Psyllid ID: psy496

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------32
Protein Sequence
MHAFYAQSITYRLKEDLAGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRTLKRSETQQYPNDQQHT
Secondary Structure (PSIPRED)
ccccccccEEEEEEcccccccccccHHHHHHHHHHHHHcccHHHHHHHccccccHHHHHHHHHHHccccccEEEEcccccccccHHHHHHHHHHHHHcccccEEEEEccccHHHHHHHHHHHHHHHccccccccccEEEEEEcccccccccEEEEEEccHHHHHHHccccccccccEEEEcccccccccHHHHHHHHHHHHHHcccccEEEEEcccccHHHHHHHccccEEEEcccccccccccHHHHHHHHHHHHHHHHHHHcccHHHHccccccccEEEccccccccccccHHHHHHHHHHHccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHccccHccHHHHcccccccHccHHHHHcHccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccEEEEEEcccccccccHHHHHHHcccccccccEEEEEcccHHHHHHHHHHHHHHHHHcccccccccEEEEEEEEccccccHccEEEEcccHHHHHHHHccccHHccEEEEEccHHHHHHHHHHHHHHHHHHHHHccccEEEEEEccccHHHHHHHHccccEEEEccccccEEEEEccccHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEccHHHHHHHHHHHHHHHHHHccccHHHHHcccccccc
Coil and Loop (DISEMBL)
MHAFYAQSITYRLKEdlagcgkttqvpqfILDDeiarnrgseccimvtqpRRISAIALINKCltlspilspsiiytstgcgkttqvpqfILDDeiarnrgseccimvtqpRRISAIAIAERVAQErdeqcgrpgssvgYQIRLekelprkrgsilyctagilpevmqsdpilsgvSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEkfsqffggapilhipgftypvqeYYLEDVLNMTRKDLKLILMSATLNAEkfsqffggapilhipgftypvqEYYLEDVLNMTRTLKrsetqqypndqqht
Flexible Loop (DISEMBL)
MHAFYAQSITYRLKEDLAGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAqerdeqcgrpgssvgyqirlekelprkrgSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRTLkrsetqqypndqqht
Low Complexity Region (SEG)
MHAFYAQSITYRLKEDLAGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRTLKRSETQQYPNDQQHT
Disordered region (IsUnstruct)
***FYAQSITYRLKEDLAGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV**************VGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMT******************
Disordered Region (DISOPRED)
MHAFYAQSITYRLKEDLAGCGKTTQVPQFILDDE******************ISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDL***************QFFGGAPILHIPGFTYPVQEYYLEDVLNMTRTL***************
Disordered Region (DISEMBL)
MHAFYAQSITYRLKEDLAGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV************SSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRTLKRS************
Disordered Region (DISPRO)
************************QV**********RNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRT****************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MHAFYAQSITYRLKEDLAGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRTLKRSETQQYPNDQQHT
Positional Conservation
no confident homologs detected

---

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	319	2.2.26 [Sep-21-2011]
Q9H2U1	1008	Probable ATP-dependent RN	yes	N/A	0.567	0.179	0.648	2e-65
Q8VHK9	1001	Probable ATP-dependent RN	yes	N/A	0.567	0.180	0.637	6e-64
P24785	1293	Dosage compensation regul	no	N/A	0.548	0.135	0.544	7e-51
Q5ZI74	1231	Putative ATP-dependent RN	no	N/A	0.545	0.141	0.508	8e-51
Q5R874	1269	ATP-dependent RNA helicas	no	N/A	0.548	0.137	0.522	2e-50
Q08211	1270	ATP-dependent RNA helicas	no	N/A	0.548	0.137	0.522	2e-50
Q28141	1287	ATP-dependent RNA helicas	no	N/A	0.548	0.135	0.516	3e-50
Q99PU8	1217	Putative ATP-dependent RN	no	N/A	0.645	0.169	0.433	8e-50
Q5BJS0	1194	Putative ATP-dependent RN	no	N/A	0.645	0.172	0.433	9e-50
Q5R607	1194	Putative ATP-dependent RN	no	N/A	0.645	0.172	0.433	2e-49

>sp|Q9H2U1|DHX36_HUMAN Probable ATP-dependent RNA helicase DHX36 OS=Homo sapiens GN=DHX36 PE=1 SV=2

 Score =  249 bits (636), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 118/182 (64%), Positives = 146/182 (80%), Gaps = 1/182 (0%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           ++I   TGCGKTTQV QFILD+ I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct: 226 TVISGETGCGKTTQVTQFILDNYIERGKGSACRIVCTQPRRISAISVAERVAAERAESCG 285

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
             G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSDP LS VSHIV+DEIHER++ SD
Sbjct: 286 -SGNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDPYLSSVSHIVLDEIHERNLQSD 344

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
            L+ ++KD+ + R DLK+ILMSATLNAEKFS++FG  P++HIPGFT+PV EY LEDV+  
Sbjct: 345 VLMTVVKDLLNFRSDLKVILMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDVIEK 404

Query: 252 TR 253
            R
Sbjct: 405 IR 406

Plays a role in degradation and deadenylation of mRNAs containing in their 3'-UTR the consensus ARE sequence element. May function in sex development and spermatogenesis.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q8VHK9|DHX36_MOUSE Probable ATP-dependent RNA helicase DHX36 OS=Mus musculus GN=Dhx36 PE=2 SV=2

 Score =  244 bits (623), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 116/182 (63%), Positives = 144/182 (79%), Gaps = 1/182 (0%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           ++I   TGCGKTTQV QFILD+ I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct: 219 TVISGETGCGKTTQVTQFILDNYIERGKGSACRIVCTQPRRISAISVAERVATERAESCG 278

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
             G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSD  LS VSHIV+DEIHER++ SD
Sbjct: 279 N-GNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDSRLSSVSHIVLDEIHERNLQSD 337

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
            L+ ++KD+   R DLK+ILMSATLNAEKFS++FG  P++HIPGFT+PV EY LED++  
Sbjct: 338 VLMTVIKDLLHFRSDLKVILMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDIIEK 397

Query: 252 TR 253
            R
Sbjct: 398 IR 399

Plays a role in degradation and deadenylation of mRNAs containing in their 3'-UTR the consensus ARE sequence element. May function in sex development and spermatogenesis.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P24785|MLE_DROME Dosage compensation regulator OS=Drosophila melanogaster GN=mle PE=2 SV=2

 Score =  201 bits (510), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 98/180 (54%), Positives = 131/180 (72%), Gaps = 5/180 (2%)

Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           II  +TGCGKTTQ+ Q+ILDD I   +G    I VTQPRRISAI++AERVA+ER EQ G 
Sbjct: 404 IIRGNTGCGKTTQIAQYILDDYICSGQGGYANIYVTQPRRISAISVAERVARERCEQLG- 462

Query: 133 PGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF 192
              +VGY +R E   PR  G+IL+CT G+L   +++   L GVSHI++DEIHER + SDF
Sbjct: 463 --DTVGYSVRFESVFPRPYGAILFCTVGVLLRKLEAG--LRGVSHIIVDEIHERDVNSDF 518

Query: 193 LLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMT 252
           LL IL+D+ D   DL +ILMSAT++  KFS++FG  P+L +PG  +PVQ+++LED++ MT
Sbjct: 519 LLVILRDMVDTYPDLHVILMSATIDTTKFSKYFGICPVLEVPGRAFPVQQFFLEDIIQMT 578

Required in males for dosage compensation of X chromosome linked genes. Mle, msl-1 and msl-3 are colocalized on X chromosome. Each of the msl proteins requires all the other msls for wild-type X-chromosome binding. Probably unwinds double-stranded DNA and RNA in a 3' to 5' direction.

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5ZI74|DHX30_CHICK Putative ATP-dependent RNA helicase DHX30 OS=Gallus gallus GN=DHX30 PE=2 SV=1

 Score =  201 bits (510), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 90/177 (50%), Positives = 131/177 (74%), Gaps = 3/177 (1%)

Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           +I   TGCGKTT++PQ +L+  I   RG+ C +++TQPRRISAI++A+RVAQE      +
Sbjct: 498 VIAGDTGCGKTTRIPQLLLEHYILEGRGARCNVVITQPRRISAISVAQRVAQELGPNMRK 557

Query: 133 PGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF 192
              +VGYQ+RLE + P + G++L+CT GIL   +Q +P L GVSH+V+DE+HER + +DF
Sbjct: 558 ---NVGYQVRLESKPPARGGALLFCTVGILLRKLQGNPSLEGVSHVVVDEVHERDVNTDF 614

Query: 193 LLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVL 249
           LL +LK +     DL+L+LMSAT + ++FS +FGG P++ +PGF YPV+EYYLE++L
Sbjct: 615 LLILLKGIQKLNPDLRLVLMSATGDNQRFSHYFGGCPVVKVPGFMYPVKEYYLEEIL 671

Associates with mitochondrial DNA.

Gallus gallus (taxid: 9031)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5R874|DHX9_PONAB ATP-dependent RNA helicase A OS=Pongo abelii GN=DHX9 PE=2 SV=1

 Score =  199 bits (507), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 94/180 (52%), Positives = 131/180 (72%), Gaps = 5/180 (2%)

Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           II  +TGCGKTTQVPQFILDD I  +R +EC I+VTQPRRISA+++AERVA ER E+   
Sbjct: 408 IIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEE--- 464

Query: 133 PGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF 192
           PG S GY +R E  LPR   SI++CT G+L   +++   + G+SH+++DEIHER + +DF
Sbjct: 465 PGKSCGYSVRFESILPRPHASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDF 522

Query: 193 LLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMT 252
           LL +L+DV     +++++LMSAT++   F ++F   PI+ + G TYPVQEY+LED + MT
Sbjct: 523 LLVVLRDVVQAYPEVRIVLMSATIDTSMFCEYFFNCPIIEVYGRTYPVQEYFLEDCIQMT 582

Component of the CRD-mediated complex that promotes MYC mRNA stability. Unwinds double-stranded DNA and RNA in a 3' to 5' direction. Alteration of secondary structure may subsequently influence interactions with proteins or other nucleic acids. Functions as a transcriptional activator. Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q08211|DHX9_HUMAN ATP-dependent RNA helicase A OS=Homo sapiens GN=DHX9 PE=1 SV=4

 Score =  199 bits (507), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 94/180 (52%), Positives = 131/180 (72%), Gaps = 5/180 (2%)

Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           II  +TGCGKTTQVPQFILDD I  +R +EC I+VTQPRRISA+++AERVA ER E+   
Sbjct: 408 IIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEE--- 464

Query: 133 PGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF 192
           PG S GY +R E  LPR   SI++CT G+L   +++   + G+SH+++DEIHER + +DF
Sbjct: 465 PGKSCGYSVRFESILPRPHASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDF 522

Query: 193 LLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMT 252
           LL +L+DV     +++++LMSAT++   F ++F   PI+ + G TYPVQEY+LED + MT
Sbjct: 523 LLVVLRDVVQAYPEVRIVLMSATIDTSMFCEYFFNCPIIEVYGRTYPVQEYFLEDCIQMT 582

Unwinds double-stranded DNA and RNA in a 3' to 5' direction. Alteration of secondary structure may subsequently influence interactions with proteins or other nucleic acids. Functions as a transcriptional activator. Component of the CRD-mediated complex that promotes MYC mRNA stability. Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q28141|DHX9_BOVIN ATP-dependent RNA helicase A OS=Bos taurus GN=DHX9 PE=2 SV=1

 Score =  199 bits (505), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 93/180 (51%), Positives = 131/180 (72%), Gaps = 5/180 (2%)

Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           II  +TGCGKTTQVPQFILDD I  +R +EC I+VTQPRRISA+++AERVA ER E+   
Sbjct: 405 IIRGATGCGKTTQVPQFILDDCIQNDRAAECNIVVTQPRRISAVSVAERVAYERGEE--- 461

Query: 133 PGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF 192
           PG S GY +R E  LPR   SI++CT G+L   +++   + G+SH+++DEIHER + +DF
Sbjct: 462 PGKSCGYSVRFESILPRPHASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDF 519

Query: 193 LLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMT 252
           LL +L+DV     +++++LMSAT++   F ++F   PI+ + G T+PVQEY+LED + MT
Sbjct: 520 LLVVLRDVVQAYPEVRIVLMSATIDTSMFCEYFFNCPIIEVYGRTFPVQEYFLEDCIQMT 579

Component of the CRD-mediated complex that promotes MYC mRNA stability. Unwinds double-stranded DNA and RNA in a 3' to 5' direction. Alteration of secondary structure may subsequently influence interactions with proteins or other nucleic acids. Functions as a transcriptional activator. Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q99PU8|DHX30_MOUSE Putative ATP-dependent RNA helicase DHX30 OS=Mus musculus GN=Dhx30 PE=2 SV=1

 Score =  197 bits (501), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 95/219 (43%), Positives = 148/219 (67%), Gaps = 13/219 (5%)

Query: 34  EIARNRG---SECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFI 90
           E+ R RG    E   +   P R + ++ I +     P++   +I   TGCGKTT++PQ +
Sbjct: 442 ELWRRRGPIWQEAPQLPVDPHRDTILSAIEQ----HPVV---VISGDTGCGKTTRIPQLL 494

Query: 91  LDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRK 150
           L+  +   RG+ C +++TQPRRISA+++A+RV+ E      R   +VG+Q+RLE + P +
Sbjct: 495 LERYVTEGRGARCNVIITQPRRISAVSVAQRVSHELGPSLRR---NVGFQVRLESKPPAR 551

Query: 151 RGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLI 210
            G++L+CT GIL   +QS+P L GVSH+++DE+HER + +DFLL +LK +      L+L+
Sbjct: 552 GGALLFCTVGILLRKLQSNPSLEGVSHVIVDEVHERDVNTDFLLILLKGLQRLNPALRLV 611

Query: 211 LMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVL 249
           LMSAT + E+FS++FGG P++ +PGF YPV+E+YLED+L
Sbjct: 612 LMSATGDNERFSRYFGGCPVIKVPGFMYPVKEHYLEDIL 650

Associates with mitochondrial DNA.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5BJS0|DHX30_RAT Putative ATP-dependent RNA helicase DHX30 OS=Rattus norvegicus GN=Dhx30 PE=1 SV=1

 Score =  197 bits (501), Expect = 9e-50,   Method: Compositional matrix adjust.
 Identities = 95/219 (43%), Positives = 148/219 (67%), Gaps = 13/219 (5%)

Query: 34  EIARNRG---SECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFI 90
           E+ R RG    E   +   P R + ++ I +     P++   +I   TGCGKTT++PQ +
Sbjct: 419 ELWRRRGPIWQEAPQLPVDPHRDTILSAIEQ----HPVV---VISGDTGCGKTTRIPQLL 471

Query: 91  LDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRK 150
           L+  +   RG+ C +++TQPRRISA+++A+RV+ E      R   +VG+Q+RLE + P +
Sbjct: 472 LERYVTEGRGARCNVIITQPRRISAVSVAQRVSHELGPSLRR---NVGFQVRLESKPPAR 528

Query: 151 RGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLI 210
            G++L+CT GIL   +QS+P L GVSH+++DE+HER + +DFLL +LK +      L+L+
Sbjct: 529 GGALLFCTVGILLRKLQSNPSLEGVSHVIVDEVHERDVNTDFLLILLKGLQRLNPALRLV 588

Query: 211 LMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVL 249
           LMSAT + E+FS++FGG P++ +PGF YPV+E+YLED+L
Sbjct: 589 LMSATGDNERFSRYFGGCPVIKVPGFMYPVKEHYLEDIL 627

Associates with mitochondrial DNA.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5R607|DHX30_PONAB Putative ATP-dependent RNA helicase DHX30 OS=Pongo abelii GN=DHX30 PE=2 SV=1

 Score =  196 bits (498), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 95/219 (43%), Positives = 147/219 (67%), Gaps = 13/219 (5%)

Query: 34  EIARNRG---SECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFI 90
           E+ R RG    E   +   P R + +  I +     P++   +I   TGCGKTT++PQ +
Sbjct: 419 ELWRRRGPVWQEAPQLPVDPHRDTILNAIEQ----HPVV---VISGDTGCGKTTRIPQLL 471

Query: 91  LDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRK 150
           L+  +   RG+ C +++TQPRRISA+++A+RV+ E      R   +VG+Q+RLE + P +
Sbjct: 472 LERYVTEGRGARCNVIITQPRRISAVSVAQRVSHELGPSLRR---NVGFQVRLESKPPAR 528

Query: 151 RGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLI 210
            G++L+CT GIL   +QS+P L GVSH+++DE+HER + +DFLL +LK +      L+L+
Sbjct: 529 GGALLFCTVGILLRKLQSNPSLEGVSHVIVDEVHERDVNTDFLLILLKGLQRLNPALRLV 588

Query: 211 LMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVL 249
           LMSAT + E+FS++FGG P++ +PGF YPV+E+YLED+L
Sbjct: 589 LMSATGDNERFSRYFGGCPVIKVPGFMYPVKEHYLEDIL 627

Associates with mitochondrial DNA.

Pongo abelii (taxid: 9601)

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	319
301607413	967	PREDICTED: probable ATP-dependent RNA he	0.567	0.187	0.681	3e-67
301607411	981	PREDICTED: probable ATP-dependent RNA he	0.567	0.184	0.675	9e-67
345327898	1002	PREDICTED: probable ATP-dependent RNA he	0.554	0.176	0.668	2e-64
395528308	962	PREDICTED: LOW QUALITY PROTEIN: probable	0.567	0.188	0.659	5e-64
114589918	1008	PREDICTED: probable ATP-dependent RNA he	0.567	0.179	0.648	1e-63
397512310	1010	PREDICTED: LOW QUALITY PROTEIN: probable	0.567	0.179	0.648	1e-63
348581698	916	PREDICTED: probable ATP-dependent RNA he	0.567	0.197	0.637	1e-63
114589920	994	PREDICTED: probable ATP-dependent RNA he	0.567	0.182	0.648	1e-63
297672311	318	PREDICTED: probable ATP-dependent RNA he	0.567	0.569	0.642	1e-63
390349687	1040	PREDICTED: probable ATP-dependent RNA he	0.695	0.213	0.562	1e-63

>gi|301607413|ref|XP_002933293.1| PREDICTED: probable ATP-dependent RNA helicase DHX36-like isoform 2 [Xenopus (Silurana) tropicalis]

 Score =  261 bits (668), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 124/182 (68%), Positives = 150/182 (82%), Gaps = 1/182 (0%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           ++I   TGCGKTTQV QFILDD I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct: 199 TVISGETGCGKTTQVTQFILDDHIKRGKGSSCYIVCTQPRRISAISVAERVAAERAEACG 258

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
           R G+S GYQIRLE ++PRK+GSILYCT GI+ + +QSDP L+ VSH+V+DEIHER++ SD
Sbjct: 259 R-GNSTGYQIRLESQMPRKQGSILYCTTGIVIQWLQSDPHLANVSHVVIDEIHERNLQSD 317

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
            L+AI+KD+   R DLK+ILMSATLNAEKFSQ+FG  P+LHIPGFTYPV+EY LEDV+ M
Sbjct: 318 VLMAIVKDLLTFRSDLKVILMSATLNAEKFSQYFGYCPMLHIPGFTYPVKEYLLEDVIEM 377

Query: 252 TR 253
            R
Sbjct: 378 LR 379

Source: Xenopus (Silurana) tropicalis

Species: Xenopus (Silurana) tropicalis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|301607411|ref|XP_002933292.1| PREDICTED: probable ATP-dependent RNA helicase DHX36-like isoform 1 [Xenopus (Silurana) tropicalis]

 Score =  259 bits (663), Expect = 9e-67,   Method: Compositional matrix adjust.
 Identities = 123/182 (67%), Positives = 149/182 (81%), Gaps = 1/182 (0%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           ++I   TGCGKTTQV QFILDD I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct: 199 TVISGETGCGKTTQVTQFILDDHIKRGKGSSCYIVCTQPRRISAISVAERVAAERAEACG 258

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
           R G+S GYQIRLE ++PRK+GSILYCT GI+ + +QSDP L+ VSH+V+DEIHER++ SD
Sbjct: 259 R-GNSTGYQIRLESQMPRKQGSILYCTTGIVIQWLQSDPHLANVSHVVIDEIHERNLQSD 317

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
            L+AI+KD+   R DLK+ILMSATLNAEKFSQ+F   P+LHIPGFTYPV+EY LEDV+ M
Sbjct: 318 VLMAIVKDLLTFRSDLKVILMSATLNAEKFSQYFDSCPMLHIPGFTYPVKEYLLEDVIEM 377

Query: 252 TR 253
            R
Sbjct: 378 LR 379

Source: Xenopus (Silurana) tropicalis

Species: Xenopus (Silurana) tropicalis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|345327898|ref|XP_001511483.2| PREDICTED: probable ATP-dependent RNA helicase DHX36 [Ornithorhynchus anatinus]

 Score =  252 bits (643), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 119/178 (66%), Positives = 146/178 (82%), Gaps = 1/178 (0%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           ++I   TGCGKTTQV QFILDD I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct: 220 TVISGETGCGKTTQVTQFILDDYIERGKGSACRIVCTQPRRISAISVAERVAAERAESCG 279

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
             G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSDP LS VSH+V+DEIHER++ SD
Sbjct: 280 N-GNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDPQLSSVSHVVLDEIHERNLQSD 338

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVL 249
            L+ ++KD+ D R DLK+ILMSATLNAEKFS++FGG P++HIPGFT+PV EY LEDV+
Sbjct: 339 VLMTVIKDLLDFRPDLKVILMSATLNAEKFSEYFGGCPMIHIPGFTFPVVEYLLEDVI 396

Source: Ornithorhynchus anatinus

Species: Ornithorhynchus anatinus

Genus: Ornithorhynchus

Family: Ornithorhynchidae

Order: Monotremata

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|395528308|ref|XP_003766272.1| PREDICTED: LOW QUALITY PROTEIN: probable ATP-dependent RNA helicase DHX36 [Sarcophilus harrisii]

 Score =  250 bits (639), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 120/182 (65%), Positives = 146/182 (80%), Gaps = 1/182 (0%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           ++I   TGCGKTTQV QFILDD I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct: 177 TVISGETGCGKTTQVTQFILDDYIERGKGSACRIVCTQPRRISAISVAERVATERAEPCG 236

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
             G S GYQIRL+  LPRK+GSILYCT GI+ + +QSDP LS VSHIV+DEIHER++ SD
Sbjct: 237 S-GHSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDPQLSSVSHIVLDEIHERNLQSD 295

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
            L+ ++KD+ + R DLK+ILMSATLNAEKFS++FGG P++HIPGFT+PV EY LEDV+  
Sbjct: 296 VLMTVIKDLLNFRPDLKVILMSATLNAEKFSEYFGGCPMIHIPGFTFPVAEYLLEDVIEK 355

Query: 252 TR 253
            R
Sbjct: 356 IR 357

Source: Sarcophilus harrisii

Species: Sarcophilus harrisii

Genus: Sarcophilus

Family: Dasyuridae

Order: Dasyuromorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|114589918|ref|XP_001147599.1| PREDICTED: probable ATP-dependent RNA helicase DHX36 isoform 6 [Pan troglodytes]

 Score =  249 bits (636), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 118/182 (64%), Positives = 146/182 (80%), Gaps = 1/182 (0%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           ++I   TGCGKTTQV QFILD+ I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct: 226 TVISGETGCGKTTQVTQFILDNYIERGKGSACRIVCTQPRRISAISVAERVAAERAESCG 285

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
             G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSDP LS VSHIV+DEIHER++ SD
Sbjct: 286 -SGNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDPYLSSVSHIVLDEIHERNLQSD 344

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
            L+ ++KD+ + R DLK+ILMSATLNAEKFS++FG  P++HIPGFT+PV EY LEDV+  
Sbjct: 345 VLMTVVKDLLNFRSDLKVILMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDVIEK 404

Query: 252 TR 253
            R
Sbjct: 405 IR 406

Source: Pan troglodytes

Species: Pan troglodytes

Genus: Pan

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|397512310|ref|XP_003826492.1| PREDICTED: LOW QUALITY PROTEIN: probable ATP-dependent RNA helicase DHX36 [Pan paniscus]

 Score =  249 bits (636), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 118/182 (64%), Positives = 146/182 (80%), Gaps = 1/182 (0%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           ++I   TGCGKTTQV QFILD+ I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct: 228 TVISGETGCGKTTQVTQFILDNYIERGKGSACRIVCTQPRRISAISVAERVAAERAESCG 287

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
             G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSDP LS VSHIV+DEIHER++ SD
Sbjct: 288 -SGNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDPYLSSVSHIVLDEIHERNLQSD 346

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
            L+ ++KD+ + R DLK+ILMSATLNAEKFS++FG  P++HIPGFT+PV EY LEDV+  
Sbjct: 347 VLMTVVKDLLNFRSDLKVILMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDVIEK 406

Query: 252 TR 253
            R
Sbjct: 407 IR 408

Source: Pan paniscus

Species: Pan paniscus

Genus: Pan

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|348581698|ref|XP_003476614.1| PREDICTED: probable ATP-dependent RNA helicase DHX36 [Cavia porcellus]

 Score =  249 bits (636), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 116/182 (63%), Positives = 146/182 (80%), Gaps = 1/182 (0%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           +++   TGCGKTTQV QFILD+ I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct: 221 TVVSGETGCGKTTQVTQFILDNYIERGKGSACRIVCTQPRRISAISVAERVAAERAESCG 280

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
             G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSDP LS VSHIV+DEIHER++ SD
Sbjct: 281 N-GNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDPHLSSVSHIVLDEIHERNLQSD 339

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
            L+ ++KD+ + R DLK+ILMSATLNAEKFS++FG  P++HIPGFT+PV EY LED++  
Sbjct: 340 VLMTVIKDLLNSRSDLKVILMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDIIEK 399

Query: 252 TR 253
            R
Sbjct: 400 IR 401

Source: Cavia porcellus

Species: Cavia porcellus

Genus: Cavia

Family: Caviidae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|114589920|ref|XP_001147378.1| PREDICTED: probable ATP-dependent RNA helicase DHX36 isoform 3 [Pan troglodytes]

 Score =  249 bits (636), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 118/182 (64%), Positives = 146/182 (80%), Gaps = 1/182 (0%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           ++I   TGCGKTTQV QFILD+ I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct: 226 TVISGETGCGKTTQVTQFILDNYIERGKGSACRIVCTQPRRISAISVAERVAAERAESCG 285

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
             G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSDP LS VSHIV+DEIHER++ SD
Sbjct: 286 -SGNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDPYLSSVSHIVLDEIHERNLQSD 344

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
            L+ ++KD+ + R DLK+ILMSATLNAEKFS++FG  P++HIPGFT+PV EY LEDV+  
Sbjct: 345 VLMTVVKDLLNFRSDLKVILMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDVIEK 404

Query: 252 TR 253
            R
Sbjct: 405 IR 406

Source: Pan troglodytes

Species: Pan troglodytes

Genus: Pan

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|297672311|ref|XP_002814249.1| PREDICTED: probable ATP-dependent RNA helicase DHX36-like, partial [Pongo abelii]

 Score =  249 bits (636), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 117/182 (64%), Positives = 146/182 (80%), Gaps = 1/182 (0%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           +++   TGCGKTTQV QFILD+ I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct: 25  TVVSGETGCGKTTQVTQFILDNYIERGKGSACRIVCTQPRRISAISVAERVAAERAESCG 84

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
             G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSDP LS VSHIV+DEIHER++ SD
Sbjct: 85  N-GNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDPYLSSVSHIVLDEIHERNLQSD 143

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
            L+ ++KD+ + R DLK+ILMSATLNAEKFS++FG  P++HIPGFT+PV EY LEDV+  
Sbjct: 144 VLMTVVKDLLNFRSDLKVILMSATLNAEKFSEYFGNCPMIHIPGFTFPVMEYLLEDVIEK 203

Query: 252 TR 253
            R
Sbjct: 204 IR 205

Source: Pongo abelii

Species: Pongo abelii

Genus: Pongo

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|390349687|ref|XP_784575.3| PREDICTED: probable ATP-dependent RNA helicase DHX36-like [Strongylocentrotus purpuratus]

 Score =  249 bits (636), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 126/224 (56%), Positives = 164/224 (73%), Gaps = 2/224 (0%)

Query: 31  LDDEIARNRGSECC-IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQF 89
           L +E+ +   SE    M T  R++ + A+ ++ L+L       +I   TGCGKTTQVPQF
Sbjct: 145 LQEELTKKENSEQYQKMQTFRRKLPSFAMKDELLSLIRSNQVVVISGETGCGKTTQVPQF 204

Query: 90  ILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPR 149
           ILDD I+R +GS C ++ TQPRRISAI +AERVA ER E+CG   +SVGYQIRLE   PR
Sbjct: 205 ILDDYISRGQGSTCRVVCTQPRRISAITVAERVAAERAERCGHE-NSVGYQIRLENTFPR 263

Query: 150 KRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKL 209
            +G ILYCT GIL + ++ D +L+ VSH+V+DE+HER ++SDFLL ILKD+  KR+DLKL
Sbjct: 264 AQGCILYCTTGILLKWLEGDKLLNSVSHVVLDEVHERDLLSDFLLIILKDLLPKRRDLKL 323

Query: 210 ILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTR 253
           ILMSATL AE FS +FG AP ++IPGFT+ V E+YLED+L +TR
Sbjct: 324 ILMSATLRAELFSDYFGQAPTVNIPGFTFGVTEFYLEDILELTR 367

Source: Strongylocentrotus purpuratus

Species: Strongylocentrotus purpuratus

Genus: Strongylocentrotus

Family: Strongylocentrotidae

Order: Echinoida

Class: Echinoidea

Phylum: Echinodermata

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	319
UNIPROTKB|E7EWK3	797	DHX36 "Probable ATP-dependent	0.567	0.227	0.648	6.4e-60
UNIPROTKB|F5GZS0	994	DHX36 "Probable ATP-dependent	0.567	0.182	0.648	3.1e-59
UNIPROTKB|Q9H2U1	1008	DHX36 "Probable ATP-dependent	0.567	0.179	0.648	3.3e-59
UNIPROTKB|I3LRU8	439	DHX36 "Uncharacterized protein	0.567	0.412	0.631	4.5e-59
UNIPROTKB|Q05B79	1010	DHX36 "Uncharacterized protein	0.567	0.179	0.637	9.3e-59
UNIPROTKB|E2QTL7	988	DHX36 "Uncharacterized protein	0.567	0.183	0.642	1e-58
UNIPROTKB|F6V8H1	1122	DHX36 "Uncharacterized protein	0.567	0.161	0.642	1.9e-58
MGI|MGI:1919412	1001	Dhx36 "DEAH (Asp-Glu-Ala-His)	0.567	0.180	0.637	5.1e-58
UNIPROTKB|E1C550	985	DHX36 "Uncharacterized protein	0.567	0.183	0.637	9.9e-58
RGD|1308767	1000	Dhx36 "DEAH (Asp-Glu-Ala-His)	0.567	0.181	0.637	1.8e-57

UNIPROTKB|E7EWK3 DHX36 "Probable ATP-dependent RNA helicase DHX36" [Homo sapiens (taxid:9606)]

 Score = 614 (221.2 bits), Expect = 6.4e-60, P = 6.4e-60
 Identities = 118/182 (64%), Positives = 146/182 (80%)

Query:    72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
             ++I   TGCGKTTQV QFILD+ I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct:   140 TVISGETGCGKTTQVTQFILDNYIERGKGSACRIVCTQPRRISAISVAERVAAERAESCG 199

Query:   132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
               G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSDP LS VSHIV+DEIHER++ SD
Sbjct:   200 S-GNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDPYLSSVSHIVLDEIHERNLQSD 258

Query:   192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
              L+ ++KD+ + R DLK+ILMSATLNAEKFS++FG  P++HIPGFT+PV EY LEDV+  
Sbjct:   259 VLMTVVKDLLNFRSDLKVILMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDVIEK 318

Query:   252 TR 253
              R
Sbjct:   319 IR 320

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0043330 "response to exogenous dsRNA" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F5GZS0 DHX36 "Probable ATP-dependent RNA helicase DHX36" [Homo sapiens (taxid:9606)]

 Score = 614 (221.2 bits), Expect = 3.1e-59, P = 3.1e-59
 Identities = 118/182 (64%), Positives = 146/182 (80%)

Query:    72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
             ++I   TGCGKTTQV QFILD+ I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct:   226 TVISGETGCGKTTQVTQFILDNYIERGKGSACRIVCTQPRRISAISVAERVAAERAESCG 285

Query:   132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
               G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSDP LS VSHIV+DEIHER++ SD
Sbjct:   286 S-GNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDPYLSSVSHIVLDEIHERNLQSD 344

Query:   192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
              L+ ++KD+ + R DLK+ILMSATLNAEKFS++FG  P++HIPGFT+PV EY LEDV+  
Sbjct:   345 VLMTVVKDLLNFRSDLKVILMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDVIEK 404

Query:   252 TR 253
              R
Sbjct:   405 IR 406

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|Q9H2U1 DHX36 "Probable ATP-dependent RNA helicase DHX36" [Homo sapiens (taxid:9606)]

 Score = 614 (221.2 bits), Expect = 3.3e-59, P = 3.3e-59
 Identities = 118/182 (64%), Positives = 146/182 (80%)

Query:    72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
             ++I   TGCGKTTQV QFILD+ I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct:   226 TVISGETGCGKTTQVTQFILDNYIERGKGSACRIVCTQPRRISAISVAERVAAERAESCG 285

Query:   132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
               G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSDP LS VSHIV+DEIHER++ SD
Sbjct:   286 S-GNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDPYLSSVSHIVLDEIHERNLQSD 344

Query:   192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
              L+ ++KD+ + R DLK+ILMSATLNAEKFS++FG  P++HIPGFT+PV EY LEDV+  
Sbjct:   345 VLMTVVKDLLNFRSDLKVILMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDVIEK 404

Query:   252 TR 253
              R
Sbjct:   405 IR 406

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0043330 "response to exogenous dsRNA" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|I3LRU8 DHX36 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 606 (218.4 bits), Expect = 4.5e-59, P = 4.5e-59
 Identities = 115/182 (63%), Positives = 145/182 (79%)

Query:    72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
             ++I   TGCGKTTQV QFILD+ I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct:   230 TVISGETGCGKTTQVTQFILDNYIERGKGSACRIVCTQPRRISAISVAERVAAERAETCG 289

Query:   132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
               G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSDP LS VSHI++DEIHER++ SD
Sbjct:   290 S-GNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDPHLSSVSHILLDEIHERNLQSD 348

Query:   192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
              L+ ++KD+   R DLK++LMSATLNAEKFS++FG  P++HIPGFT+PV EY LED++  
Sbjct:   349 VLMTVIKDLLSYRPDLKVVLMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDIIEK 408

Query:   252 TR 253
              R
Sbjct:   409 IR 410

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q05B79 DHX36 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 610 (219.8 bits), Expect = 9.3e-59, P = 9.3e-59
 Identities = 116/182 (63%), Positives = 145/182 (79%)

Query:    72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
             ++I   TGCGKTTQV QFILD+ I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct:   228 TVISGETGCGKTTQVTQFILDNYIERGKGSACRIVCTQPRRISAISVAERVAAERAESCG 287

Query:   132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
               G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSDP LS VSHIV+DEIHER++ SD
Sbjct:   288 N-GNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDPHLSSVSHIVLDEIHERNLQSD 346

Query:   192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
              L+ ++KD+   R DLK++LMSATLNAEKFS++FG  P++HIPGFT+PV EY LED++  
Sbjct:   347 VLMTVVKDLLSYRPDLKVVLMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDIIEK 406

Query:   252 TR 253
              R
Sbjct:   407 IR 408

GO:0043330 "response to exogenous dsRNA" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|E2QTL7 DHX36 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 609 (219.4 bits), Expect = 1.0e-58, P = 1.0e-58
 Identities = 117/182 (64%), Positives = 145/182 (79%)

Query:    72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
             ++I   TGCGKTTQV QFILDD I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct:   220 TVISGETGCGKTTQVTQFILDDYIERGKGSACRIVCTQPRRISAISVAERVAAERAESCG 279

Query:   132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
               G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSD  LS VSHIV+DEIHER++ SD
Sbjct:   280 N-GNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDSHLSSVSHIVLDEIHERNLQSD 338

Query:   192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
              L+ ++KD+ + R DLK+ILMSATLNAEKFS++FG  P++HIPGFT+PV EY LED++  
Sbjct:   339 VLMTVIKDLLNFRPDLKVILMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDIIEK 398

Query:   252 TR 253
              R
Sbjct:   399 IR 400

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F6V8H1 DHX36 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 609 (219.4 bits), Expect = 1.9e-58, P = 1.9e-58
 Identities = 117/182 (64%), Positives = 145/182 (79%)

Query:    72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
             ++I   TGCGKTTQV QFILDD I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct:   340 TVISGETGCGKTTQVTQFILDDYIERGKGSACRIVCTQPRRISAISVAERVAAERAESCG 399

Query:   132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
               G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSD  LS VSHIV+DEIHER++ SD
Sbjct:   400 N-GNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDSHLSSVSHIVLDEIHERNLQSD 458

Query:   192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
              L+ ++KD+ + R DLK+ILMSATLNAEKFS++FG  P++HIPGFT+PV EY LED++  
Sbjct:   459 VLMTVIKDLLNFRPDLKVILMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDIIEK 518

Query:   252 TR 253
              R
Sbjct:   519 IR 520

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:1919412 Dhx36 "DEAH (Asp-Glu-Ala-His) box polypeptide 36" [Mus musculus (taxid:10090)]

 Score = 603 (217.3 bits), Expect = 5.1e-58, P = 5.1e-58
 Identities = 116/182 (63%), Positives = 144/182 (79%)

Query:    72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
             ++I   TGCGKTTQV QFILD+ I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct:   219 TVISGETGCGKTTQVTQFILDNYIERGKGSACRIVCTQPRRISAISVAERVATERAESCG 278

Query:   132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
               G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSD  LS VSHIV+DEIHER++ SD
Sbjct:   279 N-GNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDSRLSSVSHIVLDEIHERNLQSD 337

Query:   192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
              L+ ++KD+   R DLK+ILMSATLNAEKFS++FG  P++HIPGFT+PV EY LED++  
Sbjct:   338 VLMTVIKDLLHFRSDLKVILMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDIIEK 397

Query:   252 TR 253
              R
Sbjct:   398 IR 399

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IDA

GO:0004386 "helicase activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0009615 "response to virus" evidence=IMP

GO:0016787 "hydrolase activity" evidence=IEA

GO:0043330 "response to exogenous dsRNA" evidence=IMP

UNIPROTKB|E1C550 DHX36 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 600 (216.3 bits), Expect = 9.9e-58, P = 9.9e-58
 Identities = 116/182 (63%), Positives = 144/182 (79%)

Query:    72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
             ++I   TGCGKTTQV QFILDD I R +GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct:   207 TVISGETGCGKTTQVTQFILDDYIERGKGSTCRIVCTQPRRISAISVAERVAAERAEACG 266

Query:   132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
               G S GYQIRL+  LPRK+GSILYCT GI+ + +QSD  LS +SH+V+DEIHER++ SD
Sbjct:   267 N-GKSTGYQIRLQSRLPRKQGSILYCTTGIVLQWLQSDKHLSSISHVVLDEIHERNLQSD 325

Query:   192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
              L++I+KD+ + R DLK+ILMSATLNAEKFS++F   P++HIPGFT+PV EY LEDV+  
Sbjct:   326 VLMSIIKDLLNVRLDLKVILMSATLNAEKFSEYFDNCPMIHIPGFTFPVVEYLLEDVIEK 385

Query:   252 TR 253
              R
Sbjct:   386 LR 387

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0043330 "response to exogenous dsRNA" evidence=IEA

RGD|1308767 Dhx36 "DEAH (Asp-Glu-Ala-His) box polypeptide 36" [Rattus norvegicus (taxid:10116)]

 Score = 598 (215.6 bits), Expect = 1.8e-57, P = 1.8e-57
 Identities = 116/182 (63%), Positives = 143/182 (78%)

Query:    72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
             ++I   TGCGKTTQV QFILD+ I R  GS C I+ TQPRRISAI++AERVA ER E CG
Sbjct:   218 TVISGETGCGKTTQVTQFILDNYIERGIGSACRIVCTQPRRISAISVAERVAAERAESCG 277

Query:   132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
               G+S GYQIRL+  LPRK+GSILYCT GI+ + +QSD  LS VSHIV+DEIHER++ SD
Sbjct:   278 N-GNSTGYQIRLQSRLPRKQGSILYCTTGIILQWLQSDSRLSSVSHIVLDEIHERNLQSD 336

Query:   192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM 251
              L+ ++KD+   R DLK+ILMSATLNAEKFS++FG  P++HIPGFT+PV EY LED++  
Sbjct:   337 VLMTVIKDLLHFRSDLKVILMSATLNAEKFSEYFGNCPMIHIPGFTFPVVEYLLEDIIEK 396

Query:   252 TR 253
              R
Sbjct:   397 IR 398

GO:0003725 "double-stranded RNA binding" evidence=IEA;ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

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

GO:0009615 "response to virus" evidence=IEA;ISO

GO:0043330 "response to exogenous dsRNA" evidence=IEA;ISO

---

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)
Q8VHK9	DHX36_MOUSE	3, ., 6, ., 4, ., 1, 3	0.6373	0.5673	0.1808	yes	N/A
Q9H2U1	DHX36_HUMAN	3, ., 6, ., 4, ., 1, 3	0.6483	0.5673	0.1795	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	319
COG1643	845	COG1643, HrpA, HrpA-like helicases [DNA replicatio	4e-60
TIGR01967	1283	TIGR01967, DEAH_box_HrpA, ATP-dependent helicase H	9e-39
TIGR01970	819	TIGR01970, DEAH_box_HrpB, ATP-dependent helicase H	8e-35
PRK11131	1294	PRK11131, PRK11131, ATP-dependent RNA helicase Hrp	2e-34
PRK11664	812	PRK11664, PRK11664, ATP-dependent RNA helicase Hrp	2e-28
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-19
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	2e-18
COG1643	845	COG1643, HrpA, HrpA-like helicases [DNA replicatio	8e-08
PHA02653	675	PHA02653, PHA02653, RNA helicase NPH-II; Provision	3e-07
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	2e-05

>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination, and repair]

 Score =  205 bits (524), Expect = 4e-60
 Identities = 88/175 (50%), Positives = 119/175 (68%), Gaps = 11/175 (6%)

Query: 78  TGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSV 137
           TG GKTTQ+PQF+L++      G    I  TQPRR++A ++AERVA+E  E   + G +V
Sbjct: 74  TGSGKTTQLPQFLLEEG----LGIAGKIGCTQPRRLAARSVAERVAEELGE---KLGETV 126

Query: 138 GYQIRLE-KELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAI 196
           GY IR E K  PR R  I   T GIL   +Q+DP+LSG S +++DE HERS+ +D LL +
Sbjct: 127 GYSIRFESKVSPRTR--IKVMTDGILLREIQNDPLLSGYSVVIIDEAHERSLNTDILLGL 184

Query: 197 LKDVTDKRK-DLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLN 250
           LKD+  +R+ DLKLI+MSATL+AE+FS +FG AP++ I G TYPV+  YL +   
Sbjct: 185 LKDLLARRRDDLKLIIMSATLDAERFSAYFGNAPVIEIEGRTYPVEIRYLPEAEA 239

Length = 845

>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA

 Score =  145 bits (368), Expect = 9e-39
 Identities = 72/172 (41%), Positives = 100/172 (58%), Gaps = 8/172 (4%)

Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           II   TG GKTTQ+P+  L+      RGS   I  TQPRR++A  +A+R+A+E       
Sbjct: 86  IIAGETGSGKTTQLPKICLE----LGRGSHGLIGHTQPRRLAARTVAQRIAEELGTP--- 138

Query: 133 PGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF 192
            G  VGY++R   ++      +   T GIL    Q D  LS    I++DE HERS+  DF
Sbjct: 139 LGEKVGYKVRFHDQV-SSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDF 197

Query: 193 LLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYY 244
           LL  LK +  +R DLK+I+ SAT++ E+FS+ F  API+ + G TYPV+  Y
Sbjct: 198 LLGYLKQLLPRRPDLKIIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRY 249

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 [Unknown function, Enzymes of unknown specificity]. Length = 1283

>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB

 Score =  133 bits (337), Expect = 8e-35
 Identities = 65/170 (38%), Positives = 99/170 (58%), Gaps = 12/170 (7%)

Query: 78  TGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSV 137
            G GK+T VP  +LD      +     I++ +PRR++A + A+R+A +  E     G +V
Sbjct: 26  PGAGKSTAVPLALLDAPGIGGK-----IIMLEPRRLAARSAAQRLASQLGEA---VGQTV 77

Query: 138 GYQIRLE-KELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAI 196
           GY++R E K   R R  ++  T GIL  ++Q DP L GV  ++ DE HERS+ +D  LA+
Sbjct: 78  GYRVRGENKVSRRTRLEVV--TEGILTRMIQDDPELDGVGALIFDEFHERSLDADLGLAL 135

Query: 197 LKDVTDK-RKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYL 245
             DV    R+DLK++ MSATL+ E+ S     AP++   G ++PV+  YL
Sbjct: 136 ALDVQSSLREDLKILAMSATLDGERLSSLLPDAPVVESEGRSFPVEIRYL 185

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 [Unknown function, Enzymes of unknown specificity]. Length = 819

>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional

 Score =  132 bits (335), Expect = 2e-34
 Identities = 72/191 (37%), Positives = 111/191 (58%), Gaps = 11/191 (5%)

Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           I+   TG GKTTQ+P+  L+      RG +  I  TQPRR++A  +A R+A+E + +   
Sbjct: 93  IVAGETGSGKTTQLPKICLE----LGRGVKGLIGHTQPRRLAARTVANRIAEELETE--- 145

Query: 133 PGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF 192
            G  VGY++R   ++      +   T GIL   +Q D +L     I++DE HERS+  DF
Sbjct: 146 LGGCVGYKVRFNDQV-SDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDF 204

Query: 193 LLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYY---LEDVL 249
           +L  LK++  +R DLK+I+ SAT++ E+FS+ F  API+ + G TYPV+  Y   +E+  
Sbjct: 205 ILGYLKELLPRRPDLKVIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYRPIVEEAD 264

Query: 250 NMTRKDLKLIL 260
           +  R  L+ I 
Sbjct: 265 DTERDQLQAIF 275

Length = 1294

>gnl|CDD|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional

 Score =  115 bits (289), Expect = 2e-28
 Identities = 66/174 (37%), Positives = 106/174 (60%), Gaps = 12/174 (6%)

Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           ++   TG GK+T +P  +L       +     I++ +PRR++A  +A+R+A++  E+   
Sbjct: 24  LLKAPTGAGKSTWLPLQLLQHGGINGK-----IIMLEPRRLAARNVAQRLAEQLGEK--- 75

Query: 133 PGSSVGYQIRLE-KELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
           PG +VGY++R E K  P  R  ++  T GIL  ++Q DP LSGV  +++DE HERS+ +D
Sbjct: 76  PGETVGYRMRAESKVGPNTRLEVV--TEGILTRMIQRDPELSGVGLVILDEFHERSLQAD 133

Query: 192 FLLAILKDVTDK-RKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYY 244
             LA+L DV    R DLKL++MSATL+ ++  Q    AP++   G ++PV+  Y
Sbjct: 134 LALALLLDVQQGLRDDLKLLIMSATLDNDRLQQLLPDAPVIVSEGRSFPVERRY 187

Length = 812

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

 Score = 84.5 bits (209), Expect = 1e-19
 Identities = 44/167 (26%), Positives = 71/167 (42%), Gaps = 9/167 (5%)

Query: 78  TGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGS-S 136
           TG GKT       L+   A  RG    ++V  P R  A   AE + +       +     
Sbjct: 33  TGSGKTLAALLPALE---ALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLY 89

Query: 137 VGYQIR-LEKELPRKRGSILYCTAGILPEVMQSDPI-LSGVSHIVMDEIHERSMISDFLL 194
            G   R   ++L   +  IL  T G L +++++D + LS V  +++DE H       F  
Sbjct: 90  GGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLL-DGGFGD 148

Query: 195 AILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAPILHIPGFTYP 239
            + K +    K+++L+L+SAT     E   + F   P+    GFT  
Sbjct: 149 QLEKLLKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGFTPL 195

Length = 201

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

 Score = 80.1 bits (198), Expect = 2e-18
 Identities = 38/141 (26%), Positives = 66/141 (46%), Gaps = 7/141 (4%)

Query: 78  TGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSV 137
           TG GKT      IL+   +   G    ++V  P R  A  +AER+ +   E   + G  +
Sbjct: 9   TGSGKTLAALLPILELLDSLKGGQ---VLVLAPTRELANQVAERLKELFGEG-IKVGYLI 64

Query: 138 GYQ-IRLEKELPRKRGSILYCTAGILPEVMQSDPI-LSGVSHIVMDEIHERSMISDFLLA 195
           G   I+ +++L   +  I+  T G L + ++   + L  +  +++DE H       F L 
Sbjct: 65  GGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLL-NQGFGLL 123

Query: 196 ILKDVTDKRKDLKLILMSATL 216
            LK +    KD +++L+SAT 
Sbjct: 124 GLKILLKLPKDRQVLLLSATP 144

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

>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination, and repair]

 Score = 53.5 bits (129), Expect = 8e-08
 Identities = 18/40 (45%), Positives = 26/40 (65%), Gaps = 4/40 (10%)

Query: 19  GCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAL 58
           G GKTTQ+PQF+L++      G    I  TQPRR++A ++
Sbjct: 75  GSGKTTQLPQFLLEEG----LGIAGKIGCTQPRRLAARSV 110

Length = 845

>gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional

 Score = 51.5 bits (124), Expect = 3e-07
 Identities = 25/70 (35%), Positives = 42/70 (60%), Gaps = 5/70 (7%)

Query: 178 IVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAPILHIPG 235
           +++DE+HE   I D ++A+ +   DK +   L LM+ATL  + ++  +FF     +HIPG
Sbjct: 295 VIIDEVHEHDQIGDIIIAVARKHIDKIRS--LFLMTATLEDDRDRIKEFFPNPAFVHIPG 352

Query: 236 FT-YPVQEYY 244
            T +P+ E Y
Sbjct: 353 GTLFPISEVY 362

Length = 675

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

 Score = 43.8 bits (104), Expect = 2e-05
 Identities = 40/168 (23%), Positives = 73/168 (43%), Gaps = 21/168 (12%)

Query: 64  TLSPILSPS--IIYTSTGCGKTT--QVPQFILDDEIARNRGSECCIMVTQPRRISAIAIA 119
            +  ILS    ++   TG GKT    +P  IL   + +  G +  ++   P R  A  I 
Sbjct: 7   AIPAILSGKDVLVQAPTGSGKTLAFLLP--ILQALLPKKGGPQALVLA--PTRELAEQIY 62

Query: 120 ERVAQERDEQCGRP-----GSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPI--L 172
           E + +       R      G+S+  Q R  K   + +  IL  T G L ++++   +  L
Sbjct: 63  EELKKLFKILGLRVALLTGGTSLKEQARKLK---KGKADILVGTPGRLLDLLRRGKLKLL 119

Query: 173 SGVSHIVMDEIHERSMIS-DFLLAILKDVTDKRKDLKLILMSATLNAE 219
             +  +V+DE H   ++   F   + + ++    D +++L+SATL   
Sbjct: 120 KNLKLLVLDEAHR--LLDMGFGDDLEEILSRLPPDRQILLLSATLPRN 165

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	319
KOG0922|consensus	674		100.0
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	100.0
KOG0923|consensus	902		100.0
KOG0924|consensus	1042		100.0
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	100.0
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	100.0
KOG0920|consensus	924		100.0
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	100.0
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	100.0
KOG0925|consensus	699		100.0
KOG0338|consensus	691		99.97
KOG0926|consensus	1172		99.96
KOG0330|consensus	476		99.96
KOG0331|consensus	519		99.96
KOG0343|consensus	758		99.95
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.94
KOG0346|consensus	569		99.94
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.94
KOG0342|consensus	543		99.93
KOG0335|consensus	482		99.93
KOG0340|consensus	442		99.93
PRK02362	737	ski2-like helicase; Provisional	99.93
PRK01172	674	ski2-like helicase; Provisional	99.93
PTZ00110	545	helicase; Provisional	99.93
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.93
KOG0348|consensus	708		99.93
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.93
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.92
KOG0345|consensus	567		99.92
KOG0326|consensus	459		99.92
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.92
PHA02653	675	RNA helicase NPH-II; Provisional	99.92
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.92
KOG0952|consensus	1230		99.92
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.92
COG1204	766	Superfamily II helicase [General function predicti	99.92
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.92
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.91
PRK00254	720	ski2-like helicase; Provisional	99.91
PRK13767	876	ATP-dependent helicase; Provisional	99.91
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.9
PTZ00424	401	helicase 45; Provisional	99.89
KOG0328|consensus	400		99.89
KOG0339|consensus	731		99.89
KOG0336|consensus	629		99.89
KOG0337|consensus	529		99.88
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.88
COG1202	830	Superfamily II helicase, archaea-specific [General	99.87
KOG0333|consensus	673		99.87
KOG0350|consensus	620		99.86
COG1205	851	Distinct helicase family with a unique C-terminal	99.85
KOG0334|consensus	997		99.85
KOG0347|consensus	731		99.85
KOG0951|consensus	1674		99.85
KOG0327|consensus	397		99.84
KOG4284|consensus	980		99.84
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.84
KOG0332|consensus	477		99.83
KOG0341|consensus	610		99.83
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.83
KOG0329|consensus	387		99.82
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.81
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.81
KOG0948|consensus	1041		99.81
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.8
PRK09401	1176	reverse gyrase; Reviewed	99.8
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.8
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.8
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.79
KOG0921|consensus	1282		99.79
PRK10689	1147	transcription-repair coupling factor; Provisional	99.78
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.78
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.77
KOG0344|consensus	593		99.76
PRK05580	679	primosome assembly protein PriA; Validated	99.73
PRK14701	1638	reverse gyrase; Provisional	99.73
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.73
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.72
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.7
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.68
KOG0947|consensus	1248		99.68
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.66
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.64
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.6
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.59
KOG0354|consensus	746		99.58
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.56
PHA02558	501	uvsW UvsW helicase; Provisional	99.55
PRK13766	773	Hef nuclease; Provisional	99.52
PRK09694	878	helicase Cas3; Provisional	99.5
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.48
KOG0951|consensus	1674		99.47
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.4
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.38
KOG0950|consensus	1008		99.37
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.33
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.33
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.31
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.28
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.27
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.26
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.25
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.25
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.24
KOG0949|consensus	1330		99.23
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.21
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.17
KOG0952|consensus	1230		99.17
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.1
KOG0349|consensus	725		99.09
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.06
KOG0352|consensus	641		99.0
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	98.92
PRK12904	830	preprotein translocase subunit SecA; Reviewed	98.91
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.9
PRK14873	665	primosome assembly protein PriA; Provisional	98.81
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.8
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.74
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.7
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.67
COG4096	875	HsdR Type I site-specific restriction-modification	98.65
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	98.59
KOG0351|consensus	941		98.58
KOG0353|consensus	695		98.41
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	98.39
PRK04914	956	ATP-dependent helicase HepA; Validated	98.34
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.32
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	98.25
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.23
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	98.1
PF13245	76	AAA_19: Part of AAA domain	98.1
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	98.08
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	98.08
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	98.06
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	98.02
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.01
KOG0921|consensus	1282		97.98
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.91
PRK15483	986	type III restriction-modification system StyLTI en	97.89
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.87
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.87
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	97.86
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.83
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	97.82
CHL00122	870	secA preprotein translocase subunit SecA; Validate	97.8
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.76
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	97.75
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	97.75
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.75
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	97.66
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.62
COG4889	1518	Predicted helicase [General function prediction on	97.61
COG0610	962	Type I site-specific restriction-modification syst	97.53
PRK14974	336	cell division protein FtsY; Provisional	97.53
PRK10536	262	hypothetical protein; Provisional	97.5
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	97.49
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	97.44
KOG0989|consensus	346		97.44
KOG0390|consensus	776		97.43
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.43
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	97.39
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	97.39
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.39
PRK04296	190	thymidine kinase; Provisional	97.37
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	97.36
PRK06526	254	transposase; Provisional	97.34
KOG4150|consensus	1034		97.32
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	97.32
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	97.3
PRK08181	269	transposase; Validated	97.27
KOG1803|consensus	649		97.26
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.24
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.24
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.22
KOG1123|consensus	776		97.22
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.21
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	97.2
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.16
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.11
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.09
PF05729	166	NACHT: NACHT domain	97.07
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.06
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	97.01
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	96.99
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	96.96
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.94
PRK08727	233	hypothetical protein; Validated	96.9
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	96.9
smart00382	148	AAA ATPases associated with a variety of cellular	96.9
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	96.89
KOG0387|consensus	923		96.88
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.88
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	96.87
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.86
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	96.86
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	96.84
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	96.84
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	96.81
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	96.81
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.8
PRK10867	433	signal recognition particle protein; Provisional	96.79
PRK09112	351	DNA polymerase III subunit delta'; Validated	96.78
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.77
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	96.76
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	96.72
KOG0385|consensus	971		96.69
KOG4439|consensus	901		96.68
PLN03025	319	replication factor C subunit; Provisional	96.66
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	96.65
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	96.64
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.63
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	96.6
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	96.59
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	96.56
TIGR00959	428	ffh signal recognition particle protein. This mode	96.56
PRK06835	329	DNA replication protein DnaC; Validated	96.54
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	96.54
PRK07471	365	DNA polymerase III subunit delta'; Validated	96.51
PRK10416	318	signal recognition particle-docking protein FtsY;	96.51
KOG0389|consensus	941		96.47
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	96.46
PRK05642	234	DNA replication initiation factor; Validated	96.46
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	96.45
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	96.45
PHA03333	752	putative ATPase subunit of terminase; Provisional	96.42
TIGR00376	637	DNA helicase, putative. The gene product may repre	96.4
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.4
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.38
COG2256	436	MGS1 ATPase related to the helicase subunit of the	96.37
PRK06893	229	DNA replication initiation factor; Validated	96.37
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.36
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	96.36
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	96.36
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	96.35
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.34
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	96.32
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.3
PRK08084	235	DNA replication initiation factor; Provisional	96.29
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	96.29
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.29
PRK07952	244	DNA replication protein DnaC; Validated	96.27
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	96.27
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	96.25
PRK08116	268	hypothetical protein; Validated	96.23
PRK09183	259	transposase/IS protein; Provisional	96.22
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.2
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	96.2
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	96.18
PRK13826	1102	Dtr system oriT relaxase; Provisional	96.15
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	96.14
PRK00149	450	dnaA chromosomal replication initiation protein; R	96.11
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	96.1
KOG1002|consensus	791		96.08
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	96.07
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.07
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.03
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	96.03
PRK12402	337	replication factor C small subunit 2; Reviewed	96.03
COG1484	254	DnaC DNA replication protein [DNA replication, rec	95.99
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	95.98
KOG1000|consensus	689		95.91
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	95.91
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	95.88
PRK00440	319	rfc replication factor C small subunit; Reviewed	95.79
KOG0991|consensus	333		95.77
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	95.77
PRK12377	248	putative replication protein; Provisional	95.76
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	95.76
COG3973	747	Superfamily I DNA and RNA helicases [General funct	95.75
PRK04195	482	replication factor C large subunit; Provisional	95.72
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	95.68
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	95.66
PHA03368	738	DNA packaging terminase subunit 1; Provisional	95.64
PRK14088	440	dnaA chromosomal replication initiation protein; P	95.59
PRK14087	450	dnaA chromosomal replication initiation protein; P	95.53
PRK06921	266	hypothetical protein; Provisional	95.52
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	95.5
KOG1802|consensus	935		95.5
PRK00411	394	cdc6 cell division control protein 6; Reviewed	95.5
CHL00181	287	cbbX CbbX; Provisional	95.43
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	95.42
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	95.41
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	95.4
PRK13342	413	recombination factor protein RarA; Reviewed	95.36
PRK08939	306	primosomal protein DnaI; Reviewed	95.35
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	95.35
PRK13851	344	type IV secretion system protein VirB11; Provision	95.27
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	95.25
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.24
PRK05707	328	DNA polymerase III subunit delta'; Validated	95.21
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	95.2
COG3587	985	Restriction endonuclease [Defense mechanisms]	95.2
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	95.19
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	95.18
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	95.16
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.16
KOG0384|consensus	1373		95.15
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.12
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	95.07
PRK08533	230	flagellar accessory protein FlaH; Reviewed	95.05
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	95.03
PRK14086	617	dnaA chromosomal replication initiation protein; P	95.03
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	95.03
PHA02544	316	44 clamp loader, small subunit; Provisional	95.02
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.01
PRK12422	445	chromosomal replication initiation protein; Provis	94.85
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	94.8
PRK07940	394	DNA polymerase III subunit delta'; Validated	94.78
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	94.76
KOG0780|consensus	483		94.75
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	94.74
PRK06871	325	DNA polymerase III subunit delta'; Validated	94.71
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	94.71
PRK13341	725	recombination factor protein RarA/unknown domain f	94.7
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	94.65
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	94.64
KOG0953|consensus	700		94.61
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	94.61
KOG2028|consensus	554		94.61
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	94.6
PF12846	304	AAA_10: AAA-like domain	94.53
PRK08769	319	DNA polymerase III subunit delta'; Validated	94.53
KOG0392|consensus	1549		94.51
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	94.51
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	94.46
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	94.43
KOG1805|consensus	1100		94.36
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	94.35
PRK04328	249	hypothetical protein; Provisional	94.32
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	94.29
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	94.27
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	94.25
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	94.24
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	94.18
PRK10263	1355	DNA translocase FtsK; Provisional	94.13
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	94.13
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	94.1
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	94.1
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	94.1
PRK07399	314	DNA polymerase III subunit delta'; Validated	94.05
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	94.02
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	93.99
CHL00095	821	clpC Clp protease ATP binding subunit	93.96
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	93.93
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	93.89
PRK08058	329	DNA polymerase III subunit delta'; Validated	93.88
KOG2228|consensus	408		93.87
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	93.87
PRK06090	319	DNA polymerase III subunit delta'; Validated	93.83
PRK11054	684	helD DNA helicase IV; Provisional	93.82
PF13555	62	AAA_29: P-loop containing region of AAA domain	93.82
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	93.71
PRK10865	857	protein disaggregation chaperone; Provisional	93.7
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	93.66
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	93.59
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	93.59
PRK05973	237	replicative DNA helicase; Provisional	93.5
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	93.39
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	93.36
PRK07993	334	DNA polymerase III subunit delta'; Validated	93.2
PRK11823	446	DNA repair protein RadA; Provisional	92.9
PRK06964	342	DNA polymerase III subunit delta'; Validated	92.85
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	92.83
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	92.79
PRK10436	462	hypothetical protein; Provisional	92.74
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	92.72
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	92.72
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	92.66
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	92.64
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	92.63
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	92.63
KOG0391|consensus	1958		92.63
PRK05564	313	DNA polymerase III subunit delta'; Validated	92.57
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	92.53
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	92.53
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	92.51
PRK13897	606	type IV secretion system component VirD4; Provisio	92.51
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	92.45
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	92.42
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	92.41
KOG0920|consensus	924		92.4
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	92.33
PRK13764	602	ATPase; Provisional	92.29
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	92.23
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	92.22
PTZ00293	211	thymidine kinase; Provisional	92.21
KOG0058|consensus	716		92.13
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	92.07
PRK04841	903	transcriptional regulator MalT; Provisional	92.0
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	91.93
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	91.91
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	91.88
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	91.8
TIGR02237	209	recomb_radB DNA repair and recombination protein R	91.77
PRK13850	670	type IV secretion system protein VirD4; Provisiona	91.69
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	91.6
KOG1970|consensus	634		91.54
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	91.36
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	91.31
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	91.23
cd03246	173	ABCC_Protease_Secretion This family represents the	91.19
KOG2373|consensus	514		91.18
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	91.16
COG0593	408	DnaA ATPase involved in DNA replication initiation	91.15
COG1221	403	PspF Transcriptional regulators containing an AAA-	91.14
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	91.13
PRK13880	636	conjugal transfer coupling protein TraG; Provision	91.09
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	91.06
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	91.06
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	91.04
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	91.04
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	90.95
PF00004	132	AAA: ATPase family associated with various cellula	90.93
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	90.9
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	90.85
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	90.8
cd03239	178	ABC_SMC_head The structural maintenance of chromos	90.78
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	90.7
PHA02533	534	17 large terminase protein; Provisional	90.65
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	90.62
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	90.56
PRK05917	290	DNA polymerase III subunit delta'; Validated	90.53
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	90.41
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	90.28
cd01394	218	radB RadB. The archaeal protein radB shares simila	90.27
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	90.26
PRK06067	234	flagellar accessory protein FlaH; Validated	90.22
KOG0741|consensus	744		90.07
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	90.03
PRK13876	663	conjugal transfer coupling protein TraG; Provision	89.91
COG4626	546	Phage terminase-like protein, large subunit [Gener	89.91
KOG0060|consensus	659		89.9
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	89.78
PHA02244	383	ATPase-like protein	89.76
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	89.68
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	89.65
PRK08699	325	DNA polymerase III subunit delta'; Validated	89.64
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	89.54
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	89.51
PF09439	181	SRPRB: Signal recognition particle receptor beta s	89.48
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	89.47
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	89.35
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	89.27
KOG2035|consensus	351		89.24
KOG0386|consensus	1157		89.22
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	89.19
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	89.18
PRK13822	641	conjugal transfer coupling protein TraG; Provision	89.14
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	88.93
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	88.91
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	88.9
PRK13695	174	putative NTPase; Provisional	88.82
PRK00300	205	gmk guanylate kinase; Provisional	88.79
TIGR02533	486	type_II_gspE general secretory pathway protein E.	88.77
PRK07261	171	topology modulation protein; Provisional	88.76
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	88.72
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	88.67
PRK08118	167	topology modulation protein; Reviewed	88.67
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	88.46
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	88.42
PLN02165	334	adenylate isopentenyltransferase	88.41
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	88.4
COG2204	464	AtoC Response regulator containing CheY-like recei	88.33
PRK00131	175	aroK shikimate kinase; Reviewed	88.26
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	88.22
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	88.21
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	88.19
KOG0990|consensus	360		88.1
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	88.06
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	88.02
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	88.0
TIGR00235	207	udk uridine kinase. Model contains a number of lon	87.54
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	87.45
cd00983	325	recA RecA is a bacterial enzyme which has roles in	87.45
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	87.41
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	87.39
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	87.35
PF00005	137	ABC_tran: ABC transporter This structure is on hol	87.29
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	87.16
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	87.05
PRK09354	349	recA recombinase A; Provisional	86.98
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	86.9
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	86.83
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	86.81
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	86.76
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	86.73
COG3972	660	Superfamily I DNA and RNA helicases [General funct	86.51
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	86.5
PF13173	128	AAA_14: AAA domain	86.3
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	86.28
PRK05541	176	adenylylsulfate kinase; Provisional	86.17
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	86.15
PRK09302	509	circadian clock protein KaiC; Reviewed	86.11
PRK08233	182	hypothetical protein; Provisional	86.07
KOG0745|consensus	564		86.07
PRK14530	215	adenylate kinase; Provisional	86.04
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	86.02
PRK06762	166	hypothetical protein; Provisional	86.01
KOG0726|consensus	440		85.96
PHA00012	361	I assembly protein	85.91

>KOG0922|consensus

Probab=100.00  E-value=2.1e-40  Score=318.27  Aligned_cols=254  Identities=35%  Similarity=0.511  Sum_probs=219.8

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      -.|++.+|+....++++....+|++++|.|+||||||+..+..+.++.+...    ++|.|++|+|.+|..+++++++++
T Consensus        44 ~~qR~~LPI~~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~~~----g~I~~TQPRRVAavslA~RVAeE~  119 (674)
T KOG0922|consen   44 QEQRESLPIYKYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFASS----GKIACTQPRRVAAVSLAKRVAEEM  119 (674)
T ss_pred             HHhhccCCHHHHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhcccccC----CcEEeecCchHHHHHHHHHHHHHh
Confidence            5577889999999999999999999999999999999999999998877654    369999999999999999999999


Q ss_pred             ccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccC
Q psy496          127 DEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKD  206 (319)
Q Consensus       127 ~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~  206 (319)
                      +...   |..|||.+++++.+.. +++|.++|.|.|++.+..+|.|+++++|||||||+|++++|+++++++.+...+++
T Consensus       120 ~~~l---G~~VGY~IRFed~ts~-~TrikymTDG~LLRE~l~Dp~LskYsvIIlDEAHERsl~TDiLlGlLKki~~~R~~  195 (674)
T KOG0922|consen  120 GCQL---GEEVGYTIRFEDSTSK-DTRIKYMTDGMLLREILKDPLLSKYSVIILDEAHERSLHTDILLGLLKKILKKRPD  195 (674)
T ss_pred             CCCc---CceeeeEEEecccCCC-ceeEEEecchHHHHHHhcCCccccccEEEEechhhhhhHHHHHHHHHHHHHhcCCC
Confidence            9988   9999999999998874 78999999999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEeccccChhhHhhhhCCCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCcc
Q psy496          207 LKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFT  286 (319)
Q Consensus       207 ~qiv~lSAT~~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~  286 (319)
                      +++|++|||+|.+.+.+||.+++++.++||.|||+++|+..+    ..++-.......+++  -.....|++|||++|+.
T Consensus       196 LklIimSATlda~kfS~yF~~a~i~~i~GR~fPVei~y~~~p----~~dYv~a~~~tv~~I--h~~E~~GDILvFLtGqe  269 (674)
T KOG0922|consen  196 LKLIIMSATLDAEKFSEYFNNAPILTIPGRTFPVEILYLKEP----TADYVDAALITVIQI--HLTEPPGDILVFLTGQE  269 (674)
T ss_pred             ceEEEEeeeecHHHHHHHhcCCceEeecCCCCceeEEeccCC----chhhHHHHHHHHHHH--HccCCCCCEEEEeCCHH
Confidence            999999999999999999999999999999999999999864    445555555555555  23356899999999996


Q ss_pred             c--cccccchHhHHHHhHh-----hccccCCCCCC
Q psy496          287 Y--PVQEYYLEDVLNMTRT-----LKRSETQQYPN  314 (319)
Q Consensus       287 ~--~v~~~~~~~~~~~~~~-----~~~~~~~~~~~  314 (319)
                      +  .+-....+.+.+....     |+.|+++|...
T Consensus       270 EIe~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~  304 (674)
T KOG0922|consen  270 EIEAACELLRERAKSLPEDCPELILPLYGALPSEE  304 (674)
T ss_pred             HHHHHHHHHHHHhhhccccCcceeeeecccCCHHH
Confidence            5  2222333333333333     78999987543

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

Probab=100.00  E-value=1e-37  Score=314.43  Aligned_cols=263  Identities=37%  Similarity=0.515  Sum_probs=217.7

Q ss_pred             ccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHH
Q psy496           42 ECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        42 ~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      ..+.+..++..+|+.....+++....+|++++|+||||||||++.+..+++..+.    ....|.+++|+|..|..++++
T Consensus        38 ~~~~~~~~~~~LPv~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~~----~~g~I~~tQPRRlAArsvA~R  113 (845)
T COG1643          38 NVPDILEYRSGLPVTAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGLG----IAGKIGCTQPRRLAARSVAER  113 (845)
T ss_pred             ccchhhhccccCCcHHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhcc----cCCeEEecCchHHHHHHHHHH
Confidence            3333456788999999999999999999999999999999999999999998762    245999999999999999999


Q ss_pred             HHHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhh
Q psy496          122 VAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVT  201 (319)
Q Consensus       122 ~~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~  201 (319)
                      ++++++..+   |..|||.+++++... .+++|-++|.|+|++.++.++.|+.|++||+||+|+|+++.|+++++++.+.
T Consensus       114 vAeel~~~~---G~~VGY~iRfe~~~s-~~Trik~mTdGiLlrei~~D~~Ls~ys~vIiDEaHERSl~tDilLgllk~~~  189 (845)
T COG1643         114 VAEELGEKL---GETVGYSIRFESKVS-PRTRIKVMTDGILLREIQNDPLLSGYSVVIIDEAHERSLNTDILLGLLKDLL  189 (845)
T ss_pred             HHHHhCCCc---CceeeEEEEeeccCC-CCceeEEeccHHHHHHHhhCcccccCCEEEEcchhhhhHHHHHHHHHHHHHH
Confidence            999999988   999999999999885 5789999999999999999999999999999999999999999999999966


Q ss_pred             c-cccCceEEEeccccChhhHhhhhCCCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEE
Q psy496          202 D-KRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPIL  280 (319)
Q Consensus       202 ~-~~~~~qiv~lSAT~~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LV  280 (319)
                      . .++++++|.||||+|.++|++||+++|++.++||.|||+++|.+....  +..+-..+.......   .....|++||
T Consensus       190 ~~rr~DLKiIimSATld~~rfs~~f~~apvi~i~GR~fPVei~Y~~~~~~--d~~l~~ai~~~v~~~---~~~~~GdILv  264 (845)
T COG1643         190 ARRRDDLKLIIMSATLDAERFSAYFGNAPVIEIEGRTYPVEIRYLPEAEA--DYILLDAIVAAVDIH---LREGSGSILV  264 (845)
T ss_pred             hhcCCCceEEEEecccCHHHHHHHcCCCCEEEecCCccceEEEecCCCCc--chhHHHHHHHHHHHh---ccCCCCCEEE
Confidence            6 455899999999999999999999999999999999999999766421  221222222222222   2234899999


Q ss_pred             EeCCccccccc-cchH--hHHHHhHhhccccCCCCCCccC
Q psy496          281 HIPGFTYPVQE-YYLE--DVLNMTRTLKRSETQQYPNDQQ  317 (319)
Q Consensus       281 Flp~R~~~v~~-~~~~--~~~~~~~~~~~~~~~~~~~~~~  317 (319)
                      |+||..+=-+. .-+.  ++...+..||+|++++...|++
T Consensus       265 FLpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~r  304 (845)
T COG1643         265 FLPGQREIERTAEWLEKAELGDDLEILPLYGALSAEEQVR  304 (845)
T ss_pred             ECCcHHHHHHHHHHHHhccccCCcEEeeccccCCHHHHHh
Confidence            99998652111 1122  2225688999999998877664

>KOG0923|consensus

Probab=100.00  E-value=3.6e-37  Score=293.91  Aligned_cols=258  Identities=33%  Similarity=0.489  Sum_probs=219.7

Q ss_pred             hhhhhhhcccCCCccccccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhH
Q psy496            9 ITYRLKEDLAGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      |+|-...+++|+.....-...-.   .++ + .   .+---++++|++.-..+++....++|+++|.|+||||||++.+.
T Consensus       228 idF~~e~~~~~~~e~~~~~~~~~---~~~-~-~---~iee~RksLPVy~ykdell~av~e~QVLiI~GeTGSGKTTQiPQ  299 (902)
T KOG0923|consen  228 IDFIQESKLAGSNEEDAKDAPTA---YER-R-E---SIEEVRKSLPVYPYKDELLKAVKEHQVLIIVGETGSGKTTQIPQ  299 (902)
T ss_pred             hhHHHhhhccccCccccchhhHH---HHH-H-H---HHHHHHhcCCchhhHHHHHHHHHhCcEEEEEcCCCCCccccccH
Confidence            88888888877765543221100   000 0 0   00112678999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhc
Q psy496           89 FILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQS  168 (319)
Q Consensus        89 ~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~  168 (319)
                      ++.+..+..+   ..+|-|++|+|..|..++.+++++++...   |..+||++++++++. +++-|-+||.|+|++.+..
T Consensus       300 yL~EaGytk~---gk~IgcTQPRRVAAmSVAaRVA~EMgvkL---G~eVGYsIRFEdcTS-ekTvlKYMTDGmLlREfL~  372 (902)
T KOG0923|consen  300 YLYEAGYTKG---GKKIGCTQPRRVAAMSVAARVAEEMGVKL---GHEVGYSIRFEDCTS-EKTVLKYMTDGMLLREFLS  372 (902)
T ss_pred             HHHhcccccC---CceEeecCcchHHHHHHHHHHHHHhCccc---ccccceEEEeccccC-cceeeeeecchhHHHHHhc
Confidence            9998877655   23699999999999999999999999998   999999999999987 6788999999999999999


Q ss_pred             CCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccChhhHhhhhCCCCEEEeCCccccceeeeehhh
Q psy496          169 DPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDV  248 (319)
Q Consensus       169 ~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~  248 (319)
                      .++|..++++||||||+|.+++|++.++++.+...+|++++++.|||+|.+.|..||+++|+|.++||.+||+++|...+
T Consensus       373 epdLasYSViiiDEAHERTL~TDILfgLvKDIar~RpdLKllIsSAT~DAekFS~fFDdapIF~iPGRRyPVdi~Yt~~P  452 (902)
T KOG0923|consen  373 EPDLASYSVIIVDEAHERTLHTDILFGLVKDIARFRPDLKLLISSATMDAEKFSAFFDDAPIFRIPGRRYPVDIFYTKAP  452 (902)
T ss_pred             cccccceeEEEeehhhhhhhhhhHHHHHHHHHHhhCCcceEEeeccccCHHHHHHhccCCcEEeccCcccceeeecccCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999776


Q ss_pred             hhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCccc
Q psy496          249 LNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTY  287 (319)
Q Consensus       249 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~  287 (319)
                          ..++-..+.-.++.+  ......|++|||+.|...
T Consensus       453 ----EAdYldAai~tVlqI--H~tqp~GDILVFltGQeE  485 (902)
T KOG0923|consen  453 ----EADYLDAAIVTVLQI--HLTQPLGDILVFLTGQEE  485 (902)
T ss_pred             ----chhHHHHHHhhheee--EeccCCccEEEEeccHHH
Confidence                456666665555555  333457999999999865

>KOG0924|consensus

Probab=100.00  E-value=6.5e-35  Score=279.10  Aligned_cols=231  Identities=36%  Similarity=0.520  Sum_probs=204.1

Q ss_pred             ccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           46 MVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        46 ~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      ...|++.+|+..-..+++....+|++|+|.|+||||||++.+.++++..+..    .+.|.|++|+|.+|..++++++++
T Consensus       348 i~eqrq~LPvf~~R~~ll~~ir~n~vvvivgETGSGKTTQl~QyL~edGY~~----~GmIGcTQPRRvAAiSVAkrVa~E  423 (1042)
T KOG0924|consen  348 IREQRQYLPVFACRDQLLSVIRENQVVVIVGETGSGKTTQLAQYLYEDGYAD----NGMIGCTQPRRVAAISVAKRVAEE  423 (1042)
T ss_pred             HHHHHhhcchHHHHHHHHHHHhhCcEEEEEecCCCCchhhhHHHHHhccccc----CCeeeecCchHHHHHHHHHHHHHH
Confidence            4679999999999999999999999999999999999999999888765543    358999999999999999999999


Q ss_pred             hccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhcccc
Q psy496          126 RDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRK  205 (319)
Q Consensus       126 ~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~  205 (319)
                      ++..+   |..|||.+++++.+. ..+.|-++|.|+|++....+..|..+++||+||||+|++++|++.++++.+...+.
T Consensus       424 M~~~l---G~~VGYsIRFEdvT~-~~T~IkymTDGiLLrEsL~d~~L~kYSviImDEAHERslNtDilfGllk~~larRr  499 (1042)
T KOG0924|consen  424 MGVTL---GDTVGYSIRFEDVTS-EDTKIKYMTDGILLRESLKDRDLDKYSVIIMDEAHERSLNTDILFGLLKKVLARRR  499 (1042)
T ss_pred             hCCcc---ccccceEEEeeecCC-CceeEEEeccchHHHHHhhhhhhhheeEEEechhhhcccchHHHHHHHHHHHHhhc
Confidence            99988   999999999999887 67889999999999999988899999999999999999999999999999999888


Q ss_pred             CceEEEeccccChhhHhhhhCCCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCc
Q psy496          206 DLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGF  285 (319)
Q Consensus       206 ~~qiv~lSAT~~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R  285 (319)
                      ++++|..|||||.+.|+.|||++|.|+++||.|||++.|...+    ..++-..+..-.+.+  -.....|++|||.+|+
T Consensus       500 dlKliVtSATm~a~kf~nfFgn~p~f~IpGRTyPV~~~~~k~p----~eDYVeaavkq~v~I--hl~~~~GdilIfmtGq  573 (1042)
T KOG0924|consen  500 DLKLIVTSATMDAQKFSNFFGNCPQFTIPGRTYPVEIMYTKTP----VEDYVEAAVKQAVQI--HLSGPPGDILIFMTGQ  573 (1042)
T ss_pred             cceEEEeeccccHHHHHHHhCCCceeeecCCccceEEEeccCc----hHHHHHHHHhhheEe--eccCCCCCEEEecCCC
Confidence            9999999999999999999999999999999999999998775    344445444444443  2223469999999998


Q ss_pred             cccccc
Q psy496          286 TYPVQE  291 (319)
Q Consensus       286 ~~~v~~  291 (319)
                       .+++.
T Consensus       574 -ediE~  578 (1042)
T KOG0924|consen  574 -EDIEC  578 (1042)
T ss_pred             -cchhH
Confidence             44444

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=100.00  E-value=8.5e-34  Score=289.64  Aligned_cols=248  Identities=30%  Similarity=0.453  Sum_probs=194.1

Q ss_pred             hhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCC
Q psy496           53 ISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR  132 (319)
Q Consensus        53 ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~  132 (319)
                      +|+.....+++....++++++++|+||||||++|++++++....     ..+|++++|||++|.|+++++++.++..+  
T Consensus         4 LPi~~~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~-----~~~ilvlqPrR~aA~qia~rva~~l~~~~--   76 (812)
T PRK11664          4 LPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGI-----NGKIIMLEPRRLAARNVAQRLAEQLGEKP--   76 (812)
T ss_pred             CCHHHHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCc-----CCeEEEECChHHHHHHHHHHHHHHhCccc--
Confidence            78888888999999999999999999999999999999976432     23899999999999999999999888777  


Q ss_pred             CCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhc-cccCceEEE
Q psy496          133 PGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTD-KRKDLKLIL  211 (319)
Q Consensus       133 ~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~-~~~~~qiv~  211 (319)
                       |..+|+.+++++... .+++|+|+|||+|++++..++.++++++||+||+|+|++..|+.++.+..+.. .+++.|+|+
T Consensus        77 -g~~VGy~vr~~~~~~-~~t~I~v~T~G~Llr~l~~d~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~lqlil  154 (812)
T PRK11664         77 -GETVGYRMRAESKVG-PNTRLEVVTEGILTRMIQRDPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLI  154 (812)
T ss_pred             -CceEEEEecCccccC-CCCcEEEEChhHHHHHHhhCCCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccceEEE
Confidence             899999998876554 45789999999999999888899999999999999999998888777766543 567899999


Q ss_pred             eccccChhhHhhhhCCCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCccccccc
Q psy496          212 MSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQE  291 (319)
Q Consensus       212 lSAT~~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v~~  291 (319)
                      ||||++.+.+.+||++++++.++++.+|++++|.....   .......+.......  +.. ..|++|||+||+...-.+
T Consensus       155 mSATl~~~~l~~~~~~~~~I~~~gr~~pV~~~y~~~~~---~~~~~~~v~~~l~~~--l~~-~~g~iLVFlpg~~ei~~l  228 (812)
T PRK11664        155 MSATLDNDRLQQLLPDAPVIVSEGRSFPVERRYQPLPA---HQRFDEAVARATAEL--LRQ-ESGSLLLFLPGVGEIQRV  228 (812)
T ss_pred             EecCCCHHHHHHhcCCCCEEEecCccccceEEeccCch---hhhHHHHHHHHHHHH--HHh-CCCCEEEEcCCHHHHHHH
Confidence            99999888899999999999999999999999975431   111211111111121  122 268999999998775443


Q ss_pred             cc-hHh-HHHHhHhhccccCCCCCCc
Q psy496          292 YY-LED-VLNMTRTLKRSETQQYPND  315 (319)
Q Consensus       292 ~~-~~~-~~~~~~~~~~~~~~~~~~~  315 (319)
                      .. +.+ ......+++++|.++..++
T Consensus       229 ~~~L~~~~~~~~~v~~Lhg~l~~~eq  254 (812)
T PRK11664        229 QEQLASRVASDVLLCPLYGALSLAEQ  254 (812)
T ss_pred             HHHHHHhccCCceEEEeeCCCCHHHH
Confidence            21 221 1124567888887765443

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=100.00  E-value=1e-33  Score=288.68  Aligned_cols=246  Identities=29%  Similarity=0.419  Sum_probs=191.6

Q ss_pred             hhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCC
Q psy496           54 SAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRP  133 (319)
Q Consensus        54 p~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~  133 (319)
                      |+.....+++....+|++++++|+||||||+++++++++....     ..+|++++|||++|.|+++++++.++..+   
T Consensus         2 Pi~~~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~~-----~~~ilvlqPrR~aA~qiA~rva~~~~~~~---   73 (819)
T TIGR01970         2 PIHAVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGI-----GGKIIMLEPRRLAARSAAQRLASQLGEAV---   73 (819)
T ss_pred             CchHHHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhcc-----CCeEEEEeCcHHHHHHHHHHHHHHhCCCc---
Confidence            5566667888888889999999999999999999999987632     34899999999999999999999888777   


Q ss_pred             CceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhc-cccCceEEEe
Q psy496          134 GSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTD-KRKDLKLILM  212 (319)
Q Consensus       134 g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~-~~~~~qiv~l  212 (319)
                      |..+|+.+++++... .+++|+|+|||+|++++..++.++++++|||||+|+|+++.|+.+..++.+.. .+++.|+|+|
T Consensus        74 g~~VGy~vr~~~~~s-~~t~I~v~T~G~Llr~l~~d~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~dlqlIlm  152 (819)
T TIGR01970        74 GQTVGYRVRGENKVS-RRTRLEVVTEGILTRMIQDDPELDGVGALIFDEFHERSLDADLGLALALDVQSSLREDLKILAM  152 (819)
T ss_pred             CcEEEEEEccccccC-CCCcEEEECCcHHHHHHhhCcccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCCceEEEE
Confidence            899999999876654 46789999999999999888899999999999999988888888777766644 5678999999


Q ss_pred             ccccChhhHhhhhCCCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCcccccccc
Q psy496          213 SATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEY  292 (319)
Q Consensus       213 SAT~~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v~~~  292 (319)
                      |||++.+.+.+||++++++.++++.+||+++|.....   ...+...+.......  +.. .+|++|||+||+....+..
T Consensus       153 SATl~~~~l~~~l~~~~vI~~~gr~~pVe~~y~~~~~---~~~~~~~v~~~l~~~--l~~-~~g~iLVFlpg~~eI~~l~  226 (819)
T TIGR01970       153 SATLDGERLSSLLPDAPVVESEGRSFPVEIRYLPLRG---DQRLEDAVSRAVEHA--LAS-ETGSILVFLPGQAEIRRVQ  226 (819)
T ss_pred             eCCCCHHHHHHHcCCCcEEEecCcceeeeeEEeecch---hhhHHHHHHHHHHHH--HHh-cCCcEEEEECCHHHHHHHH
Confidence            9999888899999999999999999999999976431   111111111111121  122 2689999999987754432


Q ss_pred             -chHhHH-HHhHhhccccCCCCCC
Q psy496          293 -YLEDVL-NMTRTLKRSETQQYPN  314 (319)
Q Consensus       293 -~~~~~~-~~~~~~~~~~~~~~~~  314 (319)
                       .+.+.. ....++++++.++..+
T Consensus       227 ~~L~~~~~~~~~v~pLHg~L~~~e  250 (819)
T TIGR01970       227 EQLAERLDSDVLICPLYGELSLAA  250 (819)
T ss_pred             HHHHhhcCCCcEEEEecCCCCHHH
Confidence             122211 2356788888776543

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.

>KOG0920|consensus

Probab=100.00  E-value=2.3e-33  Score=282.29  Aligned_cols=197  Identities=54%  Similarity=0.897  Sum_probs=185.3

Q ss_pred             ccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccc
Q psy496           50 PRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQ  129 (319)
Q Consensus        50 ~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~  129 (319)
                      +..+|++...+.++....++++++|+|+||||||+..+..+++..+..+  ..++|+|++|+|..|..++++++.+.+..
T Consensus       169 R~~LPa~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~--~~~~IicTQPRRIsAIsvAeRVa~ER~~~  246 (924)
T KOG0920|consen  169 RESLPAYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESG--AACNIICTQPRRISAISVAERVAKERGES  246 (924)
T ss_pred             HHhCccHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcC--CCCeEEecCCchHHHHHHHHHHHHHhccc
Confidence            5789999999999999999999999999999999999999999877665  57899999999999999999999999888


Q ss_pred             cCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceE
Q psy496          130 CGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKL  209 (319)
Q Consensus       130 ~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qi  209 (319)
                      .   |..|||+++.+.....+ +.+.+||.|.|++.+..++.+.++.++|+||+|+|++.+|+++..++.+...+|++++
T Consensus       247 ~---g~~VGYqvrl~~~~s~~-t~L~fcTtGvLLr~L~~~~~l~~vthiivDEVHER~i~~DflLi~lk~lL~~~p~Lkv  322 (924)
T KOG0920|consen  247 L---GEEVGYQVRLESKRSRE-TRLLFCTTGVLLRRLQSDPTLSGVTHIIVDEVHERSINTDFLLILLKDLLPRNPDLKV  322 (924)
T ss_pred             c---CCeeeEEEeeecccCCc-eeEEEecHHHHHHHhccCcccccCceeeeeeEEEccCCcccHHHHHHHHhhhCCCceE
Confidence            7   99999999998877654 8999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeccccChhhHhhhhCCCCEEEeCCccccceeeeehhhhhhh
Q psy496          210 ILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMT  252 (319)
Q Consensus       210 v~lSAT~~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~  252 (319)
                      |+||||+|.+.+.+||++++++.++|+.+||..+|+++.+..+
T Consensus       323 ILMSAT~dae~fs~YF~~~pvi~i~grtfpV~~~fLEDil~~~  365 (924)
T KOG0920|consen  323 ILMSATLDAELFSDYFGGCPVITIPGRTFPVKEYFLEDILSKT  365 (924)
T ss_pred             EEeeeecchHHHHHHhCCCceEeecCCCcchHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999998877653

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=100.00  E-value=1.4e-32  Score=287.09  Aligned_cols=254  Identities=33%  Similarity=0.456  Sum_probs=202.4

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      ......+|+.....+++....+|++++|+|+||||||+..+..+++.    +.+..++|++++|+|..|..+++++++++
T Consensus        60 ~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTTqlPq~lle~----~~~~~~~I~~tQPRRlAA~svA~RvA~el  135 (1283)
T TIGR01967        60 IRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLEL----GRGSHGLIGHTQPRRLAARTVAQRIAEEL  135 (1283)
T ss_pred             ccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHHHHHHHHHHc----CCCCCceEecCCccHHHHHHHHHHHHHHh
Confidence            44667899999999999999999999999999999999988777653    22334589999999999999999999999


Q ss_pred             ccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccC
Q psy496          127 DEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKD  206 (319)
Q Consensus       127 ~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~  206 (319)
                      +..+   |..|||.+++++... .+++|.++|+|+|++.+..++.|+++++|||||+|+|+++.|++++.++.+...+++
T Consensus       136 g~~l---G~~VGY~vR~~~~~s-~~T~I~~~TdGiLLr~l~~d~~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~rpd  211 (1283)
T TIGR01967       136 GTPL---GEKVGYKVRFHDQVS-SNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPD  211 (1283)
T ss_pred             CCCc---ceEEeeEEcCCcccC-CCceeeeccccHHHHHhhhCcccccCcEEEEcCcchhhccchhHHHHHHHHHhhCCC
Confidence            9888   999999999888775 478899999999999999889999999999999999999999999988888777789


Q ss_pred             ceEEEeccccChhhHhhhhCCCCEEEeCCccccceeeeehhhhhhh--hhhHHHHHHHHhhhhhhhccccCCCcEEEeCC
Q psy496          207 LKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMT--RKDLKLILMSATLNAEKFSQFFGGAPILHIPG  284 (319)
Q Consensus       207 ~qiv~lSAT~~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~  284 (319)
                      .|+|+||||++.+.++++|++++++.++|+.+||+++|........  ..+....+.......  .. ...|++|||+||
T Consensus       212 LKlIlmSATld~~~fa~~F~~apvI~V~Gr~~PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l--~~-~~~GdILVFLpg  288 (1283)
T TIGR01967       212 LKIIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYRPLVEEQEDDDLDQLEAILDAVDEL--FA-EGPGDILIFLPG  288 (1283)
T ss_pred             CeEEEEeCCcCHHHHHHHhcCCCEEEECCCcccceeEEecccccccchhhhHHHHHHHHHHHH--Hh-hCCCCEEEeCCC
Confidence            9999999999999999999999999999999999999875421110  111222222222222  22 236899999999


Q ss_pred             ccccccccchHhHHH-----HhHhhccccCCCCCC
Q psy496          285 FTYPVQEYYLEDVLN-----MTRTLKRSETQQYPN  314 (319)
Q Consensus       285 R~~~v~~~~~~~~~~-----~~~~~~~~~~~~~~~  314 (319)
                      +...-++   .+.+.     ...++++|+.++..+
T Consensus       289 ~~EI~~l---~~~L~~~~~~~~~VlpLhg~Ls~~e  320 (1283)
T TIGR01967       289 EREIRDA---AEILRKRNLRHTEILPLYARLSNKE  320 (1283)
T ss_pred             HHHHHHH---HHHHHhcCCCCcEEEeccCCCCHHH
Confidence            9774332   22222     234667787765433

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.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=100.00  E-value=1.3e-32  Score=286.65  Aligned_cols=255  Identities=31%  Similarity=0.454  Sum_probs=197.9

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      +..+..+|+....++++....+|++++|+|+||||||+.++..+++.    +.+..+.|++++|+|..|..+++++++++
T Consensus        67 ~~~~~~LPi~~~r~~Il~ai~~~~VviI~GeTGSGKTTqlPq~lle~----g~g~~g~I~~TQPRRlAArsLA~RVA~El  142 (1294)
T PRK11131         67 ITYPENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLEL----GRGVKGLIGHTQPRRLAARTVANRIAEEL  142 (1294)
T ss_pred             cCCCCCCCHHHHHHHHHHHHHhCCeEEEECCCCCCHHHHHHHHHHHc----CCCCCCceeeCCCcHHHHHHHHHHHHHHH
Confidence            55677899999999999999999999999999999999876655542    23334589999999999999999999999


Q ss_pred             ccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccC
Q psy496          127 DEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKD  206 (319)
Q Consensus       127 ~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~  206 (319)
                      +..+   |..+||.+++++... .+++|+++|||+|++++..++.|+++++|||||||+|++++|++++.++.+...+++
T Consensus       143 ~~~l---G~~VGY~vrf~~~~s-~~t~I~v~TpG~LL~~l~~d~~Ls~~~~IIIDEAHERsLn~DfLLg~Lk~lL~~rpd  218 (1294)
T PRK11131        143 ETEL---GGCVGYKVRFNDQVS-DNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPD  218 (1294)
T ss_pred             hhhh---cceeceeecCccccC-CCCCEEEEChHHHHHHHhcCCccccCcEEEecCccccccccchHHHHHHHhhhcCCC
Confidence            8776   889999999887764 568999999999999998888899999999999999999999999988888777778


Q ss_pred             ceEEEeccccChhhHhhhhCCCCEEEeCCccccceeeeehhhhhhh--hhhHHHHHHHHhhhhhhhccccCCCcEEEeCC
Q psy496          207 LKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMT--RKDLKLILMSATLNAEKFSQFFGGAPILHIPG  284 (319)
Q Consensus       207 ~qiv~lSAT~~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~  284 (319)
                      .|+|+||||++.+.++++|++++++.++++.+||+++|........  ..+....+......   +.....|++|||+||
T Consensus       219 lKvILmSATid~e~fs~~F~~apvI~V~Gr~~pVei~y~p~~~~~~~~~~d~l~~ll~~V~~---l~~~~~GdILVFLpg  295 (1294)
T PRK11131        219 LKVIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYRPIVEEADDTERDQLQAIFDAVDE---LGREGPGDILIFMSG  295 (1294)
T ss_pred             ceEEEeeCCCCHHHHHHHcCCCCEEEEcCccccceEEEeecccccchhhHHHHHHHHHHHHH---HhcCCCCCEEEEcCC
Confidence            9999999999999999999999999999999999999976431110  01111112222111   112347899999999


Q ss_pred             ccccccccc-hHhH-HHHhHhhccccCCCC
Q psy496          285 FTYPVQEYY-LEDV-LNMTRTLKRSETQQY  312 (319)
Q Consensus       285 R~~~v~~~~-~~~~-~~~~~~~~~~~~~~~  312 (319)
                      +...-++.- +... ...+.++++|+.++-
T Consensus       296 ~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~  325 (1294)
T PRK11131        296 EREIRDTADALNKLNLRHTEILPLYARLSN  325 (1294)
T ss_pred             HHHHHHHHHHHHhcCCCcceEeecccCCCH
Confidence            977533311 1110 011235566776553

>KOG0925|consensus

Probab=100.00  E-value=1.3e-32  Score=255.27  Aligned_cols=224  Identities=37%  Similarity=0.599  Sum_probs=200.8

Q ss_pred             cccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhcc
Q psy496           49 QPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDE  128 (319)
Q Consensus        49 Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~  128 (319)
                      -++.+|++....+.+....+||.++++|+||||||+..+.++++......    ..|.|++|+|..|.+++++++++++.
T Consensus        42 ~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~----~~v~CTQprrvaamsva~RVadEMDv  117 (699)
T KOG0925|consen   42 KRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHL----TGVACTQPRRVAAMSVAQRVADEMDV  117 (699)
T ss_pred             HHhcCchHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhhc----cceeecCchHHHHHHHHHHHHHHhcc
Confidence            35788999999999999999999999999999999999999988765544    47999999999999999999999999


Q ss_pred             ccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCce
Q psy496          129 QCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLK  208 (319)
Q Consensus       129 ~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~q  208 (319)
                      ..   |..|||.++++++..+ ++-+.+||.|+|++...+++.+..++++|+||||+|++.+|.+.++++.+...+|+++
T Consensus       118 ~l---G~EVGysIrfEdC~~~-~T~Lky~tDgmLlrEams~p~l~~y~viiLDeahERtlATDiLmGllk~v~~~rpdLk  193 (699)
T KOG0925|consen  118 TL---GEEVGYSIRFEDCTSP-NTLLKYCTDGMLLREAMSDPLLGRYGVIILDEAHERTLATDILMGLLKEVVRNRPDLK  193 (699)
T ss_pred             cc---chhccccccccccCCh-hHHHHHhcchHHHHHHhhCcccccccEEEechhhhhhHHHHHHHHHHHHHHhhCCCce
Confidence            88   9999999999999864 5667899999999999999999999999999999999999999999999998889999


Q ss_pred             EEEeccccChhhHhhhhCCCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCccc
Q psy496          209 LILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTY  287 (319)
Q Consensus       209 iv~lSAT~~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~  287 (319)
                      +|.+|||++..++.+||+++|++.++| .+||+++|.+.+    ..+.-..+..+++.+  ......|++|||+++..+
T Consensus       194 ~vvmSatl~a~Kfq~yf~n~Pll~vpg-~~PvEi~Yt~e~----erDylEaairtV~qi--h~~ee~GDilvFLtgeee  265 (699)
T KOG0925|consen  194 LVVMSATLDAEKFQRYFGNAPLLAVPG-THPVEIFYTPEP----ERDYLEAAIRTVLQI--HMCEEPGDILVFLTGEEE  265 (699)
T ss_pred             EEEeecccchHHHHHHhCCCCeeecCC-CCceEEEecCCC----ChhHHHHHHHHHHHH--HhccCCCCEEEEecCHHH
Confidence            999999999999999999999999999 899999999876    455556666666666  333348999999999755

>KOG0338|consensus

Probab=99.97  E-value=2.9e-30  Score=240.84  Aligned_cols=242  Identities=19%  Similarity=0.220  Sum_probs=167.3

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCC-CccEEEEecccHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRG-SECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~-~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      ++|||..+||+.+.|+|+.+++.          ||||||.+|.+|+|+++..+.++ ...+||++.||||||.|++....
T Consensus       204 PTpIQ~a~IPvallgkDIca~A~----------TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTRELaiQv~sV~~  273 (691)
T KOG0338|consen  204 PTPIQVATIPVALLGKDICACAA----------TGSGKTAAFALPILERLLYRPKKVAATRVLVLVPTRELAIQVHSVTK  273 (691)
T ss_pred             CCchhhhcccHHhhcchhhheec----------ccCCchhhhHHHHHHHHhcCcccCcceeEEEEeccHHHHHHHHHHHH
Confidence            56999999999999999999998          99999999999999999766543 45688999999999999876544


Q ss_pred             H---HhccccCCCCceEEE-EEecccccCCCCceEEEECchHHHHHHhcCCC--CCCccEEEEecccccccchhHHHHHH
Q psy496          124 Q---ERDEQCGRPGSSVGY-QIRLEKELPRKRGSILYCTAGILPEVMQSDPI--LSGVSHIVMDEIHERSMISDFLLAIL  197 (319)
Q Consensus       124 ~---~~~~~~~~~g~~vg~-~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~--l~~v~~vViDEah~~~~~~~~~~~~l  197 (319)
                      +   +....+   |..+|. .++........+++|+|+|||||++|+++.+.  ++++.++|+||||+ .+..+|...+-
T Consensus       274 qlaqFt~I~~---~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADR-MLeegFademn  349 (691)
T KOG0338|consen  274 QLAQFTDITV---GLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADR-MLEEGFADEMN  349 (691)
T ss_pred             HHHhhcccee---eeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHH-HHHHHHHHHHH
Confidence            4   444444   666652 34444444446788999999999999988775  89999999999996 34555555555


Q ss_pred             HhhhccccCceEEEecccc--ChhhHhhhhCCCCE-EEeCCc-cc--cceeeeehhhhhhhhhhHHHHHHHHhhhhhhhc
Q psy496          198 KDVTDKRKDLKLILMSATL--NAEKFSQFFGGAPI-LHIPGF-TY--PVQEYYLEDVLNMTRKDLKLILMSATLNAEKFS  271 (319)
Q Consensus       198 ~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~~-i~~~~r-~~--~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  271 (319)
                      ..+...+.++|.++|||||  .++++++.--+.|+ +.++.. ..  .+...|++-  ...+...+..+....     +.
T Consensus       350 Eii~lcpk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiRI--R~~re~dRea~l~~l-----~~  422 (691)
T KOG0338|consen  350 EIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIRI--RPKREGDREAMLASL-----IT  422 (691)
T ss_pred             HHHHhccccccceeehhhhHHHHHHHHHhhcCCCeEEEeCCccccchhhhHHHhee--ccccccccHHHHHHH-----HH
Confidence            5556677899999999999  56778876444443 333321 11  122223211  111233444433222     22


Q ss_pred             cccCCCcEEEeCCccccccccch-HhHHHHhHhhccc
Q psy496          272 QFFGGAPILHIPGFTYPVQEYYL-EDVLNMTRTLKRS  307 (319)
Q Consensus       272 ~~~~g~~LVFlp~R~~~v~~~~~-~~~~~~~~~~~~~  307 (319)
                      ..+...++||+.|...|.+.+.+ .=+-..+--||-+
T Consensus       423 rtf~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGs  459 (691)
T KOG0338|consen  423 RTFQDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGS  459 (691)
T ss_pred             HhcccceEEEEehHHHHHHHHHHHHHhhchhhhhccc
Confidence            23367899999999998887653 3333333444443

>KOG0926|consensus

Probab=99.96  E-value=3.9e-29  Score=243.03  Aligned_cols=229  Identities=33%  Similarity=0.479  Sum_probs=189.7

Q ss_pred             ccc--ccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCC-ccEEEEecccHHHHHHHHHHHH
Q psy496           47 VTQ--PRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGS-ECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        47 ~~Q--~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~-~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      -||  +..+|++..-+.++.....|..|+|||.||||||++.+..++++.+...... ...|-+++|+|.+|..++++++
T Consensus       247 EIQ~sR~~LPI~aeEq~IMEaIn~n~vvIIcGeTGsGKTTQvPQFLYEAGf~s~~~~~~gmIGITqPRRVAaiamAkRVa  326 (1172)
T KOG0926|consen  247 EIQESRLDLPIVAEEQRIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFASEQSSSPGMIGITQPRRVAAIAMAKRVA  326 (1172)
T ss_pred             HHHHHHhcCchhHHHHHHHHHhhcCCeEEEecCCCCCccccchHHHHHcccCCccCCCCCeeeecCchHHHHHHHHHHHH
Confidence            345  4578999999999999999999999999999999999999998876654222 3489999999999999999999


Q ss_pred             HHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhcc
Q psy496          124 QERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDK  203 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~  203 (319)
                      .+++. .   |..|||+++++.... +.+.|.+||.|.|++.+.++..|..|+.|||||||+|++++|++++++.++..+
T Consensus       327 ~EL~~-~---~~eVsYqIRfd~ti~-e~T~IkFMTDGVLLrEi~~DflL~kYSvIIlDEAHERSvnTDILiGmLSRiV~L  401 (1172)
T KOG0926|consen  327 FELGV-L---GSEVSYQIRFDGTIG-EDTSIKFMTDGVLLREIENDFLLTKYSVIILDEAHERSVNTDILIGMLSRIVPL  401 (1172)
T ss_pred             HHhcc-C---ccceeEEEEeccccC-CCceeEEecchHHHHHHHHhHhhhhceeEEechhhhccchHHHHHHHHHHHHHH
Confidence            99987 4   899999999988765 568899999999999999999999999999999999999999999999888653


Q ss_pred             c----------cCceEEEeccccChhhHhh---hhC-CCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhhhhh
Q psy496          204 R----------KDLKLILMSATLNAEKFSQ---FFG-GAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEK  269 (319)
Q Consensus       204 ~----------~~~qiv~lSAT~~~~~l~~---~l~-~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  269 (319)
                      +          ..+++|+||||+.+.+|.+   .|. .+|++.++.|.|||.+||....    ..++-.-+...+..+  
T Consensus       402 R~k~~ke~~~~kpLKLIIMSATLRVsDFtenk~LFpi~pPlikVdARQfPVsIHF~krT----~~DYi~eAfrKtc~I--  475 (1172)
T KOG0926|consen  402 RQKYYKEQCQIKPLKLIIMSATLRVSDFTENKRLFPIPPPLIKVDARQFPVSIHFNKRT----PDDYIAEAFRKTCKI--  475 (1172)
T ss_pred             HHHHhhhhcccCceeEEEEeeeEEecccccCceecCCCCceeeeecccCceEEEeccCC----CchHHHHHHHHHHHH--
Confidence            3          2578999999997777763   454 4679999999999999997653    233333333333333  


Q ss_pred             hccccCCCcEEEeCCcc
Q psy496          270 FSQFFGGAPILHIPGFT  286 (319)
Q Consensus       270 ~~~~~~g~~LVFlp~R~  286 (319)
                      .+..+.|.+||||.|..
T Consensus       476 H~kLP~G~ILVFvTGQq  492 (1172)
T KOG0926|consen  476 HKKLPPGGILVFVTGQQ  492 (1172)
T ss_pred             hhcCCCCcEEEEEeChH
Confidence            34567999999999974

>KOG0330|consensus

Probab=99.96  E-value=1.5e-29  Score=229.70  Aligned_cols=218  Identities=19%  Similarity=0.156  Sum_probs=153.6

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +++||.++||+.+.|+|+++.++          ||||||.+|.+||+++++...+.+.+.|+.  ||||||.|+++.+..
T Consensus        84 PT~IQ~~aiP~~L~g~dvIglAe----------TGSGKT~afaLPIl~~LL~~p~~~~~lVLt--PtRELA~QI~e~fe~  151 (476)
T KOG0330|consen   84 PTKIQSEAIPVALGGRDVIGLAE----------TGSGKTGAFALPILQRLLQEPKLFFALVLT--PTRELAQQIAEQFEA  151 (476)
T ss_pred             CchhhhhhcchhhCCCcEEEEec----------cCCCchhhhHHHHHHHHHcCCCCceEEEec--CcHHHHHHHHHHHHH
Confidence            57899999999999888777666          999999999999999999877655555555  999999999998876


Q ss_pred             HhccccCCCCceEEEEEec-----ccccCCCCceEEEECchHHHHHHhcCC--CCCCccEEEEecccccccchhHHHHHH
Q psy496          125 ERDEQCGRPGSSVGYQIRL-----EKELPRKRGSILYCTAGILPEVMQSDP--ILSGVSHIVMDEIHERSMISDFLLAIL  197 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~-----~~~~~~~~~~Iiv~Tpg~ll~~l~~~~--~l~~v~~vViDEah~~~~~~~~~~~~l  197 (319)
                      +-.. .   |..+..-+.+     ......++++|+|+|||+|.+++.+..  .+..++++|+||||+ -++++|...+-
T Consensus       152 Lg~~-i---glr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADr-lLd~dF~~~ld  226 (476)
T KOG0330|consen  152 LGSG-I---GLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADR-LLDMDFEEELD  226 (476)
T ss_pred             hccc-c---CeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHh-hhhhhhHHHHH
Confidence            6222 2   3333222221     122234678999999999999996433  489999999999995 47778887777


Q ss_pred             HhhhccccCceEEEecccc--ChhhHhhh-hCCCCEEEeCCccccc---eeeeehhhhhhhhhhHHHHHHHHhhhhhhhc
Q psy496          198 KDVTDKRKDLKLILMSATL--NAEKFSQF-FGGAPILHIPGFTYPV---QEYYLEDVLNMTRKDLKLILMSATLNAEKFS  271 (319)
Q Consensus       198 ~~~~~~~~~~qiv~lSAT~--~~~~l~~~-l~~~~~i~~~~r~~~v---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  271 (319)
                      +++...+++.|.+++||||  ++.++..- +.++..+.+..+...+   ...|+..+....+.    .+..      .++
T Consensus       227 ~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~k~K~~----yLV~------ll~  296 (476)
T KOG0330|consen  227 YILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPGKDKDT----YLVY------LLN  296 (476)
T ss_pred             HHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEeccchhcchHHhhhheEeccccccch----hHHH------HHH
Confidence            7777788899999999999  66666654 3333345555544333   34565543221111    1111      133


Q ss_pred             cccCCCcEEEeCCccccc
Q psy496          272 QFFGGAPILHIPGFTYPV  289 (319)
Q Consensus       272 ~~~~g~~LVFlp~R~~~v  289 (319)
                      +..+++++||+++-.-..
T Consensus       297 e~~g~s~iVF~~t~~tt~  314 (476)
T KOG0330|consen  297 ELAGNSVIVFCNTCNTTR  314 (476)
T ss_pred             hhcCCcEEEEEeccchHH
Confidence            445789999999876553

>KOG0331|consensus

Probab=99.96  E-value=2.4e-29  Score=240.41  Aligned_cols=230  Identities=18%  Similarity=0.173  Sum_probs=155.1

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHh----CCCCccEEEEecccHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIAR----NRGSECCIMVTQPRRISAIAIAE  120 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~----~~~~~~~vl~~~Ptr~la~q~~~  120 (319)
                      ++|||.++||.+++|+|++..+.          ||||||++|++|++.++...    .++...++|++.||||||.|+.+
T Consensus       114 PtpIQaq~wp~~l~GrD~v~iA~----------TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTRELA~QV~~  183 (519)
T KOG0331|consen  114 PTPIQAQGWPIALSGRDLVGIAR----------TGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTRELAVQVQA  183 (519)
T ss_pred             CchhhhcccceeccCCceEEEec----------cCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcHHHHHHHHH
Confidence            67999999999999999887777          99999999999999988762    12334577777799999999998


Q ss_pred             HHHHHhcc-----ccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhc-CCCCCCccEEEEecccccccchhHHH
Q psy496          121 RVAQERDE-----QCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQS-DPILSGVSHIVMDEIHERSMISDFLL  194 (319)
Q Consensus       121 ~~~~~~~~-----~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~-~~~l~~v~~vViDEah~~~~~~~~~~  194 (319)
                      .+.++...     .+.++|...+.+.+.    .....+|+|+|||||++++.. ...|++++++|+||||+ ++.++|-.
T Consensus       184 ~~~~~~~~~~~~~~cvyGG~~~~~Q~~~----l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADr-MldmGFe~  258 (519)
T KOG0331|consen  184 EAREFGKSLRLRSTCVYGGAPKGPQLRD----LERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADR-MLDMGFEP  258 (519)
T ss_pred             HHHHHcCCCCccEEEEeCCCCccHHHHH----HhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHHh-hhccccHH
Confidence            88776432     233444444433321    123467999999999999955 45699999999999995 47888888


Q ss_pred             HHHHhhhcc-ccCceEEEecccc--ChhhHhhhhCCCC-EEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhh
Q psy496          195 AILKDVTDK-RKDLKLILMSATL--NAEKFSQFFGGAP-ILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKF  270 (319)
Q Consensus       195 ~~l~~~~~~-~~~~qiv~lSAT~--~~~~l~~~l~~~~-~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (319)
                      .+.+.+... +++.|++++|||+  .++.+++-|-+.+ .+.+.+..--...+-........+..-+.......+...  
T Consensus       259 qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K~~~l~~lL~~~--  336 (519)
T KOG0331|consen  259 QIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETAKLRKLGKLLEDI--  336 (519)
T ss_pred             HHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHHHHHHHHHHHHHH--
Confidence            888888887 5666899999999  6677776443344 344433311111111222222222222222112222221  


Q ss_pred             ccccCCCcEEEeCCccccccc
Q psy496          271 SQFFGGAPILHIPGFTYPVQE  291 (319)
Q Consensus       271 ~~~~~g~~LVFlp~R~~~v~~  291 (319)
                      ....++++||||.|++.+-++
T Consensus       337 ~~~~~~KvIIFc~tkr~~~~l  357 (519)
T KOG0331|consen  337 SSDSEGKVIIFCETKRTCDEL  357 (519)
T ss_pred             hccCCCcEEEEecchhhHHHH
Confidence            123378999999999877433

>KOG0343|consensus

Probab=99.95  E-value=1.2e-28  Score=231.89  Aligned_cols=243  Identities=18%  Similarity=0.174  Sum_probs=171.9

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC--CCCccEEEEecccHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN--RGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~--~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      ..+-||+.+||..+.|.|+++++.          ||||||+||+.|++++++..+  ..-..-+|+++||||||.|++..
T Consensus        91 ~~teiQ~~~Ip~aL~G~DvlGAAk----------TGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIISPTRELA~QtFev  160 (758)
T KOG0343|consen   91 KMTEIQRDTIPMALQGHDVLGAAK----------TGSGKTLAFLVPVLEALYRLKWSPTDGLGALIISPTRELALQTFEV  160 (758)
T ss_pred             cHHHHHHhhcchhccCcccccccc----------cCCCceeeehHHHHHHHHHcCCCCCCCceeEEecchHHHHHHHHHH
Confidence            356889999999999999999999          999999999999999997532  12233455566999999999988


Q ss_pred             HHHHhccccCCCCceEEEEE-ecccccCCCCceEEEECchHHHHHHhcCCC--CCCccEEEEecccccccchhHHHHHHH
Q psy496          122 VAQERDEQCGRPGSSVGYQI-RLEKELPRKRGSILYCTAGILPEVMQSDPI--LSGVSHIVMDEIHERSMISDFLLAILK  198 (319)
Q Consensus       122 ~~~~~~~~~~~~g~~vg~~~-~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~--l~~v~~vViDEah~~~~~~~~~~~~l~  198 (319)
                      +.+.-.......|..+|..- ..+... -.+.+|+|||||||+.|+..++.  .+++.++|+||||+ .++++|...+-.
T Consensus       161 L~kvgk~h~fSaGLiiGG~~~k~E~eR-i~~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR-~LDMGFk~tL~~  238 (758)
T KOG0343|consen  161 LNKVGKHHDFSAGLIIGGKDVKFELER-ISQMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADR-MLDMGFKKTLNA  238 (758)
T ss_pred             HHHHhhccccccceeecCchhHHHHHh-hhcCCeEEechHHHHHHhhhcCCCCCCcceEEEeccHHH-HHHHhHHHHHHH
Confidence            87764444334466666332 222221 24678999999999999987776  57899999999995 588888888888


Q ss_pred             hhhccccCceEEEecccc--ChhhHhhh-hCCCCEEEeC-----CccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhh
Q psy496          199 DVTDKRKDLKLILMSATL--NAEKFSQF-FGGAPILHIP-----GFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKF  270 (319)
Q Consensus       199 ~~~~~~~~~qiv~lSAT~--~~~~l~~~-l~~~~~i~~~-----~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (319)
                      .+..+++..|.++||||.  ++.++++. +.++..+.+.     +.+..+..+|....+..    .-.++- ..+.    
T Consensus       239 Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l~~----Ki~~L~-sFI~----  309 (758)
T KOG0343|consen  239 IIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPLED----KIDMLW-SFIK----  309 (758)
T ss_pred             HHHhCChhheeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEehhh----HHHHHH-HHHH----
Confidence            888899999999999999  88999997 4455455543     22333455565443221    111111 1111    


Q ss_pred             ccccCCCcEEEeCCccccccccchHhHHH----HhHhhccccCCC
Q psy496          271 SQFFGGAPILHIPGFTYPVQEYYLEDVLN----MTRTLKRSETQQ  311 (319)
Q Consensus       271 ~~~~~g~~LVFlp~R~~~v~~~~~~~~~~----~~~~~~~~~~~~  311 (319)
                       ..+...+|||+.|-   -++.|+.++-.    -..+++++|++.
T Consensus       310 -shlk~K~iVF~Ssc---Kqvkf~~e~F~rlrpg~~l~~L~G~~~  350 (758)
T KOG0343|consen  310 -SHLKKKSIVFLSSC---KQVKFLYEAFCRLRPGIPLLALHGTMS  350 (758)
T ss_pred             -hccccceEEEEehh---hHHHHHHHHHHhcCCCCceeeeccchh
Confidence             12366899999875   45666555444    345777888763

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

Probab=99.94  E-value=3.2e-27  Score=231.98  Aligned_cols=241  Identities=21%  Similarity=0.208  Sum_probs=154.0

Q ss_pred             ccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHh-CCCCccE
Q psy496           26 VPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIAR-NRGSECC  104 (319)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~-~~~~~~~  104 (319)
                      +...+++.+.+..+..   ++|||.++||.++.|+|+++.++          ||||||.+|.+|+++.+... ...... 
T Consensus        36 l~~~ll~~l~~~gf~~---pt~IQ~~~IP~~l~g~Dvi~~A~----------TGsGKT~Af~lP~l~~l~~~~~~~~~~-  101 (513)
T COG0513          36 LSPELLQALKDLGFEE---PTPIQLAAIPLILAGRDVLGQAQ----------TGTGKTAAFLLPLLQKILKSVERKYVS-  101 (513)
T ss_pred             CCHHHHHHHHHcCCCC---CCHHHHHHHHHHhCCCCEEEECC----------CCChHHHHHHHHHHHHHhcccccCCCc-
Confidence            4444555554444433   67999999999998877555555          99999999999999997632 211111 


Q ss_pred             EEEecccHHHHHHHHHHHHHHhcccc-CCCCceEEEE-EecccccCCCCceEEEECchHHHHHHhcC-CCCCCccEEEEe
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQC-GRPGSSVGYQ-IRLEKELPRKRGSILYCTAGILPEVMQSD-PILSGVSHIVMD  181 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~-~~~g~~vg~~-~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~vViD  181 (319)
                      .|++.||||||.|+++.+..+..... ......+|.. ............+|+|+||||+++++... ..+++++++|+|
T Consensus       102 aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v~~lVlD  181 (513)
T COG0513         102 ALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLD  181 (513)
T ss_pred             eEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhcCEEEec
Confidence            66666999999999998877654321 0001111111 11111111124789999999999999555 559999999999


Q ss_pred             cccccccchhHHHHHHHhhhccccCceEEEeccccC--hhhHhh-hhCCCCEEEeCCc-----cccceeeeehhhhhhhh
Q psy496          182 EIHERSMISDFLLAILKDVTDKRKDLKLILMSATLN--AEKFSQ-FFGGAPILHIPGF-----TYPVQEYYLEDVLNMTR  253 (319)
Q Consensus       182 Eah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~--~~~l~~-~l~~~~~i~~~~r-----~~~v~~~~~~~~~~~~~  253 (319)
                      |||+ .+.+++...+.+.+...+++.|+++||||++  ...+++ ++.++..+.+...     ...++.+|....    .
T Consensus       182 EADr-mLd~Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~----~  256 (513)
T COG0513         182 EADR-MLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVE----S  256 (513)
T ss_pred             cHhh-hhcCCCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeC----C
Confidence            9996 4677788888887777888899999999993  344444 4444444555422     133455555432    1


Q ss_pred             hhHHHHHHHHhhhhhhhccccCCCcEEEeCCcccccc
Q psy496          254 KDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQ  290 (319)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v~  290 (319)
                      ..-+..+....++     ....+++|||+++...+-+
T Consensus       257 ~~~k~~~L~~ll~-----~~~~~~~IVF~~tk~~~~~  288 (513)
T COG0513         257 EEEKLELLLKLLK-----DEDEGRVIVFVRTKRLVEE  288 (513)
T ss_pred             HHHHHHHHHHHHh-----cCCCCeEEEEeCcHHHHHH
Confidence            1112222222222     1224579999999876633

>KOG0346|consensus

Probab=99.94  E-value=2.2e-27  Score=218.41  Aligned_cols=241  Identities=16%  Similarity=0.194  Sum_probs=157.2

Q ss_pred             CccccccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC--
Q psy496           21 GKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN--   98 (319)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~--   98 (319)
                      |....+.+.|-+-+|+.       ++.||..|||.+++|+|+++.+.          ||||||.+|++|+++.+....  
T Consensus        25 gLD~RllkAi~~lG~ek-------pTlIQs~aIplaLEgKDvvarAr----------TGSGKT~AYliPllqkll~~k~t   87 (569)
T KOG0346|consen   25 GLDSRLLKAITKLGWEK-------PTLIQSSAIPLALEGKDVVARAR----------TGSGKTAAYLIPLLQKLLAEKKT   87 (569)
T ss_pred             CCCHHHHHHHHHhCcCC-------cchhhhcccchhhcCcceeeeec----------cCCCchHHHHHHHHHHHHHhhhc
Confidence            55556666677777777       77999999999999999888888          999999999999999986532  


Q ss_pred             ----CCCccEEEEecccHHHHHHHHHHHHHHhccccCC-CCceEEEEEe--cccccCCCCceEEEECchHHHHHHhcCC-
Q psy496           99 ----RGSECCIMVTQPRRISAIAIAERVAQERDEQCGR-PGSSVGYQIR--LEKELPRKRGSILYCTAGILPEVMQSDP-  170 (319)
Q Consensus        99 ----~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~-~g~~vg~~~~--~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~-  170 (319)
                          .++.+.|++  ||||||+|+++.+.++....... -...+.....  .......+.++|+|+||+++++++..+. 
T Consensus        88 ~~~e~~~sa~iLv--PTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~  165 (569)
T KOG0346|consen   88 NDGEQGPSAVILV--PTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVL  165 (569)
T ss_pred             ccccccceeEEEe--chHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccc
Confidence                234445555  99999999998877763321000 0000110010  1112223578899999999999997665 


Q ss_pred             -CCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCCE-EEeCCcccc----cee
Q psy496          171 -ILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAPI-LHIPGFTYP----VQE  242 (319)
Q Consensus       171 -~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~~-i~~~~r~~~----v~~  242 (319)
                       .+..++++|+||||.. +..+.-..+.+....+++..|.++||||+  |+..+.+.+-..|+ +......-|    +..
T Consensus       166 ~~~~~l~~LVvDEADLl-lsfGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Q  244 (569)
T KOG0346|consen  166 EYLDSLSFLVVDEADLL-LSFGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQ  244 (569)
T ss_pred             hhhhheeeEEechhhhh-hhcccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccceE
Confidence             4889999999999961 22223334444445578888999999999  88899987766665 444333322    334


Q ss_pred             eeehhhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCcccccc
Q psy496          243 YYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQ  290 (319)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v~  290 (319)
                      +++... +  ...+.....-..++.      -.|.+||||++-.-+-+
T Consensus       245 y~v~cs-e--~DKflllyallKL~L------I~gKsliFVNtIdr~Yr  283 (569)
T KOG0346|consen  245 YQVKCS-E--EDKFLLLYALLKLRL------IRGKSLIFVNTIDRCYR  283 (569)
T ss_pred             EEEEec-c--chhHHHHHHHHHHHH------hcCceEEEEechhhhHH
Confidence            444442 1  111211111111111      26899999999444433

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

Probab=99.94  E-value=2.2e-26  Score=231.05  Aligned_cols=233  Identities=19%  Similarity=0.210  Sum_probs=164.8

Q ss_pred             chHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC---CCCccEEEEe
Q psy496           32 DDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN---RGSECCIMVT  108 (319)
Q Consensus        32 ~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~---~~~~~~vl~~  108 (319)
                      .+|+...+.+   +++.|.+|||.+.+|          +|+||.||||||||+++++|+++.+...+   ......++|+
T Consensus        13 ~~~~~~~~~~---~t~~Q~~a~~~i~~G----------~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYI   79 (814)
T COG1201          13 REWFKRKFTS---LTPPQRYAIPEIHSG----------ENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYI   79 (814)
T ss_pred             HHHHHHhcCC---CCHHHHHHHHHHhCC----------CceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEe
Confidence            3466665433   678899999998764          45888888999999999999999998763   2235789999


Q ss_pred             cccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCC-------CCceEEEECchHHHHHHhcC---CCCCCccEE
Q psy496          109 QPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPR-------KRGSILYCTAGILPEVMQSD---PILSGVSHI  178 (319)
Q Consensus       109 ~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~-------~~~~Iiv~Tpg~ll~~l~~~---~~l~~v~~v  178 (319)
                      +|.|+|++++.+++.......    |..+  .++.++....       +.++|+++||+.|--++.+.   ..|.+++++
T Consensus        80 sPLkALn~Di~~rL~~~~~~~----G~~v--~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~V  153 (814)
T COG1201          80 SPLKALNNDIRRRLEEPLREL----GIEV--AVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYV  153 (814)
T ss_pred             CcHHHHHHHHHHHHHHHHHHc----CCcc--ceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEE
Confidence            999999999999888775533    5555  4665555443       34689999999997777443   349999999


Q ss_pred             EEecccc-----cccchhHHHHHHHhhhccccCceEEEecccc-ChhhHhhhhCCC----CEEEeCC-ccccceeeeehh
Q psy496          179 VMDEIHE-----RSMISDFLLAILKDVTDKRKDLKLILMSATL-NAEKFSQFFGGA----PILHIPG-FTYPVQEYYLED  247 (319)
Q Consensus       179 ViDEah~-----~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~-~~~~l~~~l~~~----~~i~~~~-r~~~v~~~~~~~  247 (319)
                      ||||+|+     ||.+....+.+++.+..   +.|.|++|||. +++.+++|+.+.    .++.+.+ +...+++.....
T Consensus       154 IVDEiHel~~sKRG~~Lsl~LeRL~~l~~---~~qRIGLSATV~~~~~varfL~g~~~~~~Iv~~~~~k~~~i~v~~p~~  230 (814)
T COG1201         154 IVDEIHALAESKRGVQLALSLERLRELAG---DFQRIGLSATVGPPEEVAKFLVGFGDPCEIVDVSAAKKLEIKVISPVE  230 (814)
T ss_pred             EeehhhhhhccccchhhhhhHHHHHhhCc---ccEEEeehhccCCHHHHHHHhcCCCCceEEEEcccCCcceEEEEecCC
Confidence            9999997     88888888888887765   78999999999 999999999754    2344433 333343333322


Q ss_pred             hhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCccccccc
Q psy496          248 VLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQE  291 (319)
Q Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v~~  291 (319)
                      .....+. ....+.....+.  ..+  ...+|||+|||..+-.+
T Consensus       231 ~~~~~~~-~~~~~~~~i~~~--v~~--~~ttLIF~NTR~~aE~l  269 (814)
T COG1201         231 DLIYDEE-LWAALYERIAEL--VKK--HRTTLIFTNTRSGAERL  269 (814)
T ss_pred             ccccccc-hhHHHHHHHHHH--Hhh--cCcEEEEEeChHHHHHH
Confidence            2111111 112222223333  222  45899999999876433

>KOG0342|consensus

Probab=99.93  E-value=1.8e-26  Score=215.01  Aligned_cols=229  Identities=17%  Similarity=0.161  Sum_probs=154.9

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCC--CCccEEEEecccHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNR--GSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~--~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      .+++|+++||+++.|+|+++.+.          ||||||.||++|.++.+.....  .....+++++||||||.|++...
T Consensus       105 MT~VQ~~ti~pll~gkDvl~~AK----------TGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTRELA~Q~~~ea  174 (543)
T KOG0342|consen  105 MTPVQQKTIPPLLEGKDVLAAAK----------TGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTRELAMQIFAEA  174 (543)
T ss_pred             hhHHHHhhcCccCCCccceeeec----------cCCCceeeehhHHHHHHHhcccCCCCCeeEEEecccHHHHHHHHHHH
Confidence            67999999999999998888877          9999999999999998865431  23456777779999999999988


Q ss_pred             HHHhccccCCCCceEEEEEec-----ccccCCCCceEEEECchHHHHHHhcCCC--CCCccEEEEecccccccchhHHHH
Q psy496          123 AQERDEQCGRPGSSVGYQIRL-----EKELPRKRGSILYCTAGILPEVMQSDPI--LSGVSHIVMDEIHERSMISDFLLA  195 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~-----~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~--l~~v~~vViDEah~~~~~~~~~~~  195 (319)
                      .+++....   +..++..+.+     +.......++|+|+|||||++++.+.+.  +.+++++|+||||+ -+.++|-.+
T Consensus       175 k~Ll~~h~---~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEADr-lLd~GF~~d  250 (543)
T KOG0342|consen  175 KELLKYHE---SITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEADR-LLDIGFEED  250 (543)
T ss_pred             HHHHhhCC---CcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeecchh-hhhcccHHH
Confidence            88765442   3333333322     2222224789999999999999976654  67889999999995 466677777


Q ss_pred             HHHhhhccccCceEEEecccc--ChhhHhhh-hCCCCE-EEeCCcccc-----ceeeeehhhhhhhhhhHHHHHHHHhhh
Q psy496          196 ILKDVTDKRKDLKLILMSATL--NAEKFSQF-FGGAPI-LHIPGFTYP-----VQEYYLEDVLNMTRKDLKLILMSATLN  266 (319)
Q Consensus       196 ~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~-l~~~~~-i~~~~r~~~-----v~~~~~~~~~~~~~~~~~~~~~~~~~~  266 (319)
                      +.+++..++..+|.++||||.  -++++++- +...++ +.......+     ++..|.-..     ...+..+.-..+.
T Consensus       251 i~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~-----~~~~f~ll~~~LK  325 (543)
T KOG0342|consen  251 VEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAP-----SDSRFSLLYTFLK  325 (543)
T ss_pred             HHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEecc-----ccchHHHHHHHHH
Confidence            777777788899999999999  56677764 333333 444332222     333343332     1112111111111


Q ss_pred             hhhhccccCCCcEEEeCCccccccccchHhHHH
Q psy496          267 AEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLN  299 (319)
Q Consensus       267 ~~~~~~~~~g~~LVFlp~R~~~v~~~~~~~~~~  299 (319)
                      .   + .....++||++|-.   -+.|..++++
T Consensus       326 k---~-~~~~KiiVF~sT~~---~vk~~~~lL~  351 (543)
T KOG0342|consen  326 K---N-IKRYKIIVFFSTCM---SVKFHAELLN  351 (543)
T ss_pred             H---h-cCCceEEEEechhh---HHHHHHHHHh
Confidence            1   1 11378999999863   3455555555

>KOG0335|consensus

Probab=99.93  E-value=2.2e-26  Score=216.98  Aligned_cols=268  Identities=18%  Similarity=0.140  Sum_probs=168.2

Q ss_pred             ccchhhhhhhhcccCCCccccccccc-------cchHHHhc--cCCccccccccccchhhHHHHHHhhhcCCCCCcEEEe
Q psy496            5 YAQSITYRLKEDLAGCGKTTQVPQFI-------LDDEIARN--RGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIY   75 (319)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~--~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~   75 (319)
                      ++.+|||+++.+++.......+|..|       +++-....  +..-..++|+|+.+||.+..|++++++++        
T Consensus        48 ~~~~~nfd~~~~i~v~~~G~~~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAq--------  119 (482)
T KOG0335|consen   48 ISTGINFDKYNDIPVKVSGRDVPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQ--------  119 (482)
T ss_pred             cchhhccCCccceeeeccCCccCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEcc--------
Confidence            56789999999998655555554433       22222111  12234457999999999998888655555        


Q ss_pred             cCCCCCccchhhHHHHHHHHHhCC--------CCccEEEEecccHHHHHHHHHHHHHHhcccc-----CCCCceEEEEEe
Q psy496           76 TSTGCGKTTQVPQFILDDEIARNR--------GSECCIMVTQPRRISAIAIAERVAQERDEQC-----GRPGSSVGYQIR  142 (319)
Q Consensus        76 apTGSGKT~~~~l~il~~l~~~~~--------~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~-----~~~g~~vg~~~~  142 (319)
                        ||||||.+|++|++..+...+.        ....++++++||||||.|++++..+......     .|+|...+    
T Consensus       120 --TGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~----  193 (482)
T KOG0335|consen  120 --TGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLG----  193 (482)
T ss_pred             --CCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchh----
Confidence              9999999999999999876532        1235666666999999999999888754332     12222222    


Q ss_pred             cccccCCCCceEEEECchHHHHHH-hcCCCCCCccEEEEecccccccc-hhHHHHHHHhhhccc----cCceEEEecccc
Q psy496          143 LEKELPRKRGSILYCTAGILPEVM-QSDPILSGVSHIVMDEIHERSMI-SDFLLAILKDVTDKR----KDLKLILMSATL  216 (319)
Q Consensus       143 ~~~~~~~~~~~Iiv~Tpg~ll~~l-~~~~~l~~v~~vViDEah~~~~~-~~~~~~~l~~~~~~~----~~~qiv~lSAT~  216 (319)
                      .........++|+|+|||+|.+++ .....|++++++||||||++ ++ ++|...+-+.+....    ...|.++||||+
T Consensus       194 ~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~~~k~~vLDEADrM-lD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtf  272 (482)
T KOG0335|consen  194 AQLRFIKRGCDILVATPGRLKDLIERGKISLDNCKFLVLDEADRM-LDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATF  272 (482)
T ss_pred             hhhhhhccCccEEEecCchhhhhhhcceeehhhCcEEEecchHHh-hhhccccccHHHHhcccCCCCccceeEEEEeccC
Confidence            112222346899999999999999 45556999999999999974 44 666666655554422    367999999999


Q ss_pred             --ChhhHhhhhC-CCCEEEeC---Ccc-ccceeeeehhhhhhhhhhHHHHHHHHhhhhh---hhccccCCCcEEEeCCcc
Q psy496          217 --NAEKFSQFFG-GAPILHIP---GFT-YPVQEYYLEDVLNMTRKDLKLILMSATLNAE---KFSQFFGGAPILHIPGFT  286 (319)
Q Consensus       217 --~~~~l~~~l~-~~~~i~~~---~r~-~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~g~~LVFlp~R~  286 (319)
                        +.+.++.+|- +..++..-   ++. ..+...++..    ...+.+..++.......   .........++|||.+.+
T Consensus       273 p~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V----~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~  348 (482)
T KOG0335|consen  273 PKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFV----NEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKR  348 (482)
T ss_pred             ChhhhhhHHHHhhccceEEEEeeeccccccceeEeeee----cchhhHHHHHHHhhcccCCcccCCcccceEEEEeeccc
Confidence              5555666553 32332221   222 2222222211    13344444443333221   111111337999999987


Q ss_pred             ccccc
Q psy496          287 YPVQE  291 (319)
Q Consensus       287 ~~v~~  291 (319)
                      .+-++
T Consensus       349 ~~d~l  353 (482)
T KOG0335|consen  349 GADEL  353 (482)
T ss_pred             hhhHH
Confidence            66433

>KOG0340|consensus

Probab=99.93  E-value=1.4e-26  Score=208.27  Aligned_cols=175  Identities=21%  Similarity=0.239  Sum_probs=127.6

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      ++..|+-+..-+-.-+   +++|+|..+||.|+.|+|+++++.          ||||||++|.+|+++++.....+..+.
T Consensus        13 Gl~~Wlve~l~~l~i~---~pTpiQ~~cIpkILeGrdcig~Ak----------TGsGKT~AFaLPil~rLsedP~giFal   79 (442)
T KOG0340|consen   13 GLSPWLVEQLKALGIK---KPTPIQQACIPKILEGRDCIGCAK----------TGSGKTAAFALPILNRLSEDPYGIFAL   79 (442)
T ss_pred             CccHHHHHHHHHhcCC---CCCchHhhhhHHHhcccccccccc----------cCCCcchhhhHHHHHhhccCCCcceEE
Confidence            4556655554443332   367999999999999999999999          999999999999999998877766666


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEe-cccccCCCCceEEEECchHHHHHHhcCC-----CCCCccEE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIR-LEKELPRKRGSILYCTAGILPEVMQSDP-----ILSGVSHI  178 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~-~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~-----~l~~v~~v  178 (319)
                      |+.  ||||||.|+++++...-..........+|+... ......+++.|++++|||++-+++.++.     .+++++++
T Consensus        80 vlT--PTrELA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkfl  157 (442)
T KOG0340|consen   80 VLT--PTRELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFL  157 (442)
T ss_pred             Eec--chHHHHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeE
Confidence            666  999999999999877633221111222232111 3333445789999999999999997663     38999999


Q ss_pred             EEecccccccchhHHHHHHHhhh-ccccCceEEEecccc
Q psy496          179 VMDEIHERSMISDFLLAILKDVT-DKRKDLKLILMSATL  216 (319)
Q Consensus       179 ViDEah~~~~~~~~~~~~l~~~~-~~~~~~qiv~lSAT~  216 (319)
                      |+||||.  +....+...++.+. ..++.+|.++||||+
T Consensus       158 VlDEADr--vL~~~f~d~L~~i~e~lP~~RQtLlfSATi  194 (442)
T KOG0340|consen  158 VLDEADR--VLAGCFPDILEGIEECLPKPRQTLLFSATI  194 (442)
T ss_pred             Eecchhh--hhccchhhHHhhhhccCCCccceEEEEeeh
Confidence            9999997  33333344444443 356667999999999

>PRK02362 ski2-like helicase; Provisional

Probab=99.93  E-value=9.8e-26  Score=230.90  Aligned_cols=240  Identities=16%  Similarity=0.138  Sum_probs=151.3

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      ++|..+.+.+-+....   +++|+|.++++...         ..++|++++||||||||.++.+|+++.+..+     .+
T Consensus         7 ~lp~~~~~~l~~~g~~---~l~p~Q~~ai~~~~---------~~g~nvlv~APTGSGKTlia~lail~~l~~~-----~k   69 (737)
T PRK02362          7 PLPEGVIEFYEAEGIE---ELYPPQAEAVEAGL---------LDGKNLLAAIPTASGKTLIAELAMLKAIARG-----GK   69 (737)
T ss_pred             CCCHHHHHHHHhCCCC---cCCHHHHHHHHHHH---------hCCCcEEEECCCcchHHHHHHHHHHHHHhcC-----Cc
Confidence            4676666544333222   35688999998622         1356799999999999999999999988532     37


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc--ccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEe
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK--ELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMD  181 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~--~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViD  181 (319)
                      ++++.|+|+||.|.++.+.+.. . .   |..++......+  .......+|+|+||+++..+++... .+++++++|+|
T Consensus        70 al~i~P~raLa~q~~~~~~~~~-~-~---g~~v~~~tGd~~~~~~~l~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViD  144 (737)
T PRK02362         70 ALYIVPLRALASEKFEEFERFE-E-L---GVRVGISTGDYDSRDEWLGDNDIIVATSEKVDSLLRNGAPWLDDITCVVVD  144 (737)
T ss_pred             EEEEeChHHHHHHHHHHHHHhh-c-C---CCEEEEEeCCcCccccccCCCCEEEECHHHHHHHHhcChhhhhhcCEEEEE
Confidence            8888899999999999988642 1 1   434432211111  1111356899999999988886543 47899999999


Q ss_pred             ccccccc--chhHHHHHHHhhhccccCceEEEecccc-ChhhHhhhhCCCCEEEeCCccccceeeeehh-hhhhhh--h-
Q psy496          182 EIHERSM--ISDFLLAILKDVTDKRKDLKLILMSATL-NAEKFSQFFGGAPILHIPGFTYPVQEYYLED-VLNMTR--K-  254 (319)
Q Consensus       182 Eah~~~~--~~~~~~~~l~~~~~~~~~~qiv~lSAT~-~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~-~~~~~~--~-  254 (319)
                      |+|..+-  ....+...+..+....++.|+|++|||+ |++++++|++.. .+....|+.++....... ......  . 
T Consensus       145 E~H~l~d~~rg~~le~il~rl~~~~~~~qii~lSATl~n~~~la~wl~~~-~~~~~~rpv~l~~~v~~~~~~~~~~~~~~  223 (737)
T PRK02362        145 EVHLIDSANRGPTLEVTLAKLRRLNPDLQVVALSATIGNADELADWLDAE-LVDSEWRPIDLREGVFYGGAIHFDDSQRE  223 (737)
T ss_pred             CccccCCCcchHHHHHHHHHHHhcCCCCcEEEEcccCCCHHHHHHHhCCC-cccCCCCCCCCeeeEecCCeecccccccc
Confidence            9997321  1123333444444455678999999999 999999999643 344455665554332110 000000  0 


Q ss_pred             ---hHHHHHHHHhhhhhhhccccCCCcEEEeCCccccccc
Q psy496          255 ---DLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQE  291 (319)
Q Consensus       255 ---~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v~~  291 (319)
                         ...........+.  ..  .++++||||++|..+..+
T Consensus       224 ~~~~~~~~~~~~~~~~--~~--~~~~~LVF~~sr~~~~~~  259 (737)
T PRK02362        224 VEVPSKDDTLNLVLDT--LE--EGGQCLVFVSSRRNAEGF  259 (737)
T ss_pred             CCCccchHHHHHHHHH--HH--cCCCeEEEEeCHHHHHHH
Confidence               0001111111111  11  378999999999887544

>PRK01172 ski2-like helicase; Provisional

Probab=99.93  E-value=1.5e-25  Score=227.79  Aligned_cols=238  Identities=18%  Similarity=0.147  Sum_probs=154.0

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      .+|+.+.+. |+.   ...+..++|.++++.+.          .+++++++||||||||+++.+++++.+....     +
T Consensus         7 ~l~~~~~~~-~~~---~~~~l~~~Q~~ai~~l~----------~~~nvlv~apTGSGKTl~a~lail~~l~~~~-----k   67 (674)
T PRK01172          7 GYDDEFLNL-FTG---NDFELYDHQRMAIEQLR----------KGENVIVSVPTAAGKTLIAYSAIYETFLAGL-----K   67 (674)
T ss_pred             CCCHHHHHH-Hhh---CCCCCCHHHHHHHHHHh----------cCCcEEEECCCCchHHHHHHHHHHHHHHhCC-----c
Confidence            356554443 232   22346788999998764          3567999999999999999999998876533     6


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc--CCCCceEEEECchHHHHHHhcCCC-CCCccEEEEe
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL--PRKRGSILYCTAGILPEVMQSDPI-LSGVSHIVMD  181 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~--~~~~~~Iiv~Tpg~ll~~l~~~~~-l~~v~~vViD  181 (319)
                      ++++.|+++||.|.++.+.+...  .   |..++......+..  .....+|+|+||+++..++...+. ++++++||+|
T Consensus        68 ~v~i~P~raLa~q~~~~~~~l~~--~---g~~v~~~~G~~~~~~~~~~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViD  142 (674)
T PRK01172         68 SIYIVPLRSLAMEKYEELSRLRS--L---GMRVKISIGDYDDPPDFIKRYDVVILTSEKADSLIHHDPYIINDVGLIVAD  142 (674)
T ss_pred             EEEEechHHHHHHHHHHHHHHhh--c---CCeEEEEeCCCCCChhhhccCCEEEECHHHHHHHHhCChhHHhhcCEEEEe
Confidence            77778999999999998886422  1   45554333211111  113578999999999888866554 8999999999


Q ss_pred             ccccccc--chhHHHHHHHhhhccccCceEEEecccc-ChhhHhhhhCCCCEEEeCCccccceeeeehhhhhhhhhhHHH
Q psy496          182 EIHERSM--ISDFLLAILKDVTDKRKDLKLILMSATL-NAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKL  258 (319)
Q Consensus       182 Eah~~~~--~~~~~~~~l~~~~~~~~~~qiv~lSAT~-~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~  258 (319)
                      |+|..+-  ....+..++..+...+++.|+|++|||+ |.+++++|++. ..+....|+.|++...........+...+.
T Consensus       143 EaH~l~d~~rg~~le~ll~~~~~~~~~~riI~lSATl~n~~~la~wl~~-~~~~~~~r~vpl~~~i~~~~~~~~~~~~~~  221 (674)
T PRK01172        143 EIHIIGDEDRGPTLETVLSSARYVNPDARILALSATVSNANELAQWLNA-SLIKSNFRPVPLKLGILYRKRLILDGYERS  221 (674)
T ss_pred             cchhccCCCccHHHHHHHHHHHhcCcCCcEEEEeCccCCHHHHHHHhCC-CccCCCCCCCCeEEEEEecCeeeecccccc
Confidence            9997431  1113334444444455678999999999 99999999964 456666777777643321110000000000


Q ss_pred             -H-HHHHhhhhhhhccccCCCcEEEeCCccccccc
Q psy496          259 -I-LMSATLNAEKFSQFFGGAPILHIPGFTYPVQE  291 (319)
Q Consensus       259 -~-~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v~~  291 (319)
                       . ......+.  .  ..++++|||+++|..+.+.
T Consensus       222 ~~~~~~~i~~~--~--~~~~~vLVF~~sr~~~~~~  252 (674)
T PRK01172        222 QVDINSLIKET--V--NDGGQVLVFVSSRKNAEDY  252 (674)
T ss_pred             cccHHHHHHHH--H--hCCCcEEEEeccHHHHHHH
Confidence             0 11111110  1  1378999999999987554

>PTZ00110 helicase; Provisional

Probab=99.93  E-value=1.2e-25  Score=222.50  Aligned_cols=183  Identities=21%  Similarity=0.134  Sum_probs=125.4

Q ss_pred             ccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC---CCCc
Q psy496           26 VPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN---RGSE  102 (319)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~---~~~~  102 (319)
                      +|+++.+......+.   +++++|.++||.++.|+|          ++++||||||||++|++|++..+....   .+..
T Consensus       137 l~~~l~~~l~~~g~~---~pt~iQ~~aip~~l~G~d----------vI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~g  203 (545)
T PTZ00110        137 FPDYILKSLKNAGFT---EPTPIQVQGWPIALSGRD----------MIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDG  203 (545)
T ss_pred             CCHHHHHHHHHCCCC---CCCHHHHHHHHHHhcCCC----------EEEEeCCCChHHHHHHHHHHHHHHhcccccCCCC
Confidence            455554443333332   367899999999887544          677777999999999999998876432   1224


Q ss_pred             cEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc-----ccCCCCceEEEECchHHHHHHhcC-CCCCCcc
Q psy496          103 CCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK-----ELPRKRGSILYCTAGILPEVMQSD-PILSGVS  176 (319)
Q Consensus       103 ~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~-----~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~  176 (319)
                      ..+|+++||||||.|+.+.+.++....    +..+........     ......++|+|+|||+|++++... ..+++++
T Consensus       204 p~~LIL~PTreLa~Qi~~~~~~~~~~~----~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~  279 (545)
T PTZ00110        204 PIVLVLAPTRELAEQIREQCNKFGASS----KIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVT  279 (545)
T ss_pred             cEEEEECChHHHHHHHHHHHHHHhccc----CccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCc
Confidence            567888899999999998877764321    211211111110     111235689999999999999554 4589999


Q ss_pred             EEEEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhC
Q psy496          177 HIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFG  226 (319)
Q Consensus       177 ~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~  226 (319)
                      +|||||||.. +..++...+.+.+...+++.|++++|||+  ..+.+++.+.
T Consensus       280 ~lViDEAd~m-ld~gf~~~i~~il~~~~~~~q~l~~SAT~p~~v~~l~~~l~  330 (545)
T PTZ00110        280 YLVLDEADRM-LDMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLC  330 (545)
T ss_pred             EEEeehHHhh-hhcchHHHHHHHHHhCCCCCeEEEEEeCCCHHHHHHHHHHh
Confidence            9999999963 44555555555555667889999999999  4556666543

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

Probab=99.93  E-value=2.3e-25  Score=219.70  Aligned_cols=171  Identities=19%  Similarity=0.177  Sum_probs=116.8

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC-----CCCccEEEEecccHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN-----RGSECCIMVTQPRRISAIAI  118 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~-----~~~~~~vl~~~Ptr~la~q~  118 (319)
                      .++|+|.++||.++.|          ++++++||||||||++|++|++.++....     .....+++++.|||+||.|+
T Consensus       143 ~ptpiQ~~aip~il~g----------~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi  212 (518)
T PLN00206        143 FPTPIQMQAIPAALSG----------RSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQV  212 (518)
T ss_pred             CCCHHHHHHHHHHhcC----------CCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHHHHHH
Confidence            3578999999998764          45788888999999999999998875321     11345777777999999999


Q ss_pred             HHHHHHHhccccCCCCceEEEEEeccc-----ccCCCCceEEEECchHHHHHHhc-CCCCCCccEEEEecccccccchhH
Q psy496          119 AERVAQERDEQCGRPGSSVGYQIRLEK-----ELPRKRGSILYCTAGILPEVMQS-DPILSGVSHIVMDEIHERSMISDF  192 (319)
Q Consensus       119 ~~~~~~~~~~~~~~~g~~vg~~~~~~~-----~~~~~~~~Iiv~Tpg~ll~~l~~-~~~l~~v~~vViDEah~~~~~~~~  192 (319)
                      .+.+..+....    +..+.....+..     .....+.+|+|+|||+|.+++.. ...++++++||+||||.. ...++
T Consensus       213 ~~~~~~l~~~~----~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v~~lViDEad~m-l~~gf  287 (518)
T PLN00206        213 EDQAKVLGKGL----PFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCM-LERGF  287 (518)
T ss_pred             HHHHHHHhCCC----CceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchheeEEEeecHHHH-hhcch
Confidence            88776653321    212111111111     11123578999999999999954 445999999999999973 23333


Q ss_pred             HHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCCE
Q psy496          193 LLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAPI  230 (319)
Q Consensus       193 ~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~~  230 (319)
                      .....+.+... ++.|++++|||+  +.+.+++++...+.
T Consensus       288 ~~~i~~i~~~l-~~~q~l~~SATl~~~v~~l~~~~~~~~~  326 (518)
T PLN00206        288 RDQVMQIFQAL-SQPQVLLFSATVSPEVEKFASSLAKDII  326 (518)
T ss_pred             HHHHHHHHHhC-CCCcEEEEEeeCCHHHHHHHHHhCCCCE
Confidence            33333333333 467999999999  45677777765554

>KOG0348|consensus

Probab=99.93  E-value=7.3e-26  Score=212.61  Aligned_cols=235  Identities=23%  Similarity=0.221  Sum_probs=147.2

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC------CCCccEEEEecccHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN------RGSECCIMVTQPRRISAIAI  118 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~------~~~~~~vl~~~Ptr~la~q~  118 (319)
                      +|.+|.++||++++|+|++.          .|+||||||++|++|+++.+....      .|+.+.|++  ||||||.|+
T Consensus       160 pTsVQkq~IP~lL~grD~lV----------~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALViv--PTREL~~Q~  227 (708)
T KOG0348|consen  160 PTSVQKQAIPVLLEGRDALV----------RAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIV--PTRELALQI  227 (708)
T ss_pred             cchHhhcchhhhhcCcceEE----------EcCCCCcccHHHHHHHHHHHHhcCccccccCCceEEEEe--chHHHHHHH
Confidence            46899999999998777554          455999999999999999986533      344455555  999999999


Q ss_pred             HHHHHHHhcccc-CCCCceEEEEEe-cccccCCCCceEEEECchHHHHHHhcCCC--CCCccEEEEecccccccchhHHH
Q psy496          119 AERVAQERDEQC-GRPGSSVGYQIR-LEKELPRKRGSILYCTAGILPEVMQSDPI--LSGVSHIVMDEIHERSMISDFLL  194 (319)
Q Consensus       119 ~~~~~~~~~~~~-~~~g~~vg~~~~-~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~--l~~v~~vViDEah~~~~~~~~~~  194 (319)
                      ++.+.++..... ...|..+|...+ .+.....++.+|+|+|||||++++++...  ++.++|+|+||+|+ -+.+++-.
T Consensus       228 y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwlVlDEaDr-lleLGfek  306 (708)
T KOG0348|consen  228 YETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLVLDEADR-LLELGFEK  306 (708)
T ss_pred             HHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeeeEEEecchhH-HHhccchh
Confidence            999998866432 111333332222 22222234678999999999999977554  88999999999996 22333221


Q ss_pred             ---HHHHhhh----------ccccCceEEEecccc--ChhhHhhh-hCCCCEEEeCCc-----------------c--cc
Q psy496          195 ---AILKDVT----------DKRKDLKLILMSATL--NAEKFSQF-FGGAPILHIPGF-----------------T--YP  239 (319)
Q Consensus       195 ---~~l~~~~----------~~~~~~qiv~lSAT~--~~~~l~~~-l~~~~~i~~~~r-----------------~--~~  239 (319)
                         .+++.+.          .+++..|.+++|||+  .+..+++. +.++..+..+..                 +  -+
T Consensus       307 dit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p~~~a~~ev~~~~~~~~  386 (708)
T KOG0348|consen  307 DITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNPKDKAVQEVDDGPAGDK  386 (708)
T ss_pred             hHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcCcchhhhhhcCCcccccc
Confidence               2222221          133457899999999  56777764 333222331100                 0  01


Q ss_pred             ceeeeehhhh----hhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCccccccccch
Q psy496          240 VQEYYLEDVL----NMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYL  294 (319)
Q Consensus       240 v~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v~~~~~  294 (319)
                      ++.+-.++.+    -...+.++.++....+...+. .+....++||+.++ ..|+-+|-
T Consensus       387 l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k-~~~~qk~iVF~S~~-d~VeFHy~  443 (708)
T KOG0348|consen  387 LDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVK-FEEKQKMIVFFSCS-DSVEFHYS  443 (708)
T ss_pred             cccccCcHHhhhceEecCCchhHHHHHHHHHHHhh-hhhhceeEEEEech-hHHHHHHH
Confidence            1111111111    113567888766555554332 22255789999887 67788773

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.93  E-value=1.5e-25  Score=218.32  Aligned_cols=235  Identities=17%  Similarity=0.116  Sum_probs=147.2

Q ss_pred             ccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEE
Q psy496           26 VPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCI  105 (319)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~v  105 (319)
                      ++..+.+......+..   ++|+|.++||.++.|          ++++++||||||||++|.+|+++.+.....  .+.+
T Consensus        11 l~~~l~~~l~~~g~~~---~t~iQ~~ai~~~l~g----------~dvi~~a~TGsGKT~a~~lpil~~l~~~~~--~~~~   75 (460)
T PRK11776         11 LPPALLANLNELGYTE---MTPIQAQSLPAILAG----------KDVIAQAKTGSGKTAAFGLGLLQKLDVKRF--RVQA   75 (460)
T ss_pred             CCHHHHHHHHHCCCCC---CCHHHHHHHHHHhcC----------CCEEEECCCCCcHHHHHHHHHHHHhhhccC--CceE
Confidence            4554444433332322   568999999998754          558888889999999999999998865433  3356


Q ss_pred             EEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEe-----cccccCCCCceEEEECchHHHHHHhcC-CCCCCccEEE
Q psy496          106 MVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIR-----LEKELPRKRGSILYCTAGILPEVMQSD-PILSGVSHIV  179 (319)
Q Consensus       106 l~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~-----~~~~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~vV  179 (319)
                      +++.|||+||.|+++.+........   +..+.....     ........+.+|+|+|||++.+++... ..++++++||
T Consensus        76 lil~PtreLa~Q~~~~~~~~~~~~~---~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lV  152 (460)
T PRK11776         76 LVLCPTRELADQVAKEIRRLARFIP---NIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLV  152 (460)
T ss_pred             EEEeCCHHHHHHHHHHHHHHHhhCC---CcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEE
Confidence            6666999999999988877643221   222221111     011111245789999999999999544 4589999999


Q ss_pred             EecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCC-EEEeCCcc--ccceeeeehhhhhhhhh
Q psy496          180 MDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAP-ILHIPGFT--YPVQEYYLEDVLNMTRK  254 (319)
Q Consensus       180 iDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~-~i~~~~r~--~~v~~~~~~~~~~~~~~  254 (319)
                      +||||.. +..++...+...+...+++.|++++|||+  +...++..+...+ .+.+....  ..++.+|....    ..
T Consensus       153 iDEad~~-l~~g~~~~l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~i~~~~~~~~----~~  227 (460)
T PRK11776        153 LDEADRM-LDMGFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTHDLPAIEQRFYEVS----PD  227 (460)
T ss_pred             EECHHHH-hCcCcHHHHHHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcCCCCCCeeEEEEEeC----cH
Confidence            9999963 34444444445555566788999999999  4456666554433 34443322  22444443221    11


Q ss_pred             hHHHHHHHHhhhhhhhccccCCCcEEEeCCccccc
Q psy496          255 DLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPV  289 (319)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v  289 (319)
                      . +.......+     ....++++||||+++..+-
T Consensus       228 ~-k~~~l~~ll-----~~~~~~~~lVF~~t~~~~~  256 (460)
T PRK11776        228 E-RLPALQRLL-----LHHQPESCVVFCNTKKECQ  256 (460)
T ss_pred             H-HHHHHHHHH-----HhcCCCceEEEECCHHHHH
Confidence            1 111111111     1223678999999987653

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.92  E-value=5.1e-25  Score=214.26  Aligned_cols=236  Identities=17%  Similarity=0.096  Sum_probs=147.0

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCC----C
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNR----G  100 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~----~  100 (319)
                      .+++.+.+.+.+..+..   ++++|.++||++++|          ++++++||||||||++|.+|+++.+.....    .
T Consensus         7 ~l~~~l~~~l~~~g~~~---pt~iQ~~ai~~il~g----------~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~   73 (456)
T PRK10590          7 GLSPDILRAVAEQGYRE---PTPIQQQAIPAVLEG----------RDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGR   73 (456)
T ss_pred             CCCHHHHHHHHHCCCCC---CCHHHHHHHHHHhCC----------CCEEEECCCCCcHHHHHHHHHHHHhhhcccccccC
Confidence            45555555554443433   668999999998764          457888889999999999999998865321    1


Q ss_pred             CccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecc-----cccCCCCceEEEECchHHHHHHhcCC-CCCC
Q psy496          101 SECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLE-----KELPRKRGSILYCTAGILPEVMQSDP-ILSG  174 (319)
Q Consensus       101 ~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~-----~~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~  174 (319)
                      ...++|+++|||+||.|+.+.+..+....    +..+.......     ......+.+|+|+||++|++++.... .+++
T Consensus        74 ~~~~aLil~PtreLa~Qi~~~~~~~~~~~----~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~  149 (456)
T PRK10590         74 RPVRALILTPTRELAAQIGENVRDYSKYL----NIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQ  149 (456)
T ss_pred             CCceEEEEeCcHHHHHHHHHHHHHHhccC----CCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCccccc
Confidence            23467888899999999999888765432    22221111110     01112357899999999999985544 5899


Q ss_pred             ccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCC-EEEeCCccc---cceeeeehhh
Q psy496          175 VSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAP-ILHIPGFTY---PVQEYYLEDV  248 (319)
Q Consensus       175 v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~-~i~~~~r~~---~v~~~~~~~~  248 (319)
                      +++|||||||.. ...++...+...+...++..|++++|||+  +...+..++...+ .+.+..+..   .+..++... 
T Consensus       150 v~~lViDEah~l-l~~~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~-  227 (456)
T PRK10590        150 VEILVLDEADRM-LDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFV-  227 (456)
T ss_pred             ceEEEeecHHHH-hccccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEecccccccceeEEEEEc-
Confidence            999999999963 33344444444455566778999999999  3456666554433 344433221   222222211 


Q ss_pred             hhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCcccc
Q psy496          249 LNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       249 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~  288 (319)
                          +...+..++...     +......++|||++++..+
T Consensus       228 ----~~~~k~~~l~~l-----~~~~~~~~~lVF~~t~~~~  258 (456)
T PRK10590        228 ----DKKRKRELLSQM-----IGKGNWQQVLVFTRTKHGA  258 (456)
T ss_pred             ----CHHHHHHHHHHH-----HHcCCCCcEEEEcCcHHHH
Confidence                111111111111     1112256899999998765

>KOG0345|consensus

Probab=99.92  E-value=9.2e-25  Score=202.63  Aligned_cols=259  Identities=18%  Similarity=0.140  Sum_probs=166.1

Q ss_pred             ccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC-CC--CccE
Q psy496           28 QFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN-RG--SECC  104 (319)
Q Consensus        28 ~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~-~~--~~~~  104 (319)
                      .|+.+..-+..|+.   .||+|..+||.++.++|          |++-|+||||||+||++|+++.+..+. +.  .+.-
T Consensus        15 ~~l~~~l~~~GF~~---mTpVQa~tIPlll~~KD----------VvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vg   81 (567)
T KOG0345|consen   15 PWLLEALDESGFEK---MTPVQAATIPLLLKNKD----------VVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVG   81 (567)
T ss_pred             HHHHHHHHhcCCcc---cCHHHHhhhHHHhcCCc----------eEEEcCCCCCchhhHHHHHHHHHHhhccCCCcccee
Confidence            45544433333433   67999999999886555          667777999999999999999885433 22  2346


Q ss_pred             EEEecccHHHHHHHHHHHHHHhcccc-CCCCceEEEEEeccc--ccCCCCceEEEECchHHHHHHhc-CCC--CCCccEE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQC-GRPGSSVGYQIRLEK--ELPRKRGSILYCTAGILPEVMQS-DPI--LSGVSHI  178 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~-~~~g~~vg~~~~~~~--~~~~~~~~Iiv~Tpg~ll~~l~~-~~~--l~~v~~v  178 (319)
                      .++++||||||.|+.+....+..... ......+|...-.++  ....++++|+|+|||||.++++. ...  +.+++++
T Consensus        82 alIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~L  161 (567)
T KOG0345|consen   82 ALIISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEIL  161 (567)
T ss_pred             EEEecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceE
Confidence            77778999999999886655543311 000222332111111  11124678999999999999965 333  4599999


Q ss_pred             EEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhh-hCCCCEEEeCCcc---cc--ceeeeehhhhh
Q psy496          179 VMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQF-FGGAPILHIPGFT---YP--VQEYYLEDVLN  250 (319)
Q Consensus       179 ViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~-l~~~~~i~~~~r~---~~--v~~~~~~~~~~  250 (319)
                      |+||||+ -+.+++...+..++..+++.+|.=+||||.  .++++.+. +.++.-+.+....   .|  +..+|....  
T Consensus       162 VLDEADr-LldmgFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~--  238 (567)
T KOG0345|consen  162 VLDEADR-LLDMGFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCE--  238 (567)
T ss_pred             EecchHh-HhcccHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEec--
Confidence            9999995 477778888888888888899999999999  56677765 4454445554332   34  667777552  


Q ss_pred             hhhhhHHH-HHHHHhhhhhhhccccCCCcEEEeCCccccccccc--hHhHHHHhHhhccccCCCC
Q psy496          251 MTRKDLKL-ILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYY--LEDVLNMTRTLKRSETQQY  312 (319)
Q Consensus       251 ~~~~~~~~-~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v~~~~--~~~~~~~~~~~~~~~~~~~  312 (319)
                         +..+. .+++...+      ...+.++||-||-. +|+-.|  ++..+.....+...|-...
T Consensus       239 ---a~eK~~~lv~~L~~------~~~kK~iVFF~TCa-sVeYf~~~~~~~l~~~~i~~iHGK~~q  293 (567)
T KOG0345|consen  239 ---ADEKLSQLVHLLNN------NKDKKCIVFFPTCA-SVEYFGKLFSRLLKKREIFSIHGKMSQ  293 (567)
T ss_pred             ---HHHHHHHHHHHHhc------cccccEEEEecCcc-hHHHHHHHHHHHhCCCcEEEecchhcc
Confidence               33333 23333222      12578999998852 333322  4444455555555554443

>KOG0326|consensus

Probab=99.92  E-value=6.3e-25  Score=195.21  Aligned_cols=214  Identities=18%  Similarity=0.166  Sum_probs=150.5

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +.|+|+++||..+.|+|+++.+.          .|+|||.+|.+|+++.+.......++.|++  ||||||.|..+...+
T Consensus       108 PSPiQeesIPiaLtGrdiLaRaK----------NGTGKT~a~~IP~Lekid~~~~~IQ~~ilV--PtrelALQtSqvc~~  175 (459)
T KOG0326|consen  108 PSPIQEESIPIALTGRDILARAK----------NGTGKTAAYCIPVLEKIDPKKNVIQAIILV--PTRELALQTSQVCKE  175 (459)
T ss_pred             CCCccccccceeecchhhhhhcc----------CCCCCccceechhhhhcCccccceeEEEEe--ecchhhHHHHHHHHH
Confidence            66899999999999999999999          999999999999999998877666777777  999999998775555


Q ss_pred             HhccccCCCCceE----EEE-EecccccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHHHHH
Q psy496          125 ERDEQCGRPGSSV----GYQ-IRLEKELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLAILK  198 (319)
Q Consensus       125 ~~~~~~~~~g~~v----g~~-~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~l~  198 (319)
                      +....    |..+    |.. .+.+-.......+++|+||||++++...+. .+++...+|+||||.. +..++...+-+
T Consensus       176 lskh~----~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKl-Ls~~F~~~~e~  250 (459)
T KOG0326|consen  176 LSKHL----GIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKL-LSVDFQPIVEK  250 (459)
T ss_pred             Hhccc----CeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhh-hchhhhhHHHH
Confidence            43221    2111    111 111111123467899999999999996554 5999999999999972 55556655555


Q ss_pred             hhhccccCceEEEecccc--ChhhHh-hhhCCCCEEEeCCcc--ccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccc
Q psy496          199 DVTDKRKDLKLILMSATL--NAEKFS-QFFGGAPILHIPGFT--YPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQF  273 (319)
Q Consensus       199 ~~~~~~~~~qiv~lSAT~--~~~~l~-~~l~~~~~i~~~~r~--~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  273 (319)
                      .+.-++++.|++++|||+  .+..+. +++.++-.++.-...  ..|..+|.-.     .+..+....++.+..     .
T Consensus       251 li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM~eLtl~GvtQyYafV-----~e~qKvhCLntLfsk-----L  320 (459)
T KOG0326|consen  251 LISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLMEELTLKGVTQYYAFV-----EERQKVHCLNTLFSK-----L  320 (459)
T ss_pred             HHHhCCccceeeEEecccchhHHHHHHHhccCcceeehhhhhhhcchhhheeee-----chhhhhhhHHHHHHH-----h
Confidence            566688899999999999  455554 466665566664433  3455555432     222333344444333     1


Q ss_pred             cCCCcEEEeCCc
Q psy496          274 FGGAPILHIPGF  285 (319)
Q Consensus       274 ~~g~~LVFlp~R  285 (319)
                      .-.+++|||++.
T Consensus       321 qINQsIIFCNS~  332 (459)
T KOG0326|consen  321 QINQSIIFCNST  332 (459)
T ss_pred             cccceEEEeccc
Confidence            245789999985

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.92  E-value=1.2e-24  Score=209.98  Aligned_cols=191  Identities=15%  Similarity=0.127  Sum_probs=124.5

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCC-----
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNR-----   99 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~-----   99 (319)
                      +++..+.+...+..+..   ++++|.++||.++.|+|          ++++||||||||++|++|+++.+.....     
T Consensus        14 ~l~~~l~~~l~~~g~~~---pt~iQ~~aip~il~g~d----------vi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~   80 (423)
T PRK04837         14 ALHPQVVEALEKKGFHN---CTPIQALALPLTLAGRD----------VAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRK   80 (423)
T ss_pred             CCCHHHHHHHHHCCCCC---CCHHHHHHHHHHhCCCc----------EEEECCCCchHHHHHHHHHHHHHHhcccccccc
Confidence            45655555544433332   57899999999887654          7778889999999999999998864321     


Q ss_pred             CCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc-----ccCCCCceEEEECchHHHHHHhcC-CCCC
Q psy496          100 GSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK-----ELPRKRGSILYCTAGILPEVMQSD-PILS  173 (319)
Q Consensus       100 ~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~-----~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~  173 (319)
                      ....++++++|||+||.|+++.+..+....    |..++.......     .....+.+|+|+|||++.+++... ..++
T Consensus        81 ~~~~~~lil~PtreLa~Qi~~~~~~l~~~~----~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~  156 (423)
T PRK04837         81 VNQPRALIMAPTRELAVQIHADAEPLAQAT----GLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLG  156 (423)
T ss_pred             cCCceEEEECCcHHHHHHHHHHHHHHhccC----CceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccc
Confidence            123578888899999999988776654322    334432222111     111235689999999999999544 4589


Q ss_pred             CccEEEEecccccccchhHHHHHHHhhhccc--cCceEEEecccc--ChhhHh-hhhCCCCEEEe
Q psy496          174 GVSHIVMDEIHERSMISDFLLAILKDVTDKR--KDLKLILMSATL--NAEKFS-QFFGGAPILHI  233 (319)
Q Consensus       174 ~v~~vViDEah~~~~~~~~~~~~l~~~~~~~--~~~qiv~lSAT~--~~~~l~-~~l~~~~~i~~  233 (319)
                      +++++|+||||.. ...++...+...+...+  ...+.+++|||+  +...+. .++.+...+.+
T Consensus       157 ~v~~lViDEad~l-~~~~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v  220 (423)
T PRK04837        157 AIQVVVLDEADRM-FDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEV  220 (423)
T ss_pred             cccEEEEecHHHH-hhcccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEE
Confidence            9999999999973 23333333322222232  345678999999  334444 35544444444

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.92  E-value=3.8e-24  Score=214.20  Aligned_cols=250  Identities=22%  Similarity=0.274  Sum_probs=157.2

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHH---------HHH-hCCCCccEEEEecccHHHHH
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDD---------EIA-RNRGSECCIMVTQPRRISAI  116 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~---------l~~-~~~~~~~~vl~~~Ptr~la~  116 (319)
                      .++-..++.-. .++++....++++++++|+||||||++++.+++..         +.. ........+++++|||+||.
T Consensus       158 ~~~l~~~~~~i-Q~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~  236 (675)
T PHA02653        158 KIPLASLQPDV-QLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVR  236 (675)
T ss_pred             cccCCchhHHH-HHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHH
Confidence            44444443332 24566666678889999999999999977555432         211 01222458999999999999


Q ss_pred             HHHHHHHHHhccccCCCCceEEEEEeccccc------CCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccch
Q psy496          117 AIAERVAQERDEQCGRPGSSVGYQIRLEKEL------PRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMIS  190 (319)
Q Consensus       117 q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~------~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~  190 (319)
                      |+..++.+..+... ..|..+.  ++.+...      .....+|+++|++.      ..+.|+++++|||||||+|....
T Consensus       237 qi~~~i~~~vg~~~-~~g~~v~--v~~Gg~~~~~~~t~~k~~~Ilv~T~~L------~l~~L~~v~~VVIDEaHEr~~~~  307 (675)
T PHA02653        237 LHSITLLKSLGFDE-IDGSPIS--LKYGSIPDELINTNPKPYGLVFSTHKL------TLNKLFDYGTVIIDEVHEHDQIG  307 (675)
T ss_pred             HHHHHHHHHhCccc-cCCceEE--EEECCcchHHhhcccCCCCEEEEeCcc------cccccccCCEEEccccccCccch
Confidence            99998887665321 0122232  3322221      11245799999873      22457899999999999998888


Q ss_pred             hHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCCEEEeCCcc-ccceeeeehhhhhhh-hhh----HHHHHHH
Q psy496          191 DFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAPILHIPGFT-YPVQEYYLEDVLNMT-RKD----LKLILMS  262 (319)
Q Consensus       191 ~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~~i~~~~r~-~~v~~~~~~~~~~~~-~~~----~~~~~~~  262 (319)
                      |.++..++.....  ..|+++||||+  +.+.+.+|+++++.+.++++. +|++++|........ ...    .+.....
T Consensus       308 DllL~llk~~~~~--~rq~ILmSATl~~dv~~l~~~~~~p~~I~I~grt~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~  385 (675)
T PHA02653        308 DIIIAVARKHIDK--IRSLFLMTATLEDDRDRIKEFFPNPAFVHIPGGTLFPISEVYVKNKYNPKNKRAYIEEEKKNIVT  385 (675)
T ss_pred             hHHHHHHHHhhhh--cCEEEEEccCCcHhHHHHHHHhcCCcEEEeCCCcCCCeEEEEeecCcccccchhhhHHHHHHHHH
Confidence            8888888755432  24899999999  567888999999999999985 999999875431100 000    0111111


Q ss_pred             HhhhhhhhccccCCCcEEEeCCcccccccc-chHhHHHHhHhhccccCCC
Q psy496          263 ATLNAEKFSQFFGGAPILHIPGFTYPVQEY-YLEDVLNMTRTLKRSETQQ  311 (319)
Q Consensus       263 ~~~~~~~~~~~~~g~~LVFlp~R~~~v~~~-~~~~~~~~~~~~~~~~~~~  311 (319)
                      ....   .....++++|||+||+..+-+.. .++.......+++++|.++
T Consensus       386 ~L~~---~~~~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Ls  432 (675)
T PHA02653        386 ALKK---YTPPKGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVP  432 (675)
T ss_pred             HHHH---hhcccCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcC
Confidence            1111   11112578999999987653321 1211111246777777665

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

Probab=99.92  E-value=6.3e-25  Score=223.81  Aligned_cols=193  Identities=16%  Similarity=0.155  Sum_probs=128.5

Q ss_pred             ccccccccccchHHHhccCCc-cccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCC
Q psy496           22 KTTQVPQFILDDEIARNRGSE-CCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRG  100 (319)
Q Consensus        22 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~  100 (319)
                      ....+|.++.++..+.+.... .+++++|.++||.+++|+          |++++||||||||++|.+|+++.+....  
T Consensus        13 ~~~~~~~~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~----------nvvv~apTGSGKTla~~LPiL~~l~~~~--   80 (742)
T TIGR03817        13 RTAPWPAWAHPDVVAALEAAGIHRPWQHQARAAELAHAGR----------HVVVATGTASGKSLAYQLPVLSALADDP--   80 (742)
T ss_pred             ccCCCCCcCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCC----------CEEEECCCCCcHHHHHHHHHHHHHhhCC--
Confidence            334556555443333332221 236789999999987654          4778888999999999999999986532  


Q ss_pred             CccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc------cCCCCceEEEECchHHHHHHhc-C----
Q psy496          101 SECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE------LPRKRGSILYCTAGILPEVMQS-D----  169 (319)
Q Consensus       101 ~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~------~~~~~~~Iiv~Tpg~ll~~l~~-~----  169 (319)
                       ..++|++.||||||.|+.+.+.++.  ..   +..++  ...++.      ...++++|+++||+++...+.. .    
T Consensus        81 -~~~aL~l~PtraLa~q~~~~l~~l~--~~---~i~v~--~~~Gdt~~~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~  152 (742)
T TIGR03817        81 -RATALYLAPTKALAADQLRAVRELT--LR---GVRPA--TYDGDTPTEERRWAREHARYVLTNPDMLHRGILPSHARWA  152 (742)
T ss_pred             -CcEEEEEcChHHHHHHHHHHHHHhc--cC---CeEEE--EEeCCCCHHHHHHHhcCCCEEEEChHHHHHhhccchhHHH
Confidence             4578888899999999999888764  11   22332  111111      1124578999999998754422 1    


Q ss_pred             CCCCCccEEEEeccccc-c---cchhHHHHHHHhhhc-cccCceEEEecccc-ChhhHhhhhCCCCEEEeC
Q psy496          170 PILSGVSHIVMDEIHER-S---MISDFLLAILKDVTD-KRKDLKLILMSATL-NAEKFSQFFGGAPILHIP  234 (319)
Q Consensus       170 ~~l~~v~~vViDEah~~-~---~~~~~~~~~l~~~~~-~~~~~qiv~lSAT~-~~~~l~~~l~~~~~i~~~  234 (319)
                      ..++++++|||||+|.. +   .+...++.+++.+.. .+.+.|++++|||+ |+..+++++.+.+...++
T Consensus       153 ~~l~~l~~vViDEah~~~g~fg~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~~~~~~l~g~~~~~i~  223 (742)
T TIGR03817       153 RFLRRLRYVVIDECHSYRGVFGSHVALVLRRLRRLCARYGASPVFVLASATTADPAAAASRLIGAPVVAVT  223 (742)
T ss_pred             HHHhcCCEEEEeChhhccCccHHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCCHHHHHHHHcCCCeEEEC
Confidence            23789999999999972 2   222234444444433 34568999999999 888888776655554443

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.

