Citrus Sinensis ID: 042872

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-
Protein Sequence
MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLAETMQDSEEWDDLQAMESEACGALNNMFDKRVIDNNQANDNDNSREYIDILDDSPEPKRRPTLMELDSLSDTEDLDFTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSSKSVDCKSGVSTSSASSVSNKKRSSLISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccccEEEEEEccHHHHHHHHHHccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccHHHHHHHHHHHccccEEEEcccccccccccHHHHHHccccccEEEEEEcccccHHHHHHHHHHHHccccHHccHHHHHHHHHHHHHcccccccEEEEEEccccccccHHHHHHHHHHHHcccccccccccccccccccccccccEEEEEccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHccccccEEEccccccHHHHHHHHHccccccccHHHHHHHHHcccHHHHHccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccHHHHHHHHHHHccccEEEEEccccccccHEcccEEEEcccEEEEEcHHHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHHccccccEEEEEEcHHHHHccHHHHHHHHHHHHcccEEEEEEEcccHHHHHHHHHHHHEEEEEccccc
Coil and Loop (DISEMBL)
MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLygddgqdfisvehCGDDFIATLAETMQDSEEWDDLQAMESEACGALNNmfdkrvidnnqandndnsreyidilddspepkrrptlmeldslsdtedldftipkQKDAILnlsscpdgrsqiftpssvkhssksvdcksgvstssassvsnkkrsslisdnehgtlsfeelqalddmefANVVIFgnrafrplqhQACKAsvakqdcfvllptgggkslcyqDQIITLNlkfgipatflnsqQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCasrkdkpsckllyvtperivgnqSFSEVLKCLHrkgsirlkvlttdvvvlphtcqrqlagfvvdeahcv
Flexible Loop (DISEMBL)
MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLAETMQDSEEWDDLQAMESEACGALNNMFDKRVIDNnqandndnsreyidilddspepkrrptlmeldslsdtedlDFTIPKQKDAILNLSSCPDGRSQIFtpssvkhssksvdcksgvstssassvsnkkrsslisdnehgtLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLyvtperivgnqsFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCqrqlagfvvdeAHCV
Low Complexity Region (SEG)
MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLAETMQDSEEWDDLQAMESEACGALNNMFDKRVIDNNQANDNDNSREYIDILDDSPEPKRRPTlmeldslsdtedldFTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSSKSVDCksgvstssassvsnkkrsslisDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV
Disordered region (IsUnstruct)
*****FEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLAETM****************CGALNNMFD*******************************************************************************************************************FEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDE****
Disordered Region (DISOPRED)
*********KARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLAETMQDSEEWDDL*A**********************************************************DL**************************************************************************ALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQ*************ASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV
Disordered Region (DISEMBL)
MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLAETMQDSEEWDDLQAMESEACGALNNMFDKRVIDNNQANDNDNSREYIDILDDSPEPKRRPTLMELDSLSDTEDLDFTIPKQKDAILNLSSCPDGRSQIF**********************************ISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV
Disordered Region (DISPRO)
****DFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLAETMQDSEEWDDLQAMESEACGALNNMFDK*******************************************************************************************************************EELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLAETMQDSEEWDDLQAMESEACGALNNMFDKRVIDNNQANDNDNSREYIDILDDSPEPKRRPTLMELDSLSDTEDLDFTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSSKSVDCKSGVSTSSASSVSNKKRSSLISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	381	2.2.26 [Sep-21-2011]
Q9FT74	606	ATP-dependent DNA helicas	yes	no	0.805	0.506	0.490	6e-97
O88700	1416	Bloom syndrome protein ho	yes	no	0.307	0.082	0.329	3e-15
Q8L840	1188	ATP-dependent DNA helicas	no	no	0.356	0.114	0.308	1e-14
P54132	1417	Bloom syndrome protein OS	yes	no	0.307	0.082	0.324	2e-14
Q9FT70	1150	ATP-dependent DNA helicas	no	no	0.330	0.109	0.303	6e-14
Q9DEY9	1364	Bloom syndrome protein ho	N/A	no	0.304	0.085	0.322	7e-14
Q9VGI8	1487	Bloom syndrome protein ho	yes	no	0.519	0.133	0.278	5e-13
Q9FT72	713	ATP-dependent DNA helicas	no	no	0.304	0.162	0.296	8e-13
Q9I920	1142	Bloom syndrome protein ho	yes	no	0.307	0.102	0.307	9e-12
O18017	988	Bloom syndrome protein ho	yes	no	0.354	0.136	0.323	2e-11

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

 Score =  354 bits (909), Expect = 6e-97,   Method: Compositional matrix adjust.
 Identities = 203/414 (49%), Positives = 250/414 (60%), Gaps = 107/414 (25%)

Query: 1   MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLA 60
           M   D E EK RL+SLA + GFD+DSA K L+R + LYGDDG+DFI+VE CGDDF+A LA
Sbjct: 1   MKDQDLELEKVRLISLATKLGFDEDSAKKCLDRFVDLYGDDGRDFITVELCGDDFLAALA 60

Query: 61  ETMQDSEEWDDLQAMESEACGALNNMFDKRVIDNNQANDNDN----------SREYIDIL 110
           +  + +EEWDD+QA+ESEA G L  MFDK        N +DN          SR  + ++
Sbjct: 61  DFEEGTEEWDDIQAIESEAQGNLAEMFDK------STNPSDNGFDTDDDDDDSRVEVHVI 114

Query: 111 DDSPEPKRRPTLMELDSLSDTEDLD--FTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSS 168
           +DSPEPK++P ++ELDS SD ED++  F +P+              RSQ          S
Sbjct: 115 EDSPEPKKKPEIVELDSSSDLEDVETRFKVPR--------------RSQT--------CS 152

Query: 169 KSVDCKSGVSTSSASSVSNKKRSSLISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRP 228
           +S+D        S S++S +K S  IS+ +H T S+EELQALDD+EFAN+VIFGN+ FRP
Sbjct: 153 RSMDYSM---EDSVSTISGRKPSVQISNKDHETPSYEELQALDDLEFANLVIFGNKVFRP 209

Query: 229 LQHQACKASVAKQDCFVLLPTGGGKSLCY---------------------QDQIITLNLK 267
           LQHQAC+AS+ ++DCFVL+PTGGGKSLCY                     QDQI+ LNLK
Sbjct: 210 LQHQACRASMERKDCFVLMPTGGGKSLCYQLPATLKAGVTIVISPLLSLIQDQIVALNLK 269

Query: 268 FGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVT 327
           FGIPATFLNSQQT SQAAAVLQEL                       R+D PSCKLLYVT
Sbjct: 270 FGIPATFLNSQQTSSQAAAVLQEL-----------------------RRDNPSCKLLYVT 306

Query: 328 PERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
           PE+I G+ SF E L+CL RKG                     LAGFVVDEAHCV
Sbjct: 307 PEKIAGSSSFLETLRCLDRKG--------------------LLAGFVVDEAHCV 340

3'-5' DNA helicase that may play a role in the repair of DNA.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

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

 Score = 83.2 bits (204), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 60/182 (32%), Positives = 81/182 (44%), Gaps = 65/182 (35%)

Query: 221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------D 259
           FG   FR  Q +A  A++  +DCF+L+PTGGGKSLCYQ                     D
Sbjct: 671 FGLHNFRTNQLEAINAALLGEDCFILMPTGGGKSLCYQLPACVSPGVTIVISPLRSLIVD 730

Query: 260 QIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKP 319
           Q+  L   F IPAT+L   +T S+AA +  +L                      S+KD P
Sbjct: 731 QVQKLT-SFDIPATYLTGDKTDSEAANIYLQL----------------------SKKD-P 766

Query: 320 SCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH 379
             KLLYVTPE++  +      L+ L+ +                    + LA FV+DEAH
Sbjct: 767 IIKLLYVTPEKVCASNRLISTLENLYER--------------------KLLARFVIDEAH 806

Query: 380 CV 381
           CV
Sbjct: 807 CV 808

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

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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

 Score = 80.9 bits (198), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 85/201 (42%), Gaps = 65/201 (32%)

Query: 202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCY---- 257
            S  E      +E  N  +FGN +FRP Q +   A+++  D FVL+PTGGGKSL Y    
Sbjct: 430 WSSREFPWTRKLEVNNKKVFGNHSFRPNQREIINATMSGSDVFVLMPTGGGKSLTYQLPA 489

Query: 258 -----------------QDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQH 300
                            QDQI+ L L+  IPA  L++    ++   + QEL      S+H
Sbjct: 490 LICGGITLVISPLVSLIQDQIMNL-LQANIPAASLSAGMEWAEQLKIFQELN-----SEH 543

Query: 301 YFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVV 360
                                KLLYVTPE++  + S    L+ L+ +G            
Sbjct: 544 ------------------SKYKLLYVTPEKVAKSDSLLRHLENLNSRG------------ 573

Query: 361 VLPHTCQRQLAGFVVDEAHCV 381
                    LA FV+DEAHCV
Sbjct: 574 --------LLARFVIDEAHCV 586

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

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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

 Score = 80.5 bits (197), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 59/182 (32%), Positives = 79/182 (43%), Gaps = 65/182 (35%)

Query: 221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------D 259
           FG   FR  Q +A  A++  +DCF+L+PTGGGKSLCYQ                     D
Sbjct: 663 FGLHNFRTNQLEAINAALLGEDCFILMPTGGGKSLCYQLPACVSPGVTVVISPLRSLIVD 722

Query: 260 QIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKP 319
           Q+  L     IPAT+L   +T S+A  +  +L                      S+KD P
Sbjct: 723 QVQKLT-SLDIPATYLTGDKTDSEATNIYLQL----------------------SKKD-P 758

Query: 320 SCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH 379
             KLLYVTPE+I  +      L+ L+ +                    + LA FV+DEAH
Sbjct: 759 IIKLLYVTPEKICASNRLISTLENLYER--------------------KLLARFVIDEAH 798

Query: 380 CV 381
           CV
Sbjct: 799 CV 800

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

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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

 Score = 79.0 bits (193), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 58/191 (30%), Positives = 84/191 (43%), Gaps = 65/191 (34%)

Query: 212 DMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCY-------------- 257
           ++E  N ++FGN +FRP Q +   A+++  D FVL+PTGGGKSL Y              
Sbjct: 456 NLEVYNKLVFGNHSFRPNQREIINATMSGCDVFVLMPTGGGKSLTYQLPALLCAGITLVI 515

Query: 258 -------QDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVL 310
                  QDQI+ L L+  I A  L++    ++   +LQEL                   
Sbjct: 516 SPLVSLIQDQIMNL-LQTNISAASLSAGMEWAEQLEILQELSS----------------- 557

Query: 311 TCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQL 370
                 +K   KLLYVTPE++  ++S    L+ L+ +                      L
Sbjct: 558 ------EKSKYKLLYVTPEKVAKSESLLRHLEILNSRS--------------------LL 591

Query: 371 AGFVVDEAHCV 381
           A FV+DEAHCV
Sbjct: 592 ARFVIDEAHCV 602

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

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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

 Score = 79.0 bits (193), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 59/183 (32%), Positives = 81/183 (44%), Gaps = 67/183 (36%)

Query: 221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------D 259
           FG   FR  Q +A  A +  +DCF+L+PTGGGKSLCYQ                     D
Sbjct: 615 FGLHRFRTNQLEAINACLCGEDCFILMPTGGGKSLCYQLPGCISPGVTIVISPLRSLIVD 674

Query: 260 QIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKP 319
           Q+  L     IPAT+L   +T ++AA++  +L                      S+KD P
Sbjct: 675 QVQKLT-SLDIPATYLTGDKTDAEAASIYLQL----------------------SKKD-P 710

Query: 320 SCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQ-LAGFVVDEA 378
             KLLYVTPE++  +      ++ L+                     +RQ LA FV+DEA
Sbjct: 711 IIKLLYVTPEKVCASTRLISTMENLY---------------------ERQLLARFVIDEA 749

Query: 379 HCV 381
           HCV
Sbjct: 750 HCV 752

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

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9VGI8|BLM_DROME Bloom syndrome protein homolog OS=Drosophila melanogaster GN=mus309 PE=1 SV=1

 Score = 75.9 bits (185), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 78/280 (27%), Positives = 113/280 (40%), Gaps = 82/280 (29%)

Query: 140 KQKDAILNLSSCPDGRSQIFTPSSVKHSSKSVDCKSGVST----SSASSVSNKKRSSL-- 193
           K K+  +N+S   DG  +       +  S++   KS VS+    +S S V  K+ S+L  
Sbjct: 635 KHKETPINISLDDDGFPEYDEAMFEQMHSQAAANKSRVSSAGPSTSKSVVPTKQTSALHS 694

Query: 194 --ISDNEHGTLSFEELQA-LDDMEFANVV--------IFGNRAFRPLQHQACKASVAKQD 242
             +S N H  +  + +    D  +F +           FG ++FRP Q Q   A++   D
Sbjct: 695 QKLSGNFHANVHNDGITGEFDGQKFEHSTRLMHGLSYSFGLKSFRPNQLQVINATLLGND 754

Query: 243 CFVLLPTGGGKSLCYQ---------------------DQIITLNLKFGIPATFLNSQQTV 281
           CFVL+PTGGGKSLCYQ                     DQI  L     I A  L+ +Q +
Sbjct: 755 CFVLMPTGGGKSLCYQLPAILTEGVTIVISPLKSLIFDQINKL-ASLDICAKSLSGEQKM 813

Query: 282 SQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVL 341
           +   A+ ++L                           P  KLLYVTPE+I  +  F + L
Sbjct: 814 ADVMAIYRDLES-----------------------QPPMVKLLYVTPEKISSSARFQDTL 850

Query: 342 KCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
             L+    I                    + FV+DEAHCV
Sbjct: 851 DTLNSNNYI--------------------SRFVIDEAHCV 870

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

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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

 Score = 75.1 bits (183), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 54/182 (29%), Positives = 78/182 (42%), Gaps = 66/182 (36%)

Query: 221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------D 259
           FG+  FR  Q +A +A V+ +DCF L+PTGGGKS+CYQ                     +
Sbjct: 32  FGHADFRGKQLEAIQAVVSGRDCFCLMPTGGGKSICYQIPALAKPGIVLVVSPLIALMEN 91

Query: 260 QIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKP 319
           Q++ L  K GI A +L+S Q       + ++L  G                       KP
Sbjct: 92  QVMALKEK-GIAAEYLSSTQATHVKNKIHEDLDSG-----------------------KP 127

Query: 320 SCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH 379
           S +LLYVTPE ++  + F   L+ LH +G + L                      +DEAH
Sbjct: 128 SVRLLYVTPE-LIATKGFMLKLRKLHSRGLLNL--------------------IAIDEAH 166

Query: 380 CV 381
           C+
Sbjct: 167 CI 168

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

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9I920|BLM_CHICK Bloom syndrome protein homolog (Fragment) OS=Gallus gallus GN=BLM PE=2 SV=1

 Score = 71.6 bits (174), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 56/182 (30%), Positives = 77/182 (42%), Gaps = 65/182 (35%)

Query: 221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------D 259
           FG  +FR  Q +A  A++  +DCF+L+PTGGGKSLCYQ                     D
Sbjct: 393 FGLHSFRTNQLEAINAALLGEDCFILMPTGGGKSLCYQLPACVSAGVTVVISPLRSLIID 452

Query: 260 QIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKP 319
           Q+  L     I AT+L    T + A+    +L                      S+KD P
Sbjct: 453 QVQKLKT-LDIAATYLTGDITDADASKTYMQL----------------------SKKD-P 488

Query: 320 SCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH 379
             KLLYVTPE++  +      L+ L+ +                    + LA FV+DEAH
Sbjct: 489 IIKLLYVTPEKVCASNRLLSALENLYDR--------------------KLLARFVIDEAH 528

Query: 380 CV 381
           CV
Sbjct: 529 CV 530

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

Gallus gallus (taxid: 9031)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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

 Score = 70.5 bits (171), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 53/164 (32%), Positives = 71/164 (43%), Gaps = 29/164 (17%)

Query: 221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQT 280
           FG   FR  Q Q   +++   D FVL+PTG GKSLCYQ   + L    G+       +  
Sbjct: 243 FGFNQFRHRQKQCILSTLMGHDTFVLMPTGAGKSLCYQLPAVILP---GVTVVVSPLRSL 299

Query: 281 VSQAAAVLQELRQG---LVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSF 337
           +      ++EL  G   L         + I+    +     PS KLLYVTPE+I  +   
Sbjct: 300 IEDQKMKMKELGIGCEALTADLGAPAQEKIYAELGSG---NPSIKLLYVTPEKISASGRL 356

Query: 338 SEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
           + V   LHR+G                     LA FV+DEAHCV
Sbjct: 357 NSVFFDLHRRG--------------------LLARFVIDEAHCV 380

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

Caenorhabditis elegans (taxid: 6239)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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	381
147783250	1640	hypothetical protein VITISV_005845 [Viti	0.887	0.206	0.562	1e-113
118489987	617	unknown [Populus trichocarpa x Populus d	0.850	0.525	0.571	1e-111
224123710	588	predicted protein [Populus trichocarpa]	0.776	0.503	0.540	1e-104
296089753	591	unnamed protein product [Vitis vinifera]	0.797	0.514	0.529	1e-102
255542856	586	DNA helicase hus2, putative [Ricinus com	0.808	0.525	0.536	1e-102
357441847	603	Bloom syndrome protein-like protein [Med	0.790	0.499	0.508	1e-99
225450636	602	PREDICTED: ATP-dependent DNA helicase Q-	0.826	0.523	0.534	1e-98
356533550	612	PREDICTED: LOW QUALITY PROTEIN: ATP-depe	0.808	0.503	0.513	1e-95
30679600	606	ATP-dependent DNA helicase Q-like 1 [Ara	0.805	0.506	0.490	4e-95
449454038	601	PREDICTED: ATP-dependent DNA helicase Q-	0.816	0.517	0.483	3e-93

>gi|147783250|emb|CAN73069.1| hypothetical protein VITISV_005845 [Vitis vinifera]

 Score =  415 bits (1066), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 226/402 (56%), Positives = 267/402 (66%), Gaps = 64/402 (15%)

Query: 1   MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLA 60
           MD HD E EKARLLSLAL+FGFD++SA K L+RL+ LYGDDGQDFI+VEHCGDDF+A L 
Sbjct: 95  MDGHDLEMEKARLLSLALDFGFDEESAMKCLDRLVHLYGDDGQDFITVEHCGDDFLAALV 154

Query: 61  ETMQDSEEWDDLQAMESEACGALNNMFDKRVIDNNQANDNDNSREYIDILDDSPEPKRRP 120
           E+++DSE+WDDLQA+E+EACG LN+MFD  V+    ++       YI+  + S EP++  
Sbjct: 155 ESVEDSEDWDDLQAIETEACGTLNDMFDNDVLHGYGSDYGIYREGYINATEYSYEPQKHQ 214

Query: 121 TLMELDSLSDTEDLDFTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSSKSVDCKSGVSTS 180
             ++LDS SD+ED  F I  +K A     S PDG S  FT SS+KH+S+SVD K  V   
Sbjct: 215 NFVQLDSSSDSEDSSFRILDKKGAAPTSPSWPDGSSSAFTQSSIKHASRSVDSKISVIQG 274

Query: 181 SASSVSNKKRSSLISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAK 240
           S SS+SNK+  S +S++E+GTLS+E L  LDD E ANVVIFGNR FRPLQHQACKASV K
Sbjct: 275 SVSSISNKRARSQMSEDENGTLSYEALLDLDDFELANVVIFGNRTFRPLQHQACKASVTK 334

Query: 241 QDCFVLLPTGGGKSLCY---------------------QDQIITLNLKFGIPATFLNSQQ 279
           +DCFVL+PTGGGKSLCY                     QDQIITLNL FGIPATFL+SQQ
Sbjct: 335 RDCFVLMPTGGGKSLCYQLPATLQPGVTVVVCPLLSLIQDQIITLNLNFGIPATFLSSQQ 394

Query: 280 TVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSE 339
           T SQAAAVL+EL                       RKDKPSCKLLYVTPERI GN +F E
Sbjct: 395 TASQAAAVLKEL-----------------------RKDKPSCKLLYVTPERIAGNSTFFE 431

Query: 340 VLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
           +LK LH KG                    QLAGFVVDEAHCV
Sbjct: 432 ILKSLHWKG--------------------QLAGFVVDEAHCV 453

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118489987|gb|ABK96790.1| unknown [Populus trichocarpa x Populus deltoides]

 Score =  407 bits (1045), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 232/406 (57%), Positives = 275/406 (67%), Gaps = 82/406 (20%)

Query: 1   MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLA 60
           M   D E E+AR LSLALEFGFD++SANK L+RLISLYG+DGQDFI+VE CGDDF+  LA
Sbjct: 1   MGGRDLELERARFLSLALEFGFDEESANKCLDRLISLYGEDGQDFITVECCGDDFLVALA 60

Query: 61  ETMQDSEEW--DDLQAMESEACGALNNMFDKRV-IDNNQANDNDNSREYIDILDDSPEPK 117
           E+MQD+E+W  DDLQ +ESEACG L NMF++ V  +NN+AND+DNSR YID+ DDSPEPK
Sbjct: 61  ESMQDTEDWGDDDLQIIESEACGTLTNMFEEHVEKNNNKANDDDNSRTYIDVTDDSPEPK 120

Query: 118 RRPTLMELDSLSDTED-LDFTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSSKSVDCKSG 176
           +  T MELDS SD+E+  DF++ ++                +FTP + K  S S+DCKS 
Sbjct: 121 KTRTFMELDSSSDSEEEPDFSLEEEN-------------HDLFTPLT-KRISGSLDCKSS 166

Query: 177 VSTSSASSVSNKKRSSLISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKA 236
           V+  S SSV NK++   +S ++H +L++EELQALDD E ANVVIFGN+ FRPLQHQACKA
Sbjct: 167 VTQGSVSSVGNKRQCPRMSKDDHRSLNYEELQALDDFELANVVIFGNKTFRPLQHQACKA 226

Query: 237 SVAKQDCFVLLPTGGGKSLCY---------------------QDQIITLNLKFGIPATFL 275
           +VAKQDCFVL+PTGGGKSLCY                     QDQIITLNLKFGI ATFL
Sbjct: 227 TVAKQDCFVLMPTGGGKSLCYQLPATLKPGVTVVISPLLSLIQDQIITLNLKFGIRATFL 286

Query: 276 NSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQ 335
           NSQQT +QAAA+LQEL                       RKDKPSCKLLYVTPERI GN 
Sbjct: 287 NSQQTSAQAAAILQEL-----------------------RKDKPSCKLLYVTPERIAGNP 323

Query: 336 SFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
           +F E+LKCLH KG                    QLAGFVVDEAHCV
Sbjct: 324 AFLEILKCLHLKG--------------------QLAGFVVDEAHCV 349

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224123710|ref|XP_002330189.1| predicted protein [Populus trichocarpa] gi|222871645|gb|EEF08776.1| predicted protein [Populus trichocarpa]

 Score =  384 bits (987), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 219/405 (54%), Positives = 254/405 (62%), Gaps = 109/405 (26%)

Query: 1   MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLA 60
           M   D E E+AR LSLALEFGFD++SANK L+RLISLYGDDGQDFI+VE CGDDF+  LA
Sbjct: 1   MGGRDLELERARFLSLALEFGFDEESANKCLDRLISLYGDDGQDFITVECCGDDFLVALA 60

Query: 61  ETMQDSEEW--DDLQAMESEACGALNNMFDKRVIDNNQANDNDN-SREYIDILDDSPEPK 117
           E+MQD+E+W  DDLQ +ESEACG L NMF++ V+ NN   ++D+ SR YID+ DDSPEPK
Sbjct: 61  ESMQDTEDWGDDDLQIIESEACGTLTNMFEEHVVKNNNKANDDDNSRTYIDVTDDSPEPK 120

Query: 118 RRPTLMELDSLSDTEDLDFTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSSKSVDCKSGV 177
           +  T MELDS SD+E+                  PD                        
Sbjct: 121 KTRTFMELDSSSDSEEE-----------------PD------------------------ 139

Query: 178 STSSASSVSNKKRSSLISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKAS 237
             SS SSV NK++   +S ++H +L++EELQALDD E ANVVIFGN+ FRPLQHQACKA+
Sbjct: 140 -FSSVSSVGNKRQCPRMSKDDHRSLNYEELQALDDFELANVVIFGNKTFRPLQHQACKAT 198

Query: 238 VAKQDCFVLLPTGGGKSLCY---------------------QDQIITLNLKFGIPATFLN 276
           VAKQDCFVL+PTGGGKSLCY                     QDQIITLNLKFGIPATFLN
Sbjct: 199 VAKQDCFVLMPTGGGKSLCYQLPATLKPGVTVVISPLLSLIQDQIITLNLKFGIPATFLN 258

Query: 277 SQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQS 336
           SQQT +QAAA+LQELR                        DKPSCKLLYVTPERI GN +
Sbjct: 259 SQQTSAQAAAILQELRH-----------------------DKPSCKLLYVTPERIAGNPA 295

Query: 337 FSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
           F E+LKCLH KG                    QLAGFVVDEAHCV
Sbjct: 296 FLEILKCLHLKG--------------------QLAGFVVDEAHCV 320

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296089753|emb|CBI39572.3| unnamed protein product [Vitis vinifera]

 Score =  377 bits (968), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 213/402 (52%), Positives = 247/402 (61%), Gaps = 98/402 (24%)

Query: 1   MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLA 60
           MD HD E EKARLLSLAL+FGFD++SA K L+RL+ LYGDDGQDFI+VEHCGDDF+A L 
Sbjct: 1   MDGHDLEMEKARLLSLALDFGFDEESAMKCLDRLVHLYGDDGQDFITVEHCGDDFLAALV 60

Query: 61  ETMQDSEEWDDLQAMESEACGALNNMFDKRVIDNNQANDNDNSREYIDILDDSPEPKRRP 120
           E+++DSE+WDDLQA+E+EACG LN+MFD                                
Sbjct: 61  ESVEDSEDWDDLQAIETEACGTLNDMFDN------------------------------- 89

Query: 121 TLMELDSLSDTEDLDFTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSSKSVDCKSGVSTS 180
                                 D +    S  DG S  FT SS+KH+S+SVD K  V   
Sbjct: 90  ----------------------DVLHGYGSDYDGSSSAFTQSSIKHASRSVDSKISVIQG 127

Query: 181 SASSVSNKKRSSLISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAK 240
           S SS+SNK+  S +S++E+GTLS+E L  LDD E ANVVIFGNR FRPLQHQACKASV K
Sbjct: 128 SVSSISNKRARSQMSEDENGTLSYEALLDLDDFELANVVIFGNRTFRPLQHQACKASVTK 187

Query: 241 QDCFVLLPTGGGKSLCY---------------------QDQIITLNLKFGIPATFLNSQQ 279
           +DCFVL+PTGGGKSLCY                     QDQIITLNL FGIPATFL+SQQ
Sbjct: 188 RDCFVLMPTGGGKSLCYQLPATLQPGVTVVVCPLLSLIQDQIITLNLNFGIPATFLSSQQ 247

Query: 280 TVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSE 339
           T SQAAAVL+ELR  L+     F  Q  ++L     KDKPSCKLLYVTPERI GN +F E
Sbjct: 248 TASQAAAVLKELR--LLFPGICF--QNCYLLLSFEVKDKPSCKLLYVTPERIAGNSTFFE 303

Query: 340 VLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
           +LK LH KG                    QLAGFVVDEAHCV
Sbjct: 304 ILKSLHWKG--------------------QLAGFVVDEAHCV 325

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255542856|ref|XP_002512491.1| DNA helicase hus2, putative [Ricinus communis] gi|223548452|gb|EEF49943.1| DNA helicase hus2, putative [Ricinus communis]

 Score =  376 bits (966), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 221/412 (53%), Positives = 257/412 (62%), Gaps = 104/412 (25%)

Query: 1   MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLA 60
           M  HD E EKAR LSLA E GFD++SANK L+RLISLYGDDGQDF++VE CGDDF+A LA
Sbjct: 1   MARHDLELEKARFLSLAQECGFDEESANKCLDRLISLYGDDGQDFVTVECCGDDFLAALA 60

Query: 61  ETMQDSEEWDD-LQAMESEACGALNN-MF-DKRVIDNN----QANDNDNSREYIDILDDS 113
           E+M+DSE+WDD LQA+ESEACGAL N MF D+  I++N       +N+N+R YI++ DD 
Sbjct: 61  ESMRDSEDWDDDLQAIESEACGALANYMFSDENAINSNCTKVDNGNNENARGYINVTDDD 120

Query: 114 PEPKRRPTLMELDSLSDTE---DLDFTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSSKS 170
            EPK + T M+LDS S +E   D +F+I + K ++                         
Sbjct: 121 DEPKEKQTWMDLDSSSVSEESEDPEFSITEGKSSL------------------------- 155

Query: 171 VDCKSGVSTSSASSVSNKKRSSLISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQ 230
                  ++ SASS+ NKK+   I  +    LS+EELQALDD E ANVVIFGN +FRPLQ
Sbjct: 156 -----SATSGSASSICNKKKHPGIQKDGRPMLSYEELQALDDFELANVVIFGNMSFRPLQ 210

Query: 231 HQACKASVAKQDCFVLLPTGGGKSLCY---------------------QDQIITLNLKFG 269
           HQACKASVAK+DCFVL+PTGGGKSLCY                     QDQIITLNLKFG
Sbjct: 211 HQACKASVAKRDCFVLMPTGGGKSLCYQLPATLKPGVTVVVSPLLSLIQDQIITLNLKFG 270

Query: 270 IPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPE 329
           IPATFLNSQQT SQAAAVLQEL                       RKDKPSCKLLYVTPE
Sbjct: 271 IPATFLNSQQTASQAAAVLQEL-----------------------RKDKPSCKLLYVTPE 307

Query: 330 RIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
           RI GN  F E+LKCLH KG                    QLAGFVVDEAHCV
Sbjct: 308 RIAGNLGFLEILKCLHWKG--------------------QLAGFVVDEAHCV 339

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357441847|ref|XP_003591201.1| Bloom syndrome protein-like protein [Medicago truncatula] gi|355480249|gb|AES61452.1| Bloom syndrome protein-like protein [Medicago truncatula]

 Score =  369 bits (947), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 203/399 (50%), Positives = 247/399 (61%), Gaps = 98/399 (24%)

Query: 4   HDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLAETM 63
           HD E EK RL+SLALE GFD+ +AN+  +RL+SLYGDDG+DFI+VEHCGDDF+A L E++
Sbjct: 14  HDLELEKVRLISLALELGFDELAANQCFDRLVSLYGDDGRDFITVEHCGDDFLAALGESV 73

Query: 64  QDSEEWDDLQAMESEACGALNNMFDKRVIDNNQANDNDNSREYIDILDDSPEPKRRPTLM 123
           Q++EEWDDL  MES+A G LN++ D R          D S+ +IDI+DDSP+ K+    +
Sbjct: 74  QNTEEWDDLHEMESQAVGTLNHVLDTR---------GDGSKCFIDIIDDSPK-KQGNKFV 123

Query: 124 ELDSLSDTEDLDFTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSSKSVDCKSGVSTSSAS 183
           EL S  D ED +F +                       S V+H +  V+ + G++  S S
Sbjct: 124 ELGSSDDEEDTNFDV-----------------------SRVQHPTNLVNGRKGITQGSVS 160

Query: 184 SVSNKKRSSLISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDC 243
           S S K +SS   D  + TLS+EEL+ LDD+E ANVVIFGN++ RPLQHQACKA++AKQD 
Sbjct: 161 STSRKIKSSAAKD-RNSTLSYEELKTLDDIELANVVIFGNKSLRPLQHQACKAALAKQDS 219

Query: 244 FVLLPTGGGKSLCY---------------------QDQIITLNLKFGIPATFLNSQQTVS 282
           F+L+PTGGGKSLCY                     QDQIITLNLKFGIPATFLNSQQ  S
Sbjct: 220 FILMPTGGGKSLCYQLPATLQPGVTVVVSPLLSLIQDQIITLNLKFGIPATFLNSQQNAS 279

Query: 283 QAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLK 342
           QAAAVLQEL                       RKDKPSCKLLYVTPERI GNQSF  +LK
Sbjct: 280 QAAAVLQEL-----------------------RKDKPSCKLLYVTPERIAGNQSFVGILK 316

Query: 343 CLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
           C+H+KG                    QLAGFVVDEAHCV
Sbjct: 317 CMHQKG--------------------QLAGFVVDEAHCV 335

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225450636|ref|XP_002282715.1| PREDICTED: ATP-dependent DNA helicase Q-like 1-like [Vitis vinifera]

 Score =  366 bits (939), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 215/402 (53%), Positives = 254/402 (63%), Gaps = 87/402 (21%)

Query: 1   MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLA 60
           MD HD E EKARLLSLAL+FGFD++SA K L+RL+ LYGDDGQDFI+VEHCGDDF+A L 
Sbjct: 1   MDGHDLEMEKARLLSLALDFGFDEESAMKCLDRLVHLYGDDGQDFITVEHCGDDFLAALV 60

Query: 61  ETMQDSEEWDDLQAMESEACGALNNMFDKRVIDNNQANDNDNSREYIDILDDSPEPKRRP 120
           E+++DSE+WDDLQA+E+EACG LN+MFD  V+    ++       YI+  + S EP++  
Sbjct: 61  ESVEDSEDWDDLQAIETEACGTLNDMFDNDVLHGYGSDYGIYREGYINATEYSYEPQKHQ 120

Query: 121 TLMELDSLSDTEDLDFTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSSKSVDCKSGVSTS 180
             ++LDS SD+ED  F I  +K A     S PDG                       S+S
Sbjct: 121 NFVQLDSSSDSEDSSFRILDKKGAAPTSPSWPDG-----------------------SSS 157

Query: 181 SASSVSNKKRSSLISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAK 240
           S SS+SNK+  S +S++E+GTLS+E L  LDD E ANVVIFGNR FRPLQHQACKASV K
Sbjct: 158 SVSSISNKRARSQMSEDENGTLSYEALLDLDDFELANVVIFGNRTFRPLQHQACKASVTK 217

Query: 241 QDCFVLLPTGGGKSLCY---------------------QDQIITLNLKFGIPATFLNSQQ 279
           +DCFVL+PTGGGKSLCY                     QDQIITLNL FGIPATFL+SQQ
Sbjct: 218 RDCFVLMPTGGGKSLCYQLPATLQPGVTVVVCPLLSLIQDQIITLNLNFGIPATFLSSQQ 277

Query: 280 TVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSE 339
           T SQAAAVL+EL                       RKDKPSCKLLYVTPERI GN +F E
Sbjct: 278 TASQAAAVLKEL-----------------------RKDKPSCKLLYVTPERIAGNSTFFE 314

Query: 340 VLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
           +LK LH KG                    QLAGFVVDEAHCV
Sbjct: 315 ILKSLHWKG--------------------QLAGFVVDEAHCV 336

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356533550|ref|XP_003535326.1| PREDICTED: LOW QUALITY PROTEIN: ATP-dependent DNA helicase Q-like 1-like [Glycine max]

 Score =  356 bits (913), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 208/405 (51%), Positives = 255/405 (62%), Gaps = 97/405 (23%)

Query: 4   HDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLAETM 63
            D E EK RL+SLALEFGFD+ SANK L+RLI+LYG+DG+DFI+VEHCGDDF+A LAE+M
Sbjct: 10  QDLELEKVRLISLALEFGFDESSANKCLDRLIALYGEDGRDFITVEHCGDDFLAALAESM 69

Query: 64  QDSEEWDDLQAMESEACGALNNMFDKRVIDNNQANDNDNSRE-YIDILDDSPEPKRRP-- 120
           Q +E+WDD Q MES+ACG L ++ DK V     A+++D SR  ++DI+DDSP+P+RR   
Sbjct: 70  Q-TEDWDDQQEMESQACGTLTHVLDKTVDTCADADNDDASRSFFVDIVDDSPQPQRRKGK 128

Query: 121 ---TLMELDSLSDTEDLDFTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSSKSVDCKSGV 177
               ++ELDS SD ED+  ++ ++K  +          +Q F                 +
Sbjct: 129 SHTNVVELDS-SDDEDMHCSVSREKPTV----------TQXF---------------DFI 162

Query: 178 STSSASSVSNKKRSSLISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKAS 237
              S SS S+K +SS  S +   + ++EELQALDD+E ANVVIFGNR FRPLQHQACKA+
Sbjct: 163 IIWSVSSTSSKMQSSFASRDTSSSPTYEELQALDDIELANVVIFGNRTFRPLQHQACKAA 222

Query: 238 VAKQDCFVLLPTGGGKSLCY---------------------QDQIITLNLKFGIPATFLN 276
           +AKQD F+L+PTGGGKSLCY                     QDQIITLNLKFGIP+TFLN
Sbjct: 223 LAKQDSFILMPTGGGKSLCYQLPATLQPGVTVVVSPLLSLIQDQIITLNLKFGIPSTFLN 282

Query: 277 SQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQS 336
           SQQT SQ  AVLQEL                       RKDKPSCKLLYVTPERI GNQS
Sbjct: 283 SQQTASQVTAVLQEL-----------------------RKDKPSCKLLYVTPERIAGNQS 319

Query: 337 FSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
           F E+LK +H+KG                    QLAGFVVDEAHCV
Sbjct: 320 FLEILKFMHQKG--------------------QLAGFVVDEAHCV 344

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30679600|ref|NP_187225.2| ATP-dependent DNA helicase Q-like 1 [Arabidopsis thaliana] gi|75334309|sp|Q9FT74.1|RQL1_ARATH RecName: Full=ATP-dependent DNA helicase Q-like 1; AltName: Full=RecQ-like protein 1; Short=AtRecQ1; Short=AtRecQl1 gi|10944747|emb|CAC14163.1| DNA Helicase [Arabidopsis thaliana] gi|332640767|gb|AEE74288.1| ATP-dependent DNA helicase Q-like 1 [Arabidopsis thaliana]

 Score =  354 bits (909), Expect = 4e-95,   Method: Compositional matrix adjust.
 Identities = 203/414 (49%), Positives = 250/414 (60%), Gaps = 107/414 (25%)

Query: 1   MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLA 60
           M   D E EK RL+SLA + GFD+DSA K L+R + LYGDDG+DFI+VE CGDDF+A LA
Sbjct: 1   MKDQDLELEKVRLISLATKLGFDEDSAKKCLDRFVDLYGDDGRDFITVELCGDDFLAALA 60

Query: 61  ETMQDSEEWDDLQAMESEACGALNNMFDKRVIDNNQANDNDN----------SREYIDIL 110
           +  + +EEWDD+QA+ESEA G L  MFDK        N +DN          SR  + ++
Sbjct: 61  DFEEGTEEWDDIQAIESEAQGNLAEMFDK------STNPSDNGFDTDDDDDDSRVEVHVI 114

Query: 111 DDSPEPKRRPTLMELDSLSDTEDLD--FTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSS 168
           +DSPEPK++P ++ELDS SD ED++  F +P+              RSQ          S
Sbjct: 115 EDSPEPKKKPEIVELDSSSDLEDVETRFKVPR--------------RSQT--------CS 152

Query: 169 KSVDCKSGVSTSSASSVSNKKRSSLISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRP 228
           +S+D        S S++S +K S  IS+ +H T S+EELQALDD+EFAN+VIFGN+ FRP
Sbjct: 153 RSMDYSM---EDSVSTISGRKPSVQISNKDHETPSYEELQALDDLEFANLVIFGNKVFRP 209

Query: 229 LQHQACKASVAKQDCFVLLPTGGGKSLCY---------------------QDQIITLNLK 267
           LQHQAC+AS+ ++DCFVL+PTGGGKSLCY                     QDQI+ LNLK
Sbjct: 210 LQHQACRASMERKDCFVLMPTGGGKSLCYQLPATLKAGVTIVISPLLSLIQDQIVALNLK 269

Query: 268 FGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVT 327
           FGIPATFLNSQQT SQAAAVLQEL                       R+D PSCKLLYVT
Sbjct: 270 FGIPATFLNSQQTSSQAAAVLQEL-----------------------RRDNPSCKLLYVT 306

Query: 328 PERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
           PE+I G+ SF E L+CL RKG                     LAGFVVDEAHCV
Sbjct: 307 PEKIAGSSSFLETLRCLDRKG--------------------LLAGFVVDEAHCV 340

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449454038|ref|XP_004144763.1| PREDICTED: ATP-dependent DNA helicase Q-like 1-like [Cucumis sativus]

 Score =  348 bits (893), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 195/403 (48%), Positives = 244/403 (60%), Gaps = 92/403 (22%)

Query: 1   MDCHDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLA 60
           M  HD E E+ARLLSLA E GFD+ SA   L+R+I+LYGDDG++F+SVEHCGDDF+A LA
Sbjct: 1   MGGHDLELERARLLSLAAELGFDEQSAQACLDRIINLYGDDGKEFVSVEHCGDDFLAALA 60

Query: 61  ETMQDSEEWDDLQAMESEACGALNNMFDKRVIDNNQANDNDNSREYIDILDDSPEPKRRP 120
           E+  D+EEWDDLQAMESEACGAL+ + D+ V + + A +  N    I+I++DS E +  P
Sbjct: 61  ESAPDNEEWDDLQAMESEACGALDIILDESVQEKDGAQNVHNRECPINIIEDSSEGEENP 120

Query: 121 TLMELDSLSDT-EDLDFTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSSKSVDCKSGVST 179
            L+ +DS S++ ED +F   K+++                           V  K+  + 
Sbjct: 121 NLVNIDSSSESDEDANFNASKKRNL--------------------------VQGKNSTTR 154

Query: 180 SSASSVSNKKRSSLISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVA 239
            S  S   +++ S  S+    TL++EELQ LDD E ANVVIFGN+AFRPLQH+ACKA+ +
Sbjct: 155 GSVYSSPGERQYSRTSEAGPKTLTYEELQTLDDFELANVVIFGNKAFRPLQHEACKAAAS 214

Query: 240 KQDCFVLLPTGGGKSLCY---------------------QDQIITLNLKFGIPATFLNSQ 278
           KQDCF+L+PTGGGKSLCY                     QDQI+TLNLKFGIP+TFLNSQ
Sbjct: 215 KQDCFILMPTGGGKSLCYQLPATVQPGVTVVISPLLSLIQDQIVTLNLKFGIPSTFLNSQ 274

Query: 279 QTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFS 338
           QT SQAA VLQELRQ                       DKPSCKLLYVTPERI   QSF 
Sbjct: 275 QTSSQAAVVLQELRQ-----------------------DKPSCKLLYVTPERI-ATQSFL 310

Query: 339 EVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
           E+L+ +H K                    +QLAGFVVDEAHCV
Sbjct: 311 EILRFMHMK--------------------KQLAGFVVDEAHCV 333

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

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	381
TAIR|locus:2074429	606	RECQI1 "RECQ helicase l1" [Ara	0.829	0.521	0.346	3.2e-42
DICTYBASE|DDB_G0272384	973	DDB_G0272384 "Bloom syndrome-l	0.393	0.154	0.323	1.6e-09
TAIR|locus:2197394	1188	RECQ4A [Arabidopsis thaliana (	0.338	0.108	0.328	5.2e-09
UNIPROTKB|F1RMJ3	541	BLM "Uncharacterized protein"	0.322	0.227	0.312	8.9e-09
DICTYBASE|DDB_G0292130	1259	blm "Bloom syndrome protein" [	0.383	0.115	0.337	9.2e-09
FB|FBgn0002906	1487	Blm "Bloom syndrome helicase o	0.328	0.084	0.348	3.2e-08
TAIR|locus:2127998	713	RecQl3 "AT4G35740" [Arabidopsi	0.328	0.175	0.348	3.4e-08
RGD|1311071	621	Recql "RecQ protein-like (DNA	0.367	0.225	0.313	7.7e-08
UNIPROTKB|Q6AYJ1	621	Recql "ATP-dependent DNA helic	0.367	0.225	0.313	7.7e-08
RGD|1308810	999	Blm "Bloom syndrome, RecQ heli	0.099	0.038	0.578	1.3e-07

