG----GCTTCSEEEEEHHHHTTS-----CGGGGGGEEEEEEETGGGCCHH-------HHHHHGGGC-TT
T ss_pred             EEEecCCccccc----cccCCcEEEEeHHHHhhc-----hhhhhhcCCEEEEECCcCCCcc-------cHHHHHHhc-cc
Confidence            766666433332    346789999999976432     2345778999999999998653       455666666 56


Q ss_pred             CceEEEEeeeCchhH
Q psy12977        193 NLKRGMFSATHTEDV  207 (226)
Q Consensus       193 ~~q~v~~SAT~~~~~  207 (226)
                      ..+++++|||+++..
T Consensus       252 ~~~~l~lSATp~~~~  266 (510)
T 2oca_A          252 CMFKFGLSGSLRDGK  266 (510)
T ss_dssp             CCEEEEEESCGGGCS
T ss_pred             CcEEEEEEeCCCCCc
Confidence            789999999998664

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=99.85  E-value=2.2e-22  Score=183.01  Aligned_cols=167  Identities=18%  Similarity=0.182  Sum_probs=117.4

Q ss_pred             CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCC--CCCceEEEEcccHHHHHHH-HHHHHHHhhcCCC
Q psy12977         35 HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK--NLGFRAVIVCPTRELAKQT-YNETVRLSEGLGL  110 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~--~~~~~~iil~Pt~~L~~q~-~~~~~~~~~~~~~  110 (226)
                      +++|.|..+. .++.|+++++.+|||+|||++|++|++..+....  ..+.++||++|+++|+.|+ .+.+++++.. +.
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~-~~   85 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK-WY   85 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTT-TS
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCc-Cc
Confidence            5778886664 6677899999999999999999999988764321  1235899999999999999 9999999875 46


Q ss_pred             eEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhc----CCCCCCCCCccEEEEcccccccccCccchHHHHHHHH
Q psy12977        111 RAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQM----DPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIY  186 (226)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~----~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~  186 (226)
                      .+..+.|+....... ......++|+|+||+++.+.+..    ....+.+.+++++|+||||++....  .+...+...+
T Consensus        86 ~v~~~~g~~~~~~~~-~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~--~~~~i~~~~l  162 (699)
T 4gl2_A           86 RVIGLSGDTQLKISF-PEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEA--VYNNIMRHYL  162 (699)
T ss_dssp             CEEEEC----CCCCH-HHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTB--SSCSHHHHHH
T ss_pred             eEEEEeCCcchhhHH-HhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccc--hHHHHHHHHH
Confidence            777777664322111 11225689999999999988742    1245678899999999999886542  2222222222


Q ss_pred             Hh----c--------CCCCceEEEEeeeCch
Q psy12977        187 AA----C--------SGPNLKRGMFSATHTE  205 (226)
Q Consensus       187 ~~----~--------~~~~~q~v~~SAT~~~  205 (226)
                      ..    .        ..+.+|++++|||++.
T Consensus       163 ~~~~~~~~~~~~~~~~~~~~~il~lTATp~~  193 (699)
T 4gl2_A          163 MQKLKNNRLKKENKPVIPLPQILGLTASPGV  193 (699)
T ss_dssp             HHHHHHHHHHC----CCCCCEEEEECSCCCC
T ss_pred             HhhhcccccccccccCCCCCEEEEecccccc
Confidence            11    1        1256799999999886

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=99.85  E-value=1.2e-21  Score=179.04  Aligned_cols=164  Identities=20%  Similarity=0.207  Sum_probs=121.3

Q ss_pred             HHHhhccccCCCCcccccc-cCCCC------CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHH
Q psy12977         26 AVVSNSIFKHFEPHFTITY-LSPLG------RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTY   98 (226)
Q Consensus        26 ~~~~~~~~~~~~~~Q~~~~-~~~~~------~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~   98 (226)
                      +.+++.+| ++++.|..+. .+..+      .+.++++|||||||.+|+.+++..+..    +.+++|++||++|+.|++
T Consensus       360 ~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~----g~qvlvlaPtr~La~Q~~  434 (780)
T 1gm5_A          360 EFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA----GFQTAFMVPTSILAIQHY  434 (780)
T ss_dssp             HHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH----TSCEEEECSCHHHHHHHH
T ss_pred             HHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc----CCeEEEEeCcHHHHHHHH
Confidence            34567788 8999997664 33222      589999999999999999999988763    568999999999999999


Q ss_pred             HHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCc
Q psy12977         99 NETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGV  175 (226)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~  175 (226)
                      +.++++....+.++..+.|+.....+.   .....+.++|+|+||+.+.+       ...+.+++++|+||+|++.... 
T Consensus       435 ~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-------~~~~~~l~lVVIDEaHr~g~~q-  506 (780)
T 1gm5_A          435 RRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-------DVHFKNLGLVIIDEQHRFGVKQ-  506 (780)
T ss_dssp             HHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-------CCCCSCCCEEEEESCCCC-----
T ss_pred             HHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh-------hhhccCCceEEecccchhhHHH-
Confidence            999999988889998888776543321   11223568999999987743       3457899999999999874331 


Q ss_pred             cchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHH
Q psy12977        176 RGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKW  210 (226)
Q Consensus       176 ~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~  210 (226)
                         .    ..+... ...+++++||||+.++....
T Consensus       507 ---r----~~l~~~-~~~~~vL~mSATp~p~tl~~  533 (780)
T 1gm5_A          507 ---R----EALMNK-GKMVDTLVMSATPIPRSMAL  533 (780)
T ss_dssp             --------CCCCSS-SSCCCEEEEESSCCCHHHHH
T ss_pred             ---H----HHHHHh-CCCCCEEEEeCCCCHHHHHH
Confidence               0    111111 24689999999977655443

>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=99.83  E-value=4.5e-20  Score=165.29  Aligned_cols=145  Identities=12%  Similarity=0.095  Sum_probs=108.6

Q ss_pred             CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEE
Q psy12977         35 HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAH  113 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~  113 (226)
                      .+.+.|...+ .+.++++++++||||||||.++.+++++.       +.+++|++|+++||.|+++.+.+..   +..+.
T Consensus       217 P~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~~-------g~~vLVl~PTReLA~Qia~~l~~~~---g~~vg  286 (666)
T 3o8b_A          217 PVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ-------GYKVLVLNPSVAATLGFGAYMSKAH---GIDPN  286 (666)
T ss_dssp             CSCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHHT-------TCCEEEEESCHHHHHHHHHHHHHHH---SCCCE
T ss_pred             CcHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHHC-------CCeEEEEcchHHHHHHHHHHHHHHh---CCCee
Confidence            4445565555 55677899999999999999999888762       4589999999999999998765554   44444


Q ss_pred             EEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCC
Q psy12977        114 VIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPN  193 (226)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~  193 (226)
                      ...++..        ...+++|+|+||+++.   ..  ..+.+++++++|+||+|.+ +.   ++...+..+++.++...
T Consensus       287 ~~vG~~~--------~~~~~~IlV~TPGrLl---~~--~~l~l~~l~~lVlDEAH~l-~~---~~~~~l~~Il~~l~~~~  349 (666)
T 3o8b_A          287 IRTGVRT--------ITTGAPVTYSTYGKFL---AD--GGCSGGAYDIIICDECHST-DS---TTILGIGTVLDQAETAG  349 (666)
T ss_dssp             EECSSCE--------ECCCCSEEEEEHHHHH---HT--TSCCTTSCSEEEETTTTCC-SH---HHHHHHHHHHHHTTTTT
T ss_pred             EEECcEe--------ccCCCCEEEECcHHHH---hC--CCcccCcccEEEEccchhc-Cc---cHHHHHHHHHHhhhhcC
Confidence            4444421        3467899999999973   33  5677889999999999754 44   47778888888884322


Q ss_pred             -ceEEEEeeeCchh
Q psy12977        194 -LKRGMFSATHTED  206 (226)
Q Consensus       194 -~q~v~~SAT~~~~  206 (226)
                       ..++++|||+|+.
T Consensus       350 ~~llil~SAT~~~~  363 (666)
T 3o8b_A          350 ARLVVLATATPPGS  363 (666)
T ss_dssp             CSEEEEEESSCTTC
T ss_pred             CceEEEECCCCCcc
Confidence             2377889999874

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=99.83  E-value=3e-20  Score=176.54  Aligned_cols=173  Identities=19%  Similarity=0.217  Sum_probs=126.0

Q ss_pred             hhccccCCCCcccccc-cCCC----CC--eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHH
Q psy12977         29 SNSIFKHFEPHFTITY-LSPL----GR--QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET  101 (226)
Q Consensus        29 ~~~~~~~~~~~Q~~~~-~~~~----~~--~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~  101 (226)
                      ..++|+ ++|.|..+. .+..    ++  +.++++|||+|||.+++.+++..+..    +.+++|++||++|+.|+++.+
T Consensus       598 ~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~----g~~vlvlvPt~~La~Q~~~~~  672 (1151)
T 2eyq_A          598 DSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN----HKQVAVLVPTTLLAQQHYDNF  672 (1151)
T ss_dssp             HTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT----TCEEEEECSSHHHHHHHHHHH
T ss_pred             HhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHh----CCeEEEEechHHHHHHHHHHH
Confidence            345565 599997764 3322    55  99999999999999999888877653    569999999999999999999


Q ss_pred             HHHhhcCCCeEEEEecchhhhhh---hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccch
Q psy12977        102 VRLSEGLGLRAHVIGKIQQAAEK---FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGF  178 (226)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~  178 (226)
                      ++.+...+.++....+.......   ......+.++|+|+||+.+.       ..+.+.+++++|+||+|++...    .
T Consensus       673 ~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~-------~~~~~~~l~lvIiDEaH~~g~~----~  741 (1151)
T 2eyq_A          673 RDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-------SDVKFKDLGLLIVDEEHRFGVR----H  741 (1151)
T ss_dssp             HHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-------SCCCCSSEEEEEEESGGGSCHH----H
T ss_pred             HHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh-------CCccccccceEEEechHhcChH----H
Confidence            99988878888877654332221   11122356899999997652       3456889999999999996322    2


Q ss_pred             HHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEe
Q psy12977        179 RDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN  222 (226)
Q Consensus       179 ~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~  222 (226)
                          ...++.+ ....+++++|||+++.........+.++..+.
T Consensus       742 ----~~~l~~l-~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~  780 (1151)
T 2eyq_A          742 ----KERIKAM-RANVDILTLTATPIPRTLNMAMSGMRDLSIIA  780 (1151)
T ss_dssp             ----HHHHHHH-HTTSEEEEEESSCCCHHHHHHHTTTSEEEECC
T ss_pred             ----HHHHHHh-cCCCCEEEEcCCCChhhHHHHHhcCCCceEEe
Confidence                2333344 35789999999988777777766666555443

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=99.81  E-value=6.7e-20  Score=159.58  Aligned_cols=135  Identities=19%  Similarity=0.084  Sum_probs=105.3

Q ss_pred             CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCe-E
Q psy12977         35 HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR-A  112 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~-~  112 (226)
                      +++|.|..+. .+..+++.++.+|||+|||+.++.++...       +.+++|++|+++|+.|+.+.++++    +.. +
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~-------~~~~Lvl~P~~~L~~Q~~~~~~~~----~~~~v  161 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL-------STPTLIVVPTLALAEQWKERLGIF----GEEYV  161 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH-------CSCEEEEESSHHHHHHHHHHGGGG----CGGGE
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc-------CCCEEEEECCHHHHHHHHHHHHhC----CCcce
Confidence            5677886664 55677889999999999999998887764       458999999999999999988884    666 6


Q ss_pred             EEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCC
Q psy12977        113 HVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGP  192 (226)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~  192 (226)
                      ..+.++..          ..++|+|+|++.+.......     ..+++++|+||+|++.+.   .+..    +.+.+  +
T Consensus       162 ~~~~g~~~----------~~~~Ivv~T~~~l~~~~~~~-----~~~~~liIvDEaH~~~~~---~~~~----~~~~~--~  217 (472)
T 2fwr_A          162 GEFSGRIK----------ELKPLTVSTYDSAYVNAEKL-----GNRFMLLIFDEVHHLPAE---SYVQ----IAQMS--I  217 (472)
T ss_dssp             EEBSSSCB----------CCCSEEEEEHHHHHHTHHHH-----TTTCSEEEEETGGGTTST---TTHH----HHHTC--C
T ss_pred             EEECCCcC----------CcCCEEEEEcHHHHHHHHHh-----cCCCCEEEEECCcCCCCh---HHHH----HHHhc--C
Confidence            66665532          35789999999998876531     235899999999999876   3433    44444  5


Q ss_pred             CceEEEEeeeCc
Q psy12977        193 NLKRGMFSATHT  204 (226)
Q Consensus       193 ~~q~v~~SAT~~  204 (226)
                      ..+++++|||++
T Consensus       218 ~~~~l~lSATp~  229 (472)
T 2fwr_A          218 APFRLGLTATFE  229 (472)
T ss_dssp             CSEEEEEESCCC
T ss_pred             CCeEEEEecCcc
Confidence            678999999987

>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=99.80  E-value=1.9e-19  Score=143.51  Aligned_cols=137  Identities=19%  Similarity=0.085  Sum_probs=101.9

Q ss_pred             CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCe-E
Q psy12977         35 HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR-A  112 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~-~  112 (226)
                      ++++.|..+. .+..+++.++++|||+|||..++.++...       +.+++|++|+++|+.|+.+.+.++    +.. +
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~-------~~~~liv~P~~~L~~q~~~~~~~~----~~~~v  161 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL-------STPTLIVVPTLALAEQWKERLGIF----GEEYV  161 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS-------CSCEEEEESSHHHHHHHHHHHGGG----CGGGE
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc-------CCCEEEEeCCHHHHHHHHHHHHhC----CCCeE
Confidence            5566776554 45667789999999999999987776543       347999999999999999988773    556 6


Q ss_pred             EEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCC
Q psy12977        113 HVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGP  192 (226)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~  192 (226)
                      ..+.++..          ...+|+|+|++.+.......     ..+++++|+||+|.+.+.   .+.    .+.+.+  +
T Consensus       162 ~~~~g~~~----------~~~~i~v~T~~~l~~~~~~~-----~~~~~llIiDEaH~l~~~---~~~----~i~~~~--~  217 (237)
T 2fz4_A          162 GEFSGRIK----------ELKPLTVSTYDSAYVNAEKL-----GNRFMLLIFDEVHHLPAE---SYV----QIAQMS--I  217 (237)
T ss_dssp             EEESSSCB----------CCCSEEEEEHHHHHHTHHHH-----TTTCSEEEEECSSCCCTT---THH----HHHHTC--C
T ss_pred             EEEeCCCC----------CcCCEEEEeHHHHHhhHHHh-----cccCCEEEEECCccCCCh---HHH----HHHHhc--c
Confidence            66655432          35689999999988766531     245899999999999765   332    344455  4


Q ss_pred             CceEEEEeeeCchh
Q psy12977        193 NLKRGMFSATHTED  206 (226)
Q Consensus       193 ~~q~v~~SAT~~~~  206 (226)
                      ..+++++|||+++.
T Consensus       218 ~~~~l~LSATp~r~  231 (237)
T 2fz4_A          218 APFRLGLTATFERE  231 (237)
T ss_dssp             CSEEEEEEESCC--
T ss_pred             CCEEEEEecCCCCC
Confidence            67899999998753

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=99.79  E-value=1.1e-20  Score=163.57  Aligned_cols=139  Identities=16%  Similarity=0.142  Sum_probs=96.1

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhh
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEK  124 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (226)
                      .+.+|+|+++++|||||||++|++|+++.+..   .+.+++|++||++||.|+++.++.+    +  +....+.      
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~---~~~~~lil~Ptr~La~Q~~~~l~~~----~--v~~~~~~------   68 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECAR---RRLRTLVLAPTRVVLSEMKEAFHGL----D--VKFHTQA------   68 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHH---TTCCEEEEESSHHHHHHHHHHTTTS----C--EEEESSC------
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHh---cCCeEEEEcchHHHHHHHHHHHhcC----C--eEEeccc------
Confidence            45789999999999999999999999987653   2568999999999999999987633    2  2111100      


Q ss_pred             hCCCcCCCCCEEEECchHHHHhHhc------CCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEE
Q psy12977        125 FGPRSAQKFDVLITTPNKLVYLLQM------DPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGM  198 (226)
Q Consensus       125 ~~~~~~~~~~IiV~Tp~~l~~~~~~------~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~  198 (226)
                      .         -.++||+++.+++..      ......+.+++++|+||+|++ +.   ++...+..+.+....+++|+++
T Consensus        69 ~---------~~v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~-~~---~~~~~~~~~~~~~~~~~~~~l~  135 (440)
T 1yks_A           69 F---------SAHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL-DP---ASIAARGWAAHRARANESATIL  135 (440)
T ss_dssp             C---------CCCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC-SH---HHHHHHHHHHHHHHTTSCEEEE
T ss_pred             c---------eeccCCccceeeecccchhHhhhCcccccCccEEEEECcccc-Cc---chHHHHHHHHHHhccCCceEEE
Confidence            0         026666555432221      112345789999999999998 33   3444444444444346899999


Q ss_pred             EeeeCchhHHHHH
Q psy12977        199 FSATHTEDVAKWC  211 (226)
Q Consensus       199 ~SAT~~~~~~~~~  211 (226)
                      ||||+++.+..+.
T Consensus       136 ~SAT~~~~~~~~~  148 (440)
T 1yks_A          136 MTATPPGTSDEFP  148 (440)
T ss_dssp             ECSSCTTCCCSSC
T ss_pred             EeCCCCchhhhhh
Confidence            9999987754433

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=99.78  E-value=4.9e-19  Score=153.87  Aligned_cols=144  Identities=18%  Similarity=0.104  Sum_probs=97.7

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhh
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEK  124 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (226)
                      .+.+++++++++|||||||++|++|+++.+..   .+.+++|++|+++|+.|+.+.++      +..+........    
T Consensus        17 ~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~---~~~~~lvl~Ptr~La~Q~~~~l~------g~~v~~~~~~~~----   83 (459)
T 2z83_A           17 MLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ---QRLRTAVLAPTRVVAAEMAEALR------GLPVRYQTSAVQ----   83 (459)
T ss_dssp             GGSTTCEEEECCCTTSCTTTTHHHHHHHHHHH---TTCCEEEEECSHHHHHHHHHHTT------TSCEEECC--------
T ss_pred             HHhcCCcEEEECCCCCCHHHHHHHHHHHHHHh---CCCcEEEECchHHHHHHHHHHhc------CceEeEEecccc----
Confidence            56778999999999999999999999987653   25689999999999999999876      222221111100    


Q ss_pred             hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        125 FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       125 ~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                        .....+..+.++|.+.+.+.+..   ...+.+++++|+||||.....    ....+..+......+..|+++||||+|
T Consensus        84 --~~~t~~~~i~~~~~~~l~~~l~~---~~~l~~~~~iViDEaH~~~~~----~~~~~~~~~~~~~~~~~~~il~SAT~~  154 (459)
T 2z83_A           84 --REHQGNEIVDVMCHATLTHRLMS---PNRVPNYNLFVMDEAHFTDPA----SIAARGYIATKVELGEAAAIFMTATPP  154 (459)
T ss_dssp             ------CCCSEEEEEHHHHHHHHHS---CC-CCCCSEEEESSTTCCSHH----HHHHHHHHHHHHHTTSCEEEEECSSCT
T ss_pred             --cCCCCCcEEEEEchHHHHHHhhc---cccccCCcEEEEECCccCCch----hhHHHHHHHHHhccCCccEEEEEcCCC
Confidence              00123345778888888776664   345889999999999984211    222222222222246899999999999


Q ss_pred             hhHHHH
Q psy12977        205 EDVAKW  210 (226)
Q Consensus       205 ~~~~~~  210 (226)
                      +++..+
T Consensus       155 ~~~~~~  160 (459)
T 2z83_A          155 GTTDPF  160 (459)
T ss_dssp             TCCCSS
T ss_pred             cchhhh
Confidence            876444

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.78  E-value=1.1e-18  Score=158.22  Aligned_cols=146  Identities=23%  Similarity=0.216  Sum_probs=114.8

Q ss_pred             HHHHHHHHHHHhh-----ccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         18 ISIIVTTLAVVSN-----SIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        18 ~~~~~~~l~~~~~-----~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      ..+.|.-.+.+++     .++ +++++|.... .+++|+  +..++||+|||++|.+|++.....    +.+++|++||+
T Consensus        58 ddlLpEAFAvvREAs~R~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~----G~qv~VvTPTr  130 (997)
T 2ipc_A           58 DELLPMAFALTRESAKRYLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALT----GKGVHVVTVND  130 (997)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTT----CSCCEEEESSH
T ss_pred             HHHHHHHHHHHHHHHHHHhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHh----CCCEEEEeCCH
Confidence            4455665555554     666 8899997764 667777  999999999999999999644432    45799999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHH-HHhHhcCC----CCCCCC---CccEEE
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKL-VYLLQMDP----PALNLA---NVEWLI  163 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l-~~~~~~~~----~~~~~~---~~~~lV  163 (226)
                      +||.|.++.+..+...+++++..+.++.....+   ....++||+|+||+.+ ++++....    ....+.   .+.++|
T Consensus       131 eLA~Qdae~m~~l~~~lGLsv~~i~Gg~~~~~r---~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lI  207 (997)
T 2ipc_A          131 YLARRDAEWMGPVYRGLGLSVGVIQHASTPAER---RKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAI  207 (997)
T ss_dssp             HHHHHHHHHHHHHHHTTTCCEEECCTTCCHHHH---HHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEE
T ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEeCCCCHHHH---HHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEE
Confidence            999999999999999999999988877654332   2335689999999999 77776531    245677   899999


Q ss_pred             Eccccccccc
Q psy12977        164 VDESDKLFEA  173 (226)
Q Consensus       164 iDE~h~l~~~  173 (226)
                      +||+|.++..
T Consensus       208 IDEaDsmLiD  217 (997)
T 2ipc_A          208 IDEVDSILID  217 (997)
T ss_dssp             ETTHHHHTTS
T ss_pred             EechHHHHHh
Confidence            9999988744

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.78  E-value=2e-19  Score=160.81  Aligned_cols=166  Identities=11%  Similarity=0.009  Sum_probs=93.9

Q ss_pred             CCCCcccccc-cCC-----CCCeEEEECCCCchHhHHHHHHHHHHhcCC-----CCCCceEEEEcccHHHHHHHH-HHHH
Q psy12977         35 HFEPHFTITY-LSP-----LGRQIFACAPTGSGKTAAFLIPIIHSLRGP-----KNLGFRAVIVCPTRELAKQTY-NETV  102 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~-----~~~~~li~apTGsGKT~~~~~~~~~~~~~~-----~~~~~~~iil~Pt~~L~~q~~-~~~~  102 (226)
                      .+++.|..+. .+.     .++++++++|||+|||++++..+...+...     ...+++++|++|+++|+.|+. +.++
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~~  257 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTFT  257 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------CCT
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHHH
Confidence            6788886663 222     346799999999999999765544444322     124679999999999999998 6665


Q ss_pred             HHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcC--CCCCCCCCccEEEEcccccccccCccchHH
Q psy12977        103 RLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMD--PPALNLANVEWLIVDESDKLFEAGVRGFRD  180 (226)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~--~~~~~~~~~~~lViDE~h~l~~~~~~~~~~  180 (226)
                      .+    +.....+.+.         ....+.+|+|+||+++.......  ...+....++++|+||||++.+..    ..
T Consensus       258 ~~----~~~~~~~~~~---------~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~----~~  320 (590)
T 3h1t_A          258 PF----GDARHKIEGG---------KVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD----NS  320 (590)
T ss_dssp             TT----CSSEEECCC-----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC------------
T ss_pred             hc----chhhhhhhcc---------CCCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc----hH
Confidence            44    3333332221         23456799999999998765321  134556789999999999987641    24


Q ss_pred             HHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCe
Q psy12977        181 QLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRV  219 (226)
Q Consensus       181 ~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~  219 (226)
                      .+..+++.+  +..+++++|||+.+........++..++
T Consensus       321 ~~~~il~~~--~~~~~l~lTATP~~~~~~~~~~~f~~~~  357 (590)
T 3h1t_A          321 NWREILEYF--EPAFQIGMTATPLREDNRDTYRYFGNPI  357 (590)
T ss_dssp             -CHHHHHHS--TTSEEEEEESSCSCTTTHHHHHHSCSCS
T ss_pred             HHHHHHHhC--CcceEEEeccccccccchhHHHHcCCce
Confidence            556666677  4578999999988654444445555544

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.78  E-value=1.9e-19  Score=162.55  Aligned_cols=162  Identities=15%  Similarity=0.082  Sum_probs=105.4

Q ss_pred             Hhhcccc-----CCCCccc-----ccc-cCC------CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEccc
Q psy12977         28 VSNSIFK-----HFEPHFT-----ITY-LSP------LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPT   90 (226)
Q Consensus        28 ~~~~~~~-----~~~~~Q~-----~~~-~~~------~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt   90 (226)
                      +...+|.     .++++|+     .+. .++      +++|+++++|||||||++|+++++..+..   .+.+++|++||
T Consensus       203 l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~---~~~~~lilaPT  279 (673)
T 2wv9_A          203 LYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQ---KRLRTAVLAPT  279 (673)
T ss_dssp             EEEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHH---TTCCEEEEESS
T ss_pred             eeeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHh---CCCcEEEEccH
Confidence            4455666     8899998     553 444      79999999999999999999999987643   35689999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccc
Q psy12977         91 RELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKL  170 (226)
Q Consensus        91 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l  170 (226)
                      ++||.|+++.++.+    ++.  ...+      ........+.-+-..+.+.+.+.+..   ...+.+++++|+||+|++
T Consensus       280 r~La~Q~~~~l~~~----~i~--~~~~------~l~~v~tp~~ll~~l~~~~l~~~l~~---~~~l~~l~lvViDEaH~~  344 (673)
T 2wv9_A          280 RVVAAEMAEALRGL----PVR--YLTP------AVQREHSGNEIVDVMCHATLTHRLMS---PLRVPNYNLFVMDEAHFT  344 (673)
T ss_dssp             HHHHHHHHHHTTTS----CCE--ECCC---------CCCCSCCCEEEEEHHHHHHHHHS---SSCCCCCSEEEEESTTCC
T ss_pred             HHHHHHHHHHHhcC----Cee--eecc------cccccCCHHHHHHHHHhhhhHHHHhc---ccccccceEEEEeCCccc
Confidence            99999999887644    222  1000      00000011112333344444433332   245889999999999998


Q ss_pred             cccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHH
Q psy12977        171 FEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWC  211 (226)
Q Consensus       171 ~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~  211 (226)
                       +.   .+...+..+......+..|+++||||+++.+.++.
T Consensus       345 -~~---~~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~~~~  381 (673)
T 2wv9_A          345 -DP---ASIAARGYIATRVEAGEAAAIFMTATPPGTSDPFP  381 (673)
T ss_dssp             -CH---HHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSC
T ss_pred             -Cc---cHHHHHHHHHHhccccCCcEEEEcCCCChhhhhhc
Confidence             22   23344444444443467999999999987755443

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.77  E-value=9.6e-19  Score=150.92  Aligned_cols=140  Identities=19%  Similarity=0.158  Sum_probs=95.9

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCC
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGP  127 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (226)
                      .|+++++++|||||||.+|+.++++.+..   .+.+++|++||++|+.|+.+.+.      +..+....+....      
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~---~g~~~lvl~Pt~~La~Q~~~~~~------~~~v~~~~~~~~~------   65 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK---KRLRTVILAPTRVVASEMYEALR------GEPIRYMTPAVQS------   65 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH---TTCCEEEEESSHHHHHHHHHHTT------TSCEEEC------------
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh---CCCCEEEECcHHHHHHHHHHHhC------CCeEEEEecCccc------
Confidence            36899999999999999999998855532   25689999999999999988764      3344433332111      


Q ss_pred             CcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        128 RSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       128 ~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                      ....+..+.+.|.+.+.+.+..   ...+.+++++|+||+|++ +.   .+......+.....++.+|++++|||+++.+
T Consensus        66 ~~~~~~~~~~~~~~~l~~~l~~---~~~~~~l~~vViDEaH~~-~~---~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~  138 (431)
T 2v6i_A           66 ERTGNEIVDFMCHSTFTMKLLQ---GVRVPNYNLYIMDEAHFL-DP---ASVAARGYIETRVSMGDAGAIFMTATPPGTT  138 (431)
T ss_dssp             ---CCCSEEEEEHHHHHHHHHH---TCCCCCCSEEEEESTTCC-SH---HHHHHHHHHHHHHHTTSCEEEEEESSCTTCC
T ss_pred             cCCCCceEEEEchHHHHHHHhc---CccccCCCEEEEeCCccC-Cc---cHHHHHHHHHHHhhCCCCcEEEEeCCCCcch
Confidence            1112345677788888766554   344788999999999997 33   2344444444433346899999999999765


Q ss_pred             HH
Q psy12977        208 AK  209 (226)
Q Consensus       208 ~~  209 (226)
                      .+
T Consensus       139 ~~  140 (431)
T 2v6i_A          139 EA  140 (431)
T ss_dssp             CS
T ss_pred             hh
Confidence            43

>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=99.75  E-value=2.9e-18  Score=157.26  Aligned_cols=186  Identities=18%  Similarity=0.125  Sum_probs=121.8

Q ss_pred             HHHHHHHHhhccccCCCCcccccc--cCCCCCeEEEECCCCchHhHHHHHHHHHHh-cCCCCCCceEEEEcccHHHHHHH
Q psy12977         21 IVTTLAVVSNSIFKHFEPHFTITY--LSPLGRQIFACAPTGSGKTAAFLIPIIHSL-RGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        21 ~~~~l~~~~~~~~~~~~~~Q~~~~--~~~~~~~~li~apTGsGKT~~~~~~~~~~~-~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      .+...+.++..+ ..+++.|+...  .+..++++++.||||+|||..  +|++... ......+.++++++|+++++.|+
T Consensus        80 ~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTtl--lp~ll~~~~~~~~~g~~ilvl~P~r~La~q~  156 (773)
T 2xau_A           80 TPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQ--IPQFVLFDEMPHLENTQVACTQPRRVAAMSV  156 (773)
T ss_dssp             CHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHH--HHHHHHHHHCGGGGTCEEEEEESCHHHHHHH
T ss_pred             CHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHHH--HHHHHHHhccccCCCceEEecCchHHHHHHH
Confidence            455666676666 67777775553  555678899999999999993  4443211 11111256799999999999999


Q ss_pred             HHHHHHHh-hcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccc-ccccCc
Q psy12977         98 YNETVRLS-EGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDK-LFEAGV  175 (226)
Q Consensus        98 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~-l~~~~~  175 (226)
                      .+.+.+.. ...+..+.....       .......+.+|+++||+++.+.+..   ...+.+++++|+||+|. .++.. 
T Consensus       157 ~~~l~~~~~~~v~~~vG~~i~-------~~~~~~~~~~I~v~T~G~l~r~l~~---~~~l~~~~~lIlDEah~R~ld~d-  225 (773)
T 2xau_A          157 AQRVAEEMDVKLGEEVGYSIR-------FENKTSNKTILKYMTDGMLLREAME---DHDLSRYSCIILDEAHERTLATD-  225 (773)
T ss_dssp             HHHHHHHTTCCBTTTEEEEET-------TEEECCTTCSEEEEEHHHHHHHHHH---STTCTTEEEEEECSGGGCCHHHH-
T ss_pred             HHHHHHHhCCchhheecceec-------cccccCCCCCEEEECHHHHHHHHhh---CccccCCCEEEecCccccccchH-
Confidence            88664443 222222221111       1112235788999999999988775   24588999999999995 55541 


Q ss_pred             cchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCCC
Q psy12977        176 RGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGLR  226 (226)
Q Consensus       176 ~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  226 (226)
                       .....+..+....  +..|++++|||++.+   .+.+++.++..+.+.+|
T Consensus       226 -~~~~~l~~l~~~~--~~~~iIl~SAT~~~~---~l~~~~~~~~vi~v~gr  270 (773)
T 2xau_A          226 -ILMGLLKQVVKRR--PDLKIIIMSATLDAE---KFQRYFNDAPLLAVPGR  270 (773)
T ss_dssp             -HHHHHHHHHHHHC--TTCEEEEEESCSCCH---HHHHHTTSCCEEECCCC
T ss_pred             -HHHHHHHHHHHhC--CCceEEEEeccccHH---HHHHHhcCCCcccccCc
Confidence             2344455555444  578999999999643   34466776666766654

>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=99.70  E-value=1.9e-17  Score=155.19  Aligned_cols=156  Identities=16%  Similarity=0.070  Sum_probs=105.8

Q ss_pred             cCCCCcccccc-cCC--------------CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHH
Q psy12977         34 KHFEPHFTITY-LSP--------------LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTY   98 (226)
Q Consensus        34 ~~~~~~Q~~~~-~~~--------------~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~   98 (226)
                      ..+.|.|..+. .+.              .+++.+++++||||||+++ ++++..+.. .....++||++|+++|+.|+.
T Consensus       270 ~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~-~~~~~rvLvlvpr~eL~~Q~~  347 (1038)
T 2w00_A          270 LVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATE-LDFIDKVFFVVDRKDLDYQTM  347 (1038)
T ss_dssp             EECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTT-CTTCCEEEEEECGGGCCHHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHh-cCCCceEEEEeCcHHHHHHHH
Confidence            35788886553 221              2478999999999999997 556665543 233469999999999999999


Q ss_pred             HHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccch
Q psy12977         99 NETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGF  178 (226)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~  178 (226)
                      +.+..+....      +.++.............+++|+|+||+++...+........+....++|+||||++...     
T Consensus       348 ~~f~~f~~~~------v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~~-----  416 (1038)
T 2w00_A          348 KEYQRFSPDS------VNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQFG-----  416 (1038)
T ss_dssp             HHHHTTSTTC------SSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHHH-----
T ss_pred             HHHHHhcccc------cccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcch-----
Confidence            9998876431      11111100100001134689999999999988765322224567889999999997543     


Q ss_pred             HHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        179 RDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       179 ~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                       .....+.+.+  ++.++++||||+..
T Consensus       417 -~~~~~I~~~~--p~a~~lgfTATP~~  440 (1038)
T 2w00_A          417 -EAQKNLKKKF--KRYYQFGFTGTPIF  440 (1038)
T ss_dssp             -HHHHHHHHHC--SSEEEEEEESSCCC
T ss_pred             -HHHHHHHHhC--CcccEEEEeCCccc
Confidence             2344556666  56899999999874

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.69  E-value=5.9e-16  Score=139.71  Aligned_cols=139  Identities=14%  Similarity=0.090  Sum_probs=99.7

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhh
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEK  124 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (226)
                      ..+++++++++||||||||...    +..+...    .+++|++|+++||.|+++.+++.    +..+....|+..... 
T Consensus       151 r~l~rk~vlv~apTGSGKT~~a----l~~l~~~----~~gl~l~PtR~LA~Qi~~~l~~~----g~~v~lltG~~~~iv-  217 (677)
T 3rc3_A          151 RAMQRKIIFHSGPTNSGKTYHA----IQKYFSA----KSGVYCGPLKLLAHEIFEKSNAA----GVPCDLVTGEERVTV-  217 (677)
T ss_dssp             HTSCCEEEEEECCTTSSHHHHH----HHHHHHS----SSEEEEESSHHHHHHHHHHHHHT----TCCEEEECSSCEECC-
T ss_pred             HhcCCCEEEEEcCCCCCHHHHH----HHHHHhc----CCeEEEeCHHHHHHHHHHHHHhc----CCcEEEEECCeeEEe-
Confidence            4468899999999999999833    3333221    24599999999999999998776    667777766532211 


Q ss_pred             hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        125 FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       125 ~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                        .-.....+++++|++.+.          ....++++|+||+|.+.+.   ++...+..++..++....+++++|||.+
T Consensus       218 --~TpGr~~~il~~T~e~~~----------l~~~v~lvVIDEaH~l~d~---~~g~~~~~~l~~l~~~~i~il~~SAT~~  282 (677)
T 3rc3_A          218 --QPNGKQASHVSCTVEMCS----------VTTPYEVAVIDEIQMIRDP---ARGWAWTRALLGLCAEEVHLCGEPAAID  282 (677)
T ss_dssp             --STTCCCCSEEEEEGGGCC----------SSSCEEEEEECSGGGGGCT---TTHHHHHHHHHHCCEEEEEEEECGGGHH
T ss_pred             --cCCCcccceeEecHhHhh----------hcccCCEEEEecceecCCc---cchHHHHHHHHccCccceEEEeccchHH
Confidence              111123678888886431          2467799999999999877   6888888888888557889999999953


Q ss_pred             hhHHHHHH
Q psy12977        205 EDVAKWCR  212 (226)
Q Consensus       205 ~~~~~~~~  212 (226)
                       .+..+..
T Consensus       283 -~i~~l~~  289 (677)
T 3rc3_A          283 -LVMELMY  289 (677)
T ss_dssp             -HHHHHHH
T ss_pred             -HHHHHHH
Confidence             3444443

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.64  E-value=1.2e-16  Score=141.88  Aligned_cols=129  Identities=16%  Similarity=0.073  Sum_probs=95.4

Q ss_pred             CCCCccccc-----ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCC
Q psy12977         35 HFEPHFTIT-----YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG  109 (226)
Q Consensus        35 ~~~~~Q~~~-----~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~  109 (226)
                      ++.|.|...     ..+..|+++++.+|||+|||++|++|++.       .+.+++|++||++|+.|+.+.+..+.+..+
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~-------~~~~v~i~~pt~~l~~q~~~~~~~l~~~~~   75 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE-------VKPKVLFVVRTHNEFYPIYRDLTKIREKRN   75 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH-------HCSEEEEEESSGGGHHHHHHHHTTCCCSSC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh-------CCCeEEEEcCCHHHHHHHHHHHHHHhhhcC
Confidence            455666432     14567899999999999999999999987       256999999999999999999988877767


Q ss_pred             CeEEEEecchhh-hhh-------------------------------h------------------CCCcCCCCCEEEEC
Q psy12977        110 LRAHVIGKIQQA-AEK-------------------------------F------------------GPRSAQKFDVLITT  139 (226)
Q Consensus       110 ~~~~~~~~~~~~-~~~-------------------------------~------------------~~~~~~~~~IiV~T  139 (226)
                      .++..+.|...- ...                               .                  .+.....++|+|+|
T Consensus        76 ~~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy~~ar~~~~~adIVV~~  155 (551)
T 3crv_A           76 ITFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLYKADVIALT  155 (551)
T ss_dssp             CCEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHHHHHHHHGGGCSEEEEE
T ss_pred             ccEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCccHHHHhhhhcCCEEEeC
Confidence            777766553210 000                               0                  01113468999999


Q ss_pred             chHHHHhHhcCCCCCC-CCCccEEEEcccccccc
Q psy12977        140 PNKLVYLLQMDPPALN-LANVEWLIVDESDKLFE  172 (226)
Q Consensus       140 p~~l~~~~~~~~~~~~-~~~~~~lViDE~h~l~~  172 (226)
                      ++.+.+...+.  ... .....++|+||||++.+
T Consensus       156 ~~~l~~~~~~~--~~~~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          156 YPYFFIDRYRE--FIDIDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             THHHHCHHHHT--TSCCCSTTEEEEETTGGGGGG
T ss_pred             chHhcCHHHHH--hcCCCcCCeEEEEecccchHH
Confidence            99999876542  222 24678999999999988

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.59  E-value=1.4e-15  Score=134.62  Aligned_cols=128  Identities=15%  Similarity=0.084  Sum_probs=84.9

Q ss_pred             cccCCCCccccc-----ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhh
Q psy12977         32 IFKHFEPHFTIT-----YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE  106 (226)
Q Consensus        32 ~~~~~~~~Q~~~-----~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~  106 (226)
                      +| ++.|.|...     ..+..++++++.+|||+|||++|++|++..       +.+++|++||++|++|+.+.+..+  
T Consensus         5 ~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~-------~~~~~~~~~t~~l~~q~~~~~~~l--   74 (540)
T 2vl7_A            5 KL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL-------KKKVLIFTRTHSQLDSIYKNAKLL--   74 (540)
T ss_dssp             -----CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH-------TCEEEEEESCHHHHHHHHHHHGGG--
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC-------CCcEEEEcCCHHHHHHHHHHHHhc--
Confidence            45 678888553     245678999999999999999999998653       458999999999999999887764  


Q ss_pred             cCCCeEEEEecchh---------h-------------------------------------hhhhCCCcCCCCCEEEECc
Q psy12977        107 GLGLRAHVIGKIQQ---------A-------------------------------------AEKFGPRSAQKFDVLITTP  140 (226)
Q Consensus       107 ~~~~~~~~~~~~~~---------~-------------------------------------~~~~~~~~~~~~~IiV~Tp  140 (226)
                        +.++....+...         .                                     .....+.....++|+|+|+
T Consensus        75 --~~~~~~l~gr~~lC~~~~~~~~~~~~~c~~c~~~~~~~~~gd~~~~~~~~~~~~~~~~Cpy~~~r~~~~~adiVV~n~  152 (540)
T 2vl7_A           75 --GLKTGFLIGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYCPYYSLRANLKDKDVIAMTY  152 (540)
T ss_dssp             --TCCEEEC---------------------------------------------------------CTTGGGCSEEEEET
T ss_pred             --CCcEEEecCCccccCCchhcccccccCCCCCCchhcccccccCCcHHHHHHHhhhcCCChHHHHHHHhhcCCEEEECh
Confidence              333333222110         0                                     0000123345689999999


Q ss_pred             hHHHHhHhcCC-C----CCCCCCccEEEEccccccc
Q psy12977        141 NKLVYLLQMDP-P----ALNLANVEWLIVDESDKLF  171 (226)
Q Consensus       141 ~~l~~~~~~~~-~----~~~~~~~~~lViDE~h~l~  171 (226)
                      +.+.+...... .    ...+.+.+++|+||||++.
T Consensus       153 ~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~  188 (540)
T 2vl7_A          153 PYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLL  188 (540)
T ss_dssp             HHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGG
T ss_pred             HHhcCHHHHHhhCcccccccCcCCCEEEEEccccHH
Confidence            99987553310 1    0124667899999999994

>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=99.57  E-value=5.8e-15  Score=129.27  Aligned_cols=147  Identities=17%  Similarity=0.222  Sum_probs=100.9

Q ss_pred             CCCCcccccc-cC----CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCC
Q psy12977         35 HFEPHFTITY-LS----PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG  109 (226)
Q Consensus        35 ~~~~~Q~~~~-~~----~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~  109 (226)
                      .+.|.|.... ++    ..+++.++..+||+|||+.++..+......  ....+++|+|| .+|+.|+.++++++..  +
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~~~~--~~~~~~LIv~P-~~l~~qw~~e~~~~~~--~  111 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKE--NELTPSLVICP-LSVLKNWEEELSKFAP--H  111 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHT--TCCSSEEEEEC-STTHHHHHHHHHHHCT--T
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHHHhc--CCCCCEEEEcc-HHHHHHHHHHHHHHCC--C
Confidence            5677886553 22    457889999999999999875554444332  22458999999 5699999999999875  3


Q ss_pred             CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      .++....++..      .......+|+|+|++.+.+...     +....++++|+||||++.+..     ......+..+
T Consensus       112 ~~v~~~~g~~~------~~~~~~~~ivi~t~~~l~~~~~-----l~~~~~~~vIvDEaH~~kn~~-----~~~~~~l~~l  175 (500)
T 1z63_A          112 LRFAVFHEDRS------KIKLEDYDIILTTYAVLLRDTR-----LKEVEWKYIVIDEAQNIKNPQ-----TKIFKAVKEL  175 (500)
T ss_dssp             SCEEECSSSTT------SCCGGGSSEEEEEHHHHTTCHH-----HHTCCEEEEEEETGGGGSCTT-----SHHHHHHHTS
T ss_pred             ceEEEEecCch------hccccCCcEEEeeHHHHhccch-----hcCCCcCEEEEeCccccCCHh-----HHHHHHHHhh
Confidence            44544444431      1223567899999999865433     223468999999999986542     1233444455


Q ss_pred             CCCCceEEEEeeeCc
Q psy12977        190 SGPNLKRGMFSATHT  204 (226)
Q Consensus       190 ~~~~~q~v~~SAT~~  204 (226)
                        +..+.+++|||+.
T Consensus       176 --~~~~~l~LTaTP~  188 (500)
T 1z63_A          176 --KSKYRIALTGTPI  188 (500)
T ss_dssp             --CEEEEEEECSSCS
T ss_pred             --ccCcEEEEecCCC
Confidence              3567899999974

>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=99.56  E-value=3.1e-15  Score=140.35  Aligned_cols=159  Identities=18%  Similarity=0.088  Sum_probs=104.2

Q ss_pred             CCCCcccccc-cC--CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCe
Q psy12977         35 HFEPHFTITY-LS--PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLR  111 (226)
Q Consensus        35 ~~~~~Q~~~~-~~--~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~  111 (226)
                      ++.|.|..+. .+  ..+.+.++.++||+|||+.++..+...+...  ...+++|++|+ +|+.|+.+.+.+.+   +..
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g--~~~rvLIVvP~-sLl~Qw~~E~~~~f---~l~  226 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSG--AAERVLIIVPE-TLQHQWLVEMLRRF---NLR  226 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTS--SCCCEEEECCT-TTHHHHHHHHHHHS---CCC
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhC--CCCeEEEEeCH-HHHHHHHHHHHHHh---CCC
Confidence            5667775553 22  2356899999999999999877776666543  23489999999 99999999887665   556


Q ss_pred             EEEEecchhhhhhhC-CCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccc--hHHHHHHHHHh
Q psy12977        112 AHVIGKIQQAAEKFG-PRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG--FRDQLAVIYAA  188 (226)
Q Consensus       112 ~~~~~~~~~~~~~~~-~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~--~~~~i~~i~~~  188 (226)
                      +..+.+......... .......+|+|+|++.+....... ..+...+++++|+||+|++.......  ....+..+.  
T Consensus       227 v~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~-~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l~~L~--  303 (968)
T 3dmq_A          227 FALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRL-EHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLA--  303 (968)
T ss_dssp             CEECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTT-HHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHHHHHH--
T ss_pred             EEEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHH-HHhhhcCCCEEEehhhHhhcCCCCcchHHHHHHHHHh--
Confidence            555555443222221 233456799999999876432110 12335578999999999996543111  122333332  


Q ss_pred             cCCCCceEEEEeeeCc
Q psy12977        189 CSGPNLKRGMFSATHT  204 (226)
Q Consensus       189 ~~~~~~q~v~~SAT~~  204 (226)
                        ....+++++|||+-
T Consensus       304 --~~~~~~L~LTATPi  317 (968)
T 3dmq_A          304 --EHVPGVLLLTATPE  317 (968)
T ss_dssp             --TTCSSEEESCSSCS
T ss_pred             --hcCCcEEEEEcCCc
Confidence              34567999999974

>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=99.40  E-value=4.7e-12  Score=114.21  Aligned_cols=157  Identities=18%  Similarity=0.202  Sum_probs=102.1

Q ss_pred             CCCCcccccc-cC---------CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCC---CCceEEEEcccHHHHHHHHHHH
Q psy12977         35 HFEPHFTITY-LS---------PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKN---LGFRAVIVCPTRELAKQTYNET  101 (226)
Q Consensus        35 ~~~~~Q~~~~-~~---------~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~---~~~~~iil~Pt~~L~~q~~~~~  101 (226)
                      .+.|.|.... ++         ..++..++..++|.|||+..+..+...+.....   ...+++|++|+ +|+.|+.+++
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E~  133 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecH-HHHHHHHHHH
Confidence            5677775442 11         456789999999999999887666665543322   23469999997 8999999999