>KOG0952|consensus

Probab=99.92  E-value=9.5e-25  Score=218.01  Aligned_cols=239  Identities=16%  Similarity=0.160  Sum_probs=161.9

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC-----CCCccEEEEecccHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN-----RGSECCIMVTQPRRISAIAIA  119 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~-----~~~~~~vl~~~Ptr~la~q~~  119 (319)
                      .-.+|..++|..         -..|.|.+||||||||||..+++.|++.+....     .....+|+|++|+++||..+.
T Consensus       111 fN~iQS~vFp~a---------Y~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~  181 (1230)
T KOG0952|consen  111 FNRIQSEVFPVA---------YKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMV  181 (1230)
T ss_pred             HHHHHHHhhhhh---------hcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHH
Confidence            346788888774         235689999999999999999999999886421     123569999999999999999


Q ss_pred             HHHHHHhccccCCCCceEEEEEecccccC---CCCceEEEECchHH---HHHHhcCC-CCCCccEEEEecccc----ccc
Q psy496          120 ERVAQERDEQCGRPGSSVGYQIRLEKELP---RKRGSILYCTAGIL---PEVMQSDP-ILSGVSHIVMDEIHE----RSM  188 (319)
Q Consensus       120 ~~~~~~~~~~~~~~g~~vg~~~~~~~~~~---~~~~~Iiv~Tpg~l---l~~l~~~~-~l~~v~~vViDEah~----~~~  188 (319)
                      +.|.+.+...    |..++- ..++....   -.+++|+|+||+..   .+....+. .++.+++|||||+|.    ||+
T Consensus       182 ~~~~kkl~~~----gi~v~E-LTGD~ql~~tei~~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd~RGp  256 (1230)
T KOG0952|consen  182 DKFSKKLAPL----GISVRE-LTGDTQLTKTEIADTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHDDRGP  256 (1230)
T ss_pred             HHHhhhcccc----cceEEE-ecCcchhhHHHHHhcCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhhcCcccc
Confidence            9998876643    444441 11111111   24789999999754   34443332 378899999999996    777


Q ss_pred             chhHHHHHHHhhhc-cccCceEEEecccc-ChhhHhhhhCCC---CEEEeCCccccc--eeeeehhhhhhhhhhHHHHHH
Q psy496          189 ISDFLLAILKDVTD-KRKDLKLILMSATL-NAEKFSQFFGGA---PILHIPGFTYPV--QEYYLEDVLNMTRKDLKLILM  261 (319)
Q Consensus       189 ~~~~~~~~l~~~~~-~~~~~qiv~lSAT~-~~~~l~~~l~~~---~~i~~~~r~~~v--~~~~~~~~~~~~~~~~~~~~~  261 (319)
                      ..+.+.++..+... ....+|+|++|||+ |.+++++|++.+   .+++++++..|+  +..+...... .+......+-
T Consensus       257 vlEtiVaRtlr~vessqs~IRivgLSATlPN~eDvA~fL~vn~~~glfsFd~~yRPvpL~~~~iG~k~~-~~~~~~~~~d  335 (1230)
T KOG0952|consen  257 VLETIVARTLRLVESSQSMIRIVGLSATLPNYEDVARFLRVNPYAGLFSFDQRYRPVPLTQGFIGIKGK-KNRQQKKNID  335 (1230)
T ss_pred             hHHHHHHHHHHHHHhhhhheEEEEeeccCCCHHHHHHHhcCCCccceeeecccccccceeeeEEeeecc-cchhhhhhHH
Confidence            77777766665443 34578999999999 999999999864   467777766555  4444433222 1111222222


Q ss_pred             HHhhhhhhhccccCCCcEEEeCCcccccccc-chHhHH
Q psy496          262 SATLNAEKFSQFFGGAPILHIPGFTYPVQEY-YLEDVL  298 (319)
Q Consensus       262 ~~~~~~~~~~~~~~g~~LVFlp~R~~~v~~~-~~~~~~  298 (319)
                      ...+++.......+.+++|||++|+.+++.+ .+.+.|
T Consensus       336 ~~~~~kv~e~~~~g~qVlvFvhsR~~Ti~tA~~l~~~a  373 (1230)
T KOG0952|consen  336 EVCYDKVVEFLQEGHQVLVFVHSRNETIRTAKKLRERA  373 (1230)
T ss_pred             HHHHHHHHHHHHcCCeEEEEEecChHHHHHHHHHHHHH
Confidence            2223332222234899999999999998873 344444

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.92  E-value=1.2e-24  Score=217.91  Aligned_cols=221  Identities=19%  Similarity=0.151  Sum_probs=142.9

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++|+|.++||.++.|          ++++++||||||||++|.+|+++.+......  ..+|+++|||+||.|+++.+..
T Consensus        29 ptpiQ~~ai~~ll~g----------~dvl~~ApTGsGKT~af~lpll~~l~~~~~~--~~~LIL~PTreLa~Qv~~~l~~   96 (629)
T PRK11634         29 PSPIQAECIPHLLNG----------RDVLGMAQTGSGKTAAFSLPLLHNLDPELKA--PQILVLAPTRELAVQVAEAMTD   96 (629)
T ss_pred             CCHHHHHHHHHHHcC----------CCEEEEcCCCCcHHHHHHHHHHHHhhhccCC--CeEEEEeCcHHHHHHHHHHHHH
Confidence            668999999998764          4578888899999999999999988654333  4667777999999999998877


Q ss_pred             HhccccCCCCceEEEEEeccc-----ccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHHHHH
Q psy496          125 ERDEQCGRPGSSVGYQIRLEK-----ELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLAILK  198 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~-----~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~l~  198 (319)
                      +.+...   +..+.......+     ......++|+|+|||++++++.... .++++++|||||||++ +.+.+...+..
T Consensus        97 ~~~~~~---~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~m-l~~gf~~di~~  172 (629)
T PRK11634         97 FSKHMR---GVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEM-LRMGFIEDVET  172 (629)
T ss_pred             HHhhcC---CceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHH-hhcccHHHHHH
Confidence            654332   333321111111     1112357899999999999996544 5999999999999973 44445555555


Q ss_pred             hhhccccCceEEEecccc--ChhhHhh-hhCCCCEEEeCCccc---cceeeeehhhhhhhhhhHHHHHHHHhhhhhhhcc
Q psy496          199 DVTDKRKDLKLILMSATL--NAEKFSQ-FFGGAPILHIPGFTY---PVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQ  272 (319)
Q Consensus       199 ~~~~~~~~~qiv~lSAT~--~~~~l~~-~l~~~~~i~~~~r~~---~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  272 (319)
                      .+...+...|+++||||+  ....+.+ |+.+...+.+.....   .+...|....    .......+.. .+.     .
T Consensus       173 Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v~----~~~k~~~L~~-~L~-----~  242 (629)
T PRK11634        173 IMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVW----GMRKNEALVR-FLE-----A  242 (629)
T ss_pred             HHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCccccCCceEEEEEEec----hhhHHHHHHH-HHH-----h
Confidence            555667788999999999  3344544 555544455443321   2223332211    1111111111 111     1


Q ss_pred             ccCCCcEEEeCCccccccc
Q psy496          273 FFGGAPILHIPGFTYPVQE  291 (319)
Q Consensus       273 ~~~g~~LVFlp~R~~~v~~  291 (319)
                      .....+||||+++..+.++
T Consensus       243 ~~~~~~IVF~~tk~~a~~l  261 (629)
T PRK11634        243 EDFDAAIIFVRTKNATLEV  261 (629)
T ss_pred             cCCCCEEEEeccHHHHHHH
Confidence            1256899999998776543

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.92  E-value=6.9e-25  Score=222.19  Aligned_cols=208  Identities=18%  Similarity=0.199  Sum_probs=142.3

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc-
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE-  146 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~-  146 (319)
                      .++|++||+|||||||..+.+.+++.+...+    .+++|++|+|+||.+.++++.++-  ..   |..|+.....-+. 
T Consensus        46 ~~~N~li~aPTgsGKTlIA~lai~~~l~~~~----~k~vYivPlkALa~Ek~~~~~~~~--~~---GirV~~~TgD~~~~  116 (766)
T COG1204          46 SDENVLISAPTGSGKTLIALLAILSTLLEGG----GKVVYIVPLKALAEEKYEEFSRLE--EL---GIRVGISTGDYDLD  116 (766)
T ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHHHhcC----CcEEEEeChHHHHHHHHHHhhhHH--hc---CCEEEEecCCcccc
Confidence            3789999999999999999999999887652    389999999999999999998221  11   6666633331111 


Q ss_pred             -cCCCCceEEEECchHHHHHHhcCCC-CCCccEEEEecccc-----cccchhHHHHHHHhhhccccCceEEEecccc-Ch
Q psy496          147 -LPRKRGSILYCTAGILPEVMQSDPI-LSGVSHIVMDEIHE-----RSMISDFLLAILKDVTDKRKDLKLILMSATL-NA  218 (319)
Q Consensus       147 -~~~~~~~Iiv~Tpg~ll~~l~~~~~-l~~v~~vViDEah~-----~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~-~~  218 (319)
                       ..-.+++|+|+||+.+...+++.+. +.++++|||||+|.     ||...+.....++..   .+..|++++|||+ |.
T Consensus       117 ~~~l~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~~lE~iv~r~~~~---~~~~rivgLSATlpN~  193 (766)
T COG1204         117 DERLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLESIVARMRRL---NELIRIVGLSATLPNA  193 (766)
T ss_pred             hhhhccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcccCceehhHHHHHHhh---CcceEEEEEeeecCCH
Confidence             1124788999999999998877665 78999999999996     565555555555544   3458999999999 99


Q ss_pred             hhHhhhhCCCCEEEeCCccccce------eeeehhhhhhh--hhhHHHHHHHHhhhhhhhccccCCCcEEEeCCcccccc
Q psy496          219 EKFSQFFGGAPILHIPGFTYPVQ------EYYLEDVLNMT--RKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQ  290 (319)
Q Consensus       219 ~~l~~~l~~~~~i~~~~r~~~v~------~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v~  290 (319)
                      .++++|++.... ....++.|..      ..+....-...  .......+....+..  .  ..+|++|||||+|..+..
T Consensus       194 ~evA~wL~a~~~-~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~~--~--~~~~qvLvFv~sR~~a~~  268 (766)
T COG1204         194 EEVADWLNAKLV-ESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVLES--L--AEGGQVLVFVHSRKEAEK  268 (766)
T ss_pred             HHHHHHhCCccc-ccCCCCcccccCCccceEEEEecCccccccccchHHHHHHHHHH--H--hcCCeEEEEEecCchHHH
Confidence            999999986554 3344443321      11111110000  001112222223322  2  238999999999999877


Q ss_pred             cc
Q psy496          291 EY  292 (319)
Q Consensus       291 ~~  292 (319)
                      ++
T Consensus       269 ~A  270 (766)
T COG1204         269 TA  270 (766)
T ss_pred             HH
Confidence            63

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.92  E-value=1.5e-24  Score=215.66  Aligned_cols=220  Identities=16%  Similarity=0.151  Sum_probs=135.2

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC-----CCCccEEEEecccHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN-----RGSECCIMVTQPRRISAIAIA  119 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~-----~~~~~~vl~~~Ptr~la~q~~  119 (319)
                      ++++|.++||.++.|+          +++++||||||||++|++|+++.+....     .....++|+++|||+||.|++
T Consensus        32 ptpiQ~~~ip~~l~G~----------Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PTreLa~Qi~  101 (572)
T PRK04537         32 CTPIQALTLPVALPGG----------DVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIH  101 (572)
T ss_pred             CCHHHHHHHHHHhCCC----------CEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCcHHHHHHHH
Confidence            5789999999987644          5777788999999999999999886421     112357888889999999999


Q ss_pred             HHHHHHhccccCCCCceEEEEEecc-----cccCCCCceEEEECchHHHHHHhcC--CCCCCccEEEEecccccccchhH
Q psy496          120 ERVAQERDEQCGRPGSSVGYQIRLE-----KELPRKRGSILYCTAGILPEVMQSD--PILSGVSHIVMDEIHERSMISDF  192 (319)
Q Consensus       120 ~~~~~~~~~~~~~~g~~vg~~~~~~-----~~~~~~~~~Iiv~Tpg~ll~~l~~~--~~l~~v~~vViDEah~~~~~~~~  192 (319)
                      +.+.++....    +..++......     ........+|+|+||++|++++...  ..++++++|||||||.. +..++
T Consensus       102 ~~~~~l~~~~----~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEAh~l-ld~gf  176 (572)
T PRK04537        102 KDAVKFGADL----GLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRM-FDLGF  176 (572)
T ss_pred             HHHHHHhccC----CceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCHHHH-hhcch
Confidence            9877664322    33333222111     1112235689999999999998553  34889999999999973 23333


Q ss_pred             HHHHHHhhhcccc--CceEEEeccccC--hhhHh-hhhCCCCEEEeCCccc---cceeeeehhhhhhhhhhHHHHHHHHh
Q psy496          193 LLAILKDVTDKRK--DLKLILMSATLN--AEKFS-QFFGGAPILHIPGFTY---PVQEYYLEDVLNMTRKDLKLILMSAT  264 (319)
Q Consensus       193 ~~~~l~~~~~~~~--~~qiv~lSAT~~--~~~l~-~~l~~~~~i~~~~r~~---~v~~~~~~~~~~~~~~~~~~~~~~~~  264 (319)
                      ...+...+...+.  +.|+++||||++  ...+. .++.+...+.+.....   .+...+....    .......+..  
T Consensus       177 ~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~~~----~~~k~~~L~~--  250 (572)
T PRK04537        177 IKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPA----DEEKQTLLLG--  250 (572)
T ss_pred             HHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEeccccccccceeEEEEecC----HHHHHHHHHH--
Confidence            3333333333332  579999999993  33333 4554443444333221   1222222111    1111111111  


Q ss_pred             hhhhhhccccCCCcEEEeCCccccc
Q psy496          265 LNAEKFSQFFGGAPILHIPGFTYPV  289 (319)
Q Consensus       265 ~~~~~~~~~~~g~~LVFlp~R~~~v  289 (319)
                        .  +....++++||||+++..+-
T Consensus       251 --l--l~~~~~~k~LVF~nt~~~ae  271 (572)
T PRK04537        251 --L--LSRSEGARTMVFVNTKAFVE  271 (572)
T ss_pred             --H--HhcccCCcEEEEeCCHHHHH
Confidence              1  12223678999999987653

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.91  E-value=2.5e-24  Score=208.35  Aligned_cols=171  Identities=18%  Similarity=0.187  Sum_probs=119.6

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHh--CCCCccEEEEecccHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIAR--NRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~--~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      ++++|.++||++.+|          ++++++||||||||++|.+|+++.+...  ......+++++.||++||.|+++.+
T Consensus        24 p~~iQ~~ai~~~~~g----------~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eLa~Q~~~~~   93 (434)
T PRK11192         24 PTAIQAEAIPPALDG----------RDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVADQA   93 (434)
T ss_pred             CCHHHHHHHHHHhCC----------CCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHHHHHHHHHH
Confidence            568899999998754          4588888899999999999999987542  1223458899999999999999888


Q ss_pred             HHHhccccCCCCceEEEEEecc-----cccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHHH
Q psy496          123 AQERDEQCGRPGSSVGYQIRLE-----KELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLAI  196 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~-----~~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~  196 (319)
                      ..+....    +..++......     ......+.+|+|+|||+|++++.... .+.++++||+||||.. +..++...+
T Consensus        94 ~~l~~~~----~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~-l~~~~~~~~  168 (434)
T PRK11192         94 RELAKHT----HLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRM-LDMGFAQDI  168 (434)
T ss_pred             HHHHccC----CcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHH-hCCCcHHHH
Confidence            7764432    33333221110     11112456899999999999996554 4899999999999963 333333333


Q ss_pred             HHhhhccccCceEEEeccccC---hhhHhhhhCCCCE
Q psy496          197 LKDVTDKRKDLKLILMSATLN---AEKFSQFFGGAPI  230 (319)
Q Consensus       197 l~~~~~~~~~~qiv~lSAT~~---~~~l~~~l~~~~~  230 (319)
                      .......+...|+++||||++   ...+.+++...+.
T Consensus       169 ~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~  205 (434)
T PRK11192        169 ETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPV  205 (434)
T ss_pred             HHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCE
Confidence            333334455679999999993   4566666655443

>PRK00254 ski2-like helicase; Provisional

Probab=99.91  E-value=6e-24  Score=217.27  Aligned_cols=221  Identities=14%  Similarity=0.100  Sum_probs=142.0

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      .+|+|.++++...         ..++|++++||||||||.++.+|+++.+...+    .+++++.|+++||.|.++.+..
T Consensus        24 l~~~Q~~ai~~~~---------~~g~nvlv~apTGsGKT~~~~l~il~~l~~~~----~~~l~l~P~~aLa~q~~~~~~~   90 (720)
T PRK00254         24 LYPPQAEALKSGV---------LEGKNLVLAIPTASGKTLVAEIVMVNKLLREG----GKAVYLVPLKALAEEKYREFKD   90 (720)
T ss_pred             CCHHHHHHHHHHH---------hCCCcEEEECCCCcHHHHHHHHHHHHHHHhcC----CeEEEEeChHHHHHHHHHHHHH
Confidence            5688999997521         24577999999999999999999998876432    3788888999999999998876


Q ss_pred             HhccccCCCCceEEEEEeccc--ccCCCCceEEEECchHHHHHHhcC-CCCCCccEEEEeccccccc--chhHHHHHHHh
Q psy496          125 ERDEQCGRPGSSVGYQIRLEK--ELPRKRGSILYCTAGILPEVMQSD-PILSGVSHIVMDEIHERSM--ISDFLLAILKD  199 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~--~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~vViDEah~~~~--~~~~~~~~l~~  199 (319)
                      + .. .   |..++......+  .....+++|+|+||+++..++... ..++++++||+||+|..+.  ....+...+..
T Consensus        91 ~-~~-~---g~~v~~~~Gd~~~~~~~~~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~~rg~~le~il~~  165 (720)
T PRK00254         91 W-EK-L---GLRVAMTTGDYDSTDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGSYDRGATLEMILTH  165 (720)
T ss_pred             H-hh-c---CCEEEEEeCCCCCchhhhccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCCccchHHHHHHHHh
Confidence            3 21 1   444442221111  111135689999999998887544 4589999999999997321  11122222222


Q ss_pred             hhccccCceEEEecccc-ChhhHhhhhCCCCEEEeCCccccceee--eehhhhhhhh--hhHHHHHHHHhhhhhhhcccc
Q psy496          200 VTDKRKDLKLILMSATL-NAEKFSQFFGGAPILHIPGFTYPVQEY--YLEDVLNMTR--KDLKLILMSATLNAEKFSQFF  274 (319)
Q Consensus       200 ~~~~~~~~qiv~lSAT~-~~~~l~~~l~~~~~i~~~~r~~~v~~~--~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~  274 (319)
                         ...+.|+|++|||+ |++++++|++.. .+....|+.|+...  +.........  ......+.....+.  ..  .
T Consensus       166 ---l~~~~qiI~lSATl~n~~~la~wl~~~-~~~~~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--i~--~  237 (720)
T PRK00254        166 ---MLGRAQILGLSATVGNAEELAEWLNAE-LVVSDWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESLVYDA--VK--K  237 (720)
T ss_pred             ---cCcCCcEEEEEccCCCHHHHHHHhCCc-cccCCCCCCcceeeEecCCeeeccCcchhcchHHHHHHHHHH--HH--h
Confidence               33567999999999 999999999753 44455666665322  1111101000  00111122222232  12  2


Q ss_pred             CCCcEEEeCCccccccc
Q psy496          275 GGAPILHIPGFTYPVQE  291 (319)
Q Consensus       275 ~g~~LVFlp~R~~~v~~  291 (319)
                      ++++|||+++|..+..+
T Consensus       238 ~~~vLVF~~sr~~~~~~  254 (720)
T PRK00254        238 GKGALVFVNTRRSAEKE  254 (720)
T ss_pred             CCCEEEEEcChHHHHHH
Confidence            78999999999987554

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.91  E-value=5e-24  Score=221.05  Aligned_cols=182  Identities=23%  Similarity=0.277  Sum_probs=124.5

Q ss_pred             cchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCC----CCccEEE
Q psy496           31 LDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNR----GSECCIM  106 (319)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~----~~~~~vl  106 (319)
                      ..+|+...++.   ++|+|.++||.+.+          +++++|+||||||||++|.+|+++.+.....    ....+++
T Consensus        22 v~~~~~~~~~~---~tpiQ~~Ai~~il~----------g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~L   88 (876)
T PRK13767         22 VREWFKEKFGT---FTPPQRYAIPLIHE----------GKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCL   88 (876)
T ss_pred             HHHHHHHccCC---CCHHHHHHHHHHHc----------CCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEE
Confidence            34566665433   67899999999864          4568999999999999999999998865321    2346788


Q ss_pred             EecccHHHHHHHHHHHHHHhcc---ccCCCCc---eEEEEEecccccC-------CCCceEEEECchHHHHHHhcCC---
Q psy496          107 VTQPRRISAIAIAERVAQERDE---QCGRPGS---SVGYQIRLEKELP-------RKRGSILYCTAGILPEVMQSDP---  170 (319)
Q Consensus       107 ~~~Ptr~la~q~~~~~~~~~~~---~~~~~g~---~vg~~~~~~~~~~-------~~~~~Iiv~Tpg~ll~~l~~~~---  170 (319)
                      ++.|+|+||.|+++++...+..   .....|.   .+...+..++...       ...++|+|+||++|..++....   
T Consensus        89 yIsPtraLa~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~  168 (876)
T PRK13767         89 YVSPLRALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFRE  168 (876)
T ss_pred             EEcCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHH
Confidence            9999999999998866543211   0000011   1222233333211       1346899999999987774332   


Q ss_pred             CCCCccEEEEecccc-----cccchhHHHHHHHhhhccccCceEEEecccc-ChhhHhhhhCC
Q psy496          171 ILSGVSHIVMDEIHE-----RSMISDFLLAILKDVTDKRKDLKLILMSATL-NAEKFSQFFGG  227 (319)
Q Consensus       171 ~l~~v~~vViDEah~-----~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~-~~~~l~~~l~~  227 (319)
                      .++++++||+||+|.     ||......+..+..+.  .++.|++++|||+ |.+.+++|+..
T Consensus       169 ~l~~l~~VVIDE~H~l~~~~RG~~l~~~L~rL~~l~--~~~~q~IglSATl~~~~~va~~L~~  229 (876)
T PRK13767        169 KLRTVKWVIVDEIHSLAENKRGVHLSLSLERLEELA--GGEFVRIGLSATIEPLEEVAKFLVG  229 (876)
T ss_pred             HHhcCCEEEEechhhhccCccHHHHHHHHHHHHHhc--CCCCeEEEEecccCCHHHHHHHhcC
Confidence            378999999999997     2333344444554443  2467999999999 88999999864

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.90  E-value=2.3e-23  Score=203.70  Aligned_cols=175  Identities=21%  Similarity=0.208  Sum_probs=116.9

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCC-----CccEEEEecccHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRG-----SECCIMVTQPRRISAIAIA  119 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~-----~~~~vl~~~Ptr~la~q~~  119 (319)
                      .+++|.++||.+.+|+          +++++||||||||++|.+|+++.+......     ...+++++.|||+||.|+.
T Consensus       110 ~~~iQ~~ai~~~~~G~----------dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~PtreLa~Q~~  179 (475)
T PRK01297        110 CTPIQAQVLGYTLAGH----------DAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIA  179 (475)
T ss_pred             CCHHHHHHHHHHhCCC----------CEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCcHHHHHHHH
Confidence            5689999999987654          477788899999999999999988654311     1357777889999999999


Q ss_pred             HHHHHHhccccCCCCceEEEEEecc------cccCCCCceEEEECchHHHHHHhc-CCCCCCccEEEEecccccccchhH
Q psy496          120 ERVAQERDEQCGRPGSSVGYQIRLE------KELPRKRGSILYCTAGILPEVMQS-DPILSGVSHIVMDEIHERSMISDF  192 (319)
Q Consensus       120 ~~~~~~~~~~~~~~g~~vg~~~~~~------~~~~~~~~~Iiv~Tpg~ll~~l~~-~~~l~~v~~vViDEah~~~~~~~~  192 (319)
                      +.+..+....    +..+.......      .......++|+|+||++|+++... ...++++++|||||+|.. ...++
T Consensus       180 ~~~~~l~~~~----~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViDEah~l-~~~~~  254 (475)
T PRK01297        180 KDAAALTKYT----GLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRM-LDMGF  254 (475)
T ss_pred             HHHHHhhccC----CCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEechHHHH-Hhccc
Confidence            9887764322    33332111111      111123568999999999998844 445899999999999973 22223


Q ss_pred             HHHHHHhhhcc--ccCceEEEecccc--ChhhHhhh-hCCCCEEEeC
Q psy496          193 LLAILKDVTDK--RKDLKLILMSATL--NAEKFSQF-FGGAPILHIP  234 (319)
Q Consensus       193 ~~~~l~~~~~~--~~~~qiv~lSAT~--~~~~l~~~-l~~~~~i~~~  234 (319)
                      ...+.+.+...  ..+.|++++|||+  +...+.+. +.+...+.+.
T Consensus       255 ~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  301 (475)
T PRK01297        255 IPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIE  301 (475)
T ss_pred             HHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEec
Confidence            22222222222  2356999999998  55556554 4444344443

>PTZ00424 helicase 45; Provisional

Probab=99.89  E-value=3.5e-23  Score=198.10  Aligned_cols=175  Identities=19%  Similarity=0.136  Sum_probs=114.9

Q ss_pred             ccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEE
Q psy496           26 VPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCI  105 (319)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~v  105 (319)
                      +++.+.+.+....+.   .++++|.++||.+..|+          +++++||||||||++|.+|+++.+....  ...++
T Consensus        35 l~~~~~~~l~~~~~~---~~~~~Q~~ai~~i~~~~----------d~ii~apTGsGKT~~~~l~~l~~~~~~~--~~~~~   99 (401)
T PTZ00424         35 LNEDLLRGIYSYGFE---KPSAIQQRGIKPILDGY----------DTIGQAQSGTGKTATFVIAALQLIDYDL--NACQA   99 (401)
T ss_pred             CCHHHHHHHHHcCCC---CCCHHHHHHHHHHhCCC----------CEEEECCCCChHHHHHHHHHHHHhcCCC--CCceE
Confidence            444444444443332   36789999999987654          4778888999999999999998764322  23478


Q ss_pred             EEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc-ccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecc
Q psy496          106 MVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK-ELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEI  183 (319)
Q Consensus       106 l~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~-~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEa  183 (319)
                      +++.|+++||.|+.+.+...........+..+|.....++ .......+|+|+||+++.+.+..+. .++++++||+||+
T Consensus       100 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEa  179 (401)
T PTZ00424        100 LILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEA  179 (401)
T ss_pred             EEECCCHHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecH
Confidence            8888999999999887766543211000111111110000 1112346899999999999985544 4899999999999


Q ss_pred             cccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          184 HERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       184 h~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      |.. ...++.....+.+...+++.|++++|||+
T Consensus       180 h~~-~~~~~~~~~~~i~~~~~~~~~~i~~SAT~  211 (401)
T PTZ00424        180 DEM-LSRGFKGQIYDVFKKLPPDVQVALFSATM  211 (401)
T ss_pred             HHH-HhcchHHHHHHHHhhCCCCcEEEEEEecC
Confidence            972 12222223333444556788999999999

>KOG0328|consensus

Probab=99.89  E-value=1e-23  Score=184.75  Aligned_cols=232  Identities=17%  Similarity=0.218  Sum_probs=155.3

Q ss_pred             ccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEE
Q psy496           26 VPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCI  105 (319)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~v  105 (319)
                      +.+-++...++..++.   +..||++|||.++.|+|++++++          .|+|||.+|.+.+++.+....+..  .+
T Consensus        34 l~edlLrgiY~yGfek---PS~IQqrAi~~IlkGrdViaQaq----------SGTGKTa~~si~vlq~~d~~~r~t--Q~   98 (400)
T KOG0328|consen   34 LKEDLLRGIYAYGFEK---PSAIQQRAIPQILKGRDVIAQAQ----------SGTGKTATFSISVLQSLDISVRET--QA   98 (400)
T ss_pred             chHHHHHHHHHhccCC---chHHHhhhhhhhhcccceEEEec----------CCCCceEEEEeeeeeeccccccee--eE
Confidence            3444555556666654   45679999999999999888888          999999999999988876655433  56


Q ss_pred             EEecccHHHHHHHHHHHHHHhc---ccc--CCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCC-CCCccEEE
Q psy496          106 MVTQPRRISAIAIAERVAQERD---EQC--GRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPI-LSGVSHIV  179 (319)
Q Consensus       106 l~~~Ptr~la~q~~~~~~~~~~---~~~--~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~-l~~v~~vV  179 (319)
                      ++++||||||.|+.+.+..+-+   ..+  ..+|..+|..++    ......+++.+|||+++++++.... -..++++|
T Consensus        99 lilsPTRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedik----kld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlV  174 (400)
T KOG0328|consen   99 LILSPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIK----KLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLV  174 (400)
T ss_pred             EEecChHHHHHHHHHHHHHhcccccceEEEEecCCccchhhh----hhcccceEeeCCCchHHHHHHhccccccceeEEE
Confidence            6666999999999987766532   221  122333332222    1123578999999999999955544 78999999


Q ss_pred             EecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCCE-EEeCCcccc---ceeeeehhhhhhhh
Q psy496          180 MDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAPI-LHIPGFTYP---VQEYYLEDVLNMTR  253 (319)
Q Consensus       180 iDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~~-i~~~~r~~~---v~~~~~~~~~~~~~  253 (319)
                      +||+|+. +..++-....+....++|+.|++++|||+  +.....++|...|+ +.+.-...+   ++.+|....    .
T Consensus       175 LDEaDem-L~kgfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltlEgIKqf~v~ve----~  249 (400)
T KOG0328|consen  175 LDEADEM-LNKGFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVE----K  249 (400)
T ss_pred             eccHHHH-HHhhHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecCCCchhhhhhheeeec----h
Confidence            9999983 45566677777777788999999999999  44455566665554 333221122   445565432    2


Q ss_pred             hhHHHHHHHHhhhhhhhccccCCCcEEEeCCcc
Q psy496          254 KDLKLILMSATLNAEKFSQFFGGAPILHIPGFT  286 (319)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~  286 (319)
                      .+.+.-.....++-  +.   --+++|||+|++
T Consensus       250 EewKfdtLcdLYd~--Lt---ItQavIFcnTk~  277 (400)
T KOG0328|consen  250 EEWKFDTLCDLYDT--LT---ITQAVIFCNTKR  277 (400)
T ss_pred             hhhhHhHHHHHhhh--he---hheEEEEecccc
Confidence            23222222334443  11   347899999985

>KOG0339|consensus

Probab=99.89  E-value=4e-23  Score=193.17  Aligned_cols=172  Identities=21%  Similarity=0.178  Sum_probs=129.0

Q ss_pred             ccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHh-----CCCCccEEEEecccHHHHH
Q psy496           42 ECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIAR-----NRGSECCIMVTQPRRISAI  116 (319)
Q Consensus        42 ~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~-----~~~~~~~vl~~~Ptr~la~  116 (319)
                      -++++|||-+++|..++|++++..+.          ||||||.+|..|++.++...     +.++.+.|++  |||+||.
T Consensus       243 y~kptpiq~qalptalsgrdvigIAk----------tgSgktaAfi~pm~~himdq~eL~~g~gPi~vilv--PTrela~  310 (731)
T KOG0339|consen  243 YEKPTPIQCQALPTALSGRDVIGIAK----------TGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILV--PTRELAS  310 (731)
T ss_pred             cccCCcccccccccccccccchheee----------ccCcchhHHHHHHHHHhcchhhhcCCCCCeEEEEe--ccHHHHH
Confidence            35578999999999999999999999          99999999999999887432     3344444555  9999999


Q ss_pred             HHHHHHHHHhccccCCCCceEE-----EEEecccccCCCCceEEEECchHHHHHHhcC-CCCCCccEEEEecccccccch
Q psy496          117 AIAERVAQERDEQCGRPGSSVG-----YQIRLEKELPRKRGSILYCTAGILPEVMQSD-PILSGVSHIVMDEIHERSMIS  190 (319)
Q Consensus       117 q~~~~~~~~~~~~~~~~g~~vg-----~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~vViDEah~~~~~~  190 (319)
                      |++....++-...    |..+.     ...+.........+.|+|||||||+++++.+ ..+.+++++|+||+|+ ...+
T Consensus       311 Qi~~eaKkf~K~y----gl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~LV~DEadr-mfdm  385 (731)
T KOG0339|consen  311 QIFSEAKKFGKAY----GLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEADR-MFDM  385 (731)
T ss_pred             HHHHHHHHhhhhc----cceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceeeeEEEEechhh-hhcc
Confidence            9988666552221    22221     1122222333357889999999999999554 4599999999999996 3667


Q ss_pred             hHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCCE
Q psy496          191 DFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAPI  230 (319)
Q Consensus       191 ~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~~  230 (319)
                      ++...+..+....+|+.|.++||||+  ..+.+++-+-..|+
T Consensus       386 Gfe~qVrSI~~hirpdrQtllFsaTf~~kIe~lard~L~dpV  427 (731)
T KOG0339|consen  386 GFEPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDPV  427 (731)
T ss_pred             ccHHHHHHHHhhcCCcceEEEeeccchHHHHHHHHHHhcCCe
Confidence            77777777777789999999999999  67777764434444

>KOG0336|consensus

Probab=99.89  E-value=1.4e-23  Score=191.84  Aligned_cols=222  Identities=18%  Similarity=0.147  Sum_probs=149.8

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHh----CCCCccEEEEecccHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIAR----NRGSECCIMVTQPRRISAIAIA  119 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~----~~~~~~~vl~~~Ptr~la~q~~  119 (319)
                      +++|||.+|||++++|.|+++.++          ||+|||++|++|-+.++...    +..+...++++.|||+||.|+.
T Consensus       242 KPtPIqSQaWPI~LQG~DliGVAQ----------TgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalqie  311 (629)
T KOG0336|consen  242 KPTPIQSQAWPILLQGIDLIGVAQ----------TGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQIE  311 (629)
T ss_pred             CCCcchhcccceeecCcceEEEEe----------cCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHHHHHHH
Confidence            367999999999999999988888          99999999999976555332    2334567888889999999998


Q ss_pred             HHHHHHhccccCCCCceE-EEEEecccc-cCCCCceEEEECchHHHHHHhcC-CCCCCccEEEEecccccccchhHHHHH
Q psy496          120 ERVAQERDEQCGRPGSSV-GYQIRLEKE-LPRKRGSILYCTAGILPEVMQSD-PILSGVSHIVMDEIHERSMISDFLLAI  196 (319)
Q Consensus       120 ~~~~~~~~~~~~~~g~~v-g~~~~~~~~-~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~vViDEah~~~~~~~~~~~~  196 (319)
                      -...++.-....  ...+ |..-+.+.- ....+..|+++|||+|.++...+ ..|.++.++|+||||+ .++++|-..+
T Consensus       312 ~e~~kysyng~k--svc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlVlDEADr-MLDMgFEpqI  388 (629)
T KOG0336|consen  312 GEVKKYSYNGLK--SVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLVLDEADR-MLDMGFEPQI  388 (629)
T ss_pred             hHHhHhhhcCcc--eEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEEecchhh-hhcccccHHH
Confidence            777665322110  0011 111221111 11235679999999999998444 4599999999999995 5888999999


Q ss_pred             HHhhhccccCceEEEecccc--ChhhHhh-hhCCCCEEEeCCcc-----ccceeeeehhhhhhhhhhHHHHHHHHhhhhh
Q psy496          197 LKDVTDKRKDLKLILMSATL--NAEKFSQ-FFGGAPILHIPGFT-----YPVQEYYLEDVLNMTRKDLKLILMSATLNAE  268 (319)
Q Consensus       197 l~~~~~~~~~~qiv~lSAT~--~~~~l~~-~l~~~~~i~~~~r~-----~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~  268 (319)
                      .+.+...+|++|+++.|||.  .+..++. |+ ..|++...|..     ..|+..++-.    .+......+...+    
T Consensus       389 rkilldiRPDRqtvmTSATWP~~VrrLa~sY~-Kep~~v~vGsLdL~a~~sVkQ~i~v~----~d~~k~~~~~~f~----  459 (629)
T KOG0336|consen  389 RKILLDIRPDRQTVMTSATWPEGVRRLAQSYL-KEPMIVYVGSLDLVAVKSVKQNIIVT----TDSEKLEIVQFFV----  459 (629)
T ss_pred             HHHhhhcCCcceeeeecccCchHHHHHHHHhh-hCceEEEecccceeeeeeeeeeEEec----ccHHHHHHHHHHH----
Confidence            99999999999999999999  5666765 55 44554443332     3343333211    1222222221111    


Q ss_pred             hhccccCCCcEEEeCCcccc
Q psy496          269 KFSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       269 ~~~~~~~g~~LVFlp~R~~~  288 (319)
                       -+.+....+||||.....+
T Consensus       460 -~~ms~ndKvIiFv~~K~~A  478 (629)
T KOG0336|consen  460 -ANMSSNDKVIIFVSRKVMA  478 (629)
T ss_pred             -HhcCCCceEEEEEechhhh
Confidence             1223478899999876554

>KOG0337|consensus

Probab=99.88  E-value=3.4e-23  Score=189.96  Aligned_cols=223  Identities=16%  Similarity=0.111  Sum_probs=146.5

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++|||+++||.++++++++..+.          ||||||.+|.+|+++++.... ....+.+++.|||+||.|..+.+++
T Consensus        44 ptpiqRKTipliLe~~dvv~mar----------tgsgktaaf~ipm~e~Lk~~s-~~g~RalilsptreLa~qtlkvvkd  112 (529)
T KOG0337|consen   44 PTPIQRKTIPLILEGRDVVGMAR----------TGSGKTAAFLIPMIEKLKSHS-QTGLRALILSPTRELALQTLKVVKD  112 (529)
T ss_pred             CCchhcccccceeeccccceeee----------cCCcchhhHHHHHHHHHhhcc-ccccceeeccCcHHHHHHHHHHHHH
Confidence            77999999999999999999998          999999999999999987765 4456777777999999999987776


Q ss_pred             HhccccCCCCceEEEEEe-cccccCCCCceEEEECchHHHHHH-hcCCCCCCccEEEEecccccccchhHHHHHHHhhhc
Q psy496          125 ERDEQCGRPGSSVGYQIR-LEKELPRKRGSILYCTAGILPEVM-QSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTD  202 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~-~~~~~~~~~~~Iiv~Tpg~ll~~l-~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~  202 (319)
                      .-...-......+|+... ..-....++.+|+++|||+++... ..+..|+.+.+||+||+|. -..+++....-+.+..
T Consensus       113 lgrgt~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadr-lfemgfqeql~e~l~r  191 (529)
T KOG0337|consen  113 LGRGTKLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADR-LFEMGFQEQLHEILSR  191 (529)
T ss_pred             hccccchhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhhH-HHhhhhHHHHHHHHHh
Confidence            632110000112222111 111223357889999999998877 5555699999999999996 3455566666667777


Q ss_pred             cccCceEEEeccccC--hhhHhhh-hCCCCEEEeC--Ccccc-ceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccCC
Q psy496          203 KRKDLKLILMSATLN--AEKFSQF-FGGAPILHIP--GFTYP-VQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGG  276 (319)
Q Consensus       203 ~~~~~qiv~lSAT~~--~~~l~~~-l~~~~~i~~~--~r~~~-v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g  276 (319)
                      .+.+.|.++||||++  .-++++- +.++..+..+  .+..+ ++..+....    ..+....+....-+..     ..+
T Consensus       192 l~~~~QTllfSatlp~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~~----~a~K~aaLl~il~~~~-----~~~  262 (529)
T KOG0337|consen  192 LPESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRVR----KAEKEAALLSILGGRI-----KDK  262 (529)
T ss_pred             CCCcceEEEEeccCchhhHHHHHccCCCCceEEeehhhhcchhhhhheeeec----cHHHHHHHHHHHhccc-----ccc
Confidence            777889999999993  2344442 3333344433  22211 222222111    1222223333322221     145


Q ss_pred             CcEEEeCCcccc
Q psy496          277 APILHIPGFTYP  288 (319)
Q Consensus       277 ~~LVFlp~R~~~  288 (319)
                      +.+||++++.+.
T Consensus       263 ~t~vf~~tk~hv  274 (529)
T KOG0337|consen  263 QTIVFVATKHHV  274 (529)
T ss_pred             ceeEEecccchH
Confidence            899999998764

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.88  E-value=3.5e-22  Score=212.07  Aligned_cols=151  Identities=24%  Similarity=0.316  Sum_probs=108.7

Q ss_pred             EecCCCCCccchhhHHHHHHHHHhC--------CCCccEEEEecccHHHHHHHHHHHHHHhccc------c--CCCCceE
Q psy496           74 IYTSTGCGKTTQVPQFILDDEIARN--------RGSECCIMVTQPRRISAIAIAERVAQERDEQ------C--GRPGSSV  137 (319)
Q Consensus        74 i~apTGSGKT~~~~l~il~~l~~~~--------~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~------~--~~~g~~v  137 (319)
                      |+||||||||++|++|+++.+....        .....++||++|+|+|+.|+.+.+...+...      .  ...+..+
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            5789999999999999999987542        1235789999999999999999886532210      0  0013344


Q ss_pred             EEEEeccccc-------CCCCceEEEECchHHHHHHhcC--CCCCCccEEEEecccc-----cccchhHHHHHHHhhhcc
Q psy496          138 GYQIRLEKEL-------PRKRGSILYCTAGILPEVMQSD--PILSGVSHIVMDEIHE-----RSMISDFLLAILKDVTDK  203 (319)
Q Consensus       138 g~~~~~~~~~-------~~~~~~Iiv~Tpg~ll~~l~~~--~~l~~v~~vViDEah~-----~~~~~~~~~~~l~~~~~~  203 (319)
                      +  .+.++..       ..+.++|+|+||++|..++.++  ..++++++|||||+|.     ||.+....+.++..+.  
T Consensus        81 ~--vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~--  156 (1490)
T PRK09751         81 G--IRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALL--  156 (1490)
T ss_pred             E--EEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhC--
Confidence            3  3332221       1235789999999998887433  3589999999999996     4444555666666553  


Q ss_pred             ccCceEEEecccc-ChhhHhhhhCCC
Q psy496          204 RKDLKLILMSATL-NAEKFSQFFGGA  228 (319)
Q Consensus       204 ~~~~qiv~lSAT~-~~~~l~~~l~~~  228 (319)
                      +.+.|+|++|||+ |++++++|++..
T Consensus       157 ~~~~QrIgLSATI~n~eevA~~L~g~  182 (1490)
T PRK09751        157 HTSAQRIGLSATVRSASDVAAFLGGD  182 (1490)
T ss_pred             CCCCeEEEEEeeCCCHHHHHHHhcCC
Confidence            3467999999999 999999999753

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

Probab=99.87  E-value=1.1e-21  Score=186.00  Aligned_cols=228  Identities=17%  Similarity=0.128  Sum_probs=160.0

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ..|+|.-++.+=         .-+++|.++..+|+||||++..++=+..+...+    .+.+++.|..+||+|-++.+.+
T Consensus       217 LlPVQ~laVe~G---------LLeG~nllVVSaTasGKTLIgElAGi~~~l~~g----~KmlfLvPLVALANQKy~dF~~  283 (830)
T COG1202         217 LLPVQVLAVEAG---------LLEGENLLVVSATASGKTLIGELAGIPRLLSGG----KKMLFLVPLVALANQKYEDFKE  283 (830)
T ss_pred             ecchhhhhhhhc---------cccCCceEEEeccCCCcchHHHhhCcHHHHhCC----CeEEEEehhHHhhcchHHHHHH
Confidence            458887776552         235677888888999999999998887776644    2788888999999999999888


Q ss_pred             HhccccCCCCceEEEE-Eeccc----ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccc-----cccchhHHH
Q psy496          125 ERDEQCGRPGSSVGYQ-IRLEK----ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHE-----RSMISDFLL  194 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~-~~~~~----~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~-----~~~~~~~~~  194 (319)
                      .....-......||.. ++...    ......++|+|+|.+-+-.+++....+.++..|||||+|.     ||...|.+.
T Consensus       284 rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg~~lgdiGtVVIDEiHtL~deERG~RLdGLI  363 (830)
T COG1202         284 RYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTGKDLGDIGTVVIDEIHTLEDEERGPRLDGLI  363 (830)
T ss_pred             HhhcccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcCCcccccceEEeeeeeeccchhcccchhhHH
Confidence            7643311112333321 11111    1122357899999988777777778899999999999995     788888888


Q ss_pred             HHHHhhhccccCceEEEecccc-ChhhHhhhhCCCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccc
Q psy496          195 AILKDVTDKRKDLKLILMSATL-NAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQF  273 (319)
Q Consensus       195 ~~l~~~~~~~~~~qiv~lSAT~-~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  273 (319)
                      ++++.+.   |..|+|.+|||+ |++.+++.|+ ...+.-+.|+.|++-|..-.--....++.-.-+...-+..+... -
T Consensus       364 ~RLr~l~---~~AQ~i~LSATVgNp~elA~~l~-a~lV~y~~RPVplErHlvf~~~e~eK~~ii~~L~k~E~~~~ssk-g  438 (830)
T COG1202         364 GRLRYLF---PGAQFIYLSATVGNPEELAKKLG-AKLVLYDERPVPLERHLVFARNESEKWDIIARLVKREFSTESSK-G  438 (830)
T ss_pred             HHHHHhC---CCCeEEEEEeecCChHHHHHHhC-CeeEeecCCCCChhHeeeeecCchHHHHHHHHHHHHHHhhhhcc-C
Confidence            8877765   478999999999 9999999995 56677789999998776533211112222222333333332222 2


Q ss_pred             cCCCcEEEeCCcccccc
Q psy496          274 FGGAPILHIPGFTYPVQ  290 (319)
Q Consensus       274 ~~g~~LVFlp~R~~~v~  290 (319)
                      ..|+.|||.++|+-|.+
T Consensus       439 ~rGQtIVFT~SRrr~h~  455 (830)
T COG1202         439 YRGQTIVFTYSRRRCHE  455 (830)
T ss_pred             cCCceEEEecchhhHHH
Confidence            48999999999987743

>KOG0333|consensus

Probab=99.87  E-value=4.7e-22  Score=186.76  Aligned_cols=218  Identities=18%  Similarity=0.177  Sum_probs=137.6

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHh---------CCCCccEEEEecccHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIAR---------NRGSECCIMVTQPRRISA  115 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~---------~~~~~~~vl~~~Ptr~la  115 (319)
                      ++|||+.+||..++.+|          +|..|+||||||++|++|++..+..-         -.++.  .+++.|||+||
T Consensus       268 ptpIqR~aipl~lQ~rD----------~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gpy--aiilaptReLa  335 (673)
T KOG0333|consen  268 PTPIQRQAIPLGLQNRD----------PIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPY--AIILAPTRELA  335 (673)
T ss_pred             CchHHHhhccchhccCC----------eeeEEeccCCccccchhhHHHHHHcCCCcchhhhcccCce--eeeechHHHHH
Confidence            45999999998776555          55555599999999999998766332         22344  44445999999


Q ss_pred             HHHHHHHHHHhccccCCCCceEEEEEecccc--cCCCCceEEEECchHHHHHHhcC-CCCCCccEEEEecccccccchhH
Q psy496          116 IAIAERVAQERDEQCGRPGSSVGYQIRLEKE--LPRKRGSILYCTAGILPEVMQSD-PILSGVSHIVMDEIHERSMISDF  192 (319)
Q Consensus       116 ~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~--~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~vViDEah~~~~~~~~  192 (319)
                      +|+...-.++........-..+|.. ..+..  ..+..|+|+++|||+|++.+.+. ..+++..+||+||||+ .+++++
T Consensus       336 qqIeeEt~kf~~~lg~r~vsvigg~-s~EEq~fqls~gceiviatPgrLid~Lenr~lvl~qctyvvldeadr-miDmgf  413 (673)
T KOG0333|consen  336 QQIEEETNKFGKPLGIRTVSVIGGL-SFEEQGFQLSMGCEIVIATPGRLIDSLENRYLVLNQCTYVVLDEADR-MIDMGF  413 (673)
T ss_pred             HHHHHHHHHhcccccceEEEEeccc-chhhhhhhhhccceeeecCchHHHHHHHHHHHHhccCceEeccchhh-hhcccc
Confidence            9998765544222110001222222 22222  22357899999999999999544 4489999999999996 366666


Q ss_pred             HHHHHHhhhcccc-------------------------CceEEEecccc--ChhhHhh-hhCCCCEEEeC--Ccccc-ce
Q psy496          193 LLAILKDVTDKRK-------------------------DLKLILMSATL--NAEKFSQ-FFGGAPILHIP--GFTYP-VQ  241 (319)
Q Consensus       193 ~~~~l~~~~~~~~-------------------------~~qiv~lSAT~--~~~~l~~-~l~~~~~i~~~--~r~~~-v~  241 (319)
                      -..+.+.+...+.                         -.|.++||||+  -++.+++ ||.++.++++.  +++.| ++
T Consensus       414 E~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~pv~vtig~~gk~~~rve  493 (673)
T KOG0333|consen  414 EPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVTIGSAGKPTPRVE  493 (673)
T ss_pred             cHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCCeEEEeccCCCCccchh
Confidence            6666655543221                         17899999999  4566665 78777666665  45544 22


Q ss_pred             e--eeehhhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCcccc
Q psy496          242 E--YYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       242 ~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~  288 (319)
                      .  ++...     +...+. +...      +.+....+++||+++...+
T Consensus       494 Q~v~m~~e-----d~k~kk-L~ei------l~~~~~ppiIIFvN~kk~~  530 (673)
T KOG0333|consen  494 QKVEMVSE-----DEKRKK-LIEI------LESNFDPPIIIFVNTKKGA  530 (673)
T ss_pred             eEEEEecc-----hHHHHH-HHHH------HHhCCCCCEEEEEechhhH
Confidence            2  22222     222222 2111      1122367899999998655

>KOG0350|consensus

Probab=99.86  E-value=1.2e-21  Score=183.21  Aligned_cols=134  Identities=19%  Similarity=0.133  Sum_probs=97.4

Q ss_pred             ccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           46 MVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        46 ~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      .|+|...+|-++.--.-. ---..+++.|.||||||||++|.+||.+.+..+. -...+.+++.|||+|+.|++..+.++
T Consensus       161 FPVQ~aVlp~ll~~~~~p-~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~-v~~LRavVivPtr~L~~QV~~~f~~~  238 (620)
T KOG0350|consen  161 FPVQYAVLPSLLEEIRSP-PPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRP-VKRLRAVVIVPTRELALQVYDTFKRL  238 (620)
T ss_pred             cchHHHHHHHHHHhhcCC-CCCCCCceEEecCCCCCceeeehhHHHHHHccCC-ccceEEEEEeeHHHHHHHHHHHHHHh
Confidence            489999999886522211 1113578999999999999999999999876543 22467777779999999999999888


Q ss_pred             hccccCCCCceEEEEEe-----cccc-cCC----CCceEEEECchHHHHHHhcCC--CCCCccEEEEecccc
Q psy496          126 RDEQCGRPGSSVGYQIR-----LEKE-LPR----KRGSILYCTAGILPEVMQSDP--ILSGVSHIVMDEIHE  185 (319)
Q Consensus       126 ~~~~~~~~g~~vg~~~~-----~~~~-~~~----~~~~Iiv~Tpg~ll~~l~~~~--~l~~v~~vViDEah~  185 (319)
                      ....    |..|+....     .+.. ...    .+.+|+|+|||||++|+.+.+  .|++++++||||||+
T Consensus       239 ~~~t----gL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEADR  306 (620)
T KOG0350|consen  239 NSGT----GLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEADR  306 (620)
T ss_pred             ccCC----ceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccCCCCcchhhceEEEechHHH
Confidence            6544    444442211     1111 011    245899999999999997544  499999999999997

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

Probab=99.85  E-value=2.4e-20  Score=191.59  Aligned_cols=167  Identities=23%  Similarity=0.294  Sum_probs=121.2

Q ss_pred             hHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCC
Q psy496           55 AIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPG  134 (319)
Q Consensus        55 ~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g  134 (319)
                      .+.++.+.+....++++|+|++|||||||++|++||++.+.....   .+.|++.||++||++..++++++.....    
T Consensus        71 lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~---a~AL~lYPtnALa~DQ~~rl~~~~~~~~----  143 (851)
T COG1205          71 LYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPS---ARALLLYPTNALANDQAERLRELISDLP----  143 (851)
T ss_pred             ccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcC---ccEEEEechhhhHhhHHHHHHHHHHhCC----
Confidence            567777777777788999999999999999999999999987664   3555555999999999999999866543    


Q ss_pred             ceEEEEEecccccC-------CCCceEEEECchHHHHHH-hcCC----CCCCccEEEEecccc-cccchhHHHHHHHhh-
Q psy496          135 SSVGYQIRLEKELP-------RKRGSILYCTAGILPEVM-QSDP----ILSGVSHIVMDEIHE-RSMISDFLLAILKDV-  200 (319)
Q Consensus       135 ~~vg~~~~~~~~~~-------~~~~~Iiv~Tpg~ll~~l-~~~~----~l~~v~~vViDEah~-~~~~~~~~~~~l~~~-  200 (319)
                      ..++...-.++...       .+.++|++++|++|..++ ....    .++++++||+||+|. +|.+..-+..+++++ 
T Consensus       144 ~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrGv~GS~vA~llRRL~  223 (851)
T COG1205         144 GKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRLL  223 (851)
T ss_pred             CcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccccchhHHHHHHHHHH
Confidence            23443333222221       245789999999998855 3322    278899999999997 555555444444444 


Q ss_pred             --hc-cccCceEEEecccc-ChhhHhh-hhCCC
Q psy496          201 --TD-KRKDLKLILMSATL-NAEKFSQ-FFGGA  228 (319)
Q Consensus       201 --~~-~~~~~qiv~lSAT~-~~~~l~~-~l~~~  228 (319)
                        .. .+.+.|+|+.|||+ |+..+++ +++..
T Consensus       224 ~~~~~~~~~~q~i~~SAT~~np~e~~~~l~~~~  256 (851)
T COG1205         224 RRLRRYGSPLQIICTSATLANPGEFAEELFGRD  256 (851)
T ss_pred             HHHhccCCCceEEEEeccccChHHHHHHhcCCc
Confidence              33 34478999999999 7777665 44433

>KOG0334|consensus

Probab=99.85  E-value=8.9e-22  Score=197.85  Aligned_cols=242  Identities=17%  Similarity=0.144  Sum_probs=151.9

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC---CCCccEEEEecccHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN---RGSECCIMVTQPRRISAIAIAE  120 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~---~~~~~~vl~~~Ptr~la~q~~~  120 (319)
                      ++++||.+|||++.+|+++|..+.          ||||||.+|.+|++.++..+.   .+..+..++++|||+||.|+.+
T Consensus       387 k~~~IQ~qAiP~ImsGrdvIgvak----------TgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela~QI~r  456 (997)
T KOG0334|consen  387 KPTPIQAQAIPAIMSGRDVIGVAK----------TGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAMQIHR  456 (997)
T ss_pred             CCcchhhhhcchhccCcceEEeec----------cCCccchhhhcchhhhhhcCCChhhCCCceEEEEcCCHHHHHHHHH
Confidence            467999999999999999888887          999999999999997764321   1223455555699999999999


Q ss_pred             HHHHHhccccCCCCceEEEE---Ee--cccccCCCCceEEEECchHHHHHH-hcCCC---CCCccEEEEecccccccchh
Q psy496          121 RVAQERDEQCGRPGSSVGYQ---IR--LEKELPRKRGSILYCTAGILPEVM-QSDPI---LSGVSHIVMDEIHERSMISD  191 (319)
Q Consensus       121 ~~~~~~~~~~~~~g~~vg~~---~~--~~~~~~~~~~~Iiv~Tpg~ll~~l-~~~~~---l~~v~~vViDEah~~~~~~~  191 (319)
                      .+.++... +   |..+-..   ..  ..-......+.|+|+|||++++.+ .+...   +..+.++|+||||++ ..+.
T Consensus       457 ~~~kf~k~-l---~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~deaDrm-fdmg  531 (997)
T KOG0334|consen  457 EVRKFLKL-L---GIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEADRM-FDMG  531 (997)
T ss_pred             HHHHHHhh-c---CceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccccceeeechhhhh-heec
Confidence            88877543 2   2222111   11  111111234779999999999999 44433   455559999999973 4666


Q ss_pred             HHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCCE-EEeCCccc---cceeeeehhhhhhhhhhHHHHHHHHhh
Q psy496          192 FLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAPI-LHIPGFTY---PVQEYYLEDVLNMTRKDLKLILMSATL  265 (319)
Q Consensus       192 ~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~~-i~~~~r~~---~v~~~~~~~~~~~~~~~~~~~~~~~~~  265 (319)
                      +.....+.+...+|+.|++++|||+  ..+.+++-....|+ +.+.++..   .|...+.-.  ...+.+......-...
T Consensus       532 fePq~~~Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V~--~~e~eKf~kL~eLl~e  609 (997)
T KOG0334|consen  532 FEPQITRILQNLRPDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRVC--AIENEKFLKLLELLGE  609 (997)
T ss_pred             cCcccchHHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccceeEeccceEEEEEe--cCchHHHHHHHHHHHH
Confidence            7777777777788999999999999  45666665444555 44444432   122111111  1012222222211111


Q ss_pred             hhhhhccccCCCcEEEeCCccccccccchHhHHHHhHhhccccC
Q psy496          266 NAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRTLKRSET  309 (319)
Q Consensus       266 ~~~~~~~~~~g~~LVFlp~R~~~v~~~~~~~~~~~~~~~~~~~~  309 (319)
                      ..      ..+++||||.....+ ...+-+=+.....|+-+-|-
T Consensus       610 ~~------e~~~tiiFv~~qe~~-d~l~~~L~~ag~~~~slHGg  646 (997)
T KOG0334|consen  610 RY------EDGKTIIFVDKQEKA-DALLRDLQKAGYNCDSLHGG  646 (997)
T ss_pred             Hh------hcCCEEEEEcCchHH-HHHHHHHHhcCcchhhhcCC
Confidence            11      278999999988765 33333333333444333333

>KOG0347|consensus

Probab=99.85  E-value=1.2e-21  Score=184.88  Aligned_cols=177  Identities=21%  Similarity=0.218  Sum_probs=116.9

Q ss_pred             ccccccchHHHhccCCccccccccccchhhHHHH-HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHh-------
Q psy496           26 VPQFILDDEIARNRGSECCIMVTQPRRISAIALI-NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIAR-------   97 (319)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~-~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~-------   97 (319)
                      +|..++...-+.+|..   +|+||..+||++..| .|+++.+.          ||||||+||.+|+++.+...       
T Consensus       188 lp~~iL~aL~~~gFs~---Pt~IQsl~lp~ai~gk~DIlGaAe----------TGSGKTLAFGIPiv~~l~~~s~~s~e~  254 (731)
T KOG0347|consen  188 LPMEILRALSNLGFSR---PTEIQSLVLPAAIRGKVDILGAAE----------TGSGKTLAFGIPIVERLLESSDDSQEL  254 (731)
T ss_pred             CCHHHHHHHHhcCCCC---CccchhhcccHhhccchhcccccc----------cCCCceeeecchhhhhhhhccchHhhh
Confidence            3333444333444433   678999999999988 89999888          99999999999999854322       


Q ss_pred             ----CCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEE-EEecccccCCCCceEEEECchHHHHHHhcCC--
Q psy496           98 ----NRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGY-QIRLEKELPRKRGSILYCTAGILPEVMQSDP--  170 (319)
Q Consensus        98 ----~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~-~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~--  170 (319)
                          .++++...|++.||||||.|+.+-+.......-......+|. .+.-.....+.+++|+|+|||||..++..+.  
T Consensus       255 ~~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~  334 (731)
T KOG0347|consen  255 SNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTH  334 (731)
T ss_pred             hhHHhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhh
Confidence                233443467777999999999887765533220000112221 1111122233478899999999999995443  


Q ss_pred             --CCCCccEEEEecccccccchhHH---HHHHHhhh--ccccCceEEEecccc
Q psy496          171 --ILSGVSHIVMDEIHERSMISDFL---LAILKDVT--DKRKDLKLILMSATL  216 (319)
Q Consensus       171 --~l~~v~~vViDEah~~~~~~~~~---~~~l~~~~--~~~~~~qiv~lSAT~  216 (319)
                        .+++++++|+||+|+ .+..+.+   ..+++.+.  ...+..|.+.||||+
T Consensus       335 l~~~k~vkcLVlDEaDR-mvekghF~Els~lL~~L~e~~~~~qrQTlVFSATl  386 (731)
T KOG0347|consen  335 LGNFKKVKCLVLDEADR-MVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATL  386 (731)
T ss_pred             hhhhhhceEEEEccHHH-HhhhccHHHHHHHHHHhhhhhcccccceEEEEEEe
Confidence              388999999999996 2333333   33334333  134567999999999

>KOG0951|consensus

Probab=99.85  E-value=6.3e-21  Score=193.14  Aligned_cols=233  Identities=15%  Similarity=0.111  Sum_probs=162.2

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCC------CCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEE
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNR------GSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQI  141 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~------~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~  141 (319)
                      ..+|+++|||||+|||..+++-+++.+..+.+      -...+|+|+.|+++|++.....+.+.+...    |..|+-..
T Consensus       324 ~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~VgsfSkRla~~----GI~V~ElT  399 (1674)
T KOG0951|consen  324 GDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSFSKRLAPL----GITVLELT  399 (1674)
T ss_pred             CcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHHHhhcccc----CcEEEEec
Confidence            45789999999999999999999998865432      124589999999999999988787765433    55565322


Q ss_pred             eccc--ccCCCCceEEEECchHHHHHHhcC---CCCCCccEEEEecccc----cccchhHHHHHHHhhh-ccccCceEEE
Q psy496          142 RLEK--ELPRKRGSILYCTAGILPEVMQSD---PILSGVSHIVMDEIHE----RSMISDFLLAILKDVT-DKRKDLKLIL  211 (319)
Q Consensus       142 ~~~~--~~~~~~~~Iiv~Tpg~ll~~l~~~---~~l~~v~~vViDEah~----~~~~~~~~~~~l~~~~-~~~~~~qiv~  211 (319)
                      +...  ...-+.++++|+||+.---.-+++   ...+-++++||||.|.    ||.-.+....+...-. ......|+++
T Consensus       400 gD~~l~~~qieeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLLhDdRGpvLESIVaRt~r~ses~~e~~RlVG  479 (1674)
T KOG0951|consen  400 GDSQLGKEQIEETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLLHDDRGPVLESIVARTFRRSESTEEGSRLVG  479 (1674)
T ss_pred             ccccchhhhhhcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhcccccchHHHHHHHHHHHHhhhcccCceeee
Confidence            2111  122257889999997542222221   2356799999999986    6655554444433322 2334679999


Q ss_pred             ecccc-ChhhHhhhhCCCC--EEEe--CCccccceeeeehhhhhhhhhhHHHH-HHHHhhhhhhhccccCCCcEEEeCCc
Q psy496          212 MSATL-NAEKFSQFFGGAP--ILHI--PGFTYPVQEYYLEDVLNMTRKDLKLI-LMSATLNAEKFSQFFGGAPILHIPGF  285 (319)
Q Consensus       212 lSAT~-~~~~l~~~l~~~~--~i~~--~~r~~~v~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~g~~LVFlp~R  285 (319)
                      +|||+ |.++.+.|+...+  ++..  ..|+.|++..|+.-.  ..++..+.. +....+++.... ...+++||||++|
T Consensus       480 LSATLPNy~DV~~Fl~v~~~glf~fd~syRpvPL~qq~Igi~--ek~~~~~~qamNe~~yeKVm~~-agk~qVLVFVHsR  556 (1674)
T KOG0951|consen  480 LSATLPNYEDVASFLRVDPEGLFYFDSSYRPVPLKQQYIGIT--EKKPLKRFQAMNEACYEKVLEH-AGKNQVLVFVHSR  556 (1674)
T ss_pred             ecccCCchhhhHHHhccCcccccccCcccCcCCccceEeccc--cCCchHHHHHHHHHHHHHHHHh-CCCCcEEEEEEec
Confidence            99999 9999999987544  4444  567778877777543  223444433 345667664433 3478999999999


Q ss_pred             cccccc-cchHhHHHHhHhhccc
Q psy496          286 TYPVQE-YYLEDVLNMTRTLKRS  307 (319)
Q Consensus       286 ~~~v~~-~~~~~~~~~~~~~~~~  307 (319)
                      .++.++ ..+-|-+.-.++|.++
T Consensus       557 kET~ktA~aIRd~~le~dtls~f  579 (1674)
T KOG0951|consen  557 KETAKTARAIRDKALEEDTLSRF  579 (1674)
T ss_pred             hHHHHHHHHHHHHHhhhhHHHHH
Confidence            999898 5588888888888765

>KOG0327|consensus

Probab=99.84  E-value=1.5e-21  Score=177.81  Aligned_cols=190  Identities=19%  Similarity=0.226  Sum_probs=134.0

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      .+++-++...++-.|+.   ++.||++||+++..|.|+..+++          +|+|||.+|..++++.+....+..++.
T Consensus        32 ~L~e~LLrgiy~yGFek---PSaIQqraI~p~i~G~dv~~qaq----------sgTgKt~af~i~iLq~iD~~~ke~qal   98 (397)
T KOG0327|consen   32 NLKESLLRGIYAYGFEK---PSAIQQRAILPCIKGHDVIAQAQ----------SGTGKTAAFLISILQQIDMSVKETQAL   98 (397)
T ss_pred             CCCHHHHhHHHhhccCC---chHHHhccccccccCCceeEeee----------ccccchhhhHHHHHhhcCcchHHHHHH
Confidence            56777777777777765   45679999988888766555555          999999999999999886655544445


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEe--cccccCCCCceEEEECchHHHHHHhcCCC-CCCccEEEEe
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIR--LEKELPRKRGSILYCTAGILPEVMQSDPI-LSGVSHIVMD  181 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~--~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~-l~~v~~vViD  181 (319)
                      ++.  |+|+||.|+.+....+....-......+|....  ..........+|+++|||++.+.+..... ...++++|+|
T Consensus        99 ila--PtreLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlD  176 (397)
T KOG0327|consen   99 ILA--PTRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLD  176 (397)
T ss_pred             Hhc--chHHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccccccceeEEeec
Confidence            555  999999999965555432211111223332222  11223334578999999999999955544 6679999999


Q ss_pred             cccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCCE
Q psy496          182 EIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAPI  230 (319)
Q Consensus       182 Eah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~~  230 (319)
                      |+|++ +..++...+-..+...+++.|++++|||+  +...+.+-|...|+
T Consensus       177 EaDEm-Ls~gfkdqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv  226 (397)
T KOG0327|consen  177 EADEM-LSRGFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPV  226 (397)
T ss_pred             chHhh-hccchHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCce
Confidence            99984 45556666666666788899999999999  56677776665554

>KOG4284|consensus

Probab=99.84  E-value=2e-21  Score=186.19  Aligned_cols=188  Identities=18%  Similarity=0.205  Sum_probs=132.2

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +++||.+|||++..+-|++.++.          .|+|||++|....++.+..+...++  ++++.||||+|.|+...+.+
T Consensus        48 ptkiQaaAIP~~~~kmDliVQaK----------SGTGKTlVfsv~av~sl~~~~~~~q--~~Iv~PTREiaVQI~~tv~~  115 (980)
T KOG4284|consen   48 PTKIQAAAIPAIFSKMDLIVQAK----------SGTGKTLVFSVLAVESLDSRSSHIQ--KVIVTPTREIAVQIKETVRK  115 (980)
T ss_pred             CCchhhhhhhhhhcccceEEEec----------CCCCceEEEEeeeehhcCcccCcce--eEEEecchhhhhHHHHHHHH
Confidence            57899999999998888665555          9999999999999888876555444  44445999999999988877


Q ss_pred             Hhcccc-CCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHHHHHhh-h
Q psy496          125 ERDEQC-GRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLAILKDV-T  201 (319)
Q Consensus       125 ~~~~~~-~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~l~~~-~  201 (319)
                      .....- ..+...+|..-...+....+.++|+|+||||+..+...+. +.++++++|+||||.. +..+.+...+..+ .
T Consensus       116 v~~sf~g~~csvfIGGT~~~~d~~rlk~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL-~~t~sfq~~In~ii~  194 (980)
T KOG4284|consen  116 VAPSFTGARCSVFIGGTAHKLDLIRLKQTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKL-MDTESFQDDINIIIN  194 (980)
T ss_pred             hcccccCcceEEEecCchhhhhhhhhhhceEEecCchHHHHHHHhcCCCccceeEEEeccHHhh-hchhhHHHHHHHHHH
Confidence            633211 0002223322222233334578899999999999995554 5899999999999973 4545555555544 4


Q ss_pred             ccccCceEEEecccc--Ch-hhHhhhhCCCCEEEeCCcc---ccceeeee
Q psy496          202 DKRKDLKLILMSATL--NA-EKFSQFFGGAPILHIPGFT---YPVQEYYL  245 (319)
Q Consensus       202 ~~~~~~qiv~lSAT~--~~-~~l~~~l~~~~~i~~~~r~---~~v~~~~~  245 (319)
                      .++...|++.+|||.  |. +.+++|+.++-++....+-   +.++.+|.
T Consensus       195 slP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~  244 (980)
T KOG4284|consen  195 SLPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVV  244 (980)
T ss_pred             hcchhheeeEEeccCchhHHHHHHHHhcccceeecccCCceeechhheee
Confidence            577788999999999  44 3677788777676665442   44555443

>cd00268 DEADc DEAD-box helicases

Probab=99.84  E-value=2e-20  Score=162.56  Aligned_cols=157  Identities=23%  Similarity=0.163  Sum_probs=109.0

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +.+.|.++++.+..          +++++++||||+|||.++.+|+++.+.........+++++.|+++|+.|..+.+..
T Consensus        22 ~~~~Q~~~~~~~~~----------~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~q~~~~~~~   91 (203)
T cd00268          22 PTPIQARAIPPLLS----------GRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVARK   91 (203)
T ss_pred             CCHHHHHHHHHHhc----------CCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHHHHHHHHHH
Confidence            45678888877664          56789999999999999999999988775222345788888999999999988877


Q ss_pred             HhccccCCCCceEEEEEec----cc-ccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHHHHH
Q psy496          125 ERDEQCGRPGSSVGYQIRL----EK-ELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLAILK  198 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~----~~-~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~l~  198 (319)
                      .....    +..+......    .. .....+++|+|+||+.+.+.+.+.. .+.+++++|+||+|... ..++......
T Consensus        92 ~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~-~~~~~~~~~~  166 (203)
T cd00268          92 LGKHT----NLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRML-DMGFEDQIRE  166 (203)
T ss_pred             HhccC----CceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChHHhh-ccChHHHHHH
Confidence            64321    2232211110    00 1111357899999999999885543 48899999999999732 2222222222


Q ss_pred             hhhccccCceEEEecccc
Q psy496          199 DVTDKRKDLKLILMSATL  216 (319)
Q Consensus       199 ~~~~~~~~~qiv~lSAT~  216 (319)
                      .+...+++.+++++|||+
T Consensus       167 ~~~~l~~~~~~~~~SAT~  184 (203)
T cd00268         167 ILKLLPKDRQTLLFSATM  184 (203)
T ss_pred             HHHhCCcccEEEEEeccC
Confidence            333344578999999999

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.

>KOG0332|consensus

Probab=99.83  E-value=1.9e-20  Score=169.76  Aligned_cols=236  Identities=17%  Similarity=0.135  Sum_probs=158.0

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHH--HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCc
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALI--NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSE  102 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~--~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~  102 (319)
                      .+...++...++..|..   ++.||+.|+|.++..  ++++++++          .|+|||+||.+.+|.++......++
T Consensus        96 ~LkPellkgly~M~F~k---PskIQe~aLPlll~~Pp~nlIaQsq----------sGtGKTaaFvL~MLsrvd~~~~~PQ  162 (477)
T KOG0332|consen   96 RLKPELLKGLYAMKFQK---PSKIQETALPLLLAEPPQNLIAQSQ----------SGTGKTAAFVLTMLSRVDPDVVVPQ  162 (477)
T ss_pred             CCCHHHHhHHHHhccCC---cchHHHhhcchhhcCCchhhhhhhc----------CCCchhHHHHHHHHHhcCccccCCC
Confidence            34444555566666655   445699999998752  55555555          9999999999999999877665555


Q ss_pred             cEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCC--CCceEEEECchHHHHHHhc--CCCCCCccEE
Q psy496          103 CCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPR--KRGSILYCTAGILPEVMQS--DPILSGVSHI  178 (319)
Q Consensus       103 ~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~--~~~~Iiv~Tpg~ll~~l~~--~~~l~~v~~v  178 (319)
                      +.  |+.|+|+||.|+.+.+.+ +|...   +....|.++.......  -..+|+++|||.+++++..  -.++..++++
T Consensus       163 ~i--CLaPtrELA~Q~~eVv~e-MGKf~---~ita~yair~sk~~rG~~i~eqIviGTPGtv~Dlm~klk~id~~kikvf  236 (477)
T KOG0332|consen  163 CI--CLAPTRELAPQTGEVVEE-MGKFT---ELTASYAIRGSKAKRGNKLTEQIVIGTPGTVLDLMLKLKCIDLEKIKVF  236 (477)
T ss_pred             ce--eeCchHHHHHHHHHHHHH-hcCce---eeeEEEEecCcccccCCcchhheeeCCCccHHHHHHHHHhhChhhceEE
Confidence            54  446999999999986655 44443   5566677775532221  2357999999999999954  3458999999


Q ss_pred             EEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhh-hhCCCCEEEeCCc---cccceeeeehhhhhhh
Q psy496          179 VMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQ-FFGGAPILHIPGF---TYPVQEYYLEDVLNMT  252 (319)
Q Consensus       179 ViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~-~l~~~~~i~~~~r---~~~v~~~~~~~~~~~~  252 (319)
                      |+||||.+-...++.-..++.....+++.|+++||||.  .+..++. .+.++..+.+..+   ..++..+|+....+  
T Consensus       237 VlDEAD~Mi~tqG~~D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C~~~--  314 (477)
T KOG0332|consen  237 VLDEADVMIDTQGFQDQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIVPNANVIILKREELALDNIKQLYVLCACR--  314 (477)
T ss_pred             EecchhhhhhcccccccchhhhhhcCCcceEEeeechhHHHHHHHHHHhcCCCceeeeehhhccccchhhheeeccch--
Confidence            99999963222223334444445566789999999999  4556665 4455555555433   36777778766522  


Q ss_pred             hhhHHHHHHHHhhhhhhhccccCCCcEEEeCCcccc
Q psy496          253 RKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       253 ~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~  288 (319)
                       .+...++.. .+...     .-|+.+|||.|+.-+
T Consensus       315 -~~K~~~l~~-lyg~~-----tigqsiIFc~tk~ta  343 (477)
T KOG0332|consen  315 -DDKYQALVN-LYGLL-----TIGQSIIFCHTKATA  343 (477)
T ss_pred             -hhHHHHHHH-HHhhh-----hhhheEEEEeehhhH
Confidence             222222222 33321     157899999999765

>KOG0341|consensus

Probab=99.83  E-value=4.3e-21  Score=174.67  Aligned_cols=222  Identities=16%  Similarity=0.112  Sum_probs=139.5

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHH--------HhCCCCccEEEEecccHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEI--------ARNRGSECCIMVTQPRRISAI  116 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~--------~~~~~~~~~vl~~~Ptr~la~  116 (319)
                      ++|||-+.+|.+++|+|.++.+-          ||||||+.|.+|++--..        ..+.++.+.|+|  |+||||.
T Consensus       193 PTpIQvQGlPvvLsGRDmIGIAf----------TGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiic--PSRELAr  260 (610)
T KOG0341|consen  193 PTPIQVQGLPVVLSGRDMIGIAF----------TGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIIC--PSRELAR  260 (610)
T ss_pred             CCceeecCcceEeecCceeeEEe----------ecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEc--CcHHHHH
Confidence            57999999999999999999888          999999999999864332        234567777887  9999999


Q ss_pred             HHHHHHHHHhcccc------CCCCceEE-EEEecccccCCCCceEEEECchHHHHHHhcC-CCCCCccEEEEeccccccc
Q psy496          117 AIAERVAQERDEQC------GRPGSSVG-YQIRLEKELPRKRGSILYCTAGILPEVMQSD-PILSGVSHIVMDEIHERSM  188 (319)
Q Consensus       117 q~~~~~~~~~~~~~------~~~g~~vg-~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~vViDEah~~~~  188 (319)
                      |.+.-+..+.....      ...+..+| ..++..-.......+|+|+|||+|.+++..+ ..|.-.+++.+||||+ .+
T Consensus       261 Qt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~KK~~sLd~CRyL~lDEADR-mi  339 (610)
T KOG0341|consen  261 QTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAKKIMSLDACRYLTLDEADR-MI  339 (610)
T ss_pred             HHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHHhhccHHHHHHhhhhhHHH-Hh
Confidence            99876655432111      00122232 1122222222356799999999999999554 4588899999999996 35


Q ss_pred             chhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhh
Q psy496          189 ISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLN  266 (319)
Q Consensus       189 ~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~  266 (319)
                      +++|-..+...+......+|.++||||+  ..+.|++---..|+..--||--.-....+... +     +-..-.+.++-
T Consensus       340 DmGFEddir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVGRAGAAsldViQev-E-----yVkqEaKiVyl  413 (610)
T KOG0341|consen  340 DMGFEDDIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSALVKPVTVNVGRAGAASLDVIQEV-E-----YVKQEAKIVYL  413 (610)
T ss_pred             hccchhhHHHHHHHHhhhhheeeeeccccHHHHHHHHhhcccceEEecccccccchhHHHHH-H-----HHHhhhhhhhH
Confidence            6665555544444444577999999999  33444442212233222233222222222111 1     11112234455


Q ss_pred             hhhhccccCCCcEEEeCCcc
Q psy496          267 AEKFSQFFGGAPILHIPGFT  286 (319)
Q Consensus       267 ~~~~~~~~~g~~LVFlp~R~  286 (319)
                      .+|+.+. .-++|||+.-..
T Consensus       414 LeCLQKT-~PpVLIFaEkK~  432 (610)
T KOG0341|consen  414 LECLQKT-SPPVLIFAEKKA  432 (610)
T ss_pred             HHHhccC-CCceEEEecccc
Confidence            5566654 668999987653

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

Probab=99.83  E-value=3.1e-20  Score=156.15  Aligned_cols=154  Identities=26%  Similarity=0.250  Sum_probs=106.2

Q ss_pred             ccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           46 MVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        46 ~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      ||.|.++++.+..          ++++++.||||||||+++.+++++.+....   ..+++++.|+++|+.|..+++...
T Consensus         1 t~~Q~~~~~~i~~----------~~~~li~aptGsGKT~~~~~~~l~~~~~~~---~~~~lii~P~~~l~~q~~~~~~~~   67 (169)
T PF00270_consen    1 TPLQQEAIEAIIS----------GKNVLISAPTGSGKTLAYILPALNRLQEGK---DARVLIIVPTRALAEQQFERLRKF   67 (169)
T ss_dssp             -HHHHHHHHHHHT----------TSEEEEECSTTSSHHHHHHHHHHHHHHTTS---SSEEEEEESSHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHc----------CCCEEEECCCCCccHHHHHHHHHhhhccCC---CceEEEEeeccccccccccccccc
Confidence            3568888877653          366899999999999999999998876642   237777789999999999999888


Q ss_pred             hccccCCCCceEEEEEeccc------ccCCCCceEEEECchHHHHHHhcC-CCCCCccEEEEecccccccc--hhHHHHH
Q psy496          126 RDEQCGRPGSSVGYQIRLEK------ELPRKRGSILYCTAGILPEVMQSD-PILSGVSHIVMDEIHERSMI--SDFLLAI  196 (319)
Q Consensus       126 ~~~~~~~~g~~vg~~~~~~~------~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~vViDEah~~~~~--~~~~~~~  196 (319)
                      +...    +..+........      .....+++|+|+||+++.+.+... ..+.++++||+||+|..+..  ...+..+
T Consensus        68 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~~~~~~~~~i  143 (169)
T PF00270_consen   68 FSNT----NVRVVLLHGGQSISEDQREVLSNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDETFRAMLKSI  143 (169)
T ss_dssp             TTTT----TSSEEEESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHTTHHHHHHHH
T ss_pred             cccc----ccccccccccccccccccccccccccccccCcchhhccccccccccccceeeccCcccccccccHHHHHHHH
Confidence            6642    222221111110      001135789999999999999653 35667999999999984331  2233333


Q ss_pred             HHhhhccccCceEEEeccccC
Q psy496          197 LKDVTDKRKDLKLILMSATLN  217 (319)
Q Consensus       197 l~~~~~~~~~~qiv~lSAT~~  217 (319)
                      ++.+.. .++.+++++|||++
T Consensus       144 ~~~~~~-~~~~~~i~~SAT~~  163 (169)
T PF00270_consen  144 LRRLKR-FKNIQIILLSATLP  163 (169)
T ss_dssp             HHHSHT-TTTSEEEEEESSST
T ss_pred             HHHhcC-CCCCcEEEEeeCCC
Confidence            343332 23578999999995

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 ....

>KOG0329|consensus

Probab=99.82  E-value=4.8e-20  Score=159.79  Aligned_cols=207  Identities=19%  Similarity=0.213  Sum_probs=142.2

Q ss_pred             ccccccccccchHHHhc-----cCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHH
Q psy496           22 KTTQVPQFILDDEIARN-----RGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIA   96 (319)
Q Consensus        22 ~~~~~~~~~~~~~~~~~-----~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~   96 (319)
                      +|+++.+|++.-..-++     |.-   +.-+|..+||....|.+++.++.          +|-|||..|.+..++++..
T Consensus        40 hssgfrdfllkpellraivdcgfeh---psevqhecipqailgmdvlcqak----------sgmgktavfvl~tlqqiep  106 (387)
T KOG0329|consen   40 HSSGFRDFLLKPELLRAIVDCGFEH---PSEVQHECIPQAILGMDVLCQAK----------SGMGKTAVFVLATLQQIEP  106 (387)
T ss_pred             eccchhhhhcCHHHHHHHHhccCCC---chHhhhhhhhHHhhcchhheecc----------cCCCceeeeehhhhhhcCC
Confidence            34566666654443332     222   23679999999999999888888          9999999999999998876


Q ss_pred             hCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEE-----EEEecccccCCCCceEEEECchHHHHHHhcCC-
Q psy496           97 RNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVG-----YQIRLEKELPRKRGSILYCTAGILPEVMQSDP-  170 (319)
Q Consensus        97 ~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg-----~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~-  170 (319)
                      ..  ++..+++++.|||||.|+.+.+..+.....   +..+.     ..+..+.....+.++|+|+|||+++.+.+++. 
T Consensus       107 v~--g~vsvlvmchtrelafqi~~ey~rfskymP---~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l  181 (387)
T KOG0329|consen  107 VD--GQVSVLVMCHTRELAFQISKEYERFSKYMP---SVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSL  181 (387)
T ss_pred             CC--CeEEEEEEeccHHHHHHHHHHHHHHHhhCC---CceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccC
Confidence            44  356777778999999999776555433222   22221     12222222222357899999999999996655 


Q ss_pred             CCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCC-EEEeCCc----cccceee
Q psy496          171 ILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAP-ILHIPGF----TYPVQEY  243 (319)
Q Consensus       171 ~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~-~i~~~~r----~~~v~~~  243 (319)
                      .|++++++|+||+|.+--..|+....-+.....+++.|++++|||+  +.+-+++.|...| .+.++..    .+.++.+
T Consensus       182 ~lk~vkhFvlDEcdkmle~lDMrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~  261 (387)
T KOG0329|consen  182 NLKNVKHFVLDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQY  261 (387)
T ss_pred             chhhcceeehhhHHHHHHHHHHHHHHHHHhhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHH
Confidence            4999999999999975445556666666666778888999999999  5556666554444 3444332    2445555


Q ss_pred             eeh
Q psy496          244 YLE  246 (319)
Q Consensus       244 ~~~  246 (319)
                      |..
T Consensus       262 Yvk  264 (387)
T KOG0329|consen  262 YVK  264 (387)
T ss_pred             HHh
Confidence            643

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.81  E-value=6.6e-19  Score=182.19  Aligned_cols=210  Identities=17%  Similarity=0.177  Sum_probs=132.7

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      ++++.|.++|+.+..+..    .....+.+++||||||||.+++++++..+....     ++++++||++||.|+++.+.
T Consensus       451 ~~T~~Q~~aI~~I~~d~~----~~~~~d~Ll~adTGsGKT~val~a~l~al~~g~-----qvlvLvPT~~LA~Q~~~~f~  521 (926)
T TIGR00580       451 EETPDQLKAIEEIKADME----SPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGK-----QVAVLVPTTLLAQQHFETFK  521 (926)
T ss_pred             CCCHHHHHHHHHHHhhhc----ccCcCCEEEECCCCccHHHHHHHHHHHHHHhCC-----eEEEEeCcHHHHHHHHHHHH
Confidence            467999999999987543    344568999999999999999999998875432     56666799999999999998


Q ss_pred             HHhccccCCCCceEEEEEec----ccc-----cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHH
Q psy496          124 QERDEQCGRPGSSVGYQIRL----EKE-----LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLL  194 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~----~~~-----~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~  194 (319)
                      +.+...    +..++.-.+.    +..     ....+.+|+|+||.    ++..+..+++++++||||+|+.+...    
T Consensus       522 ~~~~~~----~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~----ll~~~v~f~~L~llVIDEahrfgv~~----  589 (926)
T TIGR00580       522 ERFANF----PVTIELLSRFRSAKEQNEILKELASGKIDILIGTHK----LLQKDVKFKDLGLLIIDEEQRFGVKQ----  589 (926)
T ss_pred             HHhccC----CcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHH----HhhCCCCcccCCEEEeecccccchhH----
Confidence            876542    3333321111    000     01124689999994    23444568999999999999854322    


Q ss_pred             HHHHhhhccccCceEEEeccccChhhHhhhh-C--CCCEEEeC-CccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhh
Q psy496          195 AILKDVTDKRKDLKLILMSATLNAEKFSQFF-G--GAPILHIP-GFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKF  270 (319)
Q Consensus       195 ~~l~~~~~~~~~~qiv~lSAT~~~~~l~~~l-~--~~~~i~~~-~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (319)
                        ...+....++.++++||||+.++.+...+ +  +..++... ....|++.++....    ....+..+    ...  .
T Consensus       590 --~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~~R~~V~t~v~~~~----~~~i~~~i----~~e--l  657 (926)
T TIGR00580       590 --KEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMEYD----PELVREAI----RRE--L  657 (926)
T ss_pred             --HHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCCCccceEEEEEecC----HHHHHHHH----HHH--H
Confidence              22233344578999999999666554432 2  22222222 12245665554321    11111111    111  1


Q ss_pred             ccccCCCcEEEeCCcccc
Q psy496          271 SQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       271 ~~~~~g~~LVFlp~R~~~  288 (319)
                      .  .+++++||+|+....
T Consensus       658 ~--~g~qv~if~n~i~~~  673 (926)
T TIGR00580       658 L--RGGQVFYVHNRIESI  673 (926)
T ss_pred             H--cCCeEEEEECCcHHH
Confidence            1  278999999987543

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.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.81  E-value=5.5e-19  Score=179.37  Aligned_cols=212  Identities=16%  Similarity=0.166  Sum_probs=132.4

Q ss_pred             ccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHH
Q psy496           42 ECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        42 ~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      +.+++++|.++|+.+..+.+    .....+++++||||||||.+|.+|++..+..+     .++++++||++||.|+++.
T Consensus       259 ~f~lt~~Q~~ai~~I~~d~~----~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~g-----~q~lilaPT~~LA~Q~~~~  329 (681)
T PRK10917        259 PFELTGAQKRVVAEILADLA----SPKPMNRLLQGDVGSGKTVVAALAALAAIEAG-----YQAALMAPTEILAEQHYEN  329 (681)
T ss_pred             CCCCCHHHHHHHHHHHHhhh----ccCCceEEEECCCCCcHHHHHHHHHHHHHHcC-----CeEEEEeccHHHHHHHHHH
Confidence            44578999999999987543    33345799999999999999999999876532     3577777999999999999


Q ss_pred             HHHHhccccCCCCceEEEEEeccc---------ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhH
Q psy496          122 VAQERDEQCGRPGSSVGYQIRLEK---------ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF  192 (319)
Q Consensus       122 ~~~~~~~~~~~~g~~vg~~~~~~~---------~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~  192 (319)
                      +.+.+...    |..++.......         .......+|+|+||+.+.+    ...+++++++||||+|+.+...  
T Consensus       330 l~~l~~~~----~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~----~v~~~~l~lvVIDE~Hrfg~~q--  399 (681)
T PRK10917        330 LKKLLEPL----GIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD----DVEFHNLGLVIIDEQHRFGVEQ--  399 (681)
T ss_pred             HHHHHhhc----CcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc----cchhcccceEEEechhhhhHHH--
Confidence            98876532    334432222111         1112357899999987643    3347899999999999854322  


Q ss_pred             HHHHHHhhhccccCceEEEeccccChhhHhh-hhCCCCEEEeCCc---cccceeeeehhhhhhhhhhHHHHHHHHhhhhh
Q psy496          193 LLAILKDVTDKRKDLKLILMSATLNAEKFSQ-FFGGAPILHIPGF---TYPVQEYYLEDVLNMTRKDLKLILMSATLNAE  268 (319)
Q Consensus       193 ~~~~l~~~~~~~~~~qiv~lSAT~~~~~l~~-~l~~~~~i~~~~r---~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~  268 (319)
                       ..   .+.......++++||||+.++.++. .+++..+..+...   ..|+...+....      ....+ .....+. 
T Consensus       400 -r~---~l~~~~~~~~iL~~SATp~prtl~~~~~g~~~~s~i~~~p~~r~~i~~~~~~~~------~~~~~-~~~i~~~-  467 (681)
T PRK10917        400 -RL---ALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDS------RRDEV-YERIREE-  467 (681)
T ss_pred             -HH---HHHhcCCCCCEEEEeCCCCHHHHHHHHcCCCceEEEecCCCCCCCcEEEEeCcc------cHHHH-HHHHHHH-
Confidence             11   1222233568999999995555443 3444333333322   234555544321      11111 1111111 


Q ss_pred             hhccccCCCcEEEeCCccc
Q psy496          269 KFSQFFGGAPILHIPGFTY  287 (319)
Q Consensus       269 ~~~~~~~g~~LVFlp~R~~  287 (319)
                       ..  .+++++||+|....
T Consensus       468 -~~--~g~q~~v~~~~ie~  483 (681)
T PRK10917        468 -IA--KGRQAYVVCPLIEE  483 (681)
T ss_pred             -HH--cCCcEEEEEccccc
Confidence             11  27799999997543

>KOG0948|consensus

Probab=99.81  E-value=1.6e-19  Score=175.53  Aligned_cols=208  Identities=17%  Similarity=0.221  Sum_probs=152.7

Q ss_pred             cccCCCccccccc---cccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHH
Q psy496           16 DLAGCGKTTQVPQ---FILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILD   92 (319)
Q Consensus        16 ~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~   92 (319)
                      +-+||.+...+|.   |+.-  ...  ....+++..-.-.+.++.  ...+.|..+++.|+++|.|.+|||.++..+|..
T Consensus        94 ~~~~c~HeVavP~~~dY~p~--~~~--~~~~~pAk~YPF~LDpFQ--~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~  167 (1041)
T KOG0948|consen   94 DREGCRHEVAVPPNYDYTPL--LPK--IFGKPPAKTYPFTLDPFQ--STAIKCIDRGESVLVSAHTSAGKTVVAEYAIAM  167 (1041)
T ss_pred             ccccceeeeecCCccccCcc--ccc--cCCCCcccCCCcccCchH--hhhhhhhcCCceEEEEeecCCCcchHHHHHHHH
Confidence            3458888888884   2220  000  111122222333333332  255667888999999999999999999999998


Q ss_pred             HHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHH-hcCCC
Q psy496           93 DEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVM-QSDPI  171 (319)
Q Consensus        93 ~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l-~~~~~  171 (319)
                      .+..++     ||+|++|-++|.+|-++.+..+++..    |...|      +.+.+..+..+|||.++|..++ ++...
T Consensus       168 sLr~kQ-----RVIYTSPIKALSNQKYREl~~EF~DV----GLMTG------DVTInP~ASCLVMTTEILRsMLYRGSEv  232 (1041)
T KOG0948|consen  168 SLREKQ-----RVIYTSPIKALSNQKYRELLEEFKDV----GLMTG------DVTINPDASCLVMTTEILRSMLYRGSEV  232 (1041)
T ss_pred             HHHhcC-----eEEeeChhhhhcchhHHHHHHHhccc----ceeec------ceeeCCCCceeeeHHHHHHHHHhccchH
Confidence            887766     99999999999999999999988754    55554      4444456679999999999998 66667


Q ss_pred             CCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc-ChhhHhhhhC-----CCCEEEeCCccccceeeee
Q psy496          172 LSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL-NAEKFSQFFG-----GAPILHIPGFTYPVQEYYL  245 (319)
Q Consensus       172 l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~-~~~~l~~~l~-----~~~~i~~~~r~~~v~~~~~  245 (319)
                      +..+.|||+||+|-+ -+.+-..-+-.-+.-++++.|.|++|||+ |+..|++|..     .|.+++.+.|+.|++++..
T Consensus       233 mrEVaWVIFDEIHYM-RDkERGVVWEETIIllP~~vr~VFLSATiPNA~qFAeWI~~ihkQPcHVVYTdyRPTPLQHyif  311 (1041)
T KOG0948|consen  233 MREVAWVIFDEIHYM-RDKERGVVWEETIILLPDNVRFVFLSATIPNARQFAEWICHIHKQPCHVVYTDYRPTPLQHYIF  311 (1041)
T ss_pred             hheeeeEEeeeehhc-cccccceeeeeeEEeccccceEEEEeccCCCHHHHHHHHHHHhcCCceEEeecCCCCcceeeee
Confidence            999999999999951 11111122233345577899999999999 9999999984     5778999999999987743

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

Probab=99.80  E-value=2.5e-19  Score=181.36  Aligned_cols=180  Identities=16%  Similarity=0.170  Sum_probs=105.3

Q ss_pred             chHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEeccc
Q psy496           32 DDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPR  111 (319)
Q Consensus        32 ~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Pt  111 (319)
                      ++.|...-+.+  ++|+|.++||.++.|++         ++++.+|||||||.++..+++. +...... .-++++++||
T Consensus         5 ~~ff~~~~G~~--PtpiQ~~~i~~il~G~~---------~v~~~apTGSGKTaa~aafll~-~~~~~~~-~~rLv~~vPt   71 (844)
T TIGR02621         5 DEWYQGLHGYS--PFPWQLSLAERFVAGQP---------PESCSTPTGLGKTSIIAAWLLA-VEIGAKV-PRRLVYVVNR   71 (844)
T ss_pred             HHHHHHHhCCC--CCHHHHHHHHHHHcCCC---------cceEecCCCCcccHHHHHhhcc-ccccccc-cceEEEeCch
Confidence            34455543333  77999999999876542         3666778999999977655552 2222222 2366667899


Q ss_pred             HHHHHHHHHHHHHHhcccc-------------------CCCCceEEEEEeccc------ccCCCCceEEEECchHHHHHH
Q psy496          112 RISAIAIAERVAQERDEQC-------------------GRPGSSVGYQIRLEK------ELPRKRGSILYCTAGILPEVM  166 (319)
Q Consensus       112 r~la~q~~~~~~~~~~~~~-------------------~~~g~~vg~~~~~~~------~~~~~~~~Iiv~Tpg~ll~~l  166 (319)
                      |+||.|+++.+.+......                   ......+. .+.++.      .....+++|+|+|++.+.+..
T Consensus        72 ReLa~Qi~~~~~~~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~-~l~GG~~~~~q~~~l~~~p~IIVgT~D~i~sr~  150 (844)
T TIGR02621        72 RTVVDQVTEEAEKIGERLPDVPEVEAALWALCSTRPEKKDRPLAIS-TLRGQFADNDEWMLDPHRPAVIVGTVDMIGSRL  150 (844)
T ss_pred             HHHHHHHHHHHHHHHHHhcccchhhhhhhhhhccccccccCCeEEE-EEECCCChHHHHHhcCCCCcEEEECHHHHcCCc
Confidence            9999999987776543210                   00011111 111111      112346789999975553333


Q ss_pred             hcC-------------CCCCCccEEEEecccccccchhHHHHHHHhhhcccc---CceEEEecccc--ChhhHhhhhC
Q psy496          167 QSD-------------PILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRK---DLKLILMSATL--NAEKFSQFFG  226 (319)
Q Consensus       167 ~~~-------------~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~---~~qiv~lSAT~--~~~~l~~~l~  226 (319)
                      ...             ..+++++++|+||||..+.+.+.+..+++.+. .++   +.|+++||||+  +...+...+.
T Consensus       151 L~~gYg~~~~~~pi~ag~L~~v~~LVLDEADLd~gF~~~l~~Il~~l~-rp~~~rprQtLLFSAT~p~ei~~l~~~~~  227 (844)
T TIGR02621       151 LFSGYGCGFKSRPLHAGFLGQDALIVHDEAHLEPAFQELLKQIMNEQQ-RPPDFLPLRVVELTATSRTDGPDRTTLLS  227 (844)
T ss_pred             cccccccccccccchhhhhccceEEEEehhhhccccHHHHHHHHHhcc-cCcccccceEEEEecCCCccHHHHHHHHc
Confidence            210             02688999999999953333333333333221 122   26999999999  3445555554

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.

>PRK09401 reverse gyrase; Reviewed

Probab=99.80  E-value=5.7e-19  Score=186.58  Aligned_cols=122  Identities=17%  Similarity=0.146  Sum_probs=83.7

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      +++++|+.++|.++.|          ++++++||||||||+ |.+++...+..  ++  .++++++|||+||.|+++.+.
T Consensus        80 ~pt~iQ~~~i~~il~g----------~dv~i~ApTGsGKT~-f~l~~~~~l~~--~g--~~alIL~PTreLa~Qi~~~l~  144 (1176)
T PRK09401         80 KPWSLQRTWAKRLLLG----------ESFAIIAPTGVGKTT-FGLVMSLYLAK--KG--KKSYIIFPTRLLVEQVVEKLE  144 (1176)
T ss_pred             CCcHHHHHHHHHHHCC----------CcEEEEcCCCCCHHH-HHHHHHHHHHh--cC--CeEEEEeccHHHHHHHHHHHH
Confidence            5678999999998754          457888889999996 55555444332  22  356666699999999999988


Q ss_pred             HHhccccCCCCceEEEEEeccc-----------ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccc
Q psy496          124 QERDEQCGRPGSSVGYQIRLEK-----------ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHE  185 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~-----------~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~  185 (319)
                      .+....    +..+........           .......+|+|+|||+|.+++. ......++++|+||||.
T Consensus       145 ~l~~~~----~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~-~l~~~~~~~lVvDEaD~  212 (1176)
T PRK09401        145 KFGEKV----GCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD-ELPKKKFDFVFVDDVDA  212 (1176)
T ss_pred             HHhhhc----CceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH-hccccccCEEEEEChHH
Confidence            875432    222221111110           0112347899999999999886 22345699999999997

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

Probab=99.80  E-value=4.2e-19  Score=181.41  Aligned_cols=175  Identities=15%  Similarity=0.179  Sum_probs=131.9

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEE
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQ  140 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~  140 (319)
                      +.+.+...+++|++|||||||||.+...++..++..+.     +++|+.|.++|.+|.++.+...++......|...|  
T Consensus       126 ~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~~q-----rviYTsPIKALsNQKyrdl~~~fgdv~~~vGL~TG--  198 (1041)
T COG4581         126 EAIAILERGESVLVCAPTSSGKTVVAEYAIALALRDGQ-----RVIYTSPIKALSNQKYRDLLAKFGDVADMVGLMTG--  198 (1041)
T ss_pred             HHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHcCC-----ceEeccchhhhhhhHHHHHHHHhhhhhhhccceec--
Confidence            33444556788999999999999999999888776655     69999999999999999998887744100033333  


Q ss_pred             EecccccCCCCceEEEECchHHHHHH-hcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc-Ch
Q psy496          141 IRLEKELPRKRGSILYCTAGILPEVM-QSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL-NA  218 (319)
Q Consensus       141 ~~~~~~~~~~~~~Iiv~Tpg~ll~~l-~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~-~~  218 (319)
                          +...+..+.++|+|.++|-+++ +....+.++.+||+||+|..+ +.+-...+-..+..++...++|+||||+ |+
T Consensus       199 ----Dv~IN~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~-D~eRG~VWEE~Ii~lP~~v~~v~LSATv~N~  273 (1041)
T COG4581         199 ----DVSINPDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIG-DRERGVVWEEVIILLPDHVRFVFLSATVPNA  273 (1041)
T ss_pred             ----ceeeCCCCceEEeeHHHHHHHhccCcccccccceEEEEeeeecc-ccccchhHHHHHHhcCCCCcEEEEeCCCCCH
Confidence                4444456789999999999998 455679999999999999632 1111112222334456678999999999 99


Q ss_pred             hhHhhhhC-----CCCEEEeCCccccceeeeehh
Q psy496          219 EKFSQFFG-----GAPILHIPGFTYPVQEYYLED  247 (319)
Q Consensus       219 ~~l~~~l~-----~~~~i~~~~r~~~v~~~~~~~  247 (319)
                      +.|+.|++     +..+++.+.|+.|.+.++...
T Consensus       274 ~EF~~Wi~~~~~~~~~vv~t~~RpvPL~~~~~~~  307 (1041)
T COG4581         274 EEFAEWIQRVHSQPIHVVSTEHRPVPLEHFVYVG  307 (1041)
T ss_pred             HHHHHHHHhccCCCeEEEeecCCCCCeEEEEecC
Confidence            99999997     456788899999998876543

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.80  E-value=2.2e-18  Score=173.71  Aligned_cols=216  Identities=15%  Similarity=0.115  Sum_probs=131.3

Q ss_pred             ccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHH
Q psy496           42 ECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        42 ~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      +.++++.|.++|+.+..+..    .....+.+++||||||||.++++|++..+..+     ..+++++||++||.|+++.
T Consensus       233 pf~lt~~Q~~ai~~I~~~~~----~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~g-----~qvlilaPT~~LA~Q~~~~  303 (630)
T TIGR00643       233 PFKLTRAQKRVVKEILQDLK----SDVPMNRLLQGDVGSGKTLVAALAMLAAIEAG-----YQVALMAPTEILAEQHYNS  303 (630)
T ss_pred             CCCCCHHHHHHHHHHHHHhc----cCCCccEEEECCCCCcHHHHHHHHHHHHHHcC-----CcEEEECCHHHHHHHHHHH
Confidence            34578899999999987532    23345789999999999999999999876542     2677777999999999999


Q ss_pred             HHHHhccccCCCCceEEEEEeccc---------ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhH
Q psy496          122 VAQERDEQCGRPGSSVGYQIRLEK---------ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF  192 (319)
Q Consensus       122 ~~~~~~~~~~~~g~~vg~~~~~~~---------~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~  192 (319)
                      +.+.+...    |..++.......         .......+|+|+||+.+.+    ...+++++++||||+|+.+.... 
T Consensus       304 ~~~l~~~~----gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~----~~~~~~l~lvVIDEaH~fg~~qr-  374 (630)
T TIGR00643       304 LRNLLAPL----GIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE----KVEFKRLALVIIDEQHRFGVEQR-  374 (630)
T ss_pred             HHHHhccc----CcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc----cccccccceEEEechhhccHHHH-
Confidence            98876532    333332211100         0112346899999997643    34578999999999998543221 


Q ss_pred             HHHHHHhhhccccCceEEEeccccChhhHhh-hhCCCCEEEeC---CccccceeeeehhhhhhhhhhHHHHHHHHhhhhh
Q psy496          193 LLAILKDVTDKRKDLKLILMSATLNAEKFSQ-FFGGAPILHIP---GFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAE  268 (319)
Q Consensus       193 ~~~~l~~~~~~~~~~qiv~lSAT~~~~~l~~-~l~~~~~i~~~---~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~  268 (319)
                       . .+........+.++++||||+.++.++. .+++.....+.   ....|+...+....    .  . ..+.....+. 
T Consensus       375 -~-~l~~~~~~~~~~~~l~~SATp~prtl~l~~~~~l~~~~i~~~p~~r~~i~~~~~~~~----~--~-~~~~~~i~~~-  444 (630)
T TIGR00643       375 -K-KLREKGQGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHD----E--K-DIVYEFIEEE-  444 (630)
T ss_pred             -H-HHHHhcccCCCCCEEEEeCCCCcHHHHHHhcCCcceeeeccCCCCCCceEEEEeCcc----h--H-HHHHHHHHHH-
Confidence             1 1111111112568999999985554443 23332222222   12245555554321    1  1 1111111111 


Q ss_pred             hhccccCCCcEEEeCCcccc
Q psy496          269 KFSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       269 ~~~~~~~g~~LVFlp~R~~~  288 (319)
                       +.  .+++++||+|.....
T Consensus       445 -l~--~g~q~~v~~~~i~~s  461 (630)
T TIGR00643       445 -IA--KGRQAYVVYPLIEES  461 (630)
T ss_pred             -HH--hCCcEEEEEcccccc
Confidence             11  267899999987554

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.79  E-value=1.2e-18  Score=170.20  Aligned_cols=156  Identities=19%  Similarity=0.184  Sum_probs=100.2

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      .+|+|.++||+++.|+          ++++++|||||||++|.+|++..   .     ...+++.|+++|+.|..+.+..
T Consensus        12 ~r~~Q~~ai~~~l~g~----------dvlv~apTGsGKTl~y~lp~l~~---~-----~~~lVi~P~~~L~~dq~~~l~~   73 (470)
T TIGR00614        12 FRPVQLEVINAVLLGR----------DCFVVMPTGGGKSLCYQLPALCS---D-----GITLVISPLISLMEDQVLQLKA   73 (470)
T ss_pred             CCHHHHHHHHHHHcCC----------CEEEEcCCCCcHhHHHHHHHHHc---C-----CcEEEEecHHHHHHHHHHHHHH
Confidence            4588999999988654          57888889999999999998742   1     2466677999999998887764


Q ss_pred             HhccccCCCCceEEEEEeccc---------ccCCCCceEEEECchHHHHH---HhcCCCCCCccEEEEecccccccch-h
Q psy496          125 ERDEQCGRPGSSVGYQIRLEK---------ELPRKRGSILYCTAGILPEV---MQSDPILSGVSHIVMDEIHERSMIS-D  191 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~---------~~~~~~~~Iiv~Tpg~ll~~---l~~~~~l~~v~~vViDEah~~~~~~-~  191 (319)
                      .        |...........         .......+|+++||+++...   +..-....++++|||||||...... +
T Consensus        74 ~--------gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~  145 (470)
T TIGR00614        74 S--------GIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHD  145 (470)
T ss_pred             c--------CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccc
Confidence            3        222221111100         01123467999999987432   1111135789999999999732111 1


Q ss_pred             H--HHHHHHhhhccccCceEEEeccccCh---hhHhhhhC
Q psy496          192 F--LLAILKDVTDKRKDLKLILMSATLNA---EKFSQFFG  226 (319)
Q Consensus       192 ~--~~~~l~~~~~~~~~~qiv~lSAT~~~---~~l~~~l~  226 (319)
                      +  ....+..+....++.+++++|||++.   +++.++++
T Consensus       146 fr~~~~~l~~l~~~~~~~~~l~lTAT~~~~~~~di~~~l~  185 (470)
T TIGR00614       146 FRPDYKALGSLKQKFPNVPIMALTATASPSVREDILRQLN  185 (470)
T ss_pred             cHHHHHHHHHHHHHcCCCceEEEecCCCHHHHHHHHHHcC
Confidence            1  11222333344467899999999943   35666664

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

>KOG0921|consensus

Probab=99.79  E-value=1.7e-19  Score=177.84  Aligned_cols=205  Identities=40%  Similarity=0.731  Sum_probs=184.1

Q ss_pred             cCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHH
Q psy496           39 RGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAI  118 (319)
Q Consensus        39 ~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~  118 (319)
                      +..+.+.+.-|+..+|+.+....++....+|..++|-+.||+|||+.+...+|+.+..+..+....+.+.+|+|..|+.+
T Consensus       363 ~d~e~~~~~a~re~lpva~~~~~i~q~v~dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisi  442 (1282)
T KOG0921|consen  363 RDEALDKITAQREELPVAQYRSEILQAVAENRVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISL  442 (1282)
T ss_pred             cccchhhhhhhhhhCcHHHHHHHHHHHHhcCceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccchHHH
Confidence            44445555678889999999999999999999999999999999999999999999988877788899999999999999


Q ss_pred             HHHHHHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHH
Q psy496          119 AERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILK  198 (319)
Q Consensus       119 ~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~  198 (319)
                      +++++...+...   |..+|++.+.++.....-.-|.++|-|.+++.+.+.  +..+.++|+||.|+|....++++-+++
T Consensus       443 aerva~er~e~~---g~tvgy~vRf~Sa~prpyg~i~fctvgvllr~~e~g--lrg~sh~i~deiherdv~~dfll~~lr  517 (1282)
T KOG0921|consen  443 AERVANERGEEV---GETCGYNVRFDSATPRPYGSIMFCTVGVLLRMMENG--LRGISHVIIDEIHERDVDTDFVLIVLR  517 (1282)
T ss_pred             HHHHHHhhHHhh---cccccccccccccccccccceeeeccchhhhhhhhc--ccccccccchhhhhhccchHHHHHHHH
Confidence            999999988877   999999999888776656679999999999988543  568899999999999999999999999


Q ss_pred             hhhccccCceEEEeccccChhhHhhhhCCCCEEEeCCccccceeeeehhh
Q psy496          199 DVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDV  248 (319)
Q Consensus       199 ~~~~~~~~~qiv~lSAT~~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~  248 (319)
                      .+....++++++++|||+|.+.+..||+.++...+.+|.+|++.+|+.+.
T Consensus       518 ~m~~ty~dl~v~lmsatIdTd~f~~~f~~~p~~~~~grt~pvq~F~led~  567 (1282)
T KOG0921|consen  518 EMISTYRDLRVVLMSATIDTDLFTNFFSSIPDVTVHGRTFPVQSFFLEDI  567 (1282)
T ss_pred             hhhccchhhhhhhhhcccchhhhhhhhccccceeeccccccHHHHHHHHh
Confidence            99999999999999999999999999999999999999999987776554

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.78  E-value=3.1e-18  Score=180.69  Aligned_cols=210  Identities=16%  Similarity=0.130  Sum_probs=130.4

Q ss_pred             ccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHH
Q psy496           42 ECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        42 ~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      +..++++|.++||.+..+.+    .....+++++|+||||||.+++.+++..+..   +  .++++++||++||.|+++.
T Consensus       598 ~~~~T~~Q~~aI~~il~d~~----~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~---g--~qvlvLvPT~eLA~Q~~~~  668 (1147)
T PRK10689        598 PFETTPDQAQAINAVLSDMC----QPLAMDRLVCGDVGFGKTEVAMRAAFLAVEN---H--KQVAVLVPTTLLAQQHYDN  668 (1147)
T ss_pred             CCCCCHHHHHHHHHHHHHhh----cCCCCCEEEEcCCCcCHHHHHHHHHHHHHHc---C--CeEEEEeCcHHHHHHHHHH
Confidence            44578999999999988654    4455789999999999999998887766532   2  3566667999999999999


Q ss_pred             HHHHhccccCCCCceEEEEEeccc----c-----cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhH
Q psy496          122 VAQERDEQCGRPGSSVGYQIRLEK----E-----LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF  192 (319)
Q Consensus       122 ~~~~~~~~~~~~g~~vg~~~~~~~----~-----~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~  192 (319)
                      +.+.+...    +..++.......    .     ....+.+|+|+||+.+    .....+++++++||||+|+.+...  
T Consensus       669 f~~~~~~~----~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL----~~~v~~~~L~lLVIDEahrfG~~~--  738 (1147)
T PRK10689        669 FRDRFANW----PVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL----QSDVKWKDLGLLIVDEEHRFGVRH--  738 (1147)
T ss_pred             HHHhhccC----CceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH----hCCCCHhhCCEEEEechhhcchhH--
Confidence            98766432    223322211111    0     0112468999999743    334457899999999999854321  


Q ss_pred             HHHHHHhhhccccCceEEEeccccChhhHh--h-hhCCCCEEEeCC-ccccceeeeehhhhhhhhhhHHHHHHHHhhhhh
Q psy496          193 LLAILKDVTDKRKDLKLILMSATLNAEKFS--Q-FFGGAPILHIPG-FTYPVQEYYLEDVLNMTRKDLKLILMSATLNAE  268 (319)
Q Consensus       193 ~~~~l~~~~~~~~~~qiv~lSAT~~~~~l~--~-~l~~~~~i~~~~-r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~  268 (319)
                          ...+...+++.|+++||||+.++.+.  . .+.+...+..+. ...+++..+....    ....+...    ... 
T Consensus       739 ----~e~lk~l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~~r~~v~~~~~~~~----~~~~k~~i----l~e-  805 (1147)
T PRK10689        739 ----KERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYD----SLVVREAI----LRE-  805 (1147)
T ss_pred             ----HHHHHhcCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCCCCCCceEEEEecC----cHHHHHHH----HHH-
Confidence                22334455688999999998444332  2 233333443322 2234554443221    11111111    111 


Q ss_pred             hhccccCCCcEEEeCCcc
Q psy496          269 KFSQFFGGAPILHIPGFT  286 (319)
Q Consensus       269 ~~~~~~~g~~LVFlp~R~  286 (319)
                       +.  .+|+++||+|+..
T Consensus       806 -l~--r~gqv~vf~n~i~  820 (1147)
T PRK10689        806 -IL--RGGQVYYLYNDVE  820 (1147)
T ss_pred             -Hh--cCCeEEEEECCHH
Confidence             11  2689999999864

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.78  E-value=3.6e-18  Score=161.18  Aligned_cols=154  Identities=18%  Similarity=0.124  Sum_probs=93.5

Q ss_pred             cccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhcc
Q psy496           49 QPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDE  128 (319)
Q Consensus        49 Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~  128 (319)
                      |.++++.+.++        ++.+++++||||||||.++.+|++..        ..+.+++.|+++|+.|.++++...+..
T Consensus         2 Q~~~~~~~~~~--------~~~~~~i~apTGsGKT~~~~~~~l~~--------~~~~~~~~P~~aL~~~~~~~~~~~~~~   65 (357)
T TIGR03158         2 QVATFEALQSK--------DADIIFNTAPTGAGKTLAWLTPLLHG--------ENDTIALYPTNALIEDQTEAIKEFVDV   65 (357)
T ss_pred             HHHHHHHHHcC--------CCCEEEEECCCCCCHHHHHHHHHHHc--------CCCEEEEeChHHHHHHHHHHHHHHHHh
Confidence            55666665432        23568999999999999999998742        124567779999999999998887632


Q ss_pred             ccCCCCceEEEEEecc------------------cc--------cCCCCceEEEECchHHHHHHhc---CC------CCC
Q psy496          129 QCGRPGSSVGYQIRLE------------------KE--------LPRKRGSILYCTAGILPEVMQS---DP------ILS  173 (319)
Q Consensus       129 ~~~~~g~~vg~~~~~~------------------~~--------~~~~~~~Iiv~Tpg~ll~~l~~---~~------~l~  173 (319)
                      .....+..+.. ..+.                  +.        .....+.|+++||+.+..+++.   .+      .+.
T Consensus        66 ~~~~~~~~v~~-~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~  144 (357)
T TIGR03158        66 FKPERDVNLLH-VSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYT  144 (357)
T ss_pred             cCCCCCceEEE-ecCCchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhhhccCcccchhhhhc
Confidence            10000111110 0000                  00        0012456888999888654432   11      258


Q ss_pred             CccEEEEecccccccchh----HHHHHHHhhhccccCceEEEeccccChh
Q psy496          174 GVSHIVMDEIHERSMISD----FLLAILKDVTDKRKDLKLILMSATLNAE  219 (319)
Q Consensus       174 ~v~~vViDEah~~~~~~~----~~~~~l~~~~~~~~~~qiv~lSAT~~~~  219 (319)
                      +++++|+||+|..+....    +.+.....+.......+++++|||++..
T Consensus       145 ~~~~iV~DE~H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~  194 (357)
T TIGR03158       145 KFSTVIFDEFHLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPA  194 (357)
T ss_pred             CCCEEEEecccccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHH
Confidence            899999999998553221    1223333332222246999999999544

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.

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.77  E-value=1.9e-18  Score=163.12  Aligned_cols=147  Identities=21%  Similarity=0.237  Sum_probs=95.8

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEE------ec-
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQI------RL-  143 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~------~~-  143 (319)
                      .++|+||||||||+++++|+++.+....   ..+++++.|+++|+.|+++++...++...   |...+...      .. 
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~~---~~~ii~v~P~~~L~~q~~~~l~~~f~~~~---~~~~~~~~~~~~~~~~~   74 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQK---ADRVIIALPTRATINAMYRRAKELFGSNL---GLLHSSSSFKRIKEMGD   74 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhCC---CCeEEEEeehHHHHHHHHHHHHHHhCccc---EEeeccHHHHHHhccCC
Confidence            4789999999999999999998754322   34788888999999999999999876432   21111000      00 


Q ss_pred             ----ccc-----cC---CCCceEEEECchHHHHHHhcCC-----CCC--CccEEEEecccccccc-hhHHHHHHHhhhcc
Q psy496          144 ----EKE-----LP---RKRGSILYCTAGILPEVMQSDP-----ILS--GVSHIVMDEIHERSMI-SDFLLAILKDVTDK  203 (319)
Q Consensus       144 ----~~~-----~~---~~~~~Iiv~Tpg~ll~~l~~~~-----~l~--~v~~vViDEah~~~~~-~~~~~~~l~~~~~~  203 (319)
                          +..     ..   ....+|+++||+.++..+....     .+.  ..+++|+||+|..... .+.+...++.+.  
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~l~~~l~~l~--  152 (358)
T TIGR01587        75 SEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLALILAVLEVLK--  152 (358)
T ss_pred             chhHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHHHHHHHHHHH--
Confidence                000     00   0135699999999988875421     111  2389999999984321 223444444443  


Q ss_pred             ccCceEEEeccccChhhHhhhhC
Q psy496          204 RKDLKLILMSATLNAEKFSQFFG  226 (319)
Q Consensus       204 ~~~~qiv~lSAT~~~~~l~~~l~  226 (319)
                      ..+.|+++||||++ +.+.+|+.
T Consensus       153 ~~~~~~i~~SATlp-~~l~~~~~  174 (358)
T TIGR01587       153 DNDVPILLMSATLP-KFLKEYAE  174 (358)
T ss_pred             HcCCCEEEEecCch-HHHHHHHh
Confidence            23678999999994 44555553

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.

>KOG0344|consensus

Probab=99.76  E-value=6.9e-19  Score=167.86  Aligned_cols=226  Identities=16%  Similarity=0.130  Sum_probs=140.7

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC---CCCccEEEEecccHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN---RGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~---~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      ++|+|+++||.++.++++++|++          ||||||++|.+|++.++....   .....+.+++.|+|+||.|+++.
T Consensus       159 Pt~iq~~aipvfl~~r~~lAcap----------TGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re  228 (593)
T KOG0344|consen  159 PTPIQKQAIPVFLEKRDVLACAP----------TGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQIYRE  228 (593)
T ss_pred             CCcccchhhhhhhcccceEEecc----------CCCcchhhhhhHHHHHHHHhhcccCccceEEEEecchHHHHHHHHHH
Confidence            56889999999998887655555          999999999999999885533   13356778888999999999999


Q ss_pred             HHHHh--ccccCCCCceEEEEEe---cc--cccCCCCceEEEECchHHHHHHhcCC---CCCCccEEEEecccccccch-
Q psy496          122 VAQER--DEQCGRPGSSVGYQIR---LE--KELPRKRGSILYCTAGILPEVMQSDP---ILSGVSHIVMDEIHERSMIS-  190 (319)
Q Consensus       122 ~~~~~--~~~~~~~g~~vg~~~~---~~--~~~~~~~~~Iiv~Tpg~ll~~l~~~~---~l~~v~~vViDEah~~~~~~-  190 (319)
                      +.++.  ....   ....+....   ..  ...+..+.+|++.||.++...+...+   +++++.|+|+||+|.. ... 
T Consensus       229 ~~k~~~~~~t~---~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~l-fe~~  304 (593)
T KOG0344|consen  229 MRKYSIDEGTS---LRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADLL-FEPE  304 (593)
T ss_pred             HHhcCCCCCCc---hhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccchhheeeeEeechHHhh-hChh
Confidence            88875  2111   111110000   00  01112457899999999999996654   6999999999999972 122 


Q ss_pred             hHHHHHHHhhhc-cccCceEEEecccc--ChhhHhhhhCCCCE-EEeCCccc---cceeeeehhhhhhhhhhHHHHHHHH
Q psy496          191 DFLLAILKDVTD-KRKDLKLILMSATL--NAEKFSQFFGGAPI-LHIPGFTY---PVQEYYLEDVLNMTRKDLKLILMSA  263 (319)
Q Consensus       191 ~~~~~~l~~~~~-~~~~~qiv~lSAT~--~~~~l~~~l~~~~~-i~~~~r~~---~v~~~~~~~~~~~~~~~~~~~~~~~  263 (319)
                      .+.......+.. ..+++++-+||||+  .+++|++-.....+ +.+..++.   .|+.......    ...-+.++...
T Consensus       305 ~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~~sa~~~V~QelvF~g----se~~K~lA~rq  380 (593)
T KOG0344|consen  305 FFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRVIVGLRNSANETVDQELVFCG----SEKGKLLALRQ  380 (593)
T ss_pred             hHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeEEEecchhHhhhhhhhheeee----cchhHHHHHHH
Confidence            233332222222 34788999999999  77788876544443 33333332   2222222111    11222222222


Q ss_pred             hhhhhhhccccCCCcEEEeCCccccccccc
Q psy496          264 TLNAEKFSQFFGGAPILHIPGFTYPVQEYY  293 (319)
Q Consensus       264 ~~~~~~~~~~~~g~~LVFlp~R~~~v~~~~  293 (319)
                      .+.     ....-++||||.+-.-+.++++
T Consensus       381 ~v~-----~g~~PP~lIfVQs~eRak~L~~  405 (593)
T KOG0344|consen  381 LVA-----SGFKPPVLIFVQSKERAKQLFE  405 (593)
T ss_pred             HHh-----ccCCCCeEEEEecHHHHHHHHH
Confidence            211     2246789999999555544443

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.73  E-value=1.8e-17  Score=167.89  Aligned_cols=224  Identities=18%  Similarity=0.107  Sum_probs=128.7

Q ss_pred             cccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           43 CCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        43 ~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      ...++.|.++++.+..+.       .+++.++.|+||||||.+|+.++.+.+..+     ..++++.|+++|+.|+.+++
T Consensus       143 ~~Lt~~Q~~ai~~i~~~~-------~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~g-----~~vLvLvPt~~L~~Q~~~~l  210 (679)
T PRK05580        143 PTLNPEQAAAVEAIRAAA-------GFSPFLLDGVTGSGKTEVYLQAIAEVLAQG-----KQALVLVPEIALTPQMLARF  210 (679)
T ss_pred             CCCCHHHHHHHHHHHhcc-------CCCcEEEECCCCChHHHHHHHHHHHHHHcC-----CeEEEEeCcHHHHHHHHHHH
Confidence            345678888888876531       456799999999999999988877665432     25677779999999999999


Q ss_pred             HHHhccccCCCCceEEEEEeccc-----ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchh----HH
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEK-----ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD----FL  193 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~-----~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~----~~  193 (319)
                      .+.++..+   ....|.....+.     .......+|+|+|++.+.      ..++++++||+||+|..+...+    .-
T Consensus       211 ~~~fg~~v---~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~------~p~~~l~liVvDEeh~~s~~~~~~p~y~  281 (679)
T PRK05580        211 RARFGAPV---AVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF------LPFKNLGLIIVDEEHDSSYKQQEGPRYH  281 (679)
T ss_pred             HHHhCCCE---EEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc------ccccCCCEEEEECCCccccccCcCCCCc
Confidence            88765332   111110000000     011134679999998764      2368899999999997432211    00


Q ss_pred             HHHHHhhhccccCceEEEeccccChhhHhhhh-CCCCEEEeCCccc---cceeeeehhhhhhhhhhHHHHHHHHhhhhhh
Q psy496          194 LAILKDVTDKRKDLKLILMSATLNAEKFSQFF-GGAPILHIPGFTY---PVQEYYLEDVLNMTRKDLKLILMSATLNAEK  269 (319)
Q Consensus       194 ~~~l~~~~~~~~~~qiv~lSAT~~~~~l~~~l-~~~~~i~~~~r~~---~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  269 (319)
                      .-.+........+.+++++|||++.+.+.... |....+....|..   ..++............+ ...+....++...
T Consensus       282 ~r~va~~ra~~~~~~~il~SATps~~s~~~~~~g~~~~~~l~~r~~~~~~p~v~~id~~~~~~~~~-~~~ls~~l~~~i~  360 (679)
T PRK05580        282 ARDLAVVRAKLENIPVVLGSATPSLESLANAQQGRYRLLRLTKRAGGARLPEVEIIDMRELLRGEN-GSFLSPPLLEAIK  360 (679)
T ss_pred             HHHHHHHHhhccCCCEEEEcCCCCHHHHHHHhccceeEEEeccccccCCCCeEEEEechhhhhhcc-cCCCCHHHHHHHH
Confidence            00111122233467999999999877766543 2333445554431   11233322100000000 0011112222211


Q ss_pred             hccccCCCcEEEeCCcccc
Q psy496          270 FSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       270 ~~~~~~g~~LVFlp~R~~~  288 (319)
                      .....++++|||+|.|+|+
T Consensus       361 ~~l~~g~qvll~~nrrGy~  379 (679)
T PRK05580        361 QRLERGEQVLLFLNRRGYA  379 (679)
T ss_pred             HHHHcCCeEEEEEcCCCCC
Confidence            1112267999999999986

>PRK14701 reverse gyrase; Provisional

Probab=99.73  E-value=4.3e-17  Score=176.10  Aligned_cols=125  Identities=16%  Similarity=0.075  Sum_probs=82.2

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      +++++|+.+||.++.|+          ++++.||||||||+++..+.+...   .++  .+++++.||++|+.|+.+.+.
T Consensus        79 ~pt~iQ~~~i~~il~G~----------d~li~APTGsGKTl~~~~~al~~~---~~g--~~aLVl~PTreLa~Qi~~~l~  143 (1638)
T PRK14701         79 EFWSIQKTWAKRILRGK----------SFSIVAPTGMGKSTFGAFIALFLA---LKG--KKCYIILPTTLLVKQTVEKIE  143 (1638)
T ss_pred             CCCHHHHHHHHHHHcCC----------CEEEEEcCCCCHHHHHHHHHHHHH---hcC--CeEEEEECHHHHHHHHHHHHH
Confidence            46789999999998754          467888899999995554443321   122  256666799999999999888


Q ss_pred             HHhccccCCCCceEEEEEec---cc------ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEeccccc
Q psy496          124 QERDEQCGRPGSSVGYQIRL---EK------ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHER  186 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~---~~------~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~  186 (319)
                      .+....-  .+..+......   ..      .......+|+|+|||+|.+.+.... ..+++++|+||||+.
T Consensus       144 ~l~~~~~--~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l~-~~~i~~iVVDEAD~m  212 (1638)
T PRK14701        144 SFCEKAN--LDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEMK-HLKFDFIFVDDVDAF  212 (1638)
T ss_pred             HHHhhcC--CceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHHh-hCCCCEEEEECceec
Confidence            7643210  01122111111   00      0111246899999999988764322 267999999999973

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.73  E-value=2.5e-17  Score=165.41  Aligned_cols=163  Identities=17%  Similarity=0.152  Sum_probs=102.5

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      .+|+|.++|+.+..|          +++++++|||||||++|.+|++..   .     ..+++++|+++|+.|..+.+..
T Consensus        26 ~r~~Q~~ai~~il~g----------~dvlv~apTGsGKTl~y~lpal~~---~-----g~tlVisPl~sL~~dqv~~l~~   87 (607)
T PRK11057         26 FRPGQQEIIDAVLSG----------RDCLVVMPTGGGKSLCYQIPALVL---D-----GLTLVVSPLISLMKDQVDQLLA   87 (607)
T ss_pred             CCHHHHHHHHHHHcC----------CCEEEEcCCCchHHHHHHHHHHHc---C-----CCEEEEecHHHHHHHHHHHHHH
Confidence            458899999998754          457888889999999999998743   1     2567777999999998887765


Q ss_pred             HhccccCCCCceEEEEEecc---------cccCCCCceEEEECchHHHHHH-hcCCCCCCccEEEEecccccccch-hH-
Q psy496          125 ERDEQCGRPGSSVGYQIRLE---------KELPRKRGSILYCTAGILPEVM-QSDPILSGVSHIVMDEIHERSMIS-DF-  192 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~---------~~~~~~~~~Iiv~Tpg~ll~~l-~~~~~l~~v~~vViDEah~~~~~~-~~-  192 (319)
                      .        |..........         ......+.+++++||+++.... .......++++|||||||...... ++ 
T Consensus        88 ~--------gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~fr  159 (607)
T PRK11057         88 N--------GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHDFR  159 (607)
T ss_pred             c--------CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCccc
Confidence            3        22222111100         0011234579999999986422 222224579999999999732111 11 


Q ss_pred             -HHHHHHhhhccccCceEEEeccccChh---hHhhhhC-CCCEEEe
Q psy496          193 -LLAILKDVTDKRKDLKLILMSATLNAE---KFSQFFG-GAPILHI  233 (319)
Q Consensus       193 -~~~~l~~~~~~~~~~qiv~lSAT~~~~---~l~~~l~-~~~~i~~  233 (319)
                       ....+..+....++.+++++|||++..   ++.+.++ ..+.+..
T Consensus       160 ~~y~~L~~l~~~~p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~~  205 (607)
T PRK11057        160 PEYAALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQI  205 (607)
T ss_pred             HHHHHHHHHHHhCCCCcEEEEecCCChhHHHHHHHHhCCCCeEEEE
Confidence             112233344444678899999999432   4555553 2344333

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.72  E-value=2.7e-17  Score=165.03  Aligned_cols=156  Identities=16%  Similarity=0.100  Sum_probs=100.7

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ..+.|.++|+++++|+          ++++++|||+|||++|.+|.+..   .     ...++++|+++|..|..+.+..
T Consensus        14 fr~~Q~~~i~~il~g~----------dvlv~~PTG~GKTl~y~lpal~~---~-----g~~lVisPl~sL~~dq~~~l~~   75 (591)
T TIGR01389        14 FRPGQEEIISHVLDGR----------DVLVVMPTGGGKSLCYQVPALLL---K-----GLTVVISPLISLMKDQVDQLRA   75 (591)
T ss_pred             CCHHHHHHHHHHHcCC----------CEEEEcCCCccHhHHHHHHHHHc---C-----CcEEEEcCCHHHHHHHHHHHHH
Confidence            4588999999988654          57888889999999999998742   1     2466777999999998887766


Q ss_pred             HhccccCCCCceEEEEEe---ccc------ccCCCCceEEEECchHHHHHH-hcCCCCCCccEEEEeccccccc---chh
Q psy496          125 ERDEQCGRPGSSVGYQIR---LEK------ELPRKRGSILYCTAGILPEVM-QSDPILSGVSHIVMDEIHERSM---ISD  191 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~---~~~------~~~~~~~~Iiv~Tpg~ll~~l-~~~~~l~~v~~vViDEah~~~~---~~~  191 (319)
                      .        |..+.....   ...      .......+|+++||+++.... .......++++|||||||..+.   ...
T Consensus        76 ~--------gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~fr  147 (591)
T TIGR01389        76 A--------GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFR  147 (591)
T ss_pred             c--------CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccH
Confidence            3        222221111   100      011234679999999986433 3333356899999999997321   111


Q ss_pred             HHHHHHHhhhccccCceEEEeccccCh---hhHhhhhC
Q psy496          192 FLLAILKDVTDKRKDLKLILMSATLNA---EKFSQFFG  226 (319)
Q Consensus       192 ~~~~~l~~~~~~~~~~qiv~lSAT~~~---~~l~~~l~  226 (319)
                      -....+..+....++..++++|||.+.   .++.++++
T Consensus       148 p~y~~l~~l~~~~~~~~vi~lTAT~~~~~~~~i~~~l~  185 (591)
T TIGR01389       148 PEYQRLGSLAERFPQVPRIALTATADAETRQDIRELLR  185 (591)
T ss_pred             HHHHHHHHHHHhCCCCCEEEEEeCCCHHHHHHHHHHcC
Confidence            112223333333344569999999933   35677775

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.

>TIGR01054 rgy reverse gyrase

Probab=99.70  E-value=7.1e-17  Score=170.96  Aligned_cols=124  Identities=16%  Similarity=0.129  Sum_probs=82.5

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      .++++|+.++|.+..|+          +++++||||||||+ |.+++...+...  +  .+++++.|||+||.|+++.+.
T Consensus        78 ~p~~iQ~~~i~~il~G~----------d~vi~ApTGsGKT~-f~l~~~~~l~~~--g--~~vLIL~PTreLa~Qi~~~l~  142 (1171)
T TIGR01054        78 EPWSIQKMWAKRVLRGD----------SFAIIAPTGVGKTT-FGLAMSLFLAKK--G--KRCYIILPTTLLVIQVAEKIS  142 (1171)
T ss_pred             CCcHHHHHHHHHHhCCC----------eEEEECCCCCCHHH-HHHHHHHHHHhc--C--CeEEEEeCHHHHHHHHHHHHH
Confidence            46789999999987654          46777889999997 556666554332  2  367777799999999999888


Q ss_pred             HHhccccCCCCceEEEE---Eeccc------ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccc
Q psy496          124 QERDEQCGRPGSSVGYQ---IRLEK------ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHE  185 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~---~~~~~------~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~  185 (319)
                      .+....-.. ...++..   .....      .......+|+|+|||+|.+++..-.  .+++++|+||||+
T Consensus       143 ~l~~~~~i~-~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l~--~~~~~iVvDEaD~  210 (1171)
T TIGR01054       143 SLAEKAGVG-TVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELG--PKFDFIFVDDVDA  210 (1171)
T ss_pred             HHHHhcCCc-eeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHhc--CCCCEEEEeChHh
Confidence            775421000 0011101   00000      1111247899999999998875422  1899999999997

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.

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

Probab=99.68  E-value=1.3e-16  Score=164.59  Aligned_cols=157  Identities=19%  Similarity=0.113  Sum_probs=96.6

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ..|.|.++|++++.|+|          +++.+|||+|||++|.+|++..   .     ...|+++|+++|+.+....+..
T Consensus       461 FRp~Q~eaI~aiL~GrD----------VLVimPTGSGKSLcYQLPAL~~---~-----GiTLVISPLiSLmqDQV~~L~~  522 (1195)
T PLN03137        461 FRPNQREIINATMSGYD----------VFVLMPTGGGKSLTYQLPALIC---P-----GITLVISPLVSLIQDQIMNLLQ  522 (1195)
T ss_pred             CCHHHHHHHHHHHcCCC----------EEEEcCCCccHHHHHHHHHHHc---C-----CcEEEEeCHHHHHHHHHHHHHh
Confidence            35889999999876654          7777779999999999999753   1     2577778999999855444433


Q ss_pred             HhccccCCCCceEEEEEec---ccc------c--CCCCceEEEECchHHHH------HHhcCCCCCCccEEEEecccccc
Q psy496          125 ERDEQCGRPGSSVGYQIRL---EKE------L--PRKRGSILYCTAGILPE------VMQSDPILSGVSHIVMDEIHERS  187 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~---~~~------~--~~~~~~Iiv~Tpg~ll~------~l~~~~~l~~v~~vViDEah~~~  187 (319)
                      .        |.........   ...      .  .....+|+++||+++..      .+........+++|||||||...
T Consensus       523 ~--------GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDEAHcVS  594 (1195)
T PLN03137        523 A--------NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEAHCVS  594 (1195)
T ss_pred             C--------CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccCcchhhh
Confidence            2        2222211110   000      0  11346899999999852      22211123458999999999732


Q ss_pred             cch-hHHHH--HHHhhhccccCceEEEeccccCh---hhHhhhhCC
Q psy496          188 MIS-DFLLA--ILKDVTDKRKDLKLILMSATLNA---EKFSQFFGG  227 (319)
Q Consensus       188 ~~~-~~~~~--~l~~~~~~~~~~qiv~lSAT~~~---~~l~~~l~~  227 (319)
                      -.. ++-..  .+..+....++.+++++|||++.   +++.+.++-
T Consensus       595 qWGhDFRpdYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L~l  640 (1195)
T PLN03137        595 QWGHDFRPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQALGL  640 (1195)
T ss_pred             hcccchHHHHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHcCC
Confidence            111 12221  12233344457789999999933   356666653

>KOG0947|consensus

Probab=99.68  E-value=1.1e-16  Score=159.22  Aligned_cols=169  Identities=17%  Similarity=0.198  Sum_probs=123.4

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEE
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGY  139 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~  139 (319)
                      +..+.+...+..|+|+|+|.+|||.++..++.-.-..     ..+.+|++|-++|.+|-++.+...++..    |...| 
T Consensus       303 k~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~h-----~TR~iYTSPIKALSNQKfRDFk~tF~Dv----gLlTG-  372 (1248)
T KOG0947|consen  303 KEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQKH-----MTRTIYTSPIKALSNQKFRDFKETFGDV----GLLTG-  372 (1248)
T ss_pred             HHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHhh-----ccceEecchhhhhccchHHHHHHhcccc----ceeec-
Confidence            3444555667889999999999999998887543222     2489999999999999999999888754    43333 


Q ss_pred             EEecccccCCCCceEEEECchHHHHHH-hcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc-C
Q psy496          140 QIRLEKELPRKRGSILYCTAGILPEVM-QSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL-N  217 (319)
Q Consensus       140 ~~~~~~~~~~~~~~Iiv~Tpg~ll~~l-~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~-~  217 (319)
                           +...+..+.++|||.++|.+++ ++...+.++++||+||+|-.+ +.+-..-+-..+..+++..++|++|||+ |
T Consensus       373 -----DvqinPeAsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiN-D~eRGvVWEEViIMlP~HV~~IlLSATVPN  446 (1248)
T KOG0947|consen  373 -----DVQINPEASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYIN-DVERGVVWEEVIIMLPRHVNFILLSATVPN  446 (1248)
T ss_pred             -----ceeeCCCcceEeehHHHHHHHHhcccchhhccceEEEeeeeecc-cccccccceeeeeeccccceEEEEeccCCC
Confidence                 3223345679999999999999 444458999999999999511 1111112223345677899999999999 9


Q ss_pred             hhhHhhhhCCC-----CEEEeCCccccceeee
Q psy496          218 AEKFSQFFGGA-----PILHIPGFTYPVQEYY  244 (319)
Q Consensus       218 ~~~l~~~l~~~-----~~i~~~~r~~~v~~~~  244 (319)
                      ...|++|.|.-     .+++...|+.|+++++
T Consensus       447 ~~EFA~WIGRtK~K~IyViST~kRPVPLEh~l  478 (1248)
T KOG0947|consen  447 TLEFADWIGRTKQKTIYVISTSKRPVPLEHYL  478 (1248)
T ss_pred             hHHHHHHhhhccCceEEEEecCCCccceEEEE
Confidence            99999999842     2344457888888764

>TIGR00595 priA primosomal protein N'

Probab=99.66  E-value=1.4e-16  Score=156.37  Aligned_cols=196  Identities=17%  Similarity=0.130  Sum_probs=108.8

Q ss_pred             EEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc------c
Q psy496           73 IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK------E  146 (319)
Q Consensus        73 li~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~------~  146 (319)
                      +|.|+||||||++|+..+.+.+....     .++++.|+++|+.|+++++.+.++..+   ....+ ......      .
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~g~-----~vLvlvP~i~L~~Q~~~~l~~~f~~~v---~vlhs-~~~~~er~~~~~~   71 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLALGK-----SVLVLVPEIALTPQMIQRFKYRFGSQV---AVLHS-GLSDSEKLQAWRK   71 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHcCC-----eEEEEeCcHHHHHHHHHHHHHHhCCcE---EEEEC-CCCHHHHHHHHHH
Confidence            47899999999999776655543322     577777999999999999988765322   10000 000000      0


Q ss_pred             cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHH----HHHHHhhhccccCceEEEeccccChhhHh
Q psy496          147 LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFL----LAILKDVTDKRKDLKLILMSATLNAEKFS  222 (319)
Q Consensus       147 ~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~----~~~l~~~~~~~~~~qiv~lSAT~~~~~l~  222 (319)
                      ......+|+|+|+..+.      ..++++++|||||+|..+...+-.    .-.+........+.++|++|||+..+.+.
T Consensus        72 ~~~g~~~IVVGTrsalf------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra~~~~~~vil~SATPsles~~  145 (505)
T TIGR00595        72 VKNGEILVVIGTRSALF------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSATPSLESYH  145 (505)
T ss_pred             HHcCCCCEEECChHHHc------CcccCCCEEEEECCCccccccccCCCCcHHHHHHHHHHhcCCCEEEEeCCCCHHHHH
Confidence            01124679999998664      236889999999999733221100    00011111223467899999999877777


Q ss_pred             hhhCCC-CEEEeCCcc----ccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCcccc
Q psy496          223 QFFGGA-PILHIPGFT----YPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       223 ~~l~~~-~~i~~~~r~----~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~  288 (319)
                      ....+. ..+....|.    .| .+.+....-......+...+.....+.  +.  .++++|||+|+|+|+
T Consensus       146 ~~~~g~~~~~~l~~r~~~~~~p-~v~vid~~~~~~~~~ls~~l~~~i~~~--l~--~g~qvLvflnrrGya  211 (505)
T TIGR00595       146 NAKQKAYRLLVLTRRVSGRKPP-EVKLIDMRKEPRQSFLSPELITAIEQT--LA--AGEQSILFLNRRGYS  211 (505)
T ss_pred             HHhcCCeEEeechhhhcCCCCC-eEEEEecccccccCCccHHHHHHHHHH--HH--cCCcEEEEEeCCcCC
Confidence            654332 233333222    22 222322100000011111222222222  22  278999999999995

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).