TAIR|locus:2074429 RECQI1 "RECQ helicase l1" [Arabidopsis thaliana (taxid:3702)]

 Score = 404 (147.3 bits), Expect = 3.2e-42, Sum P(2) = 3.2e-42
 Identities = 116/335 (34%), Positives = 162/335 (48%)

Query:    23 DQDSANKSLNRLISLYGDDGQDFISVEHCGDDFIATLAETMQDSEEWDDLQAMESEACGA 82
             DQD   + + RLISL    G D  S + C D F+    +   D  ++  ++    +   A
Sbjct:     3 DQDLELEKV-RLISLATKLGFDEDSAKKCLDRFVDLYGD---DGRDFITVELCGDDFLAA 58

Query:    83 LNNMFD-KRVIDNNQANDNDNSREYIDILDDSPEPKRRPTXXXXXXXXXXXXXXFTI--- 138
             L +  +     D+ QA +++      ++ D S  P                         
Sbjct:    59 LADFEEGTEEWDDIQAIESEAQGNLAEMFDKSTNPSDNGFDTDDDDDDSRVEVHVIEDSP 118

Query:   139 -PKQKDAILNLSSCPDGRSQIFTPSSVKHSSKSVDCXXXXXXXXXXXXXXXXXXXXXXDN 197
              PK+K  I+ L S  D    + T   V   S++                          N
Sbjct:   119 EPKKKPEIVELDSSSD-LEDVETRFKVPRRSQTCSRSMDYSMEDSVSTISGRKPSVQISN 177

Query:   198 -EHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLC 256
              +H T S+EELQALDD+EFAN+VIFGN+ FRPLQHQAC+AS+ ++DCFVL+PTGGGKSLC
Sbjct:   178 KDHETPSYEELQALDDLEFANLVIFGNKVFRPLQHQACRASMERKDCFVLMPTGGGKSLC 237

Query:   257 YQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGL---VLSQHYFLHQLIFVLTCA 313
             YQ   +   LK G+    ++   ++ Q   V   L+ G+    L+      Q   VL   
Sbjct:   238 YQ---LPATLKAGVTIV-ISPLLSLIQDQIVALNLKFGIPATFLNSQQTSSQAAAVLQ-E 292

Query:   314 SRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKG 348
              R+D PSCKLLYVTPE+I G+ SF E L+CL RKG
Sbjct:   293 LRRDNPSCKLLYVTPEKIAGSSSFLETLRCLDRKG 327

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0042631 "cellular response to water deprivation" evidence=IEP

GO:0070417 "cellular response to cold" evidence=IEP

GO:0006261 "DNA-dependent DNA replication" evidence=RCA

DICTYBASE|DDB_G0272384 DDB_G0272384 "Bloom syndrome-like protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 152 (58.6 bits), Expect = 1.6e-09, Sum P(3) = 1.6e-09
 Identities = 54/167 (32%), Positives = 80/167 (47%)

Query:   196 DNEHGTLSFE-ELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKS 254
             DN+   L  + E   L  +E  N  IFGN+ FR LQ +A  + +  +D FV LPTGGGKS
Sbjct:   450 DNDKNNLKLKREWHEL--VETCNRDIFGNKEFRNLQIEAINSILHDRDTFVSLPTGGGKS 507

Query:   255 LCYQDQIIT--LNLKFGIPATFLNSQQTVSQAAAV---LQELRQ-GLVLSQHYFLHQLIF 308
             LC+Q   I     + F I       Q  V +  ++    + +   G        L QL+ 
Sbjct:   508 LCFQIPSIVDHRGVTFVISPLLALMQDQVHKLKSLGIPAESINSSGSQRENRDVLDQLLN 567

Query:   309 VLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVL 355
               TC         KL+Y+TPER+  ++ F  +L  L+ +G +R  V+
Sbjct:   568 GETC-------KLKLIYITPERLAQSE-FLHLLDQLYDQGRLRRLVV 606

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

GO:0006310 "DNA recombination" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IC

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

GO:0016787 "hydrolase activity" evidence=IEA

TAIR|locus:2197394 RECQ4A [Arabidopsis thaliana (taxid:3702)]

 Score = 158 (60.7 bits), Expect = 5.2e-09, Sum P(2) = 5.2e-09
 Identities = 46/140 (32%), Positives = 70/140 (50%)

Query:   213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-DQIITLNLKFGI- 270
             +E  N  +FGN +FRP Q +   A+++  D FVL+PTGGGKSL YQ   +I   +   I 
Sbjct:   441 LEVNNKKVFGNHSFRPNQREIINATMSGSDVFVLMPTGGGKSLTYQLPALICGGITLVIS 500

Query:   271 PATFLNSQQTVS--QAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTP 328
             P   L   Q ++  QA      L  G+  ++   + Q +         +    KLLYVTP
Sbjct:   501 PLVSLIQDQIMNLLQANIPAASLSAGMEWAEQLKIFQEL-------NSEHSKYKLLYVTP 553

Query:   329 ERIVGNQSFSEVLKCLHRKG 348
             E++  + S    L+ L+ +G
Sbjct:   554 EKVAKSDSLLRHLENLNSRG 573

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA;IMP

GO:0006310 "DNA recombination" evidence=IEA;IMP

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

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0070417 "cellular response to cold" evidence=IEP

GO:0071215 "cellular response to abscisic acid stimulus" evidence=IEP

GO:0000723 "telomere maintenance" evidence=IMP

GO:0000724 "double-strand break repair via homologous recombination" evidence=IGI;RCA;IMP

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

GO:0043138 "3'-5' DNA helicase activity" evidence=IMP;IDA

GO:0051276 "chromosome organization" evidence=IMP

GO:0009506 "plasmodesma" evidence=IDA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

UNIPROTKB|F1RMJ3 BLM "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 147 (56.8 bits), Expect = 8.9e-09, Sum P(2) = 8.9e-09
 Identities = 40/128 (31%), Positives = 61/128 (47%)

Query:   221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQT 280
             FG   FR  Q +A  A++  +DCF+L+PTGGGKSLCYQ   +   +  G+       +  
Sbjct:   352 FGLHNFRTNQLEAINAALLGEDCFILMPTGGGKSLCYQ---LPACVSSGVTIVISPLRSL 408

Query:   281 VSQAAAVLQELR-QGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSE 339
             +      L  L      L+      +   +    S+KD P  KLLYVTPE++  +     
Sbjct:   409 IVDQVQKLTSLDIPATYLTGDKTDSEATSIYLQLSKKD-PIIKLLYVTPEKVCASNRLIS 467

Query:   340 VLKCLHRK 347
              L+ L+ +
Sbjct:   468 TLENLYNR 475

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

GO:0006310 "DNA recombination" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

DICTYBASE|DDB_G0292130 blm "Bloom syndrome protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 160 (61.4 bits), Expect = 9.2e-09, Sum P(2) = 9.2e-09
 Identities = 52/154 (33%), Positives = 72/154 (46%)

Query:   196 DNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSL 255
             DN     +F   Q + D+   N  +FG   FR  Q +   +++   D FVL+PTGGGKSL
Sbjct:   500 DNSRFKGNFPWSQKIIDI---NRSMFGFHVFRENQREIINSTLEGNDTFVLMPTGGGKSL 556

Query:   256 CYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQ-GLVLSQHYFLHQLIFVLTCAS 314
             CYQ  I  L  K G+          ++     L+ L      LS        I V     
Sbjct:   557 CYQ--IPALYQK-GLTIVISPLISLINDQVEFLETLGYPAAALSSAVSSDAAIDVYKDI- 612

Query:   315 RKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKG 348
             R + P  +LLY+TPER+V + S  E+L  L +KG
Sbjct:   613 RSNSPKIRLLYLTPERVVKSDSLIEILANLDQKG 646

GO:0044237 "cellular metabolic process" evidence=IEA

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

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

GO:0006310 "DNA recombination" evidence=IEA;ISS

GO:0006281 "DNA repair" evidence=IEA;ISS

GO:0006260 "DNA replication" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IC

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

GO:0016787 "hydrolase activity" evidence=IEA

FB|FBgn0002906 Blm "Bloom syndrome helicase ortholog" [Drosophila melanogaster (taxid:7227)]

 Score = 161 (61.7 bits), Expect = 3.2e-08, Sum P(3) = 3.2e-08
 Identities = 46/132 (34%), Positives = 68/132 (51%)

Query:   221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-DQIITLNLKFGI-PATFLNSQ 278
             FG ++FRP Q Q   A++   DCFVL+PTGGGKSLCYQ   I+T  +   I P   L   
Sbjct:   733 FGLKSFRPNQLQVINATLLGNDCFVLMPTGGGKSLCYQLPAILTEGVTIVISPLKSLIFD 792

Query:   279 QTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFS 338
             Q +++ A++  ++    +  +      +       S+   P  KLLYVTPE+I  +  F 
Sbjct:   793 Q-INKLASL--DICAKSLSGEQKMADVMAIYRDLESQP--PMVKLLYVTPEKISSSARFQ 847

Query:   339 EVLKCLHRKGSI 350
             + L  L+    I
Sbjct:   848 DTLDTLNSNNYI 859

GO:0006302 "double-strand break repair" evidence=IMP

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

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

GO:0004386 "helicase activity" evidence=ISS

GO:0003678 "DNA helicase activity" evidence=ISS

GO:0000731 "DNA synthesis involved in DNA repair" evidence=IMP

GO:0005524 "ATP binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0045003 "double-strand break repair via synthesis-dependent strand annealing" evidence=IMP

GO:0032508 "DNA duplex unwinding" evidence=IDA

GO:0000732 "strand displacement" evidence=IDA

GO:0008094 "DNA-dependent ATPase activity" evidence=IDA

GO:0000403 "Y-form DNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0000733 "DNA strand renaturation" evidence=IDA

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IDA

GO:0000724 "double-strand break repair via homologous recombination" evidence=IMP

GO:0007131 "reciprocal meiotic recombination" evidence=IMP

GO:1901291 "negative regulation of double-strand break repair via single-strand annealing" evidence=IMP

TAIR|locus:2127998 RecQl3 "AT4G35740" [Arabidopsis thaliana (taxid:3702)]

 Score = 157 (60.3 bits), Expect = 3.4e-08, P = 3.4e-08
 Identities = 47/135 (34%), Positives = 68/135 (50%)

Query:   221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQT 280
             FG+  FR  Q +A +A V+ +DCF L+PTGGGKS+CYQ   I    K GI          
Sbjct:    32 FGHADFRGKQLEAIQAVVSGRDCFCLMPTGGGKSICYQ---IPALAKPGIVLVVSPLIAL 88

Query:   281 VSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASR---KDKPSCKLLYVTPERIVGNQSF 337
             +      L+E  +G+  +++    Q   V           KPS +LLYVTPE ++  + F
Sbjct:    89 MENQVMALKE--KGIA-AEYLSSTQATHVKNKIHEDLDSGKPSVRLLYVTPE-LIATKGF 144

Query:   338 SEVLKCLHRKGSIRL 352
                L+ LH +G + L
Sbjct:   145 MLKLRKLHSRGLLNL 159

GO:0005524 "ATP binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

GO:0008152 "metabolic process" evidence=IEA

GO:0006310 "DNA recombination" evidence=IDA

GO:0009378 "four-way junction helicase activity" evidence=IDA

GO:0036310 "annealing helicase activity" evidence=IDA

GO:0043138 "3'-5' DNA helicase activity" evidence=IDA

RGD|1311071 Recql "RecQ protein-like (DNA helicase Q1-like)" [Rattus norvegicus (taxid:10116)]

 Score = 153 (58.9 bits), Expect = 7.7e-08, P = 7.7e-08
 Identities = 47/150 (31%), Positives = 73/150 (48%)

Query:   220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ 279
             +F  + FRPLQ +   A++A++D F+++PTGGGKSLCYQ   +  +   G          
Sbjct:    86 VFKLQKFRPLQLETVNATMARKDIFLVMPTGGGKSLCYQLPALCSD---GFTLVICPLIS 142

Query:   280 TVSQAAAVLQELR-QGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFS 338
              +     VLQ+L     +L+       +  V T    K+    KL+YVTPE+I  ++ F 
Sbjct:   143 LMEDQLMVLQQLGISATMLNSSSSKEHVKCVHTEMMNKNS-HLKLIYVTPEKIAKSKMFM 201

Query:   339 EVLKCLHRKGSIRLKVLTTDVVVLPHTCQR 368
               L+  +  G  RL  +  D V   H C +
Sbjct:   202 SRLEKAYEAG--RLTGVAVDEV---HCCSQ 226

GO:0000733 "DNA strand renaturation" evidence=IEA;ISO

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003678 "DNA helicase activity" evidence=ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0015630 "microtubule cytoskeleton" evidence=IEA;ISO

GO:0032508 "DNA duplex unwinding" evidence=ISO

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|Q6AYJ1 Recql "ATP-dependent DNA helicase Q1" [Rattus norvegicus (taxid:10116)]

 Score = 153 (58.9 bits), Expect = 7.7e-08, P = 7.7e-08
 Identities = 47/150 (31%), Positives = 73/150 (48%)

Query:   220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ 279
             +F  + FRPLQ +   A++A++D F+++PTGGGKSLCYQ   +  +   G          
Sbjct:    86 VFKLQKFRPLQLETVNATMARKDIFLVMPTGGGKSLCYQLPALCSD---GFTLVICPLIS 142

Query:   280 TVSQAAAVLQELR-QGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFS 338
              +     VLQ+L     +L+       +  V T    K+    KL+YVTPE+I  ++ F 
Sbjct:   143 LMEDQLMVLQQLGISATMLNSSSSKEHVKCVHTEMMNKNS-HLKLIYVTPEKIAKSKMFM 201

Query:   339 EVLKCLHRKGSIRLKVLTTDVVVLPHTCQR 368
               L+  +  G  RL  +  D V   H C +
Sbjct:   202 SRLEKAYEAG--RLTGVAVDEV---HCCSQ 226

GO:0005524 "ATP binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

RGD|1308810 Blm "Bloom syndrome, RecQ helicase-like" [Rattus norvegicus (taxid:10116)]

 Score = 120 (47.3 bits), Expect = 1.3e-07, Sum P(4) = 1.3e-07
 Identities = 22/38 (57%), Positives = 28/38 (73%)

Query:   221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ 258
             FG   FR  Q +A  A++  +DCF+L+PTGGGKSLCYQ
Sbjct:   654 FGLHNFRTNQLEAINAALLGEDCFILMPTGGGKSLCYQ 691

GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=ISO

GO:0000405 "bubble DNA binding" evidence=ISO

GO:0000723 "telomere maintenance" evidence=ISO

GO:0000729 "DNA double-strand break processing" evidence=ISO

GO:0000733 "DNA strand renaturation" evidence=ISO

GO:0000800 "lateral element" evidence=ISO

GO:0001673 "male germ cell nucleus" evidence=ISO

GO:0002039 "p53 binding" evidence=ISO

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=ISO

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

GO:0004386 "helicase activity" evidence=ISO

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

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005657 "replication fork" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006200 "ATP catabolic process" evidence=ISO

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=ISO

GO:0006310 "DNA recombination" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=ISO

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

GO:0008150 "biological_process" evidence=ND

GO:0009378 "four-way junction helicase activity" evidence=ISO

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

GO:0016363 "nuclear matrix" evidence=ISO

GO:0016605 "PML body" evidence=ISO

GO:0016887 "ATPase activity" evidence=ISO

GO:0031297 "replication fork processing" evidence=ISO

GO:0036310 "annealing helicase activity" evidence=ISO

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=ISO

GO:0045120 "pronucleus" evidence=ISO

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISO

GO:0045910 "negative regulation of DNA recombination" evidence=ISO

GO:0045950 "negative regulation of mitotic recombination" evidence=ISO

GO:0046632 "alpha-beta T cell differentiation" evidence=ISO

GO:0046641 "positive regulation of alpha-beta T cell proliferation" evidence=ISO

GO:0051098 "regulation of binding" evidence=ISO

GO:0051259 "protein oligomerization" evidence=ISO

GO:0051276 "chromosome organization" evidence=ISO

GO:0051782 "negative regulation of cell division" evidence=ISO

GO:0051880 "G-quadruplex DNA binding" evidence=ISO

GO:0000781 "chromosome, telomeric region" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.12	0.824
3rd Layer	3.6.4	0.766

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	381
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	5e-22
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	5e-21
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	4e-17
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	2e-16
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	2e-16
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	9e-06
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	0.001

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

 Score = 96.8 bits (241), Expect = 5e-22
 Identities = 58/182 (31%), Positives = 76/182 (41%), Gaps = 70/182 (38%)

Query: 221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------D 259
           FG  +FRP+Q +   A +  +DCFV++PTGGGKSLCYQ                     D
Sbjct: 7   FGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCSDGITLVISPLISLMED 66

Query: 260 QIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKP 319
           Q++ L    GIPATFLNS Q+  Q   VL +L+ G +                       
Sbjct: 67  QVLQLKA-SGIPATFLNSSQSKEQQKNVLTDLKDGKI----------------------- 102

Query: 320 SCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH 379
             KLLYVTPE+   +    + L+   RKG                          VDEAH
Sbjct: 103 --KLLYVTPEKCSASNRLLQTLE--ERKGITL---------------------IAVDEAH 137

Query: 380 CV 381
           C+
Sbjct: 138 CI 139

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

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

 Score = 94.7 bits (236), Expect = 5e-21
 Identities = 49/183 (26%), Positives = 75/183 (40%), Gaps = 72/183 (39%)

Query: 220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ--------------------- 258
           +FG  +FRP Q +   A ++ +D  V++PTGGGKSLCYQ                     
Sbjct: 12  VFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLLEGLTLVVSPLISLMK 71

Query: 259 DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDK 318
           DQ+  L    GI A +LNS  +  +   VL +L+ G +                      
Sbjct: 72  DQVDQLEAA-GIRAAYLNSTLSREERQQVLNQLKSGQL---------------------- 108

Query: 319 PSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEA 378
              KLLY++PER++ +  F E+LK                        +  ++   +DEA
Sbjct: 109 ---KLLYISPERLM-SPRFLELLK------------------------RLPISLVAIDEA 140

Query: 379 HCV 381
           HC+
Sbjct: 141 HCI 143

Length = 590

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

 Score = 82.4 bits (204), Expect = 4e-17
 Identities = 47/182 (25%), Positives = 65/182 (35%), Gaps = 72/182 (39%)

Query: 221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------D 259
           FG   FRP Q +     +  +D  V++PTGGGKSLCYQ                     D
Sbjct: 9   FGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLLKGLTVVISPLISLMKD 68

Query: 260 QIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKP 319
           Q+  L    G+ A +LNS  +  +   + + L  G +                       
Sbjct: 69  QVDQLRAA-GVAAAYLNSTLSAKEQQDIEKALVNGEL----------------------- 104

Query: 320 SCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH 379
             KLLYV PER+     F  +L+                        +  +A   VDEAH
Sbjct: 105 --KLLYVAPERLE-QDYFLNMLQ------------------------RIPIALVAVDEAH 137

Query: 380 CV 381
           CV
Sbjct: 138 CV 139

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

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

 Score = 80.7 bits (199), Expect = 2e-16
 Identities = 59/190 (31%), Positives = 82/190 (43%), Gaps = 65/190 (34%)

Query: 213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCY--------------- 257
           +E  N  +FGN +FRP Q +   A+++  D FVL+PTGGGKSL Y               
Sbjct: 448 LEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALICPGITLVIS 507

Query: 258 ------QDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLT 311
                 QDQI+ L L+  IPA  L++    ++   +LQEL                    
Sbjct: 508 PLVSLIQDQIMNL-LQANIPAASLSAGMEWAEQLEILQELSS------------------ 548

Query: 312 CASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLA 371
                +    KLLYVTPE++  + S    L+ L+ +G                     LA
Sbjct: 549 -----EYSKYKLLYVTPEKVAKSDSLLRHLENLNSRG--------------------LLA 583

Query: 372 GFVVDEAHCV 381
            FV+DEAHCV
Sbjct: 584 RFVIDEAHCV 593

Length = 1195

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

 Score = 80.1 bits (198), Expect = 2e-16
 Identities = 53/182 (29%), Positives = 69/182 (37%), Gaps = 72/182 (39%)

Query: 221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------D 259
           FG + FRP Q +   A ++ +DC V++PTGGGKSLCYQ                     D
Sbjct: 21  FGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPLISLMKD 80

Query: 260 QIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKP 319
           Q+  L L  G+ A  LNS QT  Q   V+   R G +                       
Sbjct: 81  QVDQL-LANGVAAACLNSTQTREQQLEVMAGCRTGQI----------------------- 116

Query: 320 SCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH 379
             KLLY+ PER++   +F                        L H      A   VDEAH
Sbjct: 117 --KLLYIAPERLM-MDNF------------------------LEHLAHWNPALLAVDEAH 149

Query: 380 CV 381
           C+
Sbjct: 150 CI 151

Length = 607

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

 Score = 45.3 bits (108), Expect = 9e-06
 Identities = 38/164 (23%), Positives = 60/164 (36%), Gaps = 40/164 (24%)

Query: 227 RPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQII-TLNLKFGIPATFLNS------QQ 279
            P+Q QA  A ++ +D  V  PTG GK+L +   I+  L  K G P   + +      +Q
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60

Query: 280 TVSQAAAVLQ--ELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSF 337
              +   + +   LR  L+        Q   +        K    +L  TP R++     
Sbjct: 61  IYEELKKLFKILGLRVALLTGGTSLKEQARKL-------KKGKADILVGTPGRLLDL--- 110

Query: 338 SEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
              L+    K    LK+L                  V+DEAH +
Sbjct: 111 ---LRRGKLKLLKNLKLL------------------VLDEAHRL 133

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

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

 Score = 39.4 bits (92), Expect = 0.001
 Identities = 37/167 (22%), Positives = 58/167 (34%), Gaps = 35/167 (20%)

Query: 221 FGNRAFRPLQHQACKASVA-KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ 279
           FG    RP Q +A +A ++  +D  +  PTG GK+L          LK G     L    
Sbjct: 4   FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAAL-LPALEALKRGKGGRVLVLVP 62

Query: 280 TVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKD-----KPSCKLLYVTPERIVGN 334
           T   A    +EL++   L     L  +      + R+           +L  TP R+   
Sbjct: 63  TRELAEQWAEELKK---LGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRL--- 116

Query: 335 QSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV 381
                            L +L  D + L       +   ++DEAH +
Sbjct: 117 -----------------LDLLENDKLSL-----SNVDLVILDEAHRL 141

Length = 201

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	381
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.89
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.89
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.88
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.86
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.86
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.86
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	99.84
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.83
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.82
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.81
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.8
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.79
PTZ00110	545	helicase; Provisional	99.79
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.79
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.78
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.78
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.77
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	99.77
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	99.75
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.75
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.75
PTZ00424	401	helicase 45; Provisional	99.74
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	99.72
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	99.69
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.68
PRK14701	1638	reverse gyrase; Provisional	99.65
KOG0347	731	consensus RNA helicase [RNA processing and modific	99.65
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.64
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.62
PRK13767	876	ATP-dependent helicase; Provisional	99.62
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	99.61
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.61
PRK02362	737	ski2-like helicase; Provisional	99.61
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.59
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	99.59
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	99.57
PRK00254	720	ski2-like helicase; Provisional	99.57
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	99.57
KOG0343	758	consensus RNA Helicase [RNA processing and modific	99.56
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	99.56
KOG0346	569	consensus RNA helicase [RNA processing and modific	99.55
PRK09401	1176	reverse gyrase; Reviewed	99.55
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.54
KOG0334	997	consensus RNA helicase [RNA processing and modific	99.52
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.51
PRK01172	674	ski2-like helicase; Provisional	99.51
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.49
COG1205	851	Distinct helicase family with a unique C-terminal	99.47
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	99.46
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.46
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	99.46
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.44
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.44
KOG4284	980	consensus DEAD box protein [Transcription]	99.43
PRK10689	1147	transcription-repair coupling factor; Provisional	99.42
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	99.4
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.4
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	99.36
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.3
PRK05580	679	primosome assembly protein PriA; Validated	99.26
COG1204	766	Superfamily II helicase [General function predicti	99.21
KOG0327	397	consensus Translation initiation factor 4F, helica	99.21
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.16
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.15
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.15
PHA02558	501	uvsW UvsW helicase; Provisional	99.14
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.14
PRK13766	773	Hef nuclease; Provisional	99.12
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.08
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.08
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.01
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	98.98
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	98.95
KOG0354	746	consensus DEAD-box like helicase [General function	98.94
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	98.94
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	98.88
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	98.88
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.86
PRK12904	830	preprotein translocase subunit SecA; Reviewed	98.86
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.82
COG1202	830	Superfamily II helicase, archaea-specific [General	98.8
TIGR00595	505	priA primosomal protein N'. All proteins in this f	98.77
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.73
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	98.72
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	98.67
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.66
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	98.63
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	98.56
PHA02653	675	RNA helicase NPH-II; Provisional	98.51
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	98.44
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	98.44
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	98.42
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.39
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	98.37
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	98.36
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.36
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.31
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.21
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	98.15
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	98.09
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.08
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.06
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.03
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.93
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.9
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.82
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	97.8
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	97.75
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	97.75
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	97.74
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	97.72
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	97.67
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	97.66
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	97.64
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	97.63
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	97.63
PRK09694	878	helicase Cas3; Provisional	97.62
COG4096	875	HsdR Type I site-specific restriction-modification	97.6
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	97.59
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	97.55
KOG1123	776	consensus RNA polymerase II transcription initiati	97.53
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	97.53
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	97.43
PRK04914	956	ATP-dependent helicase HepA; Validated	97.41
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	97.25
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	97.21
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	97.03
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.0
PRK15483	986	type III restriction-modification system StyLTI en	96.75
PRK14873	665	primosome assembly protein PriA; Provisional	96.75
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	96.72
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	96.65
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	96.63
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.62
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	96.56
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	96.42
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	96.33
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.27
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	96.26
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	96.23
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.15
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	96.01
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	95.98
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	95.95
COG4889	1518	Predicted helicase [General function prediction on	95.89
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	95.88
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	95.84
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	95.81
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	95.79
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	95.73
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	95.73
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	95.63
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	95.5
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	95.46
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	95.42
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.42
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	95.39
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	95.36
PRK10867	433	signal recognition particle protein; Provisional	95.34
TIGR00767	415	rho transcription termination factor Rho. Members	95.34
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	95.31
TIGR00959	428	ffh signal recognition particle protein. This mode	95.27
PRK00411	394	cdc6 cell division control protein 6; Reviewed	95.24
PRK14974	336	cell division protein FtsY; Provisional	95.22
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.13
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	95.08
PTZ00112	1164	origin recognition complex 1 protein; Provisional	95.04
PRK06526	254	transposase; Provisional	95.03
PRK10416	318	signal recognition particle-docking protein FtsY;	95.03
PRK08727	233	hypothetical protein; Validated	95.03
PRK00771	437	signal recognition particle protein Srp54; Provisi	95.02
smart00382	148	AAA ATPases associated with a variety of cellular	94.96
PF00004	132	AAA: ATPase family associated with various cellula	94.88
PRK04296	190	thymidine kinase; Provisional	94.72
PRK10875	615	recD exonuclease V subunit alpha; Provisional	94.72
PRK08181	269	transposase; Validated	94.71
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	94.69
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	94.65
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	94.64
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	94.62
COG1484	254	DnaC DNA replication protein [DNA replication, rec	94.6
PRK07952	244	DNA replication protein DnaC; Validated	94.56
KOG1002	791	consensus Nucleotide excision repair protein RAD16	94.55
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	94.39
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	94.26
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	94.1
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	94.06
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	93.97
PRK13889	988	conjugal transfer relaxase TraA; Provisional	93.86
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	93.81
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	93.64
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	93.59
TIGR02237	209	recomb_radB DNA repair and recombination protein R	93.25
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	93.04
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	92.96
PRK08084	235	DNA replication initiation factor; Provisional	92.93
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	92.9
PRK12377	248	putative replication protein; Provisional	92.81
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	92.79
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	92.78
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	92.63
PRK06921	266	hypothetical protein; Provisional	92.59
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	92.48
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	92.46
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	92.29
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	92.21
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	92.16
PRK06067	234	flagellar accessory protein FlaH; Validated	92.16
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	92.11
PRK06893	229	DNA replication initiation factor; Validated	91.96
TIGR00665	434	DnaB replicative DNA helicase. This model describe	91.93
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	91.91
PRK10865	857	protein disaggregation chaperone; Provisional	91.82
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	91.74
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	91.69
cd01394	218	radB RadB. The archaeal protein radB shares simila	91.33
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	91.32
PRK06835	329	DNA replication protein DnaC; Validated	91.29
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	91.25
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	91.23
PRK09376	416	rho transcription termination factor Rho; Provisio	91.12
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	91.11
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	90.99
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	90.95
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	90.8
PRK12608	380	transcription termination factor Rho; Provisional	90.77
PF13245	76	AAA_19: Part of AAA domain	90.76
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	90.73
KOG1805	1100	consensus DNA replication helicase [Replication, r	90.7
PF12846	304	AAA_10: AAA-like domain	90.65
PRK13826	1102	Dtr system oriT relaxase; Provisional	90.64
PRK00149	450	dnaA chromosomal replication initiation protein; R	90.61
PHA02244	383	ATPase-like protein	90.59
TIGR00376	637	DNA helicase, putative. The gene product may repre	90.59
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	90.56
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	90.54
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	90.54
PRK13833	323	conjugal transfer protein TrbB; Provisional	90.27
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	90.15
PRK05973	237	replicative DNA helicase; Provisional	90.13
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	90.0
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	89.97
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	89.94
COG0610	962	Type I site-specific restriction-modification syst	89.89
TIGR02533	486	type_II_gspE general secretory pathway protein E.	89.85
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	89.85
PRK04195	482	replication factor C large subunit; Provisional	89.79
cd00983	325	recA RecA is a bacterial enzyme which has roles in	89.79
PRK08939	306	primosomal protein DnaI; Reviewed	89.78
CHL00095	821	clpC Clp protease ATP binding subunit	89.77
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	89.75
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	89.64
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	89.62
cd03115	173	SRP The signal recognition particle (SRP) mediates	89.53
KOG4439	901	consensus RNA polymerase II transcription terminat	89.48
PRK10536	262	hypothetical protein; Provisional	89.47
cd01128	249	rho_factor Transcription termination factor rho is	89.38
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	89.38
PRK10436	462	hypothetical protein; Provisional	89.33
CHL00176	638	ftsH cell division protein; Validated	89.28
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	89.26
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	89.25
PRK08760	476	replicative DNA helicase; Provisional	89.24
PRK09354	349	recA recombinase A; Provisional	89.19
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	89.08
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	89.04
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	89.0
PRK08116	268	hypothetical protein; Validated	88.99
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	88.97
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	88.89
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	88.86
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	88.72
PRK11823	446	DNA repair protein RadA; Provisional	88.7
CHL00181	287	cbbX CbbX; Provisional	88.69
PHA02542	473	41 41 helicase; Provisional	88.67
PRK14087	450	dnaA chromosomal replication initiation protein; P	88.65
PRK09183	259	transposase/IS protein; Provisional	88.55
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	88.44
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	88.42
PRK08533	230	flagellar accessory protein FlaH; Reviewed	88.38
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	88.26
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	88.21
PRK09165	497	replicative DNA helicase; Provisional	88.14
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	88.07
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	88.0
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	87.97
KOG1803	649	consensus DNA helicase [Replication, recombination	87.94
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	87.93
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	87.87
KOG1131	755	consensus RNA polymerase II transcription initiati	87.85
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	87.79
PRK04328	249	hypothetical protein; Provisional	87.66
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	87.66
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	87.63
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	87.63
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	87.59
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	87.45
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	87.43
PRK05595	444	replicative DNA helicase; Provisional	87.39
PLN03025	319	replication factor C subunit; Provisional	87.29
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	87.23
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	87.21
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	87.01
PRK03992	389	proteasome-activating nucleotidase; Provisional	87.0
PRK08903	227	DnaA regulatory inactivator Hda; Validated	86.96
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	86.96
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	86.93
PRK00440	319	rfc replication factor C small subunit; Reviewed	86.89
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	86.75
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	86.73
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	86.73
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	86.7
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	86.66
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	86.57
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	86.54
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	86.53
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	86.34
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	86.32
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	86.23
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	86.2
PRK05642	234	DNA replication initiation factor; Validated	86.14
PRK13342	413	recombination factor protein RarA; Reviewed	86.13
PRK07004	460	replicative DNA helicase; Provisional	85.98
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	85.89
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	85.88
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	85.8
PRK08769	319	DNA polymerase III subunit delta'; Validated	85.78
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	85.77
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	85.73
PRK06321	472	replicative DNA helicase; Provisional	85.41
PRK05636	505	replicative DNA helicase; Provisional	85.21
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	85.08
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	84.86
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	84.8
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	84.79
PHA02544	316	44 clamp loader, small subunit; Provisional	84.65
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	84.6
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	84.4
PRK09302	509	circadian clock protein KaiC; Reviewed	84.31
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	84.24
PRK07773	886	replicative DNA helicase; Validated	84.15
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	84.05
PRK08506	472	replicative DNA helicase; Provisional	84.03
PRK05748	448	replicative DNA helicase; Provisional	83.95
PRK14088	440	dnaA chromosomal replication initiation protein; P	83.78
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	83.71
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	83.71
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	83.64
PF05872	502	DUF853: Bacterial protein of unknown function (DUF	83.61
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	83.53
PRK13851	344	type IV secretion system protein VirB11; Provision	83.31
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	83.27
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	83.16
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	83.12
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	83.1
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	83.08
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	82.95
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	82.27
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	82.13
PRK12422	445	chromosomal replication initiation protein; Provis	82.12
PF00154	322	RecA: recA bacterial DNA recombination protein; In	82.08
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	82.08
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	82.0
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	81.81
KOG0346	569	consensus RNA helicase [RNA processing and modific	81.53
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	81.52
PF13173	128	AAA_14: AAA domain	81.48
PHA00350	399	putative assembly protein	81.42
PRK13850	670	type IV secretion system protein VirD4; Provisiona	81.39
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	81.21
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	81.2
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	81.15
KOG0387	923	consensus Transcription-coupled repair protein CSB	81.11
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	80.86
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	80.82
PRK05707	328	DNA polymerase III subunit delta'; Validated	80.63
PRK09302	509	circadian clock protein KaiC; Reviewed	80.59
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	80.48
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	80.31
PRK13341	725	recombination factor protein RarA/unknown domain f	80.21

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

Probab=99.89  E-value=1.5e-23  Score=220.52  Aligned_cols=117  Identities=42%  Similarity=0.723  Sum_probs=107.7

Q ss_pred             HHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------HHHHHHHhhcCCcE
Q 042872          214 EFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------DQIITLNLKFGIPA  272 (381)
Q Consensus       214 ~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------dQv~~L~~~~gI~a  272 (381)
                      ...+..+|||..|||.|+++|..+++|+|+|++||||+|||+|||                     ||+.+|. ..||+|
T Consensus         6 ~~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~~G~TLVVSPLiSLM~DQV~~l~-~~Gi~A   84 (590)
T COG0514           6 QQVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLLEGLTLVVSPLISLMKDQVDQLE-AAGIRA   84 (590)
T ss_pred             HHHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhcCCCEEEECchHHHHHHHHHHHH-HcCcee
Confidence            355778899999999999999999999999999999999999999                     9999998 689999


Q ss_pred             EEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccc
Q 042872          273 TFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRL  352 (381)
Q Consensus       273 ~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l  352 (381)
                      ..+++..+.+++..++..+.+|                         .+++||.+||+|. ++.|++.|..    .    
T Consensus        85 ~~lnS~l~~~e~~~v~~~l~~g-------------------------~~klLyisPErl~-~~~f~~~L~~----~----  130 (590)
T COG0514          85 AYLNSTLSREERQQVLNQLKSG-------------------------QLKLLYISPERLM-SPRFLELLKR----L----  130 (590)
T ss_pred             ehhhcccCHHHHHHHHHHHhcC-------------------------ceeEEEECchhhc-ChHHHHHHHh----C----
Confidence            9999999999999999999876                         6899999999998 5788887763    2    


Q ss_pred             cccccccccccccccCCccEEEEeccccC
Q 042872          353 KVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       353 ~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                      +|.+|||||||||
T Consensus       131 ----------------~i~l~vIDEAHCi  143 (590)
T COG0514         131 ----------------PISLVAIDEAHCI  143 (590)
T ss_pred             ----------------CCceEEechHHHH
Confidence                            8999999999997

>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=99.89  E-value=4e-23  Score=226.84  Aligned_cols=126  Identities=52%  Similarity=0.889  Sum_probs=115.4

Q ss_pred             HHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------HHHHHHHhhcCC
Q 042872          212 DMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------DQIITLNLKFGI  270 (381)
Q Consensus       212 ~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------dQv~~L~~~~gI  270 (381)
                      +....+...||++.|||.|++||.++|.|+|++|+||||+|||+|||                     ||+.+|. ..+|
T Consensus       251 ~~~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~~gitvVISPL~SLm~DQv~~L~-~~~I  329 (941)
T KOG0351|consen  251 ELELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLLGGVTVVISPLISLMQDQVTHLS-KKGI  329 (941)
T ss_pred             HHHHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeeccccccCCceEEeccHHHHHHHHHHhhh-hcCc
Confidence            35666777899999999999999999999999999999999999999                     9999996 6899


Q ss_pred             cEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCc
Q 042872          271 PATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSI  350 (381)
Q Consensus       271 ~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~  350 (381)
                      ++..|.++++..++..+++.+.+|                       .+.++|+|+|||.+.....+...+..|+.++  
T Consensus       330 ~a~~L~s~q~~~~~~~i~q~l~~~-----------------------~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~--  384 (941)
T KOG0351|consen  330 PACFLSSIQTAAERLAILQKLANG-----------------------NPIIKILYVTPEKVVASEGLLESLADLYARG--  384 (941)
T ss_pred             ceeeccccccHHHHHHHHHHHhCC-----------------------CCeEEEEEeCHHHhhcccchhhHHHhccCCC--
Confidence            999999999999999999998844                       4679999999999999889988888888776  


Q ss_pred             cccccccccccccccccCCccEEEEeccccC
Q 042872          351 RLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       351 ~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                        .|.++||||||||
T Consensus       385 ------------------~lal~vIDEAHCV  397 (941)
T KOG0351|consen  385 ------------------LLALFVIDEAHCV  397 (941)
T ss_pred             ------------------eeEEEEecHHHHh
Confidence                              7999999999997

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

Probab=99.88  E-value=1.4e-22  Score=224.64  Aligned_cols=126  Identities=46%  Similarity=0.745  Sum_probs=108.3

Q ss_pred             HHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------HHHHHHHhhcCC
Q 042872          212 DMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------DQIITLNLKFGI  270 (381)
Q Consensus       212 ~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------dQv~~L~~~~gI  270 (381)
                      .+...++++|||..|||+|.++|+++|.|+|+|++||||+|||+||+                     ||+..|. ..||
T Consensus       447 ~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~~GiTLVISPLiSLmqDQV~~L~-~~GI  525 (1195)
T PLN03137        447 KLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALICPGITLVISPLVSLIQDQIMNLL-QANI  525 (1195)
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHcCCcEEEEeCHHHHHHHHHHHHH-hCCC
Confidence            35566778899999999999999999999999999999999999998                     7898888 5899


Q ss_pred             cEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCc
Q 042872          271 PATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSI  350 (381)
Q Consensus       271 ~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~  350 (381)
                      ++..++++....++..+++.+..                       ..+.++|||+|||+|.....+...+..+...+  
T Consensus       526 ~Aa~L~s~~s~~eq~~ilr~l~s-----------------------~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~--  580 (1195)
T PLN03137        526 PAASLSAGMEWAEQLEILQELSS-----------------------EYSKYKLLYVTPEKVAKSDSLLRHLENLNSRG--  580 (1195)
T ss_pred             eEEEEECCCCHHHHHHHHHHHHh-----------------------cCCCCCEEEEChHHhhcchHHHHHHHhhhhcc--
Confidence            99999999999988888887652                       22378999999999986555666676665554  


Q ss_pred             cccccccccccccccccCCccEEEEeccccC
Q 042872          351 RLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       351 ~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                        .|.+|||||||||
T Consensus       581 ------------------~LslIVIDEAHcV  593 (1195)
T PLN03137        581 ------------------LLARFVIDEAHCV  593 (1195)
T ss_pred             ------------------ccceeccCcchhh
Confidence                              7999999999997

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.86  E-value=1.3e-21  Score=200.26  Aligned_cols=116  Identities=47%  Similarity=0.840  Sum_probs=98.5

Q ss_pred             HHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------HHHHHHHhhcCCcEEEE
Q 042872          217 NVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------DQIITLNLKFGIPATFL  275 (381)
Q Consensus       217 ~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------dQv~~L~~~~gI~a~~l  275 (381)
                      +++.|||+.|||+|.+||+++++|+|++++||||+|||+||+                     +|+..|. .+|+++..+
T Consensus         3 l~~~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~~~~~lVi~P~~~L~~dq~~~l~-~~gi~~~~l   81 (470)
T TIGR00614         3 LKTVFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCSDGITLVISPLISLMEDQVLQLK-ASGIPATFL   81 (470)
T ss_pred             hHhhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHcCCcEEEEecHHHHHHHHHHHHH-HcCCcEEEE
Confidence            567799999999999999999999999999999999999997                     6788887 689999999


Q ss_pred             eCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcccccc
Q 042872          276 NSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVL  355 (381)
Q Consensus       276 ~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~  355 (381)
                      ++.....++..++..++.|                         .++|||+|||++..+..+...+.   ..+       
T Consensus        82 ~~~~~~~~~~~i~~~~~~~-------------------------~~~il~~TPe~l~~~~~~~~~l~---~~~-------  126 (470)
T TIGR00614        82 NSSQSKEQQKNVLTDLKDG-------------------------KIKLLYVTPEKCSASNRLLQTLE---ERK-------  126 (470)
T ss_pred             eCCCCHHHHHHHHHHHhcC-------------------------CCCEEEECHHHHcCchhHHHHHH---hcC-------
Confidence            9999888888888777644                         68999999999985444544432   222       


Q ss_pred             ccccccccccccCCccEEEEeccccC
Q 042872          356 TTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       356 ~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                   ++.+|||||||||
T Consensus       127 -------------~i~~iViDEaH~i  139 (470)
T TIGR00614       127 -------------GITLIAVDEAHCI  139 (470)
T ss_pred             -------------CcCEEEEeCCccc
Confidence                         8999999999996

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

>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=99.86  E-value=8.2e-22  Score=199.67  Aligned_cols=124  Identities=41%  Similarity=0.702  Sum_probs=115.6

Q ss_pred             HHHHHHHHhCCCCCc-HHHHHHHHHHHcC-CCEEEECCCCCCchhhHH---------------------HHHHHHHhhcC
Q 042872          213 MEFANVVIFGNRAFR-PLQHQACKASVAK-QDCFVLLPTGGGKSLCYQ---------------------DQIITLNLKFG  269 (381)
Q Consensus       213 l~~~~~~~fG~~~fR-piQ~eAI~aiL~G-rDvLviaPTGsGKTLaF~---------------------dQv~~L~~~~g  269 (381)
                      +..+++++||++.|+ +.|..|+.++..+ +||+|.||||+|||||||                     ||+..|. ++.
T Consensus         7 VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~~gITIV~SPLiALIkDQiDHL~-~LK   85 (641)
T KOG0352|consen    7 VREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVHGGITIVISPLIALIKDQIDHLK-RLK   85 (641)
T ss_pred             HHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHhCCeEEEehHHHHHHHHHHHHHH-hcC
Confidence            667889999999997 9999999999987 599999999999999999                     9999998 789