Q ss_pred             HHHhhcCCCeEEEEecchhhhh-----hh--CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccC
Q psy12977        102 VRLSEGLGLRAHVIGKIQQAAE-----KF--GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAG  174 (226)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~-----~~--~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~  174 (226)
                      .++... ......+.++.....     ..  ........+|+|+|++.+.....    .+....++++|+||+|++-...
T Consensus       134 ~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~~----~l~~~~~~~vI~DEaH~ikn~~  208 (644)
T 1z3i_X          134 GKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE----VLHKGKVGLVICDEGHRLKNSD  208 (644)
T ss_dssp             HHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT----TTTTSCCCEEEETTGGGCCTTC
T ss_pred             HHHcCC-CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhHH----HhhcCCccEEEEECceecCChh
Confidence            999765 344444444322211     00  01112357899999998876533    3344578899999999986542


Q ss_pred             ccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        175 VRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       175 ~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                           ......+..+  .....+++|||+-
T Consensus       209 -----~~~~~al~~l--~~~~rl~LTgTPi  231 (644)
T 1z3i_X          209 -----NQTYLALNSM--NAQRRVLISGTPI  231 (644)
T ss_dssp             -----HHHHHHHHHH--CCSEEEEECSSCS
T ss_pred             -----hHHHHHHHhc--ccCcEEEEecCcc
Confidence                 1222333344  3557899999963

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.37  E-value=1.3e-12  Score=120.50  Aligned_cols=151  Identities=18%  Similarity=0.162  Sum_probs=98.8

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG  126 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (226)
                      ..+++.++..++|.|||+..+..+...+.. ......++|+|| .+++.|+.+.+.++..  +..+....|.........
T Consensus       253 ~~~~~~ILademGlGKT~~ai~~i~~l~~~-~~~~~~~LIV~P-~sll~qW~~E~~~~~p--~~~v~~~~g~~~~r~~~~  328 (800)
T 3mwy_W          253 SKGDNGILADEMGLGKTVQTVAFISWLIFA-RRQNGPHIIVVP-LSTMPAWLDTFEKWAP--DLNCICYMGNQKSRDTIR  328 (800)
T ss_dssp             TTTCCEEECCCTTSSTTHHHHHHHHHHHHH-HSCCSCEEEECC-TTTHHHHHHHHHHHST--TCCEEECCCSSHHHHHHH
T ss_pred             hcCCCEEEEeCCCcchHHHHHHHHHHHHHh-cCCCCCEEEEEC-chHHHHHHHHHHHHCC--CceEEEEeCCHHHHHHHH
Confidence            467899999999999999876555444321 112346899999 7799999999998875  455555555443222110


Q ss_pred             -----------CCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCce
Q psy12977        127 -----------PRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLK  195 (226)
Q Consensus       127 -----------~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q  195 (226)
                                 ......++|+|+|++.+......    +....+++||+||||++-...     ....+.+..+  ....
T Consensus       329 ~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~----l~~~~w~~vIvDEaH~lkn~~-----s~~~~~l~~l--~~~~  397 (800)
T 3mwy_W          329 EYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE----LGSIKWQFMAVDEAHRLKNAE-----SSLYESLNSF--KVAN  397 (800)
T ss_dssp             HHHSCSCC-----CCCCCSEEEECTTHHHHTHHH----HHTSEEEEEEETTGGGGCCSS-----SHHHHHHTTS--EEEE
T ss_pred             HHHhhccccccccccccCCEEEecHHHHHhhHHH----HhcCCcceeehhhhhhhcCch-----hHHHHHHHHh--hhcc
Confidence                       12345689999999999875432    112367899999999985432     1333344444  3556


Q ss_pred             EEEEeeeCc----hhHHHHHH
Q psy12977        196 RGMFSATHT----EDVAKWCR  212 (226)
Q Consensus       196 ~v~~SAT~~----~~~~~~~~  212 (226)
                      .+++|||+-    .++..+++
T Consensus       398 rl~LTgTPiqN~l~el~~ll~  418 (800)
T 3mwy_W          398 RMLITGTPLQNNIKELAALVN  418 (800)
T ss_dssp             EEEECSCCCSSCSHHHHHHHH
T ss_pred             EEEeeCCcCCCCHHHHHHHHH
Confidence            788999963    44554443

>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=99.14  E-value=6e-11  Score=106.36  Aligned_cols=149  Identities=22%  Similarity=0.140  Sum_probs=104.7

Q ss_pred             hHHHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         17 VISIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        17 ~~~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      +..+.|+..+.+++....    .+..+|.... .+..|+  +....||+|||+++.+|++-....    |..+.+++|+.
T Consensus        53 ldd~lpeafAvvREAa~R~lg~r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~----G~~vhVvT~nd  126 (822)
T 3jux_A           53 ADEHLFEAFALVREAARRTLGMRPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALI----GKGVHLVTVND  126 (822)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTSCCCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTT----SSCEEEEESSH
T ss_pred             hHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhc----CCceEEEeccH
Confidence            345566666666655544    4455675554 444555  899999999999999998744332    56799999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchh-----------------------------------------------hhhh
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQ-----------------------------------------------AAEK  124 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~-----------------------------------------------~~~~  124 (226)
                      +||.|-++++..+.+.+|.++.++.....                                               ....
T Consensus       127 yLA~rdae~m~~l~~~Lglsvg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~  206 (822)
T 3jux_A          127 YLARRDALWMGPVYLFLGLRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKE  206 (822)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCB
T ss_pred             HHHHhHHHHHHHHHHHhCCEEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCH
Confidence            99999999999999999999988876210                                               0011


Q ss_pred             hCCCcCCCCCEEEECchHHHHhHhcC-----CCCCCCCCccEEEEccccccc
Q psy12977        125 FGPRSAQKFDVLITTPNKLVYLLQMD-----PPALNLANVEWLIVDESDKLF  171 (226)
Q Consensus       125 ~~~~~~~~~~IiV~Tp~~l~~~~~~~-----~~~~~~~~~~~lViDE~h~l~  171 (226)
                      ..+.....|||+.+|.+-+--.+-++     ..........+.|+||+|.++
T Consensus       207 ~err~aY~~DItYgTn~EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiL  258 (822)
T 3jux_A          207 ITRKEAYLCDVTYGTNNEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVL  258 (822)
T ss_dssp             CCHHHHHHSSEEEEEHHHHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHH
T ss_pred             HHHHHHhcCCCEEccCcchhhHhHHhhccCCHHHhccCCCCeEEEeccccee
Confidence            11223466899999988875433221     123335678899999999775

>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=98.93  E-value=4.2e-09  Score=94.36  Aligned_cols=144  Identities=17%  Similarity=0.172  Sum_probs=85.3

Q ss_pred             CCcccccc-cCCCCCeEEEECCCCchHh--HHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEE
Q psy12977         37 EPHFTITY-LSPLGRQIFACAPTGSGKT--AAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAH  113 (226)
Q Consensus        37 ~~~Q~~~~-~~~~~~~~li~apTGsGKT--~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~  113 (226)
                      ++.|..+. ..+.++.++++|++|||||  .+++++.+.....  ..+.++++++||...+.++.+.+.......+....
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~--~~~~~vll~APTg~AA~~L~e~~~~~~~~l~l~~~  228 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD--GERCRIRLAAPTGKAAARLTESLGKALRQLPLTDE  228 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS--SCCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCCSC
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh--cCCCeEEEEeCChhHHHHHHHHHHHHHhcCCCCHH
Confidence            56675554 5567899999999999999  5566666655422  23568999999999999999888777665543211


Q ss_pred             EEecchhhhhhhCCCcCCCCC-EEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCC
Q psy12977        114 VIGKIQQAAEKFGPRSAQKFD-VLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGP  192 (226)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~-IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~  192 (226)
                      .....       .. .....+ ++-.+|+.. . +..  .......++++|+||++.+ +.      ..+..+++.+ +.
T Consensus       229 ~~~~~-------~~-~~~Tih~ll~~~~~~~-~-~~~--~~~~~l~~d~lIIDEAsml-~~------~~~~~Ll~~l-~~  288 (608)
T 1w36_D          229 QKKRI-------PE-DASTLHRLLGAQPGSQ-R-LRH--HAGNPLHLDVLVVDEASMI-DL------PMMSRLIDAL-PD  288 (608)
T ss_dssp             CCCSC-------SC-CCBTTTSCC---------------CTTSCCSCSEEEECSGGGC-BH------HHHHHHHHTC-CT
T ss_pred             HHhcc-------ch-hhhhhHhhhccCCCch-H-HHh--ccCCCCCCCEEEEechhhC-CH------HHHHHHHHhC-CC
Confidence            10000       00 000111 111222211 0 111  1122337899999999944 32      3566677777 56


Q ss_pred             CceEEEEeee
Q psy12977        193 NLKRGMFSAT  202 (226)
Q Consensus       193 ~~q~v~~SAT  202 (226)
                      ..|++++.-.
T Consensus       289 ~~~liLvGD~  298 (608)
T 1w36_D          289 HARVIFLGDR  298 (608)
T ss_dssp             TCEEEEEECT
T ss_pred             CCEEEEEcch
Confidence            7899998755

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.83  E-value=4.5e-09  Score=94.34  Aligned_cols=70  Identities=21%  Similarity=0.188  Sum_probs=58.4

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEec
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGK  117 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~  117 (226)
                      .+.+|+++++.||||+|||++|++|++..+..   .+.+++|++||++++.|+.+.+..+....+.++..+.|
T Consensus        18 ~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~---~~~kvli~t~T~~l~~Qi~~el~~l~~~~~~~~~~l~g   87 (620)
T 4a15_A           18 SLQKSYGVALESPTGSGKTIMALKSALQYSSE---RKLKVLYLVRTNSQEEQVIKELRSLSSTMKIRAIPMQG   87 (620)
T ss_dssp             HHHHSSEEEEECCTTSCHHHHHHHHHHHHHHH---HTCEEEEEESSHHHHHHHHHHHHHHHHHSCCCEEECCC
T ss_pred             HHHcCCCEEEECCCCCCHHHHHHHHHHHhhhh---cCCeEEEECCCHHHHHHHHHHHHHHhhccCeEEEEEEC
Confidence            34578999999999999999999999987753   24699999999999999999999998766666555444

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=98.27  E-value=4.2e-06  Score=74.40  Aligned_cols=125  Identities=19%  Similarity=0.215  Sum_probs=72.8

Q ss_pred             CCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEE
Q psy12977         36 FEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHV  114 (226)
Q Consensus        36 ~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~  114 (226)
                      +++-|..+. ....++.+++.||+|+|||.... .++..+..   .+.++++++||...+.++.+..       +.....
T Consensus       190 L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~-~l~~~l~~---~g~~Vl~~ApT~~Aa~~L~e~~-------~~~a~T  258 (574)
T 3e1s_A          190 LSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTK-AVADLAES---LGLEVGLCAPTGKAARRLGEVT-------GRTAST  258 (574)
T ss_dssp             CCHHHHHHHHHHTTCSEEEEECCTTSCHHHHHH-HHHHHHHH---TTCCEEEEESSHHHHHHHHHHH-------TSCEEE
T ss_pred             CCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHHH-HHHHHHHh---cCCeEEEecCcHHHHHHhHhhh-------cccHHH
Confidence            455565553 44567889999999999997543 33343332   2457999999999888776543       211111


Q ss_pred             EecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCc
Q psy12977        115 IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNL  194 (226)
Q Consensus       115 ~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~  194 (226)
                      +.       .+..       .   .|+    .+..  ........+++|+||++.+..       ..+..+++.+ +...
T Consensus       259 ih-------~ll~-------~---~~~----~~~~--~~~~~~~~dvlIIDEasml~~-------~~~~~Ll~~~-~~~~  307 (574)
T 3e1s_A          259 VH-------RLLG-------Y---GPQ----GFRH--NHLEPAPYDLLIVDEVSMMGD-------ALMLSLLAAV-PPGA  307 (574)
T ss_dssp             HH-------HHTT-------E---ETT----EESC--SSSSCCSCSEEEECCGGGCCH-------HHHHHHHTTS-CTTC
T ss_pred             HH-------HHHc-------C---Ccc----hhhh--hhcccccCCEEEEcCccCCCH-------HHHHHHHHhC-cCCC
Confidence            10       0000       0   000    0011  122344678999999996532       2555666666 4677


Q ss_pred             eEEEEeee
Q psy12977        195 KRGMFSAT  202 (226)
Q Consensus       195 q~v~~SAT  202 (226)
                      +++++.-.
T Consensus       308 ~lilvGD~  315 (574)
T 3e1s_A          308 RVLLVGDT  315 (574)
T ss_dssp             EEEEEECT
T ss_pred             EEEEEecc
Confidence            88876544

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.26  E-value=6.6e-07  Score=80.72  Aligned_cols=65  Identities=12%  Similarity=0.249  Sum_probs=46.5

Q ss_pred             CCCcccccc-cCCCCC-eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         36 FEPHFTITY-LSPLGR-QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        36 ~~~~Q~~~~-~~~~~~-~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      +++-|..+. ..+..+ -.+|+||+|||||......+.+.+..    +.++++++||..=+.++.+.+...
T Consensus       190 LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~----~~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          190 LDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQ----GLKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             CCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHHT----TCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHhC----CCeEEEEcCchHHHHHHHHHHHhc
Confidence            445554443 223334 57999999999998766655565553    458999999999999988877654

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=98.16  E-value=6.9e-06  Score=71.05  Aligned_cols=72  Identities=17%  Similarity=0.149  Sum_probs=46.1

Q ss_pred             HHhhccccCCCCccccccc-C----CC-CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHH
Q psy12977         27 VVSNSIFKHFEPHFTITYL-S----PL-GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNE  100 (226)
Q Consensus        27 ~~~~~~~~~~~~~Q~~~~~-~----~~-~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~  100 (226)
                      .++-+.|..+++-|..+.. +    .+ ...+++.|++|||||.... .++..+....  ..++++++||..-+..+.+.
T Consensus        17 ~~~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~-~~~~~l~~~~--~~~il~~a~T~~Aa~~l~~~   93 (459)
T 3upu_A           17 RGSHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTK-FIIEALISTG--ETGIILAAPTHAAKKILSKL   93 (459)
T ss_dssp             ----CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHH-HHHHHHHHTT--CCCEEEEESSHHHHHHHHHH
T ss_pred             ccCCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHHH-HHHHHHHhcC--CceEEEecCcHHHHHHHHhh
Confidence            4566788899998866642 1    11 2489999999999997543 3344433221  13689999999888766554


Q ss_pred             H
Q psy12977        101 T  101 (226)
Q Consensus       101 ~  101 (226)
                      +
T Consensus        94 ~   94 (459)
T 3upu_A           94 S   94 (459)
T ss_dssp             H
T ss_pred             h
Confidence            3

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=98.15  E-value=2.5e-06  Score=76.61  Aligned_cols=66  Identities=14%  Similarity=0.087  Sum_probs=45.9

Q ss_pred             CCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         36 FEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        36 ~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      +++-|..+. ..+.+...+++||+|||||......+...+..   .+.++++++||..-+.++.+.+.+.
T Consensus       181 ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~~i~~l~~~---~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          181 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ---GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             CCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHHHHHHHHTS---SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHHHHHHHHHc---CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            444554443 33345678999999999998754443333321   3458999999999999998887654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.04  E-value=6.9e-06  Score=75.69  Aligned_cols=67  Identities=13%  Similarity=0.096  Sum_probs=46.9

Q ss_pred             CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         35 HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        35 ~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      .+++-|..+. ..+.+...+|+||+|||||......+...+..   .+.++++++||..-+.++.+.+.+.
T Consensus       360 ~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i~~l~~~---~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          360 QLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKI---HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHHHHHHHH---HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhC---CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            3455565443 33455668999999999998754433333321   2458999999999999999988765

>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=97.99  E-value=9.3e-06  Score=74.79  Aligned_cols=66  Identities=14%  Similarity=0.087  Sum_probs=45.1

Q ss_pred             CCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         36 FEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        36 ~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      +++-|..+. ..+.+...+++||+|||||......+......   .+.++++++||..-+.++.+.+...
T Consensus       357 Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~~~i~~l~~~---~~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          357 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ---GNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             CCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHHHHHHHHHTT---CSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHHHHHHHHHHc---CCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            344454443 23345678999999999998654433333321   3458999999999999988877654

>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=97.79  E-value=3.5e-05  Score=69.18  Aligned_cols=72  Identities=15%  Similarity=0.122  Sum_probs=56.1

Q ss_pred             ccCCCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         33 FKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        33 ~~~~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      +..+++.|..+.. ..+..++|.|++|||||.....-+...+........+++++++|+..+.++.+.+..+.
T Consensus         7 ~~~Ln~~Q~~av~-~~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~   78 (647)
T 3lfu_A            7 LDSLNDKQREAVA-APRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLM   78 (647)
T ss_dssp             HTTCCHHHHHHHT-CCSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hhcCCHHHHHHHh-CCCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHh
Confidence            4677888876664 33678999999999999887666666665433344589999999999999999888775

>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=97.73  E-value=0.00015  Score=59.48  Aligned_cols=41  Identities=15%  Similarity=0.053  Sum_probs=24.0

Q ss_pred             ccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        159 VEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       159 ~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      .+++++||+|.+....  .....+..++......+.++++.|.
T Consensus        99 ~~vL~iDEi~~l~~~~--~~~~~l~~~l~~~~~~~~~iii~~~  139 (324)
T 1l8q_A           99 VDLLLLDDVQFLSGKE--RTQIEFFHIFNTLYLLEKQIILASD  139 (324)
T ss_dssp             CSEEEEECGGGGTTCH--HHHHHHHHHHHHHHHTTCEEEEEES
T ss_pred             CCEEEEcCcccccCCh--HHHHHHHHHHHHHHHCCCeEEEEec
Confidence            4699999999886521  2334444554443234556666443

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.63  E-value=0.00023  Score=53.14  Aligned_cols=46  Identities=11%  Similarity=0.018  Sum_probs=28.2

Q ss_pred             CccEEEEcccccc-cccCccchHHHHHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        158 NVEWLIVDESDKL-FEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       158 ~~~~lViDE~h~l-~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                      +.+++|+||++.. .+.   .....+..++......+..+++.|...+++
T Consensus       100 ~~~llilDE~~~~~~~~---~~~~~l~~ll~~~~~~~~~ii~tsn~~~~~  146 (180)
T 3ec2_A          100 NSPVLVLDDLGSERLSD---WQRELISYIITYRYNNLKSTIITTNYSLQR  146 (180)
T ss_dssp             TCSEEEEETCSSSCCCH---HHHHHHHHHHHHHHHTTCEEEEECCCCSCC
T ss_pred             CCCEEEEeCCCCCcCCH---HHHHHHHHHHHHHHHcCCCEEEEcCCChhH
Confidence            4579999999953 222   244455566655533456777766666554

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.52  E-value=0.00011  Score=53.60  Aligned_cols=19  Identities=26%  Similarity=0.539  Sum_probs=16.6

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .+..+.+.||+|+|||...
T Consensus        35 ~g~~~~l~G~~G~GKTtL~   53 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLL   53 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            6788999999999999753

>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=97.42  E-value=0.0011  Score=50.25  Aligned_cols=41  Identities=15%  Similarity=0.100  Sum_probs=27.0

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      ..-.++++||+|.+...    ....+..++... ..+..+++.|..
T Consensus       101 ~~~~vliiDe~~~l~~~----~~~~l~~~l~~~-~~~~~~i~~~~~  141 (226)
T 2chg_A          101 APFKIIFLDEADALTAD----AQAALRRTMEMY-SKSCRFILSCNY  141 (226)
T ss_dssp             CSCEEEEEETGGGSCHH----HHHHHHHHHHHT-TTTEEEEEEESC
T ss_pred             cCceEEEEeChhhcCHH----HHHHHHHHHHhc-CCCCeEEEEeCC
Confidence            45679999999988654    455666666654 455666665443

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=97.39  E-value=0.0015  Score=52.13  Aligned_cols=19  Identities=32%  Similarity=0.242  Sum_probs=15.9

Q ss_pred             CCeEEEECCCCchHhHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~   67 (226)
                      .+++++.||+|+|||....
T Consensus        64 ~~~vLl~G~~GtGKT~la~   82 (272)
T 1d2n_A           64 LVSVLLEGPPHSGKTALAA   82 (272)
T ss_dssp             EEEEEEECSTTSSHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHH
Confidence            3689999999999997643

>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=97.39  E-value=0.002  Score=50.14  Aligned_cols=115  Identities=10%  Similarity=0.078  Sum_probs=62.3

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG  126 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (226)
                      ..|.-.++.|++|+|||...+-.+.....    .+.+++++.|...-  . ..  .++....+..               
T Consensus        10 ~~G~i~litG~mGsGKTT~ll~~~~r~~~----~g~kVli~~~~~d~--r-~~--~~i~srlG~~---------------   65 (223)
T 2b8t_A           10 KIGWIEFITGPMFAGKTAELIRRLHRLEY----ADVKYLVFKPKIDT--R-SI--RNIQSRTGTS---------------   65 (223)
T ss_dssp             -CCEEEEEECSTTSCHHHHHHHHHHHHHH----TTCCEEEEEECCCG--G-GC--SSCCCCCCCS---------------
T ss_pred             CCcEEEEEECCCCCcHHHHHHHHHHHHHh----cCCEEEEEEeccCc--h-HH--HHHHHhcCCC---------------
Confidence            34566889999999999876544444333    24578888776521  0 00  0111111110               


Q ss_pred             CCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        127 PRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       127 ~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                           ...+-+.+...+.+.+..   ...-.+.++||+||++.+...    ....+..+.    +.+.+++++.-
T Consensus        66 -----~~~~~~~~~~~i~~~i~~---~~~~~~~dvViIDEaQ~l~~~----~ve~l~~L~----~~gi~Vil~Gl  124 (223)
T 2b8t_A           66 -----LPSVEVESAPEILNYIMS---NSFNDETKVIGIDEVQFFDDR----ICEVANILA----ENGFVVIISGL  124 (223)
T ss_dssp             -----SCCEEESSTHHHHHHHHS---TTSCTTCCEEEECSGGGSCTH----HHHHHHHHH----HTTCEEEEECC
T ss_pred             -----ccccccCCHHHHHHHHHH---HhhCCCCCEEEEecCccCcHH----HHHHHHHHH----hCCCeEEEEec
Confidence                 012335566667766654   222345799999999965322    333443333    23566666543

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.38  E-value=0.00086  Score=50.56  Aligned_cols=40  Identities=23%  Similarity=0.215  Sum_probs=27.3

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      .|+-.++.||.|+|||...+-.+......    +.+++++.|..
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll~~~~~~~~~----g~~v~~~~~~~   41 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELLSFVEIYKLG----KKKVAVFKPKI   41 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHHHT----TCEEEEEEEC-
T ss_pred             ccEEEEEECCCCCCHHHHHHHHHHHHHHC----CCeEEEEeecc
Confidence            35667899999999998764433333322    44788888884

>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=97.34  E-value=0.00076  Score=57.91  Aligned_cols=47  Identities=15%  Similarity=0.246  Sum_probs=28.9

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                      +.+++++||+|.+.+..  .....+..++..+...+.++++.|...|.+
T Consensus       194 ~~~vL~IDEi~~l~~~~--~~q~~l~~~l~~l~~~~~~iIitt~~~~~~  240 (440)
T 2z4s_A          194 KVDILLIDDVQFLIGKT--GVQTELFHTFNELHDSGKQIVICSDREPQK  240 (440)
T ss_dssp             TCSEEEEECGGGGSSCH--HHHHHHHHHHHHHHTTTCEEEEEESSCGGG
T ss_pred             CCCEEEEeCcccccCCh--HHHHHHHHHHHHHHHCCCeEEEEECCCHHH
Confidence            45699999999987531  244455555555434566777755444443

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.31  E-value=0.00077  Score=57.69  Aligned_cols=87  Identities=17%  Similarity=0.183  Sum_probs=52.7

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCC
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGP  127 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (226)
                      ..+-.++.|++|+|||....-    .+. .    .+.++++||++++..+.+.+...    +..                
T Consensus       160 ~~~v~~I~G~aGsGKTt~I~~----~~~-~----~~~lVlTpT~~aa~~l~~kl~~~----~~~----------------  210 (446)
T 3vkw_A          160 SAKVVLVDGVPGCGKTKEILS----RVN-F----EEDLILVPGRQAAEMIRRRANAS----GII----------------  210 (446)
T ss_dssp             CSEEEEEEECTTSCHHHHHHH----HCC-T----TTCEEEESCHHHHHHHHHHHTTT----SCC----------------
T ss_pred             cccEEEEEcCCCCCHHHHHHH----Hhc-c----CCeEEEeCCHHHHHHHHHHhhhc----Ccc----------------
Confidence            335568999999999986432    222 1    25699999999998887766322    100                


Q ss_pred             CcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccc
Q psy12977        128 RSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKL  170 (226)
Q Consensus       128 ~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l  170 (226)
                         .....-|.|-++++-  +.  ........+.+|+||+-.+
T Consensus       211 ---~~~~~~V~T~dsfL~--~~--~~~~~~~~d~liiDE~sm~  246 (446)
T 3vkw_A          211 ---VATKDNVRTVDSFLM--NY--GKGARCQFKRLFIDEGLML  246 (446)
T ss_dssp             ---CCCTTTEEEHHHHHH--TT--TSSCCCCCSEEEEETGGGS
T ss_pred             ---ccccceEEEeHHhhc--CC--CCCCCCcCCEEEEeCcccC
Confidence               001122666665432  21  2222335789999999844

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=97.23  E-value=0.0034  Score=51.49  Aligned_cols=26  Identities=12%  Similarity=0.118  Sum_probs=19.5

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      .+.++++.||||+|||...-. ++..+
T Consensus        44 ~~~~lli~GpPGTGKT~~v~~-v~~~L   69 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQLVND-VMDEL   69 (318)
T ss_dssp             CCCEEEEECCCSHHHHHHHHH-HHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHH-HHHHH
Confidence            457899999999999986544 33444

>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=97.15  E-value=0.0012  Score=51.11  Aligned_cols=19  Identities=26%  Similarity=0.361  Sum_probs=16.4

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .++.+++.||+|+|||...
T Consensus        51 ~~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4678999999999999754

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=97.13  E-value=0.002  Score=48.91  Aligned_cols=40  Identities=18%  Similarity=0.140  Sum_probs=28.0

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      .|+-.++.||.|+|||...+-.+.....    .+.+++++.|..
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~~a~r~~~----~g~kV~v~k~~~   46 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIRRIRRAKI----AKQKIQVFKPEI   46 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHH----TTCCEEEEEEC-
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHH----CCCEEEEEEecc
Confidence            4566789999999999876544444332    256889998884

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=97.11  E-value=0.0005  Score=62.73  Aligned_cols=74  Identities=15%  Similarity=0.147  Sum_probs=56.8

Q ss_pred             cccCCCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhh
Q psy12977         32 IFKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE  106 (226)
Q Consensus        32 ~~~~~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~  106 (226)
                      .+..+++-|..+... .+.+++|.|+.|||||.....-+...+........++++++.|+..|.++.+.+..+..
T Consensus         8 ~l~~Ln~~Q~~av~~-~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~l~   81 (724)
T 1pjr_A            8 LLAHLNKEQQEAVRT-TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLG   81 (724)
T ss_dssp             HHTTSCHHHHHHHHC-CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHG
T ss_pred             HHhhCCHHHHHHHhC-CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhc
Confidence            456789988776543 35789999999999999876666666653333345899999999999999988887743

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=97.10  E-value=0.018  Score=43.98  Aligned_cols=40  Identities=13%  Similarity=0.044  Sum_probs=24.2

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      ..-.++|+||+|.+...    ....+...+... +....+++.|.
T Consensus       125 ~~~~vlviDe~~~l~~~----~~~~l~~~l~~~-~~~~~~i~~t~  164 (250)
T 1njg_A          125 GRFKVYLIDEVHMLSRH----SFNALLKTLEEP-PEHVKFLLATT  164 (250)
T ss_dssp             SSSEEEEEETGGGSCHH----HHHHHHHHHHSC-CTTEEEEEEES
T ss_pred             CCceEEEEECcccccHH----HHHHHHHHHhcC-CCceEEEEEeC
Confidence            34569999999987543    445555555443 34555555543

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.07  E-value=0.0011  Score=50.28  Aligned_cols=24  Identities=25%  Similarity=0.418  Sum_probs=18.1

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      +++++.||+|+|||.... .+...+
T Consensus        55 ~~~~l~G~~GtGKT~la~-~i~~~~   78 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLA-AIANEL   78 (202)
T ss_dssp             CEEEEECSTTSSHHHHHH-HHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHH
Confidence            789999999999997543 344444

>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=96.96  E-value=0.0011  Score=55.94  Aligned_cols=145  Identities=9%  Similarity=-0.027  Sum_probs=79.5

Q ss_pred             CCCCccccccc-CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCC--e
Q psy12977         35 HFEPHFTITYL-SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGL--R  111 (226)
Q Consensus        35 ~~~~~Q~~~~~-~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~--~  111 (226)
                      .+.|.|..... +...+-+++..+-+.|||......++..+..  ..+..++++.|+++-|..+++.++.+.+....  +
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~--~~g~~v~~vA~t~~qA~~vf~~i~~mi~~~P~ll~  240 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCF--NKDKAVGILAHKGSMSAEVLDRTKQAIELLPDFLQ  240 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHS--SSSCEEEEEESSHHHHHHHHHHHHHHHHHSCTTTS
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHh--CCCCeEEEEeCCHHHHHHHHHHHHHHHHhChHhhh
Confidence            45666644431 1134668999999999998766555543322  23558999999999999998888887664431  1


Q ss_pred             EEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCC
Q psy12977        112 AHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSG  191 (226)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~  191 (226)
                      -...... .  ..  -...+++.|.+.+.+  -+-+.       =.+.+++|+||+|.+.+.  +..+..+...+..  .
T Consensus       241 ~~~~~~~-~--~~--I~f~nGs~i~~lsa~--~~slr-------G~~~~~viiDE~a~~~~~--~el~~al~~~ls~--~  302 (385)
T 2o0j_A          241 PGIVEWN-K--GS--IELDNGSSIGAYASS--PDAVR-------GNSFAMIYIEDCAFIPNF--HDSWLAIQPVISS--G  302 (385)
T ss_dssp             CCEEEEC-S--SE--EEETTSCEEEEEECS--HHHHH-------TSCCSEEEEESGGGSTTH--HHHHHHHHHHHHS--T
T ss_pred             hhhccCC-c--cE--EEeCCCCEEEEEECC--CCCcc-------CCCCCEEEechhhhcCCC--HHHHHHHHHHhhc--C
Confidence            0000000 0  00  011234445444321  11111       124579999999987541  1344444433322  1


Q ss_pred             CCceEEEE
Q psy12977        192 PNLKRGMF  199 (226)
Q Consensus       192 ~~~q~v~~  199 (226)
                      ++.++++.
T Consensus       303 ~~~kiiii  310 (385)
T 2o0j_A          303 RRSKIIIT  310 (385)
T ss_dssp             TCCEEEEE
T ss_pred             CCCcEEEE
Confidence            34555544

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.91  E-value=0.0012  Score=51.46  Aligned_cols=51  Identities=20%  Similarity=0.179  Sum_probs=31.4

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETV  102 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~  102 (226)
                      ..|.-+++.||+|+|||......+......    +.+++++... .-..++.+.+.
T Consensus        21 ~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~----~~~v~~~~~e-~~~~~~~~~~~   71 (247)
T 2dr3_A           21 PERNVVLLSGGPGTGKTIFSQQFLWNGLKM----GEPGIYVALE-EHPVQVRQNMA   71 (247)
T ss_dssp             ETTCEEEEEECTTSSHHHHHHHHHHHHHHT----TCCEEEEESS-SCHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHhc----CCeEEEEEcc-CCHHHHHHHHH
Confidence            456788999999999998654444444432    3356776533 33455555444

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=96.91  E-value=0.0036  Score=51.05  Aligned_cols=41  Identities=17%  Similarity=0.111  Sum_probs=26.7

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      +.+++++||+|.+...   .....+..+++.. +.++++++.+..
T Consensus       105 ~~~vliiDEi~~l~~~---~~~~~L~~~le~~-~~~~~iI~~~n~  145 (324)
T 3u61_B          105 RQKVIVIDEFDRSGLA---ESQRHLRSFMEAY-SSNCSIIITANN  145 (324)
T ss_dssp             CEEEEEEESCCCGGGH---HHHHHHHHHHHHH-GGGCEEEEEESS
T ss_pred             CCeEEEEECCcccCcH---HHHHHHHHHHHhC-CCCcEEEEEeCC
Confidence            6679999999988622   2455666666654 345677764433

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.90  E-value=0.0044  Score=51.55  Aligned_cols=18  Identities=28%  Similarity=0.139  Sum_probs=15.5

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||...
T Consensus        45 ~~~vll~G~~G~GKT~la   62 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVS   62 (384)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            467999999999999764

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=96.88  E-value=0.0059  Score=49.30  Aligned_cols=20  Identities=25%  Similarity=0.252  Sum_probs=16.7

Q ss_pred             CCCeEEEECCCCchHhHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~   67 (226)
                      .+.++++.||+|+|||....
T Consensus        66 ~~~~vll~G~~GtGKT~la~   85 (309)
T 3syl_A           66 PTLHMSFTGNPGTGKTTVAL   85 (309)
T ss_dssp             CCCEEEEEECTTSSHHHHHH
T ss_pred             CCceEEEECCCCCCHHHHHH
Confidence            45689999999999997643

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.88  E-value=0.0042  Score=51.42  Aligned_cols=43  Identities=12%  Similarity=0.066  Sum_probs=24.0

Q ss_pred             ccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        159 VEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       159 ~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      -.++|+||+|.+.+.........+..........+..+++.|.
T Consensus       129 ~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~  171 (386)
T 2qby_A          129 QVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITN  171 (386)
T ss_dssp             CEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEES
T ss_pred             eEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEEC
Confidence            5599999999987542124555555555443233444455443

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=96.82  E-value=0.0045  Score=44.47  Aligned_cols=20  Identities=10%  Similarity=0.288  Sum_probs=17.2

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..+.++++.||+|+|||..+
T Consensus        22 ~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHH
Confidence            45688999999999999764

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.77  E-value=0.005  Score=52.04  Aligned_cols=18  Identities=28%  Similarity=0.490  Sum_probs=15.7

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||+.+
T Consensus       182 prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          182 PKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             CCCEEEESCSSSSHHHHH
T ss_pred             CCceEEeCCCCCCHHHHH
Confidence            378999999999999854

>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=96.77  E-value=0.0095  Score=48.70  Aligned_cols=18  Identities=28%  Similarity=0.444  Sum_probs=15.7

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||...
T Consensus        51 ~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           51 TSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CCEEEEECSSSSCHHHHH
T ss_pred             CCeEEEECCCCCcHHHHH
Confidence            468999999999999754

>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=96.76  E-value=0.0041  Score=55.39  Aligned_cols=72  Identities=14%  Similarity=-0.003  Sum_probs=50.7

Q ss_pred             CCCccccccc-CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCC
Q psy12977         36 FEPHFTITYL-SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG  109 (226)
Q Consensus        36 ~~~~Q~~~~~-~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~  109 (226)
                      ++|.|..... +...+..++..+-|+|||......++..+...  .+.+++++.|+++.+..+++.++.+.+..+
T Consensus       164 l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~--~~~~i~~va~t~~qA~~~~~~i~~~i~~~p  236 (592)
T 3cpe_A          164 LRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN--KDKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (592)
T ss_dssp             CCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTS--SSCEEEEEESSHHHHHHHHHHHHHHHTTSC
T ss_pred             CCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhC--CCCeEEEEECCHHHHHHHHHHHHHHHHhCh
Confidence            4566644431 12346789999999999987654444333322  245899999999999999998888876654

>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=96.75  E-value=0.0012  Score=59.56  Aligned_cols=71  Identities=20%  Similarity=0.134  Sum_probs=52.3

Q ss_pred             CCCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhh
Q psy12977         35 HFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE  106 (226)
Q Consensus        35 ~~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~  106 (226)
                      .+++-|..+... .+.+++|.|+.|||||.....-+...+........++++++.|+..+.++.+.+.....
T Consensus         2 ~L~~~Q~~av~~-~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~   72 (673)
T 1uaa_A            2 RLNPGQQQAVEF-VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   72 (673)
T ss_dssp             CCCHHHHHHHHC-CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHhC-CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHcC
Confidence            356777665532 36789999999999998766555555543222345899999999999999998887754

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.75  E-value=0.0033  Score=51.72  Aligned_cols=40  Identities=13%  Similarity=0.147  Sum_probs=26.5

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      ...+++++||+|.+...    ....+...++.. +....+++.+.
T Consensus       132 ~~~~vliiDE~~~l~~~----~~~~Ll~~le~~-~~~~~~il~~~  171 (353)
T 1sxj_D          132 PPYKIIILDEADSMTAD----AQSALRRTMETY-SGVTRFCLICN  171 (353)
T ss_dssp             CSCEEEEETTGGGSCHH----HHHHHHHHHHHT-TTTEEEEEEES
T ss_pred             CCceEEEEECCCccCHH----HHHHHHHHHHhc-CCCceEEEEeC
Confidence            35579999999988654    445666666665 34556666443

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=96.75  E-value=0.0071  Score=43.31  Aligned_cols=43  Identities=7%  Similarity=0.013  Sum_probs=27.0

Q ss_pred             cEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        160 EWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       160 ~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                      ..+++||+|.+...    ....+...++...+.+..+++.|...+++
T Consensus        77 ~~l~lDei~~l~~~----~q~~Ll~~l~~~~~~~~~iI~~tn~~~~~  119 (143)
T 3co5_A           77 GVLYVGDIAQYSRN----IQTGITFIIGKAERCRVRVIASCSYAAGS  119 (143)
T ss_dssp             SEEEEEECTTCCHH----HHHHHHHHHHHHTTTTCEEEEEEEECTTT
T ss_pred             CeEEEeChHHCCHH----HHHHHHHHHHhCCCCCEEEEEecCCCHHH
Confidence            47899999988654    34445555554434456777766655443

>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=96.74  E-value=0.012  Score=48.46  Aligned_cols=42  Identities=14%  Similarity=0.204  Sum_probs=28.3

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      .+.+++|+||+|.+ +.   .....+..+++.. ++++.+++.|...
T Consensus       133 ~~~~vlilDE~~~L-~~---~~~~~L~~~le~~-~~~~~~Il~t~~~  174 (354)
T 1sxj_E          133 HRYKCVIINEANSL-TK---DAQAALRRTMEKY-SKNIRLIMVCDSM  174 (354)
T ss_dssp             -CCEEEEEECTTSS-CH---HHHHHHHHHHHHS-TTTEEEEEEESCS
T ss_pred             CCCeEEEEeCcccc-CH---HHHHHHHHHHHhh-cCCCEEEEEeCCH
Confidence            46779999999984 43   3566777777776 4456666655443

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=96.72  E-value=0.006  Score=49.41  Aligned_cols=39  Identities=18%  Similarity=0.222  Sum_probs=26.3

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      .+-.++|+||+|.+...    ....+...++.. +..+.+++.+
T Consensus       109 ~~~~vliiDe~~~l~~~----~~~~L~~~le~~-~~~~~~i~~~  147 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQD----AQQALRRTMEMF-SSNVRFILSC  147 (327)
T ss_dssp             CSCEEEEEETGGGSCHH----HHHHHHHHHHHT-TTTEEEEEEE
T ss_pred             CCCeEEEEeCCCcCCHH----HHHHHHHHHHhc-CCCCeEEEEe
Confidence            35679999999988654    455666666654 4556666644

>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=96.70  E-value=0.018  Score=45.38  Aligned_cols=20  Identities=25%  Similarity=0.512  Sum_probs=16.7

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..+.++++.||+|+|||...
T Consensus        27 ~~~~~vll~G~~GtGKt~la   46 (265)
T 2bjv_A           27 PLDKPVLIIGERGTGKELIA   46 (265)
T ss_dssp             TSCSCEEEECCTTSCHHHHH
T ss_pred             CCCCCEEEECCCCCcHHHHH
Confidence            34578999999999999754

>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=96.70  E-value=0.013  Score=48.20  Aligned_cols=41  Identities=12%  Similarity=-0.001  Sum_probs=25.2

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      ..+.+++|+||+|.+...    ....+.+.++.- ++++-+++.|.
T Consensus       106 ~~~~kvviIdead~l~~~----a~naLLk~lEep-~~~~~~Il~t~  146 (334)
T 1a5t_A          106 LGGAKVVWVTDAALLTDA----AANALLKTLEEP-PAETWFFLATR  146 (334)
T ss_dssp             TSSCEEEEESCGGGBCHH----HHHHHHHHHTSC-CTTEEEEEEES
T ss_pred             cCCcEEEEECchhhcCHH----HHHHHHHHhcCC-CCCeEEEEEeC
Confidence            356789999999998654    334444555432 34455555443

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=96.69  E-value=0.058  Score=39.43  Aligned_cols=19  Identities=26%  Similarity=0.218  Sum_probs=16.0

Q ss_pred             CCeEEEECCCCchHhHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~   67 (226)
                      .+++++.||+|+|||....
T Consensus        43 ~~~vll~G~~G~GKT~la~   61 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVE   61 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHH
Confidence            5689999999999997543

>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=96.68  E-value=0.021  Score=48.84  Aligned_cols=135  Identities=16%  Similarity=0.184  Sum_probs=72.6

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEc-ccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVC-PTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGP  127 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~-Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (226)
                      +..+++.|++|+|||.....-+.....    .+.+++++. ++..-+  ..+.+..+....+..+......         
T Consensus        97 ~~vI~lvG~~GsGKTTt~~kLA~~l~~----~G~kVllv~~D~~r~~--a~eqL~~~~~~~gv~~~~~~~~---------  161 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGKLAYFYKK----RGYKVGLVAADVYRPA--AYDQLLQLGNQIGVQVYGEPNN---------  161 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHHHHHHHHH----TTCCEEEEEECCSCHH--HHHHHHHHHHTTTCCEECCTTC---------
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH----cCCeEEEEecCccchh--HHHHHHHHHHhcCCceeecccc---------
Confidence            456889999999999765433322222    133555544 332211  1234444544444432211110         


Q ss_pred             CcCCCCCEEEECchHHH-HhHhcCCCCCCCCCccEEEEccccccc--ccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        128 RSAQKFDVLITTPNKLV-YLLQMDPPALNLANVEWLIVDESDKLF--EAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       128 ~~~~~~~IiV~Tp~~l~-~~~~~~~~~~~~~~~~~lViDE~h~l~--~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                                ..|..+. ..+..    ....+.+++|+|++-+..  ..  ......+..+.+.. .+..-++.++|+..
T Consensus       162 ----------~dp~~i~~~al~~----a~~~~~DvvIIDTaGr~~~~~d--~~lm~el~~i~~~~-~pd~vlLVlDa~~g  224 (433)
T 3kl4_A          162 ----------QNPIEIAKKGVDI----FVKNKMDIIIVDTAGRHGYGEE--TKLLEEMKEMYDVL-KPDDVILVIDASIG  224 (433)
T ss_dssp             ----------SCHHHHHHHHHHH----TTTTTCSEEEEEECCCSSSCCT--THHHHHHHHHHHHH-CCSEEEEEEEGGGG
T ss_pred             ----------CCHHHHHHHHHHH----HHhcCCCEEEEECCCCccccCC--HHHHHHHHHHHHhh-CCcceEEEEeCccc
Confidence                      1233332 22222    112467899999997654  22  15777788877777 45566677888876


Q ss_pred             hhHHHHHHHhc
Q psy12977        205 EDVAKWCRRKL  215 (226)
Q Consensus       205 ~~~~~~~~~~~  215 (226)
                      .+..+.++.+-
T Consensus       225 q~a~~~a~~f~  235 (433)
T 3kl4_A          225 QKAYDLASRFH  235 (433)
T ss_dssp             GGGHHHHHHHH
T ss_pred             hHHHHHHHHHh
Confidence            66555555443

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=96.67  E-value=0.0079  Score=46.35  Aligned_cols=41  Identities=17%  Similarity=0.208  Sum_probs=27.9

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE   92 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~   92 (226)
                      .|+-.++.|+-|+|||...+-.+.....    .+.+++++.|.+.
T Consensus        27 ~G~l~vitG~MgsGKTT~lL~~a~r~~~----~g~kVli~k~~~d   67 (214)
T 2j9r_A           27 NGWIEVICGSMFSGKSEELIRRVRRTQF----AKQHAIVFKPCID   67 (214)
T ss_dssp             SCEEEEEECSTTSCHHHHHHHHHHHHHH----TTCCEEEEECC--
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHH----CCCEEEEEEeccC
Confidence            3455678999999999876555444433    2568999998864

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.66  E-value=0.00071  Score=55.30  Aligned_cols=19  Identities=16%  Similarity=0.345  Sum_probs=16.4

Q ss_pred             CCeEEEECCCCchHhHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~   67 (226)
                      ++++++.||+|+|||....
T Consensus       152 ~~~lll~G~~GtGKT~La~  170 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLA  170 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            5789999999999997543

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=96.65  E-value=0.0052  Score=50.94  Aligned_cols=19  Identities=32%  Similarity=0.310  Sum_probs=16.2

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .++++++.||+|+|||...
T Consensus        43 ~~~~vll~G~~G~GKT~l~   61 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAVA   61 (387)
T ss_dssp             CCCCEEECBCTTSSHHHHH
T ss_pred             CCCcEEEECCCCCCHHHHH
Confidence            4578999999999999764

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=96.65  E-value=0.0049  Score=51.26  Aligned_cols=35  Identities=17%  Similarity=0.196  Sum_probs=22.0

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEc
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVC   88 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~   88 (226)
                      .+++.||+|+|||...- .+...+....  +..++++.
T Consensus        46 ~~li~G~~G~GKTtl~~-~l~~~~~~~~--~~~~~~i~   80 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLR-KLWELYKDKT--TARFVYIN   80 (389)
T ss_dssp             EEEEECCTTSSHHHHHH-HHHHHHTTSC--CCEEEEEE
T ss_pred             eEEEECCCCCCHHHHHH-HHHHHHhhhc--CeeEEEEe
Confidence            79999999999998643 3444443211  23455553

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=96.63  E-value=0.019  Score=47.40  Aligned_cols=40  Identities=13%  Similarity=0.021  Sum_probs=24.8

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ..+-.++|+||+|.+...    ....+...++.. +..+.+++.|
T Consensus       117 ~~~~~vliiDe~~~l~~~----~~~~Ll~~le~~-~~~~~~Il~~  156 (373)
T 1jr3_A          117 RGRFKVYLIDEVHMLSRH----SFNALLKTLEEP-PEHVKFLLAT  156 (373)
T ss_dssp             SSSSEEEEEECGGGSCHH----HHHHHHHHHHSC-CSSEEEEEEE
T ss_pred             cCCeEEEEEECcchhcHH----HHHHHHHHHhcC-CCceEEEEEe
Confidence            345679999999988654    445555555543 3445555543

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.58  E-value=0.012  Score=44.64  Aligned_cols=39  Identities=13%  Similarity=0.197  Sum_probs=28.4

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEccc
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPT   90 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt   90 (226)
                      .++=.++.||.|+|||...+-.+-+....    +.+++++.|.
T Consensus        19 ~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~----~~kvl~~kp~   57 (195)
T 1w4r_A           19 RGQIQVILGPMFSGKSTELMRRVRRFQIA----QYKCLVIKYA   57 (195)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHHHT----TCCEEEEEET
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHc----CCeEEEEccc
Confidence            46667899999999997655555444432    4588999887

>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=96.54  E-value=0.0093  Score=49.58  Aligned_cols=18  Identities=28%  Similarity=0.444  Sum_probs=15.6

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||...
T Consensus        84 ~~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           84 TSGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             CCCEEEECSTTSCHHHHH
T ss_pred             CceEEEECCCCCcHHHHH
Confidence            467999999999999764

>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=96.52  E-value=0.0039  Score=60.16  Aligned_cols=70  Identities=21%  Similarity=0.207  Sum_probs=53.7