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

Probab=99.64  E-value=6.7e-16  Score=145.66  Aligned_cols=153  Identities=16%  Similarity=0.160  Sum_probs=110.9

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCC
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPR  149 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~  149 (319)
                      +|.||+.|||=|||..+.+-+...+...+   . ++++++||+-|+.|.++.+.+.++..........|-....++...+
T Consensus        30 ~NtLvvlPTGLGKT~IA~~V~~~~l~~~~---~-kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~~ltGev~p~~R~~~w  105 (542)
T COG1111          30 KNTLVVLPTGLGKTFIAAMVIANRLRWFG---G-KVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAALTGEVRPEEREELW  105 (542)
T ss_pred             cCeEEEecCCccHHHHHHHHHHHHHHhcC---C-eEEEecCCchHHHHHHHHHHHHhCCChhheeeecCCCChHHHHHHH
Confidence            58999999999999999888887765433   2 7999999999999999999998876431112222211123334445


Q ss_pred             CCceEEEECchHHHHHH-hcCCCCCCccEEEEecccccccchh-HHHHHHHhhhccccCceEEEecccc--ChhhHhhhh
Q psy496          150 KRGSILYCTAGILPEVM-QSDPILSGVSHIVMDEIHERSMISD-FLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFF  225 (319)
Q Consensus       150 ~~~~Iiv~Tpg~ll~~l-~~~~~l~~v~~vViDEah~~~~~~~-~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l  225 (319)
                      .+.+|+|+||+.+.+-+ .+..++.++.++|+||||+  ...+ ....+.+.......+.++++||||+  +.+.+.+-.
T Consensus       106 ~~~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHR--AvGnyAYv~Va~~y~~~~k~~~ilgLTASPGs~~ekI~eV~  183 (542)
T COG1111         106 AKKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHR--AVGNYAYVFVAKEYLRSAKNPLILGLTASPGSDLEKIQEVV  183 (542)
T ss_pred             hhCCEEEeccHHHHhHHhcCccChHHceEEEechhhh--ccCcchHHHHHHHHHHhccCceEEEEecCCCCCHHHHHHHH
Confidence            67889999999998877 5555699999999999997  2223 2333334444445577999999999  777777765


Q ss_pred             CCC
Q psy496          226 GGA  228 (319)
Q Consensus       226 ~~~  228 (319)
                      .+.
T Consensus       184 ~nL  186 (542)
T COG1111         184 ENL  186 (542)
T ss_pred             HhC
Confidence            543

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.60  E-value=1.7e-14  Score=122.84  Aligned_cols=163  Identities=26%  Similarity=0.228  Sum_probs=107.0

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ..+.|.++++.+.+..         +++++++|||||||.++..++++.+....   ..+++++.|++.++.|..+++..
T Consensus         9 ~~~~Q~~~~~~~~~~~---------~~~~i~~~~GsGKT~~~~~~~~~~~~~~~---~~~~l~~~p~~~~~~~~~~~~~~   76 (201)
T smart00487        9 LRPYQKEAIEALLSGL---------RDVILAAPTGSGKTLAALLPALEALKRGK---GKRVLVLVPTRELAEQWAEELKK   76 (201)
T ss_pred             CCHHHHHHHHHHHcCC---------CcEEEECCCCCchhHHHHHHHHHHhcccC---CCcEEEEeCCHHHHHHHHHHHHH
Confidence            4566777776654321         67999999999999999999888765432   23688888999999999988887


Q ss_pred             HhccccCCCCceEEEEEecccc-----cCCCCc-eEEEECchHHHHHHhcCC-CCCCccEEEEeccccccc--chhHHHH
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKE-----LPRKRG-SILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSM--ISDFLLA  195 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~-----~~~~~~-~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~--~~~~~~~  195 (319)
                      ......   +.... .......     ....+. +++++|++.+.+.+.... ....++++|+||+|....  .......
T Consensus        77 ~~~~~~---~~~~~-~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~~~~~~~~  152 (201)
T smart00487       77 LGPSLG---LKVVG-LYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEK  152 (201)
T ss_pred             HhccCC---eEEEE-EeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCCcHHHHHH
Confidence            654311   01111 1111110     011223 899999999999986544 577899999999998432  2222222


Q ss_pred             HHHhhhccccCceEEEecccc--ChhhHhhhhC
Q psy496          196 ILKDVTDKRKDLKLILMSATL--NAEKFSQFFG  226 (319)
Q Consensus       196 ~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~  226 (319)
                      .+.   ..++..+++++|||+  +.......+.
T Consensus       153 ~~~---~~~~~~~~v~~saT~~~~~~~~~~~~~  182 (201)
T smart00487      153 LLK---LLPKNVQLLLLSATPPEEIENLLELFL  182 (201)
T ss_pred             HHH---hCCccceEEEEecCCchhHHHHHHHhc
Confidence            222   234567899999999  4555554443

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.59  E-value=2.9e-14  Score=114.50  Aligned_cols=138  Identities=28%  Similarity=0.252  Sum_probs=91.6

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc--
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL--  147 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~--  147 (319)
                      +++++.+|||||||..+..++........   ..++++++|++.++.+..+.+......     +..+..........  
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~~---~~~~lv~~p~~~l~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~   72 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSLK---GGQVLVLAPTRELANQVAERLKELFGE-----GIKVGYLIGGTSIKQQ   72 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhccc---CCCEEEEcCcHHHHHHHHHHHHHHhhC-----CcEEEEEecCcchhHH
Confidence            36899999999999999888877654322   347888889999999998888776542     12222222222211  


Q ss_pred             ---CCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          148 ---PRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       148 ---~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                         .....+|+++|++.+.+.+.... ....++++|+||+|........... ...........+++++|||+
T Consensus        73 ~~~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~-~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046          73 EKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLG-LKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             HHHhcCCCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcchHHHH-HHHHhhCCccceEEEEeccC
Confidence               12467899999999988885443 3567999999999973222211111 11222234566899999995

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

>KOG0354|consensus

Probab=99.58  E-value=7.8e-15  Score=145.37  Aligned_cols=156  Identities=18%  Similarity=0.156  Sum_probs=103.6

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEE
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGY  139 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~  139 (319)
                      .+++..+- ++|++|++|||+|||.++...+++++....   +++|++++|++-|..|....+...... .   . ..+ 
T Consensus        68 ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p---~~KiVF~aP~~pLv~QQ~a~~~~~~~~-~---~-~T~-  137 (746)
T KOG0354|consen   68 EELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRP---KGKVVFLAPTRPLVNQQIACFSIYLIP-Y---S-VTG-  137 (746)
T ss_pred             HHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCC---cceEEEeeCCchHHHHHHHHHhhccCc-c---c-cee-
Confidence            45555566 889999999999999999999998876544   469999999999998887555544221 1   0 111 


Q ss_pred             EEec-----ccccCCCCceEEEECchHHHHHHhcCC--CCCCccEEEEecccccccchh-HHHHHHHhhhccc-cCceEE
Q psy496          140 QIRL-----EKELPRKRGSILYCTAGILPEVMQSDP--ILSGVSHIVMDEIHERSMISD-FLLAILKDVTDKR-KDLKLI  210 (319)
Q Consensus       140 ~~~~-----~~~~~~~~~~Iiv~Tpg~ll~~l~~~~--~l~~v~~vViDEah~~~~~~~-~~~~~l~~~~~~~-~~~qiv  210 (319)
                      ....     .........+++|+||..+.+.++...  .|+.+.++|+||||+-  ... ..-.+++...... ...|++
T Consensus       138 ~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra--~kn~~Y~~Vmr~~l~~k~~~~qIL  215 (746)
T KOG0354|consen  138 QLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRT--SKNHPYNNIMREYLDLKNQGNQIL  215 (746)
T ss_pred             eccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEcccccc--cccccHHHHHHHHHHhhhccccEE
Confidence            1111     111112356899999999988885432  2789999999999971  111 1222232222221 233999


Q ss_pred             Eecccc--ChhhHhhhhCC
Q psy496          211 LMSATL--NAEKFSQFFGG  227 (319)
Q Consensus       211 ~lSAT~--~~~~l~~~l~~  227 (319)
                      ++|||+  +.+.+.++..+
T Consensus       216 gLTASpG~~~~~v~~~I~~  234 (746)
T KOG0354|consen  216 GLTASPGSKLEQVQNVIDN  234 (746)
T ss_pred             EEecCCCccHHHHHHHHHh
Confidence            999999  67777766543

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.56  E-value=4.6e-15  Score=150.44  Aligned_cols=128  Identities=16%  Similarity=0.141  Sum_probs=92.5

Q ss_pred             cCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHH
Q psy496           39 RGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAI  118 (319)
Q Consensus        39 ~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~  118 (319)
                      +..+|..+|+|.++||.+..++++++.++          ||||||++|.+|++..+....     .++++.|+++||.|.
T Consensus        87 ~~~p~~~tp~qvQ~I~~i~l~~gvIAeaq----------TGeGKTLAf~LP~l~~aL~g~-----~v~IVTpTrELA~Qd  151 (970)
T PRK12899         87 YHQQWDMVPYDVQILGAIAMHKGFITEMQ----------TGEGKTLTAVMPLYLNALTGK-----PVHLVTVNDYLAQRD  151 (970)
T ss_pred             ccCCCCCChHHHHHhhhhhcCCCeEEEeC----------CCCChHHHHHHHHHHHHhhcC-----CeEEEeCCHHHHHHH
Confidence            34556678999999999987766555555          999999999999998776432     245556999999999


Q ss_pred             HHHHHHHhccccCCCCceEEEEEecc---cccCCCCceEEEECchHH-HHHHhcCC-CCC-------CccEEEEecccc
Q psy496          119 AERVAQERDEQCGRPGSSVGYQIRLE---KELPRKRGSILYCTAGIL-PEVMQSDP-ILS-------GVSHIVMDEIHE  185 (319)
Q Consensus       119 ~~~~~~~~~~~~~~~g~~vg~~~~~~---~~~~~~~~~Iiv~Tpg~l-l~~l~~~~-~l~-------~v~~vViDEah~  185 (319)
                      ++.+.......    |..++....+.   .....-+++|+|+|||+| +++++.+. .++       .+.++||||||.
T Consensus       152 ae~m~~L~k~l----GLsV~~i~GG~~~~eq~~~y~~DIVygTPgRLgfDyLrd~~~~~~~~~~vqr~~~~~IIDEADs  226 (970)
T PRK12899        152 CEWVGSVLRWL----GLTTGVLVSGSPLEKRKEIYQCDVVYGTASEFGFDYLRDNSIATRKEEQVGRGFYFAIIDEVDS  226 (970)
T ss_pred             HHHHHHHHhhc----CCeEEEEeCCCCHHHHHHHcCCCEEEECCChhHHHHhhCCCCCcCHHHhhcccccEEEEechhh
Confidence            99877765432    55555433211   111112578999999999 99996653 344       458999999997

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.55  E-value=1.4e-14  Score=142.67  Aligned_cols=146  Identities=11%  Similarity=0.014  Sum_probs=94.2

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      .+.+.|.++++.++.          +.+.++++|||||||.++... ........   ..++++++||++|+.|..+++.
T Consensus       114 ~~r~~Q~~av~~~l~----------~~~~il~apTGsGKT~i~~~l-~~~~~~~~---~~~vLilvpt~eL~~Q~~~~l~  179 (501)
T PHA02558        114 EPHWYQYDAVYEGLK----------NNRRLLNLPTSAGKSLIQYLL-SRYYLENY---EGKVLIIVPTTSLVTQMIDDFV  179 (501)
T ss_pred             CCCHHHHHHHHHHHh----------cCceEEEeCCCCCHHHHHHHH-HHHHHhcC---CCeEEEEECcHHHHHHHHHHHH
Confidence            345678888776553          345788999999999876442 22222222   2367777799999999999988


Q ss_pred             HHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhcc
Q psy496          124 QERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDK  203 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~  203 (319)
                      +......    ..++ .+..+... ....+|+|+||+++.+...  ..++++++||+||||..  ....+..+++.+   
T Consensus       180 ~~~~~~~----~~~~-~i~~g~~~-~~~~~I~VaT~qsl~~~~~--~~~~~~~~iIvDEaH~~--~~~~~~~il~~~---  246 (501)
T PHA02558        180 DYRLFPR----EAMH-KIYSGTAK-DTDAPIVVSTWQSAVKQPK--EWFDQFGMVIVDECHLF--TGKSLTSIITKL---  246 (501)
T ss_pred             Hhccccc----ccee-EEecCccc-CCCCCEEEeeHHHHhhchh--hhccccCEEEEEchhcc--cchhHHHHHHhh---
Confidence            7643221    1111 11111111 1246799999999876542  24789999999999973  333333333332   


Q ss_pred             ccCceEEEecccc
Q psy496          204 RKDLKLILMSATL  216 (319)
Q Consensus       204 ~~~~qiv~lSAT~  216 (319)
                      ++..++++||||+
T Consensus       247 ~~~~~~lGLTATp  259 (501)
T PHA02558        247 DNCKFKFGLTGSL  259 (501)
T ss_pred             hccceEEEEeccC
Confidence            2345799999999

>PRK13766 Hef nuclease; Provisional

Probab=99.52  E-value=5.4e-14  Score=145.52  Aligned_cols=144  Identities=15%  Similarity=0.142  Sum_probs=95.9

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc-----
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK-----  145 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~-----  145 (319)
                      +++|++|||+|||.++.+++...+..    ...++++++|+++|+.|..+.+.+.++..    +..+.. +.++.     
T Consensus        31 n~lv~~ptG~GKT~~a~~~i~~~l~~----~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~----~~~v~~-~~g~~~~~~r  101 (773)
T PRK13766         31 NTLVVLPTGLGKTAIALLVIAERLHK----KGGKVLILAPTKPLVEQHAEFFRKFLNIP----EEKIVV-FTGEVSPEKR  101 (773)
T ss_pred             CeEEEcCCCccHHHHHHHHHHHHHHh----CCCeEEEEeCcHHHHHHHHHHHHHHhCCC----CceEEE-EeCCCCHHHH
Confidence            79999999999999998888876632    13478888899999999999888876532    112221 11111     


Q ss_pred             ccCCCCceEEEECchHHHHHHhc-CCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHh
Q psy496          146 ELPRKRGSILYCTAGILPEVMQS-DPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFS  222 (319)
Q Consensus       146 ~~~~~~~~Iiv~Tpg~ll~~l~~-~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~  222 (319)
                      .....+.+|+++||+.+...+.. ...+.+++++|+||||+.... .....+.+......+..++++||||+  +.+.+.
T Consensus       102 ~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~~-~~~~~i~~~~~~~~~~~~il~lTaTP~~~~~~i~  180 (773)
T PRK13766        102 AELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGN-YAYVYIAERYHEDAKNPLVLGLTASPGSDEEKIK  180 (773)
T ss_pred             HHHHhCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCcccccc-ccHHHHHHHHHhcCCCCEEEEEEcCCCCCHHHHH
Confidence            11123567999999999877744 445889999999999973211 11112223333334456899999998  444444


Q ss_pred             hh
Q psy496          223 QF  224 (319)
Q Consensus       223 ~~  224 (319)
                      +.
T Consensus       181 ~~  182 (773)
T PRK13766        181 EV  182 (773)
T ss_pred             HH
Confidence            43

>PRK09694 helicase Cas3; Provisional

Probab=99.50  E-value=3.3e-13  Score=138.95  Aligned_cols=147  Identities=24%  Similarity=0.240  Sum_probs=88.8

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCC--CCceEEEEE----
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR--PGSSVGYQI----  141 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~--~g~~vg~~~----  141 (319)
                      +++.++|.||||||||++++.+... +...+  ...++++..||++.++++++++.+.+......  .+..-|...    
T Consensus       300 ~pgl~ileApTGsGKTEAAL~~A~~-l~~~~--~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~~v~L~Hg~a~l~~~  376 (878)
T PRK09694        300 QPGLTIIEAPTGSGKTEAALAYAWR-LIDQG--LADSIIFALPTQATANAMLSRLEALASKLFPSPNLILAHGNSRFNHL  376 (878)
T ss_pred             CCCeEEEEeCCCCCHHHHHHHHHHH-HHHhC--CCCeEEEECcHHHHHHHHHHHHHHHHHHhcCCCceEeecCcchhhhh
Confidence            4678999999999999998776554 33322  23478999999999999999987643211100  000001000    


Q ss_pred             -----ecc--------cc-------c-CCCC---ceEEEECchHHHHHHhcCC--CCCC----ccEEEEecccccccchh
Q psy496          142 -----RLE--------KE-------L-PRKR---GSILYCTAGILPEVMQSDP--ILSG----VSHIVMDEIHERSMISD  191 (319)
Q Consensus       142 -----~~~--------~~-------~-~~~~---~~Iiv~Tpg~ll~~l~~~~--~l~~----v~~vViDEah~~~~~~~  191 (319)
                           ..+        ..       . ..++   ++|+|+|.+.++.-....+  .+..    -++|||||+|.....+.
T Consensus       377 ~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~kh~~lR~~~La~svvIiDEVHAyD~ym~  456 (878)
T PRK09694        377 FQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHRFIRGFGLGRSVLIVDEVHAYDAYMY  456 (878)
T ss_pred             hhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHccchHHHHHHhhccCeEEEechhhCCHHHH
Confidence                 000        00       0 0111   5799999988875442221  1222    35899999998655544


Q ss_pred             -HHHHHHHhhhccccCceEEEeccccChh
Q psy496          192 -FLLAILKDVTDKRKDLKLILMSATLNAE  219 (319)
Q Consensus       192 -~~~~~l~~~~~~~~~~qiv~lSAT~~~~  219 (319)
                       ++...++.+...  ...+|+||||++..
T Consensus       457 ~lL~~~L~~l~~~--g~~vIllSATLP~~  483 (878)
T PRK09694        457 GLLEAVLKAQAQA--GGSVILLSATLPAT  483 (878)
T ss_pred             HHHHHHHHHHHhc--CCcEEEEeCCCCHH
Confidence             445555554443  34699999999543

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

Probab=99.48  E-value=7.9e-13  Score=106.92  Aligned_cols=133  Identities=21%  Similarity=0.222  Sum_probs=85.8

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      ++.-+|-..+|||||.-++--++......+    .++|++.|||.++..+.+.+..          ..+.+....-....
T Consensus         4 g~~~~~d~hpGaGKTr~vlp~~~~~~i~~~----~rvLvL~PTRvva~em~~aL~~----------~~~~~~t~~~~~~~   69 (148)
T PF07652_consen    4 GELTVLDLHPGAGKTRRVLPEIVREAIKRR----LRVLVLAPTRVVAEEMYEALKG----------LPVRFHTNARMRTH   69 (148)
T ss_dssp             TEEEEEE--TTSSTTTTHHHHHHHHHHHTT------EEEEESSHHHHHHHHHHTTT----------SSEEEESTTSS---
T ss_pred             CceeEEecCCCCCCcccccHHHHHHHHHcc----CeEEEecccHHHHHHHHHHHhc----------CCcccCceeeeccc
Confidence            455677888999999976665555444433    3788888999999998887743          33333333221122


Q ss_pred             CCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          149 RKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      ..+.-|-++|.+.+.+.+.....+.+++++|+||+|..+...-...+.++..... ...++|++|||+
T Consensus        70 ~g~~~i~vMc~at~~~~~~~p~~~~~yd~II~DEcH~~Dp~sIA~rg~l~~~~~~-g~~~~i~mTATP  136 (148)
T PF07652_consen   70 FGSSIIDVMCHATYGHFLLNPCRLKNYDVIIMDECHFTDPTSIAARGYLRELAES-GEAKVIFMTATP  136 (148)
T ss_dssp             -SSSSEEEEEHHHHHHHHHTSSCTTS-SEEEECTTT--SHHHHHHHHHHHHHHHT-TS-EEEEEESS-
T ss_pred             cCCCcccccccHHHHHHhcCcccccCccEEEEeccccCCHHHHhhheeHHHhhhc-cCeeEEEEeCCC
Confidence            2345689999999988886655689999999999998555555555666665443 345899999998

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 ....

>KOG0951|consensus

Probab=99.47  E-value=1.9e-13  Score=139.65  Aligned_cols=220  Identities=13%  Similarity=0.109  Sum_probs=150.5

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      ++|.+..+.+         -+.|.+|+++||+|||||.++.++++.      .....+++++.|..+.+...++.|.+.+
T Consensus      1146 ~iqtqVf~~~---------y~~nd~v~vga~~gsgkt~~ae~a~l~------~~~~~~~vyi~p~~~i~~~~~~~w~~~f 1210 (1674)
T KOG0951|consen 1146 PIQTQVFTSL---------YNTNDNVLVGAPNGSGKTACAELALLR------PDTIGRAVYIAPLEEIADEQYRDWEKKF 1210 (1674)
T ss_pred             CceEEEEeee---------ecccceEEEecCCCCchhHHHHHHhcC------CccceEEEEecchHHHHHHHHHHHHHhh
Confidence            5666666554         235688999999999999999999876      2345699999999999999988888777


Q ss_pred             ccccCCCCceEEEEEecccccC---CCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccc----cchhHHHHHHHh
Q psy496          127 DEQCGRPGSSVGYQIRLEKELP---RKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERS----MISDFLLAILKD  199 (319)
Q Consensus       127 ~~~~~~~g~~vg~~~~~~~~~~---~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~----~~~~~~~~~l~~  199 (319)
                      +...   |..+. ...++...+   ..+.+++++||...-.+ +   ..+.++++|.||+|+.|    ...+.+.+....
T Consensus      1211 ~~~~---G~~~~-~l~ge~s~~lkl~~~~~vii~tpe~~d~l-q---~iQ~v~l~i~d~lh~igg~~g~v~evi~S~r~i 1282 (1674)
T KOG0951|consen 1211 SKLL---GLRIV-KLTGETSLDLKLLQKGQVIISTPEQWDLL-Q---SIQQVDLFIVDELHLIGGVYGAVYEVICSMRYI 1282 (1674)
T ss_pred             cccc---CceEE-ecCCccccchHHhhhcceEEechhHHHHH-h---hhhhcceEeeehhhhhcccCCceEEEEeeHHHH
Confidence            6543   54442 111222111   24678999999976544 2   56889999999999844    222244443333


Q ss_pred             hhccccCceEEEecccc-ChhhHhhhhCCCCEEE--eCCccccceeeeehhhhhhhhhhHHH-HHHHHhhhhhhhccccC
Q psy496          200 VTDKRKDLKLILMSATL-NAEKFSQFFGGAPILH--IPGFTYPVQEYYLEDVLNMTRKDLKL-ILMSATLNAEKFSQFFG  275 (319)
Q Consensus       200 ~~~~~~~~qiv~lSAT~-~~~~l~~~l~~~~~i~--~~~r~~~v~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  275 (319)
                      .....+++|++.+|-.+ |..++ -.+....+++  +..|+.|.++++....+.  ...-+. .+....+.+..-....+
T Consensus      1283 a~q~~k~ir~v~ls~~lana~d~-ig~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~--~~~~~~~am~~~~~~ai~~~a~~~ 1359 (1674)
T KOG0951|consen 1283 ASQLEKKIRVVALSSSLANARDL-IGASSSGVFNFSPSVRPVPLEIHIQSVDIS--HFESRMLAMTKPTYTAIVRHAGNR 1359 (1674)
T ss_pred             HHHHHhheeEEEeehhhccchhh-ccccccceeecCcccCCCceeEEEEEeccc--hhHHHHHHhhhhHHHHHHHHhcCC
Confidence            33455688999999999 98888 3333444544  456888888887765422  333333 34456666655444458


Q ss_pred             CCcEEEeCCcccccccc
Q psy496          276 GAPILHIPGFTYPVQEY  292 (319)
Q Consensus       276 g~~LVFlp~R~~~v~~~  292 (319)
                      ++.+||+|+|..+..+.
T Consensus      1360 k~~~vf~p~rk~~~~~a 1376 (1674)
T KOG0951|consen 1360 KPAIVFLPTRKHARLVA 1376 (1674)
T ss_pred             CCeEEEeccchhhhhhh
Confidence            89999999999876553

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

Probab=99.40  E-value=1.1e-11  Score=112.39  Aligned_cols=167  Identities=17%  Similarity=0.189  Sum_probs=110.6

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      .++-|+.+-..      ++....+.+..+|+|-||+|||+...-.+-..+..++     +|.+.+|+...+..++.++..
T Consensus        98 Ls~~Q~~as~~------l~q~i~~k~~~lv~AV~GaGKTEMif~~i~~al~~G~-----~vciASPRvDVclEl~~Rlk~  166 (441)
T COG4098          98 LSPGQKKASNQ------LVQYIKQKEDTLVWAVTGAGKTEMIFQGIEQALNQGG-----RVCIASPRVDVCLELYPRLKQ  166 (441)
T ss_pred             cChhHHHHHHH------HHHHHHhcCcEEEEEecCCCchhhhHHHHHHHHhcCC-----eEEEecCcccchHHHHHHHHH
Confidence            34556655433      3444566788999999999999987666655544433     888889999999999999988


Q ss_pred             HhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchh-HHHHHHHhhhcc
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD-FLLAILKDVTDK  203 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~-~~~~~l~~~~~~  203 (319)
                      .+...      .+.  .-+++..+..+++++|+|...|++.-      +.++++||||+|......+ .+....+...+ 
T Consensus       167 aF~~~------~I~--~Lyg~S~~~fr~plvVaTtHQLlrFk------~aFD~liIDEVDAFP~~~d~~L~~Av~~ark-  231 (441)
T COG4098         167 AFSNC------DID--LLYGDSDSYFRAPLVVATTHQLLRFK------QAFDLLIIDEVDAFPFSDDQSLQYAVKKARK-  231 (441)
T ss_pred             hhccC------Cee--eEecCCchhccccEEEEehHHHHHHH------hhccEEEEeccccccccCCHHHHHHHHHhhc-
Confidence            76522      121  22333333446889999999999876      4689999999998654444 33333443333 


Q ss_pred             ccCceEEEeccccChhhHhhhh-CCCCEEEeCCccc
Q psy496          204 RKDLKLILMSATLNAEKFSQFF-GGAPILHIPGFTY  238 (319)
Q Consensus       204 ~~~~qiv~lSAT~~~~~l~~~l-~~~~~i~~~~r~~  238 (319)
                       ++--+|.+|||...+.-.+.. ++...+.++.|.+
T Consensus       232 -~~g~~IylTATp~k~l~r~~~~g~~~~~klp~RfH  266 (441)
T COG4098         232 -KEGATIYLTATPTKKLERKILKGNLRILKLPARFH  266 (441)
T ss_pred             -ccCceEEEecCChHHHHHHhhhCCeeEeecchhhc
Confidence             234578999998433333332 3334466666654

>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=99.38  E-value=1.2e-12  Score=111.03  Aligned_cols=154  Identities=16%  Similarity=0.091  Sum_probs=89.8

Q ss_pred             ccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           46 MVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        46 ~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      .+.|.+++..+...-+   ....+.++++.+|||||||.++...+.+.. .       ++++++|+..++.|....+...
T Consensus         5 r~~Q~~ai~~i~~~~~---~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~-~-------~~l~~~p~~~l~~Q~~~~~~~~   73 (184)
T PF04851_consen    5 RPYQQEAIARIINSLE---NKKEERRVLLNAPTGSGKTIIALALILELA-R-------KVLIVAPNISLLEQWYDEFDDF   73 (184)
T ss_dssp             -HHHHHHHHHHHHHHH---TTSGCSEEEEEESTTSSHHHHHHHHHHHHH-C-------EEEEEESSHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHH---hcCCCCCEEEEECCCCCcChhhhhhhhccc-c-------ceeEecCHHHHHHHHHHHHHHh
Confidence            3567777766654322   223568899999999999988876554432 2       6777779999999999888544


Q ss_pred             hccccCCC-----CceEE-E-E-----EecccccCCCCceEEEECchHHHHHHhcCC------------CCCCccEEEEe
Q psy496          126 RDEQCGRP-----GSSVG-Y-Q-----IRLEKELPRKRGSILYCTAGILPEVMQSDP------------ILSGVSHIVMD  181 (319)
Q Consensus       126 ~~~~~~~~-----g~~vg-~-~-----~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~------------~l~~v~~vViD  181 (319)
                      ........     ....+ . .     .............+.+.|.+.+........            .....++||+|
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~D  153 (184)
T PF04851_consen   74 GSEKYNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIID  153 (184)
T ss_dssp             STTSEEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEE
T ss_pred             hhhhhhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEe
Confidence            32111000     00000 0 0     000011112355699999999877763211            13567999999


Q ss_pred             cccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          182 EIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       182 Eah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      |+|...... ....+++     .+...+|+||||+
T Consensus       154 EaH~~~~~~-~~~~i~~-----~~~~~~l~lTATp  182 (184)
T PF04851_consen  154 EAHHYPSDS-SYREIIE-----FKAAFILGLTATP  182 (184)
T ss_dssp             TGGCTHHHH-HHHHHHH-----SSCCEEEEEESS-
T ss_pred             hhhhcCCHH-HHHHHHc-----CCCCeEEEEEeCc
Confidence            999732222 1222222     3455799999997

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 ....

>KOG0950|consensus

Probab=99.37  E-value=6e-12  Score=126.47  Aligned_cols=216  Identities=21%  Similarity=0.187  Sum_probs=125.0

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEE-EEEeccc
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVG-YQIRLEK  145 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg-~~~~~~~  145 (319)
                      .+++|.+.++||+.|||++..+.++......++    .++.+.|....++.-...+..+... .   |..+. |.-+...
T Consensus       238 ~e~~nliys~Pts~gktlvaeilml~~~l~~rr----~~llilp~vsiv~Ek~~~l~~~~~~-~---G~~ve~y~g~~~p  309 (1008)
T KOG0950|consen  238 LERKNLIYSLPTSAGKTLVAEILMLREVLCRRR----NVLLILPYVSIVQEKISALSPFSID-L---GFPVEEYAGRFPP  309 (1008)
T ss_pred             hcccceEEeCCCccchHHHHHHHHHHHHHHHhh----ceeEecceeehhHHHHhhhhhhccc-c---CCcchhhcccCCC
Confidence            467889999999999999999999988876654    3444446555444433333333211 1   33221 1111111


Q ss_pred             ccCCCCceEEEECchHH---HHHHhcCCCCCCccEEEEecccc-----cccchhHHHHHHHhhhccccCceEEEecccc-
Q psy496          146 ELPRKRGSILYCTAGIL---PEVMQSDPILSGVSHIVMDEIHE-----RSMISDFLLAILKDVTDKRKDLKLILMSATL-  216 (319)
Q Consensus       146 ~~~~~~~~Iiv~Tpg~l---l~~l~~~~~l~~v~~vViDEah~-----~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~-  216 (319)
                      ....++..+.++|-+.-   .+.+-....+..+++||+||.|.     ||...+.++.-+-.... ....|+|+||||+ 
T Consensus       310 ~~~~k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~lE~~l~k~~y~~~-~~~~~iIGMSATi~  388 (1008)
T KOG0950|consen  310 EKRRKRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAILELLLAKILYENL-ETSVQIIGMSATIP  388 (1008)
T ss_pred             CCcccceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccchHHHHHHHHHHHhcc-ccceeEeeeecccC
Confidence            22224567999997544   44443334577899999999997     55555554444433332 2237899999999 


Q ss_pred             ChhhHhhhhCCCCEEEeCCccccceeeeehhhhhh---hhhhHHHHHH---HHhh--h----hhhhcc-c-cCCCcEEEe
Q psy496          217 NAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNM---TRKDLKLILM---SATL--N----AEKFSQ-F-FGGAPILHI  282 (319)
Q Consensus       217 ~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~---~~~~~~~~~~---~~~~--~----~~~~~~-~-~~g~~LVFl  282 (319)
                      |...+++||. +.+....-|+.|...+......-.   ....++.+..   +..-  +    +..+.+ . .+.++|||+
T Consensus       389 N~~lL~~~L~-A~~y~t~fRPv~L~E~ik~G~~i~~~~r~~~lr~ia~l~~~~~g~~dpD~~v~L~tet~~e~~~~lvfc  467 (1008)
T KOG0950|consen  389 NNSLLQDWLD-AFVYTTRFRPVPLKEYIKPGSLIYESSRNKVLREIANLYSSNLGDEDPDHLVGLCTETAPEGSSVLVFC  467 (1008)
T ss_pred             ChHHHHHHhh-hhheecccCcccchhccCCCcccccchhhHHHHHhhhhhhhhcccCCCcceeeehhhhhhcCCeEEEEc
Confidence            9999999996 444555566666655543322111   1122222221   1100  1    000111 1 145599999


Q ss_pred             CCcccccccc
Q psy496          283 PGFTYPVQEY  292 (319)
Q Consensus       283 p~R~~~v~~~  292 (319)
                      |+|..|..+.
T Consensus       468 ~sk~~ce~~a  477 (1008)
T KOG0950|consen  468 PSKKNCENVA  477 (1008)
T ss_pred             CcccchHHHH
Confidence            9999885544

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

Probab=99.33  E-value=6.9e-12  Score=126.14  Aligned_cols=224  Identities=17%  Similarity=0.115  Sum_probs=127.9

Q ss_pred             ccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           46 MVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        46 ~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      ...|+.+...+...      .......++.|.||||||.+|+-.+-+.+..+.     .+|++.|-.+|..|+.+++...
T Consensus       200 n~~Q~~a~~~i~~~------~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~Gk-----qvLvLVPEI~Ltpq~~~rf~~r  268 (730)
T COG1198         200 NQEQQAAVEAILSS------LGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQGK-----QVLVLVPEIALTPQLLARFKAR  268 (730)
T ss_pred             CHHHHHHHHHHHHh------cccccceeEeCCCCCcHHHHHHHHHHHHHHcCC-----EEEEEeccccchHHHHHHHHHH
Confidence            34566665555442      133467999999999999999888777665443     4455559999999999999999


Q ss_pred             hccccCCCCceEEEEEecc--cccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchh---HH-HHHHHh
Q psy496          126 RDEQCGRPGSSVGYQIRLE--KELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD---FL-LAILKD  199 (319)
Q Consensus       126 ~~~~~~~~g~~vg~~~~~~--~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~---~~-~~~l~~  199 (319)
                      ++..+......++...+.+  ........+|+++|=--++      ..++++++|||||-|+-+.-.+   .. .-.+..
T Consensus       269 Fg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF------~Pf~~LGLIIvDEEHD~sYKq~~~prYhARdvA~  342 (730)
T COG1198         269 FGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALF------LPFKNLGLIIVDEEHDSSYKQEDGPRYHARDVAV  342 (730)
T ss_pred             hCCChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhc------CchhhccEEEEeccccccccCCcCCCcCHHHHHH
Confidence            8855421111111111100  0111245678888854322      1378999999999997221111   00 000011


Q ss_pred             hhccccCceEEEeccccChhhHhhhhCC-CCEEEeCCccc---cceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccC
Q psy496          200 VTDKRKDLKLILMSATLNAEKFSQFFGG-APILHIPGFTY---PVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFG  275 (319)
Q Consensus       200 ~~~~~~~~qiv~lSAT~~~~~l~~~l~~-~~~i~~~~r~~---~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  275 (319)
                      ......+..+|+-|||+..+.+..-..+ ...+....|..   +.++.++..-......+.  .+....+++.......+
T Consensus       343 ~Ra~~~~~pvvLgSATPSLES~~~~~~g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~--~lS~~Ll~~i~~~l~~g  420 (730)
T COG1198         343 LRAKKENAPVVLGSATPSLESYANAESGKYKLLRLTNRAGRARLPRVEIIDMRKEPLETGR--SLSPALLEAIRKTLERG  420 (730)
T ss_pred             HHHHHhCCCEEEecCCCCHHHHHhhhcCceEEEEccccccccCCCcceEEeccccccccCc--cCCHHHHHHHHHHHhcC
Confidence            1111225689999999988888776544 34455555544   344444433211111110  02222333322222238


Q ss_pred             CCcEEEeCCcccc
Q psy496          276 GAPILHIPGFTYP  288 (319)
Q Consensus       276 g~~LVFlp~R~~~  288 (319)
                      .++|+|+|.|+|.
T Consensus       421 eQ~llflnRRGys  433 (730)
T COG1198         421 EQVLLFLNRRGYA  433 (730)
T ss_pred             CeEEEEEccCCcc
Confidence            8999999999996

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.33  E-value=1.4e-12  Score=130.85  Aligned_cols=130  Identities=19%  Similarity=0.067  Sum_probs=88.6

Q ss_pred             HhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHH
Q psy496           36 ARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISA  115 (319)
Q Consensus        36 ~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la  115 (319)
                      +..|.-...+.++|..+.+++..|.            +..++||+|||+++.+|++-....+.     .+.++.||++||
T Consensus        48 a~~R~lg~~p~~vQlig~~~l~~G~------------Iaem~TGeGKTLva~lpa~l~aL~G~-----~V~VvTpt~~LA  110 (745)
T TIGR00963        48 ASKRVLGMRPFDVQLIGGIALHKGK------------IAEMKTGEGKTLTATLPAYLNALTGK-----GVHVVTVNDYLA  110 (745)
T ss_pred             HHHHHhCCCccchHHhhhhhhcCCc------------eeeecCCCccHHHHHHHHHHHHHhCC-----CEEEEcCCHHHH
Confidence            3333334445677877777665433            44455999999999999953333322     355556999999


Q ss_pred             HHHHHHHHHHhccccCCCCceEEEEEeccc---ccCCCCceEEEECchHH-HHHHhcC-------CCCCCccEEEEeccc
Q psy496          116 IAIAERVAQERDEQCGRPGSSVGYQIRLEK---ELPRKRGSILYCTAGIL-PEVMQSD-------PILSGVSHIVMDEIH  184 (319)
Q Consensus       116 ~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~---~~~~~~~~Iiv~Tpg~l-l~~l~~~-------~~l~~v~~vViDEah  184 (319)
                      .|.++.+...+...    |..++......+   ......++|+++||++| +++++.+       ..+.++.++||||+|
T Consensus       111 ~qdae~~~~l~~~L----GLsv~~i~g~~~~~~r~~~y~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaD  186 (745)
T TIGR00963       111 QRDAEWMGQVYRFL----GLSVGLILSGMSPEERREAYACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVD  186 (745)
T ss_pred             HHHHHHHHHHhccC----CCeEEEEeCCCCHHHHHHhcCCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHH
Confidence            99999888876543    666664443211   11112478999999999 8888544       247889999999999


Q ss_pred             cc
Q psy496          185 ER  186 (319)
Q Consensus       185 ~~  186 (319)
                      ..
T Consensus       187 s~  188 (745)
T TIGR00963       187 SI  188 (745)
T ss_pred             HH
Confidence            73

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.

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

Probab=99.31  E-value=3.4e-11  Score=118.26  Aligned_cols=181  Identities=19%  Similarity=0.222  Sum_probs=117.5

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      +.|--|.+++.-|..  |+-  ++..=+=+|+|.-|||||.++.++++..+..+.   ++-.+  .||-.||.|.++.+.
T Consensus       262 ~LT~aQ~~vi~EI~~--Dl~--~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G~---Q~ALM--APTEILA~QH~~~~~  332 (677)
T COG1200         262 KLTNAQKRVIKEILA--DLA--SPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGY---QAALM--APTEILAEQHYESLR  332 (677)
T ss_pred             CccHHHHHHHHHHHh--hhc--CchhhHHHhccCcCCCHHHHHHHHHHHHHHcCC---eeEEe--ccHHHHHHHHHHHHH
Confidence            345557777665543  221  122234578999999999999999998776533   44444  499999999999999


Q ss_pred             HHhccccCCCCceEEEEEe---ccc------ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHH
Q psy496          124 QERDEQCGRPGSSVGYQIR---LEK------ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLL  194 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~---~~~------~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~  194 (319)
                      +.+...    |..++.-..   ...      ...+...+|+|+|.-    +++.+..++++.++|+||-|++|....   
T Consensus       333 ~~l~~~----~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHA----LiQd~V~F~~LgLVIiDEQHRFGV~QR---  401 (677)
T COG1200         333 KWLEPL----GIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHA----LIQDKVEFHNLGLVIIDEQHRFGVHQR---  401 (677)
T ss_pred             HHhhhc----CCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcch----hhhcceeecceeEEEEeccccccHHHH---
Confidence            887643    334442221   111      011234689999987    445566789999999999999776542   


Q ss_pred             HHHHhhhcccc-CceEEEeccccChhhHh-hhhCCCCEEEeCCcc---ccceeeeehh
Q psy496          195 AILKDVTDKRK-DLKLILMSATLNAEKFS-QFFGGAPILHIPGFT---YPVQEYYLED  247 (319)
Q Consensus       195 ~~l~~~~~~~~-~~qiv~lSAT~~~~~l~-~~l~~~~~i~~~~r~---~~v~~~~~~~  247 (319)
                         ..+..... .+-+++||||+=+..++ ..|++-.+..++..|   .|+.+.....
T Consensus       402 ---~~L~~KG~~~Ph~LvMTATPIPRTLAlt~fgDldvS~IdElP~GRkpI~T~~i~~  456 (677)
T COG1200         402 ---LALREKGEQNPHVLVMTATPIPRTLALTAFGDLDVSIIDELPPGRKPITTVVIPH  456 (677)
T ss_pred             ---HHHHHhCCCCCcEEEEeCCCchHHHHHHHhccccchhhccCCCCCCceEEEEecc
Confidence               12222223 45689999999555544 567776665554433   5777766654

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.28  E-value=4.5e-12  Score=128.76  Aligned_cols=122  Identities=18%  Similarity=0.120  Sum_probs=83.6

Q ss_pred             cccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           43 CCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        43 ~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      ..+.++|..+++++.+|+            +..+.||+|||+++.+|++.....+.     .+.++.||++||.|.++.+
T Consensus        77 ~~p~~vQl~~~~~l~~G~------------Iaem~TGeGKTL~a~lp~~l~al~G~-----~v~VvTpt~~LA~qd~e~~  139 (790)
T PRK09200         77 MRPYDVQLIGALVLHEGN------------IAEMQTGEGKTLTATMPLYLNALEGK-----GVHLITVNDYLAKRDAEEM  139 (790)
T ss_pred             CCCchHHHHhHHHHcCCc------------eeeecCCCcchHHHHHHHHHHHHcCC-----CeEEEeCCHHHHHHHHHHH
Confidence            345577887777765443            44555999999999999985544432     3555559999999999988


Q ss_pred             HHHhccccCCCCceEEEEEeccc----ccCCCCceEEEECchHH-HHHHhc----C---CCCCCccEEEEecccc
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEK----ELPRKRGSILYCTAGIL-PEVMQS----D---PILSGVSHIVMDEIHE  185 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~----~~~~~~~~Iiv~Tpg~l-l~~l~~----~---~~l~~v~~vViDEah~  185 (319)
                      ...+...    |..+|.......    ......++|+++||+++ .+.++.    .   ..+.++.++|+||+|.
T Consensus       140 ~~l~~~l----Gl~v~~i~g~~~~~~~r~~~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDs  210 (790)
T PRK09200        140 GQVYEFL----GLTVGLNFSDIDDASEKKAIYEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDS  210 (790)
T ss_pred             HHHHhhc----CCeEEEEeCCCCcHHHHHHhcCCCEEEECCccccchhHHhccccchhhhcccccceEEEecccc
Confidence            8776543    666664443221    11113578999999988 444321    1   2468899999999996

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.27  E-value=5.3e-12  Score=125.80  Aligned_cols=126  Identities=21%  Similarity=0.112  Sum_probs=88.3

Q ss_pred             cCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHH
Q psy496           39 RGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAI  118 (319)
Q Consensus        39 ~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~  118 (319)
                      +.-...++++|..++|++++|+  ++.++          ||+|||++|.+|++.....+.     .++++.||++||.|.
T Consensus        98 R~lg~~p~~VQ~~~~~~ll~G~--Iae~~----------TGeGKTla~~lp~~~~al~G~-----~v~VvTptreLA~qd  160 (656)
T PRK12898         98 RVLGQRHFDVQLMGGLALLSGR--LAEMQ----------TGEGKTLTATLPAGTAALAGL-----PVHVITVNDYLAERD  160 (656)
T ss_pred             HHhCCCCChHHHHHHHHHhCCC--eeeee----------CCCCcHHHHHHHHHHHhhcCC-----eEEEEcCcHHHHHHH
Confidence            3445556799999999999877  66666          999999999999998765432     566666999999999


Q ss_pred             HHHHHHHhccccCCCCceEEEEEecccc---cCCCCceEEEECchHH-HHHHhcC-------------------------
Q psy496          119 AERVAQERDEQCGRPGSSVGYQIRLEKE---LPRKRGSILYCTAGIL-PEVMQSD-------------------------  169 (319)
Q Consensus       119 ~~~~~~~~~~~~~~~g~~vg~~~~~~~~---~~~~~~~Iiv~Tpg~l-l~~l~~~-------------------------  169 (319)
                      ++.+..++...    |..++......+.   .....++|+++|..-+ .+.++.+                         
T Consensus       161 ae~~~~l~~~l----Glsv~~i~gg~~~~~r~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~  236 (656)
T PRK12898        161 AELMRPLYEAL----GLTVGCVVEDQSPDERRAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRST  236 (656)
T ss_pred             HHHHHHHHhhc----CCEEEEEeCCCCHHHHHHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchh
Confidence            99888876543    6666644332111   1113678999998555 3333111                         


Q ss_pred             -CCCCCccEEEEecccc
Q psy496          170 -PILSGVSHIVMDEIHE  185 (319)
Q Consensus       170 -~~l~~v~~vViDEah~  185 (319)
                       .....+.+.||||+|.
T Consensus       237 ~~v~r~~~~aIvDEvDS  253 (656)
T PRK12898        237 QLLLRGLHFAIVDEADS  253 (656)
T ss_pred             hhcccccceeEeecccc
Confidence             1245688999999995

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

Probab=99.26  E-value=3.6e-11  Score=116.61  Aligned_cols=148  Identities=17%  Similarity=0.118  Sum_probs=92.2

Q ss_pred             ccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHH
Q psy496           42 ECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        42 ~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      ...+.+.|++++..+..-.+      .++..+++.|||+|||..+...+-..   ..     .+++++|+++|+.|.++.
T Consensus        34 ~~~lr~yQ~~al~a~~~~~~------~~~~gvivlpTGaGKT~va~~~~~~~---~~-----~~Lvlv~~~~L~~Qw~~~   99 (442)
T COG1061          34 EFELRPYQEEALDALVKNRR------TERRGVIVLPTGAGKTVVAAEAIAEL---KR-----STLVLVPTKELLDQWAEA   99 (442)
T ss_pred             CCCCcHHHHHHHHHHHhhcc------cCCceEEEeCCCCCHHHHHHHHHHHh---cC-----CEEEEECcHHHHHHHHHH
Confidence            34455778888777654111      16778999999999998876655332   11     266666999999999877


Q ss_pred             HHHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHH-hcCCCCCCccEEEEecccccccchhHHHHHHHhh
Q psy496          122 VAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVM-QSDPILSGVSHIVMDEIHERSMISDFLLAILKDV  200 (319)
Q Consensus       122 ~~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l-~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~  200 (319)
                      +...+...     ..+| ....+...... ..|.|+|.+.+.+.- .......++++||+||+|..  -.+........+
T Consensus       100 ~~~~~~~~-----~~~g-~~~~~~~~~~~-~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~--~a~~~~~~~~~~  170 (442)
T COG1061         100 LKKFLLLN-----DEIG-IYGGGEKELEP-AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHL--PAPSYRRILELL  170 (442)
T ss_pred             HHHhcCCc-----cccc-eecCceeccCC-CcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccC--CcHHHHHHHHhh
Confidence            77665432     0112 11111111111 459999999988752 22222347999999999983  333333333433


Q ss_pred             hccccCce-EEEecccc
Q psy496          201 TDKRKDLK-LILMSATL  216 (319)
Q Consensus       201 ~~~~~~~q-iv~lSAT~  216 (319)
                      ..    .. +++||||+
T Consensus       171 ~~----~~~~LGLTATp  183 (442)
T COG1061         171 SA----AYPRLGLTATP  183 (442)
T ss_pred             hc----ccceeeeccCc
Confidence            32    23 89999997

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.25  E-value=1.1e-11  Score=125.11  Aligned_cols=105  Identities=19%  Similarity=0.191  Sum_probs=73.4

Q ss_pred             EEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc------
Q psy496           72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK------  145 (319)
Q Consensus        72 vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~------  145 (319)
                      .++.++||+|||++|.+|++.......     .++++.|+++||.|.++.+.......    |..++.......      
T Consensus        86 ~Iaem~TGeGKTLta~Lpa~l~aL~g~-----~V~VVTpn~yLA~Rdae~m~~l~~~L----GLsv~~~~~~s~~~~~~~  156 (762)
T TIGR03714        86 NIAEMKTGEGKTLTATMPLYLNALTGK-----GAMLVTTNDYLAKRDAEEMGPVYEWL----GLTVSLGVVDDPDEEYDA  156 (762)
T ss_pred             ceeEecCCcchHHHHHHHHHHHhhcCC-----ceEEeCCCHHHHHHHHHHHHHHHhhc----CCcEEEEECCCCccccCH
Confidence            466777999999999999876554432     46777799999999998876665433    556654332100      


Q ss_pred             --ccCCCCceEEEECchHH-HHHHh----c---CCCCCCccEEEEecccc
Q psy496          146 --ELPRKRGSILYCTAGIL-PEVMQ----S---DPILSGVSHIVMDEIHE  185 (319)
Q Consensus       146 --~~~~~~~~Iiv~Tpg~l-l~~l~----~---~~~l~~v~~vViDEah~  185 (319)
                        ......++|+++||++| .+.+.    .   ...+.++.++|+||||.
T Consensus       157 ~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDs  206 (762)
T TIGR03714       157 NEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDS  206 (762)
T ss_pred             HHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhh
Confidence              11113678999999999 44442    1   22378899999999996

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.

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.25  E-value=1.8e-10  Score=116.22  Aligned_cols=128  Identities=15%  Similarity=0.116  Sum_probs=78.0

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc-C
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL-P  148 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~-~  148 (319)
                      .+-+|+.|||+|||......+.. +  .     .++|+++|+.+|+.|..+.+.+......    ..++. ...+... .
T Consensus       274 r~GIIvLPtGaGKTlvai~aa~~-l--~-----k~tLILvps~~Lv~QW~~ef~~~~~l~~----~~I~~-~tg~~k~~~  340 (732)
T TIGR00603       274 RSGIIVLPCGAGKSLVGVTAACT-V--K-----KSCLVLCTSAVSVEQWKQQFKMWSTIDD----SQICR-FTSDAKERF  340 (732)
T ss_pred             CCcEEEeCCCCChHHHHHHHHHH-h--C-----CCEEEEeCcHHHHHHHHHHHHHhcCCCC----ceEEE-EecCccccc
Confidence            46789999999999887654432 2  1     1456666999999999998887654321    12221 1111111 1


Q ss_pred             CCCceEEEECchHHHHHHhcC-------CCC--CCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          149 RKRGSILYCTAGILPEVMQSD-------PIL--SGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll~~l~~~-------~~l--~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      .....|+|+|+..+.......       ..+  ..++++|+||+|.  +-.......+..+    .....++||||+
T Consensus       341 ~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~--lpA~~fr~il~~l----~a~~RLGLTATP  411 (732)
T TIGR00603       341 HGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHV--VPAAMFRRVLTIV----QAHCKLGLTATL  411 (732)
T ss_pred             ccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEcccc--ccHHHHHHHHHhc----CcCcEEEEeecC
Confidence            123569999999775332111       112  4688999999997  3233333333322    233579999999

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).

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.24  E-value=2.2e-11  Score=123.98  Aligned_cols=107  Identities=16%  Similarity=0.126  Sum_probs=78.5

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc---
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE---  146 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~---  146 (319)
                      +--+..++||+|||++|.+|++.......     .+.++.|+++||.|.++.+...+...    |..+|........   
T Consensus        96 ~G~Iaem~TGeGKTL~a~Lpa~~~al~G~-----~V~VvTpn~yLA~qd~e~m~~l~~~l----GLtv~~i~gg~~~~~r  166 (896)
T PRK13104         96 EGNIAEMRTGEGKTLVATLPAYLNAISGR-----GVHIVTVNDYLAKRDSQWMKPIYEFL----GLTVGVIYPDMSHKEK  166 (896)
T ss_pred             cCccccccCCCCchHHHHHHHHHHHhcCC-----CEEEEcCCHHHHHHHHHHHHHHhccc----CceEEEEeCCCCHHHH
Confidence            44567788999999999999997665432     35566699999999999888776543    6677654332111   


Q ss_pred             cCCCCceEEEECchHH-HHHHhcCCC--C-----CCccEEEEecccc
Q psy496          147 LPRKRGSILYCTAGIL-PEVMQSDPI--L-----SGVSHIVMDEIHE  185 (319)
Q Consensus       147 ~~~~~~~Iiv~Tpg~l-l~~l~~~~~--l-----~~v~~vViDEah~  185 (319)
                      ...-.++|+++|||+| +++++.+..  +     ..+.++||||+|.
T Consensus       167 ~~~y~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDs  213 (896)
T PRK13104        167 QEAYKADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDS  213 (896)
T ss_pred             HHHhCCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhh
Confidence            1112578999999999 888865532  3     5899999999996

>KOG0949|consensus

Probab=99.23  E-value=8e-11  Score=118.40  Aligned_cols=179  Identities=17%  Similarity=0.149  Sum_probs=118.4

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEE
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGY  139 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~  139 (319)
                      ++.+.....|+.++|+|||.+|||.+-...+=..+....   ...|+++.|+++|..|+...+...++......|..+-.
T Consensus       517 ~elLDsvDr~eSavIVAPTSaGKTfisfY~iEKVLResD---~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~rg~sl~g  593 (1330)
T KOG0949|consen  517 RELLDSVDRNESAVIVAPTSAGKTFISFYAIEKVLRESD---SDVVIYVAPTKALVNQVSANVYARFDTKTFLRGVSLLG  593 (1330)
T ss_pred             HHHhhhhhcccceEEEeeccCCceeccHHHHHHHHhhcC---CCEEEEecchHHHhhhhhHHHHHhhccCccccchhhHh
Confidence            466777788899999999999999776555433333333   34799999999999999887777664332211222211


Q ss_pred             EEecccccCCCCceEEEECchHHHHHHhcCC----CCCCccEEEEecccccccchh-HHHHHHHhhhccccCceEEEecc
Q psy496          140 QIRLEKELPRKRGSILYCTAGILPEVMQSDP----ILSGVSHIVMDEIHERSMISD-FLLAILKDVTDKRKDLKLILMSA  214 (319)
Q Consensus       140 ~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~----~l~~v~~vViDEah~~~~~~~-~~~~~l~~~~~~~~~~qiv~lSA  214 (319)
                      ....+-...+-+|+|+|+-|+.+-..+.+.|    ....++++|+||+|..|-..+ .+...+-.+.    ..-++++||
T Consensus       594 ~ltqEYsinp~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll~li----~CP~L~LSA  669 (1330)
T KOG0949|consen  594 DLTQEYSINPWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLLLLI----PCPFLVLSA  669 (1330)
T ss_pred             hhhHHhcCCchhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHHHHHhc----CCCeeEEec
Confidence            2222222223478999999999988886643    378899999999998654433 3333322222    225899999


Q ss_pred             cc-ChhhHhhhhC--------CCCEEEeCCccccceeeee
Q psy496          215 TL-NAEKFSQFFG--------GAPILHIPGFTYPVQEYYL  245 (319)
Q Consensus       215 T~-~~~~l~~~l~--------~~~~i~~~~r~~~v~~~~~  245 (319)
                      |+ |+..+.+|+.        ++..+....|...+..++.
T Consensus       670 TigN~~l~qkWlnq~~R~~sr~~eli~~~erySel~l~v~  709 (1330)
T KOG0949|consen  670 TIGNPNLFQKWLNQRGRAMSRNAELIDYGERYSELGLVVY  709 (1330)
T ss_pred             ccCCHHHHHHHHHHHHhhcCCCeeeeehhhhhhhhcceee
Confidence            99 9999999996        2334555555544444433

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

Probab=99.21  E-value=3.2e-10  Score=117.25  Aligned_cols=183  Identities=15%  Similarity=0.149  Sum_probs=125.6

Q ss_pred             ccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHH
Q psy496           42 ECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        42 ~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      +...|+-|..||..+..  |.-..  ..=+=+|||.-|=|||++++-+.+.+...+.     .|.+++||..||+|.++.
T Consensus       592 PyeET~DQl~AI~eVk~--DM~~~--kpMDRLiCGDVGFGKTEVAmRAAFkAV~~GK-----QVAvLVPTTlLA~QHy~t  662 (1139)
T COG1197         592 PYEETPDQLKAIEEVKR--DMESG--KPMDRLICGDVGFGKTEVAMRAAFKAVMDGK-----QVAVLVPTTLLAQQHYET  662 (1139)
T ss_pred             CCcCCHHHHHHHHHHHH--HhccC--CcchheeecCcCCcHHHHHHHHHHHHhcCCC-----eEEEEcccHHhHHHHHHH
Confidence            44567889999988765  43222  2234689999999999999999888765543     455555999999999999


Q ss_pred             HHHHhccccCCCCceEEEEEeccccc---------CCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhH
Q psy496          122 VAQERDEQCGRPGSSVGYQIRLEKEL---------PRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF  192 (319)
Q Consensus       122 ~~~~~~~~~~~~g~~vg~~~~~~~~~---------~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~  192 (319)
                      +.+.|...    ...++.-.++....         ...+.+|+|+|.-    ++..+..+++++++||||-|++|+.-  
T Consensus       663 FkeRF~~f----PV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHr----LL~kdv~FkdLGLlIIDEEqRFGVk~--  732 (1139)
T COG1197         663 FKERFAGF----PVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHR----LLSKDVKFKDLGLLIIDEEQRFGVKH--  732 (1139)
T ss_pred             HHHHhcCC----CeeEEEecccCCHHHHHHHHHHHhcCCccEEEechH----hhCCCcEEecCCeEEEechhhcCccH--
Confidence            99988755    33444333322211         1135689999975    55666779999999999999977643  


Q ss_pred             HHHHHHhhhccccCceEEEeccccChhhHhhhhCC---CCEEE-eCCccccceeeeehh
Q psy496          193 LLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGG---APILH-IPGFTYPVQEYYLED  247 (319)
Q Consensus       193 ~~~~l~~~~~~~~~~qiv~lSAT~~~~~l~~~l~~---~~~i~-~~~r~~~v~~~~~~~  247 (319)
                       -..++   .+..+.-++-||||+=+..+.--+.+   -.++. .+....||++++.+.
T Consensus       733 -KEkLK---~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~pV~T~V~~~  787 (1139)
T COG1197         733 -KEKLK---ELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRLPVKTFVSEY  787 (1139)
T ss_pred             -HHHHH---HHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCCcceEEEEecC
Confidence             22333   34457789999999955555543322   22332 344558999888765

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

Probab=99.17  E-value=1.5e-10  Score=122.57  Aligned_cols=167  Identities=19%  Similarity=0.224  Sum_probs=99.0

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ..+.|.+||..+...   +.  ...+..+|+.+||||||..+.. ++..+.....  ..+||+++|+++|+.|..+.+..
T Consensus       414 lR~YQ~~AI~ai~~a---~~--~g~r~~Ll~maTGSGKT~tai~-li~~L~~~~~--~~rVLfLvDR~~L~~Qa~~~F~~  485 (1123)
T PRK11448        414 LRYYQEDAIQAVEKA---IV--EGQREILLAMATGTGKTRTAIA-LMYRLLKAKR--FRRILFLVDRSALGEQAEDAFKD  485 (1123)
T ss_pred             CCHHHHHHHHHHHHH---HH--hccCCeEEEeCCCCCHHHHHHH-HHHHHHhcCc--cCeEEEEecHHHHHHHHHHHHHh
Confidence            357788888776542   11  2346799999999999977543 3344443322  24788888999999999988876


Q ss_pred             HhccccCCCCceEE--EEEe-cccccCCCCceEEEECchHHHHHHhc------CCCCCCccEEEEecccccccchh----
Q psy496          125 ERDEQCGRPGSSVG--YQIR-LEKELPRKRGSILYCTAGILPEVMQS------DPILSGVSHIVMDEIHERSMISD----  191 (319)
Q Consensus       125 ~~~~~~~~~g~~vg--~~~~-~~~~~~~~~~~Iiv~Tpg~ll~~l~~------~~~l~~v~~vViDEah~~~~~~~----  191 (319)
                      .....    +....  +.+. ..+.......+|+|+|...+.+.+..      ...+..+++||+||||+ +...+    
T Consensus       486 ~~~~~----~~~~~~i~~i~~L~~~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHR-s~~~d~~~~  560 (1123)
T PRK11448        486 TKIEG----DQTFASIYDIKGLEDKFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHR-GYTLDKEMS  560 (1123)
T ss_pred             ccccc----ccchhhhhchhhhhhhcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCC-CCccccccc
Confidence            42111    10000  0111 11111223467999999998776521      13467899999999996 32100    


Q ss_pred             ----------HHHHHHHhhhccccCceEEEeccccChhhHhhhhC
Q psy496          192 ----------FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFG  226 (319)
Q Consensus       192 ----------~~~~~l~~~~~~~~~~qiv~lSAT~~~~~l~~~l~  226 (319)
                                -.....+.+.... +...|+||||+.. ...++|+
T Consensus       561 ~~~~~~~~~~~~~~~yr~iL~yF-dA~~IGLTATP~r-~t~~~FG  603 (1123)
T PRK11448        561 EGELQFRDQLDYVSKYRRVLDYF-DAVKIGLTATPAL-HTTEIFG  603 (1123)
T ss_pred             cchhccchhhhHHHHHHHHHhhc-CccEEEEecCCcc-chhHHhC
Confidence                      0012233333322 3468999999932 2345565

>KOG0952|consensus

Probab=99.17  E-value=1.5e-11  Score=124.42  Aligned_cols=209  Identities=13%  Similarity=0.116  Sum_probs=142.0

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      +.++++-+|||||||.++.+.++......+   ..+++++.|.++|.....+.+.+.....    |..++- ...+...+
T Consensus       943 d~~~~~g~ptgsgkt~~ae~a~~~~~~~~p---~~kvvyIap~kalvker~~Dw~~r~~~~----g~k~ie-~tgd~~pd 1014 (1230)
T KOG0952|consen  943 DLNFLLGAPTGSGKTVVAELAIFRALSYYP---GSKVVYIAPDKALVKERSDDWSKRDELP----GIKVIE-LTGDVTPD 1014 (1230)
T ss_pred             chhhhhcCCccCcchhHHHHHHHHHhccCC---CccEEEEcCCchhhcccccchhhhcccC----CceeEe-ccCccCCC
Confidence            356888999999999999999987765443   4699999999999998888887765432    333321 11111111


Q ss_pred             ---CCCceEEEECchHHH---HHHhcCCCCCCccEEEEecccc----cccchhHHHHHHHhhh-ccccCceEEEecccc-
Q psy496          149 ---RKRGSILYCTAGILP---EVMQSDPILSGVSHIVMDEIHE----RSMISDFLLAILKDVT-DKRKDLKLILMSATL-  216 (319)
Q Consensus       149 ---~~~~~Iiv~Tpg~ll---~~l~~~~~l~~v~~vViDEah~----~~~~~~~~~~~l~~~~-~~~~~~qiv~lSAT~-  216 (319)
                         -..++++++||+...   +-|.....+++++.+|+||.|.    |++-.+....+...+. ...+.+|++++|--+ 
T Consensus      1015 ~~~v~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~rgPVle~ivsr~n~~s~~t~~~vr~~glsta~~ 1094 (1230)
T KOG0952|consen 1015 VKAVREADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGEDRGPVLEVIVSRMNYISSQTEEPVRYLGLSTALA 1094 (1230)
T ss_pred             hhheecCceEEcccccccCccccccchhhhccccceeecccccccCCCcceEEEEeeccccCccccCcchhhhhHhhhhh
Confidence               135679999997664   4455666799999999999997    4444444444444322 244567899988777 


Q ss_pred             ChhhHhhhhCCCCE--EEeCCccccceeeeehhhhhhhhhhHH-HHHHHHhhhhhhhccccCCCcEEEeCCcccc
Q psy496          217 NAEKFSQFFGGAPI--LHIPGFTYPVQEYYLEDVLNMTRKDLK-LILMSATLNAEKFSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       217 ~~~~l~~~l~~~~~--i~~~~r~~~v~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~  288 (319)
                      |..++++|++-.+.  +....|+.|.+.++..++..  ...-+ ..+++..+.+++ ..++..++|||+.+|+-.
T Consensus      1095 na~dla~wl~~~~~~nf~~svrpvp~~~~i~gfp~~--~~cprm~smnkpa~qaik-~~sp~~p~lifv~srrqt 1166 (1230)
T KOG0952|consen 1095 NANDLADWLNIKDMYNFRPSVRPVPLEVHIDGFPGQ--HYCPRMMSMNKPAFQAIK-THSPIKPVLIFVSSRRQT 1166 (1230)
T ss_pred             ccHHHHHHhCCCCcCCCCcccccCCceEeecCCCch--hcchhhhhcccHHHHHHh-cCCCCCceEEEeeccccc
Confidence            99999999986665  44456777888887776632  22222 233344555544 345688999999998764

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.10  E-value=1e-09  Score=112.74  Aligned_cols=165  Identities=18%  Similarity=0.096  Sum_probs=95.9

Q ss_pred             HhhhcCCCCC-cEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEE
Q psy496           61 KCLTLSPILS-PSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGY  139 (319)
Q Consensus        61 ~~l~~~~~~~-~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~  139 (319)
                      +........+ .+++.||||+|||++.+.+.+...... .....+++++.|+|.+..++++++....+..........+.
T Consensus       205 ~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~-~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~~~~~~~~h~~  283 (733)
T COG1203         205 ELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEK-IKLKSRVIYVLPFRTIIEDMYRRAKEIFGLFSVIGKSLHSS  283 (733)
T ss_pred             HHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhcc-ccccceEEEEccHHHHHHHHHHHHHhhhccccccccccccc
Confidence            3333444445 899999999999999999988776553 12456999999999999999999987655332111100110


Q ss_pred             EEe---------------cccccCCCCceEEEECchHHHHHHhcCCCC-----CCccEEEEecccccccc--hhHHHHHH
Q psy496          140 QIR---------------LEKELPRKRGSILYCTAGILPEVMQSDPIL-----SGVSHIVMDEIHERSMI--SDFLLAIL  197 (319)
Q Consensus       140 ~~~---------------~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l-----~~v~~vViDEah~~~~~--~~~~~~~l  197 (319)
                      ...               ..+.....-..+.++||-............     -..+.+|+||+|.....  ..+++..+
T Consensus       284 ~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~~~~~~l~~~i  363 (733)
T COG1203         284 SKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADETMLAALLALL  363 (733)
T ss_pred             ccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhcccchHHHHHHHH
Confidence            000               000000001124444443333322111111     23578999999984433  33555555


Q ss_pred             HhhhccccCceEEEeccccCh---hhHhhhhCCC
Q psy496          198 KDVTDKRKDLKLILMSATLNA---EKFSQFFGGA  228 (319)
Q Consensus       198 ~~~~~~~~~~qiv~lSAT~~~---~~l~~~l~~~  228 (319)
                      ..+...  +..+|+||||++.   +.+.+.++..
T Consensus       364 ~~l~~~--g~~ill~SATlP~~~~~~l~~~~~~~  395 (733)
T COG1203         364 EALAEA--GVPVLLMSATLPPFLKEKLKKALGKG  395 (733)
T ss_pred             HHHHhC--CCCEEEEecCCCHHHHHHHHHHHhcc
Confidence            555544  4579999999943   3455555543

>KOG0349|consensus

Probab=99.09  E-value=6.9e-11  Score=109.90  Aligned_cols=120  Identities=18%  Similarity=0.164  Sum_probs=73.2

Q ss_pred             EEEEecccHHHHHHHHHHHHHHhcccc---CCCCceEE-EEEecccccCCCCceEEEECchHHHHHHhcC-CCCCCccEE
Q psy496          104 CIMVTQPRRISAIAIAERVAQERDEQC---GRPGSSVG-YQIRLEKELPRKRGSILYCTAGILPEVMQSD-PILSGVSHI  178 (319)
Q Consensus       104 ~vl~~~Ptr~la~q~~~~~~~~~~~~~---~~~g~~vg-~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~v  178 (319)
                      ..+++.|.||||.|..+.+.++.....   ..--..+| ...+..-....+..+|+|+||||+++.+... ..+++++++
T Consensus       288 ~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~g~~~lt~crFl  367 (725)
T KOG0349|consen  288 EAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTHCRFL  367 (725)
T ss_pred             ceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhccceeeeeeEEE
Confidence            567778999999999986655421110   00001122 1122222233456899999999999999554 458999999


Q ss_pred             EEeccccc-c-cchhHHHHHH---HhhhccccCceEEEecccc---ChhhHhh
Q psy496          179 VMDEIHER-S-MISDFLLAIL---KDVTDKRKDLKLILMSATL---NAEKFSQ  223 (319)
Q Consensus       179 ViDEah~~-~-~~~~~~~~~l---~~~~~~~~~~qiv~lSAT~---~~~~l~~  223 (319)
                      |+||+|.. + ...|.....-   ..+..-...+|.+++|||+   ++..+++
T Consensus       368 vlDead~lL~qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~e  420 (725)
T KOG0349|consen  368 VLDEADLLLGQGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGE  420 (725)
T ss_pred             EecchhhhhhcccHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhh
Confidence            99999961 1 1222222222   2222223457899999999   5666664

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

Probab=99.06  E-value=9.1e-10  Score=111.95  Aligned_cols=135  Identities=16%  Similarity=0.188  Sum_probs=81.0

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEe-ccccc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIR-LEKEL  147 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~-~~~~~  147 (319)
                      .+..+|+.+||||||......+.. +....  ...+|+++.|+++|..|..+.+........    ...+ ... .....
T Consensus       263 ~~~gli~~~TGsGKT~t~~~la~~-l~~~~--~~~~vl~lvdR~~L~~Q~~~~f~~~~~~~~----~~~~-s~~~L~~~l  334 (667)
T TIGR00348       263 ERGGLIWHTQGSGKTLTMLFAARK-ALELL--KNPKVFFVVDRRELDYQLMKEFQSLQKDCA----ERIE-SIAELKRLL  334 (667)
T ss_pred             CceeEEEEecCCCccHHHHHHHHH-HHhhc--CCCeEEEEECcHHHHHHHHHHHHhhCCCCC----cccC-CHHHHHHHH
Confidence            457999999999999877655433 33222  235788888999999999998877642111    0000 000 11111


Q ss_pred             CCCCceEEEECchHHHHHHhcC---CCCCCc-cEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          148 PRKRGSILYCTAGILPEVMQSD---PILSGV-SHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       148 ~~~~~~Iiv~Tpg~ll~~l~~~---~~l~~v-~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      ......|+|+|.+.+.+.+...   .....- -+||+||||+ +. .+.+...++   ...|+...++||||+
T Consensus       335 ~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHr-s~-~~~~~~~l~---~~~p~a~~lGfTaTP  402 (667)
T TIGR00348       335 EKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHR-SQ-YGELAKNLK---KALKNASFFGFTGTP  402 (667)
T ss_pred             hCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCcc-cc-chHHHHHHH---hhCCCCcEEEEeCCC
Confidence            1123569999999987644221   111111 2899999996 22 222222232   223466899999999

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

>KOG0352|consensus

Probab=99.00  E-value=1.5e-09  Score=101.02  Aligned_cols=221  Identities=17%  Similarity=0.101  Sum_probs=117.6

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      +.|++|+.++         ...+++|.++-|||+||+++|.+|.|-+   .+     .-++++|.-+|..+...-+..+ 
T Consensus        23 ~LQE~A~~c~---------VK~k~DVyVsMPTGaGKSLCyQLPaL~~---~g-----ITIV~SPLiALIkDQiDHL~~L-   84 (641)
T KOG0352|consen   23 RLQEQAINCI---------VKRKCDVYVSMPTGAGKSLCYQLPALVH---GG-----ITIVISPLIALIKDQIDHLKRL-   84 (641)
T ss_pred             hHHHHHHHHH---------HhccCcEEEeccCCCchhhhhhchHHHh---CC-----eEEEehHHHHHHHHHHHHHHhc-
Confidence            6677777654         3466889999999999999999997643   22     5667789999988766545443 


Q ss_pred             ccccCCCCceEEEEEe----cccccCCCCceEEEECchHHH-----HHHhcCCCCCCccEEEEecccc-----cccchh-
Q psy496          127 DEQCGRPGSSVGYQIR----LEKELPRKRGSILYCTAGILP-----EVMQSDPILSGVSHIVMDEIHE-----RSMISD-  191 (319)
Q Consensus       127 ~~~~~~~g~~vg~~~~----~~~~~~~~~~~Iiv~Tpg~ll-----~~l~~~~~l~~v~~vViDEah~-----~~~~~~-  191 (319)
                      ...+...........+    .+-.......+|++-||+..-     .++.+-..-.-++++|+||||.     ++...| 
T Consensus        85 KVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQWGHDFRPDY  164 (641)
T KOG0352|consen   85 KVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQWGHDFRPDY  164 (641)
T ss_pred             CCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHhhhccccCcch
Confidence            1111000111111111    111111124579999996541     2222111124578999999996     222223 


Q ss_pred             HHHHHHHhhhccccCceEEEeccccChh---hHhhhhC-CCCE--EEeCC-cc-ccceeeeehhhhhhhhhhHHHHHHHH
Q psy496          192 FLLAILKDVTDKRKDLKLILMSATLNAE---KFSQFFG-GAPI--LHIPG-FT-YPVQEYYLEDVLNMTRKDLKLILMSA  263 (319)
Q Consensus       192 ~~~~~l~~~~~~~~~~qiv~lSAT~~~~---~l~~~l~-~~~~--i~~~~-r~-~~v~~~~~~~~~~~~~~~~~~~~~~~  263 (319)
                      +-++.++   ..-++.-.|.++||.+++   ++..-+. ..|+  |..+. |. .-.+++|-..+ ...-..++....+.
T Consensus       165 L~LG~LR---S~~~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~FR~NLFYD~~~K~~I-~D~~~~LaDF~~~~  240 (641)
T KOG0352|consen  165 LTLGSLR---SVCPGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTFRDNLFYDNHMKSFI-TDCLTVLADFSSSN  240 (641)
T ss_pred             hhhhhHH---hhCCCCceEEeecccChhHHHHHHHHHhhcCcHHhccCcchhhhhhHHHHHHHHh-hhHhHhHHHHHHHh
Confidence            2222222   233466789999999654   3333221 2222  22111 10 00122222221 22223455555555


Q ss_pred             hhhhhhhc---cccCCCcEEEeCCccccc
Q psy496          264 TLNAEKFS---QFFGGAPILHIPGFTYPV  289 (319)
Q Consensus       264 ~~~~~~~~---~~~~g~~LVFlp~R~~~v  289 (319)
                      .-+.+.+.   +.+.|..||+|.||..+-
T Consensus       241 LG~~~~~~~~~K~~~GCGIVYCRTR~~cE  269 (641)
T KOG0352|consen  241 LGKHEKASQNKKTFTGCGIVYCRTRNECE  269 (641)
T ss_pred             cCChhhhhcCCCCcCcceEEEeccHHHHH
Confidence            55444333   234789999999998773

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

Probab=98.92  E-value=2.5e-09  Score=105.14  Aligned_cols=154  Identities=18%  Similarity=0.123  Sum_probs=92.4

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      +-|.++|..+++|++          +++.-|||.||+++|.+|.+-.   .     +..|+++|.-+|-.+..+.+... 
T Consensus        20 ~gQ~evI~~~l~g~d----------~lvvmPTGgGKSlCyQiPAll~---~-----G~TLVVSPLiSLM~DQV~~l~~~-   80 (590)
T COG0514          20 PGQQEIIDALLSGKD----------TLVVMPTGGGKSLCYQIPALLL---E-----GLTLVVSPLISLMKDQVDQLEAA-   80 (590)
T ss_pred             CCHHHHHHHHHcCCc----------EEEEccCCCCcchHhhhHHHhc---C-----CCEEEECchHHHHHHHHHHHHHc-
Confidence            558888877776655          5555569999999999997532   2     27888889999977766656543 


Q ss_pred             ccccCCCCceEEEEEec---------ccccCCCCceEEEECchHHHHHH-hcCCCCCCccEEEEecccccccch-hH--H
Q psy496          127 DEQCGRPGSSVGYQIRL---------EKELPRKRGSILYCTAGILPEVM-QSDPILSGVSHIVMDEIHERSMIS-DF--L  193 (319)
Q Consensus       127 ~~~~~~~g~~vg~~~~~---------~~~~~~~~~~Iiv~Tpg~ll~~l-~~~~~l~~v~~vViDEah~~~~~~-~~--~  193 (319)
                             |....+....         .........++++-+|+++..-. .....-..+.++||||||..+--. ||  -
T Consensus        81 -------Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~  153 (590)
T COG0514          81 -------GIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPD  153 (590)
T ss_pred             -------CceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHh
Confidence                   3222211110         01111123579999999884322 111113578999999999722111 11  1


Q ss_pred             HHHHHhhhccccCceEEEeccccChh---hHhhhhC
Q psy496          194 LAILKDVTDKRKDLKLILMSATLNAE---KFSQFFG  226 (319)
Q Consensus       194 ~~~l~~~~~~~~~~qiv~lSAT~~~~---~l~~~l~  226 (319)
                      ...+..+...-+++.++.++||.+..   ++.+-|+
T Consensus       154 Y~~lg~l~~~~~~~p~~AlTATA~~~v~~DI~~~L~  189 (590)
T COG0514         154 YRRLGRLRAGLPNPPVLALTATATPRVRDDIREQLG  189 (590)
T ss_pred             HHHHHHHHhhCCCCCEEEEeCCCChHHHHHHHHHhc
Confidence            12233333333477899999999544   5555554

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=98.91  E-value=1.9e-09  Score=109.86  Aligned_cols=103  Identities=18%  Similarity=0.143  Sum_probs=73.0

Q ss_pred             EEecCCCCCccchhhHHHH-HHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc---cC
Q psy496           73 IIYTSTGCGKTTQVPQFIL-DDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE---LP  148 (319)
Q Consensus        73 li~apTGSGKT~~~~l~il-~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~---~~  148 (319)
                      +..+.||+|||+++.+|++ +.+ .+.   ++.|+  .|++.||.|.++.+...+...    |..+|......+.   ..
T Consensus        98 Iaem~TGeGKTLva~lpa~l~aL-~G~---~V~Iv--Tpn~yLA~rd~e~~~~l~~~L----Glsv~~i~~~~~~~er~~  167 (830)
T PRK12904         98 IAEMKTGEGKTLVATLPAYLNAL-TGK---GVHVV--TVNDYLAKRDAEWMGPLYEFL----GLSVGVILSGMSPEERRE  167 (830)
T ss_pred             hhhhhcCCCcHHHHHHHHHHHHH-cCC---CEEEE--ecCHHHHHHHHHHHHHHHhhc----CCeEEEEcCCCCHHHHHH
Confidence            4445599999999999996 554 222   34444  499999999999888876543    6667644432111   11


Q ss_pred             CCCceEEEECchHH-HHHHhcCC-------CCCCccEEEEecccc
Q psy496          149 RKRGSILYCTAGIL-PEVMQSDP-------ILSGVSHIVMDEIHE  185 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~l-l~~l~~~~-------~l~~v~~vViDEah~  185 (319)
                      .-.++|+++||+++ +++++.+.       .+..+.++||||||.
T Consensus       168 ~y~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDs  212 (830)
T PRK12904        168 AYAADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDS  212 (830)
T ss_pred             hcCCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhh
Confidence            12478999999999 88885433       267899999999996

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

Probab=98.90  E-value=1e-08  Score=102.49  Aligned_cols=57  Identities=18%  Similarity=0.066  Sum_probs=45.9

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      ..+++.+++.|+||||||.+|++|++..+....   ..+++++.||++|+.|+.+.+...
T Consensus        13 l~~~~~lliEA~TGtGKTlAYLlpal~~~~~~~---~~rvlIstpT~~Lq~Ql~~~l~~l   69 (636)
T TIGR03117        13 LRQKRIGMLEASTGVGKTLAMIMAALTMLKERP---DQKIAIAVPTLALMGQLWSELERL   69 (636)
T ss_pred             HhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhcc---CceEEEECCcHHHHHHHHHHHHHH
Confidence            346788999999999999999999987665322   248899999999999998765543

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.

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.81  E-value=7.1e-09  Score=104.70  Aligned_cols=134  Identities=7%  Similarity=0.015  Sum_probs=81.2

Q ss_pred             EEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhc-cccCCCCceEEEEEecccc----
Q psy496           72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERD-EQCGRPGSSVGYQIRLEKE----  146 (319)
Q Consensus        72 vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~-~~~~~~g~~vg~~~~~~~~----  146 (319)
                      .+..+.+|||||..|+..+-+.+..++     .+|++.|...|+.|+.+++...++ ..+      ..+.......    
T Consensus       163 ~i~~~~~GSGKTevyl~~i~~~l~~Gk-----~vLvLvPEi~lt~q~~~rl~~~f~~~~v------~~lhS~l~~~~R~~  231 (665)
T PRK14873        163 AVWQALPGEDWARRLAAAAAATLRAGR-----GALVVVPDQRDVDRLEAALRALLGAGDV------AVLSAGLGPADRYR  231 (665)
T ss_pred             HHhhcCCCCcHHHHHHHHHHHHHHcCC-----eEEEEecchhhHHHHHHHHHHHcCCCcE------EEECCCCCHHHHHH
Confidence            344455799999999887766655433     455555999999999999998876 221      1111111111    


Q ss_pred             ----cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchh-----HHHHHHHhhhccccCceEEEeccccC
Q psy496          147 ----LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD-----FLLAILKDVTDKRKDLKLILMSATLN  217 (319)
Q Consensus       147 ----~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~-----~~~~~l~~~~~~~~~~qiv~lSAT~~  217 (319)
                          ......+|+|+|-.-++      ..+.++++|||||-|.-+...+     ...+ +........+..+|+.|||..
T Consensus       232 ~w~~~~~G~~~IViGtRSAvF------aP~~~LgLIIvdEEhd~sykq~~~p~yhaRd-vA~~Ra~~~~~~lvLgSaTPS  304 (665)
T PRK14873        232 RWLAVLRGQARVVVGTRSAVF------APVEDLGLVAIWDDGDDLLAEPRAPYPHARE-VALLRAHQHGCALLIGGHART  304 (665)
T ss_pred             HHHHHhCCCCcEEEEcceeEE------eccCCCCEEEEEcCCchhhcCCCCCCccHHH-HHHHHHHHcCCcEEEECCCCC
Confidence                11234679999865322      1368999999999996221111     0010 111111123668999999998


Q ss_pred             hhhHhh
Q psy496          218 AEKFSQ  223 (319)
Q Consensus       218 ~~~l~~  223 (319)
                      .+.+..
T Consensus       305 les~~~  310 (665)
T PRK14873        305 AEAQAL  310 (665)
T ss_pred             HHHHHH
Confidence            776654

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.80  E-value=1e-08  Score=104.70  Aligned_cols=108  Identities=18%  Similarity=0.115  Sum_probs=77.5

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecc---c
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLE---K  145 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~---~  145 (319)
                      ++--+...+||+|||+++.+|++.....+.   .  |.++.|++.||.+.++.+...+...    |..+|......   .
T Consensus        95 ~~G~IaEm~TGEGKTL~a~lp~~l~al~g~---~--VhIvT~ndyLA~RD~e~m~~l~~~l----Glsv~~i~~~~~~~~  165 (908)
T PRK13107         95 DSNRIAEMRTGEGKTLTATLPAYLNALTGK---G--VHVITVNDYLARRDAENNRPLFEFL----GLTVGINVAGLGQQE  165 (908)
T ss_pred             cCCccccccCCCCchHHHHHHHHHHHhcCC---C--EEEEeCCHHHHHHHHHHHHHHHHhc----CCeEEEecCCCCHHH
Confidence            344566777999999999999986665433   2  5555599999999998887776553    77777543321   1


Q ss_pred             ccCCCCceEEEECchHH-HHHHhcCC-------CCCCccEEEEecccc
Q psy496          146 ELPRKRGSILYCTAGIL-PEVMQSDP-------ILSGVSHIVMDEIHE  185 (319)
Q Consensus       146 ~~~~~~~~Iiv~Tpg~l-l~~l~~~~-------~l~~v~~vViDEah~  185 (319)
                      ....-.++|+++||+.+ ++.++.+-       ....+.+.||||+|.
T Consensus       166 r~~~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDs  213 (908)
T PRK13107        166 KKAAYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDS  213 (908)
T ss_pred             HHhcCCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhh
Confidence            11112578999999999 88775431       137789999999996

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

Probab=98.74  E-value=3.3e-07  Score=93.58  Aligned_cols=111  Identities=19%  Similarity=0.190  Sum_probs=72.1

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecc---
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLE---  144 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~---  144 (319)
                      .|+..-|.||||.|||+..++..+   +...++.  +++++.||+.|+.|.++++.++..... .....+.|+....   
T Consensus        96 rg~SFaiiAPTGvGKTTfg~~~sl---~~a~kgk--r~yii~PT~~Lv~Q~~~kl~~~~e~~~-~~~~~~~yh~~l~~~e  169 (1187)
T COG1110          96 RGKSFAIIAPTGVGKTTFGLLMSL---YLAKKGK--RVYIIVPTTTLVRQVYERLKKFAEDAG-SLDVLVVYHSALPTKE  169 (1187)
T ss_pred             cCCceEEEcCCCCchhHHHHHHHH---HHHhcCC--eEEEEecCHHHHHHHHHHHHHHHhhcC-CcceeeeeccccchHH
Confidence            567889999999999987654433   2222232  566666999999999999988754332 0011221221111   


Q ss_pred             -----cccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccc
Q psy496          145 -----KELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHE  185 (319)
Q Consensus       145 -----~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~  185 (319)
                           ....+...+|+|+|.+.|......-.. .+++++++|++|.
T Consensus       170 kee~le~i~~gdfdIlitTs~FL~k~~e~L~~-~kFdfifVDDVDA  214 (1187)
T COG1110         170 KEEALERIESGDFDILITTSQFLSKRFEELSK-LKFDFIFVDDVDA  214 (1187)
T ss_pred             HHHHHHHHhcCCccEEEEeHHHHHhhHHHhcc-cCCCEEEEccHHH
Confidence                 111223568999999999877743222 4789999999995

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

Probab=98.70  E-value=7.6e-08  Score=100.71  Aligned_cols=65  Identities=17%  Similarity=0.068  Sum_probs=48.0

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAE  120 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~  120 (319)
                      ..+.|.+.+..+..      ...+++++++.||||+|||.+|++|++.... .+    .+|+++.||++|..|+..
T Consensus       246 ~r~~Q~~~~~~i~~------~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~-~~----~~vvi~t~t~~Lq~Ql~~  310 (850)
T TIGR01407       246 YRPEQLKLAELVLD------QLTHSEKSLIEAPTGTGKTLGYLLPALYYAI-TE----KPVVISTNTKVLQSQLLE  310 (850)
T ss_pred             cCHHHHHHHHHHHH------HhccCCcEEEECCCCCchhHHHHHHHHHHhc-CC----CeEEEEeCcHHHHHHHHH
Confidence            34566665554433      2335678999999999999999999877544 22    378888899999999854

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.

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

Probab=98.67  E-value=1e-07  Score=98.99  Aligned_cols=48  Identities=27%  Similarity=0.196  Sum_probs=39.7

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIA  119 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~  119 (319)
                      ..+++.+++.|+||||||.+|++|++...  .    +.+++++.||++|+.|+.
T Consensus       261 l~~~~~~~~eA~tGtGKT~ayllp~l~~~--~----~~~vvI~t~T~~Lq~Ql~  308 (820)
T PRK07246        261 FHDGPASFIEAQTGIGKTYGYLLPLLAQS--D----QRQIIVSVPTKILQDQIM  308 (820)
T ss_pred             HhCCCcEEEECCCCCcHHHHHHHHHHHhc--C----CCcEEEEeCcHHHHHHHH
Confidence            34678899999999999999999987643  1    247888889999999994

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

Probab=98.65  E-value=1.4e-07  Score=94.64  Aligned_cols=131  Identities=18%  Similarity=0.141  Sum_probs=83.3

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL  147 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~  147 (319)
                      +++.+||+-.||+|||-.+.. ++..++..+.  .-+||++.-+++|..|....+...+-.     |..+-  . ..+..
T Consensus       184 g~~raLlvMATGTGKTrTAia-ii~rL~r~~~--~KRVLFLaDR~~Lv~QA~~af~~~~P~-----~~~~n--~-i~~~~  252 (875)
T COG4096         184 GQNRALLVMATGTGKTRTAIA-IIDRLIKSGW--VKRVLFLADRNALVDQAYGAFEDFLPF-----GTKMN--K-IEDKK  252 (875)
T ss_pred             CCceEEEEEecCCCcceeHHH-HHHHHHhcch--hheeeEEechHHHHHHHHHHHHHhCCC-----cccee--e-eeccc
Confidence            345599999999999977644 4455554332  238999999999999999877766432     11111  1 11111


Q ss_pred             CCCCceEEEECchHHHHHHhcC-C-----CCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          148 PRKRGSILYCTAGILPEVMQSD-P-----ILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       148 ~~~~~~Iiv~Tpg~ll~~l~~~-~-----~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      ....++|.++|...+...+... .     ....+++|||||||+ |...+.. +++..+..     .+++++||+
T Consensus       253 ~~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHR-gi~~~~~-~I~dYFdA-----~~~gLTATP  320 (875)
T COG4096         253 GDTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHR-GIYSEWS-SILDYFDA-----ATQGLTATP  320 (875)
T ss_pred             CCcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhh-hHHhhhH-HHHHHHHH-----HHHhhccCc
Confidence            1124679999999998877433 1     245599999999995 5544422 33333322     245569998

>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=98.59  E-value=4.8e-07  Score=82.69  Aligned_cols=145  Identities=15%  Similarity=0.062  Sum_probs=71.8

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCC-CccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRG-SECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK  145 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~-~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~  145 (319)
                      ......+++-++|+|||......+. .+...... ....+|+++|. .+..+-.+.+.+.....    ...+- ......
T Consensus        23 ~~~~g~lL~de~GlGKT~~~i~~~~-~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~----~~~v~-~~~~~~   95 (299)
T PF00176_consen   23 SPPRGGLLADEMGLGKTITAIALIS-YLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPD----SLRVI-IYDGDS   95 (299)
T ss_dssp             TTT-EEEE---TTSSHHHHHHHHHH-HHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT-----TS-EE-EESSSC
T ss_pred             cCCCCEEEEECCCCCchhhhhhhhh-hhhhccccccccceeEeecc-chhhhhhhhhccccccc----ccccc-cccccc
Confidence            3456789999999999977765543 33332221 11235555698 55566666676665321    01111 111111


Q ss_pred             ------ccCCCCceEEEECchHHHHHHhc--CCCC--CCccEEEEeccccc-ccchhHHHHHHHhhhccccCceEEEecc
Q psy496          146 ------ELPRKRGSILYCTAGILPEVMQS--DPIL--SGVSHIVMDEIHER-SMISDFLLAILKDVTDKRKDLKLILMSA  214 (319)
Q Consensus       146 ------~~~~~~~~Iiv~Tpg~ll~~l~~--~~~l--~~v~~vViDEah~~-~~~~~~~~~~l~~~~~~~~~~qiv~lSA  214 (319)
                            .......+++++|.+.+......  ...+  -+.+.||+||+|.. +...... ..+..+.    ...++++||
T Consensus        96 ~~~~~~~~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k~~~s~~~-~~l~~l~----~~~~~lLSg  170 (299)
T PF00176_consen   96 ERRRLSKNQLPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLKNKDSKRY-KALRKLR----ARYRWLLSG  170 (299)
T ss_dssp             HHHHTTSSSCCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGTTTTSHHH-HHHHCCC----ECEEEEE-S
T ss_pred             ccccccccccccceeeeccccccccccccccccccccccceeEEEeccccccccccccc-ccccccc----cceEEeecc
Confidence                  12224567999999998811100  0001  34899999999983 2222222 2222222    346788999


Q ss_pred             cc---ChhhHhh
Q psy496          215 TL---NAEKFSQ  223 (319)
Q Consensus       215 T~---~~~~l~~  223 (319)
                      |+   +..++..
T Consensus       171 TP~~n~~~dl~~  182 (299)
T PF00176_consen  171 TPIQNSLEDLYS  182 (299)
T ss_dssp             S-SSSGSHHHHH
T ss_pred             cccccccccccc
Confidence            98   3444443

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.

>KOG0351|consensus

Probab=98.58  E-value=6.2e-08  Score=100.50  Aligned_cols=211  Identities=18%  Similarity=0.077  Sum_probs=110.9

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      +-|.++|-+.+.|++          .+|..|||.||+++|.+|.+-   ..+     ..++++|...|.......+... 
T Consensus       267 ~~Q~eaI~~~l~Gkd----------~fvlmpTG~GKSLCYQlPA~l---~~g-----itvVISPL~SLm~DQv~~L~~~-  327 (941)
T KOG0351|consen  267 PNQLEAINATLSGKD----------CFVLMPTGGGKSLCYQLPALL---LGG-----VTVVISPLISLMQDQVTHLSKK-  327 (941)
T ss_pred             hhHHHHHHHHHcCCc----------eEEEeecCCceeeEeeccccc---cCC-----ceEEeccHHHHHHHHHHhhhhc-
Confidence            557777777776666          566666999999999999753   222     6777789999988776655221 


Q ss_pred             ccccCCCCceEEE-EEe-----cccccCC--CCceEEEECchHHHHHH---hcCCCCCC---ccEEEEecccccc---cc
Q psy496          127 DEQCGRPGSSVGY-QIR-----LEKELPR--KRGSILYCTAGILPEVM---QSDPILSG---VSHIVMDEIHERS---MI  189 (319)
Q Consensus       127 ~~~~~~~g~~vg~-~~~-----~~~~~~~--~~~~Iiv~Tpg~ll~~l---~~~~~l~~---v~~vViDEah~~~---~~  189 (319)
                      +..    +...+. +..     .......  ...+|++.||+.+...-   .....+..   +..+||||||..+   .+
T Consensus       328 ~I~----a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHd  403 (941)
T KOG0351|consen  328 GIP----ACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHD  403 (941)
T ss_pred             Ccc----eeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhccc
Confidence            111    111111 100     0001111  25689999998774332   11122344   8999999999711   11


Q ss_pred             hhHHHHHHHhhhccccCceEEEeccccC---hhhHhhhhC--CCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHh
Q psy496          190 SDFLLAILKDVTDKRKDLKLILMSATLN---AEKFSQFFG--GAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSAT  264 (319)
Q Consensus       190 ~~~~~~~l~~~~~~~~~~qiv~lSAT~~---~~~l~~~l~--~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~  264 (319)
                      ..-....+..+....+..-++.++||..   .+++.+-++  ++.++.. .-..+ -.+| ... ....   +..+....
T Consensus       404 FRp~Yk~l~~l~~~~~~vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~-sfnR~-NL~y-eV~-~k~~---~~~~~~~~  476 (941)
T KOG0351|consen  404 FRPSYKRLGLLRIRFPGVPFIALTATATERVREDVIRSLGLRNPELFKS-SFNRP-NLKY-EVS-PKTD---KDALLDIL  476 (941)
T ss_pred             ccHHHHHHHHHHhhCCCCCeEEeehhccHHHHHHHHHHhCCCCcceecc-cCCCC-CceE-EEE-eccC---ccchHHHH
Confidence            1111112222222334467999999983   346666654  3332221 11111 1111 110 1111   11111112


Q ss_pred             hhhhhhccccCCCcEEEeCCccccc
Q psy496          265 LNAEKFSQFFGGAPILHIPGFTYPV  289 (319)
Q Consensus       265 ~~~~~~~~~~~g~~LVFlp~R~~~v  289 (319)
                      ...  ....+.++.||+|.+|..|-
T Consensus       477 ~~~--~~~~~~~s~IIYC~sr~~ce  499 (941)
T KOG0351|consen  477 EES--KLRHPDQSGIIYCLSRKECE  499 (941)
T ss_pred             HHh--hhcCCCCCeEEEeCCcchHH
Confidence            222  12234788999999999883

>KOG0353|consensus

Probab=98.41  E-value=5.3e-07  Score=83.12  Aligned_cols=149  Identities=21%  Similarity=0.129  Sum_probs=87.5

Q ss_pred             ccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           46 MVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        46 ~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      .|.|..+|.+...|++          +++.-|||-||+++|.+|.+-   ..+     ..++++|.-.|.....-.+..+
T Consensus        96 rplq~~ain~~ma~ed----------~~lil~tgggkslcyqlpal~---adg-----~alvi~plislmedqil~lkql  157 (695)
T KOG0353|consen   96 RPLQLAAINATMAGED----------AFLILPTGGGKSLCYQLPALC---ADG-----FALVICPLISLMEDQILQLKQL  157 (695)
T ss_pred             ChhHHHHhhhhhccCc----------eEEEEeCCCccchhhhhhHHh---cCC-----ceEeechhHHHHHHHHHHHHHh
Confidence            3779999888877766          455566999999999999763   333     4555569999887666555544


Q ss_pred             hcccc--CCCCceEEEEEecccccCC--CCceEEEECchHH------HHHHhcCCCCCCccEEEEecccc-----cccch
Q psy496          126 RDEQC--GRPGSSVGYQIRLEKELPR--KRGSILYCTAGIL------PEVMQSDPILSGVSHIVMDEIHE-----RSMIS  190 (319)
Q Consensus       126 ~~~~~--~~~g~~vg~~~~~~~~~~~--~~~~Iiv~Tpg~l------l~~l~~~~~l~~v~~vViDEah~-----~~~~~  190 (319)
                       +...  ..........-+.+....+  ..-++++.||+.+      ++.+.......-+..+-+||+|.     ++...
T Consensus       158 -gi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~iaidevhccsqwghdfr~  236 (695)
T KOG0353|consen  158 -GIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHCCSQWGHDFRP  236 (695)
T ss_pred             -CcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEeecceeehhhhCcccCc
Confidence             1110  0000000000111111111  2346999999876      33332222345688999999996     22233


Q ss_pred             h-HHHHHHHhhhccccCceEEEecccc
Q psy496          191 D-FLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       191 ~-~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      | ..+.++++   ..++.-+++++||.
T Consensus       237 dy~~l~ilkr---qf~~~~iigltata  260 (695)
T KOG0353|consen  237 DYKALGILKR---QFKGAPIIGLTATA  260 (695)
T ss_pred             chHHHHHHHH---hCCCCceeeeehhh
Confidence            3 33444443   23466799999998

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=98.39  E-value=3e-06  Score=85.71  Aligned_cols=151  Identities=19%  Similarity=0.214  Sum_probs=87.4

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK  145 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~  145 (319)
                      .......+|.||.|||||++...++-+.+..    +..+++++.-++.|+.+++.++....-.     |. +-|....+.
T Consensus        46 ~~~~~V~vVRSpMGTGKTtaLi~wLk~~l~~----~~~~VLvVShRrSL~~sL~~rf~~~~l~-----gF-v~Y~d~~~~  115 (824)
T PF02399_consen   46 PQKRGVLVVRSPMGTGKTTALIRWLKDALKN----PDKSVLVVSHRRSLTKSLAERFKKAGLS-----GF-VNYLDSDDY  115 (824)
T ss_pred             CCCCCeEEEECCCCCCcHHHHHHHHHHhccC----CCCeEEEEEhHHHHHHHHHHHHhhcCCC-----cc-eeeeccccc
Confidence            4566778999999999999987776544322    2348899999999999999988753110     11 111111111


Q ss_pred             ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccc-----cccchh---HHHHHHHhhhccccCceEEEeccccC
Q psy496          146 ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHE-----RSMISD---FLLAILKDVTDKRKDLKLILMSATLN  217 (319)
Q Consensus       146 ~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~-----~~~~~~---~~~~~l~~~~~~~~~~qiv~lSAT~~  217 (319)
                      .......+-++..-+.|.+.-  ...+.++++|||||+..     .+..+.   .....+..+..  ...++|++-|++|
T Consensus       116 ~i~~~~~~rLivqIdSL~R~~--~~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~--~ak~VI~~DA~ln  191 (824)
T PF02399_consen  116 IIDGRPYDRLIVQIDSLHRLD--GSLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIR--NAKTVIVMDADLN  191 (824)
T ss_pred             cccccccCeEEEEehhhhhcc--cccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHH--hCCeEEEecCCCC
Confidence            111111234555556565443  33578899999999985     111111   12222232222  2458999999994


Q ss_pred             h---hhHhhhhCCCCE
Q psy496          218 A---EKFSQFFGGAPI  230 (319)
Q Consensus       218 ~---~~l~~~l~~~~~  230 (319)
                      .   +-++..-++.++
T Consensus       192 ~~tvdFl~~~Rp~~~i  207 (824)
T PF02399_consen  192 DQTVDFLASCRPDENI  207 (824)
T ss_pred             HHHHHHHHHhCCCCcE
Confidence            3   334443344444

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

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=98.34  E-value=2.3e-06  Score=89.59  Aligned_cols=142  Identities=12%  Similarity=0.155  Sum_probs=78.1

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      ...++|.-+.|-|||..+.+.+-.. ...+.  ..++|+++|. .|..|-...+.+.++......+.........+....
T Consensus       169 ~~R~LLADEvGLGKTIeAglil~~l-~~~g~--~~rvLIVvP~-sL~~QW~~El~~kF~l~~~i~~~~~~~~~~~~~~~p  244 (956)
T PRK04914        169 APRVLLADEVGLGKTIEAGMIIHQQ-LLTGR--AERVLILVPE-TLQHQWLVEMLRRFNLRFSLFDEERYAEAQHDADNP  244 (956)
T ss_pred             CCCEEEEeCCcCcHHHHHHHHHHHH-HHcCC--CCcEEEEcCH-HHHHHHHHHHHHHhCCCeEEEcCcchhhhcccccCc
Confidence            4579999999999998886655443 33332  2367777797 677777777765554321000000000000111112


Q ss_pred             CCCceEEEECchHHHHHH--hcCCCCCCccEEEEeccccccc---chhHHHHHHHhhhccccCceEEEecccc
Q psy496          149 RKRGSILYCTAGILPEVM--QSDPILSGVSHIVMDEIHERSM---ISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll~~l--~~~~~l~~v~~vViDEah~~~~---~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      ....+++|+|.+.+.+.-  .....-..++++|+||||....   ........++.+...  ...++++|||+
T Consensus       245 f~~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y~~v~~La~~--~~~~LLLTATP  315 (956)
T PRK04914        245 FETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVEQLAEV--IPGVLLLTATP  315 (956)
T ss_pred             cccCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhccCCCCcCHHHHHHHHHhhc--cCCEEEEEcCc
Confidence            234679999998876421  1111124789999999997211   011112333333322  23578999999

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

Probab=98.32  E-value=3.7e-06  Score=88.80  Aligned_cols=50  Identities=12%  Similarity=-0.022  Sum_probs=40.3

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAE  120 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~  120 (319)
                      .+++.++|-||||+|||.+|++|.+......+    .+|++..+|+.|-.|+..
T Consensus       274 ~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~~----~~vvIsT~T~~LQ~Ql~~  323 (928)
T PRK08074        274 RDSEHALIEAGTGTGKSLAYLLPAAYFAKKKE----EPVVISTYTIQLQQQLLE  323 (928)
T ss_pred             hcCCCEEEECCCCCchhHHHHHHHHHHhhccC----CeEEEEcCCHHHHHHHHH
Confidence            35678999999999999999999875443222    378888999999999754

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=98.25  E-value=1.5e-05  Score=75.93  Aligned_cols=130  Identities=18%  Similarity=0.153  Sum_probs=76.2

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHh-CCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIAR-NRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL  147 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~-~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~  147 (319)
                      ...+++.||||+|||+............. ..+....++.+-+.|..|....+.+++.++..       +          
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvp-------v----------  236 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIP-------V----------  236 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcc-------e----------
Confidence            46789999999999988765443222221 23445677777788888877777666654321       1          


Q ss_pred             CCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhh-hccccC-ceEEEeccccChhhHhhhh
Q psy496          148 PRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDV-TDKRKD-LKLILMSATLNAEKFSQFF  225 (319)
Q Consensus       148 ~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~-~~~~~~-~qiv~lSAT~~~~~l~~~l  225 (319)
                            ..+.++..+...+..   +.++++|+||++.+. ......+..++.+ ....++ -.++.+|||....++.+.+
T Consensus       237 ------~~~~~~~~l~~~L~~---~~~~DlVLIDTaGr~-~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~~~~~~  306 (388)
T PRK12723        237 ------KAIESFKDLKEEITQ---SKDFDLVLVDTIGKS-PKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTSDVKEIF  306 (388)
T ss_pred             ------EeeCcHHHHHHHHHH---hCCCCEEEEcCCCCC-ccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHHHHHHH
Confidence                  111133444443322   367899999999962 2221223333333 323323 4678899999655555444

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.23  E-value=2e-06  Score=88.20  Aligned_cols=104  Identities=17%  Similarity=0.142  Sum_probs=70.1

Q ss_pred             EEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc---CC
Q psy496           73 IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL---PR  149 (319)
Q Consensus        73 li~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~---~~  149 (319)
                      +.--.||+|||+++.+|++-....+.   ++.++.  |+.-||.+-++.+...+...    |..+|.........   ..
T Consensus        99 iaEM~TGEGKTLvA~l~a~l~al~G~---~VhvvT--~ndyLA~RD~e~m~~l~~~l----Gl~v~~i~~~~~~~err~~  169 (913)
T PRK13103         99 IAEMRTGEGKTLVGTLAVYLNALSGK---GVHVVT--VNDYLARRDANWMRPLYEFL----GLSVGIVTPFQPPEEKRAA  169 (913)
T ss_pred             cccccCCCCChHHHHHHHHHHHHcCC---CEEEEe--CCHHHHHHHHHHHHHHhccc----CCEEEEECCCCCHHHHHHH
Confidence            44455999999999999876554433   445555  99999999999888877654    77777443211110   01


Q ss_pred             CCceEEEECchHH-HHHHhcCC-------CCCCccEEEEecccc
Q psy496          150 KRGSILYCTAGIL-PEVMQSDP-------ILSGVSHIVMDEIHE  185 (319)
Q Consensus       150 ~~~~Iiv~Tpg~l-l~~l~~~~-------~l~~v~~vViDEah~  185 (319)
                      -.++|+++|..-+ .+.|+.+-       ...++.+.||||+|.
T Consensus       170 Y~~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDs  213 (913)
T PRK13103        170 YAADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDS  213 (913)
T ss_pred             hcCCEEEEcccccccchhhccceechhhhcccccceeEechhhh
Confidence            2478999998665 33332221       247899999999997

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=98.10  E-value=2.6e-06  Score=86.90  Aligned_cols=100  Identities=16%  Similarity=0.148  Sum_probs=67.4

Q ss_pred             CCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc---cCCCCce
Q psy496           77 STGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE---LPRKRGS  153 (319)
Q Consensus        77 pTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~---~~~~~~~  153 (319)
                      .||+|||+++.+|++-....+.   ++.++.  |+.-||.+-++.+...+...    |..+|........   ...-.++
T Consensus       101 ~TGEGKTLvA~l~a~l~al~G~---~v~vvT--~neyLA~Rd~e~~~~~~~~L----Gl~vg~i~~~~~~~~r~~~y~~d  171 (796)
T PRK12906        101 KTGEGKTLTATLPVYLNALTGK---GVHVVT--VNEYLSSRDATEMGELYRWL----GLTVGLNLNSMSPDEKRAAYNCD  171 (796)
T ss_pred             cCCCCCcHHHHHHHHHHHHcCC---CeEEEe--ccHHHHHhhHHHHHHHHHhc----CCeEEEeCCCCCHHHHHHHhcCC
Confidence            3999999999998876655543   445554  99999999999888877654    7777744321111   1112578


Q ss_pred             EEEECchH-----HHHHHhcCC---CCCCccEEEEecccc
Q psy496          154 ILYCTAGI-----LPEVMQSDP---ILSGVSHIVMDEIHE  185 (319)
Q Consensus       154 Iiv~Tpg~-----ll~~l~~~~---~l~~v~~vViDEah~  185 (319)
                      |+++|..-     |.+.+....   ....+.+.||||+|.
T Consensus       172 I~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDS  211 (796)
T PRK12906        172 ITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDS  211 (796)
T ss_pred             CeecCCccccccchhhccccchhhhhccCcceeeeccchh
Confidence            99999843     444432111   245688999999996

>PF13245 AAA_19: Part of AAA domain

Probab=98.10  E-value=9.3e-06  Score=59.19  Aligned_cols=54  Identities=26%  Similarity=0.250  Sum_probs=40.6

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      ++..++|.||+|||||......+...+...... ..+|+++.|++.++..+.+++
T Consensus         9 ~~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~-~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKTTTLAARIAELLAARADP-GKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             hCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCC-CCeEEEECCCHHHHHHHHHHH
Confidence            345677799999999987766666555332222 458999999999999998877

>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=98.08  E-value=1.7e-05  Score=68.71  Aligned_cols=126  Identities=20%  Similarity=0.229  Sum_probs=74.4

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCC
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPR  149 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~  149 (319)
                      +.+++.||||+|||+............   +....++.+-..|.-|.+..+.+++.++..+       - ....   .. 
T Consensus         2 ~vi~lvGptGvGKTTt~aKLAa~~~~~---~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~-------~-~~~~---~~-   66 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIAKLAARLKLK---GKKVALISADTYRIGAVEQLKTYAEILGVPF-------Y-VART---ES-   66 (196)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHT---T--EEEEEESTSSTHHHHHHHHHHHHHTEEE-------E-ESST---TS-
T ss_pred             EEEEEECCCCCchHhHHHHHHHHHhhc---cccceeecCCCCCccHHHHHHHHHHHhcccc-------c-hhhc---ch-
Confidence            467899999999999887655443332   4456777778899999998888998876432       0 0000   00 


Q ss_pred             CCceEEEECchHHH-HHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhc-cccCceEEEeccccChhh
Q psy496          150 KRGSILYCTAGILP-EVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTD-KRKDLKLILMSATLNAEK  220 (319)
Q Consensus       150 ~~~~Iiv~Tpg~ll-~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~-~~~~~qiv~lSAT~~~~~  220 (319)
                              .|..+. +.+.. ..-+++++|+||-+-+ +.........++.+.. ..+..-.+.+|||...+.
T Consensus        67 --------~~~~~~~~~l~~-~~~~~~D~vlIDT~Gr-~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~  129 (196)
T PF00448_consen   67 --------DPAEIAREALEK-FRKKGYDLVLIDTAGR-SPRDEELLEELKKLLEALNPDEVHLVLSATMGQED  129 (196)
T ss_dssp             --------CHHHHHHHHHHH-HHHTTSSEEEEEE-SS-SSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHH
T ss_pred             --------hhHHHHHHHHHH-HhhcCCCEEEEecCCc-chhhHHHHHHHHHHhhhcCCccceEEEecccChHH
Confidence                    122222 22211 1124689999999985 3333333334443333 345556788999994443

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 ....

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=98.08  E-value=4.3e-05  Score=72.32  Aligned_cols=132  Identities=14%  Similarity=0.169  Sum_probs=74.4

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      ...+.+.||||+|||+........ +..  .+....++..-|.|..+.+..+.+++..+..       +           
T Consensus       241 ~~vI~LVGptGvGKTTTiaKLA~~-L~~--~GkkVglI~aDt~RiaAvEQLk~yae~lgip-------v-----------  299 (436)
T PRK11889        241 VQTIALIGPTGVGKTTTLAKMAWQ-FHG--KKKTVGFITTDHSRIGTVQQLQDYVKTIGFE-------V-----------  299 (436)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHH-HHH--cCCcEEEEecCCcchHHHHHHHHHhhhcCCc-------E-----------
Confidence            367899999999999887665433 222  2334455555677766655555454432211       1           


Q ss_pred             CCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccCh---hhHhhhh
Q psy496          149 RKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNA---EKFSQFF  225 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~~---~~l~~~l  225 (319)
                           +...+|..+.+.+..-..-.++++|+||-+-+..-..+.+..+.+.+....|+..++.+|||...   ..+.+-|
T Consensus       300 -----~v~~d~~~L~~aL~~lk~~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i~~~F  374 (436)
T PRK11889        300 -----IAVRDEAAMTRALTYFKEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIITNF  374 (436)
T ss_pred             -----EecCCHHHHHHHHHHHHhccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHHHHHh
Confidence                 12235666665553222123689999999975322233344444444334455556779999833   3444445


Q ss_pred             C
Q psy496          226 G  226 (319)
Q Consensus       226 ~  226 (319)
                      .
T Consensus       375 ~  375 (436)
T PRK11889        375 K  375 (436)
T ss_pred             c
Confidence            4

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=98.06  E-value=0.00035  Score=66.03  Aligned_cols=130  Identities=19%  Similarity=0.201  Sum_probs=88.9

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      ++++.+.||||.|||+........... ..+.....++.+-..|.-|....+.+++.++..+                  
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~-~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~------------------  263 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVM-LKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPL------------------  263 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHh-hccCcceEEEEeccchhhHHHHHHHHHHHhCCce------------------
Confidence            788999999999999887655444331 1233466788888999999988888888876432                  


Q ss_pred             CCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccc-cCceEEEeccccChhhHhhhhC
Q psy496          149 RKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKR-KDLKLILMSATLNAEKFSQFFG  226 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~-~~~qiv~lSAT~~~~~l~~~l~  226 (319)
                           .++-+|.-|...+.   .+.++++|.+|-+-+ +.........++.+.... +.-..+.+|||...+++.+.+.
T Consensus       264 -----~vv~~~~el~~ai~---~l~~~d~ILVDTaGr-s~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlkei~~  333 (407)
T COG1419         264 -----EVVYSPKELAEAIE---ALRDCDVILVDTAGR-SQYDKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKEIIK  333 (407)
T ss_pred             -----EEecCHHHHHHHHH---HhhcCCEEEEeCCCC-CccCHHHHHHHHHHHhccccceEEEEEecCcchHHHHHHHH
Confidence                 33445655555542   356789999999985 444445566666665533 3346788999996666665443

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=98.02  E-value=2.7e-05  Score=81.05  Aligned_cols=66  Identities=23%  Similarity=0.202  Sum_probs=41.0

Q ss_pred             ceEEEECchHHHHHHhcCC----CC----CCccEEEEecccccccchhHH-HHHHHhhhccccCceEEEeccccChh
Q psy496          152 GSILYCTAGILPEVMQSDP----IL----SGVSHIVMDEIHERSMISDFL-LAILKDVTDKRKDLKLILMSATLNAE  219 (319)
Q Consensus       152 ~~Iiv~Tpg~ll~~l~~~~----~l----~~v~~vViDEah~~~~~~~~~-~~~l~~~~~~~~~~qiv~lSAT~~~~  219 (319)
                      +.++|+|++.++.......    .+    -.-+.|||||+|..+..+-.. ...++.....  ..++++||||+++.
T Consensus       563 apv~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaYD~~~~~~L~rlL~w~~~l--G~~VlLmSATLP~~  637 (1110)
T TIGR02562       563 APVLVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDYEPEDLPALLRLVQLAGLL--GSRVLLSSATLPPA  637 (1110)
T ss_pred             CCeEEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccCCHHHHHHHHHHHHHHHHc--CCCEEEEeCCCCHH
Confidence            4599999998876652211    01    113689999999865554433 3333322223  45799999999554

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.

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.01  E-value=7.8e-06  Score=82.21  Aligned_cols=101  Identities=17%  Similarity=0.160  Sum_probs=68.5

Q ss_pred             cCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc---CCCCc
Q psy496           76 TSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL---PRKRG  152 (319)
Q Consensus        76 apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~---~~~~~  152 (319)
                      -.||+|||+++.+|++-....+.     .|-++.|+.-||.+-++.+...+...    |..+|.........   ..-.+
T Consensus        98 M~TGEGKTLvA~l~a~l~AL~G~-----~VhvvT~NdyLA~RDae~m~~ly~~L----GLsvg~i~~~~~~~err~aY~~  168 (764)
T PRK12326         98 MATGEGKTLAGAIAAAGYALQGR-----RVHVITVNDYLARRDAEWMGPLYEAL----GLTVGWITEESTPEERRAAYAC  168 (764)
T ss_pred             ccCCCCHHHHHHHHHHHHHHcCC-----CeEEEcCCHHHHHHHHHHHHHHHHhc----CCEEEEECCCCCHHHHHHHHcC
Confidence            33999999999998876554433     34445599999999999888776654    77777543211111   01257


Q ss_pred             eEEEECch-----HHHHHHhcCC---CCCCccEEEEecccc
Q psy496          153 SILYCTAG-----ILPEVMQSDP---ILSGVSHIVMDEIHE  185 (319)
Q Consensus       153 ~Iiv~Tpg-----~ll~~l~~~~---~l~~v~~vViDEah~  185 (319)
                      +|+++|..     .|.+.+....   ....+.+.||||+|.
T Consensus       169 DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDS  209 (764)
T PRK12326        169 DVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADS  209 (764)
T ss_pred             CCEEcCCcccccccchhhhccChHhhcCCccceeeecchhh
Confidence            89999984     4455553222   256688999999996

>KOG0921|consensus

Probab=97.98  E-value=2.6e-06  Score=85.92  Aligned_cols=182  Identities=5%  Similarity=-0.191  Sum_probs=112.4

Q ss_pred             chhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccC
Q psy496           52 RISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG  131 (319)
Q Consensus        52 ~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~  131 (319)
                      +.|.-.-.+.+|+..-.|.++.+.+.+|||||.+.++.+++++.......-+-++..+|+++-|........-+.+.-+ 
T Consensus       404 cgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisiaerva~er~e~~g~tvgy~vRf~Sa~prpyg~i~fctvgv-  482 (1282)
T KOG0921|consen  404 CGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERVANERGEEVGETCGYNVRFDSATPRPYGSIMFCTVGV-  482 (1282)
T ss_pred             ccchhHHHHHHHHHHhhccccccccceeccccccchHHHHHHHHHhhHHhhcccccccccccccccccccceeeeccch-
Confidence            3344344445555556667788888899999999999999988765544445666667777766554433332222111 


Q ss_pred             CCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEE
Q psy496          132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLIL  211 (319)
Q Consensus       132 ~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~  211 (319)
                        +...++....+..-..-..-+..+|.+.++..+..+  +-+....+.||.|++.++++++...++.+      .+..+
T Consensus       483 --llr~~e~glrg~sh~i~deiherdv~~dfll~~lr~--m~~ty~dl~v~lmsatIdTd~f~~~f~~~------p~~~~  552 (1282)
T KOG0921|consen  483 --LLRMMENGLRGISHVIIDEIHERDVDTDFVLIVLRE--MISTYRDLRVVLMSATIDTDLFTNFFSSI------PDVTV  552 (1282)
T ss_pred             --hhhhhhhcccccccccchhhhhhccchHHHHHHHHh--hhccchhhhhhhhhcccchhhhhhhhccc------cceee
Confidence              111221111111100001113355666666555332  23556678899999999999988777754      35689


Q ss_pred             eccccChhhHhhhhCCCCEEEeCCccccceeee
Q psy496          212 MSATLNAEKFSQFFGGAPILHIPGFTYPVQEYY  244 (319)
Q Consensus       212 lSAT~~~~~l~~~l~~~~~i~~~~r~~~v~~~~  244 (319)
                      +++|+++..+..++-..+...+++++.+++..+
T Consensus       553 ~grt~pvq~F~led~~~~~~~vp~~~~~~k~k~  585 (1282)
T KOG0921|consen  553 HGRTFPVQSFFLEDIIQMTQFVPSEPSQKKRKK  585 (1282)
T ss_pred             ccccccHHHHHHHHhhhhhhccCCCcCccchhh
Confidence            999999998887776777777777776665443

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.91  E-value=0.00015  Score=68.53  Aligned_cols=125  Identities=16%  Similarity=0.119  Sum_probs=73.0

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE  146 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~  146 (319)
                      ..++++++.||||+|||+.............+ .....++..-+.|.-+.+..+.+.+.++..+                
T Consensus       135 ~~g~ii~lvGptGvGKTTtiakLA~~~~~~~G-~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~----------------  197 (374)
T PRK14722        135 ERGGVFALMGPTGVGKTTTTAKLAARCVMRFG-ASKVALLTTDSYRIGGHEQLRIFGKILGVPV----------------  197 (374)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHHHhcC-CCeEEEEecccccccHHHHHHHHHHHcCCce----------------
Confidence            45789999999999999887665544332222 1123344444556667766666766654221                


Q ss_pred             cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhc-cccCceEEEeccccChh
Q psy496          147 LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTD-KRKDLKLILMSATLNAE  219 (319)
Q Consensus       147 ~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~-~~~~~qiv~lSAT~~~~  219 (319)
                             ..+.+++.+...+.   .+.+.++|+||++-. ......+...+..+.. ..+...++++|||...+
T Consensus       198 -------~~~~~~~~l~~~l~---~l~~~DlVLIDTaG~-~~~d~~l~e~La~L~~~~~~~~~lLVLsAts~~~  260 (374)
T PRK14722        198 -------HAVKDGGDLQLALA---ELRNKHMVLIDTIGM-SQRDRTVSDQIAMLHGADTPVQRLLLLNATSHGD  260 (374)
T ss_pred             -------EecCCcccHHHHHH---HhcCCCEEEEcCCCC-CcccHHHHHHHHHHhccCCCCeEEEEecCccChH
Confidence                   11223333433332   235679999999985 2333445555555533 22345688899999443

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=97.89  E-value=0.00012  Score=76.14  Aligned_cols=137  Identities=15%  Similarity=0.157  Sum_probs=76.6

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH-----HHhccccCCCCceEEEEEe-c
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA-----QERDEQCGRPGSSVGYQIR-L  143 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~-----~~~~~~~~~~g~~vg~~~~-~  143 (319)
                      -++.+.-+||||||.+++-.+++....-+   ..+.++++|+.+.-..+.+.+.     ..+...  +.+..+-+.+- .
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~~~---~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~--y~~~~~~~~~~~S  134 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQKYG---LFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQF--YENTRIELYVINA  134 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHcC---CcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHH--cCCceeEEEEEec
Confidence            57999999999999999888766433322   3467777799887776655443     223221  22333332111 1


Q ss_pred             cc-----------c---------cCCCCceEEEECchHHHHHHh-----------cC-CC---CCC-ccEEEEecccccc
Q psy496          144 EK-----------E---------LPRKRGSILYCTAGILPEVMQ-----------SD-PI---LSG-VSHIVMDEIHERS  187 (319)
Q Consensus       144 ~~-----------~---------~~~~~~~Iiv~Tpg~ll~~l~-----------~~-~~---l~~-v~~vViDEah~~~  187 (319)
                      .+           .         ......+|+++|-+.+.....           +. ..   +.. =-.||+||.|...
T Consensus       135 ~k~~k~gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niqa~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIiDEPh~~~  214 (986)
T PRK15483        135 GDKKKSGRKNFPAQLSNFVKASRQNSNTIHVLLINAGMLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVIIDEPHRFP  214 (986)
T ss_pred             CcccccccccChHHHHHHHhccccCCCceEEEEEehHHhcccccccchhhhhhccCCCChHHHHHhCCCEEEEECCCCCC
Confidence            11           0         001135799999987754211           11 11   111 1478999999832


Q ss_pred             cchhHHHHHHHhhhccccCceEEEecccc
Q psy496          188 MISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       188 ~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      -....    .+.+..+.|.. ++.+|||.
T Consensus       215 ~~~k~----~~~i~~lnpl~-~lrysAT~  238 (986)
T PRK15483        215 RDNKF----YQAIEALKPQM-IIRFGATF  238 (986)
T ss_pred             cchHH----HHHHHhcCccc-EEEEeeec
Confidence            21111    23344454433 56699999

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.87  E-value=3e-05  Score=61.93  Aligned_cols=115  Identities=17%  Similarity=0.223  Sum_probs=54.8

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHh-CCCCccEEEEe-cccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIAR-NRGSECCIMVT-QPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK  145 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~-~~~~~~~vl~~-~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~  145 (319)
                      +++.++|.||+|+|||.......-...... ... ...++.+ .|...-...+.+.+...++...   ..          
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~---~~----------   68 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQLNAEAEIKN-HPDVIYVNCPSSRTPRDFAQEILEALGLPL---KS----------   68 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHHHHHHHHHCC-CEEEEEEEHHHHSSHHHHHHHHHHHHT-SS---SS----------
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHHhHHhhhccC-CCcEEEEEeCCCCCHHHHHHHHHHHhCccc---cc----------
Confidence            346789999999999988766554332211 001 1233333 3333334455555555554332   00          


Q ss_pred             ccCCCCceEEEECch----HHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          146 ELPRKRGSILYCTAG----ILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       146 ~~~~~~~~Iiv~Tpg----~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                                -.++.    .+.+.+...    ...+|||||+|... . .-....++.+.. ..+.++|+++
T Consensus        69 ----------~~~~~~l~~~~~~~l~~~----~~~~lviDe~~~l~-~-~~~l~~l~~l~~-~~~~~vvl~G  123 (131)
T PF13401_consen   69 ----------RQTSDELRSLLIDALDRR----RVVLLVIDEADHLF-S-DEFLEFLRSLLN-ESNIKVVLVG  123 (131)
T ss_dssp             ----------TS-HHHHHHHHHHHHHHC----TEEEEEEETTHHHH-T-HHHHHHHHHHTC-SCBEEEEEEE
T ss_pred             ----------cCCHHHHHHHHHHHHHhc----CCeEEEEeChHhcC-C-HHHHHHHHHHHh-CCCCeEEEEE
Confidence                      01222    334444332    22789999999831 3 334444444444 4455655543

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.87  E-value=3.4e-05  Score=66.74  Aligned_cols=61  Identities=21%  Similarity=0.203  Sum_probs=39.5

Q ss_pred             ccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHH
Q psy496           48 TQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        48 ~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      -|.+++..+..        ..++..+|+|+.|||||+.. ..+.+.+...+    .+|+++.||...+..+.+.
T Consensus         5 ~Q~~a~~~~l~--------~~~~~~~l~G~aGtGKT~~l-~~~~~~~~~~g----~~v~~~apT~~Aa~~L~~~   65 (196)
T PF13604_consen    5 EQREAVRAILT--------SGDRVSVLQGPAGTGKTTLL-KALAEALEAAG----KRVIGLAPTNKAAKELREK   65 (196)
T ss_dssp             HHHHHHHHHHH--------CTCSEEEEEESTTSTHHHHH-HHHHHHHHHTT------EEEEESSHHHHHHHHHH
T ss_pred             HHHHHHHHHHh--------cCCeEEEEEECCCCCHHHHH-HHHHHHHHhCC----CeEEEECCcHHHHHHHHHh
Confidence            36666544432        23467889999999999764 33444444432    4788888999988887665

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.86  E-value=9.3e-05  Score=69.81  Aligned_cols=132  Identities=17%  Similarity=0.208  Sum_probs=75.3

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE  146 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~  146 (319)
                      ..++.++++||+|+|||+........ +...  +....++.+-|.|..|....+.+++.++..       +         
T Consensus       204 ~~~~ii~lvGptGvGKTTt~akLA~~-l~~~--g~~V~lItaDtyR~gAveQLk~yae~lgvp-------v---------  264 (407)
T PRK12726        204 SNHRIISLIGQTGVGKTTTLVKLGWQ-LLKQ--NRTVGFITTDTFRSGAVEQFQGYADKLDVE-------L---------  264 (407)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH-HHHc--CCeEEEEeCCccCccHHHHHHHHhhcCCCC-------E---------
Confidence            34678899999999999887665543 2222  234556666678876666555555433211       1         


Q ss_pred             cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhh-ccccCceEEEeccccChhhHhhhh
Q psy496          147 LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVT-DKRKDLKLILMSATLNAEKFSQFF  225 (319)
Q Consensus       147 ~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~-~~~~~~qiv~lSAT~~~~~l~~~l  225 (319)
                             ....+|.-+.+.+.......++++|+||=+-+. ...+-.+..+..+. ...++.-++.+||+....++.+.+
T Consensus       265 -------~~~~dp~dL~~al~~l~~~~~~D~VLIDTAGr~-~~d~~~l~EL~~l~~~~~p~~~~LVLsag~~~~d~~~i~  336 (407)
T PRK12726        265 -------IVATSPAELEEAVQYMTYVNCVDHILIDTVGRN-YLAEESVSEISAYTDVVHPDLTCFTFSSGMKSADVMTIL  336 (407)
T ss_pred             -------EecCCHHHHHHHHHHHHhcCCCCEEEEECCCCC-ccCHHHHHHHHHHhhccCCceEEEECCCcccHHHHHHHH
Confidence                   112345555554432222356899999999752 22222233333333 234555567889988555555544

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.83  E-value=0.00012  Score=73.51  Aligned_cols=137  Identities=20%  Similarity=0.204  Sum_probs=74.2

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC-CCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEE
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN-RGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVG  138 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~-~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg  138 (319)
                      +..+..+-.+...+|+|++|||||+.....+ ..+.... .....+|+++.||--.|..+.+.........    +..  
T Consensus       151 k~A~~~al~~~~~vitGgpGTGKTt~v~~ll-~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~~~~~l----~~~--  223 (586)
T TIGR01447       151 KVAVALALKSNFSLITGGPGTGKTTTVARLL-LALVKQSPKQGKLRIALAAPTGKAAARLAESLRKAVKNL----AAA--  223 (586)
T ss_pred             HHHHHHHhhCCeEEEEcCCCCCHHHHHHHHH-HHHHHhccccCCCcEEEECCcHHHHHHHHHHHHhhhccc----ccc--
Confidence            3455556667899999999999998764433 2222211 1113478888999998888777665432211    000  


Q ss_pred             EEEecccccCCCCceEEEECchHHHHHHh-------cCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEE
Q psy496          139 YQIRLEKELPRKRGSILYCTAGILPEVMQ-------SDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLIL  211 (319)
Q Consensus       139 ~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~-------~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~  211 (319)
                           .. .. ....+-..|-.+++....       .......+++|||||+-+  +....+..+++.+   ++..|+|+
T Consensus       224 -----~~-~~-~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSM--vd~~l~~~ll~al---~~~~rlIl  291 (586)
T TIGR01447       224 -----EA-LI-AALPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASM--VDLPLMAKLLKAL---PPNTKLIL  291 (586)
T ss_pred             -----hh-hh-hccccccchhhhhhcccCCcchhhhcccCCCcccEEEEccccc--CCHHHHHHHHHhc---CCCCEEEE
Confidence                 00 00 000011223222222111       011223689999999998  5555555555433   45678877


Q ss_pred             eccc
Q psy496          212 MSAT  215 (319)
Q Consensus       212 lSAT  215 (319)
                      +--.
T Consensus       292 vGD~  295 (586)
T TIGR01447       292 LGDK  295 (586)
T ss_pred             ECCh
Confidence            6443

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.

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=97.82  E-value=0.00021  Score=75.50  Aligned_cols=137  Identities=15%  Similarity=0.055  Sum_probs=72.2

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEe-c--
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIR-L--  143 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~-~--  143 (319)
                      .++.+.||+=+.|.|||......+ ..+... .+....+|+++|...+ .+-.+.+.+.....     ..+.+.-. .  
T Consensus       186 ~~g~gGILADEMGLGKTlQaIalL-~~L~~~-~~~~gp~LIVvP~SlL-~nW~~Ei~kw~p~l-----~v~~~~G~~~eR  257 (1033)
T PLN03142        186 ENGINGILADEMGLGKTLQTISLL-GYLHEY-RGITGPHMVVAPKSTL-GNWMNEIRRFCPVL-----RAVKFHGNPEER  257 (1033)
T ss_pred             hcCCCEEEEeCCCccHHHHHHHHH-HHHHHh-cCCCCCEEEEeChHHH-HHHHHHHHHHCCCC-----ceEEEeCCHHHH
Confidence            456778999999999998764433 333221 1222345555696443 45555555543211     01111100 0  


Q ss_pred             ----ccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          144 ----EKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       144 ----~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                          .......+.+|+++|++.+.+....-. --++++||+||||...-........++.+   . ....+++|+|+
T Consensus       258 ~~~~~~~~~~~~~dVvITSYe~l~~e~~~L~-k~~W~~VIvDEAHrIKN~~Sklskalr~L---~-a~~RLLLTGTP  329 (1033)
T PLN03142        258 AHQREELLVAGKFDVCVTSFEMAIKEKTALK-RFSWRYIIIDEAHRIKNENSLLSKTMRLF---S-TNYRLLITGTP  329 (1033)
T ss_pred             HHHHHHHhcccCCCcceecHHHHHHHHHHhc-cCCCCEEEEcCccccCCHHHHHHHHHHHh---h-cCcEEEEecCC
Confidence                001112346799999998876542111 13578999999997221111222222222   2 22458899998

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=97.80  E-value=2.7e-05  Score=79.74  Aligned_cols=107  Identities=20%  Similarity=0.119  Sum_probs=69.4

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc--
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL--  147 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~--  147 (319)
                      +.-+.-..||.|||+++.+|++-....   |..+.|+.  ++..||..-++.+...+...    |..+|......+..  
T Consensus        90 ~G~IaEm~TGEGKTL~a~l~ayl~aL~---G~~VhVvT--~NdyLA~RD~e~m~pvy~~L----GLsvg~i~~~~~~~er  160 (870)
T CHL00122         90 DGKIAEMKTGEGKTLVATLPAYLNALT---GKGVHIVT--VNDYLAKRDQEWMGQIYRFL----GLTVGLIQEGMSSEER  160 (870)
T ss_pred             CCccccccCCCCchHHHHHHHHHHHhc---CCceEEEe--CCHHHHHHHHHHHHHHHHHc----CCceeeeCCCCChHHH
Confidence            334555569999999999988533332   22344554  99999999888776665443    77777543321111  


Q ss_pred             -CCCCceEEEECc-----hHHHHHHhcCC---CCCCccEEEEecccc
Q psy496          148 -PRKRGSILYCTA-----GILPEVMQSDP---ILSGVSHIVMDEIHE  185 (319)
Q Consensus       148 -~~~~~~Iiv~Tp-----g~ll~~l~~~~---~l~~v~~vViDEah~  185 (319)
                       ..-.++|+++|.     +.|.+.+...+   ....+.+.||||+|.
T Consensus       161 r~aY~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDS  207 (870)
T CHL00122        161 KKNYLKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDS  207 (870)
T ss_pred             HHhcCCCCEecCCccccccchhhccCcChHHhhccccceeeeecchh
Confidence             112578999998     45566653222   256789999999997

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.76  E-value=0.00023  Score=71.71  Aligned_cols=136  Identities=18%  Similarity=0.179  Sum_probs=73.4

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEE
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGY  139 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~  139 (319)
                      +..+..+..+...+|+|++|||||+.....+ ..+.........+|+++.||.-.|..+.+.+.......    +.    
T Consensus       158 k~Av~~a~~~~~~vItGgpGTGKTt~v~~ll-~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~----~~----  228 (615)
T PRK10875        158 KVAAAVALTRRISVISGGPGTGKTTTVAKLL-AALIQLADGERCRIRLAAPTGKAAARLTESLGKALRQL----PL----  228 (615)
T ss_pred             HHHHHHHhcCCeEEEEeCCCCCHHHHHHHHH-HHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhhcc----cc----
Confidence            3444445556789999999999998764433 22322222224578888999999888887665432211    00    


Q ss_pred             EEecccccCCCCceEEEECchHHHHHHhc-------CCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEe
Q psy496          140 QIRLEKELPRKRGSILYCTAGILPEVMQS-------DPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILM  212 (319)
Q Consensus       140 ~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~-------~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~l  212 (319)
                        .  +... .....-..|-.+++.....       ......++++||||+-+  +....+..+++.   .+++.|+|++
T Consensus       229 --~--~~~~-~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSM--vd~~lm~~ll~a---l~~~~rlIlv  298 (615)
T PRK10875        229 --T--DEQK-KRIPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASM--VDLPMMARLIDA---LPPHARVIFL  298 (615)
T ss_pred             --c--hhhh-hcCCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhc--ccHHHHHHHHHh---cccCCEEEEe
Confidence              0  0000 0000011122222211100       11223578999999998  555555555554   3456788776


Q ss_pred             cc
Q psy496          213 SA  214 (319)
Q Consensus       213 SA  214 (319)
                      .-
T Consensus       299 GD  300 (615)
T PRK10875        299 GD  300 (615)
T ss_pred             cc
Confidence            43

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=97.75  E-value=5.2e-05  Score=69.64  Aligned_cols=61  Identities=13%  Similarity=-0.015  Sum_probs=45.3

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCC-CccEEEEecccHHHHHHHHHHHHHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRG-SECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~-~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      ...+++++++.||||+|||.+++.|.+..+...+.. ...+++++.+|..+..|....+.+.
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            344678899999999999999999998765543321 1237888889999877776666543

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=97.75  E-value=5.2e-05  Score=69.64  Aligned_cols=61  Identities=13%  Similarity=-0.015  Sum_probs=45.3

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCC-CccEEEEecccHHHHHHHHHHHHHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRG-SECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~-~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      ...+++++++.||||+|||.+++.|.+..+...+.. ...+++++.+|..+..|....+.+.
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            344678899999999999999999998765543321 1237888889999877776666543

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.75  E-value=0.0005  Score=66.51  Aligned_cols=128  Identities=14%  Similarity=0.135  Sum_probs=69.8

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      +.++++.||||+|||+............ ..+....++-.-|.|..+....+.+++.++..+                  
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~-~~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~------------------  281 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALL-YGKKKVALITLDTYRIGAVEQLKTYAKIMGIPV------------------  281 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHh-cCCCeEEEEECCccHHHHHHHHHHHHHHhCCce------------------
Confidence            5688999999999998876544332201 122344555556777766655555655433211                  


Q ss_pred             CCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhh-ccccCceEEEeccccChhhHhh
Q psy496          149 RKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVT-DKRKDLKLILMSATLNAEKFSQ  223 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~-~~~~~~qiv~lSAT~~~~~l~~  223 (319)
                           ....+++.+.+.+..   +.++++|+||.+-...........+...+. ...+....+++|||....++.+
T Consensus       282 -----~~~~~~~~l~~~l~~---~~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~~  349 (424)
T PRK05703        282 -----EVVYDPKELAKALEQ---LRDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTKYEDLKD  349 (424)
T ss_pred             -----EccCCHHhHHHHHHH---hCCCCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHHH
Confidence                 111234445444432   346899999999752222222222222222 1223345788999995444443

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=97.66  E-value=0.00015  Score=74.55  Aligned_cols=107  Identities=21%  Similarity=0.140  Sum_probs=71.0

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc---c
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK---E  146 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~---~  146 (319)
                      +--+.-..||-|||+++.+|++-....+.   .+.|+.  +..-||..=++.+...+...    |..+|.......   +
T Consensus        99 ~G~IAEM~TGEGKTL~atlpaylnAL~Gk---gVhVVT--vNdYLA~RDae~m~~vy~~L----GLtvg~i~~~~~~~er  169 (939)
T PRK12902         99 EGQIAEMKTGEGKTLVATLPSYLNALTGK---GVHVVT--VNDYLARRDAEWMGQVHRFL----GLSVGLIQQDMSPEER  169 (939)
T ss_pred             CCceeeecCCCChhHHHHHHHHHHhhcCC---CeEEEe--CCHHHHHhHHHHHHHHHHHh----CCeEEEECCCCChHHH
Confidence            34455666999999999998875444333   345555  88889888877766665443    777875432111   1


Q ss_pred             cCCCCceEEEECchHH-----HHHHhcCC---CCCCccEEEEecccc
Q psy496          147 LPRKRGSILYCTAGIL-----PEVMQSDP---ILSGVSHIVMDEIHE  185 (319)
Q Consensus       147 ~~~~~~~Iiv~Tpg~l-----l~~l~~~~---~l~~v~~vViDEah~  185 (319)
                      ...-.++|+++|+..+     .+.+..+.   ....+.+.||||+|.
T Consensus       170 r~aY~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDS  216 (939)
T PRK12902        170 KKNYACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDS  216 (939)
T ss_pred             HHhcCCCeEEecCCcccccchhhhhcccccccccCccceEEEecccc
Confidence            1113678999999555     66664322   367789999999996

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=97.62  E-value=8.3e-05  Score=70.24  Aligned_cols=92  Identities=14%  Similarity=0.086  Sum_probs=55.9

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCC
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPR  149 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~  149 (319)
                      +.++|.|.+|||||+.+...+. .+.....  ...++++.+...+...+.+.+.....                     .
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~-~l~~~~~--~~~~~~l~~n~~l~~~l~~~l~~~~~---------------------~   57 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAK-ELQNSEE--GKKVLYLCGNHPLRNKLREQLAKKYN---------------------P   57 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHH-Hhhcccc--CCceEEEEecchHHHHHHHHHhhhcc---------------------c
Confidence            4689999999999987655433 3311112  23555666888888877776655420                     0


Q ss_pred             CCceEEEECchHHHHHHh-cCCCCCCccEEEEecccc
Q psy496          150 KRGSILYCTAGILPEVMQ-SDPILSGVSHIVMDEIHE  185 (319)
Q Consensus       150 ~~~~Iiv~Tpg~ll~~l~-~~~~l~~v~~vViDEah~  185 (319)
                      ......+..+..+..... .......+++||+||||+
T Consensus        58 ~~~~~~~~~~~~~i~~~~~~~~~~~~~DviivDEAqr   94 (352)
T PF09848_consen   58 KLKKSDFRKPTSFINNYSESDKEKNKYDVIIVDEAQR   94 (352)
T ss_pred             chhhhhhhhhHHHHhhcccccccCCcCCEEEEehhHh
Confidence            001122334444444442 334467899999999997

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>COG4889 Predicted helicase [General function prediction only]

Probab=97.61  E-value=0.0004  Score=70.69  Aligned_cols=132  Identities=16%  Similarity=0.077  Sum_probs=80.8

Q ss_pred             CccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHH
Q psy496           41 SECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAE  120 (319)
Q Consensus        41 ~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~  120 (319)
                      .+.++.|.|+.||.+..+|...   ...++-++-   .|+|||...+. +.+++..      .++|++.|.-.|-.|..+
T Consensus       158 ~~kk~R~hQq~Aid~a~~~F~~---n~RGkLIMA---cGTGKTfTsLk-isEala~------~~iL~LvPSIsLLsQTlr  224 (1518)
T COG4889         158 KPKKPRPHQQTAIDAAKEGFSD---NDRGKLIMA---CGTGKTFTSLK-ISEALAA------ARILFLVPSISLLSQTLR  224 (1518)
T ss_pred             CCCCCChhHHHHHHHHHhhccc---ccCCcEEEe---cCCCccchHHH-HHHHHhh------hheEeecchHHHHHHHHH
Confidence            3455679999999998877553   223333322   68999977644 4455443      489999999999999988


Q ss_pred             HHHHHhccccC--CC--CceEEEE---Eeccccc------------------CCCCceEEEECchHHHHHH-hcCCCCCC
Q psy496          121 RVAQERDEQCG--RP--GSSVGYQ---IRLEKEL------------------PRKRGSILYCTAGILPEVM-QSDPILSG  174 (319)
Q Consensus       121 ~~~~~~~~~~~--~~--g~~vg~~---~~~~~~~------------------~~~~~~Iiv~Tpg~ll~~l-~~~~~l~~  174 (319)
                      .|.......+.  .+  ...++-.   +...+-.                  ...+.-++++|.+.+...- .....+..
T Consensus       225 ew~~~~~l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~~i~eAQe~G~~~  304 (1518)
T COG4889         225 EWTAQKELDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLPRIKEAQEAGLDE  304 (1518)
T ss_pred             HHhhccCccceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchHHHHHHHHcCCCC
Confidence            88765221110  00  0011100   0000000                  0012238899998887766 44456889


Q ss_pred             ccEEEEecccc
Q psy496          175 VSHIVMDEIHE  185 (319)
Q Consensus       175 v~~vViDEah~  185 (319)
                      +++||.||||+
T Consensus       305 fDliicDEAHR  315 (1518)
T COG4889         305 FDLIICDEAHR  315 (1518)
T ss_pred             ccEEEecchhc
Confidence            99999999997

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=97.53  E-value=0.00033  Score=74.25  Aligned_cols=138  Identities=16%  Similarity=0.146  Sum_probs=82.1

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEe-cccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIR-LEKE  146 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~-~~~~  146 (319)
                      ..+.-+|+=-||||||....... ..+...  .....|+++.=+++|-.|+.+.+.......... . ... ... ....
T Consensus       272 ~~~~G~IWHtqGSGKTlTm~~~A-~~l~~~--~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~-~-~~~-s~~~Lk~~  345 (962)
T COG0610         272 DGKGGYIWHTQGSGKTLTMFKLA-RLLLEL--PKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFND-P-KAE-STSELKEL  345 (962)
T ss_pred             cCCceEEEeecCCchHHHHHHHH-HHHHhc--cCCCeEEEEechHHHHHHHHHHHHHHHHhhhhc-c-ccc-CHHHHHHH
Confidence            34568999999999997765443 222222  224578888899999999999888764332210 0 000 011 1111


Q ss_pred             cCCCCceEEEECchHHHHHHhcCC--CCC-CccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          147 LPRKRGSILYCTAGILPEVMQSDP--ILS-GVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       147 ~~~~~~~Iiv~Tpg~ll~~l~~~~--~l~-~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      .......|+++|-+.+-.......  .+. .==+||+||||+  ...+.....++...   ++...++|++|+
T Consensus       346 l~~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHR--SQ~G~~~~~~~~~~---~~a~~~gFTGTP  413 (962)
T COG0610         346 LEDGKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHR--SQYGELAKLLKKAL---KKAIFIGFTGTP  413 (962)
T ss_pred             HhcCCCcEEEEEecccchhhhcccccccCCCcEEEEEechhh--ccccHHHHHHHHHh---ccceEEEeeCCc
Confidence            111234699999887766663321  111 223689999996  34444444444332   346899999999

>PRK14974 cell division protein FtsY; Provisional

Probab=97.53  E-value=0.00081  Score=62.95  Aligned_cols=133  Identities=16%  Similarity=0.146  Sum_probs=67.8

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      ...++++|++|+|||+....... .+...  +....++..-+.|..+....+.++..++..+       .   ...... 
T Consensus       140 ~~vi~~~G~~GvGKTTtiakLA~-~l~~~--g~~V~li~~Dt~R~~a~eqL~~~a~~lgv~v-------~---~~~~g~-  205 (336)
T PRK14974        140 PVVIVFVGVNGTGKTTTIAKLAY-YLKKN--GFSVVIAAGDTFRAGAIEQLEEHAERLGVKV-------I---KHKYGA-  205 (336)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHH-HHHHc--CCeEEEecCCcCcHHHHHHHHHHHHHcCCce-------e---cccCCC-
Confidence            45788899999999987765442 23222  2222223223456666555555655544321       1   000000 


Q ss_pred             CCCceEEEECchH-HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhh
Q psy496          149 RKRGSILYCTAGI-LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFF  225 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~-ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l  225 (319)
                               .|-. +.+.+.. ....++++|+||++.+..-..+.+..+-+......|+..++.+|||.  +....++.|
T Consensus       206 ---------dp~~v~~~ai~~-~~~~~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl~a~~g~d~~~~a~~f  275 (336)
T PRK14974        206 ---------DPAAVAYDAIEH-AKARGIDVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAGNDAVEQAREF  275 (336)
T ss_pred             ---------CHHHHHHHHHHH-HHhCCCCEEEEECCCccCCcHHHHHHHHHHHHhhCCceEEEeeccccchhHHHHHHHH
Confidence                     1111 2222211 01246789999999963223333333322222345677788899988  433444444

>PRK10536 hypothetical protein; Provisional

Probab=97.50  E-value=0.00047  Score=61.78  Aligned_cols=46  Identities=22%  Similarity=0.156  Sum_probs=32.8

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRI  113 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~  113 (319)
                      ...+++.+++.||+|||||.......++.+....   ..+++++.|.-.
T Consensus        70 al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~---~~kIiI~RP~v~  115 (262)
T PRK10536         70 AIESKQLIFATGEAGCGKTWISAAKAAEALIHKD---VDRIIVTRPVLQ  115 (262)
T ss_pred             HHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCC---eeEEEEeCCCCC
Confidence            3344678999999999999887776666654422   447777777654

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.49  E-value=0.0015  Score=59.38  Aligned_cols=133  Identities=15%  Similarity=0.186  Sum_probs=69.4

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL  147 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~  147 (319)
                      +++.+.+.|++|+|||+.+...... +..  .+....++..-+.|.-+.+..+..+...       +..+          
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~l~~~-l~~--~~~~v~~i~~D~~ri~~~~ql~~~~~~~-------~~~~----------  133 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAKMAWQ-FHG--KKKTVGFITTDHSRIGTVQQLQDYVKTI-------GFEV----------  133 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHH-HHH--cCCeEEEEecCCCCHHHHHHHHHHhhhc-------CceE----------
Confidence            3478999999999999877654432 222  1223445554566644333323232221       1111          


Q ss_pred             CCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccChh---hHhhh
Q psy496          148 PRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAE---KFSQF  224 (319)
Q Consensus       148 ~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~~~---~l~~~  224 (319)
                            +...+|..+.+.+..-....+++++|||.+-+.....+.+..+.+.+....++..++.+|||...+   .+.+.
T Consensus       134 ------~~~~~~~~l~~~l~~l~~~~~~D~ViIDt~Gr~~~~~~~l~el~~~~~~~~~~~~~LVl~a~~~~~d~~~~~~~  207 (270)
T PRK06731        134 ------IAVRDEAAMTRALTYFKEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIITN  207 (270)
T ss_pred             ------EecCCHHHHHHHHHHHHhcCCCCEEEEECCCCCcCCHHHHHHHHHHHhhhCCCeEEEEEcCccCHHHHHHHHHH
Confidence                  111244445444422111246899999999752223334444444433344555677899998443   44444


Q ss_pred             hC
Q psy496          225 FG  226 (319)
Q Consensus       225 l~  226 (319)
                      |.
T Consensus       208 f~  209 (270)
T PRK06731        208 FK  209 (270)
T ss_pred             hC
Confidence            43

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.44  E-value=0.0014  Score=67.07  Aligned_cols=125  Identities=14%  Similarity=0.114  Sum_probs=72.1

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      ++.+.+.||||+|||+.+...........+ .....++..-+.|.-+....+.+++.++..+                  
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G-~kkV~lit~Dt~RigA~eQL~~~a~~~gvpv------------------  245 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREG-ADQLALLTTDSFRIGALEQLRIYGRILGVPV------------------  245 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcC-CCeEEEecCcccchHHHHHHHHHHHhCCCCc------------------
Confidence            567899999999999887665433222221 1123333344567666666666666543221                  


Q ss_pred             CCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhh-ccccCceEEEeccccChhhH
Q psy496          149 RKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVT-DKRKDLKLILMSATLNAEKF  221 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~-~~~~~~qiv~lSAT~~~~~l  221 (319)
                           ..+.+|..+.+.+..   +.+.++|+||=+-+. .....+...+..+. ...+...++.+|||...+.+
T Consensus       246 -----~~~~~~~~l~~al~~---~~~~D~VLIDTAGRs-~~d~~l~eel~~l~~~~~p~e~~LVLsAt~~~~~l  310 (767)
T PRK14723        246 -----HAVKDAADLRFALAA---LGDKHLVLIDTVGMS-QRDRNVSEQIAMLCGVGRPVRRLLLLNAASHGDTL  310 (767)
T ss_pred             -----cccCCHHHHHHHHHH---hcCCCEEEEeCCCCC-ccCHHHHHHHHHHhccCCCCeEEEEECCCCcHHHH
Confidence                 112256666555542   457789999999852 22222334444433 34455678889999844433

>KOG0989|consensus

Probab=97.44  E-value=0.00032  Score=63.71  Aligned_cols=155  Identities=24%  Similarity=0.290  Sum_probs=81.0

Q ss_pred             CCCccccccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC
Q psy496           19 GCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN   98 (319)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~   98 (319)
                      |.+...+.|  .-.-|++..+.....-..-|.....+++   +.+.. .+.-+.+..||+|+|||.++.... .++....
T Consensus        13 ~~~~~~~~p--~~~swteKYrPkt~de~~gQe~vV~~L~---~a~~~-~~lp~~LFyGPpGTGKTStalafa-r~L~~~~   85 (346)
T KOG0989|consen   13 GEESDKSVP--KHRSWTEKYRPKTFDELAGQEHVVQVLK---NALLR-RILPHYLFYGPPGTGKTSTALAFA-RALNCEQ   85 (346)
T ss_pred             cccccccCC--CccchHHHhCCCcHHhhcchHHHHHHHH---HHHhh-cCCceEEeeCCCCCcHhHHHHHHH-HHhcCcc
Confidence            334444455  3344777766554444455666554443   33333 566789999999999998875543 3333211


Q ss_pred             CCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHH-hcCC-CCCCcc
Q psy496           99 RGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVM-QSDP-ILSGVS  176 (319)
Q Consensus        99 ~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l-~~~~-~l~~v~  176 (319)
                             +.  |.|.+-...    +.+.       |..++    -+...          ....+.... ...+ ...-++
T Consensus        86 -------~~--~~rvl~lna----Sder-------Gisvv----r~Kik----------~fakl~~~~~~~~~~~~~~fK  131 (346)
T KOG0989|consen   86 -------LF--PCRVLELNA----SDER-------GISVV----REKIK----------NFAKLTVLLKRSDGYPCPPFK  131 (346)
T ss_pred             -------cc--ccchhhhcc----cccc-------cccch----hhhhc----------CHHHHhhccccccCCCCCcce
Confidence                   11  333321111    1111       22111    00000          011111111 1122 256689


Q ss_pred             EEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          177 HIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       177 ~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      .||+||||.  +..+...++.+.+...+...++++..--+
T Consensus       132 iiIlDEcds--mtsdaq~aLrr~mE~~s~~trFiLIcnyl  169 (346)
T KOG0989|consen  132 IIILDECDS--MTSDAQAALRRTMEDFSRTTRFILICNYL  169 (346)
T ss_pred             EEEEechhh--hhHHHHHHHHHHHhccccceEEEEEcCCh
Confidence            999999998  77777777777776666667777754433

>KOG0390|consensus

Probab=97.43  E-value=0.0013  Score=67.01  Aligned_cols=165  Identities=15%  Similarity=0.094  Sum_probs=83.6

Q ss_pred             cccccchhhHHHHHHhhhcCC--CCCcEEEecCCCCCccchhhHHHHHHHHHhCC--CCccEEEEecccHHHHHHHHHHH
Q psy496           47 VTQPRRISAIALINKCLTLSP--ILSPSIIYTSTGCGKTTQVPQFILDDEIARNR--GSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~--~~~~vli~apTGSGKT~~~~l~il~~l~~~~~--~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      |.|++.+.-+=  +++.+...  +..-.+++=..|+|||....-.+...+.....  ..-.+.++++|.- |...-.+.+
T Consensus       241 PHQ~EG~~FL~--knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~s-Lv~nWkkEF  317 (776)
T KOG0390|consen  241 PHQREGFEFLY--KNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPSS-LVNNWKKEF  317 (776)
T ss_pred             chHHHHHHHHH--hhhhcccccCCCCceEeeCCCCcchHHHHHHHHHHHHHhCcCccccccccEEEccHH-HHHHHHHHH
Confidence            66766664432  34444432  34457778889999998765544443332211  0114566666853 334444445


Q ss_pred             HHHhccccCCCCceEEEEEecccc-------------cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccc-ccc
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEKE-------------LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHE-RSM  188 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~~-------------~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~-~~~  188 (319)
                      .+..+.     +...+..+.....             .......+++-+.+.+.+.... .....++++|+||.|+ +..
T Consensus       318 ~KWl~~-----~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~-il~~~~glLVcDEGHrlkN~  391 (776)
T KOG0390|consen  318 GKWLGN-----HRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRK-ILLIRPGLLVCDEGHRLKNS  391 (776)
T ss_pred             HHhccc-----cccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHH-HhcCCCCeEEECCCCCccch
Confidence            444332     0111222221111             0111234666677766544421 2346789999999997 322


Q ss_pred             chhHHHHHHHhhhccccCceEEEeccccChhhHhhhh
Q psy496          189 ISDFLLAILKDVTDKRKDLKLILMSATLNAEKFSQFF  225 (319)
Q Consensus       189 ~~~~~~~~l~~~~~~~~~~qiv~lSAT~~~~~l~~~l  225 (319)
                      .+ .....+.   +.. ..+.|++|.|+=-.++.+||
T Consensus       392 ~s-~~~kaL~---~l~-t~rRVLLSGTp~QNdl~EyF  423 (776)
T KOG0390|consen  392 DS-LTLKALS---SLK-TPRRVLLTGTPIQNDLKEYF  423 (776)
T ss_pred             hh-HHHHHHH---hcC-CCceEEeeCCcccccHHHHH
Confidence            22 2222222   222 33678999999223444544

>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=97.43  E-value=0.00035  Score=60.68  Aligned_cols=44  Identities=20%  Similarity=0.093  Sum_probs=28.5

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRIS  114 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~l  114 (319)
                      +++.+++.||.|||||.......++.+..+   ..-+++++.|..+.
T Consensus        18 ~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g---~~~kiii~Rp~v~~   61 (205)
T PF02562_consen   18 NNDLVIVNGPAGTGKTFLALAAALELVKEG---EYDKIIITRPPVEA   61 (205)
T ss_dssp             H-SEEEEE--TTSSTTHHHHHHHHHHHHTT---S-SEEEEEE-S--T
T ss_pred             hCCeEEEECCCCCcHHHHHHHHHHHHHHhC---CCcEEEEEecCCCC
Confidence            456799999999999988877777776552   24588888787543

; GO: 0005524 ATP binding; PDB: 3B85_A.

>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=97.39  E-value=0.00069  Score=59.59  Aligned_cols=92  Identities=17%  Similarity=0.246  Sum_probs=58.1

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK  145 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~  145 (319)
                      .+.++|.+...-.|.|||.+. .|++....++++   ..+.++.| ++|..|..+.+...++..+   +..+ +.+.+.+
T Consensus        38 ~~~~~n~v~QlnMGeGKTsVI-~Pmla~~LAdg~---~LvrviVp-k~Ll~q~~~~L~~~lg~l~---~r~i-~~lpFsR  108 (229)
T PF12340_consen   38 PPSGKNSVMQLNMGEGKTSVI-VPMLALALADGS---RLVRVIVP-KALLEQMRQMLRSRLGGLL---NRRI-YHLPFSR  108 (229)
T ss_pred             CCCCCCeEeeecccCCccchH-HHHHHHHHcCCC---cEEEEEcC-HHHHHHHHHHHHHHHHHHh---CCee-EEecccC
Confidence            456788999999999999775 677766666553   24444446 4677888777777666544   4433 2333322


Q ss_pred             ccCC----------------CCceEEEECchHHHHHH
Q psy496          146 ELPR----------------KRGSILYCTAGILPEVM  166 (319)
Q Consensus       146 ~~~~----------------~~~~Iiv~Tpg~ll~~l  166 (319)
                      ....                .+..|+++||+.++...
T Consensus       109 ~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf~  145 (229)
T PF12340_consen  109 STPLTPETLEKIRQLLEECMRSGGILLATPEHILSFK  145 (229)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHHH
Confidence            2211                23459999998886543

There are two conserved sequence motifs: LLE and NMG.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.39  E-value=0.0021  Score=61.62  Aligned_cols=129  Identities=18%  Similarity=0.163  Sum_probs=71.2

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      +..++++||+|||||+............  .+....++..-+.|..+....+++++..+..       .           
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~--~G~~V~Lit~Dt~R~aA~eQLk~yAe~lgvp-------~-----------  282 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKYFLH--MGKSVSLYTTDNYRIAAIEQLKRYADTMGMP-------F-----------  282 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHh--cCCeEEEecccchhhhHHHHHHHHHHhcCCC-------e-----------
Confidence            3468899999999999887765443222  2234455555678888877666666543321       1           


Q ss_pred             CCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhh---ccccCceEEEecccc---ChhhHh
Q psy496          149 RKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVT---DKRKDLKLILMSATL---NAEKFS  222 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~---~~~~~~qiv~lSAT~---~~~~l~  222 (319)
                           +.+..+..+.+.+..    .++++|+||=+-......+.+..+.+.+.   ...+.-.++.+|||.   +...+.
T Consensus       283 -----~~~~~~~~l~~~l~~----~~~D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~~  353 (432)
T PRK12724        283 -----YPVKDIKKFKETLAR----DGSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTVL  353 (432)
T ss_pred             -----eehHHHHHHHHHHHh----CCCCEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHHH
Confidence                 000012233443331    46899999987642112222222222222   112334678899999   344555


Q ss_pred             hhhC
Q psy496          223 QFFG  226 (319)
Q Consensus       223 ~~l~  226 (319)
                      +.|.
T Consensus       354 ~~f~  357 (432)
T PRK12724        354 KAYE  357 (432)
T ss_pred             HHhc
Confidence            5554

>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=97.39  E-value=0.0013  Score=52.37  Aligned_cols=20  Identities=30%  Similarity=0.393  Sum_probs=16.6

Q ss_pred             CCCcEEEecCCCCCccchhh
Q psy496           68 ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~   87 (319)
                      .+..++|.||+|+|||....
T Consensus        18 ~~~~v~i~G~~G~GKT~l~~   37 (151)
T cd00009          18 PPKNLLLYGPPGTGKTTLAR   37 (151)
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            46789999999999996543

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.

>PRK04296 thymidine kinase; Provisional

Probab=97.37  E-value=0.0014  Score=56.43  Aligned_cols=36  Identities=25%  Similarity=0.344  Sum_probs=24.1

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecc
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQP  110 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~P  110 (319)
                      ...+++||+|+|||+.....+.+.... +    .+++++.|
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~-g----~~v~i~k~   38 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEER-G----MKVLVFKP   38 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHc-C----CeEEEEec
Confidence            457899999999998876665544332 2    25666545

>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=97.36  E-value=6.9e-05  Score=67.67  Aligned_cols=104  Identities=18%  Similarity=0.159  Sum_probs=64.2

Q ss_pred             EEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC---C
Q psy496           73 IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP---R  149 (319)
Q Consensus        73 li~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~---~  149 (319)
                      +..-.||=|||++..+|..-....   |..+.|+.  ...-||..=++.+...+...    |..+|..........   .
T Consensus        94 laEm~TGEGKTli~~l~a~~~AL~---G~~V~vvT--~NdyLA~RD~~~~~~~y~~L----Glsv~~~~~~~~~~~r~~~  164 (266)
T PF07517_consen   94 LAEMKTGEGKTLIAALPAALNALQ---GKGVHVVT--SNDYLAKRDAEEMRPFYEFL----GLSVGIITSDMSSEERREA  164 (266)
T ss_dssp             EEEESTTSHHHHHHHHHHHHHHTT---SS-EEEEE--SSHHHHHHHHHHHHHHHHHT----T--EEEEETTTEHHHHHHH
T ss_pred             eEEecCCCCcHHHHHHHHHHHHHh---cCCcEEEe--ccHHHhhccHHHHHHHHHHh----hhccccCccccCHHHHHHH
Confidence            444459999999987776544333   23455665  77778888777777666543    777876544322110   0


Q ss_pred             CCceEEEECchHH-----HHHHhcCC---CCCCccEEEEecccc
Q psy496          150 KRGSILYCTAGIL-----PEVMQSDP---ILSGVSHIVMDEIHE  185 (319)
Q Consensus       150 ~~~~Iiv~Tpg~l-----l~~l~~~~---~l~~v~~vViDEah~  185 (319)
                      -.++|+++|.+.+     .+.+....   ....+.++||||+|.
T Consensus       165 Y~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs  208 (266)
T PF07517_consen  165 YAADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDS  208 (266)
T ss_dssp             HHSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHH
T ss_pred             HhCcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccce
Confidence            1357999998555     33332221   257899999999996

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 ....