Q ss_pred             CcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCC
Q 042872          270 IPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGS  349 (381)
Q Consensus       270 I~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~  349 (381)
                      +++-.|++..+..++.+++..|.                       ..+|..++||+|||... +..|+.+|+.|+.+. 
T Consensus        86 Vp~~SLNSKlSt~ER~ri~~DL~-----------------------~ekp~~K~LYITPE~AA-t~~FQ~lLn~L~~r~-  140 (641)
T KOG0352|consen   86 VPCESLNSKLSTVERSRIMGDLA-----------------------KEKPTIKMLYITPEGAA-TDGFQKLLNGLANRD-  140 (641)
T ss_pred             CchhHhcchhhHHHHHHHHHHHH-----------------------hcCCceeEEEEchhhhh-hhhHHHHHHHHhhhc-
Confidence            99999999999999999999987                       66778999999999998 689999999999887 


Q ss_pred             ccccccccccccccccccCCccEEEEeccccC
Q 042872          350 IRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       350 ~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                         .|.|||+||||||
T Consensus       141 -------------------~L~Y~vVDEAHCV  153 (641)
T KOG0352|consen  141 -------------------VLRYIVVDEAHCV  153 (641)
T ss_pred             -------------------eeeeEEechhhhH
Confidence                               8999999999997

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.86  E-value=2.7e-21  Score=203.00  Aligned_cols=116  Identities=41%  Similarity=0.660  Sum_probs=99.6

Q ss_pred             HHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------HHHHHHHhhcCCcEE
Q 042872          215 FANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------DQIITLNLKFGIPAT  273 (381)
Q Consensus       215 ~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------dQv~~L~~~~gI~a~  273 (381)
                      ..+++.|||++|||+|.+||++++.|+|++++||||+|||+||+                     +|+..|. .+|+++.
T Consensus         3 ~~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~~g~~lVisPl~sL~~dq~~~l~-~~gi~~~   81 (591)
T TIGR01389         3 QVLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLLKGLTVVISPLISLMKDQVDQLR-AAGVAAA   81 (591)
T ss_pred             HHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHcCCcEEEEcCCHHHHHHHHHHHH-HcCCcEE
Confidence            35667899999999999999999999999999999999999998                     7888888 5899999


Q ss_pred             EEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcccc
Q 042872          274 FLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLK  353 (381)
Q Consensus       274 ~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~  353 (381)
                      .+++..+..++..++..+..|                         .++|||+|||++. +..|...+.    ..     
T Consensus        82 ~~~s~~~~~~~~~~~~~l~~~-------------------------~~~il~~tpe~l~-~~~~~~~l~----~~-----  126 (591)
T TIGR01389        82 YLNSTLSAKEQQDIEKALVNG-------------------------ELKLLYVAPERLE-QDYFLNMLQ----RI-----  126 (591)
T ss_pred             EEeCCCCHHHHHHHHHHHhCC-------------------------CCCEEEEChhHhc-ChHHHHHHh----cC-----
Confidence            999999988888888777644                         6899999999998 455554432    11     


Q ss_pred             ccccccccccccccCCccEEEEeccccC
Q 042872          354 VLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       354 ~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                     ++++|||||||||
T Consensus       127 ---------------~l~~iViDEaH~i  139 (591)
T TIGR01389       127 ---------------PIALVAVDEAHCV  139 (591)
T ss_pred             ---------------CCCEEEEeCCccc
Confidence                           7999999999996

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

>KOG0330 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.84  E-value=1.3e-21  Score=196.10  Aligned_cols=131  Identities=24%  Similarity=0.295  Sum_probs=114.7

Q ss_pred             CCCCCCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH------------------
Q 042872          197 NEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ------------------  258 (381)
Q Consensus       197 ~~~~~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~------------------  258 (381)
                      ..+...+|..|+..+++..++++ .||+.||++|.+|||.+|.|+|||+.|.||||||++|+                  
T Consensus        56 ~~e~~~sf~dLgv~~~L~~ac~~-l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lV  134 (476)
T KOG0330|consen   56 TDESFKSFADLGVHPELLEACQE-LGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALV  134 (476)
T ss_pred             hhhhhcchhhcCcCHHHHHHHHH-hCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEE
Confidence            34556789999999999999977 79999999999999999999999999999999999998                  


Q ss_pred             ------------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEE
Q 042872          259 ------------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYV  326 (381)
Q Consensus       259 ------------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~a  326 (381)
                                  +|++.|+...|+++.++.||+++..+...+.+                             ++||||+
T Consensus       135 LtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~k-----------------------------kPhilVa  185 (476)
T KOG0330|consen  135 LTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSK-----------------------------KPHILVA  185 (476)
T ss_pred             ecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhc-----------------------------CCCEEEe
Confidence                        67888887889999999999998877655543                             7899999


Q ss_pred             CccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          327 TPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       327 TPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      |||+|.         .++.+.+.++|.               +|+++|+|||+.+
T Consensus       186 TPGrL~---------dhl~~Tkgf~le---------------~lk~LVlDEADrl  216 (476)
T KOG0330|consen  186 TPGRLW---------DHLENTKGFSLE---------------QLKFLVLDEADRL  216 (476)
T ss_pred             CcHHHH---------HHHHhccCccHH---------------HhHHHhhchHHhh
Confidence            999997         456667778888               9999999999874

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.83  E-value=4.1e-20  Score=195.47  Aligned_cols=116  Identities=45%  Similarity=0.689  Sum_probs=96.7

Q ss_pred             HHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------HHHHHHHhhcCCcEE
Q 042872          215 FANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------DQIITLNLKFGIPAT  273 (381)
Q Consensus       215 ~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------dQv~~L~~~~gI~a~  273 (381)
                      ..++++|||+.|||+|.++|+++++|+|++++||||+|||+||+                     +|+..+. .+|+.+.
T Consensus        15 ~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~~g~tlVisPl~sL~~dqv~~l~-~~gi~~~   93 (607)
T PRK11057         15 QVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPLISLMKDQVDQLL-ANGVAAA   93 (607)
T ss_pred             HHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHcCCCEEEEecHHHHHHHHHHHHH-HcCCcEE
Confidence            34556799999999999999999999999999999999999997                     6777777 5799999


Q ss_pred             EEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcccc
Q 042872          274 FLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLK  353 (381)
Q Consensus       274 ~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~  353 (381)
                      .+++..+..++..++..++.|                         .++++|+|||++.. ..|.+.+..    .     
T Consensus        94 ~~~s~~~~~~~~~~~~~~~~g-------------------------~~~il~~tPe~l~~-~~~~~~l~~----~-----  138 (607)
T PRK11057         94 CLNSTQTREQQLEVMAGCRTG-------------------------QIKLLYIAPERLMM-DNFLEHLAH----W-----  138 (607)
T ss_pred             EEcCCCCHHHHHHHHHHHhCC-------------------------CCcEEEEChHHhcC-hHHHHHHhh----C-----
Confidence            999988888777777776644                         68999999999983 455443321    1     


Q ss_pred             ccccccccccccccCCccEEEEeccccC
Q 042872          354 VLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       354 ~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                     ++.+|||||||||
T Consensus       139 ---------------~l~~iVIDEaH~i  151 (607)
T PRK11057        139 ---------------NPALLAVDEAHCI  151 (607)
T ss_pred             ---------------CCCEEEEeCcccc
Confidence                           7999999999996

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.82  E-value=4e-20  Score=186.11  Aligned_cols=57  Identities=21%  Similarity=0.215  Sum_probs=49.8

Q ss_pred             CCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          201 TLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       201 ~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      ..+|+.+..-+++..++.. +||..|+|+|.+|||.++.|+|++++||||+|||+||+
T Consensus         7 ~~~f~~~~l~~~l~~~l~~-~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~l   63 (423)
T PRK04837          7 EQKFSDFALHPQVVEALEK-KGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFL   63 (423)
T ss_pred             CCCHhhCCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHH
Confidence            3567777766666666655 89999999999999999999999999999999999997

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.81  E-value=1.5e-19  Score=182.10  Aligned_cols=55  Identities=24%  Similarity=0.273  Sum_probs=48.0

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +|+.+...+.+..++.. +||..|+++|.+||++++.|+|+|+++|||+|||+||+
T Consensus         2 ~f~~l~l~~~l~~~l~~-~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~   56 (434)
T PRK11192          2 TFSELELDESLLEALQD-KGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFL   56 (434)
T ss_pred             CHhhcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHH
Confidence            46666666666666655 89999999999999999999999999999999999997

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.80  E-value=1.7e-19  Score=184.04  Aligned_cols=55  Identities=31%  Similarity=0.352  Sum_probs=48.6

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +|+.|...+++..++.+ +||..|||+|.+||+.++.|+|+|+.+|||+|||+||+
T Consensus         2 ~f~~l~l~~~l~~~l~~-~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~   56 (456)
T PRK10590          2 SFDSLGLSPDILRAVAE-QGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFT   56 (456)
T ss_pred             CHHHcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHH
Confidence            56777666666666655 89999999999999999999999999999999999997

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.79  E-value=4.6e-19  Score=186.69  Aligned_cols=56  Identities=20%  Similarity=0.223  Sum_probs=49.5

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      ++|+.+.+.+.+..++.+ +||..|+|+|.++||.++.|+|+++++|||+|||+||+
T Consensus         9 ~~f~~l~l~~~l~~~L~~-~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafl   64 (572)
T PRK04537          9 LTFSSFDLHPALLAGLES-AGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFL   64 (572)
T ss_pred             CChhhcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHH
Confidence            457777766666666655 89999999999999999999999999999999999997

>PTZ00110 helicase; Provisional

Probab=99.79  E-value=5.6e-19  Score=184.86  Aligned_cols=56  Identities=25%  Similarity=0.260  Sum_probs=48.1

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .+|+.+..-+.+..++.+ +||++|+|+|.+|||.+++|+|+|+++|||+|||++|+
T Consensus       130 ~~f~~~~l~~~l~~~l~~-~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlayl  185 (545)
T PTZ00110        130 VSFEYTSFPDYILKSLKN-AGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFL  185 (545)
T ss_pred             CCHhhcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHH
Confidence            467776655556666654 89999999999999999999999999999999999997

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.79  E-value=2.4e-18  Score=176.12  Aligned_cols=57  Identities=21%  Similarity=0.267  Sum_probs=50.2

Q ss_pred             CCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          201 TLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       201 ~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      ...|..+..-+.+..++.+ +||..|+|+|.+||+.+++|+|+++.+|||+|||+||+
T Consensus        86 ~~~f~~~~l~~~l~~~l~~-~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~  142 (475)
T PRK01297         86 KTRFHDFNLAPELMHAIHD-LGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFL  142 (475)
T ss_pred             CCCHhHCCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHH
Confidence            4467777766667667665 89999999999999999999999999999999999997

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

Probab=99.78  E-value=6.6e-19  Score=182.96  Aligned_cols=57  Identities=25%  Similarity=0.272  Sum_probs=48.9

Q ss_pred             CCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          201 TLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       201 ~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      -.+|+.+..-+.+...+.+ .||..|||+|.+|||.++.|+|+++++|||+|||++|+
T Consensus       120 i~~f~~~~l~~~l~~~L~~-~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayl  176 (518)
T PLN00206        120 ILSFSSCGLPPKLLLNLET-AGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFL  176 (518)
T ss_pred             hcCHHhCCCCHHHHHHHHH-cCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHH
Confidence            3467777655556666644 89999999999999999999999999999999999997

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.78  E-value=8.8e-19  Score=178.17  Aligned_cols=56  Identities=23%  Similarity=0.303  Sum_probs=48.0

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .+|+.+...+.+..++.+ +||..|+|+|.+|||.++.|+|+++++|||+|||++|.
T Consensus         4 ~~f~~l~l~~~l~~~l~~-~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~   59 (460)
T PRK11776          4 TAFSTLPLPPALLANLNE-LGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFG   59 (460)
T ss_pred             CChhhcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHH
Confidence            356666655666666644 89999999999999999999999999999999999997

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

Probab=99.77  E-value=2.5e-18  Score=179.05  Aligned_cols=125  Identities=21%  Similarity=0.349  Sum_probs=94.5

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-----------------------
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-----------------------  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-----------------------  258 (381)
                      ..|+.+....++..++.+ .||..|+|+|.++||.+|.|+|+++.++||+|||++|.                       
T Consensus        29 ~~F~~l~l~~~ll~~l~~-~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~P  107 (513)
T COG0513          29 PEFASLGLSPELLQALKD-LGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAP  107 (513)
T ss_pred             CCHhhcCCCHHHHHHHHH-cCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECC
Confidence            457777766777777766 89999999999999999999999999999999999998                       


Q ss_pred             ---------HHHHHHHhhc-CCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECc
Q 042872          259 ---------DQIITLNLKF-GIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTP  328 (381)
Q Consensus       259 ---------dQv~~L~~~~-gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTP  328 (381)
                               +.+..+.... +++++.++||.+...+.   ..+++                          +++|||+||
T Consensus       108 TRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~---~~l~~--------------------------~~~ivVaTP  158 (513)
T COG0513         108 TRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQI---EALKR--------------------------GVDIVVATP  158 (513)
T ss_pred             CHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHH---HHHhc--------------------------CCCEEEECc
Confidence                     1223333333 45566666666655443   22221                          489999999


Q ss_pred             cccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          329 ERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       329 ErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      +||++          +..++.++++               ++.++|+|||+.+
T Consensus       159 GRllD----------~i~~~~l~l~---------------~v~~lVlDEADrm  186 (513)
T COG0513         159 GRLLD----------LIKRGKLDLS---------------GVETLVLDEADRM  186 (513)
T ss_pred             cHHHH----------HHHcCCcchh---------------hcCEEEeccHhhh
Confidence            99972          3455678888               9999999999864

>KOG0340 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.77  E-value=8.3e-19  Score=174.65  Aligned_cols=130  Identities=20%  Similarity=0.280  Sum_probs=102.7

Q ss_pred             CCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH----------------------
Q 042872          201 TLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ----------------------  258 (381)
Q Consensus       201 ~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~----------------------  258 (381)
                      .-+|+.|.+-+++...++. +|+++|||+|..|||+||.|+|||++|.||||||++|.                      
T Consensus         6 ~~~F~~LGl~~Wlve~l~~-l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPT   84 (442)
T KOG0340|consen    6 AKPFSILGLSPWLVEQLKA-LGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPT   84 (442)
T ss_pred             cCchhhcCccHHHHHHHHH-hcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecch
Confidence            3569999988888888866 89999999999999999999999999999999999998                      


Q ss_pred             --------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccc
Q 042872          259 --------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPER  330 (381)
Q Consensus       259 --------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPEr  330 (381)
                              +|+..+++.+++++.++.|++++-.+...+..                             ++|+|++||||
T Consensus        85 rELA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~-----------------------------rPHvVvatPGR  135 (442)
T KOG0340|consen   85 RELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSD-----------------------------RPHVVVATPGR  135 (442)
T ss_pred             HHHHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhccc-----------------------------CCCeEecCccc
Confidence                    78888888889999999999776555444433                             78999999999


Q ss_pred             cccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          331 IVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       331 L~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      +...  .       ...+.       ..+-+|     .++.|+|||||+.|
T Consensus       136 lad~--l-------~sn~~-------~~~~~~-----~rlkflVlDEADrv  165 (442)
T KOG0340|consen  136 LADH--L-------SSNLG-------VCSWIF-----QRLKFLVLDEADRV  165 (442)
T ss_pred             cccc--c-------ccCCc-------cchhhh-----hceeeEEecchhhh
Confidence            9831  1       00100       000111     18999999999864

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.75  E-value=4.2e-18  Score=177.11  Aligned_cols=124  Identities=23%  Similarity=0.346  Sum_probs=97.4

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH------------------------
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ------------------------  258 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~------------------------  258 (381)
                      .|..+....++..+++ ..||+.|+|||.++||.+|.|||+++++.|||||||+|+                        
T Consensus        92 ~f~~~~ls~~~~~~lk-~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLV  170 (519)
T KOG0331|consen   92 AFQELGLSEELMKALK-EQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLV  170 (519)
T ss_pred             hhhcccccHHHHHHHH-hcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEE
Confidence            5666665554444443 489999999999999999999999999999999999998                        


Q ss_pred             --------HH----HHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEE
Q 042872          259 --------DQ----IITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYV  326 (381)
Q Consensus       259 --------dQ----v~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~a  326 (381)
                              .|    +..+....+++.++++|+.+...|.   ..+++                          +++|+|+
T Consensus       171 L~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~---~~l~~--------------------------gvdivia  221 (519)
T KOG0331|consen  171 LAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQL---RDLER--------------------------GVDVVIA  221 (519)
T ss_pred             EcCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHH---HHHhc--------------------------CCcEEEe
Confidence                    33    3344445567788888888877663   44443                          4899999


Q ss_pred             CccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          327 TPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       327 TPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      ||+||..          +.+.++++|+               ++.|+|+|||+.+
T Consensus       222 TPGRl~d----------~le~g~~~l~---------------~v~ylVLDEADrM  251 (519)
T KOG0331|consen  222 TPGRLID----------LLEEGSLNLS---------------RVTYLVLDEADRM  251 (519)
T ss_pred             CChHHHH----------HHHcCCcccc---------------ceeEEEeccHHhh
Confidence            9999962          4567888888               9999999999864

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]

Probab=99.75  E-value=2.2e-18  Score=173.16  Aligned_cols=123  Identities=40%  Similarity=0.649  Sum_probs=109.4

Q ss_pred             HHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------HHHHHHHhhcCCcEE
Q 042872          215 FANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------DQIITLNLKFGIPAT  273 (381)
Q Consensus       215 ~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------dQv~~L~~~~gI~a~  273 (381)
                      ..++..|.+++|||.|.++|++.++|+|+++++|||+|||||||                     ||+..|. .+||.+.
T Consensus        84 ~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~adg~alvi~plislmedqil~lk-qlgi~as  162 (695)
T KOG0353|consen   84 DILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCADGFALVICPLISLMEDQILQLK-QLGIDAS  162 (695)
T ss_pred             HHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhcCCceEeechhHHHHHHHHHHHH-HhCcchh
Confidence            34456699999999999999999999999999999999999999                     8999998 6999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcccc
Q 042872          274 FLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLK  353 (381)
Q Consensus       274 ~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~  353 (381)
                      .++...+.++.+.+-.++.                       .++..+++||+|||.+..++.|...|......|     
T Consensus       163 ~lnansske~~k~v~~~i~-----------------------nkdse~kliyvtpekiaksk~~mnkleka~~~~-----  214 (695)
T KOG0353|consen  163 MLNANSSKEEAKRVEAAIT-----------------------NKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAG-----  214 (695)
T ss_pred             hccCcccHHHHHHHHHHHc-----------------------CCCceeEEEEecHHHHHHHHHHHHHHHHHhhcc-----
Confidence            9999999888877777765                       456689999999999999899988888777666     


Q ss_pred             ccccccccccccccCCccEEEEeccccC
Q 042872          354 VLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       354 ~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                     .+.++.|||+||.
T Consensus       215 ---------------~~~~iaidevhcc  227 (695)
T KOG0353|consen  215 ---------------FFKLIAIDEVHCC  227 (695)
T ss_pred             ---------------eeEEEeecceeeh
Confidence                           8999999999994

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.75  E-value=4.8e-18  Score=181.00  Aligned_cols=56  Identities=20%  Similarity=0.263  Sum_probs=49.0

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .+|..|.+.+++..++.+ +||.+|+|+|.++||.++.|+|+|+.||||+|||+||+
T Consensus         6 ~~f~~l~L~~~ll~al~~-~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~   61 (629)
T PRK11634          6 TTFADLGLKAPILEALND-LGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFS   61 (629)
T ss_pred             CCHhhcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHH
Confidence            357777666666666655 89999999999999999999999999999999999996

>PTZ00424 helicase 45; Provisional

Probab=99.74  E-value=1.8e-17  Score=163.89  Aligned_cols=56  Identities=20%  Similarity=0.246  Sum_probs=48.8

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .+|+.+...+.+..++.+ +||..|+|+|.+||+.+++|+|+++.+|||+|||++|+
T Consensus        28 ~~~~~l~l~~~~~~~l~~-~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~   83 (401)
T PTZ00424         28 DSFDALKLNEDLLRGIYS-YGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFV   83 (401)
T ss_pred             CCHhhCCCCHHHHHHHHH-cCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHH
Confidence            457777766666666644 89999999999999999999999999999999999997

>KOG0338 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.72  E-value=8.2e-18  Score=173.45  Aligned_cols=126  Identities=21%  Similarity=0.270  Sum_probs=106.1

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-----------------------
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-----------------------  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-----------------------  258 (381)
                      .+|..+.+-.+++.++.. +||..|||||..+||.+|.|||+.++|.||+|||.+|+                       
T Consensus       181 ~sF~~mNLSRPlLka~~~-lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~  259 (691)
T KOG0338|consen  181 ESFQSMNLSRPLLKACST-LGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLV  259 (691)
T ss_pred             hhHHhcccchHHHHHHHh-cCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEe
Confidence            478888888888777755 99999999999999999999999999999999999998                       


Q ss_pred             ------HH----HHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECc
Q 042872          259 ------DQ----IITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTP  328 (381)
Q Consensus       259 ------dQ----v~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTP  328 (381)
                            -|    ...|..-..|.+..+.||.+...|...|+.                             .++|||+||
T Consensus       260 PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs-----------------------------~PDIVIATP  310 (691)
T KOG0338|consen  260 PTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRS-----------------------------RPDIVIATP  310 (691)
T ss_pred             ccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhh-----------------------------CCCEEEecc
Confidence                  22    233443346888888888888887777755                             699999999


Q ss_pred             cccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          329 ERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       329 ErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      |||.         .||++.-+++|+               .|..+|+|||+++
T Consensus       311 GRlI---------DHlrNs~sf~ld---------------siEVLvlDEADRM  339 (691)
T KOG0338|consen  311 GRLI---------DHLRNSPSFNLD---------------SIEVLVLDEADRM  339 (691)
T ss_pred             hhHH---------HHhccCCCcccc---------------ceeEEEechHHHH
Confidence            9996         567888889999               9999999999863

>KOG0348 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.69  E-value=8.6e-17  Score=166.66  Aligned_cols=149  Identities=23%  Similarity=0.255  Sum_probs=100.4

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-HHHHHHHh-------hcCCcEE
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-DQIITLNL-------KFGIPAT  273 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-dQv~~L~~-------~~gI~a~  273 (381)
                      -.|..|++-..+...+...++++.+|-+|.+|||.+|.|||+||-++|||||||+|+ .-+..|..       .-|+-|+
T Consensus       136 ~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~AL  215 (708)
T KOG0348|consen  136 AAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYAL  215 (708)
T ss_pred             ccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCceEE
Confidence            357777777777788888899999999999999999999999999999999999998 22222221       2255566


Q ss_pred             EEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccC-------CCCCccEEEECccccccCcchHHHHHHHHh
Q 042872          274 FLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRK-------DKPSCKLLYVTPERIVGNQSFSEVLKCLHR  346 (381)
Q Consensus       274 ~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IL~aTPErL~~~~~f~~~L~~L~~  346 (381)
                      ++...  ++-..++..-+. -+++.    +||.|-.+.+.+++       -.++++|||+|||||+         .+|..
T Consensus       216 VivPT--REL~~Q~y~~~q-KLl~~----~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLv---------DHLkn  279 (708)
T KOG0348|consen  216 VIVPT--RELALQIYETVQ-KLLKP----FHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLV---------DHLKN  279 (708)
T ss_pred             EEech--HHHHHHHHHHHH-HHhcC----ceEEeeceeecccccccHHHHHhcCceEEEcCchHHH---------HHHhc
Confidence            65432  222111221111 11111    34544444443322       2347999999999997         34555


Q ss_pred             cCCccccccccccccccccccCCccEEEEeccccC
Q 042872          347 KGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       347 ~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      ..+|.++               +|.+||+|||+.|
T Consensus       280 T~~i~~s---------------~LRwlVlDEaDrl  299 (708)
T KOG0348|consen  280 TKSIKFS---------------RLRWLVLDEADRL  299 (708)
T ss_pred             cchheee---------------eeeEEEecchhHH
Confidence            5556666               8999999999875

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

Probab=99.68  E-value=2.4e-16  Score=170.77  Aligned_cols=38  Identities=32%  Similarity=0.286  Sum_probs=37.4

Q ss_pred             hCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .||+.|+++|.+||+.+++|+|+++.+|||||||+||+
T Consensus        32 ~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~   69 (742)
T TIGR03817        32 AGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQ   69 (742)
T ss_pred             cCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHH
Confidence            89999999999999999999999999999999999998

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.

>PRK14701 reverse gyrase; Provisional

Probab=99.65  E-value=8.5e-16  Score=177.45  Aligned_cols=122  Identities=19%  Similarity=0.259  Sum_probs=93.6

Q ss_pred             HhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH------------------------HH--
Q 042872          207 LQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ------------------------DQ--  260 (381)
Q Consensus       207 L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~------------------------dQ--  260 (381)
                      .+.+.++...+++.+|| +|+++|.++|+.+++|+|++++||||+|||++++                        ++  
T Consensus        62 ~~~~~~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~~g~~aLVl~PTreLa~Qi~~  140 (1638)
T PRK14701         62 WNEVEEFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLALKGKKCYIILPTTLLVKQTVE  140 (1638)
T ss_pred             HHHHHHHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHhcCCeEEEEECHHHHHHHHHH
Confidence            34566677788888999 6999999999999999999999999999999765                        22  


Q ss_pred             -HHHHHhhc--CCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcch
Q 042872          261 -IITLNLKF--GIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSF  337 (381)
Q Consensus       261 -v~~L~~~~--gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f  337 (381)
                       +..+...+  ++++..++|+.+..++...++.+++|                         .++|||+||++|..  .+
T Consensus       141 ~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g-------------------------~~dILV~TPgrL~~--~~  193 (1638)
T PRK14701        141 KIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENG-------------------------DFDILVTTAQFLAR--NF  193 (1638)
T ss_pred             HHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcC-------------------------CCCEEEECCchhHH--hH
Confidence             23333222  46677788888888877777777654                         68999999999862  23


Q ss_pred             HHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          338 SEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       338 ~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      ..    +.. .                    ++++|||||||||
T Consensus       194 ~~----l~~-~--------------------~i~~iVVDEAD~m  212 (1638)
T PRK14701        194 PE----MKH-L--------------------KFDFIFVDDVDAF  212 (1638)
T ss_pred             HH----Hhh-C--------------------CCCEEEEECceec
Confidence            22    111 2                    7999999999996

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=99.65  E-value=1.1e-16  Score=166.17  Aligned_cols=128  Identities=23%  Similarity=0.259  Sum_probs=97.1

Q ss_pred             CCCCCCCCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcC-CCEEEECCCCCCchhhHH---------------
Q 042872          195 SDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAK-QDCFVLLPTGGGKSLCYQ---------------  258 (381)
Q Consensus       195 ~~~~~~~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~G-rDvLviaPTGsGKTLaF~---------------  258 (381)
                      +.|....++.+.|++|..        +||.+|||||.-+||++..| .|+|+.|.|||||||||.               
T Consensus       181 sAW~~l~lp~~iL~aL~~--------~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~  252 (731)
T KOG0347|consen  181 SAWKNLFLPMEILRALSN--------LGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQ  252 (731)
T ss_pred             HHHhcCCCCHHHHHHHHh--------cCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHh
Confidence            444455666666666654        89999999999999999999 699999999999999997               


Q ss_pred             ----------------------------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhh
Q 042872          259 ----------------------------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVL  310 (381)
Q Consensus       259 ----------------------------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~  310 (381)
                                                  +.+..+....+|++..++||.....|.++++.                    
T Consensus       253 e~~~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~--------------------  312 (731)
T KOG0347|consen  253 ELSNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQ--------------------  312 (731)
T ss_pred             hhhhHHhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhc--------------------
Confidence                                        22344445668999999999988888777765                    


Q ss_pred             hhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          311 TCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       311 ~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                               .++|||+|||||..  .+.+.-.++.+-     +               .|.++|||||+++
T Consensus       313 ---------~p~IVVATPGRlwe--li~e~n~~l~~~-----k---------------~vkcLVlDEaDRm  352 (731)
T KOG0347|consen  313 ---------RPDIVVATPGRLWE--LIEEDNTHLGNF-----K---------------KVKCLVLDEADRM  352 (731)
T ss_pred             ---------CCCEEEecchHHHH--HHHhhhhhhhhh-----h---------------hceEEEEccHHHH
Confidence                     68999999999972  211111112111     1               8999999999864

>cd00268 DEADc DEAD-box helicases

Probab=99.64  E-value=9.9e-16  Score=137.68  Aligned_cols=65  Identities=20%  Similarity=0.197  Sum_probs=48.5

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHH-HHHHHHhh---cCCcEEEEeCC
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQD-QIITLNLK---FGIPATFLNSQ  278 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~d-Qv~~L~~~---~gI~a~~l~g~  278 (381)
                      +...+.+ +|++.|+++|.+|++.+++|+|+++.+|||+|||++|+- -+..+...   .+.+++++.+.
T Consensus        10 i~~~l~~-~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~   78 (203)
T cd00268          10 LLRGIYA-LGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPT   78 (203)
T ss_pred             HHHHHHH-cCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCC
Confidence            3334444 899999999999999999999999999999999999862 23333322   24456666543

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.

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

Probab=99.62  E-value=9.2e-16  Score=166.85  Aligned_cols=103  Identities=25%  Similarity=0.373  Sum_probs=76.0

Q ss_pred             CCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH--------------------------------HHHHHH---Hhh
Q 042872          223 NRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ--------------------------------DQIITL---NLK  267 (381)
Q Consensus       223 ~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~--------------------------------dQv~~L---~~~  267 (381)
                      |.+|||.|.+|||.+.+|+++|++||||||||++..                                |...+|   ...
T Consensus        20 ~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn~Di~~rL~~~~~~   99 (814)
T COG1201          20 FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALNNDIRRRLEEPLRE   99 (814)
T ss_pred             cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999998765                                222222   224


Q ss_pred             cCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccc---cCcchHHHHHHH
Q 042872          268 FGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIV---GNQSFSEVLKCL  344 (381)
Q Consensus       268 ~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~---~~~~f~~~L~~L  344 (381)
                      +|+++.+.+|+++..++..+.                             ...+|||++|||.|.   +++.+++.|.  
T Consensus       100 ~G~~v~vRhGDT~~~er~r~~-----------------------------~~PPdILiTTPEsL~lll~~~~~r~~l~--  148 (814)
T COG1201         100 LGIEVAVRHGDTPQSEKQKML-----------------------------KNPPHILITTPESLAILLNSPKFRELLR--  148 (814)
T ss_pred             cCCccceecCCCChHHhhhcc-----------------------------CCCCcEEEeChhHHHHHhcCHHHHHHhc--
Confidence            455555555555554443332                             226999999999986   4455555543  


Q ss_pred             HhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          345 HRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       345 ~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                                              ++.++||||.|-
T Consensus       149 ------------------------~vr~VIVDEiHe  160 (814)
T COG1201         149 ------------------------DVRYVIVDEIHA  160 (814)
T ss_pred             ------------------------CCcEEEeehhhh
Confidence                                    899999999995

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.62  E-value=2.3e-15  Score=165.70  Aligned_cols=51  Identities=24%  Similarity=0.190  Sum_probs=41.2

Q ss_pred             HhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          207 LQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       207 L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +..++.....+.+ -+|..|||+|.+||+.+++|+|++++||||+|||+||+
T Consensus        15 ~~~l~~~v~~~~~-~~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~   65 (876)
T PRK13767         15 LDLLRPYVREWFK-EKFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAF   65 (876)
T ss_pred             HhhcCHHHHHHHH-HccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHH
Confidence            3334444333333 27889999999999999999999999999999999987

>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.61  E-value=2.2e-15  Score=154.50  Aligned_cols=49  Identities=33%  Similarity=0.399  Sum_probs=42.9

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      ++...+++++.        +||+.+||+|..+||.++.++||.|-++||||||+||+
T Consensus        13 L~~~l~~~l~~--------~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFl   61 (567)
T KOG0345|consen   13 LSPWLLEALDE--------SGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFL   61 (567)
T ss_pred             ccHHHHHHHHh--------cCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHH
Confidence            44555555444        89999999999999999999999999999999999998

>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]

Probab=99.61  E-value=1.1e-15  Score=158.12  Aligned_cols=126  Identities=22%  Similarity=0.342  Sum_probs=97.9

Q ss_pred             CCCCCCCCCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------
Q 042872          194 ISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------  258 (381)
Q Consensus       194 ~~~~~~~~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------  258 (381)
                      ...+.+..++.+.|.++..        .||+.|+|+|++|||..++.+|+|+++.||||||++|.               
T Consensus       244 lrnwEE~~~P~e~l~~I~~--------~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~  315 (673)
T KOG0333|consen  244 LRNWEESGFPLELLSVIKK--------PGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMAR  315 (673)
T ss_pred             ccChhhcCCCHHHHHHHHh--------cCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcch
Confidence            3445555677777665544        79999999999999999999999999999999999998               


Q ss_pred             ------------------------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcc
Q 042872          259 ------------------------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCAS  314 (381)
Q Consensus       259 ------------------------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~  314 (381)
                                              +....|...+|++++.+.|+.+.+++.-.+..                        
T Consensus       316 ~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~------------------------  371 (673)
T KOG0333|consen  316 LENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSM------------------------  371 (673)
T ss_pred             hhhcccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhc------------------------
Confidence                                    22345555678999999999999987666654                        


Q ss_pred             cCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          315 RKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       315 ~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                           +++|+++||++|..  .+-+.+.                  |+.     ++.+||+|||+.+
T Consensus       372 -----gceiviatPgrLid--~Lenr~l------------------vl~-----qctyvvldeadrm  408 (673)
T KOG0333|consen  372 -----GCEIVIATPGRLID--SLENRYL------------------VLN-----QCTYVVLDEADRM  408 (673)
T ss_pred             -----cceeeecCchHHHH--HHHHHHH------------------Hhc-----cCceEeccchhhh
Confidence                 68999999999973  2222111                  111     8999999999853

>PRK02362 ski2-like helicase; Provisional

Probab=99.61  E-value=2.5e-15  Score=162.18  Aligned_cols=142  Identities=20%  Similarity=0.239  Sum_probs=83.7

Q ss_pred             HHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHH-HHcCCCEEEECCCCCCchhhHHHH-HHHHHhhcCCcEEEEeCCCCH
Q 042872          204 FEELQALDDMEFANVVIFGNRAFRPLQHQACKA-SVAKQDCFVLLPTGGGKSLCYQDQ-IITLNLKFGIPATFLNSQQTV  281 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~a-iL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~~gI~a~~l~g~~~~  281 (381)
                      |+.+..-+.+..++.+ .||.+|+|+|.+|++. ++.|+|+++.+|||+|||++|.-. +..+.  .+.+++++..-  .
T Consensus         3 ~~~l~lp~~~~~~l~~-~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~--~~~kal~i~P~--r   77 (737)
T PRK02362          3 IAELPLPEGVIEFYEA-EGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIA--RGGKALYIVPL--R   77 (737)
T ss_pred             hhhcCCCHHHHHHHHh-CCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHh--cCCcEEEEeCh--H
Confidence            4455544445555544 7999999999999998 678999999999999999999622 23332  35567666543  2


Q ss_pred             HHHHHHHHHHHhchhhhhhhhhhhhhhhhh---hcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccc
Q 042872          282 SQAAAVLQELRQGLVLSQHYFLHQLIFVLT---CASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTD  358 (381)
Q Consensus       282 ~e~~~il~~lr~g~~~~~~~~~~~~~~~~~---~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~  358 (381)
                      +-..+..+.+++  +.+    +...+..++   .........++|+|+|||++..      ++    +.+...++     
T Consensus        78 aLa~q~~~~~~~--~~~----~g~~v~~~tGd~~~~~~~l~~~~IiV~Tpek~~~------ll----r~~~~~l~-----  136 (737)
T PRK02362         78 ALASEKFEEFER--FEE----LGVRVGISTGDYDSRDEWLGDNDIIVATSEKVDS------LL----RNGAPWLD-----  136 (737)
T ss_pred             HHHHHHHHHHHH--hhc----CCCEEEEEeCCcCccccccCCCCEEEECHHHHHH------HH----hcChhhhh-----
Confidence            222222333221  000    000000000   0001112357999999999852      11    11111222     


Q ss_pred             cccccccccCCccEEEEeccccC
Q 042872          359 VVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       359 ~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                ++++|||||||+|
T Consensus       137 ----------~v~lvViDE~H~l  149 (737)
T PRK02362        137 ----------DITCVVVDEVHLI  149 (737)
T ss_pred             ----------hcCEEEEECcccc
Confidence                      8999999999986

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

Probab=99.59  E-value=3.7e-15  Score=128.93  Aligned_cols=32  Identities=38%  Similarity=0.703  Sum_probs=30.3

Q ss_pred             cHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          227 RPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       227 RpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      ||+|.++++.+++|+++++.+|||+|||++|+
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~   32 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYI   32 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHH
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHH
Confidence            68999999999999999999999999999997

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 ....

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.59  E-value=1.9e-15  Score=153.24  Aligned_cols=120  Identities=22%  Similarity=0.269  Sum_probs=91.7

Q ss_pred             HhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH----------------------------
Q 042872          207 LQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ----------------------------  258 (381)
Q Consensus       207 L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~----------------------------  258 (381)
                      ++..+++.....+ .||.+|+|+|.+|+|.+|+|.|++++++||+||||+|+                            
T Consensus       225 Fq~~pevmenIkK-~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~pt  303 (629)
T KOG0336|consen  225 FQCYPEVMENIKK-TGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPT  303 (629)
T ss_pred             HhhhHHHHHHHHh-ccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEecc
Confidence            4445555555544 89999999999999999999999999999999999998                            


Q ss_pred             ----HHHHHHH---hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECcccc
Q 042872          259 ----DQIITLN---LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERI  331 (381)
Q Consensus       259 ----dQv~~L~---~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL  331 (381)
                          -|++--.   ..-|.+.++++|+-.+.++   ++.+++                          +..|+++||+||
T Consensus       304 reLalqie~e~~kysyng~ksvc~ygggnR~eq---ie~lkr--------------------------gveiiiatPgrl  354 (629)
T KOG0336|consen  304 RELALQIEGEVKKYSYNGLKSVCVYGGGNRNEQ---IEDLKR--------------------------GVEIIIATPGRL  354 (629)
T ss_pred             HHHHHHHHhHHhHhhhcCcceEEEecCCCchhH---HHHHhc--------------------------CceEEeeCCchH
Confidence                2221111   1347888888888776665   555554                          479999999999


Q ss_pred             ccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          332 VGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       332 ~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      ..          |...+.++|.               .|.|||||||+.+
T Consensus       355 nd----------L~~~n~i~l~---------------siTYlVlDEADrM  379 (629)
T KOG0336|consen  355 ND----------LQMDNVINLA---------------SITYLVLDEADRM  379 (629)
T ss_pred             hh----------hhhcCeeeee---------------eeEEEEecchhhh
Confidence            52          4445667777               8999999999863

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.57  E-value=5.1e-15  Score=153.04  Aligned_cols=126  Identities=20%  Similarity=0.310  Sum_probs=99.4

Q ss_pred             CCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH----------------------
Q 042872          201 TLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ----------------------  258 (381)
Q Consensus       201 ~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~----------------------  258 (381)
                      ..+|+...- ++.+....+..-|..|||+|-+++|.+|.||||+.+|.||||||.+|+                      
T Consensus       222 vtsfeh~gf-DkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~v  300 (731)
T KOG0339|consen  222 VTSFEHFGF-DKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGV  300 (731)
T ss_pred             cchhhhcCc-hHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCCeEE
Confidence            345666643 333444444478899999999999999999999999999999999998                      


Q ss_pred             ---------HH----HHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEE
Q 042872          259 ---------DQ----IITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLY  325 (381)
Q Consensus       259 ---------dQ----v~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~  325 (381)
                               -|    ..+|++.+||++++++||.+..+|...|+.                             ++.|||
T Consensus       301 ilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~-----------------------------g~EivV  351 (731)
T KOG0339|consen  301 ILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKE-----------------------------GAEIVV  351 (731)
T ss_pred             EEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhc-----------------------------CCeEEE
Confidence                     33    356666789999999999998887665553                             689999


Q ss_pred             ECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          326 VTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       326 aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      +|||||..          +...+..++.               ++.|||||||+.+
T Consensus       352 aTPgRlid----------~VkmKatn~~---------------rvS~LV~DEadrm  382 (731)
T KOG0339|consen  352 ATPGRLID----------MVKMKATNLS---------------RVSYLVLDEADRM  382 (731)
T ss_pred             echHHHHH----------HHHhhcccce---------------eeeEEEEechhhh
Confidence            99999972          3344566666               9999999999864

>PRK00254 ski2-like helicase; Provisional

Probab=99.57  E-value=7.9e-15  Score=157.97  Aligned_cols=144  Identities=22%  Similarity=0.231  Sum_probs=85.3

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHH-HHcCCCEEEECCCCCCchhhHHHH-HHHHHhhcCCcEEEEeCCCC
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKA-SVAKQDCFVLLPTGGGKSLCYQDQ-IITLNLKFGIPATFLNSQQT  280 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~a-iL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~~gI~a~~l~g~~~  280 (381)
                      .|+.+..-+.+...+.+ .||++|+|+|.+||+. ++.|+|+++.+|||+|||++|.-. +..+. ..+-+++++.+.  
T Consensus         2 ~~~~l~l~~~~~~~l~~-~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~-~~~~~~l~l~P~--   77 (720)
T PRK00254          2 KVDELRVDERIKRVLKE-RGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLL-REGGKAVYLVPL--   77 (720)
T ss_pred             cHHHcCCCHHHHHHHHh-CCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHH-hcCCeEEEEeCh--
Confidence            34555544555555555 8999999999999997 789999999999999999999622 23332 235567666543  


Q ss_pred             HHHHHHHHHHHHhchhhhhhhhhhhhhhhhhh---cccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcccccccc
Q 042872          281 VSQAAAVLQELRQGLVLSQHYFLHQLIFVLTC---ASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTT  357 (381)
Q Consensus       281 ~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~---~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~  357 (381)
                      ..-..++.+.++.  +.    .+...+..++-   ........++|+|+|||++..          +.+.+...++    
T Consensus        78 ~aLa~q~~~~~~~--~~----~~g~~v~~~~Gd~~~~~~~~~~~~IiV~Tpe~~~~----------ll~~~~~~l~----  137 (720)
T PRK00254         78 KALAEEKYREFKD--WE----KLGLRVAMTTGDYDSTDEWLGKYDIIIATAEKFDS----------LLRHGSSWIK----  137 (720)
T ss_pred             HHHHHHHHHHHHH--Hh----hcCCEEEEEeCCCCCchhhhccCCEEEEcHHHHHH----------HHhCCchhhh----
Confidence            2222223333221  00    00000000000   011112357999999999852          1112212223    


Q ss_pred             ccccccccccCCccEEEEeccccC
Q 042872          358 DVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       358 ~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                 ++++|||||+|++
T Consensus       138 -----------~l~lvViDE~H~l  150 (720)
T PRK00254        138 -----------DVKLVVADEIHLI  150 (720)
T ss_pred             -----------cCCEEEEcCcCcc
Confidence                       8999999999985

>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]

Probab=99.57  E-value=4e-15  Score=153.01  Aligned_cols=147  Identities=22%  Similarity=0.350  Sum_probs=87.2

Q ss_pred             CCCCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH----HHHHHHH--hhcCCcE
Q 042872          199 HGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ----DQIITLN--LKFGIPA  272 (381)
Q Consensus       199 ~~~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~----dQv~~L~--~~~gI~a  272 (381)
                      ...++...+.++.+        +||.+.|++|..+|+.+|.|+|+++.|.||+|||++|+    +.+..+.  .+.++.+
T Consensus        86 ~~~LS~~t~kAi~~--------~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~v  157 (543)
T KOG0342|consen   86 EGSLSPLTLKAIKE--------MGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGV  157 (543)
T ss_pred             ccccCHHHHHHHHh--------cCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeE
Confidence            34455555555444        89999999999999999999999999999999999998    1121111  1235566