Q ss_pred             CCCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCC--CCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         35 HFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK--NLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        35 ~~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~--~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      .+|+-|..+... .+++++|.|+.|||||...+--++..+....  ....+++++++|++.+..+.+.+....
T Consensus        10 ~~t~eQ~~~i~~-~~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~l   81 (1232)
T 3u4q_A           10 TWTDDQWNAIVS-TGQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEAL   81 (1232)
T ss_dssp             CCCHHHHHHHHC-CSSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhC-CCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHHH
Confidence            467777666543 3789999999999999987766777765422  234589999999999999998887754

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=96.50  E-value=0.03  Score=44.53  Aligned_cols=20  Identities=30%  Similarity=0.426  Sum_probs=16.7

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ...+.+++.||+|+|||...
T Consensus        49 ~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           49 EPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             CCCSEEEEESSSSSSHHHHH
T ss_pred             CCCCeEEEECCCCCcHHHHH
Confidence            34578999999999999754

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=96.49  E-value=0.08  Score=38.68  Aligned_cols=18  Identities=28%  Similarity=0.276  Sum_probs=15.6

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+++++.||+|+|||...
T Consensus        43 ~~~~ll~G~~G~GKT~l~   60 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIV   60 (195)
T ss_dssp             SCEEEEECCTTSCHHHHH
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            467999999999999764

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=96.48  E-value=0.0083  Score=49.16  Aligned_cols=18  Identities=33%  Similarity=0.475  Sum_probs=15.7

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||...
T Consensus        45 ~~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A           45 WRGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             CSEEEEESSSSSCHHHHH
T ss_pred             CceEEEECCCCccHHHHH
Confidence            478999999999999754

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=96.46  E-value=0.03  Score=49.42  Aligned_cols=60  Identities=10%  Similarity=0.140  Sum_probs=38.3

Q ss_pred             cEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc-hhHHHHHHHhcCCCe
Q psy12977        160 EWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT-EDVAKWCRRKLKRRV  219 (226)
Q Consensus       160 ~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~-~~~~~~~~~~~~~p~  219 (226)
                      -++|+||+|.+...........+.++.+.-......+++.|..+. +.+...++..+...+
T Consensus       345 ivvVIDE~~~L~~~~~~~~~~~L~~Iar~GRa~GIhLIlaTQRPs~d~I~~~Iran~~~RI  405 (574)
T 2iut_A          345 IVVVVDEFADMMMIVGKKVEELIARIAQKARAAGIHLILATQRPSVDVITGLIKANIPTRI  405 (574)
T ss_dssp             EEEEESCCTTHHHHTCHHHHHHHHHHHHHCTTTTEEEEEEESCCCTTTSCHHHHHTCCEEE
T ss_pred             EEEEEeCHHHHhhhhhHHHHHHHHHHHHHHhhCCeEEEEEecCcccccccHHHHhhhccEE
Confidence            389999999887543334666777887777666777777666554 233444444444333

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=96.43  E-value=0.022  Score=43.90  Aligned_cols=41  Identities=15%  Similarity=0.075  Sum_probs=27.1

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE   92 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~   92 (226)
                      .|.-.++.||-|+|||...+-.+ .+...   .+.+++++.|...
T Consensus        27 ~G~I~vitG~M~sGKTT~Llr~~-~r~~~---~g~kvli~kp~~D   67 (219)
T 3e2i_A           27 SGWIECITGSMFSGKSEELIRRL-RRGIY---AKQKVVVFKPAID   67 (219)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHH-HHHHH---TTCCEEEEEEC--
T ss_pred             CceEEEEECCCCCCHHHHHHHHH-HHHHH---cCCceEEEEeccC
Confidence            45667899999999997654444 33322   2457899988764

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=96.40  E-value=0.0096  Score=50.01  Aligned_cols=19  Identities=32%  Similarity=0.501  Sum_probs=16.3

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      ..+++++.||+|+|||...
T Consensus       147 ~~~~vLL~GppGtGKT~la  165 (389)
T 3vfd_A          147 PARGLLLFGPPGNGKTMLA  165 (389)
T ss_dssp             CCSEEEEESSTTSCHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3578999999999999754

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=96.29  E-value=0.035  Score=45.13  Aligned_cols=44  Identities=7%  Similarity=0.049  Sum_probs=28.4

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                      ..+.+++|+||+|.+...    ....+.+.++.- ++.+.+++.+ +-|.
T Consensus        80 ~~~~kvviIdead~lt~~----a~naLLk~LEep-~~~t~fIl~t-~~~~  123 (305)
T 2gno_A           80 LYTRKYVIVHDCERMTQQ----AANAFLKALEEP-PEYAVIVLNT-RRWH  123 (305)
T ss_dssp             SSSSEEEEETTGGGBCHH----HHHHTHHHHHSC-CTTEEEEEEE-SCGG
T ss_pred             cCCceEEEeccHHHhCHH----HHHHHHHHHhCC-CCCeEEEEEE-CChH
Confidence            346789999999998765    345566666553 4556666654 4343

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=96.28  E-value=0.028  Score=42.94  Aligned_cols=22  Identities=36%  Similarity=0.353  Sum_probs=17.5

Q ss_pred             CCCCeEEEECCCCchHhHHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~   68 (226)
                      ..|.-+.+.||+|+|||.....
T Consensus        21 ~~G~~~~i~G~~GsGKTtl~~~   42 (235)
T 2w0m_A           21 PQGFFIALTGEPGTGKTIFSLH   42 (235)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHH
T ss_pred             cCCCEEEEEcCCCCCHHHHHHH
Confidence            4567889999999999975433

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.26  E-value=0.013  Score=50.38  Aligned_cols=18  Identities=33%  Similarity=0.556  Sum_probs=15.7

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||+.+
T Consensus       243 prGILLyGPPGTGKTlLA  260 (467)
T 4b4t_H          243 PKGILLYGPPGTGKTLCA  260 (467)
T ss_dssp             CSEEEECSCTTSSHHHHH
T ss_pred             CCceEeeCCCCCcHHHHH
Confidence            388999999999999754

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=96.26  E-value=0.019  Score=46.95  Aligned_cols=17  Identities=35%  Similarity=0.536  Sum_probs=15.1

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      .++++.||+|+|||...
T Consensus        56 ~~vll~G~~GtGKT~la   72 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLA   72 (338)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECcCCCCHHHHH
Confidence            57999999999999754

>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=96.25  E-value=0.11  Score=44.51  Aligned_cols=134  Identities=16%  Similarity=0.168  Sum_probs=66.9

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEc-c-cHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVC-P-TRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG  126 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~-P-t~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (226)
                      ..-+++.|++|+|||....--+ ..+..   .+.+++++. . .+.-+   .++++.+....+..+......        
T Consensus       100 p~vIlivG~~G~GKTTt~~kLA-~~l~~---~G~kVllv~~D~~R~aa---~eqL~~~~~~~gvpv~~~~~~--------  164 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAKLA-RYFQK---RGYKVGVVCSDTWRPGA---YHQLRQLLDRYHIEVFGNPQE--------  164 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHH-HHHHT---TTCCEEEEECCCSSTHH---HHHHHHHHGGGTCEEECCTTC--------
T ss_pred             CeEEEEECcCCCCHHHHHHHHH-HHHHH---CCCeEEEEeCCCcchhH---HHHHHHHHHhcCCcEEecCCC--------
Confidence            3567899999999998654333 33332   133555544 3 33322   344555555555543221111        


Q ss_pred             CCcCCCCCEEEECchHHH-HhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCch
Q psy12977        127 PRSAQKFDVLITTPNKLV-YLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTE  205 (226)
Q Consensus       127 ~~~~~~~~IiV~Tp~~l~-~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~  205 (226)
                                 ..|..+. +.+..    ......+++|+|.+=.....  ......+..+.... .+..-++.+.|+-..
T Consensus       165 -----------~dp~~i~~~al~~----a~~~~~DvVIIDTaGrl~~d--~~lm~el~~i~~~~-~pd~vlLVvDA~~gq  226 (443)
T 3dm5_A          165 -----------KDAIKLAKEGVDY----FKSKGVDIIIVDTAGRHKED--KALIEEMKQISNVI-HPHEVILVIDGTIGQ  226 (443)
T ss_dssp             -----------CCHHHHHHHHHHH----HHHTTCSEEEEECCCCSSCC--HHHHHHHHHHHHHH-CCSEEEEEEEGGGGG
T ss_pred             -----------CCHHHHHHHHHHH----HHhCCCCEEEEECCCcccch--HHHHHHHHHHHHhh-cCceEEEEEeCCCch
Confidence                       1232222 11111    00124678888887543221  13455555555555 345556667777665


Q ss_pred             hHHHHHHHhc
Q psy12977        206 DVAKWCRRKL  215 (226)
Q Consensus       206 ~~~~~~~~~~  215 (226)
                      +..+.++.+.
T Consensus       227 ~a~~~a~~f~  236 (443)
T 3dm5_A          227 QAYNQALAFK  236 (443)
T ss_dssp             GHHHHHHHHH
T ss_pred             hHHHHHHHHH
Confidence            5555554443

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.21  E-value=0.015  Score=47.73  Aligned_cols=39  Identities=18%  Similarity=0.290  Sum_probs=26.7

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ...+++|+||+|.+...    ....+..+++.. +..+.+++.+
T Consensus       109 ~~~~viiiDe~~~l~~~----~~~~L~~~le~~-~~~~~~il~~  147 (340)
T 1sxj_C          109 KGFKLIILDEADAMTNA----AQNALRRVIERY-TKNTRFCVLA  147 (340)
T ss_dssp             CSCEEEEETTGGGSCHH----HHHHHHHHHHHT-TTTEEEEEEE
T ss_pred             CCceEEEEeCCCCCCHH----HHHHHHHHHhcC-CCCeEEEEEe
Confidence            35789999999988654    455666777665 4556666543

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=96.00  E-value=0.024  Score=44.21  Aligned_cols=41  Identities=12%  Similarity=0.217  Sum_probs=29.3

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE   92 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~   92 (226)
                      .|+-.++.|+-|+|||...+-.+.....    .+.+++++-|.+.
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~~----~g~kvli~kp~~D   58 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQI----AQYKCLVIKYAKD   58 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHT----TTCCEEEEEETTC
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHH----CCCeEEEEeecCC
Confidence            4666788999999999876555444433    3568899988764

>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=95.82  E-value=0.017  Score=52.11  Aligned_cols=65  Identities=25%  Similarity=0.199  Sum_probs=46.4

Q ss_pred             CCCCcccccc-----cCCCC-CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhh
Q psy12977         35 HFEPHFTITY-----LSPLG-RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE  106 (226)
Q Consensus        35 ~~~~~Q~~~~-----~~~~~-~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~  106 (226)
                      .|++.|..+.     .+..| +..++.+.||||||+.+.-. +....      ..++|++|+..+|.|+++.++.+.+
T Consensus         8 ~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~~-~~~~~------~~~lvv~~~~~~A~ql~~el~~~~~   78 (664)
T 1c4o_A            8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKV-IEALG------RPALVLAPNKILAAQLAAEFRELFP   78 (664)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHH-HHHHT------CCEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHHH-HHHhC------CCEEEEecCHHHHHHHHHHHHHHCC
Confidence            6667774442     12233 35678999999999876433 33332      2489999999999999999999964

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=95.81  E-value=0.018  Score=46.43  Aligned_cols=39  Identities=13%  Similarity=0.157  Sum_probs=25.4

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      +-.++|+||+|.+...    ....+...++.. ++.+.+++.|.
T Consensus       107 ~~~viiiDe~~~l~~~----~~~~L~~~le~~-~~~~~~il~~~  145 (323)
T 1sxj_B          107 KHKIVILDEADSMTAG----AQQALRRTMELY-SNSTRFAFACN  145 (323)
T ss_dssp             CCEEEEEESGGGSCHH----HHHTTHHHHHHT-TTTEEEEEEES
T ss_pred             CceEEEEECcccCCHH----HHHHHHHHHhcc-CCCceEEEEeC
Confidence            3679999999988654    344455555554 45566666543

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=95.72  E-value=0.015  Score=50.78  Aligned_cols=43  Identities=21%  Similarity=0.155  Sum_probs=28.0

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      ..-.++++||+|.+.... ++....+..+++.   .+..+++.+++.
T Consensus       147 ~~~~vliIDEid~l~~~~-~~~l~~L~~~l~~---~~~~iIli~~~~  189 (516)
T 1sxj_A          147 GKHFVIIMDEVDGMSGGD-RGGVGQLAQFCRK---TSTPLILICNER  189 (516)
T ss_dssp             TTSEEEEECSGGGCCTTS-TTHHHHHHHHHHH---CSSCEEEEESCT
T ss_pred             CCCeEEEEECCCccchhh-HHHHHHHHHHHHh---cCCCEEEEEcCC
Confidence            345699999999987642 2344555555554   355677777764

>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=95.65  E-value=0.023  Score=43.09  Aligned_cols=138  Identities=14%  Similarity=0.067  Sum_probs=73.3

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH-HHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE-LAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG  126 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~-L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (226)
                      ....+++..++|.|||.+++-.++..+..    |.+++++.-.+. ....-.+.+..+    ++.+.....+      + 
T Consensus        27 ~~g~i~v~tG~GkGKTTaA~GlalRA~g~----G~rV~~vQF~Kg~~~~gE~~~l~~L----~v~~~~~g~g------f-   91 (196)
T 1g5t_A           27 ERGIIIVFTGNGKGKTTAAFGTAARAVGH----GKNVGVVQFIKGTWPNGERNLLEPH----GVEFQVMATG------F-   91 (196)
T ss_dssp             CCCCEEEEESSSSCHHHHHHHHHHHHHHT----TCCEEEEESSCCSSCCHHHHHHGGG----TCEEEECCTT------C-
T ss_pred             cCceEEEECCCCCCHHHHHHHHHHHHHHC----CCeEEEEEeeCCCCCccHHHHHHhC----CcEEEEcccc------c-
Confidence            34679999999999999887777777753    557888743331 000001122222    3332222210      0 


Q ss_pred             CCcCCCCCEEEECch------HHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        127 PRSAQKFDVLITTPN------KLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       127 ~~~~~~~~IiV~Tp~------~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                               ...++.      .....+......+.-.++++||+||+-.....+.- -...+...+... ++..-+|+.+
T Consensus        92 ---------~~~~~~~~~~~~~a~~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l-~~~ev~~~l~~R-p~~~~vIlTG  160 (196)
T 1g5t_A           92 ---------TWETQNREADTAACMAVWQHGKRMLADPLLDMVVLDELTYMVAYDYL-PLEEVISALNAR-PGHQTVIITG  160 (196)
T ss_dssp             ---------CCCGGGHHHHHHHHHHHHHHHHHHTTCTTCSEEEEETHHHHHHTTSS-CHHHHHHHHHTS-CTTCEEEEEC
T ss_pred             ---------ccCCCCcHHHHHHHHHHHHHHHHHHhcCCCCEEEEeCCCccccCCCC-CHHHHHHHHHhC-cCCCEEEEEC
Confidence                     011111      11111111112233467899999999755444322 333455555554 4566777777


Q ss_pred             eeCchhHHHHH
Q psy12977        201 ATHTEDVAKWC  211 (226)
Q Consensus       201 AT~~~~~~~~~  211 (226)
                      --.|+++.+.+
T Consensus       161 r~ap~~l~e~A  171 (196)
T 1g5t_A          161 RGCHRDILDLA  171 (196)
T ss_dssp             SSCCHHHHHHC
T ss_pred             CCCcHHHHHhC
Confidence            77788777665

>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=95.64  E-value=0.031  Score=47.84  Aligned_cols=18  Identities=33%  Similarity=0.475  Sum_probs=15.7

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||...
T Consensus       167 ~~~vLL~GppGtGKT~lA  184 (444)
T 2zan_A          167 WRGILLFGPPGTGKSYLA  184 (444)
T ss_dssp             CSEEEEECSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            478999999999999754

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=95.59  E-value=0.022  Score=48.93  Aligned_cols=18  Identities=28%  Similarity=0.464  Sum_probs=15.3

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      .+++++||+|+|||...-
T Consensus        51 ~~vLL~GppGtGKTtlAr   68 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLAE   68 (447)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHH
Confidence            479999999999997543

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=95.58  E-value=0.019  Score=46.29  Aligned_cols=16  Identities=38%  Similarity=0.690  Sum_probs=14.1

Q ss_pred             eEEEECCCCchHhHHH
Q psy12977         51 QIFACAPTGSGKTAAF   66 (226)
Q Consensus        51 ~~li~apTGsGKT~~~   66 (226)
                      ++++.||+|+|||...
T Consensus        40 ~~ll~G~~G~GKt~la   55 (319)
T 2chq_A           40 HLLFSGPPGTGKTATA   55 (319)
T ss_dssp             CEEEESSSSSSHHHHH
T ss_pred             eEEEECcCCcCHHHHH
Confidence            5999999999999754

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=95.24  E-value=0.19  Score=39.81  Aligned_cols=25  Identities=24%  Similarity=0.187  Sum_probs=19.3

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHH
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPI   70 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~   70 (226)
                      +..|.-+++.||+|+|||......+
T Consensus        27 l~~G~i~~i~G~~GsGKTtl~~~l~   51 (279)
T 1nlf_A           27 MVAGTVGALVSPGGAGKSMLALQLA   51 (279)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHH
T ss_pred             ccCCCEEEEEcCCCCCHHHHHHHHH
Confidence            3567889999999999997654433

>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency decline, ATP-binding, DNA DAMA repair, DNA-binding, helicase, hydrolase; 1.95A {Escherichia coli} PDB: 2b2n_A* 4dfc_A

Probab=95.14  E-value=0.096  Score=45.36  Aligned_cols=53  Identities=17%  Similarity=0.170  Sum_probs=40.7

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE  106 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~  106 (226)
                      ..+....+.+-+|+||++...- +....      +..+++++|+...|.|+++.++.+.+
T Consensus        12 ~~~~~~~l~g~~gs~ka~~~a~-l~~~~------~~p~lvv~~~~~~A~~l~~~l~~~~~   64 (483)
T 3hjh_A           12 KAGEQRLLGELTGAACATLVAE-IAERH------AGPVVLIAPDMQNALRLHDEISQFTD   64 (483)
T ss_dssp             STTCEEEEECCCTTHHHHHHHH-HHHHS------SSCEEEEESSHHHHHHHHHHHHHTCS
T ss_pred             CCCCeEEEeCCCchHHHHHHHH-HHHHh------CCCEEEEeCCHHHHHHHHHHHHhhCC
Confidence            4567789999999999986432 22222      22589999999999999999998864

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=95.14  E-value=0.19  Score=43.07  Aligned_cols=40  Identities=20%  Similarity=0.043  Sum_probs=26.0

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEc
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVC   88 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~   88 (226)
                      +..|.-+++.|++|+|||...+..+.......   +..++|+.
T Consensus       200 l~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~---g~~Vl~~s  239 (454)
T 2r6a_A          200 FQRSDLIIVAARPSVGKTAFALNIAQNVATKT---NENVAIFS  239 (454)
T ss_dssp             BCTTCEEEEECCTTSCHHHHHHHHHHHHHHHS---SCCEEEEE
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHHHhC---CCcEEEEE
Confidence            34567789999999999976554444443211   33566665

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=95.06  E-value=0.068  Score=48.19  Aligned_cols=50  Identities=22%  Similarity=0.302  Sum_probs=39.1

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhh
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE  106 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~  106 (226)
                      +...+.+.||+|||+...- ++....      ..++|++|+..+|.|.++.++.+..
T Consensus        33 ~~~~l~g~~gs~k~~~~a~-~~~~~~------~~~lvv~~~~~~A~~l~~el~~~~~   82 (661)
T 2d7d_A           33 KHQTLLGATGTGKTFTVSN-LIKEVN------KPTLVIAHNKTLAGQLYSEFKEFFP   82 (661)
T ss_dssp             SEEEEEECTTSCHHHHHHH-HHHHHC------CCEEEECSSHHHHHHHHHHHHHHCT
T ss_pred             CcEEEECcCCcHHHHHHHH-HHHHhC------CCEEEEECCHHHHHHHHHHHHHHcC
Confidence            3567889999999986543 333332      1489999999999999999999965

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=94.95  E-value=0.46  Score=38.52  Aligned_cols=51  Identities=14%  Similarity=-0.018  Sum_probs=31.2

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETV  102 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~  102 (226)
                      ..|.-+++.|+||+|||...+-.+.+...+    +..++|++-- .-..|+...+.
T Consensus        66 ~~G~l~li~G~pG~GKTtl~l~ia~~~a~~----g~~vl~~slE-~s~~~l~~R~~  116 (315)
T 3bh0_A           66 KRRNFVLIAARPSMGKTAFALKQAKNMSDN----DDVVNLHSLE-MGKKENIKRLI  116 (315)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHHHHHTT----TCEEEEEESS-SCHHHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHc----CCeEEEEECC-CCHHHHHHHHH
Confidence            446778999999999997655444454442    2467776532 33344444433

>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=94.87  E-value=0.028  Score=46.96  Aligned_cols=39  Identities=21%  Similarity=0.252  Sum_probs=25.8

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEccc
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPT   90 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt   90 (226)
                      .|+-+++.+|+|+|||...+..+......    +.+++|+..-
T Consensus        73 ~G~li~I~G~pGsGKTtlal~la~~~~~~----g~~vlyi~~E  111 (366)
T 1xp8_A           73 RGRITEIYGPESGGKTTLALAIVAQAQKA----GGTCAFIDAE  111 (366)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT----TCCEEEEESS
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHHHHC----CCeEEEEECC
Confidence            35678999999999997655444444332    3367777644

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=94.80  E-value=0.072  Score=41.00  Aligned_cols=43  Identities=12%  Similarity=-0.077  Sum_probs=25.9

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCC--CCCCceEEEEcc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGP--KNLGFRAVIVCP   89 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~--~~~~~~~iil~P   89 (226)
                      ..|.-+.+.||+|+|||.....-+...+...  ...+..++++.-
T Consensus        22 ~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~   66 (243)
T 1n0w_A           22 ETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDT   66 (243)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEES
T ss_pred             cCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEEC
Confidence            4567889999999999986544443323211  001335666653

>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=94.80  E-value=0.17  Score=43.87  Aligned_cols=20  Identities=35%  Similarity=0.464  Sum_probs=16.7

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ...+.+++.||+|+|||...
T Consensus       236 ~~~~~vLL~GppGtGKT~lA  255 (489)
T 3hu3_A          236 KPPRGILLYGPPGTGKTLIA  255 (489)
T ss_dssp             CCCCEEEEECSTTSSHHHHH
T ss_pred             CCCCcEEEECcCCCCHHHHH
Confidence            34578999999999999854

>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=94.78  E-value=0.38  Score=35.22  Aligned_cols=119  Identities=10%  Similarity=0.013  Sum_probs=70.4

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.++++.-+..+.+.+...    +..+..+.++.....+.   .....+..+|+|+|..        ....+++.
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~--------~~~Gldi~   98 (172)
T 1t5i_A           31 FNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL--------FGRGMDIE   98 (172)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC--------CSTTCCGG
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhc----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCc--------hhcCcchh
Confidence            348999999999999999888765    66777777664333221   1122467789999953        22678888


Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcC
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLK  216 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~  216 (226)
                      +++++|.-+...-..    .+.+.+-+.-+.- .+..-+++++..-.....+.+.+.+.
T Consensus        99 ~~~~Vi~~d~p~~~~----~~~qr~GR~~R~g-~~g~~~~~~~~~~~~~~~~~l~~~~~  152 (172)
T 1t5i_A           99 RVNIAFNYDMPEDSD----TYLHRVARAGRFG-TKGLAITFVSDENDAKILNDVQDRFE  152 (172)
T ss_dssp             GCSEEEESSCCSSHH----HHHHHHHHHTGGG-CCCEEEEEECSHHHHHHHHHHHHHHC
T ss_pred             hCCEEEEECCCCCHH----HHHHHhcccccCC-CCcEEEEEEcChhHHHHHHHHHHHHh
Confidence            999988755442111    3455555544433 23334444433322233344444443

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=94.67  E-value=0.031  Score=56.06  Aligned_cols=42  Identities=29%  Similarity=0.364  Sum_probs=30.3

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTREL   93 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L   93 (226)
                      .++++++.+|+|+|||......+.+...+    +.+++++.....+
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~~~----G~~v~Fi~~e~~~ 1467 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQRE----GKTCAFIDAEHAL 1467 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTT----TCCEEEECTTSCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc----CCcEEEEEccccc
Confidence            47899999999999998765555554442    5578888765443

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=94.64  E-value=0.0025  Score=49.68  Aligned_cols=51  Identities=25%  Similarity=0.234  Sum_probs=29.0

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVR  103 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~  103 (226)
                      |.-+++.|+||+|||...+-.+.+...+.   +..++|+.- .+-.+++.+.+..
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~~---~~~v~~~s~-E~~~~~~~~~~~~   80 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEEY---GEPGVFVTL-EERARDLRREMAS   80 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHHH---CCCEEEEES-SSCHHHHHHHHHT
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhc---CCCceeecc-cCCHHHHHHHHHH
Confidence            56789999999999975544344433221   224566543 2334454444433

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=94.42  E-value=0.52  Score=41.88  Aligned_cols=21  Identities=19%  Similarity=0.297  Sum_probs=17.7

Q ss_pred             CCCCCeEEEECCCCchHhHHH
Q psy12977         46 SPLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~   66 (226)
                      +..++.+++.||+|+|||..+
T Consensus        57 i~~g~~vll~Gp~GtGKTtla   77 (604)
T 3k1j_A           57 ANQKRHVLLIGEPGTGKSMLG   77 (604)
T ss_dssp             HHTTCCEEEECCTTSSHHHHH
T ss_pred             ccCCCEEEEEeCCCCCHHHHH
Confidence            345789999999999999754

>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=94.42  E-value=0.02  Score=47.56  Aligned_cols=39  Identities=28%  Similarity=0.303  Sum_probs=26.1

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEccc
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPT   90 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt   90 (226)
                      .|+-+++.||+|+|||...+..+......    +.+++|+...
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~~~----g~~vlyi~~E   98 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQAA----GGIAAFIDAE   98 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT----TCCEEEEESS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC----CCeEEEEECC
Confidence            35678999999999998655544444432    3467777643

>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=94.20  E-value=0.042  Score=45.91  Aligned_cols=20  Identities=20%  Similarity=0.145  Sum_probs=15.8

Q ss_pred             CCCeEEE--ECCCCchHhHHHH
Q psy12977         48 LGRQIFA--CAPTGSGKTAAFL   67 (226)
Q Consensus        48 ~~~~~li--~apTGsGKT~~~~   67 (226)
                      .+..+++  .||+|+|||....
T Consensus        49 ~~~~~li~i~G~~G~GKT~L~~   70 (412)
T 1w5s_A           49 SDVNMIYGSIGRVGIGKTTLAK   70 (412)
T ss_dssp             CCEEEEEECTTCCSSSHHHHHH
T ss_pred             CCCEEEEeCcCcCCCCHHHHHH
Confidence            3457888  9999999997643

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=94.18  E-value=0.063  Score=48.25  Aligned_cols=43  Identities=23%  Similarity=0.283  Sum_probs=29.8

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYN   99 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~   99 (226)
                      ...++.|+-|.|||.+.-+.+ ..+..      +++|.+|+.+-+...++
T Consensus       193 ~~~vlta~RGRGKSa~lG~~~-a~~~~------~~~vtAP~~~a~~~l~~  235 (671)
T 2zpa_A          193 GVAAVTAARGRGKSALAGQLI-SRIAG------RAIVTAPAKASTDVLAQ  235 (671)
T ss_dssp             EEEEEEECTTSSHHHHHHHHH-HHSSS------CEEEECSSCCSCHHHHH
T ss_pred             CeEEEecCCCCCHHHHHHHHH-HHHHh------CcEEECCCHHHHHHHHH
Confidence            457999999999996654443 33321      36999999887665444

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=94.06  E-value=0.061  Score=46.00  Aligned_cols=40  Identities=23%  Similarity=0.071  Sum_probs=25.8

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCP   89 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~P   89 (226)
                      ..|.-+++.|++|+|||...+-.+.+.....   +..++|+..
T Consensus       198 ~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~---g~~vl~~sl  237 (444)
T 2q6t_A          198 GPGSLNIIAARPAMGKTAFALTIAQNAALKE---GVGVGIYSL  237 (444)
T ss_dssp             CTTCEEEEEECTTSCHHHHHHHHHHHHHHTT---CCCEEEEES
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHhC---CCeEEEEEC
Confidence            3456789999999999976554444444321   335666653

>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=94.04  E-value=0.042  Score=50.55  Aligned_cols=18  Identities=39%  Similarity=0.569  Sum_probs=15.7

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      -+.+++.||+|+|||...
T Consensus       238 p~GILL~GPPGTGKT~LA  255 (806)
T 3cf2_A          238 PRGILLYGPPGTGKTLIA  255 (806)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            378999999999999854

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=94.01  E-value=0.098  Score=42.27  Aligned_cols=21  Identities=29%  Similarity=0.396  Sum_probs=17.0

Q ss_pred             CCCeEEEECCCCchHhHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~   68 (226)
                      .++.+.+.||+|+|||.....
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~  124 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAK  124 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHH
Confidence            467788999999999976543

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=93.99  E-value=0.083  Score=42.99  Aligned_cols=57  Identities=14%  Similarity=0.054  Sum_probs=32.4

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCC--------CCCC----ceEEEEcccHHH-HHHHHHHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGP--------KNLG----FRAVIVCPTREL-AKQTYNETVRL  104 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~--------~~~~----~~~iil~Pt~~L-~~q~~~~~~~~  104 (226)
                      .|.-+++.||+|+|||...+..+.+.....        ...+    .+++|+.-...+ .+++.+.++.+
T Consensus        97 ~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~~~~~  166 (322)
T 2i1q_A           97 SQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHA  166 (322)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHHHHHHc
Confidence            356789999999999976544444322110        0112    578887654432 45555444443

>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=93.83  E-value=0.14  Score=42.18  Aligned_cols=44  Identities=11%  Similarity=-0.079  Sum_probs=27.2

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCC--CCCCceEEEEcccH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGP--KNLGFRAVIVCPTR   91 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~--~~~~~~~iil~Pt~   91 (226)
                      .|.-+++.||+|+|||......+.......  ...+.+++|+....
T Consensus       121 ~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~  166 (343)
T 1v5w_A          121 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTEN  166 (343)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            456789999999999986544444432211  01244778876544

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=93.78  E-value=0.41  Score=43.68  Aligned_cols=17  Identities=35%  Similarity=0.417  Sum_probs=14.7

Q ss_pred             eEEEECCCCchHhHHHH
Q psy12977         51 QIFACAPTGSGKTAAFL   67 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~   67 (226)
                      ++++.||||+|||...-
T Consensus       523 ~~Ll~Gp~GtGKT~lA~  539 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELAR  539 (758)
T ss_dssp             EEEEESCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            59999999999998643

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=93.75  E-value=1.5  Score=35.39  Aligned_cols=21  Identities=24%  Similarity=0.178  Sum_probs=16.2

Q ss_pred             CCCeEEEECCCCchHhHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~   68 (226)
                      .++-+.+.+|+|+|||.....
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~  123 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGK  123 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHH
Confidence            345678999999999976443

>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=93.61  E-value=0.15  Score=46.91  Aligned_cols=55  Identities=16%  Similarity=0.052  Sum_probs=27.8

Q ss_pred             ccEEEEcccccccccCc-------cchHHHHHHHHHhc--CCCCceEEEEeee-CchhHHHHHHH
Q psy12977        159 VEWLIVDESDKLFEAGV-------RGFRDQLAVIYAAC--SGPNLKRGMFSAT-HTEDVAKWCRR  213 (226)
Q Consensus       159 ~~~lViDE~h~l~~~~~-------~~~~~~i~~i~~~~--~~~~~q~v~~SAT-~~~~~~~~~~~  213 (226)
                      -..+.+||+|.+.....       ......+..++..+  ......++++.|| .|+.+...+.+
T Consensus       571 P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~~~V~vi~aTN~p~~lD~AllR  635 (806)
T 3cf2_A          571 PCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILR  635 (806)
T ss_dssp             SEEEECSCGGGCC--------------CHHHHHHHHHHHSSCSSSSEEEECC-CCSSSSCHHHHS
T ss_pred             CceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCchhCCHhHcC
Confidence            35899999998864311       01112334444333  1345567888888 44445444544

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=93.39  E-value=0.054  Score=45.03  Aligned_cols=39  Identities=26%  Similarity=0.288  Sum_probs=24.8

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      |.-+++.+|+|+|||...+..+.....    .+.+++|+..-.
T Consensus        61 G~i~~I~GppGsGKSTLal~la~~~~~----~gg~VlyId~E~   99 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLALHAIAEAQK----MGGVAAFIDAEH   99 (356)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHHHH----TTCCEEEEESSC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHh----cCCeEEEEeccc
Confidence            456889999999999754433333222    134677776543

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=93.07  E-value=2.5  Score=33.98  Aligned_cols=40  Identities=20%  Similarity=0.200  Sum_probs=25.4

Q ss_pred             cEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        160 EWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       160 ~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      -++|+||+|.+.+.....+...+..+....  ++..+++.+.
T Consensus       139 ~vlvlDe~~~~~~~~~~~~~~~l~~~~~~~--~~~~~i~~g~  178 (357)
T 2fna_A          139 VIIVLDEAQELVKLRGVNLLPALAYAYDNL--KRIKFIMSGS  178 (357)
T ss_dssp             EEEEEETGGGGGGCTTCCCHHHHHHHHHHC--TTEEEEEEES
T ss_pred             eEEEEECHHHhhccCchhHHHHHHHHHHcC--CCeEEEEEcC
Confidence            489999999886521225666776666554  3556666443

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=93.00  E-value=0.74  Score=33.17  Aligned_cols=75  Identities=19%  Similarity=0.255  Sum_probs=52.8

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.++++.-++.+.+.+...    +..+..+.++.....+.   .....+..+|+|+|..     ..   ..+++.
T Consensus        35 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~---~Gld~~  102 (163)
T 2hjv_A           35 PDSCIIFCRTKEHVNQLTDELDDL----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDV-----AA---RGIDIE  102 (163)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECGG-----GT---TTCCCS
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECCh-----hh---cCCchh
Confidence            347999999999999999888765    67777777764333221   1122456789999942     12   678888


Q ss_pred             CccEEEEccc
Q psy12977        158 NVEWLIVDES  167 (226)
Q Consensus       158 ~~~~lViDE~  167 (226)
                      +++++|.-+.
T Consensus       103 ~~~~Vi~~~~  112 (163)
T 2hjv_A          103 NISLVINYDL  112 (163)
T ss_dssp             CCSEEEESSC
T ss_pred             cCCEEEEeCC
Confidence            9999887554

>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=92.94  E-value=1.9  Score=31.27  Aligned_cols=75  Identities=21%  Similarity=0.166  Sum_probs=52.9

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.++++.-+..+.+.+...    +..+..+.++.....+.   .....+..+|+|+|..        ....+++.
T Consensus        34 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~--------~~~Gid~~  101 (175)
T 2rb4_A           34 IGQAIIFCQTRRNAKWLTVEMIQD----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNV--------CARGIDVK  101 (175)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCS--------CCTTTCCT
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecc--------hhcCCCcc
Confidence            458999999999999988877664    67777777764433221   1122466789999953        22678899


Q ss_pred             CccEEEEccc
Q psy12977        158 NVEWLIVDES  167 (226)
Q Consensus       158 ~~~~lViDE~  167 (226)
                      .++++|.-+.
T Consensus       102 ~~~~Vi~~d~  111 (175)
T 2rb4_A          102 QVTIVVNFDL  111 (175)
T ss_dssp             TEEEEEESSC
T ss_pred             cCCEEEEeCC
Confidence            9999986443

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=92.54  E-value=0.39  Score=36.38  Aligned_cols=22  Identities=23%  Similarity=0.036  Sum_probs=17.3

Q ss_pred             CCCCeEEEECCCCchHhHHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~   68 (226)
                      ..|.-+.+.||+|+|||.....
T Consensus        23 ~~G~~~~l~G~nGsGKSTll~~   44 (231)
T 4a74_A           23 ETQAITEVFGEFGSGKTQLAHT   44 (231)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHH
Confidence            4567789999999999975433

>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=92.42  E-value=0.17  Score=41.45  Aligned_cols=93  Identities=16%  Similarity=0.112  Sum_probs=52.6

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCC
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGP  127 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (226)
                      .| -+++.+|+|+|||...+-.+......  ..+.+++|+..-.++...   .++++    +...          +    
T Consensus        28 ~G-iteI~G~pGsGKTtL~Lq~~~~~~~~--g~g~~vlyId~E~s~~~~---ra~~l----Gvd~----------d----   83 (333)
T 3io5_A           28 SG-LLILAGPSKSFKSNFGLTMVSSYMRQ--YPDAVCLFYDSEFGITPA---YLRSM----GVDP----------E----   83 (333)
T ss_dssp             SE-EEEEEESSSSSHHHHHHHHHHHHHHH--CTTCEEEEEESSCCCCHH---HHHHT----TCCG----------G----
T ss_pred             CC-eEEEECCCCCCHHHHHHHHHHHHHhc--CCCceEEEEeccchhhHH---HHHHh----CCCH----------H----
Confidence            45 68999999999998665555444432  124588888766555321   23333    3210          0    


Q ss_pred             CcCCCCCEEEECchHHHHh----HhcCCCCCCCCCccEEEEccccccc
Q psy12977        128 RSAQKFDVLITTPNKLVYL----LQMDPPALNLANVEWLIVDESDKLF  171 (226)
Q Consensus       128 ~~~~~~~IiV~Tp~~l~~~----~~~~~~~~~~~~~~~lViDE~h~l~  171 (226)
                            ++++..|....+.    .... ..+.-.+++++|+|-+..+.
T Consensus        84 ------~llv~~~~~~E~~~l~i~~~l-~~i~~~~~~lvVIDSI~aL~  124 (333)
T 3io5_A           84 ------RVIHTPVQSLEQLRIDMVNQL-DAIERGEKVVVFIDSLGNLA  124 (333)
T ss_dssp             ------GEEEEECSBHHHHHHHHHHHH-HTCCTTCCEEEEEECSTTCB
T ss_pred             ------HeEEEcCCCHHHHHHHHHHHH-HHhhccCceEEEEecccccc
Confidence                  2445544444333    2110 01223468999999999886

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=92.31  E-value=0.62  Score=34.78  Aligned_cols=75  Identities=16%  Similarity=0.121  Sum_probs=52.3

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.+++++-++.+.+.++..    +..+..+.++.....+.   .....+..+|+|+|..     ..   ..+++.
T Consensus        54 ~~~~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~~-----~~---~Gldi~  121 (191)
T 2p6n_A           54 PPPVLIFAEKKADVDAIHEYLLLK----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDV-----AS---KGLDFP  121 (191)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECHH-----HH---TTCCCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcCc-----hh---cCCCcc
Confidence            347999999999999999888766    67777777764332221   1122456789999932     22   577888


Q ss_pred             CccEEEEccc
Q psy12977        158 NVEWLIVDES  167 (226)
Q Consensus       158 ~~~~lViDE~  167 (226)
                      +++++|.-+.
T Consensus       122 ~v~~VI~~d~  131 (191)
T 2p6n_A          122 AIQHVINYDM  131 (191)
T ss_dssp             CCSEEEESSC
T ss_pred             cCCEEEEeCC
Confidence            9998887543

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=92.21  E-value=3.4  Score=33.02  Aligned_cols=20  Identities=30%  Similarity=0.247  Sum_probs=15.8

Q ss_pred             CCCeEEEECCCCchHhHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~   67 (226)
                      .++.+.+.+++|+|||....
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~  116 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAA  116 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            55677788999999997543

>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=92.12  E-value=0.11  Score=48.32  Aligned_cols=19  Identities=26%  Similarity=0.212  Sum_probs=15.7

Q ss_pred             CCeEEEECCCCchHhHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~   67 (226)
                      ..++++.||+|+|||...-
T Consensus       191 ~~~vlL~G~pG~GKT~la~  209 (854)
T 1qvr_A          191 KNNPVLIGEPGVGKTAIVE  209 (854)
T ss_dssp             CCCCEEEECTTSCHHHHHH
T ss_pred             CCceEEEcCCCCCHHHHHH
Confidence            4579999999999997543

>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=91.93  E-value=1.1  Score=38.67  Aligned_cols=52  Identities=12%  Similarity=0.080  Sum_probs=31.4

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHH
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET  101 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~  101 (226)
                      +..|.-+++.|++|+|||...+-.+.+....   .+.+++|+.- ..-..|+...+
T Consensus       239 l~~G~l~li~G~pG~GKT~lal~~a~~~a~~---~g~~vl~~s~-E~s~~~l~~r~  290 (503)
T 1q57_A          239 ARGGEVIMVTSGSGMVMSTFVRQQALQWGTA---MGKKVGLAML-EESVEETAEDL  290 (503)
T ss_dssp             CCTTCEEEEEESSCHHHHHHHHHHHHHHTTT---SCCCEEEEES-SSCHHHHHHHH
T ss_pred             cCCCeEEEEeecCCCCchHHHHHHHHHHHHh---cCCcEEEEec-cCCHHHHHHHH
Confidence            3456778999999999998655555554432   1335666653 22334544443

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=91.80  E-value=3.5  Score=33.59  Aligned_cols=53  Identities=17%  Similarity=0.210  Sum_probs=30.6

Q ss_pred             ccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHh
Q psy12977        159 VEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRK  214 (226)
Q Consensus       159 ~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~  214 (226)
                      .+.+++|.+-..-..  ......+..+.+.+ .+...++.+.++-..++.+.++.+
T Consensus       212 ~d~vliDtaG~~~~~--~~l~~eL~~i~ral-~~de~llvLDa~t~~~~~~~~~~~  264 (328)
T 3e70_C          212 IDVVLIDTAGRSETN--RNLMDEMKKIARVT-KPNLVIFVGDALAGNAIVEQARQF  264 (328)
T ss_dssp             CSEEEEEECCSCCTT--TCHHHHHHHHHHHH-CCSEEEEEEEGGGTTHHHHHHHHH
T ss_pred             chhhHHhhccchhHH--HHHHHHHHHHHHHh-cCCCCEEEEecHHHHHHHHHHHHH
Confidence            456677776643221  14556666665555 455666677777666665555554

>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=91.63  E-value=1.6  Score=39.26  Aligned_cols=78  Identities=15%  Similarity=0.253  Sum_probs=55.8

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC---CCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG---PRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.++|+.-++.+.+.+.+.    +..+...+++.....+..   ....+..+|+|+|.-        ....+++.
T Consensus       445 ~~~vlVf~~t~~~ae~L~~~L~~~----gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~--------l~~GlDip  512 (661)
T 2d7d_A          445 NERVLVTTLTKKMSEDLTDYLKEI----GIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINL--------LREGLDIP  512 (661)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCC--------CSTTCCCT
T ss_pred             CCeEEEEECCHHHHHHHHHHHHhc----CCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecch--------hhCCcccC
Confidence            459999999999999988887775    666666665532222111   112356789999953        22688899


Q ss_pred             CccEEEEcccccc
Q psy12977        158 NVEWLIVDESDKL  170 (226)
Q Consensus       158 ~~~~lViDE~h~l  170 (226)
                      +++++|+-|++..
T Consensus       513 ~v~lVi~~d~d~~  525 (661)
T 2d7d_A          513 EVSLVAILDADKE  525 (661)
T ss_dssp             TEEEEEETTTTCC
T ss_pred             CCCEEEEeCcccc
Confidence            9999999999865

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=91.22  E-value=0.22  Score=49.47  Aligned_cols=94  Identities=22%  Similarity=0.286  Sum_probs=58.0

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPR  128 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (226)
                      |+-+.+.+|.|||||...+..+.+..+.    +..++++.+-.++....   ++.+    |+..          +     
T Consensus      1431 g~~iei~g~~~sGkttl~~~~~a~~~~~----g~~~~~i~~e~~~~~~~---~~~~----Gv~~----------~----- 1484 (1706)
T 3cmw_A         1431 GRIVEIYGPESSGKTTLTLQVIAAAQRE----GKTCAFIDAEHALDPIY---ARKL----GVDI----------D----- 1484 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHT----TCCEEEECTTSCCCHHH---HHHT----TCCG----------G-----
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHhc----CCeEEEEecCCCCCHHH---HHHc----CCCH----------H-----
Confidence            5779999999999998776655555443    55789988877776554   2233    4331          1     


Q ss_pred             cCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977        129 SAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus       129 ~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                           ++++.-|+.-.+.+..-...+.-..++.+|+|.+..+...
T Consensus      1485 -----~l~~~~p~~~e~~l~~~~~~~~s~~~~~vvvDsv~al~~~ 1524 (1706)
T 3cmw_A         1485 -----NLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTPK 1524 (1706)
T ss_dssp             -----GCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCSTTCCCT
T ss_pred             -----HeEEeCCCcHHHHHHHHHHHHHcCCCCEEEEccHHhCCcc
Confidence                 1566666443222211001122346789999999988754

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.17  E-value=0.14  Score=43.76  Aligned_cols=18  Identities=28%  Similarity=0.445  Sum_probs=15.8

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||..+
T Consensus       215 prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          215 PKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             CCEEEEESCTTSSHHHHH
T ss_pred             CCeeEEECcCCCCHHHHH
Confidence            378999999999999754

>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=91.10  E-value=0.79  Score=42.46  Aligned_cols=18  Identities=33%  Similarity=0.396  Sum_probs=15.1

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      .++++.||||+|||...-
T Consensus       589 ~~vLl~Gp~GtGKT~lA~  606 (854)
T 1qvr_A          589 GSFLFLGPTGVGKTELAK  606 (854)
T ss_dssp             EEEEEBSCSSSSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            478999999999997643

>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=91.02  E-value=0.92  Score=37.12  Aligned_cols=126  Identities=12%  Similarity=0.046  Sum_probs=73.0

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.+++++-++.+++.+++.    +..+..+.++....++.   .....+..+|+|+|.-        ....+++.
T Consensus       243 ~~~~lvf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~--------~~~Gidip  310 (395)
T 3pey_A          243 IGSSIIFVATKKTANVLYGKLKSE----GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNV--------LARGIDIP  310 (395)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGG--------GSSSCCCT
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhc----CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECCh--------hhcCCCcc
Confidence            458999999999999998888765    66677776654332221   1122456789999953        12688899


Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCC--CCceEEEEeeeCchhHHHHHHHhcCCCe
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSG--PNLKRGMFSATHTEDVAKWCRRKLKRRV  219 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~--~~~q~v~~SAT~~~~~~~~~~~~~~~p~  219 (226)
                      +++++|..+...+.... .+....++++-+....  ...-+++++..-.....+.+++++.+..
T Consensus       311 ~~~~Vi~~~~p~~~~~~-~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~  373 (395)
T 3pey_A          311 TVSMVVNYDLPTLANGQ-ADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIE  373 (395)
T ss_dssp             TEEEEEESSCCBCTTSS-BCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHTTSCC
T ss_pred             cCCEEEEcCCCCCCcCC-CCHHHhhHhccccccCCCCceEEEEEechHHHHHHHHHHHHhCCce
Confidence            99999987665432110 0223333333333211  1223334333333445566666665433

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=90.81  E-value=0.26  Score=41.71  Aligned_cols=19  Identities=26%  Similarity=0.496  Sum_probs=16.7

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      ...++++.|+||+|||...
T Consensus        52 ~~~h~~i~G~tGsGKs~~~   70 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL   70 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH
T ss_pred             CcceEEEECCCCCCHHHHH
Confidence            4578999999999999875

>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=90.58  E-value=7.6  Score=34.82  Aligned_cols=105  Identities=17%  Similarity=0.153  Sum_probs=65.6

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC---CCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG---PRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.++|+.-++.+.+.+.+.    +..+...+++.....+..   ....+..+|+|||..        ....+++.
T Consensus       439 ~~~vlVf~~t~~~ae~L~~~L~~~----gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~--------l~~GlDip  506 (664)
T 1c4o_A          439 GERTLVTVLTVRMAEELTSFLVEH----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINL--------LREGLDIP  506 (664)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCC--------CCTTCCCT
T ss_pred             CCEEEEEECCHHHHHHHHHHHHhc----CCCceeecCCCCHHHHHHHHHHhhcCCceEEEccCh--------hhcCccCC
Confidence            459999999999999988887765    666666665532222111   122466789999953        22688899


Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEE
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMF  199 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~  199 (226)
                      +++++|+=+++...-..  +....+.++-+.-.......+.+
T Consensus       507 ~v~lVI~~d~d~~G~p~--s~~~~iQr~GRagR~~~G~~i~~  546 (664)
T 1c4o_A          507 EVSLVAILDADKEGFLR--SERSLIQTIGRAARNARGEVWLY  546 (664)
T ss_dssp             TEEEEEETTTTSCSGGG--SHHHHHHHHGGGTTSTTCEEEEE
T ss_pred             CCCEEEEeCCcccCCCC--CHHHHHHHHCccCcCCCCEEEEE
Confidence            99999999987542211  23344444444332233344444

>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=90.58  E-value=1  Score=36.92  Aligned_cols=76  Identities=12%  Similarity=0.011  Sum_probs=53.7

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.+++++-++.+.+.+.+.    +..+..+.++....++.   .....+..+|+|+|..        ....+++.
T Consensus       250 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~--------~~~Gidi~  317 (391)
T 1xti_A          250 FNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL--------FGRGMDIE  317 (391)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCC--------CSSCBCCT
T ss_pred             CCcEEEEeCcHHHHHHHHHHHHhC----CCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECCh--------hhcCCCcc
Confidence            458999999999999998888765    66677776654332221   1123456789999952        22688899


Q ss_pred             CccEEEEcccc
Q psy12977        158 NVEWLIVDESD  168 (226)
Q Consensus       158 ~~~~lViDE~h  168 (226)
                      +++++|..+..
T Consensus       318 ~~~~Vi~~~~p  328 (391)
T 1xti_A          318 RVNIAFNYDMP  328 (391)
T ss_dssp             TEEEEEESSCC
T ss_pred             cCCEEEEeCCC
Confidence            99999976654

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=90.31  E-value=0.76  Score=33.16  Aligned_cols=76  Identities=18%  Similarity=0.138  Sum_probs=52.8

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.+++++-++.+.+.++..    +..+..+.++.....+.   .....+..+|+|+|..     ..   ..+++.
T Consensus        30 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~---~G~d~~   97 (165)
T 1fuk_A           30 VTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDL-----LA---RGIDVQ   97 (165)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGG-----GT---TTCCCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcCh-----hh---cCCCcc
Confidence            458999999999999998888765    66777777664333221   1122466789999943     12   577888


Q ss_pred             CccEEEEcccc
Q psy12977        158 NVEWLIVDESD  168 (226)
Q Consensus       158 ~~~~lViDE~h  168 (226)
                      +++++|.-+..
T Consensus        98 ~~~~Vi~~~~p  108 (165)
T 1fuk_A           98 QVSLVINYDLP  108 (165)
T ss_dssp             SCSEEEESSCC
T ss_pred             cCCEEEEeCCC
Confidence            99998876543

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.28  E-value=0.18  Score=43.01  Aligned_cols=18  Identities=28%  Similarity=0.508  Sum_probs=15.8

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||..+
T Consensus       215 prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          215 PKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             CCEEEEESCTTSSHHHHH
T ss_pred             CCeEEEECCCCCcHHHHH
Confidence            378999999999999864

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=90.19  E-value=0.21  Score=38.21  Aligned_cols=25  Identities=24%  Similarity=0.468  Sum_probs=18.5

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      .+.+++.||+|+|||..+ ..++..+
T Consensus        58 kn~ili~GPPGtGKTt~a-~ala~~l   82 (212)
T 1tue_A           58 KNCLVFCGPANTGKSYFG-MSFIHFI   82 (212)
T ss_dssp             CSEEEEESCGGGCHHHHH-HHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHH-HHHHHHh
Confidence            456999999999999754 4455544

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.14  E-value=0.2  Score=42.68  Aligned_cols=18  Identities=33%  Similarity=0.599  Sum_probs=15.7

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||...
T Consensus       206 prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          206 PRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             CCEEEEESCTTTTHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            378999999999999754

>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=89.85  E-value=0.19  Score=39.07  Aligned_cols=19  Identities=26%  Similarity=0.403  Sum_probs=16.0

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      ..+.+++.||+|+|||...
T Consensus        38 ~~~~vll~G~~GtGKT~la   56 (262)
T 2qz4_A           38 VPKGALLLGPPGCGKTLLA   56 (262)
T ss_dssp             CCCEEEEESCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3477999999999999754

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=89.80  E-value=0.2  Score=37.00  Aligned_cols=20  Identities=10%  Similarity=0.233  Sum_probs=16.6

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..|+-+.+.||+|+|||...
T Consensus         3 ~~g~~i~i~GpsGsGKSTL~   22 (180)
T 1kgd_A            3 HMRKTLVLLGAHGVGRRHIK   22 (180)
T ss_dssp             CCCCEEEEECCTTSSHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            35678899999999999753

>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=89.69  E-value=0.2  Score=40.33  Aligned_cols=20  Identities=25%  Similarity=0.413  Sum_probs=16.9

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..++.+++.||+|+|||...
T Consensus        47 ~~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A           47 TPSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCCSEEEEECSSSSSHHHHH
T ss_pred             CCCceEEEECCCCcCHHHHH
Confidence            34688999999999999754

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=89.67  E-value=0.18  Score=40.17  Aligned_cols=19  Identities=26%  Similarity=0.457  Sum_probs=16.4

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .++.+++.||+|+|||...
T Consensus        53 ~~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           53 PAKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             CCSEEEEESSSSSCHHHHH
T ss_pred             CCCeEEEECcCCCCHHHHH
Confidence            4578999999999999754

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=89.54  E-value=0.21  Score=36.40  Aligned_cols=18  Identities=22%  Similarity=0.327  Sum_probs=15.4

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      ++.+++.|++|+|||...
T Consensus         3 ~~~i~l~G~~GsGKST~a   20 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            467899999999999764

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=89.20  E-value=0.42  Score=48.19  Aligned_cols=40  Identities=28%  Similarity=0.349  Sum_probs=27.6

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      .|.-+++.||+|+|||...+-.+.+....    +.+++|+.--.
T Consensus       382 ~G~lilI~G~pGsGKTtLaLqia~~~a~~----G~~vlyis~E~  421 (2050)
T 3cmu_A          382 MGRIVEIYGPESSGKTTLTLQVIAAAQRE----GKTCAFIDAEH  421 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTT----TCCEEEECTTS
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHhc----CCeEEEEEcCC
Confidence            45778999999999998665555555432    34677776433

>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=89.09  E-value=0.83  Score=33.81  Aligned_cols=92  Identities=16%  Similarity=0.162  Sum_probs=52.4

Q ss_pred             CchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCE
Q psy12977         59 GSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDV  135 (226)
Q Consensus        59 GsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~I  135 (226)
                      .+.|-. .+.-++....    .+.++||.++++.-+..+.+.++..    +..+..+.++.....+.   .....+..+|
T Consensus        29 ~~~K~~-~L~~ll~~~~----~~~k~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~v   99 (185)
T 2jgn_A           29 ESDKRS-FLLDLLNATG----KDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPI   99 (185)
T ss_dssp             GGGHHH-HHHHHHHHC-----CCSCEEEEESCHHHHHHHHHHHHHT----TCCEEEEC--------CHHHHHHHHTSSSE
T ss_pred             cHHHHH-HHHHHHHhcC----CCCeEEEEECCHHHHHHHHHHHHHc----CCceEEEeCCCCHHHHHHHHHHHHcCCCeE
Confidence            455654 3344444321    3558999999999999998888764    66777666654322211   1112356789


Q ss_pred             EEECchHHHHhHhcCCCCCCCCCccEEEEccc
Q psy12977        136 LITTPNKLVYLLQMDPPALNLANVEWLIVDES  167 (226)
Q Consensus       136 iV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~  167 (226)
                      +|+|.. +    .   ..+++.+++++|.-+.
T Consensus       100 LvaT~~-~----~---~Gldi~~~~~VI~~d~  123 (185)
T 2jgn_A          100 LVATAV-A----A---RGLDISNVKHVINFDL  123 (185)
T ss_dssp             EEEEC--------------CCCSBSEEEESSC
T ss_pred             EEEcCh-h----h---cCCCcccCCEEEEeCC
Confidence            999942 1    1   5677888988887443

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=88.98  E-value=0.6  Score=40.67  Aligned_cols=61  Identities=10%  Similarity=0.169  Sum_probs=35.5

Q ss_pred             EEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc-hhHHHHHHHhcCCCeEE
Q psy12977        161 WLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT-EDVAKWCRRKLKRRVQI  221 (226)
Q Consensus       161 ~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~-~~~~~~~~~~~~~p~~i  221 (226)
                      ++|+||+|.+++.........+.++.+.-......+++.|..++ +.+..+++..+...+..
T Consensus       300 vlvIDE~~~ll~~~~~~~~~~l~~Lar~gRa~GI~LIlaTQrp~~dvl~~~i~~n~~~RI~l  361 (512)
T 2ius_A          300 VVLVDEFADLMMTVGKKVEELIARLAQKARAAGIHLVLATQRPSVDVITGLIKANIPTRIAF  361 (512)
T ss_dssp             EEEEETHHHHHHHHHHHHHHHHHHHHHHCGGGTEEEEEEESCCCTTTSCHHHHHHCCEEEEE
T ss_pred             EEEEeCHHHHHhhhhHHHHHHHHHHHHHhhhCCcEEEEEecCCccccccHHHHhhcCCeEEE
Confidence            79999999887642223444555555554334666776655555 33555565655544443

>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=88.91  E-value=0.21  Score=41.28  Aligned_cols=19  Identities=42%  Similarity=0.452  Sum_probs=16.5

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      ..+++++.||||+|||...
T Consensus        50 ~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4578999999999999854

>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=88.89  E-value=0.21  Score=39.78  Aligned_cols=19  Identities=37%  Similarity=0.529  Sum_probs=16.1

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      ..+++++.||+|+|||...
T Consensus        49 ~~~~vll~G~~GtGKT~la   67 (310)
T 1ofh_A           49 TPKNILMIGPTGVGKTEIA   67 (310)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3578999999999999754

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=88.83  E-value=0.19  Score=41.38  Aligned_cols=25  Identities=32%  Similarity=0.603  Sum_probs=18.7

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      ++.+++.||+|+|||.... .+...+
T Consensus        70 ~~~vLl~GppGtGKT~la~-~la~~l   94 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIAM-GMAQAL   94 (368)
T ss_dssp             TCEEEEEESTTSSHHHHHH-HHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH-HHHHHh
Confidence            4789999999999998643 334444

>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B*

Probab=88.65  E-value=1.1  Score=43.21  Aligned_cols=56  Identities=16%  Similarity=0.043  Sum_probs=41.6

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCC--------CCCCceEEEEcccHHHHHHHHHHHHHHh
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGP--------KNLGFRAVIVCPTRELAKQTYNETVRLS  105 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~--------~~~~~~~iil~Pt~~L~~q~~~~~~~~~  105 (226)
                      ...+|.|+-|||||....--++..+...        ...-.++++++=|++=|..+.+.+.+..
T Consensus        17 g~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~L   80 (1180)
T 1w36_B           17 GERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNI   80 (1180)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHHH
Confidence            4459999999999998766666666431        1233589999999998888877766653

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.45  E-value=0.5  Score=40.20  Aligned_cols=18  Identities=22%  Similarity=0.355  Sum_probs=15.7

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||+.+
T Consensus       216 prGvLLyGPPGTGKTlLA  233 (437)
T 4b4t_I          216 PKGVILYGAPGTGKTLLA  233 (437)
T ss_dssp             CSEEEEESSTTTTHHHHH
T ss_pred             CCCCceECCCCchHHHHH
Confidence            378999999999999854

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=88.28  E-value=0.48  Score=39.50  Aligned_cols=47  Identities=17%  Similarity=-0.048  Sum_probs=33.0

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      .-.++|+||+|.+++.........+..+.+...+.+.-+++.|.++.
T Consensus       262 ~~~~i~iDEa~~~~~~~~~~~~~~l~~~~~~~Rk~g~~~~~~tQ~~~  308 (392)
T 4ag6_A          262 ERTVLVVDEAWMLVDPQTPQAIAFLRDTSKRIRKYNGSLIVISQNVI  308 (392)
T ss_dssp             TTCEEEETTGGGGCCTTCTHHHHHHHHHHHHGGGGTCEEEEEESCGG
T ss_pred             ccEEEEEecHHHHhCcCchHHHHHHHHHHHHhhhhCeEEEEEcCCHH
Confidence            35699999999998632224666777777777556777777777654

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=88.21  E-value=0.26  Score=36.96  Aligned_cols=17  Identities=35%  Similarity=0.751  Sum_probs=14.7

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +.++++||+|+|||...
T Consensus         2 RpIVi~GPSG~GK~Tl~   18 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLL   18 (186)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            56899999999999753

>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=88.08  E-value=1.8  Score=32.71  Aligned_cols=74  Identities=19%  Similarity=0.233  Sum_probs=52.1

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.+++++-++.+.+.+...    +..+..++++.....+.   .....+..+|+|+|.-        ....+++.
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~--------~~~Gidi~   98 (212)
T 3eaq_A           31 PDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDV--------AARGLDIP   98 (212)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHH----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTT--------TTCSSSCC
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecCh--------hhcCCCCc
Confidence            348999999999999998888775    67777777764333221   1223466789999943        22678888


Q ss_pred             CccEEEEcc
Q psy12977        158 NVEWLIVDE  166 (226)
Q Consensus       158 ~~~~lViDE  166 (226)
                      +++++|.=+
T Consensus        99 ~v~~Vi~~~  107 (212)
T 3eaq_A           99 QVDLVVHYR  107 (212)
T ss_dssp             CBSEEEESS
T ss_pred             cCcEEEECC
Confidence            999888533

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=87.95  E-value=0.33  Score=35.52  Aligned_cols=21  Identities=29%  Similarity=0.192  Sum_probs=17.2

Q ss_pred             CCCCeEEEECCCCchHhHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~   67 (226)
                      ..++.+++.|++|+|||...-
T Consensus         9 ~~~~~i~i~G~~GsGKst~~~   29 (180)
T 3iij_A            9 MLLPNILLTGTPGVGKTTLGK   29 (180)
T ss_dssp             CCCCCEEEECSTTSSHHHHHH
T ss_pred             ccCCeEEEEeCCCCCHHHHHH
Confidence            456789999999999998643

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=87.83  E-value=0.27  Score=38.31  Aligned_cols=18  Identities=28%  Similarity=0.527  Sum_probs=15.3

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||...
T Consensus        45 ~~~vll~G~~GtGKT~la   62 (257)
T 1lv7_A           45 PKGVLMVGPPGTGKTLLA   62 (257)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            357999999999999754

>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=87.82  E-value=7.5  Score=33.68  Aligned_cols=80  Identities=11%  Similarity=0.057  Sum_probs=55.5

Q ss_pred             CCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCC
Q psy12977         80 LGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNL  156 (226)
Q Consensus        80 ~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~  156 (226)
                      .+.++||.++++.-++.+++.+++.... +..+..++++.....+.   .....+..+|+|+|.-     + .  ..+++
T Consensus       338 ~~~~~iVF~~s~~~~~~l~~~L~~~~~~-~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~-----~-~--~GiDi  408 (563)
T 3i5x_A          338 SNYKAIIFAPTVKFTSFLCSILKNEFKK-DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV-----G-A--RGMDF  408 (563)
T ss_dssp             TCCEEEEECSCHHHHHHHHHHHHHHHTT-TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGG-----G-T--SSCCC
T ss_pred             CCCcEEEEcCcHHHHHHHHHHHHHhccC-CceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcch-----h-h--cCCCc
Confidence            3568999999999999999988877542 56666666654332221   1122466789999963     1 2  68889


Q ss_pred             CCccEEEEcccc
Q psy12977        157 ANVEWLIVDESD  168 (226)
Q Consensus       157 ~~~~~lViDE~h  168 (226)
                      .+++++|.-..-
T Consensus       409 p~v~~VI~~~~p  420 (563)
T 3i5x_A          409 PNVHEVLQIGVP  420 (563)
T ss_dssp             TTCCEEEEESCC
T ss_pred             ccCCEEEEECCC
Confidence            999998866543

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=87.78  E-value=0.66  Score=45.19  Aligned_cols=31  Identities=13%  Similarity=0.207  Sum_probs=24.7

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      +++-+++|+||+=.-+|.   .....+...++..
T Consensus      1233 lr~~~ILiLDEaTSaLD~---~tE~~Iq~~l~~~ 1263 (1321)
T 4f4c_A         1233 VRNPKILLLDEATSALDT---ESEKVVQEALDRA 1263 (1321)
T ss_dssp             HSCCSEEEEESCCCSTTS---HHHHHHHHHHTTT
T ss_pred             HhCCCEEEEeCccccCCH---HHHHHHHHHHHHH
Confidence            456679999999988887   5777888777776

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=87.75  E-value=0.23  Score=39.84  Aligned_cols=17  Identities=18%  Similarity=0.110  Sum_probs=14.8

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +.+++.||+|+|||...
T Consensus        37 ~~lLl~GppGtGKT~la   53 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQC   53 (293)
T ss_dssp             SEEEEEECTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            67899999999999754

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=87.74  E-value=0.3  Score=35.87  Aligned_cols=19  Identities=26%  Similarity=0.254  Sum_probs=15.9

Q ss_pred             CCeEEEECCCCchHhHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~   67 (226)
                      .+.+++.|++|+|||....
T Consensus         5 ~~~i~l~G~~GsGKst~a~   23 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGS   23 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            4678999999999997643

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=87.73  E-value=0.14  Score=44.56  Aligned_cols=22  Identities=23%  Similarity=0.365  Sum_probs=18.4

Q ss_pred             cCCCCCeEEEECCCCchHhHHH
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~   66 (226)
                      .+..+.++++.||+|+|||...
T Consensus        37 al~~~~~VLL~GpPGtGKT~LA   58 (500)
T 3nbx_X           37 AALSGESVFLLGPPGIAKSLIA   58 (500)
T ss_dssp             HHHHTCEEEEECCSSSSHHHHH
T ss_pred             HHhcCCeeEeecCchHHHHHHH
Confidence            4456789999999999999753

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=87.72  E-value=0.31  Score=36.50  Aligned_cols=20  Identities=30%  Similarity=0.238  Sum_probs=16.6

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..++.+++.|++|+|||...
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~   42 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLG   42 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHH
T ss_pred             CCCCEEEEEcCCCCCHHHHH
Confidence            45678999999999999764

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=87.64  E-value=0.26  Score=36.38  Aligned_cols=20  Identities=25%  Similarity=0.320  Sum_probs=16.7

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..|..+.+.||+|+|||...
T Consensus         7 ~~g~~i~l~G~~GsGKSTl~   26 (191)
T 1zp6_A            7 LGGNILLLSGHPGSGKSTIA   26 (191)
T ss_dssp             CTTEEEEEEECTTSCHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHH
Confidence            45678899999999999753

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=87.56  E-value=0.36  Score=38.16  Aligned_cols=20  Identities=35%  Similarity=0.471  Sum_probs=17.0

Q ss_pred             CCCCCeEEEECCCCchHhHH
Q psy12977         46 SPLGRQIFACAPTGSGKTAA   65 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~   65 (226)
                      ...|..+.+.||||+|||..
T Consensus        22 i~~g~~v~i~Gp~GsGKSTl   41 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKSTT   41 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHHH
T ss_pred             hCCCCEEEEECCCCccHHHH
Confidence            45677889999999999975

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=87.45  E-value=0.63  Score=39.44  Aligned_cols=27  Identities=30%  Similarity=0.452  Sum_probs=19.4

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhc
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLR   75 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~   75 (226)
                      .+..+++.||||||||... ..++..+.
T Consensus       166 ~ggii~I~GpnGSGKTTlL-~allg~l~  192 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKSTTL-YAGLQELN  192 (418)
T ss_dssp             SSEEEEEECSTTSCHHHHH-HHHHHHHC
T ss_pred             cCCeEEEECCCCCCHHHHH-HHHHhhcC
Confidence            4566899999999999753 44455553

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=87.45  E-value=0.32  Score=36.75  Aligned_cols=19  Identities=32%  Similarity=0.440  Sum_probs=16.0

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .|+-+++.||+|+|||...
T Consensus         7 ~g~~i~l~GpsGsGKsTl~   25 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVR   25 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHH
Confidence            4677899999999999753

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=87.43  E-value=0.34  Score=36.10  Aligned_cols=20  Identities=30%  Similarity=0.411  Sum_probs=16.6

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..|.-+.+.||+|||||...
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~   23 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVR   23 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            35678899999999999753

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=87.42  E-value=0.27  Score=39.93  Aligned_cols=45  Identities=16%  Similarity=0.028  Sum_probs=28.4

Q ss_pred             HHHHHHHhhccccCCCCccccc----ccCCCCCeEEEECCCCchHhHHH
Q psy12977         22 VTTLAVVSNSIFKHFEPHFTIT----YLSPLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        22 ~~~l~~~~~~~~~~~~~~Q~~~----~~~~~~~~~li~apTGsGKT~~~   66 (226)
                      .+..+.++...+..+-..+...    ..+..++++++.||+|+|||...
T Consensus        15 ~~~~~~~~~~~~~~i~g~~~~~~~l~~~l~~~~~vll~G~pGtGKT~la   63 (331)
T 2r44_A           15 RNKIKEVIDEVGKVVVGQKYMINRLLIGICTGGHILLEGVPGLAKTLSV   63 (331)
T ss_dssp             HHHHHHHHHHHTTTCCSCHHHHHHHHHHHHHTCCEEEESCCCHHHHHHH
T ss_pred             HHHHHHHHHHhccceeCcHHHHHHHHHHHHcCCeEEEECCCCCcHHHHH
Confidence            3455556666555554433111    23345789999999999999754

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=87.42  E-value=0.54  Score=35.32  Aligned_cols=36  Identities=25%  Similarity=0.166  Sum_probs=24.1

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCP   89 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~P   89 (226)
                      ..|.-+++.||+|+|||.....-+.   .    .+.+++++.-
T Consensus        18 ~~G~~~~i~G~~GsGKTtl~~~l~~---~----~~~~v~~i~~   53 (220)
T 2cvh_A           18 APGVLTQVYGPYASGKTTLALQTGL---L----SGKKVAYVDT   53 (220)
T ss_dssp             CTTSEEEEECSTTSSHHHHHHHHHH---H----HCSEEEEEES
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHH---H----cCCcEEEEEC
Confidence            4567889999999999976443333   1    1346666653

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=87.08  E-value=0.37  Score=36.19  Aligned_cols=20  Identities=25%  Similarity=0.522  Sum_probs=16.9

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..++-+++.||+|+|||...
T Consensus        10 ~~~~~i~l~G~sGsGKsTl~   29 (204)
T 2qor_A           10 ARIPPLVVCGPSGVGKGTLI   29 (204)
T ss_dssp             CCCCCEEEECCTTSCHHHHH
T ss_pred             ccCCEEEEECCCCCCHHHHH
Confidence            46778999999999999753

>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=86.81  E-value=2  Score=35.31  Aligned_cols=75  Identities=20%  Similarity=0.165  Sum_probs=52.5

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.++++.-++.+.+.+.+.    +..+..+.++....++.   .....+..+|+|+|.-     +.   ..+++.
T Consensus       266 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~---~Gidip  333 (412)
T 3fht_A          266 IAQAMIFCHTRKTASWLAAELSKE----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNV-----CA---RGIDVE  333 (412)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGG-----GT---SSCCCT
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhC----CCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCc-----cc---cCCCcc
Confidence            348999999999999999888776    66667776664332221   1122456789999953     12   688899


Q ss_pred             CccEEEEccc
Q psy12977        158 NVEWLIVDES  167 (226)
Q Consensus       158 ~~~~lViDE~  167 (226)
                      +++++|.-+.
T Consensus       334 ~~~~Vi~~~~  343 (412)
T 3fht_A          334 QVSVVINFDL  343 (412)
T ss_dssp             TEEEEEESSC
T ss_pred             CCCEEEEECC
Confidence            9999885443

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=86.77  E-value=0.33  Score=40.19  Aligned_cols=19  Identities=42%  Similarity=0.501  Sum_probs=16.2

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      ...++++.||+|+|||...
T Consensus        71 ~~~~ill~Gp~GtGKT~la   89 (376)
T 1um8_A           71 SKSNILLIGPTGSGKTLMA   89 (376)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCCEEEECCCCCCHHHHH
Confidence            4578999999999999754

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=86.75  E-value=0.36  Score=35.45  Aligned_cols=18  Identities=17%  Similarity=0.315  Sum_probs=15.3

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      +..+++.|++|+|||...
T Consensus         3 ~~~I~i~G~~GsGKsT~~   20 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSS   20 (192)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            567899999999999753

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=86.64  E-value=0.42  Score=36.12  Aligned_cols=20  Identities=10%  Similarity=0.194  Sum_probs=17.2

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..|+-+++.||+|+|||...
T Consensus        17 ~~g~~ivl~GPSGaGKsTL~   36 (197)
T 3ney_A           17 QGRKTLVLIGASGVGRSHIK   36 (197)
T ss_dssp             CSCCEEEEECCTTSSHHHHH
T ss_pred             CCCCEEEEECcCCCCHHHHH
Confidence            56788999999999999753

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=86.63  E-value=0.42  Score=40.87  Aligned_cols=26  Identities=42%  Similarity=0.701  Sum_probs=18.9

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      .++++++.||+|+|||.... .+...+
T Consensus        62 ~~~~iLl~GppGtGKT~la~-ala~~l   87 (456)
T 2c9o_A           62 AGRAVLLAGPPGTGKTALAL-AIAQEL   87 (456)
T ss_dssp             TTCEEEEECCTTSSHHHHHH-HHHHHH
T ss_pred             CCCeEEEECCCcCCHHHHHH-HHHHHh
Confidence            34789999999999997653 333433

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=86.60  E-value=0.3  Score=42.58  Aligned_cols=27  Identities=22%  Similarity=0.214  Sum_probs=19.7

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      ..|.++++.||||||||... ..++..+
T Consensus       258 ~~g~~i~I~GptGSGKTTlL-~aL~~~i  284 (511)
T 2oap_1          258 EHKFSAIVVGETASGKTTTL-NAIMMFI  284 (511)
T ss_dssp             HTTCCEEEEESTTSSHHHHH-HHHGGGS
T ss_pred             hCCCEEEEECCCCCCHHHHH-HHHHhhC
Confidence            46788999999999999753 3344433

>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=86.60  E-value=1.9  Score=36.61  Aligned_cols=70  Identities=16%  Similarity=0.133  Sum_probs=46.9

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCcc
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVE  160 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~  160 (226)
                      +.+++|+||+++-++.+++.+++.    +.++..+++. ...........+..+|+|+|.-.        ...+++. ++
T Consensus       177 ~~~~lVF~~s~~~a~~l~~~L~~~----~~~v~~lhg~-~R~~~~~~F~~g~~~vLVaT~v~--------e~GiDip-v~  242 (440)
T 1yks_A          177 KRPTAWFLPSIRAANVMAASLRKA----GKSVVVLNRK-TFEREYPTIKQKKPDFILATDIA--------EMGANLC-VE  242 (440)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSS-SCC--------CCCSEEEESSST--------TCCTTCC-CS
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHc----CCCEEEecch-hHHHHHhhhcCCCceEEEECChh--------heeeccC-ce
Confidence            458999999999999999888775    6677777763 22222233345678999999631        1678888 88


Q ss_pred             EEEE
Q psy12977        161 WLIV  164 (226)
Q Consensus       161 ~lVi  164 (226)
                      ++|.
T Consensus       243 ~VI~  246 (440)
T 1yks_A          243 RVLD  246 (440)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            8773

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=86.56  E-value=0.34  Score=36.39  Aligned_cols=19  Identities=26%  Similarity=0.538  Sum_probs=15.0

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .|+-+.+.||+|+|||...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4677899999999999753

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=86.55  E-value=0.32  Score=34.95  Aligned_cols=16  Identities=31%  Similarity=0.353  Sum_probs=13.7

Q ss_pred             eEEEECCCCchHhHHH
Q psy12977         51 QIFACAPTGSGKTAAF   66 (226)
Q Consensus        51 ~~li~apTGsGKT~~~   66 (226)
                      .+++.|++|||||...
T Consensus         3 ~I~l~G~~GsGKsT~a   18 (179)
T 3lw7_A            3 VILITGMPGSGKSEFA   18 (179)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999754

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=86.52  E-value=0.35  Score=38.99  Aligned_cols=20  Identities=20%  Similarity=0.396  Sum_probs=16.7

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..+.++++.||||+|||...
T Consensus        23 ~~~~~vLi~Ge~GtGKt~lA   42 (304)
T 1ojl_A           23 PSDATVLIHGDSGTGKELVA   42 (304)
T ss_dssp             STTSCEEEESCTTSCHHHHH
T ss_pred             CCCCcEEEECCCCchHHHHH
Confidence            34578999999999999754

>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=86.50  E-value=0.84  Score=37.06  Aligned_cols=56  Identities=18%  Similarity=0.039  Sum_probs=31.7

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCC--CCCCceEEEEcccHHH-HHHHHHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGP--KNLGFRAVIVCPTREL-AKQTYNETVR  103 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~--~~~~~~~iil~Pt~~L-~~q~~~~~~~  103 (226)
                      .|.-+++.||+|+|||...+..+.......  ...+.+++|+.-...+ .+++.+.++.
T Consensus       106 ~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~~~~~  164 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKA  164 (324)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            457789999999999976544444432210  0113477887654332 3444444333

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=86.47  E-value=0.37  Score=34.89  Aligned_cols=18  Identities=39%  Similarity=0.652  Sum_probs=15.3

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      +..+.+.||+|||||...
T Consensus         4 ~~~i~l~G~~GsGKSTl~   21 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIG   21 (173)
T ss_dssp             CCCEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            467899999999999753

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=86.44  E-value=3  Score=34.46  Aligned_cols=75  Identities=15%  Similarity=0.100  Sum_probs=52.7

Q ss_pred             CCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCC
Q psy12977         80 LGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNL  156 (226)
Q Consensus        80 ~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~  156 (226)
                      .+.++||.+++++-++.+.+.+++.    +..+..++++....++.   .....+..+|+|+|.-     +.   ..+++
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~-----~~---~Gidi  342 (417)
T 2i4i_A          275 KDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATAV-----AA---RGLDI  342 (417)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHH-----HH---TTSCC
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHC----CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECCh-----hh---cCCCc
Confidence            4568999999999999998888765    66777777664433221   1122456789999952     22   57888


Q ss_pred             CCccEEEEcc
Q psy12977        157 ANVEWLIVDE  166 (226)
Q Consensus       157 ~~~~~lViDE  166 (226)
                      .+++++|.-+
T Consensus       343 p~v~~Vi~~~  352 (417)
T 2i4i_A          343 SNVKHVINFD  352 (417)
T ss_dssp             CCEEEEEESS
T ss_pred             ccCCEEEEEc
Confidence            8999888643

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=86.44  E-value=9.4  Score=33.34  Aligned_cols=80  Identities=11%  Similarity=0.057  Sum_probs=55.6

Q ss_pred             CCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCC
Q psy12977         80 LGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNL  156 (226)
Q Consensus        80 ~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~  156 (226)
                      .+.++||.++++.-++.+++.+++.... +..+..++++.....+.   .....+..+|+|+|..     + .  ..+++
T Consensus       287 ~~~~~iVF~~t~~~~~~l~~~L~~~~~~-~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~-----~-~--~GiDi  357 (579)
T 3sqw_A          287 SNYKAIIFAPTVKFTSFLCSILKNEFKK-DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV-----G-A--RGMDF  357 (579)
T ss_dssp             TCCEEEEECSSHHHHHHHHHHHHHHHTT-TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGG-----G-T--SSCCC
T ss_pred             CCCcEEEECCcHHHHHHHHHHHHHhhcC-CCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcch-----h-h--cCCCc
Confidence            3568999999999999999988877542 56666666654332221   1122466789999963     1 2  68889


Q ss_pred             CCccEEEEcccc
Q psy12977        157 ANVEWLIVDESD  168 (226)
Q Consensus       157 ~~~~~lViDE~h  168 (226)
                      .+++++|.-..-
T Consensus       358 p~v~~VI~~~~p  369 (579)
T 3sqw_A          358 PNVHEVLQIGVP  369 (579)
T ss_dssp             TTCCEEEEESCC
T ss_pred             ccCCEEEEcCCC
Confidence            999999876654

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=86.36  E-value=0.36  Score=39.39  Aligned_cols=17  Identities=29%  Similarity=0.411  Sum_probs=14.2

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +-+++.||||+|||...
T Consensus         4 ~~i~i~GptgsGKt~la   20 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTS   20 (322)
T ss_dssp             EEEEEECCTTSCHHHHH
T ss_pred             cEEEEECCCcCCHHHHH
Confidence            45789999999999754

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=86.35  E-value=0.36  Score=36.67  Aligned_cols=20  Identities=20%  Similarity=0.353  Sum_probs=16.5

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..++-+++.||||+|||...
T Consensus        32 ~~g~~ilI~GpsGsGKStLA   51 (205)
T 2qmh_A           32 IYGLGVLITGDSGVGKSETA   51 (205)
T ss_dssp             ETTEEEEEECCCTTTTHHHH
T ss_pred             ECCEEEEEECCCCCCHHHHH
Confidence            45677999999999999643

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=86.33  E-value=0.42  Score=35.24  Aligned_cols=19  Identities=32%  Similarity=0.469  Sum_probs=16.4

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .+..+++.|++|||||...
T Consensus         9 ~~~~I~l~G~~GsGKSTv~   27 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMA   27 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4678999999999999764

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=86.29  E-value=0.41  Score=35.66  Aligned_cols=19  Identities=32%  Similarity=0.525  Sum_probs=16.1

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .|.-+.+.||+|+|||...
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~   24 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLV   24 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHH
Confidence            5677889999999999753

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=85.87  E-value=0.96  Score=38.62  Aligned_cols=39  Identities=15%  Similarity=-0.031  Sum_probs=27.1

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCP   89 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~P   89 (226)
                      ..|.-+++.|+||+|||...+-.+.+....    +.+++|++-
T Consensus       195 ~~G~liiIaG~pG~GKTtlal~ia~~~a~~----g~~vl~fSl  233 (444)
T 3bgw_A          195 KRRNFVLIAARPSMGKTAFALKQAKNMSDN----DDVVNLHSL  233 (444)
T ss_dssp             CSSCEEEEEECSSSSHHHHHHHHHHHHHHT----TCEEEEECS
T ss_pred             CCCcEEEEEeCCCCChHHHHHHHHHHHHHc----CCEEEEEEC
Confidence            345678999999999998665555555543    446777753

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=85.83  E-value=0.8  Score=40.63  Aligned_cols=46  Identities=20%  Similarity=0.166  Sum_probs=30.4

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                      +.+-+++++||+-.-+|.   .....+...++.+. . ...+++.+.-.+.
T Consensus       507 ~~~p~illlDEpts~LD~---~~~~~i~~~l~~~~-~-~~t~i~itH~l~~  552 (598)
T 3qf4_B          507 LANPKILILDEATSNVDT---KTEKSIQAAMWKLM-E-GKTSIIIAHRLNT  552 (598)
T ss_dssp             HTCCSEEEECCCCTTCCH---HHHHHHHHHHHHHH-T-TSEEEEESCCTTH
T ss_pred             hcCCCEEEEECCccCCCH---HHHHHHHHHHHHHc-C-CCEEEEEecCHHH
Confidence            456789999999988887   56667777766662 2 3455554443333

>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=85.82  E-value=0.43  Score=39.38  Aligned_cols=20  Identities=30%  Similarity=0.353  Sum_probs=16.7

Q ss_pred             CCCeEEEECCCCchHhHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~   67 (226)
                      ..+.+++.||+|+|||...-
T Consensus       116 ~~~~vLl~GppGtGKT~la~  135 (357)
T 3d8b_A          116 PPKGILLFGPPGTGKTLIGK  135 (357)
T ss_dssp             CCSEEEEESSTTSSHHHHHH
T ss_pred             CCceEEEECCCCCCHHHHHH
Confidence            45789999999999997643

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=85.70  E-value=0.41  Score=39.40  Aligned_cols=17  Identities=24%  Similarity=0.393  Sum_probs=14.6

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +.+++.||||+|||...
T Consensus        41 ~lIvI~GPTgsGKTtLa   57 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLS   57 (339)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            46899999999999754

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=85.60  E-value=3.1  Score=34.35  Aligned_cols=74  Identities=18%  Similarity=0.147  Sum_probs=51.6

Q ss_pred             ceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCC
Q psy12977         82 FRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLAN  158 (226)
Q Consensus        82 ~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~  158 (226)
                      .++||.++++.-++.+.+.+.+.    +..+..++++....++.   .....+..+|+|+|..     +   ...+++.+
T Consensus       277 ~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~---~~Gidi~~  344 (410)
T 2j0s_A          277 TQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDV-----W---ARGLDVPQ  344 (410)
T ss_dssp             SEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGG-----G---SSSCCCTT
T ss_pred             CcEEEEEcCHHHHHHHHHHHHhC----CCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECCh-----h---hCcCCccc
Confidence            48999999999999998888765    66677776664332221   1122356789999963     1   26888999


Q ss_pred             ccEEEEccc
Q psy12977        159 VEWLIVDES  167 (226)
Q Consensus       159 ~~~lViDE~  167 (226)
                      ++++|.-+.
T Consensus       345 v~~Vi~~~~  353 (410)
T 2j0s_A          345 VSLIINYDL  353 (410)
T ss_dssp             EEEEEESSC
T ss_pred             CCEEEEECC
Confidence            999886443

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=85.56  E-value=0.86  Score=37.72  Aligned_cols=39  Identities=28%  Similarity=0.353  Sum_probs=26.7

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEccc
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPT   90 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt   90 (226)
                      .|+-+++.+++|+|||...+..+......    +.+++|+..-
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~~----g~~vlyid~E  100 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQRE----GKTCAFIDAE  100 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHT----TCCEEEEESS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHC----CCeEEEEeCC
Confidence            45778999999999998665544444432    3367777653

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=85.49  E-value=0.4  Score=35.01  Aligned_cols=21  Identities=24%  Similarity=0.254  Sum_probs=17.2

Q ss_pred             CCCCeEEEECCCCchHhHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~   67 (226)
                      ..|.-+.+.||+|+|||...-
T Consensus         7 ~~gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            7 PELSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             ESSEEEEEECCTTSCHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHH
Confidence            456778899999999997654

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=85.47  E-value=0.2  Score=39.28  Aligned_cols=19  Identities=26%  Similarity=0.454  Sum_probs=15.6

Q ss_pred             CCeEEEECCCCchHhHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~   67 (226)
                      .+.+++.||+|+|||...-
T Consensus        44 ~~~vll~G~~GtGKT~la~   62 (268)
T 2r62_A           44 PKGVLLVGPPGTGKTLLAK   62 (268)
T ss_dssp             CSCCCCBCSSCSSHHHHHH
T ss_pred             CceEEEECCCCCcHHHHHH
Confidence            3568999999999997643

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=85.47  E-value=0.39  Score=38.36  Aligned_cols=18  Identities=33%  Similarity=0.396  Sum_probs=15.4

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      .++++.||+|+|||...-
T Consensus        48 ~~~ll~G~~GtGKt~la~   65 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELAK   65 (311)
T ss_dssp             EEEEEESCSSSSHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHH
Confidence            579999999999997643

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=85.35  E-value=0.4  Score=34.78  Aligned_cols=17  Identities=29%  Similarity=0.366  Sum_probs=14.1

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      .-+++.|++|||||...
T Consensus         3 ~~I~i~G~~GsGKST~a   19 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWA   19 (181)
T ss_dssp             EEEEEECCTTSSHHHHH
T ss_pred             eEEEEecCCCCCHHHHH
Confidence            35789999999999754

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=85.30  E-value=0.44  Score=34.60  Aligned_cols=19  Identities=26%  Similarity=0.197  Sum_probs=15.9

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .+..+.+.|++|+|||...
T Consensus         7 ~g~~i~l~G~~GsGKSTl~   25 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVA   25 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            4567899999999999754

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=85.10  E-value=1.3  Score=39.14  Aligned_cols=42  Identities=17%  Similarity=0.176  Sum_probs=29.7

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      +.+-+++++||+-.-+|.   .....+...++.+. . ...+++.+.
T Consensus       496 ~~~p~illlDEpts~LD~---~~~~~i~~~l~~~~-~-~~tvi~itH  537 (582)
T 3b5x_A          496 LRDAPVLILDEATSALDT---ESERAIQAALDELQ-K-NKTVLVIAH  537 (582)
T ss_pred             HcCCCEEEEECccccCCH---HHHHHHHHHHHHHc-C-CCEEEEEec
Confidence            566789999999988887   57777777777763 2 344555444

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=84.83  E-value=0.53  Score=35.17  Aligned_cols=19  Identities=32%  Similarity=0.417  Sum_probs=16.0

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .+..+.+.||+|+|||...
T Consensus        28 ~g~~i~l~G~~GsGKSTl~   46 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIA   46 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4677899999999999754

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=84.80  E-value=0.45  Score=34.23  Aligned_cols=16  Identities=19%  Similarity=0.071  Sum_probs=13.8

Q ss_pred             eEEEECCCCchHhHHH
Q psy12977         51 QIFACAPTGSGKTAAF   66 (226)
Q Consensus        51 ~~li~apTGsGKT~~~   66 (226)
                      .+++.|++|+|||...
T Consensus         3 ~i~l~G~~GsGKsT~~   18 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVA   18 (173)
T ss_dssp             EEEEECSSSSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999754

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=84.77  E-value=0.42  Score=39.59  Aligned_cols=21  Identities=43%  Similarity=0.504  Sum_probs=17.8

Q ss_pred             cCCCCCeEEEECCCCchHhHH
Q psy12977         45 LSPLGRQIFACAPTGSGKTAA   65 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~   65 (226)
                      .+..|..+.+.||||+|||..
T Consensus       171 ~i~~G~~i~ivG~sGsGKSTl  191 (361)
T 2gza_A          171 AVQLERVIVVAGETGSGKTTL  191 (361)
T ss_dssp             HHHTTCCEEEEESSSSCHHHH
T ss_pred             HHhcCCEEEEECCCCCCHHHH
Confidence            345688999999999999974

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=84.74  E-value=0.6  Score=38.87  Aligned_cols=21  Identities=33%  Similarity=0.464  Sum_probs=17.1

Q ss_pred             CCCCCeEEEECCCCchHhHHH
Q psy12977         46 SPLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~   66 (226)
                      ...|..+++.||||+|||...
T Consensus       133 ~~~g~~i~ivG~~GsGKTTll  153 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTTI  153 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHHH
Confidence            345678999999999999753

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=84.60  E-value=0.36  Score=38.79  Aligned_cols=18  Identities=28%  Similarity=0.410  Sum_probs=15.5

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      ..++++.||+|+|||...
T Consensus        38 ~~~vll~G~~GtGKT~la   55 (324)
T 1hqc_A           38 LEHLLLFGPPGLGKTTLA   55 (324)
T ss_dssp             CCCCEEECCTTCCCHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            468999999999999754

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=84.57  E-value=0.52  Score=36.60  Aligned_cols=17  Identities=29%  Similarity=0.538  Sum_probs=14.4

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +.+++.||+|+|||...
T Consensus        50 ~g~ll~G~~G~GKTtl~   66 (254)
T 1ixz_A           50 KGVLLVGPPGVGKTHLA   66 (254)
T ss_dssp             SEEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            44999999999999754

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=84.39  E-value=0.56  Score=35.93  Aligned_cols=21  Identities=29%  Similarity=0.540  Sum_probs=16.6

Q ss_pred             CCCCCeEEEECCCCchHhHHH
Q psy12977         46 SPLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~   66 (226)
                      ...|+-+.+.||+|+|||...
T Consensus        13 ~~~G~ii~l~GpsGsGKSTLl   33 (219)
T 1s96_A           13 MAQGTLYIVSAPSGAGKSSLI   33 (219)
T ss_dssp             --CCCEEEEECCTTSCHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHH
Confidence            356788999999999999753

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=84.35  E-value=0.31  Score=39.61  Aligned_cols=18  Identities=22%  Similarity=0.372  Sum_probs=15.4

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      ..++++.||+|+|||...
T Consensus        45 ~~~vLl~G~~GtGKT~la   62 (350)
T 1g8p_A           45 IGGVLVFGDRGTGKSTAV   62 (350)
T ss_dssp             GCCEEEECCGGGCTTHHH
T ss_pred             CceEEEECCCCccHHHHH
Confidence            456999999999999754

>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=84.24  E-value=4.8  Score=35.61  Aligned_cols=76  Identities=18%  Similarity=0.225  Sum_probs=54.3

Q ss_pred             CCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCC
Q psy12977         80 LGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNL  156 (226)
Q Consensus        80 ~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~  156 (226)
                      .+.++||.|+++.-++++++.++..    +..+....++....++.   .....+..+|+|+|..        ....++.
T Consensus       266 ~~~~~IVf~~sr~~~e~la~~L~~~----g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a--------~~~GID~  333 (591)
T 2v1x_A          266 KGQSGIIYCFSQKDSEQVTVSLQNL----GIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVA--------FGMGIDK  333 (591)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTT--------SCTTCCC
T ss_pred             cCCCeEEEeCcHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEech--------hhcCCCc
Confidence            4568999999999999999988765    67777777664333221   1223567789999953        2267888


Q ss_pred             CCccEEEEccc
Q psy12977        157 ANVEWLIVDES  167 (226)
Q Consensus       157 ~~~~~lViDE~  167 (226)
                      .+++++|.-..
T Consensus       334 p~V~~VI~~~~  344 (591)
T 2v1x_A          334 PDVRFVIHHSM  344 (591)
T ss_dssp             SCEEEEEESSC
T ss_pred             ccccEEEEeCC
Confidence            99999885443

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=84.24  E-value=1.2  Score=34.34  Aligned_cols=25  Identities=40%  Similarity=0.513  Sum_probs=18.7

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhc
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLR   75 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~   75 (226)
                      ++++.+++|+|||...+--+.....
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~   32 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLR   32 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHH
Confidence            6899999999999876554444443

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=84.22  E-value=0.57  Score=35.70  Aligned_cols=22  Identities=23%  Similarity=0.365  Sum_probs=16.6

Q ss_pred             cCCCCCeEEEECCCCchHhHHH
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~   66 (226)
                      .+..|+-+.+.||+|+|||...
T Consensus        19 ~i~~G~~~~lvGpsGsGKSTLl   40 (218)
T 1z6g_A           19 SMNNIYPLVICGPSGVGKGTLI   40 (218)
T ss_dssp             ---CCCCEEEECSTTSSHHHHH
T ss_pred             ecCCCCEEEEECCCCCCHHHHH
Confidence            4456788999999999999753

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=84.13  E-value=0.6  Score=38.66  Aligned_cols=26  Identities=27%  Similarity=0.514  Sum_probs=18.4

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      .+..+++.||||||||... ..++..+
T Consensus       122 ~~g~i~I~GptGSGKTTlL-~~l~g~~  147 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTL-AAMLDYL  147 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHH-HHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH-HHHHhcc
Confidence            4557899999999999753 3334443

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=84.13  E-value=1.3  Score=35.34  Aligned_cols=19  Identities=26%  Similarity=0.246  Sum_probs=15.6

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .+.-+++.||+|+|||...
T Consensus        32 ~~~livl~G~sGsGKSTla   50 (287)
T 1gvn_B           32 SPTAFLLGGQPGSGKTSLR   50 (287)
T ss_dssp             SCEEEEEECCTTSCTHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3466899999999999754

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=84.08  E-value=0.47  Score=37.12  Aligned_cols=16  Identities=38%  Similarity=0.349  Sum_probs=13.6

Q ss_pred             eEEEECCCCchHhHHH
Q psy12977         51 QIFACAPTGSGKTAAF   66 (226)
Q Consensus        51 ~~li~apTGsGKT~~~   66 (226)
                      -+++.||+|||||...
T Consensus         3 li~I~G~~GSGKSTla   18 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMA   18 (253)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCcCHHHHH
Confidence            4689999999999754