>PRK06526 transposase; Provisional

Probab=97.34  E-value=0.00051  Score=61.91  Aligned_cols=23  Identities=17%  Similarity=0.151  Sum_probs=18.5

Q ss_pred             CCCCcEEEecCCCCCccchhhHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~   89 (319)
                      ..+++++++||+|+|||......
T Consensus        96 ~~~~nlll~Gp~GtGKThLa~al  118 (254)
T PRK06526         96 TGKENVVFLGPPGTGKTHLAIGL  118 (254)
T ss_pred             hcCceEEEEeCCCCchHHHHHHH
Confidence            45688999999999999765443

>KOG4150|consensus

Probab=97.32  E-value=0.00046  Score=67.22  Aligned_cols=225  Identities=11%  Similarity=-0.032  Sum_probs=122.3

Q ss_pred             HHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEE
Q psy496           59 INKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVG  138 (319)
Q Consensus        59 ~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg  138 (319)
                      .-+++..+..++++.+...|.|||.+++.+....-+....   ....++..|+.++++...+-+.-........-...|.
T Consensus       291 ~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~---~s~~~~~~~~~~~~~~~~~~~~V~~~~I~~~K~A~V~  367 (1034)
T KOG4150|consen  291 SLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCH---ATNSLLPSEMVEHLRNGSKGQVVHVEVIKARKSAYVE  367 (1034)
T ss_pred             hHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCc---ccceecchhHHHHhhccCCceEEEEEehhhhhcceee
Confidence            3455556666777888888999999999877665443322   3456777799999876544221111100000000011


Q ss_pred             E----EEecccccCCCCceEEEECchHHHHHHhcCC-----CCCCccEEEEecccc-cccchhHHHHHHHhhhc------
Q psy496          139 Y----QIRLEKELPRKRGSILYCTAGILPEVMQSDP-----ILSGVSHIVMDEIHE-RSMISDFLLAILKDVTD------  202 (319)
Q Consensus       139 ~----~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~-----~l~~v~~vViDEah~-~~~~~~~~~~~l~~~~~------  202 (319)
                      .    ....++.....+.+.+++.|.........+.     .+-+..+++.||+|- .++........++.+..      
T Consensus       368 ~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~~R~L~~L~~~F~  447 (1034)
T KOG4150|consen  368 MSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALAQDQLRALSDLIKGFE  447 (1034)
T ss_pred             cccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecchhhHHHHHHHHHHHHHHHHH
Confidence            0    0001111111355788999987766553221     245678899999996 23333333333333322      


Q ss_pred             cccCceEEEecccc-ChhhHh-hhhC--CCCEEEeCCccccceeeeehhh-hhhhhhhHH--HHHHHHhhhhhhhccccC
Q psy496          203 KRKDLKLILMSATL-NAEKFS-QFFG--GAPILHIPGFTYPVQEYYLEDV-LNMTRKDLK--LILMSATLNAEKFSQFFG  275 (319)
Q Consensus       203 ~~~~~qiv~lSAT~-~~~~l~-~~l~--~~~~i~~~~r~~~v~~~~~~~~-~~~~~~~~~--~~~~~~~~~~~~~~~~~~  275 (319)
                      .+.+.+++-.|||+ ++-... +.++  ...++.++|.+..-+...+-.+ ........+  .+.....+-++...+  +
T Consensus       448 ~~~~~~~~~~~~~~K~~~~~~~~~~~~~E~~Li~~DGSPs~~K~~V~WNP~~~P~~~~~~~~~i~E~s~~~~~~i~~--~  525 (1034)
T KOG4150|consen  448 ASINMGVYDGDTPYKDRTRLRSELANLSELELVTIDGSPSSEKLFVLWNPSAPPTSKSEKSSKVVEVSHLFAEMVQH--G  525 (1034)
T ss_pred             hhcCcceEeCCCCcCCHHHHHHHhcCCcceEEEEecCCCCccceEEEeCCCCCCcchhhhhhHHHHHHHHHHHHHHc--C
Confidence            34578999999999 555444 4444  3456888888776665543111 011111111  122222222322333  5


Q ss_pred             CCcEEEeCCcccc
Q psy496          276 GAPILHIPGFTYP  288 (319)
Q Consensus       276 g~~LVFlp~R~~~  288 (319)
                      -.++-|||.|+.|
T Consensus       526 ~R~IAFC~~R~~C  538 (1034)
T KOG4150|consen  526 LRCIAFCPSRKLC  538 (1034)
T ss_pred             CcEEEeccHHHHH
Confidence            6799999999877

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=97.32  E-value=0.0027  Score=57.97  Aligned_cols=167  Identities=16%  Similarity=0.147  Sum_probs=91.8

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      .-|-+++-...+..+.........-.+|-=.||.||--...-.|++......    .+.+.++.+..|-.+..+-+...-
T Consensus        40 ~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~Gr----~r~vwvS~s~dL~~Da~RDl~DIG  115 (303)
T PF13872_consen   40 ALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRGR----KRAVWVSVSNDLKYDAERDLRDIG  115 (303)
T ss_pred             HHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcCC----CceEEEECChhhhhHHHHHHHHhC
Confidence            4466655333332222222223455788888999999888777777765443    267777788888888777777652


Q ss_pred             ccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcC----CCCC--------C-ccEEEEecccccc-cch--
Q psy496          127 DEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSD----PILS--------G-VSHIVMDEIHERS-MIS--  190 (319)
Q Consensus       127 ~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~----~~l~--------~-v~~vViDEah~~~-~~~--  190 (319)
                      ......  ... .....++. ...+..|+++|.-.|...-...    ..|+        + =.+||+||+|... ...  
T Consensus       116 ~~~i~v--~~l-~~~~~~~~-~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~akn~~~~~  191 (303)
T PF13872_consen  116 ADNIPV--HPL-NKFKYGDI-IRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHKAKNLSSGS  191 (303)
T ss_pred             CCcccc--eec-hhhccCcC-CCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchhcCCCCccC
Confidence            221100  000 00111111 1123459999998776654211    0011        1 2489999999722 211  


Q ss_pred             ----hHHHHHHHhhhccccCceEEEecccc--ChhhHh
Q psy496          191 ----DFLLAILKDVTDKRKDLKLILMSATL--NAEKFS  222 (319)
Q Consensus       191 ----~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~  222 (319)
                          ......+ .+...-|+.|+|.+|||.  +++.++
T Consensus       192 ~~~sk~g~avl-~LQ~~LP~ARvvY~SATgasep~Nma  228 (303)
T PF13872_consen  192 KKPSKTGIAVL-ELQNRLPNARVVYASATGASEPRNMA  228 (303)
T ss_pred             ccccHHHHHHH-HHHHhCCCCcEEEecccccCCCceee
Confidence                1222222 233334677999999998  555543

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.30  E-value=0.0034  Score=60.47  Aligned_cols=132  Identities=15%  Similarity=0.151  Sum_probs=73.5

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE  146 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~  146 (319)
                      ..++.+.+.||||+|||+.+....-......+ .....++..-..|.-+.+....+++.++...                
T Consensus       189 ~~g~vi~lvGpnG~GKTTtlakLA~~~~~~~~-~~~v~~i~~d~~rigalEQL~~~a~ilGvp~----------------  251 (420)
T PRK14721        189 EQGGVYALIGPTGVGKTTTTAKLAARAVIRHG-ADKVALLTTDSYRIGGHEQLRIYGKLLGVSV----------------  251 (420)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHHhcC-CCeEEEEecCCcchhHHHHHHHHHHHcCCce----------------
Confidence            35678999999999999887654433222211 1233455555667777666666666654221                


Q ss_pred             cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhcc-ccCceEEEeccccChh---hHh
Q psy496          147 LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDK-RKDLKLILMSATLNAE---KFS  222 (319)
Q Consensus       147 ~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~-~~~~qiv~lSAT~~~~---~l~  222 (319)
                             ..+.++.-+...+.   .+.+.+.++||.+-+ ......+...++.+... .+...++++|||...+   .+.
T Consensus       252 -------~~v~~~~dl~~al~---~l~~~d~VLIDTaGr-sqrd~~~~~~l~~l~~~~~~~~~~LVl~at~~~~~~~~~~  320 (420)
T PRK14721        252 -------RSIKDIADLQLMLH---ELRGKHMVLIDTVGM-SQRDQMLAEQIAMLSQCGTQVKHLLLLNATSSGDTLDEVI  320 (420)
T ss_pred             -------ecCCCHHHHHHHHH---HhcCCCEEEecCCCC-CcchHHHHHHHHHHhccCCCceEEEEEcCCCCHHHHHHHH
Confidence                   00112222222222   256788999999854 22223344445555432 2344678899998444   444


Q ss_pred             hhhC
Q psy496          223 QFFG  226 (319)
Q Consensus       223 ~~l~  226 (319)
                      ..|.
T Consensus       321 ~~f~  324 (420)
T PRK14721        321 SAYQ  324 (420)
T ss_pred             HHhc
Confidence            4443

>PRK08181 transposase; Validated

Probab=97.27  E-value=0.002  Score=58.56  Aligned_cols=21  Identities=14%  Similarity=0.262  Sum_probs=17.3

Q ss_pred             CCCCcEEEecCCCCCccchhh
Q psy496           67 PILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~   87 (319)
                      ..+++++++||+|+|||....
T Consensus       104 ~~~~nlll~Gp~GtGKTHLa~  124 (269)
T PRK08181        104 AKGANLLLFGPPGGGKSHLAA  124 (269)
T ss_pred             hcCceEEEEecCCCcHHHHHH
Confidence            356789999999999996543

>KOG1803|consensus

Probab=97.26  E-value=0.0005  Score=67.47  Aligned_cols=49  Identities=24%  Similarity=0.337  Sum_probs=40.1

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      ...+|.||+|+|||......|.+.+..+.     +|++..||.+....+.+++.
T Consensus       202 ~l~~I~GPPGTGKT~TlvEiI~qlvk~~k-----~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  202 DLLIIHGPPGTGKTRTLVEIISQLVKQKK-----RVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             CceEeeCCCCCCceeeHHHHHHHHHHcCC-----eEEEEcCchHHHHHHHHHhc
Confidence            45788999999999988877776665554     89999999999998887644

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.24  E-value=0.015  Score=57.42  Aligned_cols=207  Identities=14%  Similarity=0.135  Sum_probs=100.7

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE  146 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~  146 (319)
                      ..++.+.++||||+|||+............ ..+....++..-+.|..+....+.+...+       |..+.        
T Consensus       348 ~~G~vIaLVGPtGvGKTTtaakLAa~la~~-~~gkkVaLIdtDtyRigA~EQLk~ya~iL-------gv~v~--------  411 (559)
T PRK12727        348 ERGGVIALVGPTGAGKTTTIAKLAQRFAAQ-HAPRDVALVTTDTQRVGGREQLHSYGRQL-------GIAVH--------  411 (559)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHHHHHHh-cCCCceEEEecccccccHHHHHHHhhccc-------CceeE--------
Confidence            457889999999999998875544322221 11123344444456665544433332221       11110        


Q ss_pred             cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccChhhHhhhhC
Q psy496          147 LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFG  226 (319)
Q Consensus       147 ~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~~~~l~~~l~  226 (319)
                              ...+++.+...+..   +.++++||||.+-.. .....+...+..+........+++++++....++.+.+.
T Consensus       412 --------~a~d~~~L~~aL~~---l~~~DLVLIDTaG~s-~~D~~l~eeL~~L~aa~~~a~lLVLpAtss~~Dl~eii~  479 (559)
T PRK12727        412 --------EADSAESLLDLLER---LRDYKLVLIDTAGMG-QRDRALAAQLNWLRAARQVTSLLVLPANAHFSDLDEVVR  479 (559)
T ss_pred             --------ecCcHHHHHHHHHH---hccCCEEEecCCCcc-hhhHHHHHHHHHHHHhhcCCcEEEEECCCChhHHHHHHH
Confidence                    01133445555532   356899999999752 122222222222222222346788888874444443322


Q ss_pred             CCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCcccc--ccccchHhHHHHhHhh
Q psy496          227 GAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYP--VQEYYLEDVLNMTRTL  304 (319)
Q Consensus       227 ~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~--v~~~~~~~~~~~~~~~  304 (319)
                      ...       ..+..-.++... .. ...+ ..+.+.....       +-++.-+..|.+.|  .+...-..+....-.|
T Consensus       480 ~f~-------~~~~~gvILTKl-DE-t~~l-G~aLsv~~~~-------~LPI~yvt~GQ~VPeDL~~A~~~~Lv~r~~~l  542 (559)
T PRK12727        480 RFA-------HAKPQGVVLTKL-DE-TGRF-GSALSVVVDH-------QMPITWVTDGQRVPDDLHRANAASLVLRLEDL  542 (559)
T ss_pred             HHH-------hhCCeEEEEecC-cC-ccch-hHHHHHHHHh-------CCCEEEEeCCCCchhhhhcCCHHHHHHHHHHH
Confidence            100       001111122111 10 1111 2222222211       33444444445554  4456677777777778


Q ss_pred             ccccCCCCCCccCC
Q psy496          305 KRSETQQYPNDQQH  318 (319)
Q Consensus       305 ~~~~~~~~~~~~~~  318 (319)
                      +|...-|.+.++-|
T Consensus       543 ~~~~~~~~~~~~~~  556 (559)
T PRK12727        543 RRAADKPCTPEHNH  556 (559)
T ss_pred             HhhccCCCChhhhc
Confidence            88888888887766

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.24  E-value=0.00068  Score=70.55  Aligned_cols=43  Identities=28%  Similarity=0.363  Sum_probs=31.0

Q ss_pred             CCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          169 DPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       169 ~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      .+....++++||||+|+  +..+..-.+++.+...+....+|+.+
T Consensus       115 ~p~~~~~KV~IIDEad~--lt~~a~NaLLK~LEEpP~~~~fIl~t  157 (824)
T PRK07764        115 APAESRYKIFIIDEAHM--VTPQGFNALLKIVEEPPEHLKFIFAT  157 (824)
T ss_pred             chhcCCceEEEEechhh--cCHHHHHHHHHHHhCCCCCeEEEEEe
Confidence            34457899999999998  66666667777777666666666543

>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=97.22  E-value=0.00071  Score=62.01  Aligned_cols=60  Identities=22%  Similarity=0.186  Sum_probs=45.4

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhcc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDE  128 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~  128 (319)
                      .+++++|.|+.|||||++...-+...+...+ ...-+|+++..|+.+|..+..++...++.
T Consensus        12 ~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~-~~~~~Il~lTft~~aa~e~~~ri~~~l~~   71 (315)
T PF00580_consen   12 TEGPLLVNAGAGSGKTTTLLERIAYLLYEGG-VPPERILVLTFTNAAAQEMRERIRELLEE   71 (315)
T ss_dssp             -SSEEEEEE-TTSSHHHHHHHHHHHHHHTSS-STGGGEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCchHHHHHHHHHhhcccc-CChHHheecccCHHHHHHHHHHHHHhcCc
Confidence            5688999999999999988666655544332 34457999999999999999998886543

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 ....

>KOG1123|consensus

Probab=97.22  E-value=0.00082  Score=64.64  Aligned_cols=124  Identities=15%  Similarity=0.151  Sum_probs=70.1

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEE-EEEecccccC
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVG-YQIRLEKELP  148 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg-~~~~~~~~~~  148 (319)
                      +.-+|+-|-|+|||++..-++..    -.    -++++++..-.-+.|..+++........    ..++ +.....+. -
T Consensus       321 RSGiIVLPCGAGKtLVGvTAa~t----ik----K~clvLcts~VSVeQWkqQfk~wsti~d----~~i~rFTsd~Ke~-~  387 (776)
T KOG1123|consen  321 RSGIIVLPCGAGKTLVGVTAACT----IK----KSCLVLCTSAVSVEQWKQQFKQWSTIQD----DQICRFTSDAKER-F  387 (776)
T ss_pred             cCceEEEecCCCCceeeeeeeee----ec----ccEEEEecCccCHHHHHHHHHhhcccCc----cceEEeecccccc-C
Confidence            45688899999999876444321    11    1344444666666776666655433221    1121 11111111 1


Q ss_pred             CCCceEEEECchHH-------------HHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccc
Q psy496          149 RKRGSILYCTAGIL-------------PEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSAT  215 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~l-------------l~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT  215 (319)
                      ...+.|+|+|..++             ++.+..    ..++++++||+|-  +-..++.-++..+..   . --++++||
T Consensus       388 ~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~----~EWGllllDEVHv--vPA~MFRRVlsiv~a---H-cKLGLTAT  457 (776)
T KOG1123|consen  388 PSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRG----REWGLLLLDEVHV--VPAKMFRRVLSIVQA---H-CKLGLTAT  457 (776)
T ss_pred             CCCCcEEEEeeehhhhcccccHHHHHHHHHHhc----CeeeeEEeehhcc--chHHHHHHHHHHHHH---H-hhccceeE
Confidence            23567999998665             344433    5789999999997  333333333443332   1 24799999


Q ss_pred             c
Q psy496          216 L  216 (319)
Q Consensus       216 ~  216 (319)
                      +
T Consensus       458 L  458 (776)
T KOG1123|consen  458 L  458 (776)
T ss_pred             E
Confidence            9

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.21  E-value=0.002  Score=66.52  Aligned_cols=56  Identities=18%  Similarity=0.125  Sum_probs=35.7

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHH
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIA  119 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~  119 (319)
                      +++..+..++..+|+|++|||||+..- .+++.+...+  ....|+.+.||-..|..+.
T Consensus       330 ~Ai~~~~~~~~~iitGgpGTGKTt~l~-~i~~~~~~~~--~~~~v~l~ApTg~AA~~L~  385 (720)
T TIGR01448       330 QALDTAIQHKVVILTGGPGTGKTTITR-AIIELAEELG--GLLPVGLAAPTGRAAKRLG  385 (720)
T ss_pred             HHHHHHHhCCeEEEECCCCCCHHHHHH-HHHHHHHHcC--CCceEEEEeCchHHHHHHH
Confidence            333334456789999999999997653 3444433322  1236777789988776543

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.

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=97.20  E-value=0.00087  Score=68.90  Aligned_cols=48  Identities=15%  Similarity=0.021  Sum_probs=39.1

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAE  120 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~  120 (319)
                      ++.++|-||||+|||.+|++|.+-.....+    -+|++...|..|-.|+..
T Consensus        49 ~~~lviEAgTGtGKTlaYLlPai~~A~~~~----k~vVIST~T~~LQeQL~~   96 (697)
T PRK11747         49 GRILVIEAGTGVGKTLSYLLAGIPIARAEK----KKLVISTATVALQEQLVS   96 (697)
T ss_pred             cceEEEECCCCcchhHHHHHHHHHHHHHcC----CeEEEEcCCHHHHHHHHh
Confidence            467899999999999999999875443333    279999999999989854

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.16  E-value=0.0013  Score=66.02  Aligned_cols=48  Identities=23%  Similarity=0.257  Sum_probs=32.8

Q ss_pred             HHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          164 EVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       164 ~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      +.....+.....+++||||+|+  +..+..-.+++.+...++...+|+.+
T Consensus       108 ~~~~~~P~~~~~KVvIIDEah~--Lt~~A~NALLK~LEEpp~~~~fIL~t  155 (584)
T PRK14952        108 DRAFYAPAQSRYRIFIVDEAHM--VTTAGFNALLKIVEEPPEHLIFIFAT  155 (584)
T ss_pred             HHHHhhhhcCCceEEEEECCCc--CCHHHHHHHHHHHhcCCCCeEEEEEe
Confidence            3334445567899999999998  56666667777776655565555543

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.11  E-value=0.0022  Score=67.78  Aligned_cols=123  Identities=15%  Similarity=0.129  Sum_probs=68.4

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      .++-|..++..+..         .+..++|+|+.|+|||+.. -.+.+.+...+    ..|+.+.||-..|..+.+    
T Consensus       347 Ls~eQr~Av~~il~---------s~~v~vv~G~AGTGKTT~l-~~~~~~~e~~G----~~V~~~ApTGkAA~~L~e----  408 (988)
T PRK13889        347 LSGEQADALAHVTD---------GRDLGVVVGYAGTGKSAML-GVAREAWEAAG----YEVRGAALSGIAAENLEG----  408 (988)
T ss_pred             CCHHHHHHHHHHhc---------CCCeEEEEeCCCCCHHHHH-HHHHHHHHHcC----CeEEEecCcHHHHHHHhh----
Confidence            34556666544332         1346789999999999863 33443333222    367888899776655432    


Q ss_pred             HhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHh-cCCCCCCccEEEEecccccccchhHHHHHHHhhhcc
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQ-SDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDK  203 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~-~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~  203 (319)
                      ..       |..                   -.|-..++..+. ....+...++|||||+-+  +....+..+++.... 
T Consensus       409 ~t-------Gi~-------------------a~TI~sll~~~~~~~~~l~~~~vlIVDEASM--v~~~~m~~LL~~a~~-  459 (988)
T PRK13889        409 GS-------GIA-------------------SRTIASLEHGWGQGRDLLTSRDVLVIDEAGM--VGTRQLERVLSHAAD-  459 (988)
T ss_pred             cc-------Ccc-------------------hhhHHHHHhhhcccccccccCcEEEEECccc--CCHHHHHHHHHhhhh-
Confidence            11       100                   012222332222 223366789999999997  455555555554332 


Q ss_pred             ccCceEEEeccc
Q psy496          204 RKDLKLILMSAT  215 (319)
Q Consensus       204 ~~~~qiv~lSAT  215 (319)
                       ...++|++.-+
T Consensus       460 -~garvVLVGD~  470 (988)
T PRK13889        460 -AGAKVVLVGDP  470 (988)
T ss_pred             -CCCEEEEECCH
Confidence             35577776544

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

Probab=97.09  E-value=0.00061  Score=59.48  Aligned_cols=54  Identities=26%  Similarity=0.314  Sum_probs=36.4

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHH---HhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEI---ARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~---~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ..+|+||+|||||......+.....   ........+|++++|+...+.++.+++.+
T Consensus        19 ~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen   19 ITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             -EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            4899999999999766554433311   01123345888888999999999998887

>PF05729 NACHT: NACHT domain

Probab=97.07  E-value=0.0028  Score=52.22  Aligned_cols=52  Identities=19%  Similarity=0.233  Sum_probs=30.3

Q ss_pred             EEEEecccccccchh-----HHHHHHHhhhc--cccCceEEEeccccChhhHhhhhCCC
Q psy496          177 HIVMDEIHERSMISD-----FLLAILKDVTD--KRKDLKLILMSATLNAEKFSQFFGGA  228 (319)
Q Consensus       177 ~vViDEah~~~~~~~-----~~~~~l~~~~~--~~~~~qiv~lSAT~~~~~l~~~l~~~  228 (319)
                      ++|||-+|+......     .....+..+..  ..++.++++.|.+-....+.+.+...
T Consensus        84 llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~  142 (166)
T PF05729_consen   84 LLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQA  142 (166)
T ss_pred             EEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCC
Confidence            499999998332221     23333433333  35677777766655665677777654

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.06  E-value=0.0026  Score=64.96  Aligned_cols=42  Identities=24%  Similarity=0.420  Sum_probs=28.1

Q ss_pred             CCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEe
Q psy496          169 DPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILM  212 (319)
Q Consensus       169 ~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~l  212 (319)
                      .+.-..++++||||+|+  +..+..-.+++.+...+++.++|+.
T Consensus       114 ~P~~gr~KVIIIDEah~--LT~~A~NALLKtLEEPP~~v~FILa  155 (830)
T PRK07003        114 APVDARFKVYMIDEVHM--LTNHAFNAMLKTLEEPPPHVKFILA  155 (830)
T ss_pred             ccccCCceEEEEeChhh--CCHHHHHHHHHHHHhcCCCeEEEEE
Confidence            34445789999999998  5555566667766655555555543

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.01  E-value=0.01  Score=58.07  Aligned_cols=131  Identities=16%  Similarity=0.130  Sum_probs=69.7

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL  147 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~  147 (319)
                      .++.+.+.||||+|||+......-......+ .....++..-+.|.-+.+..+.+++.++...       .  .      
T Consensus       255 ~g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G-~~kV~LI~~Dt~RigA~EQLr~~AeilGVpv-------~--~------  318 (484)
T PRK06995        255 RGGVFALMGPTGVGKTTTTAKLAARCVMRHG-ASKVALLTTDSYRIGGHEQLRIYGKILGVPV-------H--A------  318 (484)
T ss_pred             CCcEEEEECCCCccHHHHHHHHHHHHHHhcC-CCeEEEEeCCccchhHHHHHHHHHHHhCCCe-------e--c------
Confidence            4578999999999999988665433222222 1133455556778878777777777654221       0  0      


Q ss_pred             CCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhcc-ccCceEEEeccccChh---hHhh
Q psy496          148 PRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDK-RKDLKLILMSATLNAE---KFSQ  223 (319)
Q Consensus       148 ~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~-~~~~qiv~lSAT~~~~---~l~~  223 (319)
                              +..+.-+...+   ..+.+.+.++||.+-+ +.........+..+... .+...++.++||....   .+.+
T Consensus       319 --------~~~~~Dl~~aL---~~L~d~d~VLIDTaGr-~~~d~~~~e~~~~l~~~~~p~e~~LVLdAt~~~~~l~~i~~  386 (484)
T PRK06995        319 --------VKDAADLRLAL---SELRNKHIVLIDTIGM-SQRDRMVSEQIAMLHGAGAPVKRLLLLNATSHGDTLNEVVQ  386 (484)
T ss_pred             --------cCCchhHHHHH---HhccCCCeEEeCCCCc-ChhhHHHHHHHHHHhccCCCCeeEEEEeCCCcHHHHHHHHH
Confidence                    00111111111   2345678899999764 22222222222323222 1333678889998333   3444


Q ss_pred             hhC
Q psy496          224 FFG  226 (319)
Q Consensus       224 ~l~  226 (319)
                      .|.
T Consensus       387 ~f~  389 (484)
T PRK06995        387 AYR  389 (484)
T ss_pred             Hhc
Confidence            443

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.99  E-value=0.0013  Score=65.02  Aligned_cols=42  Identities=24%  Similarity=0.392  Sum_probs=29.5

Q ss_pred             CCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEe
Q psy496          169 DPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILM  212 (319)
Q Consensus       169 ~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~l  212 (319)
                      .+.-..++++||||+|+  +..+..-.+++.+...++...+|+.
T Consensus       114 ~p~~~~~kV~iIDE~~~--ls~~a~naLLk~LEepp~~~~fIla  155 (509)
T PRK14958        114 APTKGRFKVYLIDEVHM--LSGHSFNALLKTLEEPPSHVKFILA  155 (509)
T ss_pred             ccccCCcEEEEEEChHh--cCHHHHHHHHHHHhccCCCeEEEEE
Confidence            34446789999999998  5666666777766665556566553

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.96  E-value=0.0012  Score=64.40  Aligned_cols=44  Identities=18%  Similarity=0.292  Sum_probs=28.2

Q ss_pred             CCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccChh
Q psy496          172 LSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAE  219 (319)
Q Consensus       172 l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~~~  219 (319)
                      -..++++||||+|+  +..+..-.+++.+...+.  .++++-||-+..
T Consensus       119 ~g~~KV~IIDEah~--Ls~~A~NALLKtLEEPp~--~viFILaTte~~  162 (484)
T PRK14956        119 GGKYKVYIIDEVHM--LTDQSFNALLKTLEEPPA--HIVFILATTEFH  162 (484)
T ss_pred             cCCCEEEEEechhh--cCHHHHHHHHHHhhcCCC--ceEEEeecCChh
Confidence            35688999999998  666666677777655333  344443444333

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.94  E-value=0.0091  Score=57.90  Aligned_cols=55  Identities=16%  Similarity=0.184  Sum_probs=35.2

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      ..+++++|++|+|||+....... .+..  .+..+.++..-+.|..|....+.++...
T Consensus        95 p~vI~lvG~~GsGKTTtaakLA~-~L~~--~g~kV~lV~~D~~R~aa~eQL~~la~~~  149 (437)
T PRK00771         95 PQTIMLVGLQGSGKTTTAAKLAR-YFKK--KGLKVGLVAADTYRPAAYDQLKQLAEKI  149 (437)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHH-HHHH--cCCeEEEecCCCCCHHHHHHHHHHHHHc
Confidence            45788999999999988765443 3332  2334555555566776666555565543

>PRK08727 hypothetical protein; Validated

Probab=96.90  E-value=0.0049  Score=54.78  Aligned_cols=19  Identities=21%  Similarity=0.102  Sum_probs=15.5

Q ss_pred             CCcEEEecCCCCCccchhh
Q psy496           69 LSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~   87 (319)
                      .+.++++||+|||||...-
T Consensus        41 ~~~l~l~G~~G~GKThL~~   59 (233)
T PRK08727         41 SDWLYLSGPAGTGKTHLAL   59 (233)
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            3569999999999996553

>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=96.90  E-value=0.08  Score=51.26  Aligned_cols=69  Identities=16%  Similarity=0.180  Sum_probs=45.9

Q ss_pred             CceEEEECchHHHHHHhc------CCC-CCCccEEEEecccccc-cchhHHHHHHHhhhcccc-----------------
Q psy496          151 RGSILYCTAGILPEVMQS------DPI-LSGVSHIVMDEIHERS-MISDFLLAILKDVTDKRK-----------------  205 (319)
Q Consensus       151 ~~~Iiv~Tpg~ll~~l~~------~~~-l~~v~~vViDEah~~~-~~~~~~~~~l~~~~~~~~-----------------  205 (319)
                      .++||||+|=-|...+..      +.+ |+++.++|+|.+|... -+-+.+..+++.+...+.                 
T Consensus       131 ~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQNW~Hv~~v~~~lN~~P~~~~~~DfsRVR~w~Ldg  210 (442)
T PF06862_consen  131 SSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQNWEHVLHVFEHLNLQPKKSHDTDFSRVRPWYLDG  210 (442)
T ss_pred             cCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHhhHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHcC
Confidence            577999999445554532      222 8999999999999611 223355555655544332                 


Q ss_pred             ----CceEEEeccccChh
Q psy496          206 ----DLKLILMSATLNAE  219 (319)
Q Consensus       206 ----~~qiv~lSAT~~~~  219 (319)
                          -+|.|++|+..+++
T Consensus       211 ~a~~~RQtii~S~~~~pe  228 (442)
T PF06862_consen  211 QAKYYRQTIIFSSFQTPE  228 (442)
T ss_pred             cchheeEeEEecCCCCHH
Confidence                27899999998655

; GO: 0005634 nucleus

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.90  E-value=0.0014  Score=51.66  Aligned_cols=21  Identities=29%  Similarity=0.290  Sum_probs=17.3

Q ss_pred             CCcEEEecCCCCCccchhhHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~   89 (319)
                      ++.++|.||+|||||+.....
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l   22 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARAL   22 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHH
Confidence            467999999999999876443

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.

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.89  E-value=0.0017  Score=63.78  Aligned_cols=47  Identities=28%  Similarity=0.353  Sum_probs=31.8

Q ss_pred             HHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEe
Q psy496          164 EVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILM  212 (319)
Q Consensus       164 ~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~l  212 (319)
                      +.....|...+++++||||+|+  +..+..-.+++.+...++...+|+.
T Consensus       106 e~~~~~P~~~~~KVvIIDEah~--Ls~~A~NaLLK~LEePp~~v~fIla  152 (491)
T PRK14964        106 ENSCYLPISSKFKVYIIDEVHM--LSNSAFNALLKTLEEPAPHVKFILA  152 (491)
T ss_pred             HHHHhccccCCceEEEEeChHh--CCHHHHHHHHHHHhCCCCCeEEEEE
Confidence            3344456678899999999998  5555566667766665555555553

>KOG0387|consensus

Probab=96.88  E-value=0.011  Score=59.89  Aligned_cols=137  Identities=20%  Similarity=0.167  Sum_probs=70.0

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhc---cccCCCCceEE--EEE---
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERD---EQCGRPGSSVG--YQI---  141 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~---~~~~~~g~~vg--~~~---  141 (319)
                      .-=+|.=.-|=|||.+....+ ..+...++. ...+|+++|...+. |-.+.+....-   ..+ +++...+  +..   
T Consensus       225 ~GGILgDeMGLGKTIQiisFL-aaL~~S~k~-~~paLIVCP~Tii~-qW~~E~~~w~p~~rv~i-lh~t~s~~r~~~~~~  300 (923)
T KOG0387|consen  225 AGGILGDEMGLGKTIQIISFL-AALHHSGKL-TKPALIVCPATIIH-QWMKEFQTWWPPFRVFI-LHGTGSGARYDASHS  300 (923)
T ss_pred             CCCeecccccCccchhHHHHH-HHHhhcccc-cCceEEEccHHHHH-HHHHHHHHhCcceEEEE-EecCCcccccccchh
Confidence            335667779999997754432 333333221 13455556976553 33333433321   111 0011110  000   


Q ss_pred             e-cccc----cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccc-cccchhHHHHHHHhhhccccCceEEEeccc
Q psy496          142 R-LEKE----LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHE-RSMISDFLLAILKDVTDKRKDLKLILMSAT  215 (319)
Q Consensus       142 ~-~~~~----~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~-~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT  215 (319)
                      . .-+.    ......+|+++|...+. .......=...+++|+||.|. |.......++..+.-     ..+.+++|.|
T Consensus       301 ~~~~~~~L~r~~~~~~~ilitty~~~r-~~~d~l~~~~W~y~ILDEGH~IrNpns~islackki~-----T~~RiILSGT  374 (923)
T KOG0387|consen  301 SHKKDKLLIRKVATDGGILITTYDGFR-IQGDDLLGILWDYVILDEGHRIRNPNSKISLACKKIR-----TVHRIILSGT  374 (923)
T ss_pred             hhhhhhhheeeecccCcEEEEehhhhc-ccCcccccccccEEEecCcccccCCccHHHHHHHhcc-----ccceEEeeCc
Confidence            0 0000    01123468888887542 221111224689999999998 777777777665542     3356788999


Q ss_pred             c
Q psy496          216 L  216 (319)
Q Consensus       216 ~  216 (319)
                      +
T Consensus       375 P  375 (923)
T KOG0387|consen  375 P  375 (923)
T ss_pred             c
Confidence            8

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.88  E-value=0.0048  Score=56.50  Aligned_cols=89  Identities=18%  Similarity=0.189  Sum_probs=52.1

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL  147 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~  147 (319)
                      .+++++++||||+|||+.............+ +....++-.-|.|..+......++..++..       +.         
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g-~~~V~li~~D~~r~~a~eql~~~~~~~~~p-------~~---------  255 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHG-NKKVALITTDTYRIGAVEQLKTYAKILGVP-------VK---------  255 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcC-CCeEEEEECCccchhHHHHHHHHHHHhCCc-------ee---------
Confidence            3568899999999999887654433222211 134566666677776666655565543321       10         


Q ss_pred             CCCCceEEEECchHHHHHHhcCCCCCCccEEEEecc
Q psy496          148 PRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEI  183 (319)
Q Consensus       148 ~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEa  183 (319)
                             ...+++.+.+.+..   +.++++|+||.+
T Consensus       256 -------~~~~~~~l~~~l~~---~~~~d~vliDt~  281 (282)
T TIGR03499       256 -------VARDPKELRKALDR---LRDKDLILIDTA  281 (282)
T ss_pred             -------ccCCHHHHHHHHHH---ccCCCEEEEeCC
Confidence                   11134445554432   346899999975

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.87  E-value=0.0034  Score=61.56  Aligned_cols=53  Identities=23%  Similarity=0.170  Sum_probs=29.6

Q ss_pred             HHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHH
Q psy496           34 EIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        34 ~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~   89 (319)
                      |++..|.....-..-|..+...+.   +.+....-.+.++++||+|+|||+.+-..
T Consensus         4 l~~kyRP~~~~divGq~~i~~~L~---~~i~~~~l~~~~Lf~GPpGtGKTTlA~~l   56 (472)
T PRK14962          4 LYRKYRPKTFSEVVGQDHVKKLII---NALKKNSISHAYIFAGPRGTGKTTVARIL   56 (472)
T ss_pred             hHHHHCCCCHHHccCcHHHHHHHH---HHHHcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            444444443333344555433332   23333333345799999999999877543

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=96.86  E-value=0.0052  Score=58.33  Aligned_cols=69  Identities=19%  Similarity=0.166  Sum_probs=42.8

Q ss_pred             cccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHH--HHHHHHHh
Q psy496           49 QPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAI--AERVAQER  126 (319)
Q Consensus        49 Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~--~~~~~~~~  126 (319)
                      |++++..+.+.  + . ...+.++.|.|+-|+|||..+-. +.+.+..    ....+++++||-.+|..+  ...+...+
T Consensus         6 Q~~~~~~v~~~--~-~-~~~~~~~fv~G~~GtGKs~l~~~-i~~~~~~----~~~~~~~~a~tg~AA~~i~~G~T~hs~f   76 (364)
T PF05970_consen    6 QRRVFDTVIEA--I-E-NEEGLNFFVTGPAGTGKSFLIKA-IIDYLRS----RGKKVLVTAPTGIAAFNIPGGRTIHSFF   76 (364)
T ss_pred             HHHHHHHHHHH--H-H-ccCCcEEEEEcCCCCChhHHHHH-HHHHhcc----ccceEEEecchHHHHHhccCCcchHHhc
Confidence            66666665432  1 1 25678899999999999965422 2222222    123788888999988777  33444443

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=96.86  E-value=0.002  Score=65.36  Aligned_cols=43  Identities=23%  Similarity=0.410  Sum_probs=29.0

Q ss_pred             CCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          169 DPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       169 ~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      .+.+...+++||||+|.  +..+..-.+++.+...++...+|+.+
T Consensus       114 ~P~~gk~KVIIIDEad~--Ls~~A~NALLKtLEEPp~~v~fILaT  156 (709)
T PRK08691        114 APTAGKYKVYIIDEVHM--LSKSAFNAMLKTLEEPPEHVKFILAT  156 (709)
T ss_pred             hhhhCCcEEEEEECccc--cCHHHHHHHHHHHHhCCCCcEEEEEe
Confidence            34567889999999997  45555556666666555555666543

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.84  E-value=0.0021  Score=64.58  Aligned_cols=43  Identities=23%  Similarity=0.424  Sum_probs=30.6

Q ss_pred             CCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          169 DPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       169 ~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      .+....++++||||+|+  +.....-.+++.+...+++.++|+.+
T Consensus       119 ~P~~gr~KViIIDEah~--Ls~~AaNALLKTLEEPP~~v~FILaT  161 (700)
T PRK12323        119 APTAGRFKVYMIDEVHM--LTNHAFNAMLKTLEEPPEHVKFILAT  161 (700)
T ss_pred             chhcCCceEEEEEChHh--cCHHHHHHHHHhhccCCCCceEEEEe
Confidence            34456789999999998  56666667777766655566666654

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

Probab=96.84  E-value=0.0017  Score=66.47  Aligned_cols=67  Identities=16%  Similarity=0.027  Sum_probs=49.3

Q ss_pred             ccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           46 MVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        46 ~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      .+.|...+..+.      ....++..+++-||||+|||.+++.|.+......+    ..+++..+|+.+-.|+.++.
T Consensus        17 r~~Q~~~~~~v~------~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~----~~viist~t~~lq~q~~~~~   83 (654)
T COG1199          17 RPEQREMAEAVA------EALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG----KKVIISTRTKALQEQLLEED   83 (654)
T ss_pred             CHHHHHHHHHHH------HHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcC----CcEEEECCCHHHHHHHHHhh
Confidence            356777765554      23445566999999999999999999987655443    37888889998888876543

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.81  E-value=0.0052  Score=63.90  Aligned_cols=48  Identities=23%  Similarity=0.406  Sum_probs=33.0

Q ss_pred             CCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccChhhH
Q psy496          170 PILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKF  221 (319)
Q Consensus       170 ~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~~~~l  221 (319)
                      +.-...+++||||+|+  +..+..-.+++.+...++..++|+.  |-+...+
T Consensus       115 P~~gk~KViIIDEAh~--LT~eAqNALLKtLEEPP~~vrFILa--TTe~~kL  162 (944)
T PRK14949        115 PSRGRFKVYLIDEVHM--LSRSSFNALLKTLEEPPEHVKFLLA--TTDPQKL  162 (944)
T ss_pred             hhcCCcEEEEEechHh--cCHHHHHHHHHHHhccCCCeEEEEE--CCCchhc
Confidence            3345789999999998  6677777778877766566666654  5544433

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.81  E-value=0.0026  Score=60.38  Aligned_cols=48  Identities=23%  Similarity=0.346  Sum_probs=29.9

Q ss_pred             HHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEe
Q psy496          163 PEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILM  212 (319)
Q Consensus       163 l~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~l  212 (319)
                      .+.+...+.....+++||||+|.  +..+....+++.+...++..++|+.
T Consensus       108 ~~~~~~~p~~~~~kviIIDEa~~--l~~~a~naLLk~lEe~~~~~~fIl~  155 (363)
T PRK14961        108 LDNIYYSPSKSRFKVYLIDEVHM--LSRHSFNALLKTLEEPPQHIKFILA  155 (363)
T ss_pred             HHHHhcCcccCCceEEEEEChhh--cCHHHHHHHHHHHhcCCCCeEEEEE
Confidence            33333345556789999999998  4444445566666555555556554

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.80  E-value=0.011  Score=53.78  Aligned_cols=124  Identities=17%  Similarity=0.193  Sum_probs=65.1

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL  147 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~  147 (319)
                      ..+.++++||+|+|||+........ +..  .+....++-.-+.|..+....+.+.+..+..+          .......
T Consensus        71 ~~~vi~l~G~~G~GKTTt~akLA~~-l~~--~g~~V~li~~D~~r~~a~~ql~~~~~~~~i~~----------~~~~~~~  137 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIAKLANK-LKK--QGKSVLLAAGDTFRAAAIEQLEEWAKRLGVDV----------IKQKEGA  137 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH-HHh--cCCEEEEEeCCCCCHHHHHHHHHHHHhCCeEE----------EeCCCCC
Confidence            3467888999999999877655433 222  22334445545777777666666666543111          0000000


Q ss_pred             CCCCceEEEECc-hHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhc-------cccCceEEEecccc
Q psy496          148 PRKRGSILYCTA-GILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTD-------KRKDLKLILMSATL  216 (319)
Q Consensus       148 ~~~~~~Iiv~Tp-g~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~-------~~~~~qiv~lSAT~  216 (319)
                                -| ....+.+.. ....+++++|||=+-.... ...+...++.+..       ..++-.++.+|||.
T Consensus       138 ----------dp~~~~~~~l~~-~~~~~~D~ViIDT~G~~~~-d~~~~~el~~~~~~~~~~~~~~~~~~~LVl~a~~  202 (272)
T TIGR00064       138 ----------DPAAVAFDAIQK-AKARNIDVVLIDTAGRLQN-KVNLMDELKKIKRVIKKVDKDAPDEVLLVLDATT  202 (272)
T ss_pred             ----------CHHHHHHHHHHH-HHHCCCCEEEEeCCCCCcc-hHHHHHHHHHHHHHHhcccCCCCceEEEEEECCC
Confidence                      11 111222211 1125789999999986222 2222222222221       22566788899998

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.

>PRK10867 signal recognition particle protein; Provisional

Probab=96.79  E-value=0.013  Score=56.81  Aligned_cols=57  Identities=14%  Similarity=0.158  Sum_probs=37.6

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      ...++++|++|||||+........ +... .+....++..-+.|..|....+.+++..+
T Consensus       100 p~vI~~vG~~GsGKTTtaakLA~~-l~~~-~G~kV~lV~~D~~R~aa~eQL~~~a~~~g  156 (433)
T PRK10867        100 PTVIMMVGLQGAGKTTTAGKLAKY-LKKK-KKKKVLLVAADVYRPAAIEQLKTLGEQIG  156 (433)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHH-HHHh-cCCcEEEEEccccchHHHHHHHHHHhhcC
Confidence            356888999999999887655443 2222 13345666667888887766666665543

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=96.78  E-value=0.0058  Score=57.69  Aligned_cols=50  Identities=18%  Similarity=0.191  Sum_probs=33.6

Q ss_pred             HHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecc
Q psy496          163 PEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSA  214 (319)
Q Consensus       163 l~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSA  214 (319)
                      .+.+...+.-...+++||||+|.  +.......+++.+...+++..++++|.
T Consensus       130 ~~~l~~~~~~g~~rVviIDeAd~--l~~~aanaLLk~LEEpp~~~~fiLit~  179 (351)
T PRK09112        130 GHFLSQTSGDGNWRIVIIDPADD--MNRNAANAILKTLEEPPARALFILISH  179 (351)
T ss_pred             HHHhhhccccCCceEEEEEchhh--cCHHHHHHHHHHHhcCCCCceEEEEEC
Confidence            34443344456789999999998  666666677777766555555666653

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.77  E-value=0.011  Score=56.91  Aligned_cols=53  Identities=19%  Similarity=0.254  Sum_probs=34.0

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      ..++++|++|||||+........ +..  .+....++..-|.|..|....+.+++.
T Consensus       101 ~vi~lvG~~GvGKTTtaaKLA~~-l~~--~G~kV~lV~~D~~R~aA~eQLk~~a~~  153 (429)
T TIGR01425       101 NVIMFVGLQGSGKTTTCTKLAYY-YQR--KGFKPCLVCADTFRAGAFDQLKQNATK  153 (429)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH-HHH--CCCCEEEEcCcccchhHHHHHHHHhhc
Confidence            56889999999999876544332 222  233445555567787777666655554

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.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=96.76  E-value=0.0027  Score=66.25  Aligned_cols=100  Identities=19%  Similarity=0.192  Sum_probs=60.7

Q ss_pred             CCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc---ccCCCCce
Q psy496           77 STGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK---ELPRKRGS  153 (319)
Q Consensus        77 pTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~---~~~~~~~~  153 (319)
                      .||=|||+++.+|++-..+.+.   .+.|+.+..  =||..=++.+...+...    |..||.......   ....-.++
T Consensus       159 ~TGEGKTLvatlp~yLnAL~G~---gVHvVTvND--YLA~RDaewm~p~y~fl----GLtVg~i~~~~~~~~Rr~aY~~D  229 (1025)
T PRK12900        159 ATGEGKTLVSTLPTFLNALTGR---GVHVVTVND--YLAQRDKEWMNPVFEFH----GLSVGVILNTMRPEERREQYLCD  229 (1025)
T ss_pred             CCCCCcchHhHHHHHHHHHcCC---CcEEEeech--HhhhhhHHHHHHHHHHh----CCeeeeeCCCCCHHHHHHhCCCc
Confidence            3999999999999864444332   456666333  35544444444433322    888885533111   11113678


Q ss_pred             EEEECc-----hHHHHHHhcCC---CCCCccEEEEecccc
Q psy496          154 ILYCTA-----GILPEVMQSDP---ILSGVSHIVMDEIHE  185 (319)
Q Consensus       154 Iiv~Tp-----g~ll~~l~~~~---~l~~v~~vViDEah~  185 (319)
                      |+++|.     +.|.+.+..++   ....+.+.||||+|.
T Consensus       230 ItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDS  269 (1025)
T PRK12900        230 ITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDS  269 (1025)
T ss_pred             ceecCCCccccccchhccccchhhhhccCCceEEEechhh
Confidence            999998     45555553333   257789999999996

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.72  E-value=0.0049  Score=62.18  Aligned_cols=48  Identities=23%  Similarity=0.364  Sum_probs=30.8

Q ss_pred             HHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEe
Q psy496          163 PEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILM  212 (319)
Q Consensus       163 l~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~l  212 (319)
                      ++.....+....++++||||+|+  +..+..-.+++.+...++...+|+.
T Consensus       113 i~~~~~~p~~g~~KV~IIDEvh~--Ls~~a~NaLLKtLEEPP~~~~fIL~  160 (618)
T PRK14951        113 LEQAVYKPVQGRFKVFMIDEVHM--LTNTAFNAMLKTLEEPPEYLKFVLA  160 (618)
T ss_pred             HHHHHhCcccCCceEEEEEChhh--CCHHHHHHHHHhcccCCCCeEEEEE
Confidence            33334455567799999999998  5566566666666554445455543

>KOG0385|consensus

Probab=96.69  E-value=0.013  Score=59.14  Aligned_cols=137  Identities=18%  Similarity=0.068  Sum_probs=69.9

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEec----
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRL----  143 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~----  143 (319)
                      ++-|.++.-+-|=|||++-.-. +..+... ++..+.-++++|.--|.+ ..+.++++.-...    ..+-+....    
T Consensus       185 ngingILaDEMGLGKTlQtIs~-l~yl~~~-~~~~GPfLVi~P~StL~N-W~~Ef~rf~P~l~----~~~~~Gdk~eR~~  257 (971)
T KOG0385|consen  185 NGINGILADEMGLGKTLQTISL-LGYLKGR-KGIPGPFLVIAPKSTLDN-WMNEFKRFTPSLN----VVVYHGDKEERAA  257 (971)
T ss_pred             cCcccEeehhcccchHHHHHHH-HHHHHHh-cCCCCCeEEEeeHhhHHH-HHHHHHHhCCCcc----eEEEeCCHHHHHH
Confidence            4556888899999999765332 2222221 111223444449766533 2333444422110    001000110    


Q ss_pred             --ccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          144 --EKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       144 --~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                        .+.....+-+|+++|.++.++--.-- .--..+++||||||+.--....+...++.+..   + ..++++.|+
T Consensus       258 ~~r~~~~~~~fdV~iTsYEi~i~dk~~l-k~~~W~ylvIDEaHRiKN~~s~L~~~lr~f~~---~-nrLLlTGTP  327 (971)
T KOG0385|consen  258 LRRDIMLPGRFDVCITSYEIAIKDKSFL-KKFNWRYLVIDEAHRIKNEKSKLSKILREFKT---D-NRLLLTGTP  327 (971)
T ss_pred             HHHHhhccCCCceEeehHHHHHhhHHHH-hcCCceEEEechhhhhcchhhHHHHHHHHhcc---c-ceeEeeCCc
Confidence              01111235679999999887652110 11368899999999732222233344444432   2 356778887

>KOG4439|consensus

Probab=96.68  E-value=0.0029  Score=63.18  Aligned_cols=159  Identities=18%  Similarity=0.193  Sum_probs=83.5

Q ss_pred             CccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHH----hCCCCcc-EEEEecccHHHH
Q psy496           41 SECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIA----RNRGSEC-CIMVTQPRRISA  115 (319)
Q Consensus        41 ~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~----~~~~~~~-~vl~~~Ptr~la  115 (319)
                      .....+|.|..++.-+.-.     .++.++--++.-.-|=|||+..+-.+++.-..    .+++... .-|+++|.+.+ 
T Consensus       322 ~~v~LmpHQkaal~Wl~wR-----E~q~~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~PaSli-  395 (901)
T KOG4439|consen  322 LKVELMPHQKAALRWLLWR-----ESQPPSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPASLI-  395 (901)
T ss_pred             ceeecchhhhhhhhhhccc-----ccCCCCCcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCcHHHH-
Confidence            3445677887776544321     24455566778889999999776666644322    1222222 25555597554 


Q ss_pred             HHHHHHHHHHhccccCCCCceEEEEEecccc------cCCCCceEEEECchHHHH----HH---hcCCCCCC--ccEEEE
Q psy496          116 IAIAERVAQERDEQCGRPGSSVGYQIRLEKE------LPRKRGSILYCTAGILPE----VM---QSDPILSG--VSHIVM  180 (319)
Q Consensus       116 ~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~------~~~~~~~Iiv~Tpg~ll~----~l---~~~~~l~~--v~~vVi  180 (319)
                      .|....+...+...    ...|-  +-++..      ....+.+|+++|...+-+    ..   .+...|.+  ..-||+
T Consensus       396 ~qW~~Ev~~rl~~n----~LsV~--~~HG~n~r~i~~~~L~~YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVIL  469 (901)
T KOG4439|consen  396 HQWEAEVARRLEQN----ALSVY--LYHGPNKREISAKELRKYDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVIL  469 (901)
T ss_pred             HHHHHHHHHHHhhc----ceEEE--EecCCccccCCHHHHhhcceEEEeeeccccCCchhhhcccCccHHHHhhHHHhhh
Confidence            45544454443322    11111  111111      111356899999876654    22   11222444  456899


Q ss_pred             ecccc-cccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          181 DEIHE-RSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       181 DEah~-~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      ||||. +........++.+.    ... -..++|+|+
T Consensus       470 DEAH~IrN~~tq~S~AVC~L----~a~-~RWclTGTP  501 (901)
T KOG4439|consen  470 DEAHNIRNSNTQCSKAVCKL----SAK-SRWCLTGTP  501 (901)
T ss_pred             hhhhhhcccchhHHHHHHHH----hhc-ceeecccCc
Confidence            99996 33333333333222    112 357889998

>PLN03025 replication factor C subunit; Provisional

Probab=96.66  E-value=0.014  Score=54.26  Aligned_cols=22  Identities=27%  Similarity=0.332  Sum_probs=17.2

Q ss_pred             CCCCcEEEecCCCCCccchhhH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l   88 (319)
                      .+..+++++||+|+|||+.+..
T Consensus        32 ~~~~~lll~Gp~G~GKTtla~~   53 (319)
T PLN03025         32 GNMPNLILSGPPGTGKTTSILA   53 (319)
T ss_pred             CCCceEEEECCCCCCHHHHHHH
Confidence            3445699999999999977644

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=96.65  E-value=0.015  Score=60.37  Aligned_cols=106  Identities=19%  Similarity=0.195  Sum_probs=59.8

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      ++.++|.|++|+|||+..-. +.+.+...+    ..|+.+.||--.|..+.+    ..       |...           
T Consensus       368 ~~~~il~G~aGTGKTtll~~-i~~~~~~~g----~~V~~~ApTg~Aa~~L~~----~~-------g~~a-----------  420 (744)
T TIGR02768       368 GDIAVVVGRAGTGKSTMLKA-AREAWEAAG----YRVIGAALSGKAAEGLQA----ES-------GIES-----------  420 (744)
T ss_pred             CCEEEEEecCCCCHHHHHHH-HHHHHHhCC----CeEEEEeCcHHHHHHHHh----cc-------CCce-----------
Confidence            46789999999999976533 333333322    367788899776655542    11       1100           


Q ss_pred             CCCceEEEECchHHHHHH-hcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          149 RKRGSILYCTAGILPEVM-QSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll~~l-~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                              .|-..++..+ .....+...++|||||+-+  +....+..+++....  ...++|++.
T Consensus       421 --------~Ti~~~~~~~~~~~~~~~~~~llIvDEasM--v~~~~~~~Ll~~~~~--~~~kliLVG  474 (744)
T TIGR02768       421 --------RTLASLEYAWANGRDLLSDKDVLVIDEAGM--VGSRQMARVLKEAEE--AGAKVVLVG  474 (744)
T ss_pred             --------eeHHHHHhhhccCcccCCCCcEEEEECccc--CCHHHHHHHHHHHHh--cCCEEEEEC
Confidence                    0112222222 2223367889999999998  444444445543332  245677665

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.

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=96.64  E-value=0.0079  Score=59.45  Aligned_cols=43  Identities=19%  Similarity=0.322  Sum_probs=27.4

Q ss_pred             HHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCc
Q psy496          163 PEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDL  207 (319)
Q Consensus       163 l~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~  207 (319)
                      ++.....+...+.+++||||+|+  +.......+++.+...++..
T Consensus       117 ie~a~~~P~~~~~KVvIIDEa~~--Ls~~a~naLLk~LEepp~~~  159 (507)
T PRK06645        117 IESAEYKPLQGKHKIFIIDEVHM--LSKGAFNALLKTLEEPPPHI  159 (507)
T ss_pred             HHHHHhccccCCcEEEEEEChhh--cCHHHHHHHHHHHhhcCCCE
Confidence            33344456678899999999998  44455555555555444443

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=96.63  E-value=0.0035  Score=53.40  Aligned_cols=46  Identities=17%  Similarity=0.175  Sum_probs=25.8

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIA  117 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q  117 (319)
                      ..+++++++.|++|+|||..+.. +...+...+    ..++++ +..+|...
T Consensus        44 ~~~~~~l~l~G~~G~GKThLa~a-i~~~~~~~g----~~v~f~-~~~~L~~~   89 (178)
T PF01695_consen   44 IENGENLILYGPPGTGKTHLAVA-IANEAIRKG----YSVLFI-TASDLLDE   89 (178)
T ss_dssp             -SC--EEEEEESTTSSHHHHHHH-HHHHHHHTT------EEEE-EHHHHHHH
T ss_pred             cccCeEEEEEhhHhHHHHHHHHH-HHHHhccCC----cceeEe-ecCceecc
Confidence            45678999999999999976544 334444433    244443 44444433

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.

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.60  E-value=0.0035  Score=63.21  Aligned_cols=42  Identities=19%  Similarity=0.389  Sum_probs=27.8

Q ss_pred             CCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEe
Q psy496          169 DPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILM  212 (319)
Q Consensus       169 ~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~l  212 (319)
                      .+....++++||||+|+  +.....-.+++.+...++...+|+.
T Consensus       113 ~P~~gk~KV~IIDEVh~--LS~~A~NALLKtLEEPP~~v~FILa  154 (702)
T PRK14960        113 APTQGRFKVYLIDEVHM--LSTHSFNALLKTLEEPPEHVKFLFA  154 (702)
T ss_pred             hhhcCCcEEEEEechHh--cCHHHHHHHHHHHhcCCCCcEEEEE
Confidence            33446789999999998  5555556666666555555555553

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=96.59  E-value=0.016  Score=58.54  Aligned_cols=50  Identities=20%  Similarity=0.385  Sum_probs=33.3

Q ss_pred             HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          162 LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       162 ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      +++.+...+.....+++||||+|+  +.....-.+++.+...++...+|+.+
T Consensus       120 Iie~~~~~P~~a~~KVvIIDEad~--Ls~~a~naLLKtLEePp~~~~fIl~t  169 (598)
T PRK09111        120 IIESVRYRPVSARYKVYIIDEVHM--LSTAAFNALLKTLEEPPPHVKFIFAT  169 (598)
T ss_pred             HHHHHHhchhcCCcEEEEEEChHh--CCHHHHHHHHHHHHhCCCCeEEEEEe
Confidence            344445556678899999999998  45555556666666555566666543

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=96.56  E-value=0.0081  Score=60.87  Aligned_cols=50  Identities=22%  Similarity=0.381  Sum_probs=32.9

Q ss_pred             cCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccChhhH
Q psy496          168 SDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKF  221 (319)
Q Consensus       168 ~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~~~~l  221 (319)
                      ..+.-..++++||||+|+  +..+..-.+++.+...++...+|+.  |-+...+
T Consensus       113 ~~p~~g~~KV~IIDEah~--Ls~~a~NALLKtLEEPp~~v~FIL~--Tt~~~kL  162 (647)
T PRK07994        113 YAPARGRFKVYLIDEVHM--LSRHSFNALLKTLEEPPEHVKFLLA--TTDPQKL  162 (647)
T ss_pred             hhhhcCCCEEEEEechHh--CCHHHHHHHHHHHHcCCCCeEEEEe--cCCcccc
Confidence            334456789999999998  6666777777777665555555554  4444433

>TIGR00959 ffh signal recognition particle protein

Probab=96.56  E-value=0.019  Score=55.56  Aligned_cols=56  Identities=18%  Similarity=0.201  Sum_probs=36.2

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      ..++++|++|||||+........ +.. ..+....++..-+.|..|.+..+.++...+
T Consensus       100 ~vi~~vG~~GsGKTTtaakLA~~-l~~-~~g~kV~lV~~D~~R~~a~~QL~~~a~~~g  155 (428)
T TIGR00959       100 TVILMVGLQGSGKTTTCGKLAYY-LKK-KQGKKVLLVACDLYRPAAIEQLKVLGQQVG  155 (428)
T ss_pred             EEEEEECCCCCcHHHHHHHHHHH-HHH-hCCCeEEEEeccccchHHHHHHHHHHHhcC
Confidence            46888999999999887665443 221 123345566666788777666666665443

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.54  E-value=0.0082  Score=56.12  Aligned_cols=45  Identities=18%  Similarity=0.180  Sum_probs=27.3

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAI  118 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~  118 (319)
                      .+.+++++|+||+|||... ..+...+...+    ..|+++ +..++...+
T Consensus       182 ~~~~Lll~G~~GtGKThLa-~aIa~~l~~~g----~~V~y~-t~~~l~~~l  226 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLS-NCIAKELLDRG----KSVIYR-TADELIEIL  226 (329)
T ss_pred             cCCcEEEECCCCCcHHHHH-HHHHHHHHHCC----CeEEEE-EHHHHHHHH
Confidence            4588999999999999644 33444444433    256553 334443333

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.54  E-value=0.0044  Score=61.68  Aligned_cols=49  Identities=22%  Similarity=0.322  Sum_probs=32.0

Q ss_pred             HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEe
Q psy496          162 LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILM  212 (319)
Q Consensus       162 ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~l  212 (319)
                      +++.+...+...+.+++||||+|+  +..+..-.+++.+...++...+|+.
T Consensus       107 ii~~~~~~p~~g~~kViIIDEa~~--ls~~a~naLLK~LEepp~~v~fIL~  155 (546)
T PRK14957        107 ILDNIQYMPSQGRYKVYLIDEVHM--LSKQSFNALLKTLEEPPEYVKFILA  155 (546)
T ss_pred             HHHHHHhhhhcCCcEEEEEechhh--ccHHHHHHHHHHHhcCCCCceEEEE
Confidence            344444445567889999999998  5555666666666655555555553

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=96.51  E-value=0.018  Score=54.72  Aligned_cols=62  Identities=18%  Similarity=0.133  Sum_probs=39.5

Q ss_pred             eEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          153 SILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       153 ~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      .|.|-.--.+.+.+...+.-...+++||||+|.  ++....-.+++.+...++...+|++|...
T Consensus       120 ~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~--m~~~aanaLLK~LEepp~~~~~IL~t~~~  181 (365)
T PRK07471        120 VITVDEVRELISFFGLTAAEGGWRVVIVDTADE--MNANAANALLKVLEEPPARSLFLLVSHAP  181 (365)
T ss_pred             cccHHHHHHHHHHhCcCcccCCCEEEEEechHh--cCHHHHHHHHHHHhcCCCCeEEEEEECCc
Confidence            354434333444444445567889999999998  66666677777776655555566655443

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=96.51  E-value=0.032  Score=51.99  Aligned_cols=124  Identities=16%  Similarity=0.168  Sum_probs=63.2

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL  147 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~  147 (319)
                      .++.+++.||+|+|||+........ +..  .+....++-.-+.|..|.+....++...+..       +-   ......
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~-l~~--~g~~V~Li~~D~~r~~a~eql~~~a~~~~i~-------~~---~~~~~~  179 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHK-YKA--QGKKVLLAAGDTFRAAAIEQLQVWGERVGVP-------VI---AQKEGA  179 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH-HHh--cCCeEEEEecCccchhhHHHHHHHHHHcCce-------EE---EeCCCC
Confidence            4578889999999999877544322 222  2233444444466776655555555543311       10   000000


Q ss_pred             CCCCceEEEECc-hHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhh-------ccccCceEEEecccc
Q psy496          148 PRKRGSILYCTA-GILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVT-------DKRKDLKLILMSATL  216 (319)
Q Consensus       148 ~~~~~~Iiv~Tp-g~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~-------~~~~~~qiv~lSAT~  216 (319)
                                .| ....+.+.. ....++++||||=+-.. ...+.+...++.+.       ...|.-.++.++||.
T Consensus       180 ----------dpa~~v~~~l~~-~~~~~~D~ViIDTaGr~-~~~~~l~~eL~~~~~v~~~~~~~~p~~~~LVl~a~~  244 (318)
T PRK10416        180 ----------DPASVAFDAIQA-AKARGIDVLIIDTAGRL-HNKTNLMEELKKIKRVIKKADPDAPHEVLLVLDATT  244 (318)
T ss_pred             ----------CHHHHHHHHHHH-HHhCCCCEEEEeCCCCC-cCCHHHHHHHHHHHHHHhhhcCCCCceEEEEEECCC
Confidence                      11 111222211 11267899999999852 22222222222221       233555688899998

>KOG0389|consensus

Probab=96.47  E-value=0.0072  Score=61.14  Aligned_cols=141  Identities=17%  Similarity=0.148  Sum_probs=72.7

Q ss_pred             EEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccc-c-CCCCceEE-EEEecccccC
Q psy496           72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQ-C-GRPGSSVG-YQIRLEKELP  148 (319)
Q Consensus        72 vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~-~-~~~g~~vg-~~~~~~~~~~  148 (319)
                      -|+.-+-|=|||.++... +..+...+..+.-+|+|  |.--|- ...+.++++.-.. + .|+|.... -.++..-...
T Consensus       421 gILADEMGLGKTiQvIaF-layLkq~g~~gpHLVVv--PsSTle-NWlrEf~kwCPsl~Ve~YyGSq~ER~~lR~~i~~~  496 (941)
T KOG0389|consen  421 GILADEMGLGKTIQVIAF-LAYLKQIGNPGPHLVVV--PSSTLE-NWLREFAKWCPSLKVEPYYGSQDERRELRERIKKN  496 (941)
T ss_pred             ceehhhccCcchhHHHHH-HHHHHHcCCCCCcEEEe--cchhHH-HHHHHHHHhCCceEEEeccCcHHHHHHHHHHHhcc
Confidence            477778999999765332 33333333322334555  875542 2333344432111 1 12232210 0011111111


Q ss_pred             CCCceEEEECchHHH-----HHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc---Chhh
Q psy496          149 RKRGSILYCTAGILP-----EVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL---NAEK  220 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll-----~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~---~~~~  220 (319)
                      ....+++++|.....     +.+..   -.+++++|.||.|.   ....--.+.+.+...+.+. .+++++|+   |..+
T Consensus       497 ~~~ydVllTTY~la~~~kdDRsflk---~~~~n~viyDEgHm---LKN~~SeRy~~LM~I~An~-RlLLTGTPLQNNL~E  569 (941)
T KOG0389|consen  497 KDDYDVLLTTYNLAASSKDDRSFLK---NQKFNYVIYDEGHM---LKNRTSERYKHLMSINANF-RLLLTGTPLQNNLKE  569 (941)
T ss_pred             CCCccEEEEEeecccCChHHHHHHH---hccccEEEecchhh---hhccchHHHHHhccccccc-eEEeeCCcccccHHH
Confidence            235679999986542     11111   14688999999996   2233345666677666664 46778887   5555


Q ss_pred             Hhh
Q psy496          221 FSQ  223 (319)
Q Consensus       221 l~~  223 (319)
                      +-.
T Consensus       570 LiS  572 (941)
T KOG0389|consen  570 LIS  572 (941)
T ss_pred             HHH
Confidence            444

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.46  E-value=0.005  Score=60.88  Aligned_cols=44  Identities=25%  Similarity=0.395  Sum_probs=28.2

Q ss_pred             HhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEE
Q psy496          166 MQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLIL  211 (319)
Q Consensus       166 l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~  211 (319)
                      +...+.+...+++||||+|.  +..+.+..+++.+...++...+|+
T Consensus       108 ~~~~p~~~~~kVVIIDEad~--ls~~a~naLLk~LEep~~~t~~Il  151 (504)
T PRK14963        108 VLLAPLRGGRKVYILDEAHM--MSKSAFNALLKTLEEPPEHVIFIL  151 (504)
T ss_pred             HhhccccCCCeEEEEECccc--cCHHHHHHHHHHHHhCCCCEEEEE
Confidence            33345567899999999997  445555566666655444444444

>PRK05642 DNA replication initiation factor; Validated

Probab=96.46  E-value=0.018  Score=51.11  Aligned_cols=17  Identities=18%  Similarity=0.405  Sum_probs=14.5

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      ..++|+||+|+|||...
T Consensus        46 ~~l~l~G~~G~GKTHLl   62 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLL   62 (234)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            56899999999999663

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=96.45  E-value=0.0062  Score=62.87  Aligned_cols=62  Identities=15%  Similarity=0.096  Sum_probs=46.1

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++..+..++++.++-||||+|||++.+.+.+......+  ...+|++.+.|..=..|..+.+++
T Consensus        21 ~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~--~~~kIiy~sRThsQl~q~i~Elk~   82 (705)
T TIGR00604        21 DLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP--EVRKIIYASRTHSQLEQATEELRK   82 (705)
T ss_pred             HHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc--ccccEEEEcccchHHHHHHHHHHh
Confidence            44455667889999999999999999999987654322  134899988887766676666665

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).

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=96.45  E-value=0.011  Score=59.29  Aligned_cols=49  Identities=18%  Similarity=0.241  Sum_probs=30.5

Q ss_pred             HHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          163 PEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       163 l~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      .+.+...+...+.+++||||+|.  +..+..-.+++.+...++...+|+++
T Consensus       108 i~~~~~~P~~~~~KVIIIDEad~--Lt~~A~NaLLKtLEEPp~~tvfIL~T  156 (605)
T PRK05896        108 IDNINYLPTTFKYKVYIIDEAHM--LSTSAWNALLKTLEEPPKHVVFIFAT  156 (605)
T ss_pred             HHHHHhchhhCCcEEEEEechHh--CCHHHHHHHHHHHHhCCCcEEEEEEC
Confidence            34444455567789999999997  45555555556555544455555544

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=96.42  E-value=0.1  Score=52.97  Aligned_cols=144  Identities=16%  Similarity=0.155  Sum_probs=81.7

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccc-----cCCCCceEEEE----
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQ-----CGRPGSSVGYQ----  140 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~-----~~~~g~~vg~~----  140 (319)
                      .-.++.+|=|.|||.+..+.+...+...    ..+|++++|...-+.++.+++...+...     ....+..+...    
T Consensus       188 ~~tV~taPRqrGKS~iVgi~l~~La~f~----Gi~IlvTAH~~~ts~evF~rv~~~le~lg~~~~fp~~~~iv~vkgg~E  263 (752)
T PHA03333        188 CYTAATVPRRCGKTTIMAIILAAMISFL----EIDIVVQAQRKTMCLTLYNRVETVVHAYQHKPWFPEEFKIVTLKGTDE  263 (752)
T ss_pred             cceEEEeccCCCcHHHHHHHHHHHHHhc----CCeEEEECCChhhHHHHHHHHHHHHHHhccccccCCCceEEEeeCCee
Confidence            3467789999999998876665433222    2589999999999999988877765421     10001111000    


Q ss_pred             -EecccccCC--CCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccC
Q psy496          141 -IRLEKELPR--KRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLN  217 (319)
Q Consensus       141 -~~~~~~~~~--~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~  217 (319)
                       +........  ..+.|.+.+-+      .+...-.+++++|+|||..  +..+.+..++-.+...  +.+++++|-+-+
T Consensus       264 ~I~f~~p~gak~G~sti~F~Ars------~~s~RG~~~DLLIVDEAAf--I~~~~l~aIlP~l~~~--~~k~IiISS~~~  333 (752)
T PHA03333        264 NLEYISDPAAKEGKTTAHFLASS------PNAARGQNPDLVIVDEAAF--VNPGALLSVLPLMAVK--GTKQIHISSPVD  333 (752)
T ss_pred             EEEEecCcccccCcceeEEeccc------CCCcCCCCCCEEEEECccc--CCHHHHHHHHHHHccC--CCceEEEeCCCC
Confidence             000000000  00233333222      0111113578999999997  5556666665555442  446778888876


Q ss_pred             hhhHhhhhCC
Q psy496          218 AEKFSQFFGG  227 (319)
Q Consensus       218 ~~~l~~~l~~  227 (319)
                      ...+-.++.+
T Consensus       334 ~~s~tS~L~n  343 (752)
T PHA03333        334 ADSWISRVGE  343 (752)
T ss_pred             cchHHHHhhh
Confidence            6666666654

>TIGR00376 DNA helicase, putative

Probab=96.40  E-value=0.0062  Score=62.00  Aligned_cols=50  Identities=28%  Similarity=0.348  Sum_probs=39.2

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ..++|.||+|||||....-.+.+.+ ..+    .+|+++.||...+.++.+++..
T Consensus       174 ~~~lI~GpPGTGKT~t~~~ii~~~~-~~g----~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       174 DLFLIHGPPGTGKTRTLVELIRQLV-KRG----LRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHHH-HcC----CCEEEEcCcHHHHHHHHHHHHh
Confidence            6789999999999987755544433 322    2789999999999999988876

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.

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.40  E-value=0.014  Score=57.87  Aligned_cols=43  Identities=23%  Similarity=0.461  Sum_probs=31.1

Q ss_pred             CCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          169 DPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       169 ~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      .+.....+++||||+|+  +..+..-.+++.+...++..++|+.+
T Consensus       112 ~P~~~~~KVvIIDEad~--Lt~~A~NALLK~LEEpp~~t~FIL~t  154 (535)
T PRK08451        112 KPSMARFKIFIIDEVHM--LTKEAFNALLKTLEEPPSYVKFILAT  154 (535)
T ss_pred             CcccCCeEEEEEECccc--CCHHHHHHHHHHHhhcCCceEEEEEE
Confidence            45567899999999998  56666666777776665566666544

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=96.38  E-value=0.018  Score=48.13  Aligned_cols=51  Identities=20%  Similarity=0.318  Sum_probs=35.8

Q ss_pred             HHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          164 EVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       164 ~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      +.+...+.-...+++||||+|.  +..+..-++++.+...+.+..+++++-..
T Consensus        92 ~~~~~~~~~~~~KviiI~~ad~--l~~~a~NaLLK~LEepp~~~~fiL~t~~~  142 (162)
T PF13177_consen   92 EFLSLSPSEGKYKVIIIDEADK--LTEEAQNALLKTLEEPPENTYFILITNNP  142 (162)
T ss_dssp             HHCTSS-TTSSSEEEEEETGGG--S-HHHHHHHHHHHHSTTTTEEEEEEES-G
T ss_pred             HHHHHHHhcCCceEEEeehHhh--hhHHHHHHHHHHhcCCCCCEEEEEEECCh
Confidence            3333344456899999999998  77778888888887777777777766544

...

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=96.37  E-value=0.008  Score=56.72  Aligned_cols=19  Identities=32%  Similarity=0.457  Sum_probs=16.1

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      .+.+++||+|+|||+.+.+
T Consensus        49 ~SmIl~GPPG~GKTTlA~l   67 (436)
T COG2256          49 HSMILWGPPGTGKTTLARL   67 (436)
T ss_pred             ceeEEECCCCCCHHHHHHH
Confidence            5789999999999987644

>PRK06893 DNA replication initiation factor; Validated

Probab=96.37  E-value=0.018  Score=50.91  Aligned_cols=48  Identities=13%  Similarity=0.288  Sum_probs=26.6

Q ss_pred             CCccEEEEecccccccchh---HHHHHHHhhhccccCceEEEeccccChhhHh
Q psy496          173 SGVSHIVMDEIHERSMISD---FLLAILKDVTDKRKDLKLILMSATLNAEKFS  222 (319)
Q Consensus       173 ~~v~~vViDEah~~~~~~~---~~~~~l~~~~~~~~~~qiv~lSAT~~~~~l~  222 (319)
                      .+.+++||||+|......+   .+...+......  ..+++++|++..+..+.
T Consensus        90 ~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~--~~~illits~~~p~~l~  140 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQ--GKTLLLISADCSPHALS  140 (229)
T ss_pred             ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHc--CCcEEEEeCCCChHHcc
Confidence            4678999999997322222   233333333221  33566777877554443

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.36  E-value=0.02  Score=50.08  Aligned_cols=23  Identities=13%  Similarity=0.140  Sum_probs=18.6

Q ss_pred             CCCCCcEEEecCCCCCccchhhH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ...+.++++.||+|||||...-.
T Consensus        35 ~~~~~~lll~G~~G~GKT~la~~   57 (226)
T TIGR03420        35 GKGDRFLYLWGESGSGKSHLLQA   57 (226)
T ss_pred             cCCCCeEEEECCCCCCHHHHHHH
Confidence            34567899999999999977644

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.

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.36  E-value=0.015  Score=58.78  Aligned_cols=46  Identities=26%  Similarity=0.376  Sum_probs=28.9

Q ss_pred             HHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEE
Q psy496          164 EVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLIL  211 (319)
Q Consensus       164 ~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~  211 (319)
                      +.+...+.+.+.+++||||+|.  +..+..-.+++.+...++...+|+
T Consensus       110 ~~~~~~p~~~~~kVvIIDEa~~--L~~~a~naLLk~LEepp~~tv~Il  155 (585)
T PRK14950        110 ERVQFRPALARYKVYIIDEVHM--LSTAAFNALLKTLEEPPPHAIFIL  155 (585)
T ss_pred             HHHhhCcccCCeEEEEEeChHh--CCHHHHHHHHHHHhcCCCCeEEEE
Confidence            3344455678899999999997  455555555666555444443443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.36  E-value=0.0071  Score=60.22  Aligned_cols=48  Identities=23%  Similarity=0.374  Sum_probs=31.7

Q ss_pred             HHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          164 EVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       164 ~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      +.....+.....+++||||+|+  +..+..-.+++.+...++...+|+.+
T Consensus       109 ~~~~~~p~~~~~kVvIIDEad~--ls~~a~naLLK~LEepp~~~~fIL~t  156 (527)
T PRK14969        109 DNAQYAPTRGRFKVYIIDEVHM--LSKSAFNAMLKTLEEPPEHVKFILAT  156 (527)
T ss_pred             HHHhhCcccCCceEEEEcCccc--CCHHHHHHHHHHHhCCCCCEEEEEEe
Confidence            3334445567899999999998  45555556667666655566666543

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=96.35  E-value=0.027  Score=53.96  Aligned_cols=133  Identities=9%  Similarity=0.102  Sum_probs=72.0

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHH-HHHHHHHHHHHHhccccCCCCceEEEEEecc--ccc
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRI-SAIAIAERVAQERDEQCGRPGSSVGYQIRLE--KEL  147 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~-la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~--~~~  147 (319)
                      ..++.|+.|||||.+...-++..+....  ...+++++.++.. +...+.+.+...+...    |....+.....  ...
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~~--~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~----g~~~~~~~~~~~~~i~   76 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAINK--KQQNILAARKVQNSIRDSVFKDIENLLSIE----GINYEFKKSKSSMEIK   76 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhcC--CCcEEEEEehhhhHHHHHHHHHHHHHHHHc----CChhheeecCCccEEE
Confidence            4678999999999998888777666541  2368888878766 5666666666544322    21111111000  000


Q ss_pred             CCC-CceEEEECc-hHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          148 PRK-RGSILYCTA-GILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       148 ~~~-~~~Iiv~Tp-g~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      ... +..|++..- +.-- .++   ....+.++.+|||.+  +..+.+..++..+...... +.+.+|.++
T Consensus        77 ~~~~g~~i~f~g~~d~~~-~ik---~~~~~~~~~idEa~~--~~~~~~~~l~~rlr~~~~~-~~i~~t~NP  140 (396)
T TIGR01547        77 ILNTGKKFIFKGLNDKPN-KLK---SGAGIAIIWFEEASQ--LTFEDIKELIPRLRETGGK-KFIIFSSNP  140 (396)
T ss_pred             ecCCCeEEEeecccCChh-Hhh---Ccceeeeehhhhhhh--cCHHHHHHHHHHhhccCCc-cEEEEEcCc
Confidence            011 233554433 1111 111   133479999999998  3444555555444332221 246777777

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.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.34  E-value=0.022  Score=50.05  Aligned_cols=21  Identities=10%  Similarity=0.156  Sum_probs=17.2

Q ss_pred             CCCCcEEEecCCCCCccchhh
Q psy496           67 PILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~   87 (319)
                      ..+..++++||+|||||...-
T Consensus        40 ~~~~~~~l~G~~G~GKT~La~   60 (227)
T PRK08903         40 VADRFFYLWGEAGSGRSHLLQ   60 (227)
T ss_pred             CCCCeEEEECCCCCCHHHHHH
Confidence            455789999999999996654

>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=96.32  E-value=0.00058  Score=57.91  Aligned_cols=124  Identities=15%  Similarity=0.144  Sum_probs=53.2

Q ss_pred             EEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEE--EEEecccccCCC
Q psy496           73 IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVG--YQIRLEKELPRK  150 (319)
Q Consensus        73 li~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg--~~~~~~~~~~~~  150 (319)
                      +|+|+-|-|||++.-+.+...+.. +   ..+|+++.|+.+.+..+.+.....++..    |....  ............
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~-~---~~~I~vtAP~~~~~~~lf~~~~~~l~~~----~~~~~~~~~~~~~~~~~~~   72 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQK-G---KIRILVTAPSPENVQTLFEFAEKGLKAL----GYKEEKKKRIGQIIKLRFN   72 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS---------EEEE-SS--S-HHHHHCC------------------------------
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHh-c---CceEEEecCCHHHHHHHHHHHHhhcccc----ccccccccccccccccccc
Confidence            578999999998887765432221 1   2579999999998888876554432211    10000  000000001112


Q ss_pred             CceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc-Chh
Q psy496          151 RGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL-NAE  219 (319)
Q Consensus       151 ~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~-~~~  219 (319)
                      +..|.+..|+.+...-      ...+++|||||=.  +-...+.    .+..   ....++||.|+ -.|
T Consensus        73 ~~~i~f~~Pd~l~~~~------~~~DlliVDEAAa--Ip~p~L~----~ll~---~~~~vv~stTi~GYE  127 (177)
T PF05127_consen   73 KQRIEFVAPDELLAEK------PQADLLIVDEAAA--IPLPLLK----QLLR---RFPRVVFSTTIHGYE  127 (177)
T ss_dssp             CCC--B--HHHHCCT----------SCEEECTGGG--S-HHHHH----HHHC---CSSEEEEEEEBSSTT
T ss_pred             cceEEEECCHHHHhCc------CCCCEEEEechhc--CCHHHHH----HHHh---hCCEEEEEeeccccc
Confidence            3446666776544332      2458999999976  4433333    3332   22356778888 444

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.30  E-value=0.016  Score=58.13  Aligned_cols=46  Identities=17%  Similarity=0.303  Sum_probs=29.5

Q ss_pred             HHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEE
Q psy496          163 PEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLI  210 (319)
Q Consensus       163 l~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv  210 (319)
                      .+.....|.....+++||||+|+  +..+..-.+++.+...++...+|
T Consensus       108 ~~~v~~~p~~~~~kViIIDE~~~--Lt~~a~naLLKtLEepp~~~ifI  153 (559)
T PRK05563        108 RDKVKYAPSEAKYKVYIIDEVHM--LSTGAFNALLKTLEEPPAHVIFI  153 (559)
T ss_pred             HHHHhhCcccCCeEEEEEECccc--CCHHHHHHHHHHhcCCCCCeEEE
Confidence            34444456677899999999998  55555556666655544443333

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.29  E-value=0.021  Score=50.84  Aligned_cols=22  Identities=9%  Similarity=0.229  Sum_probs=17.4

Q ss_pred             CCCCCcEEEecCCCCCccchhh
Q psy496           66 SPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~   87 (319)
                      ...+.+++++||+|||||....
T Consensus        42 ~~~~~~l~l~Gp~G~GKThLl~   63 (235)
T PRK08084         42 QEHSGYIYLWSREGAGRSHLLH   63 (235)
T ss_pred             CCCCCeEEEECCCCCCHHHHHH
Confidence            3345689999999999996654

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=96.29  E-value=0.021  Score=51.55  Aligned_cols=22  Identities=27%  Similarity=0.217  Sum_probs=17.6

Q ss_pred             CCCCcEEEecCCCCCccchhhH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l   88 (319)
                      +...++++.||+|||||+.+-.
T Consensus        40 ~~~~~vll~GppGtGKTtlA~~   61 (261)
T TIGR02881        40 KQVLHMIFKGNPGTGKTTVARI   61 (261)
T ss_pred             CCcceEEEEcCCCCCHHHHHHH
Confidence            3446799999999999977643

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.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.29  E-value=0.015  Score=58.59  Aligned_cols=49  Identities=22%  Similarity=0.352  Sum_probs=32.3

Q ss_pred             HHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          163 PEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       163 l~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      .+.+...+....++++||||+|+  +..+..-.+++.+...++...+|+.+
T Consensus       108 ~~~~~~~p~~~~~KVvIIdev~~--Lt~~a~naLLk~LEepp~~~~fIl~t  156 (576)
T PRK14965        108 RENVKYLPSRSRYKIFIIDEVHM--LSTNAFNALLKTLEEPPPHVKFIFAT  156 (576)
T ss_pred             HHHHHhccccCCceEEEEEChhh--CCHHHHHHHHHHHHcCCCCeEEEEEe
Confidence            34444456678899999999998  55555566666666555555555433

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.27  E-value=0.044  Score=49.05  Aligned_cols=26  Identities=19%  Similarity=0.281  Sum_probs=18.7

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHH
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIA   96 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~   96 (319)
                      +.++++|++|+|||..... +...+..
T Consensus       100 ~~~~l~G~~GtGKThLa~a-ia~~l~~  125 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAAA-ICNELLL  125 (244)
T ss_pred             ceEEEECCCCCCHHHHHHH-HHHHHHh
Confidence            5799999999999966543 3444443

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=96.27  E-value=0.017  Score=49.36  Aligned_cols=48  Identities=21%  Similarity=0.329  Sum_probs=30.4

Q ss_pred             HHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEe
Q psy496          163 PEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILM  212 (319)
Q Consensus       163 l~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~l  212 (319)
                      .+.+...+.....+++||||+|.  +..+....+++.+...+++..+|+.
T Consensus        85 ~~~~~~~~~~~~~kviiide~~~--l~~~~~~~Ll~~le~~~~~~~~il~  132 (188)
T TIGR00678        85 VEFLSRTPQESGRRVVIIEDAER--MNEAAANALLKTLEEPPPNTLFILI  132 (188)
T ss_pred             HHHHccCcccCCeEEEEEechhh--hCHHHHHHHHHHhcCCCCCeEEEEE
Confidence            44445555677899999999998  4455555555655554444445444

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.

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=96.25  E-value=0.0057  Score=63.06  Aligned_cols=103  Identities=19%  Similarity=0.156  Sum_probs=59.7

Q ss_pred             EecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc---ccCCC
Q psy496           74 IYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK---ELPRK  150 (319)
Q Consensus        74 i~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~---~~~~~  150 (319)
                      .--.||=|||+++.+|++-....+   ..+.|+.  ..--||..=++.+...+...    |..+|.......   ....-
T Consensus        96 AEMkTGEGKTLvAtLpayLnAL~G---kgVhVVT--vNdYLA~RDae~mg~vy~fL----GLsvG~i~~~~~~~~rr~aY  166 (925)
T PRK12903         96 AEMKTGEGKTITSIAPVYLNALTG---KGVIVST--VNEYLAERDAEEMGKVFNFL----GLSVGINKANMDPNLKREAY  166 (925)
T ss_pred             eeecCCCCccHHHHHHHHHHHhcC---CceEEEe--cchhhhhhhHHHHHHHHHHh----CCceeeeCCCCChHHHHHhc
Confidence            444499999999988875333322   2345555  44446555555454443332    777775443111   11112


Q ss_pred             CceEEEECchH-----HHHHHhcC---CCCCCccEEEEecccc
Q psy496          151 RGSILYCTAGI-----LPEVMQSD---PILSGVSHIVMDEIHE  185 (319)
Q Consensus       151 ~~~Iiv~Tpg~-----ll~~l~~~---~~l~~v~~vViDEah~  185 (319)
                      .++|+++|..-     |.+.+...   .....+.+.|+||+|.
T Consensus       167 ~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDS  209 (925)
T PRK12903        167 ACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDS  209 (925)
T ss_pred             cCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchh
Confidence            57899999843     44444211   1256788999999996

>PRK08116 hypothetical protein; Validated

Probab=96.23  E-value=0.038  Score=50.22  Aligned_cols=28  Identities=25%  Similarity=0.349  Sum_probs=19.9

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHh
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIAR   97 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~   97 (319)
                      +..++++|++|+|||..+. .+.+.+...
T Consensus       114 ~~gl~l~G~~GtGKThLa~-aia~~l~~~  141 (268)
T PRK08116        114 NVGLLLWGSVGTGKTYLAA-CIANELIEK  141 (268)
T ss_pred             CceEEEECCCCCCHHHHHH-HHHHHHHHc
Confidence            3459999999999996654 355555443

>PRK09183 transposase/IS protein; Provisional

Probab=96.22  E-value=0.039  Score=49.84  Aligned_cols=24  Identities=17%  Similarity=0.180  Sum_probs=19.4

Q ss_pred             CCCCCcEEEecCCCCCccchhhHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~   89 (319)
                      ...++++++.||+|+|||......
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al  122 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIAL  122 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHH
Confidence            456789999999999999766544

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.20  E-value=0.047  Score=56.84  Aligned_cols=25  Identities=24%  Similarity=0.163  Sum_probs=18.2

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHH
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEI   95 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~   95 (319)
                      ..++|+|+||+|||++.-. +++.+.
T Consensus       782 nvLYIyG~PGTGKTATVK~-VLrELq  806 (1164)
T PTZ00112        782 QILYISGMPGTGKTATVYS-VIQLLQ  806 (1164)
T ss_pred             ceEEEECCCCCCHHHHHHH-HHHHHH
Confidence            3456999999999988755 345553

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.20  E-value=0.023  Score=57.63  Aligned_cols=47  Identities=23%  Similarity=0.296  Sum_probs=29.1

Q ss_pred             HHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEE
Q psy496          163 PEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLIL  211 (319)
Q Consensus       163 l~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~  211 (319)
                      ++.+...+.....+++||||+|.  +..+..-.+++.+...+....+|+
T Consensus       110 i~~a~~~p~~~~~KViIIDEad~--Lt~~a~naLLK~LEePp~~tvfIL  156 (620)
T PRK14948        110 IERAQFAPVQARWKVYVIDECHM--LSTAAFNALLKTLEEPPPRVVFVL  156 (620)
T ss_pred             HHHHhhChhcCCceEEEEECccc--cCHHHHHHHHHHHhcCCcCeEEEE
Confidence            33334445567789999999998  555555566666655444444443

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.18  E-value=0.018  Score=58.01  Aligned_cols=46  Identities=20%  Similarity=0.377  Sum_probs=28.0

Q ss_pred             HHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEE
Q psy496          164 EVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLIL  211 (319)
Q Consensus       164 ~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~  211 (319)
                      +.+...+.....+++||||+|.  +..+..-.+++.+....+...+|+
T Consensus       109 ~~~~~~p~~g~~kVIIIDEad~--Lt~~a~naLLk~LEEP~~~~ifIL  154 (624)
T PRK14959        109 EAIGYAPMEGRYKVFIIDEAHM--LTREAFNALLKTLEEPPARVTFVL  154 (624)
T ss_pred             HHHHhhhhcCCceEEEEEChHh--CCHHHHHHHHHHhhccCCCEEEEE
Confidence            3333344456789999999998  555555556666554334444444

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=96.15  E-value=0.049  Score=58.36  Aligned_cols=109  Identities=19%  Similarity=0.127  Sum_probs=62.6

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL  147 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~  147 (319)
                      .++..+|.|+.|+|||+..-. +.+.+...+    ..|+.+.||--.|..+.+    ..+..    +             
T Consensus       396 ~~r~~~v~G~AGTGKTt~l~~-~~~~~e~~G----~~V~g~ApTgkAA~~L~e----~~Gi~----a-------------  449 (1102)
T PRK13826        396 PARIAAVVGRAGAGKTTMMKA-AREAWEAAG----YRVVGGALAGKAAEGLEK----EAGIQ----S-------------  449 (1102)
T ss_pred             cCCeEEEEeCCCCCHHHHHHH-HHHHHHHcC----CeEEEEcCcHHHHHHHHH----hhCCC----e-------------
Confidence            357799999999999976543 333332222    378888899777655532    22111    0             


Q ss_pred             CCCCceEEEECchHHHHHH-hcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccc
Q psy496          148 PRKRGSILYCTAGILPEVM-QSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSAT  215 (319)
Q Consensus       148 ~~~~~~Iiv~Tpg~ll~~l-~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT  215 (319)
                               .|-..++-.+ .....+..-++|||||+.+  +....+..+++.+..  ...++|++.-+
T Consensus       450 ---------~TIas~ll~~~~~~~~l~~~~vlVIDEAsM--v~~~~m~~Ll~~~~~--~garvVLVGD~  505 (1102)
T PRK13826        450 ---------RTLSSWELRWNQGRDQLDNKTVFVLDEAGM--VASRQMALFVEAVTR--AGAKLVLVGDP  505 (1102)
T ss_pred             ---------eeHHHHHhhhccCccCCCCCcEEEEECccc--CCHHHHHHHHHHHHh--cCCEEEEECCH
Confidence                     0111121111 1223466778999999998  555555555555432  24577776544

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=96.14  E-value=0.0058  Score=64.00  Aligned_cols=102  Identities=19%  Similarity=0.168  Sum_probs=60.5

Q ss_pred             ecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecc----cccCCC
Q psy496           75 YTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLE----KELPRK  150 (319)
Q Consensus        75 ~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~----~~~~~~  150 (319)
                      --.||=|||+++.+|++-..+.+.   .+.|+.  ..-=||..=++.+...+...    |..+|......    .+...-
T Consensus       188 EM~TGEGKTLvAtlp~yLnAL~Gk---gVHvVT--VNDYLA~RDaewmgply~fL----GLsvg~i~~~~~~~~~rr~aY  258 (1112)
T PRK12901        188 EMATGEGKTLVATLPVYLNALTGN---GVHVVT--VNDYLAKRDSEWMGPLYEFH----GLSVDCIDKHQPNSEARRKAY  258 (1112)
T ss_pred             eecCCCCchhHHHHHHHHHHHcCC---CcEEEE--echhhhhccHHHHHHHHHHh----CCceeecCCCCCCHHHHHHhC
Confidence            344999999999999865444433   456666  33335544444444433322    77777443211    111113


Q ss_pred             CceEEEECc-----hHHHHHHhcCC---CCCCccEEEEecccc
Q psy496          151 RGSILYCTA-----GILPEVMQSDP---ILSGVSHIVMDEIHE  185 (319)
Q Consensus       151 ~~~Iiv~Tp-----g~ll~~l~~~~---~l~~v~~vViDEah~  185 (319)
                      .++|.++|.     +.|.+.+..++   ....+.+.||||+|.
T Consensus       259 ~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDS  301 (1112)
T PRK12901        259 NADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDS  301 (1112)
T ss_pred             CCcceecCCCccccccchhccccchHhhhCcCCceeEeechhh
Confidence            678999997     44555553322   256689999999996

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=96.11  E-value=0.038  Score=54.03  Aligned_cols=36  Identities=22%  Similarity=0.346  Sum_probs=23.2

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEe
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVT  108 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~  108 (319)
                      ..++++||+|+|||...- ++.+.+...  .+..+++++
T Consensus       149 ~~l~l~G~~G~GKThL~~-ai~~~~~~~--~~~~~v~yi  184 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLH-AIGNYILEK--NPNAKVVYV  184 (450)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHHh--CCCCeEEEE
Confidence            469999999999996653 344444332  123467665

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=96.10  E-value=0.043  Score=52.81  Aligned_cols=37  Identities=24%  Similarity=0.417  Sum_probs=24.2

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEec
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQ  109 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~  109 (319)
                      ..++|+||+|+|||... ..+.+.+....  +...++++.
T Consensus       137 n~l~l~G~~G~GKThL~-~ai~~~l~~~~--~~~~v~yi~  173 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLL-HAIGNEILENN--PNAKVVYVS  173 (405)
T ss_pred             CeEEEECCCCCcHHHHH-HHHHHHHHHhC--CCCcEEEEE
Confidence            45899999999999765 44555554432  234666753

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).

>KOG1002|consensus

Probab=96.08  E-value=0.05  Score=52.67  Aligned_cols=125  Identities=19%  Similarity=0.227  Sum_probs=68.6

Q ss_pred             EEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc----
Q psy496           72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL----  147 (319)
Q Consensus        72 vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~----  147 (319)
                      -++.-+-|-|||.+....++..+..      ..-++++|+.++ .|..+.+.....      |....+...+....    
T Consensus       207 GiLADEMGMGKTIQtIaLllae~~r------a~tLVvaP~VAl-mQW~nEI~~~T~------gslkv~~YhG~~R~~nik  273 (791)
T KOG1002|consen  207 GILADEMGMGKTIQTIALLLAEVDR------APTLVVAPTVAL-MQWKNEIERHTS------GSLKVYIYHGAKRDKNIK  273 (791)
T ss_pred             ceehhhhccchHHHHHHHHHhcccc------CCeeEEccHHHH-HHHHHHHHHhcc------CceEEEEEecccccCCHH
Confidence            3667779999998876666653322      124455599877 455555555443      22222222211111    


Q ss_pred             CCCCceEEEECchHHHHHHhc--------------CCCCCCccE--EEEecccc---cccchhHHHHHHHhhhccccCce
Q psy496          148 PRKRGSILYCTAGILPEVMQS--------------DPILSGVSH--IVMDEIHE---RSMISDFLLAILKDVTDKRKDLK  208 (319)
Q Consensus       148 ~~~~~~Iiv~Tpg~ll~~l~~--------------~~~l~~v~~--vViDEah~---~~~~~~~~~~~l~~~~~~~~~~q  208 (319)
                      ...+.+++.+|...+-...+.              ...|+++++  ||+||||.   |...+.      +.+..+. ..+
T Consensus       274 el~~YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~IK~R~snTA------rAV~~L~-tt~  346 (791)
T KOG1002|consen  274 ELMNYDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNIKDRQSNTA------RAVFALE-TTY  346 (791)
T ss_pred             HhhcCcEEEEecHHHHHHHHhccccccccCCcccccchhhhceeeeeehhhhcccccccccHH------HHHHhhH-hhh
Confidence            113567999999877555522              112555554  89999996   322222      1111111 225


Q ss_pred             EEEecccc
Q psy496          209 LILMSATL  216 (319)
Q Consensus       209 iv~lSAT~  216 (319)
                      .+.+|.|+
T Consensus       347 rw~LSGTP  354 (791)
T KOG1002|consen  347 RWCLSGTP  354 (791)
T ss_pred             hhhccCCc
Confidence            67899998

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

Probab=96.07  E-value=0.016  Score=56.42  Aligned_cols=70  Identities=17%  Similarity=0.092  Sum_probs=48.0

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++--|++||.-+..|-+     ...+.-.+-|-||||||.....-|- .+   +    ...++++|.+-||.|++..++.
T Consensus        13 PaGDQP~AI~~Lv~gi~-----~g~~~QtLLGvTGSGKTfT~AnVI~-~~---~----rPtLV~AhNKTLAaQLy~Efk~   79 (663)
T COG0556          13 PAGDQPEAIAELVEGIE-----NGLKHQTLLGVTGSGKTFTMANVIA-KV---Q----RPTLVLAHNKTLAAQLYSEFKE   79 (663)
T ss_pred             CCCCcHHHHHHHHHHHh-----cCceeeEEeeeccCCchhHHHHHHH-Hh---C----CCeEEEecchhHHHHHHHHHHH
Confidence            44558888877665433     2334567778999999977654432 21   1    1344455999999999999999


Q ss_pred             Hhc
Q psy496          125 ERD  127 (319)
Q Consensus       125 ~~~  127 (319)
                      ++-
T Consensus        80 fFP   82 (663)
T COG0556          80 FFP   82 (663)
T ss_pred             hCc
Confidence            875

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=96.07  E-value=0.03  Score=51.70  Aligned_cols=43  Identities=26%  Similarity=0.511  Sum_probs=29.7

Q ss_pred             CCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecc
Q psy496          170 PILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSA  214 (319)
Q Consensus       170 ~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSA  214 (319)
                      +.....+++||||||.  +..+..-..++.+...+.+..+++.+-
T Consensus       105 ~~~~~~kviiidead~--mt~~A~nallk~lEep~~~~~~il~~n  147 (325)
T COG0470         105 PLEGGYKVVIIDEADK--LTEDAANALLKTLEEPPKNTRFILITN  147 (325)
T ss_pred             CCCCCceEEEeCcHHH--HhHHHHHHHHHHhccCCCCeEEEEEcC
Confidence            3357899999999998  566666666666665555656655543

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.03  E-value=0.025  Score=46.12  Aligned_cols=21  Identities=38%  Similarity=0.616  Sum_probs=16.3

Q ss_pred             EEEecCCCCCccchhhHHHHH
Q psy496           72 SIIYTSTGCGKTTQVPQFILD   92 (319)
Q Consensus        72 vli~apTGSGKT~~~~l~il~   92 (319)
                      ++|+|++|+|||+.....+..
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~   22 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALN   22 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHH
Confidence            689999999999876554433

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.

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=96.03  E-value=0.02  Score=51.55  Aligned_cols=20  Identities=30%  Similarity=0.322  Sum_probs=16.6

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      ...++|+||+|||||+..-.
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~   62 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRN   62 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHH
Confidence            45799999999999977654

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.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=96.03  E-value=0.042  Score=51.13  Aligned_cols=20  Identities=25%  Similarity=0.409  Sum_probs=16.3

Q ss_pred             CcEEEecCCCCCccchhhHH
Q psy496           70 SPSIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~   89 (319)
                      ..++++||+|+|||+.+-..
T Consensus        37 ~~lll~Gp~GtGKT~la~~~   56 (337)
T PRK12402         37 PHLLVQGPPGSGKTAAVRAL   56 (337)
T ss_pred             ceEEEECCCCCCHHHHHHHH
Confidence            37999999999999776443

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=95.99  E-value=0.082  Score=47.64  Aligned_cols=52  Identities=10%  Similarity=0.055  Sum_probs=32.8

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      ..+.+.++++.||+|+|||..+.. +.+.+...+    .+|+++ ++.++..++...+
T Consensus       101 ~~~~~~nl~l~G~~G~GKThLa~A-i~~~l~~~g----~sv~f~-~~~el~~~Lk~~~  152 (254)
T COG1484         101 FFERGENLVLLGPPGVGKTHLAIA-IGNELLKAG----ISVLFI-TAPDLLSKLKAAF  152 (254)
T ss_pred             HhccCCcEEEECCCCCcHHHHHHH-HHHHHHHcC----CeEEEE-EHHHHHHHHHHHH
Confidence            334788999999999999966543 334444322    244442 6777766665533

>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=95.98  E-value=0.12  Score=45.38  Aligned_cols=36  Identities=22%  Similarity=0.336  Sum_probs=23.3

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEe
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVT  108 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~  108 (319)
                      ..++|+||+|+|||.. +.++.+.+.....  ..+|+|+
T Consensus        35 ~~l~l~G~~G~GKTHL-L~Ai~~~~~~~~~--~~~v~y~   70 (219)
T PF00308_consen   35 NPLFLYGPSGLGKTHL-LQAIANEAQKQHP--GKRVVYL   70 (219)
T ss_dssp             SEEEEEESTTSSHHHH-HHHHHHHHHHHCT--TS-EEEE
T ss_pred             CceEEECCCCCCHHHH-HHHHHHHHHhccc--cccceee
Confidence            4689999999999973 4555555544322  3467774

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.

>KOG1000|consensus

Probab=95.91  E-value=0.1  Score=50.54  Aligned_cols=133  Identities=15%  Similarity=0.112  Sum_probs=68.3

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecc
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLE  144 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~  144 (319)
                      ....+...+|.-.-|=|||..++- |. ..+..+    -.+++++|.... ...++.+...+....     .+-...+.+
T Consensus       210 aL~RgGR~llADeMGLGKTiQAla-IA-~yyraE----wplliVcPAsvr-ftWa~al~r~lps~~-----pi~vv~~~~  277 (689)
T KOG1000|consen  210 ALERGGRILLADEMGLGKTIQALA-IA-RYYRAE----WPLLIVCPASVR-FTWAKALNRFLPSIH-----PIFVVDKSS  277 (689)
T ss_pred             HHhcCCeEEEecccccchHHHHHH-HH-HHHhhc----CcEEEEecHHHh-HHHHHHHHHhccccc-----ceEEEeccc
Confidence            345678889999999999987633 22 222222    134455585322 223333333333221     111122233


Q ss_pred             cccCC--CCceEEEECchHHHHHHhcCCCCCCccEEEEecccc-cccch---hHHHHHHHhhhccccCceEEEecccc
Q psy496          145 KELPR--KRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHE-RSMIS---DFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       145 ~~~~~--~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~-~~~~~---~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      +....  ....|.|.+.+.+..+-.. -.-..++++|+||.|. ++...   .....+++.      -.++|++|.|+
T Consensus       278 D~~~~~~t~~~v~ivSye~ls~l~~~-l~~~~~~vvI~DEsH~Lk~sktkr~Ka~~dllk~------akhvILLSGTP  348 (689)
T KOG1000|consen  278 DPLPDVCTSNTVAIVSYEQLSLLHDI-LKKEKYRVVIFDESHMLKDSKTKRTKAATDLLKV------AKHVILLSGTP  348 (689)
T ss_pred             CCccccccCCeEEEEEHHHHHHHHHH-HhcccceEEEEechhhhhccchhhhhhhhhHHHH------hhheEEecCCc
Confidence            32211  1245888888876443311 1123589999999996 11111   112222221      23789999998

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=95.91  E-value=0.042  Score=54.16  Aligned_cols=135  Identities=16%  Similarity=0.132  Sum_probs=73.4

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCCC
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRK  150 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~~  150 (319)
                      .+++.-|=|.|||+......+..+...+ .....|+++.++++-|..+++.+.......... ....+..+     ....
T Consensus        24 ~~~l~v~RkNGKS~l~a~i~ly~l~~~g-~~~~~i~~~A~~~~QA~~~f~~~~~~i~~~~~l-~~~~~~~~-----~~~~   96 (477)
T PF03354_consen   24 EVYLEVPRKNGKSTLAAAIALYMLFLDG-EPGAEIYCAANTRDQAKIVFDEAKKMIEASPEL-RKRKKPKI-----IKSN   96 (477)
T ss_pred             EEEEEEcCccCccHHHHHHHHHHHhcCC-ccCceEEEEeCCHHHHHHHHHHHHHHHHhChhh-ccchhhhh-----hhhh
Confidence            4667778999999877665555554332 224578899999999999998887775432200 00000000     0001


Q ss_pred             CceEEEECchHHHHHHhcCC---CCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecc
Q psy496          151 RGSILYCTAGILPEVMQSDP---ILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSA  214 (319)
Q Consensus       151 ~~~Iiv~Tpg~ll~~l~~~~---~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSA  214 (319)
                      +..|.....+..++.+..++   .=.+.+++|+||+|..  ...-+...++.-...+++.+++.+|-
T Consensus        97 ~~~i~~~~~~s~~~~~s~~~~~~dG~~~~~~i~DE~h~~--~~~~~~~~l~~g~~~r~~pl~~~IST  161 (477)
T PF03354_consen   97 KKEIEFPKTGSFFKALSSDADSLDGLNPSLAIFDELHAH--KDDELYDALESGMGARPNPLIIIIST  161 (477)
T ss_pred             ceEEEEcCCCcEEEEEecCCCCccCCCCceEEEeCCCCC--CCHHHHHHHHhhhccCCCceEEEEeC
Confidence            12233333333333332211   1135789999999983  33324444444444455666666643

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.88  E-value=0.029  Score=53.88  Aligned_cols=47  Identities=19%  Similarity=0.254  Sum_probs=29.3

Q ss_pred             HHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEe
Q psy496          164 EVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILM  212 (319)
Q Consensus       164 ~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~l  212 (319)
                      +.+...+...+.+++||||+|.  +..+....+++.+...++...+|+.
T Consensus       117 ~~~~~~p~~~~~kvvIIdea~~--l~~~~~~~LLk~LEep~~~t~~Il~  163 (397)
T PRK14955        117 ENVRYGPQKGRYRVYIIDEVHM--LSIAAFNAFLKTLEEPPPHAIFIFA  163 (397)
T ss_pred             HHHhhchhcCCeEEEEEeChhh--CCHHHHHHHHHHHhcCCCCeEEEEE
Confidence            3344456778899999999998  4444444455555544444444443

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=95.79  E-value=0.081  Score=48.72  Aligned_cols=19  Identities=26%  Similarity=0.291  Sum_probs=15.6

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      .+++++||+|+|||+..-.
T Consensus        39 ~~~ll~G~~G~GKt~~~~~   57 (319)
T PRK00440         39 PHLLFAGPPGTGKTTAALA   57 (319)
T ss_pred             CeEEEECCCCCCHHHHHHH
Confidence            4589999999999976643

>KOG0991|consensus

Probab=95.77  E-value=0.026  Score=49.76  Aligned_cols=26  Identities=27%  Similarity=0.318  Sum_probs=20.3

Q ss_pred             hhhcCCCCCcEEEecCCCCCccchhh
Q psy496           62 CLTLSPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        62 ~l~~~~~~~~vli~apTGSGKT~~~~   87 (319)
                      +++...+--+++++||+|+|||++..
T Consensus        41 via~~gnmP~liisGpPG~GKTTsi~   66 (333)
T KOG0991|consen   41 VIAKEGNMPNLIISGPPGTGKTTSIL   66 (333)
T ss_pred             HHHHcCCCCceEeeCCCCCchhhHHH
Confidence            44445555689999999999998864

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.77  E-value=0.17  Score=46.88  Aligned_cols=134  Identities=18%  Similarity=0.187  Sum_probs=74.2

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      ..+++++|-.|+|||+........ +...  +.++.+...-..|+.|....+.|++..+..+          +......+
T Consensus       139 p~Vil~vGVNG~GKTTTIaKLA~~-l~~~--g~~VllaA~DTFRAaAiEQL~~w~er~gv~v----------I~~~~G~D  205 (340)
T COG0552         139 PFVILFVGVNGVGKTTTIAKLAKY-LKQQ--GKSVLLAAGDTFRAAAIEQLEVWGERLGVPV----------ISGKEGAD  205 (340)
T ss_pred             cEEEEEEecCCCchHhHHHHHHHH-HHHC--CCeEEEEecchHHHHHHHHHHHHHHHhCCeE----------EccCCCCC
Confidence            456888999999999987664332 2222  2233333445789999999998988865433          21111111


Q ss_pred             CCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhc-cc------cCceEEEecccc--Chh
Q psy496          149 RKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTD-KR------KDLKLILMSATL--NAE  219 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~-~~------~~~qiv~lSAT~--~~~  219 (319)
                      +         .....+-+.. ..-.++++|++|-|-+.. +..-+..-++.+.+ ..      |.--++.+-||.  |.-
T Consensus       206 p---------AaVafDAi~~-Akar~~DvvliDTAGRLh-nk~nLM~EL~KI~rV~~k~~~~ap~e~llvlDAttGqnal  274 (340)
T COG0552         206 P---------AAVAFDAIQA-AKARGIDVVLIDTAGRLH-NKKNLMDELKKIVRVIKKDDPDAPHEILLVLDATTGQNAL  274 (340)
T ss_pred             c---------HHHHHHHHHH-HHHcCCCEEEEeCccccc-CchhHHHHHHHHHHHhccccCCCCceEEEEEEcccChhHH
Confidence            1         1123343322 123689999999998622 22222233332222 11      222455568888  655


Q ss_pred             hHhhhhC
Q psy496          220 KFSQFFG  226 (319)
Q Consensus       220 ~l~~~l~  226 (319)
                      .-++.|.
T Consensus       275 ~QAk~F~  281 (340)
T COG0552         275 SQAKIFN  281 (340)
T ss_pred             HHHHHHH
Confidence            5555554

>PRK12377 putative replication protein; Provisional

Probab=95.76  E-value=0.083  Score=47.42  Aligned_cols=27  Identities=19%  Similarity=0.202  Sum_probs=19.1

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIA   96 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~   96 (319)
                      ..+++++||+|+|||..... +.+.+..
T Consensus       101 ~~~l~l~G~~GtGKThLa~A-Ia~~l~~  127 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAA-IGNRLLA  127 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHH-HHHHHHH
Confidence            46899999999999965433 3444443

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.76  E-value=0.098  Score=50.09  Aligned_cols=135  Identities=15%  Similarity=0.193  Sum_probs=81.6

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      ..+++++|=-|||||+...-... . +.. ++..+.++..-..|..|....+.+++..+..+        |..  +...+
T Consensus       100 P~vImmvGLQGsGKTTt~~KLA~-~-lkk-~~~kvllVaaD~~RpAA~eQL~~La~q~~v~~--------f~~--~~~~~  166 (451)
T COG0541         100 PTVILMVGLQGSGKTTTAGKLAK-Y-LKK-KGKKVLLVAADTYRPAAIEQLKQLAEQVGVPF--------FGS--GTEKD  166 (451)
T ss_pred             CeEEEEEeccCCChHhHHHHHHH-H-HHH-cCCceEEEecccCChHHHHHHHHHHHHcCCce--------ecC--CCCCC
Confidence            35688899999999988765432 1 222 45566777777899999998888887655433        011  11111


Q ss_pred             CCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhC
Q psy496          149 RKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFG  226 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~  226 (319)
                      +    +-++.-  -++..+    ...++++|+|-|-+...+.++...+...-....|+--++.+-|++  +....++-|.
T Consensus       167 P----v~Iak~--al~~ak----~~~~DvvIvDTAGRl~ide~Lm~El~~Ik~~~~P~E~llVvDam~GQdA~~~A~aF~  236 (451)
T COG0541         167 P----VEIAKA--ALEKAK----EEGYDVVIVDTAGRLHIDEELMDELKEIKEVINPDETLLVVDAMIGQDAVNTAKAFN  236 (451)
T ss_pred             H----HHHHHH--HHHHHH----HcCCCEEEEeCCCcccccHHHHHHHHHHHhhcCCCeEEEEEecccchHHHHHHHHHh
Confidence            1    111111  122222    246899999999986565555555544444466776666777777  6666655553

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=95.75  E-value=0.026  Score=55.89  Aligned_cols=66  Identities=14%  Similarity=0.051  Sum_probs=46.3

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE-EEEecccHHHHHHHHHHHHHH
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC-IMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~-vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      +|=+...+.|..++|+|..|||||++++.=+.-.++......+.+ |+++.|.|.....+.+.+-++
T Consensus       217 QneIIR~ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~vFleYis~VLPeL  283 (747)
T COG3973         217 QNEIIRFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVFLEYISRVLPEL  283 (747)
T ss_pred             HHHHHhccCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcHHHHHHHHHhchhh
Confidence            344445667888999999999999998766554444433222223 888889999988888765544

>PRK04195 replication factor C large subunit; Provisional

Probab=95.72  E-value=0.069  Score=52.67  Aligned_cols=19  Identities=26%  Similarity=0.471  Sum_probs=16.3

Q ss_pred             CCcEEEecCCCCCccchhh
Q psy496           69 LSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~   87 (319)
                      ...++|+||+|+|||+.+-
T Consensus        39 ~~~lLL~GppG~GKTtla~   57 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLAH   57 (482)
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            5679999999999997763

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.68  E-value=0.028  Score=53.25  Aligned_cols=39  Identities=18%  Similarity=0.221  Sum_probs=24.1

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhH
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      .-|..++..+.   +.+....-...++++||+|+|||+....
T Consensus        20 ig~~~~~~~l~---~~i~~~~~~~~~L~~G~~G~GKt~~a~~   58 (367)
T PRK14970         20 VGQSHITNTLL---NAIENNHLAQALLFCGPRGVGKTTCARI   58 (367)
T ss_pred             CCcHHHHHHHH---HHHHcCCCCeEEEEECCCCCCHHHHHHH
Confidence            44555544332   3333333446799999999999976643

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=95.66  E-value=0.041  Score=56.28  Aligned_cols=125  Identities=18%  Similarity=0.183  Sum_probs=73.3

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEE--EEecccc-
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGY--QIRLEKE-  146 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~--~~~~~~~-  146 (319)
                      ..++|+|.=|=|||.+.-+.+.. +.... + ..+|+++.|+.+.+..+.+...+-+...    |..-+.  ...++-. 
T Consensus       232 ~~~vlTAdRGRGKSA~lGi~~~~-~~~~~-~-~~~iiVTAP~~~nv~~Lf~fa~~~l~~l----g~~~~v~~d~~g~~~~  304 (758)
T COG1444         232 RALVLTADRGRGKSAALGIALAA-AARLA-G-SVRIIVTAPTPANVQTLFEFAGKGLEFL----GYKRKVAPDALGEIRE  304 (758)
T ss_pred             ceEEEEcCCCCcHhHHHhHHHHH-HHHhc-C-CceEEEeCCCHHHHHHHHHHHHHhHHHh----CCccccccccccceee
Confidence            38999999999999999888732 22222 1 4689999999999988887665544322    111110  0000000 


Q ss_pred             cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc-Chh
Q psy496          147 LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL-NAE  219 (319)
Q Consensus       147 ~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~-~~~  219 (319)
                      ...+...|-+-+|....         ..-+++|||||=.  +..-++..+++       ..+.++||.|+ -.|
T Consensus       305 ~~~~~~~i~y~~P~~a~---------~~~DllvVDEAAa--IplplL~~l~~-------~~~rv~~sTTIhGYE  360 (758)
T COG1444         305 VSGDGFRIEYVPPDDAQ---------EEADLLVVDEAAA--IPLPLLHKLLR-------RFPRVLFSTTIHGYE  360 (758)
T ss_pred             ecCCceeEEeeCcchhc---------ccCCEEEEehhhc--CChHHHHHHHh-------hcCceEEEeeecccc
Confidence            00111224444554322         1268999999976  44444444433       22568899999 444

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=95.64  E-value=0.12  Score=52.14  Aligned_cols=140  Identities=16%  Similarity=0.181  Sum_probs=85.0

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceE----EEEE--ec
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSV----GYQI--RL  143 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~v----g~~~--~~  143 (319)
                      +-.+...|==.|||+... +++..+...-  ...+|+++.|.+..+...++++...+....  ++..+    |-.+  ..
T Consensus       255 k~tVflVPRR~GKTwivv-~iI~~ll~s~--~Gi~IgytAH~~~ts~~vF~eI~~~le~~f--~~~~v~~vkGe~I~i~f  329 (738)
T PHA03368        255 RATVFLVPRRHGKTWFLV-PLIALALATF--RGIKIGYTAHIRKATEPVFEEIGARLRQWF--GASRVDHVKGETISFSF  329 (738)
T ss_pred             cceEEEecccCCchhhHH-HHHHHHHHhC--CCCEEEEEcCcHHHHHHHHHHHHHHHhhhc--chhheeeecCcEEEEEe
Confidence            446778889999999776 5555444321  135899999999999999988887654321  01111    1001  11


Q ss_pred             ccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccChhhHhh
Q psy496          144 EKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKFSQ  223 (319)
Q Consensus       144 ~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~~~~l~~  223 (319)
                      .+.   .++.|.+++.. =-.-++    =.+++++|+|||+.  +..+.+..++-.+...  +.++|.+|-|-..+....
T Consensus       330 ~nG---~kstI~FaSar-ntNsiR----GqtfDLLIVDEAqF--Ik~~al~~ilp~l~~~--n~k~I~ISS~Ns~~~sTS  397 (738)
T PHA03368        330 PDG---SRSTIVFASSH-NTNGIR----GQDFNLLFVDEANF--IRPDAVQTIMGFLNQT--NCKIIFVSSTNTGKASTS  397 (738)
T ss_pred             cCC---CccEEEEEecc-CCCCcc----CCcccEEEEechhh--CCHHHHHHHHHHHhcc--CccEEEEecCCCCccchH
Confidence            110   11245555331 000011    24799999999998  6667777777555444  668999998875555555


Q ss_pred             hhC
Q psy496          224 FFG  226 (319)
Q Consensus       224 ~l~  226 (319)
                      |+.
T Consensus       398 FL~  400 (738)
T PHA03368        398 FLY  400 (738)
T ss_pred             HHH
Confidence            553

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=95.59  E-value=0.17  Score=49.30  Aligned_cols=38  Identities=24%  Similarity=0.348  Sum_probs=24.3

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecc
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQP  110 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~P  110 (319)
                      ..++++||+|+|||...- .+.+.+....  +..+++++..
T Consensus       131 n~l~lyG~~G~GKTHLl~-ai~~~l~~~~--~~~~v~yi~~  168 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQ-SIGNYVVQNE--PDLRVMYITS  168 (440)
T ss_pred             CeEEEEcCCCCcHHHHHH-HHHHHHHHhC--CCCeEEEEEH
Confidence            469999999999996553 3444443322  2347777543

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=95.53  E-value=0.11  Score=50.80  Aligned_cols=46  Identities=20%  Similarity=0.137  Sum_probs=27.8

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHH
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIA  119 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~  119 (319)
                      ..++|+|++|+|||... ..+.+.+....  +..+++++.. .++...+.
T Consensus       142 npl~i~G~~G~GKTHLl-~Ai~~~l~~~~--~~~~v~yv~~-~~f~~~~~  187 (450)
T PRK14087        142 NPLFIYGESGMGKTHLL-KAAKNYIESNF--SDLKVSYMSG-DEFARKAV  187 (450)
T ss_pred             CceEEECCCCCcHHHHH-HHHHHHHHHhC--CCCeEEEEEH-HHHHHHHH
Confidence            45899999999999554 45555544322  2346777544 34444433

>PRK06921 hypothetical protein; Provisional

Probab=95.52  E-value=0.079  Score=48.07  Aligned_cols=28  Identities=14%  Similarity=0.179  Sum_probs=20.1

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIA   96 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~   96 (319)
                      .+.+++++|++|+|||.... .+...+..
T Consensus       116 ~~~~l~l~G~~G~GKThLa~-aia~~l~~  143 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLT-AAANELMR  143 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHH-HHHHHHhh
Confidence            46789999999999996543 34444443

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=95.50  E-value=0.033  Score=57.06  Aligned_cols=50  Identities=26%  Similarity=0.334  Sum_probs=32.3

Q ss_pred             HHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEe
Q psy496          161 ILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILM  212 (319)
Q Consensus       161 ~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~l  212 (319)
                      .+.+.+...|.....+++||||+|.  +..+..-.+++.+...++...+|+.
T Consensus       105 eLie~~~~~P~~g~~KV~IIDEa~~--LT~~A~NALLKtLEEPP~~tifILa  154 (725)
T PRK07133        105 ELIENVKNLPTQSKYKIYIIDEVHM--LSKSAFNALLKTLEEPPKHVIFILA  154 (725)
T ss_pred             HHHHHHHhchhcCCCEEEEEEChhh--CCHHHHHHHHHHhhcCCCceEEEEE
Confidence            3444455556678899999999998  5555566666666554444444443

>KOG1802|consensus

Probab=95.50  E-value=0.031  Score=55.81  Aligned_cols=56  Identities=20%  Similarity=0.251  Sum_probs=42.6

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      .-.+...+|+||+|+|||....-.+++-... .   ...||+.+|...++.|+++.+.+.
T Consensus       422 VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~-~---~~~VLvcApSNiAVDqLaeKIh~t  477 (935)
T KOG1802|consen  422 VLQRPLSLIQGPPGTGKTVTSATIVYHLARQ-H---AGPVLVCAPSNIAVDQLAEKIHKT  477 (935)
T ss_pred             HHcCCceeeecCCCCCceehhHHHHHHHHHh-c---CCceEEEcccchhHHHHHHHHHhc
Confidence            3345568999999999998876666554433 2   347888899999999999887764

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=95.50  E-value=0.066  Score=51.08  Aligned_cols=26  Identities=31%  Similarity=0.491  Sum_probs=19.1

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      ...+++|+||+|+|||+..-. +++.+
T Consensus        54 ~~~~~lI~G~~GtGKT~l~~~-v~~~l   79 (394)
T PRK00411         54 RPLNVLIYGPPGTGKTTTVKK-VFEEL   79 (394)
T ss_pred             CCCeEEEECCCCCCHHHHHHH-HHHHH
Confidence            346799999999999987544 33433

>CHL00181 cbbX CbbX; Provisional

Probab=95.43  E-value=0.13  Score=47.19  Aligned_cols=22  Identities=27%  Similarity=0.111  Sum_probs=17.2

Q ss_pred             CCCcEEEecCCCCCccchhhHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~   89 (319)
                      .+-++++.||+|||||+.+-..
T Consensus        58 ~~~~ill~G~pGtGKT~lAr~l   79 (287)
T CHL00181         58 PGLHMSFTGSPGTGKTTVALKM   79 (287)
T ss_pred             CCceEEEECCCCCCHHHHHHHH
Confidence            3456899999999999776443

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=95.42  E-value=0.17  Score=47.70  Aligned_cols=27  Identities=30%  Similarity=0.477  Sum_probs=19.7

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      ....+++|+||+|+|||+..- .+++.+
T Consensus        38 ~~~~~i~I~G~~GtGKT~l~~-~~~~~l   64 (365)
T TIGR02928        38 SRPSNVFIYGKTGTGKTAVTK-YVMKEL   64 (365)
T ss_pred             CCCCcEEEECCCCCCHHHHHH-HHHHHH
Confidence            344689999999999997653 344444

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=95.41  E-value=0.08  Score=55.80  Aligned_cols=41  Identities=24%  Similarity=0.255  Sum_probs=24.3

Q ss_pred             cccccchhhHHHHHHhhh--cCC---CCCcEEEecCCCCCccchhh
Q psy496           47 VTQPRRISAIALINKCLT--LSP---ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~--~~~---~~~~vli~apTGSGKT~~~~   87 (319)
                      .=|..++..+...-....  ...   ...+++++||||+|||..+-
T Consensus       569 ~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~  614 (852)
T TIGR03345       569 IGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETAL  614 (852)
T ss_pred             cChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHH
Confidence            456677766654322211  111   11358999999999997653

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.

>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=0.33  Score=45.17  Aligned_cols=131  Identities=12%  Similarity=0.135  Sum_probs=58.1

Q ss_pred             EEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH---HHhccccCCCCceEEEEEecccc-cC
Q psy496           73 IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA---QERDEQCGRPGSSVGYQIRLEKE-LP  148 (319)
Q Consensus        73 li~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~---~~~~~~~~~~g~~vg~~~~~~~~-~~  148 (319)
                      ++.++.|+|||......++........  ...++++...+.+...+.+...   .......     ........+.. ..
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~--~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~   73 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPP--GRRVIIASTYRQARDIFGRFWKGIIELLPSWF-----EIKFNEWNDRKIIL   73 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS----EEEEEESSHHHHHHHHHHHHHHHHTS-TTT-----S--EEEE-SSEEEE
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCC--CcEEEEecCHHHHHHHHHHhHHHHHHHHHHhc-----CcccccCCCCcEEe
Confidence            467889999999988777766554432  3466666555556555444222   2222211     11111111111 11


Q ss_pred             CCCceEEEECchH--HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          149 RKRGSILYCTAGI--LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~--ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      .....|.+.+.+.  -...+.+    ..++++++||+-.  ...+.....+............+.+|-|.
T Consensus        74 ~nG~~i~~~~~~~~~~~~~~~G----~~~~~i~iDE~~~--~~~~~~~~~~~~~~~~~~~~~~~~~s~p~  137 (384)
T PF03237_consen   74 PNGSRIQFRGADSPDSGDNIRG----FEYDLIIIDEAAK--VPDDAFSELIRRLRATWGGSIRMYISTPP  137 (384)
T ss_dssp             TTS-EEEEES-----SHHHHHT----S--SEEEEESGGG--STTHHHHHHHHHHHHCSTT--EEEEEE--
T ss_pred             cCceEEEEeccccccccccccc----cccceeeeeeccc--CchHHHHHHHHhhhhcccCcceEEeecCC
Confidence            2334466665432  2234444    5788999999876  33343444444444333332333566655

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.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=95.36  E-value=0.09  Score=50.80  Aligned_cols=20  Identities=40%  Similarity=0.536  Sum_probs=16.2

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      ..+++++||+|+|||+.+-.
T Consensus        36 ~~~ilL~GppGtGKTtLA~~   55 (413)
T PRK13342         36 LSSMILWGPPGTGKTTLARI   55 (413)
T ss_pred             CceEEEECCCCCCHHHHHHH
Confidence            35799999999999976643

>PRK08939 primosomal protein DnaI; Reviewed

Probab=95.35  E-value=0.18  Score=46.77  Aligned_cols=27  Identities=19%  Similarity=0.267  Sum_probs=19.4

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEI   95 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~   95 (319)
                      .++++++.|++|+|||.... ++.+.+.
T Consensus       155 ~~~gl~L~G~~G~GKThLa~-Aia~~l~  181 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYLLA-AIANELA  181 (306)
T ss_pred             CCCeEEEECCCCCCHHHHHH-HHHHHHH
Confidence            45689999999999996553 3344444

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=95.35  E-value=0.1  Score=47.84  Aligned_cols=19  Identities=26%  Similarity=0.151  Sum_probs=15.9

Q ss_pred             CCcEEEecCCCCCccchhh
Q psy496           69 LSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~   87 (319)
                      ..++++.||+|||||+.+-
T Consensus        58 ~~~vll~G~pGTGKT~lA~   76 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVAL   76 (284)
T ss_pred             CceEEEEcCCCCCHHHHHH
Confidence            4479999999999997763

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.

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=95.27  E-value=0.008  Score=56.52  Aligned_cols=44  Identities=14%  Similarity=0.068  Sum_probs=30.7

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISA  115 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la  115 (319)
                      ...+.|++|+||||||||+.. ..++..+-.     ..+++.+..+.|+.
T Consensus       159 v~~~~nilI~G~tGSGKTTll-~aLl~~i~~-----~~rivtiEd~~El~  202 (344)
T PRK13851        159 VVGRLTMLLCGPTGSGKTTMS-KTLISAIPP-----QERLITIEDTLELV  202 (344)
T ss_pred             HHcCCeEEEECCCCccHHHHH-HHHHcccCC-----CCCEEEECCCcccc
Confidence            446789999999999999765 334443322     23788888887763

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=95.25  E-value=0.1  Score=43.40  Aligned_cols=111  Identities=20%  Similarity=0.199  Sum_probs=56.9

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCC-
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPR-  149 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~-  149 (319)
                      .+.|+|++|+|||+.... +.+.+...+-.. +-+++  |-          ++        .+|..+|+.+-.-..... 
T Consensus         7 ki~ITG~PGvGKtTl~~k-i~e~L~~~g~kv-gGf~t--~E----------VR--------~gGkR~GF~Ivdl~tg~~~   64 (179)
T COG1618           7 KIFITGRPGVGKTTLVLK-IAEKLREKGYKV-GGFIT--PE----------VR--------EGGKRIGFKIVDLATGEEG   64 (179)
T ss_pred             EEEEeCCCCccHHHHHHH-HHHHHHhcCcee-eeEEe--ee----------ee--------cCCeEeeeEEEEccCCceE
Confidence            488999999999988754 344444432111 11222  21          11        126777766542221100 


Q ss_pred             -----CCceEEEECchHHHHHHhc------CCCCCCccEEEEecccccccchhHHHHHHHhhhcc
Q psy496          150 -----KRGSILYCTAGILPEVMQS------DPILSGVSHIVMDEIHERSMISDFLLAILKDVTDK  203 (319)
Q Consensus       150 -----~~~~Iiv~Tpg~ll~~l~~------~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~  203 (319)
                           ......++-.+...+.+..      ...+..-+++||||+--+-+...-+...+..+...
T Consensus        65 ~la~~~~~~~rvGkY~V~v~~le~i~~~al~rA~~~aDvIIIDEIGpMElks~~f~~~ve~vl~~  129 (179)
T COG1618          65 ILARVGFSRPRVGKYGVNVEGLEEIAIPALRRALEEADVIIIDEIGPMELKSKKFREAVEEVLKS  129 (179)
T ss_pred             EEEEcCCCCcccceEEeeHHHHHHHhHHHHHHHhhcCCEEEEecccchhhccHHHHHHHHHHhcC
Confidence                 1122334444444333311      11245579999999987544444555555555543

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.24  E-value=0.013  Score=54.57  Aligned_cols=46  Identities=20%  Similarity=0.185  Sum_probs=31.7

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRIS  114 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~l  114 (319)
                      .....|++|+|+||||||+.. ..++..+....  +..+++.+..+.|+
T Consensus       141 v~~~~nilI~G~tGSGKTTll-~aL~~~i~~~~--~~~rivtiEd~~El  186 (323)
T PRK13833        141 IDSRLNIVISGGTGSGKTTLA-NAVIAEIVASA--PEDRLVILEDTAEI  186 (323)
T ss_pred             HHcCCeEEEECCCCCCHHHHH-HHHHHHHhcCC--CCceEEEecCCccc
Confidence            345678999999999999775 44555543211  13478888878776

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=95.21  E-value=0.079  Score=49.59  Aligned_cols=51  Identities=22%  Similarity=0.304  Sum_probs=35.3

Q ss_pred             HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecc
Q psy496          162 LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSA  214 (319)
Q Consensus       162 ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSA  214 (319)
                      +.+.+...+.....+++||||+|.  +..+..-++++.+...+++..+|+.|.
T Consensus        94 l~~~~~~~~~~~~~kv~iI~~a~~--m~~~aaNaLLK~LEEPp~~~~fiL~t~  144 (328)
T PRK05707         94 LVSFVVQTAQLGGRKVVLIEPAEA--MNRNAANALLKSLEEPSGDTVLLLISH  144 (328)
T ss_pred             HHHHHhhccccCCCeEEEECChhh--CCHHHHHHHHHHHhCCCCCeEEEEEEC
Confidence            344444455677899999999998  677777777887766555555555443

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=95.20  E-value=0.033  Score=57.25  Aligned_cols=58  Identities=22%  Similarity=0.192  Sum_probs=43.9

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      +..++|.|+.|||||.+...=+...+...+ ....+|+++.-|+.+|..+.+++...++
T Consensus        15 ~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~-v~p~~IL~lTFT~kAA~em~~Rl~~~l~   72 (672)
T PRK10919         15 TGPCLVLAGAGSGKTRVITNKIAHLIRGCG-YQARHIAAVTFTNKAAREMKERVAQTLG   72 (672)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHHHHHHhcC-CCHHHeeeEechHHHHHHHHHHHHHHhC
Confidence            467899999999999887665555443322 2244789999999999999998887654

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=95.20  E-value=0.094  Score=53.90  Aligned_cols=45  Identities=16%  Similarity=0.048  Sum_probs=31.1

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHH
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIA  117 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q  117 (319)
                      -|+=|.-+||+|||.+|.-.|++.-..   -+..+.++++|+.+.-.-
T Consensus        75 lNiDI~METGTGKTy~YlrtmfeLhk~---YG~~KFIivVPs~AIkeG  119 (985)
T COG3587          75 LNIDILMETGTGKTYTYLRTMFELHKK---YGLFKFIIVVPSLAIKEG  119 (985)
T ss_pred             ceeeEEEecCCCceeeHHHHHHHHHHH---hCceeEEEEeccHHHHhh
Confidence            356778899999999998877653221   123466666799876544

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=95.19  E-value=0.074  Score=60.68  Aligned_cols=122  Identities=18%  Similarity=0.175  Sum_probs=65.9

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL  147 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~  147 (319)
                      .++..+|.|+.|+|||+..-. +.+.+...+    ..|+.+.||-..|..+.+......        ..+.  .+.....
T Consensus       445 ~~~v~ii~G~aGTGKTt~l~~-l~~~~~~~G----~~V~~lAPTgrAA~~L~e~~g~~A--------~Ti~--~~l~~l~  509 (1960)
T TIGR02760       445 TKRFIIINGFGGTGSTEIAQL-LLHLASEQG----YEIQIITAGSLSAQELRQKIPRLA--------STFI--TWVKNLF  509 (1960)
T ss_pred             CCCeEEEEECCCCCHHHHHHH-HHHHHHhcC----CeEEEEeCCHHHHHHHHHHhcchh--------hhHH--HHHHhhc
Confidence            457899999999999976533 333332222    377788899887766654322110        0000  0000000


Q ss_pred             CCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccc
Q psy496          148 PRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSAT  215 (319)
Q Consensus       148 ~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT  215 (319)
                      ..    ....|...++   .....+..-++|||||+-+  +....+..+++....  .+.|+|++.-+
T Consensus       510 ~~----~~~~tv~~fl---~~~~~l~~~~vlIVDEAsM--l~~~~~~~Ll~~a~~--~garvVlvGD~  566 (1960)
T TIGR02760       510 ND----DQDHTVQGLL---DKSSPFSNKDIFVVDEANK--LSNNELLKLIDKAEQ--HNSKLILLNDS  566 (1960)
T ss_pred             cc----ccchhHHHhh---cccCCCCCCCEEEEECCCC--CCHHHHHHHHHHHhh--cCCEEEEEcCh
Confidence            00    0011222222   2233356789999999998  555556666665533  25688877544

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.

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=95.18  E-value=0.013  Score=53.08  Aligned_cols=43  Identities=21%  Similarity=0.168  Sum_probs=29.9

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRIS  114 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~l  114 (319)
                      ..+.+++++|+||||||+.. ..+++.+...    ..+++++..+.|+
T Consensus       125 ~~~~~ili~G~tGSGKTT~l-~all~~i~~~----~~~iv~iEd~~E~  167 (270)
T PF00437_consen  125 RGRGNILISGPTGSGKTTLL-NALLEEIPPE----DERIVTIEDPPEL  167 (270)
T ss_dssp             HTTEEEEEEESTTSSHHHHH-HHHHHHCHTT----TSEEEEEESSS-S
T ss_pred             ccceEEEEECCCccccchHH-HHHhhhcccc----ccceEEeccccce
Confidence            46789999999999999877 4445544433    2377887766554

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 ....

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.16  E-value=0.035  Score=54.76  Aligned_cols=48  Identities=23%  Similarity=0.353  Sum_probs=30.2

Q ss_pred             HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEE
Q psy496          162 LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLIL  211 (319)
Q Consensus       162 ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~  211 (319)
                      +.+.....|.....+++||||+|.  +..+..-.+++.+...++...+|+
T Consensus       107 I~~~~~~~P~~~~~KVvIIDEad~--Lt~~a~naLLk~LEepp~~~v~Il  154 (486)
T PRK14953        107 LRDAVSYTPIKGKYKVYIIDEAHM--LTKEAFNALLKTLEEPPPRTIFIL  154 (486)
T ss_pred             HHHHHHhCcccCCeeEEEEEChhh--cCHHHHHHHHHHHhcCCCCeEEEE
Confidence            344445556678899999999997  445555555666555444443333

>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=95.16  E-value=0.22  Score=41.73  Aligned_cols=20  Identities=25%  Similarity=0.371  Sum_probs=15.8

Q ss_pred             cEEEecCCCCCccchhhHHH
Q psy496           71 PSIIYTSTGCGKTTQVPQFI   90 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~i   90 (319)
                      .+++.|++|||||+......
T Consensus         2 ~~~~~G~~G~GKTt~~~~la   21 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLA   21 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            36789999999998865543

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.

>KOG0384|consensus

Probab=95.15  E-value=0.1  Score=55.52  Aligned_cols=143  Identities=15%  Similarity=0.091  Sum_probs=71.6

Q ss_pred             CCCcEEEecCCCCCccch---hhHHHHHHHHHhCCCCccEEEEecccHHHHHH--HHHHHHHHhccccCCCCceEEEEEe
Q psy496           68 ILSPSIIYTSTGCGKTTQ---VPQFILDDEIARNRGSECCIMVTQPRRISAIA--IAERVAQERDEQCGRPGSSVGYQIR  142 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~---~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q--~~~~~~~~~~~~~~~~g~~vg~~~~  142 (319)
                      +++|+|+.=+-|=|||..   |+-.+++.....+     ..|++.|.--++.=  -++.|. .+.. +.|.|...+-++.
T Consensus       388 ~~~n~ILADEmgLgktvqti~fl~~l~~~~~~~g-----pflvvvplst~~~W~~ef~~w~-~mn~-i~y~g~~~sr~~i  460 (1373)
T KOG0384|consen  388 KRNNCILADEMGLGKTVQTITFLSYLFHSLQIHG-----PFLVVVPLSTITAWEREFETWT-DMNV-IVYHGNLESRQLI  460 (1373)
T ss_pred             hcccceehhhcCCCcchHHHHHHHHHHHhhhccC-----CeEEEeehhhhHHHHHHHHHHh-hhce-eeeecchhHHHHH
Confidence            568899999999999965   4444444332222     23344475443221  122233 2221 1222333221111


Q ss_pred             ------cccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchh-HHHHHHHhhhccccCceEEEeccc
Q psy496          143 ------LEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD-FLLAILKDVTDKRKDLKLILMSAT  215 (319)
Q Consensus       143 ------~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~-~~~~~l~~~~~~~~~~qiv~lSAT  215 (319)
                            .......-+.+++++|.++++.--..-.. -...++++||||+. -+.+ .+...+..+..   + ..++++.|
T Consensus       461 ~~ye~~~~~~~~~lkf~~lltTye~~LkDk~~L~~-i~w~~~~vDeahrL-kN~~~~l~~~l~~f~~---~-~rllitgT  534 (1373)
T KOG0384|consen  461 RQYEFYHSSNTKKLKFNALLTTYEIVLKDKAELSK-IPWRYLLVDEAHRL-KNDESKLYESLNQFKM---N-HRLLITGT  534 (1373)
T ss_pred             HHHHheecCCccccccceeehhhHHHhccHhhhcc-CCcceeeecHHhhc-CchHHHHHHHHHHhcc---c-ceeeecCC
Confidence                  11111112467999999988654311111 14678999999972 2233 23333333322   3 34677888


Q ss_pred             c---ChhhHhh
Q psy496          216 L---NAEKFSQ  223 (319)
Q Consensus       216 ~---~~~~l~~  223 (319)
                      +   +.+.+..
T Consensus       535 PlQNsikEL~s  545 (1373)
T KOG0384|consen  535 PLQNSLKELWS  545 (1373)
T ss_pred             CccccHHHHHH
Confidence            7   5666554

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.12  E-value=0.011  Score=55.36  Aligned_cols=44  Identities=23%  Similarity=0.071  Sum_probs=30.6

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISA  115 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la  115 (319)
                      .....+++|+|+||||||+.. ..++..+-.     ..+|+++.-+.|+.
T Consensus       157 v~~~~nili~G~tgSGKTTll-~aL~~~ip~-----~~ri~tiEd~~El~  200 (332)
T PRK13900        157 VISKKNIIISGGTSTGKTTFT-NAALREIPA-----IERLITVEDAREIV  200 (332)
T ss_pred             HHcCCcEEEECCCCCCHHHHH-HHHHhhCCC-----CCeEEEecCCCccc
Confidence            345689999999999999775 445544422     23788876666653

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=95.07  E-value=0.095  Score=49.18  Aligned_cols=49  Identities=18%  Similarity=0.320  Sum_probs=30.1

Q ss_pred             HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEe
Q psy496          162 LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILM  212 (319)
Q Consensus       162 ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~l  212 (319)
                      +.+.+...+...+.++|||||+|.  +..+....+++.+...+++..+|+.
T Consensus       105 l~~~~~~~p~~~~~~vviidea~~--l~~~~~~~Ll~~le~~~~~~~lIl~  153 (355)
T TIGR02397       105 ILDNVKYAPSSGKYKVYIIDEVHM--LSKSAFNALLKTLEEPPEHVVFILA  153 (355)
T ss_pred             HHHHHhcCcccCCceEEEEeChhh--cCHHHHHHHHHHHhCCccceeEEEE
Confidence            444455556677889999999997  4444445555655444444444443

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.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=95.05  E-value=0.057  Score=47.84  Aligned_cols=28  Identities=18%  Similarity=0.100  Sum_probs=22.2

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDD   93 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~   93 (319)
                      .+.+..++|.|++|||||+.....+...
T Consensus        21 i~~g~~~~i~G~~G~GKTtl~~~~~~~~   48 (230)
T PRK08533         21 IPAGSLILIEGDESTGKSILSQRLAYGF   48 (230)
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            5667889999999999998866555543

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=95.03  E-value=0.11  Score=45.71  Aligned_cols=17  Identities=35%  Similarity=0.538  Sum_probs=14.3

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      .+++++||+|+|||+.+
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            57999999999999665

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.

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=95.03  E-value=0.15  Score=51.37  Aligned_cols=35  Identities=23%  Similarity=0.198  Sum_probs=21.2

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEe
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVT  108 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~  108 (319)
                      .++|+|++|+|||...- .+.+.+....  ...+++|+
T Consensus       316 pL~LyG~sGsGKTHLL~-AIa~~a~~~~--~g~~V~Yi  350 (617)
T PRK14086        316 PLFIYGESGLGKTHLLH-AIGHYARRLY--PGTRVRYV  350 (617)
T ss_pred             cEEEECCCCCCHHHHHH-HHHHHHHHhC--CCCeEEEe
Confidence            48999999999996543 3333333221  12466664

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=95.03  E-value=0.027  Score=55.51  Aligned_cols=53  Identities=23%  Similarity=0.317  Sum_probs=37.0

Q ss_pred             HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccCh
Q psy496          162 LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNA  218 (319)
Q Consensus       162 ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~~  218 (319)
                      +.+.....|.-.++++.||||+|+  +....+-++++.+..-++...+|  =||-++
T Consensus       107 i~e~v~y~P~~~ryKVyiIDEvHM--LS~~afNALLKTLEEPP~hV~FI--lATTe~  159 (515)
T COG2812         107 IIEKVNYAPSEGRYKVYIIDEVHM--LSKQAFNALLKTLEEPPSHVKFI--LATTEP  159 (515)
T ss_pred             HHHHhccCCccccceEEEEecHHh--hhHHHHHHHhcccccCccCeEEE--EecCCc
Confidence            344445566778999999999998  77777888888877655554443  355533

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=95.02  E-value=0.13  Score=47.42  Aligned_cols=18  Identities=33%  Similarity=0.305  Sum_probs=13.8

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      ..++++||+|+|||+..-
T Consensus        44 ~~lll~G~~G~GKT~la~   61 (316)
T PHA02544         44 NMLLHSPSPGTGKTTVAK   61 (316)
T ss_pred             eEEEeeCcCCCCHHHHHH
Confidence            345559999999997653

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.01  E-value=0.025  Score=52.25  Aligned_cols=46  Identities=17%  Similarity=0.180  Sum_probs=31.7

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRIS  114 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~l  114 (319)
                      ...+.+++|+|+||||||+.. ..++..+-..  .+..+++++..+.|+
T Consensus       129 v~~~~~ilI~G~tGSGKTTll-~al~~~i~~~--~~~~ri~tiEd~~El  174 (299)
T TIGR02782       129 VLARKNILVVGGTGSGKTTLA-NALLAEIAKN--DPTDRVVIIEDTREL  174 (299)
T ss_pred             HHcCCeEEEECCCCCCHHHHH-HHHHHHhhcc--CCCceEEEECCchhh
Confidence            345678999999999999875 3344443221  123478888888886

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.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=94.85  E-value=0.12  Score=50.53  Aligned_cols=35  Identities=17%  Similarity=0.266  Sum_probs=22.9

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEec
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQ  109 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~  109 (319)
                      ..++|+||+|+|||...- ++.+.+...+    .+++++.
T Consensus       142 npl~L~G~~G~GKTHLl~-Ai~~~l~~~~----~~v~yi~  176 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQ-AAVHALRESG----GKILYVR  176 (445)
T ss_pred             ceEEEEcCCCCCHHHHHH-HHHHHHHHcC----CCEEEee
Confidence            458999999999996543 4444443322    3667754

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=94.80  E-value=0.063  Score=49.24  Aligned_cols=125  Identities=13%  Similarity=0.150  Sum_probs=59.5

Q ss_pred             hHHHHHHhhhcCCCC--CcEEEecCCCCCccchhhHHHHHHHHH-hCCCCccEEEEe-cccHHHHHHHHHHHHHHhcccc
Q psy496           55 AIALINKCLTLSPIL--SPSIIYTSTGCGKTTQVPQFILDDEIA-RNRGSECCIMVT-QPRRISAIAIAERVAQERDEQC  130 (319)
Q Consensus        55 ~~~~~~~~l~~~~~~--~~vli~apTGSGKT~~~~l~il~~l~~-~~~~~~~~vl~~-~Ptr~la~q~~~~~~~~~~~~~  130 (319)
                      ++..-++++..-+..  .+++|+|+|+.|||..+-...-.+... ........|+++ .|...-....+..+-..++...
T Consensus        45 ~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP~  124 (302)
T PF05621_consen   45 ALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAPY  124 (302)
T ss_pred             HHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCccc
Confidence            333334555543322  479999999999998654433222111 111112234443 4555444445554544443221


Q ss_pred             CCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccc--cc--cchhHHHHHHHhhhc
Q psy496          131 GRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHE--RS--MISDFLLAILKDVTD  202 (319)
Q Consensus       131 ~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~--~~--~~~~~~~~~l~~~~~  202 (319)
                             .    ..+.....        -...+++++.    -+++++||||+|.  .|  ....-++..++.+.+
T Consensus       125 -------~----~~~~~~~~--------~~~~~~llr~----~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~N  177 (302)
T PF05621_consen  125 -------R----PRDRVAKL--------EQQVLRLLRR----LGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGN  177 (302)
T ss_pred             -------C----CCCCHHHH--------HHHHHHHHHH----cCCcEEEeechHHHhcccHHHHHHHHHHHHHHhh
Confidence                   1    00000000        0112233322    4789999999997  12  122255566666654

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=94.78  E-value=0.15  Score=48.93  Aligned_cols=49  Identities=14%  Similarity=0.190  Sum_probs=29.4

Q ss_pred             HHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          163 PEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       163 l~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      .+.....+.....+++||||+|.  +.....-.+++.+...+++..+|+.+
T Consensus       106 ~~~~~~~p~~~~~kViiIDead~--m~~~aanaLLk~LEep~~~~~fIL~a  154 (394)
T PRK07940        106 VTIAARRPSTGRWRIVVIEDADR--LTERAANALLKAVEEPPPRTVWLLCA  154 (394)
T ss_pred             HHHHHhCcccCCcEEEEEechhh--cCHHHHHHHHHHhhcCCCCCeEEEEE
Confidence            34444455567889999999998  45554455566555444444444433

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=94.76  E-value=0.057  Score=50.59  Aligned_cols=45  Identities=24%  Similarity=0.225  Sum_probs=33.2

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISA  115 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la  115 (319)
                      -.-|.+.|.-|||||..++.+-+++....+.  .-++++..|+....
T Consensus       245 I~lV~L~G~AGtGKTlLALaAgleqv~e~~~--y~KiiVtRp~vpvG  289 (436)
T COG1875         245 IDLVSLGGKAGTGKTLLALAAGLEQVLERKR--YRKIIVTRPTVPVG  289 (436)
T ss_pred             CCeEEeeccCCccHhHHHHHHHHHHHHHHhh--hceEEEecCCcCcc
Confidence            3568889999999998887777777655432  34788888875543

>KOG0780|consensus

Probab=94.75  E-value=0.2  Score=47.28  Aligned_cols=133  Identities=16%  Similarity=0.224  Sum_probs=83.0

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCC
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPR  149 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~  149 (319)
                      .++++.|=-|||||+.......   +.+.++..+..+|.-..|+-|.+..+..+...+..+  +|       .+ ...++
T Consensus       102 sVimfVGLqG~GKTTtc~KlA~---y~kkkG~K~~LvcaDTFRagAfDQLkqnA~k~~iP~--yg-------sy-te~dp  168 (483)
T KOG0780|consen  102 SVIMFVGLQGSGKTTTCTKLAY---YYKKKGYKVALVCADTFRAGAFDQLKQNATKARVPF--YG-------SY-TEADP  168 (483)
T ss_pred             cEEEEEeccCCCcceeHHHHHH---HHHhcCCceeEEeecccccchHHHHHHHhHhhCCee--Ee-------cc-cccch
Confidence            4677899999999988765443   233456677888888899999888777766543322  01       00 00111


Q ss_pred             CCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhh
Q psy496          150 KRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFF  225 (319)
Q Consensus       150 ~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l  225 (319)
                          +.|+.-|  ++..+.    .++++||+|-.-++....+++.+.........|+.-++.+-|++  ..+..++-|
T Consensus       169 ----v~ia~eg--v~~fKk----e~fdvIIvDTSGRh~qe~sLfeEM~~v~~ai~Pd~vi~VmDasiGQaae~Qa~aF  236 (483)
T KOG0780|consen  169 ----VKIASEG--VDRFKK----ENFDVIIVDTSGRHKQEASLFEEMKQVSKAIKPDEIIFVMDASIGQAAEAQARAF  236 (483)
T ss_pred             ----HHHHHHH--HHHHHh----cCCcEEEEeCCCchhhhHHHHHHHHHHHhhcCCCeEEEEEeccccHhHHHHHHHH
Confidence                1122222  222222    57899999999875455556666655555577887777888888  666666555

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=94.74  E-value=0.04  Score=49.39  Aligned_cols=81  Identities=20%  Similarity=0.298  Sum_probs=49.5

Q ss_pred             ccEEEEecccHHHHHHHHHHHHHHhcc--ccCCCCceEEEEEecccc---cCCCCceEEEECchHHHHHHhcCCC-CCCc
Q psy496          102 ECCIMVTQPRRISAIAIAERVAQERDE--QCGRPGSSVGYQIRLEKE---LPRKRGSILYCTAGILPEVMQSDPI-LSGV  175 (319)
Q Consensus       102 ~~~vl~~~Ptr~la~q~~~~~~~~~~~--~~~~~g~~vg~~~~~~~~---~~~~~~~Iiv~Tpg~ll~~l~~~~~-l~~v  175 (319)
                      .+.+++++..-.=|..+.+.+..+.+.  .+   +....-.+..++.   ....+.+|.||||||+..++..+.. ++++
T Consensus       126 sP~~lvvs~SalRa~dl~R~l~~~~~k~~~v---~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~~l  202 (252)
T PF14617_consen  126 SPHVLVVSSSALRAADLIRALRSFKGKDCKV---AKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSNL  202 (252)
T ss_pred             CCEEEEEcchHHHHHHHHHHHHhhccCCchH---HHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCcccC
Confidence            456666666655566777766655321  11   1111112222211   1123578999999999999966654 8999


Q ss_pred             cEEEEecccc
Q psy496          176 SHIVMDEIHE  185 (319)
Q Consensus       176 ~~vViDEah~  185 (319)
                      .+||||--|.
T Consensus       203 ~~ivlD~s~~  212 (252)
T PF14617_consen  203 KRIVLDWSYL  212 (252)
T ss_pred             eEEEEcCCcc
Confidence            9999998663

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=94.71  E-value=0.2  Score=46.79  Aligned_cols=51  Identities=14%  Similarity=0.223  Sum_probs=36.9

Q ss_pred             HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecc
Q psy496          162 LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSA  214 (319)
Q Consensus       162 ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSA  214 (319)
                      +.+.+...+.-...+++|||++|.  +.....-++++.+...+++..+++.|.
T Consensus        95 l~~~~~~~~~~g~~KV~iI~~a~~--m~~~AaNaLLKtLEEPp~~~~fiL~t~  145 (325)
T PRK06871         95 INEKVSQHAQQGGNKVVYIQGAER--LTEAAANALLKTLEEPRPNTYFLLQAD  145 (325)
T ss_pred             HHHHHhhccccCCceEEEEechhh--hCHHHHHHHHHHhcCCCCCeEEEEEEC
Confidence            344445556677899999999998  667777788888877666666666554

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=94.71  E-value=0.27  Score=49.41  Aligned_cols=43  Identities=21%  Similarity=0.310  Sum_probs=27.6

Q ss_pred             hcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEE
Q psy496          167 QSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLIL  211 (319)
Q Consensus       167 ~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~  211 (319)
                      ...+...+.+++||||+|.  +..+..-.+++.+...++...+|+
T Consensus       112 ~~~p~~~~~KVvIIDEa~~--Ls~~a~naLLK~LEepp~~~vfI~  154 (563)
T PRK06647        112 MFPPASSRYRVYIIDEVHM--LSNSAFNALLKTIEEPPPYIVFIF  154 (563)
T ss_pred             HhchhcCCCEEEEEEChhh--cCHHHHHHHHHhhccCCCCEEEEE
Confidence            4455578899999999998  455555556666554444443433

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=94.70  E-value=0.2  Score=51.85  Aligned_cols=21  Identities=33%  Similarity=0.464  Sum_probs=16.9

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      ...+++++||+|+|||+.+-.
T Consensus        51 ~~~slLL~GPpGtGKTTLA~a   71 (725)
T PRK13341         51 RVGSLILYGPPGVGKTTLARI   71 (725)
T ss_pred             CCceEEEECCCCCCHHHHHHH
Confidence            345799999999999977643

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.65  E-value=0.28  Score=48.83  Aligned_cols=136  Identities=18%  Similarity=0.150  Sum_probs=64.4

Q ss_pred             CCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHH---HHH--HHhccccCCCCceEEEE-EecccccCCC
Q psy496           77 STGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAE---RVA--QERDEQCGRPGSSVGYQ-IRLEKELPRK  150 (319)
Q Consensus        77 pTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~---~~~--~~~~~~~~~~g~~vg~~-~~~~~~~~~~  150 (319)
                      .||||||....-.|++.. ..+  .+--+.++.-+..|-.-..+   .++  -++...+.+.+..+... +..-+ .-++
T Consensus         5 atgsgkt~~ma~lil~~y-~kg--yr~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkvn~fs-ehnd   80 (812)
T COG3421           5 ATGSGKTLVMAGLILECY-KKG--YRNFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKVNNFS-EHND   80 (812)
T ss_pred             ccCCChhhHHHHHHHHHH-Hhc--hhhEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeeecccC-ccCC
Confidence            399999988777776543 322  22233333333332211111   011  11222222333333311 11111 1224


Q ss_pred             CceEEEECchHHHHHH-hcC--C----CCCCccEE-EEeccccccc------chh-----HHHHHHHhhhccccCceEEE
Q psy496          151 RGSILYCTAGILPEVM-QSD--P----ILSGVSHI-VMDEIHERSM------ISD-----FLLAILKDVTDKRKDLKLIL  211 (319)
Q Consensus       151 ~~~Iiv~Tpg~ll~~l-~~~--~----~l~~v~~v-ViDEah~~~~------~~~-----~~~~~l~~~~~~~~~~qiv~  211 (319)
                      ...|.++|-+.|...+ ..+  .    +|.+..+| +-||+|....      ..+     .+.+.+......+++--++.
T Consensus        81 ~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~~nkd~~~le  160 (812)
T COG3421          81 AIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALEQNKDNLLLE  160 (812)
T ss_pred             ceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHhcCCCceeeh
Confidence            4579999998886666 222  1    25555655 6799996111      001     22222232333445655677


Q ss_pred             ecccc
Q psy496          212 MSATL  216 (319)
Q Consensus       212 lSAT~  216 (319)
                      +|||.
T Consensus       161 f~at~  165 (812)
T COG3421         161 FSATI  165 (812)
T ss_pred             hhhcC
Confidence            89998

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=94.64  E-value=0.29  Score=41.98  Aligned_cols=89  Identities=17%  Similarity=0.125  Sum_probs=48.4

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCC
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPR  149 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~  149 (319)
                      +-.+++||-.||||+-.+.-+-+....+.     ++++..|.      +-.++    +      ...+.  .+.+..   
T Consensus         5 ~l~~i~gpM~SGKT~eLl~r~~~~~~~g~-----~v~vfkp~------iD~R~----~------~~~V~--Sr~G~~---   58 (201)
T COG1435           5 WLEFIYGPMFSGKTEELLRRARRYKEAGM-----KVLVFKPA------IDTRY----G------VGKVS--SRIGLS---   58 (201)
T ss_pred             EEEEEEccCcCcchHHHHHHHHHHHHcCC-----eEEEEecc------ccccc----c------cceee--eccCCc---
Confidence            45688999999999965554433323222     55553343      11111    0      11111  111111   


Q ss_pred             CCceEEEECchHHHHHHhcCCCCCCccEEEEecccc
Q psy496          150 KRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHE  185 (319)
Q Consensus       150 ~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~  185 (319)
                       ..-+.+-.+..+.+.+........+++|.||||+-
T Consensus        59 -~~A~~i~~~~~i~~~i~~~~~~~~~~~v~IDEaQF   93 (201)
T COG1435          59 -SEAVVIPSDTDIFDEIAALHEKPPVDCVLIDEAQF   93 (201)
T ss_pred             -ccceecCChHHHHHHHHhcccCCCcCEEEEehhHh
Confidence             11256667777777775443333489999999996

>KOG0953|consensus

Probab=94.61  E-value=0.049  Score=53.40  Aligned_cols=94  Identities=19%  Similarity=0.221  Sum_probs=55.3

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCCC
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRK  150 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~~  150 (319)
                      .++=+|||-||||.-+    ++++....     .-++.-|.|.||..+++++.+. +..+   ....|-..+..... ..
T Consensus       193 Ii~H~GPTNSGKTy~A----Lqrl~~ak-----sGvycGPLrLLA~EV~~r~na~-gipC---dL~TGeE~~~~~~~-~~  258 (700)
T KOG0953|consen  193 IIMHVGPTNSGKTYRA----LQRLKSAK-----SGVYCGPLRLLAHEVYDRLNAL-GIPC---DLLTGEERRFVLDN-GN  258 (700)
T ss_pred             EEEEeCCCCCchhHHH----HHHHhhhc-----cceecchHHHHHHHHHHHhhhc-CCCc---cccccceeeecCCC-CC
Confidence            3555999999999664    45555544     3455569999999999988764 3333   33444333321111 11


Q ss_pred             CceEEEECchHHHHHHhcCCCCCCccEEEEecccc
Q psy496          151 RGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHE  185 (319)
Q Consensus       151 ~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~  185 (319)
                      .++.+-+|-+++.       .-..+++.||||+.+
T Consensus       259 ~a~hvScTVEM~s-------v~~~yeVAViDEIQm  286 (700)
T KOG0953|consen  259 PAQHVSCTVEMVS-------VNTPYEVAVIDEIQM  286 (700)
T ss_pred             cccceEEEEEEee-------cCCceEEEEehhHHh
Confidence            2345555555321       123577778888775

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=94.61  E-value=0.044  Score=48.72  Aligned_cols=54  Identities=15%  Similarity=0.134  Sum_probs=35.4

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      =.+.+..++|.|++|||||+.....+.+.+....     .++++. +.+-..++.+++..
T Consensus        17 G~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge-----~~lyvs-~ee~~~~i~~~~~~   70 (237)
T TIGR03877        17 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGE-----PGIYVA-LEEHPVQVRRNMAQ   70 (237)
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCC-----cEEEEE-eeCCHHHHHHHHHH
Confidence            3567889999999999999988777776653322     344443 34444555554443

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.

>KOG2028|consensus

Probab=94.61  E-value=0.074  Score=49.89  Aligned_cols=52  Identities=19%  Similarity=0.303  Sum_probs=29.4

Q ss_pred             cEEEEecccccc-cchhHHHHHHHhhhccccCceEEEecccc-Chh--hHhhhhCCCCEEEeC
Q psy496          176 SHIVMDEIHERS-MISDFLLAILKDVTDKRKDLKLILMSATL-NAE--KFSQFFGGAPILHIP  234 (319)
Q Consensus       176 ~~vViDEah~~~-~~~~~~~~~l~~~~~~~~~~qiv~lSAT~-~~~--~l~~~l~~~~~i~~~  234 (319)
                      ..+.|||+|++. ...|.++-.++       +--+++..||- |+.  .....+..|.++..+
T Consensus       224 TilFiDEiHRFNksQQD~fLP~VE-------~G~I~lIGATTENPSFqln~aLlSRC~VfvLe  279 (554)
T KOG2028|consen  224 TILFIDEIHRFNKSQQDTFLPHVE-------NGDITLIGATTENPSFQLNAALLSRCRVFVLE  279 (554)
T ss_pred             eEEEeHHhhhhhhhhhhcccceec-------cCceEEEecccCCCccchhHHHHhccceeEec
Confidence            468899999832 22222222211       33577888888 553  334456666666554

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.60  E-value=0.058  Score=54.72  Aligned_cols=44  Identities=20%  Similarity=0.309  Sum_probs=29.2

Q ss_pred             HhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEE
Q psy496          166 MQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLIL  211 (319)
Q Consensus       166 l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~  211 (319)
                      +...+.+.+.+++||||+|.  +..+..-.+++.+...++...+|+
T Consensus       113 ~~~~P~~~~~KVvIIdea~~--Ls~~a~naLLK~LEepp~~tifIL  156 (614)
T PRK14971        113 VRIPPQIGKYKIYIIDEVHM--LSQAAFNAFLKTLEEPPSYAIFIL  156 (614)
T ss_pred             HhhCcccCCcEEEEEECccc--CCHHHHHHHHHHHhCCCCCeEEEE
Confidence            34556688999999999998  455555556666555444444444

>PF12846 AAA_10: AAA-like domain

Probab=94.53  E-value=0.04  Score=49.97  Aligned_cols=43  Identities=26%  Similarity=0.368  Sum_probs=30.4

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAI  116 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~  116 (319)
                      |.+++|.|+||||||+.... ++......+    ..++++-|..+...
T Consensus         1 n~h~~i~G~tGsGKT~~~~~-l~~~~~~~g----~~~~i~D~~g~~~~   43 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLKN-LLEQLIRRG----PRVVIFDPKGDYSP   43 (304)
T ss_pred             CCeEEEECCCCCcHHHHHHH-HHHHHHHcC----CCEEEEcCCchHHH
Confidence            56899999999999988774 444444433    36777778766544

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=94.53  E-value=0.25  Score=46.01  Aligned_cols=52  Identities=17%  Similarity=0.190  Sum_probs=37.7

Q ss_pred             HHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecc
Q psy496          161 ILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSA  214 (319)
Q Consensus       161 ~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSA  214 (319)
                      .+.+.+...+.....+++||||+|.  +.....-+++|.+...+++..+|++|.
T Consensus       100 ~l~~~~~~~p~~g~~kV~iI~~ae~--m~~~AaNaLLKtLEEPp~~~~fiL~~~  151 (319)
T PRK08769        100 EISQKLALTPQYGIAQVVIVDPADA--INRAACNALLKTLEEPSPGRYLWLISA  151 (319)
T ss_pred             HHHHHHhhCcccCCcEEEEeccHhh--hCHHHHHHHHHHhhCCCCCCeEEEEEC
Confidence            3444454556667899999999998  677777778887777666666776655

>KOG0392|consensus

Probab=94.51  E-value=0.19  Score=53.64  Aligned_cols=140  Identities=17%  Similarity=0.107  Sum_probs=76.3

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHHHhCC----CCccEEEEecccHHHHHHHHHHHHHHhcc--ccCCCCceEEEEEecc
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEIARNR----GSECCIMVTQPRRISAIAIAERVAQERDE--QCGRPGSSVGYQIRLE  144 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~~~~~----~~~~~vl~~~Ptr~la~q~~~~~~~~~~~--~~~~~g~~vg~~~~~~  144 (319)
                      +=++|-.-|=|||++..-.+....+.++.    ......++++|. .|+-.....+.+++..  .+.|.|...   .+..
T Consensus       996 HGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPs-TLtGHW~~E~~kf~pfL~v~~yvg~p~---~r~~ 1071 (1549)
T KOG0392|consen  996 HGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPS-TLTGHWKSEVKKFFPFLKVLQYVGPPA---ERRE 1071 (1549)
T ss_pred             cceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCc-hhhhHHHHHHHHhcchhhhhhhcCChH---HHHH
Confidence            46788889999999876666555544311    112235555585 4555555666666443  111112221   2222


Q ss_pred             cccCCCCceEEEECchHHHHHH--hcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc---Chh
Q psy496          145 KELPRKRGSILYCTAGILPEVM--QSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL---NAE  219 (319)
Q Consensus       145 ~~~~~~~~~Iiv~Tpg~ll~~l--~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~---~~~  219 (319)
                      .+...++.+|+|++++.+.+-.  ..+   .++.+.|+||-|-.--..--+-..++.+.   .+ ..+.+|.|+   |+.
T Consensus      1072 lR~q~~~~~iiVtSYDv~RnD~d~l~~---~~wNYcVLDEGHVikN~ktkl~kavkqL~---a~-hRLILSGTPIQNnvl 1144 (1549)
T KOG0392|consen 1072 LRDQYKNANIIVTSYDVVRNDVDYLIK---IDWNYCVLDEGHVIKNSKTKLTKAVKQLR---AN-HRLILSGTPIQNNVL 1144 (1549)
T ss_pred             HHhhccccceEEeeHHHHHHHHHHHHh---cccceEEecCcceecchHHHHHHHHHHHh---hc-ceEEeeCCCcccCHH
Confidence            2222245789999999886433  111   35779999999952111112223333333   34 456789998   554


Q ss_pred             hH
Q psy496          220 KF  221 (319)
Q Consensus       220 ~l  221 (319)
                      ++
T Consensus      1145 eL 1146 (1549)
T KOG0392|consen 1145 EL 1146 (1549)
T ss_pred             HH
Confidence            43

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=94.51  E-value=0.065  Score=55.57  Aligned_cols=58  Identities=22%  Similarity=0.197  Sum_probs=43.5

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      ..+++|.|..|||||.+...=+...+...+ -....|+++.-|+.+|..+.+++.+..+
T Consensus        22 ~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~-v~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773         22 LGNMLVLAGAGSGKTRVLVHRIAWLMQVEN-ASPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHHHHHHcCC-CChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            367999999999999887555544332222 2345799999999999999999988765

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=94.46  E-value=0.14  Score=56.97  Aligned_cols=49  Identities=14%  Similarity=0.052  Sum_probs=31.5

Q ss_pred             CCCcEEEecCCCCCccchhhH--HHHHHHHHhCCCCccEEEEecccHHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ--FILDDEIARNRGSECCIMVTQPRRISAIAIA  119 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l--~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~  119 (319)
                      .++.++|+|..|+|||+.+-.  -++..+...   ....|+.+.||--.|..+.
T Consensus       851 ~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e~---~g~~V~glAPTgkAa~~L~  901 (1623)
T PRK14712        851 SDRFTVVQGYAGVGKTTQFRAVMSAVNMLPES---ERPRVVGLGPTHRAVGEMR  901 (1623)
T ss_pred             CCceEEEEeCCCCCHHHHHHHHHHHHHHHhhc---cCceEEEEechHHHHHHHH
Confidence            357899999999999987532  222222221   1246777789977776653

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=94.43  E-value=0.072  Score=54.65  Aligned_cols=58  Identities=21%  Similarity=0.174  Sum_probs=44.3

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      ..+++|.|+.|||||.....-+...+...+. ....|+++..|+..|.++.+++.+.++
T Consensus        14 ~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~-~p~~IL~vTFt~~Aa~em~~Rl~~~l~   71 (664)
T TIGR01074        14 TGPCLVLAGAGSGKTRVITNKIAYLIQNCGY-KARNIAAVTFTNKAAREMKERVAKTLG   71 (664)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHHHHHHhcCC-CHHHeEEEeccHHHHHHHHHHHHHHhC
Confidence            4679999999999999887666655533222 234788888999999999998887654

Designed to identify rep members of the uvrD/rep subfamily.