Q ss_pred             EEEeCCCCHHHHHHHHHHHHhchhhhhh-hhhhhhhhhhhh---cccCCCCCccEEEECccccccCcchHHHHHHHHhcC
Q 042872          273 TFLNSQQTVSQAAAVLQELRQGLVLSQH-YFLHQLIFVLTC---ASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKG  348 (381)
Q Consensus       273 ~~l~g~~~~~e~~~il~~lr~g~~~~~~-~~~~~~~~~~~~---~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g  348 (381)
                      ++++..  ++-.-++...++  .++..| -+..+.+++.+.   ...+....++|||+|||||..         ||.+.+
T Consensus       158 lIi~PT--RELA~Q~~~eak--~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlD---------HlqNt~  224 (543)
T KOG0342|consen  158 LIICPT--RELAMQIFAEAK--ELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLD---------HLQNTS  224 (543)
T ss_pred             EEeccc--HHHHHHHHHHHH--HHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHh---------HhhcCC
Confidence            666542  222212222222  112222 112222222111   112222379999999999973         333322


Q ss_pred             CccccccccccccccccccCCccEEEEeccccC
Q 042872          349 SIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       349 ~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      .+-               .+.+.++|||||++|
T Consensus       225 ~f~---------------~r~~k~lvlDEADrl  242 (543)
T KOG0342|consen  225 GFL---------------FRNLKCLVLDEADRL  242 (543)
T ss_pred             cch---------------hhccceeEeecchhh
Confidence            111               126789999999975

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=99.56  E-value=2.1e-15  Score=156.96  Aligned_cols=133  Identities=20%  Similarity=0.229  Sum_probs=94.4

Q ss_pred             hCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-HHHHHHHh-----hcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-DQIITLNL-----KFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-dQv~~L~~-----~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      -+|..+|.+|+.+||.+|.|+|||+.|.|||||||+|+ .-+.+|-.     .-|+-|+++..  +++-.-+++.-|.  
T Consensus        87 ~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIISP--TRELA~QtFevL~--  162 (758)
T KOG0343|consen   87 AKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALIISP--TRELALQTFEVLN--  162 (758)
T ss_pred             cCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeEEecc--hHHHHHHHHHHHH--
Confidence            79999999999999999999999999999999999998 22333321     12566666643  4554445555554  


Q ss_pred             hhhhhhhhhhhhhhhhhhc--ccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccE
Q 042872          295 LVLSQHYFLHQLIFVLTCA--SRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAG  372 (381)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~  372 (381)
                      ++..+|.+.-.++++....  ....-..++|||+|||||+         +||.+.-.++.+               ++.+
T Consensus       163 kvgk~h~fSaGLiiGG~~~k~E~eRi~~mNILVCTPGRLL---------QHmde~~~f~t~---------------~lQm  218 (758)
T KOG0343|consen  163 KVGKHHDFSAGLIIGGKDVKFELERISQMNILVCTPGRLL---------QHMDENPNFSTS---------------NLQM  218 (758)
T ss_pred             HHhhccccccceeecCchhHHHHHhhhcCCeEEechHHHH---------HHhhhcCCCCCC---------------cceE
Confidence            4567777776666543221  1112236899999999996         556555555555               8999


Q ss_pred             EEEeccccC
Q 042872          373 FVVDEAHCV  381 (381)
Q Consensus       373 lVIDEAHcI  381 (381)
                      +|+|||++|
T Consensus       219 LvLDEADR~  227 (758)
T KOG0343|consen  219 LVLDEADRM  227 (758)
T ss_pred             EEeccHHHH
Confidence            999999864

>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.56  E-value=1.8e-15  Score=155.95  Aligned_cols=143  Identities=24%  Similarity=0.173  Sum_probs=85.6

Q ss_pred             HHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHH-HHHHHHhh---------c--CCcEEEEeCCC
Q 042872          212 DMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQD-QIITLNLK---------F--GIPATFLNSQQ  279 (381)
Q Consensus       212 ~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~d-Qv~~L~~~---------~--gI~a~~l~g~~  279 (381)
                      +....+.+.-||..|+|+|+-+||.+..|+|++++||||+|||.+|+- -+..+...         .  ...++++..  
T Consensus        83 ~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlap--  160 (482)
T KOG0335|consen   83 EALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAP--  160 (482)
T ss_pred             HHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeC--
Confidence            344444556899999999999999999999999999999999999981 11111100         0  112222221  


Q ss_pred             CHHHHHHHHHHHHhchhhhhhhhhhhhh-hhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccc
Q 042872          280 TVSQAAAVLQELRQGLVLSQHYFLHQLI-FVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTD  358 (381)
Q Consensus       280 ~~~e~~~il~~lr~g~~~~~~~~~~~~~-~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~  358 (381)
                      +++-..++....+...+.+.+..-..+- ..+...-.....+++|+++||+||.+          +..++.|.|+     
T Consensus       161 TReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d----------~~e~g~i~l~-----  225 (482)
T KOG0335|consen  161 TRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKD----------LIERGKISLD-----  225 (482)
T ss_pred             cHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhhhhccCccEEEecCchhhh----------hhhcceeehh-----
Confidence            2333333333333222222111000000 00000011122369999999999963          5578888888     


Q ss_pred             cccccccccCCccEEEEeccccC
Q 042872          359 VVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       359 ~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                .+++||||||+.+
T Consensus       226 ----------~~k~~vLDEADrM  238 (482)
T KOG0335|consen  226 ----------NCKFLVLDEADRM  238 (482)
T ss_pred             ----------hCcEEEecchHHh
Confidence                      9999999999863

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=99.55  E-value=6.5e-15  Score=150.22  Aligned_cols=148  Identities=22%  Similarity=0.218  Sum_probs=92.0

Q ss_pred             CCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-HHHHHH-------HhhcCCcE
Q 042872          201 TLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-DQIITL-------NLKFGIPA  272 (381)
Q Consensus       201 ~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-dQv~~L-------~~~~gI~a  272 (381)
                      ..+|+.+.+-..+..+..+ +||+.||-+|..|||.+|.|+|+++-|.||||||++|+ .-+..|       ....|+.+
T Consensus        18 ~ktFe~~gLD~RllkAi~~-lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa   96 (569)
T KOG0346|consen   18 EKTFEEFGLDSRLLKAITK-LGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSA   96 (569)
T ss_pred             hccHHHhCCCHHHHHHHHH-hCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhccccccccee
Confidence            3679998866555555544 89999999999999999999999999999999999998 112222       12346777


Q ss_pred             EEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhc--------ccCCCCCccEEEECccccccCcchHHHHHHH
Q 042872          273 TFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCA--------SRKDKPSCKLLYVTPERIVGNQSFSEVLKCL  344 (381)
Q Consensus       273 ~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L  344 (381)
                      +++...   .+..++...+-..++    .+.-+.+...+.+        +..--..++|||+||.+++.         ++
T Consensus        97 ~iLvPT---kEL~qQvy~viekL~----~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~---------~~  160 (569)
T KOG0346|consen   97 VILVPT---KELAQQVYKVIEKLV----EYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLR---------HL  160 (569)
T ss_pred             EEEech---HHHHHHHHHHHHHHH----HHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHH---------HH
Confidence            777653   222222222111111    1111111111111        11122368999999999972         11


Q ss_pred             HhcCC-ccccccccccccccccccCCccEEEEeccccC
Q 042872          345 HRKGS-IRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       345 ~~~g~-~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                       ..|. ..++               .+.++|||||+.+
T Consensus       161 -~~~~~~~~~---------------~l~~LVvDEADLl  182 (569)
T KOG0346|consen  161 -AAGVLEYLD---------------SLSFLVVDEADLL  182 (569)
T ss_pred             -hhccchhhh---------------heeeEEechhhhh
Confidence             1221 1122               8999999999864

>PRK09401 reverse gyrase; Reviewed

Probab=99.55  E-value=3.1e-14  Score=160.88  Aligned_cols=51  Identities=20%  Similarity=0.120  Sum_probs=43.8

Q ss_pred             HhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          207 LQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       207 L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .+.+.++...+.+.+|+ .|+++|.++|+.++.|+|++++||||+|||+.++
T Consensus        63 ~~~~~~~~~~f~~~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~f~l  113 (1176)
T PRK09401         63 EEEYKEFEKFFKKKTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTTFGL  113 (1176)
T ss_pred             HHHHHHHHHHHHHhcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHHHHH
Confidence            34456677777788899 7999999999999999999999999999997544

>KOG0350 consensus DEAD-box ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.54  E-value=1.2e-14  Score=149.96  Aligned_cols=119  Identities=29%  Similarity=0.362  Sum_probs=84.9

Q ss_pred             HHHHHHHhCCCCCcHHHHHHHHHHH---------cCCCEEEECCCCCCchhhHH--------------------------
Q 042872          214 EFANVVIFGNRAFRPLQHQACKASV---------AKQDCFVLLPTGGGKSLCYQ--------------------------  258 (381)
Q Consensus       214 ~~~~~~~fG~~~fRpiQ~eAI~aiL---------~GrDvLviaPTGsGKTLaF~--------------------------  258 (381)
                      .+.+++ .++++.-|+|..++|.+|         .++|+.|.|||||||||||.                          
T Consensus       149 ~q~l~k-~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L  227 (620)
T KOG0350|consen  149 DQLLVK-MAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTREL  227 (620)
T ss_pred             HHHHHH-hhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCccceEEEEEeeHHHH
Confidence            334444 799999999999999997         37899999999999999998                          


Q ss_pred             -----HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECcccccc
Q 042872          259 -----DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVG  333 (381)
Q Consensus       259 -----dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~  333 (381)
                           +.+.++....|+.+..+.|+.+.+.-...+..                        ....+..+|||+||+||+ 
T Consensus       228 ~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~------------------------~~~~~~~DIlVaTPGRLV-  282 (620)
T KOG0350|consen  228 ALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLAS------------------------DPPECRIDILVATPGRLV-  282 (620)
T ss_pred             HHHHHHHHHHhccCCceEEEecccccchHHHHHHHhc------------------------CCCccccceEEcCchHHH-
Confidence                 22333333345555555555544332222221                        122236799999999998 


Q ss_pred             CcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          334 NQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       334 ~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                              +||....+++|+               .|.|+|||||+++
T Consensus       283 --------DHl~~~k~f~Lk---------------~LrfLVIDEADRl  307 (620)
T KOG0350|consen  283 --------DHLNNTKSFDLK---------------HLRFLVIDEADRL  307 (620)
T ss_pred             --------HhccCCCCcchh---------------hceEEEechHHHH
Confidence                    456667788888               9999999999864

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=99.52  E-value=2.9e-14  Score=156.19  Aligned_cols=125  Identities=24%  Similarity=0.370  Sum_probs=93.0

Q ss_pred             HHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-------------------------
Q 042872          204 FEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-------------------------  258 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-------------------------  258 (381)
                      +........+...+ +.+||..+||||.+|||+|+.|||||+++.||+|||++|.                         
T Consensus       367 W~q~gl~~~il~tl-kkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~a  445 (997)
T KOG0334|consen  367 WTQCGLSSKILETL-KKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILA  445 (997)
T ss_pred             HhhCCchHHHHHHH-HHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEc
Confidence            33333334455555 4499999999999999999999999999999999999995                         


Q ss_pred             ------HH----HHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECc
Q 042872          259 ------DQ----IITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTP  328 (381)
Q Consensus       259 ------dQ----v~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTP  328 (381)
                            -|    +..|.+..+|++++++|+....++   +..+++|                          ..|+|+||
T Consensus       446 Ptrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~q---iaelkRg--------------------------~eIvV~tp  496 (997)
T KOG0334|consen  446 PTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQ---IAELKRG--------------------------AEIVVCTP  496 (997)
T ss_pred             CCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHH---HHHHhcC--------------------------CceEEecc
Confidence                  23    455666689999999999887665   5566654                          68999999


Q ss_pred             cccccCcchHHHHHHHHhcCC-ccccccccccccccccccCCccEEEEeccccC
Q 042872          329 ERIVGNQSFSEVLKCLHRKGS-IRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       329 ErL~~~~~f~~~L~~L~~~g~-~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      +|+..      .+  ..+.|. .+|.               ++.++|+|||+.+
T Consensus       497 GRmiD------~l--~~n~grvtnlr---------------R~t~lv~deaDrm  527 (997)
T KOG0334|consen  497 GRMID------IL--CANSGRVTNLR---------------RVTYLVLDEADRM  527 (997)
T ss_pred             chhhh------hH--hhcCCcccccc---------------ccceeeechhhhh
Confidence            99973      11  112221 1222               7889999999863

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.51  E-value=7.4e-14  Score=150.09  Aligned_cols=111  Identities=16%  Similarity=0.238  Sum_probs=88.3

Q ss_pred             HHHHHHhCCCCCcHHHHHHHHHHHcC------CCEEEECCCCCCchhhHH-----------------------HH----H
Q 042872          215 FANVVIFGNRAFRPLQHQACKASVAK------QDCFVLLPTGGGKSLCYQ-----------------------DQ----I  261 (381)
Q Consensus       215 ~~~~~~fG~~~fRpiQ~eAI~aiL~G------rDvLviaPTGsGKTLaF~-----------------------dQ----v  261 (381)
                      ..+...++| ++|++|.+||+.++++      .++|+++|||||||++|+                       .|    +
T Consensus       252 ~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~g~q~lilaPT~~LA~Q~~~~l  330 (681)
T PRK10917        252 KKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENL  330 (681)
T ss_pred             HHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEeccHHHHHHHHHHH
Confidence            444556788 5999999999999986      489999999999999997                       22    3


Q ss_pred             HHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHH
Q 042872          262 ITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVL  341 (381)
Q Consensus       262 ~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L  341 (381)
                      ..+...+|+++..++|+.+..++..++..+..|                         .++|||+||+++...       
T Consensus       331 ~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g-------------------------~~~IvVgT~~ll~~~-------  378 (681)
T PRK10917        331 KKLLEPLGIRVALLTGSLKGKERREILEAIASG-------------------------EADIVIGTHALIQDD-------  378 (681)
T ss_pred             HHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCC-------------------------CCCEEEchHHHhccc-------
Confidence            344445689999999999988888888887755                         689999999988521       


Q ss_pred             HHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          342 KCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       342 ~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                              +.+.               +++++||||+|+.
T Consensus       379 --------v~~~---------------~l~lvVIDE~Hrf  395 (681)
T PRK10917        379 --------VEFH---------------NLGLVIIDEQHRF  395 (681)
T ss_pred             --------chhc---------------ccceEEEechhhh
Confidence                    1112               8999999999973

>PRK01172 ski2-like helicase; Provisional

Probab=99.51  E-value=5.7e-14  Score=149.98  Aligned_cols=140  Identities=17%  Similarity=0.150  Sum_probs=80.3

Q ss_pred             HHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHH-HHHHhhcCCcEEEEeCCCCHHH
Q 042872          205 EELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQI-ITLNLKFGIPATFLNSQQTVSQ  283 (381)
Q Consensus       205 e~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv-~~L~~~~gI~a~~l~g~~~~~e  283 (381)
                      +.+..-+.+...+.+ .||+ ++|+|.+|++.++.|+++++++|||+|||++|.-.+ ..+.  .+.+++++.+-  ..-
T Consensus         4 ~~~~l~~~~~~~~~~-~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~--~~~k~v~i~P~--raL   77 (674)
T PRK01172          4 SDLGYDDEFLNLFTG-NDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFL--AGLKSIYIVPL--RSL   77 (674)
T ss_pred             hhcCCCHHHHHHHhh-CCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHH--hCCcEEEEech--HHH
Confidence            333333334444433 5776 999999999999999999999999999999986222 2232  25677777642  222


Q ss_pred             HHHHHHHHHhchhhhhhhhhhhhhhhhhh---cccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccc
Q 042872          284 AAAVLQELRQGLVLSQHYFLHQLIFVLTC---ASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVV  360 (381)
Q Consensus       284 ~~~il~~lr~g~~~~~~~~~~~~~~~~~~---~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v  360 (381)
                      ..++.+.+++  +.    .+...+..++-   ........++|+|+|||++..      .+    ++....+.       
T Consensus        78 a~q~~~~~~~--l~----~~g~~v~~~~G~~~~~~~~~~~~dIiv~Tpek~~~------l~----~~~~~~l~-------  134 (674)
T PRK01172         78 AMEKYEELSR--LR----SLGMRVKISIGDYDDPPDFIKRYDVVILTSEKADS------LI----HHDPYIIN-------  134 (674)
T ss_pred             HHHHHHHHHH--Hh----hcCCeEEEEeCCCCCChhhhccCCEEEECHHHHHH------HH----hCChhHHh-------
Confidence            2223333321  00    00000000000   001112357999999999752      11    11111122       


Q ss_pred             cccccccCCccEEEEeccccC
Q 042872          361 VLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       361 ~~~~~~~~~L~~lVIDEAHcI  381 (381)
                              ++++|||||||++
T Consensus       135 --------~v~lvViDEaH~l  147 (674)
T PRK01172        135 --------DVGLIVADEIHII  147 (674)
T ss_pred             --------hcCEEEEecchhc
Confidence                    8999999999985

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.49  E-value=1.1e-13  Score=147.34  Aligned_cols=108  Identities=20%  Similarity=0.276  Sum_probs=85.5

Q ss_pred             HHHHhCCCCCcHHHHHHHHHHHcC------CCEEEECCCCCCchhhHH-----------------------HH----HHH
Q 042872          217 NVVIFGNRAFRPLQHQACKASVAK------QDCFVLLPTGGGKSLCYQ-----------------------DQ----IIT  263 (381)
Q Consensus       217 ~~~~fG~~~fRpiQ~eAI~aiL~G------rDvLviaPTGsGKTLaF~-----------------------dQ----v~~  263 (381)
                      +...++| ++|++|.+||+.++.+      .+.|+++|||+|||++|+                       .|    +..
T Consensus       228 ~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~g~qvlilaPT~~LA~Q~~~~~~~  306 (630)
T TIGR00643       228 FLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRN  306 (630)
T ss_pred             HHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEECCHHHHHHHHHHHHHH
Confidence            4445899 6999999999999976      258999999999999986                       22    333


Q ss_pred             HHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHH
Q 042872          264 LNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKC  343 (381)
Q Consensus       264 L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~  343 (381)
                      +...+|+++.+++|+.+..++..+++.+..|                         .++|||+||+++...         
T Consensus       307 l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g-------------------------~~~IiVgT~~ll~~~---------  352 (630)
T TIGR00643       307 LLAPLGIEVALLTGSLKGKRRKELLETIASG-------------------------QIHLVVGTHALIQEK---------  352 (630)
T ss_pred             HhcccCcEEEEEecCCCHHHHHHHHHHHhCC-------------------------CCCEEEecHHHHhcc---------
Confidence            3334589999999999988888888887755                         689999999988521         


Q ss_pred             HHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          344 LHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       344 L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                            +.+.               ++++|||||||+
T Consensus       353 ------~~~~---------------~l~lvVIDEaH~  368 (630)
T TIGR00643       353 ------VEFK---------------RLALVIIDEQHR  368 (630)
T ss_pred             ------cccc---------------ccceEEEechhh
Confidence                  1112               899999999997

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

Probab=99.47  E-value=2.4e-13  Score=149.62  Aligned_cols=106  Identities=21%  Similarity=0.250  Sum_probs=84.5

Q ss_pred             HhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH--------------------------HHHHHHHh---hcC-
Q 042872          220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ--------------------------DQIITLNL---KFG-  269 (381)
Q Consensus       220 ~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~--------------------------dQv~~L~~---~~g-  269 (381)
                      ..|+..++.+|.+|+..+.+||||+|..|||||||+||+                          ||..+|.+   .++ 
T Consensus        65 ~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnALa~DQ~~rl~~~~~~~~~  144 (851)
T COG1205          65 KAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQAERLRELISDLPG  144 (851)
T ss_pred             HhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCccEEEEechhhhHhhHHHHHHHHHHhCCC
Confidence            378888999999999999999999999999999999998                          88776653   344 


Q ss_pred             -CcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECcccccc-----CcchHHHHHH
Q 042872          270 -IPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVG-----NQSFSEVLKC  343 (381)
Q Consensus       270 -I~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~-----~~~f~~~L~~  343 (381)
                       +.+..++|++...++..++..                             .++||+++|.+|.-     .+.|+..+  
T Consensus       145 ~v~~~~y~Gdt~~~~r~~~~~~-----------------------------pp~IllTNpdMLh~~llr~~~~~~~~~--  193 (851)
T COG1205         145 KVTFGRYTGDTPPEERRAIIRN-----------------------------PPDILLTNPDMLHYLLLRNHDAWLWLL--  193 (851)
T ss_pred             cceeeeecCCCChHHHHHHHhC-----------------------------CCCEEEeCHHHHHHHhccCcchHHHHH--
Confidence             778888999888876544433                             68999999999862     12222211  


Q ss_pred             HHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          344 LHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       344 L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                                              +++++|||||+|-
T Consensus       194 ------------------------~~Lk~lVvDElHt  206 (851)
T COG1205         194 ------------------------RNLKYLVVDELHT  206 (851)
T ss_pred             ------------------------hcCcEEEEeccee
Confidence                                    1799999999994

>KOG0328 consensus Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]

Probab=99.46  E-value=7.7e-14  Score=136.51  Aligned_cols=125  Identities=17%  Similarity=0.268  Sum_probs=96.4

Q ss_pred             CCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH----------------------
Q 042872          201 TLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ----------------------  258 (381)
Q Consensus       201 ~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~----------------------  258 (381)
                      ..+|+.+..-++++... -.+||++|..+|..||+.++.||||++.++.|+|||.+|.                      
T Consensus        26 ~~~F~~Mgl~edlLrgi-Y~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPT  104 (400)
T KOG0328|consen   26 IPTFDDMGLKEDLLRGI-YAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPT  104 (400)
T ss_pred             ccchhhcCchHHHHHHH-HHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccceeeEEEecCh
Confidence            34677776655554443 3389999999999999999999999999999999999996                      


Q ss_pred             --------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccc
Q 042872          259 --------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPER  330 (381)
Q Consensus       259 --------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPEr  330 (381)
                              .-+..|+..++|.+..+.||.+..+-.+.++                             -+.++|..||+|
T Consensus       105 RELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld-----------------------------~G~hvVsGtPGr  155 (400)
T KOG0328|consen  105 RELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLD-----------------------------YGQHVVSGTPGR  155 (400)
T ss_pred             HHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhc-----------------------------ccceEeeCCCch
Confidence                    2245666677888888888877554322222                             268999999999


Q ss_pred             cccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          331 IVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       331 L~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                      ++.          |.++++++-.               .++++|+|||+-
T Consensus       156 v~d----------mikr~~L~tr---------------~vkmlVLDEaDe  180 (400)
T KOG0328|consen  156 VLD----------MIKRRSLRTR---------------AVKMLVLDEADE  180 (400)
T ss_pred             HHH----------HHHhcccccc---------------ceeEEEeccHHH
Confidence            973          5566766666               999999999973

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.46  E-value=2.6e-13  Score=150.43  Aligned_cols=113  Identities=21%  Similarity=0.240  Sum_probs=86.1

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcC------CCEEEECCCCCCchhhHH-----------------------HH-HH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAK------QDCFVLLPTGGGKSLCYQ-----------------------DQ-II  262 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~G------rDvLviaPTGsGKTLaF~-----------------------dQ-v~  262 (381)
                      +...+...|+|+ +||+|.+||+.++++      +|+|+++|||+|||++|+                       .| ..
T Consensus       440 ~~~~~~~~~~f~-~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~g~qvlvLvPT~~LA~Q~~~  518 (926)
T TIGR00580       440 WQQEFEDSFPFE-ETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFE  518 (926)
T ss_pred             HHHHHHHhCCCC-CCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHhCCeEEEEeCcHHHHHHHHH
Confidence            344556678995 999999999999975      799999999999999986                       33 22


Q ss_pred             HHH---hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHH
Q 042872          263 TLN---LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSE  339 (381)
Q Consensus       263 ~L~---~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~  339 (381)
                      .+.   ..+++++..+++..+..++..+++.++.|                         .++|||+||..+.  .    
T Consensus       519 ~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g-------------------------~~dIVIGTp~ll~--~----  567 (926)
T TIGR00580       519 TFKERFANFPVTIELLSRFRSAKEQNEILKELASG-------------------------KIDILIGTHKLLQ--K----  567 (926)
T ss_pred             HHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcC-------------------------CceEEEchHHHhh--C----
Confidence            222   24578888888888888888888887755                         6899999995432  1    


Q ss_pred             HHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          340 VLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       340 ~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                               .+.++               +|++|||||+|+.
T Consensus       568 ---------~v~f~---------------~L~llVIDEahrf  585 (926)
T TIGR00580       568 ---------DVKFK---------------DLGLLIIDEEQRF  585 (926)
T ss_pred             ---------CCCcc---------------cCCEEEeeccccc
Confidence                     12222               8999999999973

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.

>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]

Probab=99.46  E-value=9e-15  Score=147.63  Aligned_cols=123  Identities=22%  Similarity=0.298  Sum_probs=91.0

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH------------------------
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ------------------------  258 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~------------------------  258 (381)
                      +|..++--..+...+++ -|+..|||+|.+-||.+|+|||.|++|-||||||++|.                        
T Consensus       171 sF~eMKFP~~~L~~lk~-KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~g  249 (610)
T KOG0341|consen  171 SFKEMKFPKPLLRGLKK-KGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYG  249 (610)
T ss_pred             hhhhccCCHHHHHHHHh-cCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCee
Confidence            45565555555555655 79999999999999999999999999999999999996                        


Q ss_pred             -----------------HH-HHHHHhhcC---CcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCC
Q 042872          259 -----------------DQ-IITLNLKFG---IPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKD  317 (381)
Q Consensus       259 -----------------dQ-v~~L~~~~g---I~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~  317 (381)
                                       .| +..|. .-|   +++..+.|+.+..++...+   ++                        
T Consensus       250 LiicPSRELArQt~~iie~~~~~L~-e~g~P~lRs~LciGG~~v~eql~~v---~~------------------------  301 (610)
T KOG0341|consen  250 LIICPSRELARQTHDIIEQYVAALQ-EAGYPELRSLLCIGGVPVREQLDVV---RR------------------------  301 (610)
T ss_pred             EEEcCcHHHHHHHHHHHHHHHHHHH-hcCChhhhhhhhhcCccHHHHHHHH---hc------------------------
Confidence                             11 22222 223   4667777888877664443   33                        


Q ss_pred             CCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          318 KPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       318 ~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                        +.||+|+||+||.+          +..+..++|+               -+.|+++|||+++
T Consensus       302 --GvHivVATPGRL~D----------mL~KK~~sLd---------------~CRyL~lDEADRm  338 (610)
T KOG0341|consen  302 --GVHIVVATPGRLMD----------MLAKKIMSLD---------------ACRYLTLDEADRM  338 (610)
T ss_pred             --CeeEEEcCcchHHH----------HHHHhhccHH---------------HHHHhhhhhHHHH
Confidence              58999999999972          2233446666               8999999999863

>TIGR01054 rgy reverse gyrase

Probab=99.44  E-value=4.6e-13  Score=151.47  Aligned_cols=119  Identities=18%  Similarity=0.201  Sum_probs=81.5

Q ss_pred             hchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-----------------------H----HH
Q 042872          209 ALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-----------------------D----QI  261 (381)
Q Consensus       209 ~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-----------------------d----Qv  261 (381)
                      .+.++...+.+..|+ .|+|+|+++|+.++.|+|++++||||+|||+.++                       .    .+
T Consensus        63 ~~~~f~~~f~~~~g~-~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~f~l~~~~~l~~~g~~vLIL~PTreLa~Qi~~~l  141 (1171)
T TIGR01054        63 ELKEFEEFFKKAVGS-EPWSIQKMWAKRVLRGDSFAIIAPTGVGKTTFGLAMSLFLAKKGKRCYIILPTTLLVIQVAEKI  141 (1171)
T ss_pred             HHHHHHHHHHHhcCC-CCcHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEeCHHHHHHHHHHHH
Confidence            344556666666676 6999999999999999999999999999997433                       1    22


Q ss_pred             HHHHhhcCCcEE---EEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchH
Q 042872          262 ITLNLKFGIPAT---FLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFS  338 (381)
Q Consensus       262 ~~L~~~~gI~a~---~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~  338 (381)
                      ..+....|+...   .++|+.+..++...++.+++|                         .++|||+||++|..  .  
T Consensus       142 ~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~-------------------------~~dIlV~Tp~rL~~--~--  192 (1171)
T TIGR01054       142 SSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENG-------------------------DFDILITTTMFLSK--N--  192 (1171)
T ss_pred             HHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcC-------------------------CCCEEEECHHHHHH--H--
Confidence            333333344432   345666666555555555433                         68999999999862  1  


Q ss_pred             HHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          339 EVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       339 ~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                        +..+.  .                    ++.+|||||||++
T Consensus       193 --~~~l~--~--------------------~~~~iVvDEaD~~  211 (1171)
T TIGR01054       193 --YDELG--P--------------------KFDFIFVDDVDAL  211 (1171)
T ss_pred             --HHHhc--C--------------------CCCEEEEeChHhh
Confidence              22111  1                    6889999999985

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.

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.44  E-value=4.8e-13  Score=147.05  Aligned_cols=129  Identities=18%  Similarity=0.217  Sum_probs=89.5

Q ss_pred             HHHHhhchHHHHHHHH----HhCCCCC---cHHHHHHHHHHHcCCCEEEECCCCCCchhhHH------------------
Q 042872          204 FEELQALDDMEFANVV----IFGNRAF---RPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ------------------  258 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~----~fG~~~f---RpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~------------------  258 (381)
                      ++.+....++..+...    ..||..|   ||+|.++|+.++.++|+++.|+||+|||++|.                  
T Consensus        64 ~eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g~~v~IVTp  143 (970)
T PRK12899         64 PEAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTGKPVHLVTV  143 (970)
T ss_pred             HHHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhcCCeEEEeC
Confidence            5555555555554432    3578888   99999999999999999999999999999998                  


Q ss_pred             ---------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECcc
Q 042872          259 ---------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPE  329 (381)
Q Consensus       259 ---------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPE  329 (381)
                               +++..+.+.+|+++.++.|+.+..++...+                               .++|+|+||+
T Consensus       144 TrELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~y-------------------------------~~DIVygTPg  192 (970)
T PRK12899        144 NDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEIY-------------------------------QCDVVYGTAS  192 (970)
T ss_pred             CHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHc-------------------------------CCCEEEECCC
Confidence                     334455545567777777776665542111                               4799999999


Q ss_pred             cc-ccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          330 RI-VGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       330 rL-~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      +| ++      .|    +.+.+.++..        ...|+.+.++|||||+.|
T Consensus       193 RLgfD------yL----rd~~~~~~~~--------~~vqr~~~~~IIDEADsm  227 (970)
T PRK12899        193 EFGFD------YL----RDNSIATRKE--------EQVGRGFYFAIIDEVDSI  227 (970)
T ss_pred             hhHHH------Hh----hCCCCCcCHH--------HhhcccccEEEEechhhh
Confidence            99 42      11    2222222210        124568899999999865

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.43  E-value=2.4e-13  Score=143.80  Aligned_cols=125  Identities=22%  Similarity=0.261  Sum_probs=98.7

Q ss_pred             CCCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------
Q 042872          200 GTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------  258 (381)
Q Consensus       200 ~~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------  258 (381)
                      .+..|+.|.+..++..-++. -+|..|+++|..|||+++.+-|+||.+..|+|||++|.                     
T Consensus        23 ~~~~fe~l~l~r~vl~glrr-n~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~P  101 (980)
T KOG4284|consen   23 CTPGFEQLALWREVLLGLRR-NAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTP  101 (980)
T ss_pred             CCCCHHHHHHHHHHHHHHHh-hcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEec
Confidence            45679999988888777755 79999999999999999999999999999999999996                     


Q ss_pred             ---------HHHHHHHhh-cCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECc
Q 042872          259 ---------DQIITLNLK-FGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTP  328 (381)
Q Consensus       259 ---------dQv~~L~~~-~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTP  328 (381)
                               +.+.+++.. .|.++-+++||+....-..   .++                           .++|+|+||
T Consensus       102 TREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~---rlk---------------------------~~rIvIGtP  151 (980)
T KOG4284|consen  102 TREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLI---RLK---------------------------QTRIVIGTP  151 (980)
T ss_pred             chhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhh---hhh---------------------------hceEEecCc
Confidence                     334444422 3678888888876543222   222                           578999999


Q ss_pred             cccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          329 ERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       329 ErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                      |||.          +|++.+.++.+               .|.+||+|||+-
T Consensus       152 GRi~----------qL~el~~~n~s---------------~vrlfVLDEADk  178 (980)
T KOG4284|consen  152 GRIA----------QLVELGAMNMS---------------HVRLFVLDEADK  178 (980)
T ss_pred             hHHH----------HHHHhcCCCcc---------------ceeEEEeccHHh
Confidence            9996          35666666666               899999999974

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.42  E-value=7.7e-13  Score=149.40  Aligned_cols=113  Identities=21%  Similarity=0.207  Sum_probs=84.7

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcC------CCEEEECCCCCCchhhHH-----------------------HH-HH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAK------QDCFVLLPTGGGKSLCYQ-----------------------DQ-II  262 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~G------rDvLviaPTGsGKTLaF~-----------------------dQ-v~  262 (381)
                      +...+...|+| .+|++|.+||+.++.+      +|+|+++|||+|||++|+                       .| ..
T Consensus       589 ~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~g~qvlvLvPT~eLA~Q~~~  667 (1147)
T PRK10689        589 QYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYD  667 (1147)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHH
Confidence            33445566899 6999999999999987      899999999999997665                       22 23


Q ss_pred             HHHh---hcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHH
Q 042872          263 TLNL---KFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSE  339 (381)
Q Consensus       263 ~L~~---~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~  339 (381)
                      .+..   .+++++.++++..+..++..+++.+++|                         .++|||+||+.+..  .   
T Consensus       668 ~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g-------------------------~~dIVVgTp~lL~~--~---  717 (1147)
T PRK10689        668 NFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEG-------------------------KIDILIGTHKLLQS--D---  717 (1147)
T ss_pred             HHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhC-------------------------CCCEEEECHHHHhC--C---
Confidence            3332   3457777888888888887777777654                         68999999975531  1   


Q ss_pred             HHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          340 VLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       340 ~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                +.++               ++++|||||+|++
T Consensus       718 ----------v~~~---------------~L~lLVIDEahrf  734 (1147)
T PRK10689        718 ----------VKWK---------------DLGLLIVDEEHRF  734 (1147)
T ss_pred             ----------CCHh---------------hCCEEEEechhhc
Confidence                      1112               7999999999984

>KOG0326 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.40  E-value=7.1e-14  Score=138.52  Aligned_cols=125  Identities=22%  Similarity=0.308  Sum_probs=96.5

Q ss_pred             CCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH----------------------
Q 042872          201 TLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ----------------------  258 (381)
Q Consensus       201 ~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~----------------------  258 (381)
                      ...||.+-+-.++....-. .||+.|.|+|.++||.+|.|||+|+-|..|+|||.+|.                      
T Consensus        84 G~efEd~~Lkr~LLmgIfe-~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPt  162 (459)
T KOG0326|consen   84 GNEFEDYCLKRELLMGIFE-KGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPT  162 (459)
T ss_pred             CccHHHhhhhHHHHHHHHH-hccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeec
Confidence            4567777655555444433 69999999999999999999999999999999999997                      


Q ss_pred             -------HH-HHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccc
Q 042872          259 -------DQ-IITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPER  330 (381)
Q Consensus       259 -------dQ-v~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPEr  330 (381)
                             .| +..+.+.+|+++.+.+||++..+-  ++                           .-+..+|++|+||+|
T Consensus       163 relALQtSqvc~~lskh~~i~vmvttGGT~lrDD--I~---------------------------Rl~~~VH~~vgTPGR  213 (459)
T KOG0326|consen  163 RELALQTSQVCKELSKHLGIKVMVTTGGTSLRDD--IM---------------------------RLNQTVHLVVGTPGR  213 (459)
T ss_pred             chhhHHHHHHHHHHhcccCeEEEEecCCcccccc--ee---------------------------eecCceEEEEcCChh
Confidence                   23 456777788888888888775432  22                           122368999999999


Q ss_pred             cccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          331 IVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       331 L~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                      +++          |..+|...++               .+..+|+|||+-
T Consensus       214 IlD----------L~~KgVa~ls---------------~c~~lV~DEADK  238 (459)
T KOG0326|consen  214 ILD----------LAKKGVADLS---------------DCVILVMDEADK  238 (459)
T ss_pred             HHH----------HHhcccccch---------------hceEEEechhhh
Confidence            983          5566655566               899999999984

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

Probab=99.40  E-value=6.3e-13  Score=145.52  Aligned_cols=45  Identities=24%  Similarity=0.101  Sum_probs=37.7

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCC-CEEEECCCCCCchhhHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQ-DCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~Gr-DvLviaPTGsGKTLaF~  258 (381)
                      +...+....||+ |+|+|.++|+.++.|+ ++++.+|||+|||++|.
T Consensus         4 f~~ff~~~~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~a   49 (844)
T TIGR02621         4 FDEWYQGLHGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIA   49 (844)
T ss_pred             HHHHHHHHhCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHH
Confidence            344555668998 9999999999999998 67778999999999554

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.