>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_B*

Probab=83.89  E-value=0.73  Score=44.23  Aligned_cols=39  Identities=28%  Similarity=0.464  Sum_probs=28.8

Q ss_pred             EEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH
Q psy12977         53 FACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE   92 (226)
Q Consensus        53 li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~   92 (226)
                      +|.|..|||||...+.-+...+... ..+.++++++|...
T Consensus         5 lV~agAGSGKT~~l~~ri~~ll~~~-~~~~~il~lVP~q~   43 (1166)
T 3u4q_B            5 FLVGRSGSGKTKLIINSIQDELRRA-PFGKPIIFLVPDQM   43 (1166)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHHHC-TTSSCEEEECCGGG
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHhC-CCCCcEEEEecCcc
Confidence            6889999999998776666665432 23468899988763

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=83.71  E-value=0.45  Score=34.87  Aligned_cols=19  Identities=26%  Similarity=0.574  Sum_probs=15.6

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .|..+++.|++|||||...
T Consensus         3 ~g~~I~l~G~~GsGKST~~   21 (186)
T 3cm0_A            3 VGQAVIFLGPPGAGKGTQA   21 (186)
T ss_dssp             CEEEEEEECCTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3457899999999999754

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=83.65  E-value=2.3  Score=41.50  Aligned_cols=31  Identities=16%  Similarity=0.224  Sum_probs=23.2

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      +++-+++++||+=.-+|.   .....+...++.+
T Consensus       570 ~~~~~IliLDE~tSaLD~---~te~~i~~~l~~~  600 (1321)
T 4f4c_A          570 VRNPKILLLDEATSALDA---ESEGIVQQALDKA  600 (1321)
T ss_dssp             TTCCSEEEEESTTTTSCT---TTHHHHHHHHHHH
T ss_pred             ccCCCEEEEecccccCCH---HHHHHHHHHHHHH
Confidence            667789999999988887   4556666666555

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=83.65  E-value=0.53  Score=38.29  Aligned_cols=17  Identities=53%  Similarity=0.704  Sum_probs=14.2

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +-+++.||||+|||...
T Consensus        11 ~~i~i~GptgsGKt~la   27 (316)
T 3foz_A           11 KAIFLMGPTASGKTALA   27 (316)
T ss_dssp             EEEEEECCTTSCHHHHH
T ss_pred             cEEEEECCCccCHHHHH
Confidence            45789999999999754

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=83.63  E-value=0.8  Score=34.56  Aligned_cols=52  Identities=12%  Similarity=0.069  Sum_probs=27.8

Q ss_pred             ccEEEEcccccccccC--ccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHH
Q psy12977        159 VEWLIVDESDKLFEAG--VRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCR  212 (226)
Q Consensus       159 ~~~lViDE~h~l~~~~--~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~  212 (226)
                      -.++||||||.+....  ...... +...+..-.....++++++.. ++.+...++
T Consensus        88 ~~vliIDEAq~l~~~~~~~~e~~r-ll~~l~~~r~~~~~iil~tq~-~~~l~~~lr  141 (199)
T 2r2a_A           88 GSIVIVDEAQDVWPARSAGSKIPE-NVQWLNTHRHQGIDIFVLTQG-PKLLDQNLR  141 (199)
T ss_dssp             TCEEEETTGGGTSBCCCTTCCCCH-HHHGGGGTTTTTCEEEEEESC-GGGBCHHHH
T ss_pred             ceEEEEEChhhhccCccccchhHH-HHHHHHhcCcCCeEEEEECCC-HHHHhHHHH
Confidence            5599999999985321  111111 222222233456688887776 444444443

>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=83.62  E-value=2.7  Score=36.48  Aligned_cols=75  Identities=15%  Similarity=0.177  Sum_probs=53.4

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.++++.-++++++.++..    +..+...+++.....+.   .....+..+|+|+|..        ....++..
T Consensus       236 ~~~~IVf~~sr~~~e~l~~~L~~~----g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a--------~~~GiD~p  303 (523)
T 1oyw_A          236 GKSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVA--------FGMGINKP  303 (523)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTT--------SCTTTCCT
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEech--------hhCCCCcc
Confidence            457999999999999999988775    66777777664433221   1223466899999963        22678889


Q ss_pred             CccEEEEccc
Q psy12977        158 NVEWLIVDES  167 (226)
Q Consensus       158 ~~~~lViDE~  167 (226)
                      +++++|.-..
T Consensus       304 ~v~~VI~~~~  313 (523)
T 1oyw_A          304 NVRFVVHFDI  313 (523)
T ss_dssp             TCCEEEESSC
T ss_pred             CccEEEEECC
Confidence            9999886443

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=83.55  E-value=19  Score=30.37  Aligned_cols=21  Identities=29%  Similarity=0.202  Sum_probs=16.1

Q ss_pred             CCCeEEEECCCCchHhHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~   68 (226)
                      .++.+.+.+++|+|||.....
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~  117 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAK  117 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            455677889999999976543

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=83.54  E-value=3.7  Score=33.66  Aligned_cols=75  Identities=13%  Similarity=0.095  Sum_probs=52.4

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.+++++-++.+.+.+++.    +..+..+.++.....+.   .....+..+|+|+|..        ....+++.
T Consensus       258 ~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~--------~~~Gidip  325 (400)
T 1s2m_A          258 INQAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL--------LTRGIDIQ  325 (400)
T ss_dssp             CSEEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC--------SSSSCCCT
T ss_pred             CCcEEEEEecHHHHHHHHHHHHhc----CCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCc--------cccCCCcc
Confidence            458999999999999999888776    66676666654332221   1122456789999952        22678899


Q ss_pred             CccEEEEccc
Q psy12977        158 NVEWLIVDES  167 (226)
Q Consensus       158 ~~~~lViDE~  167 (226)
                      +++++|.-+.
T Consensus       326 ~~~~Vi~~~~  335 (400)
T 1s2m_A          326 AVNVVINFDF  335 (400)
T ss_dssp             TEEEEEESSC
T ss_pred             CCCEEEEeCC
Confidence            9998886443

>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=83.51  E-value=2.6  Score=33.90  Aligned_cols=76  Identities=16%  Similarity=0.233  Sum_probs=51.5

Q ss_pred             CCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCC
Q psy12977         80 LGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNL  156 (226)
Q Consensus        80 ~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~  156 (226)
                      .+.+++|.+++++-++.+.+.+++.    +..+..+.++.....+.   .....+..+|+|+|..     +.   ..+++
T Consensus       237 ~~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~-----~~---~Gid~  304 (367)
T 1hv8_A          237 KEFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDV-----MS---RGIDV  304 (367)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTT-----HH---HHCCC
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhc----CCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECCh-----hh---cCCCc
Confidence            3458999999999999998888765    66677776654332221   1122456789999952     12   35667


Q ss_pred             CCccEEEEccc
Q psy12977        157 ANVEWLIVDES  167 (226)
Q Consensus       157 ~~~~~lViDE~  167 (226)
                      .+++++|.-+.
T Consensus       305 ~~~~~Vi~~~~  315 (367)
T 1hv8_A          305 NDLNCVINYHL  315 (367)
T ss_dssp             SCCSEEEESSC
T ss_pred             ccCCEEEEecC
Confidence            88888887544

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=83.39  E-value=0.28  Score=43.85  Aligned_cols=44  Identities=16%  Similarity=0.073  Sum_probs=29.0

Q ss_pred             CCCCCEEEECchHHHHhHhcCC--C-CCCCCCccEEEEccccccccc
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDP--P-ALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~--~-~~~~~~~~~lViDE~h~l~~~  173 (226)
                      ...+||||+..+.+++...+..  + .....+-..+|+||||++.+.
T Consensus       173 ~~~ADvVV~ny~ylld~~~r~~~~~~~~i~p~~~ivI~DEAHNL~d~  219 (620)
T 4a15_A          173 LPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHNLPDI  219 (620)
T ss_dssp             GGGCSEEEEEHHHHTCHHHHHHHHHHHTCCGGGEEEEETTGGGHHHH
T ss_pred             hhcCCEEEeCchhhcCHHHHHHHHHhhccCcCCeEEEEECCCchHHH
Confidence            5678999999987765442210  0 011234569999999999764

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=83.15  E-value=0.57  Score=34.38  Aligned_cols=18  Identities=22%  Similarity=0.342  Sum_probs=15.0

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      +..+++.|++|||||...
T Consensus         3 ~~~I~l~G~~GsGKsT~a   20 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQC   20 (196)
T ss_dssp             CEEEEEECCTTSSHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            356889999999999764

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=83.13  E-value=0.64  Score=36.87  Aligned_cols=17  Identities=29%  Similarity=0.497  Sum_probs=14.4

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +.+++.||+|+|||...
T Consensus        45 ~GvlL~Gp~GtGKTtLa   61 (274)
T 2x8a_A           45 AGVLLAGPPGCGKTLLA   61 (274)
T ss_dssp             SEEEEESSTTSCHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            44999999999999754

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=83.12  E-value=0.48  Score=41.97  Aligned_cols=42  Identities=7%  Similarity=0.037  Sum_probs=28.8

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      +.+-+++++||+-.-+|.   .....+...++.+. .+ ..+++.+.
T Consensus       495 ~~~p~illlDEpts~LD~---~~~~~i~~~l~~~~-~~-~tvi~itH  536 (587)
T 3qf4_A          495 VKKPKVLILDDCTSSVDP---ITEKRILDGLKRYT-KG-CTTFIITQ  536 (587)
T ss_dssp             HTCCSEEEEESCCTTSCH---HHHHHHHHHHHHHS-TT-CEEEEEES
T ss_pred             HcCCCEEEEECCcccCCH---HHHHHHHHHHHHhC-CC-CEEEEEec
Confidence            456789999999988887   57777777777662 23 44444333

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=83.10  E-value=1.6  Score=35.85  Aligned_cols=50  Identities=16%  Similarity=0.112  Sum_probs=30.1

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNET  101 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~  101 (226)
                      ..|.-+++.|++|+|||...+-.+.....    .+..++|++. ..-..|+...+
T Consensus        44 ~~G~LiiIaG~pG~GKTt~al~ia~~~a~----~g~~Vl~fSl-Ems~~ql~~Rl   93 (338)
T 4a1f_A           44 NKGSLVIIGARPSMGKTSLMMNMVLSALN----DDRGVAVFSL-EMSAEQLALRA   93 (338)
T ss_dssp             CTTCEEEEEECTTSCHHHHHHHHHHHHHH----TTCEEEEEES-SSCHHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHH----cCCeEEEEeC-CCCHHHHHHHH
Confidence            44566899999999999865544444443    2446677653 22334444433

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=82.93  E-value=0.54  Score=38.45  Aligned_cols=19  Identities=42%  Similarity=0.872  Sum_probs=16.6

Q ss_pred             CCCCeEEEECCCCchHhHH
Q psy12977         47 PLGRQIFACAPTGSGKTAA   65 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~   65 (226)
                      ..|+.+.+.||||+|||..
T Consensus       169 ~~g~~v~i~G~~GsGKTTl  187 (330)
T 2pt7_A          169 AIGKNVIVCGGTGSGKTTY  187 (330)
T ss_dssp             HHTCCEEEEESTTSCHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            4578999999999999974

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=82.82  E-value=0.57  Score=34.42  Aligned_cols=18  Identities=22%  Similarity=0.209  Sum_probs=15.2

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      +..+++.|++|+|||...
T Consensus         5 ~~~I~l~G~~GsGKST~~   22 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLS   22 (193)
T ss_dssp             CEEEEEEESTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456899999999999754

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=82.78  E-value=0.64  Score=34.71  Aligned_cols=20  Identities=30%  Similarity=0.413  Sum_probs=16.6

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..|..+.+.||+|+|||...
T Consensus        23 ~~g~~i~l~G~sGsGKSTl~   42 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTLA   42 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHH
Confidence            45677899999999999754

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=82.69  E-value=23  Score=30.63  Aligned_cols=19  Identities=32%  Similarity=0.310  Sum_probs=15.3

Q ss_pred             CeEEEECCCCchHhHHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~   68 (226)
                      +.+.+.+++|+|||....-
T Consensus       102 ~vI~ivG~~GvGKTTl~~k  120 (504)
T 2j37_W          102 NVIMFVGLQGSGKTTTCSK  120 (504)
T ss_dssp             EEEEEECSTTSSHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4688999999999976543

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=82.61  E-value=0.76  Score=34.53  Aligned_cols=21  Identities=24%  Similarity=0.577  Sum_probs=16.5

Q ss_pred             CCCCCeEEEECCCCchHhHHH
Q psy12977         46 SPLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~   66 (226)
                      +..|+-+.+.||+|+|||...
T Consensus        17 i~~Gei~~l~GpnGsGKSTLl   37 (207)
T 1znw_A           17 AAVGRVVVLSGPSAVGKSTVV   37 (207)
T ss_dssp             --CCCEEEEECSTTSSHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHH
Confidence            356788899999999999753

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=82.32  E-value=1  Score=35.76  Aligned_cols=17  Identities=29%  Similarity=0.409  Sum_probs=14.8

Q ss_pred             eEEEECCCCchHhHHHH
Q psy12977         51 QIFACAPTGSGKTAAFL   67 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~   67 (226)
                      .+++.||+|+|||..+.
T Consensus       106 ~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A          106 TIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            59999999999998654

>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli}

Probab=81.99  E-value=0.62  Score=34.80  Aligned_cols=108  Identities=12%  Similarity=0.131  Sum_probs=62.5

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPR  128 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (226)
                      ..-.+++++-|++|+...+-.++...+.   .|.++.+++|+..-.....+       ..+..-                
T Consensus        51 ~~~~iv~g~ggs~~~~~~~a~L~~~a~~---~Gr~V~vLAp~~~s~~~l~~-------~~~l~~----------------  104 (189)
T 2l8b_A           51 PSLAIVSGQGGAAGQRERVAELVMMARE---QGREVQIIAADRRSQMNMKQ-------DERLSG----------------  104 (189)
T ss_dssp             CCEECCBCSSCSHHHHHHHHHHHHHHHH---TTCCEEEECSTTHHHHHHSC-------TTTCSS----------------
T ss_pred             CceEEEecccchHHHHHHHHHHHHHHHh---cCeEEEEEcCchHHHHHHHh-------hcCcCc----------------
Confidence            3456899999999998865555555443   36789999999866554332       111110                


Q ss_pred             cCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        129 SAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       129 ~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                           +++  |-.    .+..  ....+..=+.+||||+-.+...       .+..++......+.|++++--+
T Consensus       105 -----~t~--t~~----~ll~--~~~~~tp~s~lIVD~AekLS~k-------E~~~Lld~A~~~naqvvll~~~  158 (189)
T 2l8b_A          105 -----ELI--TGR----RQLL--EGMAFTPGSTVIVDQGEKLSLK-------ETLTLLDGAARHNVQVLITDSG  158 (189)
T ss_dssp             -----CSS--STT----TTTT--TSCCCCCCCEEEEEESSSHHHH-------HHHHHHHHHHHTTCCEEEEESS
T ss_pred             -----cee--ehh----hhhc--CCCCCCCCCEEEEechhhcCHH-------HHHHHHHHHHhcCCEEEEeCCc
Confidence                 000  110    1111  2222344458999999988554       3333433333467899987654

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=81.95  E-value=1.4  Score=36.55  Aligned_cols=25  Identities=16%  Similarity=0.195  Sum_probs=19.0

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIH   72 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~   72 (226)
                      .+.++++.||||+|||.....-+..
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~   58 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLR   58 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHH
Confidence            4678999999999999865444333

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=81.89  E-value=0.88  Score=37.06  Aligned_cols=18  Identities=28%  Similarity=0.473  Sum_probs=15.3

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      ..+++.||+|+|||...-
T Consensus        52 ~~~ll~Gp~G~GKTTLa~   69 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLAH   69 (334)
T ss_dssp             CCEEEESSTTSSHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHH
Confidence            578999999999997643

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=81.73  E-value=0.76  Score=36.23  Aligned_cols=17  Identities=29%  Similarity=0.538  Sum_probs=14.4

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +.+++.||+|+|||...
T Consensus        74 ~gvll~Gp~GtGKTtl~   90 (278)
T 1iy2_A           74 KGVLLVGPPGVGKTHLA   90 (278)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCcChHHHHH
Confidence            44999999999999754

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=81.57  E-value=4.8  Score=29.80  Aligned_cols=45  Identities=13%  Similarity=0.140  Sum_probs=24.3

Q ss_pred             EEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        52 ~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      ++|.|++|||||....- +.   . .   +..++|+......-..+.+.+...
T Consensus         2 ilV~Gg~~SGKS~~A~~-la---~-~---~~~~~yiaT~~~~d~e~~~rI~~h   46 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEA-LI---G-D---APQVLYIATSQILDDEMAARIQHH   46 (180)
T ss_dssp             EEEEECTTSSHHHHHHH-HH---C-S---CSSEEEEECCCC------CHHHHH
T ss_pred             EEEECCCCCcHHHHHHH-HH---h-c---CCCeEEEecCCCCCHHHHHHHHHH
Confidence            58999999999974332 21   1 1   335788887654433333434333

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=81.53  E-value=0.58  Score=34.44  Aligned_cols=19  Identities=21%  Similarity=0.403  Sum_probs=14.9

Q ss_pred             CCeEEEECCCCchHhHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~   67 (226)
                      |.-+++.||+|+|||...-
T Consensus         2 g~ii~l~G~~GaGKSTl~~   20 (189)
T 2bdt_A            2 KKLYIITGPAGVGKSTTCK   20 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHH
Confidence            3457899999999997543

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=81.51  E-value=0.79  Score=34.14  Aligned_cols=19  Identities=32%  Similarity=0.246  Sum_probs=15.7

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .+.-+++.|++|||||...
T Consensus         3 ~~~~I~i~G~~GsGKsT~~   21 (213)
T 2plr_A            3 KGVLIAFEGIDGSGKSSQA   21 (213)
T ss_dssp             CCEEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHH
Confidence            3567899999999999754

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=81.32  E-value=0.82  Score=32.88  Aligned_cols=18  Identities=22%  Similarity=0.289  Sum_probs=15.4

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      .++++.|++|||||...-
T Consensus         8 ~~i~l~G~~GsGKSTva~   25 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQ   25 (168)
T ss_dssp             CEEEEESCTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            578999999999998643

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=81.23  E-value=0.77  Score=34.54  Aligned_cols=16  Identities=25%  Similarity=0.324  Sum_probs=13.7

Q ss_pred             eEEEECCCCchHhHHH
Q psy12977         51 QIFACAPTGSGKTAAF   66 (226)
Q Consensus        51 ~~li~apTGsGKT~~~   66 (226)
                      .+++.|++|||||...
T Consensus         2 ~I~l~G~~GsGKsT~a   17 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQA   17 (216)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999764

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=81.13  E-value=0.8  Score=33.69  Aligned_cols=19  Identities=32%  Similarity=0.394  Sum_probs=15.8

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .+..+++.|++|||||...
T Consensus         8 ~~~~I~l~G~~GsGKsT~~   26 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQC   26 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            3467899999999999754

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=81.09  E-value=0.77  Score=39.42  Aligned_cols=26  Identities=19%  Similarity=0.130  Sum_probs=18.9

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      ...++++.||+|+|||...-. +...+
T Consensus       200 ~~~~~LL~G~pG~GKT~la~~-la~~l  225 (468)
T 3pxg_A          200 TKNNPVLIGEPGVGKTAIAEG-LAQQI  225 (468)
T ss_dssp             SSCEEEEESCTTTTTHHHHHH-HHHHH
T ss_pred             CCCCeEEECCCCCCHHHHHHH-HHHHH
Confidence            346899999999999986533 33443

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=80.98  E-value=0.79  Score=34.50  Aligned_cols=16  Identities=19%  Similarity=0.239  Sum_probs=13.7

Q ss_pred             eEEEECCCCchHhHHH
Q psy12977         51 QIFACAPTGSGKTAAF   66 (226)
Q Consensus        51 ~~li~apTGsGKT~~~   66 (226)
                      .+++.||+|||||...
T Consensus         2 ~I~l~G~~GsGKsT~a   17 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQG   17 (216)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999764

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=80.92  E-value=0.75  Score=34.26  Aligned_cols=17  Identities=29%  Similarity=0.370  Sum_probs=14.8

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      ..+++.|++|+|||...
T Consensus        19 ~~I~l~G~~GsGKSTla   35 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVG   35 (202)
T ss_dssp             SCEEEECSTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            57899999999999754

>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=80.84  E-value=4.5  Score=34.04  Aligned_cols=72  Identities=14%  Similarity=0.096  Sum_probs=51.7

Q ss_pred             eEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCc
Q psy12977         83 RAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANV  159 (226)
Q Consensus        83 ~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~  159 (226)
                      ++||.++++.-++.+.+.+.+.    +..+..++++....++.   .....+..+|+|+|.-     + .  ..+++.++
T Consensus       302 ~~lVF~~t~~~a~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v-----~-~--rGlDi~~v  369 (434)
T 2db3_A          302 GTIVFVETKRGADFLASFLSEK----EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSV-----A-S--RGLDIKNI  369 (434)
T ss_dssp             TEEEECSSHHHHHHHHHHHHHT----TCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGG-----G-T--SSCCCTTC
T ss_pred             CEEEEEeCcHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchh-----h-h--CCCCcccC
Confidence            4999999999999998887765    67777777764433221   1223467889999963     1 2  68889999


Q ss_pred             cEEEEcc
Q psy12977        160 EWLIVDE  166 (226)
Q Consensus       160 ~~lViDE  166 (226)
                      +++|.-+
T Consensus       370 ~~VI~~d  376 (434)
T 2db3_A          370 KHVINYD  376 (434)
T ss_dssp             CEEEESS
T ss_pred             CEEEEEC
Confidence            9988644

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=80.73  E-value=0.97  Score=33.50  Aligned_cols=19  Identities=32%  Similarity=0.216  Sum_probs=16.0

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .+..+++.|++|||||...
T Consensus         3 ~~~~I~l~G~~GsGKsT~~   21 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQC   21 (204)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            4567899999999999754

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=80.72  E-value=0.83  Score=33.15  Aligned_cols=17  Identities=29%  Similarity=0.343  Sum_probs=14.4

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +.+++.+++|||||...
T Consensus         5 ~~i~i~G~~GsGKsTla   21 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLA   21 (175)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CEEEEEcCCCCCHHHHH
Confidence            36889999999999754

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=80.55  E-value=0.91  Score=38.79  Aligned_cols=18  Identities=39%  Similarity=0.582  Sum_probs=15.7

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+++++.||+|+|||...
T Consensus        50 ~~~iLl~GppGtGKT~la   67 (444)
T 1g41_A           50 PKNILMIGPTGVGKTEIA   67 (444)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            478999999999999754

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=80.37  E-value=5.5  Score=35.84  Aligned_cols=70  Identities=14%  Similarity=0.153  Sum_probs=49.5

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCcc
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVE  160 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~  160 (226)
                      +.++||++|+++-++.+++.+++.    +.++..+++. ...........+..+|+|+|.-     +.   ..+++. ++
T Consensus       410 ~~~~lVF~~s~~~~e~la~~L~~~----g~~v~~lHg~-eR~~v~~~F~~g~~~VLVaTdv-----~e---~GIDip-v~  475 (673)
T 2wv9_A          410 AGKTVWFVASVKMSNEIAQCLQRA----GKRVIQLNRK-SYDTEYPKCKNGDWDFVITTDI-----SE---MGANFG-AS  475 (673)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTT----TCCEEEECSS-SHHHHGGGGGTCCCSEEEECGG-----GG---TTCCCC-CS
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhC----CCeEEEeChH-HHHHHHHHHHCCCceEEEECch-----hh---cceeeC-Cc
Confidence            458999999999999988877665    6777777764 2223333344577899999953     12   567777 88


Q ss_pred             EEEE
Q psy12977        161 WLIV  164 (226)
Q Consensus       161 ~lVi  164 (226)
                      ++|.
T Consensus       476 ~VI~  479 (673)
T 2wv9_A          476 RVID  479 (673)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7763

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=80.22  E-value=0.76  Score=35.10  Aligned_cols=21  Identities=29%  Similarity=0.547  Sum_probs=13.3

Q ss_pred             CCCCCeEEEECCCCchHhHHH
Q psy12977         46 SPLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~   66 (226)
                      +..|.-+.+.||+|+|||...
T Consensus        24 v~~G~ii~l~Gp~GsGKSTl~   44 (231)
T 3lnc_A           24 KSVGVILVLSSPSGCGKTTVA   44 (231)
T ss_dssp             EECCCEEEEECSCC----CHH
T ss_pred             cCCCCEEEEECCCCCCHHHHH
Confidence            456778899999999999653

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=80.17  E-value=0.94  Score=33.07  Aligned_cols=17  Identities=24%  Similarity=0.231  Sum_probs=14.4

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      ..+++.|++|||||...
T Consensus         3 ~~I~l~G~~GsGKsT~a   19 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIG   19 (184)
T ss_dssp             CSEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            45889999999999754

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=80.04  E-value=0.93  Score=33.88  Aligned_cols=20  Identities=30%  Similarity=0.059  Sum_probs=16.1

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..+.-+.+.|++|+|||...
T Consensus        19 ~~~~~i~i~G~~GsGKSTl~   38 (207)
T 2qt1_A           19 SKTFIIGISGVTNSGKTTLA   38 (207)
T ss_dssp             CCCEEEEEEESTTSSHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHH
Confidence            44567889999999999753

---

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	226
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	7e-17
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	2e-16
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	3e-16
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	2e-15
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	2e-14
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	9e-14
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	2e-12
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	1e-11
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	4e-10
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	4e-09
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	4e-09
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	3e-08
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	4e-07
d1e9ra_	433	c.37.1.11 (A:) Bacterial conjugative coupling prot	6e-04
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	0.002
d1yksa1	140	c.37.1.14 (A:185-324) YFV helicase domain {Yellow	0.003

>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 = 74.6 bits (182), Expect = 7e-17
 Identities = 35/190 (18%), Positives = 65/190 (34%), Gaps = 29/190 (15%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
                A APTG GKT+  L   +      K    R  ++ PT  L  Q      + +E  
Sbjct: 58  KESFAATAPTGVGKTSFGLAMSLFLALKGK----RCYVIFPTSLLVIQAAETIRKYAEKA 113

Query: 109 GLRAHVIGKIQQAAEKFGPR-----SAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLI 163
           G+    +            +     + + F ++ITT   L    +       L + +++ 
Sbjct: 114 GVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRE------LGHFDFIF 167

Query: 164 VDESDKLFEAGVR--------GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKL 215
           VD+ D + +A           GF   L               + +AT  +      + +L
Sbjct: 168 VDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVG-EARGCLMVSTATAKKGK----KAEL 222

Query: 216 KRR-VQINVG 224
            R+ +  ++G
Sbjct: 223 FRQLLNFDIG 232

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

 Score = 73.0 bits (178), Expect = 2e-16
 Identities = 59/187 (31%), Positives = 94/187 (50%), Gaps = 17/187 (9%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSL--------RGPKNLGFRAVIVCPTRELAKQTYNE 100
            R I ACA TGSGKTAAFLIPII+ L        R  K    + +I+ PTRELA Q  +E
Sbjct: 58  HRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSE 117

Query: 101 TVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVE 160
           + + S    LR+ V+        +          +L+ TP +LV  ++ +   ++L   +
Sbjct: 118 SQKFSLNTPLRSCVVYGGADTHSQIR-EVQMGCHLLVATPGRLVDFIEKN--KISLEFCK 174

Query: 161 WLIVDESDKLFEAGVRGFRDQLAVIYAACSGP---NLKRGMFSATHTEDVAKWCRRKLKR 217
           ++++DE+D++ +    GF  Q+  I    + P   N +  MFSAT  +++ K     L  
Sbjct: 175 YIVLDEADRMLD---MGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYN 231

Query: 218 RVQINVG 224
            + + VG
Sbjct: 232 YIFMTVG 238

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 72.0 bits (176), Expect = 3e-16
 Identities = 50/175 (28%), Positives = 86/175 (49%), Gaps = 10/175 (5%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
              I A A TGSGKTA+F IP+I      +N G  A+I+ PTRELA Q  +E   L    
Sbjct: 42  EYNIVAQARTGSGKTASFAIPLIE--LVNENNGIEAIILTPTRELAIQVADEIESLKGNK 99

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
            L+   I   +    +   ++ +  ++++ TP +++  +      LNL NV++ I+DE+D
Sbjct: 100 NLKIAKIYGGKAIYPQI--KALKNANIVVGTPGRILDHINR--GTLNLKNVKYFILDEAD 155

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           ++      GF   +  I  AC+  + +  +FSAT   ++    ++ +     I  
Sbjct: 156 EMLN---MGFIKDVEKILNACN-KDKRILLFSATMPREILNLAKKYMGDYSFIKA 206

>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 = 71.5 bits (174), Expect = 2e-15
 Identities = 29/167 (17%), Positives = 46/167 (27%), Gaps = 26/167 (15%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
            R        G+GKT  +L  I+         G R +I+ PTR +A +           L
Sbjct: 9   KRLTIMDLHPGAGKTKRYLPAIVREAIKR---GLRTLILAPTRVVAAEMEEA-------L 58

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
                        AE  G        V +         L        + N   +I+DE+ 
Sbjct: 59  RGLPIRYQTPAIRAEHTGR-----EIVDLMCHATFTMRLLSPI---RVPNYNLIIMDEAH 110

Query: 169 KLFEAG--VRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRR 213
               A    RG+      +              +AT       + + 
Sbjct: 111 FTDPASIAARGYISTRVEM------GEAAGIFMTATPPGSRDPFPQS 151

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.6 bits (164), Expect = 2e-14
 Identities = 43/176 (24%), Positives = 85/176 (48%), Gaps = 7/176 (3%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  + A A +G+GKTA F I I+  +        +A+++ PTRELA+Q     + L + +
Sbjct: 49  GYDVIAQAQSGTGKTATFAISILQQIE-LDLKATQALVLAPTRELAQQIQKVVMALGDYM 107

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
           G   H          +      +   +++ TP ++  +L      L+   ++  ++DE+D
Sbjct: 108 GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRY--LSPKYIKMFVLDEAD 165

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG 224
           ++     RGF+DQ+  I+   +  N +  + SAT   DV +  ++ ++  ++I V 
Sbjct: 166 EMLS---RGFKDQIYDIFQKLN-SNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK 217

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 65.6 bits (159), Expect = 9e-14
 Identities = 39/175 (22%), Positives = 78/175 (44%), Gaps = 9/175 (5%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  + A A +G+GKT  F I  +  +        +A+++ PTRELA Q     + L+  +
Sbjct: 47  GHDVLAQAQSGTGKTGTFSIAALQRIDTSVK-APQALMLAPTRELALQIQKVVMALAFHM 105

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
            ++ H    I   +        +   +++ TP ++     +         ++  I+DE+D
Sbjct: 106 DIKVHAC--IGGTSFVEDAEGLRDAQIVVGTPGRVFD--NIQRRRFRTDKIKMFILDEAD 161

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           ++      GF++Q+  I+     P  +  + SAT   DV +   + ++  V+I V
Sbjct: 162 EMLS---SGFKEQIYQIFTLLP-PTTQVVLLSATMPNDVLEVTTKFMRNPVRILV 212

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.2 bits (150), Expect = 2e-12
 Identities = 39/176 (22%), Positives = 82/176 (46%), Gaps = 8/176 (4%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR + A + +G+GKTA F I ++  L        +A+I+ PTRELA Q     + L + +
Sbjct: 54  GRDVIAQSQSGTGKTATFSISVLQCLDIQVR-ETQALILAPTRELAVQIQKGLLALGDYM 112

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
            ++ H          +   +      V+  TP ++  +++          ++ L++DE+D
Sbjct: 113 NVQCHAC-IGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSL--RTRAIKMLVLDEAD 169

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG 224
           ++     +GF++Q+  +Y     P  +  + SAT   ++ +   + +   ++I V 
Sbjct: 170 EMLN---KGFKEQIYDVYRYLP-PATQVVLISATLPHEILEMTNKFMTDPIRILVK 221

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.5 bits (143), Expect = 1e-11
 Identities = 42/176 (23%), Positives = 79/176 (44%), Gaps = 7/176 (3%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  +   A +G GKTA F++  +  L          +++C TRELA Q   E  R S+ +
Sbjct: 38  GMDVLCQAKSGMGKTAVFVLATLQQLEPVTG-QVSVLVMCHTRELAFQISKEYERFSKYM 96

Query: 109 GLRAHVIGKIQQAAEKFGPR-SAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES 167
                 +     + +K           +++ TP +++        +LNL +++  I+DE 
Sbjct: 97  PNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILA--LARNKSLNLKHIKHFILDEC 154

Query: 168 DKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
           DK+ E      R  +  I+        +  MFSAT ++++   CR+ ++  ++I V
Sbjct: 155 DKMLEQL--DMRRDVQEIFRMTP-HEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 207

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 202

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 55.0 bits (131), Expect = 4e-10
 Identities = 33/169 (19%), Positives = 57/169 (33%), Gaps = 14/169 (8%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G+ +    PT +GKT    + ++          +    V P R LA + Y    +  +  
Sbjct: 40  GKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLY----VVPLRALAGEKYESFKKWEKIG 95

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
                  G  +   E          D+++TT  K   L  +   A  +  V  L+VDE  
Sbjct: 96  LRIGISTGDYESRDEHL-----GDCDIIVTTSEKADSL--IRNRASWIKAVSCLVVDEIH 148

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT--HTEDVAKWCRRKL 215
            L         + L       +   L+    SAT  +  ++A+W     
Sbjct: 149 LLDSEKRGATLEILVTKMRRMN-KALRVIGLSATAPNVTEIAEWLDADY 196

>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 = 52.7 bits (125), Expect = 4e-09
 Identities = 33/177 (18%), Positives = 58/177 (32%), Gaps = 13/177 (7%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR      PTG GK+  + IP +             V+V P      +   + ++ +   
Sbjct: 40  GRDCLVVMPTGGGKSLCYQIPALLLNG-------LTVVVSPLIS-LMKDQVDQLQANGVA 91

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
               +     +Q  E        +  +L   P +   +L      L   N   L VDE+ 
Sbjct: 92  AACLNSTQTREQQLEVMTGCRTGQIRLLYIAPER--LMLDNFLEHLAHWNPVLLAVDEAH 149

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRR---VQIN 222
            + + G     +  A+       P L     +AT  +   +   R L      +QI+
Sbjct: 150 CISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQIS 206

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 52.7 bits (125), Expect = 4e-09
 Identities = 50/176 (28%), Positives = 81/176 (46%), Gaps = 8/176 (4%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR I A A  G+GKTAAF+IP +     PK    +A+I+ PTRELA QT      L +  
Sbjct: 38  GRDILARAKNGTGKTAAFVIPTLEK-VKPKLNKIQALIMVPTRELALQTSQVVRTLGKHC 96

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
           G+   V             R  +   +L+ TP +++          +L++    I+DE+D
Sbjct: 97  GISCMVTTGGTNL-RDDILRLNETVHILVGTPGRVLD--LASRKVADLSDCSLFIMDEAD 153

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG 224
           K+     +   +Q   I +    P  +  +FSAT    V ++  + L +  +IN+ 
Sbjct: 154 KMLSRDFKTIIEQ---ILSFLP-PTHQSLLFSATFPLTVKEFMVKHLHKPYEINLM 205

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (118), Expect = 3e-08
 Identities = 46/174 (26%), Positives = 82/174 (47%), Gaps = 7/174 (4%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           GR I A A  G+GK+ A+LIP++  L   K    +A+++ PTRELA Q     +++S+ +
Sbjct: 40  GRDILARAKNGTGKSGAYLIPLLERLD-LKKDNIQAMVIVPTRELALQVSQICIQVSKHM 98

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
           G    +             R      V+I TP +++    +      + +V+ +++DE+D
Sbjct: 99  GGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILD--LIKKGVAKVDHVQMIVLDEAD 156

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN 222
           KL     + F   +  I       N +  ++SAT    V K+    L++  +IN
Sbjct: 157 KLLS---QDFVQIMEDIILTLP-KNRQILLYSATFPLSVQKFMNSHLEKPYEIN 206

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 46.7 bits (109), Expect = 4e-07
 Identities = 25/162 (15%), Positives = 48/162 (29%), Gaps = 11/162 (6%)

Query: 48  LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG 107
                    PTG GKT   ++   + L      G + +++ PT+ L  Q      RL   
Sbjct: 22  KETNCLIVLPTGLGKTLIAMMIAEYRLT---KYGGKVLMLAPTKPLVLQHAESFRRLFNL 78

Query: 108 LGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES 167
              +   +   +        RS       +           +    ++L +V  ++ DE+
Sbjct: 79  PPEKIVALTGEK----SPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEA 134

Query: 168 DKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAK 209
            +            +A  Y      N      +A+      K
Sbjct: 135 HRA---VGNYAYVFIAREYKRQ-AKNPLVIGLTASPGSTPEK 172

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]} Length = 433

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

 Score = 38.0 bits (87), Expect = 6e-04
 Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 4/64 (6%)

Query: 50  RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG 109
           R +     TG+GK+   L  + ++       G R VIV P  ++  +   +   +     
Sbjct: 51  RHLLVNGATGTGKS-VLLRELAYTGL---LRGDRMVIVDPNGDMLSKFGRDKDIILNPYD 106

Query: 110 LRAH 113
            R  
Sbjct: 107 QRTK 110

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 36.2 bits (82), Expect = 0.002
 Identities = 32/175 (18%), Positives = 65/175 (37%), Gaps = 4/175 (2%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G  +   + TG+GKT A+L+PI+  ++  +      +         +  +          
Sbjct: 38  GESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCP 97

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             R  V   +    +K            I           +   AL++     L+VDE+D
Sbjct: 98  KDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEAD 157

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV 223
            + +    GF   +  I A     +L+  +FSAT  E +  + ++ ++    ++V
Sbjct: 158 LMLD---MGFITDVDQIAARMP-KDLQMLVFSATIPEKLKPFLKKYMENPTFVHV 208

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 140

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 = 34.7 bits (78), Expect = 0.003
 Identities = 26/154 (16%), Positives = 43/154 (27%), Gaps = 22/154 (14%)

Query: 49  GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGL 108
           G         G+GKT  FL  I+           R +++ PTR +  +       L    
Sbjct: 7   GMTTVLDFHPGAGKTRRFLPQILAECARR---RLRTLVLAPTRVVLSEMKEAFHGLDVKF 63

Query: 109 GLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD 168
             +A       +                      L Y +      +N   +   I+DE+ 
Sbjct: 64  HTQAFSAHGSGREVIDA------------MCHATLTYRMLEPTRVVNWEVI---IMDEAH 108

Query: 169 KLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT 202
            L  A +   R   A              + +AT
Sbjct: 109 FLDPASI-AARGWAAHR---ARANESATILMTAT 138

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	226
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	100.0
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.96
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.95
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.94
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.92
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.84
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.82
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.77
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.76
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.75
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.73
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.72
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.14
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	99.0
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.96
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.95
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.51
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.99
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.97
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.91
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.74
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.65
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.57
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.52
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.5
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.41
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	97.24
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.13
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	97.12
d1okkd2	207	GTPase domain of the signal recognition particle r	97.1
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.1
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.04
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.03
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.0
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	96.98
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	96.95
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.83
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	96.53
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	96.31
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	96.27
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	95.96
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	95.6
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	95.51
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	95.35
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	95.28
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	95.15
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	95.03
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	94.82
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	94.79
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	94.36
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	94.18
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.85
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	93.72
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	93.41
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	93.4
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	93.33
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	93.21
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	93.1
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	92.79
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	92.71
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	92.65
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	92.54
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	92.49
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	92.39
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	92.16
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	92.14
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	92.12
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	92.04
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	91.97
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	91.92
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	91.88
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	91.86
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	91.75
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	91.63
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	91.59
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	91.45
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	91.43
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	91.08
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	91.02
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	90.94
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	90.58
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	90.53
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	90.36
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	90.32
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	90.24
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	90.14
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	90.01
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	89.98
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	89.81
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	89.78
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	89.64
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	89.59
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	89.42
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	89.39
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	89.07
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	89.0
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	88.84
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	88.78
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	88.74
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	88.43
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	88.39
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	88.09
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	87.99
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	87.98
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	87.85
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	87.79
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	87.5
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	87.48
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	87.22
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	87.08
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	87.0
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	86.52
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	86.5
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	86.47
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	86.24
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	86.13
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	85.78
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	85.74
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	85.7
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	84.97
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	84.82
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	84.72
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	84.69
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	84.15
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	83.92
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	83.48
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	83.43
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	82.99
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	82.77
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	82.09
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	81.96
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	81.6
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	81.59
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	81.24
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	80.77
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	80.72
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	80.48

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.6e-42  Score=269.87  Aligned_cols=200  Identities=22%  Similarity=0.306  Sum_probs=179.8

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      .+-+.+++++.+.+|++++|+|+++. .++.|+|++++||||||||++|++|+++.+.. ...+++++|++||++||.|+
T Consensus        18 ~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~-~~~~~~alil~Pt~eL~~Q~   96 (218)
T d2g9na1          18 NLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIEL-DLKATQALVLAPTRELAQQI   96 (218)
T ss_dssp             CCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCT-TCCSCCEEEECSSHHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecc-cccCccEEEEcccchhhhhH
Confidence            46789999999999999999998774 78899999999999999999999999999864 44678999999999999999


Q ss_pred             HHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccc
Q psy12977         98 YNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG  177 (226)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~  177 (226)
                      ++.++.+.+..+.......++............+.++|+|+||+++.+++.+  +...+++++++|+||||.+++.   +
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~--~~~~~~~l~~lVlDEaD~ll~~---~  171 (218)
T d2g9na1          97 QKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNR--RYLSPKYIKMFVLDEADEMLSR---G  171 (218)
T ss_dssp             HHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHT--TSSCSTTCCEEEEESHHHHHHT---T
T ss_pred             HHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhc--CCcccccceEEEeeecchhhcC---c
Confidence            9999999999998888777776665555556667899999999999999987  6788999999999999999998   6


Q ss_pred             hHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        178 FRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       178 ~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      |...+..+++.+ +.+.|++++|||+|+++.+++++++++|+.|.|++
T Consensus       172 f~~~~~~Il~~~-~~~~Q~il~SAT~~~~v~~~~~~~l~~pv~i~v~~  218 (218)
T d2g9na1         172 FKDQIYDIFQKL-NSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKK  218 (218)
T ss_dssp             CHHHHHHHHHHS-CTTCEEEEEESCCCHHHHHHHHHHCSSCEEEECCC
T ss_pred             hHHHHHHHHHhC-CCCCeEEEEEecCCHHHHHHHHHHCCCCEEEEEeC
Confidence            999999999999 67899999999999999999999999999999975

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=8.3e-43  Score=273.94  Aligned_cols=200  Identities=22%  Similarity=0.302  Sum_probs=178.1

Q ss_pred             HHHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      +++-+.+++++++.+|..++|+|+.+ +.+++|+|+++.||||||||++|++|+++.+.. ...+++++|++||++|+.|
T Consensus        22 l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~-~~~~~~~lil~PtreLa~Q  100 (222)
T d2j0sa1          22 MGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI-QVRETQALILAPTRELAVQ  100 (222)
T ss_dssp             GCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCT-TSCSCCEEEECSSHHHHHH
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccc-cccCceeEEecchHHHHHH
Confidence            45788999999999999999999777 478899999999999999999999999999864 3456899999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +++.++.+.+..+.++....++....... ..+..+++|+|+||+++.+++..  ....+++++++|+||||.+++.   
T Consensus       101 i~~~~~~l~~~~~i~~~~~~g~~~~~~~~-~~l~~~~~Ilv~TPgrl~~~~~~--~~~~~~~l~~lVlDEaD~ll~~---  174 (222)
T d2j0sa1         101 IQKGLLALGDYMNVQCHACIGGTNVGEDI-RKLDYGQHVVAGTPGRVFDMIRR--RSLRTRAIKMLVLDEADEMLNK---  174 (222)
T ss_dssp             HHHHHHHHTTTTTCCEEEECTTSCHHHHH-HHHHHCCSEEEECHHHHHHHHHT--TSSCCTTCCEEEEETHHHHTST---
T ss_pred             HHHHHHHHhCccceeEEEEeecccchhhH-HHhccCCeEEeCCCCcHHhcccc--cccccccceeeeecchhHhhhc---
Confidence            99999999998888888887776544332 23456789999999999999887  6788999999999999999998   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      +|...+..+++.+ ++.+|++++|||+|+++.+++++++++|+.|.|++
T Consensus       175 ~f~~~i~~I~~~l-~~~~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V~r  222 (222)
T d2j0sa1         175 GFKEQIYDVYRYL-PPATQVVLISATLPHEILEMTNKFMTDPIRILVKR  222 (222)
T ss_dssp             TTHHHHHHHHTTS-CTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCG
T ss_pred             CcHHHHHHHHHhC-CCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEEeC
Confidence            6999999999998 67899999999999999999999999999999875

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.2e-41  Score=264.85  Aligned_cols=196  Identities=25%  Similarity=0.348  Sum_probs=169.6

Q ss_pred             HHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      .+-+++++++.+.+|++++|+|+++ +.+++|+|++++||||||||++|++|+++.+.. ...++++++++|+++|+.|+
T Consensus         9 ~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~-~~~~~~~lil~pt~el~~q~   87 (206)
T d1veca_           9 CLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDL-KKDNIQAMVIVPTRELALQV   87 (206)
T ss_dssp             CCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCT-TSCSCCEEEECSCHHHHHHH
T ss_pred             CcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccc-cccCcceEEEeecchhhHHH
Confidence            4678999999999999999999777 488899999999999999999999999999864 45578999999999999999


Q ss_pred             HHHHHHHhhcCC-CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         98 YNETVRLSEGLG-LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        98 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      ++.+..+.+... .......++.. .......+..+++|+|+||+++.+++..  +...+++++++|+||||.+++.   
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~l~~~~~ivv~TPgrl~~~~~~--~~~~~~~l~~lVlDEaD~ll~~---  161 (206)
T d1veca_          88 SQICIQVSKHMGGAKVMATTGGTN-LRDDIMRLDDTVHVVIATPGRILDLIKK--GVAKVDHVQMIVLDEADKLLSQ---  161 (206)
T ss_dssp             HHHHHHHTTTSSSCCEEEECSSSC-HHHHHHHTTSCCSEEEECHHHHHHHHHT--TCSCCTTCCEEEEETHHHHTST---
T ss_pred             HHHHHHHhhcccCcccccccCCcc-HHHHHHHHHhccCeEEeCCccccccccc--hhccccccceEEEecccccccc---
Confidence            999999877654 34444444432 2333334567899999999999999987  7788999999999999999998   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEe
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN  222 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~  222 (226)
                      +|...+..+++.+ +++.|++++|||+|+++.+++++++++|+.|+
T Consensus       162 ~f~~~i~~I~~~~-~~~~Q~~l~SAT~~~~v~~l~~~~l~~P~~I~  206 (206)
T d1veca_         162 DFVQIMEDIILTL-PKNRQILLYSATFPLSVQKFMNSHLEKPYEIN  206 (206)
T ss_dssp             TTHHHHHHHHHHS-CTTCEEEEEESCCCHHHHHHHHHHCSSCEEEC
T ss_pred             chHHHHHHHHHhC-CCCCEEEEEEecCCHHHHHHHHHHCCCCEEEC
Confidence            6999999999999 67899999999999999999999999999874

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.5e-41  Score=263.30  Aligned_cols=199  Identities=24%  Similarity=0.313  Sum_probs=171.4

Q ss_pred             HHHHHHHHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      ++-+++++++++++|+.++|+|+.+ +.+++|+|++++||||||||++|++|+++.+.. ...++++++++|+++|+.|+
T Consensus         7 ~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~-~~~~~~~lil~PtreL~~qi   85 (207)
T d1t6na_           7 LLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEP-VTGQVSVLVMCHTRELAFQI   85 (207)
T ss_dssp             CCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCC-CTTCCCEEEECSCHHHHHHH
T ss_pred             CcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecc-cCCCceEEEEeccchhhHHH
Confidence            4578999999999999999999777 488899999999999999999999999999864 45568999999999999999