>KOG1805|consensus

Probab=94.36  E-value=0.061  Score=55.88  Aligned_cols=50  Identities=20%  Similarity=0.208  Sum_probs=35.9

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      -.+|-|=+|+|||+.....+ +.+...++    +||.++=|..++..+.-++...
T Consensus       687 y~LI~GMPGTGKTTtI~~LI-kiL~~~gk----kVLLtsyThsAVDNILiKL~~~  736 (1100)
T KOG1805|consen  687 YALILGMPGTGKTTTISLLI-KILVALGK----KVLLTSYTHSAVDNILIKLKGF  736 (1100)
T ss_pred             hheeecCCCCCchhhHHHHH-HHHHHcCC----eEEEEehhhHHHHHHHHHHhcc
Confidence            36788889999998876543 44444442    7888888888888887666543

>TIGR01075 uvrD DNA helicase II

Probab=94.35  E-value=0.066  Score=55.47  Aligned_cols=58  Identities=19%  Similarity=0.145  Sum_probs=43.7

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      +..++|.|..|||||.+...=+...+...+ -...+|+++.-|+.+|..+.+++.+.++
T Consensus        17 ~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~-v~p~~IL~lTFTnkAA~em~~Rl~~~~~   74 (715)
T TIGR01075        17 PGNLLVLAGAGSGKTRVLTHRIAWLLSVEN-ASPHSIMAVTFTNKAAAEMRHRIGALLG   74 (715)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHHHHHHcCC-CCHHHeEeeeccHHHHHHHHHHHHHHhc
Confidence            467999999999999887555544333222 2345889989999999999999888765

Designed to identify uvrD members of the uvrD/rep subfamily.

>PRK04328 hypothetical protein; Provisional

Probab=94.32  E-value=0.13  Score=46.09  Aligned_cols=31  Identities=19%  Similarity=0.258  Sum_probs=25.0

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIA   96 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~   96 (319)
                      .+.+..++|.|++|||||+.....+.+.+..
T Consensus        20 ip~gs~ili~G~pGsGKT~l~~~fl~~~~~~   50 (249)
T PRK04328         20 IPERNVVLLSGGPGTGKSIFSQQFLWNGLQM   50 (249)
T ss_pred             CcCCcEEEEEcCCCCCHHHHHHHHHHHHHhc
Confidence            4678889999999999998887777665543

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=94.29  E-value=0.18  Score=56.56  Aligned_cols=49  Identities=14%  Similarity=0.108  Sum_probs=31.1

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAI  118 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~  118 (319)
                      ++.++|+|..|+|||+..- .+.+.+..-.......|+.+.||--.|..+
T Consensus       984 dr~~~I~G~AGTGKTT~l~-~v~~~~~~l~~~~~~~V~glAPTgrAAk~L 1032 (1747)
T PRK13709        984 DRFTVVQGYAGVGKTTQFR-AVMSAVNTLPESERPRVVGLGPTHRAVGEM 1032 (1747)
T ss_pred             CcEEEEEeCCCCCHHHHHH-HHHHHHHHhhcccCceEEEECCcHHHHHHH
Confidence            4689999999999997753 233332211111134677788997776654

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=94.27  E-value=0.32  Score=46.23  Aligned_cols=27  Identities=37%  Similarity=0.518  Sum_probs=20.0

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHh
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIAR   97 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~   97 (319)
                      .|++|.|+||+|||...-. +++.+...
T Consensus        43 ~n~~iyG~~GTGKT~~~~~-v~~~l~~~   69 (366)
T COG1474          43 SNIIIYGPTGTGKTATVKF-VMEELEES   69 (366)
T ss_pred             ccEEEECCCCCCHhHHHHH-HHHHHHhh
Confidence            4699999999999977544 55665544

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.25  E-value=0.29  Score=49.71  Aligned_cols=45  Identities=18%  Similarity=0.279  Sum_probs=29.4

Q ss_pred             hcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          167 QSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       167 ~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      ...+.+.+.+++||||+|.  +.....-.+++.+...++...+|+++
T Consensus       120 ~~~P~~~~~KVvIIdEad~--Lt~~a~naLLK~LEePp~~tv~IL~t  164 (620)
T PRK14954        120 RYGPQKGRYRVYIIDEVHM--LSTAAFNAFLKTLEEPPPHAIFIFAT  164 (620)
T ss_pred             HhhhhcCCCEEEEEeChhh--cCHHHHHHHHHHHhCCCCCeEEEEEe
Confidence            4446678899999999998  44444555666655544454555544

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=94.24  E-value=0.055  Score=45.68  Aligned_cols=47  Identities=19%  Similarity=0.176  Sum_probs=28.6

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      .++|.||+|||||+.....+...+..+.     .++++. +.+...++.+++.
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~~~g~-----~v~~~s-~e~~~~~~~~~~~   47 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGLARGE-----PGLYVT-LEESPEELIENAE   47 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHCCC-----cEEEEE-CCCCHHHHHHHHH
Confidence            3789999999999887776666543222     344442 3344455544443

A related protein is found in archaea.

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=94.18  E-value=0.14  Score=49.70  Aligned_cols=27  Identities=26%  Similarity=0.213  Sum_probs=21.1

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchhh
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~~   87 (319)
                      .++.....+++++++||+|+|||..+-
T Consensus       186 ~l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        186 TILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             HHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            444455567899999999999997764

>PRK10263 DNA translocase FtsK; Provisional

Probab=94.13  E-value=0.44  Score=51.66  Aligned_cols=40  Identities=23%  Similarity=0.300  Sum_probs=27.6

Q ss_pred             CCCcEEEeCCccccccc--cc--hHhHHHHhHhhccccCCCCCC
Q psy496          275 GGAPILHIPGFTYPVQE--YY--LEDVLNMTRTLKRSETQQYPN  314 (319)
Q Consensus       275 ~g~~LVFlp~R~~~v~~--~~--~~~~~~~~~~~~~~~~~~~~~  314 (319)
                      .|.+|..-++...|+++  .|  -++|...++.++..+.-.|-+
T Consensus      1227 ~GDmL~~~~g~~~p~RvqgafvsD~Ei~~vv~~~k~~~~p~y~~ 1270 (1355)
T PRK10263       1227 MGDMLYSGPNSTLPVRVHGAFVRDQEVHAVVQDWKARGRPQYVD 1270 (1355)
T ss_pred             CccEEEecCCCCceeEEEeccCCHHHHHHHHHHHHhcCCCchhh
Confidence            56666655566666655  55  577888888888877766644

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=94.13  E-value=0.051  Score=49.68  Aligned_cols=37  Identities=19%  Similarity=0.204  Sum_probs=25.6

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEe
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVT  108 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~  108 (319)
                      ...-++|+||||||||+... .+++.+....   ...|+.+
T Consensus       124 ~~GLILVTGpTGSGKSTTlA-amId~iN~~~---~~HIlTI  160 (353)
T COG2805         124 PRGLILVTGPTGSGKSTTLA-AMIDYINKHK---AKHILTI  160 (353)
T ss_pred             CCceEEEeCCCCCcHHHHHH-HHHHHHhccC---CcceEEe
Confidence            45779999999999998753 4666665543   2355554

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=94.10  E-value=0.15  Score=50.84  Aligned_cols=26  Identities=23%  Similarity=0.169  Sum_probs=21.3

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchh
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ++=...+.++.+.|+||+|||||+.+
T Consensus       353 ~isl~i~~G~~vaIvG~SGsGKSTLl  378 (529)
T TIGR02868       353 GVSLDLPPGERVAILGPSGSGKSTLL  378 (529)
T ss_pred             cceEEEcCCCEEEEECCCCCCHHHHH
Confidence            44455678999999999999999765

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.

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=94.10  E-value=0.16  Score=58.17  Aligned_cols=48  Identities=15%  Similarity=0.132  Sum_probs=31.7

Q ss_pred             CCCcEEEecCCCCCccchhh---HHHHHHHHHhCCCCccEEEEecccHHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVP---QFILDDEIARNRGSECCIMVTQPRRISAIAIA  119 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~---l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~  119 (319)
                      .+..++|.|+.|+|||+..-   -++.+. +...   ...|+.+.||-..|..+.
T Consensus      1035 ~~~~~~i~G~AGtGKTt~l~~~~~~i~~~-~~~~---g~~v~glApT~~Aa~~L~ 1085 (1960)
T TIGR02760      1035 KDRFVAVQGLAGVGKTTMLESRYKPVLQA-FESE---QLQVIGLAPTHEAVGELK 1085 (1960)
T ss_pred             CCcEEEEEeCCCCCHHHhHHHHHHHHHHH-HHhc---CCeEEEEeChHHHHHHHH
Confidence            34678999999999998762   223332 2222   246777789977776663

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.

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=94.10  E-value=0.092  Score=45.95  Aligned_cols=46  Identities=20%  Similarity=0.238  Sum_probs=29.1

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC-CCCccEEEEecc
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN-RGSECCIMVTQP  110 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~-~~~~~~vl~~~P  110 (319)
                      -.+.++.+.|.|++|||||......+........ .+....++++..
T Consensus        15 G~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~   61 (226)
T cd01393          15 GIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDT   61 (226)
T ss_pred             CCcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEec
Confidence            3566788999999999999877665554432220 011235666544

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.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=94.05  E-value=0.3  Score=45.37  Aligned_cols=58  Identities=17%  Similarity=0.232  Sum_probs=38.9

Q ss_pred             EEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecc
Q psy496          154 ILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSA  214 (319)
Q Consensus       154 Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSA  214 (319)
                      |-|-.-..+.+.+...+.....+++|||++|.  +..+..-.+++.+...+ +..+|+++.
T Consensus       104 I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~--m~~~aaNaLLK~LEEPp-~~~fILi~~  161 (314)
T PRK07399        104 IRLEQIREIKRFLSRPPLEAPRKVVVIEDAET--MNEAAANALLKTLEEPG-NGTLILIAP  161 (314)
T ss_pred             CcHHHHHHHHHHHccCcccCCceEEEEEchhh--cCHHHHHHHHHHHhCCC-CCeEEEEEC
Confidence            33333344566666667778999999999998  56666666777666544 656666554

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=94.02  E-value=0.079  Score=52.29  Aligned_cols=52  Identities=17%  Similarity=0.086  Sum_probs=34.9

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      .+.+..++|.||+|+|||+..+..+.+.+....     +++|+ -..|-..|+.++..
T Consensus       260 ~~~gs~~li~G~~G~GKt~l~~~f~~~~~~~ge-----~~~y~-s~eEs~~~i~~~~~  311 (484)
T TIGR02655       260 FFKDSIILATGATGTGKTLLVSKFLENACANKE-----RAILF-AYEESRAQLLRNAY  311 (484)
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHHHHCCC-----eEEEE-EeeCCHHHHHHHHH
Confidence            567788999999999999988777666543322     44443 34455566666554

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.

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=93.99  E-value=0.059  Score=47.35  Aligned_cols=34  Identities=29%  Similarity=0.255  Sum_probs=27.6

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHH-hC
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIA-RN   98 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~-~~   98 (319)
                      =.+.+..++|.|++|||||......+.+.+.. ..
T Consensus        15 Gip~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge   49 (226)
T PF06745_consen   15 GIPKGSVVLISGPPGSGKTTLALQFLYNGLKNFGE   49 (226)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT-
T ss_pred             CCCCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCC
Confidence            35678899999999999999888888877766 44

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 ....

>CHL00095 clpC Clp protease ATP binding subunit

Probab=93.96  E-value=0.18  Score=53.19  Aligned_cols=40  Identities=20%  Similarity=0.212  Sum_probs=24.4

Q ss_pred             cccccchhhHHHHHHh--hhcCCCC---CcEEEecCCCCCccchh
Q psy496           47 VTQPRRISAIALINKC--LTLSPIL---SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~--l~~~~~~---~~vli~apTGSGKT~~~   86 (319)
                      .-|..++..+...-..  .+....+   ..++++||||+|||..+
T Consensus       512 ~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA  556 (821)
T CHL00095        512 IGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELT  556 (821)
T ss_pred             cChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHH
Confidence            5577887776542211  1111222   35789999999999665

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=93.93  E-value=0.041  Score=51.27  Aligned_cols=47  Identities=17%  Similarity=0.223  Sum_probs=31.4

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRIS  114 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~l  114 (319)
                      +...+.+++|+|+||||||+.. ..++..+...  .+..+++++..+.|+
T Consensus       144 ~v~~~~~ilI~G~tGSGKTTll-~aL~~~~~~~--~~~~rivtIEd~~El  190 (319)
T PRK13894        144 AVRAHRNILVIGGTGSGKTTLV-NAIINEMVIQ--DPTERVFIIEDTGEI  190 (319)
T ss_pred             HHHcCCeEEEECCCCCCHHHHH-HHHHHhhhhc--CCCceEEEEcCCCcc
Confidence            3456789999999999999554 4455443211  123478887777765

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=93.89  E-value=0.059  Score=52.79  Aligned_cols=48  Identities=23%  Similarity=0.157  Sum_probs=36.4

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      .++++.||||||||..+.+|.+-   ...    ..++++-|.-|+....+..+.+
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll---~~~----~s~iV~D~KgEl~~~t~~~r~~   92 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLL---NYP----GSMIVTDPKGELYEKTAGYRKK   92 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHH---hcc----CCEEEEECCCcHHHHHHHHHHH
Confidence            57999999999999999888652   211    1678888999988776664444

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

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=93.88  E-value=0.31  Score=45.64  Aligned_cols=46  Identities=13%  Similarity=0.196  Sum_probs=32.1

Q ss_pred             HhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          166 MQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       166 l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      +...+...+.+++||||+|.  +..+..-.+++.+...+++..+|+.+
T Consensus       102 ~~~~~~~~~~kvviI~~a~~--~~~~a~NaLLK~LEEPp~~~~~Il~t  147 (329)
T PRK08058        102 FSKSGVESNKKVYIIEHADK--MTASAANSLLKFLEEPSGGTTAILLT  147 (329)
T ss_pred             HhhCCcccCceEEEeehHhh--hCHHHHHHHHHHhcCCCCCceEEEEe
Confidence            33445567899999999998  56666667777776655566666544

>KOG2228|consensus

Probab=93.87  E-value=1.3  Score=41.29  Aligned_cols=129  Identities=18%  Similarity=0.184  Sum_probs=64.3

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEeccc----HHHHHHHHHHHHHHhccccCCCCceEEEEEec
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPR----RISAIAIAERVAQERDEQCGRPGSSVGYQIRL  143 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Pt----r~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~  143 (319)
                      +...+++.||-|||||...--.+.. ..  ..+.+..++=+.++    +.+...+.++++..+...    +...|     
T Consensus        48 EsnsviiigprgsgkT~li~~~Ls~-~q--~~~E~~l~v~Lng~~~~dk~al~~I~rql~~e~~~~----~k~~g-----  115 (408)
T KOG2228|consen   48 ESNSVIIIGPRGSGKTILIDTRLSD-IQ--ENGENFLLVRLNGELQTDKIALKGITRQLALELNRI----VKSFG-----  115 (408)
T ss_pred             CCCceEEEccCCCCceEeeHHHHhh-HH--hcCCeEEEEEECccchhhHHHHHHHHHHHHHHHhhh----heeec-----
Confidence            3457999999999999766554444 21  22223344444443    223344555555443321    11111     


Q ss_pred             ccccCCCCceEEEECchHHHHHHhcCCCCCCc-cEEEEecccccccchh--HHHHHHHhhhccccCceEEEeccccCh
Q psy496          144 EKELPRKRGSILYCTAGILPEVMQSDPILSGV-SHIVMDEIHERSMISD--FLLAILKDVTDKRKDLKLILMSATLNA  218 (319)
Q Consensus       144 ~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v-~~vViDEah~~~~~~~--~~~~~l~~~~~~~~~~qiv~lSAT~~~  218 (319)
                       .-..         +-..++..+..+..-... =.+|+||+|....+..  .+.............+-+++++.-+|.
T Consensus       116 -sfte---------~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrld~  183 (408)
T KOG2228|consen  116 -SFTE---------NLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRLDI  183 (408)
T ss_pred             -ccch---------hHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeeccccH
Confidence             0000         113455555444433344 4578899996222221  333444444433445567788777743

>cd01131 PilT Pilus retraction ATPase PilT

Probab=93.87  E-value=0.06  Score=46.50  Aligned_cols=37  Identities=19%  Similarity=0.268  Sum_probs=23.2

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecc
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQP  110 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~P  110 (319)
                      ..++|+||||||||+.. ..++..+....   ..+++.+.-
T Consensus         2 GlilI~GptGSGKTTll-~~ll~~~~~~~---~~~i~t~e~   38 (198)
T cd01131           2 GLVLVTGPTGSGKSTTL-AAMIDYINKNK---THHILTIED   38 (198)
T ss_pred             cEEEEECCCCCCHHHHH-HHHHHHhhhcC---CcEEEEEcC
Confidence            35889999999999886 33444443322   235665443

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.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=93.83  E-value=0.38  Score=44.78  Aligned_cols=52  Identities=17%  Similarity=0.245  Sum_probs=36.3

Q ss_pred             HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccc
Q psy496          162 LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSAT  215 (319)
Q Consensus       162 ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT  215 (319)
                      +.+.+...+.....+++|||++|.  +.....-++++.+...+++..+|+.|..
T Consensus        96 l~~~~~~~~~~~~~kV~iI~~ae~--m~~~AaNaLLKtLEEPp~~t~fiL~t~~  147 (319)
T PRK06090         96 CNRLAQESSQLNGYRLFVIEPADA--MNESASNALLKTLEEPAPNCLFLLVTHN  147 (319)
T ss_pred             HHHHHhhCcccCCceEEEecchhh--hCHHHHHHHHHHhcCCCCCeEEEEEECC
Confidence            334444455677899999999998  6666777778877776666656665443

>PRK11054 helD DNA helicase IV; Provisional

Probab=93.82  E-value=0.14  Score=52.72  Aligned_cols=57  Identities=16%  Similarity=0.113  Sum_probs=41.1

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      .+++|.|..|||||.+..--+...+.. .......|+++..++.+|..+.+++...++
T Consensus       210 ~~~lV~agaGSGKT~vl~~r~ayLl~~-~~~~~~~IL~ltft~~AA~em~eRL~~~lg  266 (684)
T PRK11054        210 DSLLVLAGAGSGKTSVLVARAGWLLAR-GQAQPEQILLLAFGRQAAEEMDERIRERLG  266 (684)
T ss_pred             CCeEEEEeCCCCHHHHHHHHHHHHHHh-CCCCHHHeEEEeccHHHHHHHHHHHHHhcC
Confidence            568999999999998875544333322 222334788888999999999988876554

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=93.82  E-value=0.033  Score=38.73  Aligned_cols=19  Identities=26%  Similarity=0.331  Sum_probs=15.9

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      .+...+|.|++|||||+.+
T Consensus        22 ~g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   22 RGDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            3457999999999999765

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=93.71  E-value=0.21  Score=48.91  Aligned_cols=41  Identities=22%  Similarity=0.415  Sum_probs=26.0

Q ss_pred             CCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEe
Q psy496          170 PILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILM  212 (319)
Q Consensus       170 ~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~l  212 (319)
                      +...+.+++||||+|.  +..+..-.+++.+...++...+|+.
T Consensus       117 ~~~~~~kvvIIdead~--lt~~~~n~LLk~lEep~~~~~~Il~  157 (451)
T PRK06305        117 PSKSRYKIYIIDEVHM--LTKEAFNSLLKTLEEPPQHVKFFLA  157 (451)
T ss_pred             hhcCCCEEEEEecHHh--hCHHHHHHHHHHhhcCCCCceEEEE
Confidence            3456789999999997  4444444555555554445455543

>PRK10865 protein disaggregation chaperone; Provisional

Probab=93.70  E-value=0.76  Score=48.65  Aligned_cols=47  Identities=19%  Similarity=0.160  Sum_probs=26.8

Q ss_pred             cccccchhhHHHHHHhhh--cCCCC---CcEEEecCCCCCccchhhHHHHHHH
Q psy496           47 VTQPRRISAIALINKCLT--LSPIL---SPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~--~~~~~---~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      .-|..++..+...-....  ....+   ..++++||||+|||+.+-. +.+.+
T Consensus       571 iGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~a-La~~l  622 (857)
T PRK10865        571 IGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKA-LANFM  622 (857)
T ss_pred             eCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHH-HHHHh
Confidence            456666666544322211  11112   4689999999999987633 33433

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=93.66  E-value=0.36  Score=40.68  Aligned_cols=23  Identities=17%  Similarity=0.112  Sum_probs=19.1

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.++.+.|.||+|||||+.+
T Consensus        23 ~~i~~Ge~~~i~G~nGsGKStLl   45 (178)
T cd03247          23 LELKQGEKIALLGRSGSGKSTLL   45 (178)
T ss_pred             EEEcCCCEEEEECCCCCCHHHHH
Confidence            34567889999999999999754

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.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=93.59  E-value=0.071  Score=50.19  Aligned_cols=42  Identities=17%  Similarity=0.140  Sum_probs=27.1

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRI  113 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~  113 (319)
                      .+..++|+||||||||+..- .++..+...   ...+|+.+.-..|
T Consensus       121 ~~g~ili~G~tGSGKTT~l~-al~~~i~~~---~~~~i~tiEdp~E  162 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTLA-SMIDYINKN---AAGHIITIEDPIE  162 (343)
T ss_pred             cCcEEEEECCCCCCHHHHHH-HHHHhhCcC---CCCEEEEEcCChh
Confidence            45789999999999998763 344444322   1246777554444

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.

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=93.59  E-value=0.15  Score=55.45  Aligned_cols=63  Identities=22%  Similarity=0.216  Sum_probs=49.8

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhcc
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDE  128 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~  128 (319)
                      .+.+++++|.|..|||||.+...-+++.+...+.-.--.|+|+.-|++.|..+..|+.+.+..
T Consensus        13 ~~~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~~L~~   75 (1139)
T COG1074          13 SPPGQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDRLKE   75 (1139)
T ss_pred             cCCCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHHHHHH
Confidence            456789999999999999988888888777643122347888889999999998888776544

>PRK05973 replicative DNA helicase; Provisional

Probab=93.50  E-value=0.094  Score=46.71  Aligned_cols=59  Identities=8%  Similarity=0.041  Sum_probs=38.5

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +++.+-.+.+..++|.|++|+|||+.....+.+....+.     .++++ ..-+-..++.+++..
T Consensus        55 ~~l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge-----~vlyf-SlEes~~~i~~R~~s  113 (237)
T PRK05973         55 EELFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGR-----TGVFF-TLEYTEQDVRDRLRA  113 (237)
T ss_pred             HHhcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCC-----eEEEE-EEeCCHHHHHHHHHH
Confidence            456667788899999999999999888777766543322     34443 222233555555543

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=93.39  E-value=0.44  Score=49.53  Aligned_cols=17  Identities=29%  Similarity=0.374  Sum_probs=14.3

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      .++++.||||+|||..+
T Consensus       485 ~~~lf~Gp~GvGKT~lA  501 (731)
T TIGR02639       485 GSFLFTGPTGVGKTELA  501 (731)
T ss_pred             eeEEEECCCCccHHHHH
Confidence            35899999999999655

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=93.36  E-value=0.087  Score=46.18  Aligned_cols=17  Identities=24%  Similarity=0.454  Sum_probs=13.7

Q ss_pred             EEEecCCCCCccchhhH
Q psy496           72 SIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        72 vli~apTGSGKT~~~~l   88 (319)
                      ++|.|+.|||||+.+.-
T Consensus         1 ~vv~G~pGsGKSt~i~~   17 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKK   17 (234)
T ss_pred             CEEEcCCCCCHHHHHHH
Confidence            47899999999986533

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

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=93.20  E-value=0.49  Score=44.40  Aligned_cols=53  Identities=13%  Similarity=0.162  Sum_probs=37.6

Q ss_pred             hHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecc
Q psy496          160 GILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSA  214 (319)
Q Consensus       160 g~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSA  214 (319)
                      -.+.+.+...+.....+++|||++|.  +.....-+++|.+..-+++.-++++|.
T Consensus        94 R~l~~~~~~~~~~g~~kV~iI~~ae~--m~~~AaNaLLKtLEEPp~~t~fiL~t~  146 (334)
T PRK07993         94 REVTEKLYEHARLGGAKVVWLPDAAL--LTDAAANALLKTLEEPPENTWFFLACR  146 (334)
T ss_pred             HHHHHHHhhccccCCceEEEEcchHh--hCHHHHHHHHHHhcCCCCCeEEEEEEC
Confidence            33445555566678899999999998  677777778887777655655555554

>PRK11823 DNA repair protein RadA; Provisional

Probab=92.90  E-value=0.17  Score=49.44  Aligned_cols=57  Identities=23%  Similarity=0.079  Sum_probs=34.8

Q ss_pred             HHhhh-cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           60 NKCLT-LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        60 ~~~l~-~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      ++++. =...+..++|.|++|+|||+.....+.+....     ..+++|+.- .+-..|+..+.
T Consensus        70 D~~LgGGi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~-----g~~vlYvs~-Ees~~qi~~ra  127 (446)
T PRK11823         70 DRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLAAA-----GGKVLYVSG-EESASQIKLRA  127 (446)
T ss_pred             HHHhcCCccCCEEEEEECCCCCCHHHHHHHHHHHHHhc-----CCeEEEEEc-cccHHHHHHHH
Confidence            34443 34567789999999999998776655543311     126666543 34445655543

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=92.85  E-value=0.47  Score=44.63  Aligned_cols=54  Identities=17%  Similarity=0.156  Sum_probs=37.1

Q ss_pred             hHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccc
Q psy496          160 GILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSAT  215 (319)
Q Consensus       160 g~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT  215 (319)
                      ..+.+.+...+.-...+++|||++|.  +.....-++++.+...+++..+|++|.-
T Consensus       118 R~l~~~~~~~~~~~~~kV~iI~~ae~--m~~~AaNaLLKtLEEPp~~t~fiL~t~~  171 (342)
T PRK06964        118 RALLDFCGVGTHRGGARVVVLYPAEA--LNVAAANALLKTLEEPPPGTVFLLVSAR  171 (342)
T ss_pred             HHHHHHhccCCccCCceEEEEechhh--cCHHHHHHHHHHhcCCCcCcEEEEEECC
Confidence            33444444455567899999999998  6777777777777765566555555543

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=92.83  E-value=0.051  Score=50.02  Aligned_cols=17  Identities=35%  Similarity=0.440  Sum_probs=14.8

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      .|+++.||||||||+.+
T Consensus        98 SNILLiGPTGsGKTlLA  114 (408)
T COG1219          98 SNILLIGPTGSGKTLLA  114 (408)
T ss_pred             ccEEEECCCCCcHHHHH
Confidence            58999999999999554

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=92.79  E-value=0.61  Score=49.40  Aligned_cols=41  Identities=22%  Similarity=0.208  Sum_probs=25.4

Q ss_pred             cccccchhhHHHHHHhhhc--CC---CCCcEEEecCCCCCccchhh
Q psy496           47 VTQPRRISAIALINKCLTL--SP---ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~--~~---~~~~vli~apTGSGKT~~~~   87 (319)
                      .-|..++..+...-.....  ..   ....+++.||||+|||+.+-
T Consensus       568 ~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~  613 (852)
T TIGR03346       568 VGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAK  613 (852)
T ss_pred             CCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHH
Confidence            5577777776543222111  11   23468899999999997653

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.

>PRK10436 hypothetical protein; Provisional

Probab=92.74  E-value=0.1  Score=51.09  Aligned_cols=37  Identities=19%  Similarity=0.140  Sum_probs=24.6

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEec
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQ  109 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~  109 (319)
                      .+..++++||||||||+.. ..+++.+...    ..+|+.+.
T Consensus       217 ~~GliLvtGpTGSGKTTtL-~a~l~~~~~~----~~~i~TiE  253 (462)
T PRK10436        217 PQGLILVTGPTGSGKTVTL-YSALQTLNTA----QINICSVE  253 (462)
T ss_pred             cCCeEEEECCCCCChHHHH-HHHHHhhCCC----CCEEEEec
Confidence            4578999999999999875 3455554322    23566543

>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=92.72  E-value=0.19  Score=41.32  Aligned_cols=21  Identities=19%  Similarity=0.162  Sum_probs=17.6

Q ss_pred             CCCCCcEEEecCCCCCccchh
Q psy496           66 SPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~   86 (319)
                      ..+++.+.|.|++|||||+.+
T Consensus        22 i~~g~~~~i~G~nGsGKStll   42 (157)
T cd00267          22 LKAGEIVALVGPNGSGKSTLL   42 (157)
T ss_pred             EcCCCEEEEECCCCCCHHHHH
Confidence            456788999999999999654

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.

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=92.72  E-value=0.069  Score=49.70  Aligned_cols=39  Identities=21%  Similarity=0.154  Sum_probs=26.1

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHH
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRIS  114 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~l  114 (319)
                      .|++|+|.||||||+..     +.+...- ...-+|+++.-|.||
T Consensus       174 ~NILisGGTGSGKTTlL-----Nal~~~i-~~~eRvItiEDtaEL  212 (355)
T COG4962         174 CNILISGGTGSGKTTLL-----NALSGFI-DSDERVITIEDTAEL  212 (355)
T ss_pred             eeEEEeCCCCCCHHHHH-----HHHHhcC-CCcccEEEEeehhhh
Confidence            58999999999999653     2222211 112289998888776

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=92.66  E-value=0.49  Score=49.27  Aligned_cols=41  Identities=22%  Similarity=0.176  Sum_probs=25.4

Q ss_pred             cccccchhhHHHHHHhhhc--C---CCCCcEEEecCCCCCccchhh
Q psy496           47 VTQPRRISAIALINKCLTL--S---PILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~--~---~~~~~vli~apTGSGKT~~~~   87 (319)
                      .=|..++..+...-.....  .   ....+++++||||+|||..+-
T Consensus       461 iGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk  506 (758)
T PRK11034        461 FGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTV  506 (758)
T ss_pred             eCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHH
Confidence            4577777666543222111  1   122468999999999997763

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=92.64  E-value=0.055  Score=46.16  Aligned_cols=21  Identities=33%  Similarity=0.340  Sum_probs=18.0

Q ss_pred             CCCCCcEEEecCCCCCccchh
Q psy496           66 SPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.+++|+||||||||+.+
T Consensus        22 v~~g~~i~I~G~tGSGKTTll   42 (186)
T cd01130          22 VEARKNILISGGTGSGKTTLL   42 (186)
T ss_pred             HhCCCEEEEECCCCCCHHHHH
Confidence            445789999999999999875

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=92.63  E-value=0.13  Score=48.92  Aligned_cols=43  Identities=19%  Similarity=0.106  Sum_probs=27.6

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRI  113 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~  113 (319)
                      .+..++|+||||||||+.. ..+++.+....  +..+++.+.-..|
T Consensus       148 ~~GlilI~G~TGSGKTT~l-~al~~~i~~~~--~~~~IvtiEdp~E  190 (372)
T TIGR02525       148 AAGLGLICGETGSGKSTLA-ASIYQHCGETY--PDRKIVTYEDPIE  190 (372)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHHhcC--CCceEEEEecCch
Confidence            4568999999999999876 44555554321  1236777544434

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=92.63  E-value=0.19  Score=52.23  Aligned_cols=58  Identities=22%  Similarity=0.216  Sum_probs=43.0

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      .+.++|.|..|||||.+...=+...+...+ -..-+|+++.-|+.+|..+.+++.+..+
T Consensus        17 ~g~~lV~AgaGSGKT~~l~~ria~Li~~~~-i~P~~IL~lTFT~kAA~em~~Rl~~~~~   74 (726)
T TIGR01073        17 EGPLLIMAGAGSGKTRVLTHRIAHLIAEKN-VAPWNILAITFTNKAAREMKERVEKLLG   74 (726)
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHHHHHcCC-CCHHHeeeeeccHHHHHHHHHHHHHHhc
Confidence            467999999999999887665554443222 2234788888999999999988887654

Designed to identify pcrA members of the uvrD/rep subfamily.

>KOG0391|consensus

Probab=92.63  E-value=0.16  Score=53.89  Aligned_cols=136  Identities=16%  Similarity=0.158  Sum_probs=72.5

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEE--EEEe--
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVG--YQIR--  142 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg--~~~~--  142 (319)
                      .+|=|-|+.-+-|=|||..-.- ++.++.. +++.++--|++.||-.+-+     |.-+++..+  .|..+-  |...  
T Consensus       632 eknlNGILADEmGLGKTIQtIS-llAhLAC-eegnWGPHLIVVpTsviLn-----WEMElKRwc--PglKILTYyGs~kE  702 (1958)
T KOG0391|consen  632 EKNLNGILADEMGLGKTIQTIS-LLAHLAC-EEGNWGPHLIVVPTSVILN-----WEMELKRWC--PGLKILTYYGSHKE  702 (1958)
T ss_pred             HhcccceehhhhcccchhHHHH-HHHHHHh-cccCCCCceEEeechhhhh-----hhHHHhhhC--CcceEeeecCCHHH
Confidence            3566789999999999977543 3334333 3344444444448855422     222222111  022221  1111  


Q ss_pred             -cccccCC---CCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          143 -LEKELPR---KRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       143 -~~~~~~~---~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                       -+....+   +..|++|+++..+++-+..-. -.++.++|+||+|..   ..+-..++..+...+.. |.+++..|.
T Consensus       703 rkeKRqgW~kPnaFHVCItSYklv~qd~~AFk-rkrWqyLvLDEaqnI---KnfksqrWQAllnfnsq-rRLLLtgTP  775 (1958)
T KOG0391|consen  703 RKEKRQGWAKPNAFHVCITSYKLVFQDLTAFK-RKRWQYLVLDEAQNI---KNFKSQRWQALLNFNSQ-RRLLLTGTP  775 (1958)
T ss_pred             HHHHhhcccCCCeeEEeehhhHHHHhHHHHHH-hhccceeehhhhhhh---cchhHHHHHHHhccchh-heeeecCCc
Confidence             1111111   234899999988876662211 146889999999972   22333444445444433 567777776

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=92.57  E-value=1  Score=41.74  Aligned_cols=44  Identities=20%  Similarity=0.284  Sum_probs=30.1

Q ss_pred             cCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          168 SDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       168 ~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      ..|...+.+++||||+|.  +..+..-.+++.+...+++..+|+.+
T Consensus        87 ~~p~~~~~kv~iI~~ad~--m~~~a~naLLK~LEepp~~t~~il~~  130 (313)
T PRK05564         87 KKPYEGDKKVIIIYNSEK--MTEQAQNAFLKTIEEPPKGVFIILLC  130 (313)
T ss_pred             cCcccCCceEEEEechhh--cCHHHHHHHHHHhcCCCCCeEEEEEe
Confidence            456678899999999998  55555666677666655555455443

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=92.53  E-value=0.17  Score=45.56  Aligned_cols=54  Identities=20%  Similarity=0.177  Sum_probs=36.1

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      -.+.+.+++|.|++|||||......+.+.+....     .++++ .+.+...++.+.+..
T Consensus        19 G~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge-----~vlyv-s~~e~~~~l~~~~~~   72 (260)
T COG0467          19 GLPRGSVVLITGPPGTGKTIFALQFLYEGAREGE-----PVLYV-STEESPEELLENARS   72 (260)
T ss_pred             CCcCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCC-----cEEEE-EecCCHHHHHHHHHH
Confidence            3578899999999999999888887776654422     23332 445555555554443

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=92.53  E-value=0.069  Score=49.51  Aligned_cols=21  Identities=38%  Similarity=0.327  Sum_probs=18.2

Q ss_pred             CCCCCcEEEecCCCCCccchh
Q psy496           66 SPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.+++|+||||||||+..
T Consensus       141 v~~~~~ili~G~tGsGKTTll  161 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTFL  161 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHHH
Confidence            446789999999999999865

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.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=92.51  E-value=0.094  Score=54.02  Aligned_cols=30  Identities=27%  Similarity=0.263  Sum_probs=24.4

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchhhHHH
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQVPQFI   90 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~~l~i   90 (319)
                      +.+..+.+.+-++|+||.|+|||+....+.
T Consensus        29 ~~L~~~~~~RL~li~APAGfGKttl~aq~~   58 (894)
T COG2909          29 DRLRRANDYRLILISAPAGFGKTTLLAQWR   58 (894)
T ss_pred             HHHhcCCCceEEEEeCCCCCcHHHHHHHHH
Confidence            456667777889999999999998876654

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=92.51  E-value=0.18  Score=50.98  Aligned_cols=51  Identities=12%  Similarity=0.004  Sum_probs=39.4

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ...+++++.||||||||..+.+|-+-..  .     ..++++-|.-|+....+...++
T Consensus       156 ~g~~hvLviapTgSGKg~g~VIPnLL~~--~-----~S~VV~DpKGEl~~~Ta~~R~~  206 (606)
T PRK13897        156 DGFQHALLFAPTGSGKGVGFVIPNLLFW--E-----DSVVVHDIKLENYELTSGWREK  206 (606)
T ss_pred             cCCceEEEEcCCCCCcceEEehhhHHhC--C-----CCEEEEeCcHHHHHHHHHHHHH
Confidence            3457899999999999999999976531  1     2688888999998777764443

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=92.45  E-value=0.15  Score=48.27  Aligned_cols=28  Identities=29%  Similarity=0.348  Sum_probs=21.3

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEI   95 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~   95 (319)
                      ..+..++|+||||||||+.. ..++..+.
T Consensus       132 ~~~glilI~GpTGSGKTTtL-~aLl~~i~  159 (358)
T TIGR02524       132 PQEGIVFITGATGSGKSTLL-AAIIRELA  159 (358)
T ss_pred             ccCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            35789999999999999876 44555443

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.

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=92.42  E-value=0.087  Score=50.29  Aligned_cols=46  Identities=15%  Similarity=0.104  Sum_probs=34.6

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      ++++.||||||||..+.+|-+-.  .     ...++++-|.-++....+....
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~--~-----~~s~vv~D~Kge~~~~t~~~r~   46 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLT--W-----PGSVVVLDPKGENFELTSEHRR   46 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhc--C-----CCCEEEEccchhHHHHHHHHHH
Confidence            47899999999999998876532  1     1378888899998876665443

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.

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=92.41  E-value=0.056  Score=42.25  Aligned_cols=17  Identities=35%  Similarity=0.468  Sum_probs=14.3

Q ss_pred             EEEecCCCCCccchhhH
Q psy496           72 SIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        72 vli~apTGSGKT~~~~l   88 (319)
                      ++|+|++|||||+..-.
T Consensus         2 I~I~G~~gsGKST~a~~   18 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKE   18 (121)
T ss_dssp             EEEEESTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            78999999999977633

...

>KOG0920|consensus

Probab=92.40  E-value=0.026  Score=58.91  Aligned_cols=54  Identities=57%  Similarity=1.010  Sum_probs=49.1

Q ss_pred             hhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCccccccccchHhHHHHhHhhc
Q psy496          252 TRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRTLK  305 (319)
Q Consensus       252 ~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v~~~~~~~~~~~~~~~~  305 (319)
                      .+++++.++|+.+++++.+...++|...+-+|||.|||.++|+||++.+++-..
T Consensus       316 ~~p~LkvILMSAT~dae~fs~YF~~~pvi~i~grtfpV~~~fLEDil~~~~~~~  369 (924)
T KOG0920|consen  316 RNPDLKVILMSATLDAELFSDYFGGCPVITIPGRTFPVKEYFLEDILSKTGYVS  369 (924)
T ss_pred             hCCCceEEEeeeecchHHHHHHhCCCceEeecCCCcchHHHHHHHHHHHhcccc
Confidence            368899999999999999999899999999999999999999999999995433

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=92.33  E-value=0.51  Score=48.83  Aligned_cols=117  Identities=21%  Similarity=0.281  Sum_probs=59.1

Q ss_pred             cccccchhhHHHHHHhh--hcCC---CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHH
Q psy496           47 VTQPRRISAIALINKCL--TLSP---ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l--~~~~---~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      .=|..|+.++...-..-  +...   .-.+.+..||||.|||...- .+.+.+....   ...|=+  -+-|--.  ...
T Consensus       494 iGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAk-aLA~~Lfg~e---~aliR~--DMSEy~E--kHs  565 (786)
T COG0542         494 IGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAK-ALAEALFGDE---QALIRI--DMSEYME--KHS  565 (786)
T ss_pred             eChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHH-HHHHHhcCCC---ccceee--chHHHHH--HHH
Confidence            44777777765422211  1111   22468889999999997652 2333333322   122222  3333211  122


Q ss_pred             HHHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHH
Q psy496          122 VAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILK  198 (319)
Q Consensus       122 ~~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~  198 (319)
                      ++++.|....|    |||..                 -|.|.+..+.+|    +++|.+||+..  .+.+++--.+.
T Consensus       566 VSrLIGaPPGY----VGyee-----------------GG~LTEaVRr~P----ySViLlDEIEK--AHpdV~nilLQ  615 (786)
T COG0542         566 VSRLIGAPPGY----VGYEE-----------------GGQLTEAVRRKP----YSVILLDEIEK--AHPDVFNLLLQ  615 (786)
T ss_pred             HHHHhCCCCCC----ceecc-----------------ccchhHhhhcCC----CeEEEechhhh--cCHHHHHHHHH
Confidence            45555544432    22111                 123455555544    78999999998  55554443333

>PRK13764 ATPase; Provisional

Probab=92.29  E-value=0.14  Score=51.58  Aligned_cols=42  Identities=17%  Similarity=0.071  Sum_probs=27.0

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRIS  114 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~l  114 (319)
                      ...+++|+||||||||+.. ..+++.+...+    ..|+.+.-.+|+
T Consensus       256 ~~~~ILIsG~TGSGKTTll-~AL~~~i~~~~----riV~TiEDp~El  297 (602)
T PRK13764        256 RAEGILIAGAPGAGKSTFA-QALAEFYADMG----KIVKTMESPRDL  297 (602)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHhhCC----CEEEEECCCccc
Confidence            4578999999999999865 44555554322    234455444454

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=92.23  E-value=0.45  Score=45.35  Aligned_cols=50  Identities=22%  Similarity=0.068  Sum_probs=30.9

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      ...+..++|.|++|+|||+.....+.+.. ..+    .+++|+.-. +-..|+..+
T Consensus        79 i~~GslvLI~G~pG~GKStLllq~a~~~a-~~g----~~VlYvs~E-Es~~qi~~R  128 (372)
T cd01121          79 LVPGSVILIGGDPGIGKSTLLLQVAARLA-KRG----GKVLYVSGE-ESPEQIKLR  128 (372)
T ss_pred             ccCCeEEEEEeCCCCCHHHHHHHHHHHHH-hcC----CeEEEEECC-cCHHHHHHH
Confidence            45578899999999999987766544332 221    267776432 333455443

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.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=92.22  E-value=0.067  Score=52.18  Aligned_cols=29  Identities=24%  Similarity=0.205  Sum_probs=20.5

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIA   96 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~   96 (319)
                      ..+.-++++||||||||+.. ..+++.+..
T Consensus       256 ~p~GliLvTGPTGSGKTTTL-Y~~L~~ln~  284 (500)
T COG2804         256 RPQGLILVTGPTGSGKTTTL-YAALSELNT  284 (500)
T ss_pred             CCCeEEEEeCCCCCCHHHHH-HHHHHHhcC
Confidence            34577999999999999774 344444443

>PTZ00293 thymidine kinase; Provisional

Probab=92.21  E-value=0.28  Score=42.86  Aligned_cols=38  Identities=18%  Similarity=0.112  Sum_probs=24.6

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEeccc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPR  111 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Pt  111 (319)
                      +.-.+++||-+||||+-.+..+.+....+.     +++++.|.
T Consensus         4 G~i~vi~GpMfSGKTteLLr~i~~y~~ag~-----kv~~~kp~   41 (211)
T PTZ00293          4 GTISVIIGPMFSGKTTELMRLVKRFTYSEK-----KCVVIKYS   41 (211)
T ss_pred             eEEEEEECCCCChHHHHHHHHHHHHHHcCC-----ceEEEEec
Confidence            345788999999999877665544433322     45554464

>KOG0058|consensus

Probab=92.13  E-value=0.074  Score=53.82  Aligned_cols=36  Identities=14%  Similarity=-0.041  Sum_probs=27.4

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHh
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIAR   97 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~   97 (319)
                      +++-...+.++++-++||.|||||+++.+  +.+++..
T Consensus       485 k~lsfti~pGe~vALVGPSGsGKSTiasL--L~rfY~P  520 (716)
T KOG0058|consen  485 KNLSFTIRPGEVVALVGPSGSGKSTIASL--LLRFYDP  520 (716)
T ss_pred             cCceeeeCCCCEEEEECCCCCCHHHHHHH--HHHhcCC
Confidence            35556677899999999999999988744  4555543

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=92.07  E-value=0.13  Score=46.36  Aligned_cols=30  Identities=27%  Similarity=0.264  Sum_probs=23.8

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEI   95 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~   95 (319)
                      .+.+..++|+|++|||||+.....+.+.+.
T Consensus        33 ip~gs~~lI~G~pGtGKT~l~~qf~~~~a~   62 (259)
T TIGR03878        33 IPAYSVINITGVSDTGKSLMVEQFAVTQAS   62 (259)
T ss_pred             eECCcEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            456788999999999999888776665543

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=92.00  E-value=1.1  Score=47.56  Aligned_cols=27  Identities=22%  Similarity=0.320  Sum_probs=21.3

Q ss_pred             hcCCCCCcEEEecCCCCCccchhhHHH
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQVPQFI   90 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~~l~i   90 (319)
                      ........++|+||.|.|||+....++
T Consensus        27 ~~~~~~~~~~v~apaG~GKTtl~~~~~   53 (903)
T PRK04841         27 SGANNYRLVLVTSPAGYGKTTLISQWA   53 (903)
T ss_pred             hcccCCCeEEEECCCCCCHHHHHHHHH
Confidence            334456789999999999999886655

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=91.93  E-value=0.12  Score=51.93  Aligned_cols=26  Identities=23%  Similarity=0.188  Sum_probs=20.1

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      .+..++++||||||||+.. ..+++.+
T Consensus       315 ~~Glilv~G~tGSGKTTtl-~a~l~~~  340 (564)
T TIGR02538       315 PQGMVLVTGPTGSGKTVSL-YTALNIL  340 (564)
T ss_pred             cCCeEEEECCCCCCHHHHH-HHHHHhh
Confidence            4578999999999999885 4455554

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=91.91  E-value=0.21  Score=44.14  Aligned_cols=33  Identities=15%  Similarity=-0.103  Sum_probs=24.7

Q ss_pred             hcCCCCCcEEEecCCCCCccchhhHHHHHHHHH
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQVPQFILDDEIA   96 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~   96 (319)
                      .-.+.++.++|+|++|+|||+.....+.+....
T Consensus         8 ~Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~   40 (242)
T cd00984           8 GGLQPGDLIIIAARPSMGKTAFALNIAENIAKK   40 (242)
T ss_pred             cCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence            334567889999999999998776666655444

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.

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=91.88  E-value=0.56  Score=39.25  Aligned_cols=23  Identities=22%  Similarity=0.150  Sum_probs=19.0

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.++.+.|.||.|||||+.+
T Consensus        23 ~~i~~G~~~~l~G~nGsGKstLl   45 (171)
T cd03228          23 LTIKPGEKVAIVGPSGSGKSTLL   45 (171)
T ss_pred             EEEcCCCEEEEECCCCCCHHHHH
Confidence            34567889999999999999654

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). 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.

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=91.80  E-value=0.13  Score=49.62  Aligned_cols=44  Identities=27%  Similarity=0.289  Sum_probs=29.0

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAI  116 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~  116 (319)
                      .+++++|.|+||||||..+.. ++..+...+    .++++.-|..++..
T Consensus        41 ~~~h~~i~g~tGsGKt~~i~~-l~~~~~~~~----~~~vi~D~kg~~~~   84 (410)
T cd01127          41 EEAHTMIIGTTGTGKTTQIRE-LLASIRARG----DRAIIYDPNGGFVS   84 (410)
T ss_pred             hhccEEEEcCCCCCHHHHHHH-HHHHHHhcC----CCEEEEeCCcchhH
Confidence            457899999999999986433 344443322    25677677766543

TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=91.77  E-value=0.2  Score=43.36  Aligned_cols=29  Identities=21%  Similarity=0.227  Sum_probs=22.6

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      .+.++.+.|+||+|||||......+.+..
T Consensus         9 i~~g~i~~i~G~~GsGKT~l~~~~~~~~~   37 (209)
T TIGR02237         9 VERGTITQIYGPPGSGKTNICMILAVNAA   37 (209)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            35678899999999999988766655443

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=91.69  E-value=0.19  Score=51.47  Aligned_cols=50  Identities=12%  Similarity=-0.017  Sum_probs=37.7

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      ..++++++.||||||||..+.+|-+-.  ..     ..++++-|.-|+....+...+
T Consensus       137 ~~~~hvlviApTgSGKgvg~VIPnLL~--~~-----gS~VV~DpKGE~~~~Ta~~R~  186 (670)
T PRK13850        137 GEQPHSLVVAPTRAGKGVGVVIPTLLT--FK-----GSVIALDVKGELFELTSRARK  186 (670)
T ss_pred             CCCceEEEEecCCCCceeeehHhHHhc--CC-----CCEEEEeCCchHHHHHHHHHH
Confidence            445789999999999999998886543  11     268888899998776665443

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=91.60  E-value=0.081  Score=41.45  Aligned_cols=17  Identities=35%  Similarity=0.272  Sum_probs=14.2

Q ss_pred             EEEecCCCCCccchhhH
Q psy496           72 SIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        72 vli~apTGSGKT~~~~l   88 (319)
                      ++|+|++|||||+..-.
T Consensus         1 I~i~G~~GsGKtTia~~   17 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKE   17 (129)
T ss_dssp             EEEEESTTSSHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHH
Confidence            57999999999987633

...

>KOG1970|consensus

Probab=91.54  E-value=0.2  Score=49.29  Aligned_cols=59  Identities=15%  Similarity=0.160  Sum_probs=34.2

Q ss_pred             ccchHHHhccCCccccccccccchhhHHHHHHhhh---cCCCCCcEEEecCCCCCccchhhH
Q psy496           30 ILDDEIARNRGSECCIMVTQPRRISAIALINKCLT---LSPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~---~~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      -.+.|++........-..+..+-|..+.+--+.++   ....++.++|+||+|||||++.-.
T Consensus        68 ~~elW~eKy~P~t~eeLAVHkkKI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkv  129 (634)
T KOG1970|consen   68 EFELWVEKYKPRTLEELAVHKKKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKV  129 (634)
T ss_pred             ccchhHHhcCcccHHHHhhhHHhHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHH
Confidence            35567676554433333445554444433222222   223566899999999999998744

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=91.36  E-value=0.088  Score=42.33  Aligned_cols=16  Identities=31%  Similarity=0.466  Sum_probs=13.8

Q ss_pred             EEEecCCCCCccchhh
Q psy496           72 SIIYTSTGCGKTTQVP   87 (319)
Q Consensus        72 vli~apTGSGKT~~~~   87 (319)
                      ++++|++|||||+.+-
T Consensus         2 ii~~G~pgsGKSt~a~   17 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAK   17 (143)
T ss_dssp             EEEEESTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            7899999999997753

...

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=91.31  E-value=0.26  Score=51.51  Aligned_cols=63  Identities=17%  Similarity=0.126  Sum_probs=44.1

Q ss_pred             CceEEEECchHHHHHH-hcCCCCCCccEEEEeccccc-ccchh-HHHHHHHhhhccccCceEEEecccc
Q psy496          151 RGSILYCTAGILPEVM-QSDPILSGVSHIVMDEIHER-SMISD-FLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       151 ~~~Iiv~Tpg~ll~~l-~~~~~l~~v~~vViDEah~~-~~~~~-~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      ++.|+++||.+|..-+ .+...+..+..+|+||||+. +-..+ +...+.   ...++..-+.+|||.+
T Consensus         7 ~ggi~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~~~~eaFI~rly---r~~n~~gfIkafSdsP   72 (814)
T TIGR00596         7 EGGIFSITSRILVVDLLTGIIPPELITGILVLRADRIIESSQEAFILRLY---RQKNKTGFIKAFSDNP   72 (814)
T ss_pred             cCCEEEEechhhHhHHhcCCCCHHHccEEEEeecccccccccHHHHHHHH---HHhCCCcceEEecCCC
Confidence            4569999999996555 66667999999999999972 12222 333222   2334456789999998

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

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=91.23  E-value=0.51  Score=42.98  Aligned_cols=39  Identities=26%  Similarity=0.378  Sum_probs=23.3

Q ss_pred             chHHHHHHhcCCCCCCccEEEEecccccccch-hHHHHHHHhh
Q psy496          159 AGILPEVMQSDPILSGVSHIVMDEIHERSMIS-DFLLAILKDV  200 (319)
Q Consensus       159 pg~ll~~l~~~~~l~~v~~vViDEah~~~~~~-~~~~~~l~~~  200 (319)
                      ||-|...+.   .|+.-+++.|||+|+.+... +.+...++..
T Consensus        91 ~gDlaaiLt---~Le~~DVLFIDEIHrl~~~vEE~LYpaMEDf  130 (332)
T COG2255          91 PGDLAAILT---NLEEGDVLFIDEIHRLSPAVEEVLYPAMEDF  130 (332)
T ss_pred             hhhHHHHHh---cCCcCCeEEEehhhhcChhHHHHhhhhhhhe
Confidence            444555553   25677899999999844333 3444554443

>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=91.19  E-value=0.4  Score=40.19  Aligned_cols=22  Identities=23%  Similarity=0.145  Sum_probs=18.5

Q ss_pred             cCCCCCcEEEecCCCCCccchh
Q psy496           65 LSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ....++.+.|.||+|||||+.+
T Consensus        24 ~i~~Ge~~~i~G~nGsGKStLl   45 (173)
T cd03246          24 SIEPGESLAIIGPSGSGKSTLA   45 (173)
T ss_pred             EECCCCEEEEECCCCCCHHHHH
Confidence            3567889999999999999754

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

>KOG2373|consensus

Probab=91.18  E-value=0.51  Score=44.09  Aligned_cols=113  Identities=15%  Similarity=0.130  Sum_probs=56.5

Q ss_pred             hhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH-hccccCCCCceEEEE
Q psy496           62 CLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE-RDEQCGRPGSSVGYQ  140 (319)
Q Consensus        62 ~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~-~~~~~~~~g~~vg~~  140 (319)
                      ++.-...++-.+++||||||||+...-+.++....+-....+..=+  |..-||.-...+++.. +....      -.|.
T Consensus       266 ~LkGhR~GElTvlTGpTGsGKTTFlsEYsLDL~~QGVnTLwgSFEi--~n~rla~~mL~Qyagyrl~drl------~~y~  337 (514)
T KOG2373|consen  266 YLKGHRPGELTVLTGPTGSGKTTFLSEYSLDLFTQGVNTLWGSFEI--PNKRLAHWMLVQYAGYRLLDRL------NSYK  337 (514)
T ss_pred             HhccCCCCceEEEecCCCCCceeEehHhhHHHHhhhhhheeeeeec--chHHHHHHHHHHHccCchHhhh------hhhh
Confidence            4444556778999999999999987777666443322211222222  4444444333323221 00000      0000


Q ss_pred             EecccccCCCCceEEEECc------hHHHHHHhcCCCCCCccEEEEecccc
Q psy496          141 IRLEKELPRKRGSILYCTA------GILPEVMQSDPILSGVSHIVMDEIHE  185 (319)
Q Consensus       141 ~~~~~~~~~~~~~Iiv~Tp------g~ll~~l~~~~~l~~v~~vViDEah~  185 (319)
                      -+.+.   .++....++|-      ...++.+.......++.+||||...-
T Consensus       338 HWadr---FErlplyfmtfhgqq~~~~vi~~i~ha~yV~di~HViIDNLQF  385 (514)
T KOG2373|consen  338 HWADR---FERLPLYFMTFHGQQFMEKVINEIAHAIYVEDIQHVIIDNLQF  385 (514)
T ss_pred             HHHHH---HhccchHhhhhcccchHHHHHHHHHHHHHHHhhhhhhhhhHHH
Confidence            11000   02223444442      22344554445577899999999884

>TIGR00763 lon ATP-dependent protease La

Probab=91.16  E-value=0.37  Score=50.46  Aligned_cols=19  Identities=21%  Similarity=0.085  Sum_probs=15.7

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      .+..+++.||+|+|||+.+
T Consensus       346 ~~~~lll~GppG~GKT~lA  364 (775)
T TIGR00763       346 KGPILCLVGPPGVGKTSLG  364 (775)
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            4457999999999999665

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=91.15  E-value=1  Score=43.28  Aligned_cols=37  Identities=24%  Similarity=0.412  Sum_probs=23.5

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEe
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVT  108 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~  108 (319)
                      ...++|+||+|+|||-..-.+.- ....  .++.++++++
T Consensus       113 ~nplfi~G~~GlGKTHLl~Aign-~~~~--~~~~a~v~y~  149 (408)
T COG0593         113 YNPLFIYGGVGLGKTHLLQAIGN-EALA--NGPNARVVYL  149 (408)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHH-HHHh--hCCCceEEec
Confidence            56799999999999965433322 2222  2345677773

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=91.14  E-value=1  Score=43.15  Aligned_cols=27  Identities=26%  Similarity=0.307  Sum_probs=21.6

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchhh
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~~   87 (319)
                      .+-.-++.+..|+|.|+||+||+..+-
T Consensus        93 qik~~ap~~~~vLi~GetGtGKel~A~  119 (403)
T COG1221          93 QIKAYAPSGLPVLIIGETGTGKELFAR  119 (403)
T ss_pred             HHHhhCCCCCcEEEecCCCccHHHHHH
Confidence            333457788999999999999997663

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=91.13  E-value=0.097  Score=47.66  Aligned_cols=21  Identities=24%  Similarity=0.420  Sum_probs=17.6

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      .++.++++||+|||||...--
T Consensus        32 ~~~pvLl~G~~GtGKT~li~~   52 (272)
T PF12775_consen   32 NGRPVLLVGPSGTGKTSLIQN   52 (272)
T ss_dssp             CTEEEEEESSTTSSHHHHHHH
T ss_pred             cCCcEEEECCCCCchhHHHHh
Confidence            468899999999999976543

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=91.09  E-value=0.23  Score=50.73  Aligned_cols=46  Identities=15%  Similarity=-0.020  Sum_probs=35.3

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAE  120 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~  120 (319)
                      ..+++++.||||||||..+.+|.+-.  .     ...++++-|..|+....+.
T Consensus       174 g~~HvlviapTgSGKgvg~ViPnLL~--~-----~~S~VV~D~KGE~~~~Tag  219 (636)
T PRK13880        174 GPEHVLTYAPTRSGKGVGLVVPTLLS--W-----GHSSVITDLKGELWALTAG  219 (636)
T ss_pred             CCceEEEEecCCCCCceEEEccchhh--C-----CCCEEEEeCcHHHHHHHHH
Confidence            45789999999999999998887642  1     1268888899998655554

>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=91.06  E-value=0.55  Score=39.58  Aligned_cols=22  Identities=18%  Similarity=0.148  Sum_probs=18.5

Q ss_pred             cCCCCCcEEEecCCCCCccchh
Q psy496           65 LSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ....++.+.|.||.|||||+.+
T Consensus        22 ~i~~G~~~~i~G~nGsGKSTLl   43 (178)
T cd03229          22 NIEAGEIVALLGPSGSGKSTLL   43 (178)
T ss_pred             EEcCCCEEEEECCCCCCHHHHH
Confidence            4567889999999999999754

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.

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=91.06  E-value=1.5  Score=39.68  Aligned_cols=16  Identities=31%  Similarity=0.542  Sum_probs=14.3

Q ss_pred             CcEEEecCCCCCccch
Q psy496           70 SPSIIYTSTGCGKTTQ   85 (319)
Q Consensus        70 ~~vli~apTGSGKT~~   85 (319)
                      +||+..||+|+|||..
T Consensus       152 knVLFyGppGTGKTm~  167 (368)
T COG1223         152 KNVLFYGPPGTGKTMM  167 (368)
T ss_pred             ceeEEECCCCccHHHH
Confidence            7899999999999943

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=91.04  E-value=0.11  Score=46.89  Aligned_cols=29  Identities=24%  Similarity=0.238  Sum_probs=22.2

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhH
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      +.++.....+.++++.||+|+|||..+..
T Consensus        12 ~~~l~~l~~g~~vLL~G~~GtGKT~lA~~   40 (262)
T TIGR02640        12 SRALRYLKSGYPVHLRGPAGTGKTTLAMH   40 (262)
T ss_pred             HHHHHHHhcCCeEEEEcCCCCCHHHHHHH
Confidence            34455556678999999999999977643

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=91.04  E-value=0.093  Score=42.18  Aligned_cols=18  Identities=33%  Similarity=0.569  Sum_probs=15.0

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      +|+|.||+|+|||..+-.
T Consensus         1 ~vlL~G~~G~GKt~l~~~   18 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARE   18 (139)
T ss_dssp             EEEEEESSSSSHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHH
Confidence            489999999999976643

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=90.95  E-value=0.26  Score=43.23  Aligned_cols=30  Identities=20%  Similarity=0.055  Sum_probs=23.5

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      -.+.+..++|.|++|||||+.....+.+.+
T Consensus        16 Gi~~G~~~~i~G~~G~GKT~l~~~~~~~~~   45 (229)
T TIGR03881        16 GIPRGFFVAVTGEPGTGKTIFCLHFAYKGL   45 (229)
T ss_pred             CCcCCeEEEEECCCCCChHHHHHHHHHHHH
Confidence            356788999999999999987766555544

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.

>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=90.93  E-value=0.11  Score=40.88  Aligned_cols=16  Identities=31%  Similarity=0.407  Sum_probs=13.6

Q ss_pred             EEEecCCCCCccchhh
Q psy496           72 SIIYTSTGCGKTTQVP   87 (319)
Q Consensus        72 vli~apTGSGKT~~~~   87 (319)
                      +++.||+|+|||+.+-
T Consensus         1 ill~G~~G~GKT~l~~   16 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLAR   16 (132)
T ss_dssp             EEEESSTTSSHHHHHH
T ss_pred             CEEECcCCCCeeHHHH
Confidence            6899999999997653

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 ....

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=90.90  E-value=0.45  Score=48.78  Aligned_cols=71  Identities=17%  Similarity=0.115  Sum_probs=46.3

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++-.|..+|..+.++-.     ...+..++.|-||||||..... +++..   +    ..+|+++|.+.+|.|+++.+..
T Consensus        10 ~~~~Q~~ai~~l~~~~~-----~~~~~~~l~Gvtgs~kt~~~a~-~~~~~---~----~p~Lvi~~n~~~A~ql~~el~~   76 (655)
T TIGR00631        10 PAGDQPKAIAKLVEGLT-----DGEKHQTLLGVTGSGKTFTMAN-VIAQV---N----RPTLVIAHNKTLAAQLYNEFKE   76 (655)
T ss_pred             CChHHHHHHHHHHHhhh-----cCCCcEEEECCCCcHHHHHHHH-HHHHh---C----CCEEEEECCHHHHHHHHHHHHH
Confidence            44457777766654331     1122446899999999976543 22221   1    1456666999999999999988


Q ss_pred             Hhcc
Q psy496          125 ERDE  128 (319)
Q Consensus       125 ~~~~  128 (319)
                      ++..
T Consensus        77 f~p~   80 (655)
T TIGR00631        77 FFPE   80 (655)
T ss_pred             hCCC
Confidence            8754

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

>PF10412 TrwB_AAD_bind: Type IV secretion-system coupling protein DNA-binding domain; InterPro: IPR019476 The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein

Probab=90.85  E-value=0.3  Score=46.79  Aligned_cols=45  Identities=24%  Similarity=0.237  Sum_probs=29.7

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIA  117 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q  117 (319)
                      ..+++++.|.||||||.+ +..++..+...+    -++++.-|.-+....
T Consensus        14 e~~~~li~G~~GsGKT~~-i~~ll~~~~~~g----~~~iI~D~kg~~~~~   58 (386)
T PF10412_consen   14 ENRHILIIGATGSGKTQA-IRHLLDQIRARG----DRAIIYDPKGEFTER   58 (386)
T ss_dssp             GGG-EEEEE-TTSSHHHH-HHHHHHHHHHTT-----EEEEEEETTHHHHH
T ss_pred             hhCcEEEECCCCCCHHHH-HHHHHHHHHHcC----CEEEEEECCchHHHH
Confidence            357799999999999974 456676665544    266666787665443

It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells []. This protein forms hexamers from six structurally very similar protomers []. This hexamer contains a central channel running from the cytosolic pole (formed by the all-alpha domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-alpha domain appears to be the DNA-binding domain of the structure. ; PDB: 1E9S_D 1E9R_F 1GKI_B 1GL7_G 1GL6_A.

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=90.80  E-value=0.41  Score=48.85  Aligned_cols=48  Identities=19%  Similarity=0.259  Sum_probs=32.8

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHH--HHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRI--SAIAIAE  120 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~--la~q~~~  120 (319)
                      ...+++|.|+||||||..+...+.+.+.. +    ..++++-|-..  +...+..
T Consensus       175 ~~~H~lv~G~TGsGKT~l~~~l~~q~i~~-g----~~viv~DpKgD~~l~~~~~~  224 (634)
T TIGR03743       175 RVGHTLVLGTTGVGKTRLAELLITQDIRR-G----DVVIVIDPKGDADLKRRMRA  224 (634)
T ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHHHHc-C----CeEEEEeCCCchHHHHHHHH
Confidence            45789999999999998875555444433 2    26788778754  4444443

Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.

>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=90.78  E-value=0.9  Score=38.48  Aligned_cols=16  Identities=31%  Similarity=0.397  Sum_probs=13.9

Q ss_pred             cEEEecCCCCCccchh
Q psy496           71 PSIIYTSTGCGKTTQV   86 (319)
Q Consensus        71 ~vli~apTGSGKT~~~   86 (319)
                      ..+|.||+|||||..+
T Consensus        24 ~~~i~G~NGsGKSnil   39 (178)
T cd03239          24 FNAIVGPNGSGKSNIV   39 (178)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            6789999999999764

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.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=90.70  E-value=0.33  Score=42.48  Aligned_cols=53  Identities=19%  Similarity=0.072  Sum_probs=33.0

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      .+.+..++|.|++|+|||......+.+.+....     .++++. +.+-..++.+++..
T Consensus        13 i~~g~~~li~G~~G~GKt~~~~~~~~~~~~~g~-----~~~y~s-~e~~~~~l~~~~~~   65 (224)
T TIGR03880        13 FPEGHVIVVIGEYGTGKTTFSLQFLYQGLKNGE-----KAMYIS-LEEREERILGYAKS   65 (224)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCC-----eEEEEE-CCCCHHHHHHHHHH
Confidence            456788999999999999877666655543322     444442 23334555554433

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.

>PHA02533 17 large terminase protein; Provisional

Probab=90.65  E-value=1.9  Score=43.21  Aligned_cols=136  Identities=18%  Similarity=0.098  Sum_probs=70.4

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecc-ccc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLE-KEL  147 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~-~~~  147 (319)
                      ++-.++..+=..|||+......+.......   ...+++++|++.-|..+.+++..........  ...+...... .-.
T Consensus        74 ~R~~ii~~aRq~GKStl~a~~al~~a~~~~---~~~v~i~A~~~~QA~~vF~~ik~~ie~~P~l--~~~~i~~~~~~~I~  148 (534)
T PHA02533         74 NRFNACNLSRQLGKTTVVAIFLLHYVCFNK---DKNVGILAHKASMAAEVLDRTKQAIELLPDF--LQPGIVEWNKGSIE  148 (534)
T ss_pred             CeEEEEEEcCcCChHHHHHHHHHHHHHhCC---CCEEEEEeCCHHHHHHHHHHHHHHHHhCHHH--hhcceeecCccEEE
Confidence            455678888899999888755544333322   3488888899999999888777554322100  0001000000 000


Q ss_pred             CCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          148 PRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       148 ~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      ...++.|.+.|.+.  +-.++    .+..++|+||+|...-..++..++...+.. ....+++.+|.+-
T Consensus       149 l~NGS~I~~lss~~--~t~rG----~~~~~liiDE~a~~~~~~e~~~ai~p~las-g~~~r~iiiSTp~  210 (534)
T PHA02533        149 LENGSKIGAYASSP--DAVRG----NSFAMIYIDECAFIPNFIDFWLAIQPVISS-GRSSKIIITSTPN  210 (534)
T ss_pred             eCCCCEEEEEeCCC--CccCC----CCCceEEEeccccCCCHHHHHHHHHHHHHc-CCCceEEEEECCC
Confidence            01233454444321  11111    256789999999732222344333333332 2234666666665

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=90.62  E-value=0.17  Score=45.80  Aligned_cols=41  Identities=22%  Similarity=0.155  Sum_probs=25.7

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRI  113 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~  113 (319)
                      ....++|+|+||||||+.. ..+++.+..    ...+++.+.-..|
T Consensus        79 ~~GlilisG~tGSGKTT~l-~all~~i~~----~~~~iitiEdp~E  119 (264)
T cd01129          79 PHGIILVTGPTGSGKTTTL-YSALSELNT----PEKNIITVEDPVE  119 (264)
T ss_pred             CCCEEEEECCCCCcHHHHH-HHHHhhhCC----CCCeEEEECCCce
Confidence            3467999999999999876 334444422    1236666544433

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=90.56  E-value=0.75  Score=41.19  Aligned_cols=28  Identities=18%  Similarity=0.023  Sum_probs=20.3

Q ss_pred             CCCCC-cEEEecCCCCCccchhhHHHHHHH
Q psy496           66 SPILS-PSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        66 ~~~~~-~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      ..+++ .+.++|+-|||||...- +++..+
T Consensus        47 i~d~qg~~~vtGevGsGKTv~~R-al~~s~   75 (269)
T COG3267          47 IADGQGILAVTGEVGSGKTVLRR-ALLASL   75 (269)
T ss_pred             HhcCCceEEEEecCCCchhHHHH-HHHHhc
Confidence            34455 89999999999998766 444433

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=90.53  E-value=2.1  Score=39.25  Aligned_cols=53  Identities=25%  Similarity=0.231  Sum_probs=39.4

Q ss_pred             HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          162 LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       162 ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      +.+.+...+.-...+++|||++|.  +..+..-++++.+...+++..++++|...
T Consensus        83 l~~~~~~~p~e~~~kv~ii~~ad~--mt~~AaNaLLK~LEEPp~~~~fiL~~~~~  135 (290)
T PRK05917         83 IKKQIWIHPYESPYKIYIIHEADR--MTLDAISAFLKVLEDPPQHGVIILTSAKP  135 (290)
T ss_pred             HHHHHhhCccCCCceEEEEechhh--cCHHHHHHHHHHhhcCCCCeEEEEEeCCh
Confidence            444444456667899999999998  67777778888887766677777776654

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=90.41  E-value=0.49  Score=52.13  Aligned_cols=124  Identities=14%  Similarity=0.153  Sum_probs=69.6

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL  147 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~  147 (319)
                      .+.+++|.|..|||||.+..--++..+...  ...-+++++.=|+.+|..+..++.+.+....   ..... ........
T Consensus        13 ~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~--~~~~~il~~tFt~~aa~e~~~ri~~~l~~~~---~~~p~-~~~L~~q~   86 (1232)
T TIGR02785        13 RGQNILVSASAGSGKTAVLVERIIKKILRG--VDIDRLLVVTFTNAAAREMKERIEEALQKAL---QQEPN-SKHLRRQL   86 (1232)
T ss_pred             CCCCEEEEecCCCcHHHHHHHHHHHHHhcC--CCHhhEEEEeccHHHHHHHHHHHHHHHHHHH---hcCch-hHHHHHHH
Confidence            467899999999999988766666655432  1123577877999999999888887765432   10000 00000000


Q ss_pred             CCCCceEEEECchHHH-HHHhcCCCCCCc--cEEEEecccccccchhHHHHHHH
Q psy496          148 PRKRGSILYCTAGILP-EVMQSDPILSGV--SHIVMDEIHERSMISDFLLAILK  198 (319)
Q Consensus       148 ~~~~~~Iiv~Tpg~ll-~~l~~~~~l~~v--~~vViDEah~~~~~~~~~~~~l~  198 (319)
                       ..-...-|+|-..+. +.++.....-++  .+=|.||....-+..+.+..++.
T Consensus        87 -~~~~~~~i~Tihsf~~~~~~~~~~~l~ldP~F~i~de~e~~ll~~e~~~~~~e  139 (1232)
T TIGR02785        87 -ALLNTANISTLHSFCLKVIRKHYYLLDLDPSFRILTDTEQLLLIKEVVDDVFE  139 (1232)
T ss_pred             -hhccCCeEeeHHHHHHHHHHHhhhhcCCCCCceeCCHHHHHHHHHHHHHHHHH
Confidence             011225577865554 444443322222  44568888753333444444443

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.

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=90.28  E-value=0.53  Score=39.92  Aligned_cols=58  Identities=21%  Similarity=0.144  Sum_probs=31.9

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhC-----CCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARN-----RGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~-----~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      +.++.+++.|++|+|||+.....+........     .....+|+++..--. ..++.+++...
T Consensus        30 ~~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~   92 (193)
T PF13481_consen   30 PRGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRAL   92 (193)
T ss_dssp             -TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHH
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHH
Confidence            35678999999999999887666655442110     012457777644322 34555555544

>cd01394 radB RadB

Probab=90.27  E-value=0.33  Score=42.28  Aligned_cols=30  Identities=20%  Similarity=0.222  Sum_probs=23.5

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      -.+.+..++|+|++|||||+.....+.+..
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~~a~~~~   44 (218)
T cd01394          15 GVERGTVTQVYGPPGTGKTNIAIQLAVETA   44 (218)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            345678899999999999988777665543

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=90.26  E-value=0.14  Score=47.12  Aligned_cols=19  Identities=21%  Similarity=0.244  Sum_probs=15.5

Q ss_pred             CCcEEEecCCCCCccchhh
Q psy496           69 LSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~   87 (319)
                      +..++|+||||||||....
T Consensus         4 ~~ii~I~GpTasGKS~LAl   22 (300)
T PRK14729          4 NKIVFIFGPTAVGKSNILF   22 (300)
T ss_pred             CcEEEEECCCccCHHHHHH
Confidence            4568999999999996553

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=90.22  E-value=0.34  Score=42.77  Aligned_cols=31  Identities=26%  Similarity=0.257  Sum_probs=24.2

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEI   95 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~   95 (319)
                      =.+.+..++|.|++|||||+.....+.+.+.
T Consensus        21 G~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~   51 (234)
T PRK06067         21 GIPFPSLILIEGDHGTGKSVLSQQFVYGALK   51 (234)
T ss_pred             CCcCCcEEEEECCCCCChHHHHHHHHHHHHh
Confidence            3567788999999999999887776665543

>KOG0741|consensus

Probab=90.07  E-value=2.1  Score=42.31  Aligned_cols=48  Identities=10%  Similarity=-0.002  Sum_probs=31.5

Q ss_pred             hHHHHHHhhhcCCCCC-----cEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEE
Q psy496           55 AIALINKCLTLSPILS-----PSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMV  107 (319)
Q Consensus        55 ~~~~~~~~l~~~~~~~-----~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~  107 (319)
                      .+.+|..++.+..+..     .+++.||.|||||+.+.-..     .....+..+++.
T Consensus       519 il~~G~llv~qvk~s~~s~lvSvLl~Gp~~sGKTaLAA~iA-----~~S~FPFvKiiS  571 (744)
T KOG0741|consen  519 ILDDGKLLVQQVKNSERSPLVSVLLEGPPGSGKTALAAKIA-----LSSDFPFVKIIS  571 (744)
T ss_pred             HHhhHHHHHHHhhccccCcceEEEEecCCCCChHHHHHHHH-----hhcCCCeEEEeC
Confidence            4566777777665443     58999999999996553332     234455666665

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=90.03  E-value=0.16  Score=44.33  Aligned_cols=21  Identities=24%  Similarity=0.215  Sum_probs=18.1

Q ss_pred             cCCCCCcEEEecCCCCCccch
Q psy496           65 LSPILSPSIIYTSTGCGKTTQ   85 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~   85 (319)
                      ....++.+.|+||.|||||+.
T Consensus        24 ~v~~Gevv~iiGpSGSGKSTl   44 (240)
T COG1126          24 SVEKGEVVVIIGPSGSGKSTL   44 (240)
T ss_pred             eEcCCCEEEEECCCCCCHHHH
Confidence            456789999999999999964

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=89.91  E-value=0.33  Score=49.68  Aligned_cols=48  Identities=13%  Similarity=-0.075  Sum_probs=36.1

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      ..++++++.||||||||..+.+|-+-..  .     ..++++-|.-|+....+..
T Consensus       142 ~g~~hvLviApTrSGKgvg~VIPnLL~~--~-----~S~VV~D~KGEl~~~Ta~~  189 (663)
T PRK13876        142 DGPEHVLCFAPTRSGKGVGLVVPTLLTW--P-----GSAIVHDIKGENWQLTAGF  189 (663)
T ss_pred             cCCceEEEEecCCCCcceeEehhhHHhC--C-----CCEEEEeCcchHHHHHHHH
Confidence            4568999999999999999988865431  1     2677778888886665553

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=89.91  E-value=2.4  Score=42.10  Aligned_cols=135  Identities=13%  Similarity=0.093  Sum_probs=70.7

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCCC
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRK  150 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~~  150 (319)
                      ..+|.-|-+-|||+.+.-.++..+.... .....+.+++|+.+-|.+.+...+......-         .++........
T Consensus        88 e~fI~v~RkngKt~l~A~i~~~~~l~~~-~~~~~~~i~A~s~~qa~~~F~~ar~mv~~~~---------~l~~~~~~q~~  157 (546)
T COG4626          88 EAFIFIPRKNGKSTLAAGIMMTALLLNW-RSGAGIYILAPSVEQAANSFNPARDMVKRDD---------DLRDLCNVQTH  157 (546)
T ss_pred             EEEEEEecCCchHHHHHHHHHHHHHhhh-hcCCcEEEEeccHHHHHHhhHHHHHHHHhCc---------chhhhhccccc
Confidence            4788888999999877644444333222 2234677777999988888776655432110         01100111111


Q ss_pred             CceEEEECchHHHHHHhcCC---CCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          151 RGSILYCTAGILPEVMQSDP---ILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       151 ~~~Iiv~Tpg~ll~~l~~~~---~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      +..|...--...++.+..++   +=.+..+.|+||.|..+-..+++- .++.=...+++.+++..|-..
T Consensus       158 s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~~~~~~~-~~~~g~~ar~~~l~~~ITT~g  225 (546)
T COG4626         158 SRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGKQEDMYS-EAKGGLGARPEGLVVYITTSG  225 (546)
T ss_pred             eeEEEecccceeeeeeccCCCcccCCCcceEEEehhhhhcCHHHHHH-HHHhhhccCcCceEEEEecCC
Confidence            11122222222233332222   234578999999998543223333 333223355677888887644

>KOG0060|consensus

Probab=89.90  E-value=0.14  Score=50.65  Aligned_cols=34  Identities=24%  Similarity=0.279  Sum_probs=24.6

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHH
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIA   96 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~   96 (319)
                      ++-...+.+++++|+||+|||||..+  =++-.+|.
T Consensus       453 ~Ls~~V~~g~~LLItG~sG~GKtSLl--RvlggLWp  486 (659)
T KOG0060|consen  453 NLSLEVPSGQNLLITGPSGCGKTSLL--RVLGGLWP  486 (659)
T ss_pred             eeeeEecCCCeEEEECCCCCchhHHH--HHHhcccc
Confidence            44455778999999999999999543  33444554

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=89.78  E-value=0.41  Score=48.66  Aligned_cols=47  Identities=19%  Similarity=0.054  Sum_probs=36.1

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      ..+++++.||||||||..+.+|-+-  ...     ..++++-|..|++...+..
T Consensus       210 g~~H~lv~ApTgsGKgvg~VIPnLL--~~~-----gS~VV~DpKgE~~~~Ta~~  256 (623)
T TIGR02767       210 GSTHMIFFAGSGGFKTTSVVVPTAL--KYG-----GPLVCLDPSTEVAPMVCEH  256 (623)
T ss_pred             CCceEEEEeCCCCCccceeehhhhh--cCC-----CCEEEEEChHHHHHHHHHH
Confidence            4578999999999999999999632  111     2688888999997766653

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>PHA02244 ATPase-like protein

Probab=89.76  E-value=0.3  Score=46.32  Aligned_cols=28  Identities=14%  Similarity=0.191  Sum_probs=21.8

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhh
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~   87 (319)
                      ..+...+..+.+++|.||||||||..+.
T Consensus       110 ~ri~r~l~~~~PVLL~GppGtGKTtLA~  137 (383)
T PHA02244        110 ADIAKIVNANIPVFLKGGAGSGKNHIAE  137 (383)
T ss_pred             HHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            4555556677899999999999997653

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=89.68  E-value=0.52  Score=47.92  Aligned_cols=30  Identities=17%  Similarity=0.258  Sum_probs=20.7

Q ss_pred             EEEECchHHHHHHhcCCCCCCccEEEEecccc
Q psy496          154 ILYCTAGILPEVMQSDPILSGVSHIVMDEIHE  185 (319)
Q Consensus       154 Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~  185 (319)
                      -+=+-||++++-++....  .=-++++||+|.
T Consensus       399 YIGamPGrIiQ~mkka~~--~NPv~LLDEIDK  428 (782)
T COG0466         399 YIGAMPGKIIQGMKKAGV--KNPVFLLDEIDK  428 (782)
T ss_pred             ccccCChHHHHHHHHhCC--cCCeEEeechhh
Confidence            445579999999843221  123689999997

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=89.65  E-value=0.21  Score=46.47  Aligned_cols=48  Identities=23%  Similarity=0.075  Sum_probs=32.5

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHH
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRIS  114 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~l  114 (319)
                      .+..+....++++++|+||||||+.. .+++..+-.     ..+++.+.-+.|+
T Consensus       135 yL~~~ie~~~siii~G~t~sGKTt~l-nall~~Ip~-----~~rivtIEdt~E~  182 (312)
T COG0630         135 YLWLAIEARKSIIICGGTASGKTTLL-NALLDFIPP-----EERIVTIEDTPEL  182 (312)
T ss_pred             HHHHHHHcCCcEEEECCCCCCHHHHH-HHHHHhCCc-----hhcEEEEeccccc
Confidence            35666777899999999999999764 333333222     3477776666554

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=89.64  E-value=1.1  Score=41.98  Aligned_cols=51  Identities=14%  Similarity=0.195  Sum_probs=32.6

Q ss_pred             HHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          161 ILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       161 ~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      .+.+.+...+.....+++|+|++|.  ++....-..++.+...++...+|+.|
T Consensus       100 ~l~~~~~~~p~~~~~kV~iiEp~~~--Ld~~a~naLLk~LEep~~~~~~Ilvt  150 (325)
T PRK08699        100 EIIDNVYLTSVRGGLRVILIHPAES--MNLQAANSLLKVLEEPPPQVVFLLVS  150 (325)
T ss_pred             HHHHHHhhCcccCCceEEEEechhh--CCHHHHHHHHHHHHhCcCCCEEEEEe
Confidence            3445555566678899999999998  56665666666555544444455543

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=89.54  E-value=0.69  Score=48.13  Aligned_cols=101  Identities=17%  Similarity=0.202  Sum_probs=0.0

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      ...+++.||+|||||+.+                                 +.++...+...        ..+...+-..
T Consensus       487 ~~giLL~GppGtGKT~la---------------------------------kalA~e~~~~f--------i~v~~~~l~~  525 (733)
T TIGR01243       487 PKGVLLFGPPGTGKTLLA---------------------------------KAVATESGANF--------IAVRGPEILS  525 (733)
T ss_pred             CceEEEECCCCCCHHHHH---------------------------------HHHHHhcCCCE--------EEEehHHHhh


Q ss_pred             CCCceEEEECchHHHHHHhcCCCCCCccEEEEecccc----------cccchhHHHHHHHhhhccccCceEEEeccc
Q psy496          149 RKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHE----------RSMISDFLLAILKDVTDKRKDLKLILMSAT  215 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~----------~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT  215 (319)
                           -.++-.+..++.+.....-..-.+++|||+|.          .+.....+-.++..+-...+...++++-||
T Consensus       526 -----~~vGese~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v~vI~aT  597 (733)
T TIGR01243       526 -----KWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNVVVIAAT  597 (733)
T ss_pred             -----cccCcHHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCCCCEEEEEeC

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.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=89.51  E-value=0.17  Score=43.04  Aligned_cols=20  Identities=15%  Similarity=0.194  Sum_probs=16.4

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      ++.++|.||+|||||+.+-.
T Consensus         2 g~~i~l~G~sGsGKsTl~~~   21 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSLLAA   21 (186)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            45789999999999987643

>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=89.48  E-value=0.19  Score=42.77  Aligned_cols=22  Identities=23%  Similarity=0.439  Sum_probs=15.5

Q ss_pred             CCcEEEecCCCCCccchhhHHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFI   90 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~i   90 (319)
                      ...++|+||.|||||..|....
T Consensus         3 ~~~vlL~Gps~SGKTaLf~~L~   24 (181)
T PF09439_consen    3 RPTVLLVGPSGSGKTALFSQLV   24 (181)
T ss_dssp             --EEEEE-STTSSHHHHHHHHH
T ss_pred             CceEEEEcCCCCCHHHHHHHHh
Confidence            3569999999999997765443

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=89.47  E-value=0.2  Score=47.07  Aligned_cols=42  Identities=21%  Similarity=0.154  Sum_probs=28.2

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRIS  114 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~l  114 (319)
                      ....+++++|+||||||+.+- .++..+..     ..+++++.-+.|+
T Consensus       176 ~~~~~ili~G~tGsGKTTll~-al~~~i~~-----~~riv~iEd~~El  217 (340)
T TIGR03819       176 AARLAFLISGGTGSGKTTLLS-ALLALVAP-----DERIVLVEDAAEL  217 (340)
T ss_pred             hCCCeEEEECCCCCCHHHHHH-HHHccCCC-----CCcEEEECCccee
Confidence            456799999999999997653 23332221     2367777777676

Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=89.35  E-value=0.33  Score=48.83  Aligned_cols=55  Identities=18%  Similarity=0.156  Sum_probs=38.1

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHH-HHHHHHhc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIA-ERVAQERD  127 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~-~~~~~~~~  127 (319)
                      -+.|++..++-+|||......+...+...    .+.+++++||.++|.... .++.-.+.
T Consensus        33 v~~Vv~~k~aQ~GkT~~~~n~~g~~i~~~----P~~~l~v~Pt~~~a~~~~~~rl~Pmi~   88 (557)
T PF05876_consen   33 VREVVVMKSAQVGKTELLLNWIGYSIDQD----PGPMLYVQPTDDAAKDFSKERLDPMIR   88 (557)
T ss_pred             ccEEEEEEcchhhHhHHHHhhceEEEEeC----CCCEEEEEEcHHHHHHHHHHHHHHHHH
Confidence            46799999999999996555443333222    247888889999999875 44554443

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 [].

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=89.27  E-value=0.44  Score=41.72  Aligned_cols=29  Identities=24%  Similarity=0.266  Sum_probs=23.1

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      .+.+..++|+|++|||||......+.+..
T Consensus        20 i~~g~i~~i~G~~GsGKT~l~~~la~~~~   48 (225)
T PRK09361         20 FERGTITQIYGPPGSGKTNICLQLAVEAA   48 (225)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            45678899999999999988776665544

>KOG2035|consensus

Probab=89.24  E-value=1.4  Score=40.10  Aligned_cols=41  Identities=20%  Similarity=0.319  Sum_probs=31.3

Q ss_pred             CCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccc
Q psy496          173 SGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSAT  215 (319)
Q Consensus       173 ~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT  215 (319)
                      ..+++|||.|+|+  +..|...++.+-+.+...+.|+|+.--.
T Consensus       126 r~fKvvvi~ead~--LT~dAQ~aLRRTMEkYs~~~RlIl~cns  166 (351)
T KOG2035|consen  126 RPFKVVVINEADE--LTRDAQHALRRTMEKYSSNCRLILVCNS  166 (351)
T ss_pred             cceEEEEEechHh--hhHHHHHHHHHHHHHHhcCceEEEEecC
Confidence            4689999999999  7777777777777777778888776333

>KOG0386|consensus

Probab=89.22  E-value=0.26  Score=51.51  Aligned_cols=155  Identities=16%  Similarity=0.053  Sum_probs=74.4

Q ss_pred             cccchhhH-HHHHHhhhcC-CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           49 QPRRISAI-ALINKCLTLS-PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        49 Q~~~ip~~-~~~~~~l~~~-~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      |-..++.+ ++|-.=+.+. ++|=|=++.-++|-|||.+-.-.+..-....+..+...|++  |+-.|..     |..++
T Consensus       391 ~GG~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQtIsLitYLmE~K~~~GP~Lviv--PlstL~N-----W~~Ef  463 (1157)
T KOG0386|consen  391 QGGELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEHKQMQGPFLIIV--PLSTLVN-----WSSEF  463 (1157)
T ss_pred             cCCCCchhhhhhhHHHhhccCCCcccccchhcccchHHHHHHHHHHHHHHcccCCCeEEec--cccccCC-----chhhc
Confidence            33344433 2333333334 35557888999999999776544433222222222234444  8766543     33333


Q ss_pred             ccccCCCCceEEEEEe-----cccccCCCCceEEEECchHHHHHHhcCCCCCC--ccEEEEecccccccchhHHHHHHHh
Q psy496          127 DEQCGRPGSSVGYQIR-----LEKELPRKRGSILYCTAGILPEVMQSDPILSG--VSHIVMDEIHERSMISDFLLAILKD  199 (319)
Q Consensus       127 ~~~~~~~g~~vg~~~~-----~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~--v~~vViDEah~~~~~~~~~~~~l~~  199 (319)
                      ....-.....++.+..     ........+.+|+++|.+.+++   ....|+.  ..++||||.|++.....-+-..+  
T Consensus       464 ~kWaPSv~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik---dk~lLsKI~W~yMIIDEGHRmKNa~~KLt~~L--  538 (1157)
T KOG0386|consen  464 PKWAPSVQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK---DKALLSKISWKYMIIDEGHRMKNAICKLTDTL--  538 (1157)
T ss_pred             cccccceeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC---CHHHHhccCCcceeecccccccchhhHHHHHh--
Confidence            2221000111111111     1111112466899999988765   2222333  56789999997432221111111  


Q ss_pred             hhccccCceEEEecccc
Q psy496          200 VTDKRKDLKLILMSATL  216 (319)
Q Consensus       200 ~~~~~~~~qiv~lSAT~  216 (319)
                       .......+.++++.|.
T Consensus       539 -~t~y~~q~RLLLTGTP  554 (1157)
T KOG0386|consen  539 -NTHYRAQRRLLLTGTP  554 (1157)
T ss_pred             -hccccchhhhhhcCCh
Confidence             1112233567778887

>TIGR02012 tigrfam_recA protein RecA

Probab=89.19  E-value=0.57  Score=43.65  Aligned_cols=42  Identities=21%  Similarity=0.095  Sum_probs=29.5

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEeccc
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPR  111 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Pt  111 (319)
                      =.+.+..+.|.||+|||||+..+..+.+.....     ..++++..-
T Consensus        51 Glp~G~iteI~G~~GsGKTtLaL~~~~~~~~~g-----~~v~yId~E   92 (321)
T TIGR02012        51 GLPRGRIIEIYGPESSGKTTLALHAIAEAQKAG-----GTAAFIDAE   92 (321)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcC-----CcEEEEccc
Confidence            466778999999999999988777665543322     255665443

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=89.18  E-value=0.76  Score=45.38  Aligned_cols=32  Identities=28%  Similarity=0.361  Sum_probs=26.6

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIA   96 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~   96 (319)
                      =.+.+..++|+|++|||||+.....+.+.+..
T Consensus        17 Glp~g~~~Li~G~pGsGKT~la~qfl~~g~~~   48 (484)
T TIGR02655        17 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIH   48 (484)
T ss_pred             CCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHh
Confidence            35678899999999999999988887776554

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.

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=89.14  E-value=0.49  Score=48.33  Aligned_cols=48  Identities=19%  Similarity=0.103  Sum_probs=36.6

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      .++++++.||||||||..+.+|-+-   ..    ...++++-|..|+....+...
T Consensus       223 g~~H~Lv~ApTgsGKt~g~VIPnLL---~~----~gS~VV~DpKgEl~~~Ta~~R  270 (641)
T PRK13822        223 GSTHGLVFAGSGGFKTTSVVVPTAL---KW----GGPLVVLDPSTEVAPMVSEHR  270 (641)
T ss_pred             CCceEEEEeCCCCCccceEehhhhh---cC----CCCEEEEeCcHHHHHHHHHHH
Confidence            4578999999999999999999642   11    136888889999877666533

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=88.93  E-value=0.9  Score=37.87  Aligned_cols=25  Identities=32%  Similarity=0.279  Sum_probs=18.8

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHH
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEI   95 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~   95 (319)
                      -+.|..++|.|||+++.--.+...-
T Consensus         4 ~i~vy~g~G~Gkt~~a~g~~~ra~~   28 (159)
T cd00561           4 LIQVYTGNGKGKTTAALGLALRALG   28 (159)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4667788899999998766666543

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.

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=88.91  E-value=0.45  Score=42.84  Aligned_cols=32  Identities=28%  Similarity=0.180  Sum_probs=23.9

Q ss_pred             hhcCCCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           63 LTLSPILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        63 l~~~~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      +.-...+..++|.|++|+|||+.....+.+..
T Consensus        24 ~gG~~~g~~~~i~g~~G~GKT~l~~~~~~~~~   55 (271)
T cd01122          24 TKGLRKGELIILTAGTGVGKTTFLREYALDLI   55 (271)
T ss_pred             eEEEcCCcEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            33455678899999999999987766655543

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>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=88.90  E-value=0.41  Score=41.27  Aligned_cols=28  Identities=25%  Similarity=0.284  Sum_probs=18.3

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      ..+.+++|.|.||||||...-..+...+
T Consensus        36 ~~~~h~li~G~tgsGKS~~l~~ll~~l~   63 (205)
T PF01580_consen   36 KKNPHLLIAGATGSGKSTLLRTLLLSLA   63 (205)
T ss_dssp             GGS-SEEEE--TTSSHHHHHHHHHHHHH
T ss_pred             CCCceEEEEcCCCCCccHHHHHHHHHHH
Confidence            3445899999999999988765544443

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.

>PRK13695 putative NTPase; Provisional

Probab=88.82  E-value=2.1  Score=35.85  Aligned_cols=18  Identities=39%  Similarity=0.316  Sum_probs=15.3

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|+|++|||||+.+..
T Consensus         2 ~i~ltG~~G~GKTTll~~   19 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLK   19 (174)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            378999999999988764

>PRK00300 gmk guanylate kinase; Provisional

Probab=88.79  E-value=0.27  Score=42.25  Aligned_cols=19  Identities=26%  Similarity=0.256  Sum_probs=16.3

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      .++.++|.||+|||||+..
T Consensus         4 ~g~~i~i~G~sGsGKstl~   22 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLV   22 (205)
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5678999999999999754

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=88.77  E-value=0.21  Score=49.25  Aligned_cols=26  Identities=27%  Similarity=0.222  Sum_probs=18.9

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      .+..++++||||||||+.. ..+++.+
T Consensus       241 ~~GlilitGptGSGKTTtL-~a~L~~l  266 (486)
T TIGR02533       241 PHGIILVTGPTGSGKTTTL-YAALSRL  266 (486)
T ss_pred             CCCEEEEEcCCCCCHHHHH-HHHHhcc
Confidence            3457899999999999876 3344544

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>PRK07261 topology modulation protein; Provisional

Probab=88.76  E-value=0.21  Score=42.05  Aligned_cols=18  Identities=28%  Similarity=0.338  Sum_probs=15.3

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|.|++|||||+.+-.
T Consensus         2 ri~i~G~~GsGKSTla~~   19 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARK   19 (171)
T ss_pred             EEEEEcCCCCCHHHHHHH
Confidence            478999999999987744

>TIGR03263 guanyl_kin guanylate kinase

Probab=88.72  E-value=0.26  Score=41.41  Aligned_cols=18  Identities=33%  Similarity=0.327  Sum_probs=15.0

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      ++.++|.||+|||||+..
T Consensus         1 g~ii~l~G~~GsGKsTl~   18 (180)
T TIGR03263         1 GLLIVISGPSGVGKSTLV   18 (180)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            356899999999999854

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=88.67  E-value=0.26  Score=39.89  Aligned_cols=15  Identities=27%  Similarity=0.525  Sum_probs=12.9

Q ss_pred             EEEecCCCCCccchh
Q psy496           72 SIIYTSTGCGKTTQV   86 (319)
Q Consensus        72 vli~apTGSGKT~~~   86 (319)
                      ++|+||||||||+..
T Consensus         2 i~i~GpsGsGKstl~   16 (137)
T cd00071           2 IVLSGPSGVGKSTLL   16 (137)
T ss_pred             EEEECCCCCCHHHHH
Confidence            678999999999744

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>PRK08118 topology modulation protein; Reviewed

Probab=88.67  E-value=0.21  Score=41.87  Aligned_cols=16  Identities=38%  Similarity=0.474  Sum_probs=14.0

Q ss_pred             cEEEecCCCCCccchh
Q psy496           71 PSIIYTSTGCGKTTQV   86 (319)
Q Consensus        71 ~vli~apTGSGKT~~~   86 (319)
                      .++|.|++|||||+..
T Consensus         3 rI~I~G~~GsGKSTla   18 (167)
T PRK08118          3 KIILIGSGGSGKSTLA   18 (167)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5899999999999754

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=88.46  E-value=0.22  Score=41.88  Aligned_cols=18  Identities=22%  Similarity=0.311  Sum_probs=15.5

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      +.++|.||+|||||+..-
T Consensus         2 ~~~~i~G~sGsGKttl~~   19 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLD   19 (179)
T ss_pred             cEEEEECCCCCCHHHHHH
Confidence            468899999999998764

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=88.42  E-value=0.24  Score=41.66  Aligned_cols=19  Identities=16%  Similarity=0.146  Sum_probs=16.1

Q ss_pred             CCcEEEecCCCCCccchhh
Q psy496           69 LSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~   87 (319)
                      ++.++++|++|||||+..-
T Consensus         2 ~~~i~l~G~~gsGKst~a~   20 (175)
T cd00227           2 GRIIILNGGSSAGKSSIAR   20 (175)
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            4678999999999998763

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PLN02165 adenylate isopentenyltransferase

Probab=88.41  E-value=0.23  Score=46.37  Aligned_cols=23  Identities=22%  Similarity=0.186  Sum_probs=18.7

Q ss_pred             CCCCCcEEEecCCCCCccchhhH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ...+..++|.||||||||+.+..
T Consensus        40 ~~~g~iivIiGPTGSGKStLA~~   62 (334)
T PLN02165         40 NCKDKVVVIMGATGSGKSRLSVD   62 (334)
T ss_pred             CCCCCEEEEECCCCCcHHHHHHH
Confidence            44567899999999999977644

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=88.40  E-value=0.94  Score=49.60  Aligned_cols=60  Identities=17%  Similarity=0.179  Sum_probs=45.3

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhcc
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDE  128 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~  128 (319)
                      ...++++|.|+-|||||.....=++..+... . ....|+++.-|+..|..+..++...+..
T Consensus         8 dp~~~~~~~a~agsgkt~~l~~~~~~~~~~~-~-~~~~i~~~t~t~~aa~em~~Ri~~~L~~   67 (1141)
T TIGR02784         8 DPKTSAWVSANAGSGKTHVLTQRVIRLLLNG-V-PPSKILCLTYTKAAAAEMQNRVFDRLGE   67 (1141)
T ss_pred             CCCCCEEEEEECCCCHHHHHHHHHHHHHHcC-C-CCCeEEEEecCHHHHHHHHHHHHHHHHH
Confidence            3456799999999999988776666555432 2 2348899999999999998888776643

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=88.33  E-value=3.7  Score=40.16  Aligned_cols=52  Identities=15%  Similarity=0.274  Sum_probs=29.4

Q ss_pred             hhHHHHHHhhhc-CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEE
Q psy496           54 SAIALINKCLTL-SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMV  107 (319)
Q Consensus        54 p~~~~~~~~l~~-~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~  107 (319)
                      |++.+-.+.+.. ++.+-+|+|.|+|||||-+++-  .++..-.+.+++...|-|
T Consensus       148 ~am~~l~~~i~kvA~s~a~VLI~GESGtGKElvAr--~IH~~S~R~~~PFVavNc  200 (464)
T COG2204         148 PAMQQLRRLIAKVAPSDASVLITGESGTGKELVAR--AIHQASPRAKGPFIAVNC  200 (464)
T ss_pred             HHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHH--HHHhhCcccCCCceeeec
Confidence            334443344433 4566789999999999996652  223333333444444444

>PRK00131 aroK shikimate kinase; Reviewed

Probab=88.26  E-value=0.28  Score=40.63  Aligned_cols=20  Identities=20%  Similarity=0.114  Sum_probs=16.8

Q ss_pred             CCCcEEEecCCCCCccchhh
Q psy496           68 ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~   87 (319)
                      ++..++++|++|||||+..-
T Consensus         3 ~~~~i~l~G~~GsGKstla~   22 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIGR   22 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHHH
Confidence            45679999999999998764

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=88.22  E-value=0.22  Score=42.01  Aligned_cols=17  Identities=29%  Similarity=0.393  Sum_probs=14.3

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      .++++.||||+|||..+
T Consensus         4 ~~~ll~GpsGvGKT~la   20 (171)
T PF07724_consen    4 SNFLLAGPSGVGKTELA   20 (171)
T ss_dssp             EEEEEESSTTSSHHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            46899999999999644

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=88.21  E-value=0.24  Score=43.73  Aligned_cols=23  Identities=22%  Similarity=0.109  Sum_probs=19.2

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.++.+.|.||+|||||+..
T Consensus        26 l~i~~Ge~vaI~GpSGSGKSTLL   48 (226)
T COG1136          26 LEIEAGEFVAIVGPSGSGKSTLL   48 (226)
T ss_pred             EEEcCCCEEEEECCCCCCHHHHH
Confidence            34667899999999999999753

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=88.19  E-value=0.35  Score=48.11  Aligned_cols=21  Identities=33%  Similarity=0.463  Sum_probs=16.7

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      ..+.++++||+|||||+++-.
T Consensus        44 ~~~iLlLtGP~G~GKtttv~~   64 (519)
T PF03215_consen   44 PKRILLLTGPSGCGKTTTVKV   64 (519)
T ss_pred             CcceEEEECCCCCCHHHHHHH
Confidence            345788899999999987633

>KOG0990|consensus

Probab=88.10  E-value=1.9  Score=39.94  Aligned_cols=38  Identities=16%  Similarity=0.254  Sum_probs=25.2

Q ss_pred             CccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          174 GVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       174 ~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      .++++|+||||.  +..+...++.+.+.....+.++...+
T Consensus       131 ~fKlvILDEADa--MT~~AQnALRRviek~t~n~rF~ii~  168 (360)
T KOG0990|consen  131 AFKLVILDEADA--MTRDAQNALRRVIEKYTANTRFATIS  168 (360)
T ss_pred             ceeEEEecchhH--hhHHHHHHHHHHHHHhccceEEEEec
Confidence            689999999998  45554444445555555666666443

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=88.06  E-value=0.53  Score=47.82  Aligned_cols=41  Identities=20%  Similarity=0.246  Sum_probs=30.9

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRI  113 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~  113 (319)
                      ...+.+|.|+||||||..+.+.+.+.+...     ..++++-|...
T Consensus       179 ~~gHtlV~GtTGsGKT~l~~~li~q~i~~g-----~~vi~fDpkgD  219 (643)
T TIGR03754       179 RVGHTLVLGTTRVGKTRLAELLITQDIRRG-----DVVIVFDPKGD  219 (643)
T ss_pred             ccCceEEECCCCCCHHHHHHHHHHHHHHcC-----CeEEEEeCCCC
Confidence            457899999999999999887666655432     26777778663

Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=88.02  E-value=0.39  Score=38.79  Aligned_cols=28  Identities=21%  Similarity=0.115  Sum_probs=22.0

Q ss_pred             HHHhhhcCCCCCcEEEecCCCCCccchh
Q psy496           59 INKCLTLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        59 ~~~~l~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ++.+....+.+..+++.|+.|+|||+..
T Consensus        12 ~~~l~~~l~~~~~i~l~G~lGaGKTtl~   39 (133)
T TIGR00150        12 GKAFAKPLDFGTVVLLKGDLGAGKTTLV   39 (133)
T ss_pred             HHHHHHhCCCCCEEEEEcCCCCCHHHHH
Confidence            4455555677889999999999999654

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=88.00  E-value=0.48  Score=39.91  Aligned_cols=45  Identities=13%  Similarity=0.138  Sum_probs=29.2

Q ss_pred             EEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        72 vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++|.|++|||||......+..    .    ..+++++...+..-....+++..
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~----~----~~~~~y~at~~~~d~em~~rI~~   46 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE----L----GGPVTYIATAEAFDDEMAERIAR   46 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh----c----CCCeEEEEccCcCCHHHHHHHHH
Confidence            689999999999887655432    1    12566665665555555555544

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.

>TIGR00235 udk uridine kinase

Probab=87.54  E-value=0.26  Score=42.75  Aligned_cols=19  Identities=32%  Similarity=0.067  Sum_probs=15.9

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      .+..+.|+|++|||||+..
T Consensus         5 ~g~vi~I~G~sGsGKSTl~   23 (207)
T TIGR00235         5 KGIIIGIGGGSGSGKTTVA   23 (207)
T ss_pred             CeEEEEEECCCCCCHHHHH
Confidence            4567889999999999754

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=87.45  E-value=0.36  Score=37.45  Aligned_cols=23  Identities=22%  Similarity=0.105  Sum_probs=18.9

Q ss_pred             CCCCCcEEEecCCCCCccchhhH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ...++.+.|.||+|||||+.+.+
T Consensus        12 i~~ge~v~I~GpSGsGKSTLl~~   34 (107)
T cd00820          12 VYGKVGVLITGDSGIGKTELALE   34 (107)
T ss_pred             EcCCEEEEEEcCCCCCHHHHHHH
Confidence            34567899999999999987655

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=87.45  E-value=0.84  Score=42.61  Aligned_cols=44  Identities=18%  Similarity=0.095  Sum_probs=30.2

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRI  113 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~  113 (319)
                      =.+.+..+.|.||+|||||+..+..+.+.....     ..++++.+-..
T Consensus        51 Glp~G~iteI~Gp~GsGKTtLal~~~~~~~~~g-----~~~vyId~E~~   94 (325)
T cd00983          51 GYPKGRIIEIYGPESSGKTTLALHAIAEAQKLG-----GTVAFIDAEHA   94 (325)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHcC-----CCEEEECcccc
Confidence            356678899999999999988777665543222     25666655433

RecA couples ATP hydrolysis to DNA strand exchange.

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=87.41  E-value=0.29  Score=42.55  Aligned_cols=22  Identities=18%  Similarity=0.131  Sum_probs=15.1

Q ss_pred             cCCCCCcEEEecCCCCCccchh
Q psy496           65 LSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ++..+.++++.||.|||||..+
T Consensus        18 AAaG~h~lLl~GppGtGKTmlA   39 (206)
T PF01078_consen   18 AAAGGHHLLLIGPPGTGKTMLA   39 (206)
T ss_dssp             HHHCC--EEEES-CCCTHHHHH
T ss_pred             HHcCCCCeEEECCCCCCHHHHH
Confidence            3445689999999999999654

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=87.39  E-value=0.4  Score=40.09  Aligned_cols=32  Identities=25%  Similarity=0.292  Sum_probs=17.0

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHHh
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIAR   97 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~   97 (319)
                      ......+++|.|+.|+|||...-. +++.+...
T Consensus        20 ~~~~~~~~ll~G~~G~GKT~ll~~-~~~~~~~~   51 (185)
T PF13191_consen   20 QSGSPRNLLLTGESGSGKTSLLRA-LLDRLAER   51 (185)
T ss_dssp             SS-----EEE-B-TTSSHHHHHHH-HHHHHHHH
T ss_pred             HcCCCcEEEEECCCCCCHHHHHHH-HHHHHHhc
Confidence            344567899999999999976543 44444443

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=87.35  E-value=0.46  Score=47.52  Aligned_cols=51  Identities=24%  Similarity=0.262  Sum_probs=32.5

Q ss_pred             HHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhH
Q psy496           34 EIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        34 ~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      |.+..|........-|..++..+..   . ..++..+.+++.||+|+|||+++-.
T Consensus        55 ~~~~~rp~~f~~iiGqs~~i~~l~~---a-l~~~~~~~vLi~Ge~GtGKt~lAr~  105 (531)
T TIGR02902        55 LSEKTRPKSFDEIIGQEEGIKALKA---A-LCGPNPQHVIIYGPPGVGKTAAARL  105 (531)
T ss_pred             HHHhhCcCCHHHeeCcHHHHHHHHH---H-HhCCCCceEEEECCCCCCHHHHHHH
Confidence            3344443333334567766655542   2 2456678899999999999987643

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=87.29  E-value=0.3  Score=38.90  Aligned_cols=21  Identities=24%  Similarity=0.158  Sum_probs=17.7

Q ss_pred             CCCCCcEEEecCCCCCccchh
Q psy496           66 SPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...++.+.|.|++|||||+.+
T Consensus         8 i~~g~~~~i~G~nGsGKStLl   28 (137)
T PF00005_consen    8 IKPGEIVAIVGPNGSGKSTLL   28 (137)
T ss_dssp             EETTSEEEEEESTTSSHHHHH
T ss_pred             EcCCCEEEEEccCCCccccce
Confidence            346788999999999999765

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=87.16  E-value=0.33  Score=34.23  Aligned_cols=15  Identities=33%  Similarity=0.432  Sum_probs=13.0

Q ss_pred             EEEecCCCCCccchh
Q psy496           72 SIIYTSTGCGKTTQV   86 (319)
Q Consensus        72 vli~apTGSGKT~~~   86 (319)
                      +.++|+.|||||+..
T Consensus         2 i~i~G~~gsGKst~~   16 (69)
T cd02019           2 IAITGGSGSGKSTVA   16 (69)
T ss_pred             EEEECCCCCCHHHHH
Confidence            678999999999765

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=87.05  E-value=0.92  Score=47.11  Aligned_cols=105  Identities=21%  Similarity=0.165  Sum_probs=59.5

Q ss_pred             EEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC---
Q psy496           72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP---  148 (319)
Q Consensus        72 vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~---  148 (319)
                      -+.---||=|||+...+|..-....+.   ...++.  ..-=||.--+..+...+...    |..+|.....-....   
T Consensus        96 ~iaEM~TGEGKTL~atlp~ylnaL~gk---gVhvVT--vNdYLA~RDae~m~~l~~~L----GlsvG~~~~~m~~~ek~~  166 (822)
T COG0653          96 DIAEMRTGEGKTLVATLPAYLNALAGK---GVHVVT--VNDYLARRDAEWMGPLYEFL----GLSVGVILAGMSPEEKRA  166 (822)
T ss_pred             ceeeeecCCchHHHHHHHHHHHhcCCC---CcEEee--ehHHhhhhCHHHHHHHHHHc----CCceeeccCCCChHHHHH
Confidence            344444999999999888753333322   234443  33334444444444443333    788886655322111   


Q ss_pred             CCCceEEEECchHH-----HHHHhc---CCCCCCccEEEEecccc
Q psy496          149 RKRGSILYCTAGIL-----PEVMQS---DPILSGVSHIVMDEIHE  185 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~l-----l~~l~~---~~~l~~v~~vViDEah~  185 (319)
                      .-.++|.++|...+     .+.+..   ......+.+-|+||+|.
T Consensus       167 aY~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDS  211 (822)
T COG0653         167 AYACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDS  211 (822)
T ss_pred             HHhcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhh
Confidence            12578999998444     333322   22255688899999996

>PRK09354 recA recombinase A; Provisional

Probab=86.98  E-value=0.92  Score=42.74  Aligned_cols=44  Identities=20%  Similarity=0.095  Sum_probs=30.6

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRI  113 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~  113 (319)
                      =.+.+..+.|.||+|||||+..+..+.+.....     ..++++..-..
T Consensus        56 Gip~G~IteI~G~~GsGKTtLal~~~~~~~~~G-----~~~~yId~E~s   99 (349)
T PRK09354         56 GLPRGRIVEIYGPESSGKTTLALHAIAEAQKAG-----GTAAFIDAEHA   99 (349)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcC-----CcEEEECCccc
Confidence            356678899999999999998877776654322     25666544433

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=86.90  E-value=0.99  Score=47.26  Aligned_cols=19  Identities=21%  Similarity=0.085  Sum_probs=16.0

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      .+..+++.||+|+|||+.+
T Consensus       348 ~g~~i~l~GppG~GKTtl~  366 (784)
T PRK10787        348 KGPILCLVGPPGVGKTSLG  366 (784)
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            4567999999999999665

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=86.83  E-value=0.26  Score=40.74  Aligned_cols=15  Identities=27%  Similarity=0.448  Sum_probs=12.6

Q ss_pred             EEEecCCCCCccchh
Q psy496           72 SIIYTSTGCGKTTQV   86 (319)
Q Consensus        72 vli~apTGSGKT~~~   86 (319)
                      ++++||+|||||+.+
T Consensus         1 i~l~G~~GsGKSTla   15 (163)
T TIGR01313         1 FVLMGVAGSGKSTIA   15 (163)
T ss_pred             CEEECCCCCCHHHHH
Confidence            468999999999665

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=86.81  E-value=2.5  Score=41.45  Aligned_cols=38  Identities=16%  Similarity=0.135  Sum_probs=26.3

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchh
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      +=|..++-.+++.-++++.  .+.+|+|+|+||+||-+.+
T Consensus       226 IG~S~am~~ll~~i~~VA~--Sd~tVLi~GETGtGKElvA  263 (550)
T COG3604         226 IGRSPAMRQLLKEIEVVAK--SDSTVLIRGETGTGKELVA  263 (550)
T ss_pred             eecCHHHHHHHHHHHHHhc--CCCeEEEecCCCccHHHHH
Confidence            4455566555555555544  4588999999999998554

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=86.76  E-value=1.3  Score=41.14  Aligned_cols=30  Identities=17%  Similarity=0.151  Sum_probs=23.2

Q ss_pred             hcCCCCCcEEEecCCCCCccchhhHHHHHH
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQVPQFILDD   93 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~~l~il~~   93 (319)
                      ........++|.|+.|||||.+....+..+
T Consensus        18 ~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A   47 (309)
T PF10236_consen   18 DKSSKNNRYVLTGERGSGKSVLLAQAVHYA   47 (309)
T ss_pred             cccCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            344556789999999999998887766544

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=86.73  E-value=0.69  Score=46.58  Aligned_cols=28  Identities=21%  Similarity=0.198  Sum_probs=20.6

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEI   95 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~   95 (319)
                      ...+++++.|+||||||.++ ..++..+.
T Consensus       174 ~e~~h~li~G~tGsGKs~~i-~~ll~~~~  201 (566)
T TIGR02759       174 SETQHILIHGTTGSGKSVAI-RKLLRWIR  201 (566)
T ss_pred             ccccceEEEcCCCCCHHHHH-HHHHHHHH
Confidence            34678999999999999754 33555543

The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM).

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=86.51  E-value=2.6  Score=41.35  Aligned_cols=51  Identities=20%  Similarity=0.122  Sum_probs=36.8

Q ss_pred             EEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           73 IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        73 li~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      .|.|=.|||||....+-.   ..-..+.+.-+|+++.=|+.|+.++...+.+++
T Consensus       180 rIrGLAGSGKT~~La~Ka---a~lh~knPd~~I~~Tfftk~L~s~~r~lv~~F~  230 (660)
T COG3972         180 RIRGLAGSGKTELLAHKA---AELHSKNPDSRIAFTFFTKILASTMRTLVPEFF  230 (660)
T ss_pred             hhhcccCCCchhHHHHHH---HHHhcCCCCceEEEEeehHHHHHHHHHHHHHHH
Confidence            566778999997764432   223345667799999999999998877766653

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=86.50  E-value=0.34  Score=38.59  Aligned_cols=34  Identities=21%  Similarity=0.099  Sum_probs=23.9

Q ss_pred             HHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHH
Q psy496           59 INKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDD   93 (319)
Q Consensus        59 ~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~   93 (319)
                      ++.+....+++..+++.|+-|||||+..- .+.+.
T Consensus         5 a~~l~~~l~~g~vi~L~GdLGaGKTtf~r-~l~~~   38 (123)
T PF02367_consen    5 AKKLAQILKPGDVILLSGDLGAGKTTFVR-GLARA   38 (123)
T ss_dssp             HHHHHHHHSS-EEEEEEESTTSSHHHHHH-HHHHH
T ss_pred             HHHHHHhCCCCCEEEEECCCCCCHHHHHH-HHHHH
Confidence            45555666788899999999999996543 34443

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>PF13173 AAA_14: AAA domain

Probab=86.30  E-value=0.51  Score=37.48  Aligned_cols=22  Identities=32%  Similarity=0.311  Sum_probs=18.0

Q ss_pred             CCCcEEEecCCCCCccchhhHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~   89 (319)
                      |++.++|.||.|+|||+.....
T Consensus         1 n~~~~~l~G~R~vGKTtll~~~   22 (128)
T PF13173_consen    1 NRKIIILTGPRGVGKTTLLKQL   22 (128)
T ss_pred             CCCeEEEECCCCCCHHHHHHHH
Confidence            4678999999999999876444

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=86.28  E-value=1.1  Score=38.39  Aligned_cols=35  Identities=29%  Similarity=0.238  Sum_probs=24.6

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEec
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQ  109 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~  109 (319)
                      .-++|....|=|||++++=-++..+-.     ..+|.+++
T Consensus        29 Gli~V~TG~GKGKTTAAlG~alRa~Gh-----G~rv~vvQ   63 (198)
T COG2109          29 GLIIVFTGNGKGKTTAALGLALRALGH-----GLRVGVVQ   63 (198)
T ss_pred             CeEEEEecCCCChhHHHHHHHHHHhcC-----CCEEEEEE
Confidence            447778889999999987777765422     23677665

>PRK05541 adenylylsulfate kinase; Provisional

Probab=86.17  E-value=0.41  Score=40.19  Aligned_cols=21  Identities=33%  Similarity=0.188  Sum_probs=17.4

Q ss_pred             CCCCcEEEecCCCCCccchhh
Q psy496           67 PILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~   87 (319)
                      +.+..++++|++|||||+..-
T Consensus         5 ~~~~~I~i~G~~GsGKst~a~   25 (176)
T PRK05541          5 PNGYVIWITGLAGSGKTTIAK   25 (176)
T ss_pred             CCCCEEEEEcCCCCCHHHHHH
Confidence            456689999999999998763

>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

Probab=86.15  E-value=0.36  Score=44.73  Aligned_cols=18  Identities=28%  Similarity=0.255  Sum_probs=15.3

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      ..++|+||||||||....
T Consensus         5 ~~i~i~GptgsGKt~la~   22 (307)
T PRK00091          5 KVIVIVGPTASGKTALAI   22 (307)
T ss_pred             eEEEEECCCCcCHHHHHH
Confidence            468899999999997764

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=86.11  E-value=0.76  Score=45.66  Aligned_cols=36  Identities=22%  Similarity=0.270  Sum_probs=27.8

Q ss_pred             Hhh-hcCCCCCcEEEecCCCCCccchhhHHHHHHHHH
Q psy496           61 KCL-TLSPILSPSIIYTSTGCGKTTQVPQFILDDEIA   96 (319)
Q Consensus        61 ~~l-~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~   96 (319)
                      +++ +-.+.++.++|.|++|||||+.....+.+.+..
T Consensus        22 ~~l~GG~p~Gs~~li~G~pGsGKT~l~~qf~~~~~~~   58 (509)
T PRK09302         22 DITHGGLPKGRPTLVSGTAGTGKTLFALQFLVNGIKR   58 (509)
T ss_pred             HhhcCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence            444 346788999999999999998887776666544

>PRK08233 hypothetical protein; Provisional

Probab=86.07  E-value=0.36  Score=40.45  Aligned_cols=18  Identities=33%  Similarity=0.285  Sum_probs=14.8

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      ..+.|.|++|||||+...
T Consensus         4 ~iI~I~G~~GsGKtTla~   21 (182)
T PRK08233          4 KIITIAAVSGGGKTTLTE   21 (182)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            457889999999998763

>KOG0745|consensus

Probab=86.07  E-value=0.4  Score=46.05  Aligned_cols=17  Identities=35%  Similarity=0.470  Sum_probs=14.7

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      .|+|+.||||||||+..
T Consensus       227 SNvLllGPtGsGKTlla  243 (564)
T KOG0745|consen  227 SNVLLLGPTGSGKTLLA  243 (564)
T ss_pred             ccEEEECCCCCchhHHH
Confidence            57999999999999543

>PRK14530 adenylate kinase; Provisional

Probab=86.04  E-value=0.37  Score=41.97  Aligned_cols=19  Identities=26%  Similarity=0.431  Sum_probs=16.0

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      .+++|.|++|||||+..-.
T Consensus         4 ~~I~i~G~pGsGKsT~~~~   22 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSN   22 (215)
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4689999999999987644

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=86.02  E-value=3.2  Score=40.08  Aligned_cols=54  Identities=13%  Similarity=0.263  Sum_probs=34.0

Q ss_pred             ccEEEEecccccccchhHHHHHHHhhhc---cccCceEEEecccc-ChhhHhhhhCCC
Q psy496          175 VSHIVMDEIHERSMISDFLLAILKDVTD---KRKDLKLILMSATL-NAEKFSQFFGGA  228 (319)
Q Consensus       175 v~~vViDEah~~~~~~~~~~~~l~~~~~---~~~~~qiv~lSAT~-~~~~l~~~l~~~  228 (319)
                      .-+||||.+..+....+++...+..-..   ...-..+|++|... ..+.+.+.+.+.
T Consensus       149 ~PVVVIdnF~~k~~~~~~iy~~laeWAa~Lv~~nIAHVIFlT~dv~~~k~LskaLPn~  206 (431)
T PF10443_consen  149 RPVVVIDNFLHKAEENDFIYDKLAEWAASLVQNNIAHVIFLTDDVSYSKPLSKALPNR  206 (431)
T ss_pred             CCEEEEcchhccCcccchHHHHHHHHHHHHHhcCccEEEEECCCCchhhhHHHhCCCC
Confidence            4689999998754443444433333221   22345789998888 777888888654

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>PRK06762 hypothetical protein; Provisional

Probab=86.01  E-value=0.36  Score=40.00  Aligned_cols=17  Identities=41%  Similarity=0.442  Sum_probs=14.5

Q ss_pred             cEEEecCCCCCccchhh
Q psy496           71 PSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~   87 (319)
                      .++++|++|||||+..-
T Consensus         4 li~i~G~~GsGKST~A~   20 (166)
T PRK06762          4 LIIIRGNSGSGKTTIAK   20 (166)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47889999999998763

>KOG0726|consensus

Probab=85.96  E-value=0.86  Score=41.73  Aligned_cols=17  Identities=35%  Similarity=0.481  Sum_probs=14.5

Q ss_pred             CCcEEEecCCCCCccch
Q psy496           69 LSPSIIYTSTGCGKTTQ   85 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~   85 (319)
                      .+-|+++|++|+|||+.
T Consensus       219 PKGVIlyG~PGTGKTLL  235 (440)
T KOG0726|consen  219 PKGVILYGEPGTGKTLL  235 (440)
T ss_pred             CCeeEEeCCCCCchhHH
Confidence            36699999999999954

>PHA00012 I assembly protein

Probab=85.91  E-value=2.5  Score=39.49  Aligned_cols=24  Identities=25%  Similarity=0.278  Sum_probs=18.3

Q ss_pred             EEEecCCCCCccchhhHHHHHHHH
Q psy496           72 SIIYTSTGCGKTTQVPQFILDDEI   95 (319)
Q Consensus        72 vli~apTGSGKT~~~~l~il~~l~   95 (319)
                      -+|+|-.|||||.....-+...+.
T Consensus         4 ylITGkPGSGKSl~aV~~I~~~L~   27 (361)
T PHA00012          4 YVVTGKLGAGKTLVAVSRIQDKLV   27 (361)
T ss_pred             EEEecCCCCCchHHHHHHHHHHHH
Confidence            578999999999877665555443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	319
3llm_A	235	Crystal Structure Analysis Of A Rna Helicase Length		1e-42
3kx2_B	767	Crystal Structure Of Prp43p In Complex With Adp Len		9e-37
2xau_A	773	Crystal Structure Of The Prp43p Deah-Box Rna Helica		9e-37

>pdb|3LLM|A Chain A, Crystal Structure Analysis Of A Rna Helicase Length = 235

Iteration: 1
 Score =  170 bits (431), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 80/161 (49%), Positives = 114/161 (70%), Gaps = 5/161 (3%)
Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           II  +TGCGKTTQVPQFILDD I  +R +EC I+VTQPRRISA+++AERVA ER E+   
Sbjct: 80  IIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEE--- 136
Query: 133 PGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF 192
           PG S GY +R E  LPR   SI +CT G+L   +++   + G+SH+++DEIHER + +DF
Sbjct: 137 PGKSCGYSVRFESILPRPHASIXFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDF 194
Query: 193 LLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHI 233
           LL +L+DV     +++++L SAT++   F ++F   PI+ +
Sbjct: 195 LLVVLRDVVQAYPEVRIVLXSATIDTSXFCEYFFNCPIIEV 235

>pdb|3KX2|B Chain B, Crystal Structure Of Prp43p In Complex With Adp Length = 767

Iteration: 1
 Score =  150 bits (379), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 80/173 (46%), Positives = 114/173 (65%), Gaps = 8/173 (4%)
Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           +    TG GKTTQ+PQF+L DE+     ++  +  TQPRR++A+++A+RVA+E D + G 
Sbjct: 113 VFVGETGSGKTTQIPQFVLFDEMPHLENTQ--VACTQPRRVAAMSVAQRVAEEMDVKLG- 169
Query: 133 PGSSVGYQIRLEKELPRKRGSIL-YCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
               VGY IR E +   K  +IL Y T G+L      D  LS  S I++DE HER++ +D
Sbjct: 170 --EEVGYSIRFENKTSNK--TILKYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATD 225
Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYY 244
            L+ +LK V  +R DLK+I+MSATL+AEKF ++F  AP+L +PG TYPV+ YY
Sbjct: 226 ILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFNDAPLLAVPGRTYPVELYY 278

>pdb|2XAU|A Chain A, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In Complex With Adp Length = 773

Iteration: 1
 Score =  150 bits (379), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 80/173 (46%), Positives = 114/173 (65%), Gaps = 8/173 (4%)
Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           +    TG GKTTQ+PQF+L DE+     ++  +  TQPRR++A+++A+RVA+E D + G 
Sbjct: 113 VFVGETGSGKTTQIPQFVLFDEMPHLENTQ--VACTQPRRVAAMSVAQRVAEEMDVKLG- 169
Query: 133 PGSSVGYQIRLEKELPRKRGSIL-YCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
               VGY IR E +   K  +IL Y T G+L      D  LS  S I++DE HER++ +D
Sbjct: 170 --EEVGYSIRFENKTSNK--TILKYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATD 225
Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYY 244
            L+ +LK V  +R DLK+I+MSATL+AEKF ++F  AP+L +PG TYPV+ YY
Sbjct: 226 ILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFNDAPLLAVPGRTYPVELYY 278

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	319
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	5e-90
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	3e-19
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	5e-61
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	2e-06
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	3e-27
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	3e-27
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	1e-05
1yks_A	440	Genome polyprotein [contains: flavivirin protease	9e-27
1yks_A	440	Genome polyprotein [contains: flavivirin protease	4e-05
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	2e-26
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	3e-05
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	7e-26
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	1e-05
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	6e-25
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	1e-23
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	3e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05

>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} Length = 235

 Score =  267 bits (685), Expect = 5e-90
 Identities = 81/161 (50%), Positives = 115/161 (71%), Gaps = 5/161 (3%)

Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           II  +TGCGKTTQVPQFILDD I  +R +EC I+VTQPRRISA+++AERVA ER E    
Sbjct: 80  IIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGE---E 136

Query: 133 PGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF 192
           PG S GY +R E  LPR   SI++CT G+L   +++   + G+SH+++DEIHER + +DF
Sbjct: 137 PGKSCGYSVRFESILPRPHASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDF 194

Query: 193 LLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHI 233
           LL +L+DV     +++++LMSAT++   F ++F   PI+ +
Sbjct: 195 LLVVLRDVVQAYPEVRIVLMSATIDTSMFCEYFFNCPIIEV 235

>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} Length = 235

 Score = 83.9 bits (208), Expect = 3e-19
 Identities = 29/40 (72%), Positives = 35/40 (87%)

Query: 19  GCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAL 58
           GCGKTTQVPQFILDD I  +R +EC I+VTQPRRISA+++
Sbjct: 86  GCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSV 125

>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* Length = 773

 Score =  206 bits (526), Expect = 5e-61
 Identities = 77/176 (43%), Positives = 111/176 (63%), Gaps = 6/176 (3%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
            +    TG GKTTQ+PQF+L DE+     +   +  TQPRR++A+++A+RVA+E D    
Sbjct: 112 MVFVGETGSGKTTQIPQFVLFDEMPHLENT--QVACTQPRRVAAMSVAQRVAEEMD---V 166

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
           + G  VGY IR E      +  + Y T G+L      D  LS  S I++DE HER++ +D
Sbjct: 167 KLGEEVGYSIRFE-NKTSNKTILKYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATD 225

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLED 247
            L+ +LK V  +R DLK+I+MSATL+AEKF ++F  AP+L +PG TYPV+ YY  +
Sbjct: 226 ILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFNDAPLLAVPGRTYPVELYYTPE 281

>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* Length = 773

 Score = 48.5 bits (116), Expect = 2e-06
 Identities = 18/41 (43%), Positives = 28/41 (68%), Gaps = 2/41 (4%)

Query: 18  AGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAL 58
            G GKTTQ+PQF+L DE+     +   +  TQPRR++A+++
Sbjct: 118 TGSGKTTQIPQFVLFDEMPHLENT--QVACTQPRRVAAMSV 156

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666

 Score =  111 bits (278), Expect = 3e-27
 Identities = 22/173 (12%), Positives = 48/173 (27%), Gaps = 25/173 (14%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           + ++  TG GK+T+VP                 ++V  P   + +     +++       
Sbjct: 235 AHLHAPTGSGKSTKVPAAYAAQGYK--------VLVLNPSVAATLGFGAYMSKAHGI--- 283

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
               ++   +R           + Y T G    +            I+ DE H     + 
Sbjct: 284 --DPNIRTGVRTI----TTGAPVTYSTYGKF--LADGGCSGGAYDIIICDECHSTDSTTI 335

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYY 244
             +  + D  +      ++L +AT                +I           
Sbjct: 336 LGIGTVLDQAETAGARLVVLATATPPGSVTVPHP------NIEEVALSNTGEI 382

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A Length = 431

 Score =  109 bits (274), Expect = 3e-27
 Identities = 25/181 (13%), Positives = 56/181 (30%), Gaps = 18/181 (9%)

Query: 78  TGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSV 137
            G GKT +V   ++ + + +        ++  P R+ A  + E +  E       P   +
Sbjct: 11  PGAGKTRRVLPQLVREAVKKRLR----TVILAPTRVVASEMYEALRGE-------PIRYM 59

Query: 138 GYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAIL 197
              ++ E+        + +         +     +   +  +MDE H     S      +
Sbjct: 60  TPAVQSER---TGNEIVDFMCHSTFTMKLLQGVRVPNYNLYIMDEAHFLDPASVAARGYI 116

Query: 198 KDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYY--LEDVLNMTRKD 255
           +       D   I M+AT      + F      +       P + +    E +     + 
Sbjct: 117 ETR-VSMGDAGAIFMTATPPGTTEA-FPPSNSPIIDEETRIPDKAWNSGYEWITEFDGRT 174

Query: 256 L 256
           +
Sbjct: 175 V 175

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A Length = 431

 Score = 45.6 bits (108), Expect = 1e-05
 Identities = 8/37 (21%), Positives = 17/37 (45%), Gaps = 4/37 (10%)

Query: 19 GCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISA 55
          G GKT +V   ++ + + +        ++  P R+ A
Sbjct: 12 GAGKTRRVLPQLVREAVKKRLR----TVILAPTRVVA 44

>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 =  108 bits (271), Expect = 9e-27
 Identities = 30/164 (18%), Positives = 45/164 (27%), Gaps = 16/164 (9%)

Query: 78  TGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSV 137
            G GKT +    IL +   R        +V  P R+    + E             G  V
Sbjct: 17  PGAGKTRRFLPQILAECARRRL----RTLVLAPTRVVLSEMKEAFH----------GLDV 62

Query: 138 GYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAIL 197
            +  +        R  I       L   M     +     I+MDE H     S       
Sbjct: 63  KFHTQAFSAHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFLDPASIAARGWA 122

Query: 198 KDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQ 241
                +  +   ILM+AT       +F      +       P +
Sbjct: 123 AHRA-RANESATILMTATPPGTSD-EFPHSNGEIEDVQTDIPSE 164

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A* Length = 440

 Score = 44.1 bits (104), Expect = 4e-05
 Identities = 13/66 (19%), Positives = 23/66 (34%), Gaps = 5/66 (7%)

Query: 19 GCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTST 78
          G GKT +    IL +   R        +V  P R+    +      L      +  +++ 
Sbjct: 18 GAGKTRRFLPQILAECARRRL----RTLVLAPTRVVLSEMKEAFHGLDVKFH-TQAFSAH 72

Query: 79 GCGKTT 84
          G G+  
Sbjct: 73 GSGREV 78

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A Length = 459

 Score =  107 bits (268), Expect = 2e-26
 Identities = 32/182 (17%), Positives = 53/182 (29%), Gaps = 25/182 (13%)

Query: 78  TGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSV 137
            G GKT ++   I+ D I +         V  P R+    +A  +A+         G  V
Sbjct: 30  PGSGKTRKILPQIIKDAIQQRLR----TAVLAPTRV----VAAEMAEALR------GLPV 75

Query: 138 GYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAIL 197
            YQ    +   +    +       L   + S   +   +  VMDE H     S      +
Sbjct: 76  RYQTSAVQREHQGNEIVDVMCHATLTHRLMSPNRVPNYNLFVMDEAHFTDPASIAARGYI 135

Query: 198 KDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLK 257
                +  +   I M+AT                  P    P+ +   E          +
Sbjct: 136 ATKV-ELGEAAAIFMTATPPGTTDP----------FPDSNAPIHDLQDEIPDRAWSSGYE 184

Query: 258 LI 259
            I
Sbjct: 185 WI 186

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A Length = 459

 Score = 44.4 bits (105), Expect = 3e-05
 Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 4/37 (10%)

Query: 19 GCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISA 55
          G GKT ++   I+ D I +         V  P R+ A
Sbjct: 31 GSGKTRKILPQIIKDAIQQRLR----TAVLAPTRVVA 63

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A Length = 451

 Score =  105 bits (264), Expect = 7e-26
 Identities = 32/181 (17%), Positives = 58/181 (32%), Gaps = 18/181 (9%)

Query: 78  TGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSV 137
            G GKT ++   I+ + + R        ++  P R+ A  + E +           G  +
Sbjct: 28  PGAGKTKRILPSIVREALLRRL----RTLILAPTRVVAAEMEEALR----------GLPI 73

Query: 138 GYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAIL 197
            YQ    K     R  +           + S   +   + IVMDE H     S      +
Sbjct: 74  RYQTPAVKSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSVAARGYI 133

Query: 198 KDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYY--LEDVLNMTRKD 255
                +  +   I M+AT            +PI  I     P + +    + + +   K 
Sbjct: 134 STR-VEMGEAAAIFMTATPPGSTDPFPQSNSPIEDIER-EIPERSWNTGFDWITDYQGKT 191

Query: 256 L 256
           +
Sbjct: 192 V 192

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A Length = 451

 Score = 45.2 bits (107), Expect = 1e-05
 Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 5/66 (7%)

Query: 19 GCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTST 78
          G GKT ++   I+ + + R        ++  P R+ A  +    L   PI   +    S 
Sbjct: 29 GAGKTKRILPSIVREALLRRL----RTLILAPTRVVAAEMEEA-LRGLPIRYQTPAVKSD 83

Query: 79 GCGKTT 84
            G+  
Sbjct: 84 HTGREI 89

>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 Length = 618

 Score =  104 bits (260), Expect = 6e-25
 Identities = 31/174 (17%), Positives = 55/174 (31%), Gaps = 16/174 (9%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           +I+    G GKT ++   I+ + + R        ++  P R+ A  + E +         
Sbjct: 189 TIMDLHPGAGKTKRILPSIVREALKRRL----RTLILAPTRVVAAEMEEALRGLP----- 239

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
                + YQ    K     R  +           + S   +   + IVMDE H     S 
Sbjct: 240 -----IRYQTPAVKSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSV 294

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYL 245
                +     +  +   I M+AT            +PI  I     P + +  
Sbjct: 295 AARGYISTR-VEMGEAAAIFMTATPPGSTDPFPQSNSPIEDIER-EIPERSWNT 346

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus} Length = 673

 Score =  100 bits (250), Expect = 1e-23
 Identities = 30/173 (17%), Positives = 53/173 (30%), Gaps = 32/173 (18%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           +++    G GKT ++   I+ D I +         V  P R+ A  +AE +         
Sbjct: 244 TVLDLHPGAGKTRRILPQIIKDAIQKRL----RTAVLAPTRVVAAEMAEALRGL------ 293

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
            P   +   ++ E         +       L   + S   +   +  VMDE H     S 
Sbjct: 294 -PVRYLTPAVQREHS---GNEIVDVMCHATLTHRLMSPLRVPNYNLFVMDEAHFTDPASI 349

Query: 192 FLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYY 244
                +     +  +   I M+AT                  PG + P  +  
Sbjct: 350 AARGYIATRV-EAGEAAAIFMTATP-----------------PGTSDPFPDTN 384

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus} Length = 673

 Score = 41.5 bits (97), Expect = 3e-04
 Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 4/37 (10%)

Query: 19  GCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISA 55
           G GKT ++   I+ D I +         V  P R+ A
Sbjct: 251 GAGKTRRILPQIIKDAIQKRL----RTAVLAPTRVVA 283

>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 = 68.0 bits (165), Expect = 1e-12
 Identities = 38/293 (12%), Positives = 89/293 (30%), Gaps = 78/293 (26%)

Query: 52  RISAIALINKCLTLSPILSPS---IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVT 108
           R+     + + L     L P+   +I    G GKT       +  ++  +   +C +   
Sbjct: 133 RLQPYLKLRQALL---ELRPAKNVLIDGVLGSGKTW------VALDVCLSYKVQCKM--- 180

Query: 109 QPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQS 168
              +I  + +           C  P + +    +L  ++        + +     +   +
Sbjct: 181 -DFKIFWLNLK---------NCNSPETVLEMLQKLLYQIDPN-----WTS---RSDHSSN 222

Query: 169 DP-----ILSGVSHIVMDEIHERSMISDFLLAILKDVTDKR--KDLKL---ILMSATLNA 218
                  I + +  ++  + +E       LL +L +V + +      L   IL++ T   
Sbjct: 223 IKLRIHSIQAELRRLLKSKPYENC-----LL-VLLNVQNAKAWNAFNLSCKILLT-TRFK 275

Query: 219 EKFSQFFGGAPILHIP------GFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQ 272
           +  + F   A   HI         T    +  L   L+   +DL               +
Sbjct: 276 Q-VTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP-------------RE 321

Query: 273 FFGGAPILHIPGFTYPVQEY-----YLEDVLN--MTRTLKRSETQQYPNDQQH 318
                P   +      +++        + V    +T  ++ S     P + + 
Sbjct: 322 VLTTNP-RRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK 373

>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 = 57.6 bits (138), Expect = 2e-09
 Identities = 51/341 (14%), Positives = 103/341 (30%), Gaps = 90/341 (26%)

Query: 17  LAGCGKTTQVPQFILDDEIARNRGSECC-------IMVTQPRRISAI--ALINKCLTLSP 67
           + G GKT       +  ++  +   +C        + +        +   L      + P
Sbjct: 158 VLGSGKTW------VALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP 211

Query: 68  ILSPSIIYTSTGCGKTTQV----------PQF-----ILDD----EIARNRGSECCIMV- 107
             +    ++S    +   +            +     +L +    +        C I++ 
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLT 271

Query: 108 TQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILP-EVM 166
           T+ ++++    A        +       S+       K L  K    L C    LP EV+
Sbjct: 272 TRFKQVTDFLSAATTTHISLDH-----HSMTLTPDEVKSLLLK---YLDCRPQDLPREVL 323

Query: 167 QSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS-ATLNAEKFSQFF 225
            ++P    +S I+ + I +     D      K V   +    +I  S   L   ++ + F
Sbjct: 324 TTNPRR--LS-IIAESIRDGLATWDN----WKHVNCDKLT-TIIESSLNVLEPAEYRKMF 375

Query: 226 GGAPIL----HIPGFTYPVQEYYLEDVL-----NMTRKDLKLI---LMSATLNAEKFSQF 273
               +     HIP             +L     ++ + D+ ++   L   +L  EK    
Sbjct: 376 DRLSVFPPSAHIP-----------TILLSLIWFDVIKSDVMVVVNKLHKYSL-VEK---- 419

Query: 274 FGGAPILHIPGFTYPVQEYYLEDVLNMT--RTLKRSETQQY 312
                       T  +   YLE  + +     L RS    Y
Sbjct: 420 -------QPKESTISIPSIYLELKVKLENEYALHRSIVDHY 453

>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 = 44.8 bits (105), Expect = 3e-05
 Identities = 51/335 (15%), Positives = 102/335 (30%), Gaps = 87/335 (25%)

Query: 30  ILDD----EIARNRGSECCIMVT----------QPRRISAIALINKCLTLSPILSPSIIY 75
           +L +    +        C I++T               + I+L +  +TL+P    S++ 
Sbjct: 249 VLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL 308

Query: 76  TSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER-----DEQC 130
               C +   +P              E     T PRR+S IA + R             C
Sbjct: 309 KYLDC-RPQDLP-------------REVL--TTNPRRLSIIAESIRDGLATWDNWKHVNC 352

Query: 131 GRPGSSVGYQIR-LEKELPRKRGSILYCTAGILPE-------VMQ---SDPILSGVSHIV 179
            +  + +   +  LE    RK    ++    + P        ++     D I S V  + 
Sbjct: 353 DKLTTIIESSLNVLEPAEYRK----MFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVV- 407

Query: 180 MDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILH---IPGF 236
           ++++H+ S++        K   +    +  I +   +  E           LH   +   
Sbjct: 408 VNKLHKYSLV-------EKQPKESTISIPSIYLELKVKLENEYA-------LHRSIVD-- 451

Query: 237 TYPVQEYYLEDVLNMTRKDLKLIL------MSATLNAEKFSQF--------FGGAPILHI 282
            Y + + +  D L     D +         +    + E+ + F        F    I H 
Sbjct: 452 HYNIPKTFDSDDLIPPYLD-QYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHD 510

Query: 283 PGFTYPVQEYYLEDVLNMTRTLKRSETQQYPNDQQ 317
              T       + + L   +  K       P  ++
Sbjct: 511 S--TAWNASGSILNTLQQLKFYKPYICDNDPKYER 543

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	319
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.96
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.95
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.94
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.94
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.93
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.93
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.93
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.93
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.92
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.91
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.91
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.91
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.91
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.91
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.91
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.91
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.91
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.91
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.91
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.9
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.9
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.9
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.9
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.9
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.9
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.9
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.9
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.89
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.89
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.89
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.89
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.89
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.89
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.89
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.89
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.88
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.88
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.88
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.87
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.87
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.86
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.85
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.84
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.83
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.83
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.83
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.82
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.81
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.81
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.81
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.8
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.8
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.78
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.78
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.78
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.78
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.76
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.76
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.76
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.74
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.72
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.72
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.7
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.7
3h1t_A	590	Type I site-specific restriction-modification syst	99.63
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.62
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.59
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.59
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.59
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.58
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.51
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.43
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.42
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.24
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.14
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.13
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.08
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.84
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.71
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.56
3jux_A	822	Protein translocase subunit SECA; protein transloc	98.2
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.14
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.78
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.77
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.43
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	97.21
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.01
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	96.96
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.95
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	96.82
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	96.8
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.78
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.76
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	96.7
2chg_A	226	Replication factor C small subunit; DNA-binding pr	96.57
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.56
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.48
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	96.44
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	96.44
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.42
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	96.22
3bos_A	242	Putative DNA replication factor; P-loop containing	96.2
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.15
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	96.14
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	96.14
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	96.07
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	96.06
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	96.03
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	95.99
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	95.95
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	95.9
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	95.88
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	95.87
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	95.87
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	95.81
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	95.77
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	95.75
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	95.64
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	95.49
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	95.45
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	95.28
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	95.26
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	95.13
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	95.12
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	95.1
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	95.05
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	94.95
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	94.92
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	94.81
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	94.8
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	94.78
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	94.76
2chq_A	319	Replication factor C small subunit; DNA-binding pr	94.75
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	94.67
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	94.38
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	93.95
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	93.47
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	93.35
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	93.33
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	93.15
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	92.68
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	92.57
2xxa_A	433	Signal recognition particle protein; protein trans	92.47
2eyu_A	261	Twitching motility protein PILT; pilus retraction	92.33
3co5_A	143	Putative two-component system transcriptional RES	92.2
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	91.8
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	91.07
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	91.07
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	90.97
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	90.88
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	90.82
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	90.56
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	90.51
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	90.43
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	90.4
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	90.26
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	90.23
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	90.19
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	90.12
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	90.07
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	90.02
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	89.94
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	89.83
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	89.49
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	89.36
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	89.36
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	89.27
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	89.25
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	89.21
2ewv_A	372	Twitching motility protein PILT; pilus retraction	89.14
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	89.12
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	89.05
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	88.89
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	88.89
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	88.85
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	88.78
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	88.74
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	88.67
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	88.52
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	88.41
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	88.41
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	88.32
1p9r_A	418	General secretion pathway protein E; bacterial typ	88.32
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	88.3
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	88.29
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	88.26
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	88.21
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	88.14
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	88.07
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	88.06
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	88.02
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	87.97
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	87.93
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	87.93
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	87.87
2cvh_A	220	DNA repair and recombination protein RADB; filamen	87.85
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	87.79
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	87.77
2qgz_A	308	Helicase loader, putative primosome component; str	87.73
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	87.57
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	87.53
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	87.38
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	87.35
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	87.31
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	87.13
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	87.05
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	86.88
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	86.88
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	86.87
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	86.75
1tue_A	212	Replication protein E1; helicase, replication, E1E	86.61
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	86.59
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	86.52
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	86.47
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	86.44
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	86.42
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	86.4
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	86.39
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	86.27
4a74_A	231	DNA repair and recombination protein RADA; hydrola	86.08
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	86.03
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	85.99
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	85.9
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	85.82
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	85.47
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	85.46
3pvs_A	447	Replication-associated recombination protein A; ma	85.44
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	85.14
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	85.07
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	85.03
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	85.02
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	84.95
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	84.92
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	84.88
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	84.85
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	84.81
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	84.54
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	84.49
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	84.46
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	84.43
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	84.41
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	84.4
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	84.12
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	84.01
2vli_A	183	Antibiotic resistance protein; transferase, tunica	83.98
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	83.91
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	83.9
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	83.89
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	83.83
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	83.83
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	83.74
1via_A	175	Shikimate kinase; structural genomics, transferase	83.73
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	83.57
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	83.54
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	83.52
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	83.51
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	83.49
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	83.38
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	83.37
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	83.35
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	83.34
1sgw_A	214	Putative ABC transporter; structural genomics, P p	83.25
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	83.25
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	83.2
2r6a_A	454	DNAB helicase, replicative helicase; replication,	83.15
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	83.12
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	83.05
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	83.04
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	83.02
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	83.01
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	82.91
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	82.89
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	82.88
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	82.86
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	82.61
2l8b_A	189	Protein TRAI, DNA helicase I; RECD, hydrolase; NMR	82.6
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	82.58
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	82.54
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	82.49
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	82.45
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	82.43
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	82.42
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	82.42
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	82.33
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	82.3
3kta_A	182	Chromosome segregation protein SMC; structural mai	82.27
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	82.24
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	82.2
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	82.19
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	82.16
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	82.1
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	82.04
1u94_A	356	RECA protein, recombinase A; homologous recombinat	82.03
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	81.97
2ghi_A	260	Transport protein; multidrug resistance protein, M	81.96
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	81.94
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	81.91
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	81.86
1ji0_A	240	ABC transporter; ATP binding protein, structural g	81.82
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	81.73
1g6h_A	257	High-affinity branched-chain amino acid transport	81.7
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	81.68
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	81.56
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	81.5
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	81.48
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	81.47
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	81.43
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	81.41
2og2_A	359	Putative signal recognition particle receptor; nuc	81.36
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	81.19
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	81.19
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	81.17
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	81.17
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	81.14
1b0u_A	262	Histidine permease; ABC transporter, transport pro	81.08
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	81.06
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	81.04
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	81.0
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	80.98
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	80.9
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	80.84
2z43_A	324	DNA repair and recombination protein RADA; archaea	80.79
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	80.76
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	80.73
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	80.6
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	80.59
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	80.53
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	80.48
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	80.44
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	80.41
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	80.36
2r44_A	331	Uncharacterized protein; putative ATPase, structur	80.34
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	80.22
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	80.22
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	80.21
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	80.2
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	80.04
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	80.01

>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=99.96  E-value=4.6e-29  Score=220.70  Aligned_cols=174  Identities=48%  Similarity=0.822  Sum_probs=146.3

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ..++|.++++.+..          +++++++||||||||+++.+++++.....+.+....++++.|+|+++.|+++++..
T Consensus        62 ~~~~q~~~i~~i~~----------g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~  131 (235)
T 3llm_A           62 VKKFESEILEAISQ----------NSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAF  131 (235)
T ss_dssp             GGGGHHHHHHHHHH----------CSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhc----------CCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHH
Confidence            44666777666654          56789999999999999999999887766555566889999999999999999998


Q ss_pred             HhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccc
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKR  204 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~  204 (319)
                      .++..+   |..+|+..+.+......+++|+|+|||++++++..  .++++++||+||+|++++..++....++.+....
T Consensus       132 ~~~~~~---~~~~g~~~~~~~~~~~~~~~Ivv~Tpg~l~~~l~~--~l~~~~~lVlDEah~~~~~~~~~~~~l~~i~~~~  206 (235)
T 3llm_A          132 ERGEEP---GKSCGYSVRFESILPRPHASIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAY  206 (235)
T ss_dssp             TTTCCT---TSSEEEEETTEEECCCSSSEEEEEEHHHHHHHHHH--CCTTCCEEEECCTTSCCHHHHHHHHHHHHHHHHC
T ss_pred             Hhcccc---CceEEEeechhhccCCCCCeEEEECHHHHHHHHHh--hhcCCcEEEEECCccCCcchHHHHHHHHHHHhhC
Confidence            887766   88889888777665545688999999999999965  4899999999999998889998888888887766


Q ss_pred             cCceEEEeccccChhhHhhhhCCCCEEEe
Q psy496          205 KDLKLILMSATLNAEKFSQFFGGAPILHI  233 (319)
Q Consensus       205 ~~~qiv~lSAT~~~~~l~~~l~~~~~i~~  233 (319)
                      ++.|+++||||++.+.+++||++++++.+
T Consensus       207 ~~~~~il~SAT~~~~~~~~~~~~~pvi~v  235 (235)
T 3llm_A          207 PEVRIVLMSATIDTSMFCEYFFNCPIIEV  235 (235)
T ss_dssp             TTSEEEEEECSSCCHHHHHHTTSCCCEEC
T ss_pred             CCCeEEEEecCCCHHHHHHHcCCCCEEeC
Confidence            78899999999977789999998887653

>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=99.95  E-value=1.6e-27  Score=243.64  Aligned_cols=226  Identities=37%  Similarity=0.570  Sum_probs=174.5

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++++|+.+|+.+..         .+++++|+||||||||++++..++......+  ...++++++|+|+||.|+++++++
T Consensus        94 P~~~q~~~i~~~l~---------~~~~vii~gpTGSGKTtllp~ll~~~~~~~~--~g~~ilvl~P~r~La~q~~~~l~~  162 (773)
T 2xau_A           94 PVHAQRDEFLKLYQ---------NNQIMVFVGETGSGKTTQIPQFVLFDEMPHL--ENTQVACTQPRRVAAMSVAQRVAE  162 (773)
T ss_dssp             GGGGGHHHHHHHHH---------HCSEEEEECCTTSSHHHHHHHHHHHHHCGGG--GTCEEEEEESCHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHh---------CCCeEEEECCCCCCHHHHHHHHHHHhccccC--CCceEEecCchHHHHHHHHHHHHH
Confidence            34567777766654         3567999999999999966555444332221  124688888999999999999998


Q ss_pred             HhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccc
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKR  204 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~  204 (319)
                      .++..+   +..+|+.++.++... .+++|+++|||++.+.+..++.+.++++||+||+|+|++..+.+...++.+....
T Consensus       163 ~~~~~v---~~~vG~~i~~~~~~~-~~~~I~v~T~G~l~r~l~~~~~l~~~~~lIlDEah~R~ld~d~~~~~l~~l~~~~  238 (773)
T 2xau_A          163 EMDVKL---GEEVGYSIRFENKTS-NKTILKYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRR  238 (773)
T ss_dssp             HTTCCB---TTTEEEEETTEEECC-TTCSEEEEEHHHHHHHHHHSTTCTTEEEEEECSGGGCCHHHHHHHHHHHHHHHHC
T ss_pred             HhCCch---hheecceeccccccC-CCCCEEEECHHHHHHHHhhCccccCCCEEEecCccccccchHHHHHHHHHHHHhC
Confidence            887766   888888877665543 4678999999999999977888999999999999998888888888888887766


Q ss_pred             cCceEEEeccccChhhHhhhhCCCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCC
Q psy496          205 KDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPG  284 (319)
Q Consensus       205 ~~~qiv~lSAT~~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~  284 (319)
                      ++.|+++||||++.+.+++|+++.+++.++++.+|++++|....    ..+....+.....+.  .....+|++|||++|
T Consensus       239 ~~~~iIl~SAT~~~~~l~~~~~~~~vi~v~gr~~pv~~~~~~~~----~~~~~~~~l~~l~~~--~~~~~~g~iLVF~~~  312 (773)
T 2xau_A          239 PDLKIIIMSATLDAEKFQRYFNDAPLLAVPGRTYPVELYYTPEF----QRDYLDSAIRTVLQI--HATEEAGDILLFLTG  312 (773)
T ss_dssp             TTCEEEEEESCSCCHHHHHHTTSCCEEECCCCCCCEEEECCSSC----CSCHHHHHHHHHHHH--HHHSCSCEEEEECSC
T ss_pred             CCceEEEEeccccHHHHHHHhcCCCcccccCcccceEEEEecCC----chhHHHHHHHHHHHH--HHhcCCCCEEEECCC
Confidence            78899999999999999999999999999999999999987653    122222222222222  112237899999999


Q ss_pred             ccccccc
Q psy496          285 FTYPVQE  291 (319)
Q Consensus       285 R~~~v~~  291 (319)
                      +..+.++
T Consensus       313 ~~~i~~l  319 (773)
T 2xau_A          313 EDEIEDA  319 (773)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9877554

>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=99.94  E-value=3.4e-26  Score=249.31  Aligned_cols=252  Identities=16%  Similarity=0.113  Sum_probs=166.4

Q ss_pred             cchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCC------CCccE
Q psy496           31 LDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNR------GSECC  104 (319)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~------~~~~~  104 (319)
                      +++|....|..-....++|.+++|.+..         .++|++++||||||||.++.+++++.+.....      ....+
T Consensus        66 Lp~~~~~~f~g~~~ln~iQs~~~~~al~---------~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k  136 (1724)
T 4f92_B           66 LPKYAQAGFEGFKTLNRIQSKLYRAALE---------TDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFK  136 (1724)
T ss_dssp             SCGGGSTTCTTCSBCCHHHHHTHHHHHT---------CCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCE
T ss_pred             cCHHHHHhcCCCCCCCHHHHHHHHHHHc---------CCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCE
Confidence            4556555554334467899999988653         56889999999999999999999999865321      12458


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC----CCCceEEEECchHHHHHHhcCC---CCCCccE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP----RKRGSILYCTAGILPEVMQSDP---ILSGVSH  177 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~----~~~~~Iiv~Tpg~ll~~l~~~~---~l~~v~~  177 (319)
                      ++|++|+|+||.|..+.+.+.++..    |..++.  ..++...    ...++|+|+||+++..++.+..   .++++++
T Consensus       137 ~lyiaP~kALa~e~~~~l~~~~~~~----gi~V~~--~tGd~~~~~~~~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~  210 (1724)
T 4f92_B          137 IIYIAPMRSLVQEMVGSFGKRLATY----GITVAE--LTGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVRL  210 (1724)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHTTT----TCCEEE--CCSSCSSCCTTGGGCSEEEECHHHHHHHTTSSTTHHHHTTEEE
T ss_pred             EEEECCHHHHHHHHHHHHHHHHhhC----CCEEEE--EECCCCCCccccCCCCEEEECHHHHHHHHcCCccchhhcCcCE
Confidence            9999999999999999998877643    555542  2222111    1357899999999855554432   2789999


Q ss_pred             EEEecccc----cccchhHHHHHHHhh-hccccCceEEEecccc-ChhhHhhhhCCCC---EEEeC--Cccccceeeeeh
Q psy496          178 IVMDEIHE----RSMISDFLLAILKDV-TDKRKDLKLILMSATL-NAEKFSQFFGGAP---ILHIP--GFTYPVQEYYLE  246 (319)
Q Consensus       178 vViDEah~----~~~~~~~~~~~l~~~-~~~~~~~qiv~lSAT~-~~~~l~~~l~~~~---~i~~~--~r~~~v~~~~~~  246 (319)
                      |||||+|.    ||...+.++.++... ...+++.|+|+||||+ |++++++|++..+   .+.++  .|+.|++.++..
T Consensus       211 vIiDEvH~l~d~RG~~lE~~l~rl~~~~~~~~~~~riI~LSATl~N~~dvA~wL~~~~~~~~~~~~~~~RPvpL~~~~~~  290 (1724)
T 4f92_B          211 IILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVG  290 (1724)
T ss_dssp             EEETTGGGGGSTTHHHHHHHHHHHHHHHHHHTCCCEEEEEECSCTTHHHHHHHTTCCHHHHEEECCGGGCSSCEEEECCE
T ss_pred             EEEecchhcCCccHHHHHHHHHHHHHHHHhCCCCCcEEEEecccCCHHHHHHHhCCCCCCCeEEECCCCccCccEEEEec
Confidence            99999995    555555555544333 3356688999999999 9999999998642   34444  455566555543


Q ss_pred             hhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCcccccccc-chHhHHH
Q psy496          247 DVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEY-YLEDVLN  299 (319)
Q Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v~~~-~~~~~~~  299 (319)
                      .. ..........+....++.. .....++++||||++|+.+.+.. ++.+.+.
T Consensus       291 ~~-~~~~~~~~~~~~~~~~~~v-~~~~~~~~~LVF~~sR~~~~~~A~~l~~~~~  342 (1724)
T 4f92_B          291 IT-EKKAIKRFQIMNEIVYEKI-MEHAGKNQVLVFVHSRKETGKTARAIRDMCL  342 (1724)
T ss_dssp             EC-CCCHHHHHHHHHHHHHHHH-TTCCSSCCEEEECSSTTTTHHHHHHHHHHHH
T ss_pred             cC-CcchhhhhHHHHHHHHHHH-HHHhcCCcEEEECCCHHHHHHHHHHHHHHHh
Confidence            22 1111111112222222221 22234789999999999987663 3444433