>KOG0337 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.36  E-value=3.3e-13  Score=137.33  Aligned_cols=148  Identities=20%  Similarity=0.245  Sum_probs=90.0

Q ss_pred             CCCCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-HHHHHHHh--hcCCcEEEE
Q 042872          199 HGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-DQIITLNL--KFGIPATFL  275 (381)
Q Consensus       199 ~~~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-dQv~~L~~--~~gI~a~~l  275 (381)
                      .-.+....++++.        .-||..|+|+|+..||.+|.|+|++..+-||||||.||. ..+++|..  ..|+++.++
T Consensus        25 smgL~~~v~raI~--------kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~Ralil   96 (529)
T KOG0337|consen   25 SMGLDYKVLRAIH--------KKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALIL   96 (529)
T ss_pred             ccCCCHHHHHHHH--------HhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeec
Confidence            3345555554433        379999999999999999999999999999999999998 44555543  346777776


Q ss_pred             eCCCCHHHH-HHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccc
Q 042872          276 NSQQTVSQA-AAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKV  354 (381)
Q Consensus       276 ~g~~~~~e~-~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~  354 (381)
                      .+..-...| -.+++.+-+|.-+-+.-.+++.-.  -......+..++||++||++++.. .         -.-.++|+ 
T Consensus        97 sptreLa~qtlkvvkdlgrgt~lr~s~~~ggD~~--eeqf~~l~~npDii~ATpgr~~h~-~---------vem~l~l~-  163 (529)
T KOG0337|consen   97 SPTRELALQTLKVVKDLGRGTKLRQSLLVGGDSI--EEQFILLNENPDIIIATPGRLLHL-G---------VEMTLTLS-  163 (529)
T ss_pred             cCcHHHHHHHHHHHHHhccccchhhhhhcccchH--HHHHHHhccCCCEEEecCceeeee-e---------hheecccc-
Confidence            653222111 122233333321111111110000  000112344689999999999831 1         11124555 


Q ss_pred             cccccccccccccCCccEEEEeccccC
Q 042872          355 LTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       355 ~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                    .+.|||+|||+.|
T Consensus       164 --------------sveyVVfdEadrl  176 (529)
T KOG0337|consen  164 --------------SVEYVVFDEADRL  176 (529)
T ss_pred             --------------ceeeeeehhhhHH
Confidence                          8999999999864

>KOG0329 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.30  E-value=2.5e-12  Score=124.69  Aligned_cols=121  Identities=20%  Similarity=0.294  Sum_probs=87.6

Q ss_pred             HHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-------------------------
Q 042872          204 FEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-------------------------  258 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-------------------------  258 (381)
                      |..+-+-+++..+.. .-||+.|.++|.+|||.+.-|.|+++.|..|-|||.+|.                         
T Consensus        44 frdfllkpellraiv-dcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtrel  122 (387)
T KOG0329|consen   44 FRDFLLKPELLRAIV-DCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTREL  122 (387)
T ss_pred             hhhhhcCHHHHHHHH-hccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHHH
Confidence            444433333333333 389999999999999999999999999999999999997                         


Q ss_pred             -----HHHHHHHhhc-CCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccc
Q 042872          259 -----DQIITLNLKF-GIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIV  332 (381)
Q Consensus       259 -----dQv~~L~~~~-gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~  332 (381)
                           ....++.+.+ ++++.++.||.....-...++.                             .+||+++||+|++
T Consensus       123 afqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~-----------------------------~PhivVgTPGril  173 (387)
T KOG0329|consen  123 AFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKN-----------------------------CPHIVVGTPGRIL  173 (387)
T ss_pred             HHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhC-----------------------------CCeEEEcCcHHHH
Confidence                 1223333222 5677777777654433333322                             5899999999997


Q ss_pred             cCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccc
Q 042872          333 GNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH  379 (381)
Q Consensus       333 ~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAH  379 (381)
                      .          |.+.++++|+               +++.+||||++
T Consensus       174 A----------Lvr~k~l~lk---------------~vkhFvlDEcd  195 (387)
T KOG0329|consen  174 A----------LVRNRSLNLK---------------NVKHFVLDECD  195 (387)
T ss_pred             H----------HHHhccCchh---------------hcceeehhhHH
Confidence            2          5667788888               99999999986

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.26  E-value=2.7e-11  Score=130.52  Aligned_cols=100  Identities=23%  Similarity=0.317  Sum_probs=82.0

Q ss_pred             CCcHHHHHHHHHHHcC---CCEEEECCCCCCchhhHH------------------------HHHHHHHhhcCCcEEEEeC
Q 042872          225 AFRPLQHQACKASVAK---QDCFVLLPTGGGKSLCYQ------------------------DQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~G---rDvLviaPTGsGKTLaF~------------------------dQv~~L~~~~gI~a~~l~g  277 (381)
                      .+++.|.+|++.++.+   +++++.+|||+|||.+|+                        ++...|.+.+|+++..++|
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s  223 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHS  223 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEEC
Confidence            5889999999999984   789999999999999996                        3456676667888889999


Q ss_pred             CCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcccccccc
Q 042872          278 QQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTT  357 (381)
Q Consensus       278 ~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~  357 (381)
                      +.+..++...+.++..|                         .++|||+||..+.. +                ++    
T Consensus       224 ~~s~~~r~~~~~~~~~g-------------------------~~~IVVgTrsal~~-p----------------~~----  257 (679)
T PRK05580        224 GLSDGERLDEWRKAKRG-------------------------EAKVVIGARSALFL-P----------------FK----  257 (679)
T ss_pred             CCCHHHHHHHHHHHHcC-------------------------CCCEEEeccHHhcc-c----------------cc----
Confidence            98888887777777654                         68999999988751 0                11    


Q ss_pred             ccccccccccCCccEEEEeccccC
Q 042872          358 DVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       358 ~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                 ++++|||||+|+.
T Consensus       258 -----------~l~liVvDEeh~~  270 (679)
T PRK05580        258 -----------NLGLIIVDEEHDS  270 (679)
T ss_pred             -----------CCCEEEEECCCcc
Confidence                       8999999999963

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.21  E-value=2.5e-11  Score=132.52  Aligned_cols=104  Identities=20%  Similarity=0.316  Sum_probs=71.2

Q ss_pred             hCCCCCcHHHHHHHHHHHc-CCCEEEECCCCCCchhhHH-------------------------HHHHHHH--hhcCCcE
Q 042872          221 FGNRAFRPLQHQACKASVA-KQDCFVLLPTGGGKSLCYQ-------------------------DQIITLN--LKFGIPA  272 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~-GrDvLviaPTGsGKTLaF~-------------------------dQv~~L~--~~~gI~a  272 (381)
                      .|+.+..|.|++++...+. ++|+|+++|||+|||+++.                         +.+.++.  +.+|+++
T Consensus        27 ~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~~~k~vYivPlkALa~Ek~~~~~~~~~~GirV  106 (766)
T COG1204          27 DGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEEFSRLEELGIRV  106 (766)
T ss_pred             CChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhcCCcEEEEeChHHHHHHHHHHhhhHHhcCCEE
Confidence            5676777888888888765 5999999999999999886                         2223333  2566666


Q ss_pred             EEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccc
Q 042872          273 TFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRL  352 (381)
Q Consensus       273 ~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l  352 (381)
                      ...+|+.....                                ..-.+++|||+|||++-+          +.++...  
T Consensus       107 ~~~TgD~~~~~--------------------------------~~l~~~~ViVtT~EK~Ds----------l~R~~~~--  142 (766)
T COG1204         107 GISTGDYDLDD--------------------------------ERLARYDVIVTTPEKLDS----------LTRKRPS--  142 (766)
T ss_pred             EEecCCcccch--------------------------------hhhccCCEEEEchHHhhH----------hhhcCcc--
Confidence            66666654221                                111268999999999952          1111111  


Q ss_pred             cccccccccccccccCCccEEEEeccccC
Q 042872          353 KVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       353 ~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                   +.+.+++|||||+|.|
T Consensus       143 -------------~~~~V~lvViDEiH~l  158 (766)
T COG1204         143 -------------WIEEVDLVVIDEIHLL  158 (766)
T ss_pred             -------------hhhcccEEEEeeeeec
Confidence                         2238999999999975

>KOG0327 consensus Translation initiation factor 4F, helicase subunit (eIF-4A) and related helicases [Translation, ribosomal structure and biogenesis]

Probab=99.21  E-value=1.7e-11  Score=123.39  Aligned_cols=124  Identities=18%  Similarity=0.274  Sum_probs=89.8

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH------------------------
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ------------------------  258 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~------------------------  258 (381)
                      +|+.+++-++++.-. -.+||++|+.+|+.||..+..|.|+++.+++|+|||.+|.                        
T Consensus        27 sfddm~L~e~LLrgi-y~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalilaPtre  105 (397)
T KOG0327|consen   27 SFDDMNLKESLLRGI-YAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTRE  105 (397)
T ss_pred             hhhhcCCCHHHHhHH-HhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhcchHH
Confidence            677776555444433 3489999999999999999999999999999999999997                        


Q ss_pred             ------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccc
Q 042872          259 ------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIV  332 (381)
Q Consensus       259 ------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~  332 (381)
                            ..++.++...++++..+.|+.........+...                            .++|++.||+|+.
T Consensus       106 La~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~----------------------------~~hivvGTpgrV~  157 (397)
T KOG0327|consen  106 LAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKD----------------------------KPHIVVGTPGRVF  157 (397)
T ss_pred             HHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhcc----------------------------CceeecCCchhHH
Confidence                  112344444567777777776655443333331                            4799999999997


Q ss_pred             cCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          333 GNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       333 ~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                      .          +..++++..+               .++++|+|||+-
T Consensus       158 d----------ml~~~~l~~~---------------~iKmfvlDEaDE  180 (397)
T KOG0327|consen  158 D----------MLNRGSLSTD---------------GIKMFVLDEADE  180 (397)
T ss_pred             H----------hhcccccccc---------------ceeEEeecchHh
Confidence            3          2233344444               799999999974

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.16  E-value=1.7e-10  Score=126.17  Aligned_cols=120  Identities=18%  Similarity=0.179  Sum_probs=85.5

Q ss_pred             chHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHH
Q 042872          210 LDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQII  262 (381)
Q Consensus       210 l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~  262 (381)
                      +.-+..++.+.+|+ .|+++|..+++.++.|+  |+.|+||+|||++|.                           +.+.
T Consensus        64 fA~vrea~~R~~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~G~~v~VvTpt~~LA~qd~e~~~  140 (790)
T PRK09200         64 FAVVREAAKRVLGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALEGKGVHLITVNDYLAKRDAEEMG  140 (790)
T ss_pred             HHHHHHHHHHHhCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHHHHHH
Confidence            33355677788999 79999999999999887  999999999999997                           3455


Q ss_pred             HHHhhcCCcEEEEeCCCC-HHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHH
Q 042872          263 TLNLKFGIPATFLNSQQT-VSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVL  341 (381)
Q Consensus       263 ~L~~~~gI~a~~l~g~~~-~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L  341 (381)
                      .+...+|+++.++.|+.+ ..+++..    .                           .++|+|+||+++.- ..++..+
T Consensus       141 ~l~~~lGl~v~~i~g~~~~~~~r~~~----y---------------------------~~dIvygT~~~l~f-DyLrd~~  188 (790)
T PRK09200        141 QVYEFLGLTVGLNFSDIDDASEKKAI----Y---------------------------EADIIYTTNSELGF-DYLRDNL  188 (790)
T ss_pred             HHHhhcCCeEEEEeCCCCcHHHHHHh----c---------------------------CCCEEEECCccccc-hhHHhcc
Confidence            666677899998888887 4443211    1                           57999999999941 1111111


Q ss_pred             HHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          342 KCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       342 ~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      ..  ..               ...+++.+.++||||||.|
T Consensus       189 ~~--~~---------------~~~~~r~~~~~IvDEaDsi  211 (790)
T PRK09200        189 AD--SK---------------EDKVQRPLNYAIIDEIDSI  211 (790)
T ss_pred             cc--ch---------------hhhcccccceEEEeccccc
Confidence            00  00               0123348999999999986

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.15  E-value=1.3e-10  Score=126.50  Aligned_cols=43  Identities=28%  Similarity=0.295  Sum_probs=31.0

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +..+..+.+|+   +|+|.+++..+..++..++.|+||+|||+||.
T Consensus        59 vrEa~~R~lgl---rpydVQlig~l~l~~G~Iaem~TGeGKTLta~  101 (762)
T TIGR03714        59 VREADKRVLGM---FPYDVQVLGAIVLHQGNIAEMKTGEGKTLTAT  101 (762)
T ss_pred             HHHHHHhhcCC---CccHHHHHHHHHhcCCceeEecCCcchHHHHH
Confidence            45566677887   34455555555545557999999999999998

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

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.15  E-value=1.7e-10  Score=125.23  Aligned_cols=121  Identities=16%  Similarity=0.160  Sum_probs=84.3

Q ss_pred             hchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHH
Q 042872          209 ALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQI  261 (381)
Q Consensus       209 ~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv  261 (381)
                      ++.-+..+..+.+|+ .|+++|..+.+.++.|+  |+.|+||+|||++|.                           +++
T Consensus        41 afA~vrEa~~R~lg~-~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~G~~V~VvTpt~~LA~qdae~~  117 (745)
T TIGR00963        41 AFAVVREASKRVLGM-RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALTGKGVHVVTVNDYLAQRDAEWM  117 (745)
T ss_pred             HHHHHHHHHHHHhCC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHhCCCEEEEcCCHHHHHHHHHHH
Confidence            344466678888999 58899999999998887  999999999999987                           445


Q ss_pred             HHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHH
Q 042872          262 ITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVL  341 (381)
Q Consensus       262 ~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L  341 (381)
                      ..+...+|+++.+++|+.+..++....                               .++|+|+||.+|.- ..++..+
T Consensus       118 ~~l~~~LGLsv~~i~g~~~~~~r~~~y-------------------------------~~dIvyGT~~rlgf-DyLrd~~  165 (745)
T TIGR00963       118 GQVYRFLGLSVGLILSGMSPEERREAY-------------------------------ACDITYGTNNELGF-DYLRDNM  165 (745)
T ss_pred             HHHhccCCCeEEEEeCCCCHHHHHHhc-------------------------------CCCEEEECCCchhh-HHHhccc
Confidence            566656788888888887765432221                               47899999999930 1111110


Q ss_pred             HHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          342 KCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       342 ~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      .         +  . .+.+     .++.+.++||||||.|
T Consensus       166 ~---------~--~-~~~~-----~~r~l~~aIIDEaDs~  188 (745)
T TIGR00963       166 A---------H--S-KEEK-----VQRPFHFAIIDEVDSI  188 (745)
T ss_pred             c---------c--c-hhhh-----hccccceeEeecHHHH
Confidence            0         0  0 0011     2238999999999975

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.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.14  E-value=2e-10  Score=119.33  Aligned_cols=122  Identities=15%  Similarity=0.114  Sum_probs=73.6

Q ss_pred             CCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhh
Q 042872          224 RAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFL  303 (381)
Q Consensus       224 ~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~  303 (381)
                      -.||++|.+|++.++.+++.++.+|||+|||+++..-...+......+++++...  .+-..+..+.++.=.+..     
T Consensus       113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~~~~~vLilvpt--~eL~~Q~~~~l~~~~~~~-----  185 (501)
T PHA02558        113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLENYEGKVLIIVPT--TSLVTQMIDDFVDYRLFP-----  185 (501)
T ss_pred             CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhcCCCeEEEEECc--HHHHHHHHHHHHHhcccc-----
Confidence            4799999999999999999999999999999987532222222334477777653  222222333332100000     


Q ss_pred             hhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          304 HQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       304 ~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      ...+ ..-..+.......+|+|+||+++...+  ..           .++               .+++|||||||++
T Consensus       186 ~~~~-~~i~~g~~~~~~~~I~VaT~qsl~~~~--~~-----------~~~---------------~~~~iIvDEaH~~  234 (501)
T PHA02558        186 REAM-HKIYSGTAKDTDAPIVVSTWQSAVKQP--KE-----------WFD---------------QFGMVIVDECHLF  234 (501)
T ss_pred             ccce-eEEecCcccCCCCCEEEeeHHHHhhch--hh-----------hcc---------------ccCEEEEEchhcc
Confidence            0000 000112223345789999999986321  00           011               7899999999975

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.14  E-value=2.4e-10  Score=98.19  Aligned_cols=38  Identities=37%  Similarity=0.622  Sum_probs=35.6

Q ss_pred             hCCCCCcHHHHHHHHHHHcC-CCEEEECCCCCCchhhHH
Q 042872          221 FGNRAFRPLQHQACKASVAK-QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~G-rDvLviaPTGsGKTLaF~  258 (381)
                      +++..++++|.+++..++.+ +.+++.+|||+|||.++.
T Consensus         4 ~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~   42 (201)
T smart00487        4 FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAAL   42 (201)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHH
Confidence            67889999999999999999 999999999999999776

>PRK13766 Hef nuclease; Provisional

Probab=99.12  E-value=2.5e-10  Score=123.53  Aligned_cols=52  Identities=27%  Similarity=0.218  Sum_probs=37.8

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ++|++|.+++..++.+ |+|+++|||+|||++|+--+..+....+-+++++..
T Consensus        15 ~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~~~~~vLvl~P   66 (773)
T PRK13766         15 EARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHKKGGKVLILAP   66 (773)
T ss_pred             CccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHhCCCeEEEEeC
Confidence            6899999999999887 999999999999998862222221123445555554

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.08  E-value=6.6e-10  Score=119.51  Aligned_cols=136  Identities=21%  Similarity=0.207  Sum_probs=86.5

Q ss_pred             hHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHH
Q 042872          211 DDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIIT  263 (381)
Q Consensus       211 ~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~  263 (381)
                      .-+..+..+.+|.. |+|+|..+++.++.|+  |+.|+||+|||++|.                           +.+..
T Consensus        90 A~~rEa~~R~lg~~-p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~G~~v~VvTptreLA~qdae~~~~  166 (656)
T PRK12898         90 ALVREASGRVLGQR-HFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALAGLPVHVITVNDYLAERDAELMRP  166 (656)
T ss_pred             HHHHHHHHHHhCCC-CChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhcCCeEEEEcCcHHHHHHHHHHHHH
Confidence            33555677789994 7799999999999999  999999999999998                           44566


Q ss_pred             HHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHH
Q 042872          264 LNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKC  343 (381)
Q Consensus       264 L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~  343 (381)
                      +...+|+++.+++|+++..+++..                               ..++|+|+|...+.- ..++..+..
T Consensus       167 l~~~lGlsv~~i~gg~~~~~r~~~-------------------------------y~~dIvygT~~e~~F-DyLrd~~~~  214 (656)
T PRK12898        167 LYEALGLTVGCVVEDQSPDERRAA-------------------------------YGADITYCTNKELVF-DYLRDRLAL  214 (656)
T ss_pred             HHhhcCCEEEEEeCCCCHHHHHHH-------------------------------cCCCEEEECCCchhh-hhccccccc
Confidence            665679999999988765432211                               157999999888741 111211110


Q ss_pred             HHhcCC--ccccccccccccccccccCCccEEEEeccccC
Q 042872          344 LHRKGS--IRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       344 L~~~g~--~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      -...+.  ..+..|.+..--.....++.+.+.|||||+.|
T Consensus       215 ~~~~~~~~~~~~~l~~~~~~~~~~v~r~~~~aIvDEvDSi  254 (656)
T PRK12898        215 GQRASDARLALESLHGRSSRSTQLLLRGLHFAIVDEADSV  254 (656)
T ss_pred             cccccchhhhhhhhccccCchhhhcccccceeEeecccce
Confidence            000000  00001111000112234568999999999975

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=99.08  E-value=1.5e-10  Score=127.51  Aligned_cols=40  Identities=20%  Similarity=0.406  Sum_probs=36.4

Q ss_pred             HHhCCCCCcHHHHHHHHHHHc-CCCEEEECCCCCCchhhHH
Q 042872          219 VIFGNRAFRPLQHQACKASVA-KQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       219 ~~fG~~~fRpiQ~eAI~aiL~-GrDvLviaPTGsGKTLaF~  258 (381)
                      ..|+|++|..+|.++.|.+.. +.+.|++||||+|||.+|.
T Consensus       104 ~~f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~  144 (1230)
T KOG0952|consen  104 GFFSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAE  144 (1230)
T ss_pred             hcccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHH
Confidence            458999999999999999985 5799999999999998887

>KOG0344 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.01  E-value=4.4e-10  Score=118.06  Aligned_cols=128  Identities=32%  Similarity=0.405  Sum_probs=82.0

Q ss_pred             HHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-HHHHHHHh------hcCCcEEEEeCCCCHHHHHHHHHHH
Q 042872          219 VIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-DQIITLNL------KFGIPATFLNSQQTVSQAAAVLQEL  291 (381)
Q Consensus       219 ~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-dQv~~L~~------~~gI~a~~l~g~~~~~e~~~il~~l  291 (381)
                      ...||..|+|+|.+|||.++.++|+|+++|||+|||++|. .-+..|..      +-|+.++++..  ...-..++.+..
T Consensus       152 ~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~p--treLa~Qi~re~  229 (593)
T KOG0344|consen  152 QELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSP--TRELAAQIYREM  229 (593)
T ss_pred             hhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhcccCccceEEEEecc--hHHHHHHHHHHH
Confidence            3489999999999999999999999999999999999998 22333332      34677777654  344333444433


Q ss_pred             Hhchhhhhhhhhhhhhhhhhhc------------ccCCCCCccEEEECccccccCcchHHHHHHHHhcCC--cccccccc
Q 042872          292 RQGLVLSQHYFLHQLIFVLTCA------------SRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGS--IRLKVLTT  357 (381)
Q Consensus       292 r~g~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~--~~l~~~~~  357 (381)
                      +        .+.+........+            .......+++++.||-++..          +...++  +.|.    
T Consensus       230 ~--------k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~----------~~~~~~~~idl~----  287 (593)
T KOG0344|consen  230 R--------KYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVG----------LLGLGKLNIDLS----  287 (593)
T ss_pred             H--------hcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHHHHH----------HhcCCCccchhh----
Confidence            2        1111111110000            01122368999999999762          222333  3444    


Q ss_pred             ccccccccccCCccEEEEeccccC
Q 042872          358 DVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       358 ~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                 .|.++|+|||+.+
T Consensus       288 -----------~V~~lV~dEaD~l  300 (593)
T KOG0344|consen  288 -----------KVEWLVVDEADLL  300 (593)
T ss_pred             -----------eeeeEeechHHhh
Confidence                       8999999999864

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=98.98  E-value=1.9e-09  Score=118.80  Aligned_cols=116  Identities=16%  Similarity=0.223  Sum_probs=83.3

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITLN  265 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L~  265 (381)
                      +..+..+.+|.. +.++|.-.--++..|+  |+.|+||+|||++|.                           +++..+.
T Consensus        71 vrEa~~R~lg~~-~ydvQliGg~~Lh~G~--Iaem~TGeGKTL~a~Lpa~~~al~G~~V~VvTpn~yLA~qd~e~m~~l~  147 (896)
T PRK13104         71 VREVSLRTLGLR-HFDVQLIGGMVLHEGN--IAEMRTGEGKTLVATLPAYLNAISGRGVHIVTVNDYLAKRDSQWMKPIY  147 (896)
T ss_pred             HHHHHHHHcCCC-cchHHHhhhhhhccCc--cccccCCCCchHHHHHHHHHHHhcCCCEEEEcCCHHHHHHHHHHHHHHh
Confidence            555677789985 6699988887777776  999999999999997                           4556666


Q ss_pred             hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECcccc-ccCcchHHHHHHH
Q 042872          266 LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERI-VGNQSFSEVLKCL  344 (381)
Q Consensus       266 ~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL-~~~~~f~~~L~~L  344 (381)
                      ..+|+++.++.|+.+..++....                               .++|+|+||++| ++      .|+  
T Consensus       148 ~~lGLtv~~i~gg~~~~~r~~~y-------------------------------~~dIvygT~grlgfD------yLr--  188 (896)
T PRK13104        148 EFLGLTVGVIYPDMSHKEKQEAY-------------------------------KADIVYGTNNEYGFD------YLR--  188 (896)
T ss_pred             cccCceEEEEeCCCCHHHHHHHh-------------------------------CCCEEEECChhhhHH------HHh--
Confidence            66788888888887766542222                               479999999998 31      111  


Q ss_pred             HhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          345 HRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       345 ~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                        .+ +.+        .+...+|+.+.++||||||.|
T Consensus       189 --d~-~~~--------~~~~~v~r~l~~~IvDEaDsi  214 (896)
T PRK13104        189 --DN-MAF--------SLTDKVQRELNFAIVDEVDSI  214 (896)
T ss_pred             --cC-Ccc--------chHhhhccccceEEeccHhhh
Confidence              11 000        122335668999999999975

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

Probab=98.95  E-value=1.5e-09  Score=112.78  Aligned_cols=103  Identities=24%  Similarity=0.334  Sum_probs=81.3

Q ss_pred             CCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-------------------------HHHHHHHhhcCCc---EE
Q 042872          222 GNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-------------------------DQIITLNLKFGIP---AT  273 (381)
Q Consensus       222 G~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-------------------------dQv~~L~~~~gI~---a~  273 (381)
                      +.-++|.+|......++.+ ++|+++|||-|||++.+                         .+...+.+-+|++   ++
T Consensus        12 ~~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~~kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~   90 (542)
T COG1111          12 NTIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFGGKVLFLAPTKPLVLQHAEFCRKVTGIPEDEIA   90 (542)
T ss_pred             ccccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcCCeEEEecCCchHHHHHHHHHHHHhCCChhhee
Confidence            4447999999999999886 99999999999998866                         4566666666774   56


Q ss_pred             EEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcccc
Q 042872          274 FLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLK  353 (381)
Q Consensus       274 ~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~  353 (381)
                      .++|....++|...+..                              -+|+|+||..+.+  +       | ..|-++++
T Consensus        91 ~ltGev~p~~R~~~w~~------------------------------~kVfvaTPQvveN--D-------l-~~Grid~~  130 (542)
T COG1111          91 ALTGEVRPEEREELWAK------------------------------KKVFVATPQVVEN--D-------L-KAGRIDLD  130 (542)
T ss_pred             eecCCCChHHHHHHHhh------------------------------CCEEEeccHHHHh--H-------H-hcCccChH
Confidence            88888888887776654                              4699999999974  1       1 24556666


Q ss_pred             ccccccccccccccCCccEEEEecccc
Q 042872          354 VLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       354 ~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                                     .+.++|+||||+
T Consensus       131 ---------------dv~~lifDEAHR  142 (542)
T COG1111         131 ---------------DVSLLIFDEAHR  142 (542)
T ss_pred             ---------------HceEEEechhhh
Confidence                           899999999996

>KOG0354 consensus DEAD-box like helicase [General function prediction only]

Probab=98.94  E-value=1.2e-09  Score=118.03  Aligned_cols=55  Identities=18%  Similarity=0.291  Sum_probs=41.3

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHH-HHHHHhhcCCcEEEEeCCCC
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQ-IITLNLKFGIPATFLNSQQT  280 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~~gI~a~~l~g~~~  280 (381)
                      .+|++|.+.+..+| |+++|+++|||+|||.+.+-- ...|...-.-+++++....+
T Consensus        62 ~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~p  117 (746)
T KOG0354|consen   62 ELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRP  117 (746)
T ss_pred             cccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCcceEEEeeCCch
Confidence            68999999999999 999999999999999887622 23333223456666665544

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=98.94  E-value=4.2e-09  Score=105.24  Aligned_cols=30  Identities=33%  Similarity=0.446  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHcCCC--EEEECCCCCCchhhHH
Q 042872          229 LQHQACKASVAKQD--CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       229 iQ~eAI~aiL~GrD--vLviaPTGsGKTLaF~  258 (381)
                      +|.++++++.++++  +++.+|||+|||+||+
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~   32 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWL   32 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHH
Confidence            49999999999875  7889999999999996

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.

>KOG0349 consensus Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]

Probab=98.88  E-value=8.2e-10  Score=113.44  Aligned_cols=55  Identities=22%  Similarity=0.273  Sum_probs=49.0

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .|+++..++++..+-.+ +.+.-||.+|.|+||.||.|-|||..|.||||||-+|.
T Consensus         3 af~e~gv~pel~~a~~e-~dw~lptdvqaeaiplilgggdvlmaaetgsgktgaf~   57 (725)
T KOG0349|consen    3 AFEEFGVLPELGMATDE-LDWTLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFC   57 (725)
T ss_pred             chHhhCcchHhhhhhhh-hccccccccccccccEEecCCcEEEEeccCCCCcccee
Confidence            47888888887777655 78889999999999999999999999999999998885

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=98.88  E-value=1.8e-09  Score=124.46  Aligned_cols=38  Identities=26%  Similarity=0.451  Sum_probs=26.1

Q ss_pred             CccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          320 SCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       320 ~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      .++|||+|||+|..      +|.   .+....|+               +|.+|||||+|++
T Consensus        99 ppdILVTTPEsL~~------LLt---sk~r~~L~---------------~Vr~VIVDE~H~L  136 (1490)
T PRK09751         99 PPDILITTPESLYL------MLT---SRARETLR---------------GVETVIIDEVHAV  136 (1490)
T ss_pred             CCCEEEecHHHHHH------HHh---hhhhhhhc---------------cCCEEEEecHHHh
Confidence            58999999999962      111   11111223               8999999999975

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

Probab=98.86  E-value=7.6e-09  Score=115.46  Aligned_cols=125  Identities=21%  Similarity=0.259  Sum_probs=82.7

Q ss_pred             HhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhh
Q 042872          220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQ  299 (381)
Q Consensus       220 ~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~  299 (381)
                      .+||+ +-++|++||-.+..|..|||+||||+|||++. +-...+...-|-+++...+          ++++.++++...
T Consensus       115 ~~~F~-LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVa-eyAi~~al~~~qrviYTsP----------IKALsNQKyrdl  182 (1041)
T COG4581         115 EYPFE-LDPFQQEAIAILERGESVLVCAPTSSGKTVVA-EYAIALALRDGQRVIYTSP----------IKALSNQKYRDL  182 (1041)
T ss_pred             hCCCC-cCHHHHHHHHHHhCCCcEEEEccCCCCcchHH-HHHHHHHHHcCCceEeccc----------hhhhhhhHHHHH
Confidence            37884 66999999999999999999999999999886 2333333344556444333          444444443333


Q ss_pred             hhhhh--hhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEec
Q 042872          300 HYFLH--QLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDE  377 (381)
Q Consensus       300 ~~~~~--~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDE  377 (381)
                      ...+.  ....++-.....-+++..++|+|.|.|.+          |.-+|+..+               +.+.+||+||
T Consensus       183 ~~~fgdv~~~vGL~TGDv~IN~~A~clvMTTEILRn----------Mlyrg~~~~---------------~~i~~ViFDE  237 (1041)
T COG4581         183 LAKFGDVADMVGLMTGDVSINPDAPCLVMTTEILRN----------MLYRGSESL---------------RDIEWVVFDE  237 (1041)
T ss_pred             HHHhhhhhhhccceecceeeCCCCceEEeeHHHHHH----------HhccCcccc---------------cccceEEEEe
Confidence            22222  22234444566778889999999888762          222332232               3899999999


Q ss_pred             cccC
Q 042872          378 AHCV  381 (381)
Q Consensus       378 AHcI  381 (381)
                      +|||
T Consensus       238 vHyi  241 (1041)
T COG4581         238 VHYI  241 (1041)
T ss_pred             eeec
Confidence            9997

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=98.86  E-value=9.8e-09  Score=112.83  Aligned_cols=117  Identities=18%  Similarity=0.171  Sum_probs=84.9

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITLN  265 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L~  265 (381)
                      +..+..+.+|+ .|+++|.-..-++..|+  |+.|+||+|||++|.                           +++..+.
T Consensus        70 vrEa~~R~lg~-~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~G~~V~IvTpn~yLA~rd~e~~~~l~  146 (830)
T PRK12904         70 VREASKRVLGM-RHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALTGKGVHVVTVNDYLAKRDAEWMGPLY  146 (830)
T ss_pred             HHHHHHHHhCC-CCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHcCCCEEEEecCHHHHHHHHHHHHHHH
Confidence            55677788999 57799999988888886  999999999999987                           4566666


Q ss_pred             hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHH
Q 042872          266 LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLH  345 (381)
Q Consensus       266 ~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~  345 (381)
                      ..+|+++.+++|+++..++....                               .++|+|+||.+|.- .    .|+.  
T Consensus       147 ~~LGlsv~~i~~~~~~~er~~~y-------------------------------~~dI~ygT~~elgf-D----yLrd--  188 (830)
T PRK12904        147 EFLGLSVGVILSGMSPEERREAY-------------------------------AADITYGTNNEFGF-D----YLRD--  188 (830)
T ss_pred             hhcCCeEEEEcCCCCHHHHHHhc-------------------------------CCCeEEECCcchhh-h----hhhc--
Confidence            67799999999888877654443                               47899999999931 1    1111  


Q ss_pred             hcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          346 RKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       346 ~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                        + +..        -.....++.+.++|||||+.|
T Consensus       189 --~-~~~--------~~~~~~~r~~~~aIvDEaDsi  213 (830)
T PRK12904        189 --N-MVF--------SLEERVQRGLNYAIVDEVDSI  213 (830)
T ss_pred             --c-ccc--------chhhhcccccceEEEechhhh
Confidence              0 000        011123458999999999975

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

Probab=98.82  E-value=8.1e-09  Score=89.64  Aligned_cols=50  Identities=22%  Similarity=0.383  Sum_probs=39.6

Q ss_pred             CCcHHHHHHHHHHHc-------CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          225 AFRPLQHQACKASVA-------KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~-------GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      ++||+|.+|+..++.       .+.+++.+|||+|||.++..-+..+..    +++++...
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~----~~l~~~p~   59 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR----KVLIVAPN   59 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC----EEEEEESS
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc----ceeEecCH
Confidence            578999999999984       689999999999999998754555542    77777654

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 ....

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

Probab=98.80  E-value=1e-08  Score=108.32  Aligned_cols=39  Identities=26%  Similarity=0.313  Sum_probs=35.7

Q ss_pred             HhCCCCCcHHHHHHHHHH-HcCCCEEEECCCCCCchhhHH
Q 042872          220 IFGNRAFRPLQHQACKAS-VAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       220 ~fG~~~fRpiQ~eAI~ai-L~GrDvLviaPTGsGKTLaF~  258 (381)
                      ..|++.++|+|.-|+.+- |.|+|.||+.+|+|||||+--
T Consensus       211 ~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgE  250 (830)
T COG1202         211 REGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGE  250 (830)
T ss_pred             hcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHH
Confidence            379999999999999995 689999999999999999864

>TIGR00595 priA primosomal protein N'

Probab=98.77  E-value=1.5e-08  Score=106.20  Aligned_cols=81  Identities=22%  Similarity=0.339  Sum_probs=64.1

Q ss_pred             EEECCCCCCchhhHH------------------------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhh
Q 042872          244 FVLLPTGGGKSLCYQ------------------------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQ  299 (381)
Q Consensus       244 LviaPTGsGKTLaF~------------------------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~  299 (381)
                      |+.+|||+|||.+|+                        ++...|.+.++.++.+++|+.+..++...+..+.+|     
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g-----   75 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNG-----   75 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcC-----
Confidence            467899999999987                        345677767888888999998888888888777655     


Q ss_pred             hhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccc
Q 042872          300 HYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH  379 (381)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAH  379 (381)
                                          .++|||+|+..+.. +                +               .++++|||||+|
T Consensus        76 --------------------~~~IVVGTrsalf~-p----------------~---------------~~l~lIIVDEeh  103 (505)
T TIGR00595        76 --------------------EILVVIGTRSALFL-P----------------F---------------KNLGLIIVDEEH  103 (505)
T ss_pred             --------------------CCCEEECChHHHcC-c----------------c---------------cCCCEEEEECCC
Confidence                                67899999887651 0                1               189999999999


Q ss_pred             cC
Q 042872          380 CV  381 (381)
Q Consensus       380 cI  381 (381)
                      +.
T Consensus       104 ~~  105 (505)
T TIGR00595       104 DS  105 (505)
T ss_pred             cc
Confidence            73

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).

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

Probab=98.73  E-value=2.1e-08  Score=103.31  Aligned_cols=49  Identities=31%  Similarity=0.485  Sum_probs=39.8

Q ss_pred             CCcHHHHHHHHHHHc----CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          225 AFRPLQHQACKASVA----KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~----GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      .+||+|++|+.++..    ++..++++|||+|||++++.-+..+.    -++.++..
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~----~~~Lvlv~   88 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELK----RSTLVLVP   88 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhc----CCEEEEEC
Confidence            689999999999998    89999999999999999974444443    34666654

>KOG0332 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.72  E-value=1.1e-08  Score=103.52  Aligned_cols=56  Identities=21%  Similarity=0.214  Sum_probs=48.9

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcC--CCEEEECCCCCCchhhHH
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAK--QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~G--rDvLviaPTGsGKTLaF~  258 (381)
                      -+|++|++-+++...+-. ++|..|+.+|..|+|.+|..  ++.|+.+..|+|||.||.
T Consensus        90 ksFeeL~LkPellkgly~-M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFv  147 (477)
T KOG0332|consen   90 KSFEELRLKPELLKGLYA-MKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFV  147 (477)
T ss_pred             ccHHhhCCCHHHHhHHHH-hccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHH
Confidence            368888877777666644 89999999999999999986  899999999999999997

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=98.67  E-value=7.9e-08  Score=77.80  Aligned_cols=37  Identities=30%  Similarity=0.343  Sum_probs=23.9

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhh-cCCcEEEEeC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLK-FGIPATFLNS  277 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~-~gI~a~~l~g  277 (381)
                      +.+++.+|||+|||.++...+..+... ..-+++++..
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p   38 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAP   38 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcC
Confidence            468999999999998887444443321 2235555544

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

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.66  E-value=7.1e-08  Score=106.61  Aligned_cols=117  Identities=17%  Similarity=0.139  Sum_probs=79.5

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITLN  265 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L~  265 (381)
                      +..++.+.+|+. ++++|.-.--.+..|+  |+.|+||.|||++|.                           +++..+.
T Consensus        71 vrEaa~R~lgm~-~ydVQliGgl~L~~G~--IaEm~TGEGKTL~a~lp~~l~al~g~~VhIvT~ndyLA~RD~e~m~~l~  147 (908)
T PRK13107         71 VREASKRVFEMR-HFDVQLLGGMVLDSNR--IAEMRTGEGKTLTATLPAYLNALTGKGVHVITVNDYLARRDAENNRPLF  147 (908)
T ss_pred             HHHHHHHHhCCC-cCchHHhcchHhcCCc--cccccCCCCchHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHHHHHHHHH
Confidence            556777889994 7799998877777776  999999999999997                           4455565


Q ss_pred             hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHH
Q 042872          266 LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLH  345 (381)
Q Consensus       266 ~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~  345 (381)
                      ..+|+++.++.++++..++..                               .-.++|+|+||.+|.- .    .|+.  
T Consensus       148 ~~lGlsv~~i~~~~~~~~r~~-------------------------------~Y~~dI~YgT~~e~gf-D----yLrd--  189 (908)
T PRK13107        148 EFLGLTVGINVAGLGQQEKKA-------------------------------AYNADITYGTNNEFGF-D----YLRD--  189 (908)
T ss_pred             HhcCCeEEEecCCCCHHHHHh-------------------------------cCCCCeEEeCCCcccc-h----hhhc--
Confidence            567787777777766433211                               1157999999999930 1    1211  


Q ss_pred             hcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          346 RKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       346 ~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                        + +.++        .....|+.+.++|||||+.|
T Consensus       190 --n-m~~~--------~~~~vqr~~~~aIvDEvDsi  214 (908)
T PRK13107        190 --N-MAFS--------PQERVQRPLHYALIDEVDSI  214 (908)
T ss_pred             --c-Cccc--------hhhhhccccceeeecchhhh
Confidence              0 0000        11234568999999999865

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=98.63  E-value=8.1e-08  Score=94.32  Aligned_cols=36  Identities=14%  Similarity=-0.038  Sum_probs=23.5

Q ss_pred             CEEEECCCCCCchhhHHHHH-HHHHhhcCCcEEEEeC
Q 042872          242 DCFVLLPTGGGKSLCYQDQI-ITLNLKFGIPATFLNS  277 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv-~~L~~~~gI~a~~l~g  277 (381)
                      |+++.+|||+|||++|+-.+ ..+....+-+++++.+
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~~~~~ii~v~P   37 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQKADRVIIALP   37 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhCCCCeEEEEee
Confidence            68999999999999997332 2222223345655544

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.

>TIGR00603 rad25 DNA repair helicase rad25

Probab=98.56  E-value=2.3e-07  Score=101.28  Aligned_cols=50  Identities=24%  Similarity=0.339  Sum_probs=37.9

Q ss_pred             CCcHHHHHHHHHHHc-C--CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          225 AFRPLQHQACKASVA-K--QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~-G--rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      .+||+|.+|+..++. |  +..++++|||+|||++.+.-+..    .+-++++++..
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~----l~k~tLILvps  307 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACT----VKKSCLVLCTS  307 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHH----hCCCEEEEeCc
Confidence            589999999999884 4  47899999999999998633332    34567676653

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).

>PHA02653 RNA helicase NPH-II; Provisional

Probab=98.51  E-value=2e-07  Score=101.10  Aligned_cols=30  Identities=20%  Similarity=0.179  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHcCCCEEEECCCCCCchhhH
Q 042872          228 PLQHQACKASVAKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       228 piQ~eAI~aiL~GrDvLviaPTGsGKTLaF  257 (381)
                      .+|.++++.++.|+|+++.|+||+|||.++
T Consensus       167 ~iQ~qil~~i~~gkdvIv~A~TGSGKTtqv  196 (675)
T PHA02653        167 DVQLKIFEAWISRKPVVLTGGTGVGKTSQV  196 (675)
T ss_pred             HHHHHHHHHHHhCCCEEEECCCCCCchhHH
Confidence            589999999999999999999999999873

>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]

Probab=98.44  E-value=9.6e-07  Score=97.61  Aligned_cols=123  Identities=19%  Similarity=0.194  Sum_probs=80.3

Q ss_pred             HhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhh
Q 042872          220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQ  299 (381)
Q Consensus       220 ~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~  299 (381)
                      .|+| ++-++|++||-++..|..|+|.|+|.+|||++. +-...|..+.+.+++....          +++|.+.++.++
T Consensus       293 ~~pF-elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVA-EYAialaq~h~TR~iYTSP----------IKALSNQKfRDF  360 (1248)
T KOG0947|consen  293 IYPF-ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVA-EYAIALAQKHMTRTIYTSP----------IKALSNQKFRDF  360 (1248)
T ss_pred             hCCC-CccHHHHHHHHHHHcCCeEEEEecCCCCcchHH-HHHHHHHHhhccceEecch----------hhhhccchHHHH
Confidence            4666 466789999999999999999999999999997 5555666555666654332          445544433332


Q ss_pred             hhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccc
Q 042872          300 HYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH  379 (381)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAH  379 (381)
                      ...+.-  .++-...-.-+|....||+|.|+|.+         -|++.. -               ..+.+.+||+||+|
T Consensus       361 k~tF~D--vgLlTGDvqinPeAsCLIMTTEILRs---------MLYrga-d---------------liRDvE~VIFDEVH  413 (1248)
T KOG0947|consen  361 KETFGD--VGLLTGDVQINPEASCLIMTTEILRS---------MLYRGA-D---------------LIRDVEFVIFDEVH  413 (1248)
T ss_pred             HHhccc--cceeecceeeCCCcceEeehHHHHHH---------HHhccc-c---------------hhhccceEEEeeee
Confidence            111100  01222233467788999999999863         123222 1               11279999999999


Q ss_pred             cC
Q 042872          380 CV  381 (381)
Q Consensus       380 cI  381 (381)
                      -|
T Consensus       414 Yi  415 (1248)
T KOG0947|consen  414 YI  415 (1248)
T ss_pred             ec
Confidence            75

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=98.44  E-value=5.9e-07  Score=99.24  Aligned_cols=115  Identities=20%  Similarity=0.167  Sum_probs=60.4

Q ss_pred             HHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhh
Q 042872          232 QACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLT  311 (381)
Q Consensus       232 eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~  311 (381)
                      +.+.++.+++++++.+|||+|||.+|.-.+..-. ..+.+++++..  .+.-..++.+.+..-    ........ .++.
T Consensus        12 ~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~-~~~~~ilvlqP--rR~aA~qia~rva~~----l~~~~g~~-VGy~   83 (812)
T PRK11664         12 ELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHG-GINGKIIMLEP--RRLAARNVAQRLAEQ----LGEKPGET-VGYR   83 (812)
T ss_pred             HHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcC-CcCCeEEEECC--hHHHHHHHHHHHHHH----hCcccCce-EEEE
Confidence            4455556789999999999999999952221111 12235555432  232222222222100    00000111 1111


Q ss_pred             hcc-cCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          312 CAS-RKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       312 ~~~-~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                      ... .......+|+|+|||+|..      .+   ..  ...|+               ++++|||||||-
T Consensus        84 vr~~~~~~~~t~I~v~T~G~Llr------~l---~~--d~~L~---------------~v~~IIlDEaHE  127 (812)
T PRK11664         84 MRAESKVGPNTRLEVVTEGILTR------MI---QR--DPELS---------------GVGLVILDEFHE  127 (812)
T ss_pred             ecCccccCCCCcEEEEChhHHHH------HH---hh--CCCcC---------------cCcEEEEcCCCc
Confidence            111 1223356899999999862      11   11  23344               899999999994

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

Probab=98.42  E-value=7.8e-07  Score=86.77  Aligned_cols=117  Identities=16%  Similarity=0.156  Sum_probs=77.6

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITLN  265 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L~  265 (381)
                      +..++.+.+|+ .|++.|.-++-++..|+  |+.+.||=|||++-.                           +++..+-
T Consensus        66 ~rea~~r~~g~-~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~G~~V~vvT~NdyLA~RD~~~~~~~y  142 (266)
T PF07517_consen   66 VREAARRTLGL-RPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQGKGVHVVTSNDYLAKRDAEEMRPFY  142 (266)
T ss_dssp             HHHHHHHHTS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTTSS-EEEEESSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCC-cccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHhcCCcEEEeccHHHhhccHHHHHHHH
Confidence            55566677888 58899999998888887  999999999998765                           4566666


Q ss_pred             hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHH
Q 042872          266 LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLH  345 (381)
Q Consensus       266 ~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~  345 (381)
                      ..+|+.+..+.++.+..+++...                               .++|+|+|...+.-     ..|+.-.
T Consensus       143 ~~LGlsv~~~~~~~~~~~r~~~Y-------------------------------~~dI~Y~t~~~~~f-----D~Lrd~~  186 (266)
T PF07517_consen  143 EFLGLSVGIITSDMSSEERREAY-------------------------------AADIVYGTNSEFGF-----DYLRDNL  186 (266)
T ss_dssp             HHTT--EEEEETTTEHHHHHHHH-------------------------------HSSEEEEEHHHHHH-----HHHHHTT
T ss_pred             HHhhhccccCccccCHHHHHHHH-------------------------------hCcccccccchhhH-----HHHHHHH
Confidence            67899998888887766554433                               35799999888851     2232211


Q ss_pred             hcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          346 RKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       346 ~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      ..+.             ....++.+.++|||||+.|
T Consensus       187 ~~~~-------------~~~~~r~~~~~ivDEvDs~  209 (266)
T PF07517_consen  187 ALSK-------------NEQVQRGFDFAIVDEVDSI  209 (266)
T ss_dssp             -SSG-------------GG--SSSSSEEEECTHHHH
T ss_pred             hhcc-------------chhccCCCCEEEEeccceE
Confidence            1110             0112458999999999853

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 ....