Q ss_pred             HHHHHHHhhcCC-CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         98 YNETVRLSEGLG-LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        98 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      .+.++.+....+ .+.....|+..............++|+|+||+++.+++.+  +.+++++++++|+||||.+++..  
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~--~~~~l~~l~~lVlDEaD~ll~~~--  161 (207)
T d1t6na_          86 SKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN--KSLNLKHIKHFILDECDKMLEQL--  161 (207)
T ss_dssp             HHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT--TSSCCTTCCEEEEESHHHHHSSH--
T ss_pred             HHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccC--CceeccccceeehhhhhhhhhcC--
Confidence            999999988765 4455555554443333333356799999999999999987  67889999999999999999742  


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEec
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~  223 (226)
                      ++...+..+++.+ ++..|++++|||+|+++++++++++++|+.|.|
T Consensus       162 ~~~~~i~~I~~~~-~~~~Q~il~SAT~~~~v~~l~~~~l~~P~~I~V  207 (207)
T d1t6na_         162 DMRRDVQEIFRMT-PHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV  207 (207)
T ss_dssp             HHHHHHHHHHHTS-CSSSEEEEEESCCCTTTHHHHHTTCSSCEEEEC
T ss_pred             CcHHHHHHHHHhC-CCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEeC
Confidence            5888999999988 678999999999999999999999999999875

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=4e-40  Score=257.17  Aligned_cols=196  Identities=22%  Similarity=0.295  Sum_probs=169.7

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      .+-+++++++++++|++++|+|..+. .++.|+|+++++|||||||++|++|+++.+.. ...++++++++||++++.|+
T Consensus        16 ~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~-~~~~~~~lil~pt~el~~q~   94 (212)
T d1qdea_          16 ELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDT-SVKAPQALMLAPTRELALQI   94 (212)
T ss_dssp             TCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCT-TCCSCCEEEECSSHHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhc-cCCCcceEEEcccHHHhhhh
Confidence            56789999999999999999998875 78899999999999999999999999999863 55678999999999999999


Q ss_pred             HHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccc
Q psy12977         98 YNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRG  177 (226)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~  177 (226)
                      ...+..+............++.....+.  ....+++|+|+||+++.+++..  +...+++++++|+||||.+++.   +
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~IvI~TP~~l~~~~~~--~~~~l~~l~~lVlDEad~lld~---~  167 (212)
T d1qdea_          95 QKVVMALAFHMDIKVHACIGGTSFVEDA--EGLRDAQIVVGTPGRVFDNIQR--RRFRTDKIKMFILDEADEMLSS---G  167 (212)
T ss_dssp             HHHHHHHTTTSCCCEEEECC------------CTTCSEEEECHHHHHHHHHT--TSSCCTTCCEEEEETHHHHHHT---T
T ss_pred             hhhhcccccccccceeeEeeccchhHHH--HHhcCCcEEEECCCcccccccc--CceecCcceEEeehhhhhhccc---c
Confidence            9999999888887777766655443332  2335789999999999999988  6788999999999999999998   6


Q ss_pred             hHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEec
Q psy12977        178 FRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       178 ~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~  223 (226)
                      |...+..+++.+ ++.+|++++|||+|+++++++++++++|+.|.|
T Consensus       168 f~~~v~~I~~~~-~~~~Q~vl~SAT~~~~v~~l~~~~l~~Pv~i~v  212 (212)
T d1qdea_         168 FKEQIYQIFTLL-PPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV  212 (212)
T ss_dssp             CHHHHHHHHHHS-CTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC-
T ss_pred             hHHHHHHHHHhC-CCCCeEEEEEeeCCHHHHHHHHHHCCCCEEEeC
Confidence            999999999998 678999999999999999999999999999875

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=100.00  E-value=1.4e-39  Score=253.66  Aligned_cols=196  Identities=28%  Similarity=0.380  Sum_probs=171.6

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCC-CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLG-RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~-~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      .+.+++++++.+++|++++|+|+.+. .+++| +|+++++|||+|||++|.+|+++....  ..+++++|++||++||.|
T Consensus        10 ~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~--~~~~~~lil~pt~~l~~q   87 (208)
T d1hv8a1          10 NLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE--NNGIEAIILTPTRELAIQ   87 (208)
T ss_dssp             SCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS--SSSCCEEEECSCHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccccccccc--ccCcceEEEeeccccchh
Confidence            46788999999999999999998775 55666 599999999999999999999988754  456799999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +.+.++.+....+.++....++........  ...++||+|+||+++.+++++  +.+++++++++|+||||.+++.   
T Consensus        88 ~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~--~l~~~~IlV~TP~~l~~~l~~--~~~~~~~l~~lViDEad~l~~~---  160 (208)
T d1hv8a1          88 VADEIESLKGNKNLKIAKIYGGKAIYPQIK--ALKNANIVVGTPGRILDHINR--GTLNLKNVKYFILDEADEMLNM---  160 (208)
T ss_dssp             HHHHHHHHHCSSCCCEEEECTTSCHHHHHH--HHHTCSEEEECHHHHHHHHHT--TCSCTTSCCEEEEETHHHHHTT---
T ss_pred             hhhhhhhhcccCCeEEEEeeCCCChHHHHH--hcCCCCEEEEChHHHHHHHHc--CCCCcccCcEEEEEChHHhhcC---
Confidence            999999999998888888777654433321  224689999999999999987  6788999999999999999988   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      ++...+.++++.+ ++++|++++|||+|+++.++++++++||..|+++
T Consensus       161 ~~~~~i~~I~~~~-~~~~Q~i~~SAT~~~~v~~~~~~~l~~~~~I~~~  207 (208)
T d1hv8a1         161 GFIKDVEKILNAC-NKDKRILLFSATMPREILNLAKKYMGDYSFIKAK  207 (208)
T ss_dssp             TTHHHHHHHHHTS-CSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECC
T ss_pred             CChHHHHHHHHhC-CCCCeEEEEEccCCHHHHHHHHHHCCCCeEEEEE
Confidence            6889999999988 6789999999999999999999999999999875

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=100.00  E-value=1.8e-39  Score=257.72  Aligned_cols=201  Identities=29%  Similarity=0.399  Sum_probs=173.6

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCC--------CCCCceEEEEc
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGP--------KNLGFRAVIVC   88 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~--------~~~~~~~iil~   88 (226)
                      +.+-+++++++.+.+|.+++|+|..+. .+++|+|++++||||||||++|++|+++.+...        ...+++++|++
T Consensus        26 l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~~~alil~  105 (238)
T d1wrba1          26 LKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILA  105 (238)
T ss_dssp             GSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEEC
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCCCceEEEec
Confidence            345677888999999999999997775 778999999999999999999999999988432        33467899999


Q ss_pred             ccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccc
Q psy12977         89 PTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESD  168 (226)
Q Consensus        89 Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h  168 (226)
                      ||++||.|+.+.+..+....+.++....++....... +....++||+|+||+++.+++..  +...+.+++++|+||+|
T Consensus       106 pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~ivV~TP~~l~~~~~~--~~~~l~~v~~lViDEaD  182 (238)
T d1wrba1         106 PTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQI-REVQMGCHLLVATPGRLVDFIEK--NKISLEFCKYIVLDEAD  182 (238)
T ss_dssp             SSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHH-HHHSSCCSEEEECHHHHHHHHHT--TSBCCTTCCEEEEETHH
T ss_pred             cchhhhcchheeeeecccCCCcEEEEEeccchhhHHH-hhcccCCceeecCHHHHHhHHcc--Cceeccccceeeeehhh
Confidence            9999999999999999999898888887665443332 23557899999999999999987  67789999999999999


Q ss_pred             cccccCccchHHHHHHHHHhcCC---CCceEEEEeeeCchhHHHHHHHhcCCCeEEecC
Q psy12977        169 KLFEAGVRGFRDQLAVIYAACSG---PNLKRGMFSATHTEDVAKWCRRKLKRRVQINVG  224 (226)
Q Consensus       169 ~l~~~~~~~~~~~i~~i~~~~~~---~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~  224 (226)
                      .+++.   +|...+..+++.+..   .+.|++++|||+|+++++++++++++|++|.|.
T Consensus       183 ~ll~~---~f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~~i~vg  238 (238)
T d1wrba1         183 RMLDM---GFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG  238 (238)
T ss_dssp             HHHHT---TCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC
T ss_pred             hhhhh---ccHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEEeC
Confidence            99988   699999999987632   357999999999999999999999999999874

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.4e-38  Score=247.56  Aligned_cols=200  Identities=27%  Similarity=0.367  Sum_probs=178.7

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      +.+-+++++++.+.+|.+++|+|+++. .+++|+|+++.||||||||++|++|+++.+.. ...+.++++++|+.+++.|
T Consensus         6 l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~-~~~~~~~~~~~~~~~~~~~   84 (206)
T d1s2ma1           6 FYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKP-KLNKIQALIMVPTRELALQ   84 (206)
T ss_dssp             GCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCT-TSCSCCEEEECSSHHHHHH
T ss_pred             cCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhcccccccccc-ccccccceeeccchhhhhh
Confidence            457889999999999999999998774 78899999999999999999999999999864 4456789999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      .......+....+.++....|+....... ..+..+++|+|+||+++.+++..  ....+++++++|+||||.+++.   
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~l~~~~~Ili~TP~~l~~~l~~--~~~~l~~l~~lV~DEaD~l~~~---  158 (206)
T d1s2ma1          85 TSQVVRTLGKHCGISCMVTTGGTNLRDDI-LRLNETVHILVGTPGRVLDLASR--KVADLSDCSLFIMDEADKMLSR---  158 (206)
T ss_dssp             HHHHHHHHTTTTTCCEEEECSSSCHHHHH-HHTTSCCSEEEECHHHHHHHHHT--TCSCCTTCCEEEEESHHHHSSH---
T ss_pred             hhhhhhhcccccCeeEEeecCccchhhHH-HHhcccceEEEECCccccccccc--ceeecccceEEEeechhhhhhh---
Confidence            99999999999999988887776544433 34567899999999999999987  6788999999999999999998   


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEecCC
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINVGL  225 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~~~  225 (226)
                      +|...+..+++.+ ++.+|++++|||+|+++.+++++|+++|+.|++.+
T Consensus       159 ~f~~~v~~I~~~l-~~~~Q~il~SATl~~~v~~~~~~~l~~P~~I~~~~  206 (206)
T d1s2ma1         159 DFKTIIEQILSFL-PPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLME  206 (206)
T ss_dssp             HHHHHHHHHHTTS-CSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCS
T ss_pred             hhHHHHHHHHHhC-CCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEeeC
Confidence            7999999999999 67899999999999999999999999999998864

>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=100.00  E-value=7.6e-37  Score=238.09  Aligned_cols=197  Identities=24%  Similarity=0.339  Sum_probs=168.8

Q ss_pred             HHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHH
Q psy12977         19 SIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQT   97 (226)
Q Consensus        19 ~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~   97 (226)
                      ++-+.+++++++.+|++++|+|+++. .+++|+|++++||||||||++|++|+++.... ...+...++++|+.+++.+.
T Consensus         7 ~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~-~~~~~~~~~~~~~~~~~~~~   85 (209)
T d1q0ua_           7 PFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKP-ERAEVQAVITAPTRELATQI   85 (209)
T ss_dssp             CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCT-TSCSCCEEEECSSHHHHHHH
T ss_pred             CcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeecccccc-ccccccccccccccchhHHH
Confidence            46788999999999999999998885 77899999999999999999999999999874 44567889999999999999


Q ss_pred             HHHHHHHhhcCC----CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccccc
Q psy12977         98 YNETVRLSEGLG----LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEA  173 (226)
Q Consensus        98 ~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~  173 (226)
                      .+.+....+...    .......++.. ..........+++|+|+||+++..++.+  ....+++++++|+||||.+++.
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~Ilv~TP~~l~~~~~~--~~~~~~~l~~lViDEad~ll~~  162 (209)
T d1q0ua_          86 YHETLKITKFCPKDRMIVARCLIGGTD-KQKALEKLNVQPHIVIGTPGRINDFIRE--QALDVHTAHILVVDEADLMLDM  162 (209)
T ss_dssp             HHHHHHHHTTSCGGGCCCEEEECCCSH-HHHTTCCCSSCCSEEEECHHHHHHHHHT--TCCCGGGCCEEEECSHHHHHHT
T ss_pred             HHHHHhhhccccccccccccccccchh-hHHHHHHhccCceEEEecCchhhhhhhh--hccccccceEEEEeeccccccc
Confidence            998887766543    33444444433 3333445678899999999999999887  5677899999999999999998


Q ss_pred             CccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEec
Q psy12977        174 GVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQINV  223 (226)
Q Consensus       174 ~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~~  223 (226)
                         ++...+..+++.+ +++.|++++|||+|+++.+++++++++|+.|+|
T Consensus       163 ---~f~~~v~~I~~~~-~~~~Q~il~SATl~~~v~~l~~~~l~~p~~i~V  208 (209)
T d1q0ua_         163 ---GFITDVDQIAARM-PKDLQMLVFSATIPEKLKPFLKKYMENPTFVHV  208 (209)
T ss_dssp             ---TCHHHHHHHHHTS-CTTCEEEEEESCCCGGGHHHHHHHCSSCEEEEC
T ss_pred             ---ccHHHHHHHHHHC-CCCCEEEEEEccCCHHHHHHHHHHCCCCEEEEe
Confidence               6899999999998 678999999999999999999999999999986

>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=99.96  E-value=5.3e-29  Score=192.38  Aligned_cols=191  Identities=19%  Similarity=0.173  Sum_probs=141.6

Q ss_pred             HHHHHHHHHHHhhccccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHH
Q psy12977         18 ISIIVTTLAVVSNSIFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQ   96 (226)
Q Consensus        18 ~~~~~~~l~~~~~~~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q   96 (226)
                      .++....++.+++.++++++|.|.++. .+.+|+|+++++|||+|||.++.++++..+..    +.++++++|+++|+.|
T Consensus         8 ~~~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~----~~~vl~l~P~~~L~~q   83 (202)
T d2p6ra3           8 ESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK----GGKSLYVVPLRALAGE   83 (202)
T ss_dssp             HHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT----TCCEEEEESSHHHHHH
T ss_pred             hhhhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhc----cCcceeecccHHHHHH
Confidence            356777888999999999999998875 77789999999999999999998988887764    4589999999999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCcc
Q psy12977         97 TYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVR  176 (226)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~  176 (226)
                      +.+.++++.+.. ..+....++...    .......++++++||..+..++..  ....+.+++++|+||+|.+.++.+.
T Consensus        84 ~~~~~~~~~~~~-~~v~~~~~~~~~----~~~~~~~~~ii~~~~~~~~~~~~~--~~~~~~~~~~ii~DE~h~~~~~~r~  156 (202)
T d2p6ra3          84 KYESFKKWEKIG-LRIGISTGDYES----RDEHLGDCDIIVTTSEKADSLIRN--RASWIKAVSCLVVDEIHLLDSEKRG  156 (202)
T ss_dssp             HHHHHTTTTTTT-CCEEEECSSCBC----CSSCSTTCSEEEEEHHHHHHHHHT--TCSGGGGCCEEEETTGGGGGCTTTH
T ss_pred             HHHHHHHHhhcc-ccceeeccCccc----ccccccccceeeeccHHHHHHHhc--cchhhhhhhhccccHHHHhcccccc
Confidence            999998876643 344444433221    123346789999999999998876  5567889999999999998876322


Q ss_pred             chHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCCCeEEe
Q psy12977        177 GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKRRVQIN  222 (226)
Q Consensus       177 ~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~p~~i~  222 (226)
                      .....+...++.. ++++|++++|||+|+ .+++ .+|+..+.++.
T Consensus       157 ~~~~~~l~~i~~~-~~~~~~l~lSATl~n-~~~~-~~~l~~~~~~s  199 (202)
T d2p6ra3         157 ATLEILVTKMRRM-NKALRVIGLSATAPN-VTEI-AEWLDADYYVS  199 (202)
T ss_dssp             HHHHHHHHHHHHH-CTTCEEEEEECCCTT-HHHH-HHHTTCEEEEC
T ss_pred             hHHHHHHHHHHhc-CCCCcEEEEcCCCCc-HHHH-HHHcCCCeeeC
Confidence            2233333334444 568899999999975 3444 47776666553

>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=99.95  E-value=3.3e-28  Score=188.33  Aligned_cols=187  Identities=20%  Similarity=0.208  Sum_probs=131.8

Q ss_pred             HHHHHHHHhhc-cccCCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHH
Q psy12977         21 IVTTLAVVSNS-IFKHFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTY   98 (226)
Q Consensus        21 ~~~~l~~~~~~-~~~~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~   98 (226)
                      -+-..+.+++. +|+.++|.|..+. .+.+|+|+++++|||+|||++|.+|++..       ..++++++|+++|+.|+.
T Consensus        10 ~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~-------~~~~~~v~P~~~L~~q~~   82 (206)
T d1oywa2          10 ESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL-------NGLTVVVSPLISLMKDQV   82 (206)
T ss_dssp             HHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS-------SSEEEEECSCHHHHHHHH
T ss_pred             CHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc-------cCceEEeccchhhhhhHH
Confidence            33444556665 8999999997774 77789999999999999999999998753       348999999999999999


Q ss_pred             HHHHHHhhcCCCeEEEEecc-h--hhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCc
Q psy12977         99 NETVRLSEGLGLRAHVIGKI-Q--QAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGV  175 (226)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~-~--~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~  175 (226)
                      +.++..+..    ....... .  ..............+|+++||..+......  .......++++|+||+|.+.+++.
T Consensus        83 ~~l~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~--~~~~~~~v~~lviDEaH~~~~~~~  156 (206)
T d1oywa2          83 DQLQANGVA----AACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFL--EHLAHWNPVLLAVDEAHCISQWGH  156 (206)
T ss_dssp             HHHHHTTCC----EEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHH--HHHTTSCEEEEEESSGGGGCTTSS
T ss_pred             HHHHhhccc----ccccccccccccchhHHHHHhcCCceEEEEechhhhchhhc--ccchhheeeeeeeeeeeeeecccc
Confidence            999877532    2222111 1  111111122346688999999988655433  344577899999999999887643


Q ss_pred             cc--hHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHh--cCCCeEEec
Q psy12977        176 RG--FRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRK--LKRRVQINV  223 (226)
Q Consensus       176 ~~--~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~--~~~p~~i~~  223 (226)
                      ..  ....+..+...+  +++|++++|||+|+++.+.+.++  +.+|+ ++|
T Consensus       157 ~~~~~~~~~~~l~~~~--~~~~ii~lSATl~~~v~~di~~~L~l~~p~-v~v  205 (206)
T d1oywa2         157 DFRPEYAALGQLRQRF--PTLPFMALTATADDTTRQDIVRLLGLNDPL-IQI  205 (206)
T ss_dssp             CCCHHHHGGGGHHHHC--TTSCEEEEESCCCHHHHHHHHHHHTCCSCE-EEE
T ss_pred             chHHHHHHHHHHHHhC--CCCceEEEEeCCCHHHHHHHHHHcCCCCCc-EEe
Confidence            21  122334445555  57899999999999886545443  78995 544

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.94  E-value=7.1e-28  Score=190.42  Aligned_cols=177  Identities=19%  Similarity=0.122  Sum_probs=124.2

Q ss_pred             HHHHhhccccCCCCccccc-ccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHH
Q psy12977         25 LAVVSNSIFKHFEPHFTIT-YLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVR  103 (226)
Q Consensus        25 l~~~~~~~~~~~~~~Q~~~-~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~  103 (226)
                      ...+-+.++++|+++|..+ +.++.|+|+++.+|||+|||.+++++++....+    +.+++|++|+++|++|+.+.+++
T Consensus        33 ~~~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~----~~rvliv~Pt~~La~Q~~~~l~~  108 (237)
T d1gkub1          33 FVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK----GKRCYVIFPTSLLVIQAAETIRK  108 (237)
T ss_dssp             HHHHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT----SCCEEEEESCHHHHHHHHHHHHH
T ss_pred             HHHHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHh----cCeEEEEeccHHHHHHHHHHHHH
Confidence            3444455788999999766 577899999999999999999999988877653    45899999999999999999999


Q ss_pred             HhhcCCCeEE----EEecchhhhh-hhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccch
Q psy12977        104 LSEGLGLRAH----VIGKIQQAAE-KFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGF  178 (226)
Q Consensus       104 ~~~~~~~~~~----~~~~~~~~~~-~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~  178 (226)
                      +.+..+....    ...+...... ........+++|+|+||+++.+...      .+.+++++|+||+|.+++.+.  .
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~~~------~~~~~~~vVvDE~d~~l~~~~--~  180 (237)
T d1gkub1         109 YAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYR------ELGHFDFIFVDDVDAILKASK--N  180 (237)
T ss_dssp             HHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCST------TSCCCSEEEESCHHHHHTSTH--H
T ss_pred             HHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHhhh------hcCCCCEEEEEChhhhhhccc--c
Confidence            9887765432    2222211111 1111223567899999998766433      367899999999999887631  1


Q ss_pred             HHHHHHHHH---------hcCCCCceEEEEeeeCchhHHHHHHH
Q psy12977        179 RDQLAVIYA---------ACSGPNLKRGMFSATHTEDVAKWCRR  213 (226)
Q Consensus       179 ~~~i~~i~~---------~~~~~~~q~v~~SAT~~~~~~~~~~~  213 (226)
                      ...+...+.         ...+...|++++|||+++..+..+.+
T Consensus       181 ~~~~~~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~l~r  224 (237)
T d1gkub1         181 VDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFR  224 (237)
T ss_dssp             HHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTHHHHH
T ss_pred             hhHHHHhcCChHHHHHHHhhCCCCCeEEEEeCCCCcccHHHHHH
Confidence            122222211         11246789999999998765444433

>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=99.92  E-value=2.4e-25  Score=171.11  Aligned_cols=164  Identities=16%  Similarity=0.126  Sum_probs=120.5

Q ss_pred             CCCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEE
Q psy12977         35 HFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHV  114 (226)
Q Consensus        35 ~~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~  114 (226)
                      +|.+.|..+.....++|.++++|||+|||++++.++...+.+.   +.++++++|+++|++|+.+.+.++....+.++..
T Consensus         9 ~pr~~Q~~~~~~~~~~n~lv~~pTGsGKT~i~~~~~~~~~~~~---~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~~   85 (200)
T d1wp9a1           9 QPRIYQEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKY---GGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVA   85 (200)
T ss_dssp             CCCHHHHHHHHHGGGSCEEEECCTTSCHHHHHHHHHHHHHHHS---CSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEE
T ss_pred             CCCHHHHHHHHHHhcCCeEEEeCCCCcHHHHHHHHHHHHHHhc---CCcEEEEcCchHHHHHHHHHHHHhhcccccceee
Confidence            5667786665334567899999999999998888776666432   3479999999999999999999998877777766


Q ss_pred             EecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCc
Q psy12977        115 IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNL  194 (226)
Q Consensus       115 ~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~  194 (226)
                      ..++.......  .....++++++||+.+...+..  ....+.+++++|+||||.+.+..  ............  ...+
T Consensus        86 ~~~~~~~~~~~--~~~~~~~i~i~t~~~~~~~~~~--~~~~~~~~~~vIiDE~H~~~~~~--~~~~~~~~~~~~--~~~~  157 (200)
T d1wp9a1          86 LTGEKSPEERS--KAWARAKVIVATPQTIENDLLA--GRISLEDVSLIVFDEAHRAVGNY--AYVFIAREYKRQ--AKNP  157 (200)
T ss_dssp             ECSCSCHHHHH--HHHHHCSEEEECHHHHHHHHHT--TSCCTTSCSEEEEETGGGCSTTC--HHHHHHHHHHHH--CSSC
T ss_pred             eecccchhHHH--HhhhcccccccccchhHHHHhh--hhhhccccceEEEEehhhhhcch--hHHHHHHHHHhc--CCCC
Confidence            55544332221  1223468999999999998877  66778899999999999887652  223333333333  3578


Q ss_pred             eEEEEeeeCchhHHH
Q psy12977        195 KRGMFSATHTEDVAK  209 (226)
Q Consensus       195 q~v~~SAT~~~~~~~  209 (226)
                      +++++|||++.....
T Consensus       158 ~~l~~SATp~~~~~~  172 (200)
T d1wp9a1         158 LVIGLTASPGSTPEK  172 (200)
T ss_dssp             CEEEEESCSCSSHHH
T ss_pred             cEEEEEecCCCcHHH
Confidence            999999998654443

>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=99.84  E-value=1.5e-21  Score=158.55  Aligned_cols=140  Identities=19%  Similarity=0.165  Sum_probs=96.6

Q ss_pred             cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhh
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEK  124 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (226)
                      ++.+++++++.||||||||.+|+.+++.....   .+.+++|++|+++||+|+++.++.+..    .....        .
T Consensus         5 ~~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~---~~~~~lvi~Ptr~La~q~~~~l~~~~~----~~~~~--------~   69 (305)
T d2bmfa2           5 IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIK---RGLRTLILAPTRVVAAEMEEALRGLPI----RYQTP--------A   69 (305)
T ss_dssp             SSSTTCEEEECCCTTSSTTTTHHHHHHHHHHH---HTCCEEEEESSHHHHHHHHHHTTTSCC----BCCC----------
T ss_pred             HhhcCCcEEEEECCCCCHHHHHHHHHHHHHHh---cCCEEEEEccHHHHHHHHHHHHhcCCc----ceeee--------E
Confidence            45688999999999999999888887765543   256899999999999999887765432    21111        1


Q ss_pred             hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        125 FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       125 ~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      ..........++++|++.+......   ...+.+++++|+||+|.+.++.   + .....+......+..+++++|||+|
T Consensus        70 ~~~~~~~~~~i~~~t~~~l~~~~~~---~~~~~~~~~vViDE~H~~~~~~---~-~~~~~l~~~~~~~~~~~v~~SAT~~  142 (305)
T d2bmfa2          70 IRAEHTGREIVDLMCHATFTMRLLS---PIRVPNYNLIIMDEAHFTDPAS---I-AARGYISTRVEMGEAAGIFMTATPP  142 (305)
T ss_dssp             ------CCCSEEEEEHHHHHHHHTS---SSCCCCCSEEEEESTTCCSHHH---H-HHHHHHHHHHHHTSCEEEEECSSCT
T ss_pred             EeecccCccccccCCcHHHHHHHhc---CccccceeEEEeeeeeecchhh---H-HHHHHHHHhhccccceEEEeecCCC
Confidence            1112335567999999988877664   4457889999999999886652   1 1111122122236789999999987


Q ss_pred             hh
Q psy12977        205 ED  206 (226)
Q Consensus       205 ~~  206 (226)
                      ..
T Consensus       143 ~~  144 (305)
T d2bmfa2         143 GS  144 (305)
T ss_dssp             TC
T ss_pred             cc
Confidence            54

>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=99.82  E-value=1.4e-20  Score=135.40  Aligned_cols=137  Identities=20%  Similarity=0.165  Sum_probs=92.1

Q ss_pred             CCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh
Q psy12977         46 SPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF  125 (226)
Q Consensus        46 ~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (226)
                      +..|++.++.+|||+|||..++..++.....   .+.++++++|++++++|..+.+...    +..+.....        
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~---~~~~vli~~p~~~l~~q~~~~~~~~----~~~~~~~~~--------   68 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECAR---RRLRTLVLAPTRVVLSEMKEAFHGL----DVKFHTQAF--------   68 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHH---TTCCEEEEESSHHHHHHHHHHTTTS----CEEEESSCC--------
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhh---cCceeeeeecchhHHHHHHHHhhhh----hhhhccccc--------
Confidence            4568999999999999998776666655543   2458999999999999988765332    222211111        


Q ss_pred             CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCc
Q psy12977        126 GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHT  204 (226)
Q Consensus       126 ~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~  204 (226)
                      .........+.+.|...+.+...   ....+.+++++|+||||.+....  .....+......  .++.++++||||+|
T Consensus        69 ~~~~~~~~~~~~~~~~~l~~~~~---~~~~~~~~~lvIiDEaH~~~~~~--~~~~~~~~~~~~--~~~~~~l~lTATPp  140 (140)
T d1yksa1          69 SAHGSGREVIDAMCHATLTYRML---EPTRVVNWEVIIMDEAHFLDPAS--IAARGWAAHRAR--ANESATILMTATPP  140 (140)
T ss_dssp             CCCCCSSCCEEEEEHHHHHHHHT---SSSCCCCCSEEEETTTTCCSHHH--HHHHHHHHHHHH--TTSCEEEEECSSCT
T ss_pred             ccccccccchhhhhHHHHHHHHh---ccccccceeEEEEccccccChhh--HHHHHHHHHHhh--CCCCCEEEEEcCCC
Confidence            12223445688888887776554   35568899999999999875441  111222222222  36789999999997

>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=99.77  E-value=3.1e-19  Score=143.69  Aligned_cols=150  Identities=13%  Similarity=0.051  Sum_probs=100.3

Q ss_pred             CCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEE
Q psy12977         37 EPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVI  115 (226)
Q Consensus        37 ~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  115 (226)
                      ...|..+. .++.+++.++.+|||+|||+.....+......   ...+++|++|+++|++|+.+.+.+++......+...
T Consensus       115 rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~~~~~~---~~~k~Liivp~~~Lv~Q~~~~f~~~~~~~~~~~~~~  191 (282)
T d1rifa_         115 HWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN---YEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKI  191 (282)
T ss_dssp             CHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHH---CSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEEC
T ss_pred             chHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHHHhhhc---ccceEEEEEcCchhHHHHHHHHHHhhccccccceee
Confidence            33454442 44456788999999999998754433332222   234899999999999999999998876544445444


Q ss_pred             ecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCce
Q psy12977        116 GKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLK  195 (226)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q  195 (226)
                      .++...    ........+++++|++.+.....     ..+++++++|+||||++.+.       .+..++..+ .+...
T Consensus       192 ~~g~~~----~~~~~~~~~i~i~t~qs~~~~~~-----~~~~~f~~VIvDEaH~~~a~-------~~~~il~~~-~~~~~  254 (282)
T d1rifa_         192 GGGASK----DDKYKNDAPVVVGTWQTVVKQPK-----EWFSQFGMMMNDECHLATGK-------SISSIISGL-NNCMF  254 (282)
T ss_dssp             STTCSS----TTCCCTTCSEEEECHHHHTTSCG-----GGGGGEEEEEEETGGGCCHH-------HHHHHTTTC-TTCCE
T ss_pred             cceecc----cccccccceEEEEeeehhhhhcc-----cccCCCCEEEEECCCCCCch-------hHHHHHHhc-cCCCe
Confidence            444221    12233567899999987654432     23568999999999987543       445566665 23334


Q ss_pred             EEEEeeeCchh
Q psy12977        196 RGMFSATHTED  206 (226)
Q Consensus       196 ~v~~SAT~~~~  206 (226)
                      .+++|||+++.
T Consensus       255 rlGlTaT~~~~  265 (282)
T d1rifa_         255 KFGLSGSLRDG  265 (282)
T ss_dssp             EEEECSSCCTT
T ss_pred             EEEEEeecCCC
Confidence            68999998754

>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=99.76  E-value=4.4e-18  Score=132.37  Aligned_cols=166  Identities=20%  Similarity=0.227  Sum_probs=120.6

Q ss_pred             HHHhhccccCCCCcccccc-----cCCCC--CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHH
Q psy12977         26 AVVSNSIFKHFEPHFTITY-----LSPLG--RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTY   98 (226)
Q Consensus        26 ~~~~~~~~~~~~~~Q~~~~-----~~~~~--~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~   98 (226)
                      ..+.+..--++|+-|..+.     .+.++  .+.+++|.||||||..|+..++..+.+    +.++++++|+..|+.|.+
T Consensus        46 ~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~----g~qv~~l~Pt~~La~Q~~  121 (233)
T d2eyqa3          46 QLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN----HKQVAVLVPTTLLAQQHY  121 (233)
T ss_dssp             HHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT----TCEEEEECSSHHHHHHHH
T ss_pred             HhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHc----CCceEEEccHHHhHHHHH
Confidence            3333333345666664432     12222  478999999999999999999998864    679999999999999999


Q ss_pred             HHHHHHhhcCCCeEEEEecchhhhhh---hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCc
Q psy12977         99 NETVRLSEGLGLRAHVIGKIQQAAEK---FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGV  175 (226)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~  175 (226)
                      +.+++++..++..+....+.....++   ......+..+|+|+|...+.       ..++++++.++|+||-|...-.  
T Consensus       122 ~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~-------~~~~f~~LgLiIiDEeH~fg~k--  192 (233)
T d2eyqa3         122 DNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-------SDVKFKDLGLLIVDEEHRFGVR--  192 (233)
T ss_dssp             HHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-------SCCCCSSEEEEEEESGGGSCHH--
T ss_pred             HHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc-------cCCccccccceeeechhhhhhH--
Confidence            99999999999999888776544332   22344677899999987553       3566889999999999976332  


Q ss_pred             cchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHH
Q psy12977        176 RGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWC  211 (226)
Q Consensus       176 ~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~  211 (226)
                          +. ..+...  ..++.++++|||+-++....+
T Consensus       193 ----Q~-~~l~~~--~~~~~~l~~SATPiprtl~~~  221 (233)
T d2eyqa3         193 ----HK-ERIKAM--RANVDILTLTATPIPRTLNMA  221 (233)
T ss_dssp             ----HH-HHHHHH--HTTSEEEEEESSCCCHHHHHH
T ss_pred             ----HH-HHHHhh--CCCCCEEEEecchhHHHHHHH
Confidence                21 222222  357899999999777665544

>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=99.75  E-value=7.9e-18  Score=120.93  Aligned_cols=128  Identities=13%  Similarity=0.044  Sum_probs=86.3

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPR  128 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (226)
                      .+..++.+|||+|||..+...+.   .    .+.+++|++|+++|++|+.+.+.+.....   ......+.        .
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~~---~----~~~~vli~~P~~~l~~q~~~~~~~~~~~~---~~~~~~~~--------~   69 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAYA---A----QGYKVLVLNPSVAATLGFGAYMSKAHGVD---PNIRTGVR--------T   69 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHHH---T----TTCCEEEEESCHHHHHHHHHHHHHHHSCC---CEEECSSC--------E
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHH---H----cCCcEEEEcChHHHHHHHHHHHHHHhhcc---cccccccc--------c
Confidence            46679999999999975432221   1    25589999999999999999988875432   22222221        1


Q ss_pred             cCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcC-CCCceEEEEeeeC
Q psy12977        129 SAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACS-GPNLKRGMFSATH  203 (226)
Q Consensus       129 ~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~-~~~~q~v~~SAT~  203 (226)
                      ......+.++|.+.......     ..+++++++|+||+|.+...    ....+..+++.+. .++.+++++|||+
T Consensus        70 ~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~vIiDE~H~~~~~----~~~~~~~~l~~~~~~~~~~~l~~TATP  136 (136)
T d1a1va1          70 ITTGSPITYSTYGKFLADGG-----CSGGAYDIIICDECHSTDAT----SILGIGTVLDQAETAGARLVVLATATP  136 (136)
T ss_dssp             ECCCCSEEEEEHHHHHHTTG-----GGGCCCSEEEEETTTCCSHH----HHHHHHHHHHHTTTTTCSEEEEEESSC
T ss_pred             cccccceEEEeeeeeccccc-----hhhhcCCEEEEecccccCHH----HHHHHHHHHHHHHHCCCCcEEEEeCCC
Confidence            12345688999887765533     34678999999999987443    3334445554442 3567899999995

>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=99.73  E-value=1.1e-17  Score=128.54  Aligned_cols=135  Identities=20%  Similarity=0.084  Sum_probs=92.4

Q ss_pred             CCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEE
Q psy12977         36 FEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHV  114 (226)
Q Consensus        36 ~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~  114 (226)
                      +.+.|..+. .+.++++.++.+|||+|||+.++..+ ..+      +.+++|++|+++|+.|+.+.++.+...   .+..
T Consensus        71 Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~-~~~------~~~~Liv~p~~~L~~q~~~~~~~~~~~---~~~~  140 (206)
T d2fz4a1          71 LRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAI-NEL------STPTLIVVPTLALAEQWKERLGIFGEE---YVGE  140 (206)
T ss_dssp             CCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHH-HHS------CSCEEEEESSHHHHHHHHHHHGGGCGG---GEEE
T ss_pred             cCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHH-HHh------cCceeEEEcccchHHHHHHHHHhhccc---chhh
Confidence            445665553 45567788899999999998765443 332      237899999999999999988776432   2222


Q ss_pred             EecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCc
Q psy12977        115 IGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNL  194 (226)
Q Consensus       115 ~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~  194 (226)
                      ..+.          .....+|+++|.+.+.......     ..+++++|+||||++.+.   .    ..++++.+  +..
T Consensus       141 ~~~~----------~~~~~~i~i~t~~~~~~~~~~~-----~~~~~lvIiDEaH~~~a~---~----~~~i~~~~--~~~  196 (206)
T d2fz4a1         141 FSGR----------IKELKPLTVSTYDSAYVNAEKL-----GNRFMLLIFDEVHHLPAE---S----YVQIAQMS--IAP  196 (206)
T ss_dssp             ESSS----------CBCCCSEEEEEHHHHHHTHHHH-----TTTCSEEEEECSSCCCTT---T----HHHHHHTC--CCS
T ss_pred             cccc----------cccccccccceehhhhhhhHhh-----CCcCCEEEEECCeeCCcH---H----HHHHHhcc--CCC
Confidence            2222          2234579999999887765442     346789999999998544   2    23445444  345


Q ss_pred             eEEEEeeeCc
Q psy12977        195 KRGMFSATHT  204 (226)
Q Consensus       195 q~v~~SAT~~  204 (226)
                      ..+++|||+.
T Consensus       197 ~~lgLTATl~  206 (206)
T d2fz4a1         197 FRLGLTATFE  206 (206)
T ss_dssp             EEEEEEESCC
T ss_pred             cEEEEecCCC
Confidence            6788999974

>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=99.72  E-value=1.1e-17  Score=132.31  Aligned_cols=157  Identities=19%  Similarity=0.191  Sum_probs=113.1

Q ss_pred             CCCCcccccc-c----CCCC--CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         35 HFEPHFTITY-L----SPLG--RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        35 ~~~~~Q~~~~-~----~~~~--~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      ++|+-|..+. .    +.++  .+-+++|.||||||..|+..++..+.+    |.++++++||..|+.|.++.++++++.
T Consensus        83 eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~----g~q~~~m~Pt~~La~Qh~~~~~~~f~~  158 (264)
T d1gm5a3          83 KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA----GFQTAFMVPTSILAIQHYRRTVESFSK  158 (264)
T ss_dssp             CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH----TSCEEEECSCHHHHHHHHHHHHHHHTC
T ss_pred             cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc----ccceeEEeehHhhhHHHHHHHHHhhhh
Confidence            5677775542 1    1122  367999999999999999999888864    568999999999999999999999999


Q ss_pred             CCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHH
Q psy12977        108 LGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAV  184 (226)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~  184 (226)
                      .+..+....++....++.   .....+.++|+|||..-+..       .+.++++.++|+||-|...-....        
T Consensus       159 ~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~-------~~~f~~LglviiDEqH~fgv~Qr~--------  223 (264)
T d1gm5a3         159 FNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-------DVHFKNLGLVIIDEQHRFGVKQRE--------  223 (264)
T ss_dssp             SSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-------CCCCSCCCEEEEESCCCC-----C--------
T ss_pred             ccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcC-------CCCccccceeeeccccccchhhHH--------
Confidence            999998887765544322   22335779999999876543       344678999999999987543110        


Q ss_pred             HHHhcCCCCceEEEEeeeCchhHHHHH
Q psy12977        185 IYAACSGPNLKRGMFSATHTEDVAKWC  211 (226)
Q Consensus       185 i~~~~~~~~~q~v~~SAT~~~~~~~~~  211 (226)
                      .+.+- ...+.++++|||+-++...+.
T Consensus       224 ~l~~~-~~~~~~l~~SATPiprtl~~~  249 (264)
T d1gm5a3         224 ALMNK-GKMVDTLVMSATPIPRSMALA  249 (264)
T ss_dssp             CCCSS-SSCCCEEEEESSCCCHHHHHH
T ss_pred             HHHHh-CcCCCEEEEECCCCHHHHHHH
Confidence            11111 346889999999666554433

>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=99.14  E-value=1.1e-09  Score=87.71  Aligned_cols=145  Identities=18%  Similarity=0.154  Sum_probs=89.4

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCC---CCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK---NLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAE  123 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~---~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (226)
                      ..+...++.-..|.|||+..+..+...+....   ....+++|+||.. +..|+.+++.++.......+ ...++..+..
T Consensus        77 ~~~~g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~s-l~~qW~~Ei~k~~~~~~~~v-~~~~~~~~~~  154 (298)
T d1z3ix2          77 ENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSS-LVRNWYNEVGKWLGGRVQPV-AIDGGSKDEI  154 (298)
T ss_dssp             TTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECHH-HHHHHHHHHHHHHGGGCCEE-EECSSCHHHH
T ss_pred             ccCCceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccch-hhHHHHHHHHhhcCCceeEE-EEeCchHHHH
Confidence            34567899999999999865443333333222   2234799999985 88999999999876533333 3333322211


Q ss_pred             h-------hCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceE
Q psy12977        124 K-------FGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKR  196 (226)
Q Consensus       124 ~-------~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~  196 (226)
                      .       .........+++++|.+.+.....    .+...+.+++|+||+|.+-...     .........+  .....
T Consensus       155 ~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~----~l~~~~~~~vI~DEaH~ikn~~-----s~~~~a~~~l--~~~~r  223 (298)
T d1z3ix2         155 DSKLVNFISQQGMRIPTPILIISYETFRLHAE----VLHKGKVGLVICDEGHRLKNSD-----NQTYLALNSM--NAQRR  223 (298)
T ss_dssp             HHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT----TTTTSCCCEEEETTGGGCCTTC-----HHHHHHHHHH--CCSEE
T ss_pred             HHHHHHhhhccCccccceEEEEeecccccchh----cccccceeeeeccccccccccc-----chhhhhhhcc--cccee
Confidence            1       111223456899999888765433    2333467899999999986542     1122223334  34567


Q ss_pred             EEEeeeCc
Q psy12977        197 GMFSATHT  204 (226)
Q Consensus       197 v~~SAT~~  204 (226)
                      +++|||+-
T Consensus       224 llLTGTPi  231 (298)
T d1z3ix2         224 VLISGTPI  231 (298)
T ss_dssp             EEECSSCS
T ss_pred             eeecchHH
Confidence            88999954

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=99.00  E-value=5e-10  Score=87.00  Aligned_cols=188  Identities=18%  Similarity=0.146  Sum_probs=130.8

Q ss_pred             hHHHHHHHHHHHhhcccc----CCCCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccH
Q psy12977         17 VISIIVTTLAVVSNSIFK----HFEPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTR   91 (226)
Q Consensus        17 ~~~~~~~~l~~~~~~~~~----~~~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~   91 (226)
                      ...+.|+..+.+++....    ++..+|...- .+..|+  +....||-|||+...+|++-....    |..+-+++.+-
T Consensus        58 LDdlLpEAFAlVREAakRtlG~RhyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al~----g~~vhvvTvNd  131 (273)
T d1tf5a3          58 TDDLLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT----GKGVHVVTVNE  131 (273)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT----SSCEEEEESSH
T ss_pred             cchhHHHHHHHHHHHHHHhhceEEehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhc----CCCceEEecCc
Confidence            355677777888877666    3444564443 444554  889999999999988887655443    55789999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcC-----CCCCCCCCccEEEEcc
Q psy12977         92 ELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMD-----PPALNLANVEWLIVDE  166 (226)
Q Consensus        92 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~-----~~~~~~~~~~~lViDE  166 (226)
                      .||..=.+++..+.+.+|.++.+........++   .....+||+.+|...+--.+-++     ..........+.|+||
T Consensus       132 yLA~RDae~m~~iy~~lGlsvg~~~~~~~~~~r---~~~Y~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDE  208 (273)
T d1tf5a3         132 YLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEK---REAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDE  208 (273)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEECCTTSCHHHH---HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEET
T ss_pred             cccchhhhHHhHHHHHcCCCccccccccCHHHH---HHHhhCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEc
Confidence            999999999999999999999988766544433   24467999999998886433222     1223366788999999


Q ss_pred             ccccc-ccCc-------c--chH-HHHHHHHHhcCCCCceEEEEeeeCchhHHHHHHHhcCC
Q psy12977        167 SDKLF-EAGV-------R--GFR-DQLAVIYAACSGPNLKRGMFSATHTEDVAKWCRRKLKR  217 (226)
Q Consensus       167 ~h~l~-~~~~-------~--~~~-~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~~~~~~  217 (226)
                      +|.++ |.+.       .  ... -....++    ....++.+||.|-..+..++.+-|--+
T Consensus       209 vDsiliDeartpliisg~~~~~a~it~q~~f----~~y~~l~gmtgta~~~~~e~~~iy~l~  266 (273)
T d1tf5a3         209 VDSILIDEARTPLIISGQSMTLATITFQNYF----RMYEKLAGMTGTAKTEEEEFRNIYNMQ  266 (273)
T ss_dssp             HHHHHTTTTTCEEEEEEEEEEEEEEEHHHHH----TTSSEEEEEESCCGGGHHHHHHHHCCC
T ss_pred             chhhhhhccCCceEeccCccchhhhhHHHHH----HHHHHHhCCccccHHHHHHHHhccCCc
Confidence            99775 3320       0  000 0112222    234588899999888888888777543

>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=98.95  E-value=2e-09  Score=82.86  Aligned_cols=147  Identities=16%  Similarity=0.226  Sum_probs=89.6

Q ss_pred             CCCCcccccc-----cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCC
Q psy12977         35 HFEPHFTITY-----LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLG  109 (226)
Q Consensus        35 ~~~~~Q~~~~-----~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~  109 (226)
                      ++.|.|....     ....+...++..+.|.|||...+..+........  ..+++|++| ..+..|+.+++..+.... 
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~~~~~~~~~--~~~~LIv~p-~~l~~~W~~e~~~~~~~~-   87 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENE--LTPSLVICP-LSVLKNWEEELSKFAPHL-   87 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTTC--CSSEEEEEC-STTHHHHHHHHHHHCTTS-
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhhhhhhhccc--ccccceecc-hhhhhHHHHHHHhhcccc-
Confidence            4566674442     1123456899999999999987554444443322  337899998 568899999888886533 


Q ss_pred             CeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        110 LRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                       .+........      .....+.+++++|.+.+.+....     .--..+++|+||+|.+-...   .  ........+
T Consensus        88 -~~~~~~~~~~------~~~~~~~~vvi~~~~~~~~~~~l-----~~~~~~~vI~DEah~~k~~~---s--~~~~~~~~l  150 (230)
T d1z63a1          88 -RFAVFHEDRS------KIKLEDYDIILTTYAVLLRDTRL-----KEVEWKYIVIDEAQNIKNPQ---T--KIFKAVKEL  150 (230)
T ss_dssp             -CEEECSSSTT------SCCGGGSSEEEEEHHHHTTCHHH-----HTCCEEEEEEETGGGGSCTT---S--HHHHHHHTS
T ss_pred             -cceeeccccc------hhhccCcCEEEeeHHHHHhHHHH-----hcccceEEEEEhhhcccccc---h--hhhhhhhhh
Confidence             3332222211      11234568999998877543321     12356899999999886542   1  112223344


Q ss_pred             CCCCceEEEEeeeCc
Q psy12977        190 SGPNLKRGMFSATHT  204 (226)
Q Consensus       190 ~~~~~q~v~~SAT~~  204 (226)
                        .....+++|||+-
T Consensus       151 --~a~~r~~LTgTPi  163 (230)
T d1z63a1         151 --KSKYRIALTGTPI  163 (230)
T ss_dssp             --CEEEEEEECSSCS
T ss_pred             --ccceEEEEecchH
Confidence              2345688999943