>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=99.94  E-value=5.6e-27  Score=255.41  Aligned_cols=241  Identities=13%  Similarity=0.126  Sum_probs=163.9

Q ss_pred             chHHHhccCC-ccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecc
Q psy496           32 DDEIARNRGS-ECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQP  110 (319)
Q Consensus        32 ~~~~~~~~~~-~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~P  110 (319)
                      +..++..+.. -....|+|.++++.+.+         .++|++++||||||||+++.+|+++.+....   ..+++|++|
T Consensus       913 ~~~~e~l~~~~f~~fnpiQ~q~~~~l~~---------~~~nvlv~APTGSGKTliaelail~~l~~~~---~~kavyi~P  980 (1724)
T 4f92_B          913 NSAFESLYQDKFPFFNPIQTQVFNTVYN---------SDDNVFVGAPTGSGKTICAEFAILRMLLQSS---EGRCVYITP  980 (1724)
T ss_dssp             CHHHHTTTTTTCSBCCHHHHHHHHHHHS---------CCSCEEEECCTTSCCHHHHHHHHHHHHHHCT---TCCEEEECS
T ss_pred             CHHHHHHHHhcCCCCCHHHHHHHHHHhc---------CCCcEEEEeCCCCCchHHHHHHHHHHHHhCC---CCEEEEEcC
Confidence            4445555433 23357999999988753         4578999999999999999999999887644   347899999


Q ss_pred             cHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc---CCCCceEEEECchHHHHHHhc---CCCCCCccEEEEeccc
Q psy496          111 RRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL---PRKRGSILYCTAGILPEVMQS---DPILSGVSHIVMDEIH  184 (319)
Q Consensus       111 tr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~---~~~~~~Iiv~Tpg~ll~~l~~---~~~l~~v~~vViDEah  184 (319)
                      +|+||.|.++.+.+.++...   |..++.... +...   ...+++|+|+|||++..+++.   ...++++++||+||+|
T Consensus       981 ~raLa~q~~~~~~~~f~~~~---g~~V~~ltG-d~~~~~~~~~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H 1056 (1724)
T 4f92_B          981 MEALAEQVYMDWYEKFQDRL---NKKVVLLTG-ETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVH 1056 (1724)
T ss_dssp             CHHHHHHHHHHHHHHHTTTS---CCCEEECCS-CHHHHHHHHHHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGG
T ss_pred             hHHHHHHHHHHHHHHhchhc---CCEEEEEEC-CCCcchhhcCCCCEEEECHHHHHHHHhCcccccccceeeEEEeechh
Confidence            99999999999988877654   666653221 1111   113568999999998766643   2237899999999999


Q ss_pred             c----cccchhHHHHHHHhhhc-cccCceEEEecccc-ChhhHhhhhCCC--CEEEe--CCccccceeeeehhhhhhhhh
Q psy496          185 E----RSMISDFLLAILKDVTD-KRKDLKLILMSATL-NAEKFSQFFGGA--PILHI--PGFTYPVQEYYLEDVLNMTRK  254 (319)
Q Consensus       185 ~----~~~~~~~~~~~l~~~~~-~~~~~qiv~lSAT~-~~~~l~~~l~~~--~~i~~--~~r~~~v~~~~~~~~~~~~~~  254 (319)
                      .    +|...+..+.+++.+.. .+++.|+|+||||+ |++++++|++..  ..+.+  ..|+.|++.++......  +.
T Consensus      1057 ~l~d~rg~~le~il~rl~~i~~~~~~~~riI~lSATl~N~~dla~WL~~~~~~~~~~~~~~RPvpL~~~i~~~~~~--~~ 1134 (1724)
T 4f92_B         1057 LIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNIS--HT 1134 (1724)
T ss_dssp             GGGSTTHHHHHHHHHHHHHHHHTTSSCCEEEEEESCBTTHHHHHHHHTCCSTTEEECCGGGCSSCEEEEEEEECCC--SH
T ss_pred             hcCCCCCccHHHHHHHHHHHHhhcCCCceEEEEeCCCCCHHHHHHHhCCCCCCeEEeCCCCCCCCeEEEEEeccCC--Cc
Confidence            6    33334455555554443 55678999999999 999999999753  34444  45666666665443322  22


Q ss_pred             hHHHHHH-HHhhhhhhhccccCCCcEEEeCCccccccc
Q psy496          255 DLKLILM-SATLNAEKFSQFFGGAPILHIPGFTYPVQE  291 (319)
Q Consensus       255 ~~~~~~~-~~~~~~~~~~~~~~g~~LVFlp~R~~~v~~  291 (319)
                      ..+...+ ....... .....++++|||+++|..+...
T Consensus      1135 ~~~~~~~~~~~~~~i-~~~~~~~~~lVF~~sR~~~~~~ 1171 (1724)
T 4f92_B         1135 QTRLLSMAKPVYHAI-TKHSPKKPVIVFVPSRKQTRLT 1171 (1724)
T ss_dssp             HHHHHTTHHHHHHHH-HHHCSSSCEEEEESSHHHHHHH
T ss_pred             hhhhhhhcchHHHHH-HHhcCCCCeeeeCCCHHHHHHH
Confidence            2222222 2222221 2233478999999999887544

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=99.93  E-value=2.7e-26  Score=233.03  Aligned_cols=220  Identities=16%  Similarity=0.158  Sum_probs=152.4

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      ++.++|.++++.+.          ++++++++||||||||+++++++++.+..+     .++++++|+|+||.|.++++.
T Consensus        25 ~l~~~Q~~~i~~i~----------~~~~~lv~apTGsGKT~~~~l~il~~~~~~-----~~~l~i~P~r~La~q~~~~~~   89 (702)
T 2p6r_A           25 ELFPPQAEAVEKVF----------SGKNLLLAMPTAAGKTLLAEMAMVREAIKG-----GKSLYVVPLRALAGEKYESFK   89 (702)
T ss_dssp             CCCCCCHHHHHHHT----------TCSCEEEECSSHHHHHHHHHHHHHHHHHTT-----CCEEEEESSHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHh----------CCCcEEEEcCCccHHHHHHHHHHHHHHHhC-----CcEEEEeCcHHHHHHHHHHHH
Confidence            35689999998854          257899999999999999999999886532     378888899999999999884


Q ss_pred             HHhccccCCCCceEEEEEeccccc--CCCCceEEEECchHHHHHHhcCCC-CCCccEEEEecccc-----cccchhHHHH
Q psy496          124 QERDEQCGRPGSSVGYQIRLEKEL--PRKRGSILYCTAGILPEVMQSDPI-LSGVSHIVMDEIHE-----RSMISDFLLA  195 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~~~--~~~~~~Iiv~Tpg~ll~~l~~~~~-l~~v~~vViDEah~-----~~~~~~~~~~  195 (319)
                      . +...    |..++.........  ...+++|+|+|||++.+++..++. ++++++||+||+|+     |+...+.++.
T Consensus        90 ~-~~~~----g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~~~ll~  164 (702)
T 2p6r_A           90 K-WEKI----GLRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVT  164 (702)
T ss_dssp             T-TTTT----TCCEEEECSSCBCCSSCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHHHH
T ss_pred             H-HHhc----CCEEEEEeCCCCcchhhccCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCCCCcccHHHHHHH
Confidence            3 2221    44444322211111  113678999999999999977666 89999999999998     4444555555


Q ss_pred             HHHhhhccccCceEEEecccc-ChhhHhhhhCCCCEEEeCCccccceeeeehhh-hhhhhhhH---HHH-HHHHhhhhhh
Q psy496          196 ILKDVTDKRKDLKLILMSATL-NAEKFSQFFGGAPILHIPGFTYPVQEYYLEDV-LNMTRKDL---KLI-LMSATLNAEK  269 (319)
Q Consensus       196 ~l~~~~~~~~~~qiv~lSAT~-~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~-~~~~~~~~---~~~-~~~~~~~~~~  269 (319)
                      .++.   .+++.|+|+||||+ |.+++++|++ .+.+..++|++|++..+.... ....+...   +.. ......+.  
T Consensus       165 ~l~~---~~~~~~ii~lSATl~n~~~~~~~l~-~~~~~~~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  238 (702)
T 2p6r_A          165 KMRR---MNKALRVIGLSATAPNVTEIAEWLD-ADYYVSDWRPVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVEEC--  238 (702)
T ss_dssp             HHHH---HCTTCEEEEEECCCTTHHHHHHHTT-CEEEECCCCSSCEEEEEECSSEEEEEETTEEEEEECCHHHHHHHH--
T ss_pred             HHHh---cCcCceEEEECCCcCCHHHHHHHhC-CCcccCCCCCccceEEEeeCCeeeccCcchhhhhhhhHHHHHHHH--
Confidence            4443   34578999999999 7999999996 667888899999876553221 00000000   000 11111111  


Q ss_pred             hccccCCCcEEEeCCccccccc
Q psy496          270 FSQFFGGAPILHIPGFTYPVQE  291 (319)
Q Consensus       270 ~~~~~~g~~LVFlp~R~~~v~~  291 (319)
                      ..  .++++|||+++|..+.+.
T Consensus       239 ~~--~~~~~LVF~~s~~~~~~~  258 (702)
T 2p6r_A          239 VA--ENGGVLVFESTRRGAEKT  258 (702)
T ss_dssp             HH--TTCCEEEECSSHHHHHHH
T ss_pred             Hh--cCCCEEEEcCCHHHHHHH
Confidence            11  378999999999887544

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=99.93  E-value=3.8e-26  Score=209.35  Aligned_cols=188  Identities=16%  Similarity=0.073  Sum_probs=128.3

Q ss_pred             ccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEE
Q psy496           26 VPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCI  105 (319)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~v  105 (319)
                      ++..+.+...+..+.   .++++|.++||.++.|        .+++++++||||||||++|.+|+++.+.....+  .++
T Consensus        99 l~~~l~~~l~~~g~~---~pt~iQ~~ai~~il~~--------~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~--~~~  165 (300)
T 3fmo_B           99 LKPQLLQGVYAMGFN---RPSKIQENALPLMLAE--------PPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKY--PQC  165 (300)
T ss_dssp             CCHHHHHHHHHTTCC---SCCHHHHHHHHHHTSS--------SCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCS--CCE
T ss_pred             CCHHHHHHHHHcCCC---CCCHHHHHHHHHHHcC--------CCCeEEEECCCCCCccHHHHHHHHHhhhccCCC--ceE
Confidence            444444444333332   3568899999998653        347899999999999999999999987654433  356


Q ss_pred             EEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc--cCCCCceEEEECchHHHHHHhc--CCCCCCccEEEEe
Q psy496          106 MVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE--LPRKRGSILYCTAGILPEVMQS--DPILSGVSHIVMD  181 (319)
Q Consensus       106 l~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~--~~~~~~~Iiv~Tpg~ll~~l~~--~~~l~~v~~vViD  181 (319)
                      ++++|||+||.|+++.+..+.....   +..++........  .....++|+|+|||+|++++..  ...++++++||||
T Consensus       166 lil~PtreLa~Q~~~~~~~l~~~~~---~~~~~~~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlD  242 (300)
T 3fmo_B          166 LCLSPTYELALQTGKVIEQMGKFYP---ELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLD  242 (300)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTST---TCCEEEESTTCCCCTTCCCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEET
T ss_pred             EEEcCcHHHHHHHHHHHHHHHhhCC---CcEEEEEeCCccHhhhhcCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEe
Confidence            7777999999999998887754322   3344433332221  1123568999999999999954  3348999999999


Q ss_pred             cccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCC
Q psy496          182 EIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAP  229 (319)
Q Consensus       182 Eah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~  229 (319)
                      |||...-...+.......+...+++.|+++||||+  +...+++.+...|
T Consensus       243 Ead~l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~~~v~~~a~~~l~~p  292 (300)
T 3fmo_B          243 EADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP  292 (300)
T ss_dssp             THHHHHHSTTHHHHHHHHHTTSCTTCEEEEEESCCCHHHHHHHHHHSSSC
T ss_pred             CHHHHhhccCcHHHHHHHHHhCCCCCEEEEEeccCCHHHHHHHHHHCCCC
Confidence            99973211234444444444466788999999999  5566666544333

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.93  E-value=2.5e-26  Score=233.63  Aligned_cols=176  Identities=19%  Similarity=0.130  Sum_probs=129.3

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      .+.++|.++++.+         ...+++++++||||||||+++++++++.+...+    .++++++|+|+||.|.++++.
T Consensus        30 ~l~~~Q~~~i~~~---------~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~----~~il~i~P~r~La~q~~~~~~   96 (715)
T 2va8_A           30 KLNPPQTEAVKKG---------LLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNG----GKAIYVTPLRALTNEKYLTFK   96 (715)
T ss_dssp             BCCHHHHHHHHTT---------TTTTCCEEEECCTTSCHHHHHHHHHHHHHHHSC----SEEEEECSCHHHHHHHHHHHG
T ss_pred             CCCHHHHHHHHHH---------hcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHCC----CeEEEEeCcHHHHHHHHHHHH
Confidence            3568899988762         123688999999999999999999998876432    489999999999999999984


Q ss_pred             HHhccccCCCCceEEEEEe----cccccCCCCceEEEECchHHHHHHhcCCC-CCCccEEEEeccccccc--chhHHHHH
Q psy496          124 QERDEQCGRPGSSVGYQIR----LEKELPRKRGSILYCTAGILPEVMQSDPI-LSGVSHIVMDEIHERSM--ISDFLLAI  196 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~----~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~-l~~v~~vViDEah~~~~--~~~~~~~~  196 (319)
                      . +...    |..++....    .+...  .+++|+|+|||++.+++..++. ++++++||+||+|+.+-  ....+...
T Consensus        97 ~-~~~~----g~~v~~~~G~~~~~~~~~--~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~~~~~l~~i  169 (715)
T 2va8_A           97 D-WELI----GFKVAMTSGDYDTDDAWL--KNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPERGPVVESV  169 (715)
T ss_dssp             G-GGGG----TCCEEECCSCSSSCCGGG--GGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTTTHHHHHHH
T ss_pred             H-hhcC----CCEEEEEeCCCCCchhhc--CCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcccchHHHHH
Confidence            3 2221    334432211    11111  2578999999999999877666 89999999999998431  11122223


Q ss_pred             HHhhhccccCceEEEecccc-ChhhHhhhhCCCCEEEeCCccccceeee
Q psy496          197 LKDVTDKRKDLKLILMSATL-NAEKFSQFFGGAPILHIPGFTYPVQEYY  244 (319)
Q Consensus       197 l~~~~~~~~~~qiv~lSAT~-~~~~l~~~l~~~~~i~~~~r~~~v~~~~  244 (319)
                      +..+    ++.|+|+||||+ |.+++++|++ .+.+..++|++|++.++
T Consensus       170 ~~~~----~~~~ii~lSATl~n~~~~~~~l~-~~~~~~~~r~~~l~~~~  213 (715)
T 2va8_A          170 TIRA----KRRNLLALSATISNYKQIAKWLG-AEPVATNWRPVPLIEGV  213 (715)
T ss_dssp             HHHH----HTSEEEEEESCCTTHHHHHHHHT-CEEEECCCCSSCEEEEE
T ss_pred             HHhc----ccCcEEEEcCCCCCHHHHHHHhC-CCccCCCCCCCCceEEE
Confidence            3222    267999999999 8999999996 56788888988887654

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=99.93  E-value=2.7e-26  Score=220.55  Aligned_cols=254  Identities=17%  Similarity=0.162  Sum_probs=153.4

Q ss_pred             cchhhhhhhhcccCCCcccccc------------ccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEE
Q psy496            6 AQSITYRLKEDLAGCGKTTQVP------------QFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSI   73 (319)
Q Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vl   73 (319)
                      ..+++|+.+.+++..-....+|            +.+.+......+   ..++|+|.++||.+++|          ++++
T Consensus        31 ~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~---~~pt~iQ~~ai~~i~~g----------~d~i   97 (434)
T 2db3_A           31 ASGIHFSKYNNIPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGY---KIPTPIQKCSIPVISSG----------RDLM   97 (434)
T ss_dssp             CCCTTGGGGGGSCEEEESSSCCCCCCCGGGSCCCHHHHHHHHHTTC---CSCCHHHHHHHHHHHTT----------CCEE
T ss_pred             ccccChhhhcCceeEecCCCCCCCcCChhhcCCCHHHHHHHHHcCC---CCCCHHHHHHHHHHhcC----------CCEE
Confidence            5678999887765322222222            222222222222   23679999999998754          5688


Q ss_pred             EecCCCCCccchhhHHHHHHHHHhCC---CCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEec-----cc
Q psy496           74 IYTSTGCGKTTQVPQFILDDEIARNR---GSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRL-----EK  145 (319)
Q Consensus        74 i~apTGSGKT~~~~l~il~~l~~~~~---~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~-----~~  145 (319)
                      ++||||||||++|++|+++.+.....   ....++++++|||+||.|+++.+.++....    +..++.....     ..
T Consensus        98 ~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~----~~~~~~~~gg~~~~~~~  173 (434)
T 2db3_A           98 ACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFES----YLKIGIVYGGTSFRHQN  173 (434)
T ss_dssp             EECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTS----SCCCCEECTTSCHHHHH
T ss_pred             EECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEecCHHHHHHHHHHHHHHhccC----CcEEEEEECCCCHHHHH
Confidence            88889999999999999998876432   224578888899999999999888775432    1222211111     11


Q ss_pred             ccCCCCceEEEECchHHHHHHhcC-CCCCCccEEEEecccccccchhHHHHHHHhhhc--cccCceEEEecccc--Chhh
Q psy496          146 ELPRKRGSILYCTAGILPEVMQSD-PILSGVSHIVMDEIHERSMISDFLLAILKDVTD--KRKDLKLILMSATL--NAEK  220 (319)
Q Consensus       146 ~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~--~~~~~qiv~lSAT~--~~~~  220 (319)
                      .....+++|+|+|||+|++++... ..+++++++|+||||+. ...++.....+.+..  .+++.|+++||||+  +.+.
T Consensus       174 ~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVlDEah~~-~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~  252 (434)
T 2db3_A          174 ECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRM-LDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQR  252 (434)
T ss_dssp             HHHTTCCSEEEECHHHHHHHHHTTSCCCTTCCEEEEETHHHH-TSTTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHH
T ss_pred             HHhhcCCCEEEEChHHHHHHHHhCCcccccCCeEEEccHhhh-hccCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHH
Confidence            111245789999999999999554 45899999999999973 333333333333332  35678999999999  3444


Q ss_pred             Hhh-hhCCCCEEEeCCc---cccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCcccc
Q psy496          221 FSQ-FFGGAPILHIPGF---TYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       221 l~~-~l~~~~~i~~~~r---~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~  288 (319)
                      +++ |+.+...+.+...   ...+...+....    .......+...      +... ++.+|||++++..+
T Consensus       253 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~----~~~k~~~l~~~------l~~~-~~~~lVF~~t~~~a  313 (434)
T 2db3_A          253 MAGEFLKNYVFVAIGIVGGACSDVKQTIYEVN----KYAKRSKLIEI------LSEQ-ADGTIVFVETKRGA  313 (434)
T ss_dssp             HHHTTCSSCEEEEESSTTCCCTTEEEEEEECC----GGGHHHHHHHH------HHHC-CTTEEEECSSHHHH
T ss_pred             HHHHhccCCEEEEeccccccccccceEEEEeC----cHHHHHHHHHH------HHhC-CCCEEEEEeCcHHH
Confidence            544 5554434444321   122333332211    11112222211      1111 34599999998765

>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=99.92  E-value=1.4e-24  Score=205.40  Aligned_cols=239  Identities=14%  Similarity=0.095  Sum_probs=147.1

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      ++++.+.+...+..+.   .++++|.+++|.+..+        .+++++++||||||||++|++|+++.+.....  ..+
T Consensus        31 ~l~~~l~~~l~~~g~~---~~~~~Q~~~i~~~~~~--------~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~--~~~   97 (412)
T 3fht_A           31 RLKPQLLQGVYAMGFN---RPSKIQENALPLMLAE--------PPQNLIAQSQSGTGKTAAFVLAMLSQVEPANK--YPQ   97 (412)
T ss_dssp             TCCHHHHHHHHHTTCC---SCCHHHHHHHHHHHSS--------SCCCEEEECCTTSCHHHHHHHHHHHHCCTTSC--SCC
T ss_pred             CCCHHHHHHHHHcCCC---CCCHHHHHHHHHHhcC--------CCCeEEEECCCCchHHHHHHHHHHHHhhhcCC--CCC
Confidence            3444444443333222   3568899999998753        45789999999999999999999987754433  336


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc--CCCCceEEEECchHHHHHHhcC--CCCCCccEEEE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL--PRKRGSILYCTAGILPEVMQSD--PILSGVSHIVM  180 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~--~~~~~~Iiv~Tpg~ll~~l~~~--~~l~~v~~vVi  180 (319)
                      +++++|+++|+.|+++.+.++.....   +..++.........  .....+|+|+||+++.+++...  ..+.++++||+
T Consensus        98 ~lil~P~~~L~~q~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iVi  174 (412)
T 3fht_A           98 CLCLSPTYELALQTGKVIEQMGKFYP---ELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVL  174 (412)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTST---TCCEEEECTTCCCCTTCCCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEE
T ss_pred             EEEECCCHHHHHHHHHHHHHHHhhcc---cceEEEeecCcchhhhhcCCCCEEEECchHHHHHHHhcCCcChhhCcEEEE
Confidence            77778999999999998887754332   44455444322211  1234689999999999998553  34789999999


Q ss_pred             ecccccccchhHHHHHHHhhhccccCceEEEeccccC--hhhHhh-hhCCCCEEEeCCccc---cceeeeehhhhhhhhh
Q psy496          181 DEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLN--AEKFSQ-FFGGAPILHIPGFTY---PVQEYYLEDVLNMTRK  254 (319)
Q Consensus       181 DEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~--~~~l~~-~l~~~~~i~~~~r~~---~v~~~~~~~~~~~~~~  254 (319)
                      ||+|.......+...........+++.|++++|||++  ...+.. ++.+...+.+.....   .+...+....    ..
T Consensus       175 DEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~  250 (412)
T 3fht_A          175 DEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCS----SR  250 (412)
T ss_dssp             ETHHHHHSTTTTHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGSSCTTEEEEEEECS----SH
T ss_pred             eCHHHHhhcCCcHHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccccccCceEEEEEcC----Ch
Confidence            9999732212222233333334556789999999993  334444 454444444433222   2223332221    11


Q ss_pred             hHHHHHHHHhhhhhhhccccCCCcEEEeCCcccc
Q psy496          255 DLKLILMSATLNAEKFSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~  288 (319)
                      ..+.......     +....++++|||++++..+
T Consensus       251 ~~~~~~l~~~-----~~~~~~~~~lvf~~~~~~~  279 (412)
T 3fht_A          251 DEKFQALCNL-----YGAITIAQAMIFCHTRKTA  279 (412)
T ss_dssp             HHHHHHHHHH-----HHHHSSSEEEEECSSHHHH
T ss_pred             HHHHHHHHHH-----HhhcCCCCEEEEeCCHHHH
Confidence            1111111111     1112367899999998765

>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=99.91  E-value=5.2e-25  Score=224.14  Aligned_cols=234  Identities=15%  Similarity=0.101  Sum_probs=152.5

Q ss_pred             cccccccchHHHhccCCccccccccccchhh-HHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCcc
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISA-IALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSEC  103 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~-~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~  103 (319)
                      ++|+.+.+ ++.....  .++.++|.++++. +.          .+++++++||||||||+++++++++.+...+    .
T Consensus         7 ~l~~~~~~-~l~~~g~--~~l~~~Q~~~i~~~~~----------~~~~~lv~apTGsGKT~~~~l~il~~~~~~~----~   69 (720)
T 2zj8_A            7 RVDERIKS-TLKERGI--ESFYPPQAEALKSGIL----------EGKNALISIPTASGKTLIAEIAMVHRILTQG----G   69 (720)
T ss_dssp             CSCHHHHH-HHHHTTC--CBCCHHHHHHHTTTGG----------GTCEEEEECCGGGCHHHHHHHHHHHHHHHHC----S
T ss_pred             CCCHHHHH-HHHHCCC--CCCCHHHHHHHHHHhc----------CCCcEEEEcCCccHHHHHHHHHHHHHHHhCC----C
Confidence            45655543 3333211  1356889999887 43          2578999999999999999999998876443    4


Q ss_pred             EEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc--CCCCceEEEECchHHHHHHhcCCC-CCCccEEEE
Q psy496          104 CIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL--PRKRGSILYCTAGILPEVMQSDPI-LSGVSHIVM  180 (319)
Q Consensus       104 ~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~--~~~~~~Iiv~Tpg~ll~~l~~~~~-l~~v~~vVi  180 (319)
                      ++++++|+|+||.|+++++.++ ...    |..++.........  ...+++|+|+|||++..++..++. ++++++||+
T Consensus        70 ~~l~i~P~raLa~q~~~~~~~l-~~~----g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIi  144 (720)
T 2zj8_A           70 KAVYIVPLKALAEEKFQEFQDW-EKI----GLRVAMATGDYDSKDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVA  144 (720)
T ss_dssp             EEEEECSSGGGHHHHHHHTGGG-GGG----TCCEEEECSCSSCCCGGGGGCSEEEECHHHHHHHHHHTCTTGGGEEEEEE
T ss_pred             EEEEEcCcHHHHHHHHHHHHHH-Hhc----CCEEEEecCCCCccccccCCCCEEEECHHHHHHHHHcChhhhhcCCEEEE
Confidence            8999999999999999998533 211    44444322211100  012578999999999998866655 899999999


Q ss_pred             ecccc-----cccchhHHHHHHHhhhccccCceEEEecccc-ChhhHhhhhCCCCEEEeCCccccceeeeehhh-hhhhh
Q psy496          181 DEIHE-----RSMISDFLLAILKDVTDKRKDLKLILMSATL-NAEKFSQFFGGAPILHIPGFTYPVQEYYLEDV-LNMTR  253 (319)
Q Consensus       181 DEah~-----~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~-~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~-~~~~~  253 (319)
                      ||+|.     |+...+.++..++      ++.|+|++|||+ |.+++++|++ .+.+..+.|+.|++..+.... .....
T Consensus       145 DE~H~l~~~~r~~~~~~ll~~l~------~~~~ii~lSATl~n~~~~~~~l~-~~~~~~~~rp~~l~~~~~~~~~~~~~~  217 (720)
T 2zj8_A          145 DEIHLIGSRDRGATLEVILAHML------GKAQIIGLSATIGNPEELAEWLN-AELIVSDWRPVKLRRGVFYQGFVTWED  217 (720)
T ss_dssp             ETGGGGGCTTTHHHHHHHHHHHB------TTBEEEEEECCCSCHHHHHHHTT-EEEEECCCCSSEEEEEEEETTEEEETT
T ss_pred             ECCcccCCCcccHHHHHHHHHhh------cCCeEEEEcCCcCCHHHHHHHhC-CcccCCCCCCCcceEEEEeCCeeeccc
Confidence            99995     3333333333333      267999999999 8999999996 456777888888776543211 00000


Q ss_pred             h--hHHHHHHHHhhhhhhhccccCCCcEEEeCCccccccc
Q psy496          254 K--DLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQE  291 (319)
Q Consensus       254 ~--~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v~~  291 (319)
                      .  ...........+.  ..  .++++|||+++|..+.++
T Consensus       218 ~~~~~~~~~~~~~~~~--~~--~~~~~LVF~~sr~~~~~~  253 (720)
T 2zj8_A          218 GSIDRFSSWEELVYDA--IR--KKKGALIFVNMRRKAERV  253 (720)
T ss_dssp             SCEEECSSTTHHHHHH--HH--TTCCEEEECSCHHHHHHH
T ss_pred             cchhhhhHHHHHHHHH--Hh--CCCCEEEEecCHHHHHHH
Confidence            0  0000000111111  11  278999999999887544

>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=99.91  E-value=7.7e-25  Score=212.50  Aligned_cols=225  Identities=14%  Similarity=0.097  Sum_probs=123.0

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++++|.+++|.++.+        .+++++++||||||||++|++|+++.+.....  ..++++++|+++||.|+++.+.+
T Consensus       115 p~~~Q~~ai~~il~~--------~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~--~~~~lil~Pt~~La~Q~~~~~~~  184 (479)
T 3fmp_B          115 PSKIQENALPLMLAE--------PPQNLIAQSQSGTGKTAAFVLAMLSQVEPANK--YPQCLCLSPTYELALQTGKVIEQ  184 (479)
T ss_dssp             CCHHHHHHHHHHTSB--------SCCEEEEECCSSSSHHHHHHHHHHTTCCTTSC--SCCEEEECSSHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHcC--------CCCcEEEEcCCCCchhHHHHHHHHHHHhhcCC--CCcEEEEeChHHHHHHHHHHHHH
Confidence            568899999998653        35789999999999999999999987755433  23677777999999999988887


Q ss_pred             HhccccCCCCceEEEEEeccccc--CCCCceEEEECchHHHHHHhcCC--CCCCccEEEEecccccccchhHHHHHHHhh
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKEL--PRKRGSILYCTAGILPEVMQSDP--ILSGVSHIVMDEIHERSMISDFLLAILKDV  200 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~~--~~~~~~Iiv~Tpg~ll~~l~~~~--~l~~v~~vViDEah~~~~~~~~~~~~l~~~  200 (319)
                      +.....   +..+++........  .....+|+|+|||++++++....  .+.++++||+||+|.......+........
T Consensus       185 ~~~~~~---~~~~~~~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~i~  261 (479)
T 3fmp_B          185 MGKFYP---ELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQ  261 (479)
T ss_dssp             HHTTST---TCCEEEESTTCCCCTTCCCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHHHHHTSTTHHHHHHHHH
T ss_pred             HHhhCC---CceEEEEeCCccccccccCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHHHHhhcCCcHHHHHHHH
Confidence            754332   34444433322211  12346799999999999995533  468999999999997322223443444444


Q ss_pred             hccccCceEEEeccccC--hhhHhh-hhCCCCEEEeCCcccc---ceeeeehhhhhhhhhhHHHHHHHHhhhhhhhcccc
Q psy496          201 TDKRKDLKLILMSATLN--AEKFSQ-FFGGAPILHIPGFTYP---VQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFF  274 (319)
Q Consensus       201 ~~~~~~~qiv~lSAT~~--~~~l~~-~l~~~~~i~~~~r~~~---v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  274 (319)
                      ...+++.|++++|||++  ...++. ++.+...+.+......   +...+....    ....+...+   ...  +....
T Consensus       262 ~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~----~~~~~~~~l---~~~--~~~~~  332 (479)
T 3fmp_B          262 RMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCS----SRDEKFQAL---CNL--YGAIT  332 (479)
T ss_dssp             TTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC-------------------------------------------
T ss_pred             hhCCccceEEEEeCCCCHHHHHHHHHHcCCCeEEeccccccCcCCceEEEEEeC----CHHHHHHHH---HHH--Hhhcc
Confidence            44566889999999993  334554 4444444444332211   112221111    011111111   111  11223


Q ss_pred             CCCcEEEeCCccccccc
Q psy496          275 GGAPILHIPGFTYPVQE  291 (319)
Q Consensus       275 ~g~~LVFlp~R~~~v~~  291 (319)
                      .+++||||+++..+.++
T Consensus       333 ~~~~lvF~~s~~~~~~l  349 (479)
T 3fmp_B          333 IAQAMIFCHTRKTASWL  349 (479)
T ss_dssp             -----------------
T ss_pred             CCceEEEeCcHHHHHHH
Confidence            67899999999876444

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=99.91  E-value=5.9e-25  Score=192.84  Aligned_cols=169  Identities=20%  Similarity=0.155  Sum_probs=114.0

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHh----CCCCccEEEEecccHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIAR----NRGSECCIMVTQPRRISAIAIAE  120 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~----~~~~~~~vl~~~Ptr~la~q~~~  120 (319)
                      ++++|.+++|.+.+|          ++++++||||||||++|.+|++..+...    ......+++++.||++||.|+.+
T Consensus        43 ~~~~Q~~~i~~~~~~----------~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~  112 (228)
T 3iuy_A           43 PTPIQSQAWPIILQG----------IDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEA  112 (228)
T ss_dssp             CCHHHHHHHHHHHTT----------CCEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCC----------CCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCCHHHHHHHHH
Confidence            568899999988753          5688999999999999999999876432    11224567888899999999999


Q ss_pred             HHHHHhccccCCCCceEEEEEeccc-----ccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHH
Q psy496          121 RVAQERDEQCGRPGSSVGYQIRLEK-----ELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLL  194 (319)
Q Consensus       121 ~~~~~~~~~~~~~g~~vg~~~~~~~-----~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~  194 (319)
                      ++.+....     +..+........     .....+.+|+|+|||++.+.+..+. .+++++++|+||||.. ...++..
T Consensus       113 ~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~-~~~~~~~  186 (228)
T 3iuy_A          113 ECSKYSYK-----GLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKM-LDMEFEP  186 (228)
T ss_dssp             HHHHHCCT-----TCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTCCEEEECCHHHH-HHTTCHH
T ss_pred             HHHHhccc-----CceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccceEEEEECHHHH-hccchHH
Confidence            88886421     222221111111     0111346899999999999885544 4899999999999962 2222333


Q ss_pred             HHHHhhhccccCceEEEecccc--ChhhHhhhhCCCC
Q psy496          195 AILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAP  229 (319)
Q Consensus       195 ~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~  229 (319)
                      ...+.+...+++.|++++|||+  +.+.+.+.+.+.|
T Consensus       187 ~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p  223 (228)
T 3iuy_A          187 QIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDP  223 (228)
T ss_dssp             HHHHHHHHSCSSCEEEEEESCCCHHHHHHHHTTCSSC
T ss_pred             HHHHHHHhCCcCCeEEEEEeeCCHHHHHHHHHHCCCC
Confidence            3334444456688999999999  3455555433333

>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=99.91  E-value=3.4e-24  Score=226.17  Aligned_cols=177  Identities=18%  Similarity=0.177  Sum_probs=133.0

Q ss_pred             cccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           43 CCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        43 ~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      .+++++|.++|+.+.          .+++++++||||||||++|.+|++..+...     .++++++|+|+|+.|+++.+
T Consensus       183 f~ltp~Q~~AI~~i~----------~g~dvLV~ApTGSGKTlva~l~i~~~l~~g-----~rvlvl~PtraLa~Q~~~~l  247 (1108)
T 3l9o_A          183 FTLDPFQDTAISCID----------RGESVLVSAHTSAGKTVVAEYAIAQSLKNK-----QRVIYTSPIKALSNQKYREL  247 (1108)
T ss_dssp             SCCCHHHHHHHHHHT----------TTCCEEEECCSSSHHHHHHHHHHHHHHHTT-----CEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHH----------cCCCEEEECCCCCChHHHHHHHHHHHHhcC-----CeEEEEcCcHHHHHHHHHHH
Confidence            345688888888764          457799999999999999999999887443     37888889999999999999


Q ss_pred             HHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCC-CCCccEEEEecccccccchhHHHHHHHhhh
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPI-LSGVSHIVMDEIHERSMISDFLLAILKDVT  201 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~-l~~v~~vViDEah~~~~~~~~~~~~l~~~~  201 (319)
                      .+.++        .+|.  ..++.....+++|+|+|||+|.+++..... +.++++|||||||.. ...++...+...+.
T Consensus       248 ~~~~~--------~Vgl--ltGd~~~~~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l-~d~~rg~~~e~ii~  316 (1108)
T 3l9o_A          248 LAEFG--------DVGL--MTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYM-RDKERGVVWEETII  316 (1108)
T ss_dssp             HHHTS--------SEEE--ECSSCBCCCSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGT-TSHHHHHHHHHHHH
T ss_pred             HHHhC--------CccE--EeCccccCCCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhc-cccchHHHHHHHHH
Confidence            98865        2332  222222335678999999999999966554 889999999999963 23333333333444


Q ss_pred             ccccCceEEEecccc-ChhhHhhhhCC-----CCEEEeCCccccceeeee
Q psy496          202 DKRKDLKLILMSATL-NAEKFSQFFGG-----APILHIPGFTYPVQEYYL  245 (319)
Q Consensus       202 ~~~~~~qiv~lSAT~-~~~~l~~~l~~-----~~~i~~~~r~~~v~~~~~  245 (319)
                      .++++.|+|+||||+ +...+++|++.     ..++..+.++.|++.++.
T Consensus       317 ~l~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~rp~pl~~~~~  366 (1108)
T 3l9o_A          317 LLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLF  366 (1108)
T ss_dssp             HSCTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECCCSSCEEEEEE
T ss_pred             hcCCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCCcccceEEEe
Confidence            566789999999999 88888888752     445677788888876553

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=99.91  E-value=1.4e-24  Score=192.54  Aligned_cols=174  Identities=18%  Similarity=0.088  Sum_probs=119.2

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC---CCCccEEEEecccHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN---RGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~---~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      ++++|.++||.+..|          ++++++||||||||++|.+|++..+....   .....++++++|||+|+.|+.+.
T Consensus        52 ~~~~Q~~~i~~~~~g----------~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~  121 (242)
T 3fe2_A           52 PTAIQAQGWPVALSG----------LDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQV  121 (242)
T ss_dssp             CCHHHHHHHHHHHHT----------CCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCC----------CCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEEeCcHHHHHHHHHH
Confidence            578999999998864          46888999999999999999998876432   12244678888999999999988


Q ss_pred             HHHHhccccCCCCceEEEEEecccc-----cCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHH
Q psy496          122 VAQERDEQCGRPGSSVGYQIRLEKE-----LPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLA  195 (319)
Q Consensus       122 ~~~~~~~~~~~~g~~vg~~~~~~~~-----~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~  195 (319)
                      +.+.....    +..++........     ....+++|+|+|||++.+.+.... .+++++++|+||||.. ...++...
T Consensus       122 ~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~lViDEah~l-~~~~~~~~  196 (242)
T 3fe2_A          122 AAEYCRAC----RLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRM-LDMGFEPQ  196 (242)
T ss_dssp             HHHHHHHT----TCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHHTSCCCTTCCEEEETTHHHH-HHTTCHHH
T ss_pred             HHHHHhhc----CceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCCcccccEEEEeCHHHH-hhhCcHHH
Confidence            87764332    2233221111110     001246799999999999995444 5899999999999962 22233333


Q ss_pred             HHHhhhccccCceEEEecccc--ChhhHhhh-hCCCCEEEe
Q psy496          196 ILKDVTDKRKDLKLILMSATL--NAEKFSQF-FGGAPILHI  233 (319)
Q Consensus       196 ~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~-l~~~~~i~~  233 (319)
                      ....+...+++.|+++||||+  +.+.+.+. +.+...+.+
T Consensus       197 ~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~l~~~~~i~~  237 (242)
T 3fe2_A          197 IRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINI  237 (242)
T ss_dssp             HHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEEEE
T ss_pred             HHHHHHhCCccceEEEEEeecCHHHHHHHHHHCCCCEEEEe
Confidence            344444556788999999999  45556654 444333444

>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=99.91  E-value=4.4e-24  Score=200.42  Aligned_cols=238  Identities=15%  Similarity=0.121  Sum_probs=147.7

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      ++++.+.+...+..+.   .++++|.++++.+..+        .+++++++||||||||+++++|+++.+.....  ..+
T Consensus        11 ~l~~~l~~~l~~~~~~---~~~~~Q~~~i~~~~~~--------~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~--~~~   77 (395)
T 3pey_A           11 GLAPELLKGIYAMKFQ---KPSKIQERALPLLLHN--------PPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDA--SPQ   77 (395)
T ss_dssp             CCCHHHHHHHHHTTCC---SCCHHHHHHHHHHHCS--------SCCCEEEECCTTSCHHHHHHHHHHHHCCTTCC--SCC
T ss_pred             CCCHHHHHHHHHCCCC---CCCHHHHHHHHHHHcC--------CCCeEEEECCCCCcHHHHHHHHHHHHhccCCC--Ccc
Confidence            4555555554443332   3568899999988653        34789999999999999999999987654332  346


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecc-cccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEec
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLE-KELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDE  182 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~-~~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDE  182 (319)
                      +++++|+++|+.|+++.+.+.....    +..++...... ......+++|+|+||+++.+.+.... .+.++++||+||
T Consensus        78 ~lil~P~~~L~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDE  153 (395)
T 3pey_A           78 AICLAPSRELARQTLEVVQEMGKFT----KITSQLIVPDSFEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDE  153 (395)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTS----CCCEEEESTTSSCTTSCBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEET
T ss_pred             EEEECCCHHHHHHHHHHHHHHhccc----CeeEEEEecCchhhhccCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEC
Confidence            7888899999999999888764322    32333222111 11112357899999999999985544 488999999999


Q ss_pred             ccccccchhHHHHHHHhhhccccCceEEEeccccC--hhhHhhhh-CCCCEEEeCCcccc---ceeeeehhhhhhhhhhH
Q psy496          183 IHERSMISDFLLAILKDVTDKRKDLKLILMSATLN--AEKFSQFF-GGAPILHIPGFTYP---VQEYYLEDVLNMTRKDL  256 (319)
Q Consensus       183 ah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~--~~~l~~~l-~~~~~i~~~~r~~~---v~~~~~~~~~~~~~~~~  256 (319)
                      +|......++...........+++.|++++|||++  ...+...+ .+...+........   +...+....    ....
T Consensus       154 ah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~  229 (395)
T 3pey_A          154 ADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCK----NEAD  229 (395)
T ss_dssp             HHHHHHSTTHHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGGGCSCTTEEEEEEECS----SHHH
T ss_pred             hhhhcCccccHHHHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEccccccccccccEEEEEcC----chHH
Confidence            99743223344444444444556789999999993  34555444 34333443333222   222232221    1111


Q ss_pred             HHHHHHHhhhhhhhccccCCCcEEEeCCcccc
Q psy496          257 KLILMSATLNAEKFSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       257 ~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~  288 (319)
                      +.......     .....++++|||++++..+
T Consensus       230 ~~~~l~~~-----~~~~~~~~~lvf~~~~~~~  256 (395)
T 3pey_A          230 KFDVLTEL-----YGLMTIGSSIIFVATKKTA  256 (395)
T ss_dssp             HHHHHHHH-----HTTTTSSEEEEECSCHHHH
T ss_pred             HHHHHHHH-----HHhccCCCEEEEeCCHHHH
Confidence            11111111     1112367899999998765

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.91  E-value=3.4e-24  Score=203.34  Aligned_cols=235  Identities=16%  Similarity=0.112  Sum_probs=139.3

Q ss_pred             ccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCC-----
Q psy496           26 VPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRG-----  100 (319)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~-----  100 (319)
                      +++.+.+......+.   .++++|.++||.+..          +++++++||||||||++|.+|+++.+......     
T Consensus        22 l~~~l~~~l~~~~~~---~~~~~Q~~~i~~i~~----------~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~   88 (417)
T 2i4i_A           22 MGEIIMGNIELTRYT---RPTPVQKHAIPIIKE----------KRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRA   88 (417)
T ss_dssp             CCHHHHHHHHHHTCC---SCCHHHHHHHHHHHT----------TCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHH
T ss_pred             CCHHHHHHHHHCCCC---CCCHHHHHHHHHHcc----------CCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhc
Confidence            444444443333332   357889999998764          35688999999999999999999887654321     


Q ss_pred             -----------CccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc-----ccCCCCceEEEECchHHHH
Q psy496          101 -----------SECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK-----ELPRKRGSILYCTAGILPE  164 (319)
Q Consensus       101 -----------~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~-----~~~~~~~~Iiv~Tpg~ll~  164 (319)
                                 ...++++++|||+|+.|+++.+.+.....    +..++.......     .....+++|+|+||++|.+
T Consensus        89 ~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~  164 (417)
T 2i4i_A           89 MKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRS----RVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVD  164 (417)
T ss_dssp             HHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTS----SCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHH
T ss_pred             cccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcC----CceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHH
Confidence                       12468888899999999999988765432    223322111111     0112356899999999999


Q ss_pred             HHhcCC-CCCCccEEEEecccccccchhHHHHHHHhhhc---cc--cCceEEEecccc--ChhhHhh-hhCCCCEEEeCC
Q psy496          165 VMQSDP-ILSGVSHIVMDEIHERSMISDFLLAILKDVTD---KR--KDLKLILMSATL--NAEKFSQ-FFGGAPILHIPG  235 (319)
Q Consensus       165 ~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~---~~--~~~qiv~lSAT~--~~~~l~~-~l~~~~~i~~~~  235 (319)
                      ++.... .++++++||+||+|.. ...++.. .++.+..   .+  ...|++++|||+  +.+.+.. |+.+...+.+..
T Consensus       165 ~l~~~~~~~~~~~~iViDEah~~-~~~~~~~-~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  242 (417)
T 2i4i_A          165 MMERGKIGLDFCKYLVLDEADRM-LDMGFEP-QIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGR  242 (417)
T ss_dssp             HHHTTSBCCTTCCEEEESSHHHH-HHTTCHH-HHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC-
T ss_pred             HHHcCCcChhhCcEEEEEChhHh-hccCcHH-HHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCC
Confidence            996544 4889999999999972 1111222 2222221   22  267899999999  3344444 454433333322


Q ss_pred             cc---ccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCCcccc
Q psy496          236 FT---YPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       236 r~---~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~  288 (319)
                      ..   ..+...+....    .......+... +..    ...++++|||++++..+
T Consensus       243 ~~~~~~~i~~~~~~~~----~~~~~~~l~~~-l~~----~~~~~~~lVf~~~~~~~  289 (417)
T 2i4i_A          243 VGSTSENITQKVVWVE----ESDKRSFLLDL-LNA----TGKDSLTLVFVETKKGA  289 (417)
T ss_dssp             ---CCSSEEEEEEECC----GGGHHHHHHHH-HHT----CCTTCEEEEECSSHHHH
T ss_pred             CCCCccCceEEEEEec----cHhHHHHHHHH-HHh----cCCCCeEEEEECCHHHH
Confidence            11   12222232211    11111222111 111    11367899999998765

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=99.91  E-value=2.4e-24  Score=188.20  Aligned_cols=192  Identities=18%  Similarity=0.125  Sum_probs=123.0

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      .+++.+.+...+..+.   .+++.|.++++.+..|          ++++++||||||||.+|.+|+++.+.....  ..+
T Consensus        20 ~l~~~l~~~l~~~g~~---~~~~~Q~~~i~~~~~~----------~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~--~~~   84 (224)
T 1qde_A           20 ELDENLLRGVFGYGFE---EPSAIQQRAIMPIIEG----------HDVLAQAQSGTGKTGTFSIAALQRIDTSVK--APQ   84 (224)
T ss_dssp             TCCHHHHHHHHHHTCC---SCCHHHHHHHHHHHTT----------CCEEEECCTTSSHHHHHHHHHHHHCCTTCC--SCC
T ss_pred             CCCHHHHHHHHHCCCC---CCcHHHHHHHHHHhcC----------CCEEEECCCCCcHHHHHHHHHHHHHhccCC--Cce
Confidence            3455555444333322   2568899999987653          568999999999999999999987754332  347


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEe----cccccCCCCceEEEECchHHHHHHhcC-CCCCCccEEE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIR----LEKELPRKRGSILYCTAGILPEVMQSD-PILSGVSHIV  179 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~----~~~~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~vV  179 (319)
                      +++++|+++|+.|+.+.+.+.....    +..++....    .+......+++|+|+||+++.+.+... ..+++++++|
T Consensus        85 ~lil~Pt~~L~~q~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~iV  160 (224)
T 1qde_A           85 ALMLAPTRELALQIQKVVMALAFHM----DIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFI  160 (224)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTS----CCCEEEECC----------CTTCSEEEECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             EEEEECCHHHHHHHHHHHHHHhccc----CceEEEEeCCcchHHHHhcCCCCCEEEECHHHHHHHHHhCCcchhhCcEEE
Confidence            7888899999999999888765432    222221111    111111124789999999999988554 3488999999


Q ss_pred             EecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhh-hhCCCCEEEeCCc
Q psy496          180 MDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQ-FFGGAPILHIPGF  236 (319)
Q Consensus       180 iDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~-~l~~~~~i~~~~r  236 (319)
                      +||||.. ...++...+.+.+...+++.|++++|||+  +.+.+.+ |+.++..+.++.+
T Consensus       161 iDEah~~-~~~~~~~~l~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~~  219 (224)
T 1qde_A          161 LDEADEM-LSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKD  219 (224)
T ss_dssp             EETHHHH-HHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC----
T ss_pred             EcChhHH-hhhhhHHHHHHHHHhCCccCeEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            9999962 12222222333333455678999999999  3445444 5655444555443

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.91  E-value=2.5e-24  Score=189.76  Aligned_cols=175  Identities=18%  Similarity=0.160  Sum_probs=119.2

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCC--CCccEEEEecccHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNR--GSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~--~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      ++++|.++++.+..|          ++++++||||||||++|.+|+++.+.....  ....++++++|+++|+.|+++.+
T Consensus        48 ~~~~Q~~~i~~~~~~----------~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~  117 (236)
T 2pl3_A           48 VTEIQKQTIGLALQG----------KDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVL  117 (236)
T ss_dssp             CCHHHHHHHHHHHTT----------CCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCC----------CCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEEeCCHHHHHHHHHHH
Confidence            568899999988753          568999999999999999999988765321  12347888889999999999988


Q ss_pred             HHHhccccCCCCceEEEEEecc----cccCCCCceEEEECchHHHHHHhcC--CCCCCccEEEEecccccccchhHHHHH
Q psy496          123 AQERDEQCGRPGSSVGYQIRLE----KELPRKRGSILYCTAGILPEVMQSD--PILSGVSHIVMDEIHERSMISDFLLAI  196 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~----~~~~~~~~~Iiv~Tpg~ll~~l~~~--~~l~~v~~vViDEah~~~~~~~~~~~~  196 (319)
                      .+.....    +..++......    ......+++|+|+|||++.+.+...  ..+.+++++|+||||.. ...++...+
T Consensus       118 ~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~~-~~~~~~~~~  192 (236)
T 2pl3_A          118 RKVGKNH----DFSAGLIIGGKDLKHEAERINNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRI-LDMGFADTM  192 (236)
T ss_dssp             HHHTTTS----SCCEEEECCC--CHHHHHHHTTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEETTHHHH-HHTTTHHHH
T ss_pred             HHHhCCC----CeeEEEEECCCCHHHHHHhCCCCCEEEECHHHHHHHHHhcCCcccccccEEEEeChHHH-hcCCcHHHH
Confidence            8765322    22333211111    0011135689999999999988543  34789999999999962 222233333


Q ss_pred             HHhhhccccCceEEEecccc--ChhhHhhhh-CCCCEEEeC
Q psy496          197 LKDVTDKRKDLKLILMSATL--NAEKFSQFF-GGAPILHIP  234 (319)
Q Consensus       197 l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l-~~~~~i~~~  234 (319)
                      .+.+...+++.|+++||||+  +.+.+++.+ .++..+.++
T Consensus       193 ~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~  233 (236)
T 2pl3_A          193 NAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVH  233 (236)
T ss_dssp             HHHHHTSCTTSEEEEEESSCCHHHHHHHHHSCSSCEEEECC
T ss_pred             HHHHHhCCCCCeEEEEEeeCCHHHHHHHHHhCCCCEEEEeC
Confidence            33344455678999999999  455666654 444344443

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=99.91  E-value=3.1e-24  Score=190.26  Aligned_cols=177  Identities=18%  Similarity=0.143  Sum_probs=120.1

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++++|.+++|.+..|          ++++++||||||||++|.+|+++.+.... ....+++++.|||+|+.|+++.+.+
T Consensus        52 ~~~~Q~~~i~~~~~~----------~~~l~~a~TGsGKT~~~~l~~l~~l~~~~-~~~~~~lil~Pt~~L~~q~~~~~~~  120 (245)
T 3dkp_A           52 PTPIQMQAIPVMLHG----------RELLASAPTGSGKTLAFSIPILMQLKQPA-NKGFRALIISPTRELASQIHRELIK  120 (245)
T ss_dssp             CCHHHHHHHHHHHTT----------CCEEEECCTTSCHHHHHHHHHHHHHCSCC-SSSCCEEEECSSHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCC----------CCEEEECCCCCcHHHHHHHHHHHHHhhcc-cCCceEEEEeCCHHHHHHHHHHHHH
Confidence            578999999998754          45889999999999999999998875321 2234788888999999999999988


Q ss_pred             HhccccCCCCceEEEEEecc------cccCCCCceEEEECchHHHHHHhcC---CCCCCccEEEEecccccccc--hhHH
Q psy496          125 ERDEQCGRPGSSVGYQIRLE------KELPRKRGSILYCTAGILPEVMQSD---PILSGVSHIVMDEIHERSMI--SDFL  193 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~------~~~~~~~~~Iiv~Tpg~ll~~l~~~---~~l~~v~~vViDEah~~~~~--~~~~  193 (319)
                      .....    +..+.......      ......+++|+|+|||++.+++...   ..+++++++|+||||.....  .++.
T Consensus       121 ~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~  196 (245)
T 3dkp_A          121 ISEGT----GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFR  196 (245)
T ss_dssp             HTTTS----CCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEEESSHHHHHHHC--CHH
T ss_pred             Hhccc----CceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEEEeChHHhcccccccHH
Confidence            75432    22222111100      1111245789999999999999654   34889999999999973211  2344


Q ss_pred             HHHHHhhhc-cccCceEEEecccc--ChhhHhhh-hCCCCEEEeCCc
Q psy496          194 LAILKDVTD-KRKDLKLILMSATL--NAEKFSQF-FGGAPILHIPGF  236 (319)
Q Consensus       194 ~~~l~~~~~-~~~~~qiv~lSAT~--~~~~l~~~-l~~~~~i~~~~r  236 (319)
                      ..+.+.+.. .+++.|+++||||+  +.+.+.+. +.++..+.++.+
T Consensus       197 ~~~~~i~~~~~~~~~~~~~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  243 (245)
T 3dkp_A          197 DQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR  243 (245)
T ss_dssp             HHHHHHHHHCCCTTCEEEEEESSCCHHHHHHHHHHSSSCEEEEECC-
T ss_pred             HHHHHHHHhcCCCCcEEEEEeccCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            444444333 23577999999999  45566654 444444555443

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=99.90  E-value=8.6e-24  Score=182.15  Aligned_cols=183  Identities=17%  Similarity=0.149  Sum_probs=121.2

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      .+++.+.+...+..+.   ++++.|.++++.+..+          ++++++||||||||.+|.+|+++.+.....  ..+
T Consensus         9 ~l~~~l~~~l~~~g~~---~~~~~Q~~~i~~~~~~----------~~~lv~apTGsGKT~~~~~~~~~~~~~~~~--~~~   73 (206)
T 1vec_A            9 CLKRELLMGIFEMGWE---KPSPIQEESIPIALSG----------RDILARAKNGTGKSGAYLIPLLERLDLKKD--NIQ   73 (206)
T ss_dssp             CCCHHHHHHHHTTTCC---SCCHHHHHHHHHHHTT----------CCEEEECCSSSTTHHHHHHHHHHHCCTTSC--SCC
T ss_pred             CCCHHHHHHHHHCCCC---CCCHHHHHHHHHHccC----------CCEEEECCCCCchHHHHHHHHHHHhcccCC--Cee
Confidence            3455554443333222   3568899999988753          568999999999999999999987644332  346


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc-----ccCCCCceEEEECchHHHHHHhcCC-CCCCccEE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK-----ELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHI  178 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~-----~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~v  178 (319)
                      ++++.|+++|+.|+++.+.+......   +..++.......     .....+++|+|+||+++.+.+.... .+++++++
T Consensus        74 ~lil~Pt~~L~~q~~~~~~~~~~~~~---~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~l  150 (206)
T 1vec_A           74 AMVIVPTRELALQVSQICIQVSKHMG---GAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMI  150 (206)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHTTTSS---SCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEE
T ss_pred             EEEEeCcHHHHHHHHHHHHHHHhhcC---CceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCCcCcccCCEE
Confidence            77788999999999998888754321   223332221111     1112457899999999999885544 58899999


Q ss_pred             EEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhh-hhC
Q psy496          179 VMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQ-FFG  226 (319)
Q Consensus       179 ViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~-~l~  226 (319)
                      |+||+|.. ...++...+.+.+...+++.|++++|||+  +...+.+ ++.
T Consensus       151 ViDEah~~-~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~  200 (206)
T 1vec_A          151 VLDEADKL-LSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLE  200 (206)
T ss_dssp             EEETHHHH-TSTTTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCS
T ss_pred             EEEChHHh-HhhCcHHHHHHHHHhCCccceEEEEEeeCCHHHHHHHHHHcC
Confidence            99999972 22233332333333345578999999999  3444444 454

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.90  E-value=4.7e-24  Score=186.02  Aligned_cols=190  Identities=18%  Similarity=0.128  Sum_probs=122.8

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      .+++.+.+...+..+.   +++++|.++++.+.+|          ++++++||||||||.+|.+|+++.+.....  ..+
T Consensus        10 ~l~~~l~~~l~~~g~~---~~~~~Q~~~i~~~~~~----------~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~--~~~   74 (219)
T 1q0u_A           10 PFQPFIIEAIKTLRFY---KPTEIQERIIPGALRG----------ESMVGQSQTGTGKTHAYLLPIMEKIKPERA--EVQ   74 (219)
T ss_dssp             CCCHHHHHHHHHTTCC---SCCHHHHHHHHHHHHT----------CCEEEECCSSHHHHHHHHHHHHHHCCTTSC--SCC
T ss_pred             CCCHHHHHHHHHCCCC---CCCHHHHHHHHHHhCC----------CCEEEECCCCChHHHHHHHHHHHHHHhCcC--Cce
Confidence            3455555444333222   2568899999998764          568889999999999999999987654332  346


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc-----ccCCCCceEEEECchHHHHHHhcCC-CCCCccEE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK-----ELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHI  178 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~-----~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~v  178 (319)
                      +++++||++|+.|+++.+.+.........+..++......+     .....+.+|+|+|||++.+.+.... .+++++++
T Consensus        75 ~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~l  154 (219)
T 1q0u_A           75 AVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHIL  154 (219)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEE
T ss_pred             EEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCCCCcCcceEE
Confidence            77778999999999998887754321000122221111111     1111356899999999999885543 48899999


Q ss_pred             EEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCCE
Q psy496          179 VMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAPI  230 (319)
Q Consensus       179 ViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~~  230 (319)
                      |+||||.. ...++...+.+.+...+++.|++++|||+  +...+.+.+.+.|.
T Consensus       155 ViDEah~~-~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~  207 (219)
T 1q0u_A          155 VVDEADLM-LDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPT  207 (219)
T ss_dssp             EECSHHHH-HHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCE
T ss_pred             EEcCchHH-hhhChHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHcCCCe
Confidence            99999972 12222223333333455678999999999  44455554434443

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=99.90  E-value=9.3e-24  Score=188.28  Aligned_cols=168  Identities=23%  Similarity=0.189  Sum_probs=118.3

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++++|.++++.+..|          ++++++||||||||++|.+|+++.+.....  ..++++++|+|+|+.|+++.+.+
T Consensus        66 ~~~~Q~~~i~~i~~~----------~~~lv~a~TGsGKT~~~~~~il~~l~~~~~--~~~~lil~Ptr~L~~q~~~~~~~  133 (249)
T 3ber_A           66 PTKIQIEAIPLALQG----------RDIIGLAETGSGKTGAFALPILNALLETPQ--RLFALVLTPTRELAFQISEQFEA  133 (249)
T ss_dssp             CCHHHHHHHHHHHTT----------CCEEEECCTTSCHHHHHHHHHHHHHHHSCC--SSCEEEECSSHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCC----------CCEEEEcCCCCCchhHhHHHHHHHHhcCCC--CceEEEEeCCHHHHHHHHHHHHH
Confidence            568899999988753          568999999999999999999998876543  34677778999999999998877


Q ss_pred             HhccccCCCCceEEEEEecccc-----cCCCCceEEEECchHHHHHHhcC--CCCCCccEEEEecccccccchhHHHHHH
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKE-----LPRKRGSILYCTAGILPEVMQSD--PILSGVSHIVMDEIHERSMISDFLLAIL  197 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~-----~~~~~~~Iiv~Tpg~ll~~l~~~--~~l~~v~~vViDEah~~~~~~~~~~~~l  197 (319)
                      .....    +..++........     ....+++|+|+|||++.+.+...  ..+.+++++|+||||.. ...++...+.
T Consensus       134 ~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l-~~~~~~~~l~  208 (249)
T 3ber_A          134 LGSSI----GVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRI-LNMDFETEVD  208 (249)
T ss_dssp             HHGGG----TCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSHHHH-HHTTCHHHHH
T ss_pred             HhccC----CeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcChhhh-hccChHHHHH
Confidence            65432    3333322211110     01135689999999999998542  35889999999999962 2333433444


Q ss_pred             HhhhccccCceEEEecccc--ChhhHhhhhCCCC
Q psy496          198 KDVTDKRKDLKLILMSATL--NAEKFSQFFGGAP  229 (319)
Q Consensus       198 ~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~  229 (319)
                      +.+...+++.|+++||||+  +.+.+.+.+...|
T Consensus       209 ~i~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~p  242 (249)
T 3ber_A          209 KILKVIPRDRKTFLFSATMTKKVQKLQRAALKNP  242 (249)
T ss_dssp             HHHHSSCSSSEEEEEESSCCHHHHHHHHHHCSSC
T ss_pred             HHHHhCCCCCeEEEEeccCCHHHHHHHHHHCCCC
Confidence            4444455678999999999  4556666544444

>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=99.90  E-value=1.1e-23  Score=199.53  Aligned_cols=218  Identities=18%  Similarity=0.155  Sum_probs=137.9

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++++|.++++.+..          +++++++||||||||++|++|+++.+.....  ..++++++|+++|+.|+.+.+.+
T Consensus        63 ~~~~Q~~~i~~~~~----------~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~--~~~~lil~P~~~L~~q~~~~~~~  130 (414)
T 3eiq_A           63 PSAIQQRAILPCIK----------GYDVIAQAQSGTGKTATFAISILQQIELDLK--ATQALVLAPTRELAQQIQKVVMA  130 (414)
T ss_dssp             CCHHHHHHHHHHHT----------TCCEEECCCSCSSSHHHHHHHHHHHCCTTSC--SCCEEEECSSHHHHHHHHHHHHH
T ss_pred             CCHHHHHHhHHHhC----------CCCEEEECCCCCcccHHHHHHHHHHHhhcCC--ceeEEEEeChHHHHHHHHHHHHH
Confidence            56889999988775          3558899999999999999999987654322  34678888999999999998888


Q ss_pred             HhccccCCCCceEEEEEecccc------cCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHHHH
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKE------LPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLAIL  197 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~------~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~l  197 (319)
                      .....    +..++........      .....++|+|+||++|.+.+..+. .+.++++||+||+|+. ...++.....
T Consensus       131 ~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~-~~~~~~~~~~  205 (414)
T 3eiq_A          131 LGDYM----GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEM-LSRGFKDQIY  205 (414)
T ss_dssp             HGGGS----CCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEECSHHHH-HHTTTHHHHH
T ss_pred             Hhccc----CceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEEECHHHh-hccCcHHHHH
Confidence            75432    3333322211111      111456899999999999995544 4788999999999973 2223333444


Q ss_pred             HhhhccccCceEEEeccccC--hhhHh-hhhCCCCEEEeCCcccc---ceeeeehhhhhhhhhhHHHHHHHHhhhhhhhc
Q psy496          198 KDVTDKRKDLKLILMSATLN--AEKFS-QFFGGAPILHIPGFTYP---VQEYYLEDVLNMTRKDLKLILMSATLNAEKFS  271 (319)
Q Consensus       198 ~~~~~~~~~~qiv~lSAT~~--~~~l~-~~l~~~~~i~~~~r~~~---v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  271 (319)
                      ..+...+++.|++++|||++  ...+. .++.+...+........   +...+....  ....... .+.    +.  +.
T Consensus       206 ~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~-~l~----~~--~~  276 (414)
T 3eiq_A          206 DIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVE--REEWKLD-TLC----DL--YE  276 (414)
T ss_dssp             HHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCCCCCCTTSCCEEEEECS--SSTTHHH-HHH----HH--HH
T ss_pred             HHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecCCccCCCCceEEEEEeC--hHHhHHH-HHH----HH--HH
Confidence            44455667889999999993  33443 44544444444333222   223333221  1111111 111    11  11


Q ss_pred             cccCCCcEEEeCCcccc
Q psy496          272 QFFGGAPILHIPGFTYP  288 (319)
Q Consensus       272 ~~~~g~~LVFlp~R~~~  288 (319)
                      ...++++|||++++..+
T Consensus       277 ~~~~~~~lvf~~~~~~~  293 (414)
T 3eiq_A          277 TLTITQAVIFINTRRKV  293 (414)
T ss_dssp             SSCCSSCEEECSCHHHH
T ss_pred             hCCCCcEEEEeCCHHHH
Confidence            22367999999998655

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.90  E-value=3.8e-23  Score=216.42  Aligned_cols=177  Identities=18%  Similarity=0.195  Sum_probs=129.2

Q ss_pred             ccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHH
Q psy496           42 ECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        42 ~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      +.++.++|.++++.+..          +++++++||||||||+++.++++..+..+     .++++++|+++|+.|.++.
T Consensus        84 ~f~L~~~Q~eai~~l~~----------g~~vLV~apTGSGKTlva~lai~~~l~~g-----~rvL~l~PtkaLa~Q~~~~  148 (1010)
T 2xgj_A           84 PFTLDPFQDTAISCIDR----------GESVLVSAHTSAGKTVVAEYAIAQSLKNK-----QRVIYTSPIKALSNQKYRE  148 (1010)
T ss_dssp             SSCCCHHHHHHHHHHHH----------TCEEEEECCTTSCHHHHHHHHHHHHHHTT-----CEEEEEESSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHc----------CCCEEEECCCCCChHHHHHHHHHHHhccC-----CeEEEECChHHHHHHHHHH
Confidence            34467889999988765          35689999999999999999998876432     3788888999999999999


Q ss_pred             HHHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhc-CCCCCCccEEEEecccccccc-hhHHHHHHHh
Q psy496          122 VAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQS-DPILSGVSHIVMDEIHERSMI-SDFLLAILKD  199 (319)
Q Consensus       122 ~~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~-~~~l~~v~~vViDEah~~~~~-~~~~~~~l~~  199 (319)
                      +.+.++        .+|.  ..++.......+|+|+||++|.+++.. ...+.++++|||||+|..+-. .+..  .-..
T Consensus       149 l~~~~~--------~vgl--ltGd~~~~~~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~rg~~--~e~i  216 (1010)
T 2xgj_A          149 LLAEFG--------DVGL--MTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVV--WEET  216 (1010)
T ss_dssp             HHHHHS--------CEEE--ECSSCEECTTCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHH--HHHH
T ss_pred             HHHHhC--------CEEE--EeCCCccCCCCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccchhHH--HHHH
Confidence            998875        2221  112222234578999999999988844 455899999999999973211 1111  1122


Q ss_pred             hhccccCceEEEecccc-ChhhHhhhhC-----CCCEEEeCCccccceeeee
Q psy496          200 VTDKRKDLKLILMSATL-NAEKFSQFFG-----GAPILHIPGFTYPVQEYYL  245 (319)
Q Consensus       200 ~~~~~~~~qiv~lSAT~-~~~~l~~~l~-----~~~~i~~~~r~~~v~~~~~  245 (319)
                      +..++++.|+|+||||+ |...+++|++     ...++..+.++.|++.++.
T Consensus       217 l~~l~~~~~il~LSATi~n~~e~a~~l~~~~~~~~~vi~~~~rp~pl~~~~~  268 (1010)
T 2xgj_A          217 IILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLF  268 (1010)
T ss_dssp             HHHSCTTCEEEEEECCCTTHHHHHHHHHHHHTSCEEEEEECCCSSCEEEEEE
T ss_pred             HHhcCCCCeEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCCcccceEEEE
Confidence            23345678999999999 8889999985     3445667788888776654

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=99.90  E-value=8.9e-24  Score=186.76  Aligned_cols=166  Identities=20%  Similarity=0.198  Sum_probs=112.4

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++++|.++++.+..|          ++++++||||||||.+|.+|+++.+.....  ..++++++|+|+|+.|+++.+.+
T Consensus        53 ~~~~Q~~ai~~i~~~----------~~~li~apTGsGKT~~~~l~~l~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~~~  120 (237)
T 3bor_A           53 PSAIQQRAIIPCIKG----------YDVIAQAQSGTGKTATFAISILQQLEIEFK--ETQALVLAPTRELAQQIQKVILA  120 (237)
T ss_dssp             CCHHHHHHHHHHHTT----------CCEEECCCSSHHHHHHHHHHHHHHCCTTSC--SCCEEEECSSHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCC----------CCEEEECCCCCcHHHHHHHHHHHHHHhcCC--CceEEEEECcHHHHHHHHHHHHH
Confidence            568899999988753          568899999999999999999987654322  34677788999999999998887


Q ss_pred             HhccccCCCCceEEEEEeccc------ccCCCCceEEEECchHHHHHHhcC-CCCCCccEEEEecccccccchhHHHHHH
Q psy496          125 ERDEQCGRPGSSVGYQIRLEK------ELPRKRGSILYCTAGILPEVMQSD-PILSGVSHIVMDEIHERSMISDFLLAIL  197 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~------~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~vViDEah~~~~~~~~~~~~l  197 (319)
                      .....    +..+........      ......++|+|+|||++.+.+... ..+.++++||+||||.. ...++...+.
T Consensus       121 ~~~~~----~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~-~~~~~~~~l~  195 (237)
T 3bor_A          121 LGDYM----GATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEM-LSRGFKDQIY  195 (237)
T ss_dssp             HTTTT----TCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHH-HHTTCHHHHH
T ss_pred             Hhhhc----CceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEEEECCchHh-hccCcHHHHH
Confidence            65322    222221111100      111123689999999999998554 34888999999999962 1222222223


Q ss_pred             HhhhccccCceEEEecccc--ChhhHhh-hhCC
Q psy496          198 KDVTDKRKDLKLILMSATL--NAEKFSQ-FFGG  227 (319)
Q Consensus       198 ~~~~~~~~~~qiv~lSAT~--~~~~l~~-~l~~  227 (319)
                      ..+...+++.|++++|||+  +.+.+.+ |+.+
T Consensus       196 ~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~l~~  228 (237)
T 3bor_A          196 EIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRD  228 (237)
T ss_dssp             HHHHHSCTTCEEEEECSSCCHHHHHHHHHHCSS
T ss_pred             HHHHhCCCCCeEEEEEEecCHHHHHHHHHHCCC
Confidence            3333445678999999999  4455555 4443

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=99.90  E-value=8.5e-24  Score=185.97  Aligned_cols=168  Identities=17%  Similarity=0.139  Sum_probs=113.7

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++++|.++++.+..          +++++++||||||||.+|.+|+++.+.....  ..++++++|+++|+.|+.+.+.+
T Consensus        47 ~~~~Q~~~i~~~~~----------~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~~~  114 (230)
T 2oxc_A           47 PSPVQLKAIPLGRC----------GLDLIVQAKSGTGKTCVFSTIALDSLVLENL--STQILILAPTREIAVQIHSVITA  114 (230)
T ss_dssp             CCHHHHHHHHHHHT----------TCCEEEECCTTSSHHHHHHHHHHHHCCTTSC--SCCEEEECSSHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhC----------CCCEEEECCCCCcHHHHHHHHHHHHHHhcCC--CceEEEEeCCHHHHHHHHHHHHH
Confidence            56889999998765          3568999999999999999999987654332  34678888999999999999887


Q ss_pred             HhccccCCCCceEEEEEeccc----ccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchh-HHHHHHH
Q psy496          125 ERDEQCGRPGSSVGYQIRLEK----ELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISD-FLLAILK  198 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~----~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~-~~~~~l~  198 (319)
                      ......   +..++.......    .....+++|+|+|||++.+.+..+. .+.+++++|+||+|... ..+ +...+..
T Consensus       115 ~~~~~~---~~~~~~~~g~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~-~~~~~~~~~~~  190 (230)
T 2oxc_A          115 IGIKME---GLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLL-EEGSFQEQINW  190 (230)
T ss_dssp             HTTTST---TCCEEEECTTSCHHHHHHHTTSCSEEEECHHHHHHHHHTTSSCGGGCCEEEESSHHHHH-STTSSHHHHHH
T ss_pred             HhcccC---CceEEEEeCCCCHHHHHHhccCCCEEEECHHHHHHHHhcCCcccccCCEEEeCCchHhh-cCcchHHHHHH
Confidence            754321   333332211111    0111357899999999999885543 47899999999999731 111 2222222


Q ss_pred             hhhccccCceEEEeccccCh--hh-HhhhhCCC
Q psy496          199 DVTDKRKDLKLILMSATLNA--EK-FSQFFGGA  228 (319)
Q Consensus       199 ~~~~~~~~~qiv~lSAT~~~--~~-l~~~l~~~  228 (319)
                      .+...+++.|++++|||++.  .. +.+|++++
T Consensus       191 i~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~p  223 (230)
T 2oxc_A          191 IYSSLPASKQMLAVSATYPEFLANALTKYMRDP  223 (230)
T ss_dssp             HHHHSCSSCEEEEEESCCCHHHHHHHTTTCSSC
T ss_pred             HHHhCCCCCeEEEEEeccCHHHHHHHHHHcCCC
Confidence            23334557899999999933  23 34455543

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=99.89  E-value=9e-24  Score=189.76  Aligned_cols=170  Identities=16%  Similarity=0.161  Sum_probs=118.1

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCC--CCccEEEEecccHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNR--GSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~--~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      ++++|.+++|.+..+          ++++++||||||||++|.+|+++.+.....  ....++++++|||+||.|+++.+
T Consensus        77 ~~~~Q~~~i~~~~~~----------~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~q~~~~~  146 (262)
T 3ly5_A           77 MTEIQHKSIRPLLEG----------RDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVL  146 (262)
T ss_dssp             CCHHHHHHHHHHHHT----------CCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCC----------CcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHHHHHHHH
Confidence            568999999998864          457888889999999999999998865221  11346888889999999999999


Q ss_pred             HHHhccccCCCCceEEEEEeccccc-----CCCCceEEEECchHHHHHHhcCC--CCCCccEEEEecccccccchhHHHH
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEKEL-----PRKRGSILYCTAGILPEVMQSDP--ILSGVSHIVMDEIHERSMISDFLLA  195 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~~~-----~~~~~~Iiv~Tpg~ll~~l~~~~--~l~~v~~vViDEah~~~~~~~~~~~  195 (319)
                      .+.....    +..++.........     ...+.+|+|+|||++.+++....  .++++++||+||||.. ...++...
T Consensus       147 ~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEah~l-~~~~~~~~  221 (262)
T 3ly5_A          147 KELMTHH----VHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRI-LDVGFEEE  221 (262)
T ss_dssp             HHHTTTC----CSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSHHHH-HHTTCHHH
T ss_pred             HHHHhhc----CceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEcChHHH-hhhhHHHH
Confidence            8876533    33333222211100     01236799999999999885543  5889999999999962 22223333


Q ss_pred             HHHhhhccccCceEEEecccc--ChhhHhhh-hCCCC
Q psy496          196 ILKDVTDKRKDLKLILMSATL--NAEKFSQF-FGGAP  229 (319)
Q Consensus       196 ~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~-l~~~~  229 (319)
                      +.+.+...+++.|+++||||+  +.+.+++. +.+.+
T Consensus       222 l~~i~~~~~~~~q~l~~SAT~~~~v~~~~~~~l~~~~  258 (262)
T 3ly5_A          222 LKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEP  258 (262)
T ss_dssp             HHHHHHHSCSSSEEEEECSSCCHHHHHHHHHHCSSCC
T ss_pred             HHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHcCCCC
Confidence            333334455678999999999  45566664 44443

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=99.89  E-value=2.5e-23  Score=185.34  Aligned_cols=173  Identities=17%  Similarity=0.145  Sum_probs=115.4

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC-------CCCccEEEEecccHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN-------RGSECCIMVTQPRRISAIA  117 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~-------~~~~~~vl~~~Ptr~la~q  117 (319)
                      ++++|.+++|.+..|          ++++++||||||||.+|.+|+++.+....       .....++++++|||+|+.|
T Consensus        46 ~~~~Q~~~i~~i~~~----------~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q  115 (253)
T 1wrb_A           46 PTPIQKNAIPAILEH----------RDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQ  115 (253)
T ss_dssp             CCHHHHHHHHHHHTT----------CCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHH
T ss_pred             CCHHHHHHHHHHhCC----------CCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCceEEEEECCHHHHHH
Confidence            568999999988753          56889999999999999999998876432       1223478888899999999


Q ss_pred             HHHHHHHHhccccCCCCceEEEEEeccc-----ccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchh
Q psy496          118 IAERVAQERDEQCGRPGSSVGYQIRLEK-----ELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISD  191 (319)
Q Consensus       118 ~~~~~~~~~~~~~~~~g~~vg~~~~~~~-----~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~  191 (319)
                      +.+.+.+.....    +..+........     .....+++|+|+||+++.+.+.... .+++++++|+||||.. ...+
T Consensus       116 ~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~-~~~~  190 (253)
T 1wrb_A          116 ILSESQKFSLNT----PLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRM-LDMG  190 (253)
T ss_dssp             HHHHHHHHHTTS----SCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHH-HHTT
T ss_pred             HHHHHHHHhccC----CceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHcCCCChhhCCEEEEeCHHHH-HhCc
Confidence            999888765432    222221111110     0111356899999999999985544 5889999999999972 1111


Q ss_pred             ---HHHHHHHhhhcccc--CceEEEecccc--ChhhHhhh-hCCCCEEEe
Q psy496          192 ---FLLAILKDVTDKRK--DLKLILMSATL--NAEKFSQF-FGGAPILHI  233 (319)
Q Consensus       192 ---~~~~~l~~~~~~~~--~~qiv~lSAT~--~~~~l~~~-l~~~~~i~~  233 (319)
                         .+..+++.+ ..+.  +.|+++||||+  +.+.+++. +.+...+.+
T Consensus       191 ~~~~~~~i~~~~-~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~  239 (253)
T 1wrb_A          191 FEPQIRKIIEES-NMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTV  239 (253)
T ss_dssp             CHHHHHHHHHSS-CCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEE
T ss_pred             hHHHHHHHHhhc-cCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEE
Confidence               222222221 1222  67999999999  44566654 443333433

>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=99.89  E-value=2.7e-23  Score=197.06  Aligned_cols=218  Identities=16%  Similarity=0.130  Sum_probs=134.8

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++++|.++++.+..|          ++++++||||||||++|++|+++.+.....  ..++++++|+++|+.|+++.+.+
T Consensus        60 ~~~~Q~~ai~~i~~~----------~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~~~  127 (410)
T 2j0s_A           60 PSAIQQRAIKQIIKG----------RDVIAQSQSGTGKTATFSISVLQCLDIQVR--ETQALILAPTRELAVQIQKGLLA  127 (410)
T ss_dssp             CCHHHHHHHHHHHTT----------CCEEEECCTTSSHHHHHHHHHHHTCCTTSC--SCCEEEECSSHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCC----------CCEEEECCCCCCchHHHHHHHHHHHhhccC--CceEEEEcCcHHHHHHHHHHHHH
Confidence            568899999988753          568999999999999999999987643322  34777888999999999998887


Q ss_pred             HhccccCCCCceEEEEEecccc-----cCCCCceEEEECchHHHHHHhcC-CCCCCccEEEEecccccccchhHHHHHHH
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKE-----LPRKRGSILYCTAGILPEVMQSD-PILSGVSHIVMDEIHERSMISDFLLAILK  198 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~-----~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~vViDEah~~~~~~~~~~~~l~  198 (319)
                      .....    +..++........     .....++|+|+|||++.+.+... ..+.++++||+||+|.. ...++.....+
T Consensus       128 ~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vViDEah~~-~~~~~~~~~~~  202 (410)
T 2j0s_A          128 LGDYM----NVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM-LNKGFKEQIYD  202 (410)
T ss_dssp             HTTTT----TCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHH-TSTTTHHHHHH
T ss_pred             HhccC----CeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEEEccHHHH-HhhhhHHHHHH
Confidence            64322    3333322211110     00124579999999999998554 34788999999999973 22333333333


Q ss_pred             hhhccccCceEEEeccccCh--hhH-hhhhCCCCEEEeCCccc---cceeeeehhhhhhhhhhHHHHHHHHhhhhhhhcc
Q psy496          199 DVTDKRKDLKLILMSATLNA--EKF-SQFFGGAPILHIPGFTY---PVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQ  272 (319)
Q Consensus       199 ~~~~~~~~~qiv~lSAT~~~--~~l-~~~l~~~~~i~~~~r~~---~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  272 (319)
                      .+...+++.|++++|||++.  ..+ ..++.+...+.+.....   .+...+....    ....+.......+.     .
T Consensus       203 i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~k~~~l~~~~~-----~  273 (410)
T 2j0s_A          203 VYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVE----REEWKFDTLCDLYD-----T  273 (410)
T ss_dssp             HHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGGGCSCTTEEEEEEEES----STTHHHHHHHHHHH-----H
T ss_pred             HHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCccccCCCceEEEEEeC----cHHhHHHHHHHHHH-----h
Confidence            44445567899999999933  333 34554433333332221   2233333221    11111111111111     1


Q ss_pred             ccCCCcEEEeCCcccc
Q psy496          273 FFGGAPILHIPGFTYP  288 (319)
Q Consensus       273 ~~~g~~LVFlp~R~~~  288 (319)
                      ...+++|||++++..+
T Consensus       274 ~~~~~~lVf~~~~~~~  289 (410)
T 2j0s_A          274 LTITQAVIFCNTKRKV  289 (410)
T ss_dssp             HTSSEEEEECSSHHHH
T ss_pred             cCCCcEEEEEcCHHHH
Confidence            1257899999998665

>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=99.89  E-value=1.9e-23  Score=201.79  Aligned_cols=197  Identities=18%  Similarity=0.170  Sum_probs=130.9

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      .+|+|+ +||.++.+         +++++++||||||||++|++|++..+...+    .++++++|||+||.|+++.+. 
T Consensus         5 ~~~iq~-~i~~~l~~---------~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~----~~~lvl~Ptr~La~Q~~~~l~-   69 (451)
T 2jlq_A            5 GEPDYE-VDEDIFRK---------KRLTIMDLHPGAGKTKRILPSIVREALLRR----LRTLILAPTRVVAAEMEEALR-   69 (451)
T ss_dssp             CSCCCC-CCGGGGST---------TCEEEECCCTTSSCCTTHHHHHHHHHHHTT----CCEEEEESSHHHHHHHHHHTT-
T ss_pred             CCCcHH-HHHHHHhc---------CCeEEEECCCCCCHhhHHHHHHHHHHHhcC----CcEEEECCCHHHHHHHHHHhc-
Confidence            457775 68887653         345689999999999999999998766533    367777799999999998763 


Q ss_pred             HhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccc
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKR  204 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~  204 (319)
                               |..+++...........+..|.++|+|.+.+.+.....++++++|||||+|+++...+.....+... ...
T Consensus        70 ---------g~~v~~~~~~~~~~~~~~~~i~~~t~~~l~~~l~~~~~l~~~~~iViDEah~~~~~~~~~~~~~~~~-~~~  139 (451)
T 2jlq_A           70 ---------GLPIRYQTPAVKSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSVAARGYISTR-VEM  139 (451)
T ss_dssp             ---------TSCEEECCTTCSCCCCSSCCEEEEEHHHHHHHHHHCSCCCCCSEEEEETTTCCSHHHHHHHHHHHHH-HHT
T ss_pred             ---------CceeeeeeccccccCCCCceEEEEChHHHHHHhhCcccccCCCEEEEeCCccCCcchHHHHHHHHHh-hcC
Confidence                     3444544433222222345699999999999998778899999999999998644444443333322 234


Q ss_pred             cCceEEEeccccChhhHhhhhCCCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccCCCcEEEeCC
Q psy496          205 KDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGGAPILHIPG  284 (319)
Q Consensus       205 ~~~qiv~lSAT~~~~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~  284 (319)
                      ++.|+++||||++.+....+.++.+++.+. +..|... |..                 ..+.  +.. .++++|||+++
T Consensus       140 ~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~-~~~p~~~-~~~-----------------~~~~--l~~-~~~~~lVF~~s  197 (451)
T 2jlq_A          140 GEAAAIFMTATPPGSTDPFPQSNSPIEDIE-REIPERS-WNT-----------------GFDW--ITD-YQGKTVWFVPS  197 (451)
T ss_dssp             TSCEEEEECSSCTTCCCSSCCCSSCEEEEE-CCCCSSC-CSS-----------------SCHH--HHH-CCSCEEEECSS
T ss_pred             CCceEEEEccCCCccchhhhcCCCceEecC-ccCCchh-hHH-----------------HHHH--HHh-CCCCEEEEcCC
Confidence            578999999999655444455555555443 2233111 100                 0000  111 26799999999


Q ss_pred             cccc
Q psy496          285 FTYP  288 (319)
Q Consensus       285 R~~~  288 (319)
                      +..+
T Consensus       198 ~~~a  201 (451)
T 2jlq_A          198 IKAG  201 (451)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9776

>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=99.89  E-value=1.7e-23  Score=194.61  Aligned_cols=232  Identities=16%  Similarity=0.135  Sum_probs=144.6

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      ++++.+.+...+..+.   ++++.|.++++.+..+         +++++++||||||||+++.+|++..+...   ...+
T Consensus        12 ~l~~~~~~~l~~~g~~---~~~~~Q~~~i~~~~~~---------~~~~l~~~~TGsGKT~~~~~~~~~~~~~~---~~~~   76 (367)
T 1hv8_A           12 NLSDNILNAIRNKGFE---KPTDIQMKVIPLFLND---------EYNIVAQARTGSGKTASFAIPLIELVNEN---NGIE   76 (367)
T ss_dssp             SCCHHHHHHHHHHTCC---SCCHHHHHHHHHHHHT---------CSEEEEECCSSSSHHHHHHHHHHHHSCSS---SSCC
T ss_pred             CCCHHHHHHHHHcCCC---CCCHHHHHHHHHHhCC---------CCCEEEECCCCChHHHHHHHHHHHHhccc---CCCc
Confidence            4555555544444332   2568899999988753         35789999999999999999988765432   2347


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc----cCCCCceEEEECchHHHHHHhcCC-CCCCccEEE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE----LPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIV  179 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~----~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vV  179 (319)
                      +++++|+++|+.|+++.+.+..+..    +..++........    ....+.+|+|+||+++.+.+.... .+.+++++|
T Consensus        77 ~lil~P~~~L~~q~~~~~~~~~~~~----~~~v~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iI  152 (367)
T 1hv8_A           77 AIILTPTRELAIQVADEIESLKGNK----NLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRGTLNLKNVKYFI  152 (367)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHHCSS----CCCEEEECTTSCHHHHHHHHHTCSEEEECHHHHHHHHHTTCSCTTSCCEEE
T ss_pred             EEEEcCCHHHHHHHHHHHHHHhCCC----CceEEEEECCcchHHHHhhcCCCCEEEecHHHHHHHHHcCCcccccCCEEE
Confidence            8888899999999999998876543    2223211111110    001246799999999999985544 488999999


Q ss_pred             EecccccccchhHHHHHHHhhhccccCceEEEeccccChh---hHhhhhCCCCEEEeCCccccceeeeehhhhhhhhhhH
Q psy496          180 MDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAE---KFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDL  256 (319)
Q Consensus       180 iDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~~~---~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~  256 (319)
                      +||+|.. ....+.....+.+...+++.+++++|||++..   .+..++++...+... ....++..+....    ....
T Consensus       153 iDEah~~-~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~----~~~~  226 (367)
T 1hv8_A          153 LDEADEM-LNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAK-INANIEQSYVEVN----ENER  226 (367)
T ss_dssp             EETHHHH-HTTTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECC-SSSSSEEEEEECC----GGGH
T ss_pred             EeCchHh-hhhchHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEec-CCCCceEEEEEeC----hHHH
Confidence            9999973 22223333333344455678999999999432   344566544333332 2234444443221    1111


Q ss_pred             HHHHHHHhhhhhhhccccCCCcEEEeCCcccc
Q psy496          257 KLILMSATLNAEKFSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       257 ~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~  288 (319)
                      ...+...      +. ..++++|||++++..+
T Consensus       227 ~~~l~~~------l~-~~~~~~lvf~~~~~~~  251 (367)
T 1hv8_A          227 FEALCRL------LK-NKEFYGLVFCKTKRDT  251 (367)
T ss_dssp             HHHHHHH------HC-STTCCEEEECSSHHHH
T ss_pred             HHHHHHH------Hh-cCCCcEEEEECCHHHH
Confidence            1111111      11 2377899999998665

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=99.89  E-value=5.3e-23  Score=179.26  Aligned_cols=168  Identities=16%  Similarity=0.127  Sum_probs=115.1

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +++.|.++++.+.++          +++++++|||||||.++.+|+++.+....  ...++++++|+++|+.|+++.+.+
T Consensus        37 ~~~~Q~~~i~~~~~~----------~~~li~~~TGsGKT~~~~~~~~~~~~~~~--~~~~~lil~Pt~~L~~q~~~~~~~  104 (220)
T 1t6n_A           37 PSEVQHECIPQAILG----------MDVLCQAKSGMGKTAVFVLATLQQLEPVT--GQVSVLVMCHTRELAFQISKEYER  104 (220)
T ss_dssp             CCHHHHHHHHHHHTT----------CCEEEECCTTSCHHHHHHHHHHHHCCCCT--TCCCEEEECSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCC----------CCEEEECCCCCchhhhhhHHHHHhhhccC--CCEEEEEEeCCHHHHHHHHHHHHH
Confidence            568899999988753          45899999999999999999988754322  234788888999999999998887


Q ss_pred             HhccccCCCCceEEEEEecccc------cCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHHHH
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKE------LPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLAIL  197 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~------~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~l  197 (319)
                      ......   +..++........      ......+|+|+||+++.+.+.... .+.+++++|+||||......++.....
T Consensus       105 ~~~~~~---~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~  181 (220)
T 1t6n_A          105 FSKYMP---NVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQ  181 (220)
T ss_dssp             HTTTST---TCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHHHHHHHH
T ss_pred             HHhhCC---CceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcCHHHHhcccCcHHHHH
Confidence            754321   3333321111110      001235799999999999885543 488999999999997321223333333


Q ss_pred             HhhhccccCceEEEecccc--ChhhHhh-hhCC
Q psy496          198 KDVTDKRKDLKLILMSATL--NAEKFSQ-FFGG  227 (319)
Q Consensus       198 ~~~~~~~~~~qiv~lSAT~--~~~~l~~-~l~~  227 (319)
                      +.+...+++.|++++|||+  +.+.+.+ |+.+
T Consensus       182 ~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~  214 (220)
T 1t6n_A          182 EIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQD  214 (220)
T ss_dssp             HHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSS
T ss_pred             HHHHhCCCcCeEEEEEeecCHHHHHHHHHHcCC
Confidence            3333455678999999999  4556655 4543

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=99.89  E-value=3.8e-23  Score=178.12  Aligned_cols=168  Identities=20%  Similarity=0.140  Sum_probs=114.5

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC-CCCccEEEEecccHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN-RGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~-~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      ++++|.++++.+.++          ++++++||||||||.++.+|+++.+.... .....++++++|+++|+.|+.+.+.
T Consensus        24 ~~~~Q~~~i~~~~~~----------~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~~q~~~~~~   93 (207)
T 2gxq_A           24 PTPIQAAALPLALEG----------KDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELT   93 (207)
T ss_dssp             CCHHHHHHHHHHHTT----------CCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHcCC----------CCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHHHHHHHHHH
Confidence            568899999987753          56899999999999999999998765321 1224578888899999999999998


Q ss_pred             HHhccccCCCCceEEEEEeccc-----ccCCCCceEEEECchHHHHHHhc-CCCCCCccEEEEecccccccchhHHHHHH
Q psy496          124 QERDEQCGRPGSSVGYQIRLEK-----ELPRKRGSILYCTAGILPEVMQS-DPILSGVSHIVMDEIHERSMISDFLLAIL  197 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~-----~~~~~~~~Iiv~Tpg~ll~~l~~-~~~l~~v~~vViDEah~~~~~~~~~~~~l  197 (319)
                      +....      ..+........     .....+++|+|+||+++.+.+.. ...+.+++++|+||||.. ...++.....
T Consensus        94 ~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~-~~~~~~~~~~  166 (207)
T 2gxq_A           94 AVAPH------LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEM-LSMGFEEEVE  166 (207)
T ss_dssp             HHCTT------SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHH-HHTTCHHHHH
T ss_pred             HHhhc------ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHh-hccchHHHHH
Confidence            87542      11211111100     00012467999999999998854 345889999999999962 1222222222


Q ss_pred             HhhhccccCceEEEecccc--ChhhHhhhhCCCC
Q psy496          198 KDVTDKRKDLKLILMSATL--NAEKFSQFFGGAP  229 (319)
Q Consensus       198 ~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~  229 (319)
                      ..+...+++.|++++|||+  +.+.+.+++...|
T Consensus       167 ~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p  200 (207)
T 2gxq_A          167 ALLSATPPSRQTLLFSATLPSWAKRLAERYMKNP  200 (207)
T ss_dssp             HHHHTSCTTSEEEEECSSCCHHHHHHHHHHCSSC
T ss_pred             HHHHhCCccCeEEEEEEecCHHHHHHHHHHcCCC
Confidence            2333455678999999999  4556666554444

>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=99.89  E-value=5.1e-23  Score=203.47  Aligned_cols=176  Identities=21%  Similarity=0.186  Sum_probs=115.7

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCC--CCccEEEEecccHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNR--GSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~--~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      ++|+|.++||.++.        .++++++++||||||||++|.+|+++.+.....  ....++++++||++||.|+++.+
T Consensus        95 ~~~~Q~~~i~~~l~--------~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~La~Q~~~~~  166 (563)
T 3i5x_A           95 LTPVQQKTIKPILS--------SEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEV  166 (563)
T ss_dssp             CCHHHHHHHHHHHS--------SSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhc--------CCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHHHHHHHHHH
Confidence            57899999998872        245789999999999999999999998876442  12347888889999999999999


Q ss_pred             HHHhccccCCCCceEEEEEecccc------cCCCCceEEEECchHHHHHHhcC--CCCCCccEEEEecccccc-----cc
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEKE------LPRKRGSILYCTAGILPEVMQSD--PILSGVSHIVMDEIHERS-----MI  189 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~~------~~~~~~~Iiv~Tpg~ll~~l~~~--~~l~~v~~vViDEah~~~-----~~  189 (319)
                      .+.........+..+.........      ....+++|+|+|||++++++...  ..++++++||+||||+..     ..
T Consensus       167 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~~f~~~  246 (563)
T 3i5x_A          167 KKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDD  246 (563)
T ss_dssp             HHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTSTTTHHH
T ss_pred             HHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccceEEEEeCHHHHhccchHHH
Confidence            886432110001112111111110      00124679999999999988543  247889999999999721     11


Q ss_pred             hhHHHHHHHhhh-ccccCceEEEeccccC--hhhHhhhhCCC
Q psy496          190 SDFLLAILKDVT-DKRKDLKLILMSATLN--AEKFSQFFGGA  228 (319)
Q Consensus       190 ~~~~~~~l~~~~-~~~~~~qiv~lSAT~~--~~~l~~~l~~~  228 (319)
                      ...+...+.... ...++.|+++||||++  ...+..++...
T Consensus       247 ~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~  288 (563)
T 3i5x_A          247 LETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNK  288 (563)
T ss_dssp             HHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCS
T ss_pred             HHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCC
Confidence            112222222222 1334779999999993  45666655443

>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=99.88  E-value=4.1e-22  Score=188.17  Aligned_cols=232  Identities=15%  Similarity=0.091  Sum_probs=141.3

Q ss_pred             ccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEE
Q psy496           26 VPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCI  105 (319)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~v  105 (319)
                      +++.+.+...+..+.   .+++.|.++++.+..+          ++++++||||||||+++.+|++..+.....  ..++
T Consensus        28 l~~~l~~~l~~~g~~---~~~~~Q~~~i~~i~~~----------~~~li~a~TGsGKT~~~~~~~~~~~~~~~~--~~~~   92 (400)
T 1s2m_A           28 LKRELLMGIFEAGFE---KPSPIQEEAIPVAITG----------RDILARAKNGTGKTAAFVIPTLEKVKPKLN--KIQA   92 (400)
T ss_dssp             CCHHHHHHHHHTTCC---SCCHHHHHHHHHHHHT----------CCEEEECCTTSCHHHHHHHHHHHHCCTTSC--SCCE
T ss_pred             CCHHHHHHHHHCCCC---CCCHHHHHHHHHHhcC----------CCEEEECCCCcHHHHHHHHHHHHHHhhccC--CccE
Confidence            444444444443332   2568999999988754          458999999999999999999887644322  3467


Q ss_pred             EEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc-----ccCCCCceEEEECchHHHHHHhcC-CCCCCccEEE
Q psy496          106 MVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK-----ELPRKRGSILYCTAGILPEVMQSD-PILSGVSHIV  179 (319)
Q Consensus       106 l~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~-----~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~vV  179 (319)
                      ++++|+++|+.|+++.+.+.....    +..++.......     .....+++|+|+||+++.+.+... ..+.++++||
T Consensus        93 lil~P~~~L~~q~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vI  168 (400)
T 1s2m_A           93 LIMVPTRELALQTSQVVRTLGKHC----GISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFI  168 (400)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTT----TCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEE
T ss_pred             EEEcCCHHHHHHHHHHHHHHhccc----CceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEE
Confidence            788899999999999888775432    333332221111     111245689999999999988554 4588999999


Q ss_pred             EecccccccchhHHHHHHHhh-hccccCceEEEeccccCh--h-hHhhhhCCCCEEEeCCcc--ccceeeeehhhhhhhh
Q psy496          180 MDEIHERSMISDFLLAILKDV-TDKRKDLKLILMSATLNA--E-KFSQFFGGAPILHIPGFT--YPVQEYYLEDVLNMTR  253 (319)
Q Consensus       180 iDEah~~~~~~~~~~~~l~~~-~~~~~~~qiv~lSAT~~~--~-~l~~~l~~~~~i~~~~r~--~~v~~~~~~~~~~~~~  253 (319)
                      +||+|.. ...++. ..+..+ ...++..+++++|||++.  . .+..++.....+......  ..+..++....    .
T Consensus       169 iDEaH~~-~~~~~~-~~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~  242 (400)
T 1s2m_A          169 MDEADKM-LSRDFK-TIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLMEELTLKGITQYYAFVE----E  242 (400)
T ss_dssp             EESHHHH-SSHHHH-HHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCSSCBCTTEEEEEEECC----G
T ss_pred             EeCchHh-hhhchH-HHHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEeccccccCCceeEEEEec----h
Confidence            9999962 222333 333333 334567899999999932  2 344455543333332221  12233332211    1


Q ss_pred             hhHHHHHHHHhhhhhhhccccCCCcEEEeCCcccc
Q psy496          254 KDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~  288 (319)
                      ......+ ...+.     ...++++|||++++..+
T Consensus       243 ~~k~~~l-~~~~~-----~~~~~~~lVf~~~~~~~  271 (400)
T 1s2m_A          243 RQKLHCL-NTLFS-----KLQINQAIIFCNSTNRV  271 (400)
T ss_dssp             GGHHHHH-HHHHH-----HSCCSEEEEECSSHHHH
T ss_pred             hhHHHHH-HHHHh-----hcCCCcEEEEEecHHHH
Confidence            1111111 11111     12367899999998665

>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=99.88  E-value=1.6e-22  Score=189.98  Aligned_cols=220  Identities=15%  Similarity=0.126  Sum_probs=137.9

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +++.|.++++.+..          +++++++||||||||.++.+|++..+....  ...++++++|+++|+.|+.+.+.+
T Consensus        31 ~~~~Q~~~i~~~~~----------~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~--~~~~~lil~P~~~L~~q~~~~~~~   98 (391)
T 1xti_A           31 PSEVQHECIPQAIL----------GMDVLCQAKSGMGKTAVFVLATLQQLEPVT--GQVSVLVMCHTRELAFQISKEYER   98 (391)
T ss_dssp             CCHHHHHHHHHHTT----------TCCEEEECSSCSSHHHHHHHHHHHHCCCCT--TCCCEEEECSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhc----------CCcEEEECCCCCcHHHHHHHHHHHhhcccC--CCeeEEEECCCHHHHHHHHHHHHH
Confidence            56889999988764          356999999999999999999987754322  234788888999999999998888


Q ss_pred             HhccccCCCCceEEEEEecccc------cCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHHHH
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKE------LPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLAIL  197 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~------~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~l  197 (319)
                      ......   +..++........      .....++|+|+||+++.+.+.... .+.++++||+||+|......++.....
T Consensus        99 ~~~~~~---~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~~~~~~~~~~  175 (391)
T 1xti_A           99 FSKYMP---NVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQ  175 (391)
T ss_dssp             HTTTCT---TCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHHHHTSSHHHHHHHH
T ss_pred             HHhhCC---CeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHHHHhhccchHHHHH
Confidence            754322   3333322111110      001235799999999999885544 488999999999997422234444444


Q ss_pred             HhhhccccCceEEEecccc--Chhh-HhhhhCCCCEEEeCCcc----ccceeeeehhhhhhhhhhHHHHHHHHhhhhhhh
Q psy496          198 KDVTDKRKDLKLILMSATL--NAEK-FSQFFGGAPILHIPGFT----YPVQEYYLEDVLNMTRKDLKLILMSATLNAEKF  270 (319)
Q Consensus       198 ~~~~~~~~~~qiv~lSAT~--~~~~-l~~~l~~~~~i~~~~r~----~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (319)
                      +.+...+++.|++++|||+  +... +..++.+...+.+....    ..+...+....    .......+.. .+.    
T Consensus       176 ~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~l~~-~l~----  246 (391)
T 1xti_A          176 EIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLK----DNEKNRKLFD-LLD----  246 (391)
T ss_dssp             HHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCCCCCCCCTTCEEEEEECC----GGGHHHHHHH-HHH----
T ss_pred             HHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCccccCcccceEEEEEcC----chhHHHHHHH-HHH----
Confidence            4444455678999999999  3333 44455544444443321    22333333221    1111111111 111    


Q ss_pred             ccccCCCcEEEeCCccccc
Q psy496          271 SQFFGGAPILHIPGFTYPV  289 (319)
Q Consensus       271 ~~~~~g~~LVFlp~R~~~v  289 (319)
                       ...++++|||++++..+.
T Consensus       247 -~~~~~~~lvf~~~~~~~~  264 (391)
T 1xti_A          247 -VLEFNQVVIFVKSVQRCI  264 (391)
T ss_dssp             -HSCCSEEEEECSCHHHHH
T ss_pred             -hcCCCcEEEEeCcHHHHH
Confidence             123688999999987653

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.88  E-value=1.1e-22  Score=212.69  Aligned_cols=178  Identities=17%  Similarity=0.173  Sum_probs=128.5

Q ss_pred             cccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           43 CCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        43 ~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      .++.+.|.++|+.+..|          ++++++||||||||+++.+++...+...     .++++++|+++|+.|+++++
T Consensus        38 f~l~~~Q~~aI~~il~g----------~~vlv~apTGsGKTlv~~~~i~~~~~~g-----~~vlvl~PtraLa~Q~~~~l  102 (997)
T 4a4z_A           38 FELDTFQKEAVYHLEQG----------DSVFVAAHTSAGKTVVAEYAIAMAHRNM-----TKTIYTSPIKALSNQKFRDF  102 (997)
T ss_dssp             SCCCHHHHHHHHHHHTT----------CEEEEECCTTSCSHHHHHHHHHHHHHTT-----CEEEEEESCGGGHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHcC----------CCEEEEECCCCcHHHHHHHHHHHHHhcC-----CeEEEEeCCHHHHHHHHHHH
Confidence            34568899999887653          5689999999999999999887754332     37888889999999999999


Q ss_pred             HHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHHHHHhhh
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLAILKDVT  201 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~l~~~~  201 (319)
                      .+.+.      +..++..  .++.......+|+|+|||+|.+++.... .+.++++|||||+|.. ...+....+.+.+.
T Consensus       103 ~~~~~------~~~v~~l--~G~~~~~~~~~IlV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l-~d~~~g~~~e~ii~  173 (997)
T 4a4z_A          103 KETFD------DVNIGLI--TGDVQINPDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYV-NDQDRGVVWEEVII  173 (997)
T ss_dssp             HTTC--------CCEEEE--CSSCEECTTSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCC-CTTCTTCCHHHHHH
T ss_pred             HHHcC------CCeEEEE--eCCCccCCCCCEEEECHHHHHHHHHhCchhhcCCCEEEEECcccc-cccchHHHHHHHHH
Confidence            88653      2233322  1222223457899999999999885444 4899999999999962 12221112223333


Q ss_pred             ccccCceEEEecccc-ChhhHhhhhC-----CCCEEEeCCccccceeee
Q psy496          202 DKRKDLKLILMSATL-NAEKFSQFFG-----GAPILHIPGFTYPVQEYY  244 (319)
Q Consensus       202 ~~~~~~qiv~lSAT~-~~~~l~~~l~-----~~~~i~~~~r~~~v~~~~  244 (319)
                      ..+++.++|++|||+ |..++++|++     ...++..+.|+.|++.++
T Consensus       174 ~l~~~v~iIlLSAT~~n~~ef~~~l~~~~~~~~~vi~~~~r~~pl~~~v  222 (997)
T 4a4z_A          174 MLPQHVKFILLSATVPNTYEFANWIGRTKQKNIYVISTPKRPVPLEINI  222 (997)
T ss_dssp             HSCTTCEEEEEECCCTTHHHHHHHHHHHHTCCEEEEECSSCSSCEEEEE
T ss_pred             hcccCCCEEEEcCCCCChHHHHHHHhcccCCceEEEecCCCCccceEEE
Confidence            456688999999999 9999999995     234677788888887654

>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=99.87  E-value=2.6e-23  Score=195.48  Aligned_cols=238  Identities=15%  Similarity=0.111  Sum_probs=125.4

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      .+++.+.+...+..+.   .+++.|.++++.+..+          ++++++||||||||.++.+|+++.+.....  ..+
T Consensus        27 ~l~~~l~~~l~~~g~~---~~~~~Q~~~i~~i~~~----------~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~--~~~   91 (394)
T 1fuu_A           27 ELDENLLRGVFGYGFE---EPSAIQQRAIMPIIEG----------HDVLAQAQSGTGKTGTFSIAALQRIDTSVK--APQ   91 (394)
T ss_dssp             CCCHHHHHHHHHHTCC---SCCHHHHHHHHHHHHT----------CCEEECCCSSHHHHHHHHHHHHHHCCTTCC--SCC
T ss_pred             CCCHHHHHHHHHcCCC---CCCHHHHHHHHHHhCC----------CCEEEECCCCChHHHHHHHHHHHHhhccCC--CCC
Confidence            4566666655444332   3568899999998764          458889999999999999999987654332  346


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc----ccCCCCceEEEECchHHHHHHhcCC-CCCCccEEE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK----ELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIV  179 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~----~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vV  179 (319)
                      +++++|+++|+.|+.+.+.+.....    +..++.......    .....+++|+|+||+++.+.+.... .+.+++++|
T Consensus        92 ~lil~P~~~L~~q~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~vI  167 (394)
T 1fuu_A           92 ALMLAPTRELALQIQKVVMALAFHM----DIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFI  167 (394)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTS----CCCEEEECSSCCHHHHHHHHHHCSEEEECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             EEEEcCCHHHHHHHHHHHHHHhccC----CeeEEEEeCCCchHHHHhhcCCCCEEEECHHHHHHHHHhCCcchhhCcEEE
Confidence            7788899999999999888775432    333332211111    0001146799999999999885543 478999999


Q ss_pred             EecccccccchhHHHHHHHhhhccccCceEEEeccccCh---hhHhhhhCCCCEEEeCCcccc---ceeeeehhhhhhhh
Q psy496          180 MDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNA---EKFSQFFGGAPILHIPGFTYP---VQEYYLEDVLNMTR  253 (319)
Q Consensus       180 iDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~~---~~l~~~l~~~~~i~~~~r~~~---v~~~~~~~~~~~~~  253 (319)
                      +||+|.. ...++.....+.+...++..|++++|||++.   +.+..++.+...+........   +...+....    .
T Consensus       168 iDEah~~-~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~  242 (394)
T 1fuu_A          168 LDEADEM-LSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVE----E  242 (394)
T ss_dssp             EETHHHH-HHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC---------------------
T ss_pred             EEChHHh-hCCCcHHHHHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecCccccCCCceEEEEEcC----c
Confidence            9999972 1122222233333345567899999999932   234456654444444332221   112222111    1


Q ss_pred             hhHHHHHHHHhhhhhhhccccCCCcEEEeCCccccccc
Q psy496          254 KDLKLILMSATLNAEKFSQFFGGAPILHIPGFTYPVQE  291 (319)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~g~~LVFlp~R~~~v~~  291 (319)
                      ...+.......     +....++++|||++++..+.+.
T Consensus       243 ~~~~~~~l~~~-----~~~~~~~~~lVf~~~~~~~~~l  275 (394)
T 1fuu_A          243 EEYKYECLTDL-----YDSISVTQAVIFCNTRRKVEEL  275 (394)
T ss_dssp             --------------------------------------
T ss_pred             hhhHHHHHHHH-----HhcCCCCcEEEEECCHHHHHHH
Confidence            11111111111     1112367899999999876443

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.87  E-value=3.4e-22  Score=198.56  Aligned_cols=176  Identities=22%  Similarity=0.185  Sum_probs=114.9

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCC--CCccEEEEecccHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNR--GSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~--~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      ++|+|.++|+.++.        ..+++++++||||||||++|.+|+++.+.....  ....++++++||++||.|+++.+
T Consensus        44 ~~~~Q~~~i~~il~--------~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~La~Q~~~~~  115 (579)
T 3sqw_A           44 LTPVQQKTIKPILS--------SEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEV  115 (579)
T ss_dssp             CCHHHHHHHHHHHC--------SSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHc--------cCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHHHHHHHHHHH
Confidence            57999999998872        245789999999999999999999998876431  22357888889999999999998


Q ss_pred             HHHhccccCCCCceEEEEEecccc------cCCCCceEEEECchHHHHHHhcC--CCCCCccEEEEeccccccc--chhH
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEKE------LPRKRGSILYCTAGILPEVMQSD--PILSGVSHIVMDEIHERSM--ISDF  192 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~~------~~~~~~~Iiv~Tpg~ll~~l~~~--~~l~~v~~vViDEah~~~~--~~~~  192 (319)
                      .+............+.........      ....+++|+|+|||+|++++...  ..++++++||+||||+..-  ....
T Consensus       116 ~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~gf~~~  195 (579)
T 3sqw_A          116 KKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDD  195 (579)
T ss_dssp             HHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTSTTTHHH
T ss_pred             HHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccccCCEEEEEChHHhhcCCCHHH
Confidence            886532110001111111111110      00124679999999999988542  3478899999999997311  1122


Q ss_pred             HHHHHHhhhc----cccCceEEEeccccC--hhhHhhhhCCC
Q psy496          193 LLAILKDVTD----KRKDLKLILMSATLN--AEKFSQFFGGA  228 (319)
Q Consensus       193 ~~~~l~~~~~----~~~~~qiv~lSAT~~--~~~l~~~l~~~  228 (319)
                      +..++..+..    ..++.|+++||||++  ...+..++...
T Consensus       196 ~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~  237 (579)
T 3sqw_A          196 LETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNK  237 (579)
T ss_dssp             HHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCS
T ss_pred             HHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCC
Confidence            2222222221    234679999999993  35566555443

>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=99.86  E-value=2.5e-22  Score=184.64  Aligned_cols=210  Identities=16%  Similarity=0.085  Sum_probs=132.1

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +++.|.++++.+.+          +++++++||||||||+++++|+++.        ..++++++|+++|+.|+++.+.+
T Consensus        17 l~~~Q~~~i~~i~~----------~~~~lv~~~TGsGKT~~~~~~~~~~--------~~~~liv~P~~~L~~q~~~~~~~   78 (337)
T 2z0m_A           17 FTEVQSKTIPLMLQ----------GKNVVVRAKTGSGKTAAYAIPILEL--------GMKSLVVTPTRELTRQVASHIRD   78 (337)
T ss_dssp             CCHHHHHHHHHHHT----------TCCEEEECCTTSSHHHHHHHHHHHH--------TCCEEEECSSHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhc----------CCCEEEEcCCCCcHHHHHHHHHHhh--------cCCEEEEeCCHHHHHHHHHHHHH
Confidence            56889999998764          3579999999999999999998763        13677888999999999999887


Q ss_pred             HhccccCCCCceEEEEEecccc----cCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHHHHHh
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKE----LPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLAILKD  199 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~----~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~l~~  199 (319)
                      .....    +..++........    ....+++|+|+||+++.+.+.... .+.+++++|+||+|... ..++.......
T Consensus        79 ~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~-~~~~~~~~~~~  153 (337)
T 2z0m_A           79 IGRYM----DTKVAEVYGGMPYKAQINRVRNADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMF-EMGFIDDIKII  153 (337)
T ss_dssp             HTTTS----CCCEEEECTTSCHHHHHHHHTTCSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHH-HTTCHHHHHHH
T ss_pred             Hhhhc----CCcEEEEECCcchHHHHhhcCCCCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhh-ccccHHHHHHH
Confidence            64322    3333322111100    001246799999999999885543 47899999999999721 11122222222


Q ss_pred             hhccccCceEEEeccccCh---hhHhhhhCCCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhhccccCC
Q psy496          200 VTDKRKDLKLILMSATLNA---EKFSQFFGGAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKFSQFFGG  276 (319)
Q Consensus       200 ~~~~~~~~qiv~lSAT~~~---~~l~~~l~~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g  276 (319)
                      +...+...+++++|||++.   +.+..|+.+...+........++..+....     ...+..+     ..  +....++
T Consensus       154 ~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~-----~~--~~~~~~~  221 (337)
T 2z0m_A          154 LAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEACIGLANVEHKFVHVK-----DDWRSKV-----QA--LRENKDK  221 (337)
T ss_dssp             HHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEECSGGGGGEEEEEEECS-----SSSHHHH-----HH--HHTCCCS
T ss_pred             HhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceeeecccccCCceEEEEEeC-----hHHHHHH-----HH--HHhCCCC
Confidence            2334456788999999933   345567765544443333333444333221     1111111     11  1223378


Q ss_pred             CcEEEeCCccccc
Q psy496          277 APILHIPGFTYPV  289 (319)
Q Consensus       277 ~~LVFlp~R~~~v  289 (319)
                      ++|||++++..+.
T Consensus       222 ~~lvf~~~~~~~~  234 (337)
T 2z0m_A          222 GVIVFVRTRNRVA  234 (337)
T ss_dssp             SEEEECSCHHHHH
T ss_pred             cEEEEEcCHHHHH
Confidence            8999999987653

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.85  E-value=3.3e-22  Score=190.27  Aligned_cols=121  Identities=14%  Similarity=-0.008  Sum_probs=87.9

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      +++++|.+++|.+..|          ++++++||||||||++++++++.....     ..++++++||++|+.|+++++.
T Consensus        21 ~~~~~Q~~~i~~i~~~----------~~~lv~apTGsGKT~~~l~~~~~~~~~-----~~~~lil~Pt~~L~~q~~~~~~   85 (414)
T 3oiy_A           21 DLTGYQRLWAKRIVQG----------KSFTMVAPTGVGKTTFGMMTALWLARK-----GKKSALVFPTVTLVKQTLERLQ   85 (414)
T ss_dssp             CCCHHHHHHHHHHTTT----------CCEECCSCSSSSHHHHHHHHHHHHHTT-----TCCEEEEESSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHhcC----------CCEEEEeCCCCCHHHHHHHHHHHHhcC-----CCEEEEEECCHHHHHHHHHHHH
Confidence            3568999999988643          568888899999999998888775522     2367777799999999999998


Q ss_pred             HHhccccCCCCceEEEEEecccc---------cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccc
Q psy496          124 QERDEQCGRPGSSVGYQIRLEKE---------LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHE  185 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~~---------~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~  185 (319)
                      ++..  .   |..++........         .....++|+|+|||++.+++.. ..+.++++||+||+|.
T Consensus        86 ~~~~--~---~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~-~~~~~~~~iViDEaH~  150 (414)
T 3oiy_A           86 KLAD--E---KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK-LSQKRFDFVFVDDVDA  150 (414)
T ss_dssp             HHCC--S---SCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH-HTTCCCSEEEESCHHH
T ss_pred             HHcc--C---CceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH-hccccccEEEEeChHh
Confidence            8643  2   4344322211111         0012378999999999888753 4467899999999995

>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=99.84  E-value=9e-21  Score=183.35  Aligned_cols=137  Identities=21%  Similarity=0.200  Sum_probs=97.9

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK  145 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~  145 (319)
                      ..++++++++||||||||++|++|+++.+...+    .++++++|||+||.|+++++.          |..+++......
T Consensus        18 l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~~----~~~lvl~Ptr~La~Q~~~~l~----------g~~v~~~~~~~~   83 (459)
T 2z83_A           18 LRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQR----LRTAVLAPTRVVAAEMAEALR----------GLPVRYQTSAVQ   83 (459)
T ss_dssp             GSTTCEEEECCCTTSCTTTTHHHHHHHHHHHTT----CCEEEEECSHHHHHHHHHHTT----------TSCEEECC----
T ss_pred             HhcCCcEEEECCCCCCHHHHHHHHHHHHHHhCC----CcEEEECchHHHHHHHHHHhc----------CceEeEEecccc
Confidence            445788999999999999999999998876533    467888899999999998775          223333222111


Q ss_pred             ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccC
Q psy496          146 ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLN  217 (319)
Q Consensus       146 ~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~  217 (319)
                      ........+.++|.+.+.+.+...+.++++++|||||||+++.........+..... .++.|+++||||++
T Consensus        84 ~~~t~~~~i~~~~~~~l~~~l~~~~~l~~~~~iViDEaH~~~~~~~~~~~~~~~~~~-~~~~~~il~SAT~~  154 (459)
T 2z83_A           84 REHQGNEIVDVMCHATLTHRLMSPNRVPNYNLFVMDEAHFTDPASIAARGYIATKVE-LGEAAAIFMTATPP  154 (459)
T ss_dssp             ----CCCSEEEEEHHHHHHHHHSCC-CCCCSEEEESSTTCCSHHHHHHHHHHHHHHH-TTSCEEEEECSSCT
T ss_pred             cCCCCCcEEEEEchHHHHHHhhccccccCCcEEEEECCccCCchhhHHHHHHHHHhc-cCCccEEEEEcCCC
Confidence            111123457889999999888887889999999999999865444444444444332 35789999999994

>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=2.2e-21  Score=193.48  Aligned_cols=134  Identities=16%  Similarity=0.197  Sum_probs=93.7

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecc
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLE  144 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~  144 (319)
                      ...++++++++||||||||++|++++++.        ..++++++|||+||.|+++++.+.++..+   +..+|+     
T Consensus       228 ~L~~~~~vlv~ApTGSGKT~a~~l~ll~~--------g~~vLVl~PTReLA~Qia~~l~~~~g~~v---g~~vG~-----  291 (666)
T 3o8b_A          228 VPQSFQVAHLHAPTGSGKSTKVPAAYAAQ--------GYKVLVLNPSVAATLGFGAYMSKAHGIDP---NIRTGV-----  291 (666)
T ss_dssp             CCSSCEEEEEECCTTSCTTTHHHHHHHHT--------TCCEEEEESCHHHHHHHHHHHHHHHSCCC---EEECSS-----
T ss_pred             HHHcCCeEEEEeCCchhHHHHHHHHHHHC--------CCeEEEEcchHHHHHHHHHHHHHHhCCCe---eEEECc-----
Confidence            34567889999999999999999998762        12677778999999999999988876543   333331     


Q ss_pred             cccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccC
Q psy496          145 KELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLN  217 (319)
Q Consensus       145 ~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~  217 (319)
                       .....+.+|+|+|||+|++  .....++++++|||||||+++...+..+..+...........++++|||++
T Consensus       292 -~~~~~~~~IlV~TPGrLl~--~~~l~l~~l~~lVlDEAH~l~~~~~~~l~~Il~~l~~~~~~llil~SAT~~  361 (666)
T 3o8b_A          292 -RTITTGAPVTYSTYGKFLA--DGGCSGGAYDIIICDECHSTDSTTILGIGTVLDQAETAGARLVVLATATPP  361 (666)
T ss_dssp             -CEECCCCSEEEEEHHHHHH--TTSCCTTSCSEEEETTTTCCSHHHHHHHHHHHHHTTTTTCSEEEEEESSCT
T ss_pred             -EeccCCCCEEEECcHHHHh--CCCcccCcccEEEEccchhcCccHHHHHHHHHHhhhhcCCceEEEECCCCC
Confidence             1123467899999999843  233347889999999999865444333333333332222334778899994

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.83  E-value=4.6e-21  Score=202.24  Aligned_cols=121  Identities=13%  Similarity=-0.019  Sum_probs=88.7

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      +++++|.++||.++.          +++++++||||||||++++.+++..+..     ..++++++|||+||.|+++++.
T Consensus        78 ~pt~iQ~~ai~~il~----------g~dvlv~ApTGSGKTl~~l~~il~~~~~-----~~~~Lil~PtreLa~Q~~~~l~  142 (1104)
T 4ddu_A           78 DLTGYQRLWAKRIVQ----------GKSFTMVAPTGVGKTTFGMMTALWLARK-----GKKSALVFPTVTLVKQTLERLQ  142 (1104)
T ss_dssp             CCCHHHHHHHHHHTT----------TCCEEECCSTTCCHHHHHHHHHHHHHTT-----TCCEEEEESSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHc----------CCCEEEEeCCCCcHHHHHHHHHHHHHhc-----CCeEEEEechHHHHHHHHHHHH
Confidence            467999999999875          3568899999999999888887776522     2367777799999999999998


Q ss_pred             HHhccccCCCCceEEEEEecccc---------cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccc
Q psy496          124 QERDEQCGRPGSSVGYQIRLEKE---------LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHE  185 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~~---------~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~  185 (319)
                      ++.  ..   +..++........         .....++|+|+|||+|.+++.. ..++++++||+||||.
T Consensus       143 ~l~--~~---~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~-l~~~~l~~lViDEaH~  207 (1104)
T 4ddu_A          143 KLA--DE---KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK-LSQKRFDFVFVDDVDA  207 (1104)
T ss_dssp             TTS--CT---TSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH-HHTSCCSEEEESCHHH
T ss_pred             Hhh--CC---CCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh-hcccCcCEEEEeCCCc
Confidence            843  22   4444433222111         0112378999999999888753 3467899999999995

>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=99.83  E-value=1e-20  Score=188.90  Aligned_cols=149  Identities=19%  Similarity=0.165  Sum_probs=105.7

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      ..+|+|+.++|.++          ++++++++||||||||++|++|+++.+...+    .++++++|||+||.|+++.+.
T Consensus       171 ~~lpiq~~~i~~l~----------~g~dvlv~a~TGSGKT~~~~lpil~~l~~~~----~~vLvl~PtreLa~Qi~~~l~  236 (618)
T 2whx_A          171 IGEPDYEVDEDIFR----------KKRLTIMDLHPGAGKTKRILPSIVREALKRR----LRTLILAPTRVVAAEMEEALR  236 (618)
T ss_dssp             CCCCCCCCCGGGGS----------TTCEEEECCCTTSSTTTTHHHHHHHHHHHTT----CCEEEEESSHHHHHHHHHHTT
T ss_pred             cCCCccccCHHHHh----------cCCeEEEEcCCCCCHHHHHHHHHHHHHHhCC----CeEEEEcChHHHHHHHHHHhc
Confidence            34677777766654          4677888899999999999999998876532    367777799999999997664


Q ss_pred             HHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhcc
Q psy496          124 QERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDK  203 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~  203 (319)
                                +..+++..............+.++|.+.+.+.+...+.++++++|||||||+++...+.....+.... .
T Consensus       237 ----------~~~v~~~~~~l~~~~tp~~~i~~~t~~~l~~~l~~~~~l~~~~~iViDEah~~~~~~~~~~~~i~~~l-~  305 (618)
T 2whx_A          237 ----------GLPIRYQTPAVKSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSVAARGYISTRV-E  305 (618)
T ss_dssp             ----------TSCEEECCTTSSCCCCSSSCEEEEEHHHHHHHHHHCSSCCCCSEEEEESTTCCSHHHHHHHHHHHHHH-H
T ss_pred             ----------CCceeEecccceeccCCCceEEEEChHHHHHHHhccccccCCeEEEEECCCCCCccHHHHHHHHHHHh-c
Confidence                      22344333321112223455888999999988877788999999999999986443333333333322 1


Q ss_pred             ccCceEEEeccccC
Q psy496          204 RKDLKLILMSATLN  217 (319)
Q Consensus       204 ~~~~qiv~lSAT~~  217 (319)
                      .++.|+++||||++
T Consensus       306 ~~~~q~il~SAT~~  319 (618)
T 2whx_A          306 MGEAAAIFMTATPP  319 (618)
T ss_dssp             HTSCEEEEECSSCT
T ss_pred             ccCccEEEEECCCc
Confidence            25789999999993

>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=99.82  E-value=3.9e-20  Score=181.53  Aligned_cols=158  Identities=15%  Similarity=0.049  Sum_probs=108.0

Q ss_pred             cccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           43 CCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        43 ~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      .+++++|.++++.++.          ++++++++|||||||.+|.+|+++.+.....+...++++++|+++|+.|+.+.+
T Consensus         6 ~~~~~~Q~~~i~~~~~----------~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~   75 (556)
T 4a2p_A            6 KKARSYQIELAQPAIN----------GKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVF   75 (556)
T ss_dssp             --CCHHHHHHHHHHHT----------TCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHc----------CCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHH
Confidence            3457899999998864          356899999999999999999998876644333457888889999999999999


Q ss_pred             HHHhccccCCCCceEEEEEecccccC------CCCceEEEECchHHHHHHhcCC--CCCCccEEEEecccccccchhHHH
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEKELP------RKRGSILYCTAGILPEVMQSDP--ILSGVSHIVMDEIHERSMISDFLL  194 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~~~~------~~~~~Iiv~Tpg~ll~~l~~~~--~l~~v~~vViDEah~~~~~~~~~~  194 (319)
                      .+.+...    +..++... ++....      ..+++|+|+||++|.+++....  .+.++++||+||||...-. ....
T Consensus        76 ~~~~~~~----~~~~~~~~-g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~-~~~~  149 (556)
T 4a2p_A           76 KHHFERQ----GYSVQGIS-GENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGN-HPYN  149 (556)
T ss_dssp             HHHHGGG----TCCEEECC-CC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTT-SHHH
T ss_pred             HHHhccc----CceEEEEe-CCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCc-chHH
Confidence            8876432    22222111 111000      1246799999999999996543  5889999999999974322 1222


Q ss_pred             HHHHhhhc-----cccCceEEEecccc
Q psy496          195 AILKDVTD-----KRKDLKLILMSATL  216 (319)
Q Consensus       195 ~~l~~~~~-----~~~~~qiv~lSAT~  216 (319)
                      ..+.....     ..+..++++||||+
T Consensus       150 ~~~~~~~~~~~~~~~~~~~~l~lSAT~  176 (556)
T 4a2p_A          150 VLMTRYLEQKFNSASQLPQILGLTASV  176 (556)
T ss_dssp             HHHHHHHHHHHCC---CCEEEEEESCC
T ss_pred             HHHHHHHHhhhcccCCCCeEEEEeCCc
Confidence            22222211     24567999999999

>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=99.81  E-value=3.4e-20  Score=184.39  Aligned_cols=157  Identities=15%  Similarity=0.074  Sum_probs=105.2

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ..|.|.++|+.++.          ++++++.+|||||||++|.+|++..        ..++++++|+++|+.|..+.+.+
T Consensus        45 ~rp~Q~~~i~~il~----------g~d~lv~~pTGsGKTl~~~lpal~~--------~g~~lVisP~~~L~~q~~~~l~~  106 (591)
T 2v1x_A           45 FRPLQLETINVTMA----------GKEVFLVMPTGGGKSLCYQLPALCS--------DGFTLVICPLISLMEDQLMVLKQ  106 (591)
T ss_dssp             CCTTHHHHHHHHHT----------TCCEEEECCTTSCTTHHHHHHHHTS--------SSEEEEECSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHc----------CCCEEEEECCCChHHHHHHHHHHHc--------CCcEEEEeCHHHHHHHHHHHHHh
Confidence            46899999999875          3568889999999999999998752        23788889999999999998877


Q ss_pred             HhccccCCCCceEEEEEecccc---------c--CCCCceEEEECchHHH------HHHhcCCCCCCccEEEEecccccc
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKE---------L--PRKRGSILYCTAGILP------EVMQSDPILSGVSHIVMDEIHERS  187 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~---------~--~~~~~~Iiv~Tpg~ll------~~l~~~~~l~~v~~vViDEah~~~  187 (319)
                      . +.       .++........         .  .....+|+++||++|.      +.+.....+.++++|||||||...
T Consensus       107 ~-gi-------~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~~~~i~~iViDEAH~is  178 (591)
T 2v1x_A          107 L-GI-------SATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCS  178 (591)
T ss_dssp             H-TC-------CEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHHHHHTTCEEEEEEETGGGGS
T ss_pred             c-CC-------cEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHhhhhccCCcEEEEECccccc
Confidence            5 22       22211110000         0  1235789999999774      333332336789999999999732


Q ss_pred             c-----chhHHHHHHHhhhccccCceEEEeccccCh---hhHhhhhCCCC
Q psy496          188 M-----ISDFLLAILKDVTDKRKDLKLILMSATLNA---EKFSQFFGGAP  229 (319)
Q Consensus       188 ~-----~~~~~~~~l~~~~~~~~~~qiv~lSAT~~~---~~l~~~l~~~~  229 (319)
                      .     ..+.  ..+..+....++.++++||||++.   +++.++++...
T Consensus       179 ~~g~dfr~~~--~~l~~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~~~  226 (591)
T 2v1x_A          179 QWGHDFRPDY--KALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEK  226 (591)
T ss_dssp             TTCTTCCGGG--GGGGHHHHHCTTSEEEEEESSCCHHHHHHHHHHTTCCS
T ss_pred             ccccccHHHH--HHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHHhCCCC
Confidence            1     1111  111223333457899999999943   46677776443

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.81  E-value=7.5e-20  Score=175.54  Aligned_cols=135  Identities=16%  Similarity=0.173  Sum_probs=94.6

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL  147 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~  147 (319)
                      ++++++++||||||||++|++|+++.+...+    .++++++||++||.|+++.+.          |..+++........
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~~g----~~~lvl~Pt~~La~Q~~~~~~----------~~~v~~~~~~~~~~   66 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVKKR----LRTVILAPTRVVASEMYEALR----------GEPIRYMTPAVQSE   66 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHHTT----CCEEEEESSHHHHHHHHHHTT----------TSCEEEC-------
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHhCC----CCEEEECcHHHHHHHHHHHhC----------CCeEEEEecCcccc
Confidence            3688999999999999999999997665433    367777799999999987664          22333222211111


Q ss_pred             CCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccC
Q psy496          148 PRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLN  217 (319)
Q Consensus       148 ~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~  217 (319)
                      ...+..+.+.|.|.+.+.+.....++++++|||||+|+++...+.....++... .+++.++++||||++
T Consensus        67 ~~~~~~~~~~~~~~l~~~l~~~~~~~~l~~vViDEaH~~~~~~~~~~~~l~~~~-~~~~~~~l~~SAT~~  135 (431)
T 2v6i_A           67 RTGNEIVDFMCHSTFTMKLLQGVRVPNYNLYIMDEAHFLDPASVAARGYIETRV-SMGDAGAIFMTATPP  135 (431)
T ss_dssp             --CCCSEEEEEHHHHHHHHHHTCCCCCCSEEEEESTTCCSHHHHHHHHHHHHHH-HTTSCEEEEEESSCT
T ss_pred             CCCCceEEEEchHHHHHHHhcCccccCCCEEEEeCCccCCccHHHHHHHHHHHh-hCCCCcEEEEeCCCC
Confidence            112345778899999888866777999999999999996554444455555443 235789999999994

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.81  E-value=1.2e-19  Score=177.80  Aligned_cols=159  Identities=16%  Similarity=0.062  Sum_probs=111.3

Q ss_pred             cccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           43 CCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        43 ~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      .+++++|.++++.++.          ++++++++|||||||.+|.+|+++.+.....+...++++++|+++|+.|..+.+
T Consensus         3 ~~~~~~Q~~~i~~~~~----------~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~   72 (555)
T 3tbk_A            3 LKPRNYQLELALPAKK----------GKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVF   72 (555)
T ss_dssp             CCCCHHHHHHHHHHHT----------TCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHhC----------CCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHH
Confidence            4567899999998764          357899999999999999999998887654333457888889999999999999


Q ss_pred             HHHhccccCCCCceEEEEEecccccC-----CCCceEEEECchHHHHHHhcCC--CCCCccEEEEecccccccchhHHHH
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEKELP-----RKRGSILYCTAGILPEVMQSDP--ILSGVSHIVMDEIHERSMISDFLLA  195 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~~~~-----~~~~~Iiv~Tpg~ll~~l~~~~--~l~~v~~vViDEah~~~~~~~~~~~  195 (319)
                      .+.+...    +..++..........     ..+.+|+|+||+++.+.+....  .+.++++||+||||...-.. ....
T Consensus        73 ~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~-~~~~  147 (555)
T 3tbk_A           73 SRYFERL----GYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNH-PYNQ  147 (555)
T ss_dssp             HHHHHTT----TCCEEEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTC-HHHH
T ss_pred             HHHhccC----CcEEEEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcc-hHHH
Confidence            8876432    333332221111111     0236799999999999996543  58899999999999843221 1222


Q ss_pred             HHHhhhc------cccCceEEEecccc
Q psy496          196 ILKDVTD------KRKDLKLILMSATL  216 (319)
Q Consensus       196 ~l~~~~~------~~~~~qiv~lSAT~  216 (319)
                      .+.....      ..+..+++++|||+
T Consensus       148 ~~~~~~~~~~~~~~~~~~~~l~lSAT~  174 (555)
T 3tbk_A          148 IMFRYLDHKLGESRDPLPQVVGLTASV  174 (555)
T ss_dssp             HHHHHHHHHTSSCCSCCCEEEEEESCC
T ss_pred             HHHHHHHhhhccccCCCCeEEEEecCc
Confidence            2222211      12567999999999

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.80  E-value=9.7e-20  Score=183.28  Aligned_cols=155  Identities=17%  Similarity=0.141  Sum_probs=104.4

Q ss_pred             ccccccc-----cchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHH
Q psy496           44 CIMVTQP-----RRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAI  118 (319)
Q Consensus        44 ~~~~~Q~-----~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~  118 (319)
                      .++++|+     .+||.++.    ......+++++++||||||||++|++|+++.+...+    .++++++|||+||.|+
T Consensus       215 ~pt~IQ~~~r~~~aIp~~l~----~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~~----~~~lilaPTr~La~Q~  286 (673)
T 2wv9_A          215 YVSAIVQGERVEEPVPEAYN----PEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQKR----LRTAVLAPTRVVAAEM  286 (673)
T ss_dssp             EEEEEECC-------CCCCC----GGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHTT----CCEEEEESSHHHHHHH
T ss_pred             ccCceeeccccccchHHHhh----HHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhCC----CcEEEEccHHHHHHHH
Confidence            4678999     89998763    233446789999999999999999999998876533    3677777999999999


Q ss_pred             HHHHHHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHH
Q psy496          119 AERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILK  198 (319)
Q Consensus       119 ~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~  198 (319)
                      ++.+..+          .+++.............-+-+.+.+.+.+.+.....++++++|||||+|+++...+.....+.
T Consensus       287 ~~~l~~~----------~i~~~~~~l~~v~tp~~ll~~l~~~~l~~~l~~~~~l~~l~lvViDEaH~~~~~~~~~~~~l~  356 (673)
T 2wv9_A          287 AEALRGL----------PVRYLTPAVQREHSGNEIVDVMCHATLTHRLMSPLRVPNYNLFVMDEAHFTDPASIAARGYIA  356 (673)
T ss_dssp             HHHTTTS----------CCEECCC---CCCCSCCCEEEEEHHHHHHHHHSSSCCCCCSEEEEESTTCCCHHHHHHHHHHH
T ss_pred             HHHHhcC----------CeeeecccccccCCHHHHHHHHHhhhhHHHHhcccccccceEEEEeCCcccCccHHHHHHHHH
Confidence            9877532          122211110101111233556677777777766677999999999999996544444444444


Q ss_pred             hhhccccCceEEEeccccC
Q psy496          199 DVTDKRKDLKLILMSATLN  217 (319)
Q Consensus       199 ~~~~~~~~~qiv~lSAT~~  217 (319)
                      .... +++.|+++||||++
T Consensus       357 ~~~~-~~~~~vl~~SAT~~  374 (673)
T 2wv9_A          357 TRVE-AGEAAAIFMTATPP  374 (673)
T ss_dssp             HHHH-TTSCEEEEECSSCT
T ss_pred             Hhcc-ccCCcEEEEcCCCC
Confidence            4432 24679999999993

>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=99.80  E-value=5e-19  Score=180.43  Aligned_cols=211  Identities=19%  Similarity=0.171  Sum_probs=132.5

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      ++++.|.++|+.+..+..    .....+++++||||||||+++++|++..+..+.     ++++++||++||.|+++.+.
T Consensus       368 ~lt~~Q~~ai~~I~~~l~----~~~~~~~Ll~a~TGSGKTlvall~il~~l~~g~-----qvlvlaPtr~La~Q~~~~l~  438 (780)
T 1gm5_A          368 KLTNAQKRAHQEIRNDMI----SEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGF-----QTAFMVPTSILAIQHYRRTV  438 (780)
T ss_dssp             CCCHHHHHHHHHHHHHHH----SSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTS-----CEEEECSCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhhcc----ccCCCcEEEEcCCCCCHHHHHHHHHHHHHHcCC-----eEEEEeCcHHHHHHHHHHHH
Confidence            567899999999887532    334468999999999999999999998876533     67777899999999999999


Q ss_pred             HHhccccCCCCceEEEEEecccc---------cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHH
Q psy496          124 QERDEQCGRPGSSVGYQIRLEKE---------LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLL  194 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~~---------~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~  194 (319)
                      +.+...    |..++........         ......+|+|+||+.+.+    ...+.+++++|+||+|+.+...    
T Consensus       439 ~~~~~~----gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~----~~~~~~l~lVVIDEaHr~g~~q----  506 (780)
T 1gm5_A          439 ESFSKF----NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE----DVHFKNLGLVIIDEQHRFGVKQ----  506 (780)
T ss_dssp             HHHTCS----SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH----CCCCSCCCEEEEESCCCC--------
T ss_pred             HHhhhc----CceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh----hhhccCCceEEecccchhhHHH----
Confidence            887532    3333321111100         011247899999997754    4458899999999999854321    


Q ss_pred             HHHHhhhccccCceEEEeccccChhhHhh-hhCCCCEEEeCC---ccccceeeeehhhhhhhhhhHHHHHHHHhhhhhhh
Q psy496          195 AILKDVTDKRKDLKLILMSATLNAEKFSQ-FFGGAPILHIPG---FTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEKF  270 (319)
Q Consensus       195 ~~l~~~~~~~~~~qiv~lSAT~~~~~l~~-~l~~~~~i~~~~---r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (319)
                        ...+.....+.++++||||+.++.++. ++++.....++.   ...|+...+....    .  ... +.....+.  +
T Consensus       507 --r~~l~~~~~~~~vL~mSATp~p~tl~~~~~g~~~~s~i~~~p~~r~~i~~~~~~~~----~--~~~-l~~~i~~~--l  575 (780)
T 1gm5_A          507 --REALMNKGKMVDTLVMSATPIPRSMALAFYGDLDVTVIDEMPPGRKEVQTMLVPMD----R--VNE-VYEFVRQE--V  575 (780)
T ss_dssp             ---CCCCSSSSCCCEEEEESSCCCHHHHHHHTCCSSCEEECCCCSSCCCCEECCCCSS----T--HHH-HHHHHHHH--T
T ss_pred             --HHHHHHhCCCCCEEEEeCCCCHHHHHHHHhCCcceeeeeccCCCCcceEEEEeccc----h--HHH-HHHHHHHH--H
Confidence              122233345679999999996666654 455444333332   2235554443321    1  111 11111111  1


Q ss_pred             ccccCCCcEEEeCCcccc
Q psy496          271 SQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       271 ~~~~~g~~LVFlp~R~~~  288 (319)
                        ..+++++||+|.....
T Consensus       576 --~~g~qvlVf~~~ie~s  591 (780)
T 1gm5_A          576 --MRGGQAFIVYPLIEES  591 (780)
T ss_dssp             --TTSCCBCCBCCCC---
T ss_pred             --hcCCcEEEEecchhhh
Confidence              1278999999986553

>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=99.78  E-value=1.1e-18  Score=167.92  Aligned_cols=136  Identities=20%  Similarity=0.117  Sum_probs=89.2

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE  146 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~  146 (319)
                      .++++++++||||||||++|++|+++.+...+    .++++++||++||.|+++.+...          .+++.......
T Consensus         6 ~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~~----~~~lil~Ptr~La~Q~~~~l~~~----------~v~~~~~~~~~   71 (440)
T 1yks_A            6 KKGMTTVLDFHPGAGKTRRFLPQILAECARRR----LRTLVLAPTRVVLSEMKEAFHGL----------DVKFHTQAFSA   71 (440)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHTT----CCEEEEESSHHHHHHHHHHTTTS----------CEEEESSCCCC
T ss_pred             hCCCCEEEEcCCCCCHHHHHHHHHHHHHHhcC----CeEEEEcchHHHHHHHHHHHhcC----------CeEEeccccee
Confidence            46789999999999999999999998776543    36677779999999999877522          23322211000


Q ss_pred             cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccC
Q psy496          147 LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLN  217 (319)
Q Consensus       147 ~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~  217 (319)
                      ......-+-..+.+.+...+.....+++++++|+||+|+++...+.....+..+.. .++.|+++||||++
T Consensus        72 v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~~~~~~~~~~~~~~~~~-~~~~~~l~~SAT~~  141 (440)
T 1yks_A           72 HGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR-ANESATILMTATPP  141 (440)
T ss_dssp             CCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHH-TTSCEEEEECSSCT
T ss_pred             ccCCccceeeecccchhHhhhCcccccCccEEEEECccccCcchHHHHHHHHHHhc-cCCceEEEEeCCCC
Confidence            11011123334445555555556668999999999999853333333344444332 34679999999993

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.78  E-value=1.1e-18  Score=176.49  Aligned_cols=159  Identities=16%  Similarity=0.089  Sum_probs=110.7

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +++.|.++++.++.          ++++++++|||||||+++.+|+++.+.....+...++++++||++|+.|..+.+.+
T Consensus        14 lr~~Q~~~i~~~l~----------g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~~   83 (696)
T 2ykg_A           14 PRNYQLELALPAMK----------GKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFSK   83 (696)
T ss_dssp             CCHHHHHHHHHHHT----------TCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHc----------CCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHHH
Confidence            56889999988764          46799999999999999999999887665433335788888999999999998888


Q ss_pred             HhccccCCCCceEEEEEecccccC-----CCCceEEEECchHHHHHHhcCC--CCCCccEEEEecccccccchh---HHH
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKELP-----RKRGSILYCTAGILPEVMQSDP--ILSGVSHIVMDEIHERSMISD---FLL  194 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~~~-----~~~~~Iiv~Tpg~ll~~l~~~~--~l~~v~~vViDEah~~~~~~~---~~~  194 (319)
                      .+...    +..++..........     ..+.+|+|+|||+|.+.+..+.  .+.++++||+||||+..-...   ...
T Consensus        84 ~~~~~----~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~~~~~~i~~  159 (696)
T 2ykg_A           84 YFERH----GYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMF  159 (696)
T ss_dssp             HTTTT----TCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTTCHHHHHHH
T ss_pred             HhccC----CceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCcccHHHHHH
Confidence            76432    333432221111100     0246899999999999996553  488999999999998332211   111


Q ss_pred             HHHHh-hh-ccccCceEEEeccccC
Q psy496          195 AILKD-VT-DKRKDLKLILMSATLN  217 (319)
Q Consensus       195 ~~l~~-~~-~~~~~~qiv~lSAT~~  217 (319)
                      ..+.. +. ...+..++++||||+.
T Consensus       160 ~~l~~~~~~~~~~~~~il~LTATp~  184 (696)
T 2ykg_A          160 NYLDQKLGGSSGPLPQVIGLTASVG  184 (696)
T ss_dssp             HHHHHHHTTCCSCCCEEEEEESCCC
T ss_pred             HHHHHhhcccCCCCCeEEEEeCccc
Confidence            11211 11 1235679999999994

>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=99.78  E-value=1.6e-19  Score=177.29  Aligned_cols=207  Identities=16%  Similarity=0.103  Sum_probs=124.7

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ..+.|.++|+.+..|          +++++.+|||||||++|.+|++..   .     ..+++++|+++|+.|..+.+..
T Consensus        26 ~r~~Q~~~i~~il~g----------~d~lv~apTGsGKTl~~~lp~l~~---~-----g~~lvi~P~~aL~~q~~~~l~~   87 (523)
T 1oyw_A           26 FRPGQEEIIDTVLSG----------RDCLVVMPTGGGKSLCYQIPALLL---N-----GLTVVVSPLISLMKDQVDQLQA   87 (523)
T ss_dssp             CCTTHHHHHHHHHTT----------CCEEEECSCHHHHHHHHHHHHHHS---S-----SEEEEECSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHcC----------CCEEEECCCCcHHHHHHHHHHHHh---C-----CCEEEECChHHHHHHHHHHHHH
Confidence            468899999998754          468889999999999999998743   1     3688888999999999988876


Q ss_pred             HhccccCCCCceEEEEEeccc---------ccCCCCceEEEECchHHHHHH-hcCCCCCCccEEEEeccccccc---chh
Q psy496          125 ERDEQCGRPGSSVGYQIRLEK---------ELPRKRGSILYCTAGILPEVM-QSDPILSGVSHIVMDEIHERSM---ISD  191 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~---------~~~~~~~~Iiv~Tpg~ll~~l-~~~~~l~~v~~vViDEah~~~~---~~~  191 (319)
                      .        |..+........         .......+|+++||+++.... .......++++|||||||...-   ...
T Consensus        88 ~--------gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~i~~~g~~fr  159 (523)
T 1oyw_A           88 N--------GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFR  159 (523)
T ss_dssp             T--------TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCCC
T ss_pred             c--------CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCccccCcCCCccH
Confidence            4        222221111100         000124679999999985321 1111236899999999997321   111


Q ss_pred             HHHHHHHhhhccccCceEEEeccccCh---hhHhhhhC-CCCEEEeCCccccceeeeehhhhhhhhhhHHHHHHHHhhhh
Q psy496          192 FLLAILKDVTDKRKDLKLILMSATLNA---EKFSQFFG-GAPILHIPGFTYPVQEYYLEDVLNMTRKDLKLILMSATLNA  267 (319)
Q Consensus       192 ~~~~~l~~~~~~~~~~qiv~lSAT~~~---~~l~~~l~-~~~~i~~~~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~  267 (319)
                      .....+..+....++.+++++|||++.   +++.++++ ..+.+.+.+...|. ..|.-..  . ...... +...    
T Consensus       160 ~~~~~l~~l~~~~~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~~~~~~r~~-l~~~v~~--~-~~~~~~-l~~~----  230 (523)
T 1oyw_A          160 PEYAALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPN-IRYMLME--K-FKPLDQ-LMRY----  230 (523)
T ss_dssp             HHHHGGGGHHHHCTTSCEEEEESCCCHHHHHHHHHHHTCCSCEEEECCCCCTT-EEEEEEE--C-SSHHHH-HHHH----
T ss_pred             HHHHHHHHHHHhCCCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEEeCCCCCCc-eEEEEEe--C-CCHHHH-HHHH----
Confidence            122233333344457899999999943   46777775 34444444333332 2222111  0 111111 1111    


Q ss_pred             hhhccccCCCcEEEeCCcccc
Q psy496          268 EKFSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       268 ~~~~~~~~g~~LVFlp~R~~~  288 (319)
                        +....++++|||+++|..+
T Consensus       231 --l~~~~~~~~IVf~~sr~~~  249 (523)
T 1oyw_A          231 --VQEQRGKSGIIYCNSRAKV  249 (523)
T ss_dssp             --HHHTTTCCEEEECSSHHHH
T ss_pred             --HHhcCCCcEEEEeCCHHHH
Confidence              1111367899999999765

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=99.78  E-value=7.7e-20  Score=157.91  Aligned_cols=157  Identities=18%  Similarity=0.071  Sum_probs=98.2

Q ss_pred             ccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC-CCCccEEEEecccHHHHHH-HH
Q psy496           42 ECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN-RGSECCIMVTQPRRISAIA-IA  119 (319)
Q Consensus        42 ~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~-~~~~~~vl~~~Ptr~la~q-~~  119 (319)
                      ..++.+.|.++++.+..          ++++++++|||||||.++.+++++.+.... .....++++++|+++|+.| ..
T Consensus        31 ~~~l~~~Q~~~i~~~~~----------~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~  100 (216)
T 3b6e_A           31 ELQLRPYQMEVAQPALE----------GKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFR  100 (216)
T ss_dssp             CCCCCHHHHHHHHHHHT----------TCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHhc----------CCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHH
Confidence            34567889999987764          367999999999999999999987765422 1123467777799999999 55


Q ss_pred             HHHHHHhccccCCCCceEEEEEecccccC------CCCceEEEECchHHHHHHhcC-------CCCCCccEEEEeccccc
Q psy496          120 ERVAQERDEQCGRPGSSVGYQIRLEKELP------RKRGSILYCTAGILPEVMQSD-------PILSGVSHIVMDEIHER  186 (319)
Q Consensus       120 ~~~~~~~~~~~~~~g~~vg~~~~~~~~~~------~~~~~Iiv~Tpg~ll~~l~~~-------~~l~~v~~vViDEah~~  186 (319)
                      +.+.+....     +..++... .+....      ....+|+|+||+++.+.+...       ..+.++++||+||||..
T Consensus       101 ~~~~~~~~~-----~~~v~~~~-g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~  174 (216)
T 3b6e_A          101 KEFQPFLKK-----WYRVIGLS-GDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHT  174 (216)
T ss_dssp             HTHHHHHTT-----TSCEEECC-C---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC---
T ss_pred             HHHHHHhcc-----CceEEEEe-CCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhh
Confidence            656555432     11222110 111000      013679999999999988553       34789999999999973


Q ss_pred             ccchhHHHHHHHhhhc--------------cccCceEEEeccc
Q psy496          187 SMISDFLLAILKDVTD--------------KRKDLKLILMSAT  215 (319)
Q Consensus       187 ~~~~~~~~~~l~~~~~--------------~~~~~qiv~lSAT  215 (319)
                      . ...+....+..+..              ..+..++++||||
T Consensus       175 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          175 N-KEAVYNNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             c-cCCcHHHHHHHHHHHhcccccccccccCCCCcceEEEeecC
Confidence            2 11122222222211              1156799999998

>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=99.76  E-value=1.6e-18  Score=178.15  Aligned_cols=158  Identities=14%  Similarity=0.046  Sum_probs=110.0

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      +++++|.++++.+..          ++++++++|||||||.+|.+|+++.+.....+...++++++|+++|+.|..+.+.
T Consensus       248 ~l~~~Q~~~i~~~l~----------~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~  317 (797)
T 4a2q_A          248 KARSYQIELAQPAIN----------GKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFK  317 (797)
T ss_dssp             CCCHHHHHHHHHHHT----------TCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh----------CCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHH
Confidence            356889999888754          3568999999999999999999988876543334578888899999999999998


Q ss_pred             HHhccccCCCCceEEEEEeccccc-----CCCCceEEEECchHHHHHHhcCC--CCCCccEEEEecccccccchhHHHHH
Q psy496          124 QERDEQCGRPGSSVGYQIRLEKEL-----PRKRGSILYCTAGILPEVMQSDP--ILSGVSHIVMDEIHERSMISDFLLAI  196 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~~~-----~~~~~~Iiv~Tpg~ll~~l~~~~--~l~~v~~vViDEah~~~~~~~~~~~~  196 (319)
                      +.+...    +..++.........     ...+++|+|+||++|.+.+....  .+.++++||+||||...... ....+
T Consensus       318 ~~~~~~----~~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~~-~~~~i  392 (797)
T 4a2q_A          318 HHFERQ----GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNH-PYNVL  392 (797)
T ss_dssp             HHHGGG----TCCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTTS-HHHHH
T ss_pred             HhcccC----CceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCCc-cHHHH
Confidence            876432    22232111111000     01256799999999999996543  47899999999999743222 22333


Q ss_pred             HHhhhc-----cccCceEEEecccc
Q psy496          197 LKDVTD-----KRKDLKLILMSATL  216 (319)
Q Consensus       197 l~~~~~-----~~~~~qiv~lSAT~  216 (319)
                      +..+..     ..+..++++||||+
T Consensus       393 ~~~~~~~~~~~~~~~~~~l~lSATp  417 (797)
T 4a2q_A          393 MTRYLEQKFNSASQLPQILGLTASV  417 (797)
T ss_dssp             HHHHHHHHHTTCCCCCEEEEEESCC
T ss_pred             HHHHHHHhhccCCCCCeEEEEcCCc
Confidence            222221     24567999999999

>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=99.76  E-value=1.1e-17  Score=177.50  Aligned_cols=211  Identities=16%  Similarity=0.136  Sum_probs=130.9

Q ss_pred             cccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           43 CCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        43 ~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      .+.++.|.++|+.+.....    .....+++++||||||||++++.+++..+..+     .++++++||++||.|.++.+
T Consensus       602 ~~~t~~Q~~ai~~il~~~~----~g~p~d~ll~~~TGsGKT~val~aa~~~~~~g-----~~vlvlvPt~~La~Q~~~~~  672 (1151)
T 2eyq_A          602 FETTPDQAQAINAVLSDMC----QPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNH-----KQVAVLVPTTLLAQQHYDNF  672 (1151)
T ss_dssp             SCCCHHHHHHHHHHHHHHH----SSSCCEEEEECCCCTTTHHHHHHHHHHHHTTT-----CEEEEECSSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHh----cCCcCcEEEECCCCCCHHHHHHHHHHHHHHhC-----CeEEEEechHHHHHHHHHHH
Confidence            3457999999998876322    22234899999999999999998887765432     27888889999999999999


Q ss_pred             HHHhccccCCCCceEEEEEecccc---------cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHH
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEKE---------LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFL  193 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~~---------~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~  193 (319)
                      .+.+...    +..++........         ....+.+|+|+||+.+    .....++++++||+||+|+.+...   
T Consensus       673 ~~~~~~~----~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll----~~~~~~~~l~lvIiDEaH~~g~~~---  741 (1151)
T 2eyq_A          673 RDRFANW----PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLL----QSDVKFKDLGLLIVDEEHRFGVRH---  741 (1151)
T ss_dssp             HHHSTTT----TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHH----HSCCCCSSEEEEEEESGGGSCHHH---
T ss_pred             HHHhhcC----CCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHH----hCCccccccceEEEechHhcChHH---
Confidence            8876532    3334322211110         0112478999999855    344568899999999999854322   


Q ss_pred             HHHHHhhhccccCceEEEeccccChhhHhhhhCCCCEEE-eC---CccccceeeeehhhhhhhhhhHHHHHHHHhhhhhh
Q psy496          194 LAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILH-IP---GFTYPVQEYYLEDVLNMTRKDLKLILMSATLNAEK  269 (319)
Q Consensus       194 ~~~l~~~~~~~~~~qiv~lSAT~~~~~l~~~l~~~~~i~-~~---~r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  269 (319)
                      ...++.   ..++.++++||||+.++.+...+....-.. +.   ....++..++....    .......+    ...  
T Consensus       742 ~~~l~~---l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~~~~~~r~~i~~~~~~~~----~~~i~~~i----l~~--  808 (1151)
T 2eyq_A          742 KERIKA---MRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYD----SMVVREAI----LRE--  808 (1151)
T ss_dssp             HHHHHH---HHTTSEEEEEESSCCCHHHHHHHTTTSEEEECCCCCCBCBCEEEEEEECC----HHHHHHHH----HHH--
T ss_pred             HHHHHH---hcCCCCEEEEcCCCChhhHHHHHhcCCCceEEecCCCCccccEEEEecCC----HHHHHHHH----HHH--
Confidence            222232   334679999999996665555444332222 21   12234444433221    11111111    111  


Q ss_pred             hccccCCCcEEEeCCcccc
Q psy496          270 FSQFFGGAPILHIPGFTYP  288 (319)
Q Consensus       270 ~~~~~~g~~LVFlp~R~~~  288 (319)
                      ..  .+++++||++++..+
T Consensus       809 l~--~g~qvlvf~~~v~~~  825 (1151)
T 2eyq_A          809 IL--RGGQVYYLYNDVENI  825 (1151)
T ss_dssp             HT--TTCEEEEECCCSSCH
T ss_pred             Hh--cCCeEEEEECCHHHH
Confidence            11  278999999998654

>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=99.76  E-value=1.2e-19  Score=191.13  Aligned_cols=148  Identities=18%  Similarity=0.111  Sum_probs=101.7

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      ++|.++||.++.|          ++++++||||||||+ |.+|++..+...+    .++++++|||+||.|+++.+.+..
T Consensus        59 ~iQ~~ai~~il~g----------~dvlv~apTGSGKTl-~~lp~l~~~~~~~----~~~lil~PtreLa~Q~~~~l~~l~  123 (1054)
T 1gku_B           59 AIQKMWAKRILRK----------ESFAATAPTGVGKTS-FGLAMSLFLALKG----KRCYVIFPTSLLVIQAAETIRKYA  123 (1054)
T ss_dssp             HHHHHHHHHHHTT----------CCEECCCCBTSCSHH-HHHHHHHHHHTTS----CCEEEEESCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC----------CCEEEEcCCCCCHHH-HHHHHHHHHhhcC----CeEEEEeccHHHHHHHHHHHHHHH
Confidence            8999999998764          568888889999998 8888887765432    366777799999999999998876


Q ss_pred             ccccCCCCc----eEEEEEecccc-------cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHH
Q psy496          127 DEQCGRPGS----SVGYQIRLEKE-------LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLA  195 (319)
Q Consensus       127 ~~~~~~~g~----~vg~~~~~~~~-------~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~  195 (319)
                      ...    +.    .++........       ....+++|+|+|||+|++++..   ++++++||+||||+..-....+..
T Consensus       124 ~~~----~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~~~IlV~TP~~L~~~l~~---L~~l~~lViDEah~~l~~~~~~~~  196 (1054)
T 1gku_B          124 EKA----GVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRE---LGHFDFIFVDDVDAILKASKNVDK  196 (1054)
T ss_dssp             TTT----CCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCSTT---SCCCSEEEESCHHHHHTSTHHHHH
T ss_pred             hhc----CCCccceEEEEeCCCChhhHHHHHhhccCCCEEEEcHHHHHHHHHH---hccCCEEEEeChhhhhhccccHHH
Confidence            432    22    23211111000       0001278999999999998865   779999999999973222222333


Q ss_pred             HHHhhh--------ccccCceEEEecccc
Q psy496          196 ILKDVT--------DKRKDLKLILMSATL  216 (319)
Q Consensus       196 ~l~~~~--------~~~~~~qiv~lSAT~  216 (319)
                      .++.+.        ..++..|++++|||+
T Consensus       197 i~~~lgf~~~~~~~~~~~~~q~~l~SAT~  225 (1054)
T 1gku_B          197 LLHLLGFHYDLKTKSWVGEARGCLMVSTA  225 (1054)
T ss_dssp             HHHHTTEEEETTTTEEEECCSSEEEECCC
T ss_pred             HHHHhCcchhhhhhhcccCCceEEEEecC
Confidence            333331        113467899999999

>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=99.74  E-value=6.3e-18  Score=152.93  Aligned_cols=147  Identities=12%  Similarity=0.005  Sum_probs=99.3

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      ++.+.|.++++.+..+          .+.++++|||||||.++..++...+.. +   ..++++++|+++|+.|..+++.
T Consensus       113 ~l~~~Q~~ai~~~l~~----------~~~ll~~~tGsGKT~~~~~~~~~~~~~-~---~~~~lil~Pt~~L~~q~~~~l~  178 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVN----------RRRILNLPTSAGRSLIQALLARYYLEN-Y---EGKILIIVPTTALTTQMADDFV  178 (282)
T ss_dssp             CCCHHHHHHHHHHHHH----------SEEEECCCTTSCHHHHHHHHHHHHHHH-C---SSEEEEECSSHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHhc----------CCeEEEcCCCCCcHHHHHHHHHHHHHc-C---CCeEEEEECCHHHHHHHHHHHH
Confidence            4557799998877653          346789999999999998877765543 2   2378888899999999999998


Q ss_pred             HHhccccCCCCceEEEEEecccccC---CCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhh
Q psy496          124 QERDEQCGRPGSSVGYQIRLEKELP---RKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDV  200 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~~~~---~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~  200 (319)
                      +.....    +..++. +..+....   ..+.+|+|+||+.+.+...  ..+.++++||+||||..  ....+.   ..+
T Consensus       179 ~~~~~~----~~~~~~-~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~--~~~~~~~~vIiDEaH~~--~~~~~~---~il  246 (282)
T 1rif_A          179 DYRLFS----HAMIKK-IGGGASKDDKYKNDAPVVVGTWQTVVKQPK--EWFSQFGMMMNDECHLA--TGKSIS---SII  246 (282)
T ss_dssp             HHTSCC----GGGEEE-CSTTCSSTTCCCTTCSEEEECHHHHTTSCG--GGGGGEEEEEEETGGGC--CHHHHH---HHT
T ss_pred             Hhcccc----cceEEE-EeCCCcchhhhccCCcEEEEchHHHHhhHH--HHHhhCCEEEEECCccC--CcccHH---HHH
Confidence            764321    112221 11111111   1457899999998765422  24678999999999983  333222   223


Q ss_pred             hccccCceEEEecccc
Q psy496          201 TDKRKDLKLILMSATL  216 (319)
Q Consensus       201 ~~~~~~~qiv~lSAT~  216 (319)
                      ....+..+++++|||+
T Consensus       247 ~~~~~~~~~l~lSATp  262 (282)
T 1rif_A          247 SGLNNCMFKFGLSGSL  262 (282)
T ss_dssp             TTCTTCCEEEEECSSC
T ss_pred             HHhhcCCeEEEEeCCC
Confidence            3344577999999999