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.39  E-value=1.3e-06  Score=96.99  Aligned_cols=116  Identities=19%  Similarity=0.197  Sum_probs=81.2

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITLN  265 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L~  265 (381)
                      +..+..+.+|. .+.++|.-.--++..|+  |+-|.||.|||++..                           +.+..+-
T Consensus        71 vrEa~~R~lGm-~~ydVQliGg~~Lh~G~--iaEM~TGEGKTLvA~l~a~l~al~G~~VhvvT~ndyLA~RD~e~m~~l~  147 (913)
T PRK13103         71 AREAGKRVMGM-RHFDVQLIGGMTLHEGK--IAEMRTGEGKTLVGTLAVYLNALSGKGVHVVTVNDYLARRDANWMRPLY  147 (913)
T ss_pred             HHHHHHHHhCC-CcchhHHHhhhHhccCc--cccccCCCCChHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHh
Confidence            55567778997 56799998877776665  899999999998865                           3455555


Q ss_pred             hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHH
Q 042872          266 LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLH  345 (381)
Q Consensus       266 ~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~  345 (381)
                      ..+|+++.++++.++..+++...                               .++|+|+|.--+.-     ..|+   
T Consensus       148 ~~lGl~v~~i~~~~~~~err~~Y-------------------------------~~dI~YGT~~e~gF-----DYLr---  188 (913)
T PRK13103        148 EFLGLSVGIVTPFQPPEEKRAAY-------------------------------AADITYGTNNEFGF-----DYLR---  188 (913)
T ss_pred             cccCCEEEEECCCCCHHHHHHHh-------------------------------cCCEEEEccccccc-----chhh---
Confidence            56789998888888777665444                               47899999777620     1111   


Q ss_pred             hcCCccccccccccc-cccccccCCccEEEEeccccC
Q 042872          346 RKGSIRLKVLTTDVV-VLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       346 ~~g~~~l~~~~~~~v-~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                 .+++ .....+|+.+.+.||||+|.|
T Consensus       189 -----------D~~~~~~~~~vqr~l~~aIVDEvDsi  214 (913)
T PRK13103        189 -----------DNMAFSLDDKFQRELNFAVIDEVDSI  214 (913)
T ss_pred             -----------ccceechhhhcccccceeEechhhhe
Confidence                       0111 022345668999999999986

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=98.37  E-value=1.4e-06  Score=95.77  Aligned_cols=120  Identities=16%  Similarity=0.148  Sum_probs=85.5

Q ss_pred             chHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHH
Q 042872          210 LDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQII  262 (381)
Q Consensus       210 l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~  262 (381)
                      +.-+..++.+.+|+ .|+++|.-+.-++..|+  |+.|.||.|||++..                           +++.
T Consensus        66 fA~vrEa~~R~~g~-~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~G~~v~vvT~neyLA~Rd~e~~~  142 (796)
T PRK12906         66 FAVAREGAKRVLGL-RPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALTGKGVHVVTVNEYLSSRDATEMG  142 (796)
T ss_pred             HHHHHHHHHHHhCC-CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHcCCCeEEEeccHHHHHhhHHHHH
Confidence            33356677888998 58899999988888887  999999999998865                           4456


Q ss_pred             HHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHH
Q 042872          263 TLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLK  342 (381)
Q Consensus       263 ~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~  342 (381)
                      .+-..+|+++.++.++++..+++...                               .++|+|+|.--+.- ..++..+.
T Consensus       143 ~~~~~LGl~vg~i~~~~~~~~r~~~y-------------------------------~~dI~Y~t~~e~gf-DyLRD~m~  190 (796)
T PRK12906        143 ELYRWLGLTVGLNLNSMSPDEKRAAY-------------------------------NCDITYSTNSELGF-DYLRDNMV  190 (796)
T ss_pred             HHHHhcCCeEEEeCCCCCHHHHHHHh-------------------------------cCCCeecCCccccc-cchhhccc
Confidence            66667899999998888777664443                               57899999877751 12221110


Q ss_pred             HHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          343 CLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       343 ~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                               ++        .....++.+.+.|||||+.|
T Consensus       191 ---------~~--------~~~~v~r~~~~aIvDEvDSi  212 (796)
T PRK12906        191 ---------VY--------KEQMVQRPLNYAIVDEVDSI  212 (796)
T ss_pred             ---------cc--------hhhhhccCcceeeeccchhe
Confidence                     00        01224557899999999875

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=98.36  E-value=1.2e-06  Score=96.93  Aligned_cols=114  Identities=18%  Similarity=0.174  Sum_probs=60.6

Q ss_pred             HHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhh
Q 042872          232 QACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLT  311 (381)
Q Consensus       232 eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~  311 (381)
                      +.+.++..++++++.+|||+|||.+|.--+.... ..+.+++++..  .+.-..++.+.+..-    ........+ ++.
T Consensus         9 ~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~-~~~~~ilvlqP--rR~aA~qiA~rva~~----~~~~~g~~V-Gy~   80 (819)
T TIGR01970         9 ALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAP-GIGGKIIMLEP--RRLAARSAAQRLASQ----LGEAVGQTV-GYR   80 (819)
T ss_pred             HHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhh-ccCCeEEEEeC--cHHHHHHHHHHHHHH----hCCCcCcEE-EEE
Confidence            4445555778999999999999999962222111 12345555543  232222222222100    000000111 111


Q ss_pred             hc-ccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccc
Q 042872          312 CA-SRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH  379 (381)
Q Consensus       312 ~~-~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAH  379 (381)
                      .. ........+|+|+||++|+.      .   +..  ...|+               ++++|||||||
T Consensus        81 vr~~~~~s~~t~I~v~T~G~Llr------~---l~~--d~~L~---------------~v~~VIiDEaH  123 (819)
T TIGR01970        81 VRGENKVSRRTRLEVVTEGILTR------M---IQD--DPELD---------------GVGALIFDEFH  123 (819)
T ss_pred             EccccccCCCCcEEEECCcHHHH------H---Hhh--Ccccc---------------cCCEEEEeccc
Confidence            11 11223357899999999962      1   211  22344               89999999999

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.

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

Probab=98.36  E-value=1.9e-06  Score=98.09  Aligned_cols=53  Identities=21%  Similarity=0.181  Sum_probs=37.2

Q ss_pred             CCcHHHHHHHHHHH----cC-CCEEEECCCCCCchhhHHHHHHHHHhhcC-CcEEEEeC
Q 042872          225 AFRPLQHQACKASV----AK-QDCFVLLPTGGGKSLCYQDQIITLNLKFG-IPATFLNS  277 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL----~G-rDvLviaPTGsGKTLaF~dQv~~L~~~~g-I~a~~l~g  277 (381)
                      .+|++|.+||.++.    .| +.+|++||||+|||++..--+..|..... -+++++.-
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li~~L~~~~~~~rVLfLvD  471 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALMYRLLKAKRFRRILFLVD  471 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHHHHHHhcCccCeEEEEec
Confidence            58999999999886    34 68999999999999876533444432222 35656543

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.31  E-value=2.8e-06  Score=92.58  Aligned_cols=117  Identities=18%  Similarity=0.201  Sum_probs=84.3

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITLN  265 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L~  265 (381)
                      +..+..+.+|+ .++++|.-+.-.++.|+  ++.|.||.|||++..                           +.+..+-
T Consensus        67 vREa~~R~lg~-r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~G~~VhvvT~NdyLA~RDae~m~~ly  143 (764)
T PRK12326         67 AREAAERTLGL-RPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQGRRVHVITVNDYLARRDAEWMGPLY  143 (764)
T ss_pred             HHHHHHHHcCC-CcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHcCCCeEEEcCCHHHHHHHHHHHHHHH
Confidence            55567778999 47799999999999885  789999999998765                           4455555


Q ss_pred             hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHH
Q 042872          266 LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLH  345 (381)
Q Consensus       266 ~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~  345 (381)
                      ..+|+++.++.+..+..+++...                               .++|+|+|..-+.- ..++..+..  
T Consensus       144 ~~LGLsvg~i~~~~~~~err~aY-------------------------------~~DItYgTn~e~gF-DyLRDnm~~--  189 (764)
T PRK12326        144 EALGLTVGWITEESTPEERRAAY-------------------------------ACDVTYASVNEIGF-DVLRDQLVT--  189 (764)
T ss_pred             HhcCCEEEEECCCCCHHHHHHHH-------------------------------cCCCEEcCCccccc-ccchhhhcc--
Confidence            57899999888888777655444                               47899999877651 222222110  


Q ss_pred             hcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          346 RKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       346 ~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                     -....+++.+.+.|||||+.|
T Consensus       190 ---------------~~~~~v~R~~~faIVDEvDSi  210 (764)
T PRK12326        190 ---------------DVADLVSPNPDVAIIDEADSV  210 (764)
T ss_pred             ---------------ChHhhcCCccceeeecchhhh
Confidence                           012235568999999999975

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.21  E-value=7.7e-06  Score=90.78  Aligned_cols=117  Identities=16%  Similarity=0.231  Sum_probs=82.1

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITLN  265 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L~  265 (381)
                      +..+..+.+|.. +.++|.-.--++..|+  |+-|.||-||||++.                           +++..+-
T Consensus        74 vREa~~R~lG~r-~ydVQliGgl~Lh~G~--IAEM~TGEGKTL~atlpaylnAL~GkgVhVVTvNdYLA~RDae~m~~vy  150 (939)
T PRK12902         74 VREASKRVLGMR-HFDVQLIGGMVLHEGQ--IAEMKTGEGKTLVATLPSYLNALTGKGVHVVTVNDYLARRDAEWMGQVH  150 (939)
T ss_pred             HHHHHHHHhCCC-cchhHHHhhhhhcCCc--eeeecCCCChhHHHHHHHHHHhhcCCCeEEEeCCHHHHHhHHHHHHHHH
Confidence            556777889994 6699998887777665  899999999999875                           4455555


Q ss_pred             hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHH
Q 042872          266 LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLH  345 (381)
Q Consensus       266 ~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~  345 (381)
                      ..+|+.+.++.++++..+++...                               .++|+|+|+..+.- ..++..+..  
T Consensus       151 ~~LGLtvg~i~~~~~~~err~aY-------------------------------~~DItYgTn~e~gF-DYLRDnm~~--  196 (939)
T PRK12902        151 RFLGLSVGLIQQDMSPEERKKNY-------------------------------ACDITYATNSELGF-DYLRDNMAT--  196 (939)
T ss_pred             HHhCCeEEEECCCCChHHHHHhc-------------------------------CCCeEEecCCcccc-cchhhhhcc--
Confidence            56788887777776665543322                               57999999988851 222222210  


Q ss_pred             hcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          346 RKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       346 ~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                     .....+++.+.+.|||||+.|
T Consensus       197 ---------------~~~~~vqR~~~faIVDEvDSI  217 (939)
T PRK12902        197 ---------------DISEVVQRPFNYCVIDEVDSI  217 (939)
T ss_pred             ---------------cccccccCccceEEEecccce
Confidence                           012235668999999999976

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=98.15  E-value=1.8e-06  Score=97.59  Aligned_cols=40  Identities=23%  Similarity=0.467  Sum_probs=36.0

Q ss_pred             HHhCCCCCcHHHHHHHHHHHcC-CCEEEECCCCCCchhhHH
Q 042872          219 VIFGNRAFRPLQHQACKASVAK-QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       219 ~~fG~~~fRpiQ~eAI~aiL~G-rDvLviaPTGsGKTLaF~  258 (381)
                      ..+|+..|.++|....++++.+ .+++++||||+|||-+.+
T Consensus       303 aF~g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAv  343 (1674)
T KOG0951|consen  303 AFFGKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAV  343 (1674)
T ss_pred             hcccchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHH
Confidence            3479999999999999999988 589999999999998776

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=98.09  E-value=1.4e-05  Score=91.86  Aligned_cols=31  Identities=26%  Similarity=0.276  Sum_probs=20.0

Q ss_pred             HHHHHHHHHc-CCCEEEECCCCCCchhhHHHHH
Q 042872          230 QHQACKASVA-KQDCFVLLPTGGGKSLCYQDQI  261 (381)
Q Consensus       230 Q~eAI~aiL~-GrDvLviaPTGsGKTLaF~dQv  261 (381)
                      .++.|...+. ++.++++++||||||... .|+
T Consensus        78 ~r~~Il~ai~~~~VviI~GeTGSGKTTql-Pq~  109 (1294)
T PRK11131         78 KKQDILEAIRDHQVVIVAGETGSGKTTQL-PKI  109 (1294)
T ss_pred             HHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHH
Confidence            3444555554 455677799999999843 443

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

Probab=98.08  E-value=1.5e-05  Score=85.96  Aligned_cols=108  Identities=18%  Similarity=0.247  Sum_probs=82.9

Q ss_pred             HHHHhCCCCCcHHHHHHHHHHHcC------CCEEEECCCCCCchhhHH-----------------------HH----HHH
Q 042872          217 NVVIFGNRAFRPLQHQACKASVAK------QDCFVLLPTGGGKSLCYQ-----------------------DQ----IIT  263 (381)
Q Consensus       217 ~~~~fG~~~fRpiQ~eAI~aiL~G------rDvLviaPTGsGKTLaF~-----------------------dQ----v~~  263 (381)
                      +...+.| ++|..|+.+|..|...      .+-|+++--|||||++.+                       .|    +..
T Consensus       255 ~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G~Q~ALMAPTEILA~QH~~~~~~  333 (677)
T COG1200         255 FLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGYQAALMAPTEILAEQHYESLRK  333 (677)
T ss_pred             HHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHcCCeeEEeccHHHHHHHHHHHHHH
Confidence            3344677 5889999999999842      356899999999998876                       22    344


Q ss_pred             HHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHH
Q 042872          264 LNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKC  343 (381)
Q Consensus       264 L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~  343 (381)
                      +-..+||++..++|......++.++..+.+|                         ..+|||.|==-+-      +    
T Consensus       334 ~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G-------------------------~~~ivVGTHALiQ------d----  378 (677)
T COG1200         334 WLEPLGIRVALLTGSLKGKARKEILEQLASG-------------------------EIDIVVGTHALIQ------D----  378 (677)
T ss_pred             HhhhcCCeEEEeecccchhHHHHHHHHHhCC-------------------------CCCEEEEcchhhh------c----
Confidence            4446799999999999999999999999877                         7899999933222      1    


Q ss_pred             HHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          344 LHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       344 L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                           ++...               ++.++||||=|+
T Consensus       379 -----~V~F~---------------~LgLVIiDEQHR  395 (677)
T COG1200         379 -----KVEFH---------------NLGLVIIDEQHR  395 (677)
T ss_pred             -----ceeec---------------ceeEEEEecccc
Confidence                 12222               899999999996

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

Probab=98.06  E-value=1.3e-05  Score=87.70  Aligned_cols=98  Identities=23%  Similarity=0.338  Sum_probs=81.3

Q ss_pred             CCcHHHHHHHHHHHcC----CCEEEECCCCCCchhhHH-----------------------HH-HHHHHhhcCCcEEEEe
Q 042872          225 AFRPLQHQACKASVAK----QDCFVLLPTGGGKSLCYQ-----------------------DQ-IITLNLKFGIPATFLN  276 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~G----rDvLviaPTGsGKTLaF~-----------------------dQ-v~~L~~~~gI~a~~l~  276 (381)
                      .+.+.|..|+..++..    +-.|+-+-||||||-+|+                       .| +.+|...||.++.+++
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlH  277 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLH  277 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhc
Confidence            4668899999999765    678999999999999998                       44 5778888999999999


Q ss_pred             CCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccc
Q 042872          277 SQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLT  356 (381)
Q Consensus       277 g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~  356 (381)
                      ++.+..++...+.++++|                         ..+||++|==.|+     ...                
T Consensus       278 S~Ls~~er~~~W~~~~~G-------------------------~~~vVIGtRSAlF-----~Pf----------------  311 (730)
T COG1198         278 SGLSPGERYRVWRRARRG-------------------------EARVVIGTRSALF-----LPF----------------  311 (730)
T ss_pred             ccCChHHHHHHHHHHhcC-------------------------CceEEEEechhhc-----Cch----------------
Confidence            999999999999998877                         7899999844433     110                


Q ss_pred             cccccccccccCCccEEEEeccc
Q 042872          357 TDVVVLPHTCQRQLAGFVVDEAH  379 (381)
Q Consensus       357 ~~~v~~~~~~~~~L~~lVIDEAH  379 (381)
                                 .+|++|||||=|
T Consensus       312 -----------~~LGLIIvDEEH  323 (730)
T COG1198         312 -----------KNLGLIIVDEEH  323 (730)
T ss_pred             -----------hhccEEEEeccc
Confidence                       189999999988

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.03  E-value=1.6e-05  Score=88.16  Aligned_cols=118  Identities=16%  Similarity=0.164  Sum_probs=77.9

Q ss_pred             HHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHH
Q 042872          212 DMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITL  264 (381)
Q Consensus       212 ~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L  264 (381)
                      -+..++.+.+|+. ++++|.-+.-++..  .-|+-|.||-||||++.                           ++...+
T Consensus        64 vvrEa~~R~lG~r-~ydvQlig~l~L~~--G~IaEm~TGEGKTL~a~l~ayl~aL~G~~VhVvT~NdyLA~RD~e~m~pv  140 (870)
T CHL00122         64 LTREASFRTLGLR-HFDVQLIGGLVLND--GKIAEMKTGEGKTLVATLPAYLNALTGKGVHIVTVNDYLAKRDQEWMGQI  140 (870)
T ss_pred             HHHHHHHHHhCCC-CCchHhhhhHhhcC--CccccccCCCCchHHHHHHHHHHHhcCCceEEEeCCHHHHHHHHHHHHHH
Confidence            3556777889995 77999887665554  46999999999999876                           344555


Q ss_pred             HhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHH
Q 042872          265 NLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCL  344 (381)
Q Consensus       265 ~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L  344 (381)
                      -+.+|+.+.++.++++..+++...                               .++|+|+|.--+.- ..++..+.  
T Consensus       141 y~~LGLsvg~i~~~~~~~err~aY-------------------------------~~DItYgTn~e~gF-DyLRDnm~--  186 (870)
T CHL00122        141 YRFLGLTVGLIQEGMSSEERKKNY-------------------------------LKDITYVTNSELGF-DYLRDNMA--  186 (870)
T ss_pred             HHHcCCceeeeCCCCChHHHHHhc-------------------------------CCCCEecCCccccc-cchhhccC--
Confidence            556677777776666665543333                               46899999876641 11211110  


Q ss_pred             HhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          345 HRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       345 ~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                             ++        .....++.+.+.|||||+.|
T Consensus       187 -------~~--------~~~~v~r~~~faIVDEvDSi  208 (870)
T CHL00122        187 -------LS--------LSDVVQRPFNYCIIDEVDSI  208 (870)
T ss_pred             -------cC--------hHHhhccccceeeeecchhh
Confidence                   00        11224558999999999975

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

Probab=97.93  E-value=5.9e-05  Score=83.71  Aligned_cols=60  Identities=28%  Similarity=0.335  Sum_probs=42.7

Q ss_pred             hCCCCCcHHHHH---HHHHHH-cCCCEEEECCCCCCchhhHH----------------------HHH-----HHHHhhcC
Q 042872          221 FGNRAFRPLQHQ---ACKASV-AKQDCFVLLPTGGGKSLCYQ----------------------DQI-----ITLNLKFG  269 (381)
Q Consensus       221 fG~~~fRpiQ~e---AI~aiL-~GrDvLviaPTGsGKTLaF~----------------------dQv-----~~L~~~~g  269 (381)
                      -|| ++||.|.+   +|...+ .++.+++.|+||+|||++|+                      +|+     ..|.+.++
T Consensus       242 ~~~-e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~~~~~vvI~t~T~~Lq~Ql~~~~i~~l~~~~~  320 (820)
T PRK07246        242 LGL-EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQSDQRQIIVSVPTKILQDQIMAEEVKAIQEVFH  320 (820)
T ss_pred             CCC-ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHHHHHHHHHHHhcC
Confidence            356 69999999   444444 46789999999999999998                      333     33444566


Q ss_pred             CcEEEEeCCCCH
Q 042872          270 IPATFLNSQQTV  281 (381)
Q Consensus       270 I~a~~l~g~~~~  281 (381)
                      +++.++.|+...
T Consensus       321 ~~~~~~kg~~~y  332 (820)
T PRK07246        321 IDCHSLKGPQNY  332 (820)
T ss_pred             CcEEEEECCccc
Confidence            777667766554

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

Probab=97.90  E-value=2.9e-05  Score=84.15  Aligned_cols=52  Identities=19%  Similarity=0.128  Sum_probs=36.1

Q ss_pred             CcHHHHHHHHHHHc----------CCCEEEECCCCCCchhhHHHHHHHHHhhcCC-cEEEEeC
Q 042872          226 FRPLQHQACKASVA----------KQDCFVLLPTGGGKSLCYQDQIITLNLKFGI-PATFLNS  277 (381)
Q Consensus       226 fRpiQ~eAI~aiL~----------GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI-~a~~l~g  277 (381)
                      +|+.|.+||..++.          .+..++.+|||||||++..--+..|....+. ++++++-
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~~~~~~~~vl~lvd  301 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFVVD  301 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHHhhcCCCeEEEEEC
Confidence            68899999998752          2578999999999998876444444333333 4555543

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

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

Probab=97.82  E-value=0.00013  Score=81.90  Aligned_cols=36  Identities=28%  Similarity=0.322  Sum_probs=29.6

Q ss_pred             CCCCCcHHHHHHHHHH---H-cCCCEEEECCCCCCchhhHH
Q 042872          222 GNRAFRPLQHQACKAS---V-AKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       222 G~~~fRpiQ~eAI~ai---L-~GrDvLviaPTGsGKTLaF~  258 (381)
                      || ++||.|.+-+..+   + .++.+++-||||+|||++|+
T Consensus       255 ~~-e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYL  294 (928)
T PRK08074        255 KY-EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYL  294 (928)
T ss_pred             CC-cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHH
Confidence            44 7999999955444   3 56789999999999999998

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

Probab=97.80  E-value=0.00016  Score=81.20  Aligned_cols=122  Identities=19%  Similarity=0.218  Sum_probs=86.8

Q ss_pred             HHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhh------HH-----------------HHH-
Q 042872          206 ELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLC------YQ-----------------DQI-  261 (381)
Q Consensus       206 ~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLa------F~-----------------dQv-  261 (381)
                      .+..+.++...+.+..|+ .|.-.|+-+..-++.|+..-++||||.|||--      |.                 .|+ 
T Consensus        64 ~~~e~e~~~~fF~k~~G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~kgkr~yii~PT~~Lv~Q~~  142 (1187)
T COG1110          64 YLWEYEEFEEFFKKATGF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAKKGKRVYIIVPTTTLVRQVY  142 (1187)
T ss_pred             HHHHHHHHHHHHHHhhCC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEecCHHHHHHHH
Confidence            344456677777788898 68889999999999999999999999999921      11                 332 


Q ss_pred             ---HHHHhhcC-CcEEE-EeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcc
Q 042872          262 ---ITLNLKFG-IPATF-LNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQS  336 (381)
Q Consensus       262 ---~~L~~~~g-I~a~~-l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~  336 (381)
                         ..+....| ..+.+ .++..+..++++.++++.+|                         +++|+|+|-.-|.  +.
T Consensus       143 ~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~g-------------------------dfdIlitTs~FL~--k~  195 (1187)
T COG1110         143 ERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESG-------------------------DFDILITTSQFLS--KR  195 (1187)
T ss_pred             HHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcC-------------------------CccEEEEeHHHHH--hh
Confidence               23332223 33322 67777888888999998876                         8999999977765  33


Q ss_pred             hHHHHHHHHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          337 FSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       337 f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                      |-    .|.+ -                    +..++++|.++-
T Consensus       196 ~e----~L~~-~--------------------kFdfifVDDVDA  214 (1187)
T COG1110         196 FE----ELSK-L--------------------KFDFIFVDDVDA  214 (1187)
T ss_pred             HH----Hhcc-c--------------------CCCEEEEccHHH
Confidence            32    2221 1                    688999998764

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=97.75  E-value=0.00012  Score=84.60  Aligned_cols=127  Identities=17%  Similarity=0.122  Sum_probs=60.8

Q ss_pred             hCCCCCcHHHH--HHHHHHHc-CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhh
Q 042872          221 FGNRAFRPLQH--QACKASVA-KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVL  297 (381)
Q Consensus       221 fG~~~fRpiQ~--eAI~aiL~-GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~  297 (381)
                      ..|..--|+..  +.|...+. ++-+++.++||||||--. .|+.. ....+....+++.+.-+-....+-..+..-   
T Consensus        60 ~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTTql-Pq~ll-e~~~~~~~~I~~tQPRRlAA~svA~RvA~e---  134 (1283)
T TIGR01967        60 IRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQL-PKICL-ELGRGSHGLIGHTQPRRLAARTVAQRIAEE---  134 (1283)
T ss_pred             ccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHHHH-HHHHH-HcCCCCCceEecCCccHHHHHHHHHHHHHH---
Confidence            34443335543  45555554 456678889999999632 44321 112344444444332222222222222100   


Q ss_pred             hhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEec
Q 042872          298 SQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDE  377 (381)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDE  377 (381)
                       ......+.+.+..-......+..+|+|+|||+|+.         .+....  .|+               ++.+|||||
T Consensus       135 -lg~~lG~~VGY~vR~~~~~s~~T~I~~~TdGiLLr---------~l~~d~--~L~---------------~~~~IIIDE  187 (1283)
T TIGR01967       135 -LGTPLGEKVGYKVRFHDQVSSNTLVKLMTDGILLA---------ETQQDR--FLS---------------RYDTIIIDE  187 (1283)
T ss_pred             -hCCCcceEEeeEEcCCcccCCCceeeeccccHHHH---------HhhhCc--ccc---------------cCcEEEEcC
Confidence             00111111111011112233467899999999972         111111  122               899999999


Q ss_pred             cc
Q 042872          378 AH  379 (381)
Q Consensus       378 AH  379 (381)
                      ||
T Consensus       188 aH  189 (1283)
T TIGR01967       188 AH  189 (1283)
T ss_pred             cc
Confidence            99

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.

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=97.75  E-value=0.00018  Score=79.93  Aligned_cols=119  Identities=14%  Similarity=0.139  Sum_probs=78.7

Q ss_pred             hHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHH
Q 042872          211 DDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIIT  263 (381)
Q Consensus       211 ~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~  263 (381)
                      .-+..+..+.+|+ .++++|.-..-.+..|+  |+-|.||=||||+..                           ++...
T Consensus        65 AvvREA~~R~lG~-r~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL~GkgVhVVTvNdYLA~RDae~mg~  141 (925)
T PRK12903         65 AVAREATKRVLGK-RPYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLNALTGKGVIVSTVNEYLAERDAEEMGK  141 (925)
T ss_pred             HHHHHHHHHHhCC-CcCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHHHhcCCceEEEecchhhhhhhHHHHHH
Confidence            3355677788999 57799999888887775  899999999998764                           33444


Q ss_pred             HHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHH
Q 042872          264 LNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKC  343 (381)
Q Consensus       264 L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~  343 (381)
                      +-..+|+.+.++..+++..+++...                               .++|+|+|.--|.    | ..|+.
T Consensus       142 vy~fLGLsvG~i~~~~~~~~rr~aY-------------------------------~~DItYgTn~E~g----F-DYLRD  185 (925)
T PRK12903        142 VFNFLGLSVGINKANMDPNLKREAY-------------------------------ACDITYSVHSELG----F-DYLRD  185 (925)
T ss_pred             HHHHhCCceeeeCCCCChHHHHHhc-------------------------------cCCCeeecCcccc----h-hhhhh
Confidence            4445566666666555554433222                               5789999976664    1 12221


Q ss_pred             HHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          344 LHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       344 L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      -.     .        .......|+.+.|.|||||+.|
T Consensus       186 nm-----~--------~~~~~~vqR~~~faIVDEVDSI  210 (925)
T PRK12903        186 NM-----V--------SSKEEKVQRGLNFCLIDEVDSI  210 (925)
T ss_pred             cc-----c--------ccHHHhcCcccceeeeccchhe
Confidence            10     0        1133456678999999999875

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=97.74  E-value=1.5e-05  Score=90.28  Aligned_cols=34  Identities=29%  Similarity=0.576  Sum_probs=29.2

Q ss_pred             CCcHHHHHHHHHHHcC-CCEEEECCCCCCchhhHH
Q 042872          225 AFRPLQHQACKASVAK-QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~G-rDvLviaPTGsGKTLaF~  258 (381)
                      .|.|+|.++.+.+.+. +++||.+|+|+|||+|..
T Consensus      1143 ~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae 1177 (1674)
T KOG0951|consen 1143 DFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAE 1177 (1674)
T ss_pred             ccCCceEEEEeeeecccceEEEecCCCCchhHHHH
Confidence            3478999999998765 578999999999999976

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

Probab=97.72  E-value=0.00022  Score=81.02  Aligned_cols=109  Identities=18%  Similarity=0.209  Sum_probs=83.8

Q ss_pred             HHHHHhCCCCCcHHHHHHHHHHHc----C--CCEEEECCCCCCchhhHH-----------------------HH-HHHHH
Q 042872          216 ANVVIFGNRAFRPLQHQACKASVA----K--QDCFVLLPTGGGKSLCYQ-----------------------DQ-IITLN  265 (381)
Q Consensus       216 ~~~~~fG~~~fRpiQ~eAI~aiL~----G--rDvLviaPTGsGKTLaF~-----------------------dQ-v~~L~  265 (381)
                      .+...|+| .-||=|..||..++.    +  .|-|+|+--|.|||-+.+                       +| ...++
T Consensus       586 ~F~~~FPy-eET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~GKQVAvLVPTTlLA~QHy~tFk  664 (1139)
T COG1197         586 EFEASFPY-EETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMDGKQVAVLVPTTLLAQQHYETFK  664 (1139)
T ss_pred             HHHhcCCC-cCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcCCCeEEEEcccHHhHHHHHHHHH
Confidence            34455777 468899999999973    4  499999999999996655                       33 55555


Q ss_pred             h---hcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHH
Q 042872          266 L---KFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLK  342 (381)
Q Consensus       266 ~---~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~  342 (381)
                      .   .+.|++..+.-=.+..+++.+++.++.|                         ..+|||+|=--|..         
T Consensus       665 eRF~~fPV~I~~LSRF~s~kE~~~il~~la~G-------------------------~vDIvIGTHrLL~k---------  710 (1139)
T COG1197         665 ERFAGFPVRIEVLSRFRSAKEQKEILKGLAEG-------------------------KVDIVIGTHRLLSK---------  710 (1139)
T ss_pred             HHhcCCCeeEEEecccCCHHHHHHHHHHHhcC-------------------------CccEEEechHhhCC---------
Confidence            4   4578888898888899999999999987                         78999999544432         


Q ss_pred             HHHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          343 CLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       343 ~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                            ++..+               +|+++||||=|+
T Consensus       711 ------dv~Fk---------------dLGLlIIDEEqR  727 (1139)
T COG1197         711 ------DVKFK---------------DLGLLIIDEEQR  727 (1139)
T ss_pred             ------CcEEe---------------cCCeEEEechhh
Confidence                  12222               899999999885

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

Probab=97.67  E-value=0.00013  Score=78.98  Aligned_cols=23  Identities=26%  Similarity=0.219  Sum_probs=19.9

Q ss_pred             HHHcCCCEEEECCCCCCchhhHH
Q 042872          236 ASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       236 aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      ++..++.+++.||||+|||++|+
T Consensus        12 al~~~~~lliEA~TGtGKTlAYL   34 (636)
T TIGR03117        12 SLRQKRIGMLEASTGVGKTLAMI   34 (636)
T ss_pred             HHhcCCeEEEEcCCCCcHHHHHH
Confidence            34467889999999999999998

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.

>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]

Probab=97.66  E-value=6.3e-05  Score=83.58  Aligned_cols=133  Identities=20%  Similarity=0.162  Sum_probs=77.2

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHH--HHHHcCCCEEEECCCCCCchhhHHH-H-HHHHHh----hcCCcEEEEeCCCCHHHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQAC--KASVAKQDCFVLLPTGGGKSLCYQD-Q-IITLNL----KFGIPATFLNSQQTVSQA  284 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI--~aiL~GrDvLviaPTGsGKTLaF~d-Q-v~~L~~----~~gI~a~~l~g~~~~~e~  284 (381)
                      ....-.+..|...+..+|.+|+  +.++.+++++..+||++|||++.-- . ...|..    -++++.+.+     ..+.
T Consensus       211 ~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr~~llilp~vsi-----v~Ek  285 (1008)
T KOG0950|consen  211 VSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRRNVLLILPYVSI-----VQEK  285 (1008)
T ss_pred             HHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHhhceeEecceeeh-----hHHH
Confidence            3333445678889999999997  5678899999999999999999740 0 111111    122222221     2222


Q ss_pred             HHHHHHHHhchhhhhhhhhhhhhhh--hhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccc
Q 042872          285 AAVLQELRQGLVLSQHYFLHQLIFV--LTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVL  362 (381)
Q Consensus       285 ~~il~~lr~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~  362 (381)
                      ..-+..+.        ..+...+..  ..+...+..+.-++-++|-|+..+      .+..|...|  +++         
T Consensus       286 ~~~l~~~~--------~~~G~~ve~y~g~~~p~~~~k~~sv~i~tiEkans------lin~lie~g--~~~---------  340 (1008)
T KOG0950|consen  286 ISALSPFS--------IDLGFPVEEYAGRFPPEKRRKRESVAIATIEKANS------LINSLIEQG--RLD---------  340 (1008)
T ss_pred             Hhhhhhhc--------cccCCcchhhcccCCCCCcccceeeeeeehHhhHh------HHHHHHhcC--Ccc---------
Confidence            22222211        111111111  111122333457899999999852      456666777  333         


Q ss_pred             cccccCCccEEEEeccccC
Q 042872          363 PHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       363 ~~~~~~~L~~lVIDEAHcI  381 (381)
                            .++.|||||-|+|
T Consensus       341 ------~~g~vvVdElhmi  353 (1008)
T KOG0950|consen  341 ------FLGMVVVDELHMI  353 (1008)
T ss_pred             ------ccCcEEEeeeeee
Confidence                  7999999999986

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=97.64  E-value=0.00013  Score=79.97  Aligned_cols=105  Identities=18%  Similarity=0.207  Sum_probs=74.5

Q ss_pred             CCCcHHHHHHHHHHH----cCCCEEEECCCCCCchh------hHH--------------------HHHHHHHh-hcCCcE
Q 042872          224 RAFRPLQHQACKASV----AKQDCFVLLPTGGGKSL------CYQ--------------------DQIITLNL-KFGIPA  272 (381)
Q Consensus       224 ~~fRpiQ~eAI~aiL----~GrDvLviaPTGsGKTL------aF~--------------------dQv~~L~~-~~gI~a  272 (381)
                      -.+|++|.+-++-+.    +|-++|+.=.-|-|||+      +|+                    ..+..+.. .-++++
T Consensus       166 g~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQtIs~l~yl~~~~~~~GPfLVi~P~StL~NW~~Ef~rf~P~l~~  245 (971)
T KOG0385|consen  166 GELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIAPKSTLDNWMNEFKRFTPSLNV  245 (971)
T ss_pred             CccchhhhccHHHHHHHHhcCcccEeehhcccchHHHHHHHHHHHHHhcCCCCCeEEEeeHhhHHHHHHHHHHhCCCcce
Confidence            368999999887765    57889999999999994      233                    23333332 137889


Q ss_pred             EEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccc
Q 042872          273 TFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRL  352 (381)
Q Consensus       273 ~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l  352 (381)
                      +++.|+  ..++....+.+.                        ..+.++|+++|-|+++....+   |.+.        
T Consensus       246 ~~~~Gd--k~eR~~~~r~~~------------------------~~~~fdV~iTsYEi~i~dk~~---lk~~--------  288 (971)
T KOG0385|consen  246 VVYHGD--KEERAALRRDIM------------------------LPGRFDVCITSYEIAIKDKSF---LKKF--------  288 (971)
T ss_pred             EEEeCC--HHHHHHHHHHhh------------------------ccCCCceEeehHHHHHhhHHH---HhcC--------
Confidence            999886  466666665542                        223799999999999854443   3332        


Q ss_pred             cccccccccccccccCCccEEEEeccccC
Q 042872          353 KVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       353 ~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                      .-.|+||||||+|
T Consensus       289 ----------------~W~ylvIDEaHRi  301 (971)
T KOG0385|consen  289 ----------------NWRYLVIDEAHRI  301 (971)
T ss_pred             ----------------CceEEEechhhhh
Confidence                            5679999999986

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=97.63  E-value=0.00024  Score=69.67  Aligned_cols=71  Identities=25%  Similarity=0.253  Sum_probs=45.2

Q ss_pred             HhCCCCCcHHHHH----HHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCC-----cEEEEeCCCCHHHHHHHHHH
Q 042872          220 IFGNRAFRPLQHQ----ACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGI-----PATFLNSQQTVSQAAAVLQE  290 (381)
Q Consensus       220 ~fG~~~fRpiQ~e----AI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI-----~a~~l~g~~~~~e~~~il~~  290 (381)
                      .|.|+ |||.|.+    ++..+..|+++++.+|||+|||++|+--+..+....+.     ++++.+..  ..+..+.+..
T Consensus         4 ~FPy~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T--~~~~~q~i~~   80 (289)
T smart00489        4 YFPYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRT--VSEIEKRLEE   80 (289)
T ss_pred             cCCCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEecc--HHHHHHHHHH
Confidence            37775 6999999    45555578999999999999999998222111112222     55555543  3344445555


Q ss_pred             HHh
Q 042872          291 LRQ  293 (381)
Q Consensus       291 lr~  293 (381)
                      +++
T Consensus        81 l~~   83 (289)
T smart00489       81 LRK   83 (289)
T ss_pred             HHh
Confidence            553

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=97.63  E-value=0.00024  Score=69.67  Aligned_cols=71  Identities=25%  Similarity=0.253  Sum_probs=45.2

Q ss_pred             HhCCCCCcHHHHH----HHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCC-----cEEEEeCCCCHHHHHHHHHH
Q 042872          220 IFGNRAFRPLQHQ----ACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGI-----PATFLNSQQTVSQAAAVLQE  290 (381)
Q Consensus       220 ~fG~~~fRpiQ~e----AI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI-----~a~~l~g~~~~~e~~~il~~  290 (381)
                      .|.|+ |||.|.+    ++..+..|+++++.+|||+|||++|+--+..+....+.     ++++.+..  ..+..+.+..
T Consensus         4 ~FPy~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T--~~~~~q~i~~   80 (289)
T smart00488        4 YFPYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRT--VSEIEKRLEE   80 (289)
T ss_pred             cCCCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEecc--HHHHHHHHHH
Confidence            37775 6999999    45555578999999999999999998222111112222     55555543  3344445555


Q ss_pred             HHh
Q 042872          291 LRQ  293 (381)
Q Consensus       291 lr~  293 (381)
                      +++
T Consensus        81 l~~   83 (289)
T smart00488       81 LRK   83 (289)
T ss_pred             HHh
Confidence            553

>PRK09694 helicase Cas3; Provisional

Probab=97.62  E-value=0.0003  Score=78.78  Aligned_cols=38  Identities=21%  Similarity=0.120  Sum_probs=30.0

Q ss_pred             hCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      |+...|||+|..+......+.-+++.+|||+|||.+.+
T Consensus       282 ~~~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL  319 (878)
T PRK09694        282 DNGYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAAL  319 (878)
T ss_pred             cCCCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHH
Confidence            54558999999886544445668999999999998876

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

Probab=97.60  E-value=0.00019  Score=79.17  Aligned_cols=54  Identities=22%  Similarity=0.206  Sum_probs=37.6

Q ss_pred             CCCCCcHHHHHHHHHHH----cC-CCEEEECCCCCCchhhHHHHHHHHHhhcC-C-cEEEEe
Q 042872          222 GNRAFRPLQHQACKASV----AK-QDCFVLLPTGGGKSLCYQDQIITLNLKFG-I-PATFLN  276 (381)
Q Consensus       222 G~~~fRpiQ~eAI~aiL----~G-rDvLviaPTGsGKTLaF~dQv~~L~~~~g-I-~a~~l~  276 (381)
                      +-..+|.+|..||..+.    .| +.+|++|.||+|||.+...-+..|.+ .| + ++.+|.
T Consensus       162 s~i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAiaii~rL~r-~~~~KRVLFLa  222 (875)
T COG4096         162 SAIGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAIAIIDRLIK-SGWVKRVLFLA  222 (875)
T ss_pred             ccccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHHHHHHHHHh-cchhheeeEEe
Confidence            44468999999999876    34 35999999999999776533444442 22 2 455554

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

Probab=97.59  E-value=0.00025  Score=66.68  Aligned_cols=127  Identities=18%  Similarity=0.110  Sum_probs=65.0

Q ss_pred             HHHHHHHHHH-------------cCCCEEEECCCCCCchhhHHHHHHHHHhhcCC----cEEEEeCCCCHHHHHHHHHHH
Q 042872          229 LQHQACKASV-------------AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGI----PATFLNSQQTVSQAAAVLQEL  291 (381)
Q Consensus       229 iQ~eAI~aiL-------------~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI----~a~~l~g~~~~~e~~~il~~l  291 (381)
                      +|.+++.-++             ..+.+|+.-.+|.|||+..+--+..+......    ++.++.+......+...+...
T Consensus         1 ~Q~~~v~~m~~~~~~~~~~~~~~~~~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~~l~~~W~~E~~~~   80 (299)
T PF00176_consen    1 HQLEAVRWMLDRELVEEYPNSESPPRGGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPSSLLSQWKEEIEKW   80 (299)
T ss_dssp             HHHHHHHHHHHHH----TTSSSTTT-EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-TTTHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhhhhcccccccCCCCEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeeccchhhhhhhhhccc
Confidence            4777776653             23577888899999998876333334322222    377777776666665555553


Q ss_pred             HhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccc--cCcchHHHHHHHHhcCCccccccccccccccccccCC
Q 042872          292 RQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIV--GNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQ  369 (381)
Q Consensus       292 r~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~--~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~  369 (381)
                      ..+.....+++....  ............++++++|.+.+.  ..+.....+..    .                    +
T Consensus        81 ~~~~~~~v~~~~~~~--~~~~~~~~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~----~--------------------~  134 (299)
T PF00176_consen   81 FDPDSLRVIIYDGDS--ERRRLSKNQLPKYDVVITTYETLRKARKKKDKEDLKQ----I--------------------K  134 (299)
T ss_dssp             SGT-TS-EEEESSSC--HHHHTTSSSCCCSSEEEEEHHHHH--TSTHTTHHHHT----S--------------------E
T ss_pred             ccccccccccccccc--ccccccccccccceeeecccccccccccccccccccc----c--------------------c
Confidence            211000000000000  000012334557899999999987  11222222221    1                    5


Q ss_pred             ccEEEEeccccC
Q 042872          370 LAGFVVDEAHCV  381 (381)
Q Consensus       370 L~~lVIDEAHcI  381 (381)
                      ..+|||||||.+
T Consensus       135 ~~~vIvDEaH~~  146 (299)
T PF00176_consen  135 WDRVIVDEAHRL  146 (299)
T ss_dssp             EEEEEETTGGGG
T ss_pred             ceeEEEeccccc
Confidence            889999999974

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.

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=97.55  E-value=0.00019  Score=81.46  Aligned_cols=129  Identities=14%  Similarity=0.059  Sum_probs=70.1

Q ss_pred             CCcHHHHHHHHHHH----cCCCEEEECCCCCCchhhHHHHHHHHHhhcCC--cEEEEeCCCCHHHHHHHHHHHHhchhhh
Q 042872          225 AFRPLQHQACKASV----AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGI--PATFLNSQQTVSQAAAVLQELRQGLVLS  298 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL----~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI--~a~~l~g~~~~~e~~~il~~lr~g~~~~  298 (381)
                      .+||+|.+++.-++    .|...|+.-..|-|||+.-+--+..+....++  +++++.+......+..-+...-.. ..-
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIalL~~L~~~~~~~gp~LIVvP~SlL~nW~~Ei~kw~p~-l~v  247 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPKSTLGNWMNEIRRFCPV-LRA  247 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHHHHHHHHhcCCCCCEEEEeChHHHHHHHHHHHHHCCC-Cce
Confidence            68999999998765    57889999999999997543223333322233  456666655555544444332100 000


Q ss_pred             hhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEecc
Q 042872          299 QHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEA  378 (381)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEA  378 (381)
                      ..+.-.+.............+.++|||+|.+.+....   ..|..    -                    .-.+||||||
T Consensus       248 ~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~---~~L~k----~--------------------~W~~VIvDEA  300 (1033)
T PLN03142        248 VKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEK---TALKR----F--------------------SWRYIIIDEA  300 (1033)
T ss_pred             EEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHH---HHhcc----C--------------------CCCEEEEcCc
Confidence            0000000000000000012236899999999886321   11111    0                    5679999999


Q ss_pred             ccC
Q 042872          379 HCV  381 (381)
Q Consensus       379 HcI  381 (381)
                      |+|
T Consensus       301 HrI  303 (1033)
T PLN03142        301 HRI  303 (1033)
T ss_pred             ccc
Confidence            986

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=97.53  E-value=0.00013  Score=77.01  Aligned_cols=125  Identities=18%  Similarity=0.217  Sum_probs=78.4

Q ss_pred             CCcHHHHHHHHHHHc-C--CCEEEECCCCCCchhhHHHHHHHHHhhcCCcE-EEEeCCCCHHHHHHHHHHHHhchhhhhh
Q 042872          225 AFRPLQHQACKASVA-K--QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPA-TFLNSQQTVSQAAAVLQELRQGLVLSQH  300 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~-G--rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a-~~l~g~~~~~e~~~il~~lr~g~~~~~~  300 (381)
                      .+||+|..++..... |  |.-++++|-|+||||+-.--+..    ..-++ +.+++.++.++++.+.....       -
T Consensus       302 ~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~t----ikK~clvLcts~VSVeQWkqQfk~ws-------t  370 (776)
T KOG1123|consen  302 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACT----IKKSCLVLCTSAVSVEQWKQQFKQWS-------T  370 (776)
T ss_pred             ccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeee----ecccEEEEecCccCHHHHHHHHHhhc-------c
Confidence            468999999999873 3  68999999999999886311111    12234 34578888888877776642       1


Q ss_pred             hhhhhhhhhhhhcccCCCCCccEEEECccccccCc--c--hHHHHHHHHhcCCccccccccccccccccccCCccEEEEe
Q 042872          301 YFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQ--S--FSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVD  376 (381)
Q Consensus       301 ~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~--~--f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVID  376 (381)
                      +...+....+..+......++.|+|.|--++..+.  .  -...+..|..+                     .-+++|+|
T Consensus       371 i~d~~i~rFTsd~Ke~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~---------------------EWGllllD  429 (776)
T KOG1123|consen  371 IQDDQICRFTSDAKERFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGR---------------------EWGLLLLD  429 (776)
T ss_pred             cCccceEEeeccccccCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcC---------------------eeeeEEee
Confidence            11222222233333444456889999988887431  1  12233333211                     68899999


Q ss_pred             ccccC
Q 042872          377 EAHCV  381 (381)
Q Consensus       377 EAHcI  381 (381)
                      |+|.|
T Consensus       430 EVHvv  434 (776)
T KOG1123|consen  430 EVHVV  434 (776)
T ss_pred             hhccc
Confidence            99976

>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]

Probab=97.53  E-value=0.0002  Score=78.28  Aligned_cols=33  Identities=24%  Similarity=0.321  Sum_probs=30.1

Q ss_pred             CcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          226 FRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       226 fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +-|+|..||.++-.+..|||.|-|.+|||++.-
T Consensus       130 LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAe  162 (1041)
T KOG0948|consen  130 LDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAE  162 (1041)
T ss_pred             cCchHhhhhhhhcCCceEEEEeecCCCcchHHH
Confidence            348899999999999999999999999998874

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

Probab=97.43  E-value=0.00033  Score=77.93  Aligned_cols=37  Identities=30%  Similarity=0.531  Sum_probs=31.8

Q ss_pred             hCCCCCcHHHHHHHH----HHHcCCCEEEECCCCCCchhhHH
Q 042872          221 FGNRAFRPLQHQACK----ASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~----aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .||+ +||.|.+.+.    ++..|+++++.||||+|||++|+
T Consensus       242 ~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayL  282 (850)
T TIGR01407       242 LGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYL  282 (850)
T ss_pred             cCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHH
Confidence            6885 9999998666    44468999999999999999997

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.