>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=98.51  E-value=3.4e-07  Score=74.79  Aligned_cols=141  Identities=16%  Similarity=0.099  Sum_probs=79.5

Q ss_pred             CCcccccc-cCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEE
Q psy12977         37 EPHFTITY-LSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVI  115 (226)
Q Consensus        37 ~~~Q~~~~-~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  115 (226)
                      +.-|..+. ..+.++-.+++||+|||||......+..........+.++++.+||..=+.++.+.........+......
T Consensus       150 ~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~~~~~~~~~~~~~~~  229 (359)
T d1w36d1         150 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQK  229 (359)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCCSCCC
T ss_pred             ccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHHHHHHhhcCchhhhh
Confidence            34465553 45567889999999999998753322222222233466899999999988888776655443332211000


Q ss_pred             ecchhhhhhhCCCcCCCCCEEEECchHHHH------hHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        116 GKIQQAAEKFGPRSAQKFDVLITTPNKLVY------LLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~------~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      ....               --..|..++..      .+..  ........+++||||+-.+..       ..+..++..+
T Consensus       230 ~~~~---------------~~~~t~~~ll~~~~~~~~~~~--~~~~~l~~d~lIIDEaSmv~~-------~l~~~ll~~~  285 (359)
T d1w36d1         230 KRIP---------------EDASTLHRLLGAQPGSQRLRH--HAGNPLHLDVLVVDEASMIDL-------PMMSRLIDAL  285 (359)
T ss_dssp             CSCS---------------CCCBTTTSCC-------------CTTSCCSCSEEEECSGGGCBH-------HHHHHHHHTC
T ss_pred             hhhh---------------hhhhHHHHHHhhhhcchHHHH--hhhcccccceeeehhhhccCH-------HHHHHHHHHh
Confidence            0000               00111111111      1111  233455788999999986532       2455666666


Q ss_pred             CCCCceEEEEeee
Q psy12977        190 SGPNLKRGMFSAT  202 (226)
Q Consensus       190 ~~~~~q~v~~SAT  202 (226)
                       ++.++++++.=.
T Consensus       286 -~~~~~lILvGD~  297 (359)
T d1w36d1         286 -PDHARVIFLGDR  297 (359)
T ss_dssp             -CTTCEEEEEECT
T ss_pred             -cCCCEEEEECCh
Confidence             567899988644

>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=97.99  E-value=3.2e-05  Score=58.09  Aligned_cols=108  Identities=17%  Similarity=0.218  Sum_probs=64.9

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRS  129 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (226)
                      ..++++||+|+|||... .++.+.....   +..++++ +..+...+..+.+..-                         
T Consensus        37 n~l~l~G~~G~GKTHLl-~A~~~~~~~~---~~~~~~~-~~~~~~~~~~~~~~~~-------------------------   86 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHLL-QAAGNEAKKR---GYRVIYS-SADDFAQAMVEHLKKG-------------------------   86 (213)
T ss_dssp             SSEEEECSSSSSHHHHH-HHHHHHHHHT---TCCEEEE-EHHHHHHHHHHHHHHT-------------------------
T ss_pred             CcEEEECCCCCcHHHHH-HHHHHHhccC---ccceEEe-chHHHHHHHHHHHHcc-------------------------
Confidence            34899999999999643 4445544322   2344444 5555555544433211                         


Q ss_pred             CCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhH
Q psy12977        130 AQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       130 ~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~  207 (226)
                               ....+.+.         +...+++++|++|.+.+..  .....+..++..+...+.++++.|...|++.
T Consensus        87 ---------~~~~~~~~---------~~~~dll~iDDi~~i~~~~--~~~~~lf~lin~~~~~~~~iiits~~~p~~l  144 (213)
T d1l8qa2          87 ---------TINEFRNM---------YKSVDLLLLDDVQFLSGKE--RTQIEFFHIFNTLYLLEKQIILASDRHPQKL  144 (213)
T ss_dssp             ---------CHHHHHHH---------HHTCSEEEEECGGGGTTCH--HHHHHHHHHHHHHHHTTCEEEEEESSCGGGC
T ss_pred             ---------chhhHHHH---------HhhccchhhhhhhhhcCch--HHHHHHHHHHHHHhhccceEEEecCCcchhc
Confidence                     11122222         3367899999999886542  3455666677666567788888777666543

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=97.97  E-value=3.9e-06  Score=66.71  Aligned_cols=79  Identities=16%  Similarity=0.187  Sum_probs=57.3

Q ss_pred             HhhccccCCCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         28 VSNSIFKHFEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        28 ~~~~~~~~~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      +.+.....+++-|..+... .+.+++|.|++|||||...+.-+...+........+++++++++..+..+...+.+....
T Consensus         4 ~~~~~~~~L~~eQ~~~v~~-~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~~~~   82 (318)
T d1pjra1           4 LSEQLLAHLNKEQQEAVRT-TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGG   82 (318)
T ss_dssp             HHHHHHTTSCHHHHHHHHC-CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHGG
T ss_pred             hHHHHHHhCCHHHHHHHhC-CCCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhhccc
Confidence            4455556678878665432 346799999999999998776666555543333458999999999999998888766443

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=97.91  E-value=4.3e-06  Score=65.87  Aligned_cols=70  Identities=20%  Similarity=0.133  Sum_probs=49.3

Q ss_pred             CCCcccccccCCCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhh
Q psy12977         36 FEPHFTITYLSPLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE  106 (226)
Q Consensus        36 ~~~~Q~~~~~~~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~  106 (226)
                      ++|-|..+... ...+++|.|++|||||...+.-+...+........+++++++|++.+..+.+.+.+...
T Consensus         2 L~~eQ~~av~~-~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1           2 LNPGQQQAVEF-VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             CCHHHHHHHHC-CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             cCHHHHHHHhC-CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            46666555432 34678999999999998766544444432222345899999999999999888877654

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=97.74  E-value=4.4e-05  Score=57.05  Aligned_cols=137  Identities=17%  Similarity=0.158  Sum_probs=72.2

Q ss_pred             CCCe-EEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC
Q psy12977         48 LGRQ-IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG  126 (226)
Q Consensus        48 ~~~~-~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (226)
                      ..++ +++.||||+|||....--+.....+  . ..-+++-+.+...+-  .++++.+.+..+..+........      
T Consensus         8 ~~~~vi~lvGp~GvGKTTTiaKLA~~~~~~--g-~kV~lit~Dt~R~gA--~eQL~~~a~~l~v~~~~~~~~~~------   76 (207)
T d1ls1a2           8 KDRNLWFLVGLQGSGKTTTAAKLALYYKGK--G-RRPLLVAADTQRPAA--REQLRLLGEKVGVPVLEVMDGES------   76 (207)
T ss_dssp             CSSEEEEEECCTTTTHHHHHHHHHHHHHHT--T-CCEEEEECCSSCHHH--HHHHHHHHHHHTCCEEECCTTCC------
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHHC--C-CcEEEEecccccchH--HHHHHHHHHhcCCccccccccch------
Confidence            3445 5679999999998755433333332  1 223344444333322  25566666655665543322211      


Q ss_pred             CCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchh
Q psy12977        127 PRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTED  206 (226)
Q Consensus       127 ~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~  206 (226)
                                   +..+.....   ......+.+++++|=+-+.....  .....+..+.+.. ++..-++.++|+...+
T Consensus        77 -------------~~~~~~~~~---~~~~~~~~d~vlIDTaGr~~~d~--~~~~el~~~~~~~-~~~~~llv~~a~~~~~  137 (207)
T d1ls1a2          77 -------------PESIRRRVE---EKARLEARDLILVDTAGRLQIDE--PLMGELARLKEVL-GPDEVLLVLDAMTGQE  137 (207)
T ss_dssp             -------------HHHHHHHHH---HHHHHHTCCEEEEECCCCSSCCH--HHHHHHHHHHHHH-CCSEEEEEEEGGGTHH
T ss_pred             -------------hhHHHHHHH---HHHhhccCcceeecccccchhhh--hhHHHHHHHHhhc-CCceEEEEeccccchh
Confidence                         111111100   00113456788888877654331  4666777777666 4555667778887776


Q ss_pred             HHHHHHHh
Q psy12977        207 VAKWCRRK  214 (226)
Q Consensus       207 ~~~~~~~~  214 (226)
                      ..+.++.+
T Consensus       138 ~~~~~~~f  145 (207)
T d1ls1a2         138 ALSVARAF  145 (207)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            66666554

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.65  E-value=0.00028  Score=53.51  Aligned_cols=40  Identities=13%  Similarity=0.044  Sum_probs=26.9

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      .+.+++|+||+|.+...    ....+..+++.. ++.+.+++.+-
T Consensus       114 ~~~kviiIde~d~l~~~----~q~~Llk~lE~~-~~~~~~il~tn  153 (239)
T d1njfa_         114 GRFKVYLIDEVHMLSRH----SFNALLKTLEEP-PEHVKFLLATT  153 (239)
T ss_dssp             SSSEEEEEETGGGSCHH----HHHHHHHHHHSC-CTTEEEEEEES
T ss_pred             CCCEEEEEECcccCCHH----HHHHHHHHHhcC-CCCeEEEEEcC
Confidence            45679999999998654    445666666654 45666666543

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.57  E-value=0.00044  Score=51.35  Aligned_cols=42  Identities=12%  Similarity=0.002  Sum_probs=29.0

Q ss_pred             CCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEee
Q psy12977        155 NLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSA  201 (226)
Q Consensus       155 ~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SA  201 (226)
                      .....+++|+||+|.+...    ....+..+++.- ++++.+++.+.
T Consensus       105 ~~~~~kviIide~d~l~~~----a~n~Llk~lEep-~~~~~fIl~t~  146 (207)
T d1a5ta2         105 RLGGAKVVWVTDAALLTDA----AANALLKTLEEP-PAETWFFLATR  146 (207)
T ss_dssp             TTSSCEEEEESCGGGBCHH----HHHHHHHHHTSC-CTTEEEEEEES
T ss_pred             ccCccceEEechhhhhhhh----hhHHHHHHHHhh-cccceeeeeec
Confidence            3456789999999998765    556666777664 45566666443

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.50  E-value=0.00041  Score=51.18  Aligned_cols=103  Identities=10%  Similarity=-0.006  Sum_probs=61.1

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH--HHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE--LAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF  125 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~--L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (226)
                      .+.++++.||+|+|||...... .+.+.......+-++++.|...  -.+|+.+                          
T Consensus        14 ~~~~~l~~G~~g~gk~~~a~~l-~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~--------------------------   66 (198)
T d2gnoa2          14 EGISILINGEDLSYPREVSLEL-PEYVEKFPPKASDVLEIDPEGENIGIDDIRT--------------------------   66 (198)
T ss_dssp             SSEEEEEECSSSSHHHHHHHHH-HHHHHTSCCCTTTEEEECCSSSCBCHHHHHH--------------------------
T ss_pred             CCceEEEECCCCCCHHHHHHHH-HHHHhccccCCCCEEEEeCCcCCCCHHHHHH--------------------------
Confidence            3468999999999999765432 3444333333455677666411  0122211                          


Q ss_pred             CCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        126 GPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       126 ~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                                       +.+.+..   .-.....+++|+||||.|...    ....+..+++.- ++++.++++|..
T Consensus        67 -----------------i~~~~~~---~~~~~~~KviIId~ad~l~~~----aqNaLLK~LEEP-p~~t~fiLit~~  118 (198)
T d2gnoa2          67 -----------------IKDFLNY---SPELYTRKYVIVHDCERMTQQ----AANAFLKALEEP-PEYAVIVLNTRR  118 (198)
T ss_dssp             -----------------HHHHHTS---CCSSSSSEEEEETTGGGBCHH----HHHHTHHHHHSC-CTTEEEEEEESC
T ss_pred             -----------------HHHHHhh---CcccCCCEEEEEeCccccchh----hhhHHHHHHhCC-CCCceeeeccCC
Confidence                             2222221   111345679999999999765    666777777765 556677766554

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=97.41  E-value=0.00033  Score=52.23  Aligned_cols=128  Identities=13%  Similarity=0.103  Sum_probs=67.5

Q ss_pred             EEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCC
Q psy12977         52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQ  131 (226)
Q Consensus        52 ~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (226)
                      +++.||||+|||.+..--+.. +... + ..-+++.+.+...+  -.++++.+.+..++.+........           
T Consensus        12 i~lvGptGvGKTTTiAKLA~~-~~~~-g-~kV~lit~Dt~R~g--A~eQL~~~a~~l~v~~~~~~~~~d-----------   75 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLARQ-FEQQ-G-KSVMLAAGDTFRAA--AVEQLQVWGQRNNIPVIAQHTGAD-----------   75 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH-HHTT-T-CCEEEECCCTTCHH--HHHHHHHHHHHTTCCEECCSTTCC-----------
T ss_pred             EEEECCCCCCHHHHHHHHHHH-HHHC-C-CcEEEEeccccccc--chhhhhhhhhhcCCcccccccCCC-----------
Confidence            568999999999876544333 3322 1 23455555554443  246677777776776543322211           


Q ss_pred             CCCEEEECchHHH-HhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcC-----CCCceEEEEeeeCch
Q psy12977        132 KFDVLITTPNKLV-YLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACS-----GPNLKRGMFSATHTE  205 (226)
Q Consensus       132 ~~~IiV~Tp~~l~-~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~-----~~~~q~v~~SAT~~~  205 (226)
                              +..+. +....    ....+.++++||=+=+.....  .....+..+.+...     .+...++.++|+...
T Consensus        76 --------~~~~l~~~~~~----a~~~~~d~ilIDTaGr~~~d~--~~~~el~~l~~~~~~~~~~~p~~~~LVl~a~~~~  141 (211)
T d2qy9a2          76 --------SASVIFDAIQA----AKARNIDVLIADTAGRLQNKS--HLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQ  141 (211)
T ss_dssp             --------HHHHHHHHHHH----HHHTTCSEEEECCCCCGGGHH--HHHHHHHHHHHHHTTTCTTCCSEEEEEEEGGGTH
T ss_pred             --------HHHHHHHHHHH----HHHcCCCEEEeccCCCccccH--HHHHHHHHHHHHHhhhcccCcceeeeehhcccCc
Confidence                    11111 11110    012356788888876543221  35555665555442     134456677888664


Q ss_pred             hHHH
Q psy12977        206 DVAK  209 (226)
Q Consensus       206 ~~~~  209 (226)
                      +...
T Consensus       142 ~~~~  145 (211)
T d2qy9a2         142 NAVS  145 (211)
T ss_dssp             HHHH
T ss_pred             chHH
Confidence            4333

>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=97.24  E-value=0.00066  Score=50.85  Aligned_cols=50  Identities=12%  Similarity=0.096  Sum_probs=28.9

Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHHH
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWCR  212 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~~  212 (226)
                      ..+.+|+||+|.+...    ....+..++... +..+.++..+....+.......
T Consensus       108 ~~~viiiDe~d~l~~~----~~~~l~~~~~~~-~~~~~~i~~~~~~~~~~~~l~s  157 (237)
T d1sxjd2         108 PYKIIILDEADSMTAD----AQSALRRTMETY-SGVTRFCLICNYVTRIIDPLAS  157 (237)
T ss_dssp             SCEEEEETTGGGSCHH----HHHHHHHHHHHT-TTTEEEEEEESCGGGSCHHHHH
T ss_pred             CceEEEEecccccCHH----HHHHHhhccccc-cccccccccccccccccccccc
Confidence            4558999999998765    344455555444 4555666554444333333333

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=97.13  E-value=0.00057  Score=50.99  Aligned_cols=60  Identities=15%  Similarity=-0.002  Sum_probs=37.7

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEE
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHV  114 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~  114 (226)
                      +-+++.||||+|||....--+.....+   ...-+++-+.+...+-.  ++++.+.+.++..+..
T Consensus        12 ~vi~lvGptGvGKTTTiAKLAa~~~~~---~~kV~lit~Dt~R~gA~--eQL~~~a~~l~i~~~~   71 (213)
T d1vmaa2          12 FVIMVVGVNGTGKTTSCGKLAKMFVDE---GKSVVLAAADTFRAAAI--EQLKIWGERVGATVIS   71 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHT---TCCEEEEEECTTCHHHH--HHHHHHHHHHTCEEEC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHC---CCceEEEeecccccchh--HHHHHHhhhcCccccc
Confidence            346789999999998765433333332   13356677776655543  6677777666766543

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=97.12  E-value=0.0026  Score=45.66  Aligned_cols=118  Identities=17%  Similarity=0.150  Sum_probs=81.5

Q ss_pred             CCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCC
Q psy12977         80 LGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNL  156 (226)
Q Consensus        80 ~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~  156 (226)
                      .+.++||.|+++.-|+.+.+.+++.    |++...+.++....++.   .....+..+|+|+|.-        ....++.
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v--------~~~GiDi   97 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEH----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINL--------LREGLDI   97 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCC--------CCTTCCC
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhc----CCceEEEecccchHHHHHHHHHHHCCCeEEEEeeee--------eeeeccC
Confidence            3669999999999999999888776    88888888876544332   2344688899999963        2278999


Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHH
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWC  211 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~  211 (226)
                      ++++++|+=.++...-.  +.....+.++-+...+.+...+++.....+.+...+
T Consensus        98 p~V~~Vi~~~~~~~~~~--~~~~~~iq~~GR~gR~~~g~~~~~~~~~~~~~~~~i  150 (174)
T d1c4oa2          98 PEVSLVAILDADKEGFL--RSERSLIQTIGRAARNARGEVWLYADRVSEAMQRAI  150 (174)
T ss_dssp             TTEEEEEETTTTSCSGG--GSHHHHHHHHGGGTTSTTCEEEEECSSCCHHHHHHH
T ss_pred             CCCcEEEEecccccccc--chhHHHHHHhhhhhhcCCCeeEEeecCCCHHHHHHH
Confidence            99999999887754322  023445555555554455566666555555555444

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=97.10  E-value=0.00057  Score=50.78  Aligned_cols=59  Identities=15%  Similarity=0.108  Sum_probs=32.6

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEccc-HHHHHHHHHHHHHHhhcCCCeE
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPT-RELAKQTYNETVRLSEGLGLRA  112 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt-~~L~~q~~~~~~~~~~~~~~~~  112 (226)
                      .++-+++.||||+|||....--+.. +... . ..-+++-+.+ |.=+.   ++++.+.+.++..+
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~~-~~~~-g-~kV~lit~Dt~R~gA~---eQL~~~a~~l~i~~   64 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGRY-YQNL-G-KKVMFCAGDTFRAAGG---TQLSEWGKRLSIPV   64 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHH-HHTT-T-CCEEEECCCCSSTTHH---HHHHHHHHHHTCCE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH-HHHC-C-CcEEEEEeccccccch---hhHhhcccccCceE
Confidence            3466788999999999875543333 3222 2 2244555554 33332   34445555556554

>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=97.10  E-value=0.00084  Score=49.96  Aligned_cols=132  Identities=13%  Similarity=0.072  Sum_probs=61.4

Q ss_pred             EEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCC
Q psy12977         52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQ  131 (226)
Q Consensus        52 ~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (226)
                      +.+.||||+|||....--+..... .  ...-+++-+.+...+-.  ++++.+.+..+..+.....              
T Consensus        15 i~lvGptGvGKTTTiAKLA~~~~~-~--g~kV~lit~Dt~R~ga~--eQL~~~a~~l~v~~~~~~~--------------   75 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAYFYKK-K--GFKVGLVGADVYRPAAL--EQLQQLGQQIGVPVYGEPG--------------   75 (211)
T ss_dssp             EEEECSCCC----HHHHHHHHHHH-T--TCCEEEEECCCSSHHHH--HHHHHHHHHHTCCEECCTT--------------
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH-C--CCceEEEEeeccccchh--HHHHHhccccCcceeeccc--------------
Confidence            567999999999875433333222 2  12356666665554442  6666676666666543222              


Q ss_pred             CCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHH
Q psy12977        132 KFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWC  211 (226)
Q Consensus       132 ~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~  211 (226)
                              ++.+...+.+.-......+.++++||=+=+............+..+.... ++..-.+.++|+...+..+.+
T Consensus        76 --------~~~~~~~~~~a~~~~~~~~~d~IlIDTaGr~~~~~~~~~~~el~~~~~~~-~~~~~~LVl~a~~~~~~~~~~  146 (211)
T d1j8yf2          76 --------EKDVVGIAKRGVEKFLSEKMEIIIVDTAGRHGYGEEAALLEEMKNIYEAI-KPDEVTLVIDASIGQKAYDLA  146 (211)
T ss_dssp             --------CCCHHHHHHHHHHHHHHTTCSEEEEECCCSCCTTCHHHHHHHHHHHHHHH-CCSEEEEEEEGGGGGGHHHHH
T ss_pred             --------chhhhHHHHHHHHHhhccCCceEEEecCCcCccchhhHHHHHHHHHHhhc-CCceEEEEEecccCcchHHHH
Confidence                    22221111100000012356678888665421110001234566666666 344455666777654443333

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.04  E-value=0.00045  Score=51.62  Aligned_cols=44  Identities=11%  Similarity=0.117  Sum_probs=28.2

Q ss_pred             CCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        155 NLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       155 ~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      ......++|+||+|.+.+.    ....+...++.. ...+.+++.+...
T Consensus        98 ~~~~~kviiiDe~d~~~~~----~~~~ll~~~e~~-~~~~~~i~~~~~~  141 (224)
T d1sxjb2          98 PPGKHKIVILDEADSMTAG----AQQALRRTMELY-SNSTRFAFACNQS  141 (224)
T ss_dssp             CTTCCEEEEEESGGGSCHH----HHHTTHHHHHHT-TTTEEEEEEESCG
T ss_pred             CCcceEEEEEecccccchh----HHHHHhhhcccc-ccceeeeeccCch
Confidence            3445679999999998776    344454555554 4556666655553

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.03  E-value=0.00019  Score=54.45  Aligned_cols=39  Identities=15%  Similarity=0.213  Sum_probs=25.8

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ...+++|+||+|.+...    ....+..+++.. +.++.+++.+
T Consensus       130 ~~~~iiiide~d~l~~~----~~~~l~~~~e~~-~~~~~~Il~t  168 (252)
T d1sxje2         130 HRYKCVIINEANSLTKD----AQAALRRTMEKY-SKNIRLIMVC  168 (252)
T ss_dssp             -CCEEEEEECTTSSCHH----HHHHHHHHHHHS-TTTEEEEEEE
T ss_pred             CCceEEEeccccccccc----cchhhhcccccc-cccccceeee
Confidence            45679999999988654    555566667665 4556666543

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=97.00  E-value=0.0014  Score=48.97  Aligned_cols=42  Identities=17%  Similarity=0.154  Sum_probs=25.3

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeee
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSAT  202 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT  202 (226)
                      .....++++||+|.+...    ....+..++... ...+.+++.+..
T Consensus       107 ~~~~~iilide~d~~~~~----~~~~ll~~l~~~-~~~~~~i~~~n~  148 (231)
T d1iqpa2         107 GASFKIIFLDEADALTQD----AQQALRRTMEMF-SSNVRFILSCNY  148 (231)
T ss_dssp             GCSCEEEEEETGGGSCHH----HHHHHHHHHHHT-TTTEEEEEEESC
T ss_pred             CCCceEEeehhhhhcchh----HHHHHhhhcccC-CcceEEEeccCC
Confidence            345679999999988765    344455555544 344555554333

>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=96.98  E-value=0.0015  Score=48.63  Aligned_cols=41  Identities=17%  Similarity=0.233  Sum_probs=26.4

Q ss_pred             CCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        155 NLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       155 ~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      ...+.+.+|+||+|.+...    ....+..+++.. ...+.+++.+
T Consensus        96 ~~~~~kiiiiDe~d~~~~~----~~~~Ll~~le~~-~~~~~~~~~~  136 (227)
T d1sxjc2          96 FSKGFKLIILDEADAMTNA----AQNALRRVIERY-TKNTRFCVLA  136 (227)
T ss_dssp             SSCSCEEEEETTGGGSCHH----HHHHHHHHHHHT-TTTEEEEEEE
T ss_pred             cCCCeEEEEEeccccchhh----HHHHHHHHhhhc-ccceeecccc
Confidence            3445679999999988765    445566666665 3455555543

>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=96.95  E-value=0.006  Score=46.19  Aligned_cols=17  Identities=35%  Similarity=0.380  Sum_probs=15.0

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +.+++.||+|+|||...
T Consensus        41 ~~vLL~GppGtGKT~la   57 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            57999999999999764

>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=96.83  E-value=0.0087  Score=45.33  Aligned_cols=17  Identities=29%  Similarity=0.538  Sum_probs=15.1

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +.+++.||+|+|||...
T Consensus        43 ~giLl~GppGtGKT~la   59 (247)
T d1ixza_          43 KGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             SEEEEECCTTSSHHHHH
T ss_pred             ceEEEecCCCCChhHHH
Confidence            67999999999999754

>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=96.53  E-value=0.0089  Score=43.56  Aligned_cols=20  Identities=25%  Similarity=0.180  Sum_probs=16.5

Q ss_pred             CCCeEEEECCCCchHhHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~   67 (226)
                      ...|+++.||+|.|||....
T Consensus        42 ~k~n~lLvG~pGVGKTalv~   61 (195)
T d1jbka_          42 TKNNPVLIGEPGVGKTAIVE   61 (195)
T ss_dssp             SSCEEEEECCTTSCHHHHHH
T ss_pred             CCCCeEEEecCCcccHHHHH
Confidence            34689999999999997653

>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=96.31  E-value=0.011  Score=45.00  Aligned_cols=18  Identities=28%  Similarity=0.527  Sum_probs=15.6

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+|||...
T Consensus        45 ~~~iLL~GppGtGKT~la   62 (256)
T d1lv7a_          45 PKGVLMVGPPGTGKTLLA   62 (256)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEeeCCCCCCccHHH
Confidence            477999999999999864

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=96.27  E-value=0.015  Score=41.83  Aligned_cols=106  Identities=18%  Similarity=0.186  Sum_probs=74.1

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC---CCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG---PRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.+++|.++++.-++.+.+.++..    +..+..+.++....++..   ....+..+|+|||.-        ....++..
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~~~----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv--------~~rGiDip   98 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLKEA----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINL--------LREGLDIP   98 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCC--------CSSSCCCT
T ss_pred             CCeEEEEeehhhhhHHHHHHHHhC----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhH--------HHccCCCC
Confidence            458999999999998888876655    888888888866544432   334678899999953        22789999


Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEe
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFS  200 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~S  200 (226)
                      +++++|.-++......  ..+...+.++-+.-.....-.+++.
T Consensus        99 ~v~~VI~~d~p~~~~~--~s~~~yi~R~GRagR~g~~~~~~~~  139 (181)
T d1t5la2          99 EVSLVAILDADKEGFL--RSERSLIQTIGRAARNANGHVIMYA  139 (181)
T ss_dssp             TEEEEEETTTTSCSGG--GSHHHHHHHHGGGTTSTTCEEEEEC
T ss_pred             CCCEEEEecCCccccc--ccHHHHHHHHHhhccccCceeEeec
Confidence            9999999988854221  1355667777666533334444433

>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=95.96  E-value=0.022  Score=43.20  Aligned_cols=17  Identities=41%  Similarity=0.634  Sum_probs=15.0

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +.+++.||+|+|||...
T Consensus        39 ~giLL~GppGtGKT~l~   55 (258)
T d1e32a2          39 RGILLYGPPGTGKTLIA   55 (258)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             ceeEEecCCCCCchHHH
Confidence            67999999999999753

>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=95.60  E-value=0.0048  Score=45.52  Aligned_cols=93  Identities=15%  Similarity=0.144  Sum_probs=68.4

Q ss_pred             CCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCC
Q psy12977         80 LGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNL  156 (226)
Q Consensus        80 ~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~  156 (226)
                      ++.++-++||..+-.+...+.+++..+  +.++..++|.....+..   .....+..+|+|||.-.     .   ..++.
T Consensus        30 rGgQvy~V~p~I~~~e~~~~~l~~~~p--~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvI-----E---vGiDv   99 (211)
T d2eyqa5          30 RGGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTII-----E---TGIDI   99 (211)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCT--TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTT-----G---GGSCC
T ss_pred             cCCeEEEEEcCccchhhHHHHHHHhCC--ceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhh-----h---hccCC
Confidence            467999999999999999888888876  45677777665444332   23346778999999631     2   67889


Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      .+..++|+++||++.       ..++.++...+
T Consensus       100 pnA~~iiI~~a~rfG-------LaQLhQLRGRV  125 (211)
T d2eyqa5         100 PTANTIIIERADHFG-------LAQLHQLRGRV  125 (211)
T ss_dssp             TTEEEEEETTTTSSC-------HHHHHHHHTTC
T ss_pred             CCCcEEEEecchhcc-------cccccccccee
Confidence            999999999999863       33566666555

>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=95.51  E-value=0.015  Score=47.35  Aligned_cols=51  Identities=22%  Similarity=0.304  Sum_probs=40.2

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      ++.++.|-||||||+... .++....      ..++|++|+...|.|+++.++.+...
T Consensus        32 ~~q~l~GltGS~ka~~iA-~l~~~~~------rp~LVVt~n~~~A~qL~~dL~~~l~~   82 (413)
T d1t5la1          32 KHQTLLGATGTGKTFTIS-NVIAQVN------KPTLVIAHNKTLAGQLYSELKEFFPH   82 (413)
T ss_dssp             SEEEEEECTTSCHHHHHH-HHHHHHT------CCEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CcEEEeCCCCcHHHHHHH-HHHHHhC------CCEEEEeCCHHHHHHHHHHHHHHcCC
Confidence            678899999999997543 3334332      25899999999999999999998643

>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=95.35  E-value=0.047  Score=43.95  Aligned_cols=47  Identities=23%  Similarity=0.218  Sum_probs=18.7

Q ss_pred             EEEEcccccccccCcc-chHHHHHHHHHhcCCCCceEEEEeeeCchhHHH
Q psy12977        161 WLIVDESDKLFEAGVR-GFRDQLAVIYAACSGPNLKRGMFSATHTEDVAK  209 (226)
Q Consensus       161 ~lViDE~h~l~~~~~~-~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~  209 (226)
                      .+++||+|.+++.+.. +..+.-..+.-.+.....|+|+  ||-|++...
T Consensus       118 ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~rg~~~~I~--~tT~~ey~~  165 (387)
T d1qvra2         118 ILFIDELHTVVGAGKAEGAVDAGNMLKPALARGELRLIG--ATTLDEYRE  165 (387)
T ss_dssp             EEEECCC-------------------HHHHHTTCCCEEE--EECHHHHHH
T ss_pred             EEEeccHHHHhcCCCCCCcccHHHHHHHHHhCCCcceee--ecCHHHHHH
Confidence            6899999999875421 2233334444444456777777  444555543

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=95.28  E-value=0.0038  Score=49.37  Aligned_cols=42  Identities=29%  Similarity=0.508  Sum_probs=30.9

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTREL   93 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L   93 (226)
                      ..+++++++|+||||||.. +-.++..+.    ...+.+.+-.+.|+
T Consensus       164 ~~~~nili~G~tgSGKTT~-l~al~~~i~----~~~rivtiEd~~El  205 (323)
T d1g6oa_         164 AIGKNVIVCGGTGSGKTTY-IKSIMEFIP----KEERIISIEDTEEI  205 (323)
T ss_dssp             HHTCCEEEEESTTSSHHHH-HHHHGGGSC----TTCCEEEEESSCCC
T ss_pred             HhCCCEEEEeeccccchHH-HHHHhhhcc----cccceeeccchhhh
Confidence            4578999999999999985 355555543    24478888787776

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.15  E-value=0.0092  Score=41.95  Aligned_cols=25  Identities=32%  Similarity=0.554  Sum_probs=19.0

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLR   75 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~   75 (226)
                      |++++.||+|+|||... ..++..+.
T Consensus         2 k~v~ItG~~GtGKTtl~-~~i~~~l~   26 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLI-HKASEVLK   26 (189)
T ss_dssp             CCEEEESCCSSCHHHHH-HHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHH-HHHHHHHH
Confidence            78999999999999843 44455553

>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=95.03  E-value=0.011  Score=44.78  Aligned_cols=16  Identities=25%  Similarity=0.123  Sum_probs=13.0

Q ss_pred             EEEECCCCchHhHHHH
Q psy12977         52 IFACAPTGSGKTAAFL   67 (226)
Q Consensus        52 ~li~apTGsGKT~~~~   67 (226)
                      +++.||+|+|||...-
T Consensus        49 l~l~GppGtGKT~l~~   64 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLAK   64 (287)
T ss_dssp             EECTTCCSSSHHHHHH
T ss_pred             EEeECCCCCCHHHHHH
Confidence            4668999999998653

>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=94.82  E-value=0.034  Score=42.48  Aligned_cols=45  Identities=20%  Similarity=0.204  Sum_probs=27.4

Q ss_pred             EEEEcccccccccCc-cchHHHHHHHHH-hcCCCCceEEEEeeeCchhH
Q psy12977        161 WLIVDESDKLFEAGV-RGFRDQLAVIYA-ACSGPNLKRGMFSATHTEDV  207 (226)
Q Consensus       161 ~lViDE~h~l~~~~~-~~~~~~i~~i~~-~~~~~~~q~v~~SAT~~~~~  207 (226)
                      ++++||+|.+++.+. .+....+..+++ .+.....|+++  +|-|++.
T Consensus       113 IlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~rg~i~vIg--atT~eey  159 (268)
T d1r6bx2         113 ILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIG--STTYQEF  159 (268)
T ss_dssp             EEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEE--EECHHHH
T ss_pred             eEEecchHHHhcCCCCCCccccHHHHhhHHHhCCCCeEEE--eCCHHHH
Confidence            888999999986542 123344555554 55455677776  4544444

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=94.79  E-value=0.1  Score=38.77  Aligned_cols=39  Identities=21%  Similarity=0.174  Sum_probs=26.2

Q ss_pred             ccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEE
Q psy12977        159 VEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMF  199 (226)
Q Consensus       159 ~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~  199 (226)
                      --.+++||.|.+.+.....+...+.......  .....++.
T Consensus       137 ~~~i~id~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~i~~  175 (283)
T d2fnaa2         137 NVIIVLDEAQELVKLRGVNLLPALAYAYDNL--KRIKFIMS  175 (283)
T ss_dssp             CEEEEEETGGGGGGCTTCCCHHHHHHHHHHC--TTEEEEEE
T ss_pred             ccccccchhhhhcccchHHHHHHHHHHHHhh--hhhhhhhc
Confidence            3478999999988766556777776666544  34444443

>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=94.36  E-value=0.26  Score=34.33  Aligned_cols=91  Identities=11%  Similarity=0.001  Sum_probs=61.2

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.|+++.-++.+.+.++..    +..+..++++....++.   .....+..+|+|+|..        ....+++.
T Consensus        27 ~~k~iIF~~~~~~~~~l~~~L~~~----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~--------~~~Gid~~   94 (168)
T d1t5ia_          27 FNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL--------FGRGMDIE   94 (168)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC--------CSTTCCGG
T ss_pred             CCeEEEEEeeeecchhhhhhhccc----cccccccccccchhhhhhhhhhhccccceeeecccc--------ccchhhcc
Confidence            347999999999999888877665    77777777775444332   1233577889999954        22678888


Q ss_pred             CccEEEEcccccccccCccchHHHHHHHHH
Q psy12977        158 NVEWLIVDESDKLFEAGVRGFRDQLAVIYA  187 (226)
Q Consensus       158 ~~~~lViDE~h~l~~~~~~~~~~~i~~i~~  187 (226)
                      .++++|.-+.-....    .+.+.+.+.-+
T Consensus        95 ~~~~vi~~~~p~~~~----~yiqr~GR~gR  120 (168)
T d1t5ia_          95 RVNIAFNYDMPEDSD----TYLHRVARAGR  120 (168)
T ss_dssp             GCSEEEESSCCSSHH----HHHHHHHHHTG
T ss_pred             cchhhhhhhcccchh----hHhhhhhhccc
Confidence            999888766543222    25555555444

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=94.18  E-value=0.15  Score=34.58  Aligned_cols=66  Identities=18%  Similarity=0.242  Sum_probs=48.4

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCCCCCEEEECchHHHHhHhcCCCCCCCCCcc
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQKFDVLITTPNKLVYLLQMDPPALNLANVE  160 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~  160 (226)
                      +.++||.|+|+.-|+++++.+++.    +..+..+.++..    .........+++|||..     +.   ..++ .+++
T Consensus        35 ~~k~IVFc~t~~~ae~la~~L~~~----G~~~~~~H~~~~----~~~~~~~~~~vlvaTd~-----~~---~GiD-~~v~   97 (138)
T d1jr6a_          35 GGRHLIFCHSKKKCDELAAKLVAL----GINAVAYYRGLD----VSVIPTNGDVVVVATDA-----LM---TGFT-GDFD   97 (138)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHH----TCEEEEECTTCC----SCCCTTSSCEEEEESSS-----SC---SSSC-CCBS
T ss_pred             CCCEEEEeCcHHHHHHHHHHHhcc----ccchhhhhccch----hhhhhhhhcceeehhHH-----HH---hccc-cccc
Confidence            347999999999999999988776    777777776643    23344577899999963     12   4566 6787


Q ss_pred             EEE
Q psy12977        161 WLI  163 (226)
Q Consensus       161 ~lV  163 (226)
                      ++|
T Consensus        98 ~Vi  100 (138)
T d1jr6a_          98 SVI  100 (138)
T ss_dssp             EEE
T ss_pred             eEE
Confidence            775

>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=93.85  E-value=0.014  Score=48.07  Aligned_cols=21  Identities=33%  Similarity=0.415  Sum_probs=17.6

Q ss_pred             CCCCeEEEECCCCchHhHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~   67 (226)
                      ...+|+++.||||+|||+.+-
T Consensus        47 i~ksNILliGPTGvGKTlLAr   67 (443)
T d1g41a_          47 VTPKNILMIGPTGVGKTEIAR   67 (443)
T ss_dssp             CCCCCEEEECCTTSSHHHHHH
T ss_pred             cccccEEEECCCCCCHHHHHH
Confidence            346799999999999998653

>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=93.72  E-value=0.022  Score=42.21  Aligned_cols=18  Identities=28%  Similarity=0.473  Sum_probs=15.5

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      .++++.||+|+|||..+-
T Consensus        36 ~~~L~~GPpGtGKT~lA~   53 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLAH   53 (238)
T ss_dssp             CCEEEESSTTSSHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHH
Confidence            579999999999998653

>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=93.41  E-value=0.026  Score=38.57  Aligned_cols=19  Identities=37%  Similarity=0.579  Sum_probs=16.1

Q ss_pred             CCeEEEECCCCchHhHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~   67 (226)
                      .+++++.||+|+|||....
T Consensus         2 ~k~I~l~G~~GsGKSTvak   20 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGR   20 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            4789999999999997643

>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=93.40  E-value=0.017  Score=45.06  Aligned_cols=19  Identities=37%  Similarity=0.529  Sum_probs=16.4

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      ..+++++.||||+|||..+
T Consensus        48 ~~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            4578999999999999865

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=93.33  E-value=0.047  Score=44.11  Aligned_cols=43  Identities=28%  Similarity=0.366  Sum_probs=26.5

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTREL   93 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L   93 (226)
                      ...+++++.|+||+|||......+.+.+..    +..++|+=|-.++
T Consensus        48 ~~~~H~~I~G~tGsGKT~~l~~li~~~~~~----g~~~iiiD~kge~   90 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVLLRELAYTGLLR----GDRMVIVDPNGDM   90 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHHHHHHHHHHHHT----TCEEEEEEETTHH
T ss_pred             cccceEEEEeCCCCcHHHHHHHHHHHHHhC----CCCEEEEeCChhH
Confidence            335789999999999998754444444432    2244444444433

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=93.21  E-value=0.012  Score=44.38  Aligned_cols=31  Identities=16%  Similarity=0.134  Sum_probs=24.0

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      +.+-+++|+||+=.-+|.   .....+...++.+
T Consensus       155 ~~~p~ililDEpts~LD~---~~~~~i~~~l~~l  185 (241)
T d2pmka1         155 VNNPKILIFDEATSALDY---ESEHVIMRNMHKI  185 (241)
T ss_dssp             TTCCSEEEECCCCSCCCH---HHHHHHHHHHHHH
T ss_pred             hcccchhhhhCCccccCH---HHHHHHHHHHHHH
Confidence            556789999999988887   5666677666666

>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=93.10  E-value=0.026  Score=41.91  Aligned_cols=18  Identities=28%  Similarity=0.456  Sum_probs=15.4

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      .++++.||+|+|||...-
T Consensus        36 ~~~Ll~GPpG~GKTtla~   53 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAH   53 (239)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            579999999999997653

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.79  E-value=0.15  Score=41.23  Aligned_cols=58  Identities=19%  Similarity=0.110  Sum_probs=38.7

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCC--------CCCceEEEEcccHHHHHHHHHHHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPK--------NLGFRAVIVCPTRELAKQTYNETVRL  104 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~--------~~~~~~iil~Pt~~L~~q~~~~~~~~  104 (226)
                      .....++|.|..|||||.+..--++..+....        .....+++++=|+.=|..+.+.+...
T Consensus        14 p~~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~~   79 (485)
T d1w36b1          14 PLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSN   79 (485)
T ss_dssp             CCSSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHHH
Confidence            34567899999999999876665555553221        11235888999987666666554443

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=92.71  E-value=0.023  Score=39.62  Aligned_cols=20  Identities=25%  Similarity=0.320  Sum_probs=16.8

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      +.|+-+++.||+|||||...
T Consensus         2 ~~g~iI~l~G~~GsGKSTia   21 (176)
T d1zp6a1           2 LGGNILLLSGHPGSGKSTIA   21 (176)
T ss_dssp             CTTEEEEEEECTTSCHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHH
Confidence            46777899999999999853

>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=92.65  E-value=0.54  Score=31.66  Aligned_cols=88  Identities=14%  Similarity=0.115  Sum_probs=51.1

Q ss_pred             EEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCC
Q psy12977         52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQ  131 (226)
Q Consensus        52 ~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (226)
                      -++.||=.||||.-.+ -.+++...   .+.+++++-|...--            + +..+....+            ..
T Consensus         5 ~~i~GpMfsGKTteLi-~~~~~~~~---~~~kv~~ikp~~D~R------------~-~~~i~s~~g------------~~   55 (139)
T d2b8ta1           5 EFITGPMFAGKTAELI-RRLHRLEY---ADVKYLVFKPKIDTR------------S-IRNIQSRTG------------TS   55 (139)
T ss_dssp             EEEECSTTSCHHHHHH-HHHHHHHH---TTCCEEEEEECCCGG------------G-CSSCCCCCC------------CS
T ss_pred             EEEEccccCHHHHHHH-HHHHHHHH---CCCcEEEEEEccccc------------c-cceEEcccC------------ce
Confidence            4788999999997543 33333322   255788888875420            0 111111111            11


Q ss_pred             CCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccc
Q psy12977        132 KFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLF  171 (226)
Q Consensus       132 ~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~  171 (226)
                      ...+.+.....+.+.+...   ....+.+++.+||++-+.
T Consensus        56 ~~~~~~~~~~~~~~~~~~~---~~~~~~dvI~IDE~QFf~   92 (139)
T d2b8ta1          56 LPSVEVESAPEILNYIMSN---SFNDETKVIGIDEVQFFD   92 (139)
T ss_dssp             SCCEEESSTHHHHHHHHST---TSCTTCCEEEECSGGGSC
T ss_pred             eeeEEeccchhhHHHHHhh---ccccCcCEEEechhhhcc
Confidence            2335666666666666542   224688999999999763

>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=92.54  E-value=0.026  Score=39.53  Aligned_cols=17  Identities=18%  Similarity=0.255  Sum_probs=15.1

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +.+++.||+|+|||...
T Consensus         8 K~I~i~G~~GsGKTTla   24 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLV   24 (192)
T ss_dssp             EEEEEECCTTSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            78999999999999754

>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=92.49  E-value=0.06  Score=39.66  Aligned_cols=39  Identities=23%  Similarity=0.169  Sum_probs=27.3

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCP   89 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~P   89 (226)
                      ..|.-+++.|+||+|||...+--+.+....    +..+++++-
T Consensus        24 ~~gsl~li~G~pGsGKT~l~~qia~~~~~~----~~~~~~is~   62 (242)
T d1tf7a2          24 FKDSIILATGATGTGKTLLVSRFVENACAN----KERAILFAY   62 (242)
T ss_dssp             ESSCEEEEEECTTSSHHHHHHHHHHHHHTT----TCCEEEEES
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHHHHh----ccccceeec
Confidence            346778999999999998665555555543    445677653

>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=92.39  E-value=0.21  Score=36.00  Aligned_cols=75  Identities=15%  Similarity=0.177  Sum_probs=53.8

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.++|+.-++.+.+.++..    +..+....++.....+.   .....+..+|+|+|..        ....++..
T Consensus        30 ~~~~IIF~~t~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~--------~~~GiD~p   97 (200)
T d1oywa3          30 GKSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVA--------FGMGINKP   97 (200)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTT--------SCTTTCCT
T ss_pred             CCCEEEEEeeehhhHHhhhhhccC----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecch--------hhhccCCC
Confidence            447999999999999988877665    67777777665433322   1233577899999974        22688899


Q ss_pred             CccEEEEccc
Q psy12977        158 NVEWLIVDES  167 (226)
Q Consensus       158 ~~~~lViDE~  167 (226)
                      +++++|.=++
T Consensus        98 ~v~~VI~~~~  107 (200)
T d1oywa3          98 NVRFVVHFDI  107 (200)
T ss_dssp             TCCEEEESSC
T ss_pred             CCCEEEECCC
Confidence            9998885443

>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=92.16  E-value=0.031  Score=38.69  Aligned_cols=17  Identities=29%  Similarity=0.333  Sum_probs=14.4

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      -++++.||+|||||...
T Consensus         5 ~~I~i~G~pGsGKTTia   21 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLG   21 (173)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            46889999999999754

>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=92.14  E-value=0.18  Score=35.00  Aligned_cols=75  Identities=17%  Similarity=0.113  Sum_probs=54.8

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC---CCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG---PRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      ..++||.|.++.-++++++.+...    +..+..+.++.....+..   ....+...|+|+|.-.      .  ..+++.
T Consensus        27 ~~k~iIF~~s~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv~------~--rGiDi~   94 (162)
T d1fuka_          27 VTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLL------A--RGIDVQ   94 (162)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGG------T--TTCCCC
T ss_pred             CCcEEEEEEEEchHHHHHHHHhhc----CceEEEeccCCchhhHHHHHHHHhhcccceeeccccc------c--ccccCC
Confidence            347999999999999998877665    777777777654433322   2335678899999642      2  688899


Q ss_pred             CccEEEEccc
Q psy12977        158 NVEWLIVDES  167 (226)
Q Consensus       158 ~~~~lViDE~  167 (226)
                      +++++|.=+.
T Consensus        95 ~v~~VI~~d~  104 (162)
T d1fuka_          95 QVSLVINYDL  104 (162)
T ss_dssp             SCSEEEESSC
T ss_pred             CceEEEEecc
Confidence            9999998664

>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=92.12  E-value=0.31  Score=33.32  Aligned_cols=75  Identities=16%  Similarity=0.227  Sum_probs=52.2

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.|++++-++++.+.++..    +..+..+.++....++.   .....+...|+|+|...     .   ..+++.
T Consensus        28 ~~k~IIF~~s~~~~~~l~~~L~~~----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~~-----~---~Gid~~   95 (155)
T d1hv8a2          28 EFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVM-----S---RGIDVN   95 (155)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTH-----H---HHCCCS
T ss_pred             CCCEEEEECchHHHHHHHhhhccc----ccccccccccchhhhhhhhhhhhhcccceeeeehhHH-----h---hhhhhc
Confidence            347999999999999988887765    77777777664333321   12234667899999531     1   467788


Q ss_pred             CccEEEEccc
Q psy12977        158 NVEWLIVDES  167 (226)
Q Consensus       158 ~~~~lViDE~  167 (226)
                      .++++|.=++
T Consensus        96 ~v~~Vi~~d~  105 (155)
T d1hv8a2          96 DLNCVINYHL  105 (155)
T ss_dssp             CCSEEEESSC
T ss_pred             cCcEEEEecC
Confidence            8998886443