>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=99.72  E-value=3.1e-18  Score=163.87  Aligned_cols=159  Identities=16%  Similarity=0.102  Sum_probs=108.0

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +.+.|.++++.+..+           ++++++|||+|||.++..+++..+...    ..++++++|+++|+.|..+.+.+
T Consensus        10 l~~~Q~~~i~~~~~~-----------~~ll~~~tG~GKT~~~~~~~~~~~~~~----~~~~liv~P~~~L~~q~~~~~~~   74 (494)
T 1wp9_A           10 PRIYQEVIYAKCKET-----------NCLIVLPTGLGKTLIAMMIAEYRLTKY----GGKVLMLAPTKPLVLQHAESFRR   74 (494)
T ss_dssp             CCHHHHHHHHHGGGS-----------CEEEECCTTSCHHHHHHHHHHHHHHHS----CSCEEEECSSHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHhhC-----------CEEEEcCCCCCHHHHHHHHHHHHHhcC----CCeEEEEECCHHHHHHHHHHHHH
Confidence            457788888766542           799999999999999999988876522    24788888999999999999998


Q ss_pred             HhccccCCCCceEEEEEecccc----cCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHHHHHh
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKE----LPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLAILKD  199 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~----~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~l~~  199 (319)
                      .++..    +..++........    ....+.+|+|+||+.+.+.+.... .+.++++||+||||...- ........+.
T Consensus        75 ~~~~~----~~~v~~~~g~~~~~~~~~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~-~~~~~~~~~~  149 (494)
T 1wp9_A           75 LFNLP----PEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVG-NYAYVFIARE  149 (494)
T ss_dssp             HBCSC----GGGEEEECSCSCHHHHHHHHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCST-TCHHHHHHHH
T ss_pred             HhCcc----hhheEEeeCCcchhhhhhhccCCCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCC-CCcHHHHHHH
Confidence            86531    1122211111000    001245799999999999885443 488999999999997321 1122233344


Q ss_pred             hhccccCceEEEecccc--ChhhHhh
Q psy496          200 VTDKRKDLKLILMSATL--NAEKFSQ  223 (319)
Q Consensus       200 ~~~~~~~~qiv~lSAT~--~~~~l~~  223 (319)
                      +....+..++++||||+  +.+.+.+
T Consensus       150 ~~~~~~~~~~l~lTaTp~~~~~~~~~  175 (494)
T 1wp9_A          150 YKRQAKNPLVIGLTASPGSTPEKIME  175 (494)
T ss_dssp             HHHHCSSCCEEEEESCSCSSHHHHHH
T ss_pred             HHhcCCCCeEEEEecCCCCCcHHHHH
Confidence            43344567899999999  4444444

>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=99.72  E-value=7.9e-18  Score=175.64  Aligned_cols=159  Identities=14%  Similarity=0.040  Sum_probs=108.2

Q ss_pred             cccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           43 CCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        43 ~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      .++++.|.++++.++.          ++++++++|||||||.++.+|+++.+.....+...++++++|+++|+.|..+.+
T Consensus       247 ~~~r~~Q~~ai~~il~----------g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~  316 (936)
T 4a2w_A          247 KKARSYQIELAQPAIN----------GKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVF  316 (936)
T ss_dssp             -CCCHHHHHHHHHHHT----------TCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHc----------CCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHH
Confidence            3456889999888754          356899999999999999999988765543222457888889999999999999


Q ss_pred             HHHhccccCCCCceEEEEEecccccC-----CCCceEEEECchHHHHHHhcCC--CCCCccEEEEecccccccchhHHHH
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEKELP-----RKRGSILYCTAGILPEVMQSDP--ILSGVSHIVMDEIHERSMISDFLLA  195 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~~~~-----~~~~~Iiv~Tpg~ll~~l~~~~--~l~~v~~vViDEah~~~~~~~~~~~  195 (319)
                      .+.+...    +..++..........     ..+.+|+|+||++|.+.+....  .+.++++||+||||...-.. ....
T Consensus       317 ~~~~~~~----~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~~-~~~~  391 (936)
T 4a2w_A          317 KHHFERQ----GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNH-PYNV  391 (936)
T ss_dssp             HHHHHTT----TCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTTC-HHHH
T ss_pred             HHHhccc----CceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCCc-cHHH
Confidence            8876432    222221111110000     1245799999999999996543  47889999999999733221 2233


Q ss_pred             HHHhhhc-----cccCceEEEecccc
Q psy496          196 ILKDVTD-----KRKDLKLILMSATL  216 (319)
Q Consensus       196 ~l~~~~~-----~~~~~qiv~lSAT~  216 (319)
                      .+..+..     ..+..++++||||+
T Consensus       392 i~~~~~~~~~~~~~~~~~~l~LSATp  417 (936)
T 4a2w_A          392 LMTRYLEQKFNSASQLPQILGLTASV  417 (936)
T ss_dssp             HHHHHHHHHHTTCSCCCEEEEEESCC
T ss_pred             HHHHHHHHhhccCCCcCeEEEecCCc
Confidence            3322222     24567999999999

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.70  E-value=3.8e-17  Score=159.45  Aligned_cols=148  Identities=11%  Similarity=0.019  Sum_probs=101.4

Q ss_pred             cccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           43 CCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        43 ~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      .++++.|.++++.+..+          .+++++||||||||+++..++...+....    .++++++|+++|+.|..+++
T Consensus       112 ~~l~~~Q~~ai~~~~~~----------~~~ll~~~tGsGKT~~~~~~~~~~~~~~~----~~vlvl~P~~~L~~Q~~~~~  177 (510)
T 2oca_A          112 IEPHWYQKDAVFEGLVN----------RRRILNLPTSAGRSLIQALLARYYLENYE----GKILIIVPTTALTTQMADDF  177 (510)
T ss_dssp             ECCCHHHHHHHHHHHHH----------SEEEEECCSTTTHHHHHHHHHHHHHHHCS----SEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhc----------CCcEEEeCCCCCHHHHHHHHHHHHHhCCC----CeEEEEECcHHHHHHHHHHH
Confidence            35678999999988764          45899999999999999998887665322    37788889999999999999


Q ss_pred             HHHhccccCCCCceEEEEEeccccc---CCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHh
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEKEL---PRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKD  199 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~~~---~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~  199 (319)
                      .+.....    +..++. +..+...   .....+|+|+||+.+.+.  ....+.++++||+||+|..+  .......   
T Consensus       178 ~~~~~~~----~~~v~~-~~~~~~~~~~~~~~~~I~i~T~~~l~~~--~~~~~~~~~liIiDE~H~~~--~~~~~~i---  245 (510)
T 2oca_A          178 VDYRLFS----HAMIKK-IGGGASKDDKYKNDAPVVVGTWQTVVKQ--PKEWFSQFGMMMNDECHLAT--GKSISSI---  245 (510)
T ss_dssp             HHTTSSC----GGGEEE-CGGGCCTTGGGCTTCSEEEEEHHHHTTS--CGGGGGGEEEEEEETGGGCC--HHHHHHH---
T ss_pred             HHhhcCC----ccceEE-EecCCccccccccCCcEEEEeHHHHhhc--hhhhhhcCCEEEEECCcCCC--cccHHHH---
Confidence            7652211    222221 1111111   114578999999976543  12347889999999999833  2222222   


Q ss_pred             hhccccCceEEEecccc
Q psy496          200 VTDKRKDLKLILMSATL  216 (319)
Q Consensus       200 ~~~~~~~~qiv~lSAT~  216 (319)
                      +....+..++++||||+
T Consensus       246 l~~~~~~~~~l~lSATp  262 (510)
T 2oca_A          246 ISGLNNCMFKFGLSGSL  262 (510)
T ss_dssp             GGGCTTCCEEEEEESCG
T ss_pred             HHhcccCcEEEEEEeCC
Confidence            23344567899999999

>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=99.70  E-value=2.6e-18  Score=173.77  Aligned_cols=163  Identities=18%  Similarity=0.122  Sum_probs=103.6

Q ss_pred             cccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCC-CCccEEEEecccHHHHHHH-HH
Q psy496           43 CCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNR-GSECCIMVTQPRRISAIAI-AE  120 (319)
Q Consensus        43 ~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~-~~~~~vl~~~Ptr~la~q~-~~  120 (319)
                      .++.+.|.++++.++.          +++++|++|||||||+++.+|+++.+..... +...++++++|+++|+.|. .+
T Consensus         6 ~~l~~~Q~~~i~~il~----------g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~   75 (699)
T 4gl2_A            6 LQLRPYQMEVAQPALE----------GKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRK   75 (699)
T ss_dssp             -CCCHHHHHHHHHHHS----------SCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHH
T ss_pred             CCccHHHHHHHHHHHh----------CCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHH
Confidence            3456889999988765          4679999999999999999999987765421 1113566777999999999 99


Q ss_pred             HHHHHhccccCCCCceEEEEEeccc-ccCCCCceEEEECchHHHHHHhcC-------CCCCCccEEEEecccccc---cc
Q psy496          121 RVAQERDEQCGRPGSSVGYQIRLEK-ELPRKRGSILYCTAGILPEVMQSD-------PILSGVSHIVMDEIHERS---MI  189 (319)
Q Consensus       121 ~~~~~~~~~~~~~g~~vg~~~~~~~-~~~~~~~~Iiv~Tpg~ll~~l~~~-------~~l~~v~~vViDEah~~~---~~  189 (319)
                      .+.+.+.... ..+...|....... .....+.+|+|+||++|.+.+...       ..+.++++|||||||...   ..
T Consensus        76 ~l~~~~~~~~-~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~  154 (699)
T 4gl2_A           76 EFQPFLKKWY-RVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVY  154 (699)
T ss_dssp             THHHHHTTTS-CEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSS
T ss_pred             HHHHHcCcCc-eEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchH
Confidence            8988775311 00111121111000 000135689999999999888332       247889999999999621   11


Q ss_pred             hhHHHHHHHh-hhccc---------cCceEEEecccc
Q psy496          190 SDFLLAILKD-VTDKR---------KDLKLILMSATL  216 (319)
Q Consensus       190 ~~~~~~~l~~-~~~~~---------~~~qiv~lSAT~  216 (319)
                      .......+.. +....         +..++++||||+
T Consensus       155 ~~i~~~~l~~~~~~~~~~~~~~~~~~~~~il~lTATp  191 (699)
T 4gl2_A          155 NNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLTASP  191 (699)
T ss_dssp             CSHHHHHHHHHHHHHHHHC----CCCCCEEEEECSCC
T ss_pred             HHHHHHHHHhhhcccccccccccCCCCCEEEEecccc
Confidence            1122111111 11111         567999999999

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.63  E-value=7.2e-16  Score=153.25  Aligned_cols=163  Identities=18%  Similarity=0.054  Sum_probs=85.8

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC-----CCCccEEEEecccHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN-----RGSECCIMVTQPRRISAIAI  118 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~-----~~~~~~vl~~~Ptr~la~q~  118 (319)
                      .+.+.|.++++.+...-.     ..+.++++++|||||||.++... +..+...+     .....++++++|+++|+.|.
T Consensus       178 ~lr~~Q~~ai~~~~~~~~-----~~~~~~ll~~~TGsGKT~~~~~~-~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~  251 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVL-----QGKKRSLITMATGTGKTVVAFQI-SWKLWSARWNRTGDYRKPRILFLADRNVLVDDP  251 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHH-----TTCSEEEEEECTTSCHHHHHHHH-HHHHHHTTCCSSCSSSCCCEEEEEC--------
T ss_pred             CchHHHHHHHHHHHHHHh-----cCCCceEEEecCCCChHHHHHHH-HHHHHhcccccccccCCCeEEEEeCCHHHHHHH
Confidence            467889999988765221     23366899999999999996554 44444332     01234677777999999999


Q ss_pred             H-HHHHHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhc-----CCCCCCccEEEEecccccccch-h
Q psy496          119 A-ERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQS-----DPILSGVSHIVMDEIHERSMIS-D  191 (319)
Q Consensus       119 ~-~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~-----~~~l~~v~~vViDEah~~~~~~-~  191 (319)
                      . +.+..+        +..++. +. . .......+|+|+||++|.+....     ......+++||+||||+..... .
T Consensus       252 ~~~~~~~~--------~~~~~~-~~-~-~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~~~  320 (590)
T 3h1t_A          252 KDKTFTPF--------GDARHK-IE-G-GKVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARDNS  320 (590)
T ss_dssp             ---CCTTT--------CSSEEE-CC-C---CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC--------
T ss_pred             HHHHHHhc--------chhhhh-hh-c-cCCCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccchH
Confidence            8 544322        222221 11 1 11224568999999999887532     2235678999999999732110 1


Q ss_pred             HHHHHHHhhhccccCceEEEecccc---ChhhHhhhhCC
Q psy496          192 FLLAILKDVTDKRKDLKLILMSATL---NAEKFSQFFGG  227 (319)
Q Consensus       192 ~~~~~l~~~~~~~~~~qiv~lSAT~---~~~~l~~~l~~  227 (319)
                      .+..+++.    .+..++++||||+   +......+|+.
T Consensus       321 ~~~~il~~----~~~~~~l~lTATP~~~~~~~~~~~f~~  355 (590)
T 3h1t_A          321 NWREILEY----FEPAFQIGMTATPLREDNRDTYRYFGN  355 (590)
T ss_dssp             -CHHHHHH----STTSEEEEEESSCSCTTTHHHHHHSCS
T ss_pred             HHHHHHHh----CCcceEEEeccccccccchhHHHHcCC
Confidence            22222222    2346899999998   23456667764

>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=99.62  E-value=4.8e-17  Score=164.36  Aligned_cols=121  Identities=19%  Similarity=0.151  Sum_probs=85.0

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      .++++|..++|++++|+  ++.++          ||||||++|.+|++.....   +.+  ++++.|||+||.|.++.+.
T Consensus        83 ~pt~VQ~~~ip~ll~G~--Iaea~----------TGeGKTlaf~LP~~l~aL~---g~~--vlVltptreLA~qd~e~~~  145 (844)
T 1tf5_A           83 FPFKVQLMGGVALHDGN--IAEMK----------TGEGKTLTSTLPVYLNALT---GKG--VHVVTVNEYLASRDAEQMG  145 (844)
T ss_dssp             CCCHHHHHHHHHHHTTS--EEECC----------TTSCHHHHHHHHHHHHHTT---SSC--EEEEESSHHHHHHHHHHHH
T ss_pred             CCcHHHHHhhHHHhCCC--EEEcc----------CCcHHHHHHHHHHHHHHHc---CCC--EEEEeCCHHHHHHHHHHHH
Confidence            56799999999998776  55555          9999999999999843332   223  4555599999999998777


Q ss_pred             HHhccccCCCCceEEEEEeccc---ccCCCCceEEEECchHH-HHHHhc-------CCCCCCccEEEEecccc
Q psy496          124 QERDEQCGRPGSSVGYQIRLEK---ELPRKRGSILYCTAGIL-PEVMQS-------DPILSGVSHIVMDEIHE  185 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~---~~~~~~~~Iiv~Tpg~l-l~~l~~-------~~~l~~v~~vViDEah~  185 (319)
                      .+....    |..++....+.+   ......++|+|+|||+| ++++..       ...+..+.++|+||||+
T Consensus       146 ~l~~~l----gl~v~~i~gg~~~~~r~~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~  214 (844)
T 1tf5_A          146 KIFEFL----GLTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDS  214 (844)
T ss_dssp             HHHHHT----TCCEEECCTTSCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHH
T ss_pred             HHHhhc----CCeEEEEeCCCCHHHHHHhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhh
Confidence            764432    445543222111   11112468999999999 555522       23478999999999997

>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=99.59  E-value=6e-16  Score=149.48  Aligned_cols=136  Identities=16%  Similarity=0.081  Sum_probs=92.4

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      ++.+.|.++++.+..          ++++++++|||||||.++..++...   .     .++++++|+++|+.|..+++.
T Consensus        93 ~l~~~Q~~ai~~i~~----------~~~~ll~~~TGsGKT~~~l~~i~~~---~-----~~~Lvl~P~~~L~~Q~~~~~~  154 (472)
T 2fwr_A           93 SLRDYQEKALERWLV----------DKRGCIVLPTGSGKTHVAMAAINEL---S-----TPTLIVVPTLALAEQWKERLG  154 (472)
T ss_dssp             CBCHHHHHHHHHHTT----------TTEEEEECCTTSCHHHHHHHHHHHH---C-----SCEEEEESSHHHHHHHHHHGG
T ss_pred             CcCHHHHHHHHHHHh----------cCCEEEEeCCCCCHHHHHHHHHHHc---C-----CCEEEEECCHHHHHHHHHHHH
Confidence            456777777776543          3459999999999999998887653   1     256666799999999999888


Q ss_pred             HHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhcc
Q psy496          124 QERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDK  203 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~  203 (319)
                      + ++..      .++  ...+..  ....+|+|+||+.+...+..-  ..++++||+||+|...  .......++    .
T Consensus       155 ~-~~~~------~v~--~~~g~~--~~~~~Ivv~T~~~l~~~~~~~--~~~~~liIvDEaH~~~--~~~~~~~~~----~  215 (472)
T 2fwr_A          155 I-FGEE------YVG--EFSGRI--KELKPLTVSTYDSAYVNAEKL--GNRFMLLIFDEVHHLP--AESYVQIAQ----M  215 (472)
T ss_dssp             G-GCGG------GEE--EBSSSC--BCCCSEEEEEHHHHHHTHHHH--TTTCSEEEEETGGGTT--STTTHHHHH----T
T ss_pred             h-CCCc------ceE--EECCCc--CCcCCEEEEEcHHHHHHHHHh--cCCCCEEEEECCcCCC--ChHHHHHHH----h
Confidence            7 4322      033  111111  124679999999998776321  2468999999999732  111222222    2


Q ss_pred             ccCceEEEecccc
Q psy496          204 RKDLKLILMSATL  216 (319)
Q Consensus       204 ~~~~qiv~lSAT~  216 (319)
                      .+..+++++|||+
T Consensus       216 ~~~~~~l~lSATp  228 (472)
T 2fwr_A          216 SIAPFRLGLTATF  228 (472)
T ss_dssp             CCCSEEEEEESCC
T ss_pred             cCCCeEEEEecCc
Confidence            2356899999999

>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=99.59  E-value=1e-16  Score=161.69  Aligned_cols=121  Identities=15%  Similarity=0.061  Sum_probs=85.7

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      .++++|..++|++++|+  ++.++          ||||||++|.+|++.....   +.++.|++  |||+||.|.++.+.
T Consensus        74 ~p~~VQ~~~i~~ll~G~--Iaem~----------TGsGKTlaf~LP~l~~~l~---g~~vlVlt--PTreLA~Q~~e~~~  136 (853)
T 2fsf_A           74 RHFDVQLLGGMVLNERC--IAEMR----------TGEGKTLTATLPAYLNALT---GKGVHVVT--VNDYLAQRDAENNR  136 (853)
T ss_dssp             CCCHHHHHHHHHHHSSE--EEECC----------TTSCHHHHHHHHHHHHHTT---SSCCEEEE--SSHHHHHHHHHHHH
T ss_pred             CCChHHHhhcccccCCe--eeeec----------CCchHHHHHHHHHHHHHHc---CCcEEEEc--CCHHHHHHHHHHHH
Confidence            46799999999998766  55555          9999999999999865432   33455555  99999999998777


Q ss_pred             HHhccccCCCCceEEEEEeccc---ccCCCCceEEEECchHH-HHHHhcC-------CCCCCccEEEEecccc
Q psy496          124 QERDEQCGRPGSSVGYQIRLEK---ELPRKRGSILYCTAGIL-PEVMQSD-------PILSGVSHIVMDEIHE  185 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~---~~~~~~~~Iiv~Tpg~l-l~~l~~~-------~~l~~v~~vViDEah~  185 (319)
                      .+....    |..++....+.+   ......++|+|+|||+| +++++.+       ..+++++++|+||||+
T Consensus       137 ~l~~~l----gl~v~~i~GG~~~~~r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~  205 (853)
T 2fsf_A          137 PLFEFL----GLTVGINLPGMPAPAKREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDS  205 (853)
T ss_dssp             HHHHHT----TCCEEECCTTCCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHH
T ss_pred             HHHHhc----CCeEEEEeCCCCHHHHHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHH
Confidence            764432    444442221111   00112468999999999 7777433       3478999999999997

>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=99.59  E-value=2.6e-16  Score=159.16  Aligned_cols=121  Identities=17%  Similarity=0.118  Sum_probs=85.6

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      .++++|..++|++.+|+  ++.++          ||+|||++|.+|++......   .+  ++++.||++||.|.++.+.
T Consensus       111 rP~~VQ~~~ip~Ll~G~--Iaem~----------TGeGKTLa~~LP~~l~aL~g---~~--v~VvTpTreLA~Qdae~m~  173 (922)
T 1nkt_A          111 RPFDVQVMGAAALHLGN--VAEMK----------TGEGKTLTCVLPAYLNALAG---NG--VHIVTVNDYLAKRDSEWMG  173 (922)
T ss_dssp             CCCHHHHHHHHHHHTTE--EEECC----------TTSCHHHHTHHHHHHHHTTT---SC--EEEEESSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhHhcCC--EEEec----------CCCccHHHHHHHHHHHHHhC---CC--eEEEeCCHHHHHHHHHHHH
Confidence            56799999999998765  55555          99999999999997443332   23  5555599999999998877


Q ss_pred             HHhccccCCCCceEEEEEecccc---cCCCCceEEEECchHH-HHHHhcC-------CCCCCccEEEEecccc
Q psy496          124 QERDEQCGRPGSSVGYQIRLEKE---LPRKRGSILYCTAGIL-PEVMQSD-------PILSGVSHIVMDEIHE  185 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~~---~~~~~~~Iiv~Tpg~l-l~~l~~~-------~~l~~v~~vViDEah~  185 (319)
                      .+....    |..++......+.   .....++|+++|||+| ++++..+       ..+.++.++||||||+
T Consensus       174 ~l~~~l----GLsv~~i~gg~~~~~r~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDs  242 (922)
T 1nkt_A          174 RVHRFL----GLQVGVILATMTPDERRVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDS  242 (922)
T ss_dssp             HHHHHT----TCCEEECCTTCCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHH
T ss_pred             HHHhhc----CCeEEEEeCCCCHHHHHHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHH
Confidence            764432    5555533221110   0012468999999999 6776332       3478899999999997

>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=99.58  E-value=1.4e-15  Score=134.43  Aligned_cols=136  Identities=16%  Similarity=0.096  Sum_probs=89.9

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      ...+.|.++++.+.          ++++++++||||+|||.++..++...        ..++++++|+++|+.|..+.+.
T Consensus        93 ~l~~~Q~~ai~~~~----------~~~~~ll~~~tG~GKT~~a~~~~~~~--------~~~~liv~P~~~L~~q~~~~~~  154 (237)
T 2fz4_A           93 SLRDYQEKALERWL----------VDKRGCIVLPTGSGKTHVAMAAINEL--------STPTLIVVPTLALAEQWKERLG  154 (237)
T ss_dssp             CCCHHHHHHHHHHT----------TTSEEEEEESSSTTHHHHHHHHHHHS--------CSCEEEEESSHHHHHHHHHHHG
T ss_pred             CcCHHHHHHHHHHH----------hCCCEEEEeCCCCCHHHHHHHHHHHc--------CCCEEEEeCCHHHHHHHHHHHH
Confidence            34566777766543          23459999999999999988776542        1256677799999999998887


Q ss_pred             HHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhcc
Q psy496          124 QERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDK  203 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~  203 (319)
                      + ++..      .++. ...+.   ....+|+|+|++.+......  ....+++|||||+|..  .......+++    .
T Consensus       155 ~-~~~~------~v~~-~~g~~---~~~~~i~v~T~~~l~~~~~~--~~~~~~llIiDEaH~l--~~~~~~~i~~----~  215 (237)
T 2fz4_A          155 I-FGEE------YVGE-FSGRI---KELKPLTVSTYDSAYVNAEK--LGNRFMLLIFDEVHHL--PAESYVQIAQ----M  215 (237)
T ss_dssp             G-GCGG------GEEE-ESSSC---BCCCSEEEEEHHHHHHTHHH--HTTTCSEEEEECSSCC--CTTTHHHHHH----T
T ss_pred             h-CCCC------eEEE-EeCCC---CCcCCEEEEeHHHHHhhHHH--hcccCCEEEEECCccC--CChHHHHHHH----h
Confidence            7 4322      0331 11111   12467999999998776632  1246899999999973  2222222222    2


Q ss_pred             ccCceEEEecccc
Q psy496          204 RKDLKLILMSATL  216 (319)
Q Consensus       204 ~~~~qiv~lSAT~  216 (319)
                      .+..++++||||+
T Consensus       216 ~~~~~~l~LSATp  228 (237)
T 2fz4_A          216 SIAPFRLGLTATF  228 (237)
T ss_dssp             CCCSEEEEEEESC
T ss_pred             ccCCEEEEEecCC
Confidence            2356889999998

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.51  E-value=5.8e-14  Score=141.11  Aligned_cols=141  Identities=16%  Similarity=0.081  Sum_probs=88.7

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK  145 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~  145 (319)
                      +-++++++++||||||||+    +++..+...+     ..++++|||+||.|+++++.+.        |..++.......
T Consensus       152 ~l~rk~vlv~apTGSGKT~----~al~~l~~~~-----~gl~l~PtR~LA~Qi~~~l~~~--------g~~v~lltG~~~  214 (677)
T 3rc3_A          152 AMQRKIIFHSGPTNSGKTY----HAIQKYFSAK-----SGVYCGPLKLLAHEIFEKSNAA--------GVPCDLVTGEER  214 (677)
T ss_dssp             TSCCEEEEEECCTTSSHHH----HHHHHHHHSS-----SEEEEESSHHHHHHHHHHHHHT--------TCCEEEECSSCE
T ss_pred             hcCCCEEEEEcCCCCCHHH----HHHHHHHhcC-----CeEEEeCHHHHHHHHHHHHHhc--------CCcEEEEECCee
Confidence            3467899999999999998    3444444433     2255679999999999998764        333332222211


Q ss_pred             ccC---CCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccc-cCceEEEecccc-Chhh
Q psy496          146 ELP---RKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKR-KDLKLILMSATL-NAEK  220 (319)
Q Consensus       146 ~~~---~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~-~~~qiv~lSAT~-~~~~  220 (319)
                      ...   ....+++++|++.+       .....++++||||+|++ ...++...+...+...+ ++.+++++|||. ..+.
T Consensus       215 ~iv~TpGr~~~il~~T~e~~-------~l~~~v~lvVIDEaH~l-~d~~~g~~~~~~l~~l~~~~i~il~~SAT~~~i~~  286 (677)
T 3rc3_A          215 VTVQPNGKQASHVSCTVEMC-------SVTTPYEVAVIDEIQMI-RDPARGWAWTRALLGLCAEEVHLCGEPAAIDLVME  286 (677)
T ss_dssp             ECCSTTCCCCSEEEEEGGGC-------CSSSCEEEEEECSGGGG-GCTTTHHHHHHHHHHCCEEEEEEEECGGGHHHHHH
T ss_pred             EEecCCCcccceeEecHhHh-------hhcccCCEEEEecceec-CCccchHHHHHHHHccCccceEEEeccchHHHHHH
Confidence            110   01234666665432       23578899999999985 33344444444444444 678999999998 6666


Q ss_pred             HhhhhCCCCEE
Q psy496          221 FSQFFGGAPIL  231 (319)
Q Consensus       221 l~~~l~~~~~i  231 (319)
                      +..+.+....+
T Consensus       287 l~~~~~~~~~v  297 (677)
T 3rc3_A          287 LMYTTGEEVEV  297 (677)
T ss_dssp             HHHHHTCCEEE
T ss_pred             HHHhcCCceEE
Confidence            77666544333

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.43  E-value=1.5e-14  Score=146.10  Aligned_cols=123  Identities=16%  Similarity=0.105  Sum_probs=88.2

Q ss_pred             ccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHH
Q psy496           42 ECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        42 ~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      ...++++|..++|++++|+  ++.++          ||||||++|.+|++.....   +.++.|++  ||++||.|.++.
T Consensus        77 G~~Pt~VQ~~~ip~LlqG~--Iaeak----------TGeGKTLvf~Lp~~L~aL~---G~qv~VvT--PTreLA~Qdae~  139 (997)
T 2ipc_A           77 GMRHFDVQLIGGAVLHEGK--IAEMK----------TGEGKTLVATLAVALNALT---GKGVHVVT--VNDYLARRDAEW  139 (997)
T ss_dssp             CCCCCHHHHHHHHHHHTTS--EEECC----------STHHHHHHHHHHHHHHHTT---CSCCEEEE--SSHHHHHHHHHH
T ss_pred             CCCCcHHHHhhcccccCCc--eeecc----------CCCchHHHHHHHHHHHHHh---CCCEEEEe--CCHHHHHHHHHH
Confidence            3466899999999998876  55555          9999999999999644332   22445555  999999999998


Q ss_pred             HHHHhccccCCCCceEEEEEecccc---cCCCCceEEEECchHH-HHHHhcC-------CCCC---CccEEEEecccc
Q psy496          122 VAQERDEQCGRPGSSVGYQIRLEKE---LPRKRGSILYCTAGIL-PEVMQSD-------PILS---GVSHIVMDEIHE  185 (319)
Q Consensus       122 ~~~~~~~~~~~~g~~vg~~~~~~~~---~~~~~~~Iiv~Tpg~l-l~~l~~~-------~~l~---~v~~vViDEah~  185 (319)
                      +..++...    |..++........   .....++|+|+|||++ +++++.+       ..+.   ++.++||||+|.
T Consensus       140 m~~l~~~l----GLsv~~i~Gg~~~~~r~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDs  213 (997)
T 2ipc_A          140 MGPVYRGL----GLSVGVIQHASTPAERRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDS  213 (997)
T ss_dssp             HHHHHHTT----TCCEEECCTTCCHHHHHHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHH
T ss_pred             HHHHHHhc----CCeEEEEeCCCCHHHHHHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHH
Confidence            87775533    5555533221110   0012478999999999 8888443       2477   899999999996

>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=99.42  E-value=1.4e-13  Score=143.86  Aligned_cols=172  Identities=17%  Similarity=0.141  Sum_probs=107.7

Q ss_pred             ccccccccchhhHHHHHHhhh----cCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLT----LSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIA  119 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~----~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~  119 (319)
                      .+.+.|..|++.+..+-.-=.    -..++++.+++++||||||.++ ++++..+...  +...++|+++|+++|+.|+.
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~--~~~~rvLvlvpr~eL~~Q~~  347 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATEL--DFIDKVFFVVDRKDLDYQTM  347 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTC--TTCCEEEEEECGGGCCHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhc--CCCceEEEEeCcHHHHHHHH
Confidence            457899999998876321100    0123467999999999999997 6666544321  22247888889999999999


Q ss_pred             HHHHHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcC---CCCCCccEEEEecccccccchhHHHHH
Q psy496          120 ERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSD---PILSGVSHIVMDEIHERSMISDFLLAI  196 (319)
Q Consensus       120 ~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~---~~l~~v~~vViDEah~~~~~~~~~~~~  196 (319)
                      +.+.......+ .++....   ...........+|+|+||+++.+.+...   +.+....+||+||||+ +...+..   
T Consensus       348 ~~f~~f~~~~v-~~~~s~~---~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHr-s~~~~~~---  419 (1038)
T 2w00_A          348 KEYQRFSPDSV-NGSENTA---GLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHR-SQFGEAQ---  419 (1038)
T ss_dssp             HHHHTTSTTCS-SSSCCCH---HHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCT-THHHHHH---
T ss_pred             HHHHHhccccc-ccccCHH---HHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccch-hcchHHH---
Confidence            88877543221 0010000   0001111234679999999999887432   2367789999999997 2222222   


Q ss_pred             HHhhhccccCceEEEecccc-Ch------hhHhhhhCC
Q psy496          197 LKDVTDKRKDLKLILMSATL-NA------EKFSQFFGG  227 (319)
Q Consensus       197 l~~~~~~~~~~qiv~lSAT~-~~------~~l~~~l~~  227 (319)
                       +.+....++.++++||||+ ..      .....+||+
T Consensus       420 -~~I~~~~p~a~~lgfTATP~~~~~~~~~~~t~~~FG~  456 (1038)
T 2w00_A          420 -KNLKKKFKRYYQFGFTGTPIFPENALGSETTASVFGR  456 (1038)
T ss_dssp             -HHHHHHCSSEEEEEEESSCCCSTTCTTSCCHHHHHCS
T ss_pred             -HHHHHhCCcccEEEEeCCccccccchhhhHHHHHhCC
Confidence             2222333467999999999 32      345667764

>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=99.24  E-value=1.7e-11  Score=119.10  Aligned_cols=150  Identities=16%  Similarity=0.058  Sum_probs=88.8

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +.|.|.++++.+....      ..+.+.+++.+||+|||.++...+ ..+...+..  .++|+++|+ .|+.|..+.+.+
T Consensus        38 L~~~Q~~~v~~l~~~~------~~~~~~ilad~~GlGKT~~ai~~i-~~~~~~~~~--~~~LIv~P~-~l~~qw~~e~~~  107 (500)
T 1z63_A           38 LRPYQIKGFSWMRFMN------KLGFGICLADDMGLGKTLQTIAVF-SDAKKENEL--TPSLVICPL-SVLKNWEEELSK  107 (500)
T ss_dssp             CCHHHHHHHHHHHHHH------HTTCCEEECCCTTSCHHHHHHHHH-HHHHHTTCC--SSEEEEECS-TTHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHh------hCCCCEEEEeCCCCcHHHHHHHHH-HHHHhcCCC--CCEEEEccH-HHHHHHHHHHHH
Confidence            4578888887654321      235679999999999999875544 444433322  345666695 577888887777


Q ss_pred             HhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccc
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKR  204 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~  204 (319)
                      ...      +..+...............+|+++|++.+.+...  ....++++||+||||...-........+.   .. 
T Consensus       108 ~~~------~~~v~~~~g~~~~~~~~~~~ivi~t~~~l~~~~~--l~~~~~~~vIvDEaH~~kn~~~~~~~~l~---~l-  175 (500)
T 1z63_A          108 FAP------HLRFAVFHEDRSKIKLEDYDIILTTYAVLLRDTR--LKEVEWKYIVIDEAQNIKNPQTKIFKAVK---EL-  175 (500)
T ss_dssp             HCT------TSCEEECSSSTTSCCGGGSSEEEEEHHHHTTCHH--HHTCCEEEEEEETGGGGSCTTSHHHHHHH---TS-
T ss_pred             HCC------CceEEEEecCchhccccCCcEEEeeHHHHhccch--hcCCCcCEEEEeCccccCCHhHHHHHHHH---hh-
Confidence            642      1122211111111111345799999999876542  11246899999999973211111222222   22 


Q ss_pred             cCceEEEecccc
Q psy496          205 KDLKLILMSATL  216 (319)
Q Consensus       205 ~~~qiv~lSAT~  216 (319)
                      +..+.+++|||+
T Consensus       176 ~~~~~l~LTaTP  187 (500)
T 1z63_A          176 KSKYRIALTGTP  187 (500)
T ss_dssp             CEEEEEEECSSC
T ss_pred             ccCcEEEEecCC
Confidence            234789999999

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.14  E-value=4.9e-11  Score=117.60  Aligned_cols=65  Identities=12%  Similarity=-0.043  Sum_probs=49.4

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      |.|.+.+..+..      ....++++++.||||||||.+|++|++.   .     ..+++++.||++|+.|+.+.+...
T Consensus         6 ~~Q~~~~~~v~~------~l~~~~~~~~~a~TGtGKT~~~l~p~l~---~-----~~~v~i~~pt~~l~~q~~~~~~~l   70 (551)
T 3crv_A            6 DWQEKLKDKVIE------GLRNNFLVALNAPTGSGKTLFSLLVSLE---V-----KPKVLFVVRTHNEFYPIYRDLTKI   70 (551)
T ss_dssp             HHHHHHHHHHHH------HHHTTCEEEEECCTTSSHHHHHHHHHHH---H-----CSEEEEEESSGGGHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHH------HHHcCCcEEEECCCCccHHHHHHHHHHh---C-----CCeEEEEcCCHHHHHHHHHHHHHH
Confidence            556666554432      1224578999999999999999999987   1     237888889999999998777654

>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=99.13  E-value=2e-11  Score=127.73  Aligned_cols=160  Identities=10%  Similarity=0.078  Sum_probs=92.9

Q ss_pred             cccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           43 CCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        43 ~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      .++.|.|..++..+..        ..+.+++|+++||+|||.++...+...+....   ..++++++|+ .|+.|..+.+
T Consensus       152 ~~LrpyQ~eav~~~l~--------~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~---~~rvLIVvP~-sLl~Qw~~E~  219 (968)
T 3dmq_A          152 TSLIPHQLNIAHDVGR--------RHAPRVLLADEVGLGKTIEAGMILHQQLLSGA---AERVLIIVPE-TLQHQWLVEM  219 (968)
T ss_dssp             SCCCHHHHHHHHHHHH--------SSSCEEEECCCTTSCHHHHHHHHHHHHHHTSS---CCCEEEECCT-TTHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHH--------hcCCCEEEECCCCCcHHHHHHHHHHHHHHhCC---CCeEEEEeCH-HHHHHHHHHH
Confidence            3445667766654432        22567999999999999998777665543322   2367777799 8889988888


Q ss_pred             HHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcC--CCCCCccEEEEecccccccch---hHHHHHH
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSD--PILSGVSHIVMDEIHERSMIS---DFLLAIL  197 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~--~~l~~v~~vViDEah~~~~~~---~~~~~~l  197 (319)
                      .+.++..+..++..................+|+|+|++.+.+.....  ....++++||+||+|...-..   ......+
T Consensus       220 ~~~f~l~v~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l  299 (968)
T 3dmq_A          220 LRRFNLRFALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAI  299 (968)
T ss_dssp             HHHSCCCCEECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHH
T ss_pred             HHHhCCCEEEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCcchHHHHHH
Confidence            77665332000000000000000112235679999999886532111  113579999999999732111   1112233


Q ss_pred             HhhhccccCceEEEecccc
Q psy496          198 KDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       198 ~~~~~~~~~~qiv~lSAT~  216 (319)
                      +.+..  ...+++++|||+
T Consensus       300 ~~L~~--~~~~~L~LTATP  316 (968)
T 3dmq_A          300 EQLAE--HVPGVLLLTATP  316 (968)
T ss_dssp             HHHHT--TCSSEEESCSSC
T ss_pred             HHHhh--cCCcEEEEEcCC
Confidence            33322  233689999998

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.08  E-value=1.1e-10  Score=114.93  Aligned_cols=66  Identities=11%  Similarity=0.028  Sum_probs=50.5

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +.+.|.+++..+...      ..+++++++.||||+|||.+|++|++..        ..+++++.||++|+.|+.+.+..
T Consensus         8 ~r~~Q~~~~~~v~~~------~~~~~~~~~~a~TGtGKT~~~l~~~~~~--------~~~~~~~~~t~~l~~q~~~~~~~   73 (540)
T 2vl7_A            8 LRQWQAEKLGEAINA------LKHGKTLLLNAKPGLGKTVFVEVLGMQL--------KKKVLIFTRTHSQLDSIYKNAKL   73 (540)
T ss_dssp             -CCHHHHHHHHHHHH------HHTTCEEEEECCTTSCHHHHHHHHHHHH--------TCEEEEEESCHHHHHHHHHHHGG
T ss_pred             CCHHHHHHHHHHHHH------HHcCCCEEEEcCCCCcHHHHHHHHHHhC--------CCcEEEEcCCHHHHHHHHHHHHh
Confidence            447788877665432      1245789999999999999999998653        23788888999999999987765

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.84  E-value=1.1e-08  Score=105.03  Aligned_cols=136  Identities=18%  Similarity=0.060  Sum_probs=79.4

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK  145 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~  145 (319)
                      ...+.+.+|+.++|+|||.++...+..........  ..+|+++| ..+..|..+.+.+....      ..+........
T Consensus       252 ~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~--~~~LIV~P-~sll~qW~~E~~~~~p~------~~v~~~~g~~~  322 (800)
T 3mwy_W          252 WSKGDNGILADEMGLGKTVQTVAFISWLIFARRQN--GPHIIVVP-LSTMPAWLDTFEKWAPD------LNCICYMGNQK  322 (800)
T ss_dssp             HTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCC--SCEEEECC-TTTHHHHHHHHHHHSTT------CCEEECCCSSH
T ss_pred             hhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCC--CCEEEEEC-chHHHHHHHHHHHHCCC------ceEEEEeCCHH
Confidence            34567899999999999988766665444333322  24566669 55667777777766421      11110000000


Q ss_pred             -----------------ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEeccccc-ccchhHHHHHHHhhhccccCc
Q psy496          146 -----------------ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHER-SMISDFLLAILKDVTDKRKDL  207 (319)
Q Consensus       146 -----------------~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~-~~~~~~~~~~l~~~~~~~~~~  207 (319)
                                       .....+.+|+++|++.+.+....-. -..+++||+||||.. +... .....+.   .. +..
T Consensus       323 ~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~l~-~~~w~~vIvDEaH~lkn~~s-~~~~~l~---~l-~~~  396 (800)
T 3mwy_W          323 SRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAELG-SIKWQFMAVDEAHRLKNAES-SLYESLN---SF-KVA  396 (800)
T ss_dssp             HHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHHHH-TSEEEEEEETTGGGGCCSSS-HHHHHHT---TS-EEE
T ss_pred             HHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHHHh-cCCcceeehhhhhhhcCchh-HHHHHHH---Hh-hhc
Confidence                             0112346799999999976542111 136889999999972 1222 2222222   22 233


Q ss_pred             eEEEecccc
Q psy496          208 KLILMSATL  216 (319)
Q Consensus       208 qiv~lSAT~  216 (319)
                      +.+++|||+
T Consensus       397 ~rl~LTgTP  405 (800)
T 3mwy_W          397 NRMLITGTP  405 (800)
T ss_dssp             EEEEECSCC
T ss_pred             cEEEeeCCc
Confidence            678999998

>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=98.71  E-value=8.9e-08  Score=95.99  Aligned_cols=158  Identities=15%  Similarity=0.019  Sum_probs=90.0

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCC--CCccEEEEecccHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNR--GSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~--~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      +.|.|.+++..+.....- ....++...+++.+||+|||.++...+...+.....  ....++|+++|+ .+..|..+.+
T Consensus        56 LrpyQ~~gv~~l~~~~~~-~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E~  133 (644)
T 1z3i_X           56 LRPHQREGVKFLWDCVTG-RRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (644)
T ss_dssp             CCHHHHHHHHHHHHHHTT-SSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhhhc-ccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecH-HHHHHHHHHH
Confidence            346777777655431100 011456678999999999999887766554332211  112346666697 6777877777


Q ss_pred             HHHhccccCCCCceEEEEEecccc--------------cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccc-
Q psy496          123 AQERDEQCGRPGSSVGYQIRLEKE--------------LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERS-  187 (319)
Q Consensus       123 ~~~~~~~~~~~g~~vg~~~~~~~~--------------~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~-  187 (319)
                      .+......    ..+.  +..+..              ......+|+|+|++.+...... ..-.++++||+||+|... 
T Consensus       134 ~~~~~~~~----~~~~--~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~~~-l~~~~~~~vI~DEaH~ikn  206 (644)
T 1z3i_X          134 GKWLGGRV----QPVA--IDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEV-LHKGKVGLVICDEGHRLKN  206 (644)
T ss_dssp             HHHHGGGC----CEEE--ECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTT-TTTSCCCEEEETTGGGCCT
T ss_pred             HHHcCCCe----eEEE--EeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhHHH-hhcCCccEEEEECceecCC
Confidence            77654321    1111  111100              0012357999999988765421 112468899999999722 


Q ss_pred             cchhHHHHHHHhhhccccCceEEEecccc
Q psy496          188 MISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       188 ~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      ...... ..+..+   . ..+.+++|||+
T Consensus       207 ~~~~~~-~al~~l---~-~~~rl~LTgTP  230 (644)
T 1z3i_X          207 SDNQTY-LALNSM---N-AQRRVLISGTP  230 (644)
T ss_dssp             TCHHHH-HHHHHH---C-CSEEEEECSSC
T ss_pred             hhhHHH-HHHHhc---c-cCcEEEEecCc
Confidence            222222 222222   2 33779999998

>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=98.56  E-value=7.2e-08  Score=96.02  Aligned_cols=143  Identities=15%  Similarity=0.130  Sum_probs=73.3

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccch--hhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQ--VPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~--~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +.|+.+++.++          .++.++|+|++|||||+.  +.++.+..+..   ....+|+++.||..+|.++.+.+..
T Consensus       152 ~~Q~~Ai~~~l----------~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~---~~~~~vll~APTg~AA~~L~e~~~~  218 (608)
T 1w36_D          152 NWQKVAAAVAL----------TRRISVISGGPGTGKTTTVAKLLAALIQMAD---GERCRIRLAAPTGKAAARLTESLGK  218 (608)
T ss_dssp             CHHHHHHHHHH----------TBSEEEEECCTTSTHHHHHHHHHHHHHHTCS---SCCCCEEEEBSSHHHHHHHHHHHTH
T ss_pred             HHHHHHHHHHh----------cCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh---cCCCeEEEEeCChhHHHHHHHHHHH
Confidence            45666655543          357899999999999944  44555443211   1234788888999999998876654


Q ss_pred             HhccccCCCCceEE--EEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhc
Q psy496          125 ERDEQCGRPGSSVG--YQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTD  202 (319)
Q Consensus       125 ~~~~~~~~~g~~vg--~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~  202 (319)
                      .....    +....  ..+..+..+.   -.++-.+|+.. ...........++++||||+++  +....+..+++.   
T Consensus       219 ~~~~l----~l~~~~~~~~~~~~~Ti---h~ll~~~~~~~-~~~~~~~~~l~~d~lIIDEAsm--l~~~~~~~Ll~~---  285 (608)
T 1w36_D          219 ALRQL----PLTDEQKKRIPEDASTL---HRLLGAQPGSQ-RLRHHAGNPLHLDVLVVDEASM--IDLPMMSRLIDA---  285 (608)
T ss_dssp             HHHHS----SCCSCCCCSCSCCCBTT---TSCC------------CTTSCCSCSEEEECSGGG--CBHHHHHHHHHT---
T ss_pred             HHhcC----CCCHHHHhccchhhhhh---HhhhccCCCch-HHHhccCCCCCCCEEEEechhh--CCHHHHHHHHHh---
Confidence            32211    10000  0000000000   01222233321 1111111223789999999997  444444444443   


Q ss_pred             cccCceEEEeccc
Q psy496          203 KRKDLKLILMSAT  215 (319)
Q Consensus       203 ~~~~~qiv~lSAT  215 (319)
                      .++..|+|++.-.
T Consensus       286 l~~~~~liLvGD~  298 (608)
T 1w36_D          286 LPDHARVIFLGDR  298 (608)
T ss_dssp             CCTTCEEEEEECT
T ss_pred             CCCCCEEEEEcch
Confidence            3456788887544

>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=98.20  E-value=6.4e-07  Score=89.48  Aligned_cols=61  Identities=18%  Similarity=0.019  Sum_probs=41.8

Q ss_pred             EEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEe
Q psy496           73 IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIR  142 (319)
Q Consensus        73 li~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~  142 (319)
                      +.--.||+|||+++.+|++-....+   .++.|+  .|++.||.+-++.+...+...    |..+|....
T Consensus        92 iaEM~TGEGKTLva~lp~~lnAL~G---~~vhVv--T~ndyLA~rdae~m~~l~~~L----glsvg~i~~  152 (822)
T 3jux_A           92 VAEMKTGEGKTLAATMPIYLNALIG---KGVHLV--TVNDYLARRDALWMGPVYLFL----GLRVGVINS  152 (822)
T ss_dssp             EEECCTTSCHHHHTHHHHHHHHTTS---SCEEEE--ESSHHHHHHHHHHHHHHHHHT----TCCEEEEET
T ss_pred             hhhccCCCCccHHHHHHHHHHHhcC---CceEEE--eccHHHHHhHHHHHHHHHHHh----CCEEEEEcC
Confidence            3444499999999999987433332   234444  599999999988777765433    666665443

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.14  E-value=1.7e-06  Score=86.20  Aligned_cols=54  Identities=13%  Similarity=0.058  Sum_probs=45.9

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      +++++++.||||+|||.+|++|++..+...+    .+++++.||++++.|+.+.+...
T Consensus        21 ~~~~~~~~apTGtGKT~a~l~p~l~~~~~~~----~kvli~t~T~~l~~Qi~~el~~l   74 (620)
T 4a15_A           21 KSYGVALESPTGSGKTIMALKSALQYSSERK----LKVLYLVRTNSQEEQVIKELRSL   74 (620)
T ss_dssp             HSSEEEEECCTTSCHHHHHHHHHHHHHHHHT----CEEEEEESSHHHHHHHHHHHHHH
T ss_pred             cCCCEEEECCCCCCHHHHHHHHHHHhhhhcC----CeEEEECCCHHHHHHHHHHHHHH
Confidence            4678999999999999999999998876533    37888899999999998877664

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=97.78  E-value=5.8e-05  Score=74.51  Aligned_cols=60  Identities=15%  Similarity=0.077  Sum_probs=40.8

Q ss_pred             HHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           58 LINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        58 ~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      ..+.++..+..++.++|+|++|||||+.... ++..+...+    .+|+++.||..+|..+.+..
T Consensus       193 ~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~~-l~~~l~~~g----~~Vl~~ApT~~Aa~~L~e~~  252 (574)
T 3e1s_A          193 EQASVLDQLAGHRLVVLTGGPGTGKSTTTKA-VADLAESLG----LEVGLCAPTGKAARRLGEVT  252 (574)
T ss_dssp             HHHHHHHHHTTCSEEEEECCTTSCHHHHHHH-HHHHHHHTT----CCEEEEESSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCEEEEEcCCCCCHHHHHHH-HHHHHHhcC----CeEEEecCcHHHHHHhHhhh
Confidence            3445555555678999999999999976433 444443332    36778889999887776543

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=97.77  E-value=5.1e-05  Score=72.77  Aligned_cols=68  Identities=16%  Similarity=0.216  Sum_probs=44.4

Q ss_pred             ccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           46 MVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        46 ~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      ++-|++++..+...   +..  ...+++|.|+.|||||+.. ..++..+...+.   ..|+++.||..+|..+.+++
T Consensus        27 n~~Q~~av~~~~~~---i~~--~~~~~li~G~aGTGKT~ll-~~~~~~l~~~~~---~~il~~a~T~~Aa~~l~~~~   94 (459)
T 3upu_A           27 TEGQKNAFNIVMKA---IKE--KKHHVTINGPAGTGATTLT-KFIIEALISTGE---TGIILAAPTHAAKKILSKLS   94 (459)
T ss_dssp             CHHHHHHHHHHHHH---HHS--SSCEEEEECCTTSCHHHHH-HHHHHHHHHTTC---CCEEEEESSHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH---Hhc--CCCEEEEEeCCCCCHHHHH-HHHHHHHHhcCC---ceEEEecCcHHHHHHHHhhh
Confidence            45677777665432   111  2248999999999999765 344555544432   35777889988887776544

>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=97.43  E-value=0.00054  Score=59.26  Aligned_cols=112  Identities=17%  Similarity=0.136  Sum_probs=59.9

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL  147 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~  147 (319)
                      .+..++++|++|||||++.+..+.+.... +    .+++++.|...-      + ..  . .+   ....|        .
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~~~-g----~kVli~~~~~d~------r-~~--~-~i---~srlG--------~   64 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLEYA-D----VKYLVFKPKIDT------R-SI--R-NI---QSRTG--------T   64 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHHHT-T----CCEEEEEECCCG------G-GC--S-SC---CCCCC--------C
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHHhc-C----CEEEEEEeccCc------h-HH--H-HH---HHhcC--------C
Confidence            45678899999999999876655544332 2    256776665320      0 00  0 00   11111        0


Q ss_pred             CCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEe
Q psy496          148 PRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILM  212 (319)
Q Consensus       148 ~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~l  212 (319)
                      .  ...+-+.+...+.+.+.....-.++++|||||++.  +..+ ....++.+...  +..+++.
T Consensus        65 ~--~~~~~~~~~~~i~~~i~~~~~~~~~dvViIDEaQ~--l~~~-~ve~l~~L~~~--gi~Vil~  122 (223)
T 2b8t_A           65 S--LPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQF--FDDR-ICEVANILAEN--GFVVIIS  122 (223)
T ss_dssp             S--SCCEEESSTHHHHHHHHSTTSCTTCCEEEECSGGG--SCTH-HHHHHHHHHHT--TCEEEEE
T ss_pred             C--ccccccCCHHHHHHHHHHHhhCCCCCEEEEecCcc--CcHH-HHHHHHHHHhC--CCeEEEE
Confidence            0  01133456666777665433334689999999996  3334 23333444332  4455443

>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=97.21  E-value=0.0024  Score=60.64  Aligned_cols=134  Identities=13%  Similarity=0.079  Sum_probs=71.2

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      ...++++|++|||||+....... .+..  .+....++..-+.|..+......+....+..       +-   .....  
T Consensus        97 ~~vI~lvG~~GsGKTTt~~kLA~-~l~~--~G~kVllv~~D~~r~~a~eqL~~~~~~~gv~-------~~---~~~~~--  161 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGKLAY-FYKK--RGYKVGLVAADVYRPAAYDQLLQLGNQIGVQ-------VY---GEPNN--  161 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHHHHH-HHHH--TTCCEEEEEECCSCHHHHHHHHHHHHTTTCC-------EE---CCTTC--
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH-HHHH--cCCeEEEEecCccchhHHHHHHHHHHhcCCc-------ee---ecccc--
Confidence            46788999999999988755432 2222  2334555555677777666555555543321       10   00000  


Q ss_pred             CCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccc--cchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhh
Q psy496          149 RKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERS--MISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQF  224 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~--~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~  224 (319)
                              ..|..+...........+++++|||++-...  ........+........++.-+++++|+.  +....++.
T Consensus       162 --------~dp~~i~~~al~~a~~~~~DvvIIDTaGr~~~~~d~~lm~el~~i~~~~~pd~vlLVlDa~~gq~a~~~a~~  233 (433)
T 3kl4_A          162 --------QNPIEIAKKGVDIFVKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLASR  233 (433)
T ss_dssp             --------SCHHHHHHHHHHHTTTTTCSEEEEEECCCSSSCCTTHHHHHHHHHHHHHCCSEEEEEEEGGGGGGGHHHHHH
T ss_pred             --------CCHHHHHHHHHHHHHhcCCCEEEEECCCCccccCCHHHHHHHHHHHHhhCCcceEEEEeCccchHHHHHHHH
Confidence                    0122222221111123578999999998633  33333333333333334565677788887  55455554


Q ss_pred             h
Q psy496          225 F  225 (319)
Q Consensus       225 l  225 (319)
                      |
T Consensus       234 f  234 (433)
T 3kl4_A          234 F  234 (433)
T ss_dssp             H
T ss_pred             H
Confidence            4

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.01  E-value=0.0017  Score=54.17  Aligned_cols=38  Identities=21%  Similarity=0.225  Sum_probs=25.8

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEeccc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPR  111 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Pt  111 (319)
                      +...+++||.|||||+.....+.+... .+    .+++++.|.
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~~~-~g----~~v~~~~~~   40 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIYKL-GK----KKVAVFKPK   40 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHH-TT----CEEEEEEEC
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHHH-CC----CeEEEEeec
Confidence            456889999999999987655443322 22    256676676

>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=96.96  E-value=0.0027  Score=53.45  Aligned_cols=39  Identities=18%  Similarity=0.088  Sum_probs=27.1

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEeccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPR  111 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Pt  111 (319)
                      .++..+++||.|||||++.+-.+.+.. ..+    .+++++.|.
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~~a~r~~-~~g----~kV~v~k~~   45 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIRRIRRAK-IAK----QKIQVFKPE   45 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHH-HTT----CCEEEEEEC
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHH-HCC----CEEEEEEec
Confidence            356788899999999988766554433 222    267776676

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.95  E-value=0.00044  Score=69.14  Aligned_cols=51  Identities=29%  Similarity=0.359  Sum_probs=40.0

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      ...+|.||+|||||....-.+.+.+.. +    .+||+++||..++.++.+++...
T Consensus       206 ~~~lI~GPPGTGKT~ti~~~I~~l~~~-~----~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          206 ELAIIHGPPGTGKTTTVVEIILQAVKQ-G----LKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHHT-T----CCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHHhC-C----CeEEEEcCchHHHHHHHHHHHhc
Confidence            468999999999998876655554432 2    37899999999999999888653

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=96.82  E-value=0.0057  Score=55.63  Aligned_cols=127  Identities=13%  Similarity=0.048  Sum_probs=63.1

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCC---CccEEEEecccH-HHHHHHHHHHHHHhccccCCCCceEEEEE
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRG---SECCIMVTQPRR-ISAIAIAERVAQERDEQCGRPGSSVGYQI  141 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~---~~~~vl~~~Ptr-~la~q~~~~~~~~~~~~~~~~g~~vg~~~  141 (319)
                      ...+.+++|+||+|+|||+..-. +++.+......   +...++.+.-.. .-..+++..+...+.      |....   
T Consensus        42 ~~~~~~lli~GpPGTGKT~~v~~-v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I~~~L~------g~~~~---  111 (318)
T 3te6_A           42 SSQNKLFYITNADDSTKFQLVND-VMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAIS------KENLC---  111 (318)
T ss_dssp             TTCCCEEEEECCCSHHHHHHHHH-HHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHHHHHHS------CCC-----
T ss_pred             CCCCCeEEEECCCCCCHHHHHHH-HHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHHHHHhc------CCCCC---
Confidence            34567899999999999977644 45555432211   123455543111 011122222222221      21100   


Q ss_pred             ecccccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          142 RLEKELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       142 ~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                            . ..      +-..|.+.+.... .-...-++++||+|... ..+++...++.........-+|+.++|+
T Consensus       112 ------~-~~------~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~-~q~~L~~l~~~~~~~~s~~~vI~i~n~~  173 (318)
T 3te6_A          112 ------G-DI------SLEALNFYITNVPKAKKRKTLILIQNPENLL-SEKILQYFEKWISSKNSKLSIICVGGHN  173 (318)
T ss_dssp             ------C-CC------CHHHHHHHHHHSCGGGSCEEEEEEECCSSSC-CTHHHHHHHHHHHCSSCCEEEEEECCSS
T ss_pred             ------c-hH------HHHHHHHHHHHhhhccCCceEEEEecHHHhh-cchHHHHHHhcccccCCcEEEEEEecCc
Confidence                  0 00      1122333332211 12345689999999854 5566666665433333345677889998

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=96.80  E-value=0.0018  Score=61.49  Aligned_cols=99  Identities=14%  Similarity=0.114  Sum_probs=56.5

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK  145 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~  145 (319)
                      .......+|.|+.|||||+.+.-.+     ...     .++++.||++++..+.+++.+.        |.          
T Consensus       158 ~~~~~v~~I~G~aGsGKTt~I~~~~-----~~~-----~~lVlTpT~~aa~~l~~kl~~~--------~~----------  209 (446)
T 3vkw_A          158 VSSAKVVLVDGVPGCGKTKEILSRV-----NFE-----EDLILVPGRQAAEMIRRRANAS--------GI----------  209 (446)
T ss_dssp             CCCSEEEEEEECTTSCHHHHHHHHC-----CTT-----TCEEEESCHHHHHHHHHHHTTT--------SC----------
T ss_pred             cccccEEEEEcCCCCCHHHHHHHHh-----ccC-----CeEEEeCCHHHHHHHHHHhhhc--------Cc----------
Confidence            3455678899999999998753321     111     3455569999998887766331        10          


Q ss_pred             ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHH
Q psy496          146 ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILK  198 (319)
Q Consensus       146 ~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~  198 (319)
                       ..  ..+.-+.|-+.++-.-.. ......+++||||+-+  +..+.+...+.
T Consensus       210 -~~--~~~~~V~T~dsfL~~~~~-~~~~~~d~liiDE~sm--~~~~~l~~l~~  256 (446)
T 3vkw_A          210 -IV--ATKDNVRTVDSFLMNYGK-GARCQFKRLFIDEGLM--LHTGCVNFLVE  256 (446)
T ss_dssp             -CC--CCTTTEEEHHHHHHTTTS-SCCCCCSEEEEETGGG--SCHHHHHHHHH
T ss_pred             -cc--cccceEEEeHHhhcCCCC-CCCCcCCEEEEeCccc--CCHHHHHHHHH
Confidence             00  011224555543321111 1123589999999986  55554444443

>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=96.78  E-value=0.0058  Score=55.01  Aligned_cols=130  Identities=15%  Similarity=0.190  Sum_probs=64.5

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE  146 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~  146 (319)
                      ..++.+++.|++|+|||+.......  ......+....++-.-+.|..+.+..+.+.+..+.       .+-        
T Consensus       103 ~~g~vi~lvG~~GsGKTTl~~~LA~--~l~~~~G~~V~lv~~D~~r~~a~eqL~~~~~~~gl-------~~~--------  165 (296)
T 2px0_A          103 IHSKYIVLFGSTGAGKTTTLAKLAA--ISMLEKHKKIAFITTDTYRIAAVEQLKTYAELLQA-------PLE--------  165 (296)
T ss_dssp             CCSSEEEEEESTTSSHHHHHHHHHH--HHHHTTCCCEEEEECCCSSTTHHHHHHHHHTTTTC-------CCC--------
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHH--HHHHhcCCEEEEEecCcccchHHHHHHHHHHhcCC-------CeE--------
Confidence            3567899999999999987654332  22222232344444456565554444434332221       110        


Q ss_pred             cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccChhhHhhh
Q psy496          147 LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLNAEKFSQF  224 (319)
Q Consensus       147 ~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~~~~l~~~  224 (319)
                      ..        ..|+.+...+..   +.+++++|+|.+-........+..+.+.+....++..+++++||.+...+.++
T Consensus       166 ~~--------~~~~~l~~al~~---~~~~dlvIiDT~G~~~~~~~~~~el~~~l~~~~~~~~~lVl~at~~~~~~~~~  232 (296)
T 2px0_A          166 VC--------YTKEEFQQAKEL---FSEYDHVFVDTAGRNFKDPQYIDELKETIPFESSIQSFLVLSATAKYEDMKHI  232 (296)
T ss_dssp             BC--------SSHHHHHHHHHH---GGGSSEEEEECCCCCTTSHHHHHHHHHHSCCCTTEEEEEEEETTBCHHHHHHH
T ss_pred             ec--------CCHHHHHHHHHH---hcCCCEEEEeCCCCChhhHHHHHHHHHHHhhcCCCeEEEEEECCCCHHHHHHH
Confidence            00        123334333321   36789999997754222222233333333222234457777777654444443

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=96.76  E-value=0.0061  Score=50.07  Aligned_cols=21  Identities=24%  Similarity=0.080  Sum_probs=17.5

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      .++.+++.||+|||||+.+-.
T Consensus        37 ~g~~~~l~G~~G~GKTtL~~~   57 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHLAVA   57 (180)
T ss_dssp             GCCEEEECCSSSSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            467899999999999976543

>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=96.70  E-value=0.014  Score=49.23  Aligned_cols=41  Identities=20%  Similarity=0.358  Sum_probs=24.5

Q ss_pred             CCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecc
Q psy496          172 LSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSA  214 (319)
Q Consensus       172 l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSA  214 (319)
                      ...-.+|||||+|.  +..+....+++.+...+.+..+|+.+.
T Consensus       124 ~~~~~vlviDe~~~--l~~~~~~~l~~~l~~~~~~~~~i~~t~  164 (250)
T 1njg_A          124 RGRFKVYLIDEVHM--LSRHSFNALLKTLEEPPEHVKFLLATT  164 (250)
T ss_dssp             SSSSEEEEEETGGG--SCHHHHHHHHHHHHSCCTTEEEEEEES
T ss_pred             cCCceEEEEECccc--ccHHHHHHHHHHHhcCCCceEEEEEeC
Confidence            34567999999998  444444445555544444555555543

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=96.57  E-value=0.025  Score=47.05  Aligned_cols=19  Identities=21%  Similarity=0.314  Sum_probs=15.5

Q ss_pred             CCcEEEecCCCCCccchhh
Q psy496           69 LSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~   87 (319)
                      ..+++|+||+|+|||+..-
T Consensus        38 ~~~~ll~G~~G~GKT~l~~   56 (226)
T 2chg_A           38 IPHLLFSGPPGTGKTATAI   56 (226)
T ss_dssp             CCCEEEECSTTSSHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            3459999999999997653

>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=96.56  E-value=0.0074  Score=57.34  Aligned_cols=55  Identities=18%  Similarity=0.178  Sum_probs=36.2

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      ...++++|++|+|||+....... .+..  .+....++..-|.|..|....+.+....
T Consensus       100 p~vIlivG~~G~GKTTt~~kLA~-~l~~--~G~kVllv~~D~~R~aa~eqL~~~~~~~  154 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAKLAR-YFQK--RGYKVGVVCSDTWRPGAYHQLRQLLDRY  154 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHH-HHHT--TTCCEEEEECCCSSTHHHHHHHHHHGGG
T ss_pred             CeEEEEECcCCCCHHHHHHHHHH-HHHH--CCCeEEEEeCCCcchhHHHHHHHHHHhc
Confidence            45788999999999988755432 2222  2334555555688887776666666544

>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=96.48  E-value=0.014  Score=52.70  Aligned_cols=51  Identities=18%  Similarity=0.040  Sum_probs=29.9

Q ss_pred             HHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhh
Q psy496           34 EIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        34 ~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~   87 (319)
                      |.+..+.....-..-|...+..+   .+.+........+++.||+|+|||+..-
T Consensus        16 ~~~k~rP~~~~~ivg~~~~~~~l---~~~l~~~~~~~~~L~~G~~G~GKT~la~   66 (324)
T 3u61_B           16 LEQKYRPSTIDECILPAFDKETF---KSITSKGKIPHIILHSPSPGTGKTTVAK   66 (324)
T ss_dssp             HHHHSCCCSTTTSCCCHHHHHHH---HHHHHTTCCCSEEEECSSTTSSHHHHHH
T ss_pred             HHHhhCCCCHHHHhCcHHHHHHH---HHHHHcCCCCeEEEeeCcCCCCHHHHHH
Confidence            55555544444445555554433   3444444444567888889999997653

>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=96.44  E-value=0.0065  Score=51.97  Aligned_cols=41  Identities=17%  Similarity=0.120  Sum_probs=28.4

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRR  112 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr  112 (319)
                      ..+...+++|+-|||||++.+--+.+......     +++++.|..
T Consensus        26 ~~G~l~vitG~MgsGKTT~lL~~a~r~~~~g~-----kVli~k~~~   66 (214)
T 2j9r_A           26 QNGWIEVICGSMFSGKSEELIRRVRRTQFAKQ-----HAIVFKPCI   66 (214)
T ss_dssp             CSCEEEEEECSTTSCHHHHHHHHHHHHHHTTC-----CEEEEECC-
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHHHHHCCC-----EEEEEEecc
Confidence            34556778999999999988776655543332     677777864

>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=96.44  E-value=0.0093  Score=54.60  Aligned_cols=50  Identities=22%  Similarity=0.364  Sum_probs=29.7

Q ss_pred             HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          162 LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       162 ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      +.+.+...+......++||||+|.  +..+....+++.+...+++..+|+.+
T Consensus       107 l~~~~~~~~~~~~~~vliiDe~~~--l~~~~~~~Ll~~le~~~~~~~~Il~~  156 (373)
T 1jr3_A          107 LLDNVQYAPARGRFKVYLIDEVHM--LSRHSFNALLKTLEEPPEHVKFLLAT  156 (373)
T ss_dssp             HHHHTTSCCSSSSSEEEEEECGGG--SCHHHHHHHHHHHHSCCSSEEEEEEE
T ss_pred             HHHHHhhccccCCeEEEEEECcch--hcHHHHHHHHHHHhcCCCceEEEEEe
Confidence            444444444566788999999998  44444445555554444454455443

>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=96.42  E-value=0.031  Score=50.88  Aligned_cols=51  Identities=14%  Similarity=0.206  Sum_probs=31.9

Q ss_pred             HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecc
Q psy496          162 LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSA  214 (319)
Q Consensus       162 ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSA  214 (319)
                      +.+.+...+.....+++||||+|.  +..+..-.+++.+...+++..+|+.+.
T Consensus        96 l~~~~~~~~~~~~~kvviIdead~--l~~~a~naLLk~lEep~~~~~~Il~t~  146 (334)
T 1a5t_A           96 VTEKLNEHARLGGAKVVWVTDAAL--LTDAAANALLKTLEEPPAETWFFLATR  146 (334)
T ss_dssp             HHHHTTSCCTTSSCEEEEESCGGG--BCHHHHHHHHHHHTSCCTTEEEEEEES
T ss_pred             HHHHHhhccccCCcEEEEECchhh--cCHHHHHHHHHHhcCCCCCeEEEEEeC
Confidence            334444445567799999999998  455555556666655444555555543

>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=96.22  E-value=0.02  Score=52.61  Aligned_cols=18  Identities=22%  Similarity=0.409  Sum_probs=15.6

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      +++|+||+|+|||+..-.
T Consensus        46 ~~li~G~~G~GKTtl~~~   63 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLRK   63 (389)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            799999999999977643

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=96.20  E-value=0.0063  Score=51.79  Aligned_cols=21  Identities=10%  Similarity=0.188  Sum_probs=17.6

Q ss_pred             CCCCcEEEecCCCCCccchhh
Q psy496           67 PILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~   87 (319)
                      ..+.+++|+||+|+|||+..-
T Consensus        50 ~~~~~~ll~G~~G~GKT~la~   70 (242)
T 3bos_A           50 DGVQAIYLWGPVKSGRTHLIH   70 (242)
T ss_dssp             CSCSEEEEECSTTSSHHHHHH
T ss_pred             CCCCeEEEECCCCCCHHHHHH
Confidence            356889999999999997653

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.15  E-value=0.0028  Score=50.98  Aligned_cols=20  Identities=15%  Similarity=0.195  Sum_probs=17.1

Q ss_pred             CCCcEEEecCCCCCccchhh
Q psy496           68 ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~   87 (319)
                      .++.++|.||+|||||+..-
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~   54 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQ   54 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            57889999999999997653

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=96.14  E-value=0.016  Score=51.73  Aligned_cols=21  Identities=24%  Similarity=0.098  Sum_probs=17.0

Q ss_pred             CCCCcEEEecCCCCCccchhh
Q psy496           67 PILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~   87 (319)
                      ....+++++||+|+|||+.+-
T Consensus        65 ~~~~~vll~G~~GtGKT~la~   85 (309)
T 3syl_A           65 TPTLHMSFTGNPGTGKTTVAL   85 (309)
T ss_dssp             CCCCEEEEEECTTSSHHHHHH
T ss_pred             CCCceEEEECCCCCCHHHHHH
Confidence            345679999999999997653

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=96.14  E-value=0.037  Score=50.54  Aligned_cols=22  Identities=32%  Similarity=0.385  Sum_probs=18.1

Q ss_pred             CCCCcEEEecCCCCCccchhhH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ....+++|+||+|+|||+..-.
T Consensus        42 ~~~~~vll~G~~G~GKT~l~~~   63 (387)
T 2v1u_A           42 EKPSNALLYGLTGTGKTAVARL   63 (387)
T ss_dssp             CCCCCEEECBCTTSSHHHHHHH
T ss_pred             CCCCcEEEECCCCCCHHHHHHH
Confidence            4567899999999999977643

>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=96.07  E-value=0.024  Score=51.36  Aligned_cols=50  Identities=20%  Similarity=0.300  Sum_probs=27.9

Q ss_pred             HHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhh
Q psy496           34 EIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        34 ~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~   87 (319)
                      |.+..+........-|...+..+.   ..+... ...++++.||+|+|||+.+-
T Consensus        27 ~~~k~~p~~~~~i~g~~~~~~~l~---~~l~~~-~~~~~ll~G~~G~GKT~la~   76 (353)
T 1sxj_D           27 WVEKYRPKNLDEVTAQDHAVTVLK---KTLKSA-NLPHMLFYGPPGTGKTSTIL   76 (353)
T ss_dssp             HHHHTCCSSTTTCCSCCTTHHHHH---HHTTCT-TCCCEEEECSTTSSHHHHHH
T ss_pred             HHHhcCCCCHHHhhCCHHHHHHHH---HHHhcC-CCCEEEEECCCCCCHHHHHH
Confidence            445544433333344555554432   222222 12459999999999997653

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=96.06  E-value=0.0098  Score=58.95  Aligned_cols=59  Identities=22%  Similarity=0.156  Sum_probs=44.7

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhcc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDE  128 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~  128 (319)
                      ++.++|.|+.|||||.....-+...+...+ ....+|+++.+|+.+|.++.+++.+..+.
T Consensus        22 ~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~-~~~~~iL~ltft~~aa~e~~~rl~~~~~~   80 (647)
T 3lfu_A           22 RSNLLVLAGAGSGKTRVLVHRIAWLMSVEN-CSPYSIMAVTFTNKAAAEMRHRIGQLMGT   80 (647)
T ss_dssp             SSCEEEEECTTSCHHHHHHHHHHHHHHTSC-CCGGGEEEEESSHHHHHHHHHHHHHHHCS
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHhCC-CChhhEEEEeccHHHHHHHHHHHHHHhcc
Confidence            567999999999999887665554443322 23447888889999999999999887653

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=96.03  E-value=0.0083  Score=54.22  Aligned_cols=20  Identities=40%  Similarity=0.692  Sum_probs=16.7

Q ss_pred             CCCcEEEecCCCCCccchhh
Q psy496           68 ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~   87 (319)
                      ....++|+||+|+|||+..-
T Consensus        36 ~~~~lll~G~~GtGKT~la~   55 (324)
T 1l8q_A           36 LYNPIFIYGSVGTGKTHLLQ   55 (324)
T ss_dssp             SCSSEEEECSSSSSHHHHHH
T ss_pred             CCCeEEEECCCCCcHHHHHH
Confidence            35689999999999997653

>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=95.99  E-value=0.046  Score=48.77  Aligned_cols=39  Identities=18%  Similarity=0.276  Sum_probs=23.5

Q ss_pred             CCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          173 SGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       173 ~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      .+..++||||+|.  +..+....+++.+...+++.++|+.+
T Consensus       109 ~~~~vliiDe~~~--l~~~~~~~L~~~le~~~~~~~~i~~~  147 (327)
T 1iqp_A          109 ASFKIIFLDEADA--LTQDAQQALRRTMEMFSSNVRFILSC  147 (327)
T ss_dssp             CSCEEEEEETGGG--SCHHHHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCCeEEEEeCCCc--CCHHHHHHHHHHHHhcCCCCeEEEEe
Confidence            4578999999998  44444444444444444455666543

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=95.95  E-value=0.11  Score=48.41  Aligned_cols=55  Identities=16%  Similarity=0.145  Sum_probs=41.0

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      +.+++..+-+.|||.+....++..+...   +...|+++.|++.-|..+.+.+.....
T Consensus       179 R~~vi~~sRq~GKT~l~a~~~l~~a~~~---~g~~v~~vA~t~~qA~~vf~~i~~mi~  233 (385)
T 2o0j_A          179 RMTVCNLSRQLGKTTVVAIFLAHFVCFN---KDKAVGILAHKGSMSAEVLDRTKQAIE  233 (385)
T ss_dssp             SEEEEEECSSSCHHHHHHHHHHHHHHSS---SSCEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEcCcCChhHHHHHHHHHHHHhC---CCCeEEEEeCCHHHHHHHHHHHHHHHH
Confidence            5588999999999988766665433332   245788999999999888877766543

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=95.90  E-value=0.025  Score=51.47  Aligned_cols=43  Identities=14%  Similarity=0.351  Sum_probs=27.3

Q ss_pred             CCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          172 LSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       172 l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      ..+.+++|+||+|.  +..+....+++.+...+++..+|+.|-..
T Consensus       132 ~~~~~vlilDE~~~--L~~~~~~~L~~~le~~~~~~~~Il~t~~~  174 (354)
T 1sxj_E          132 AHRYKCVIINEANS--LTKDAQAALRRTMEKYSKNIRLIMVCDSM  174 (354)
T ss_dssp             --CCEEEEEECTTS--SCHHHHHHHHHHHHHSTTTEEEEEEESCS
T ss_pred             CCCCeEEEEeCccc--cCHHHHHHHHHHHHhhcCCCEEEEEeCCH
Confidence            34678999999998  55555555555555544555666665544

>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=95.88  E-value=0.13  Score=50.54  Aligned_cols=57  Identities=16%  Similarity=0.112  Sum_probs=42.8

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhcc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDE  128 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~  128 (319)
                      .+.+++.++-|+|||.+....++..+...   +...++++.|++..|..+...+...+..
T Consensus       178 ~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~---~~~~i~~va~t~~qA~~~~~~i~~~i~~  234 (592)
T 3cpe_A          178 KRMTVCNLSRQLGKTTVVAIFLAHFVCFN---KDKAVGILAHKGSMSAEVLDRTKQAIEL  234 (592)
T ss_dssp             CSEEEEEECSSSCHHHHHHHHHHHHHHTS---SSCEEEEEESSHHHHHHHHHHHHHHHTT
T ss_pred             ccEEEEEEcCccChHHHHHHHHHHHHHhC---CCCeEEEEECCHHHHHHHHHHHHHHHHh
Confidence            35689999999999988766555444332   2458899999999999988877766543

>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=95.87  E-value=0.0062  Score=60.54  Aligned_cols=52  Identities=21%  Similarity=0.307  Sum_probs=38.8

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +...+|.||+|||||......+ ..+....   ..+|+++.||..++.++.+++.+
T Consensus       195 ~~~~li~GppGTGKT~~~~~~i-~~l~~~~---~~~ilv~a~tn~A~~~l~~~l~~  246 (624)
T 2gk6_A          195 RPLSLIQGPPGTGKTVTSATIV-YHLARQG---NGPVLVCAPSNIAVDQLTEKIHQ  246 (624)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHH-HHHHTSS---SCCEEEEESSHHHHHHHHHHHHT
T ss_pred             CCCeEEECCCCCCHHHHHHHHH-HHHHHcC---CCeEEEEeCcHHHHHHHHHHHHh
Confidence            4678999999999998765433 3333211   34788888999999999988765

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=95.87  E-value=0.01  Score=60.66  Aligned_cols=62  Identities=16%  Similarity=0.200  Sum_probs=42.9

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      .+++..+..+...+|.||+|||||......+. .+....   ..+|+++.||..++.++.+++.+.
T Consensus       366 ~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i~-~l~~~~---~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          366 SNAVSHVLQRPLSLIQGPPGTGKTVTSATIVY-HLSKIH---KDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             HHHHHHHTTCSEEEEECSTTSSHHHHHHHHHH-HHHHHH---CCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhcCCCEEEECCCCCCHHHHHHHHHH-HHHhCC---CCeEEEEcCcHHHHHHHHHHHHhh
Confidence            33343333456789999999999987654443 333211   237888889999999999988763

>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=95.81  E-value=0.046  Score=50.09  Aligned_cols=27  Identities=22%  Similarity=0.269  Sum_probs=19.5

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      .....++|+||+|+|||+..-. +.+.+
T Consensus        43 ~~~~~vll~G~~G~GKT~la~~-l~~~~   69 (384)
T 2qby_B           43 EVKFSNLFLGLTGTGKTFVSKY-IFNEI   69 (384)
T ss_dssp             CCCCEEEEEECTTSSHHHHHHH-HHHHH
T ss_pred             CCCCcEEEECCCCCCHHHHHHH-HHHHH
Confidence            3456899999999999977633 34443

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=95.77  E-value=0.019  Score=49.11  Aligned_cols=49  Identities=14%  Similarity=-0.026  Sum_probs=27.0

Q ss_pred             HHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccH
Q psy496           59 INKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRR  112 (319)
Q Consensus        59 ~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr  112 (319)
                      |.........+...+++|+-|||||+..+.-+.+. ...+    .+++++.|..
T Consensus        18 ~~~m~~~~~~G~I~vitG~M~sGKTT~Llr~~~r~-~~~g----~kvli~kp~~   66 (219)
T 3e2i_A           18 GSHMYETYHSGWIECITGSMFSGKSEELIRRLRRG-IYAK----QKVVVFKPAI   66 (219)
T ss_dssp             ---------CCEEEEEEECTTSCHHHHHHHHHHHH-HHTT----CCEEEEEEC-
T ss_pred             CceEeeccCCceEEEEECCCCCCHHHHHHHHHHHH-HHcC----CceEEEEecc
Confidence            33333334566788999999999998776555433 3222    2567766763

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=95.75  E-value=0.011  Score=49.77  Aligned_cols=39  Identities=18%  Similarity=0.084  Sum_probs=28.0

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEeccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPR  111 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Pt  111 (319)
                      .++-.+++||.|||||+-.+..+-+....+     .+++++.|.
T Consensus        19 ~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~~-----~kvl~~kp~   57 (195)
T 1w4r_A           19 RGQIQVILGPMFSGKSTELMRRVRRFQIAQ-----YKCLVIKYA   57 (195)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHHHTT-----CCEEEEEET
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHcC-----CeEEEEccc
Confidence            356789999999999988777666554443     267776665

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=95.64  E-value=0.052  Score=48.92  Aligned_cols=50  Identities=14%  Similarity=0.240  Sum_probs=32.9

Q ss_pred             HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          162 LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       162 ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      +.+.....+...+.+++||||+|.  +..+..-.+++.+...+++..+|+.+
T Consensus        70 li~~~~~~p~~~~~kvviIdead~--lt~~a~naLLk~LEep~~~t~fIl~t  119 (305)
T 2gno_A           70 IKDFLNYSPELYTRKYVIVHDCER--MTQQAANAFLKALEEPPEYAVIVLNT  119 (305)
T ss_dssp             HHHHHTSCCSSSSSEEEEETTGGG--BCHHHHHHTHHHHHSCCTTEEEEEEE
T ss_pred             HHHHHhhccccCCceEEEeccHHH--hCHHHHHHHHHHHhCCCCCeEEEEEE
Confidence            444445555567899999999998  55555556666665555555555553

>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=95.49  E-value=0.017  Score=57.71  Aligned_cols=69  Identities=19%  Similarity=0.112  Sum_probs=40.0

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++..|..+|..+..+-   .  ......++.|-||||||..+...+ ...   +    ..+|++.|+..+|.|++..+..
T Consensus        13 p~~~Q~~~i~~l~~~~---~--~~~~~~~l~g~~gs~k~~~~a~~~-~~~---~----~~~lvv~~~~~~A~~l~~el~~   79 (661)
T 2d7d_A           13 PQGDQPKAIEKLVKGI---Q--EGKKHQTLLGATGTGKTFTVSNLI-KEV---N----KPTLVIAHNKTLAGQLYSEFKE   79 (661)
T ss_dssp             CCTTHHHHHHHHHHHH---H--TTCSEEEEEECTTSCHHHHHHHHH-HHH---C----CCEEEECSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHH---h--cCCCcEEEECcCCcHHHHHHHHHH-HHh---C----CCEEEEECCHHHHHHHHHHHHH
Confidence            4455666665443321   1  111235677889999986553322 221   1    1366666888888888887777


Q ss_pred             Hh
Q psy496          125 ER  126 (319)
Q Consensus       125 ~~  126 (319)
                      ++
T Consensus        80 ~~   81 (661)
T 2d7d_A           80 FF   81 (661)
T ss_dssp             HC
T ss_pred             Hc
Confidence            64

>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=95.45  E-value=0.048  Score=47.10  Aligned_cols=40  Identities=18%  Similarity=0.105  Sum_probs=28.1

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRR  112 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr  112 (319)
                      .++..+++|+-|||||++.+--+.+....+     .+++++.|..
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~~~g-----~kvli~kp~~   57 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQIAQ-----YKCLVIKYAK   57 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHTTT-----CCEEEEEETT
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHCC-----CeEEEEeecC
Confidence            356688899999999998877665554332     2677766753

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=95.28  E-value=0.019  Score=61.51  Aligned_cols=59  Identities=17%  Similarity=0.187  Sum_probs=45.1

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhC-CCCccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARN-RGSECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~-~~~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      +++++|.|+.|||||.+...=++..+.... .-..-+|+++.+|+.+|..+.+++...++
T Consensus        23 ~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~l~   82 (1232)
T 3u4q_A           23 GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEALE   82 (1232)
T ss_dssp             SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHHHH
Confidence            689999999999999987665655554321 11334799999999999999998887654

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=95.26  E-value=0.014  Score=59.75  Aligned_cols=53  Identities=21%  Similarity=0.281  Sum_probs=39.0

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      .+...+|.||+|||||+..... +..+....   ..+|+++.||..++.++.+++..
T Consensus       370 ~~~~~lI~GppGTGKT~ti~~~-i~~l~~~~---~~~ilv~a~tn~A~~~l~~~l~~  422 (800)
T 2wjy_A          370 QRPLSLIQGPPGTGKTVTSATI-VYHLARQG---NGPVLVCAPSNIAVDQLTEKIHQ  422 (800)
T ss_dssp             TSSEEEEECCTTSCHHHHHHHH-HHHHHTTC---SSCEEEEESSHHHHHHHHHHHHT
T ss_pred             cCCeEEEEcCCCCCHHHHHHHH-HHHHHHcC---CCcEEEEcCcHHHHHHHHHHHHH
Confidence            3467899999999999876443 33343311   24788888999999999888765

>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=95.13  E-value=0.077  Score=47.49  Aligned_cols=46  Identities=20%  Similarity=0.193  Sum_probs=26.7

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAI  116 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~  116 (319)
                      .++.+.++|++|+|||+.......  ..... +....++-.-+.+..+.
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~--~~~~~-~~~v~l~~~d~~~~~~~  142 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLAL--YYKGK-GRRPLLVAADTQRPAAR  142 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHH--HHHHT-TCCEEEEECCSSCHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH--HHHHc-CCeEEEecCCcccHhHH
Confidence            456788899999999977644332  22222 22334444445665544

>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=95.12  E-value=0.11  Score=46.05  Aligned_cols=38  Identities=11%  Similarity=0.156  Sum_probs=22.5

Q ss_pred             CccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          174 GVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       174 ~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      ...++||||+|.  +..+....+++.+...+++..+|+.+
T Consensus       107 ~~~viiiDe~~~--l~~~~~~~L~~~le~~~~~~~~il~~  144 (323)
T 1sxj_B          107 KHKIVILDEADS--MTAGAQQALRRTMELYSNSTRFAFAC  144 (323)
T ss_dssp             CCEEEEEESGGG--SCHHHHHTTHHHHHHTTTTEEEEEEE
T ss_pred             CceEEEEECccc--CCHHHHHHHHHHHhccCCCceEEEEe
Confidence            378999999997  33333333444443344455666654

>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=95.10  E-value=0.024  Score=56.66  Aligned_cols=58  Identities=21%  Similarity=0.194  Sum_probs=44.1

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      +++++|.|+.|||||.....-+...+...+. ....|+++..|+.+|.++.+++...++
T Consensus        15 ~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~-~~~~IL~lTfT~~Aa~em~~Rl~~~l~   72 (673)
T 1uaa_A           15 TGPCLVLAGAGSGKTRVITNKIAHLIRGCGY-QARHIAAVTFTNKAAREMKERVGQTLG   72 (673)
T ss_dssp             SSEEEECCCTTSCHHHHHHHHHHHHHHHHCC-CGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CCCEEEEeCCCCChHHHHHHHHHHHHHhcCC-CHHHeEEEeccHHHHHHHHHHHHHHcC
Confidence            5789999999999998876555554443221 234788888999999999999987754

>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=95.05  E-value=0.02  Score=57.38  Aligned_cols=75  Identities=19%  Similarity=0.149  Sum_probs=50.6

Q ss_pred             CCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHH
Q psy496           40 GSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIA  119 (319)
Q Consensus        40 ~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~  119 (319)
                      .++.+++..|..+|..+..+-+     ......++.|.||||||..+...+ ...  +.     .+|++.|+..+|.|++
T Consensus         4 ~~~~~~~~~q~~ai~~l~~~~~-----~~~~~~~l~g~tgs~kt~~~a~~~-~~~--~~-----~~lvv~~~~~~A~ql~   70 (664)
T 1c4o_A            4 YRGPSPKGDQPKAIAGLVEALR-----DGERFVTLLGATGTGKTVTMAKVI-EAL--GR-----PALVLAPNKILAAQLA   70 (664)
T ss_dssp             CCSCCCCTTHHHHHHHHHHHHH-----TTCSEEEEEECTTSCHHHHHHHHH-HHH--TC-----CEEEEESSHHHHHHHH
T ss_pred             CCCCCCCCCChHHHHHHHHHHh-----cCCCcEEEEcCCCcHHHHHHHHHH-HHh--CC-----CEEEEecCHHHHHHHH
Confidence            4455677889999877654321     112346788999999997664332 221  11     3666669999999999


Q ss_pred             HHHHHHhc
Q psy496          120 ERVAQERD  127 (319)
Q Consensus       120 ~~~~~~~~  127 (319)
                      ..+..++.
T Consensus        71 ~el~~~~~   78 (664)
T 1c4o_A           71 AEFRELFP   78 (664)
T ss_dssp             HHHHHHCT
T ss_pred             HHHHHHCC
Confidence            99888753

>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=94.95  E-value=0.2  Score=47.35  Aligned_cols=26  Identities=31%  Similarity=0.424  Sum_probs=19.1

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEI   95 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~   95 (319)
                      ...++|+||+|+|||+.+- .+.+.+.
T Consensus       130 ~~~lll~Gp~G~GKTtLa~-aia~~l~  155 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQ-SIGNYVV  155 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHH-HHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHH
Confidence            5689999999999997653 3344443

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=94.92  E-value=0.082  Score=47.44  Aligned_cols=21  Identities=24%  Similarity=0.346  Sum_probs=17.5

Q ss_pred             CCCCCcEEEecCCCCCccchh
Q psy496           66 SPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~   86 (319)
                      +..+.+++|+||+|+|||..+
T Consensus        22 a~~~~~vLi~Ge~GtGKt~lA   42 (304)
T 1ojl_A           22 APSDATVLIHGDSGTGKELVA   42 (304)
T ss_dssp             CSTTSCEEEESCTTSCHHHHH
T ss_pred             hCCCCcEEEECCCCchHHHHH
Confidence            455678999999999999664

>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=94.81  E-value=0.13  Score=46.40  Aligned_cols=54  Identities=17%  Similarity=0.160  Sum_probs=30.2

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      .++.++++|++|||||+.......  ..... +....++-.-+.|..+.+..+.+.+
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~--~l~~~-g~kV~lv~~D~~r~~a~eqL~~~~~  156 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAK--MFVDE-GKSVVLAAADTFRAAAIEQLKIWGE  156 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHH--HHHHT-TCCEEEEEECTTCHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHH--HHHhc-CCEEEEEccccccHHHHHHHHHHHH
Confidence            356788999999999987654332  22222 2233444444566555443333443

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=94.80  E-value=0.034  Score=56.22  Aligned_cols=58  Identities=21%  Similarity=0.177  Sum_probs=43.6

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      +++++|.|+.|||||.+...-+...+...+ -....|+++..|+.+|.++.+++...++
T Consensus        24 ~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~-~~p~~IL~vTFTnkAA~Em~~Rl~~~l~   81 (724)
T 1pjr_A           24 EGPLLIMAGAGSGKTRVLTHRIAYLMAEKH-VAPWNILAITFTNKAAREMRERVQSLLG   81 (724)
T ss_dssp             SSCEEEEECTTSCHHHHHHHHHHHHHHTTC-CCGGGEEEEESSHHHHHHHHHHHHHHHG
T ss_pred             CCCEEEEEcCCCCHHHHHHHHHHHHHHhcC-CCHHHeEEEeccHHHHHHHHHHHHHHhc
Confidence            467999999999999887655554443222 2234788888999999999998887654

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=94.78  E-value=0.14  Score=48.40  Aligned_cols=21  Identities=24%  Similarity=0.374  Sum_probs=17.2

Q ss_pred             CcEEEecCCCCCccchhhHHH
Q psy496           70 SPSIIYTSTGCGKTTQVPQFI   90 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~i   90 (319)
                      .+++++|++|+|||+......
T Consensus       100 ~vI~ivG~~GvGKTTla~~La  120 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLA  120 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            579999999999998775543

>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=94.76  E-value=0.11  Score=47.05  Aligned_cols=39  Identities=18%  Similarity=0.316  Sum_probs=23.8

Q ss_pred             CCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          173 SGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       173 ~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      .+.+++|+||+|.  +..+....+++.+...+...++++.+
T Consensus       109 ~~~~viiiDe~~~--l~~~~~~~L~~~le~~~~~~~~il~~  147 (340)
T 1sxj_C          109 KGFKLIILDEADA--MTNAAQNALRRVIERYTKNTRFCVLA  147 (340)
T ss_dssp             CSCEEEEETTGGG--SCHHHHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCceEEEEeCCCC--CCHHHHHHHHHHHhcCCCCeEEEEEe
Confidence            4689999999997  44444444444444444455555543

>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=94.75  E-value=0.065  Score=47.58  Aligned_cols=17  Identities=24%  Similarity=0.288  Sum_probs=14.6

Q ss_pred             cEEEecCCCCCccchhh
Q psy496           71 PSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~   87 (319)
                      +++++||+|+|||+..-
T Consensus        40 ~~ll~G~~G~GKt~la~   56 (319)
T 2chq_A           40 HLLFSGPPGTGKTATAI   56 (319)
T ss_dssp             CEEEESSSSSSHHHHHH
T ss_pred             eEEEECcCCcCHHHHHH
Confidence            59999999999997653

>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=94.67  E-value=0.05  Score=54.40  Aligned_cols=15  Identities=7%  Similarity=0.166  Sum_probs=12.4

Q ss_pred             CCCcEEEeCCccccc
Q psy496          275 GGAPILHIPGFTYPV  289 (319)
Q Consensus       275 ~g~~LVFlp~R~~~v  289 (319)
                      ++++|||++|+..+-
T Consensus       439 ~~~vlVf~~t~~~ae  453 (664)
T 1c4o_A          439 GERTLVTVLTVRMAE  453 (664)
T ss_dssp             TCEEEEECSSHHHHH
T ss_pred             CCEEEEEECCHHHHH
Confidence            678999999987663

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=94.38  E-value=0.19  Score=50.82  Aligned_cols=16  Identities=38%  Similarity=0.453  Sum_probs=14.3

Q ss_pred             cEEEecCCCCCccchh
Q psy496           71 PSIIYTSTGCGKTTQV   86 (319)
Q Consensus        71 ~vli~apTGSGKT~~~   86 (319)
                      +++++||||+|||..+
T Consensus       523 ~~Ll~Gp~GtGKT~lA  538 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELA  538 (758)
T ss_dssp             EEEEESCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5999999999999765

>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=93.95  E-value=0.15  Score=46.40  Aligned_cols=57  Identities=21%  Similarity=0.214  Sum_probs=32.2

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      +.+..+.+.||+|||||+..-...  .+.... +....+.-....|..+.+..+.++...
T Consensus       127 ~~g~vi~lvG~nGaGKTTll~~La--g~l~~~-~g~V~l~g~D~~r~~a~eql~~~~~~~  183 (328)
T 3e70_C          127 EKPYVIMFVGFNGSGKTTTIAKLA--NWLKNH-GFSVVIAASDTFRAGAIEQLEEHAKRI  183 (328)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHH--HHHHHT-TCCEEEEEECCSSTTHHHHHHHHHHHT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHH--HHHHhc-CCEEEEEeecccccchHHHHHHHHHHc
Confidence            457789999999999998764332  233322 223333333344544554444455443

>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=93.47  E-value=0.15  Score=52.39  Aligned_cols=17  Identities=29%  Similarity=0.411  Sum_probs=14.9

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      .+++++||||+|||+.+
T Consensus       589 ~~vLl~Gp~GtGKT~lA  605 (854)
T 1qvr_A          589 GSFLFLGPTGVGKTELA  605 (854)
T ss_dssp             EEEEEBSCSSSSHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            47999999999999765

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=93.35  E-value=0.065  Score=53.38  Aligned_cols=96  Identities=18%  Similarity=0.246  Sum_probs=58.6

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCC
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPR  149 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~  149 (319)
                      ...+|+|+-|.|||++.-+.+-.. .  .     .++++.|+.+.+..+.+...+    .                    
T Consensus       193 ~~~vlta~RGRGKSa~lG~~~a~~-~--~-----~~~vtAP~~~a~~~l~~~~~~----~--------------------  240 (671)
T 2zpa_A          193 GVAAVTAARGRGKSALAGQLISRI-A--G-----RAIVTAPAKASTDVLAQFAGE----K--------------------  240 (671)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHS-S--S-----CEEEECSSCCSCHHHHHHHGG----G--------------------
T ss_pred             CeEEEecCCCCCHHHHHHHHHHHH-H--h-----CcEEECCCHHHHHHHHHHhhC----C--------------------
Confidence            568999999999997776655332 1  1     358888998877655442211    0                    


Q ss_pred             CCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          150 KRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       150 ~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                          |-+..|+-++.      .+.+.+++|||||=.  +....+..++.       ....++||.|+
T Consensus       241 ----i~~~~Pd~~~~------~~~~~dlliVDEAAa--Ip~pll~~ll~-------~~~~v~~~tTv  288 (671)
T 2zpa_A          241 ----FRFIAPDALLA------SDEQADWLVVDEAAA--IPAPLLHQLVS-------RFPRTLLTTTV  288 (671)
T ss_dssp             ----CCBCCHHHHHH------SCCCCSEEEEETGGG--SCHHHHHHHHT-------TSSEEEEEEEB
T ss_pred             ----eEEeCchhhhh------CcccCCEEEEEchhc--CCHHHHHHHHh-------hCCeEEEEecC
Confidence                22335554332      124689999999986  44444433333       11246777777

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=93.33  E-value=0.037  Score=43.74  Aligned_cols=21  Identities=24%  Similarity=0.317  Sum_probs=17.8

Q ss_pred             CCCCCcEEEecCCCCCccchh
Q psy496           66 SPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~   86 (319)
                      +..+.+++|.||+|||||..+
T Consensus        21 a~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           21 SETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TTCCSCEEEESSTTSSHHHHH
T ss_pred             hCCCCCEEEECCCCCCHHHHH
Confidence            456688999999999999665

>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=93.15  E-value=0.35  Score=45.58  Aligned_cols=54  Identities=17%  Similarity=0.171  Sum_probs=32.2

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      .++.++++|++|||||+.......  .... .+....++-.-+.+..+....+.+..
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~--~l~~-~g~~Vllvd~D~~r~aa~~qL~~~~~  150 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLAL--YYKG-KGRRPLLVAADTQRPAAREQLRLLGE  150 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHH--HHHT-TTCCEEEEECCSSCHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH--HHHH-cCCeEEEeeccccCchhHHHHHHhcc
Confidence            356788899999999987654332  2222 23344555555777766544444443

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=92.68  E-value=0.45  Score=42.49  Aligned_cols=53  Identities=17%  Similarity=0.159  Sum_probs=30.8

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      +..++++|++|+|||+........ +..  .+....++-.-+.|..+....+.+..
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~-~~~--~g~~v~l~~~D~~r~~a~~ql~~~~~  150 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYF-YKK--KGFKVGLVGADVYRPAALEQLQQLGQ  150 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHH-HHH--TTCCEEEEECCCSSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHH--CCCeEEEEecCCCCHHHHHHHHHHhc
Confidence            557888999999999876543322 222  22344444445666655544444443

>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=92.57  E-value=0.076  Score=49.95  Aligned_cols=42  Identities=14%  Similarity=0.184  Sum_probs=26.1

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRIS  114 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~l  114 (319)
                      .+.+++|.|+||||||..+ ..++..+...+    ..++++-|..++
T Consensus        52 ~~~h~~i~G~tGsGKs~~~-~~li~~~~~~g----~~viv~Dpkge~   93 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL-RELAYTGLLRG----DRMVIVDPNGDM   93 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH-HHHHHHHHHTT----CEEEEEEETTHH
T ss_pred             CcceEEEECCCCCCHHHHH-HHHHHHHHHCC----CcEEEEeCCCch
Confidence            4578999999999999975 33444433322    144444454444

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=92.47  E-value=0.37  Score=45.49  Aligned_cols=55  Identities=20%  Similarity=0.170  Sum_probs=33.2

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      ..+++++|++|+|||+........ +... .+.+..++-.-|.|..+....+.+...
T Consensus       100 ~~vI~ivG~~GvGKTT~a~~LA~~-l~~~-~G~kVllvd~D~~r~~a~~ql~~~~~~  154 (433)
T 2xxa_A          100 PAVVLMAGLQGAGKTTSVGKLGKF-LREK-HKKKVLVVSADVYRPAAIKQLETLAEQ  154 (433)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHHHH-HHHT-SCCCEEEEECCCSSTTHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHHh-cCCeEEEEecCCCCccHHHHHHhhccc
Confidence            357888999999999887554432 2222 133455555567776665544444443

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=92.33  E-value=0.068  Score=46.98  Aligned_cols=23  Identities=22%  Similarity=0.375  Sum_probs=19.6

Q ss_pred             CCCCCcEEEecCCCCCccchhhH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      .+.++.++|+||||||||+.+-.
T Consensus        22 i~~g~~v~i~Gp~GsGKSTll~~   44 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKSTTIAS   44 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHHHHHH
T ss_pred             hCCCCEEEEECCCCccHHHHHHH
Confidence            56788999999999999987643

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=92.20  E-value=0.047  Score=43.07  Aligned_cols=20  Identities=20%  Similarity=0.150  Sum_probs=16.6

Q ss_pred             CCCCcEEEecCCCCCccchh
Q psy496           67 PILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~   86 (319)
                      ..+.+++++||+|+|||..+
T Consensus        25 ~~~~~vll~G~~GtGKt~lA   44 (143)
T 3co5_A           25 KRTSPVFLTGEAGSPFETVA   44 (143)
T ss_dssp             TCSSCEEEEEETTCCHHHHH
T ss_pred             CCCCcEEEECCCCccHHHHH
Confidence            45678999999999999654

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=91.80  E-value=0.053  Score=44.47  Aligned_cols=21  Identities=10%  Similarity=0.238  Sum_probs=17.1

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      .++.++|+||+|||||+..-.
T Consensus         4 ~g~~i~i~GpsGsGKSTL~~~   24 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIKNT   24 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            356789999999999986643

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=91.07  E-value=0.13  Score=42.71  Aligned_cols=24  Identities=25%  Similarity=0.214  Sum_probs=18.1

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHH
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      .+++|+||+|+|||+.+- .+...+
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            789999999999997653 333433

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=91.07  E-value=0.18  Score=42.95  Aligned_cols=31  Identities=32%  Similarity=0.368  Sum_probs=24.0

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIA   96 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~   96 (319)
                      .+.++.++|+|++|+|||+.....+.+....
T Consensus        27 l~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~   57 (251)
T 2zts_A           27 FPEGTTVLLTGGTGTGKTTFAAQFIYKGAEE   57 (251)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence            4567889999999999998877666654444

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=90.97  E-value=0.73  Score=44.23  Aligned_cols=22  Identities=23%  Similarity=0.258  Sum_probs=18.2

Q ss_pred             CCCCcEEEecCCCCCccchhhH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ..++.+.|.|++|||||+.+-.
T Consensus       291 ~~GeVI~LVGpNGSGKTTLl~~  312 (503)
T 2yhs_A          291 KAPFVILMVGVNGVGKTTTIGK  312 (503)
T ss_dssp             CTTEEEEEECCTTSSHHHHHHH
T ss_pred             cCCeEEEEECCCcccHHHHHHH
Confidence            4567899999999999987644

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=90.88  E-value=0.06  Score=52.13  Aligned_cols=23  Identities=26%  Similarity=0.211  Sum_probs=18.8

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      .....+++++|+||||||||+..
T Consensus       255 ~~v~~g~~i~I~GptGSGKTTlL  277 (511)
T 2oap_1          255 LAIEHKFSAIVVGETASGKTTTL  277 (511)
T ss_dssp             HHHHTTCCEEEEESTTSSHHHHH
T ss_pred             HHHhCCCEEEEECCCCCCHHHHH
Confidence            34456788999999999999765

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=90.82  E-value=0.14  Score=43.47  Aligned_cols=28  Identities=25%  Similarity=0.361  Sum_probs=21.9

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDD   93 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~   93 (319)
                      .+.++.++|.||+|||||+.....+...
T Consensus        20 l~~G~~~~i~G~~GsGKTtl~~~~~~~~   47 (247)
T 2dr3_A           20 IPERNVVLLSGGPGTGKTIFSQQFLWNG   47 (247)
T ss_dssp             EETTCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4567889999999999998865554443

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=90.56  E-value=0.19  Score=42.14  Aligned_cols=30  Identities=27%  Similarity=0.164  Sum_probs=22.8

Q ss_pred             Hhhh-cCCCCCcEEEecCCCCCccchhhHHH
Q psy496           61 KCLT-LSPILSPSIIYTSTGCGKTTQVPQFI   90 (319)
Q Consensus        61 ~~l~-~~~~~~~vli~apTGSGKT~~~~l~i   90 (319)
                      +++. -.+.++.++|.||+|||||+.....+
T Consensus        14 ~~~~ggi~~G~~~~i~G~~GsGKTtl~~~l~   44 (235)
T 2w0m_A           14 KLIQGGIPQGFFIALTGEPGTGKTIFSLHFI   44 (235)
T ss_dssp             GGGTTSEETTCEEEEECSTTSSHHHHHHHHH
T ss_pred             HHhcCCCcCCCEEEEEcCCCCCHHHHHHHHH
Confidence            4443 46678899999999999998765544

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=90.51  E-value=0.18  Score=45.35  Aligned_cols=20  Identities=30%  Similarity=0.338  Sum_probs=16.6

Q ss_pred             CCCCcEEEecCCCCCccchh
Q psy496           67 PILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~   86 (319)
                      ....+++|+||+|+|||+.+
T Consensus        53 ~~~~~vll~G~~GtGKT~la   72 (338)
T 3pfi_A           53 ECLDHILFSGPAGLGKTTLA   72 (338)
T ss_dssp             SCCCCEEEECSTTSSHHHHH
T ss_pred             CCCCeEEEECcCCCCHHHHH
Confidence            44568999999999999765

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=90.43  E-value=0.086  Score=42.53  Aligned_cols=21  Identities=24%  Similarity=0.346  Sum_probs=17.1

Q ss_pred             CCCCcEEEecCCCCCccchhh
Q psy496           67 PILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~   87 (319)
                      ....+++|+||+|+|||+.+-
T Consensus        41 ~~~~~~ll~G~~G~GKT~l~~   61 (195)
T 1jbk_A           41 RTKNNPVLIGEPGVGKTAIVE   61 (195)
T ss_dssp             SSSCEEEEECCTTSCHHHHHH
T ss_pred             CCCCceEEECCCCCCHHHHHH
Confidence            345779999999999997653

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=90.40  E-value=0.087  Score=43.67  Aligned_cols=22  Identities=32%  Similarity=0.332  Sum_probs=17.8

Q ss_pred             CCCCcEEEecCCCCCccchhhH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ..++.+.|.||+|||||+..-.
T Consensus         5 ~~g~ii~l~Gp~GsGKSTl~~~   26 (205)
T 3tr0_A            5 NKANLFIISAPSGAGKTSLVRA   26 (205)
T ss_dssp             CCCCEEEEECCTTSCHHHHHHH
T ss_pred             CCCcEEEEECcCCCCHHHHHHH
Confidence            3567899999999999987643

>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=90.26  E-value=0.11  Score=43.62  Aligned_cols=22  Identities=18%  Similarity=0.077  Sum_probs=18.0

Q ss_pred             CCCCcEEEecCCCCCccchhhH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l   88 (319)
                      +.+..++|+||+|||||+..-.
T Consensus         6 ~~g~~i~l~GpsGsGKsTl~~~   27 (208)
T 3tau_A            6 ERGLLIVLSGPSGVGKGTVREA   27 (208)
T ss_dssp             CCCCEEEEECCTTSCHHHHHHH
T ss_pred             CCCcEEEEECcCCCCHHHHHHH
Confidence            4567899999999999987543

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=90.23  E-value=0.082  Score=43.00  Aligned_cols=22  Identities=36%  Similarity=0.523  Sum_probs=18.3

Q ss_pred             CCCCcEEEecCCCCCccchhhH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l   88 (319)
                      +.++.+.+.||+|||||+.+-.
T Consensus         7 ~~gei~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A            7 PELSLVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             ESSEEEEEECCTTSCHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHH
Confidence            4567899999999999987653

>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=90.19  E-value=0.087  Score=43.17  Aligned_cols=22  Identities=18%  Similarity=0.096  Sum_probs=18.0

Q ss_pred             CCCCCcEEEecCCCCCccchhh
Q psy496           66 SPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~   87 (319)
                      ...++.++|.||+|||||+..-
T Consensus         6 i~~g~~i~l~G~~GsGKSTl~~   27 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTIAE   27 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHH
Confidence            4457789999999999998653

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=90.12  E-value=0.095  Score=43.60  Aligned_cols=24  Identities=25%  Similarity=0.176  Sum_probs=17.9

Q ss_pred             cCCCCCcEEEecCCCCCccchhhH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ....+..++|.|++|||||+..-.
T Consensus        21 ~~~~~~~i~l~G~~GsGKsTl~~~   44 (199)
T 3vaa_A           21 QSNAMVRIFLTGYMGAGKTTLGKA   44 (199)
T ss_dssp             ---CCCEEEEECCTTSCHHHHHHH
T ss_pred             ecCCCCEEEEEcCCCCCHHHHHHH
Confidence            345567899999999999987643

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=90.07  E-value=0.094  Score=43.79  Aligned_cols=21  Identities=24%  Similarity=0.420  Sum_probs=16.4

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      .++.+.|.||+|||||+..-+
T Consensus         3 ~g~~i~lvGpsGaGKSTLl~~   23 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLLKK   23 (198)
T ss_dssp             --CCEEEECCTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            356799999999999987644

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=90.02  E-value=0.094  Score=48.33  Aligned_cols=27  Identities=22%  Similarity=0.164  Sum_probs=21.2

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchhh
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~~   87 (319)
                      ++-...+.++.++|+||||||||+.+-
T Consensus       167 ~l~~~i~~G~~i~ivG~sGsGKSTll~  193 (361)
T 2gza_A          167 FLRRAVQLERVIVVAGETGSGKTTLMK  193 (361)
T ss_dssp             HHHHHHHTTCCEEEEESSSSCHHHHHH
T ss_pred             HHHHHHhcCCEEEEECCCCCCHHHHHH
Confidence            344455678999999999999998653

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=89.94  E-value=1.1  Score=43.24  Aligned_cols=51  Identities=20%  Similarity=0.277  Sum_probs=30.0

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      .+++++|++|+|||+.+...... +...  +....++-.-|.|..+....+.+.
T Consensus       102 ~vI~ivG~~GvGKTTl~~kLA~~-l~~~--G~kVllVd~D~~r~aa~~qL~~~~  152 (504)
T 2j37_W          102 NVIMFVGLQGSGKTTTCSKLAYY-YQRK--GWKTCLICADTFRAGAFDQLKQNA  152 (504)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH-HHHT--TCCEEEEEECCSSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH-HHhC--CCeEEEEeccccchhHHHHHHHHh
Confidence            46888999999999887554432 2222  233445554456666544433333

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=89.49  E-value=0.12  Score=43.80  Aligned_cols=28  Identities=21%  Similarity=0.224  Sum_probs=18.2

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchhhH
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ++=...+.++.+.|.||+|||||+.+-+
T Consensus        15 ~isl~i~~G~~~~lvGpsGsGKSTLl~~   42 (218)
T 1z6g_A           15 VPRGSMNNIYPLVICGPSGVGKGTLIKK   42 (218)
T ss_dssp             -------CCCCEEEECSTTSSHHHHHHH
T ss_pred             CCceecCCCCEEEEECCCCCCHHHHHHH
Confidence            3334456788999999999999987643

>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=89.36  E-value=0.11  Score=41.94  Aligned_cols=18  Identities=22%  Similarity=0.252  Sum_probs=15.3

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      ..++|+|++|||||+..-
T Consensus         4 ~~i~l~G~~GsGKST~a~   21 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVR   21 (178)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            568999999999998763

>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=89.36  E-value=0.1  Score=41.59  Aligned_cols=18  Identities=22%  Similarity=0.226  Sum_probs=15.0

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|+|++|||||+..-.
T Consensus         3 ~I~l~G~~GsGKsT~a~~   20 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKL   20 (179)
T ss_dssp             EEEEECCTTSCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            478999999999987643

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=89.27  E-value=0.12  Score=42.77  Aligned_cols=22  Identities=18%  Similarity=0.105  Sum_probs=17.7

Q ss_pred             CCCCcEEEecCCCCCccchhhH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ..+..+.|.||+|||||+..-.
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~~~   25 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVRKR   25 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHH
Confidence            3567899999999999987643

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=89.25  E-value=0.086  Score=42.49  Aligned_cols=21  Identities=29%  Similarity=0.376  Sum_probs=17.3

Q ss_pred             CCCCcEEEecCCCCCccchhh
Q psy496           67 PILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~   87 (319)
                      ....+++|+||+|+|||+..-
T Consensus        41 ~~~~~vll~G~~G~GKT~la~   61 (187)
T 2p65_A           41 RTKNNPILLGDPGVGKTAIVE   61 (187)
T ss_dssp             SSSCEEEEESCGGGCHHHHHH
T ss_pred             CCCCceEEECCCCCCHHHHHH
Confidence            446789999999999997654

>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=89.21  E-value=0.13  Score=47.36  Aligned_cols=21  Identities=24%  Similarity=0.302  Sum_probs=17.4

Q ss_pred             CCCCcEEEecCCCCCccchhh
Q psy496           67 PILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~   87 (319)
                      ..++.++|+||||||||+..-
T Consensus       121 ~~~g~i~I~GptGSGKTTlL~  141 (356)
T 3jvv_A          121 VPRGLVLVTGPTGSGKSTTLA  141 (356)
T ss_dssp             CSSEEEEEECSTTSCHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHH
Confidence            445689999999999997753

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=89.14  E-value=0.13  Score=47.60  Aligned_cols=23  Identities=22%  Similarity=0.375  Sum_probs=19.2

Q ss_pred             CCCCCcEEEecCCCCCccchhhH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ...++.++|+||||||||+..-.
T Consensus       133 ~~~g~~i~ivG~~GsGKTTll~~  155 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTTIAS  155 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHHHHH
Confidence            45678999999999999987644

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=89.12  E-value=0.15  Score=43.43  Aligned_cols=23  Identities=26%  Similarity=0.479  Sum_probs=14.8

Q ss_pred             CCCCCcEEEecCCCCCccchhhH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      .+.++.+.|.||+|||||+..-.
T Consensus        24 v~~G~ii~l~Gp~GsGKSTl~~~   46 (231)
T 3lnc_A           24 KSVGVILVLSSPSGCGKTTVANK   46 (231)
T ss_dssp             EECCCEEEEECSCC----CHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHHHH
Confidence            44677899999999999988643

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=89.05  E-value=0.13  Score=41.34  Aligned_cols=19  Identities=21%  Similarity=0.198  Sum_probs=15.9

Q ss_pred             CCcEEEecCCCCCccchhh
Q psy496           69 LSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~   87 (319)
                      +..+.|.|+.|||||+..-
T Consensus         4 ~~~i~l~G~~GsGKSTl~~   22 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIGR   22 (173)
T ss_dssp             CCCEEEECCTTSCHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            4579999999999998653

>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=88.89  E-value=0.18  Score=43.81  Aligned_cols=21  Identities=29%  Similarity=0.507  Sum_probs=17.1

Q ss_pred             CCCCCcEEEecCCCCCccchh
Q psy496           66 SPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~   86 (319)
                      +..+.+++|+||+|+|||..+
T Consensus        26 ~~~~~~vll~G~~GtGKt~la   46 (265)
T 2bjv_A           26 APLDKPVLIIGERGTGKELIA   46 (265)
T ss_dssp             TTSCSCEEEECCTTSCHHHHH
T ss_pred             hCCCCCEEEECCCCCcHHHHH
Confidence            345578999999999999654

>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=88.89  E-value=0.18  Score=46.71  Aligned_cols=24  Identities=25%  Similarity=0.308  Sum_probs=19.3

Q ss_pred             CCCcEEEecCCCCCccchhhHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFIL   91 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il   91 (319)
                      .+.+++|.|+||||||+..-..+.
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~   57 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLL   57 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHH
Confidence            567899999999999987655443

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=88.85  E-value=0.13  Score=41.90  Aligned_cols=20  Identities=30%  Similarity=0.328  Sum_probs=16.5

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      ..+++++|++|||||+..-.
T Consensus         5 ~~~i~l~G~~GsGKst~a~~   24 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQ   24 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            35789999999999987644

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=88.78  E-value=0.16  Score=42.62  Aligned_cols=21  Identities=24%  Similarity=0.257  Sum_probs=17.8

Q ss_pred             CCCCCcEEEecCCCCCccchh
Q psy496           66 SPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...++.+.|.||+|||||+.+
T Consensus        19 ~~~g~~v~I~G~sGsGKSTl~   39 (208)
T 3c8u_A           19 QPGRQLVALSGAPGSGKSTLS   39 (208)
T ss_dssp             CCSCEEEEEECCTTSCTHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHH
Confidence            456778999999999999865

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=88.74  E-value=0.15  Score=42.58  Aligned_cols=22  Identities=23%  Similarity=0.505  Sum_probs=17.8

Q ss_pred             CCCCcEEEecCCCCCccchhhH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ..+..++|+||+|||||+..-.
T Consensus        10 ~~~~~i~l~G~sGsGKsTl~~~   31 (204)
T 2qor_A           10 ARIPPLVVCGPSGVGKGTLIKK   31 (204)
T ss_dssp             CCCCCEEEECCTTSCHHHHHHH
T ss_pred             ccCCEEEEECCCCCCHHHHHHH
Confidence            4567899999999999986543

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=88.67  E-value=1.2  Score=40.05  Aligned_cols=23  Identities=26%  Similarity=0.365  Sum_probs=17.8

Q ss_pred             CCCCcEEEecCCCCCccchhhHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~   89 (319)
                      ..++.++++|++|+|||+.....
T Consensus       103 ~~~~vI~ivG~~G~GKTT~~~~L  125 (320)
T 1zu4_A          103 NRLNIFMLVGVNGTGKTTSLAKM  125 (320)
T ss_dssp             TSCEEEEEESSTTSSHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHH
Confidence            34567889999999999876443

>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=88.52  E-value=0.14  Score=46.62  Aligned_cols=22  Identities=36%  Similarity=0.353  Sum_probs=18.2

Q ss_pred             cCCCCCcEEEecCCCCCccchh
Q psy496           65 LSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ..+.+++++|+||||||||+.+
T Consensus       167 ~i~~g~~v~i~G~~GsGKTTll  188 (330)
T 2pt7_A          167 GIAIGKNVIVCGGTGSGKTTYI  188 (330)
T ss_dssp             HHHHTCCEEEEESTTSCHHHHH
T ss_pred             hccCCCEEEEECCCCCCHHHHH
Confidence            3456789999999999999854

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=88.41  E-value=0.16  Score=46.32  Aligned_cols=19  Identities=21%  Similarity=0.232  Sum_probs=15.8

Q ss_pred             CCcEEEecCCCCCccchhh
Q psy496           69 LSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~   87 (319)
                      +..++|+||||||||+...
T Consensus        40 ~~lIvI~GPTgsGKTtLa~   58 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSI   58 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4578999999999997653

>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=88.41  E-value=0.15  Score=42.35  Aligned_cols=17  Identities=35%  Similarity=0.622  Sum_probs=14.5

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      +.++|+||+|+|||+..
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            45899999999999764

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=88.32  E-value=0.24  Score=44.53  Aligned_cols=29  Identities=14%  Similarity=0.024  Sum_probs=23.7

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhH
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      +++-...+.++.+.|.||+|||||+.+-+
T Consensus       117 ~~vsl~i~~Ge~vaIvGpsGsGKSTLl~l  145 (305)
T 2v9p_A          117 KLWLKGIPKKNCLAFIGPPNTGKSMLCNS  145 (305)
T ss_dssp             HHHHHTCTTCSEEEEECSSSSSHHHHHHH
T ss_pred             ccceEEecCCCEEEEECCCCCcHHHHHHH
Confidence            35556788899999999999999977644

>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=88.32  E-value=0.16  Score=47.81  Aligned_cols=22  Identities=23%  Similarity=0.240  Sum_probs=18.2

Q ss_pred             CCCCCcEEEecCCCCCccchhh
Q psy496           66 SPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~   87 (319)
                      ...++.++|+||||||||+..-
T Consensus       164 ~~~ggii~I~GpnGSGKTTlL~  185 (418)
T 1p9r_A          164 KRPHGIILVTGPTGSGKSTTLY  185 (418)
T ss_dssp             TSSSEEEEEECSTTSCHHHHHH
T ss_pred             HhcCCeEEEECCCCCCHHHHHH
Confidence            3567789999999999998753

>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=88.30  E-value=0.2  Score=42.27  Aligned_cols=19  Identities=21%  Similarity=0.246  Sum_probs=15.7

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      .+..++|.||||||||+..
T Consensus        33 ~g~~ilI~GpsGsGKStLA   51 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSETA   51 (205)
T ss_dssp             TTEEEEEECCCTTTTHHHH
T ss_pred             CCEEEEEECCCCCCHHHHH
Confidence            4566899999999999665

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=88.29  E-value=0.38  Score=43.20  Aligned_cols=34  Identities=12%  Similarity=-0.063  Sum_probs=26.3

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHH
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDD   93 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~   93 (319)
                      ++++.-.+.++.++|+|++|+|||+.....+.+.
T Consensus        59 D~~lgGl~~G~l~li~G~pG~GKTtl~l~ia~~~   92 (315)
T 3bh0_A           59 DRMTYGYKRRNFVLIAARPSMGKTAFALKQAKNM   92 (315)
T ss_dssp             HHHHSSBCTTCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HhhcCCCCCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            4555567788999999999999998766655544

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=88.26  E-value=0.19  Score=42.22  Aligned_cols=21  Identities=10%  Similarity=0.169  Sum_probs=17.2

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      .++.++|+||+|+|||+..-.
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~   38 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNA   38 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHHHH
Confidence            467799999999999986543

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=88.21  E-value=0.23  Score=45.14  Aligned_cols=39  Identities=18%  Similarity=0.113  Sum_probs=24.2

Q ss_pred             cccchhhHHHHHHhhhcCC-CCCcEEEecCCCCCccchhh
Q psy496           49 QPRRISAIALINKCLTLSP-ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        49 Q~~~ip~~~~~~~~l~~~~-~~~~vli~apTGSGKT~~~~   87 (319)
                      |......+..-.+.+.... .+..++++||+|+|||+.+-
T Consensus        49 ~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~   88 (368)
T 3uk6_A           49 QLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAM   88 (368)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHH
Confidence            4444444333334443333 34689999999999997653

>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=88.14  E-value=0.18  Score=41.01  Aligned_cols=21  Identities=29%  Similarity=0.419  Sum_probs=17.1

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      ...+++++|++|||||+..-.
T Consensus        10 ~~~~i~i~G~~GsGKst~~~~   30 (180)
T 3iij_A           10 LLPNILLTGTPGVGKTTLGKE   30 (180)
T ss_dssp             CCCCEEEECSTTSSHHHHHHH
T ss_pred             cCCeEEEEeCCCCCHHHHHHH
Confidence            346799999999999987643

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=88.07  E-value=0.16  Score=42.17  Aligned_cols=22  Identities=23%  Similarity=0.249  Sum_probs=17.6

Q ss_pred             CCCCcEEEecCCCCCccchhhH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ..+..++|.|+.|||||+..-.
T Consensus        27 ~~g~~i~l~G~~GsGKSTl~~~   48 (200)
T 4eun_A           27 EPTRHVVVMGVSGSGKTTIAHG   48 (200)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHH
Confidence            3567899999999999987643

>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=88.06  E-value=0.14  Score=46.26  Aligned_cols=18  Identities=28%  Similarity=0.202  Sum_probs=14.8

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      ..++|+||||||||+...
T Consensus         4 ~~i~i~GptgsGKt~la~   21 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSV   21 (322)
T ss_dssp             EEEEEECCTTSCHHHHHH
T ss_pred             cEEEEECCCcCCHHHHHH
Confidence            457889999999997653

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=88.02  E-value=0.17  Score=42.39  Aligned_cols=23  Identities=17%  Similarity=0.218  Sum_probs=17.7

Q ss_pred             cCCCCCcEEEecCCCCCccchhh
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~   87 (319)
                      ....++.+.|.||+|||||+.+-
T Consensus        16 ~i~~Gei~~l~GpnGsGKSTLl~   38 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKSTVVR   38 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHHHHH
T ss_pred             CCCCCCEEEEECCCCCCHHHHHH
Confidence            45678899999999999998763

>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=87.97  E-value=0.17  Score=43.22  Aligned_cols=23  Identities=17%  Similarity=0.271  Sum_probs=18.0

Q ss_pred             CCCCCcEEEecCCCCCccchhhH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      .+.++.++|.||+|||||+.+-.
T Consensus        13 ~~~G~ii~l~GpsGsGKSTLlk~   35 (219)
T 1s96_A           13 MAQGTLYIVSAPSGAGKSSLIQA   35 (219)
T ss_dssp             --CCCEEEEECCTTSCHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHH
Confidence            46778899999999999987543

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=87.93  E-value=0.16  Score=40.83  Aligned_cols=19  Identities=16%  Similarity=0.303  Sum_probs=16.5

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      |+++|.|+.|||||++.-.
T Consensus         8 ~~i~l~G~~GsGKSTva~~   26 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQE   26 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            6899999999999987643

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=87.87  E-value=0.15  Score=44.34  Aligned_cols=18  Identities=39%  Similarity=0.436  Sum_probs=14.9

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|+||+|||||+..-.
T Consensus         3 li~I~G~~GSGKSTla~~   20 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQ   20 (253)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHH
Confidence            478999999999987643

>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=87.85  E-value=0.27  Score=40.94  Aligned_cols=31  Identities=26%  Similarity=0.043  Sum_probs=23.9

Q ss_pred             Hhhh-cCCCCCcEEEecCCCCCccchhhHHHH
Q psy496           61 KCLT-LSPILSPSIIYTSTGCGKTTQVPQFIL   91 (319)
Q Consensus        61 ~~l~-~~~~~~~vli~apTGSGKT~~~~l~il   91 (319)
                      +++. -.+.++.++|.||+|||||+.....+.
T Consensus        11 ~~l~Ggi~~G~~~~i~G~~GsGKTtl~~~l~~   42 (220)
T 2cvh_A           11 SLLGGGFAPGVLTQVYGPYASGKTTLALQTGL   42 (220)
T ss_dssp             HHTTSSBCTTSEEEEECSTTSSHHHHHHHHHH
T ss_pred             HhhcCCCcCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4443 567788999999999999987765544

>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=87.79  E-value=0.16  Score=41.02  Aligned_cols=21  Identities=14%  Similarity=0.224  Sum_probs=17.0

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      .+..++|.|+.|||||+..-.
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~   27 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASE   27 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHH
Confidence            356789999999999987643

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=87.77  E-value=0.15  Score=42.59  Aligned_cols=26  Identities=23%  Similarity=-0.003  Sum_probs=19.8

Q ss_pred             hhhcCCCCCcEEEecCCCCCccchhh
Q psy496           62 CLTLSPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        62 ~l~~~~~~~~vli~apTGSGKT~~~~   87 (319)
                      ++.....+..+.|+|++|||||+..-
T Consensus        14 ~~~~~~~~~~i~i~G~~GsGKSTl~~   39 (207)
T 2qt1_A           14 LVPRGSKTFIIGISGVTNSGKTTLAK   39 (207)
T ss_dssp             CCCCSCCCEEEEEEESTTSSHHHHHH
T ss_pred             ccccCCCCeEEEEECCCCCCHHHHHH
Confidence            34445566788999999999997653

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=87.73  E-value=0.32  Score=43.61  Aligned_cols=26  Identities=15%  Similarity=0.239  Sum_probs=19.0

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEI   95 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~   95 (319)
                      +.+++++||+|+|||..... +...+.
T Consensus       152 ~~~lll~G~~GtGKT~La~a-ia~~~~  177 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAA-MAHELS  177 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHH-HHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHH-HHHHHH
Confidence            57899999999999976543 334433

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=87.57  E-value=0.17  Score=40.81  Aligned_cols=17  Identities=24%  Similarity=0.261  Sum_probs=14.6

Q ss_pred             cEEEecCCCCCccchhh
Q psy496           71 PSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~   87 (319)
                      .++++|++|||||+..-
T Consensus         4 ~I~i~G~~GsGKST~a~   20 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWAR   20 (181)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEecCCCCCHHHHHH
Confidence            57899999999998763

>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=87.53  E-value=0.16  Score=40.57  Aligned_cols=18  Identities=22%  Similarity=0.209  Sum_probs=15.1

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|.|+.|||||+..-.
T Consensus         3 ~i~l~G~~GsGKsT~~~~   20 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAK   20 (173)
T ss_dssp             EEEEECSSSSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            478999999999987643

>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=87.38  E-value=0.18  Score=41.03  Aligned_cols=20  Identities=20%  Similarity=0.207  Sum_probs=16.3

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      +..++|+|++|||||+..-.
T Consensus         3 ~~~I~i~G~~GsGKsT~~~~   22 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSSQL   22 (192)
T ss_dssp             CCEEEEECCTTSCHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            35689999999999987643

>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=87.35  E-value=0.98  Score=44.97  Aligned_cols=14  Identities=0%  Similarity=-0.128  Sum_probs=11.9

Q ss_pred             CCCcEEEeCCcccc
Q psy496          275 GGAPILHIPGFTYP  288 (319)
Q Consensus       275 ~g~~LVFlp~R~~~  288 (319)
                      ++++|||++|+..+
T Consensus       445 ~~~vlVf~~t~~~a  458 (661)
T 2d7d_A          445 NERVLVTTLTKKMS  458 (661)
T ss_dssp             TCEEEEECSSHHHH
T ss_pred             CCeEEEEECCHHHH
Confidence            67899999998765

>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=87.31  E-value=0.19  Score=41.12  Aligned_cols=20  Identities=25%  Similarity=0.217  Sum_probs=16.7

Q ss_pred             CCCcEEEecCCCCCccchhh
Q psy496           68 ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~   87 (319)
                      .+.+++|+|++|||||++.-
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~   28 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAE   28 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            45679999999999998763

>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=87.13  E-value=0.19  Score=43.29  Aligned_cols=20  Identities=25%  Similarity=0.541  Sum_probs=16.3

Q ss_pred             CCCcEEEecCCCCCccchhh
Q psy496           68 ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~   87 (319)
                      ....++++||+|+|||+.+-
T Consensus        38 ~~~~vll~G~~GtGKT~la~   57 (262)
T 2qz4_A           38 VPKGALLLGPPGCGKTLLAK   57 (262)
T ss_dssp             CCCEEEEESCTTSSHHHHHH
T ss_pred             CCceEEEECCCCCCHHHHHH
Confidence            34679999999999997653

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=87.05  E-value=0.2  Score=44.24  Aligned_cols=19  Identities=21%  Similarity=0.300  Sum_probs=16.3

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      ....+++.||+|+|||+.+
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            4578999999999999765

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=86.88  E-value=0.21  Score=43.77  Aligned_cols=20  Identities=25%  Similarity=0.330  Sum_probs=16.7

Q ss_pred             CCCCcEEEecCCCCCccchh
Q psy496           67 PILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~   86 (319)
                      .....++|+||+|+|||+.+
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            45577999999999999665

>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=86.88  E-value=0.19  Score=41.71  Aligned_cols=23  Identities=17%  Similarity=0.056  Sum_probs=18.8

Q ss_pred             CCCCCcEEEecCCCCCccchhhH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ...+..+.|.||+|||||+..-.
T Consensus        22 ~~~g~~i~l~G~sGsGKSTl~~~   44 (200)
T 3uie_A           22 DQKGCVIWVTGLSGSGKSTLACA   44 (200)
T ss_dssp             TSCCEEEEEECSTTSSHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHH
Confidence            45678899999999999987643

>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=86.87  E-value=0.19  Score=45.43  Aligned_cols=18  Identities=22%  Similarity=0.250  Sum_probs=15.0

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      ..++|+||||||||+...
T Consensus        11 ~~i~i~GptgsGKt~la~   28 (316)
T 3foz_A           11 KAIFLMGPTASGKTALAI   28 (316)
T ss_dssp             EEEEEECCTTSCHHHHHH
T ss_pred             cEEEEECCCccCHHHHHH
Confidence            458899999999997653

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=86.75  E-value=0.34  Score=42.77  Aligned_cols=31  Identities=23%  Similarity=0.090  Sum_probs=24.6

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHH
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFI   90 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~i   90 (319)
                      +++....+.++.++|.||+|||||+.....+
T Consensus        26 d~i~~~l~~G~~~~i~G~~G~GKTTl~~~ia   56 (296)
T 1cr0_A           26 NDKTLGARGGEVIMVTSGSGMGKSTFVRQQA   56 (296)
T ss_dssp             HHHHCSBCTTCEEEEEESTTSSHHHHHHHHH
T ss_pred             HHHhcCCCCCeEEEEEeCCCCCHHHHHHHHH
Confidence            3555667889999999999999998765543

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=86.61  E-value=0.37  Score=40.82  Aligned_cols=28  Identities=14%  Similarity=0.122  Sum_probs=21.0

Q ss_pred             HHHhhhcCCCCCcEEEecCCCCCccchh
Q psy496           59 INKCLTLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        59 ~~~~l~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      -+..+...++...+++.||+|+|||+.+
T Consensus        48 l~~~~~~iPkkn~ili~GPPGtGKTt~a   75 (212)
T 1tue_A           48 LKSFLKGTPKKNCLVFCGPANTGKSYFG   75 (212)
T ss_dssp             HHHHHHTCTTCSEEEEESCGGGCHHHHH
T ss_pred             HHHHHhcCCcccEEEEECCCCCCHHHHH
Confidence            3445555666566999999999999765

>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=86.59  E-value=0.17  Score=41.48  Aligned_cols=19  Identities=32%  Similarity=0.408  Sum_probs=15.6

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      +.++|.||+|||||+..-.
T Consensus         3 ~ii~l~G~~GaGKSTl~~~   21 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKR   21 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHH
Confidence            4578999999999987644

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=86.52  E-value=0.2  Score=41.82  Aligned_cols=20  Identities=30%  Similarity=0.036  Sum_probs=16.5

Q ss_pred             CCCcEEEecCCCCCccchhh
Q psy496           68 ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~   87 (319)
                      .+..+.|.||+|||||+..-
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~   24 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQ   24 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHH
Confidence            45678899999999998763

>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=86.47  E-value=0.24  Score=43.68  Aligned_cols=20  Identities=25%  Similarity=0.285  Sum_probs=16.6

Q ss_pred             CCCcEEEecCCCCCccchhh
Q psy496           68 ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~   87 (319)
                      ...+++++||+|+|||+.+-
T Consensus        49 ~~~~vll~G~~GtGKT~la~   68 (310)
T 1ofh_A           49 TPKNILMIGPTGVGKTEIAR   68 (310)
T ss_dssp             CCCCEEEECCTTSSHHHHHH
T ss_pred             CCceEEEECCCCCCHHHHHH
Confidence            35689999999999997653

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=86.44  E-value=0.18  Score=42.71  Aligned_cols=23  Identities=17%  Similarity=0.020  Sum_probs=19.2

Q ss_pred             CCCCCcEEEecCCCCCccchhhH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ...++.+.|.||+|||||+.+-+
T Consensus        19 i~~Ge~~~liG~nGsGKSTLl~~   41 (208)
T 3b85_A           19 IDTNTIVFGLGPAGSGKTYLAMA   41 (208)
T ss_dssp             HHHCSEEEEECCTTSSTTHHHHH
T ss_pred             ccCCCEEEEECCCCCCHHHHHHH
Confidence            46788899999999999987644

>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=86.42  E-value=0.22  Score=44.32  Aligned_cols=20  Identities=30%  Similarity=0.526  Sum_probs=17.0

Q ss_pred             CCCCcEEEecCCCCCccchh
Q psy496           67 PILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~   86 (319)
                      ..+..++++||+|||||+.+
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            45678999999999999765

>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=86.40  E-value=0.46  Score=42.97  Aligned_cols=19  Identities=26%  Similarity=0.293  Sum_probs=16.0

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      +.+++.||+|+|||+.+-.
T Consensus        52 ~~~ll~Gp~G~GKTTLa~~   70 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLAHI   70 (334)
T ss_dssp             CCEEEESSTTSSHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHH
Confidence            6799999999999977533

>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=86.39  E-value=0.2  Score=43.69  Aligned_cols=21  Identities=19%  Similarity=0.202  Sum_probs=17.1

Q ss_pred             CCCCcEEEecCCCCCccchhh
Q psy496           67 PILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~   87 (319)
                      ....+++++||+|+|||+.+-
T Consensus        62 ~~~~~vLl~G~~GtGKT~la~   82 (272)
T 1d2n_A           62 TPLVSVLLEGPPHSGKTALAA   82 (272)
T ss_dssp             CSEEEEEEECSTTSSHHHHHH
T ss_pred             CCCeEEEEECCCCCcHHHHHH
Confidence            345689999999999997653

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=86.27  E-value=0.19  Score=40.93  Aligned_cols=20  Identities=30%  Similarity=0.376  Sum_probs=16.4

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      +..+++.|+.|||||+..-.
T Consensus         4 g~~I~l~G~~GsGKST~~~~   23 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASR   23 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            45689999999999987644

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=86.08  E-value=0.24  Score=41.59  Aligned_cols=26  Identities=15%  Similarity=0.144  Sum_probs=21.0

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFI   90 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~i   90 (319)
                      -.+.++.+.|.||+|||||+.+...+
T Consensus        21 gi~~G~~~~l~G~nGsGKSTll~~l~   46 (231)
T 4a74_A           21 GIETQAITEVFGEFGSGKTQLAHTLA   46 (231)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHH
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHH
Confidence            45678899999999999998765443

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=86.03  E-value=0.23  Score=42.86  Aligned_cols=19  Identities=21%  Similarity=0.244  Sum_probs=15.6

Q ss_pred             CCcEEEecCCCCCccchhh
Q psy496           69 LSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~   87 (319)
                      ...+++.||+|||||+.+-
T Consensus        45 ~~~vll~G~~GtGKT~la~   63 (257)
T 1lv7_A           45 PKGVLMVGPPGTGKTLLAK   63 (257)
T ss_dssp             CCEEEEECCTTSCHHHHHH
T ss_pred             CCeEEEECcCCCCHHHHHH
Confidence            3469999999999997653

>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=85.99  E-value=1.2  Score=47.56  Aligned_cols=62  Identities=16%  Similarity=0.187  Sum_probs=45.4

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhC-------CCCccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARN-------RGSECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~-------~~~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      .+-+...+|.|+-|||||.+...-++..+...+       .-..-.||++.=|+.+|..+..|+.+.+.
T Consensus        13 ~pl~g~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~L~   81 (1180)
T 1w36_B           13 LPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNIH   81 (1180)
T ss_dssp             CCCSSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHHHH
Confidence            344456699999999999887777777665321       11234788888999999999888877654

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=85.90  E-value=0.26  Score=45.04  Aligned_cols=19  Identities=32%  Similarity=0.279  Sum_probs=16.3

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      ...++++.||+|||||+.+
T Consensus        50 ~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4578999999999999765

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=85.82  E-value=0.24  Score=41.04  Aligned_cols=19  Identities=16%  Similarity=0.324  Sum_probs=16.0

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      ..++|+|+.|||||+..-.
T Consensus        19 ~~I~l~G~~GsGKSTla~~   37 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEA   37 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4699999999999987643

>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=85.47  E-value=0.24  Score=40.41  Aligned_cols=20  Identities=25%  Similarity=0.177  Sum_probs=16.3

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      +..++++|+.|||||+..-.
T Consensus         5 ~~~I~l~G~~GsGKST~~~~   24 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQA   24 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            45689999999999987643

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=85.46  E-value=0.27  Score=42.28  Aligned_cols=23  Identities=22%  Similarity=0.085  Sum_probs=19.2

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      .....++.+.|.||+|||||+.+
T Consensus        26 l~i~~Ge~~~iiG~nGsGKSTLl   48 (235)
T 3tif_A           26 LNIKEGEFVSIMGPSGSGKSTML   48 (235)
T ss_dssp             EEECTTCEEEEECSTTSSHHHHH
T ss_pred             EEEcCCCEEEEECCCCCcHHHHH
Confidence            34567889999999999999764

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=85.44  E-value=0.41  Score=45.37  Aligned_cols=18  Identities=33%  Similarity=0.519  Sum_probs=15.5

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      .+++++||+|+|||+.+-
T Consensus        51 ~~vLL~GppGtGKTtlAr   68 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLAE   68 (447)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHH
Confidence            579999999999997653

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=85.14  E-value=0.25  Score=44.85  Aligned_cols=18  Identities=22%  Similarity=0.255  Sum_probs=15.2

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      ..++|+||||||||+...
T Consensus         6 ~~i~i~GptGsGKTtla~   23 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAM   23 (323)
T ss_dssp             EEEEEECCTTSCHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHH
Confidence            468999999999997653

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=85.07  E-value=0.29  Score=43.42  Aligned_cols=20  Identities=20%  Similarity=0.245  Sum_probs=16.3

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      +..++|+||+|||||+..-.
T Consensus        33 ~~livl~G~sGsGKSTla~~   52 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSLRSA   52 (287)
T ss_dssp             CEEEEEECCTTSCTHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            45688999999999987643

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=85.03  E-value=0.28  Score=41.23  Aligned_cols=19  Identities=26%  Similarity=0.249  Sum_probs=15.9

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      ..+.|.||+|||||+..-+
T Consensus         6 ~~i~i~G~~GsGKSTl~~~   24 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKA   24 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4688999999999987643

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=85.02  E-value=0.26  Score=44.98  Aligned_cols=18  Identities=28%  Similarity=0.159  Sum_probs=15.1

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      ..++|+||||||||+...
T Consensus         8 ~lI~I~GptgSGKTtla~   25 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSI   25 (340)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             ceEEEECCCcCcHHHHHH
Confidence            368899999999997663

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=84.95  E-value=0.29  Score=40.02  Aligned_cols=21  Identities=24%  Similarity=0.273  Sum_probs=17.0

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      ++..++|.|++|||||+..-.
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~   28 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQCEK   28 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            345789999999999987643

>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=84.92  E-value=0.44  Score=45.92  Aligned_cols=19  Identities=32%  Similarity=0.611  Sum_probs=16.1

Q ss_pred             CCcEEEecCCCCCccchhh
Q psy496           69 LSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~   87 (319)
                      ...++++||+|+|||+.+-
T Consensus        77 ~~~lLL~GppGtGKTtla~   95 (516)
T 1sxj_A           77 FRAAMLYGPPGIGKTTAAH   95 (516)
T ss_dssp             CSEEEEECSTTSSHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            3689999999999997654

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=84.88  E-value=0.27  Score=41.13  Aligned_cols=18  Identities=33%  Similarity=0.431  Sum_probs=15.0

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|+|++|||||+..-.
T Consensus         2 ~I~l~G~~GsGKsT~a~~   19 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQ   19 (216)
T ss_dssp             EEEEECSTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            378999999999987644

>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=84.85  E-value=0.3  Score=43.49  Aligned_cols=19  Identities=32%  Similarity=0.473  Sum_probs=16.2

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      ...+++|+||+|+|||+.+
T Consensus        37 ~~~~vll~G~~GtGKT~la   55 (324)
T 1hqc_A           37 PLEHLLLFGPPGLGKTTLA   55 (324)
T ss_dssp             CCCCCEEECCTTCCCHHHH
T ss_pred             CCCcEEEECCCCCCHHHHH
Confidence            4468999999999999665

>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=84.81  E-value=0.36  Score=40.88  Aligned_cols=31  Identities=19%  Similarity=0.073  Sum_probs=23.5

Q ss_pred             Hhh-hcCCCCCcEEEecCCCCCccchhhHHHH
Q psy496           61 KCL-TLSPILSPSIIYTSTGCGKTTQVPQFIL   91 (319)
Q Consensus        61 ~~l-~~~~~~~~vli~apTGSGKT~~~~l~il   91 (319)
                      +++ .-.+.++.++|.||+|||||+.....+.
T Consensus        15 ~~l~ggi~~G~~~~i~G~~GsGKTtl~~~l~~   46 (243)
T 1n0w_A           15 KLLQGGIETGSITEMFGEFRTGKTQICHTLAV   46 (243)
T ss_dssp             HHTTTSEETTSEEEEECCTTSSHHHHHHHHHH
T ss_pred             HhhcCCCcCCeEEEEECCCCCcHHHHHHHHHH
Confidence            344 3456788999999999999987765544

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=84.54  E-value=0.85  Score=43.13  Aligned_cols=36  Identities=11%  Similarity=-0.093  Sum_probs=27.3

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHH
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEI   95 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~   95 (319)
                      ++++.-.+.++.++|+|++|+|||+.....+.+...
T Consensus       188 D~~lgGl~~G~liiIaG~pG~GKTtlal~ia~~~a~  223 (444)
T 3bgw_A          188 DRMTYGYKRRNFVLIAARPSMGKTAFALKQAKNMSD  223 (444)
T ss_dssp             HHHHSSBCSSCEEEEEECSSSSHHHHHHHHHHHHHH
T ss_pred             HhhcCCCCCCcEEEEEeCCCCChHHHHHHHHHHHHH
Confidence            345555677889999999999999887766655443

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=84.49  E-value=0.28  Score=39.94  Aligned_cols=19  Identities=26%  Similarity=0.377  Sum_probs=15.7

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      ..++|.|++|||||+..-.
T Consensus         4 ~~I~l~G~~GsGKsT~a~~   22 (196)
T 1tev_A            4 LVVFVLGGPGAGKGTQCAR   22 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4588999999999987643

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=84.46  E-value=0.29  Score=41.41  Aligned_cols=19  Identities=32%  Similarity=0.438  Sum_probs=16.0

Q ss_pred             CCcEEEecCCCCCccchhh
Q psy496           69 LSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~   87 (319)
                      ...++|.|++|||||+..-
T Consensus         7 ~~~I~l~G~~GsGKsT~a~   25 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSS   25 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            4568999999999998763

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=84.43  E-value=0.3  Score=39.60  Aligned_cols=20  Identities=25%  Similarity=0.115  Sum_probs=16.6

Q ss_pred             CCCcEEEecCCCCCccchhh
Q psy496           68 ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~   87 (319)
                      .+..+++.|+.|||||+..-
T Consensus         4 ~g~~i~l~G~~GsGKST~~~   23 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVSM   23 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            45678999999999998763

>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=84.41  E-value=0.29  Score=40.97  Aligned_cols=18  Identities=28%  Similarity=0.340  Sum_probs=15.0

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      +++|+|++|||||+..-.
T Consensus         2 ~I~l~G~~GsGKsT~a~~   19 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGER   19 (216)
T ss_dssp             EEEEECSTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            378999999999987644

>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=84.40  E-value=0.3  Score=43.92  Aligned_cols=18  Identities=28%  Similarity=0.451  Sum_probs=15.6

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      ...++++||+|+|||+.+
T Consensus        51 ~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           51 TSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CCEEEEECSSSSCHHHHH
T ss_pred             CCeEEEECCCCCcHHHHH
Confidence            467999999999999765

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=84.12  E-value=1.2  Score=39.86  Aligned_cols=22  Identities=27%  Similarity=0.264  Sum_probs=18.1

Q ss_pred             CCCCcEEEecCCCCCccchhhH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ..++.+.+.||+|||||+..-.
T Consensus        98 ~~g~vi~lvG~nGsGKTTll~~  119 (302)
T 3b9q_A           98 RKPAVIMIVGVNGGGKTTSLGK  119 (302)
T ss_dssp             SSCEEEEEECCTTSCHHHHHHH
T ss_pred             CCCcEEEEEcCCCCCHHHHHHH
Confidence            3567899999999999987644

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=84.01  E-value=0.31  Score=40.02  Aligned_cols=17  Identities=47%  Similarity=0.501  Sum_probs=14.3

Q ss_pred             cEEEecCCCCCccchhh
Q psy496           71 PSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~   87 (319)
                      .+.|.||+|||||+.+-
T Consensus         2 ~i~l~G~nGsGKTTLl~   18 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVK   18 (178)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999998753

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=83.98  E-value=0.37  Score=38.95  Aligned_cols=19  Identities=26%  Similarity=0.204  Sum_probs=11.8

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      ..++|.|+.|||||+..-.
T Consensus         6 ~~I~l~G~~GsGKST~a~~   24 (183)
T 2vli_A            6 PIIWINGPFGVGKTHTAHT   24 (183)
T ss_dssp             CEEEEECCC----CHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4688999999999987643

>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=83.91  E-value=0.4  Score=43.99  Aligned_cols=20  Identities=30%  Similarity=0.282  Sum_probs=16.6

Q ss_pred             CCCCcEEEecCCCCCccchh
Q psy496           67 PILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~   86 (319)
                      ....+++++||+|+|||+.+
T Consensus        70 ~~~~~ill~Gp~GtGKT~la   89 (376)
T 1um8_A           70 LSKSNILLIGPTGSGKTLMA   89 (376)
T ss_dssp             CCCCCEEEECCTTSSHHHHH
T ss_pred             cCCCCEEEECCCCCCHHHHH
Confidence            34568999999999999765

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=83.90  E-value=0.35  Score=41.62  Aligned_cols=23  Identities=22%  Similarity=0.343  Sum_probs=19.3

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.++.+.|.||+|||||+.+
T Consensus        26 l~i~~Ge~~~i~G~nGsGKSTLl   48 (237)
T 2cbz_A           26 FSIPEGALVAVVGQVGCGKSSLL   48 (237)
T ss_dssp             EEECTTCEEEEECSTTSSHHHHH
T ss_pred             EEECCCCEEEEECCCCCCHHHHH
Confidence            34567889999999999999765

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=83.89  E-value=0.35  Score=38.67  Aligned_cols=19  Identities=32%  Similarity=0.571  Sum_probs=15.6

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      ..++|+|+.|||||+..-.
T Consensus         3 ~~I~l~G~~GsGKsT~a~~   21 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRE   21 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            3589999999999987643

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=83.83  E-value=0.75  Score=44.38  Aligned_cols=37  Identities=24%  Similarity=0.312  Sum_probs=29.1

Q ss_pred             HHhhh-cCCCCCcEEEecCCCCCccchhhHHHHHHHHH
Q psy496           60 NKCLT-LSPILSPSIIYTSTGCGKTTQVPQFILDDEIA   96 (319)
Q Consensus        60 ~~~l~-~~~~~~~vli~apTGSGKT~~~~l~il~~l~~   96 (319)
                      +++.. ..+.++.++|.||+|||||+.....++..+..
T Consensus        29 d~i~~G~i~~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~~   66 (525)
T 1tf7_A           29 DDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIE   66 (525)
T ss_dssp             HHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHH
T ss_pred             HHhcCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHh
Confidence            35555 67889999999999999999887765565554

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=83.83  E-value=0.33  Score=43.79  Aligned_cols=19  Identities=16%  Similarity=0.303  Sum_probs=15.9

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      ....++++||+|+|||+.+
T Consensus        44 ~~~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A           44 PWRGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             CCSEEEEESSSSSCHHHHH
T ss_pred             CCceEEEECCCCccHHHHH
Confidence            3467999999999999665

>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=83.74  E-value=0.3  Score=43.91  Aligned_cols=19  Identities=26%  Similarity=0.517  Sum_probs=15.9

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      ...+++++||+|+|||..+
T Consensus        44 ~~~~vLl~G~~GtGKT~la   62 (350)
T 1g8p_A           44 GIGGVLVFGDRGTGKSTAV   62 (350)
T ss_dssp             GGCCEEEECCGGGCTTHHH
T ss_pred             CCceEEEECCCCccHHHHH
Confidence            3456999999999999765

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=83.73  E-value=0.36  Score=38.96  Aligned_cols=18  Identities=22%  Similarity=0.263  Sum_probs=15.2

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      +++|.|+.|||||+..-.
T Consensus         6 ~i~i~G~~GsGKsTla~~   23 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARA   23 (175)
T ss_dssp             CEEEECCTTSCHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHH
Confidence            589999999999987643

>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=83.57  E-value=0.33  Score=41.74  Aligned_cols=16  Identities=25%  Similarity=0.385  Sum_probs=14.1

Q ss_pred             cEEEecCCCCCccchh
Q psy496           71 PSIIYTSTGCGKTTQV   86 (319)
Q Consensus        71 ~vli~apTGSGKT~~~   86 (319)
                      .++|.||+|||||+.+
T Consensus        51 g~ll~G~~G~GKTtl~   66 (254)
T 1ixz_A           51 GVLLVGPPGVGKTHLA   66 (254)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4999999999999765

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=83.54  E-value=0.31  Score=43.25  Aligned_cols=18  Identities=28%  Similarity=0.185  Sum_probs=15.0

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      ...++++||+|+|||..+
T Consensus        36 p~~lLl~GppGtGKT~la   53 (293)
T 3t15_A           36 PLILGIWGGKGQGKSFQC   53 (293)
T ss_dssp             CSEEEEEECTTSCHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            356899999999999654

>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=83.52  E-value=0.38  Score=39.62  Aligned_cols=20  Identities=25%  Similarity=0.096  Sum_probs=16.6

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      +..++|.|+.|||||+..-.
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~   23 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMN   23 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHH
Confidence            45689999999999988643

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=83.51  E-value=0.44  Score=40.54  Aligned_cols=23  Identities=22%  Similarity=0.241  Sum_probs=18.2

Q ss_pred             CCCCCcEEEecCCCCCccchhhH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ..+.+.++|.||+||||++....
T Consensus        26 ~~k~kiI~llGpPGsGKgTqa~~   48 (217)
T 3umf_A           26 LAKAKVIFVLGGPGSGKGTQCEK   48 (217)
T ss_dssp             TTSCEEEEEECCTTCCHHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHHH
Confidence            34556788899999999988754

>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=83.49  E-value=0.39  Score=38.96  Aligned_cols=19  Identities=21%  Similarity=0.326  Sum_probs=15.6

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      ..++|+|++|||||+..-.
T Consensus         3 ~~I~l~G~~GsGKsT~a~~   21 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRR   21 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHH
Confidence            3589999999999987643

>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=83.38  E-value=0.73  Score=42.11  Aligned_cols=34  Identities=24%  Similarity=0.169  Sum_probs=25.3

Q ss_pred             HHhhh--cCCCCCcEEEecCCCCCccchhhHHHHHH
Q psy496           60 NKCLT--LSPILSPSIIYTSTGCGKTTQVPQFILDD   93 (319)
Q Consensus        60 ~~~l~--~~~~~~~vli~apTGSGKT~~~~l~il~~   93 (319)
                      +.++.  -.+.++.++|.||+|||||+.....+...
T Consensus        50 D~~Lg~GGl~~G~iv~I~G~pGsGKTtLal~la~~~   85 (349)
T 2zr9_A           50 DVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANA   85 (349)
T ss_dssp             HHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             HHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34454  45678899999999999998876655443

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=83.37  E-value=0.33  Score=39.41  Aligned_cols=18  Identities=28%  Similarity=0.422  Sum_probs=15.1

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|.|+.|||||+..-.
T Consensus         3 ~I~i~G~~GsGKsT~~~~   20 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAK   20 (194)
T ss_dssp             EEEEEECTTSCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            478999999999987644

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=83.35  E-value=1  Score=41.07  Aligned_cols=35  Identities=20%  Similarity=0.090  Sum_probs=26.1

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      ++++.-...++.++|.|++|+|||+.....+.+..
T Consensus        37 D~~~gGl~~G~LiiIaG~pG~GKTt~al~ia~~~a   71 (338)
T 4a1f_A           37 DNYTSGFNKGSLVIIGARPSMGKTSLMMNMVLSAL   71 (338)
T ss_dssp             HHHHCSBCTTCEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             HHHhcCCCCCcEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            34455567788999999999999987766555443

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=83.34  E-value=0.32  Score=42.96  Aligned_cols=18  Identities=28%  Similarity=0.377  Sum_probs=15.4

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      .++++.||+|+|||+.+-
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            479999999999997653

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=83.25  E-value=0.42  Score=40.58  Aligned_cols=22  Identities=23%  Similarity=0.067  Sum_probs=18.7

Q ss_pred             cCCCCCcEEEecCCCCCccchh
Q psy496           65 LSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ..+.++.+.|.||.|||||+.+
T Consensus        31 ~i~~Ge~~~iiG~NGsGKSTLl   52 (214)
T 1sgw_A           31 TIEKGNVVNFHGPNGIGKTTLL   52 (214)
T ss_dssp             EEETTCCEEEECCTTSSHHHHH
T ss_pred             EEcCCCEEEEECCCCCCHHHHH
Confidence            4567889999999999999765

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=83.25  E-value=0.57  Score=43.21  Aligned_cols=18  Identities=22%  Similarity=0.372  Sum_probs=15.8

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      ..+++|+||+|+|||+.+
T Consensus       148 ~~~vLL~GppGtGKT~la  165 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLA  165 (389)
T ss_dssp             CSEEEEESSTTSCHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            578999999999999765

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=83.20  E-value=0.39  Score=41.20  Aligned_cols=20  Identities=30%  Similarity=0.439  Sum_probs=16.5

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      ...+.|.||+|||||+..-.
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~   46 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQR   46 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            46799999999999987643

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=83.15  E-value=1  Score=42.57  Aligned_cols=35  Identities=11%  Similarity=0.014  Sum_probs=26.7

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      ++++.-.+.++.++|.|++|+|||+.....+.+..
T Consensus       194 D~~~gGl~~G~liiI~G~pG~GKTtl~l~ia~~~~  228 (454)
T 2r6a_A          194 DRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVA  228 (454)
T ss_dssp             HHHHSSBCTTCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             HhhcCCCCCCCEEEEECCCCCCHHHHHHHHHHHHH
Confidence            45555677889999999999999987766555443

>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=83.12  E-value=0.22  Score=43.25  Aligned_cols=19  Identities=21%  Similarity=0.249  Sum_probs=15.6

Q ss_pred             CCcEEEecCCCCCccchhh
Q psy496           69 LSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~   87 (319)
                      ...++++||+|+|||+.+-
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            4569999999999997653

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=83.05  E-value=0.4  Score=42.39  Aligned_cols=23  Identities=22%  Similarity=0.133  Sum_probs=19.3

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.++.+.|.||+|||||+.+
T Consensus        29 l~i~~Ge~~~iiGpnGsGKSTLl   51 (275)
T 3gfo_A           29 MNIKRGEVTAILGGNGVGKSTLF   51 (275)
T ss_dssp             EEEETTSEEEEECCTTSSHHHHH
T ss_pred             EEEcCCCEEEEECCCCCCHHHHH
Confidence            34567889999999999999765

>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=83.04  E-value=0.86  Score=43.93  Aligned_cols=28  Identities=21%  Similarity=0.297  Sum_probs=20.9

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      .+..+++|.|+||||||++.-..+...+
T Consensus       165 ~~~pHlLIaG~TGSGKSt~L~~li~sLl  192 (512)
T 2ius_A          165 AKMPHLLVAGTTGSGASVGVNAMILSML  192 (512)
T ss_dssp             GGSCSEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             ccCceEEEECCCCCCHHHHHHHHHHHHH
Confidence            3457899999999999987655444433

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=83.02  E-value=0.44  Score=40.07  Aligned_cols=20  Identities=25%  Similarity=0.187  Sum_probs=16.6

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      ...++|.|+.|||||+..-.
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~   24 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCEL   24 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            35689999999999987644

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=83.01  E-value=0.37  Score=39.44  Aligned_cols=18  Identities=33%  Similarity=0.362  Sum_probs=15.4

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      ..++|+|++|||||+..-
T Consensus        13 ~~I~l~G~~GsGKsT~a~   30 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCE   30 (199)
T ss_dssp             CEEEEEECTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            468999999999998763

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=82.91  E-value=0.39  Score=41.22  Aligned_cols=24  Identities=21%  Similarity=-0.011  Sum_probs=18.3

Q ss_pred             cCCCCCcEEEecCCCCCccchhhH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ..+.+..+-|.||.|||||+..-.
T Consensus        21 ~i~~g~iigI~G~~GsGKSTl~k~   44 (245)
T 2jeo_A           21 QSMRPFLIGVSGGTASGKSTVCEK   44 (245)
T ss_dssp             --CCSEEEEEECSTTSSHHHHHHH
T ss_pred             cCCCCEEEEEECCCCCCHHHHHHH
Confidence            455667889999999999987643

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=82.89  E-value=0.41  Score=40.20  Aligned_cols=20  Identities=30%  Similarity=0.464  Sum_probs=16.4

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      +..+++.|+.|||||+..-.
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~   23 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPN   23 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            45689999999999987644

>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=82.88  E-value=0.51  Score=43.33  Aligned_cols=32  Identities=22%  Similarity=0.080  Sum_probs=23.4

Q ss_pred             HHhhh--cCCCCCcEEEecCCCCCccchhhHHHH
Q psy496           60 NKCLT--LSPILSPSIIYTSTGCGKTTQVPQFIL   91 (319)
Q Consensus        60 ~~~l~--~~~~~~~vli~apTGSGKT~~~~l~il   91 (319)
                      +.++.  -.+.+..++|.||+|||||+.....+.
T Consensus        50 D~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~   83 (356)
T 3hr8_A           50 DIATGVGGYPRGRIVEIFGQESSGKTTLALHAIA   83 (356)
T ss_dssp             HHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHH
T ss_pred             HHHhccCCccCCcEEEEECCCCCCHHHHHHHHHH
Confidence            34444  455678999999999999987655443

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=82.86  E-value=0.51  Score=37.95  Aligned_cols=22  Identities=23%  Similarity=0.149  Sum_probs=18.6

Q ss_pred             cCCCCCcEEEecCCCCCccchh
Q psy496           65 LSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ..+.++.+.|.||.|||||+.+
T Consensus        29 ~i~~Ge~v~L~G~nGaGKTTLl   50 (158)
T 1htw_A           29 HTEKAIMVYLNGDLGAGKTTLT   50 (158)
T ss_dssp             CCSSCEEEEEECSTTSSHHHHH
T ss_pred             ccCCCCEEEEECCCCCCHHHHH
Confidence            3477889999999999999765

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=82.61  E-value=0.39  Score=39.14  Aligned_cols=21  Identities=24%  Similarity=0.101  Sum_probs=17.3

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      .+..+++.|+.|||||+..-.
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~   32 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATR   32 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHH
Confidence            456789999999999987644

>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli}

Probab=82.60  E-value=0.88  Score=37.67  Aligned_cols=47  Identities=13%  Similarity=0.107  Sum_probs=32.8