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=97.41  E-value=0.00033  Score=79.11  Aligned_cols=129  Identities=16%  Similarity=0.051  Sum_probs=69.8

Q ss_pred             CCcHHHHHHHHHHHcC--CCEEEECCCCCCchhhHHHHHHHHHhhcC--CcEEEEeCCCCHHHHHHHHHHHHhchhhhhh
Q 042872          225 AFRPLQHQACKASVAK--QDCFVLLPTGGGKSLCYQDQIITLNLKFG--IPATFLNSQQTVSQAAAVLQELRQGLVLSQH  300 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~G--rDvLviaPTGsGKTLaF~dQv~~L~~~~g--I~a~~l~g~~~~~e~~~il~~lr~g~~~~~~  300 (381)
                      .+.|+|.+++..++..  ..+|+.-..|-|||+-..--+..+. ..|  -++.+++...-..++..-+..   -+-....
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~-~~g~~~rvLIVvP~sL~~QW~~El~~---kF~l~~~  227 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQL-LTGRAERVLILVPETLQHQWLVEMLR---RFNLRFS  227 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHH-HcCCCCcEEEEcCHHHHHHHHHHHHH---HhCCCeE
Confidence            4779999999887654  4789999999999976642233332 123  367777765333333222211   0000111


Q ss_pred             hhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          301 YFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       301 ~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                      .+...............-...+++|+|-+.+..++.+.+.+..    .                    ...+|||||||+
T Consensus       228 i~~~~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~~~l~~----~--------------------~wdlvIvDEAH~  283 (956)
T PRK04914        228 LFDEERYAEAQHDADNPFETEQLVICSLDFLRRNKQRLEQALA----A--------------------EWDLLVVDEAHH  283 (956)
T ss_pred             EEcCcchhhhcccccCccccCcEEEEEHHHhhhCHHHHHHHhh----c--------------------CCCEEEEechhh
Confidence            1111100000000011112467999999888754444333321    1                    688999999998


Q ss_pred             C
Q 042872          381 V  381 (381)
Q Consensus       381 I  381 (381)
                      +
T Consensus       284 l  284 (956)
T PRK04914        284 L  284 (956)
T ss_pred             h
Confidence            5

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=97.25  E-value=0.001  Score=75.01  Aligned_cols=117  Identities=15%  Similarity=0.103  Sum_probs=75.4

Q ss_pred             HHHHHHHHhC-------------CCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------
Q 042872          213 MEFANVVIFG-------------NRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------  258 (381)
Q Consensus       213 l~~~~~~~fG-------------~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------  258 (381)
                      +..++.+.+|             + .+.++|.-.--++..|+  |+-|.||=||||+..                     
T Consensus       114 vrEaarR~~G~~~~~~g~~~~wdm-~~ydVQLiGgivLh~G~--IAEM~TGEGKTLvatlp~yLnAL~G~gVHvVTvNDY  190 (1025)
T PRK12900        114 VKETCRRLKGHTYQVMGREMTWDM-VPYDVQLIGGIVLHSGK--ISEMATGEGKTLVSTLPTFLNALTGRGVHVVTVNDY  190 (1025)
T ss_pred             HHHHHHHHhCCcccccccccccCc-cccchHHhhhHHhhcCC--ccccCCCCCcchHhHHHHHHHHHcCCCcEEEeechH
Confidence            4446666677             3 46688888877777776  889999999998864                     


Q ss_pred             ------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccc
Q 042872          259 ------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIV  332 (381)
Q Consensus       259 ------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~  332 (381)
                            ++...+-..+|+.+.++..+++..+++...                               .++|.|+|.--+-
T Consensus       191 LA~RDaewm~p~y~flGLtVg~i~~~~~~~~Rr~aY-------------------------------~~DItYgTn~EfG  239 (1025)
T PRK12900        191 LAQRDKEWMNPVFEFHGLSVGVILNTMRPEERREQY-------------------------------LCDITYGTNNEFG  239 (1025)
T ss_pred             hhhhhHHHHHHHHHHhCCeeeeeCCCCCHHHHHHhC-------------------------------CCcceecCCCccc
Confidence                  344555545677766666655555443222                               5799999976664


Q ss_pred             cCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          333 GNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       333 ~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      - ..++..+..                 ......|+.+.|.|||||+.|
T Consensus       240 F-DYLRDnma~-----------------~~~~~vqR~~~faIVDEvDSv  270 (1025)
T PRK12900        240 F-DYLRDNMAG-----------------TPEEMVQRDFYFAIVDEVDSV  270 (1025)
T ss_pred             c-ccchhcccc-----------------chhhhhccCCceEEEechhhh
Confidence            1 222211110                 011235668999999999865

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=97.21  E-value=0.00098  Score=72.65  Aligned_cols=73  Identities=21%  Similarity=0.291  Sum_probs=48.4

Q ss_pred             HHhCCCCCcHHHHHHHHHHH----cCCCEEEECCCCCCchhhHHHHHHHHHhhcC--CcEEEEeCCCCHHHHHHHHHHHH
Q 042872          219 VIFGNRAFRPLQHQACKASV----AKQDCFVLLPTGGGKSLCYQDQIITLNLKFG--IPATFLNSQQTVSQAAAVLQELR  292 (381)
Q Consensus       219 ~~fG~~~fRpiQ~eAI~aiL----~GrDvLviaPTGsGKTLaF~dQv~~L~~~~g--I~a~~l~g~~~~~e~~~il~~lr  292 (381)
                      ..|.|+.+||.|.+.+..+.    .|+.+|+-+|||+|||++-+--..+.....+  .+++.+  ..+..+..+++++++
T Consensus         4 v~FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~--sRThsQl~q~i~Elk   81 (705)
T TIGR00604         4 VYFPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYA--SRTHSQLEQATEELR   81 (705)
T ss_pred             eecCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEE--cccchHHHHHHHHHH
Confidence            45899989999999887765    5789999999999999887622211111122  233333  334555666676666


Q ss_pred             h
Q 042872          293 Q  293 (381)
Q Consensus       293 ~  293 (381)
                      +
T Consensus        82 ~   82 (705)
T TIGR00604        82 K   82 (705)
T ss_pred             h
Confidence            4

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).

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

Probab=97.03  E-value=0.0018  Score=66.01  Aligned_cols=52  Identities=29%  Similarity=0.395  Sum_probs=35.7

Q ss_pred             CCcHHHHHHHHHHH----cCCCEEEECCCCCCch-hhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          225 AFRPLQHQACKASV----AKQDCFVLLPTGGGKS-LCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL----~GrDvLviaPTGsGKT-LaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      +++|.|+.|-..++    +.+|.|+-|=||+||| ..|+ -+.. ....|-++.+...-
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMif~-~i~~-al~~G~~vciASPR  153 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIFQ-GIEQ-ALNQGGRVCIASPR  153 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhHH-HHHH-HHhcCCeEEEecCc
Confidence            68899998887776    4689999999999999 4554 2221 11345555554443

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

Probab=97.00  E-value=0.0019  Score=69.30  Aligned_cols=59  Identities=24%  Similarity=0.299  Sum_probs=42.0

Q ss_pred             HHhCCCCCcHHHHHHHHHHH----cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          219 VIFGNRAFRPLQHQACKASV----AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       219 ~~fG~~~fRpiQ~eAI~aiL----~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ..|.+.++|+.|.+.+..+.    .|+-+++-||||+|||++|+--........+.++++.++
T Consensus         9 ~~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~~~viist~   71 (654)
T COG1199           9 VAFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKVIISTR   71 (654)
T ss_pred             hhCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcCCcEEEECC
Confidence            34777789999999987654    345699999999999999984333333334455555544

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=96.75  E-value=0.0071  Score=68.50  Aligned_cols=38  Identities=21%  Similarity=0.371  Sum_probs=28.6

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCc-EEEEeCC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIP-ATFLNSQ  278 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~-a~~l~g~  278 (381)
                      .++.+.|+||+|||.+|+..+..|...+|.. .+++.+.
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~~~~~~fii~vp~   98 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQKYGLFKFIIVVPT   98 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHcCCcEEEEEeCC
Confidence            3789999999999999987677777667765 3444443

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.75  E-value=0.0041  Score=68.00  Aligned_cols=74  Identities=11%  Similarity=0.076  Sum_probs=59.2

Q ss_pred             CCCCchhhHH-----------------------HH-HHHHHhhcC-CcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhh
Q 042872          249 TGGGKSLCYQ-----------------------DQ-IITLNLKFG-IPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFL  303 (381)
Q Consensus       249 TGsGKTLaF~-----------------------dQ-v~~L~~~~g-I~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~  303 (381)
                      +|||||-+|+                       .| +..|...+| -.+++++++.+..++...+.++++|         
T Consensus       169 ~GSGKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G---------  239 (665)
T PRK14873        169 PGEDWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRG---------  239 (665)
T ss_pred             CCCcHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCC---------
Confidence            5999999998                       34 466777787 7788999999999998888888766         


Q ss_pred             hhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccc
Q 042872          304 HQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH  379 (381)
Q Consensus       304 ~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAH  379 (381)
                                      ..+|||+|---++. |                               -.++++|||||=|
T Consensus       240 ----------------~~~IViGtRSAvFa-P-------------------------------~~~LgLIIvdEEh  267 (665)
T PRK14873        240 ----------------QARVVVGTRSAVFA-P-------------------------------VEDLGLVAIWDDG  267 (665)
T ss_pred             ----------------CCcEEEEcceeEEe-c-------------------------------cCCCCEEEEEcCC
Confidence                            68899999666651 1                               1289999999987

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=96.72  E-value=0.0036  Score=71.03  Aligned_cols=35  Identities=17%  Similarity=0.150  Sum_probs=27.2

Q ss_pred             hCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      ||. .+.++|.-.--++..|+  |+-|.||=||||+..
T Consensus       166 W~m-~~yDVQliGgivLh~G~--IAEM~TGEGKTLvAt  200 (1112)
T PRK12901        166 WDM-VHYDVQLIGGVVLHQGK--IAEMATGEGKTLVAT  200 (1112)
T ss_pred             CCC-cccchHHhhhhhhcCCc--eeeecCCCCchhHHH
Confidence            565 35588887777776665  899999999998864

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]

Probab=96.65  E-value=0.0012  Score=74.09  Aligned_cols=29  Identities=17%  Similarity=0.331  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHcCCCEEEECCCCCCchhh
Q 042872          228 PLQHQACKASVAKQDCFVLLPTGGGKSLC  256 (381)
Q Consensus       228 piQ~eAI~aiL~GrDvLviaPTGsGKTLa  256 (381)
                      .+|++-...+=.++.++++|||-+|||.+
T Consensus       514 ~WQ~elLDsvDr~eSavIVAPTSaGKTfi  542 (1330)
T KOG0949|consen  514 EWQRELLDSVDRNESAVIVAPTSAGKTFI  542 (1330)
T ss_pred             HHHHHHhhhhhcccceEEEeeccCCceec
Confidence            57999998888899999999999999954

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=96.63  E-value=0.0062  Score=66.06  Aligned_cols=25  Identities=36%  Similarity=0.262  Sum_probs=19.1

Q ss_pred             HHHHHHHHcCCCEEEECCCCCCchh
Q 042872          231 HQACKASVAKQDCFVLLPTGGGKSL  255 (381)
Q Consensus       231 ~eAI~aiL~GrDvLviaPTGsGKTL  255 (381)
                      .+.+.++-.++=+++++.||+|||-
T Consensus        57 ~~il~~ve~nqvlIviGeTGsGKST   81 (674)
T KOG0922|consen   57 DQILYAVEDNQVLIVIGETGSGKST   81 (674)
T ss_pred             HHHHHHHHHCCEEEEEcCCCCCccc
Confidence            3455555667778999999999993

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=96.62  E-value=0.0051  Score=57.20  Aligned_cols=16  Identities=31%  Similarity=0.372  Sum_probs=13.4

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      +++++|||+|||-+-.
T Consensus         4 i~lvGptGvGKTTt~a   19 (196)
T PF00448_consen    4 IALVGPTGVGKTTTIA   19 (196)
T ss_dssp             EEEEESTTSSHHHHHH
T ss_pred             EEEECCCCCchHhHHH
Confidence            5789999999996654

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 ....

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=96.56  E-value=0.01  Score=65.00  Aligned_cols=36  Identities=31%  Similarity=0.248  Sum_probs=28.8

Q ss_pred             CCCCCcHHHHHHHHHH---HcC------CCEEEECCCCCCchhhHH
Q 042872          222 GNRAFRPLQHQACKAS---VAK------QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       222 G~~~fRpiQ~eAI~ai---L~G------rDvLviaPTGsGKTLaF~  258 (381)
                      || ++|+.|.+-+..+   +.+      +.+++-||||+|||++|+
T Consensus        23 ~~-e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYL   67 (697)
T PRK11747         23 GF-IPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYL   67 (697)
T ss_pred             CC-CcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHH
Confidence            45 7999999955444   444      568899999999999998

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

Probab=96.42  E-value=0.013  Score=65.77  Aligned_cols=26  Identities=27%  Similarity=0.256  Sum_probs=18.1

Q ss_pred             HHHHHHHcCCCEEEECCCCCCchhhH
Q 042872          232 QACKASVAKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       232 eAI~aiL~GrDvLviaPTGsGKTLaF  257 (381)
                      +.+.++-...=+++.+|||+|||--.
T Consensus        57 ~i~~ai~~~~vvii~getGsGKTTql   82 (845)
T COG1643          57 EILKAIEQNQVVIIVGETGSGKTTQL   82 (845)
T ss_pred             HHHHHHHhCCEEEEeCCCCCChHHHH
Confidence            34444445566788899999999543

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=96.33  E-value=0.0015  Score=54.45  Aligned_cols=19  Identities=21%  Similarity=0.324  Sum_probs=13.3

Q ss_pred             CCCEEEECCCCCCchhhHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~  258 (381)
                      ++-+++.+|+|+|||.+..
T Consensus         4 ~~~~~i~G~~G~GKT~~~~   22 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIK   22 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHH
Confidence            4568999999999998764

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=96.27  E-value=0.018  Score=53.12  Aligned_cols=52  Identities=19%  Similarity=0.198  Sum_probs=34.0

Q ss_pred             CCcHHHHHHHHHHHcCC-C-EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          225 AFRPLQHQACKASVAKQ-D-CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~Gr-D-vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ++++-|++|+..++... . +++.+|.|+|||.+...-...+. ..|.+++.+..
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~~-~~g~~v~~~ap   54 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLLKALAEALE-AAGKRVIGLAP   54 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHHH-HTT--EEEEES
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHHH-hCCCeEEEECC
Confidence            36789999999998654 3 56669999999976543333344 45777766654

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=96.26  E-value=0.0071  Score=69.32  Aligned_cols=111  Identities=17%  Similarity=0.242  Sum_probs=69.2

Q ss_pred             CCCcHHHHHHHHHHH----cCCCEEEECCCCCCch---hhHH-----------------------HHHHHHHhhcCCcEE
Q 042872          224 RAFRPLQHQACKASV----AKQDCFVLLPTGGGKS---LCYQ-----------------------DQIITLNLKFGIPAT  273 (381)
Q Consensus       224 ~~fRpiQ~eAI~aiL----~GrDvLviaPTGsGKT---LaF~-----------------------dQv~~L~~~~gI~a~  273 (381)
                      -++|.+|.+-++-++    .+.++|+.=.-|-|||   ++|+                       .....+..+..+.++
T Consensus       369 ~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqti~fl~~l~~~~~~~gpflvvvplst~~~W~~ef~~w~~mn~i  448 (1373)
T KOG0384|consen  369 NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITFLSYLFHSLQIHGPFLVVVPLSTITAWEREFETWTDMNVI  448 (1373)
T ss_pred             chhhhhhcccchhHHHHHHhcccceehhhcCCCcchHHHHHHHHHHHhhhccCCeEEEeehhhhHHHHHHHHHHhhhcee
Confidence            579999999998766    6889999999999999   4565                       112233333455566


Q ss_pred             EEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcccc
Q 042872          274 FLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLK  353 (381)
Q Consensus       274 ~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~  353 (381)
                      ++.|.....+   +++.-.         +++        .+....=++++|++|-|.++....++..+            
T Consensus       449 ~y~g~~~sr~---~i~~ye---------~~~--------~~~~~~lkf~~lltTye~~LkDk~~L~~i------------  496 (1373)
T KOG0384|consen  449 VYHGNLESRQ---LIRQYE---------FYH--------SSNTKKLKFNALLTTYEIVLKDKAELSKI------------  496 (1373)
T ss_pred             eeecchhHHH---HHHHHH---------hee--------cCCccccccceeehhhHHHhccHhhhccC------------
Confidence            6655433222   122110         000        11112226899999999998655443221            


Q ss_pred             ccccccccccccccCCccEEEEeccccC
Q 042872          354 VLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       354 ~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                     .-.+++|||||++
T Consensus       497 ---------------~w~~~~vDeahrL  509 (1373)
T KOG0384|consen  497 ---------------PWRYLLVDEAHRL  509 (1373)
T ss_pred             ---------------CcceeeecHHhhc
Confidence                           4678999999975

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

Probab=96.23  E-value=0.049  Score=49.46  Aligned_cols=50  Identities=16%  Similarity=0.120  Sum_probs=30.0

Q ss_pred             CCCEEEECCCCCCchhhHHHH-HHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQ-IITLNLKFGIPATFLNSQQTVSQAAAVLQELR  292 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQ-v~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr  292 (381)
                      |+=.++-+.+|+|||--.+.+ +.+.. ..+.++++|...  +-..+++-++++
T Consensus         4 g~~~~~d~hpGaGKTr~vlp~~~~~~i-~~~~rvLvL~PT--Rvva~em~~aL~   54 (148)
T PF07652_consen    4 GELTVLDLHPGAGKTRRVLPEIVREAI-KRRLRVLVLAPT--RVVAEEMYEALK   54 (148)
T ss_dssp             TEEEEEE--TTSSTTTTHHHHHHHHHH-HTT--EEEEESS--HHHHHHHHHHTT
T ss_pred             CceeEEecCCCCCCcccccHHHHHHHH-HccCeEEEeccc--HHHHHHHHHHHh
Confidence            445688899999999877643 33333 568899999863  444455555554

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 ....

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.15  E-value=0.056  Score=45.53  Aligned_cols=39  Identities=18%  Similarity=0.346  Sum_probs=26.1

Q ss_pred             EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHH
Q 042872          243 CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVS  282 (381)
Q Consensus       243 vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~  282 (381)
                      +++.+|+|+|||.........+. ..+.+++++.......
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~-~~~~~v~~~~~e~~~~   40 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIA-TKGGKVVYVDIEEEIE   40 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHH-hcCCEEEEEECCcchH
Confidence            57899999999977643333333 3577777776654443

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.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=96.01  E-value=0.041  Score=60.71  Aligned_cols=37  Identities=16%  Similarity=0.164  Sum_probs=32.2

Q ss_pred             HhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhH
Q 042872          220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       220 ~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF  257 (381)
                      .+++ .+++.|++||..++..+-+++.++.|+|||-+-
T Consensus       319 ~~~~-~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l  355 (720)
T TIGR01448       319 KLRK-GLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT  355 (720)
T ss_pred             hcCC-CCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH
Confidence            3555 689999999999998888999999999999765

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.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.98  E-value=0.04  Score=56.55  Aligned_cols=40  Identities=20%  Similarity=0.275  Sum_probs=25.9

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcC-CcEEEEeCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFG-IPATFLNSQQ  279 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~g-I~a~~l~g~~  279 (381)
                      |+-+++++|||+|||.+...-...+....| .++.+++.+.
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~  177 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDS  177 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEeccc
Confidence            678899999999999887633333332344 3555555443

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=95.95  E-value=0.0084  Score=59.91  Aligned_cols=37  Identities=16%  Similarity=0.207  Sum_probs=26.5

Q ss_pred             EEEECCCCCCchhhHHHHHHHH--HhhcCCcEEEEeCCCC
Q 042872          243 CFVLLPTGGGKSLCYQDQIITL--NLKFGIPATFLNSQQT  280 (381)
Q Consensus       243 vLviaPTGsGKTLaF~dQv~~L--~~~~gI~a~~l~g~~~  280 (381)
                      +||.+..|+|||++....+..+  . ..+..+..+++...
T Consensus         4 ~~I~G~aGTGKTvla~~l~~~l~~~-~~~~~~~~l~~n~~   42 (352)
T PF09848_consen    4 ILITGGAGTGKTVLALNLAKELQNS-EEGKKVLYLCGNHP   42 (352)
T ss_pred             EEEEecCCcCHHHHHHHHHHHhhcc-ccCCceEEEEecch
Confidence            5788999999999987667666  3 34566666665433

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=95.89  E-value=0.043  Score=61.81  Aligned_cols=37  Identities=22%  Similarity=0.277  Sum_probs=29.8

Q ss_pred             CCCCCcHHHHHHHHHHHcC----CCEEEECCCCCCchhhHH
Q 042872          222 GNRAFRPLQHQACKASVAK----QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       222 G~~~fRpiQ~eAI~aiL~G----rDvLviaPTGsGKTLaF~  258 (381)
                      .-++|||+|++||.+++.|    ..-=++|..|+|||.+-+
T Consensus       158 ~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsL  198 (1518)
T COG4889         158 KPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSL  198 (1518)
T ss_pred             CCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHH
Confidence            3457999999999999964    224577888999998877

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=95.88  E-value=0.018  Score=63.37  Aligned_cols=32  Identities=25%  Similarity=0.177  Sum_probs=27.2

Q ss_pred             cHHHHHHHHHHHcC---C-CEEEECCCCCCchhhHH
Q 042872          227 RPLQHQACKASVAK---Q-DCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       227 RpiQ~eAI~aiL~G---r-DvLviaPTGsGKTLaF~  258 (381)
                      ++.|..+...++.+   . .+++.||||+|||.+.+
T Consensus       197 ~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl  232 (733)
T COG1203         197 YELQEKALELILRLEKRSLLVVLEAPTGYGKTEASL  232 (733)
T ss_pred             hHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHH
Confidence            68899999988853   4 67889999999999987

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=95.84  E-value=0.0043  Score=70.15  Aligned_cols=53  Identities=21%  Similarity=0.309  Sum_probs=34.4

Q ss_pred             CCcHHHHHHHHHHHc-CCCEEEECCCCCCchhhHHH-HHHHHHhhcCCcEEEEeC
Q 042872          225 AFRPLQHQACKASVA-KQDCFVLLPTGGGKSLCYQD-QIITLNLKFGIPATFLNS  277 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~-GrDvLviaPTGsGKTLaF~d-Qv~~L~~~~gI~a~~l~g  277 (381)
                      .|-|+|.+.+..+.. ..+.++.+|||+|||++|.. -+..+...-+-+++.+..
T Consensus       927 ~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p~~kvvyIap  981 (1230)
T KOG0952|consen  927 YFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYPGSKVVYIAP  981 (1230)
T ss_pred             ccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCCCccEEEEcC
Confidence            455677776665543 36789999999999999962 234444333455555543

>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=95.81  E-value=0.093  Score=42.60  Aligned_cols=37  Identities=24%  Similarity=0.359  Sum_probs=23.1

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ++.+++.+|+|+|||.....-...+. ..+.++..+..
T Consensus        19 ~~~v~i~G~~G~GKT~l~~~i~~~~~-~~~~~v~~~~~   55 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLARAIANELF-RPGAPFLYLNA   55 (151)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhh-cCCCCeEEEeh
Confidence            67899999999999966532222222 23555555543

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.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.79  E-value=0.039  Score=61.38  Aligned_cols=39  Identities=18%  Similarity=0.125  Sum_probs=23.7

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcC-CcEEEEeCCC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFG-IPATFLNSQQ  279 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~g-I~a~~l~g~~  279 (381)
                      +=+++++|||+|||-++..-...+....| -++.++..+.
T Consensus       186 ~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt  225 (767)
T PRK14723        186 GVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDS  225 (767)
T ss_pred             eEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCcc
Confidence            34678999999999887633333322334 3555555543

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=95.73  E-value=0.045  Score=60.78  Aligned_cols=107  Identities=14%  Similarity=0.161  Sum_probs=69.8

Q ss_pred             CcHHHHHHHHHHH----cCCCEEEECCCCCCch---hhHH----------------------HHHHHHHhh-cCCcEEEE
Q 042872          226 FRPLQHQACKASV----AKQDCFVLLPTGGGKS---LCYQ----------------------DQIITLNLK-FGIPATFL  275 (381)
Q Consensus       226 fRpiQ~eAI~aiL----~GrDvLviaPTGsGKT---LaF~----------------------dQv~~L~~~-~gI~a~~l  275 (381)
                      +.++|.--|+-+.    .+-+.|+.=.-|-|||   ++|+                      ..++.+.+. -.+++...
T Consensus       400 LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQvIaFlayLkq~g~~gpHLVVvPsSTleNWlrEf~kwCPsl~Ve~Y  479 (941)
T KOG0389|consen  400 LKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQVIAFLAYLKQIGNPGPHLVVVPSSTLENWLREFAKWCPSLKVEPY  479 (941)
T ss_pred             ccchhhhhHHHHHHHHHccccceehhhccCcchhHHHHHHHHHHHcCCCCCcEEEecchhHHHHHHHHHHhCCceEEEec
Confidence            5588988887654    3446677788999999   3444                      333444321 13445555


Q ss_pred             eCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcccccc
Q 042872          276 NSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVL  355 (381)
Q Consensus       276 ~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~  355 (381)
                      +|.+  .+++.+-..+.                       +....++||++|--.+.+++.=+..|++.           
T Consensus       480 yGSq--~ER~~lR~~i~-----------------------~~~~~ydVllTTY~la~~~kdDRsflk~~-----------  523 (941)
T KOG0389|consen  480 YGSQ--DERRELRERIK-----------------------KNKDDYDVLLTTYNLAASSKDDRSFLKNQ-----------  523 (941)
T ss_pred             cCcH--HHHHHHHHHHh-----------------------ccCCCccEEEEEeecccCChHHHHHHHhc-----------
Confidence            5543  44444433333                       33448999999999988777666666543           


Q ss_pred             ccccccccccccCCccEEEEeccccC
Q 042872          356 TTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       356 ~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                   ++.++|.||+|.+
T Consensus       524 -------------~~n~viyDEgHmL  536 (941)
T KOG0389|consen  524 -------------KFNYVIYDEGHML  536 (941)
T ss_pred             -------------cccEEEecchhhh
Confidence                         7999999999974

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=95.73  E-value=0.056  Score=49.45  Aligned_cols=37  Identities=16%  Similarity=0.197  Sum_probs=23.9

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      .++++++.+|||.|||-...--...+. ..|.++.++.
T Consensus        46 ~~~~l~l~G~~G~GKThLa~ai~~~~~-~~g~~v~f~~   82 (178)
T PF01695_consen   46 NGENLILYGPPGTGKTHLAVAIANEAI-RKGYSVLFIT   82 (178)
T ss_dssp             C--EEEEEESTTSSHHHHHHHHHHHHH-HTT--EEEEE
T ss_pred             cCeEEEEEhhHhHHHHHHHHHHHHHhc-cCCcceeEee
Confidence            478999999999999966543344444 3678887765

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.

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=95.63  E-value=0.051  Score=60.76  Aligned_cols=117  Identities=20%  Similarity=0.229  Sum_probs=77.4

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITLN  265 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L~  265 (381)
                      +..+....+|...|. +|.-.-  +.-..--++-|.||=||||+..                           .+...|-
T Consensus        69 ~REa~~Rvlg~~~~d-VQliG~--i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~gkgVhvVTvNdYLA~RDae~m~~l~  145 (822)
T COG0653          69 VREASKRVLGMRHFD-VQLLGG--IVLHLGDIAEMRTGEGKTLVATLPAYLNALAGKGVHVVTVNDYLARRDAEWMGPLY  145 (822)
T ss_pred             hhHHHHHhcCCChhh-HHHhhh--hhhcCCceeeeecCCchHHHHHHHHHHHhcCCCCcEEeeehHHhhhhCHHHHHHHH
Confidence            445566678886554 555444  3334456889999999998865                           5666666


Q ss_pred             hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHH
Q 042872          266 LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLH  345 (381)
Q Consensus       266 ~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~  345 (381)
                      ..+|+.+.+...+++..++....                               .++|.|.|--.|-- ..++..+.   
T Consensus       146 ~~LGlsvG~~~~~m~~~ek~~aY-------------------------------~~DItY~TnnElGF-DYLRDNm~---  190 (822)
T COG0653         146 EFLGLSVGVILAGMSPEEKRAAY-------------------------------ACDITYGTNNELGF-DYLRDNMV---  190 (822)
T ss_pred             HHcCCceeeccCCCChHHHHHHH-------------------------------hcCceeccccccCc-chhhhhhh---
Confidence            67788888888887777765555                               46899999777641 22221111   


Q ss_pred             hcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          346 RKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       346 ~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                    ......+|+.+.|-||||++-|
T Consensus       191 --------------~~~ee~vqr~~~faIvDEvDSI  212 (822)
T COG0653         191 --------------TSQEEKVQRGLNFAIVDEVDSI  212 (822)
T ss_pred             --------------ccHHHhhhccCCeEEEcchhhe
Confidence                          1123456778999999998754

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.50  E-value=0.082  Score=54.51  Aligned_cols=41  Identities=15%  Similarity=0.198  Sum_probs=26.2

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHh---hcCCcEEEEeCCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNL---KFGIPATFLNSQQT  280 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~---~~gI~a~~l~g~~~  280 (381)
                      ++-+++++|||+|||-+...-...+..   ..|.++.+++.+.-
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~  217 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNY  217 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCc
Confidence            356889999999999776533333331   13556766766653

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=95.46  E-value=0.099  Score=54.69  Aligned_cols=38  Identities=11%  Similarity=0.116  Sum_probs=24.5

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCC
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQT  280 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~  280 (381)
                      =+++++|+|+|||-+-..-...+. ..|.++.++..+.-
T Consensus       102 vi~lvG~~GvGKTTtaaKLA~~l~-~~G~kV~lV~~D~~  139 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLAYYYQ-RKGFKPCLVCADTF  139 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH-HCCCCEEEEcCccc
Confidence            367889999999966543333343 34667777666543

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.

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=95.42  E-value=0.035  Score=61.87  Aligned_cols=24  Identities=21%  Similarity=0.200  Sum_probs=17.0

Q ss_pred             HHHHHHHcCCCEEEECCCCCCchh
Q 042872          232 QACKASVAKQDCFVLLPTGGGKSL  255 (381)
Q Consensus       232 eAI~aiL~GrDvLviaPTGsGKTL  255 (381)
                      +.+.+|-.+-=||+++.||||||-
T Consensus       263 ~IMEaIn~n~vvIIcGeTGsGKTT  286 (1172)
T KOG0926|consen  263 RIMEAINENPVVIICGETGSGKTT  286 (1172)
T ss_pred             HHHHHhhcCCeEEEecCCCCCccc
Confidence            344555444456888999999994

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=95.42  E-value=0.18  Score=44.61  Aligned_cols=45  Identities=11%  Similarity=0.090  Sum_probs=30.0

Q ss_pred             EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          243 CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       243 vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      +++.+|+|+|||..-+.-+.... +.|-++..+....+.++....+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~-~~g~~v~~~s~e~~~~~~~~~~   46 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGL-ARGEPGLYVTLEESPEELIENA   46 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH-HCCCcEEEEECCCCHHHHHHHH
Confidence            68899999999976542233332 4688888887776665543333

A related protein is found in archaea.

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

Probab=95.39  E-value=0.045  Score=49.02  Aligned_cols=66  Identities=17%  Similarity=0.299  Sum_probs=40.5

Q ss_pred             CcHHHHHHHHHHHcCCC-EEEECCCCCCchhhHHHHHHHH-------HhhcCCcEEEEeCCCCHHHHHHHHHHHHh
Q 042872          226 FRPLQHQACKASVAKQD-CFVLLPTGGGKSLCYQDQIITL-------NLKFGIPATFLNSQQTVSQAAAVLQELRQ  293 (381)
Q Consensus       226 fRpiQ~eAI~aiL~GrD-vLviaPTGsGKTLaF~dQv~~L-------~~~~gI~a~~l~g~~~~~e~~~il~~lr~  293 (381)
                      +.+.|.+||..++.... +++.+|.|+|||-+-...+..+       ....+-+++++.  .+......++..+..
T Consensus         2 ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~--~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    2 LNESQREAIQSALSSNGITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVS--PSNAAVDNILERLKK   75 (236)
T ss_dssp             --HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEE--SSHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeec--CCchhHHHHHHHHHh
Confidence            45789999999999999 9999999999995443334444       112333443333  344455556666554

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=95.36  E-value=0.078  Score=49.86  Aligned_cols=31  Identities=13%  Similarity=0.079  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHH----cCC-CEEEECCCCCCchhhHH
Q 042872          228 PLQHQACKASV----AKQ-DCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       228 piQ~eAI~aiL----~Gr-DvLviaPTGsGKTLaF~  258 (381)
                      +.+.+++..+.    .+. -+++.+|+|+|||....
T Consensus        26 ~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        26 KGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            44555665543    233 57889999999997764

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.

>PRK10867 signal recognition particle protein; Provisional

Probab=95.34  E-value=0.12  Score=53.97  Aligned_cols=41  Identities=12%  Similarity=0.002  Sum_probs=28.0

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHH
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVS  282 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~  282 (381)
                      =+++++|+|+|||-+-..-...|....|.++.++..+.-+.
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~~D~~R~  142 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAADVYRP  142 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEEccccch
Confidence            36788999999997665444555533377777777765443

>TIGR00767 rho transcription termination factor Rho

Probab=95.34  E-value=0.056  Score=56.29  Aligned_cols=53  Identities=11%  Similarity=0.167  Sum_probs=30.8

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhh-cCCcEEEEeCCCCHHHHHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLK-FGIPATFLNSQQTVSQAAAVLQEL  291 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~-~gI~a~~l~g~~~~~e~~~il~~l  291 (381)
                      .|+-+++++|+|+|||.....-...+... +.+.++++..+....+...+++.+
T Consensus       167 ~Gq~~~IvG~~g~GKTtL~~~i~~~I~~nhfdv~v~VlLIgER~~EVtDLqrsI  220 (415)
T TIGR00767       167 KGQRGLIVAPPKAGKTVLLQKIAQAITRNHPEVELIVLLIDERPEEVTDMQRSV  220 (415)
T ss_pred             CCCEEEEECCCCCChhHHHHHHHHhhcccCCceEEEEEEcCCCCccHHHHHHHh
Confidence            68899999999999997654222333222 344444444443333444445444

Members of this family differ in the specificity of RNA binding.

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=95.31  E-value=0.051  Score=53.59  Aligned_cols=18  Identities=28%  Similarity=0.468  Sum_probs=15.6

Q ss_pred             CCEEEECCCCCCchhhHH
Q 042872          241 QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~  258 (381)
                      ..+++.+|+|+|||.+..
T Consensus        41 ~~i~I~G~~GtGKT~l~~   58 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVTK   58 (365)
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            579999999999997764

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.

>TIGR00959 ffh signal recognition particle protein

Probab=95.27  E-value=0.13  Score=53.65  Aligned_cols=40  Identities=15%  Similarity=0.087  Sum_probs=27.1

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCH
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTV  281 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~  281 (381)
                      -+++++|+|+|||-+-..-...+....|.++.++..+.-+
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~~D~~R  140 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDLYR  140 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEeccccc
Confidence            3688899999999776544444432356777777766543

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=95.24  E-value=0.075  Score=53.08  Aligned_cols=38  Identities=18%  Similarity=0.281  Sum_probs=25.3

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhc-CCcEEEEeCC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKF-GIPATFLNSQ  278 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~-gI~a~~l~g~  278 (381)
                      ..+++.+|+|+|||.+...-+..+.... ++..+.++..
T Consensus        56 ~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~   94 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQ   94 (394)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECC
Confidence            5799999999999987643334443222 4666666654

>PRK14974 cell division protein FtsY; Provisional

Probab=95.22  E-value=0.15  Score=51.65  Aligned_cols=39  Identities=15%  Similarity=0.101  Sum_probs=26.3

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCH
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTV  281 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~  281 (381)
                      =+++++|+|+|||-+-..-...|. ..|.+++++.+++-+
T Consensus       142 vi~~~G~~GvGKTTtiakLA~~l~-~~g~~V~li~~Dt~R  180 (336)
T PRK14974        142 VIVFVGVNGTGKTTTIAKLAYYLK-KNGFSVVIAAGDTFR  180 (336)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH-HcCCeEEEecCCcCc
Confidence            367889999999976543334444 457777777766543

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.13  E-value=0.18  Score=49.32  Aligned_cols=38  Identities=16%  Similarity=0.117  Sum_probs=26.4

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      +=+++++|||+|||-+...-...+. ..|-++.++..+.
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~l~-~~g~~V~li~~D~  110 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANKLK-KQGKSVLLAAGDT  110 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHH-hcCCEEEEEeCCC
Confidence            4467789999999977654444454 4567777777664

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.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.08  E-value=0.088  Score=55.07  Aligned_cols=39  Identities=18%  Similarity=0.251  Sum_probs=25.2

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQT  280 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~  280 (381)
                      +.+++++|||+|||-....-...+. ..|.++.++..+.-
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~-~~GkkVglI~aDt~  280 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFH-GKKKTVGFITTDHS  280 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHH-HcCCcEEEEecCCc
Confidence            5678999999999977653333333 34556666655543

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=95.04  E-value=0.76  Score=52.64  Aligned_cols=53  Identities=13%  Similarity=0.081  Sum_probs=31.5

Q ss_pred             CcHHHHHHHHHHHc----C---CCE-EEECCCCCCchhhHHHHHHHHHh---hcC---CcEEEEeCC
Q 042872          226 FRPLQHQACKASVA----K---QDC-FVLLPTGGGKSLCYQDQIITLNL---KFG---IPATFLNSQ  278 (381)
Q Consensus       226 fRpiQ~eAI~aiL~----G---rDv-LviaPTGsGKTLaF~dQv~~L~~---~~g---I~a~~l~g~  278 (381)
                      .|.-|.+.|..+|.    |   ..+ ++.++||+|||++--.-+..|..   ..+   +.++.+++.
T Consensus       759 hREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm  825 (1164)
T PTZ00112        759 CREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGM  825 (1164)
T ss_pred             ChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCC
Confidence            35667777666552    2   245 59999999999886522333321   222   445666653

>PRK06526 transposase; Provisional

Probab=95.03  E-value=0.048  Score=52.81  Aligned_cols=35  Identities=26%  Similarity=0.265  Sum_probs=22.9

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEE
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATF  274 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~  274 (381)
                      .++++++++|+|+|||-...--...+. ..|.++.+
T Consensus        97 ~~~nlll~Gp~GtGKThLa~al~~~a~-~~g~~v~f  131 (254)
T PRK06526         97 GKENVVFLGPPGTGKTHLAIGLGIRAC-QAGHRVLF  131 (254)
T ss_pred             cCceEEEEeCCCCchHHHHHHHHHHHH-HCCCchhh
Confidence            567999999999999966542223333 24555544

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=95.03  E-value=0.21  Score=50.00  Aligned_cols=39  Identities=13%  Similarity=0.034  Sum_probs=25.4

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      ++=+++++|+|+|||-+...-...+. ..|-++.++..+.
T Consensus       114 ~~vi~lvGpnGsGKTTt~~kLA~~l~-~~g~~V~Li~~D~  152 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIGKLAHKYK-AQGKKVLLAAGDT  152 (318)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHH-hcCCeEEEEecCc
Confidence            44567889999999977653333343 3466666666554

>PRK08727 hypothetical protein; Validated

Probab=95.03  E-value=0.06  Score=50.97  Aligned_cols=15  Identities=27%  Similarity=0.341  Sum_probs=12.9

Q ss_pred             CEEEECCCCCCchhh
Q 042872          242 DCFVLLPTGGGKSLC  256 (381)
Q Consensus       242 DvLviaPTGsGKTLa  256 (381)
                      -+++.+|+|+|||-.
T Consensus        43 ~l~l~G~~G~GKThL   57 (233)
T PRK08727         43 WLYLSGPAGTGKTHL   57 (233)
T ss_pred             eEEEECCCCCCHHHH
Confidence            489999999999944

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=95.02  E-value=0.17  Score=53.00  Aligned_cols=39  Identities=15%  Similarity=0.191  Sum_probs=26.5

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQT  280 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~  280 (381)
                      .-++++++||+|||.+-..-...|. ..|.++.++..+.-
T Consensus        96 ~vI~lvG~~GsGKTTtaakLA~~L~-~~g~kV~lV~~D~~  134 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTAAKLARYFK-KKGLKVGLVAADTY  134 (437)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHH-HcCCeEEEecCCCC
Confidence            3578899999999977654444454 35667776665543

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=94.96  E-value=0.057  Score=43.14  Aligned_cols=19  Identities=21%  Similarity=0.380  Sum_probs=16.2

Q ss_pred             CCCEEEECCCCCCchhhHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~  258 (381)
                      ++.+++.+|+|+|||..-.
T Consensus         2 ~~~~~l~G~~G~GKTtl~~   20 (148)
T smart00382        2 GEVILIVGPPGSGKTTLAR   20 (148)
T ss_pred             CCEEEEECCCCCcHHHHHH
Confidence            5678999999999997764

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.

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=94.88  E-value=0.057  Score=44.48  Aligned_cols=32  Identities=22%  Similarity=0.315  Sum_probs=23.3

Q ss_pred             EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          243 CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       243 vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      +++.+|.|+|||...    ..+...++.+.+.+.+.
T Consensus         1 ill~G~~G~GKT~l~----~~la~~l~~~~~~i~~~   32 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLA----RALAQYLGFPFIEIDGS   32 (132)
T ss_dssp             EEEESSTTSSHHHHH----HHHHHHTTSEEEEEETT
T ss_pred             CEEECcCCCCeeHHH----HHHHhhccccccccccc
Confidence            588999999999764    44555567777666654

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 ....