>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=92.04  E-value=0.034  Score=41.52  Aligned_cols=25  Identities=16%  Similarity=0.224  Sum_probs=19.1

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHhc
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSLR   75 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~~   75 (226)
                      .++++.||+|+|||... -.+...+.
T Consensus        44 ~~lll~GppGtGKT~l~-~~l~~~l~   68 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL-RKLWELYK   68 (276)
T ss_dssp             CEEEEECCTTSSHHHHH-HHHHHHHT
T ss_pred             CceEEECCCCCCHHHHH-HHHHHHHh
Confidence            68999999999999764 33555554

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=91.97  E-value=0.042  Score=38.12  Aligned_cols=19  Identities=32%  Similarity=0.469  Sum_probs=16.1

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .+-++++.||+|+|||...
T Consensus         4 k~~~I~i~G~~GsGKTT~~   22 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMA   22 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHH
Confidence            4567999999999999864

>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=91.92  E-value=0.035  Score=37.79  Aligned_cols=17  Identities=29%  Similarity=0.366  Sum_probs=14.0

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +-+++.|++|||||...
T Consensus         3 klIii~G~pGsGKTTla   19 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEEEECCTTSSHHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            44789999999999753

>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=91.88  E-value=0.048  Score=40.51  Aligned_cols=43  Identities=21%  Similarity=0.155  Sum_probs=25.2

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeC
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATH  203 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~  203 (226)
                      .....+++||+|.+.... +++...+......   ....+++.+++.
T Consensus       122 ~~~~vi~ide~~~~~~~~-~~~~~~~~~~~~~---~~~~ii~i~~~~  164 (253)
T d1sxja2         122 GKHFVIIMDEVDGMSGGD-RGGVGQLAQFCRK---TSTPLILICNER  164 (253)
T ss_dssp             TTSEEEEECSGGGCCTTS-TTHHHHHHHHHHH---CSSCEEEEESCT
T ss_pred             ccceEEEeeeccccccch-hhhhHHHhhhhcc---cccccccccccc
Confidence            345689999999887653 2344444444333   344566655553

>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=91.86  E-value=0.028  Score=42.15  Aligned_cols=24  Identities=25%  Similarity=0.285  Sum_probs=17.5

Q ss_pred             CeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         50 RQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      +.+++.||||+|||... -.+...+
T Consensus        33 ~~ilL~GpPGtGKT~la-~~la~~~   56 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLR-SAIFEET   56 (273)
T ss_dssp             EEEEEECCTTSCTHHHH-HHHHHHT
T ss_pred             EEEEEECCCCCCHHHHH-HHHHHHh
Confidence            56999999999999854 3344433

>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=91.75  E-value=0.67  Score=32.13  Aligned_cols=77  Identities=14%  Similarity=0.103  Sum_probs=56.6

Q ss_pred             CceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhh---CCCcCCCCCEEEECchHHHHhHhcCCCCCCCC
Q psy12977         81 GFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKF---GPRSAQKFDVLITTPNKLVYLLQMDPPALNLA  157 (226)
Q Consensus        81 ~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~  157 (226)
                      +.++||.|+++.-++.+...+...    +..+..+.++....++.   .....+..+|+|||..        ....+++.
T Consensus        32 ~~k~iVF~~~~~~~~~l~~~L~~~----g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~--------~~~Gid~~   99 (171)
T d1s2ma2          32 INQAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL--------LTRGIDIQ   99 (171)
T ss_dssp             CSEEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC--------SSSSCCCT
T ss_pred             CCceEEEEeeeehhhHhHHhhhcc----cccccccccccchhhhhhhhhhcccCccccccchhH--------hhhccccc
Confidence            458999999999999988888766    77777777665433222   2234577899999974        23788999


Q ss_pred             CccEEEEccccc
Q psy12977        158 NVEWLIVDESDK  169 (226)
Q Consensus       158 ~~~~lViDE~h~  169 (226)
                      +++++|.-++..
T Consensus       100 ~v~~VI~~d~p~  111 (171)
T d1s2ma2         100 AVNVVINFDFPK  111 (171)
T ss_dssp             TEEEEEESSCCS
T ss_pred             eeEEEEecCCcc
Confidence            999999766653

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=91.63  E-value=0.05  Score=37.66  Aligned_cols=19  Identities=21%  Similarity=0.288  Sum_probs=15.9

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      +.+-+++.|++|||||...
T Consensus         2 ~~kiI~l~G~~GsGKsTva   20 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4577899999999999754

>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=91.59  E-value=0.039  Score=38.06  Aligned_cols=27  Identities=4%  Similarity=-0.166  Sum_probs=19.2

Q ss_pred             CCceEEEEeeeCchhHHHHHHHhcCCC
Q psy12977        192 PNLKRGMFSATHTEDVAKWCRRKLKRR  218 (226)
Q Consensus       192 ~~~q~v~~SAT~~~~~~~~~~~~~~~p  218 (226)
                      ....++-.|.--|+++.+.++.++.++
T Consensus       145 ~~~~~id~~~~~~~~~~~~I~~i~~~~  171 (176)
T d2bdta1         145 DERYFYNTSHLQPTNLNDIVKNLKTNP  171 (176)
T ss_dssp             CTTSEEECSSSCGGGHHHHHHHHHHCG
T ss_pred             CCeEEEECCCCCHHHHHHHHHHHHhcC
Confidence            445566666667788888888887664

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=91.45  E-value=0.019  Score=43.64  Aligned_cols=30  Identities=17%  Similarity=0.164  Sum_probs=24.2

Q ss_pred             CCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        157 ANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       157 ~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      .+-+++|+||+-.-+|.   .....+...++.+
T Consensus       171 ~~p~ililDEpts~LD~---~t~~~i~~~l~~l  200 (255)
T d2hyda1         171 NNPPILILDEATSALDL---ESESIIQEALDVL  200 (255)
T ss_dssp             HCCSEEEEESTTTTCCH---HHHHHHHHHHHHH
T ss_pred             cCCCEEEEeCccccCCH---HHHHHHHHHHHHH
Confidence            45679999999998887   5677777777777

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=91.43  E-value=0.33  Score=36.69  Aligned_cols=43  Identities=21%  Similarity=0.274  Sum_probs=27.7

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAK   95 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~   95 (226)
                      |+-+.+.+|+|+|||...+..+...-..    +..++|+-.-..+-.
T Consensus        57 g~itei~G~~~sGKT~l~l~~~~~aqk~----g~~v~yiDtE~~~~~   99 (268)
T d1xp8a1          57 GRITEIYGPESGGKTTLALAIVAQAQKA----GGTCAFIDAEHALDP   99 (268)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHT----TCCEEEEESSCCCCH
T ss_pred             ceEEEEecCCccchHHHHHHHHHHHHhC----CCEEEEEECCccCCH
Confidence            4667899999999998665554444332    346777754433433

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=91.08  E-value=0.11  Score=39.54  Aligned_cols=92  Identities=21%  Similarity=0.335  Sum_probs=51.4

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCC
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPR  128 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (226)
                      |+-+.+.+|+|+|||...+..+......    +.+++|+-.-..+..+.   ++++    +...          +     
T Consensus        60 g~i~e~~G~~~~GKT~l~l~~~~~~q~~----g~~~vyIDtE~~~~~e~---a~~~----GvD~----------d-----  113 (269)
T d1mo6a1          60 GRVIEIYGPESSGKTTVALHAVANAQAA----GGVAAFIDAEHALDPDY---AKKL----GVDT----------D-----  113 (269)
T ss_dssp             SSEEEEECSSSSSHHHHHHHHHHHHHHT----TCEEEEEESSCCCCHHH---HHHH----TCCG----------G-----
T ss_pred             ceeEEEecCCCcHHHHHHHHHHHHHhcC----CCEEEEEECCccCCHHH---HHHh----CCCH----------H-----
Confidence            5668899999999998766555544432    45778775544443332   3333    2210          1     


Q ss_pred             cCCCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccccccc
Q psy12977        129 SAQKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLF  171 (226)
Q Consensus       129 ~~~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~  171 (226)
                           ++++..|....+.+..-.....-..++++|+|-+-.+.
T Consensus       114 -----~il~~~~~~~E~~~~~~~~l~~~~~~~liIiDSi~al~  151 (269)
T d1mo6a1         114 -----SLLVSQPDTGEQALEIADMLIRSGALDIVVIDSVAALV  151 (269)
T ss_dssp             -----GCEEECCSSHHHHHHHHHHHHHTTCEEEEEEECSTTCC
T ss_pred             -----HeEEecCCCHHHHHHHHHHHHhcCCCCEEEEecccccc
Confidence                 14444444443333210011113467899999998776

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=91.02  E-value=0.059  Score=37.35  Aligned_cols=20  Identities=35%  Similarity=0.330  Sum_probs=16.9

Q ss_pred             CCCCeEEEECCCCchHhHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~   66 (226)
                      ..|..++++|++|+|||...
T Consensus         4 ~~g~~I~l~G~~GsGKTTia   23 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKDAIA   23 (183)
T ss_dssp             TCCEEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHH
Confidence            46677889999999999764

>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=90.94  E-value=0.087  Score=42.47  Aligned_cols=26  Identities=31%  Similarity=0.498  Sum_probs=19.7

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhc
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLR   75 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~   75 (226)
                      +.-+++.||||||||... ..+++.+.
T Consensus       158 ~GliLvtGpTGSGKSTTl-~~~l~~~~  183 (401)
T d1p9ra_         158 HGIILVTGPTGSGKSTTL-YAGLQELN  183 (401)
T ss_dssp             SEEEEEECSTTSCHHHHH-HHHHHHHC
T ss_pred             hceEEEEcCCCCCccHHH-HHHhhhhc
Confidence            345899999999999864 55666664

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.58  E-value=0.049  Score=41.08  Aligned_cols=41  Identities=12%  Similarity=0.148  Sum_probs=28.6

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEE
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMF  199 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~  199 (226)
                      +.+-+++++||+=.-+|.   .....+...+..+....-..+++
T Consensus       167 ~~~p~ililDEpTs~LD~---~~~~~i~~~l~~l~~~~~~Tvi~  207 (251)
T d1jj7a_         167 IRKPCVLILDDATSALDA---NSQLQVEQLLYESPERYSRSVLL  207 (251)
T ss_dssp             TTCCSEEEEESTTTTCCH---HHHHHHHHHHHTCGGGGGCEEEE
T ss_pred             ccCCcEEEecCcCcccCh---hhHHHHHHHHHHHhhhcCCEEEE
Confidence            566789999999988887   56777777777663322344444

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=90.53  E-value=0.034  Score=42.06  Aligned_cols=31  Identities=16%  Similarity=0.239  Sum_probs=23.7

Q ss_pred             CCCccEEEEcccccccccCccchHHHHHHHHHhc
Q psy12977        156 LANVEWLIVDESDKLFEAGVRGFRDQLAVIYAAC  189 (226)
Q Consensus       156 ~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~  189 (226)
                      +.+-+++|+||+=.-+|.   .....+...++.+
T Consensus       168 ~~~p~ililDEpts~LD~---~~~~~i~~~l~~l  198 (253)
T d3b60a1         168 LRDSPILILDEATSALDT---ESERAIQAALDEL  198 (253)
T ss_dssp             HHCCSEEEEETTTSSCCH---HHHHHHHHHHHHH
T ss_pred             hcCCCEEEeccccccCCH---HHHHHHHHHHHHh
Confidence            335679999999988887   5667777777666

>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=90.36  E-value=0.096  Score=38.24  Aligned_cols=44  Identities=7%  Similarity=-0.105  Sum_probs=26.8

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcC--CCCCCceEEEEccc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRG--PKNLGFRAVIVCPT   90 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~--~~~~~~~~iil~Pt   90 (226)
                      ..|+-+++.||+|+|||...+-.+.+....  ....+..++++.-.
T Consensus        32 ~~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~   77 (251)
T d1szpa2          32 ETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE   77 (251)
T ss_dssp             ESSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESS
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeec
Confidence            456789999999999997554433333221  12234467776543

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=90.32  E-value=0.064  Score=37.23  Aligned_cols=18  Identities=28%  Similarity=0.283  Sum_probs=15.2

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      +++++.|++|+|||...-
T Consensus         1 k~I~liG~~GsGKsTi~k   18 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLAR   18 (161)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            578999999999997643

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=90.24  E-value=0.064  Score=37.04  Aligned_cols=21  Identities=24%  Similarity=0.102  Sum_probs=16.1

Q ss_pred             CCCeEEEECCCCchHhHHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~   68 (226)
                      +++-+++.||+|||||...-.
T Consensus         5 ~~~iivl~G~~GsGKsT~a~~   25 (171)
T d1knqa_           5 DHHIYVLMGVSGSGKSAVASE   25 (171)
T ss_dssp             TSEEEEEECSTTSCHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            345578999999999986543

>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=90.14  E-value=0.062  Score=42.81  Aligned_cols=19  Identities=42%  Similarity=0.501  Sum_probs=16.3

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .-.+++..||||+|||..+
T Consensus        67 p~~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          67 SKSNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCcceeeeCCCCccHHHHH
Confidence            3478999999999999865

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.01  E-value=0.11  Score=36.91  Aligned_cols=28  Identities=14%  Similarity=0.017  Sum_probs=20.7

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      ..|+-+++.||+|+|||...+-.+.+..
T Consensus        21 ~~G~v~~i~G~~GsGKT~l~l~la~~~~   48 (242)
T d1n0wa_          21 ETGSITEMFGEFRTGKTQICHTLAVTCQ   48 (242)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             cCCEEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            3567899999999999976554444444

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=89.98  E-value=0.37  Score=38.74  Aligned_cols=53  Identities=30%  Similarity=0.359  Sum_probs=39.7

Q ss_pred             CCC-CeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhh
Q psy12977         47 PLG-RQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSE  106 (226)
Q Consensus        47 ~~~-~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~  106 (226)
                      ..| +...+.|.+||+|++... .+.....      ..++|++|+...|.++++.+..+..
T Consensus        25 ~~g~~~~~L~GlsgS~ka~~~A-~l~~~~~------rp~LvVt~~~~~A~~l~~dL~~~l~   78 (408)
T d1c4oa1          25 RDGERFVTLLGATGTGKTVTMA-KVIEALG------RPALVLAPNKILAAQLAAEFRELFP   78 (408)
T ss_dssp             HTTCSEEEEEECTTSCHHHHHH-HHHHHHT------CCEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             hcCCCcEEEecCCCCHHHHHHH-HHHHHhC------CCEEEEeCCHHHHHHHHHHHHHhcC
Confidence            344 457899999999997532 3333332      2578999999999999999998864

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=89.81  E-value=0.14  Score=35.53  Aligned_cols=141  Identities=13%  Similarity=0.050  Sum_probs=73.2

Q ss_pred             EEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhCCCcCC
Q psy12977         52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFGPRSAQ  131 (226)
Q Consensus        52 ~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (226)
                      +.+-...|-|||.+++--++..+-.    +.+++++-=.+--...  .. ..+.+..+........+-..... ....  
T Consensus         5 i~vytG~GKGKTTAAlG~alRA~G~----G~rV~ivQFlKg~~~~--ge-~~~~~~~~~~~~~~~~~~~~~~~-~~e~--   74 (157)
T d1g5ta_           5 IIVFTGNGKGKTTAAFGTAARAVGH----GKNVGVVQFIKGTWPN--GE-RNLLEPHGVEFQVMATGFTWETQ-NREA--   74 (157)
T ss_dssp             EEEEESSSSCHHHHHHHHHHHHHHT----TCCEEEEESSCCSSCC--HH-HHHHGGGTCEEEECCTTCCCCGG-GHHH--
T ss_pred             EEEEeCCCCCcHHHHHHHHHHHhcC----CCEEEEEEEecCCccc--ch-hhhhcccCcEEEEecCCCcccCC-ChHH--
Confidence            5566778999999988777777643    5577777643321100  00 11122223333221111000000 0000  


Q ss_pred             CCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHHHHHHHhcCCCCceEEEEeeeCchhHHHHH
Q psy12977        132 KFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQLAVIYAACSGPNLKRGMFSATHTEDVAKWC  211 (226)
Q Consensus       132 ~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i~~i~~~~~~~~~q~v~~SAT~~~~~~~~~  211 (226)
                        +.  ......+....   ..+.-...++||+||+-..++.+.- -.+.+..+++.- ++..-+|+..-..|+++.+.+
T Consensus        75 --~~--~~a~~~~~~a~---~~~~~~~~dllILDEi~~Ai~~gli-~~~~v~~ll~~r-p~~~evVlTGr~~p~~L~e~A  145 (157)
T d1g5ta_          75 --DT--AACMAVWQHGK---RMLADPLLDMVVLDELTYMVAYDYL-PLEEVISALNAR-PGHQTVIITGRGCHRDILDLA  145 (157)
T ss_dssp             --HH--HHHHHHHHHHH---HHTTCTTCSEEEEETHHHHHHTTSS-CHHHHHHHHHTS-CTTCEEEEECSSCCHHHHHHC
T ss_pred             --HH--HHHHHHHHHHH---HHhhcCccCEEeHHHHHHHHHcCCC-CHHHHHHHHHhC-CCCCEEEEECCCCCHHHHHhc
Confidence              00  00011112111   2344556899999999988776432 345666666665 567788887667888887665

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.78  E-value=0.15  Score=37.32  Aligned_cols=53  Identities=9%  Similarity=-0.058  Sum_probs=31.8

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCC--CCCCceEEEEcccHHHHHHHHH
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGP--KNLGFRAVIVCPTRELAKQTYN   99 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~--~~~~~~~iil~Pt~~L~~q~~~   99 (226)
                      ..|+-+++.||+|+|||...+-.+.+.....  ......++++........+...
T Consensus        35 p~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (258)
T d1v5wa_          35 ESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLR   89 (258)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHH
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHHHHH
Confidence            4567899999999999986655554444321  1223456666555444443333

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.59  E-value=0.67  Score=30.89  Aligned_cols=37  Identities=11%  Similarity=0.274  Sum_probs=25.4

Q ss_pred             EEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH
Q psy12977         52 IFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE   92 (226)
Q Consensus        52 ~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~   92 (226)
                      -++.||=.||||.-. +-.+.....   .+.+++++-|...
T Consensus         5 ~li~GpMfsGKTt~L-i~~~~~~~~---~g~~v~~ikp~~D   41 (133)
T d1xbta1           5 QVILGPMFSGKSTEL-MRRVRRFQI---AQYKCLVIKYAKD   41 (133)
T ss_dssp             EEEECCTTSCHHHHH-HHHHHHHHT---TTCCEEEEEETTC
T ss_pred             EEEEecccCHHHHHH-HHHHHHHHH---cCCcEEEEecccc
Confidence            478899999999854 444444432   3557888888754

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=89.42  E-value=0.19  Score=36.49  Aligned_cols=28  Identities=18%  Similarity=0.035  Sum_probs=21.6

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      ..|+-+++.|++|+|||...+-.+.+..
T Consensus        32 ~~G~l~~i~G~~G~GKT~~~l~~a~~~~   59 (258)
T d2i1qa2          32 ESQSVTEFAGVFGSGKTQIMHQSCVNLQ   59 (258)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            4467789999999999987665555554

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=89.39  E-value=0.14  Score=34.98  Aligned_cols=35  Identities=29%  Similarity=0.338  Sum_probs=21.5

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcc
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCP   89 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~P   89 (226)
                      -+.++|++|||||.. +-.++..+..   .+.++.++..
T Consensus         4 vi~itG~~GSGKTTL-~~~L~~~l~~---~g~~v~v~~~   38 (170)
T d1np6a_           4 LLAFAAWSGTGKTTL-LKKLIPALCA---RGIRPGLIKH   38 (170)
T ss_dssp             EEEEECCTTSCHHHH-HHHHHHHHHH---TTCCEEEEEE
T ss_pred             EEEEEcCCCCCHHHH-HHHHHHHHHH---CCCeEEEecc
Confidence            367999999999974 3444454432   2345555543

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=89.07  E-value=0.1  Score=38.36  Aligned_cols=43  Identities=16%  Similarity=0.016  Sum_probs=27.1

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCC--CCCCceEEEEcc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGP--KNLGFRAVIVCP   89 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~--~~~~~~~iil~P   89 (226)
                      ..|+-+++.||+|+|||...+-.+.+.....  ...+..++++.-
T Consensus        34 p~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~   78 (254)
T d1pzna2          34 ETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDT   78 (254)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEES
T ss_pred             cCCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEec
Confidence            4467789999999999986655555554321  112345666543

>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=89.00  E-value=2.4  Score=29.06  Aligned_cols=95  Identities=17%  Similarity=0.105  Sum_probs=63.0

Q ss_pred             ECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHHHHHHHHHHHHHhhcCCCeEEEEecchhhhhhhC---CCcCC
Q psy12977         55 CAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRELAKQTYNETVRLSEGLGLRAHVIGKIQQAAEKFG---PRSAQ  131 (226)
Q Consensus        55 ~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~  131 (226)
                      .-+....|.. ++..++....     +.++|+.|++++-++.+.+.++..    +..+..+.++....++..   ....+
T Consensus        14 ~v~~~~~K~~-~L~~ll~~~~-----~~k~iiF~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~fk~g   83 (168)
T d2j0sa2          14 AVEREEWKFD-TLCDLYDTLT-----ITQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFRSG   83 (168)
T ss_dssp             EESSTTHHHH-HHHHHHHHHT-----SSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHHT
T ss_pred             EecChHHHHH-HHHHHHHhCC-----CCceEEEeeeHHHHHHHHHHhhhc----ccchhhhhhhhhHHHHHHHHHHHhcC
Confidence            3344445644 3444554432     458999999999999988877765    666666666654443321   22346


Q ss_pred             CCCEEEECchHHHHhHhcCCCCCCCCCccEEEEccc
Q psy12977        132 KFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDES  167 (226)
Q Consensus       132 ~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~  167 (226)
                      ..+|+|+|--.      .  ..+++.+++++|.=++
T Consensus        84 ~~~iLv~Td~~------~--rGiDi~~v~~VIn~d~  111 (168)
T d2j0sa2          84 ASRVLISTDVW------A--RGLDVPQVSLIINYDL  111 (168)
T ss_dssp             SSCEEEECGGG------S--SSCCCTTEEEEEESSC
T ss_pred             CccEEeccchh------c--ccccccCcceEEEecC
Confidence            67899999642      2  7899999999986554

>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=88.84  E-value=0.48  Score=35.32  Aligned_cols=40  Identities=15%  Similarity=0.153  Sum_probs=26.3

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCP   89 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~P   89 (226)
                      ..|.-+++.|+||+|||....-.+.+....   .+.+++++..
T Consensus        33 ~~G~l~vi~G~~G~GKT~~~~~la~~~a~~---~g~~v~~~s~   72 (277)
T d1cr2a_          33 RGGEVIMVTSGSGMGKSTFVRQQALQWGTA---MGKKVGLAML   72 (277)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHHHHHHHT---SCCCEEEEES
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHhhhhh---cccceeEeee
Confidence            346778999999999997554444444332   2446777763

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=88.78  E-value=0.11  Score=36.15  Aligned_cols=18  Identities=17%  Similarity=0.315  Sum_probs=14.9

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      ++-+++.|++|+|||...
T Consensus         1 ~kiI~i~G~~GsGKsT~~   18 (190)
T d1khta_           1 NKVVVVTGVPGVGSTTSS   18 (190)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            356889999999999753

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.74  E-value=0.075  Score=37.49  Aligned_cols=20  Identities=25%  Similarity=0.461  Sum_probs=16.0

Q ss_pred             CCCeEEEECCCCchHhHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~   67 (226)
                      .|..++++|++|||||...-
T Consensus        18 ~g~vI~L~G~pGSGKTTiAk   37 (195)
T d1x6va3          18 RGCTVWLTGLSGAGKTTVSM   37 (195)
T ss_dssp             CCEEEEEESSCHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            45677899999999997643

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.43  E-value=0.11  Score=36.96  Aligned_cols=17  Identities=35%  Similarity=0.751  Sum_probs=14.7

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +.+++.||+|+|||...
T Consensus         2 rpIvl~GpsG~GK~tl~   18 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLL   18 (186)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            56899999999999753

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=88.39  E-value=0.14  Score=35.43  Aligned_cols=23  Identities=30%  Similarity=0.479  Sum_probs=16.7

Q ss_pred             eEEEECCCCchHhHHHHHHHHHHh
Q psy12977         51 QIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      .+++.||+|+|||.. +-.++..+
T Consensus         2 ki~I~G~~G~GKSTL-l~~i~~~l   24 (178)
T d1ye8a1           2 KIIITGEPGVGKTTL-VKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHH-HHHHHHHH
T ss_pred             EEEEECCCCcHHHHH-HHHHHhcC
Confidence            478999999999984 33444444

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.09  E-value=0.11  Score=36.52  Aligned_cols=16  Identities=25%  Similarity=0.389  Sum_probs=13.7

Q ss_pred             CeEEEECCCCchHhHH
Q psy12977         50 RQIFACAPTGSGKTAA   65 (226)
Q Consensus        50 ~~~li~apTGsGKT~~   65 (226)
                      .-++++|++|||||..
T Consensus        15 ~liil~G~pGsGKST~   30 (172)
T d1yj5a2          15 EVVVAVGFPGAGKSTF   30 (172)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             EEEEEECCCCCCHHHH
Confidence            4578999999999974

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=87.99  E-value=2.4  Score=28.31  Aligned_cols=41  Identities=20%  Similarity=0.189  Sum_probs=26.8

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTRE   92 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~   92 (226)
                      .|.=-++.||=.||||.-. +-.+++...   .+.+++++-|...
T Consensus         6 ~G~l~lI~GpMfSGKTteL-i~~~~~~~~---~g~~vl~i~~~~D   46 (141)
T d1xx6a1           6 HGWVEVIVGPMYSGKSEEL-IRRIRRAKI---AKQKIQVFKPEID   46 (141)
T ss_dssp             CCEEEEEECSTTSSHHHHH-HHHHHHHHH---TTCCEEEEEEC--
T ss_pred             ceeEEEEEeccccHHHHHH-HHHHHHhhh---cCCcEEEEEeccc
Confidence            4555688999999999754 434444332   3557899999764

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.98  E-value=0.13  Score=38.93  Aligned_cols=25  Identities=24%  Similarity=0.377  Sum_probs=18.4

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      .+.+++.||+|+|||... -.+...+
T Consensus        41 ~~giLL~Gp~GtGKT~l~-~ala~~~   65 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLLA-KAIANEC   65 (265)
T ss_dssp             CCEEEEBCCTTSSHHHHH-HHHHHHT
T ss_pred             CCeEEEECCCCCcchhHH-HHHHHHh
Confidence            477999999999999753 3344443

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=87.85  E-value=0.14  Score=36.14  Aligned_cols=20  Identities=25%  Similarity=0.351  Sum_probs=16.3

Q ss_pred             CCCeEEEECCCCchHhHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~   67 (226)
                      .|-.+++.||+|||||...-
T Consensus         2 ~~~riil~G~pGSGKsT~a~   21 (190)
T d1ak2a1           2 KGVRAVLLGPPGAGKGTQAP   21 (190)
T ss_dssp             CCCEEEEECCTTSSHHHHHH
T ss_pred             CccEEEEECCCCCCHHHHHH
Confidence            35678899999999998654

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=87.79  E-value=0.16  Score=35.32  Aligned_cols=17  Identities=18%  Similarity=0.227  Sum_probs=14.4

Q ss_pred             eEEEECCCCchHhHHHH
Q psy12977         51 QIFACAPTGSGKTAAFL   67 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~   67 (226)
                      ++++.||+|||||....
T Consensus         2 ~I~i~G~pGSGKsT~a~   18 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAE   18 (182)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999998653

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=87.50  E-value=0.21  Score=39.55  Aligned_cols=26  Identities=23%  Similarity=0.207  Sum_probs=19.7

Q ss_pred             CCCeEEEECCCCchHhHHHHHHHHHHh
Q psy12977         48 LGRQIFACAPTGSGKTAAFLIPIIHSL   74 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~~~~~~~~   74 (226)
                      .++.+++.||+|+|||... .+++..+
T Consensus       153 ~~~~~~~~g~~~~gk~~~~-~~~~~~~  178 (362)
T d1svma_         153 KKRYWLFKGPIDSGKTTLA-AALLELC  178 (362)
T ss_dssp             TCCEEEEECSTTSSHHHHH-HHHHHHH
T ss_pred             CcCeEEEECCCCCCHHHHH-HHHHHHc
Confidence            4578999999999999743 4555554

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.48  E-value=0.13  Score=36.63  Aligned_cols=17  Identities=29%  Similarity=0.718  Sum_probs=14.4

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      +.+++.||+|+|||...
T Consensus         1 rpIvl~GPsGsGK~tl~   17 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTLL   17 (190)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            45899999999999853

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=87.22  E-value=0.14  Score=35.90  Aligned_cols=18  Identities=22%  Similarity=0.488  Sum_probs=14.7

Q ss_pred             eEEEECCCCchHhHHHHH
Q psy12977         51 QIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~   68 (226)
                      ++++.||+|||||...-.
T Consensus         2 ~I~i~G~pGsGKsT~a~~   19 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVK   19 (181)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            578999999999986443

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=87.08  E-value=0.16  Score=35.68  Aligned_cols=18  Identities=28%  Similarity=0.613  Sum_probs=15.5

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      |+-+++.||+|+|||...
T Consensus         2 G~iivl~GpsG~GK~tl~   19 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVV   19 (182)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            567899999999999853

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=87.00  E-value=0.091  Score=40.95  Aligned_cols=19  Identities=21%  Similarity=0.275  Sum_probs=16.5

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      .++++++.||+|+|||...
T Consensus        27 ~~h~vLl~G~pG~GKT~la   45 (333)
T d1g8pa_          27 GIGGVLVFGDRGTGKSTAV   45 (333)
T ss_dssp             GGCCEEEECCGGGCTTHHH
T ss_pred             CCCeEEEECCCCccHHHHH
Confidence            4588999999999999763

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=86.52  E-value=0.16  Score=35.90  Aligned_cols=17  Identities=18%  Similarity=0.288  Sum_probs=14.3

Q ss_pred             eEEEECCCCchHhHHHH
Q psy12977         51 QIFACAPTGSGKTAAFL   67 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~   67 (226)
                      .+++.||+|||||....
T Consensus         5 ~I~i~GppGsGKsT~a~   21 (189)
T d1zaka1           5 KVMISGAPASGKGTQCE   21 (189)
T ss_dssp             CEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            48899999999997653

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=86.50  E-value=0.18  Score=36.44  Aligned_cols=19  Identities=32%  Similarity=0.616  Sum_probs=16.1

Q ss_pred             CCCeEEEECCCCchHhHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~   66 (226)
                      +|+-+++.||+|+|||...
T Consensus         1 ~G~livi~GPSG~GK~tl~   19 (205)
T d1s96a_           1 QGTLYIVSAPSGAGKSSLI   19 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4677899999999999754

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=86.47  E-value=0.22  Score=34.49  Aligned_cols=19  Identities=26%  Similarity=0.284  Sum_probs=15.5

Q ss_pred             CeEEEECCCCchHhHHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~   68 (226)
                      +.+++.|++|+|||...-.
T Consensus         3 ~~Iil~G~~GsGKSTia~~   21 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRE   21 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHH
Confidence            6788999999999976543

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=86.24  E-value=0.15  Score=35.62  Aligned_cols=16  Identities=19%  Similarity=0.196  Sum_probs=13.8

Q ss_pred             eEEEECCCCchHhHHH
Q psy12977         51 QIFACAPTGSGKTAAF   66 (226)
Q Consensus        51 ~~li~apTGsGKT~~~   66 (226)
                      ++++.||+|||||...
T Consensus         2 ~I~i~G~pGSGKsT~~   17 (179)
T d1e4va1           2 RIILLGAPVAGKGTQA   17 (179)
T ss_dssp             EEEEEESTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4788999999999864

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.13  E-value=0.21  Score=35.25  Aligned_cols=18  Identities=11%  Similarity=0.228  Sum_probs=15.6

Q ss_pred             CCeEEEECCCCchHhHHH
Q psy12977         49 GRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~   66 (226)
                      .+.+++.||+|+||+...
T Consensus         3 ~k~ivl~Gpsg~GK~tl~   20 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIK   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            477899999999999864

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=85.78  E-value=0.99  Score=33.32  Aligned_cols=60  Identities=13%  Similarity=0.036  Sum_probs=34.0

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcC------CCCCCceEEEEcccHHHHHHHHHHHHHHhhc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRG------PKNLGFRAVIVCPTRELAKQTYNETVRLSEG  107 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~------~~~~~~~~iil~Pt~~L~~q~~~~~~~~~~~  107 (226)
                      ..|.-.++.|++|+|||...+..++.....      ....+.+++|+. ...-..++.+.+..+...
T Consensus        27 ~pg~~~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~-~E~~~~~~~~Rl~~~~~~   92 (274)
T d1nlfa_          27 VAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLP-AEDPPTAIHHRLHALGAH   92 (274)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEE-SSSCHHHHHHHHHHHHTT
T ss_pred             cCCcEEEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEe-ccchHHHHHHHHHHHhhc
Confidence            347888999999999997654433332211      111233566654 333345555556555543

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=85.74  E-value=0.25  Score=34.57  Aligned_cols=17  Identities=24%  Similarity=0.227  Sum_probs=14.1

Q ss_pred             eEEEECCCCchHhHHHH
Q psy12977         51 QIFACAPTGSGKTAAFL   67 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~   67 (226)
                      .+++.||+|||||....
T Consensus         2 ~I~i~G~pGSGKsT~a~   18 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQAD   18 (182)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999998653

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=85.70  E-value=0.24  Score=35.68  Aligned_cols=40  Identities=23%  Similarity=0.298  Sum_probs=24.5

Q ss_pred             CCCCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcc
Q psy12977         47 PLGRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCP   89 (226)
Q Consensus        47 ~~~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~P   89 (226)
                      ..|.-+++.|++|+|||...+-.+.+.....   +..++++..
T Consensus        24 ~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~---~~~~~~~s~   63 (242)
T d1tf7a1          24 PIGRSTLVSGTSGTGKTLFSIQFLYNGIIEF---DEPGVFVTF   63 (242)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHHH---CCCEEEEES
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHHHHhc---CCCcccccc
Confidence            3567899999999999975443333333221   224566543

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=84.97  E-value=0.48  Score=35.61  Aligned_cols=41  Identities=29%  Similarity=0.350  Sum_probs=27.3

Q ss_pred             CCeEEEECCCCchHhHHHHHHHHHHhcCCCCCCceEEEEcccHHH
Q psy12977         49 GRQIFACAPTGSGKTAAFLIPIIHSLRGPKNLGFRAVIVCPTREL   93 (226)
Q Consensus        49 ~~~~li~apTGsGKT~~~~~~~~~~~~~~~~~~~~~iil~Pt~~L   93 (226)
                      |+-+.+.+|+|+|||...+..+......    +..++|+---...
T Consensus        54 g~itei~G~~gsGKTtl~l~~~~~~q~~----g~~~vyidtE~~~   94 (263)
T d1u94a1          54 GRIVEIYGPESSGKTTLTLQVIAAAQRE----GKTCAFIDAEHAL   94 (263)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHT----TCCEEEEESSCCC
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcC----CCEEEEEcccccc
Confidence            3668899999999998765555555432    4467776544333

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=84.82  E-value=0.18  Score=35.63  Aligned_cols=16  Identities=31%  Similarity=0.486  Sum_probs=13.7

Q ss_pred             eEEEECCCCchHhHHH
Q psy12977         51 QIFACAPTGSGKTAAF   66 (226)
Q Consensus        51 ~~li~apTGsGKT~~~   66 (226)
                      -+++.||+|||||...
T Consensus         8 iI~i~G~pGSGKsT~a   23 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQC   23 (194)
T ss_dssp             EEEEEESTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999854

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=84.72  E-value=0.21  Score=35.41  Aligned_cols=17  Identities=29%  Similarity=0.450  Sum_probs=13.9

Q ss_pred             CeEEEECCCCchHhHHH
Q psy12977         50 RQIFACAPTGSGKTAAF   66 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~   66 (226)
                      .-+++.||+|||||...
T Consensus         9 ~iI~i~GppGSGKsT~a   25 (196)
T d1ukza_           9 SVIFVLGGPGAGKGTQC   25 (196)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            35789999999999754

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=84.69  E-value=0.22  Score=35.24  Aligned_cols=20  Identities=30%  Similarity=0.393  Sum_probs=15.9

Q ss_pred             CCCeEEEECCCCchHhHHHH
Q psy12977         48 LGRQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        48 ~~~~~li~apTGsGKT~~~~   67 (226)
                      ..+-+++.||+|||||...-
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~   26 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCE   26 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            34668899999999997543

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=84.15  E-value=0.24  Score=35.15  Aligned_cols=19  Identities=21%  Similarity=0.113  Sum_probs=15.2

Q ss_pred             CeEEEECCCCchHhHHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~~   68 (226)
                      -.+++.||+|||||.....
T Consensus         7 mrIiliG~PGSGKtT~a~~   25 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVSSR   25 (189)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             eeEEEECCCCCCHHHHHHH
Confidence            4688999999999976433

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.92  E-value=0.25  Score=34.54  Aligned_cols=18  Identities=22%  Similarity=0.368  Sum_probs=14.5

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      -.+++.||+|||||...-
T Consensus         3 mrIvl~G~pGSGKtT~a~   20 (180)
T d1akya1           3 IRMVLIGPPGAGKGTQAP   20 (180)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            357888999999998643

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.48  E-value=0.25  Score=34.81  Aligned_cols=17  Identities=24%  Similarity=0.413  Sum_probs=14.0

Q ss_pred             eEEEECCCCchHhHHHH
Q psy12977         51 QIFACAPTGSGKTAAFL   67 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~   67 (226)
                      -+++.||+|||||....
T Consensus         3 iI~i~GppGSGKsT~a~   19 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCA   19 (194)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            36899999999997653

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=83.43  E-value=0.26  Score=33.91  Aligned_cols=18  Identities=22%  Similarity=0.150  Sum_probs=14.3

Q ss_pred             eEEEECCCCchHhHHHHH
Q psy12977         51 QIFACAPTGSGKTAAFLI   68 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~~   68 (226)
                      ++++.|++|+|||...-.
T Consensus         3 ~IvliG~~G~GKSTig~~   20 (165)
T d2iyva1           3 KAVLVGLPGSGKSTIGRR   20 (165)
T ss_dssp             SEEEECSTTSSHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHH
Confidence            477889999999986433

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=82.99  E-value=0.25  Score=38.38  Aligned_cols=16  Identities=25%  Similarity=0.326  Sum_probs=12.8

Q ss_pred             eEEEECCCCchHhHHH
Q psy12977         51 QIFACAPTGSGKTAAF   66 (226)
Q Consensus        51 ~~li~apTGsGKT~~~   66 (226)
                      ++++.||+|+|||+..
T Consensus       125 ~~l~~G~pG~GKT~la  140 (321)
T d1w44a_         125 MVIVTGKGNSGKTPLV  140 (321)
T ss_dssp             EEEEECSSSSCHHHHH
T ss_pred             eEEEECCCCccHHHHH
Confidence            3556899999999854

>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=82.77  E-value=2.1  Score=30.36  Aligned_cols=76  Identities=13%  Similarity=0.054  Sum_probs=46.0

Q ss_pred             ceEEEEcccHHHHHHHHHHHHHHhhcCC--------------------------CeEEEEecchhhhhhhC---CCcCCC
Q psy12977         82 FRAVIVCPTRELAKQTYNETVRLSEGLG--------------------------LRAHVIGKIQQAAEKFG---PRSAQK  132 (226)
Q Consensus        82 ~~~iil~Pt~~L~~q~~~~~~~~~~~~~--------------------------~~~~~~~~~~~~~~~~~---~~~~~~  132 (226)
                      ..+||.||||.-|+..+..+........                          ..+..++++-....+..   ....+.
T Consensus        41 ~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~r~~ie~~f~~g~  120 (201)
T d2p6ra4          41 GGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGN  120 (201)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTTS
T ss_pred             CcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhhHHHHHHHHhCCC
Confidence            3689999999988888877766543211                          11344444432222211   112466


Q ss_pred             CCEEEECchHHHHhHhcCCCCCCCCCccEEEEc
Q psy12977        133 FDVLITTPNKLVYLLQMDPPALNLANVEWLIVD  165 (226)
Q Consensus       133 ~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViD  165 (226)
                      .+|+|||..-        ...+++.....+|.|
T Consensus       121 i~vlvaT~~l--------~~Gin~p~~~vvi~~  145 (201)
T d2p6ra4         121 IKVVVATPTL--------AAGVNLPARRVIVRS  145 (201)
T ss_dssp             CCEEEECSTT--------TSSSCCCBSEEEECC
T ss_pred             ceEEEechHH--------HhhcCCCCceEEEec
Confidence            8999999862        157777777676653

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=82.09  E-value=0.37  Score=35.80  Aligned_cols=22  Identities=18%  Similarity=0.244  Sum_probs=17.5

Q ss_pred             cCCCCCeEEEECCCCchHhHHH
Q psy12977         45 LSPLGRQIFACAPTGSGKTAAF   66 (226)
Q Consensus        45 ~~~~~~~~li~apTGsGKT~~~   66 (226)
                      ....+.++++.|++|+||+..+
T Consensus        19 ~a~~~~pvlI~Ge~GtGK~~~A   40 (247)
T d1ny5a2          19 ISCAECPVLITGESGVGKEVVA   40 (247)
T ss_dssp             HTTCCSCEEEECSTTSSHHHHH
T ss_pred             HhCCCCCEEEECCCCcCHHHHH
Confidence            3455678999999999999643

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=81.96  E-value=0.28  Score=34.30  Aligned_cols=18  Identities=33%  Similarity=0.392  Sum_probs=13.5

Q ss_pred             CCeEE-EECCCCchHhHHH
Q psy12977         49 GRQIF-ACAPTGSGKTAAF   66 (226)
Q Consensus        49 ~~~~l-i~apTGsGKT~~~   66 (226)
                      ++-++ |.||+|||||...
T Consensus        21 ~~~iIgI~G~~GSGKSTla   39 (198)
T d1rz3a_          21 GRLVLGIDGLSRSGKTTLA   39 (198)
T ss_dssp             SSEEEEEEECTTSSHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHH
Confidence            34344 9999999999753

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=81.60  E-value=0.29  Score=33.93  Aligned_cols=23  Identities=17%  Similarity=0.222  Sum_probs=15.8

Q ss_pred             EEEECCCCchHhHHHHHHHHHHhc
Q psy12977         52 IFACAPTGSGKTAAFLIPIIHSLR   75 (226)
Q Consensus        52 ~li~apTGsGKT~~~~~~~~~~~~   75 (226)
                      +++.|++|+|||...- -+...+.
T Consensus         4 ivi~G~~GsGKTT~~~-~La~~L~   26 (194)
T d1nksa_           4 GIVTGIPGVGKSTVLA-KVKEILD   26 (194)
T ss_dssp             EEEEECTTSCHHHHHH-HHHHHHH
T ss_pred             EEEECCCCCCHHHHHH-HHHHHHH
Confidence            5789999999997542 2334443

>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=81.59  E-value=0.33  Score=37.51  Aligned_cols=17  Identities=35%  Similarity=0.581  Sum_probs=14.5

Q ss_pred             eEEEECCCCchHhHHHH
Q psy12977         51 QIFACAPTGSGKTAAFL   67 (226)
Q Consensus        51 ~~li~apTGsGKT~~~~   67 (226)
                      ++++.||||+|||..+-
T Consensus        54 ~~lf~Gp~GvGKT~lak   70 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVTV   70 (315)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCcchhHHHHH
Confidence            68899999999997643

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=81.24  E-value=0.73  Score=32.59  Aligned_cols=34  Identities=24%  Similarity=0.272  Sum_probs=20.3

Q ss_pred             CeEEEECC-CCchHhHHHHHHHHHHhcCCCCCCceEEEE
Q psy12977         50 RQIFACAP-TGSGKTAAFLIPIIHSLRGPKNLGFRAVIV   87 (226)
Q Consensus        50 ~~~li~ap-TGsGKT~~~~~~~~~~~~~~~~~~~~~iil   87 (226)
                      |.+.|++- ||.|||...+.-+....+    .|.+++++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~----~G~rVl~i   36 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKA----AGYRTAGY   36 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHH----TTCCEEEE
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHH----CCCeEEEE
Confidence            45666766 799999875443322222    24566665

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

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: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=80.77  E-value=4.5  Score=30.94  Aligned_cols=72  Identities=10%  Similarity=-0.023  Sum_probs=34.8

Q ss_pred             CCCCEEEECchHHHHhHhcCCCCCCCCCccEEEEcccccccccCccchHHHH----HHHHHhcC----CCCceEEEEeee
Q psy12977        131 QKFDVLITTPNKLVYLLQMDPPALNLANVEWLIVDESDKLFEAGVRGFRDQL----AVIYAACS----GPNLKRGMFSAT  202 (226)
Q Consensus       131 ~~~~IiV~Tp~~l~~~~~~~~~~~~~~~~~~lViDE~h~l~~~~~~~~~~~i----~~i~~~~~----~~~~q~v~~SAT  202 (226)
                      ...-++|.+|+.=-+.=..  +.--+.--+++|+-=+|.....   .....+    ...+..+.    ...++++.+||.
T Consensus       165 ~D~~v~v~~p~~GD~iQ~~--k~gilE~aDi~vvNKaD~~~~~---~~~~~~~~~~~~~l~~~~~~~~~~~p~V~~~Sa~  239 (323)
T d2qm8a1         165 TDFFLVLMLPGAGDELQGI--KKGIFELADMIAVNKADDGDGE---RRASAAASEYRAALHILTPPSATWTPPVVTISGL  239 (323)
T ss_dssp             SSEEEEEECSCC------C--CTTHHHHCSEEEEECCSTTCCH---HHHHHHHHHHHHHHTTBCCSBTTBCCCEEEEBTT
T ss_pred             cceEEEEeeccchhhhhhh--hhhHhhhhheeeEeccccccch---HHHHHHHHHHHHHhhcccccccCCCCceEEEEec
Confidence            3455888888753222111  1111334568888777744222   122222    22222221    235789999998


Q ss_pred             CchhH
Q psy12977        203 HTEDV  207 (226)
Q Consensus       203 ~~~~~  207 (226)
                      -.+-+
T Consensus       240 ~g~Gi  244 (323)
T d2qm8a1         240 HGKGL  244 (323)
T ss_dssp             TTBSH
T ss_pred             CCCCH
Confidence            66433

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=80.72  E-value=0.76  Score=31.30  Aligned_cols=23  Identities=17%  Similarity=0.037  Sum_probs=15.9

Q ss_pred             EEEECCCCchHhHHHHHHHHHHhc
Q psy12977         52 IFACAPTGSGKTAAFLIPIIHSLR   75 (226)
Q Consensus        52 ~li~apTGsGKT~~~~~~~~~~~~   75 (226)
                      +-+.|+.|||||... --++..+.
T Consensus         4 i~I~G~~gSGKTTli-~~l~~~L~   26 (165)
T d1xjca_           4 WQVVGYKHSGKTTLM-EKWVAAAV   26 (165)
T ss_dssp             EEEECCTTSSHHHHH-HHHHHHHH
T ss_pred             EEEEeCCCCCHHHHH-HHHHHHHH
Confidence            459999999999743 33444443

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

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: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=80.48  E-value=2  Score=32.00  Aligned_cols=18  Identities=28%  Similarity=0.311  Sum_probs=14.6

Q ss_pred             CeEEEECCCCchHhHHHH
Q psy12977         50 RQIFACAPTGSGKTAAFL   67 (226)
Q Consensus        50 ~~~li~apTGsGKT~~~~   67 (226)
                      +-+.+.|.-|.|||..+.
T Consensus        45 ~~v~I~GmgGiGKTtLA~   62 (277)
T d2a5yb3          45 FFLFLHGRAGSGKSVIAS   62 (277)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            457799999999998543