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIA  119 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~  119 (319)
                      .+..+|.|+-||+|+.....-++......++    .|.++.|+...+..+.
T Consensus        51 ~~~~iv~g~ggs~~~~~~~a~L~~~a~~~Gr----~V~vLAp~~~s~~~l~   97 (189)
T 2l8b_A           51 PSLAIVSGQGGAAGQRERVAELVMMAREQGR----EVQIIAADRRSQMNMK   97 (189)
T ss_dssp             CCEECCBCSSCSHHHHHHHHHHHHHHHHTTC----CEEEECSTTHHHHHHS
T ss_pred             CceEEEecccchHHHHHHHHHHHHHHHhcCe----EEEEEcCchHHHHHHH
Confidence            3778889999999998865555544444332    6777779977665554

>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=82.58  E-value=0.42  Score=43.69  Aligned_cols=20  Identities=25%  Similarity=0.353  Sum_probs=16.3

Q ss_pred             CCCcEEEecCCCCCccchhh
Q psy496           68 ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~   87 (319)
                      ....++++||+|+|||+.+-
T Consensus        83 ~~~~iLL~GppGtGKT~la~  102 (355)
T 2qp9_X           83 PTSGILLYGPPGTGKSYLAK  102 (355)
T ss_dssp             CCCCEEEECSTTSCHHHHHH
T ss_pred             CCceEEEECCCCCcHHHHHH
Confidence            34679999999999997653

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=82.54  E-value=0.38  Score=39.04  Aligned_cols=19  Identities=26%  Similarity=0.408  Sum_probs=15.6

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      ..++|+|++|||||+..-.
T Consensus         7 ~~I~l~G~~GsGKsT~~~~   25 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQCAN   25 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHH
Confidence            3588999999999987643

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=82.49  E-value=0.54  Score=38.96  Aligned_cols=20  Identities=25%  Similarity=0.353  Sum_probs=16.5

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      ++.+.|.||+|||||+.+-.
T Consensus         1 G~~i~i~G~nG~GKTTll~~   20 (189)
T 2i3b_A            1 ARHVFLTGPPGVGKTTLIHK   20 (189)
T ss_dssp             CCCEEEESCCSSCHHHHHHH
T ss_pred             CCEEEEECCCCChHHHHHHH
Confidence            35688999999999987644

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=82.45  E-value=0.4  Score=39.62  Aligned_cols=19  Identities=21%  Similarity=0.183  Sum_probs=15.9

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      ..++|.|+.|||||+..-.
T Consensus         5 ~~I~i~G~~GsGKsT~~~~   23 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATL   23 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHH
Confidence            4688999999999987644

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=82.43  E-value=0.43  Score=42.78  Aligned_cols=21  Identities=24%  Similarity=0.319  Sum_probs=17.5

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      .++.+.+.||+|||||+..-.
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~  121 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAK  121 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHH
Confidence            467899999999999987644

>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=82.42  E-value=0.43  Score=43.60  Aligned_cols=21  Identities=19%  Similarity=0.186  Sum_probs=17.1

Q ss_pred             CCCCcEEEecCCCCCccchhh
Q psy496           67 PILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~   87 (319)
                      .....++|+||+|+|||+.+-
T Consensus       115 ~~~~~vLl~GppGtGKT~la~  135 (357)
T 3d8b_A          115 GPPKGILLFGPPGTGKTLIGK  135 (357)
T ss_dssp             SCCSEEEEESSTTSSHHHHHH
T ss_pred             CCCceEEEECCCCCCHHHHHH
Confidence            345789999999999997653

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=82.42  E-value=0.41  Score=38.01  Aligned_cols=17  Identities=24%  Similarity=0.473  Sum_probs=14.6

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      ...+|.||+|||||+.+
T Consensus        24 g~~~I~G~NGsGKStil   40 (149)
T 1f2t_A           24 GINLIIGQNGSGKSSLL   40 (149)
T ss_dssp             EEEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            46789999999999774

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=82.33  E-value=0.44  Score=41.29  Aligned_cols=23  Identities=22%  Similarity=0.031  Sum_probs=19.2

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.++.+.|.||+|||||+.+
T Consensus        30 l~i~~Ge~~~i~G~nGsGKSTLl   52 (247)
T 2ff7_A           30 LSIKQGEVIGIVGRSGSGKSTLT   52 (247)
T ss_dssp             EEEETTCEEEEECSTTSSHHHHH
T ss_pred             EEEcCCCEEEEECCCCCCHHHHH
Confidence            34567889999999999999765

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=82.30  E-value=0.39  Score=44.17  Aligned_cols=18  Identities=17%  Similarity=0.370  Sum_probs=15.3

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      ..+|+||||||||+.+-.
T Consensus        25 ~~~i~G~NGaGKTTll~a   42 (365)
T 3qf7_A           25 ITVVEGPNGAGKSSLFEA   42 (365)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            678999999999988743

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=82.27  E-value=0.58  Score=37.81  Aligned_cols=18  Identities=22%  Similarity=0.248  Sum_probs=15.1

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      ...+|.||+|||||+.+-
T Consensus        27 g~~~i~G~NGsGKStll~   44 (182)
T 3kta_A           27 GFTAIVGANGSGKSNIGD   44 (182)
T ss_dssp             SEEEEEECTTSSHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            378899999999997753

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=82.24  E-value=0.45  Score=40.71  Aligned_cols=22  Identities=27%  Similarity=0.144  Sum_probs=18.7

Q ss_pred             cCCCCCcEEEecCCCCCccchh
Q psy496           65 LSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ..+.++.+.|.||+|||||+.+
T Consensus        30 ~i~~Ge~~~i~G~nGsGKSTLl   51 (229)
T 2pze_A           30 KIERGQLLAVAGSTGAGKTSLL   51 (229)
T ss_dssp             EEETTCEEEEECCTTSSHHHHH
T ss_pred             EEcCCCEEEEECCCCCCHHHHH
Confidence            4567889999999999999765

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=82.20  E-value=0.42  Score=40.70  Aligned_cols=22  Identities=23%  Similarity=0.137  Sum_probs=18.5

Q ss_pred             cCCCCCcEEEecCCCCCccchh
Q psy496           65 LSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ..+.++.+.|.||.|||||+.+
T Consensus        26 ~i~~Ge~~~iiG~nGsGKSTLl   47 (224)
T 2pcj_A           26 SVKKGEFVSIIGASGSGKSTLL   47 (224)
T ss_dssp             EEETTCEEEEEECTTSCHHHHH
T ss_pred             EEcCCCEEEEECCCCCCHHHHH
Confidence            4557788999999999999764

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=82.19  E-value=0.4  Score=38.16  Aligned_cols=18  Identities=17%  Similarity=0.004  Sum_probs=14.9

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|.|+.|||||+..-.
T Consensus         2 ~I~l~G~~GsGKsT~a~~   19 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSL   19 (168)
T ss_dssp             EEEEESCTTSCHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            478999999999987643

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=82.16  E-value=0.38  Score=45.02  Aligned_cols=18  Identities=33%  Similarity=0.364  Sum_probs=14.7

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|+||||||||+....
T Consensus         4 ~i~i~GptgsGKttla~~   21 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLSIQ   21 (409)
T ss_dssp             EEEEEECSSSSHHHHHHH
T ss_pred             EEEEECcchhhHHHHHHH
Confidence            578999999999976533

>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=82.10  E-value=0.68  Score=43.78  Aligned_cols=20  Identities=20%  Similarity=0.200  Sum_probs=16.5

Q ss_pred             CCCcEEEecCCCCCccchhh
Q psy496           68 ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~   87 (319)
                      .+.++++.||+|+|||+.+-
T Consensus        62 ~~~~iLl~GppGtGKT~la~   81 (456)
T 2c9o_A           62 AGRAVLLAGPPGTGKTALAL   81 (456)
T ss_dssp             TTCEEEEECCTTSSHHHHHH
T ss_pred             CCCeEEEECCCcCCHHHHHH
Confidence            34679999999999997663

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=82.04  E-value=0.45  Score=39.40  Aligned_cols=21  Identities=19%  Similarity=-0.020  Sum_probs=17.2

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      .+..++|+|+.|||||+..-.
T Consensus         9 ~~~~I~l~G~~GsGKST~~~~   29 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQSKL   29 (212)
T ss_dssp             CSCEEEEEESTTSSHHHHHHH
T ss_pred             cCCEEEEEcCCCCCHHHHHHH
Confidence            356789999999999987644

>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=82.03  E-value=0.93  Score=41.58  Aligned_cols=28  Identities=32%  Similarity=0.293  Sum_probs=22.6

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDD   93 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~   93 (319)
                      .+.+..++|.|++|||||+.....+.+.
T Consensus        60 l~~G~ii~I~G~pGsGKTtLal~la~~~   87 (356)
T 1u94_A           60 LPMGRIVEIYGPESSGKTTLTLQVIAAA   87 (356)
T ss_dssp             EETTSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            5677899999999999998876655543

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=81.97  E-value=0.42  Score=41.27  Aligned_cols=23  Identities=22%  Similarity=0.053  Sum_probs=19.4

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.++.+.|.||+|||||+.+
T Consensus        23 l~i~~Ge~~~i~G~nGsGKSTLl   45 (243)
T 1mv5_A           23 FEAQPNSIIAFAGPSGGGKSTIF   45 (243)
T ss_dssp             EEECTTEEEEEECCTTSSHHHHH
T ss_pred             EEEcCCCEEEEECCCCCCHHHHH
Confidence            34567889999999999999765

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=81.96  E-value=0.46  Score=41.49  Aligned_cols=23  Identities=26%  Similarity=0.319  Sum_probs=19.6

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.++.+.|.||+|||||+.+
T Consensus        41 l~i~~Ge~~~i~G~nGsGKSTLl   63 (260)
T 2ghi_A           41 FFIPSGTTCALVGHTGSGKSTIA   63 (260)
T ss_dssp             EEECTTCEEEEECSTTSSHHHHH
T ss_pred             EEECCCCEEEEECCCCCCHHHHH
Confidence            44667889999999999999765

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=81.94  E-value=0.46  Score=41.09  Aligned_cols=22  Identities=23%  Similarity=0.249  Sum_probs=17.9

Q ss_pred             CCCCcEEEecCCCCCccchhhH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ..+..+.|.||+|||||+..-+
T Consensus        25 ~~g~~I~I~G~~GsGKSTl~k~   46 (252)
T 4e22_A           25 AIAPVITVDGPSGAGKGTLCKA   46 (252)
T ss_dssp             TTSCEEEEECCTTSSHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHH
Confidence            4567899999999999987633

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=81.91  E-value=0.41  Score=39.65  Aligned_cols=17  Identities=29%  Similarity=0.204  Sum_probs=14.4

Q ss_pred             cEEEecCCCCCccchhh
Q psy496           71 PSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~   87 (319)
                      .+.|.|+.|||||+..-
T Consensus         4 ~i~l~G~~GsGKST~~~   20 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIAN   20 (206)
T ss_dssp             EEEEECSTTSCHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47889999999998763

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=81.86  E-value=0.65  Score=41.75  Aligned_cols=22  Identities=23%  Similarity=0.184  Sum_probs=18.7

Q ss_pred             CCCCCcEEEecCCCCCccchhh
Q psy496           66 SPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~   87 (319)
                      ...+..+.|.||+|||||+.+-
T Consensus        87 ~~~g~ivgI~G~sGsGKSTL~~  108 (312)
T 3aez_A           87 RPVPFIIGVAGSVAVGKSTTAR  108 (312)
T ss_dssp             SCCCEEEEEECCTTSCHHHHHH
T ss_pred             CCCCEEEEEECCCCchHHHHHH
Confidence            5667889999999999998763

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=81.82  E-value=0.47  Score=40.85  Aligned_cols=23  Identities=26%  Similarity=0.273  Sum_probs=19.1

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.++.+.|.||+|||||+.+
T Consensus        27 l~i~~Ge~~~l~G~nGsGKSTLl   49 (240)
T 1ji0_A           27 LKVPRGQIVTLIGANGAGKTTTL   49 (240)
T ss_dssp             EEEETTCEEEEECSTTSSHHHHH
T ss_pred             EEEcCCCEEEEECCCCCCHHHHH
Confidence            34567888999999999999765

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=81.73  E-value=0.56  Score=41.07  Aligned_cols=26  Identities=15%  Similarity=0.132  Sum_probs=21.3

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFIL   91 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il   91 (319)
                      .+.++.++|.||+|||||+.....+.
T Consensus        27 l~~G~i~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           27 MVAGTVGALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             ccCCCEEEEEcCCCCCHHHHHHHHHH
Confidence            45778899999999999987765544

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=81.70  E-value=0.48  Score=41.27  Aligned_cols=23  Identities=22%  Similarity=0.248  Sum_probs=19.1

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.++.+.|.||+|||||+.+
T Consensus        28 l~i~~Ge~~~liG~nGsGKSTLl   50 (257)
T 1g6h_A           28 ISVNKGDVTLIIGPNGSGKSTLI   50 (257)
T ss_dssp             CEEETTCEEEEECSTTSSHHHHH
T ss_pred             EEEeCCCEEEEECCCCCCHHHHH
Confidence            34567889999999999999765

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=81.68  E-value=0.41  Score=39.58  Aligned_cols=17  Identities=29%  Similarity=0.456  Sum_probs=14.4

Q ss_pred             cEEEecCCCCCccchhh
Q psy496           71 PSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~   87 (319)
                      .+.|+|+.|||||+..-
T Consensus         3 ~i~i~G~~GsGKSTl~~   19 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQ   19 (204)
T ss_dssp             EEEEEECTTSSHHHHHH
T ss_pred             EEEEECCCCcCHHHHHH
Confidence            47899999999998653

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=81.56  E-value=0.43  Score=45.05  Aligned_cols=19  Identities=26%  Similarity=0.433  Sum_probs=15.8

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      ....+|+.||+|||||..+
T Consensus       214 ~prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          214 APKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             CCCEEEEESCTTSSHHHHH
T ss_pred             CCCeeEEECcCCCCHHHHH
Confidence            3567999999999999654

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=81.50  E-value=0.43  Score=39.11  Aligned_cols=18  Identities=28%  Similarity=0.488  Sum_probs=15.0

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|.|+.|||||+..-.
T Consensus         2 ~I~i~G~~GsGKsT~~~~   19 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAE   19 (205)
T ss_dssp             EEEEECCTTSCHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHH
Confidence            478999999999987643

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=81.48  E-value=0.49  Score=39.04  Aligned_cols=19  Identities=26%  Similarity=0.396  Sum_probs=15.8

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      ..++|.|++|||||+..-.
T Consensus        21 ~~I~l~G~~GsGKST~a~~   39 (201)
T 2cdn_A           21 MRVLLLGPPGAGKGTQAVK   39 (201)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4689999999999987643

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=81.47  E-value=0.49  Score=41.55  Aligned_cols=23  Identities=22%  Similarity=0.137  Sum_probs=19.2

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      .....++.+.|.||+|||||+.+
T Consensus        32 l~i~~Ge~~~liG~nGsGKSTLl   54 (266)
T 4g1u_C           32 LHIASGEMVAIIGPNGAGKSTLL   54 (266)
T ss_dssp             EEEETTCEEEEECCTTSCHHHHH
T ss_pred             EEEcCCCEEEEECCCCCcHHHHH
Confidence            34567889999999999999765

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=81.43  E-value=0.46  Score=39.21  Aligned_cols=18  Identities=33%  Similarity=0.420  Sum_probs=15.1

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      ..++|+|+.|||||+..-
T Consensus        16 ~~I~l~G~~GsGKsT~~~   33 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCE   33 (203)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHH
Confidence            458899999999998763

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=81.41  E-value=0.49  Score=39.24  Aligned_cols=21  Identities=19%  Similarity=0.112  Sum_probs=17.2

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      .+..++|+|+.|||||+..-.
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~   28 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQSRK   28 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHH
Confidence            345789999999999988754

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=81.36  E-value=1.7  Score=39.89  Aligned_cols=22  Identities=27%  Similarity=0.264  Sum_probs=18.1

Q ss_pred             CCCCcEEEecCCCCCccchhhH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ..++.+.+.||+|||||+..-.
T Consensus       155 ~~g~vi~lvG~nGsGKTTll~~  176 (359)
T 2og2_A          155 RKPAVIMIVGVNGGGKTTSLGK  176 (359)
T ss_dssp             SSSEEEEEECCTTSCHHHHHHH
T ss_pred             CCCeEEEEEcCCCChHHHHHHH
Confidence            3567899999999999987644

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=81.19  E-value=0.51  Score=40.90  Aligned_cols=24  Identities=21%  Similarity=0.221  Sum_probs=19.6

Q ss_pred             hcCCCCCcEEEecCCCCCccchhh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~~   87 (319)
                      .....++.+.|.||+|||||+.+-
T Consensus        24 l~i~~Ge~~~l~G~nGsGKSTLlk   47 (250)
T 2d2e_A           24 LVVPKGEVHALMGPNGAGKSTLGK   47 (250)
T ss_dssp             EEEETTCEEEEECSTTSSHHHHHH
T ss_pred             EEEcCCCEEEEECCCCCCHHHHHH
Confidence            345678899999999999998753

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=81.19  E-value=0.49  Score=41.61  Aligned_cols=25  Identities=16%  Similarity=0.017  Sum_probs=20.4

Q ss_pred             hhhcCCCCCcEEEecCCCCCccchh
Q psy496           62 CLTLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        62 ~l~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      +-...+.++.+.|.||+|||||+.+
T Consensus        38 vsl~i~~Ge~~~i~G~nGsGKSTLl   62 (271)
T 2ixe_A           38 LTFTLYPGKVTALVGPNGSGKSTVA   62 (271)
T ss_dssp             EEEEECTTCEEEEECSTTSSHHHHH
T ss_pred             eEEEECCCCEEEEECCCCCCHHHHH
Confidence            3345678899999999999999765

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=81.17  E-value=0.46  Score=41.78  Aligned_cols=16  Identities=31%  Similarity=0.580  Sum_probs=14.0

Q ss_pred             cEEEecCCCCCccchh
Q psy496           71 PSIIYTSTGCGKTTQV   86 (319)
Q Consensus        71 ~vli~apTGSGKT~~~   86 (319)
                      .+++.||+|||||+.+
T Consensus        46 GvlL~Gp~GtGKTtLa   61 (274)
T 2x8a_A           46 GVLLAGPPGCGKTLLA   61 (274)
T ss_dssp             EEEEESSTTSCHHHHH
T ss_pred             eEEEECCCCCcHHHHH
Confidence            3999999999999765

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=81.17  E-value=0.44  Score=39.89  Aligned_cols=18  Identities=28%  Similarity=0.235  Sum_probs=15.0

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      +++|.|++|||||+..-.
T Consensus         2 ~I~l~G~~GsGKsT~a~~   19 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQF   19 (214)
T ss_dssp             EEEEEESTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            378999999999987644

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=81.14  E-value=0.55  Score=40.85  Aligned_cols=20  Identities=25%  Similarity=0.111  Sum_probs=17.5

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      +++++|.|+.|||||+..-.
T Consensus        48 g~~i~l~G~~GsGKSTl~~~   67 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKI   67 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            78999999999999987643

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=81.08  E-value=0.52  Score=41.24  Aligned_cols=23  Identities=26%  Similarity=0.187  Sum_probs=19.4

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      .....++.+.|.||+|||||+.+
T Consensus        27 l~i~~Ge~~~liG~nGsGKSTLl   49 (262)
T 1b0u_A           27 LQARAGDVISIIGSSGSGKSTFL   49 (262)
T ss_dssp             EEECTTCEEEEECCTTSSHHHHH
T ss_pred             EEEcCCCEEEEECCCCCCHHHHH
Confidence            34567889999999999999765

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=81.06  E-value=0.47  Score=41.51  Aligned_cols=16  Identities=25%  Similarity=0.385  Sum_probs=14.1

Q ss_pred             cEEEecCCCCCccchh
Q psy496           71 PSIIYTSTGCGKTTQV   86 (319)
Q Consensus        71 ~vli~apTGSGKT~~~   86 (319)
                      .++|.||+|||||+.+
T Consensus        75 gvll~Gp~GtGKTtl~   90 (278)
T 1iy2_A           75 GVLLVGPPGVGKTHLA   90 (278)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCcChHHHHH
Confidence            3999999999999765

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=81.04  E-value=0.49  Score=44.24  Aligned_cols=20  Identities=30%  Similarity=0.388  Sum_probs=16.2

Q ss_pred             CCCCcEEEecCCCCCccchh
Q psy496           67 PILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~   86 (319)
                      +....+|+.||+|||||..+
T Consensus       180 ~~prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          180 AQPKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             CCCCCEEEESCSSSSHHHHH
T ss_pred             CCCCceEEeCCCCCCHHHHH
Confidence            34567999999999999654

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=81.00  E-value=0.48  Score=38.47  Aligned_cols=18  Identities=33%  Similarity=0.292  Sum_probs=14.9

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|+|+.|||||+..-.
T Consensus         2 ~I~l~G~~GsGKsT~~~~   19 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKK   19 (195)
T ss_dssp             EEEEECSTTSCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            478999999999987643

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=80.90  E-value=0.46  Score=39.45  Aligned_cols=21  Identities=24%  Similarity=-0.091  Sum_probs=17.1

Q ss_pred             CCCCcEEEecCCCCCccchhh
Q psy496           67 PILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~   87 (319)
                      ..+..+.|.|++|||||+..-
T Consensus        20 ~~~~~i~i~G~~GsGKstl~~   40 (201)
T 1rz3_A           20 AGRLVLGIDGLSRSGKTTLAN   40 (201)
T ss_dssp             SSSEEEEEEECTTSSHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHH
Confidence            345678899999999998764

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=80.84  E-value=0.59  Score=39.34  Aligned_cols=19  Identities=26%  Similarity=0.401  Sum_probs=15.4

Q ss_pred             cEEEecCCCCCccchhhHH
Q psy496           71 PSIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~   89 (319)
                      ++++.||+||||++.....
T Consensus         2 ~Iil~GpPGsGKgTqa~~L   20 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRL   20 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3678999999999887553

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=80.79  E-value=0.68  Score=41.68  Aligned_cols=28  Identities=18%  Similarity=0.176  Sum_probs=22.3

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILD   92 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~   92 (319)
                      -.+.++.++|.||+|||||+.....+.+
T Consensus       103 Gl~~G~i~~i~G~~GsGKT~la~~la~~  130 (324)
T 2z43_A          103 GIETRTMTEFFGEFGSGKTQLCHQLSVN  130 (324)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCCCcEEEEECCCCCCHhHHHHHHHHH
Confidence            4566789999999999999877665544

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=80.76  E-value=0.54  Score=41.25  Aligned_cols=24  Identities=21%  Similarity=0.069  Sum_probs=20.0

Q ss_pred             hcCCCCCcEEEecCCCCCccchhh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~~   87 (319)
                      ...+.++.+.|.||+|||||+.+-
T Consensus        41 l~i~~Ge~~~l~G~NGsGKSTLlk   64 (267)
T 2zu0_C           41 LDVHPGEVHAIMGPNGSGKSTLSA   64 (267)
T ss_dssp             EEECTTCEEEEECCTTSSHHHHHH
T ss_pred             EEEcCCCEEEEECCCCCCHHHHHH
Confidence            446778899999999999998753

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=80.73  E-value=1.3  Score=41.78  Aligned_cols=35  Identities=17%  Similarity=0.071  Sum_probs=26.2

Q ss_pred             HHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           60 NKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        60 ~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      ++++.-.+.++.++|+|++|+|||+.....+.+..
T Consensus       191 D~~lgGl~~G~l~ii~G~pg~GKT~lal~ia~~~a  225 (444)
T 2q6t_A          191 DQLIGTLGPGSLNIIAARPAMGKTAFALTIAQNAA  225 (444)
T ss_dssp             HHHHCCCCTTCEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             hhhcCCcCCCcEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            44555567788999999999999987766555443

>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=80.60  E-value=0.88  Score=43.59  Aligned_cols=21  Identities=24%  Similarity=0.287  Sum_probs=17.2

Q ss_pred             CCCCCcEEEecCCCCCccchh
Q psy496           66 SPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~   86 (319)
                      +.....++|+||+|+|||+.+
T Consensus       235 ~~~~~~vLL~GppGtGKT~lA  255 (489)
T 3hu3_A          235 VKPPRGILLYGPPGTGKTLIA  255 (489)
T ss_dssp             CCCCCEEEEECSTTSSHHHHH
T ss_pred             CCCCCcEEEECcCCCCHHHHH
Confidence            345577999999999999765

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=80.59  E-value=0.5  Score=39.47  Aligned_cols=23  Identities=13%  Similarity=0.007  Sum_probs=18.6

Q ss_pred             CCCCCcEEEecCCCCCccchhhH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ...+..+++.|+.|||||+..-.
T Consensus        22 ~~~~~~i~~~G~~GsGKsT~~~~   44 (211)
T 1m7g_A           22 NQRGLTIWLTGLSASGKSTLAVE   44 (211)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHH
Confidence            45567899999999999987643

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=80.53  E-value=0.55  Score=40.95  Aligned_cols=23  Identities=22%  Similarity=0.024  Sum_probs=19.4

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.++.+.|.||+|||||+.+
T Consensus        36 l~i~~Gei~~l~G~NGsGKSTLl   58 (256)
T 1vpl_A           36 FEIEEGEIFGLIGPNGAGKTTTL   58 (256)
T ss_dssp             EEECTTCEEEEECCTTSSHHHHH
T ss_pred             EEEcCCcEEEEECCCCCCHHHHH
Confidence            34567889999999999999765

>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=80.48  E-value=0.56  Score=42.42  Aligned_cols=23  Identities=35%  Similarity=0.339  Sum_probs=18.6

Q ss_pred             CCCCCcEEEecCCCCCccchhhH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ...+..++|+||+|+|||+..-.
T Consensus        42 ~~~~~~vli~G~~G~GKTtl~~~   64 (386)
T 2qby_A           42 EEKPNNIFIYGLTGTGKTAVVKF   64 (386)
T ss_dssp             TCCCCCEEEEECTTSSHHHHHHH
T ss_pred             CCCCCeEEEECCCCCCHHHHHHH
Confidence            34567899999999999977643

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=80.44  E-value=0.49  Score=38.83  Aligned_cols=19  Identities=26%  Similarity=0.149  Sum_probs=15.6

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      ..+.|+|++|||||+..-.
T Consensus         9 ~~I~i~G~~GsGKST~~~~   27 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAAL   27 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4688999999999987633

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=80.41  E-value=0.56  Score=41.06  Aligned_cols=23  Identities=22%  Similarity=0.182  Sum_probs=19.4

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      .....++.+.|.||+|||||+.+
T Consensus        28 l~i~~Ge~~~liG~nGsGKSTLl   50 (266)
T 2yz2_A           28 LVINEGECLLVAGNTGSGKSTLL   50 (266)
T ss_dssp             EEECTTCEEEEECSTTSSHHHHH
T ss_pred             EEEcCCCEEEEECCCCCcHHHHH
Confidence            44667889999999999999765

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=80.36  E-value=0.5  Score=44.66  Aligned_cols=20  Identities=25%  Similarity=0.341  Sum_probs=16.2

Q ss_pred             CCCCcEEEecCCCCCccchh
Q psy496           67 PILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~   86 (319)
                      +...-+|+.||+|||||+.+
T Consensus       213 ~~prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          213 KPPKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             CCCCEEEEESCTTSSHHHHH
T ss_pred             CCCCeEEEECCCCCcHHHHH
Confidence            34467999999999999654

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=80.34  E-value=0.37  Score=43.22  Aligned_cols=18  Identities=22%  Similarity=0.143  Sum_probs=15.7

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      +.++++.||+|+|||...
T Consensus        46 ~~~vll~G~pGtGKT~la   63 (331)
T 2r44_A           46 GGHILLEGVPGLAKTLSV   63 (331)
T ss_dssp             TCCEEEESCCCHHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHH
Confidence            468999999999999655

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=80.22  E-value=0.36  Score=46.50  Aligned_cols=19  Identities=11%  Similarity=0.076  Sum_probs=16.0

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      .+.++++.||+|+|||..+
T Consensus        40 ~~~~VLL~GpPGtGKT~LA   58 (500)
T 3nbx_X           40 SGESVFLLGPPGIAKSLIA   58 (500)
T ss_dssp             HTCEEEEECCSSSSHHHHH
T ss_pred             cCCeeEeecCchHHHHHHH
Confidence            4578999999999999654

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=80.22  E-value=0.56  Score=40.78  Aligned_cols=22  Identities=23%  Similarity=0.249  Sum_probs=18.6

Q ss_pred             cCCCCCcEEEecCCCCCccchh
Q psy496           65 LSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ..+.++.+.|.||+|||||+.+
T Consensus        27 ~i~~Ge~~~l~G~nGsGKSTLl   48 (253)
T 2nq2_C           27 DLNKGDILAVLGQNGCGKSTLL   48 (253)
T ss_dssp             EEETTCEEEEECCSSSSHHHHH
T ss_pred             EECCCCEEEEECCCCCCHHHHH
Confidence            4567888999999999999765

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=80.21  E-value=1  Score=42.77  Aligned_cols=22  Identities=18%  Similarity=0.265  Sum_probs=17.6

Q ss_pred             CCCCcEEEecCCCCCccchhhH
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l   88 (319)
                      ....++++.||+|+|||+.+-.
T Consensus       199 ~~~~~~LL~G~pG~GKT~la~~  220 (468)
T 3pxg_A          199 RTKNNPVLIGEPGVGKTAIAEG  220 (468)
T ss_dssp             SSSCEEEEESCTTTTTHHHHHH
T ss_pred             cCCCCeEEECCCCCCHHHHHHH
Confidence            4456899999999999976643

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=80.20  E-value=0.51  Score=44.47  Aligned_cols=19  Identities=32%  Similarity=0.434  Sum_probs=15.7

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      ...-+++.||+|||||..+
T Consensus       205 ~prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          205 PPRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             CCCEEEEESCTTTTHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3466999999999999654

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=80.04  E-value=0.43  Score=41.27  Aligned_cols=21  Identities=24%  Similarity=0.159  Sum_probs=16.7

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      .+..++++|++|||||+..-.
T Consensus        31 ~~~~i~l~G~~GsGKSTla~~   51 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTIHRI   51 (253)
T ss_dssp             SCEEEEEESCGGGTTHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            345789999999999987533

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=80.01  E-value=0.59  Score=40.96  Aligned_cols=23  Identities=17%  Similarity=0.172  Sum_probs=19.5

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.++.+.|.||.|||||+.+
T Consensus        45 l~i~~Gei~~liG~NGsGKSTLl   67 (263)
T 2olj_A           45 VHIREGEVVVVIGPSGSGKSTFL   67 (263)
T ss_dssp             EEECTTCEEEEECCTTSSHHHHH
T ss_pred             EEEcCCCEEEEEcCCCCcHHHHH
Confidence            44567889999999999999765

---

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	319
d1a1va1	136	c.37.1.14 (A:190-325) HCV helicase domain {Human h	2e-21
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	1e-17
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	4e-04
d1yksa1	140	c.37.1.14 (A:185-324) YFV helicase domain {Yellow	8e-09
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	2e-04
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	0.004

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 136

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

 Score = 86.1 bits (212), Expect = 2e-21
 Identities = 18/144 (12%), Positives = 40/144 (27%), Gaps = 19/144 (13%)

Query: 72  SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCG 131
           + ++  TG GK+T+VP                 ++V  P   + +     +++       
Sbjct: 11  AHLHAPTGSGKSTKVPAAYAAQG--------YKVLVLNPSVAATLGFGAYMSKAHGVDPN 62

Query: 132 RPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISD 191
                          +           +     +            I+ DE H     S 
Sbjct: 63  IR-----------TGVRTITTGSPITYSTYGKFLADGGCSGGAYDIIICDECHSTDATSI 111

Query: 192 FLLAILKDVTDKRKDLKLILMSAT 215
             +  + D  +      ++L +AT
Sbjct: 112 LGIGTVLDQAETAGARLVVLATAT 135

>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 = 79.6 bits (195), Expect = 1e-17
 Identities = 30/161 (18%), Positives = 52/161 (32%), Gaps = 15/161 (9%)

Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           I+    G GKT +    I+ + I R        ++  P R+ A  + E +          
Sbjct: 13  IMDLHPGAGKTKRYLPAIVREAIKRGLR----TLILAPTRVVAAEMEEALR--------- 59

Query: 133 PGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF 192
            G  + YQ    +     R  +           + S   +   + I+MDE H     S  
Sbjct: 60  -GLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTDPASIA 118

Query: 193 LLAILKDVTDKRKDLKLILMSATLNAEKFSQFFGGAPILHI 233
               +    +   +   I M+AT    +       API+  
Sbjct: 119 ARGYISTRVE-MGEAAGIFMTATPPGSRDPFPQSNAPIMDE 158

>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 = 39.1 bits (90), Expect = 4e-04
 Identities = 14/82 (17%), Positives = 26/82 (31%), Gaps = 7/82 (8%)

Query: 19 GCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTST 78
          G GKT +    I+ + I R        ++  P R+ A   + + L   PI   +    + 
Sbjct: 19 GAGKTKRYLPAIVREAIKRGLR----TLILAPTRVVAAE-MEEALRGLPIRYQTPAIRAE 73

Query: 79 GCGKTTQV--PQFILDDEIARN 98
            G+              +   
Sbjct: 74 HTGREIVDLMCHATFTMRLLSP 95

>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 = 51.6 bits (122), Expect = 8e-09
 Identities = 24/143 (16%), Positives = 39/143 (27%), Gaps = 15/143 (10%)

Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           ++    G GKT +    IL +   R   +                      + ++   G 
Sbjct: 11  VLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLS-----------EMKEAFHGL 59

Query: 133 PGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF 192
               V +  +        R  I       L   M     +     I+MDE H     S  
Sbjct: 60  D---VKFHTQAFSAHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFLDPASIA 116

Query: 193 LLAILKDVTDKRKDLKLILMSAT 215
                     +  +   ILM+AT
Sbjct: 117 ARGWAAHR-ARANESATILMTAT 138

>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 = 40.0 bits (93), Expect = 2e-04
 Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 7/87 (8%)

Query: 134 GSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPI-LSGVSHIVMDEIHERSMISDF 192
           G ++  QI+       K  +I+  T G + + +    + L  V + ++DE     +   F
Sbjct: 109 GKAIYPQIKA-----LKNANIVVGTPGRILDHINRGTLNLKNVKYFILDEAD-EMLNMGF 162

Query: 193 LLAILKDVTDKRKDLKLILMSATLNAE 219
           +  + K +    KD +++L SAT+  E
Sbjct: 163 IKDVEKILNACNKDKRILLFSATMPRE 189

>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 = 35.3 bits (80), Expect = 0.004
 Identities = 31/166 (18%), Positives = 61/166 (36%), Gaps = 18/166 (10%)

Query: 73  IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGR 132
           ++   T  GKT      ++     R        +   P R  A    E   +        
Sbjct: 44  LLAMPTAAGKTLLAEMAMV-----REAIKGGKSLYVVPLRALAGEKYESFKKWEKIGLRI 98

Query: 133 PGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPI-LSGVSHIVMDEIHE-----R 186
             S+  Y+ R E         I+  T+     ++++    +  VS +V+DEIH      R
Sbjct: 99  GISTGDYESRDE---HLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKR 155

Query: 187 SMISDFLLAILKDVTDKRKDLKLILMSATL-NAEKFSQFFGGAPIL 231
               + L+  ++ +    K L++I +SAT  N  + +++      +
Sbjct: 156 GATLEILVTKMRRM---NKALRVIGLSATAPNVTEIAEWLDADYYV 198

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	319
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.95
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.95
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.95
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.94
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.94
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.93
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.92
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.92
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.92
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.9
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.83
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.81
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.8
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.8
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.79
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.78
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.63
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.62
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.46
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.46
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.33
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	98.15
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.14
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.89
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.85
d1okkd2	207	GTPase domain of the signal recognition particle r	97.78
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.75
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.56
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.2
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.18
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	97.08
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.04
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	97.0
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	96.99
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	96.95
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	96.83
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	96.81
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	96.78
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.52
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	96.43
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	96.35
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	96.3
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	95.89
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	95.41
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	94.86
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	94.68
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	93.73
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	93.36
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	93.33
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.26
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	93.18
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	93.08
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	93.05
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	93.0
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	92.73
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	92.65
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	92.56
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	92.43
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	92.43
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	92.37
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	92.36
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	92.23
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	92.21
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	92.17
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	91.94
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	91.91
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	91.62
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	91.57
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	91.5
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	91.15
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	90.93
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	90.87
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	90.85
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	90.77
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	90.72
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	90.59
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	90.27
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	89.84
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	89.75
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	89.53
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	89.45
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	89.31
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	89.28
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	89.13
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	89.08
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	89.05
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	89.02
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	88.87
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	88.76
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	88.58
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	88.57
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	88.36
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	88.33
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	88.29
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	88.16
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	88.14
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	87.67
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	87.47
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	87.3
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	87.18
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	87.01
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	86.88
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	86.34
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	86.12
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	86.0
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	85.97
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	85.93
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	85.89
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	85.71
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	85.64
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	85.59
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	85.29
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	85.24
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	85.13
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	85.09
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	85.06
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	84.97
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	84.31
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	84.24
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	84.18
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	84.06
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	83.89
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	83.62
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	83.0
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	82.73
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	82.45
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	82.21
d2awna2	232	Maltose transport protein MalK, N-terminal domain	82.18
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	82.12
d1g2912	240	Maltose transport protein MalK, N-terminal domain	81.23
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	81.17
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	80.09

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=4e-29  Score=217.27  Aligned_cols=186  Identities=19%  Similarity=0.147  Sum_probs=130.4

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      ++++.+.+...+..+..   ++++|.++||.++.|+|          +++.||||||||++|.+|+++.+......+  +
T Consensus        23 ~L~~~l~~~L~~~g~~~---pt~IQ~~aIp~il~g~d----------vi~~a~TGSGKTlayllPil~~l~~~~~~~--~   87 (222)
T d2j0sa1          23 GLREDLLRGIYAYGFEK---PSAIQQRAIKQIIKGRD----------VIAQSQSGTGKTATFSISVLQCLDIQVRET--Q   87 (222)
T ss_dssp             CCCHHHHHHHHHHTCCS---CCHHHHHHHHHHHTTCC----------EEEECCTTSSHHHHHHHHHHHTCCTTSCSC--C
T ss_pred             CCCHHHHHHHHHCCCCC---CCHHHHHHHHHHHCCCC----------eEEEcCcchhhhhhhcccccccccccccCc--e
Confidence            35555555444444433   67899999999987654          667777999999999999999887655444  4


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc-----ccCCCCceEEEECchHHHHHHhcC-CCCCCccEE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK-----ELPRKRGSILYCTAGILPEVMQSD-PILSGVSHI  178 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~-----~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~v  178 (319)
                      .+++.||||||.|+++.+..+....    +..+........     .....+++|+|+|||++.+++... ..+++++++
T Consensus        88 ~lil~PtreLa~Qi~~~~~~l~~~~----~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~l  163 (222)
T d2j0sa1          88 ALILAPTRELAVQIQKGLLALGDYM----NVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKML  163 (222)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTT----TCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEE
T ss_pred             eEEecchHHHHHHHHHHHHHHhCcc----ceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceee
Confidence            5555699999999998877764322    333322221111     011135789999999999998544 458999999


Q ss_pred             EEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCCE
Q psy496          179 VMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAPI  230 (319)
Q Consensus       179 ViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~~  230 (319)
                      |+||||.. +..++...+...+...+++.|++++|||+  +.+.+++.+...|+
T Consensus       164 VlDEaD~l-l~~~f~~~i~~I~~~l~~~~Q~ilfSAT~~~~v~~l~~~~l~~Pv  216 (222)
T d2j0sa1         164 VLDEADEM-LNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPI  216 (222)
T ss_dssp             EEETHHHH-TSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCE
T ss_pred             eecchhHh-hhcCcHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCE
Confidence            99999972 44445555555556677889999999999  45677775554453

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=6.4e-29  Score=213.75  Aligned_cols=186  Identities=17%  Similarity=0.153  Sum_probs=130.1

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      .+++.+.+...+..+..   ++|+|+++||.+++|+|          ++++||||||||++|.+|+++++.....++  .
T Consensus         9 ~L~~~l~~~l~~~g~~~---pt~iQ~~aip~il~g~d----------vl~~a~TGsGKTlayllP~l~~~~~~~~~~--~   73 (206)
T d1veca_           9 CLKRELLMGIFEMGWEK---PSPIQEESIPIALSGRD----------ILARAKNGTGKSGAYLIPLLERLDLKKDNI--Q   73 (206)
T ss_dssp             CCCHHHHHHHHTTTCCS---CCHHHHHHHHHHHTTCC----------EEEECCSSSTTHHHHHHHHHHHCCTTSCSC--C
T ss_pred             CcCHHHHHHHHHCCCCC---CCHHHHHHHHHHHcCCC----------EEeeccCccccccccccchhhcccccccCc--c
Confidence            44555544443333332   67899999999997755          677777999999999999999876655544  4


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEec-----ccccCCCCceEEEECchHHHHHHhcC-CCCCCccEE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRL-----EKELPRKRGSILYCTAGILPEVMQSD-PILSGVSHI  178 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~-----~~~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~v  178 (319)
                      ++++.|+|+||.|+.+.+........   +.........     ........++|+|+|||++.+++..+ ..+++++++
T Consensus        74 ~lil~pt~el~~q~~~~~~~~~~~~~---~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~~~l~~l  150 (206)
T d1veca_          74 AMVIVPTRELALQVSQICIQVSKHMG---GAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMI  150 (206)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHTTTSS---SCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEE
T ss_pred             eEEEeecchhhHHHHHHHHHHhhccc---CcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchhccccccceE
Confidence            55566999999999988776644322   2222211111     11112346789999999999999554 458999999


Q ss_pred             EEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCC
Q psy496          179 VMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAP  229 (319)
Q Consensus       179 ViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~  229 (319)
                      |+||||.. +..++...+.+.+...+++.|++++|||+  +.+.+++.+.+.|
T Consensus       151 VlDEaD~l-l~~~f~~~i~~I~~~~~~~~Q~~l~SAT~~~~v~~l~~~~l~~P  202 (206)
T d1veca_         151 VLDEADKL-LSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKP  202 (206)
T ss_dssp             EEETHHHH-TSTTTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSC
T ss_pred             EEeccccc-cccchHHHHHHHHHhCCCCCEEEEEEecCCHHHHHHHHHHCCCC
Confidence            99999962 44455555555555677789999999999  4567777655544

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=2.2e-28  Score=212.15  Aligned_cols=189  Identities=19%  Similarity=0.150  Sum_probs=128.3

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      ++++.+.+...+..+..   ++++|+++||.++.|+|          ++++||||||||++|.+|+++.+.....+  .+
T Consensus        18 ~L~~~l~~~L~~~g~~~---pt~iQ~~aip~il~g~d----------vl~~a~TGsGKTlayllp~l~~i~~~~~~--~~   82 (218)
T d2g9na1          18 NLSESLLRGIYAYGFEK---PSAIQQRAILPCIKGYD----------VIAQAQSGTGKTATFAISILQQIELDLKA--TQ   82 (218)
T ss_dssp             CCCHHHHHHHHHHTCCS---CCHHHHHHHHHHHHTCC----------EEEECCTTSSHHHHHHHHHHHHCCTTCCS--CC
T ss_pred             CCCHHHHHHHHHCCCCC---CCHHHHHHHHHHHcCCC----------EEEEcccchhhhhhhhhhhhheecccccC--cc
Confidence            34555554443333333   67899999999987655          67777799999999999999988655444  45


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecc--cccCCCCceEEEECchHHHHHHhc-CCCCCCccEEEEe
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLE--KELPRKRGSILYCTAGILPEVMQS-DPILSGVSHIVMD  181 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~--~~~~~~~~~Iiv~Tpg~ll~~l~~-~~~l~~v~~vViD  181 (319)
                      +++++||++||.|+++.+...............+.....+  .......++|+|+|||++.+++.. ...+++++++|+|
T Consensus        83 alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVlD  162 (218)
T d2g9na1          83 ALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLD  162 (218)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEE
T ss_pred             EEEEcccchhhhhHHHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEEEee
Confidence            6666699999999999888775543211011111111111  111223578999999999999954 4559999999999


Q ss_pred             cccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCC
Q psy496          182 EIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAP  229 (319)
Q Consensus       182 Eah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~  229 (319)
                      |||+. ...++...+.+.+...+++.|++++|||+  +.+.+++.+...|
T Consensus       163 EaD~l-l~~~f~~~~~~Il~~~~~~~Q~il~SAT~~~~v~~~~~~~l~~p  211 (218)
T d2g9na1         163 EADEM-LSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDP  211 (218)
T ss_dssp             SHHHH-HHTTCHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSC
T ss_pred             ecchh-hcCchHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHCCCC
Confidence            99972 33334444555555567789999999999  4567776554444

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.94  E-value=4.3e-28  Score=209.41  Aligned_cols=190  Identities=18%  Similarity=0.153  Sum_probs=128.5

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      ++++.+.+...+.++..   ++++|.++||.+++|+|          ++++||||||||.+|.+|+++++.....++  .
T Consensus        16 ~l~~~l~~~L~~~g~~~---pt~iQ~~aip~il~g~d----------vl~~a~TGsGKT~a~~lp~i~~l~~~~~~~--~   80 (212)
T d1qdea_          16 ELDENLLRGVFGYGFEE---PSAIQQRAIMPIIEGHD----------VLAQAQSGTGKTGTFSIAALQRIDTSVKAP--Q   80 (212)
T ss_dssp             TCCHHHHHHHHHHTCCS---CCHHHHHHHHHHHTTCC----------EEEECCTTSSHHHHHHHHHHHHCCTTCCSC--C
T ss_pred             CCCHHHHHHHHHCCCCC---CCHHHHHHHHHHHcCCC----------EEeecccccchhhhhHhhhHhhhhccCCCc--c
Confidence            34555555444443333   67899999999987544          677777999999999999999987655544  5


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecc
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEI  183 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEa  183 (319)
                      +++++||++++.|....+...............+.....++.....+++|+|+|||++.+++.... .+++++++|+|||
T Consensus        81 ~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEa  160 (212)
T d1qdea_          81 ALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEA  160 (212)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CTTCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETH
T ss_pred             eEEEcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHHhcCCcEEEECCCccccccccCceecCcceEEeehhh
Confidence            555669999999999888765432210001111111111122222457899999999999995544 5999999999999


Q ss_pred             cccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCCE
Q psy496          184 HERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAPI  230 (319)
Q Consensus       184 h~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~~  230 (319)
                      |.. ...++...+.+.+...+++.|++++|||+  +.+.+++.+...|+
T Consensus       161 d~l-ld~~f~~~v~~I~~~~~~~~Q~vl~SAT~~~~v~~l~~~~l~~Pv  208 (212)
T d1qdea_         161 DEM-LSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPV  208 (212)
T ss_dssp             HHH-HHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCE
T ss_pred             hhh-cccchHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHHCCCCE
Confidence            972 33345555555555577788999999999  45788887665553

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=7.8e-28  Score=207.04  Aligned_cols=186  Identities=16%  Similarity=0.111  Sum_probs=126.7

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      ++++.+.+...+..+..   ++|+|.++||.+++|+          ++++.||||||||++|.+|+++.+.....+  .+
T Consensus         7 ~L~~~l~~~l~~~g~~~---pt~iQ~~aip~il~g~----------dvl~~A~TGsGKTla~~lp~l~~~~~~~~~--~~   71 (207)
T d1t6na_           7 LLKPELLRAIVDCGFEH---PSEVQHECIPQAILGM----------DVLCQAKSGMGKTAVFVLATLQQLEPVTGQ--VS   71 (207)
T ss_dssp             CCCHHHHHHHHHTTCCC---CCHHHHHHHHHHHTTC----------CEEEECCTTSCHHHHHHHHHHHHCCCCTTC--CC
T ss_pred             CcCHHHHHHHHHCCCCC---CCHHHHHHHHHHHcCC----------CeEEEeccccccccccccceeeeecccCCC--ce
Confidence            34554554444443333   6789999999999765          477777799999999999999887554433  45


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecc------cccCCCCceEEEECchHHHHHHhcCC-CCCCccE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLE------KELPRKRGSILYCTAGILPEVMQSDP-ILSGVSH  177 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~------~~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~  177 (319)
                      +++++|+|+||.|+.+.+........   ...........      .......++|+|+|||++.+++..+. .++++++
T Consensus        72 ~lil~PtreL~~qi~~~~~~~~~~~~---~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~  148 (207)
T d1t6na_          72 VLVMCHTRELAFQISKEYERFSKYMP---NVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKH  148 (207)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHTTTST---TCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCE
T ss_pred             EEEEeccchhhHHHHHHHHHHHhhCC---CceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccce
Confidence            66667999999999998877644321   11122111110      11111357899999999999996544 5899999


Q ss_pred             EEEecccccccc-hhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCC
Q psy496          178 IVMDEIHERSMI-SDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAP  229 (319)
Q Consensus       178 vViDEah~~~~~-~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~  229 (319)
                      +|+||||+. +. .++.....+.+...+++.|++++|||+  +.+.+++.+-..|
T Consensus       149 lVlDEaD~l-l~~~~~~~~i~~I~~~~~~~~Q~il~SAT~~~~v~~l~~~~l~~P  202 (207)
T d1t6na_         149 FILDECDKM-LEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDP  202 (207)
T ss_dssp             EEEESHHHH-HSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSC
T ss_pred             eehhhhhhh-hhcCCcHHHHHHHHHhCCCCCEEEEEeeeCCHHHHHHHHHHCCCC
Confidence            999999972 22 234433444444566788999999999  5677777554444

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.93  E-value=5.7e-27  Score=201.71  Aligned_cols=183  Identities=17%  Similarity=0.206  Sum_probs=126.1

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      ++++.+.+...+..+..   ++|+|.++||.++.|+         .+++++||||||||.+|.+|+++.....   ...+
T Consensus        10 ~l~~~l~~~l~~~g~~~---pt~iQ~~~ip~~l~g~---------~d~iv~a~TGsGKT~~~~l~~~~~~~~~---~~~~   74 (208)
T d1hv8a1          10 NLSDNILNAIRNKGFEK---PTDIQMKVIPLFLNDE---------YNIVAQARTGSGKTASFAIPLIELVNEN---NGIE   74 (208)
T ss_dssp             SCCHHHHHHHHHHTCCS---CCHHHHHHHHHHHHTC---------SEEEEECCSSSSHHHHHHHHHHHHSCSS---SSCC
T ss_pred             CCCHHHHHHHHHCCCCC---CCHHHHHHHHHHHcCC---------CCeeeechhcccccceeecccccccccc---cCcc
Confidence            46766666544444433   5688999999988753         3578888899999999999998764432   2456


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc----ccCCCCceEEEECchHHHHHHhcCC-CCCCccEEE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK----ELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIV  179 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~----~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vV  179 (319)
                      +++++||++||.|+.+.+..+....    +..+........    .....+++|+|+|||++.+++..+. .+++++++|
T Consensus        75 ~lil~pt~~l~~q~~~~~~~~~~~~----~~~v~~~~g~~~~~~~~~~l~~~~IlV~TP~~l~~~l~~~~~~~~~l~~lV  150 (208)
T d1hv8a1          75 AIILTPTRELAIQVADEIESLKGNK----NLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRGTLNLKNVKYFI  150 (208)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHHCSS----CCCEEEECTTSCHHHHHHHHHTCSEEEECHHHHHHHHHTTCSCTTSCCEEE
T ss_pred             eEEEeeccccchhhhhhhhhhcccC----CeEEEEeeCCCChHHHHHhcCCCCEEEEChHHHHHHHHcCCCCcccCcEEE
Confidence            7777799999999999888775433    333332211111    0011357899999999999995544 599999999


Q ss_pred             EecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhh-hhCC
Q psy496          180 MDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQ-FFGG  227 (319)
Q Consensus       180 iDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~-~l~~  227 (319)
                      +||||.. ...++...+.+.+...+++.|++++|||+  +...+++ |+.+
T Consensus       151 iDEad~l-~~~~~~~~i~~I~~~~~~~~Q~i~~SAT~~~~v~~~~~~~l~~  200 (208)
T d1hv8a1         151 LDEADEM-LNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGD  200 (208)
T ss_dssp             EETHHHH-HTTTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCS
T ss_pred             EEChHHh-hcCCChHHHHHHHHhCCCCCeEEEEEccCCHHHHHHHHHHCCC
Confidence            9999962 22333333444445566788999999999  3456665 4543

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=99.92  E-value=8.1e-26  Score=198.36  Aligned_cols=171  Identities=19%  Similarity=0.140  Sum_probs=117.4

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhC-------CCCccEEEEecccHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARN-------RGSECCIMVTQPRRISAIA  117 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~-------~~~~~~vl~~~Ptr~la~q  117 (319)
                      ++++|..+||.++.|+          +++++||||||||++|.+|+++.+....       .....++++++||++||.|
T Consensus        44 pt~iQ~~~ip~il~g~----------dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~~~alil~pt~el~~q  113 (238)
T d1wrba1          44 PTPIQKNAIPAILEHR----------DIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQ  113 (238)
T ss_dssp             CCHHHHHHHHHHHTTC----------CEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHH
T ss_pred             CCHHHHHHhhhhhCCC----------CEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCCCceEEEeccchhhhcc
Confidence            6789999999998654          5788888999999999999999985432       2234567777799999999


Q ss_pred             HHHHHHHHhccccCCCCceEEEEEec-----ccccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchh
Q psy496          118 IAERVAQERDEQCGRPGSSVGYQIRL-----EKELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISD  191 (319)
Q Consensus       118 ~~~~~~~~~~~~~~~~g~~vg~~~~~-----~~~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~  191 (319)
                      +.+.+.......    +..+......     +......+++|+|+|||+|.+++..+. .+.+++++|+||+|.. +..+
T Consensus       114 ~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v~~lViDEaD~l-l~~~  188 (238)
T d1wrba1         114 ILSESQKFSLNT----PLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRM-LDMG  188 (238)
T ss_dssp             HHHHHHHHHTTS----SCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHH-HHTT
T ss_pred             hheeeeecccCC----CcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceeccccceeeeehhhhh-hhhc
Confidence            998776654322    2222211111     111222467899999999999995544 5999999999999972 2222


Q ss_pred             HHHHHHHhhhc----cccCceEEEecccc--ChhhHhhhhCCCCE
Q psy496          192 FLLAILKDVTD----KRKDLKLILMSATL--NAEKFSQFFGGAPI  230 (319)
Q Consensus       192 ~~~~~l~~~~~----~~~~~qiv~lSAT~--~~~~l~~~l~~~~~  230 (319)
                      +...+.+.+..    ...+.|++++|||+  +.+.+++-|...|+
T Consensus       189 f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~  233 (238)
T d1wrba1         189 FEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYI  233 (238)
T ss_dssp             CHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCE
T ss_pred             cHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHHHHHHHCCCCE
Confidence            23222222222    22367999999999  56777765444443

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.92  E-value=1.9e-25  Score=191.77  Aligned_cols=189  Identities=17%  Similarity=0.118  Sum_probs=126.1

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      ++++.+.+..-+..+..   ++++|+++||.+++|+|          ++++||||||||++|.+|+++.+......  ..
T Consensus         7 ~L~~~l~~~l~~~g~~~---pt~iQ~~aip~~l~G~d----------vii~a~TGSGKTlayllp~l~~~~~~~~~--~~   71 (209)
T d1q0ua_           7 PFQPFIIEAIKTLRFYK---PTEIQERIIPGALRGES----------MVGQSQTGTGKTHAYLLPIMEKIKPERAE--VQ   71 (209)
T ss_dssp             CCCHHHHHHHHHTTCCS---CCHHHHHHHHHHHHTCC----------EEEECCSSHHHHHHHHHHHHHHCCTTSCS--CC
T ss_pred             CcCHHHHHHHHHCCCCC---CCHHHHHHHHHHHCCCC----------eEeecccccccceeeeeeecccccccccc--cc
Confidence            45665555443333322   67899999999998664          77777799999999999999887654433  45


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecc-----cccCCCCceEEEECchHHHHHHhcC-CCCCCccEE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLE-----KELPRKRGSILYCTAGILPEVMQSD-PILSGVSHI  178 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~-----~~~~~~~~~Iiv~Tpg~ll~~l~~~-~~l~~v~~v  178 (319)
                      .+++.|+++++.+.++.+..............+.......     ......+++|+|+||+++.+++.+. ..+++++++
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l~~l  151 (209)
T d1q0ua_          72 AVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHIL  151 (209)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEE
T ss_pred             ccccccccchhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhccccccceEE
Confidence            5666699999999887766553322111122222111111     1112245789999999999998554 458999999


Q ss_pred             EEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCC
Q psy496          179 VMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAP  229 (319)
Q Consensus       179 ViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~  229 (319)
                      |+||||.. ...++...+...+...+++.|++++|||+  +.+.+++.+...|
T Consensus       152 ViDEad~l-l~~~f~~~v~~I~~~~~~~~Q~il~SATl~~~v~~l~~~~l~~p  203 (209)
T d1q0ua_         152 VVDEADLM-LDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENP  203 (209)
T ss_dssp             EECSHHHH-HHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSC
T ss_pred             EEeecccc-cccccHHHHHHHHHHCCCCCEEEEEEccCCHHHHHHHHHHCCCC
Confidence            99999972 22233444444445567789999999999  5567776544333

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.92  E-value=2e-25  Score=191.60  Aligned_cols=185  Identities=18%  Similarity=0.092  Sum_probs=129.8

Q ss_pred             cccccccchHHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccE
Q psy496           25 QVPQFILDDEIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECC  104 (319)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~  104 (319)
                      ++++.+.+...+..+..   ++|+|..+||+++.|+|          +++.||||||||++|.+|+++.+.....+.  +
T Consensus         7 ~L~~~l~~~L~~~g~~~---pt~iQ~~aip~il~g~d----------vi~~a~tGsGKTlay~lp~i~~~~~~~~~~--~   71 (206)
T d1s2ma1           7 YLKRELLMGIFEAGFEK---PSPIQEEAIPVAITGRD----------ILARAKNGTGKTAAFVIPTLEKVKPKLNKI--Q   71 (206)
T ss_dssp             CCCHHHHHHHHHTTCCS---CCHHHHHHHHHHHHTCC----------EEEECCTTSCHHHHHHHHHHHHCCTTSCSC--C
T ss_pred             CCCHHHHHHHHHCCCCC---CCHHHHHHHHHHHcCCC----------EEEecCCcchhhhhhccccccccccccccc--c
Confidence            45655555554444433   67899999999998655          677777999999999999999876655443  4


Q ss_pred             EEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecc-----cccCCCCceEEEECchHHHHHHhcCC-CCCCccEE
Q psy496          105 IMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLE-----KELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHI  178 (319)
Q Consensus       105 vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~-----~~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~v  178 (319)
                      .+++.|+++++.+............    +..+.......     .......++|+|+|||+|.+++.... .+.+++++
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~l  147 (206)
T d1s2ma1          72 ALIMVPTRELALQTSQVVRTLGKHC----GISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLF  147 (206)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTT----TCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEE
T ss_pred             ceeeccchhhhhhhhhhhhhccccc----CeeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeecccceEE
Confidence            5556699999999988776654322    33333222111     11122468899999999999996544 48999999


Q ss_pred             EEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHhhhhCCCC
Q psy496          179 VMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFSQFFGGAP  229 (319)
Q Consensus       179 ViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~~~l~~~~  229 (319)
                      |+||||.. +..++...+...+...+++.|++++|||+  +...+++.+...|
T Consensus       148 V~DEaD~l-~~~~f~~~v~~I~~~l~~~~Q~il~SATl~~~v~~~~~~~l~~P  199 (206)
T d1s2ma1         148 IMDEADKM-LSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKP  199 (206)
T ss_dssp             EEESHHHH-SSHHHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSC
T ss_pred             Eeechhhh-hhhhhHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCC
Confidence            99999973 34445555555555577788999999999  5567776554444

>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=99.90  E-value=5.2e-25  Score=188.15  Aligned_cols=166  Identities=17%  Similarity=0.169  Sum_probs=118.5

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++|.|.++++.+.+          +++++++||||||||+++.++++..+...+     ++++++|+++|+.|..+++.+
T Consensus        26 l~~~Q~~ai~~l~~----------~~~~il~apTGsGKT~~a~l~i~~~~~~~~-----~vl~l~P~~~L~~q~~~~~~~   90 (202)
T d2p6ra3          26 LFPPQAEAVEKVFS----------GKNLLLAMPTAAGKTLLAEMAMVREAIKGG-----KSLYVVPLRALAGEKYESFKK   90 (202)
T ss_dssp             CCCCCHHHHHHHTT----------CSCEEEECSSHHHHHHHHHHHHHHHHHTTC-----CEEEEESSHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHc----------CCCEEEEcCCCCchhHHHHHHHHHHhhccC-----cceeecccHHHHHHHHHHHHH
Confidence            56899999988653          467899999999999999999988765433     678888999999999998876


Q ss_pred             HhccccCCCCceEEEEEe--cccccCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccc--hhHHHHHHHh
Q psy496          125 ERDEQCGRPGSSVGYQIR--LEKELPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMI--SDFLLAILKD  199 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~--~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~--~~~~~~~l~~  199 (319)
                      +....     ..++....  ...........++++||..+...+.... .+.++++||+||+|.....  .......++.
T Consensus        91 ~~~~~-----~~v~~~~~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~~r~~~~~~~l~~  165 (202)
T d2p6ra3          91 WEKIG-----LRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTK  165 (202)
T ss_dssp             TTTTT-----CCEEEECSSCBCCSSCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHHHHH
T ss_pred             Hhhcc-----ccceeeccCcccccccccccceeeeccHHHHHHHhccchhhhhhhhccccHHHHhcccccchHHHHHHHH
Confidence            54422     12221111  1111112356799999999988885544 4889999999999963211  1123334455


Q ss_pred             hhccccCceEEEecccc-ChhhHhhhhCCCCE
Q psy496          200 VTDKRKDLKLILMSATL-NAEKFSQFFGGAPI  230 (319)
Q Consensus       200 ~~~~~~~~qiv~lSAT~-~~~~l~~~l~~~~~  230 (319)
                      +...+++.|+|+||||+ |++++++|++....
T Consensus       166 i~~~~~~~~~l~lSATl~n~~~~~~~l~~~~~  197 (202)
T d2p6ra3         166 MRRMNKALRVIGLSATAPNVTEIAEWLDADYY  197 (202)
T ss_dssp             HHHHCTTCEEEEEECCCTTHHHHHHHTTCEEE
T ss_pred             HHhcCCCCcEEEEcCCCCcHHHHHHHcCCCee
Confidence            55556688999999999 99999999965433

>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=99.83  E-value=6e-21  Score=171.59  Aligned_cols=136  Identities=18%  Similarity=0.133  Sum_probs=95.9

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE  146 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~  146 (319)
                      .++++++|.||||||||++|+.++++.....+    .++++++|||+||.|++++++.......   ...      .+. 
T Consensus         7 ~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~----~~~lvi~Ptr~La~q~~~~l~~~~~~~~---~~~------~~~-   72 (305)
T d2bmfa2           7 RKKRLTIMDLHPGAGKTKRYLPAIVREAIKRG----LRTLILAPTRVVAAEMEEALRGLPIRYQ---TPA------IRA-   72 (305)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHHT----CCEEEEESSHHHHHHHHHHTTTSCCBCC---C------------
T ss_pred             hcCCcEEEEECCCCCHHHHHHHHHHHHHHhcC----CEEEEEccHHHHHHHHHHHHhcCCccee---eeE------Eee-
Confidence            46788999999999999999888887665543    2677778999999999987765421111   111      111 


Q ss_pred             cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEeccccC
Q psy496          147 LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATLN  217 (319)
Q Consensus       147 ~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~~  217 (319)
                      .......++++|++.+..++.....+.+++++|+||+|............++.+.. .+..+++++|||++
T Consensus        73 ~~~~~~~i~~~t~~~l~~~~~~~~~~~~~~~vViDE~H~~~~~~~~~~~~l~~~~~-~~~~~~v~~SAT~~  142 (305)
T d2bmfa2          73 EHTGREIVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTDPASIAARGYISTRVE-MGEAAGIFMTATPP  142 (305)
T ss_dssp             ---CCCSEEEEEHHHHHHHHTSSSCCCCCSEEEEESTTCCSHHHHHHHHHHHHHHH-HTSCEEEEECSSCT
T ss_pred             cccCccccccCCcHHHHHHHhcCccccceeEEEeeeeeecchhhHHHHHHHHHhhc-cccceEEEeecCCC
Confidence            11234569999999998888777778999999999999854333334444444332 35679999999983

>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=99.81  E-value=8.1e-21  Score=165.72  Aligned_cols=154  Identities=18%  Similarity=0.089  Sum_probs=98.2

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ++++|+.+||.++.|+          +++++||||||||+++.++++.....+     .+++++.|+++|+.|+++++.+
T Consensus        44 p~~~Q~~~i~~~l~g~----------~~~i~apTGsGKT~~~~~~~~~~~~~~-----~rvliv~Pt~~La~Q~~~~l~~  108 (237)
T d1gkub1          44 PRAIQKMWAKRILRKE----------SFAATAPTGVGKTSFGLAMSLFLALKG-----KRCYVIFPTSLLVIQAAETIRK  108 (237)
T ss_dssp             CCHHHHHHHHHHHTTC----------CEECCCCBTSCSHHHHHHHHHHHHTTS-----CCEEEEESCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHCCC----------CEEEEecCCChHHHHHHHHHHHHHHhc-----CeEEEEeccHHHHHHHHHHHHH
Confidence            4688999999988654          477778899999999998887654432     2677777999999999999888


Q ss_pred             HhccccCCCCceEEEEEecccc-------cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccc---hhHHH
Q psy496          125 ERDEQCGRPGSSVGYQIRLEKE-------LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMI---SDFLL  194 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~~~~~-------~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~---~~~~~  194 (319)
                      +........+...+........       ......+|+|+||++|.+...   .+++++++|+||+|...-.   .+...
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~~~---~~~~~~~vVvDE~d~~l~~~~~~~~~~  185 (237)
T d1gkub1         109 YAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYR---ELGHFDFIFVDDVDAILKASKNVDKLL  185 (237)
T ss_dssp             HHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCST---TSCCCSEEEESCHHHHHTSTHHHHHHH
T ss_pred             HHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHhhh---hcCCCCEEEEEChhhhhhcccchhHHH
Confidence            7543211112222211111000       011245799999998876542   4678999999999962111   11111


Q ss_pred             HHHH-------hhhccccCceEEEecccc
Q psy496          195 AILK-------DVTDKRKDLKLILMSATL  216 (319)
Q Consensus       195 ~~l~-------~~~~~~~~~qiv~lSAT~  216 (319)
                      ..+.       .........|++++|||+
T Consensus       186 ~~~g~~~~~~~~~~~~~~~~~~i~~SAT~  214 (237)
T d1gkub1         186 HLLGFHYDLKTKSWVGEARGCLMVSTATA  214 (237)
T ss_dssp             HHTTEEEETTTTEEEECCSSEEEECCCCS
T ss_pred             HhcCChHHHHHHHhhCCCCCeEEEEeCCC
Confidence            1110       111133466899999999

>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=99.80  E-value=2.1e-20  Score=159.49  Aligned_cols=171  Identities=15%  Similarity=0.074  Sum_probs=107.2

Q ss_pred             cccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHH
Q psy496           45 IMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQ  124 (319)
Q Consensus        45 ~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~  124 (319)
                      ..|.|.++|+++.+|          +++++++|||||||.+|.+|++..        ..+++++.|+++|+.|..+.+..
T Consensus        26 ~rp~Q~~ai~~~l~g----------~~vlv~apTGsGKT~~~~~~~~~~--------~~~~~~v~P~~~L~~q~~~~l~~   87 (206)
T d1oywa2          26 FRPGQEEIIDTVLSG----------RDCLVVMPTGGGKSLCYQIPALLL--------NGLTVVVSPLISLMKDQVDQLQA   87 (206)
T ss_dssp             CCTTHHHHHHHHHTT----------CCEEEECSCHHHHHHHHHHHHHHS--------SSEEEEECSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHcC----------CCEEEEcCCCCCCcchhhhhhhhc--------cCceEEeccchhhhhhHHHHHHh
Confidence            458899999987653          458888899999999999998652        23677888999999999998876


Q ss_pred             HhccccCCCCceEEEEEe-cccccCCCCceEEEECchHHHHHH-hcCCCCCCccEEEEecccccccc---hhHHHHHHHh
Q psy496          125 ERDEQCGRPGSSVGYQIR-LEKELPRKRGSILYCTAGILPEVM-QSDPILSGVSHIVMDEIHERSMI---SDFLLAILKD  199 (319)
Q Consensus       125 ~~~~~~~~~g~~vg~~~~-~~~~~~~~~~~Iiv~Tpg~ll~~l-~~~~~l~~v~~vViDEah~~~~~---~~~~~~~l~~  199 (319)
                      .........+...+.... ...........|+++||..+.... .......+++++|+||+|.....   .......+..
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~~~~~~~~~~~~~~~~~  167 (206)
T d1oywa2          88 NGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQ  167 (206)
T ss_dssp             TTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCCCHHHHGGGG
T ss_pred             hcccccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcccchhheeeeeeeeeeeeeeccccchHHHHHHHHH
Confidence            633211000000000000 000001134679999998875443 22334678999999999962111   1111122233


Q ss_pred             hhccccCceEEEeccccCh---hhHhhhhC-CCCEEEe
Q psy496          200 VTDKRKDLKLILMSATLNA---EKFSQFFG-GAPILHI  233 (319)
Q Consensus       200 ~~~~~~~~qiv~lSAT~~~---~~l~~~l~-~~~~i~~  233 (319)
                      +....++.|+++||||++.   +++.++++ +.|++.+
T Consensus       168 l~~~~~~~~ii~lSATl~~~v~~di~~~L~l~~p~v~v  205 (206)
T d1oywa2         168 LRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQI  205 (206)
T ss_dssp             HHHHCTTSCEEEEESCCCHHHHHHHHHHHTCCSCEEEE
T ss_pred             HHHhCCCCceEEEEeCCCHHHHHHHHHHcCCCCCcEEe
Confidence            3334467899999999944   47888875 5555443

>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=99.80  E-value=4e-19  Score=140.86  Aligned_cols=136  Identities=20%  Similarity=0.114  Sum_probs=96.7

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccc
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEK  145 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~  145 (319)
                      ..++++++|++|||||||.+++..++......+    .+++++.|+++++.|..+.+...          ..++......
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~~----~~vli~~p~~~l~~q~~~~~~~~----------~~~~~~~~~~   69 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECARRR----LRTLVLAPTRVVLSEMKEAFHGL----------DVKFHTQAFS   69 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTT----CCEEEEESSHHHHHHHHHHTTTS----------CEEEESSCCC
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhhcC----ceeeeeecchhHHHHHHHHhhhh----------hhhhcccccc
Confidence            356899999999999999998777776665543    37788889999999988765322          2232222222


Q ss_pred             ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          146 ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       146 ~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      ........+.+.|...+.+.......+.++++||+||+|..+.........+..... .++.++|+||||+
T Consensus        70 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~-~~~~~~l~lTATP  139 (140)
T d1yksa1          70 AHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR-ANESATILMTATP  139 (140)
T ss_dssp             CCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHH-TTSCEEEEECSSC
T ss_pred             cccccccchhhhhHHHHHHHHhccccccceeEEEEccccccChhhHHHHHHHHHHhh-CCCCCEEEEEcCC
Confidence            222234568888888888888777789999999999999854444444444444433 3467999999997

>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=99.79  E-value=4.8e-20  Score=156.13  Aligned_cols=148  Identities=17%  Similarity=0.139  Sum_probs=99.4

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc---
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE---  146 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~---  146 (319)
                      +|+++++|||||||.++.+++...+...+    .++++++|+++|+.|.++.+.+.++..    +..++........   
T Consensus        24 ~n~lv~~pTGsGKT~i~~~~~~~~~~~~~----~~il~i~P~~~L~~q~~~~~~~~~~~~----~~~v~~~~~~~~~~~~   95 (200)
T d1wp9a1          24 TNCLIVLPTGLGKTLIAMMIAEYRLTKYG----GKVLMLAPTKPLVLQHAESFRRLFNLP----PEKIVALTGEKSPEER   95 (200)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHHHSC----SCEEEECSSHHHHHHHHHHHHHHBCSC----GGGEEEECSCSCHHHH
T ss_pred             CCeEEEeCCCCcHHHHHHHHHHHHHHhcC----CcEEEEcCchHHHHHHHHHHHHhhccc----ccceeeeecccchhHH
Confidence            57899999999999998888776654432    268888899999999999999886543    2233211111000   


Q ss_pred             -cCCCCceEEEECchHHHHHHhcCC-CCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc--ChhhHh
Q psy496          147 -LPRKRGSILYCTAGILPEVMQSDP-ILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL--NAEKFS  222 (319)
Q Consensus       147 -~~~~~~~Iiv~Tpg~ll~~l~~~~-~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~--~~~~l~  222 (319)
                       ....+.+++++||+.+...+.... .+++++++|+||+|....... .......+.....+.+++++|||+  +.+.+.
T Consensus        96 ~~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~~~-~~~~~~~~~~~~~~~~~l~~SATp~~~~~~~~  174 (200)
T d1wp9a1          96 SKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYA-YVFIAREYKRQAKNPLVIGLTASPGSTPEKIM  174 (200)
T ss_dssp             HHHHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCH-HHHHHHHHHHHCSSCCEEEEESCSCSSHHHHH
T ss_pred             HHhhhcccccccccchhHHHHhhhhhhccccceEEEEehhhhhcchh-HHHHHHHHHhcCCCCcEEEEEecCCCcHHHHH
Confidence             001234699999999998885544 478999999999997432222 222222333334466899999999  456666


Q ss_pred             hhhC
Q psy496          223 QFFG  226 (319)
Q Consensus       223 ~~l~  226 (319)
                      +++.
T Consensus       175 ~~~~  178 (200)
T d1wp9a1         175 EVIN  178 (200)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            6554

>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=99.78  E-value=6.2e-19  Score=140.42  Aligned_cols=131  Identities=17%  Similarity=0.185  Sum_probs=91.6

Q ss_pred             CCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccc
Q psy496           67 PILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKE  146 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~  146 (319)
                      +++++.+|.||||||||+.++..+.+      .  ..++++++|+++|+.|..+++.+.++...       +....... 
T Consensus         6 ~~~~~~ll~apTGsGKT~~~~~~~~~------~--~~~vli~~P~~~l~~q~~~~~~~~~~~~~-------~~~~~~~~-   69 (136)
T d1a1va1           6 QSFQVAHLHAPTGSGKSTKVPAAYAA------Q--GYKVLVLNPSVAATLGFGAYMSKAHGVDP-------NIRTGVRT-   69 (136)
T ss_dssp             SSCEEEEEECCTTSCTTTHHHHHHHT------T--TCCEEEEESCHHHHHHHHHHHHHHHSCCC-------EEECSSCE-
T ss_pred             cCCCEEEEEeCCCCCHHHHHHHHHHH------c--CCcEEEEcChHHHHHHHHHHHHHHhhccc-------cccccccc-
Confidence            35688999999999999876554321      1  22677778999999999999988765432       22222221 


Q ss_pred             cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          147 LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       147 ~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                       ......+.++|.+.+....  ...+.++++||+||+|+.+...+.....+.......++.+++++|||+
T Consensus        70 -~~~~~~~~~~~~~~~~~~~--~~~~~~~~~vIiDE~H~~~~~~~~~~~~~l~~~~~~~~~~~l~~TATP  136 (136)
T d1a1va1          70 -ITTGSPITYSTYGKFLADG--GCSGGAYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLATATP  136 (136)
T ss_dssp             -ECCCCSEEEEEHHHHHHTT--GGGGCCCSEEEEETTTCCSHHHHHHHHHHHHHTTTTTCSEEEEEESSC
T ss_pred             -cccccceEEEeeeeecccc--chhhhcCCEEEEecccccCHHHHHHHHHHHHHHHHCCCCcEEEEeCCC
Confidence             1234568899998776554  235789999999999986555554455555555556677999999995

>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=99.63  E-value=1e-15  Score=134.46  Aligned_cols=170  Identities=20%  Similarity=0.212  Sum_probs=112.7

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVA  123 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~  123 (319)
                      +.|.-|.+++.-+..  |+-  .+..-+-+|+|.||||||.+++..++..+..+.     .++++.||..||.|.++++.
T Consensus        83 eLT~~Q~~ai~ei~~--d~~--~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~-----q~~~m~Pt~~La~Qh~~~~~  153 (264)
T d1gm5a3          83 KLTNAQKRAHQEIRN--DMI--SEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGF-----QTAFMVPTSILAIQHYRRTV  153 (264)
T ss_dssp             CCCHHHHHHHHHHHH--HHH--SSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTS-----CEEEECSCHHHHHHHHHHHH
T ss_pred             cCCchHHHHHHHHHH--Hhh--ccCcceeeeeccccccccHHHHHHHHHHHhccc-----ceeEEeehHhhhHHHHHHHH
Confidence            456678888776654  321  334457899999999999999999988776654     56666699999999999999


Q ss_pred             HHhccccCCCCceEEEEEecccc---------cCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHH
Q psy496          124 QERDEQCGRPGSSVGYQIRLEKE---------LPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLL  194 (319)
Q Consensus       124 ~~~~~~~~~~g~~vg~~~~~~~~---------~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~  194 (319)
                      +.+...    |..+..-......         ..+...+|+|||.--+.    .+..+++++++||||-|+.|....   
T Consensus       154 ~~f~~~----~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~----~~~~f~~LglviiDEqH~fgv~Qr---  222 (264)
T d1gm5a3         154 ESFSKF----NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQ----EDVHFKNLGLVIIDEQHRFGVKQR---  222 (264)
T ss_dssp             HHHTCS----SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHH----HCCCCSCCCEEEEESCCCC--------
T ss_pred             Hhhhhc----cccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhc----CCCCccccceeeeccccccchhhH---
Confidence            988643    3333311110000         01235789999987544    334578999999999998665432   


Q ss_pred             HHHHhhhccccCceEEEeccccChhhHhh-hhCCCCEEEeCCc
Q psy496          195 AILKDVTDKRKDLKLILMSATLNAEKFSQ-FFGGAPILHIPGF  236 (319)
Q Consensus       195 ~~l~~~~~~~~~~qiv~lSAT~~~~~l~~-~l~~~~~i~~~~r  236 (319)
                         ..+.....+..++++|||+-++.++. .+|+-.+..+..+
T Consensus       223 ---~~l~~~~~~~~~l~~SATPiprtl~~~~~g~~~~s~i~e~  262 (264)
T d1gm5a3         223 ---EALMNKGKMVDTLVMSATPIPRSMALAFYGDLDVTVIDEM  262 (264)
T ss_dssp             ---CCCCSSSSCCCEEEEESSCCCHHHHHHHTCCSSCEEECCC
T ss_pred             ---HHHHHhCcCCCEEEEECCCCHHHHHHHHcCCCCeEeeCCC
Confidence               12222334567999999996666654 5666666655544

>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=99.62  E-value=4.5e-15  Score=128.02  Aligned_cols=161  Identities=16%  Similarity=0.157  Sum_probs=109.5

Q ss_pred             ccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHH
Q psy496           42 ECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAER  121 (319)
Q Consensus        42 ~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~  121 (319)
                      +...++-|.+++..+...-    ..+...+.+|+|.||||||.+|+..+...+..+.     .++++.|+..||.|.+++
T Consensus        53 P~~lt~~Q~~~~~~i~~~~----~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~-----qv~~l~Pt~~La~Q~~~~  123 (233)
T d2eyqa3          53 PFETTPDQAQAINAVLSDM----CQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHK-----QVAVLVPTTLLAQQHYDN  123 (233)
T ss_dssp             CSCCCHHHHHHHHHHHHHH----HSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTC-----EEEEECSSHHHHHHHHHH
T ss_pred             ccccchhHHHHHHHHHHHH----hccCccCeEEEcCCCCCcHHHHHHHHHHHHHcCC-----ceEEEccHHHhHHHHHHH
Confidence            4445666888876665421    2444568999999999999999999888765433     677777999999999999


Q ss_pred             HHHHhccccCCCCceEEEEEeccc---------ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhH
Q psy496          122 VAQERDEQCGRPGSSVGYQIRLEK---------ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDF  192 (319)
Q Consensus       122 ~~~~~~~~~~~~g~~vg~~~~~~~---------~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~  192 (319)
                      +.+.++..    +..+..-.....         .....+.+|+|+|--.+.    ....++++++|||||-|+.|....-
T Consensus       124 ~~~~~~~~----~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~----~~~~f~~LgLiIiDEeH~fg~kQ~~  195 (233)
T d2eyqa3         124 FRDRFANW----PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ----SDVKFKDLGLLIVDEEHRFGVRHKE  195 (233)
T ss_dssp             HHHHSTTT----TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH----SCCCCSSEEEEEEESGGGSCHHHHH
T ss_pred             HHHHHhhC----CCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc----cCCccccccceeeechhhhhhHHHH
Confidence            99886643    333331111100         011235689999987544    3345789999999999987654432


Q ss_pred             HHHHHHhhhccccCceEEEeccccChhhHhhhh
Q psy496          193 LLAILKDVTDKRKDLKLILMSATLNAEKFSQFF  225 (319)
Q Consensus       193 ~~~~l~~~~~~~~~~qiv~lSAT~~~~~l~~~l  225 (319)
                      .   ++   ....+..++++|||+-++.++.-.
T Consensus       196 ~---l~---~~~~~~~~l~~SATPiprtl~~~~  222 (233)
T d2eyqa3         196 R---IK---AMRANVDILTLTATPIPRTLNMAM  222 (233)
T ss_dssp             H---HH---HHHTTSEEEEEESSCCCHHHHHHH
T ss_pred             H---HH---hhCCCCCEEEEecchhHHHHHHHH
Confidence            1   22   223466899999999777766543

>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=99.46  E-value=5.3e-14  Score=119.44  Aligned_cols=131  Identities=18%  Similarity=0.124  Sum_probs=81.5

Q ss_pred             HHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEE
Q psy496           59 INKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVG  138 (319)
Q Consensus        59 ~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg  138 (319)
                      +.+++....++++.+|++|||||||.++...+ ..+     +  .++|+++|+++|+.|..+.+.......       ++
T Consensus        75 Q~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~-~~~-----~--~~~Liv~p~~~L~~q~~~~~~~~~~~~-------~~  139 (206)
T d2fz4a1          75 QEKALERWLVDKRGCIVLPTGSGKTHVAMAAI-NEL-----S--TPTLIVVPTLALAEQWKERLGIFGEEY-------VG  139 (206)
T ss_dssp             HHHHHHHHTTTSEEEEEESSSTTHHHHHHHHH-HHS-----C--SCEEEEESSHHHHHHHHHHHGGGCGGG-------EE
T ss_pred             HHHHHHHHHhCCCcEEEeCCCCCceehHHhHH-HHh-----c--CceeEEEcccchHHHHHHHHHhhcccc-------hh
Confidence            34444445566788999999999998764433 221     1  245666699999999988876643221       22


Q ss_pred             EEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          139 YQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       139 ~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      . ... ..  .....++++|...+......  ...++++||+||+|...  .+.....++    ..+...+++||||+
T Consensus       140 ~-~~~-~~--~~~~~i~i~t~~~~~~~~~~--~~~~~~lvIiDEaH~~~--a~~~~~i~~----~~~~~~~lgLTATl  205 (206)
T d2fz4a1         140 E-FSG-RI--KELKPLTVSTYDSAYVNAEK--LGNRFMLLIFDEVHHLP--AESYVQIAQ----MSIAPFRLGLTATF  205 (206)
T ss_dssp             E-ESS-SC--BCCCSEEEEEHHHHHHTHHH--HTTTCSEEEEECSSCCC--TTTHHHHHH----TCCCSEEEEEEESC
T ss_pred             h-ccc-cc--ccccccccceehhhhhhhHh--hCCcCCEEEEECCeeCC--cHHHHHHHh----ccCCCcEEEEecCC
Confidence            1 111 11  12345999999888766532  13578999999999732  232222222    22344678999997

>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=99.46  E-value=4.9e-14  Score=125.43  Aligned_cols=133  Identities=12%  Similarity=0.080  Sum_probs=82.4

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEeccccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKEL  147 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~  147 (319)
                      ++++.++.+|||||||......+ ..+....   ..++|+++|+++|+.|.++.+.+.....    ...++ .+..+...
T Consensus       127 ~~~~~il~~pTGsGKT~i~~~i~-~~~~~~~---~~k~Liivp~~~Lv~Q~~~~f~~~~~~~----~~~~~-~~~~g~~~  197 (282)
T d1rifa_         127 VNRRRILNLPTSAGRSLIQALLA-RYYLENY---EGKILIIVPTTALTTQMADDFVDYRLFS----HAMIK-KIGGGASK  197 (282)
T ss_dssp             HHSEEEECCCTTSCHHHHHHHHH-HHHHHHC---SSEEEEECSSHHHHHHHHHHHHHHTSCC----GGGEE-ECSTTCSS
T ss_pred             hcCCceeEEEcccCccHHHHHHH-HHhhhcc---cceEEEEEcCchhHHHHHHHHHHhhccc----cccce-eecceecc
Confidence            35668889999999998765433 3333333   2378888899999999999888764321    11111 11111111


Q ss_pred             ---CCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          148 ---PRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       148 ---~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                         ......++++|++.+.+...  ..++++++||+||||.  .....+..   .+....+....++||||+
T Consensus       198 ~~~~~~~~~i~i~t~qs~~~~~~--~~~~~f~~VIvDEaH~--~~a~~~~~---il~~~~~~~~rlGlTaT~  262 (282)
T d1rifa_         198 DDKYKNDAPVVVGTWQTVVKQPK--EWFSQFGMMMNDECHL--ATGKSISS---IISGLNNCMFKFGLSGSL  262 (282)
T ss_dssp             TTCCCTTCSEEEECHHHHTTSCG--GGGGGEEEEEEETGGG--CCHHHHHH---HTTTCTTCCEEEEECSSC
T ss_pred             cccccccceEEEEeeehhhhhcc--cccCCCCEEEEECCCC--CCchhHHH---HHHhccCCCeEEEEEeec
Confidence               11245799999987654432  2467899999999997  33333322   233333333458999999

>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=98.33  E-value=1.2e-06  Score=74.08  Aligned_cols=155  Identities=14%  Similarity=0.071  Sum_probs=80.5

Q ss_pred             ccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           46 MVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        46 ~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      .|.|.+++.-+...      ...+...+++=++|.|||..... ++..+.......  ++++++|. .+..+..+.+.+.
T Consensus        14 ~~yQ~~~v~~~~~~------~~~~~g~iLaDe~GlGKT~~~i~-~~~~~~~~~~~~--~~LIv~p~-~l~~~W~~e~~~~   83 (230)
T d1z63a1          14 RPYQIKGFSWMRFM------NKLGFGICLADDMGLGKTLQTIA-VFSDAKKENELT--PSLVICPL-SVLKNWEEELSKF   83 (230)
T ss_dssp             CHHHHHHHHHHHHH------HHTTCCEEECCCTTSCHHHHHHH-HHHHHHHTTCCS--SEEEEECS-TTHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHh------hhcCCCEEEEeCCCCChHHHHHH-hhhhhhhccccc--ccceecch-hhhhHHHHHHHhh
Confidence            36677776433221      12345678888899999988644 344444433322  44555574 3445555555554


Q ss_pred             hccccCCCCceEEEEEecccccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhcccc
Q psy496          126 RDEQCGRPGSSVGYQIRLEKELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRK  205 (319)
Q Consensus       126 ~~~~~~~~g~~vg~~~~~~~~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~  205 (319)
                      ...      ..+...............+++++|.+.+.+...-.  --..+.+|+||+|............+.   ... 
T Consensus        84 ~~~------~~~~~~~~~~~~~~~~~~~vvi~~~~~~~~~~~l~--~~~~~~vI~DEah~~k~~~s~~~~~~~---~l~-  151 (230)
T d1z63a1          84 APH------LRFAVFHEDRSKIKLEDYDIILTTYAVLLRDTRLK--EVEWKYIVIDEAQNIKNPQTKIFKAVK---ELK-  151 (230)
T ss_dssp             CTT------SCEEECSSSTTSCCGGGSSEEEEEHHHHTTCHHHH--TCCEEEEEEETGGGGSCTTSHHHHHHH---TSC-
T ss_pred             ccc------ccceeeccccchhhccCcCEEEeeHHHHHhHHHHh--cccceEEEEEhhhcccccchhhhhhhh---hhc-
Confidence            321      11211111111111234579999998775433110  125678999999973211111111122   222 


Q ss_pred             CceEEEecccc---ChhhHh
Q psy496          206 DLKLILMSATL---NAEKFS  222 (319)
Q Consensus       206 ~~qiv~lSAT~---~~~~l~  222 (319)
                      ....+++|||+   +++++.
T Consensus       152 a~~r~~LTgTPi~n~~~dl~  171 (230)
T d1z63a1         152 SKYRIALTGTPIENKVDDLW  171 (230)
T ss_dssp             EEEEEEECSSCSTTCHHHHH
T ss_pred             cceEEEEecchHHhHHHHHH
Confidence            23578999999   455543

>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=98.15  E-value=1.3e-05  Score=70.25  Aligned_cols=137  Identities=18%  Similarity=0.082  Sum_probs=74.3

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCC---CCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEe
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNR---GSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIR  142 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~---~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~  142 (319)
                      ...+...+++=+.|.|||....-.+ ..+.....   ....++|+++|.. +..|-.+.+.+.+....    ..+-  ..
T Consensus        76 ~~~~~g~iLaDemGlGKT~qaia~l-~~l~~~~~~~~~~~~~~LIV~P~s-l~~qW~~Ei~k~~~~~~----~~v~--~~  147 (298)
T d1z3ix2          76 IENSYGCIMADEMGLGKTLQCITLI-WTLLKQSPDCKPEIDKVIVVSPSS-LVRNWYNEVGKWLGGRV----QPVA--ID  147 (298)
T ss_dssp             STTCCEEEECCCTTSCHHHHHHHHH-HHHHHCCTTSSCSCSCEEEEECHH-HHHHHHHHHHHHHGGGC----CEEE--EC
T ss_pred             hccCCceEEEeCCCCCHHHHHHHHH-HHHHHhcccccCCCCcEEEEccch-hhHHHHHHHHhhcCCce----eEEE--Ee
Confidence            3456678888899999997654333 33333221   1122466666975 55676666766554321    1111  11


Q ss_pred             ccc--------------ccCCCCceEEEECchHHHHHHhcCCCCCCccEEEEeccccc-ccchhHHHHHHHhhhccccCc
Q psy496          143 LEK--------------ELPRKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHER-SMISDFLLAILKDVTDKRKDL  207 (319)
Q Consensus       143 ~~~--------------~~~~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~-~~~~~~~~~~l~~~~~~~~~~  207 (319)
                      ...              ........++++|.+.+......- .-.+++++|+||+|.. ........ .+..+    ...
T Consensus       148 ~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~~l-~~~~~~~vI~DEaH~ikn~~s~~~~-a~~~l----~~~  221 (298)
T d1z3ix2         148 GGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEVL-HKGKVGLVICDEGHRLKNSDNQTYL-ALNSM----NAQ  221 (298)
T ss_dssp             SSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTTT-TTSCCCEEEETTGGGCCTTCHHHHH-HHHHH----CCS
T ss_pred             CchHHHHHHHHHHhhhccCccccceEEEEeecccccchhcc-cccceeeeecccccccccccchhhh-hhhcc----ccc
Confidence            000              001123568899988776554221 1235789999999972 22222222 22222    133


Q ss_pred             eEEEecccc
Q psy496          208 KLILMSATL  216 (319)
Q Consensus       208 qiv~lSAT~  216 (319)
                      ..+++|||+
T Consensus       222 ~rllLTGTP  230 (298)
T d1z3ix2         222 RRVLISGTP  230 (298)
T ss_dssp             EEEEECSSC
T ss_pred             eeeeecchH
Confidence            678999999

>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=98.14  E-value=3e-06  Score=76.66  Aligned_cols=57  Identities=28%  Similarity=0.412  Sum_probs=40.7

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQE  125 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~  125 (319)
                      .+..++|+||+|||||+.... ++..+.........+|+++.||-..|..+.+.....
T Consensus       162 ~~~~~vI~G~pGTGKTt~i~~-~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~~~~  218 (359)
T d1w36d1         162 TRRISVISGGPGTGKTTTVAK-LLAALIQMADGERCRIRLAAPTGKAAARLTESLGKA  218 (359)
T ss_dssp             TBSEEEEECCTTSTHHHHHHH-HHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTHH
T ss_pred             cCCeEEEEcCCCCCceehHHH-HHHHHHHHHhccCCeEEEecCcHHHHHHHHHHHHHH
Confidence            467899999999999987543 233333333334568999999999998887766544

>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=97.89  E-value=2.8e-05  Score=64.85  Aligned_cols=133  Identities=13%  Similarity=0.102  Sum_probs=75.8

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCC
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPR  149 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~  149 (319)
                      ..++++||||+|||+........ +..+  +.+..++.+-..|.-|.+..+.+++.++..+       .   ...+..+ 
T Consensus        12 ~vi~lvGptGvGKTTTiAKLAa~-~~~~--~~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~-------~---~~~~~~d-   77 (213)
T d1vmaa2          12 FVIMVVGVNGTGKTTSCGKLAKM-FVDE--GKSVVLAAADTFRAAAIEQLKIWGERVGATV-------I---SHSEGAD-   77 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH-HHHT--TCCEEEEEECTTCHHHHHHHHHHHHHHTCEE-------E---CCSTTCC-
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH-HHHC--CCceEEEeecccccchhHHHHHHhhhcCccc-------c---ccCCCCc-
Confidence            45778999999999988765533 3222  3356777777899999988888888776442       0   0001000 


Q ss_pred             CCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhc-------cccCceEEEeccccC---hh
Q psy496          150 KRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTD-------KRKDLKLILMSATLN---AE  219 (319)
Q Consensus       150 ~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~-------~~~~~qiv~lSAT~~---~~  219 (319)
                               +..+...........++++|+||=+-+. .....+...++.+..       ..|...++.+|||..   ..
T Consensus        78 ---------~~~~~~~~~~~~~~~~~d~ilIDTaGr~-~~d~~~~~el~~~~~~~~~~~~~~p~~~~LVl~a~~~~~~~~  147 (213)
T d1vmaa2          78 ---------PAAVAFDAVAHALARNKDVVIIDTAGRL-HTKKNLMEELRKVHRVVKKKIPDAPHETLLVIDATTGQNGLV  147 (213)
T ss_dssp             ---------HHHHHHHHHHHHHHTTCSEEEEEECCCC-SCHHHHHHHHHHHHHHGGGTCTTCCSEEEEEEEGGGHHHHHH
T ss_pred             ---------HHHHHHHHHHHHHHcCCCEEEEeccccc-cchHHHHHHHHHHHhhhhhccccccceeEEeeccccCcchhh
Confidence                     1111222211112357889999999852 222222222322221       114456888999993   34


Q ss_pred             hHhhhhC
Q psy496          220 KFSQFFG  226 (319)
Q Consensus       220 ~l~~~l~  226 (319)
                      .+.+++.
T Consensus       148 ~~~~~~~  154 (213)
T d1vmaa2         148 QAKIFKE  154 (213)
T ss_dssp             HHHHHHH
T ss_pred             hhhhhcc
Confidence            4445553

>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=97.85  E-value=2.2e-05  Score=65.24  Aligned_cols=124  Identities=15%  Similarity=0.130  Sum_probs=71.5

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP  148 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~  148 (319)
                      .+.++++||||+|||+........ +..  ++.+..++.+-..|..|.+..+.+++.++..+       -   ...+.. 
T Consensus        10 ~~vi~lvGp~GvGKTTTiaKLA~~-~~~--~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~-------~---~~~~~~-   75 (207)
T d1ls1a2          10 RNLWFLVGLQGSGKTTTAAKLALY-YKG--KGRRPLLVAADTQRPAAREQLRLLGEKVGVPV-------L---EVMDGE-   75 (207)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHH-HHH--TTCCEEEEECCSSCHHHHHHHHHHHHHHTCCE-------E---ECCTTC-
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH-HHH--CCCcEEEEecccccchHHHHHHHHHHhcCCcc-------c---cccccc-
Confidence            345677999999999888765433 222  23345666667899999998888888876442       0   000000 


Q ss_pred             CCCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhh-ccccCceEEEecccc
Q psy496          149 RKRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVT-DKRKDLKLILMSATL  216 (319)
Q Consensus       149 ~~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~-~~~~~~qiv~lSAT~  216 (319)
                               .+..+.........+.+.++++||=+-+. .........++.+. ...++..++.++|+.
T Consensus        76 ---------~~~~~~~~~~~~~~~~~~d~vlIDTaGr~-~~d~~~~~el~~~~~~~~~~~~llv~~a~~  134 (207)
T d1ls1a2          76 ---------SPESIRRRVEEKARLEARDLILVDTAGRL-QIDEPLMGELARLKEVLGPDEVLLVLDAMT  134 (207)
T ss_dssp             ---------CHHHHHHHHHHHHHHHTCCEEEEECCCCS-SCCHHHHHHHHHHHHHHCCSEEEEEEEGGG
T ss_pred             ---------hhhHHHHHHHHHHhhccCcceeecccccc-hhhhhhHHHHHHHHhhcCCceEEEEecccc
Confidence                     01111111111112357789999999863 33333333333333 244566678888888

>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=97.78  E-value=2.4e-05  Score=64.96  Aligned_cols=59  Identities=14%  Similarity=0.046  Sum_probs=42.3

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccc
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQ  129 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~  129 (319)
                      +.+.++++||||+|||+....... .+.  ..+.+..++.+-..|..|.+..+.+++.++..
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~-~~~--~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~i~   63 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGR-YYQ--NLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIP   63 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHH-HHH--TTTCCEEEECCCCSSTTHHHHHHHHHHHHTCC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH-HHH--HCCCcEEEEEeccccccchhhHhhcccccCce
Confidence            346788899999999999877543 222  22334555565678999988888898887654

>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=97.75  E-value=4.7e-05  Score=63.26  Aligned_cols=133  Identities=12%  Similarity=0.113  Sum_probs=74.3

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCC
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPR  149 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~  149 (319)
                      ..++++||||+|||+....... .+.  ..+....++.+-..|..|.+..+.+++.++..+          ....+..  
T Consensus        10 ~vi~lvGptGvGKTTTiAKLA~-~~~--~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~----------~~~~~~~--   74 (211)
T d2qy9a2          10 FVILMVGVNGVGKTTTIGKLAR-QFE--QQGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPV----------IAQHTGA--   74 (211)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH-HHH--TTTCCEEEECCCTTCHHHHHHHHHHHHHTTCCE----------ECCSTTC--
T ss_pred             EEEEEECCCCCCHHHHHHHHHH-HHH--HCCCcEEEEecccccccchhhhhhhhhhcCCcc----------cccccCC--
Confidence            4577899999999999877543 222  223355666666789999988888888876432          0000100  


Q ss_pred             CCceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhc-------cccCceEEEeccccCh---h
Q psy496          150 KRGSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTD-------KRKDLKLILMSATLNA---E  219 (319)
Q Consensus       150 ~~~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~-------~~~~~qiv~lSAT~~~---~  219 (319)
                              -+..++..........++++++||=+-+. .....+...++.+..       ..|.-.++.+||+...   .
T Consensus        75 --------d~~~~l~~~~~~a~~~~~d~ilIDTaGr~-~~d~~~~~el~~l~~~~~~~~~~~p~~~~LVl~a~~~~~~~~  145 (211)
T d2qy9a2          75 --------DSASVIFDAIQAAKARNIDVLIADTAGRL-QNKSHLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVS  145 (211)
T ss_dssp             --------CHHHHHHHHHHHHHHTTCSEEEECCCCCG-GGHHHHHHHHHHHHHHHTTTCTTCCSEEEEEEEGGGTHHHHH
T ss_pred             --------CHHHHHHHHHHHHHHcCCCEEEeccCCCc-cccHHHHHHHHHHHHHHhhhcccCcceeeeehhcccCcchHH
Confidence                    11112222111111357899999999752 222222333332221       1245567889999943   3


Q ss_pred             hHhhhhC
Q psy496          220 KFSQFFG  226 (319)
Q Consensus       220 ~l~~~l~  226 (319)
                      .+.+++.
T Consensus       146 ~~~~~~~  152 (211)
T d2qy9a2         146 QAKLFHE  152 (211)
T ss_dssp             HHHHHHH
T ss_pred             HHhhhhh
Confidence            4444553

>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=97.56  E-value=0.00012  Score=60.79  Aligned_cols=57  Identities=14%  Similarity=0.134  Sum_probs=37.3

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccc
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQ  129 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~  129 (319)
                      ..++++||||+|||+....... .+..  ++.+..++.+-..|.-|....+.+++.++..
T Consensus        13 ~vi~lvGptGvGKTTTiAKLA~-~~~~--~g~kV~lit~Dt~R~ga~eQL~~~a~~l~v~   69 (211)
T d1j8yf2          13 YVIMLVGVQGTGKATTAGKLAY-FYKK--KGFKVGLVGADVYRPAALEQLQQLGQQIGVP   69 (211)
T ss_dssp             EEEEEECSCCC----HHHHHHH-HHHH--TTCCEEEEECCCSSHHHHHHHHHHHHHHTCC
T ss_pred             EEEEEECCCCCCHHHHHHHHHH-HHHH--CCCceEEEEeeccccchhHHHHHhccccCcc
Confidence            4577799999999999876553 2322  2334566666678999998888898887654

>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=97.20  E-value=0.00019  Score=61.92  Aligned_cols=58  Identities=21%  Similarity=0.181  Sum_probs=42.5

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      +.+++|.|+.|||||++...-+...+...+ ....+|+++.+|+.+|..+..++.+..+
T Consensus        14 ~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~-~~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1          14 TGPCLVLAGAGSGKTRVITNKIAHLIRGCG-YQARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             SSEEEECCCTTSCHHHHHHHHHHHHHHHHC-CCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CCCEEEEeeCCccHHHHHHHHHHHHHHhcC-CChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            466999999999999887654444333322 2334789999999999999888877644

>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=97.18  E-value=0.00072  Score=55.58  Aligned_cols=50  Identities=14%  Similarity=0.199  Sum_probs=33.9

Q ss_pred             HHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecc
Q psy496          163 PEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSA  214 (319)
Q Consensus       163 l~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSA  214 (319)
                      .+.+...+.....+++||||+|.  +..+..-.+++.+...+++..+++.+-
T Consensus        97 ~~~~~~~~~~~~~kviIide~d~--l~~~a~n~Llk~lEep~~~~~fIl~t~  146 (207)
T d1a5ta2          97 TEKLNEHARLGGAKVVWVTDAAL--LTDAAANALLKTLEEPPAETWFFLATR  146 (207)
T ss_dssp             HHHTTSCCTTSSCEEEEESCGGG--BCHHHHHHHHHHHTSCCTTEEEEEEES
T ss_pred             hhhhhhccccCccceEEechhhh--hhhhhhHHHHHHHHhhcccceeeeeec
Confidence            44444445567789999999998  566666677777766656666666443

>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=97.04  E-value=0.00087  Score=55.32  Aligned_cols=40  Identities=18%  Similarity=0.291  Sum_probs=25.0

Q ss_pred             CCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          172 LSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       172 l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      ..+..++|+||+|.  +..+....+++.+....+...+++.+
T Consensus        97 ~~~~kiiiiDe~d~--~~~~~~~~Ll~~le~~~~~~~~~~~~  136 (227)
T d1sxjc2          97 SKGFKLIILDEADA--MTNAAQNALRRVIERYTKNTRFCVLA  136 (227)
T ss_dssp             SCSCEEEEETTGGG--SCHHHHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCCeEEEEEecccc--chhhHHHHHHHHhhhcccceeecccc
Confidence            45667999999998  44454555555555544455555543

>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=97.00  E-value=0.00029  Score=60.01  Aligned_cols=104  Identities=19%  Similarity=0.164  Sum_probs=63.4

Q ss_pred             EEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccC---C
Q psy496           73 IIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELP---R  149 (319)
Q Consensus        73 li~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~---~  149 (319)
                      +..-.||=|||++..+|..-..+.+.   .+.|+.  ..--||..=++.+...+...    |..+|......+...   .
T Consensus        97 iaem~TGEGKTL~a~l~a~l~al~g~---~vhvvT--vNdyLA~RDae~m~~iy~~l----Glsvg~~~~~~~~~~r~~~  167 (273)
T d1tf5a3          97 IAEMKTGEGKTLTSTLPVYLNALTGK---GVHVVT--VNEYLASRDAEQMGKIFEFL----GLTVGLNLNSMSKDEKREA  167 (273)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHTTSS---CEEEEE--SSHHHHHHHHHHHHHHHHHT----TCCEEECCTTSCHHHHHHH
T ss_pred             heeecCCCcchhHHHHHHHHHHhcCC---CceEEe--cCccccchhhhHHhHHHHHc----CCCccccccccCHHHHHHH
Confidence            44455999999999888765444333   456666  55557666666555554433    777774432211111   1


Q ss_pred             CCceEEEECchHH-----HHHHhcC---CCCCCccEEEEecccc
Q psy496          150 KRGSILYCTAGIL-----PEVMQSD---PILSGVSHIVMDEIHE  185 (319)
Q Consensus       150 ~~~~Iiv~Tpg~l-----l~~l~~~---~~l~~v~~vViDEah~  185 (319)
                      -.++|+++|..-+     .+.+...   .....+.+.|+||+|.
T Consensus       168 Y~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDs  211 (273)
T d1tf5a3         168 YAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDS  211 (273)
T ss_dssp             HHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHH
T ss_pred             hhCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchh
Confidence            2578999998444     3433221   1256799999999996

>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=96.99  E-value=0.00059  Score=59.29  Aligned_cols=56  Identities=21%  Similarity=0.184  Sum_probs=41.9

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      ..++|.|+.|||||++...-+...+.. ......+|+++.+++.+|..+..++....
T Consensus        25 g~~lV~g~aGSGKTt~l~~ri~~ll~~-~~~~p~~il~lt~t~~aa~~~~~~~~~~~   80 (318)
T d1pjra1          25 GPLLIMAGAGSGKTRVLTHRIAYLMAE-KHVAPWNILAITFTNKAAREMRERVQSLL   80 (318)
T ss_dssp             SCEEEEECTTSCHHHHHHHHHHHHHHT-TCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCEEEEecCCccHHHHHHHHHHHHHHc-CCCCHHHeEeEeccHHHHHHHHHHHHhhc
Confidence            569999999999999876655444433 32334578888899999999988887653

>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=96.95  E-value=0.00071  Score=56.71  Aligned_cols=40  Identities=20%  Similarity=0.362  Sum_probs=26.4

Q ss_pred             CCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          172 LSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       172 l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      -...+++||||+|.  +..+..-.+++.+...+++.++++.+
T Consensus       113 ~~~~kviiIde~d~--l~~~~q~~Llk~lE~~~~~~~~il~t  152 (239)
T d1njfa_         113 RGRFKVYLIDEVHM--LSRHSFNALLKTLEEPPEHVKFLLAT  152 (239)
T ss_dssp             SSSSEEEEEETGGG--SCHHHHHHHHHHHHSCCTTEEEEEEE
T ss_pred             cCCCEEEEEECccc--CCHHHHHHHHHHHhcCCCCeEEEEEc
Confidence            45678999999998  55555555566655544555665543

>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=96.83  E-value=0.00074  Score=55.96  Aligned_cols=40  Identities=25%  Similarity=0.444  Sum_probs=25.0

Q ss_pred             ccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHH
Q psy496           46 MVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        46 ~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~   89 (319)
                      ...|...+..+.   +.+. .....+++++||+|+|||+..-..
T Consensus        14 iig~~~~~~~l~---~~i~-~~~~~~lll~Gp~G~GKTtl~~~i   53 (237)
T d1sxjd2          14 VTAQDHAVTVLK---KTLK-SANLPHMLFYGPPGTGKTSTILAL   53 (237)
T ss_dssp             CCSCCTTHHHHH---HHTT-CTTCCCEEEECSTTSSHHHHHHHH
T ss_pred             ccCcHHHHHHHH---HHHH-cCCCCeEEEECCCCCChHHHHHHH
Confidence            345555554443   2332 333456999999999999776443

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.81  E-value=0.00034  Score=58.66  Aligned_cols=39  Identities=15%  Similarity=0.363  Sum_probs=23.7

Q ss_pred             CCccEEEEecccccccchhHHHHHHHhhhccccCceEEEec
Q psy496          173 SGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMS  213 (319)
Q Consensus       173 ~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lS  213 (319)
                      ....++||||+|.  +..+....+.+.+...+++.++++.+
T Consensus       130 ~~~~iiiide~d~--l~~~~~~~l~~~~e~~~~~~~~Il~t  168 (252)
T d1sxje2         130 HRYKCVIINEANS--LTKDAQAALRRTMEKYSKNIRLIMVC  168 (252)
T ss_dssp             -CCEEEEEECTTS--SCHHHHHHHHHHHHHSTTTEEEEEEE
T ss_pred             CCceEEEeccccc--cccccchhhhcccccccccccceeee
Confidence            4567999999997  44444444445444445555666543

>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=96.78  E-value=0.0017  Score=53.56  Aligned_cols=52  Identities=21%  Similarity=0.181  Sum_probs=31.8

Q ss_pred             HHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHH
Q psy496           34 EIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        34 ~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~   89 (319)
                      |.+..+.+...-..-|...+..+.   +.+ ...+..+++++||+|+|||+++-..
T Consensus         5 w~eKyrP~~~~d~ig~~~~~~~L~---~~~-~~~~~~~~ll~Gp~G~GKTt~a~~l   56 (224)
T d1sxjb2           5 WVEKYRPQVLSDIVGNKETIDRLQ---QIA-KDGNMPHMIISGMPGIGKTTSVHCL   56 (224)
T ss_dssp             HHHHTCCSSGGGCCSCTHHHHHHH---HHH-HSCCCCCEEEECSTTSSHHHHHHHH
T ss_pred             hHhHhCCCCHHHhcCCHHHHHHHH---HHH-HcCCCCeEEEECCCCCCchhhHHHH
Confidence            556655444444455665544433   222 2334457999999999999876443

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.52  E-value=0.0018  Score=52.82  Aligned_cols=53  Identities=13%  Similarity=0.217  Sum_probs=38.6

Q ss_pred             HHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhhccccCceEEEecccc
Q psy496          162 LPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVTDKRKDLKLILMSATL  216 (319)
Q Consensus       162 ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~~~~~~~qiv~lSAT~  216 (319)
                      +.+.+...+...+.+++||||||.  +..+..-++++.+...+++..+++.+...
T Consensus        67 i~~~~~~~~~~~~~KviIId~ad~--l~~~aqNaLLK~LEEPp~~t~fiLit~~~  119 (198)
T d2gnoa2          67 IKDFLNYSPELYTRKYVIVHDCER--MTQQAANAFLKALEEPPEYAVIVLNTRRW  119 (198)
T ss_dssp             HHHHHTSCCSSSSSEEEEETTGGG--BCHHHHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             HHHHHhhCcccCCCEEEEEeCccc--cchhhhhHHHHHHhCCCCCceeeeccCCh
Confidence            344445555567889999999998  67777777888777766777777765543

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.43  E-value=0.014  Score=47.73  Aligned_cols=17  Identities=47%  Similarity=0.763  Sum_probs=14.1

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      ..++|+||+|||||...
T Consensus        37 n~l~l~G~~G~GKTHLl   53 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHLL   53 (213)
T ss_dssp             SSEEEECSSSSSHHHHH
T ss_pred             CcEEEECCCCCcHHHHH
Confidence            44899999999999543

>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=96.30  E-value=0.009  Score=49.04  Aligned_cols=50  Identities=16%  Similarity=0.156  Sum_probs=29.7

Q ss_pred             HHHhccCCccccccccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhh
Q psy496           34 EIARNRGSECCIMVTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        34 ~~~~~~~~~~~~~~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~   87 (319)
                      |.+..+.....-...|..++..+..   .+. ..+..+++++||+|+|||+.+-
T Consensus        14 w~~ky~P~~~~diig~~~~~~~l~~---~i~-~~~~~~lll~Gp~G~GKTtla~   63 (231)
T d1iqpa2          14 WVEKYRPQRLDDIVGQEHIVKRLKH---YVK-TGSMPHLLFAGPPGVGKTTAAL   63 (231)
T ss_dssp             HHHHTCCCSTTTCCSCHHHHHHHHH---HHH-HTCCCEEEEESCTTSSHHHHHH
T ss_pred             HHHHhCCCCHHHccCcHHHHHHHHH---HHH-cCCCCeEEEECCCCCcHHHHHH
Confidence            4444443333334556666555432   232 2344579999999999997764

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=95.89  E-value=0.0083  Score=52.27  Aligned_cols=40  Identities=28%  Similarity=0.239  Sum_probs=24.3

Q ss_pred             cccccchhhHHHHHH-hhh-cCCCC---CcEEEecCCCCCccchh
Q psy496           47 VTQPRRISAIALINK-CLT-LSPIL---SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~-~l~-~~~~~---~~vli~apTGSGKT~~~   86 (319)
                      .=|..|+..+...-. ... ....+   .+++++||||+|||..+
T Consensus        26 ~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~la   70 (315)
T d1qvra3          26 VGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELA   70 (315)
T ss_dssp             CSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHH
T ss_pred             eCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHH
Confidence            447777777655322 111 11111   25788999999999665

>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=95.41  E-value=0.024  Score=43.16  Aligned_cols=99  Identities=15%  Similarity=0.087  Sum_probs=56.1

Q ss_pred             EEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHhccccCCCCceEEEEEecccccCCCC
Q psy496           72 SIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQERDEQCGRPGSSVGYQIRLEKELPRKR  151 (319)
Q Consensus        72 vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~~~~~~~~g~~vg~~~~~~~~~~~~~  151 (319)
                      -++.||-.||||+-.+.-+-+. ...+    .+++++.|...-      |    .+..       +.  .+.+.    ..
T Consensus         5 ~~i~GpMfsGKTteLi~~~~~~-~~~~----~kv~~ikp~~D~------R----~~~~-------i~--s~~g~----~~   56 (139)
T d2b8ta1           5 EFITGPMFAGKTAELIRRLHRL-EYAD----VKYLVFKPKIDT------R----SIRN-------IQ--SRTGT----SL   56 (139)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHH-HHTT----CCEEEEEECCCG------G----GCSS-------CC--CCCCC----SS
T ss_pred             EEEEccccCHHHHHHHHHHHHH-HHCC----CcEEEEEEcccc------c----ccce-------EE--cccCc----ee
Confidence            5789999999998865554332 2222    156666676221      0    0100       10  11111    11


Q ss_pred             ceEEEECchHHHHHHhcCCCCCCccEEEEecccccccchhHHHHHHHhhh
Q psy496          152 GSILYCTAGILPEVMQSDPILSGVSHIVMDEIHERSMISDFLLAILKDVT  201 (319)
Q Consensus       152 ~~Iiv~Tpg~ll~~l~~~~~l~~v~~vViDEah~~~~~~~~~~~~l~~~~  201 (319)
                      ..+.+.....+++.+.......++++|.|||++-.   .+........+.
T Consensus        57 ~~~~~~~~~~~~~~~~~~~~~~~~dvI~IDE~QFf---~d~i~~~~~~~~  103 (139)
T d2b8ta1          57 PSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFF---DDRICEVANILA  103 (139)
T ss_dssp             CCEEESSTHHHHHHHHSTTSCTTCCEEEECSGGGS---CTHHHHHHHHHH
T ss_pred             eeEEeccchhhHHHHHhhccccCcCEEEechhhhc---chhHHHHHHHHH
Confidence            22566666777777766666678999999999973   243444444443

>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=94.86  E-value=0.002  Score=56.65  Aligned_cols=43  Identities=26%  Similarity=0.204  Sum_probs=29.4

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRIS  114 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~l  114 (319)
                      ...+.|++|+|+||||||+.. ..++..+-     ...+++++.-+.|+
T Consensus       163 v~~~~nili~G~tgSGKTT~l-~al~~~i~-----~~~rivtiEd~~El  205 (323)
T d1g6oa_         163 IAIGKNVIVCGGTGSGKTTYI-KSIMEFIP-----KEERIISIEDTEEI  205 (323)
T ss_dssp             HHHTCCEEEEESTTSSHHHHH-HHHGGGSC-----TTCCEEEEESSCCC
T ss_pred             HHhCCCEEEEeeccccchHHH-HHHhhhcc-----cccceeeccchhhh
Confidence            345578999999999999864 34443322     23478887777665

>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=94.68  E-value=0.012  Score=45.54  Aligned_cols=39  Identities=15%  Similarity=0.035  Sum_probs=25.2

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEeccc
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPR  111 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Pt  111 (319)
                      ++++|+||+|||||+... .++..+...+  ....++...|.
T Consensus         2 k~v~ItG~~GtGKTtl~~-~i~~~l~~~~--~~v~~~~~~~~   40 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIH-KASEVLKSSG--VPVDGFYTEEV   40 (189)
T ss_dssp             CCEEEESCCSSCHHHHHH-HHHHHHHHTT--CCCEEEECCEE
T ss_pred             cEEEEECCCCCcHHHHHH-HHHHHHHHCC--CEEEEEEeccc
Confidence            579999999999998554 4455554433  23445554454

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=93.73  E-value=0.008  Score=45.62  Aligned_cols=17  Identities=24%  Similarity=0.280  Sum_probs=14.5

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      +.++|+|++|||||+.+
T Consensus         3 klIii~G~pGsGKTTla   19 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEEEECCTTSSHHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            45788999999999864

>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=93.36  E-value=0.053  Score=48.67  Aligned_cols=62  Identities=18%  Similarity=0.232  Sum_probs=44.1

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHhC------CC-CccEEEEecccHHHHHHHHHHHHHHhc
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIARN------RG-SECCIMVTQPRRISAIAIAERVAQERD  127 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~------~~-~~~~vl~~~Ptr~la~q~~~~~~~~~~  127 (319)
                      .|-+++++|.|+-|||||.+...=++..+....      ++ ..-.|+++.=|+.+|..+..|+.+.++
T Consensus        13 ~p~~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~~L~   81 (485)
T d1w36b1          13 LPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNIH   81 (485)
T ss_dssp             CCCSSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHHHHH
Confidence            677889999999999999887666665554321      01 123577777899999998888766543

>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=93.33  E-value=0.046  Score=49.20  Aligned_cols=69  Identities=16%  Similarity=0.139  Sum_probs=46.6

Q ss_pred             cccccchhhHHHHHHhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHHHHHh
Q psy496           47 VTQPRRISAIALINKCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERVAQER  126 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~~~~~  126 (319)
                      =-|.+||..+.+|-+     .+.+..+|.|-||||||....- +++.   .+    ..+|++.|+...|.++++.+..++
T Consensus        14 gDQP~aI~~l~~~l~-----~g~~~q~l~GltGS~ka~~iA~-l~~~---~~----rp~LVVt~n~~~A~qL~~dL~~~l   80 (413)
T d1t5la1          14 GDQPQAIAKLVDGLR-----RGVKHQTLLGATGTGKTFTISN-VIAQ---VN----KPTLVIAHNKTLAGQLYSELKEFF   80 (413)
T ss_dssp             TTHHHHHHHHHHHHH-----HTCSEEEEEECTTSCHHHHHHH-HHHH---HT----CCEEEECSSHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHh-----cCCCcEEEeCCCCcHHHHHHHH-HHHH---hC----CCEEEEeCCHHHHHHHHHHHHHHc
Confidence            347777766654322     2235678999999999955432 2222   12    257777899999999999999887


Q ss_pred             cc
Q psy496          127 DE  128 (319)
Q Consensus       127 ~~  128 (319)
                      +.
T Consensus        81 ~~   82 (413)
T d1t5la1          81 PH   82 (413)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>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=93.26  E-value=0.011  Score=53.88  Aligned_cols=18  Identities=28%  Similarity=0.344  Sum_probs=15.6

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      .+|+|+.||||||||+.+
T Consensus        49 ksNILliGPTGvGKTlLA   66 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIA   66 (443)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             cccEEEECCCCCCHHHHH
Confidence            468999999999999654

>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=93.18  E-value=0.012  Score=45.24  Aligned_cols=18  Identities=28%  Similarity=0.355  Sum_probs=15.3

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      +++|+||+|||||+..-.
T Consensus         6 ~I~i~G~pGsGKTTia~~   23 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKE   23 (173)
T ss_dssp             CEEEECSTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            589999999999987643

>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=93.08  E-value=0.013  Score=44.32  Aligned_cols=19  Identities=26%  Similarity=0.282  Sum_probs=15.9

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      +++++.||+|||||+..-.
T Consensus         3 k~I~l~G~~GsGKSTvak~   21 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQ   21 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHH
Confidence            5789999999999987643

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=93.05  E-value=0.015  Score=44.92  Aligned_cols=21  Identities=29%  Similarity=0.327  Sum_probs=17.1

Q ss_pred             CCCCcEEEecCCCCCccchhh
Q psy496           67 PILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~~   87 (319)
                      |.+-+++|+||+|||||+..-
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~   23 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAE   23 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHH
T ss_pred             CCCCEEEEEeCCCCCHHHHHH
Confidence            345579999999999998763

>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=93.00  E-value=0.034  Score=49.76  Aligned_cols=25  Identities=16%  Similarity=0.244  Sum_probs=18.7

Q ss_pred             CCCcEEEecCCCCCccchhhHHHHH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQFILD   92 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l~il~   92 (319)
                      .+++++|.|+||||||..+...+.+
T Consensus        49 ~~~H~~I~G~tGsGKT~~l~~li~~   73 (433)
T d1e9ra_          49 EPRHLLVNGATGTGKSVLLRELAYT   73 (433)
T ss_dssp             GGGCEEEEECTTSSHHHHHHHHHHH
T ss_pred             ccceEEEEeCCCCcHHHHHHHHHHH
Confidence            3567999999999999875443333

>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=92.73  E-value=0.015  Score=44.56  Aligned_cols=18  Identities=33%  Similarity=0.403  Sum_probs=15.0

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      +.++|+||+|||||+.+-
T Consensus         3 klI~i~G~~GsGKTTva~   20 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCK   20 (176)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            358899999999998753

>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=92.65  E-value=0.016  Score=45.00  Aligned_cols=20  Identities=20%  Similarity=0.207  Sum_probs=17.1

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      |+.++|.|++|||||+..-.
T Consensus         1 ~kiI~i~G~~GsGKsT~~~~   20 (190)
T d1khta_           1 NKVVVVTGVPGVGSTTSSQL   20 (190)
T ss_dssp             CCEEEEECCTTSCHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            57899999999999987644

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=92.56  E-value=0.017  Score=44.47  Aligned_cols=20  Identities=20%  Similarity=0.165  Sum_probs=16.5

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      ++.++|+|++|||||+..-.
T Consensus         3 ~kiI~l~G~~GsGKsTva~~   22 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRC   22 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            46789999999999987633

>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=92.43  E-value=0.016  Score=44.74  Aligned_cols=18  Identities=22%  Similarity=0.242  Sum_probs=15.5

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      ++.++|.||+|||||+..
T Consensus         4 g~iI~l~G~~GsGKSTia   21 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIA   21 (176)
T ss_dssp             TEEEEEEECTTSCHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            466889999999999865

>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=92.43  E-value=0.012  Score=45.56  Aligned_cols=18  Identities=22%  Similarity=0.267  Sum_probs=15.6

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      ++++|.||+|||||+.+-
T Consensus         8 K~I~i~G~~GsGKTTla~   25 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVN   25 (192)
T ss_dssp             EEEEEECCTTSHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            569999999999998764

>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=92.37  E-value=0.019  Score=47.17  Aligned_cols=18  Identities=33%  Similarity=0.438  Sum_probs=15.6

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      ..+++++||+|+|||+.+
T Consensus        35 ~~~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2          35 LDHVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             CCCEEEESSTTSSHHHHH
T ss_pred             CCeEEEECCCCCcHHHHH
Confidence            457999999999999765

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=92.36  E-value=0.018  Score=44.36  Aligned_cols=21  Identities=14%  Similarity=0.224  Sum_probs=17.2

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      .++.++|+|++|||||+..-.
T Consensus         5 ~~~iivl~G~~GsGKsT~a~~   25 (171)
T d1knqa_           5 DHHIYVLMGVSGSGKSAVASE   25 (171)
T ss_dssp             TSEEEEEECSTTSCHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            456788999999999988644

>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=92.23  E-value=0.022  Score=46.10  Aligned_cols=32  Identities=28%  Similarity=0.381  Sum_probs=24.6

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHHHHh
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDEIAR   97 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l~~~   97 (319)
                      .+.+..++|.|++|||||+.....+.+.....
T Consensus        23 i~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~   54 (242)
T d1tf7a1          23 LPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEF   54 (242)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHHHH
T ss_pred             CcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence            56788999999999999987766555544443

>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=92.21  E-value=0.02  Score=49.55  Aligned_cols=18  Identities=28%  Similarity=0.344  Sum_probs=15.6

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      ..+++++||||+|||+.+
T Consensus        49 ~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            478999999999999665

>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=92.17  E-value=0.38  Score=36.16  Aligned_cols=38  Identities=18%  Similarity=0.098  Sum_probs=24.4

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccH
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRR  112 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr  112 (319)
                      .--+|+||-.||||+-.+.-+-.. ...+    -+++++.|..
T Consensus         8 ~l~lI~GpMfSGKTteLi~~~~~~-~~~g----~~vl~i~~~~   45 (141)
T d1xx6a1           8 WVEVIVGPMYSGKSEELIRRIRRA-KIAK----QKIQVFKPEI   45 (141)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHH-HHTT----CCEEEEEEC-
T ss_pred             eEEEEEeccccHHHHHHHHHHHHh-hhcC----CcEEEEEecc
Confidence            446889999999998875554332 2222    1566766863

>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=91.94  E-value=0.059  Score=44.26  Aligned_cols=18  Identities=33%  Similarity=0.608  Sum_probs=15.5

Q ss_pred             CcEEEecCCCCCccchhh
Q psy496           70 SPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~   87 (319)
                      ..++++||+|+|||+++-
T Consensus        53 ~~lll~GPpG~GKTt~a~   70 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAAH   70 (253)
T ss_dssp             SEEEEECSTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            569999999999997764

>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=91.91  E-value=0.023  Score=46.73  Aligned_cols=18  Identities=33%  Similarity=0.547  Sum_probs=15.5

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      ..+++++||+|+|||+.+
T Consensus        35 ~~~~Ll~GPpG~GKTtla   52 (239)
T d1ixsb2          35 LEHLLLFGPPGLGKTTLA   52 (239)
T ss_dssp             CCCEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            357999999999999765

>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=91.62  E-value=0.025  Score=43.58  Aligned_cols=20  Identities=10%  Similarity=-0.069  Sum_probs=16.8

Q ss_pred             CCCcEEEecCCCCCccchhh
Q psy496           68 ILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~   87 (319)
                      .+.+++++|++|||||+..-
T Consensus         5 ~g~~I~l~G~~GsGKTTia~   24 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIAR   24 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            45678899999999998863

>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=91.57  E-value=0.2  Score=37.31  Aligned_cols=37  Identities=14%  Similarity=0.040  Sum_probs=23.2

Q ss_pred             CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEeccc
Q psy496           70 SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPR  111 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Pt  111 (319)
                      .--+|+||-.||||+-.+.-+-.. ...+    -+++++.|.
T Consensus         3 ~L~li~GpMfsGKTt~Li~~~~~~-~~~g----~~v~~ikp~   39 (133)
T d1xbta1           3 QIQVILGPMFSGKSTELMRRVRRF-QIAQ----YKCLVIKYA   39 (133)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH-HTTT----CCEEEEEET
T ss_pred             EEEEEEecccCHHHHHHHHHHHHH-HHcC----CcEEEEecc
Confidence            446889999999998765443322 2222    256666675

>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=91.50  E-value=0.028  Score=46.65  Aligned_cols=17  Identities=24%  Similarity=0.329  Sum_probs=14.8

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      ..+++.||+|||||+.+
T Consensus        33 ~~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEEECCTTSCTHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            45999999999999765

>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=91.15  E-value=0.041  Score=43.06  Aligned_cols=21  Identities=29%  Similarity=0.126  Sum_probs=15.3

Q ss_pred             CCCcEE-EecCCCCCccchhhH
Q psy496           68 ILSPSI-IYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vl-i~apTGSGKT~~~~l   88 (319)
                      .+..++ |+|++|||||+..-.
T Consensus        20 ~~~~iIgI~G~~GSGKSTla~~   41 (198)
T d1rz3a_          20 AGRLVLGIDGLSRSGKTTLANQ   41 (198)
T ss_dssp             SSSEEEEEEECTTSSHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHH
Confidence            344444 899999999987643

>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=90.93  E-value=0.037  Score=43.37  Aligned_cols=20  Identities=25%  Similarity=0.313  Sum_probs=16.4

Q ss_pred             CCCCcEEEecCCCCCccchh
Q psy496           67 PILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        67 ~~~~~vli~apTGSGKT~~~   86 (319)
                      ++...++++|++|||||+.+
T Consensus        12 ~~p~liil~G~pGsGKST~a   31 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFI   31 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHH
Confidence            44567899999999999754

>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=90.87  E-value=0.049  Score=42.88  Aligned_cols=28  Identities=14%  Similarity=0.040  Sum_probs=22.4

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDD   93 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~   93 (319)
                      .+.++.++|.||+|||||+.....+.+.
T Consensus        20 i~~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          20 IETGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CcCCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            4578899999999999998776655543

>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=90.85  E-value=0.037  Score=49.63  Aligned_cols=28  Identities=21%  Similarity=0.190  Sum_probs=20.7

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      ...+.-++++||||||||+..-. +++.+
T Consensus       155 ~~~~GliLvtGpTGSGKSTTl~~-~l~~~  182 (401)
T d1p9ra_         155 KRPHGIILVTGPTGSGKSTTLYA-GLQEL  182 (401)
T ss_dssp             TSSSEEEEEECSTTSCHHHHHHH-HHHHH
T ss_pred             hhhhceEEEEcCCCCCccHHHHH-Hhhhh
Confidence            34557899999999999987644 44444

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=90.77  E-value=0.033  Score=45.97  Aligned_cols=25  Identities=16%  Similarity=0.243  Sum_probs=18.8

Q ss_pred             CCcEEEecCCCCCccchhhHHHHHHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      ..+++|.||+|+|||++. ..+.+.+
T Consensus        43 ~~~lll~GppGtGKT~l~-~~l~~~l   67 (276)
T d1fnna2          43 YPRATLLGRPGTGKTVTL-RKLWELY   67 (276)
T ss_dssp             CCEEEEECCTTSSHHHHH-HHHHHHH
T ss_pred             CCceEEECCCCCCHHHHH-HHHHHHH
Confidence            467999999999999775 3344444

>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=90.72  E-value=0.062  Score=43.78  Aligned_cols=29  Identities=28%  Similarity=0.171  Sum_probs=23.8

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      .+.+..++|.|++|||||+.....+.+..
T Consensus        23 i~~gsl~li~G~pGsGKT~l~~qia~~~~   51 (242)
T d1tf7a2          23 FFKDSIILATGATGTGKTLLVSRFVENAC   51 (242)
T ss_dssp             EESSCEEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             CcCCeEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            56788999999999999988877666643

>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=90.59  E-value=0.035  Score=42.93  Aligned_cols=15  Identities=53%  Similarity=0.594  Sum_probs=13.4

Q ss_pred             EEEecCCCCCccchh
Q psy496           72 SIIYTSTGCGKTTQV   86 (319)
Q Consensus        72 vli~apTGSGKT~~~   86 (319)
                      ++|+||+|||||+.+
T Consensus         3 i~I~G~~G~GKSTLl   17 (178)
T d1ye8a1           3 IIITGEPGVGKTTLV   17 (178)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCcHHHHHH
Confidence            789999999999854

>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=90.27  E-value=0.42  Score=38.03  Aligned_cols=123  Identities=12%  Similarity=0.101  Sum_probs=61.1

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchhhHHHHHHHHHhCC---CCccEEEEecccHHHHH-----HHHHHHHHHhccccCC
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQVPQFILDDEIARNR---GSECCIMVTQPRRISAI-----AIAERVAQERDEQCGR  132 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~~l~il~~l~~~~~---~~~~~vl~~~Ptr~la~-----q~~~~~~~~~~~~~~~  132 (319)
                      .++... ...|+++.||+|.|||+.+.-. ...+.....   -...+++.+.+.+.+|-     +..+++...+......
T Consensus        36 ~iL~r~-~k~n~lLvG~pGVGKTalv~~L-A~ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~  113 (195)
T d1jbka_          36 QVLQRR-TKNNPVLIGEPGVGKTAIVEGL-AQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQ  113 (195)
T ss_dssp             HHHTSS-SSCEEEEECCTTSCHHHHHHHH-HHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHS
T ss_pred             HHHhcc-CCCCeEEEecCCcccHHHHHHH-HHHHHhCCCCHHHcCceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcC
Confidence            444333 3468999999999999776433 333333211   11346777766665542     2333333332211000


Q ss_pred             CCceEEEEEe----ccc--c---cC----------CCCce-EEEECchHHHHHHhcCCC-CCCccEEEEecccc
Q psy496          133 PGSSVGYQIR----LEK--E---LP----------RKRGS-ILYCTAGILPEVMQSDPI-LSGVSHIVMDEIHE  185 (319)
Q Consensus       133 ~g~~vg~~~~----~~~--~---~~----------~~~~~-Iiv~Tpg~ll~~l~~~~~-l~~v~~vViDEah~  185 (319)
                      .|..+=+.-.    .+.  .   .+          ...-. |.-+||+...+.+..++. ...+..|-++|-+.
T Consensus       114 ~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~rg~l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep~~  187 (195)
T d1jbka_         114 EGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSV  187 (195)
T ss_dssp             TTTEEEEEETGGGGTT------CCCCHHHHHHHHHTTSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCCH
T ss_pred             CCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHhCCCceEEecCCHHHHHHHHHcCHHHHhcCCEeecCCCCH
Confidence            0221111100    000  0   00          01122 445678888877777665 46678888888763

>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=89.84  E-value=0.048  Score=42.03  Aligned_cols=19  Identities=21%  Similarity=0.251  Sum_probs=15.7

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      +|++|.|++|||||+..-.
T Consensus         1 k~I~liG~~GsGKsTi~k~   19 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLARA   19 (161)
T ss_dssp             CCEEEECCTTSCHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHH
Confidence            4688999999999987643

>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=89.75  E-value=0.059  Score=44.02  Aligned_cols=29  Identities=14%  Similarity=0.153  Sum_probs=23.7

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      .+.++.++|.||+|||||+.....+.+..
T Consensus        33 lp~G~~~li~G~pGsGKT~~~lq~~~~~~   61 (254)
T d1pzna2          33 IETQAITEVFGEFGSGKTQLAHTLAVMVQ   61 (254)
T ss_dssp             EESSEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             ccCCEEEEEEcCCCCCHHHHHHHHHHHhh
Confidence            56788999999999999988877665543

>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=89.53  E-value=0.05  Score=48.12  Aligned_cols=19  Identities=32%  Similarity=0.336  Sum_probs=16.0

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      .-.|+|..||||+|||+.+
T Consensus        67 p~~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          67 SKSNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCcceeeeCCCCccHHHHH
Confidence            3467999999999999765

>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=89.45  E-value=0.049  Score=42.92  Aligned_cols=18  Identities=28%  Similarity=0.289  Sum_probs=15.4

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|.||+|||||+..-.
T Consensus         5 ~I~i~GppGsGKsT~a~~   22 (189)
T d1zaka1           5 KVMISGAPASGKGTQCEL   22 (189)
T ss_dssp             CEEEEESTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            588999999999988744

>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=89.31  E-value=0.062  Score=41.70  Aligned_cols=18  Identities=28%  Similarity=0.403  Sum_probs=15.2

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      +++|.||+|||||+..-+
T Consensus         2 ~I~i~G~pGSGKsT~a~~   19 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEK   19 (182)
T ss_dssp             EEEEECSTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            378999999999998753

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=89.28  E-value=0.055  Score=42.42  Aligned_cols=18  Identities=22%  Similarity=0.254  Sum_probs=15.5

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      ++.++|+||+|||||+..
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            467899999999999864

>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=89.13  E-value=0.061  Score=41.63  Aligned_cols=19  Identities=32%  Similarity=0.571  Sum_probs=16.1

Q ss_pred             CcEEEecCCCCCccchhhH
Q psy496           70 SPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~~l   88 (319)
                      +++++.|+.|||||+..-.
T Consensus         3 ~~Iil~G~~GsGKSTia~~   21 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRE   21 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHH
Confidence            5688999999999987744

>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=89.08  E-value=0.052  Score=42.85  Aligned_cols=20  Identities=25%  Similarity=0.350  Sum_probs=16.3

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      ...++|.||+|||||+..-.
T Consensus         6 p~iI~i~G~pGSGKsT~a~~   25 (194)
T d1qf9a_           6 PNVVFVLGGPGSGKGTQCAN   25 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            35688999999999987643

>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=89.05  E-value=0.064  Score=42.17  Aligned_cols=20  Identities=30%  Similarity=0.506  Sum_probs=16.4

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      +-.+++.||+|||||+..-+
T Consensus         3 ~~riil~G~pGSGKsT~a~~   22 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAPK   22 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHH
Confidence            44678899999999998754

>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=89.02  E-value=0.055  Score=45.03  Aligned_cols=17  Identities=18%  Similarity=0.214  Sum_probs=14.6

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      ..+|+.||+|||||..+
T Consensus        41 ~~vLL~GppGtGKT~la   57 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            45999999999999665

>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=88.87  E-value=0.16  Score=42.15  Aligned_cols=31  Identities=23%  Similarity=0.097  Sum_probs=22.9

Q ss_pred             hhhcCCCCCcEEEecCCCCCccchhhHHHHH
Q psy496           62 CLTLSPILSPSIIYTSTGCGKTTQVPQFILD   92 (319)
Q Consensus        62 ~l~~~~~~~~vli~apTGSGKT~~~~l~il~   92 (319)
                      ++.=...++.++|.|+||+|||+.....+.+
T Consensus        28 ~~~G~~~G~l~vi~G~~G~GKT~~~~~la~~   58 (277)
T d1cr2a_          28 KTLGARGGEVIMVTSGSGMGKSTFVRQQALQ   58 (277)
T ss_dssp             HHCSBCTTCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HhcCCCCCeEEEEEeCCCCCHHHHHHHHHHh
Confidence            3333566889999999999999766555444

>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=88.76  E-value=0.055  Score=42.15  Aligned_cols=18  Identities=28%  Similarity=0.235  Sum_probs=15.0

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      ++++.||+|||||+..-.
T Consensus         2 ~I~i~G~pGSGKsT~~~~   19 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQF   19 (179)
T ss_dssp             EEEEEESTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            378899999999998743

>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=88.58  E-value=0.081  Score=43.05  Aligned_cols=30  Identities=10%  Similarity=0.047  Sum_probs=24.2

Q ss_pred             cCCCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           65 LSPILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      -.+.++.++|+|++|||||......+.+..
T Consensus        33 Gip~G~~~~i~G~~GsGKT~lalq~~~~~~   62 (258)
T d1v5wa_          33 GIESMAITEAFGEFRTGKTQLSHTLCVTAQ   62 (258)
T ss_dssp             SBCSSEEEEEECCTTCTHHHHHHHHHHHTT
T ss_pred             CCcCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            367788999999999999988777665543

>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=88.57  E-value=0.06  Score=42.01  Aligned_cols=18  Identities=28%  Similarity=0.444  Sum_probs=15.4

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      +++|.||+|||||+..-.
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            478899999999998755

>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=88.36  E-value=0.032  Score=43.80  Aligned_cols=20  Identities=25%  Similarity=0.152  Sum_probs=15.9

Q ss_pred             CCcEEEecCCCCCccchhhH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l   88 (319)
                      +..++++|++|||||+.+-.
T Consensus        19 g~vI~L~G~pGSGKTTiAk~   38 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMA   38 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            34677899999999987643

>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=88.33  E-value=0.068  Score=42.24  Aligned_cols=21  Identities=29%  Similarity=0.444  Sum_probs=16.6

Q ss_pred             CCcEEEecCCCCCccchhhHH
Q psy496           69 LSPSIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~~l~   89 (319)
                      ...++|.||+|||||+.+-..
T Consensus         8 ~~iI~i~GppGSGKsT~a~~L   28 (196)
T d1ukza_           8 VSVIFVLGGPGAGKGTQCEKL   28 (196)
T ss_dssp             CEEEEEECSTTSSHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHH
Confidence            346888999999999887543

>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=88.29  E-value=0.07  Score=42.19  Aligned_cols=21  Identities=24%  Similarity=0.248  Sum_probs=17.1

Q ss_pred             CCCcEEEecCCCCCccchhhH
Q psy496           68 ILSPSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~~l   88 (319)
                      +...++|.||+|||||+..-.
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~   27 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEK   27 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHH
Confidence            346788999999999987753

>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=88.16  E-value=0.073  Score=41.95  Aligned_cols=17  Identities=35%  Similarity=0.622  Sum_probs=14.3

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      +.++|+||+|||||+..
T Consensus         2 rpIvl~GpsG~GK~tl~   18 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLL   18 (186)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            35899999999999754

>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=88.14  E-value=0.083  Score=41.22  Aligned_cols=17  Identities=29%  Similarity=0.446  Sum_probs=14.7

Q ss_pred             EEEecCCCCCccchhhH
Q psy496           72 SIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        72 vli~apTGSGKT~~~~l   88 (319)
                      ++|.||+|||||+..-.
T Consensus         3 I~i~G~pGSGKsT~a~~   19 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADR   19 (182)
T ss_dssp             EEEECSTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            78899999999998744

>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=87.67  E-value=0.13  Score=44.31  Aligned_cols=40  Identities=25%  Similarity=0.241  Sum_probs=25.3

Q ss_pred             cccccchhhHHHHHHhhh--cCCC---CCcEEEecCCCCCccchh
Q psy496           47 VTQPRRISAIALINKCLT--LSPI---LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        47 ~~Q~~~ip~~~~~~~~l~--~~~~---~~~vli~apTGSGKT~~~   86 (319)
                      .=|..|+..+...-....  ....   -.+++++||||+|||..+
T Consensus        25 iGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~la   69 (315)
T d1r6bx3          25 FGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVT   69 (315)
T ss_dssp             CSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHH
T ss_pred             cChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHH
Confidence            558888887765322111  1111   236889999999999655

>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=87.47  E-value=0.085  Score=42.58  Aligned_cols=27  Identities=11%  Similarity=0.086  Sum_probs=21.8

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILD   92 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~   92 (319)
                      .+.++.++|.||+|||||+.....+.+
T Consensus        31 i~~G~~~li~G~pGsGKT~l~lq~~~~   57 (251)
T d1szpa2          31 VETGSITELFGEFRTGKSQLCHTLAVT   57 (251)
T ss_dssp             EESSSEEEEEESTTSSHHHHHHHHTTT
T ss_pred             CcCCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            567889999999999999876655443

>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=87.30  E-value=0.082  Score=41.57  Aligned_cols=18  Identities=28%  Similarity=0.436  Sum_probs=15.3

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|.||+|||||+..-.
T Consensus         3 iI~i~GppGSGKsT~a~~   20 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCAR   20 (194)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            478999999999998754

>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=87.18  E-value=0.082  Score=40.17  Aligned_cols=25  Identities=24%  Similarity=0.235  Sum_probs=17.5

Q ss_pred             cEEEecCCCCCccchhhHHHHHHHHH
Q psy496           71 PSIIYTSTGCGKTTQVPQFILDDEIA   96 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~il~~l~~   96 (319)
                      ++.|+|+.|||||+..-. +++.+..
T Consensus         4 vi~itG~~GSGKTTL~~~-L~~~l~~   28 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKK-LIPALCA   28 (170)
T ss_dssp             EEEEECCTTSCHHHHHHH-HHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHH-HHHHHHH
Confidence            478899999999986544 3344433

>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=87.01  E-value=0.094  Score=41.50  Aligned_cols=16  Identities=31%  Similarity=0.677  Sum_probs=14.0

Q ss_pred             cEEEecCCCCCccchh
Q psy496           71 PSIIYTSTGCGKTTQV   86 (319)
Q Consensus        71 ~vli~apTGSGKT~~~   86 (319)
                      .++|+||+|||||+..
T Consensus         2 pIvl~GPsGsGK~tl~   17 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLL   17 (190)
T ss_dssp             CEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4889999999999864

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=86.88  E-value=0.059  Score=44.56  Aligned_cols=22  Identities=23%  Similarity=0.077  Sum_probs=15.7

Q ss_pred             EEEecCCCCCccchhhHHHHHHH
Q psy496           72 SIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        72 vli~apTGSGKT~~~~l~il~~l   94 (319)
                      ++++||+|+|||++.-. +.+.+
T Consensus        49 l~l~GppGtGKT~l~~~-l~~~l   70 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLAKF-TVKRV   70 (287)
T ss_dssp             EECTTCCSSSHHHHHHH-HHHHH
T ss_pred             EEeECCCCCCHHHHHHH-HHHHH
Confidence            46689999999977643 44444

>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=86.34  E-value=0.11  Score=41.83  Aligned_cols=18  Identities=22%  Similarity=0.408  Sum_probs=15.3

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      +..++|+||+|||||+..
T Consensus         2 G~livi~GPSG~GK~tl~   19 (205)
T d1s96a_           2 GTLYIVSAPSGAGKSSLI   19 (205)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456889999999999765

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=86.12  E-value=0.12  Score=41.41  Aligned_cols=23  Identities=22%  Similarity=0.056  Sum_probs=19.5

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.++.+.|.||.|||||+.+
T Consensus        22 ~~i~~Gei~~l~G~NGsGKSTLl   44 (200)
T d1sgwa_          22 MTIEKGNVVNFHGPNGIGKTTLL   44 (200)
T ss_dssp             EEEETTCCEEEECCTTSSHHHHH
T ss_pred             EEEcCCCEEEEECCCCChHHHHH
Confidence            34567889999999999999765

>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=86.00  E-value=0.13  Score=40.68  Aligned_cols=18  Identities=28%  Similarity=0.383  Sum_probs=15.2

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|.||+|||||+..-.
T Consensus         8 rIiliG~PGSGKtT~a~~   25 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSR   25 (189)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            578889999999988754

>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=85.97  E-value=0.14  Score=41.18  Aligned_cols=29  Identities=21%  Similarity=0.069  Sum_probs=23.8

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      .+.++.++|.|++|+|||+.....+.+..
T Consensus        31 l~~G~l~~i~G~~G~GKT~~~l~~a~~~~   59 (258)
T d2i1qa2          31 LESQSVTEFAGVFGSGKTQIMHQSCVNLQ   59 (258)
T ss_dssp             EETTEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             ccCCeEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            55678999999999999988777766554

>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=85.93  E-value=0.092  Score=40.55  Aligned_cols=18  Identities=28%  Similarity=0.422  Sum_probs=14.8

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++|.|+.|||||+..-.
T Consensus         3 iivi~G~~GsGKTT~~~~   20 (194)
T d1nksa_           3 IGIVTGIPGVGKSTVLAK   20 (194)
T ss_dssp             EEEEEECTTSCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            467899999999988744

>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=85.89  E-value=0.12  Score=42.83  Aligned_cols=25  Identities=20%  Similarity=-0.025  Sum_probs=20.2

Q ss_pred             hhhcCCCCCcEEEecCCCCCccchh
Q psy496           62 CLTLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        62 ~l~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      +-...+.++.+.|.||+|||||+.+
T Consensus        22 isl~i~~Ge~vaIvG~sGsGKSTLl   46 (241)
T d2pmka1          22 INLSIKQGEVIGIVGRSGSGKSTLT   46 (241)
T ss_dssp             EEEEEETTCEEEEECSTTSSHHHHH
T ss_pred             eEEEEcCCCEEEEECCCCCCHHHHH
Confidence            3345677899999999999999754

>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=85.71  E-value=0.12  Score=39.64  Aligned_cols=18  Identities=22%  Similarity=0.337  Sum_probs=14.7

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      ++++.|+.|||||+..-.
T Consensus         3 ~IvliG~~G~GKSTig~~   20 (165)
T d2iyva1           3 KAVLVGLPGSGKSTIGRR   20 (165)
T ss_dssp             SEEEECSTTSSHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHH
Confidence            477779999999987644

>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=85.64  E-value=0.13  Score=42.82  Aligned_cols=27  Identities=15%  Similarity=0.035  Sum_probs=21.5

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchhh
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQVP   87 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~~   87 (319)
                      ++-...+.++.+.|.||+|||||+..-
T Consensus        32 ~isl~i~~Ge~vaivG~sGsGKSTLl~   58 (251)
T d1jj7a_          32 GLTFTLRPGEVTALVGPNGSGKSTVAA   58 (251)
T ss_dssp             EEEEEECTTCEEEEECSTTSSHHHHHH
T ss_pred             ceEEEEcCCCEEEEECCCCCcHHHHHH
Confidence            344456788999999999999997653

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.59  E-value=0.11  Score=41.42  Aligned_cols=15  Identities=20%  Similarity=0.193  Sum_probs=12.8

Q ss_pred             EEEecCCCCCccchh
Q psy496           72 SIIYTSTGCGKTTQV   86 (319)
Q Consensus        72 vli~apTGSGKT~~~   86 (319)
                      +-|+|++|||||+..
T Consensus         5 IgI~G~~gSGKSTla   19 (213)
T d1uj2a_           5 IGVSGGTASGKSSVC   19 (213)
T ss_dssp             EEEECSTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            457999999999776

>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=85.29  E-value=0.13  Score=40.35  Aligned_cols=17  Identities=12%  Similarity=0.305  Sum_probs=14.7

Q ss_pred             CcEEEecCCCCCccchh
Q psy496           70 SPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        70 ~~vli~apTGSGKT~~~   86 (319)
                      +.++|+||+||||++..
T Consensus         4 k~ivl~Gpsg~GK~tl~   20 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIK   20 (178)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            46899999999999765

>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=85.24  E-value=0.12  Score=40.18  Aligned_cols=19  Identities=32%  Similarity=0.592  Sum_probs=15.3

Q ss_pred             cEEEecCCCCCccchhhHH
Q psy496           71 PSIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~   89 (319)
                      .+++.||+|||||+..-..
T Consensus         4 rIvl~G~pGSGKtT~a~~L   22 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPNL   22 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3678899999999887443

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=85.13  E-value=0.12  Score=42.89  Aligned_cols=26  Identities=19%  Similarity=0.013  Sum_probs=20.9

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchh
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ++-...+.++.+.|.||+|||||+.+
T Consensus        20 ~isl~i~~Ge~vaivG~sGsGKSTLl   45 (242)
T d1mv5a_          20 DISFEAQPNSIIAFAGPSGGGKSTIF   45 (242)
T ss_dssp             EEEEEECTTEEEEEECCTTSSHHHHH
T ss_pred             eeEEEEcCCCEEEEECCCCCCHHHHH
Confidence            34445678899999999999999755

>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=85.09  E-value=0.24  Score=40.93  Aligned_cols=22  Identities=27%  Similarity=0.386  Sum_probs=17.6

Q ss_pred             cCCCCCcEEEecCCCCCccchh
Q psy496           65 LSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        65 ~~~~~~~vli~apTGSGKT~~~   86 (319)
                      .+..+..|+|.|++|||||..+
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            3555678999999999999544

>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=85.06  E-value=0.14  Score=42.66  Aligned_cols=26  Identities=15%  Similarity=0.022  Sum_probs=21.5

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchh
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ++-...+.++.+.|.|++|||||+..
T Consensus        36 ~isl~i~~Ge~vaivG~sGsGKSTLl   61 (255)
T d2hyda1          36 DINLSIEKGETVAFVGMSGGGKSTLI   61 (255)
T ss_dssp             EEEEEECTTCEEEEECSTTSSHHHHH
T ss_pred             ceEEEEcCCCEEEEECCCCCcHHHHH
Confidence            44456778899999999999999765

>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=84.97  E-value=0.13  Score=42.92  Aligned_cols=18  Identities=22%  Similarity=0.268  Sum_probs=15.4

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      ...+++.||+|||||..+
T Consensus        45 ~~~iLL~GppGtGKT~la   62 (256)
T d1lv7a_          45 PKGVLMVGPPGTGKTLLA   62 (256)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEeeCCCCCCccHHH
Confidence            467999999999999765

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=84.31  E-value=0.14  Score=40.32  Aligned_cols=18  Identities=17%  Similarity=0.076  Sum_probs=15.1

Q ss_pred             cEEEecCCCCCccchhhH
Q psy496           71 PSIIYTSTGCGKTTQVPQ   88 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l   88 (319)
                      .++++|.+|||||+.+-.
T Consensus         4 li~l~GlpgsGKSTla~~   21 (213)
T d1bifa1           4 LIVMVGLPARGKTYISKK   21 (213)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            378899999999988744

>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=84.24  E-value=0.96  Score=40.04  Aligned_cols=71  Identities=21%  Similarity=0.157  Sum_probs=44.0

Q ss_pred             ccccccccchhhHHHHHHhhhcCCCC-CcEEEecCCCCCccchhhHHHHHHHHHhCCCCccEEEEecccHHHHHHHHHHH
Q psy496           44 CIMVTQPRRISAIALINKCLTLSPIL-SPSIIYTSTGCGKTTQVPQFILDDEIARNRGSECCIMVTQPRRISAIAIAERV  122 (319)
Q Consensus        44 ~~~~~Q~~~ip~~~~~~~~l~~~~~~-~~vli~apTGSGKT~~~~l~il~~l~~~~~~~~~~vl~~~Ptr~la~q~~~~~  122 (319)
                      .++--|.+||.-+.++      ..++ +...|.|-+||+|+....     .+.....   ..++++.|+...|.++++.+
T Consensus         8 ~p~~dqp~aI~~l~~~------L~~g~~~~~L~GlsgS~ka~~~A-----~l~~~~~---rp~LvVt~~~~~A~~l~~dL   73 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEA------LRDGERFVTLLGATGTGKTVTMA-----KVIEALG---RPALVLAPNKILAAQLAAEF   73 (408)
T ss_dssp             CCCTTHHHHHHHHHHH------HHTTCSEEEEEECTTSCHHHHHH-----HHHHHHT---CCEEEEESSHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHH------HhcCCCcEEEecCCCCHHHHHHH-----HHHHHhC---CCEEEEeCCHHHHHHHHHHH
Confidence            3333455565544332      2233 457899999999994432     2222111   14566669999999999999


Q ss_pred             HHHhcc
Q psy496          123 AQERDE  128 (319)
Q Consensus       123 ~~~~~~  128 (319)
                      ..+++.
T Consensus        74 ~~~l~~   79 (408)
T d1c4oa1          74 RELFPE   79 (408)
T ss_dssp             HHHCTT
T ss_pred             HHhcCc
Confidence            888653

>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=84.18  E-value=0.14  Score=42.35  Aligned_cols=18  Identities=22%  Similarity=0.302  Sum_probs=15.2

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      ...+|+.||+|||||+.+
T Consensus        42 ~~giLl~GppGtGKT~la   59 (247)
T d1ixza_          42 PKGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             CSEEEEECCTTSSHHHHH
T ss_pred             CceEEEecCCCCChhHHH
Confidence            356999999999999665

>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=84.06  E-value=0.15  Score=42.50  Aligned_cols=18  Identities=28%  Similarity=0.412  Sum_probs=15.0

Q ss_pred             CCcEEEecCCCCCccchh
Q psy496           69 LSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        69 ~~~vli~apTGSGKT~~~   86 (319)
                      ...+|+.||+|||||...
T Consensus        38 ~~giLL~GppGtGKT~l~   55 (258)
T d1e32a2          38 PRGILLYGPPGTGKTLIA   55 (258)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CceeEEecCCCCCchHHH
Confidence            456999999999999653

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=83.89  E-value=0.18  Score=40.05  Aligned_cols=19  Identities=26%  Similarity=0.270  Sum_probs=15.4

Q ss_pred             cEEEecCCCCCccchhhHH
Q psy496           71 PSIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        71 ~vli~apTGSGKT~~~~l~   89 (319)
                      .+.|.||+||||+++.-..
T Consensus         5 iI~I~GppGSGKgT~ak~L   23 (225)
T d1ckea_           5 VITIDGPSGAGKGTLCKAM   23 (225)
T ss_dssp             EEEEECCTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4677899999999987553

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=83.62  E-value=0.17  Score=41.47  Aligned_cols=25  Identities=20%  Similarity=0.038  Sum_probs=20.3

Q ss_pred             hhhcCCCCCcEEEecCCCCCccchh
Q psy496           62 CLTLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        62 ~l~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      +-...+.++.+.|.||+|||||+..
T Consensus        24 isl~i~~Ge~~~iiG~sGsGKSTLl   48 (230)
T d1l2ta_          24 VNLNIKEGEFVSIMGPSGSGKSTML   48 (230)
T ss_dssp             EEEEECTTCEEEEECSTTSSHHHHH
T ss_pred             eEEEEcCCCEEEEECCCCCCcchhh
Confidence            3345678899999999999999763

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=83.00  E-value=0.18  Score=41.95  Aligned_cols=26  Identities=19%  Similarity=0.167  Sum_probs=21.3

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchh
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ++-...+.++.+.|.||+|||||+.+
T Consensus        33 ~isl~i~~Ge~iaivG~sGsGKSTLl   58 (253)
T d3b60a1          33 NINLKIPAGKTVALVGRSGSGKSTIA   58 (253)
T ss_dssp             EEEEEECTTCEEEEEECTTSSHHHHH
T ss_pred             ceEEEEcCCCEEEEECCCCChHHHHH
Confidence            34445678899999999999999765

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=82.73  E-value=0.17  Score=40.35  Aligned_cols=18  Identities=22%  Similarity=0.185  Sum_probs=14.5

Q ss_pred             EEEecCCCCCccchhhHH
Q psy496           72 SIIYTSTGCGKTTQVPQF   89 (319)
Q Consensus        72 vli~apTGSGKT~~~~l~   89 (319)
                      +.|.||.|||||++.-+.
T Consensus         6 IaIdGp~GsGKgT~ak~L   23 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKII   23 (223)
T ss_dssp             EEEECSSCSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            457799999999987553

>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=82.45  E-value=0.43  Score=39.76  Aligned_cols=29  Identities=31%  Similarity=0.303  Sum_probs=23.4

Q ss_pred             CCCCCcEEEecCCCCCccchhhHHHHHHH
Q psy496           66 SPILSPSIIYTSTGCGKTTQVPQFILDDE   94 (319)
Q Consensus        66 ~~~~~~vli~apTGSGKT~~~~l~il~~l   94 (319)
                      .+.++.+.+.||+|||||...+..+.+..
T Consensus        51 i~~g~itei~G~~gsGKTtl~l~~~~~~q   79 (263)
T d1u94a1          51 LPMGRIVEIYGPESSGKTTLTLQVIAAAQ   79 (263)
T ss_dssp             EETTSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             ccCceEEEEecCCCcHHHHHHHHHHHHHH
Confidence            45678999999999999988777666543

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.21  E-value=0.24  Score=41.80  Aligned_cols=26  Identities=27%  Similarity=0.065  Sum_probs=20.8

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchh
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ++=...+.++.+.|.||+|||||+.+
T Consensus        54 ~isl~i~~Ge~vaivG~nGsGKSTLl   79 (281)
T d1r0wa_          54 NINLNIEKGEMLAITGSTGSGKTSLL   79 (281)
T ss_dssp             EEEEEECTTCEEEEEESTTSSHHHHH
T ss_pred             CeEEEEcCCCEEEEECCCCChHHHHH
Confidence            33345678899999999999999765

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=82.18  E-value=0.21  Score=40.98  Aligned_cols=24  Identities=21%  Similarity=0.183  Sum_probs=19.7

Q ss_pred             hhcCCCCCcEEEecCCCCCccchh
Q psy496           63 LTLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        63 l~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      -...++++.+.|.||+|||||+.+
T Consensus        20 sl~i~~Gei~~liGpsGsGKSTLl   43 (232)
T d2awna2          20 NLDIHEGEFVVFVGPSGCGKSTLL   43 (232)
T ss_dssp             EEEECTTCEEEEECCTTSSHHHHH
T ss_pred             EEEEcCCCEEEEECCCCChHHHHH
Confidence            344578899999999999999764

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.12  E-value=0.19  Score=42.01  Aligned_cols=19  Identities=32%  Similarity=0.552  Sum_probs=15.7

Q ss_pred             CCCcEEEecCCCCCccchh
Q psy496           68 ILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        68 ~~~~vli~apTGSGKT~~~   86 (319)
                      ....+|++||+|||||...
T Consensus        40 ~~~giLL~Gp~GtGKT~l~   58 (265)
T d1r7ra3          40 PSKGVLFYGPPGCGKTLLA   58 (265)
T ss_dssp             CCCEEEEBCCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCcchhHH
Confidence            3466999999999999654

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=81.23  E-value=0.24  Score=40.83  Aligned_cols=23  Identities=30%  Similarity=0.341  Sum_probs=19.1

Q ss_pred             hcCCCCCcEEEecCCCCCccchh
Q psy496           64 TLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        64 ~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ...+.++.+-|.||+|||||+.+
T Consensus        24 l~i~~Ge~~~liG~sGaGKSTll   46 (240)
T d1g2912          24 LEVKDGEFMILLGPSGCGKTTTL   46 (240)
T ss_dssp             EEEETTCEEEEECSTTSSHHHHH
T ss_pred             eEEcCCCEEEEECCCCChHHHHH
Confidence            34567889999999999999764

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=81.17  E-value=0.23  Score=40.95  Aligned_cols=26  Identities=19%  Similarity=0.186  Sum_probs=20.6

Q ss_pred             HhhhcCCCCCcEEEecCCCCCccchh
Q psy496           61 KCLTLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        61 ~~l~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      ++-.....++.+.|.||+|||||+..
T Consensus        23 ~vsl~i~~Ge~~~iiG~sGsGKSTLl   48 (240)
T d3dhwc1          23 NVSLHVPAGQIYGVIGASGAGKSTLI   48 (240)
T ss_dssp             EEEEEECSSCEEEEEESTTSSHHHHH
T ss_pred             ceeEEEcCCCEEEEECCCCCCHHHHH
Confidence            33445677899999999999999764

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=80.09  E-value=0.28  Score=40.44  Aligned_cols=24  Identities=25%  Similarity=0.272  Sum_probs=20.0

Q ss_pred             hhcCCCCCcEEEecCCCCCccchh
Q psy496           63 LTLSPILSPSIIYTSTGCGKTTQV   86 (319)
Q Consensus        63 l~~~~~~~~vli~apTGSGKT~~~   86 (319)
                      -...+.++.+.|.||.|||||+.+
T Consensus        26 sl~v~~Ge~~~liGpsGaGKSTLl   49 (239)
T d1v43a3          26 NLTIKDGEFLVLLGPSGCGKTTTL   49 (239)
T ss_dssp             EEEECTTCEEEEECCTTSSHHHHH
T ss_pred             eEEECCCCEEEEECCCCChHHHHH
Confidence            344677889999999999999765