>PRK04296 thymidine kinase; Provisional

Probab=94.72  E-value=0.13  Score=47.31  Aligned_cols=34  Identities=15%  Similarity=0.200  Sum_probs=24.9

Q ss_pred             EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          243 CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       243 vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      +++.+|.|+|||......+.++. ..|.++.++.+
T Consensus         5 ~litG~~GsGKTT~~l~~~~~~~-~~g~~v~i~k~   38 (190)
T PRK04296          5 EFIYGAMNSGKSTELLQRAYNYE-ERGMKVLVFKP   38 (190)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHH-HcCCeEEEEec
Confidence            57889999999977665565554 35777777755

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=94.72  E-value=0.29  Score=53.37  Aligned_cols=42  Identities=17%  Similarity=0.147  Sum_probs=33.3

Q ss_pred             HHHHhCCCC-CcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          217 NVVIFGNRA-FRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       217 ~~~~fG~~~-fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +...|+... ..+.|++|+-..+..+-+++.++.|+|||-+-.
T Consensus       143 l~~lf~~~~~~~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~  185 (615)
T PRK10875        143 LDALFGPVTDEVDWQKVAAAVALTRRISVISGGPGTGKTTTVA  185 (615)
T ss_pred             HHHhcCcCCCCCHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHH
Confidence            334465542 358999999999999999999999999997653

>PRK08181 transposase; Validated

Probab=94.71  E-value=0.18  Score=49.50  Aligned_cols=48  Identities=25%  Similarity=0.220  Sum_probs=28.3

Q ss_pred             HHHHHHHHH----HHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          228 PLQHQACKA----SVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       228 piQ~eAI~a----iL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      +.|..++..    +-.++++++.+|+|+|||-...--...+. ..|.++.++.
T Consensus        90 ~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~Aia~~a~-~~g~~v~f~~  141 (269)
T PRK08181         90 KAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAAAIGLALI-ENGWRVLFTR  141 (269)
T ss_pred             HHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHHHHHHHHH-HcCCceeeee
Confidence            445544432    23578999999999999943321122223 3466666554

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=94.69  E-value=0.13  Score=52.54  Aligned_cols=26  Identities=23%  Similarity=0.289  Sum_probs=19.4

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHh
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNL  266 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~  266 (381)
                      .++++.+|||+|||++-..-+.++..
T Consensus        43 ~n~~iyG~~GTGKT~~~~~v~~~l~~   68 (366)
T COG1474          43 SNIIIYGPTGTGKTATVKFVMEELEE   68 (366)
T ss_pred             ccEEEECCCCCCHhHHHHHHHHHHHh
Confidence            36999999999999987633444443

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=94.65  E-value=0.2  Score=47.48  Aligned_cols=52  Identities=17%  Similarity=0.191  Sum_probs=33.9

Q ss_pred             HHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          237 SVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       237 iL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      +..|.-+++.+|||+|||..-......+....|-+++++.-..+..+....+
T Consensus        27 ~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS~E~~~~~~~~r~   78 (271)
T cd01122          27 LRKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLEEPVVRTARRL   78 (271)
T ss_pred             EcCCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEEcccCHHHHHHHH
Confidence            3456778999999999996543223333333478888887777665544333

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=94.64  E-value=0.28  Score=49.97  Aligned_cols=79  Identities=14%  Similarity=0.244  Sum_probs=48.2

Q ss_pred             EEEECCCCCCchhhHH--------------------------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchh
Q 042872          243 CFVLLPTGGGKSLCYQ--------------------------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLV  296 (381)
Q Consensus       243 vLviaPTGsGKTLaF~--------------------------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~  296 (381)
                      +|+++-.|+|||-+..                          +|+..+.++.|++++.-..+.+..  .-+.+++..   
T Consensus       142 il~vGVNG~GKTTTIaKLA~~l~~~g~~VllaA~DTFRAaAiEQL~~w~er~gv~vI~~~~G~DpA--aVafDAi~~---  216 (340)
T COG0552         142 ILFVGVNGVGKTTTIAKLAKYLKQQGKSVLLAAGDTFRAAAIEQLEVWGERLGVPVISGKEGADPA--AVAFDAIQA---  216 (340)
T ss_pred             EEEEecCCCchHhHHHHHHHHHHHCCCeEEEEecchHHHHHHHHHHHHHHHhCCeEEccCCCCCcH--HHHHHHHHH---
Confidence            5788999999995543                          666666666666655432222221  122222221   


Q ss_pred             hhhhhhhhhhhhhhhhcccCCCCCccEEEE-CccccccCcchHHHHHHHH
Q 042872          297 LSQHYFLHQLIFVLTCASRKDKPSCKLLYV-TPERIVGNQSFSEVLKCLH  345 (381)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~IL~a-TPErL~~~~~f~~~L~~L~  345 (381)
                                         ....++++|++ |-|||.+...+.+-|.+..
T Consensus       217 -------------------Akar~~DvvliDTAGRLhnk~nLM~EL~KI~  247 (340)
T COG0552         217 -------------------AKARGIDVVLIDTAGRLHNKKNLMDELKKIV  247 (340)
T ss_pred             -------------------HHHcCCCEEEEeCcccccCchhHHHHHHHHH
Confidence                               11225788877 9999998777777776654

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=94.62  E-value=0.3  Score=45.35  Aligned_cols=50  Identities=16%  Similarity=0.123  Sum_probs=34.7

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      .|+=+++.++||+|||..-+.-+..+....|.+++.+....+..+....+
T Consensus        12 ~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~E~~~~~~~~r~   61 (242)
T cd00984          12 PGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEMSKEQLLQRL   61 (242)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeCCCCHHHHHHHH
Confidence            45567889999999995543334444434488999999888877655444

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.

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=94.60  E-value=0.22  Score=48.28  Aligned_cols=50  Identities=22%  Similarity=0.226  Sum_probs=34.7

Q ss_pred             cHHHHHHHHHHH-------cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          227 RPLQHQACKASV-------AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       227 RpiQ~eAI~aiL-------~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ...+..++..+.       .++++++.+|+|.|||-...-....+. +.|+++.+++-
T Consensus        85 ~~~~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g~sv~f~~~  141 (254)
T COG1484          85 PGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLAIAIGNELL-KAGISVLFITA  141 (254)
T ss_pred             cchhHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHHHHHHHHHH-HcCCeEEEEEH
Confidence            344555444443       577999999999999966554455566 56888888763

>PRK07952 DNA replication protein DnaC; Validated

Probab=94.56  E-value=0.22  Score=48.17  Aligned_cols=48  Identities=15%  Similarity=-0.004  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHc-------C-CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          228 PLQHQACKASVA-------K-QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       228 piQ~eAI~aiL~-------G-rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      +.|..|+..+..       + ..+++.+++|+|||-...--...+. ..|.++.++.
T Consensus        79 ~~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~-~~g~~v~~it  134 (244)
T PRK07952         79 EGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELL-LRGKSVLIIT  134 (244)
T ss_pred             chHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHH-hcCCeEEEEE
Confidence            446556555442       1 4689999999999965543334444 3467776663

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=94.55  E-value=0.16  Score=54.45  Aligned_cols=31  Identities=16%  Similarity=0.214  Sum_probs=19.5

Q ss_pred             cHHHHHHHHHHHcCCC-----EEEECCCCCCchhhH
Q 042872          227 RPLQHQACKASVAKQD-----CFVLLPTGGGKSLCY  257 (381)
Q Consensus       227 RpiQ~eAI~aiL~GrD-----vLviaPTGsGKTLaF  257 (381)
                      -|+|.|-+.-+-...+     .++.-.-|-|||+--
T Consensus       186 L~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQt  221 (791)
T KOG1002|consen  186 LPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQT  221 (791)
T ss_pred             hhhhHHHHHHHHHhhhhhhccceehhhhccchHHHH
Confidence            4788888765544333     344456789998644

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=94.39  E-value=0.18  Score=55.72  Aligned_cols=26  Identities=23%  Similarity=0.189  Sum_probs=17.8

Q ss_pred             HHHHHHHHcCCCEEEECCCCCCchhh
Q 042872          231 HQACKASVAKQDCFVLLPTGGGKSLC  256 (381)
Q Consensus       231 ~eAI~aiL~GrDvLviaPTGsGKTLa  256 (381)
                      .+-+..+-.++=|++++.||||||--
T Consensus       362 ~~ll~~ir~n~vvvivgETGSGKTTQ  387 (1042)
T KOG0924|consen  362 DQLLSVIRENQVVVIVGETGSGKTTQ  387 (1042)
T ss_pred             HHHHHHHhhCcEEEEEecCCCCchhh
Confidence            33344444566678889999999943

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=94.26  E-value=0.15  Score=57.77  Aligned_cols=28  Identities=21%  Similarity=0.179  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHcCCCEEEECCCCCCchh
Q 042872          228 PLQHQACKASVAKQDCFVLLPTGGGKSL  255 (381)
Q Consensus       228 piQ~eAI~aiL~GrDvLviaPTGsGKTL  255 (381)
                      ..+.+.|.++.+..-+++.+.||+|||-
T Consensus       176 ~~r~~Il~~i~~~qVvvIsGeTGcGKTT  203 (924)
T KOG0920|consen  176 KMRDTILDAIEENQVVVISGETGCGKTT  203 (924)
T ss_pred             HHHHHHHHHHHhCceEEEeCCCCCCchh
Confidence            4577777777777788888999999994

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.10  E-value=0.28  Score=50.99  Aligned_cols=40  Identities=15%  Similarity=0.078  Sum_probs=26.8

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHH-hhcCCcEEEEeCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLN-LKFGIPATFLNSQQ  279 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~-~~~gI~a~~l~g~~  279 (381)
                      |+-+++++|||+|||-+-..-...+. ...|.++.++..+.
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~  261 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDT  261 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCc
Confidence            56788999999999966543333333 23466777777664

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=94.06  E-value=0.11  Score=59.13  Aligned_cols=106  Identities=17%  Similarity=0.227  Sum_probs=65.4

Q ss_pred             CCCCCcHHHHHHHHHHHc--CC--CEEEECCCCCCchhh------HH--------------------HHHHHHHhh-cCC
Q 042872          222 GNRAFRPLQHQACKASVA--KQ--DCFVLLPTGGGKSLC------YQ--------------------DQIITLNLK-FGI  270 (381)
Q Consensus       222 G~~~fRpiQ~eAI~aiL~--Gr--DvLviaPTGsGKTLa------F~--------------------dQv~~L~~~-~gI  270 (381)
                      .-.+++++|..-+.-..+  +.  +-|..=.+|-|||+.      |+                    .....+..+ -.|
T Consensus       391 ~GG~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQtIsLitYLmE~K~~~GP~LvivPlstL~NW~~Ef~kWaPSv  470 (1157)
T KOG0386|consen  391 QGGELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEHKQMQGPFLIIVPLSTLVNWSSEFPKWAPSV  470 (1157)
T ss_pred             cCCCCchhhhhhhHHHhhccCCCcccccchhcccchHHHHHHHHHHHHHHcccCCCeEEeccccccCCchhhccccccce
Confidence            334788888887766542  33  455666899999953      43                    111111100 123


Q ss_pred             cEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCc
Q 042872          271 PATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSI  350 (381)
Q Consensus       271 ~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~  350 (381)
                      ..+...|  +.++|......++.|                         +++||++|-|-+...+.+   |...      
T Consensus       471 ~~i~YkG--tp~~R~~l~~qir~g-------------------------KFnVLlTtyEyiikdk~l---LsKI------  514 (1157)
T KOG0386|consen  471 QKIQYKG--TPQQRSGLTKQQRHG-------------------------KFNVLLTTYEYIIKDKAL---LSKI------  514 (1157)
T ss_pred             eeeeeeC--CHHHHhhHHHHHhcc-------------------------cceeeeeeHHHhcCCHHH---Hhcc------
Confidence            3333333  466666677777655                         799999999999865444   3322      


Q ss_pred             cccccccccccccccccCCccEEEEeccccC
Q 042872          351 RLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       351 ~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                        +-.++||||.|.|
T Consensus       515 ------------------~W~yMIIDEGHRm  527 (1157)
T KOG0386|consen  515 ------------------SWKYMIIDEGHRM  527 (1157)
T ss_pred             ------------------CCcceeecccccc
Confidence                              5678999999986

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=93.97  E-value=0.16  Score=56.36  Aligned_cols=51  Identities=16%  Similarity=0.016  Sum_probs=36.0

Q ss_pred             CCcHHHHHHHHHHHcC-CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          225 AFRPLQHQACKASVAK-QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~G-rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      .+++-|++|+..++.+ +=+++.++.|+|||-.. ..+...-...|.++..+.
T Consensus       352 ~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll-~~i~~~~~~~g~~V~~~A  403 (744)
T TIGR02768       352 RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWEAAGYRVIGAA  403 (744)
T ss_pred             CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHHhCCCeEEEEe
Confidence            5789999999999885 45688899999999665 333322224566665553

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.

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=93.86  E-value=0.25  Score=56.56  Aligned_cols=50  Identities=18%  Similarity=-0.001  Sum_probs=36.6

Q ss_pred             CCcHHHHHHHHHHHcCCC-EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEE
Q 042872          225 AFRPLQHQACKASVAKQD-CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFL  275 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrD-vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l  275 (381)
                      .+++-|++||..++.+++ +++.++.|+|||-+- ..+..+-...|.+++.+
T Consensus       346 ~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~l-~~~~~~~e~~G~~V~~~  396 (988)
T PRK13889        346 VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAML-GVAREAWEAAGYEVRGA  396 (988)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHHH-HHHHHHHHHcCCeEEEe
Confidence            589999999999999876 578899999999763 33333333456665544

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=93.81  E-value=0.12  Score=47.42  Aligned_cols=36  Identities=22%  Similarity=0.260  Sum_probs=22.7

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      ++.+++.+|+|+|||....--...+. ..+.+++.+.
T Consensus        38 ~~~lll~G~~G~GKT~la~~~~~~~~-~~~~~~~~i~   73 (226)
T TIGR03420        38 DRFLYLWGESGSGKSHLLQAACAAAE-ERGKSAIYLP   73 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHH-hcCCcEEEEe
Confidence            46899999999999966532222222 2355555554

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=93.64  E-value=0.26  Score=48.23  Aligned_cols=40  Identities=18%  Similarity=0.233  Sum_probs=26.8

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcC-CcEEEEeCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFG-IPATFLNSQQ  279 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~g-I~a~~l~g~~  279 (381)
                      ++-+++++|||+|||-+...-...+....| .++.++..+.
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~  234 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDT  234 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCc
Confidence            456788999999999776533444443323 6777777664

>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=93.59  E-value=0.46  Score=45.97  Aligned_cols=34  Identities=21%  Similarity=0.389  Sum_probs=30.1

Q ss_pred             CCcHHHHHHHHHHHc---CCCEEEECCCCCCchhhHH
Q 042872          225 AFRPLQHQACKASVA---KQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~---GrDvLviaPTGsGKTLaF~  258 (381)
                      -.||.|.+......+   |++.+..+-.|.|||-+-.
T Consensus        23 liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI~   59 (229)
T PF12340_consen   23 LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVIV   59 (229)
T ss_pred             eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccchHH
Confidence            689999999999985   6899999999999996655

There are two conserved sequence motifs: LLE and NMG.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=93.25  E-value=0.7  Score=42.10  Aligned_cols=40  Identities=13%  Similarity=0.192  Sum_probs=27.1

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      .|+=+++.+|+|+|||..-+.-..... ..|-+++.+....
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~-~~g~~v~yi~~e~   50 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAA-RQGKKVVYIDTEG   50 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH-hCCCeEEEEECCC
Confidence            355678999999999976543233333 3577888887653

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=93.04  E-value=0.44  Score=49.67  Aligned_cols=51  Identities=27%  Similarity=0.385  Sum_probs=38.2

Q ss_pred             cCCCEEEECCCCCCchhhHH----------------------------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQ----------------------------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQE  290 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~----------------------------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~  290 (381)
                      .++-+.+++|||-|||-+-+                            +|+..++..+|++..++...   .+-...+..
T Consensus       202 ~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~vv~~~---~el~~ai~~  278 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLEVVYSP---KELAEAIEA  278 (407)
T ss_pred             cCcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHHHHHHHhCCceEEecCH---HHHHHHHHH
Confidence            37788999999999995533                            89999998899999888754   344444555


Q ss_pred             HH
Q 042872          291 LR  292 (381)
Q Consensus       291 lr  292 (381)
                      ++
T Consensus       279 l~  280 (407)
T COG1419         279 LR  280 (407)
T ss_pred             hh
Confidence            44

>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=92.96  E-value=0.24  Score=46.93  Aligned_cols=34  Identities=24%  Similarity=0.142  Sum_probs=26.4

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      ..++.|..++.+++...-+++.+|.|+|||+...
T Consensus         4 p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~   37 (205)
T PF02562_consen    4 PKNEEQKFALDALLNNDLVIVNGPAGTGKTFLAL   37 (205)
T ss_dssp             --SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHH
T ss_pred             CCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHH
Confidence            4568899999999987888999999999998876

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PRK08084 DNA replication initiation factor; Provisional

Probab=92.93  E-value=0.26  Score=46.69  Aligned_cols=36  Identities=14%  Similarity=0.232  Sum_probs=21.0

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      +..+++.+|+|+|||-..+-....+. ..|.++..+.
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a~~~~~~-~~~~~v~y~~   80 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHAACAELS-QRGRAVGYVP   80 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHH-hCCCeEEEEE
Confidence            35789999999999944321122222 2355555543

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=92.90  E-value=0.66  Score=50.33  Aligned_cols=31  Identities=16%  Similarity=0.126  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          228 PLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       228 piQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +.|++|+..++.++=+++.++.|+|||-+-.
T Consensus       148 ~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~  178 (586)
T TIGR01447       148 NWQKVAVALALKSNFSLITGGPGTGKTTTVA  178 (586)
T ss_pred             HHHHHHHHHHhhCCeEEEEcCCCCCHHHHHH
Confidence            7899999999999999999999999997754

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.

>PRK12377 putative replication protein; Provisional

Probab=92.81  E-value=0.75  Score=44.63  Aligned_cols=35  Identities=14%  Similarity=-0.006  Sum_probs=22.9

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      ..+++.+|+|+|||-...--...+. ..|.++.+++
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~l~-~~g~~v~~i~  136 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNRLL-AKGRSVIVVT  136 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHH-HcCCCeEEEE
Confidence            5789999999999944332233444 3467776654

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=92.79  E-value=1.2  Score=47.74  Aligned_cols=32  Identities=25%  Similarity=0.364  Sum_probs=25.4

Q ss_pred             CcHHHHHHHHHHHcCCC--EEEECCCCCCchhhH
Q 042872          226 FRPLQHQACKASVAKQD--CFVLLPTGGGKSLCY  257 (381)
Q Consensus       226 fRpiQ~eAI~aiL~GrD--vLviaPTGsGKTLaF  257 (381)
                      +.+.|.+.+..++....  +||.+|||||||.+-
T Consensus       242 ~~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTTL  275 (500)
T COG2804         242 MSPFQLARLLRLLNRPQGLILVTGPTGSGKTTTL  275 (500)
T ss_pred             CCHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHH
Confidence            34778889988887654  678899999999664

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=92.78  E-value=0.26  Score=49.78  Aligned_cols=32  Identities=25%  Similarity=0.316  Sum_probs=27.3

Q ss_pred             CcHHHHHHHHHH------HcCCCEEEECCCCCCchhhH
Q 042872          226 FRPLQHQACKAS------VAKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       226 fRpiQ~eAI~ai------L~GrDvLviaPTGsGKTLaF  257 (381)
                      +.+-|++++..+      ..+..+++.+|-|+|||..+
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~   39 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLI   39 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHH
Confidence            456788888777      57889999999999999887

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=92.63  E-value=0.1  Score=53.21  Aligned_cols=33  Identities=33%  Similarity=0.560  Sum_probs=23.8

Q ss_pred             HcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEE
Q 042872          238 VAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATF  274 (381)
Q Consensus       238 L~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~  274 (381)
                      |...++|+++|||||||+..+    .|.+.++++.++
T Consensus        95 L~KSNILLiGPTGsGKTlLAq----TLAk~LnVPFai  127 (408)
T COG1219          95 LSKSNILLIGPTGSGKTLLAQ----TLAKILNVPFAI  127 (408)
T ss_pred             eeeccEEEECCCCCcHHHHHH----HHHHHhCCCeee
Confidence            455699999999999999875    344445565443

>PRK06921 hypothetical protein; Provisional

Probab=92.59  E-value=1.1  Score=43.61  Aligned_cols=37  Identities=24%  Similarity=0.315  Sum_probs=23.4

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      +..+++.+|||+|||-...--...+....|..++.+.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~  153 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFP  153 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEE
Confidence            5689999999999994432223333322266666654

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=92.48  E-value=0.63  Score=48.63  Aligned_cols=20  Identities=25%  Similarity=0.218  Sum_probs=16.0

Q ss_pred             cCCCEEEECCCCCCchhhHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~  258 (381)
                      .|+-+.+++|||+|||-+..
T Consensus       190 ~g~vi~lvGpnG~GKTTtla  209 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTA  209 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            35568889999999997664

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.46  E-value=0.61  Score=50.40  Aligned_cols=39  Identities=13%  Similarity=0.149  Sum_probs=24.2

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhc-CCcEEEEeCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKF-GIPATFLNSQ  278 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~-gI~a~~l~g~  278 (381)
                      |+-+.+++|||+|||-+...-...+.... +.++.++..+
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtD  389 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTD  389 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecc
Confidence            56778889999999977643333333222 3456555544

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=92.29  E-value=0.4  Score=50.95  Aligned_cols=40  Identities=18%  Similarity=0.216  Sum_probs=25.8

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcC-CcEEEEeCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFG-IPATFLNSQQ  279 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~g-I~a~~l~g~~  279 (381)
                      |+=+++++|||+|||-+...-...+....| .++.++..+.
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt  296 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDS  296 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCc
Confidence            344778899999999887644434433344 4666666554

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=92.21  E-value=0.58  Score=45.15  Aligned_cols=17  Identities=24%  Similarity=0.303  Sum_probs=14.5

Q ss_pred             CCEEEECCCCCCchhhH
Q 042872          241 QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF  257 (381)
                      ..+++.+|.|+|||...
T Consensus        31 ~~~ll~Gp~G~GKT~la   47 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLA   47 (305)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            46899999999999664

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=92.16  E-value=0.51  Score=43.71  Aligned_cols=50  Identities=12%  Similarity=0.151  Sum_probs=29.6

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      .|.-+++.+|+|+|||.--+.-+.+-....|-+++.+.-..+.++..+.+
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~ee~~~~l~~~~   67 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFEEPPEELIENM   67 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESSS-HHHHHHHH
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEecCCHHHHHHHH
Confidence            46788999999999996543222222212388898888776665543333

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 ....

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=92.16  E-value=1.4  Score=41.27  Aligned_cols=49  Identities=16%  Similarity=0.087  Sum_probs=31.0

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      .|.=+++.+++|+|||.-....+.... ..|-++..+....+..+....+
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~~-~~g~~~~y~~~e~~~~~~~~~~   72 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGAL-KQGKKVYVITTENTSKSYLKQM   72 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHHH-hCCCEEEEEEcCCCHHHHHHHH
Confidence            356788889999999965532222222 3577888887766665543333

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=92.11  E-value=0.38  Score=46.02  Aligned_cols=17  Identities=18%  Similarity=0.100  Sum_probs=14.9

Q ss_pred             CCEEEECCCCCCchhhH
Q 042872          241 QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF  257 (381)
                      .++++.+|+|+|||...
T Consensus        43 ~~vll~GppGtGKTtlA   59 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVA   59 (261)
T ss_pred             ceEEEEcCCCCCHHHHH
Confidence            47899999999999765

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=91.96  E-value=0.31  Score=45.92  Aligned_cols=34  Identities=12%  Similarity=-0.019  Sum_probs=19.7

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      -+++.+|+|+|||-.-+--...+. ..+.++.++.
T Consensus        41 ~l~l~G~~G~GKThL~~ai~~~~~-~~~~~~~y~~   74 (229)
T PRK06893         41 FFYIWGGKSSGKSHLLKAVSNHYL-LNQRTAIYIP   74 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHH-HcCCCeEEee
Confidence            368999999999944331222233 2345555544

>TIGR00665 DnaB replicative DNA helicase

Probab=91.93  E-value=1.1  Score=45.88  Aligned_cols=49  Identities=16%  Similarity=0.158  Sum_probs=33.0

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      |.=+++.++||.|||.--+.-+.......|.++.++...++..+....+
T Consensus       195 G~l~vi~g~pg~GKT~~~l~~a~~~a~~~g~~vl~~SlEm~~~~i~~R~  243 (434)
T TIGR00665       195 SDLIILAARPSMGKTAFALNIAENAAIKEGKPVAFFSLEMSAEQLAMRM  243 (434)
T ss_pred             CeEEEEEeCCCCChHHHHHHHHHHHHHhCCCeEEEEeCcCCHHHHHHHH
Confidence            3446778999999996554334444434578888888888877654333

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=91.91  E-value=0.52  Score=46.57  Aligned_cols=18  Identities=22%  Similarity=0.327  Sum_probs=15.4

Q ss_pred             CCEEEECCCCCCchhhHH
Q 042872          241 QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~  258 (381)
                      +.+++.+|+|+|||....
T Consensus        52 ~~~ll~GppG~GKT~la~   69 (328)
T PRK00080         52 DHVLLYGPPGLGKTTLAN   69 (328)
T ss_pred             CcEEEECCCCccHHHHHH
Confidence            479999999999997753

>PRK10865 protein disaggregation chaperone; Provisional

Probab=91.82  E-value=0.43  Score=53.80  Aligned_cols=17  Identities=18%  Similarity=0.215  Sum_probs=15.2

Q ss_pred             CCEEEECCCCCCchhhH
Q 042872          241 QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF  257 (381)
                      .++++++|+|.|||..-
T Consensus       200 ~n~lL~G~pGvGKT~l~  216 (857)
T PRK10865        200 NNPVLIGEPGVGKTAIV  216 (857)
T ss_pred             CceEEECCCCCCHHHHH
Confidence            48999999999999775

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=91.74  E-value=0.76  Score=47.92  Aligned_cols=40  Identities=18%  Similarity=0.101  Sum_probs=25.4

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      .++-+++++|||+|||-+...-...+. ..|.++.++..+.
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~-~~g~~V~lItaDt  244 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLL-KQNRTVGFITTDT  244 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH-HcCCeEEEEeCCc
Confidence            366788999999999966652222232 3455666665543

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=91.69  E-value=0.8  Score=48.19  Aligned_cols=51  Identities=14%  Similarity=0.020  Sum_probs=34.9

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQE  290 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~  290 (381)
                      .|.-+++.+|+|+|||..-+.-+.... +.|-+++.+...-+.++.....+.
T Consensus       262 ~gs~~li~G~~G~GKt~l~~~f~~~~~-~~ge~~~y~s~eEs~~~i~~~~~~  312 (484)
T TIGR02655       262 KDSIILATGATGTGKTLLVSKFLENAC-ANKERAILFAYEESRAQLLRNAYS  312 (484)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHH-HCCCeEEEEEeeCCHHHHHHHHHH
Confidence            467789999999999976542233333 468888888887776665444433

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.

>cd01394 radB RadB

Probab=91.33  E-value=0.97  Score=41.53  Aligned_cols=40  Identities=15%  Similarity=0.169  Sum_probs=26.3

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQT  280 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~  280 (381)
                      |+=+++.+++|+|||..-+..+..+. ..|-+++.+.....
T Consensus        19 g~i~~i~G~~GsGKT~l~~~~a~~~~-~~g~~v~yi~~e~~   58 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQLAVETA-GQGKKVAYIDTEGL   58 (218)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH-hcCCeEEEEECCCC
Confidence            44578999999999966543333333 35778878766543

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=91.32  E-value=0.8  Score=48.10  Aligned_cols=70  Identities=14%  Similarity=0.252  Sum_probs=37.9

Q ss_pred             CCCCHHHHhhchHHHHHHHHHhC-CCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          200 GTLSFEELQALDDMEFANVVIFG-NRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       200 ~~~~fe~L~~l~~l~~~~~~~fG-~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      ...+|+.+..+++....+..... +..+..++..-   .-..+.+|+.+|+|+|||...    +.+....+++.+.+.
T Consensus        50 ~~~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g---~~~~~giLL~GppGtGKT~la----~alA~~~~~~~~~i~  120 (495)
T TIGR01241        50 PKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLG---AKIPKGVLLVGPPGTGKTLLA----KAVAGEAGVPFFSIS  120 (495)
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcC---CCCCCcEEEECCCCCCHHHHH----HHHHHHcCCCeeecc
Confidence            35667777666655444433221 11121111110   111357999999999999774    344445667665554

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>PRK06835 DNA replication protein DnaC; Validated

Probab=91.29  E-value=2  Score=43.35  Aligned_cols=37  Identities=16%  Similarity=0.161  Sum_probs=23.7

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ++.+++.+|||+|||-...--...+. ..|..++.++.
T Consensus       183 ~~~Lll~G~~GtGKThLa~aIa~~l~-~~g~~V~y~t~  219 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSNCIAKELL-DRGKSVIYRTA  219 (329)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHH-HCCCeEEEEEH
Confidence            57899999999999954321223333 34666666543

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=91.25  E-value=0.3  Score=51.40  Aligned_cols=46  Identities=22%  Similarity=0.190  Sum_probs=29.5

Q ss_pred             HHHHHHHHhCCC--CCcHHH----HHHH-HHHHcCCCEEEECCCCCCchhhHH
Q 042872          213 MEFANVVIFGNR--AFRPLQ----HQAC-KASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       213 l~~~~~~~fG~~--~fRpiQ----~eAI-~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +...+....||.  .|+.-|    ...+ +-+-.+.|++.++|+|+|||-.|.
T Consensus       175 Wid~LlrSiG~~P~~~~~r~k~~~L~rl~~fve~~~Nli~lGp~GTGKThla~  227 (449)
T TIGR02688       175 WIDVLIRSIGYEPEGFEARQKLLLLARLLPLVEPNYNLIELGPKGTGKSYIYN  227 (449)
T ss_pred             HHHHHHHhcCCCcccCChHHHHHHHHhhHHHHhcCCcEEEECCCCCCHHHHHH
Confidence            334444557886  344322    2222 444467899999999999998875

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>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=91.23  E-value=0.25  Score=46.54  Aligned_cols=49  Identities=18%  Similarity=0.223  Sum_probs=33.6

Q ss_pred             CcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCC---cEEEEe
Q 042872          226 FRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGI---PATFLN  276 (381)
Q Consensus       226 fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI---~a~~l~  276 (381)
                      +++-|.++|..  ....++|.|+.|||||.+-..-+..|-...++   ++++++
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lT   52 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLT   52 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEE
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecc
Confidence            36789999988  67899999999999999886555554433333   355554

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 ....

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=91.12  E-value=1.1  Score=46.93  Aligned_cols=64  Identities=11%  Similarity=0.151  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHH---cCCCEEEECCCCCCchhhHHHHHHHHHh-hcCCcEEEEeCCCCHHHHHHHHHHH
Q 042872          228 PLQHQACKASV---AKQDCFVLLPTGGGKSLCYQDQIITLNL-KFGIPATFLNSQQTVSQAAAVLQEL  291 (381)
Q Consensus       228 piQ~eAI~aiL---~GrDvLviaPTGsGKTLaF~dQv~~L~~-~~gI~a~~l~g~~~~~e~~~il~~l  291 (381)
                      +.=..+|..++   .|+..++++|.|.|||.....-...+.. .+.+.+.++..+...++...+.+.+
T Consensus       154 ~~~~rvID~l~PIGkGQR~lIvgppGvGKTTLaK~Ian~I~~nhFDv~~~VvLIgER~~EVtdiqrsI  221 (416)
T PRK09376        154 DLSTRIIDLIAPIGKGQRGLIVAPPKAGKTVLLQNIANSITTNHPEVHLIVLLIDERPEEVTDMQRSV  221 (416)
T ss_pred             ccceeeeeeecccccCceEEEeCCCCCChhHHHHHHHHHHHhhcCCeEEEEEEeCCchhHHHHHHHHh
Confidence            33444555443   7899999999999999655322233322 3566655444443444544555554

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=91.11  E-value=1  Score=44.38  Aligned_cols=39  Identities=18%  Similarity=0.214  Sum_probs=24.6

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      .+..+++++|+|.|||..+.--...+. ..+.++.++..+
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~l~~~l~-~~~~~v~~i~~D  112 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAKMAWQFH-GKKKTVGFITTD  112 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHH-HcCCeEEEEecC
Confidence            346788899999999988752223333 234555555544

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=90.99  E-value=1.9  Score=45.45  Aligned_cols=38  Identities=21%  Similarity=0.357  Sum_probs=25.8

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      =+++++|||+|||-+...-...+....|-++.++..+.
T Consensus       225 vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Lit~Dt  262 (432)
T PRK12724        225 VVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDN  262 (432)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEecccc
Confidence            37788999999997764333333334567777777665

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=90.95  E-value=0.96  Score=51.12  Aligned_cols=28  Identities=11%  Similarity=0.194  Sum_probs=20.3

Q ss_pred             HHHHHHHHH----c--CCCEEEECCCCCCchhhH
Q 042872          230 QHQACKASV----A--KQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       230 Q~eAI~aiL----~--GrDvLviaPTGsGKTLaF  257 (381)
                      |.+-|..++    .  ..++++++|.|.|||.+-
T Consensus       192 r~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~  225 (852)
T TIGR03345       192 RDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVV  225 (852)
T ss_pred             CHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHH
Confidence            444455544    2  258999999999999775

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.

>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]

Probab=90.80  E-value=0.44  Score=52.62  Aligned_cols=57  Identities=21%  Similarity=0.208  Sum_probs=44.6

Q ss_pred             hCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH------------------------HHHHHHHhhcCCcEEEEe
Q 042872          221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ------------------------DQIITLNLKFGIPATFLN  276 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~------------------------dQv~~L~~~~gI~a~~l~  276 (381)
                      +|+.++..-|..|+.++|...=.|+.+|.|+|||++-.                        ||+.....+.|++++-+.
T Consensus       406 ~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~~~~~VLvcApSNiAVDqLaeKIh~tgLKVvRl~  485 (935)
T KOG1802|consen  406 PNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQHAGPVLVCAPSNIAVDQLAEKIHKTGLKVVRLC  485 (935)
T ss_pred             CCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHhcCCceEEEcccchhHHHHHHHHHhcCceEeeee
Confidence            45666667899999999999889999999999996644                        665544446788887776


Q ss_pred             C
Q 042872          277 S  277 (381)
Q Consensus       277 g  277 (381)
                      +
T Consensus       486 a  486 (935)
T KOG1802|consen  486 A  486 (935)
T ss_pred             h
Confidence            4

>PRK12608 transcription termination factor Rho; Provisional

Probab=90.77  E-value=0.68  Score=47.92  Aligned_cols=63  Identities=11%  Similarity=0.202  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHH---cCCCEEEECCCCCCchhhHHHHHHHHHhhc-CCc-EEEEeCCCCHHHHHHHHHHH
Q 042872          228 PLQHQACKASV---AKQDCFVLLPTGGGKSLCYQDQIITLNLKF-GIP-ATFLNSQQTVSQAAAVLQEL  291 (381)
Q Consensus       228 piQ~eAI~aiL---~GrDvLviaPTGsGKTLaF~dQv~~L~~~~-gI~-a~~l~g~~~~~e~~~il~~l  291 (381)
                      ++-..+|..+.   .|..+++++|.|+|||..-.+-+..+.... .+. ++++.+.... +....++.+
T Consensus       118 ~~~~RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~la~~i~~~~~dv~~vv~lIgER~~-EV~df~~~i  185 (380)
T PRK12608        118 DLSMRVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPE-EVTDMRRSV  185 (380)
T ss_pred             chhHhhhhheeecCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEEecCCCC-CHHHHHHHH
Confidence            44455787776   688999999999999988755455554322 454 3445555443 334444444

>PF13245 AAA_19: Part of AAA domain

Probab=90.76  E-value=0.95  Score=36.08  Aligned_cols=45  Identities=27%  Similarity=0.308  Sum_probs=27.2

Q ss_pred             HHHHHHHcCCCEEE-ECCCCCCchhhHHHHHHHHHhh---cCCcEEEEe
Q 042872          232 QACKASVAKQDCFV-LLPTGGGKSLCYQDQIITLNLK---FGIPATFLN  276 (381)
Q Consensus       232 eAI~aiL~GrDvLv-iaPTGsGKTLaF~dQv~~L~~~---~gI~a~~l~  276 (381)
                      +||...+.+..+++ .+|.|+|||-+...-+..+...   .+-++.++.
T Consensus         1 ~av~~al~~~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a   49 (76)
T PF13245_consen    1 EAVRRALAGSPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLA   49 (76)
T ss_pred             CHHHHHHhhCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEEC
Confidence            35665555666555 9999999996665444444421   144555554

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.73  E-value=0.99  Score=48.13  Aligned_cols=15  Identities=20%  Similarity=0.138  Sum_probs=13.1

Q ss_pred             EEEECCCCCCchhhH
Q 042872          243 CFVLLPTGGGKSLCY  257 (381)
Q Consensus       243 vLviaPTGsGKTLaF  257 (381)
                      .|+.+|.|.|||.+.
T Consensus        41 ~Lf~Gp~G~GKTt~A   55 (509)
T PRK14958         41 YLFTGTRGVGKTTIS   55 (509)
T ss_pred             EEEECCCCCCHHHHH
Confidence            589999999999665

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]

Probab=90.70  E-value=0.92  Score=51.84  Aligned_cols=34  Identities=26%  Similarity=0.295  Sum_probs=27.6

Q ss_pred             CCcHHHHHHHHHHHcCCC-EEEECCCCCCchhhHH
Q 042872          225 AFRPLQHQACKASVAKQD-CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrD-vLviaPTGsGKTLaF~  258 (381)
                      .+...|++|+-.+|..+| .|+.+-.|+|||-+..
T Consensus       669 ~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~  703 (1100)
T KOG1805|consen  669 RLNNDQRQALLKALAAEDYALILGMPGTGKTTTIS  703 (1100)
T ss_pred             hcCHHHHHHHHHHHhccchheeecCCCCCchhhHH
Confidence            455679999999999887 4777788999996654

>PF12846 AAA_10: AAA-like domain

Probab=90.65  E-value=0.47  Score=44.41  Aligned_cols=19  Identities=26%  Similarity=0.424  Sum_probs=16.2

Q ss_pred             CCCEEEECCCCCCchhhHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~  258 (381)
                      +++++++++||+|||....
T Consensus         1 n~h~~i~G~tGsGKT~~~~   19 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLK   19 (304)
T ss_pred             CCeEEEECCCCCcHHHHHH
Confidence            3689999999999997765

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=90.64  E-value=1.1  Score=51.98  Aligned_cols=50  Identities=14%  Similarity=-0.015  Sum_probs=35.6

Q ss_pred             CCcHHHHHHHHHHHcC-CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEE
Q 042872          225 AFRPLQHQACKASVAK-QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFL  275 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~G-rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l  275 (381)
                      .+++-|.+||..+..+ +=++++++-|+|||-+.- .+..+-...|.+++.+
T Consensus       381 ~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l~-~~~~~~e~~G~~V~g~  431 (1102)
T PRK13826        381 RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMMK-AAREAWEAAGYRVVGG  431 (1102)
T ss_pred             CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHHH-HHHHHHHHcCCeEEEE
Confidence            6889999999988754 446888999999997763 3333333456666544

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=90.61  E-value=0.67  Score=48.00  Aligned_cols=17  Identities=24%  Similarity=0.251  Sum_probs=14.3

Q ss_pred             CCEEEECCCCCCchhhH
Q 042872          241 QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF  257 (381)
                      +.+++.+|+|+|||-..
T Consensus       149 ~~l~l~G~~G~GKThL~  165 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLL  165 (450)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            45899999999999654

>PHA02244 ATPase-like protein

Probab=90.59  E-value=0.94  Score=46.96  Aligned_cols=38  Identities=18%  Similarity=0.192  Sum_probs=26.8

Q ss_pred             HHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          236 ASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       236 aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      .+-.+.++++.+|||+|||...    ..+....+.+.+.+++
T Consensus       115 ~l~~~~PVLL~GppGtGKTtLA----~aLA~~lg~pfv~In~  152 (383)
T PHA02244        115 IVNANIPVFLKGGAGSGKNHIA----EQIAEALDLDFYFMNA  152 (383)
T ss_pred             HHhcCCCEEEECCCCCCHHHHH----HHHHHHhCCCEEEEec
Confidence            3446789999999999999664    2333345777766653

>TIGR00376 DNA helicase, putative

Probab=90.59  E-value=1.1  Score=49.07  Aligned_cols=51  Identities=20%  Similarity=0.221  Sum_probs=35.3

Q ss_pred             CCCcHHHHHHHHHHHcC-CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEE
Q 042872          224 RAFRPLQHQACKASVAK-QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFL  275 (381)
Q Consensus       224 ~~fRpiQ~eAI~aiL~G-rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l  275 (381)
                      ..+.+.|.+||..++.. ..+++.+|+|+|||-+-..-+..+. ..|.++.++
T Consensus       156 ~~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~-~~g~~VLv~  207 (637)
T TIGR00376       156 PNLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLV-KRGLRVLVT  207 (637)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHH-HcCCCEEEE
Confidence            35678999999999987 5678999999999965543333333 234444443

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.

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=90.56  E-value=0.75  Score=50.84  Aligned_cols=17  Identities=18%  Similarity=0.212  Sum_probs=15.5

Q ss_pred             CCEEEECCCCCCchhhH
Q 042872          241 QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF  257 (381)
                      .++++++|+|.|||...
T Consensus       204 ~n~lL~G~pG~GKT~l~  220 (731)
T TIGR02639       204 NNPLLVGEPGVGKTAIA  220 (731)
T ss_pred             CceEEECCCCCCHHHHH
Confidence            58999999999999875

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=90.54  E-value=2.1  Score=39.60  Aligned_cols=38  Identities=16%  Similarity=0.241  Sum_probs=25.8

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      |+=+++.+|+|+|||..-+..+.... ..|-+++.+...
T Consensus        23 g~i~~i~G~~GsGKT~l~~~la~~~~-~~~~~v~yi~~e   60 (225)
T PRK09361         23 GTITQIYGPPGSGKTNICLQLAVEAA-KNGKKVIYIDTE   60 (225)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH-HCCCeEEEEECC
Confidence            55678999999999855433333333 347788887766

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.54  E-value=0.65  Score=49.43  Aligned_cols=16  Identities=25%  Similarity=0.358  Sum_probs=13.8

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      .|+.+|.|+|||-+..
T Consensus        43 ~Lf~GP~GtGKTTlAr   58 (484)
T PRK14956         43 YIFFGPRGVGKTTIAR   58 (484)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6999999999997653

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=90.27  E-value=0.32  Score=49.07  Aligned_cols=31  Identities=16%  Similarity=0.258  Sum_probs=25.4

Q ss_pred             CcHHHHHHHHHHHc-CCCEEEECCCCCCchhh
Q 042872          226 FRPLQHQACKASVA-KQDCFVLLPTGGGKSLC  256 (381)
Q Consensus       226 fRpiQ~eAI~aiL~-GrDvLviaPTGsGKTLa  256 (381)
                      +++.|.+.+..++. ++++++.++||||||-.
T Consensus       129 ~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTl  160 (323)
T PRK13833        129 MTEAQASVIRSAIDSRLNIVISGGTGSGKTTL  160 (323)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH
Confidence            67788888877765 56999999999999944

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=90.15  E-value=0.6  Score=44.97  Aligned_cols=44  Identities=18%  Similarity=0.186  Sum_probs=31.4

Q ss_pred             HHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          231 HQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       231 ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      ..++..+..|+.+++.+|+|+|||.+..    .+...+|.+...+++.
T Consensus        12 ~~~l~~l~~g~~vLL~G~~GtGKT~lA~----~la~~lg~~~~~i~~~   55 (262)
T TIGR02640        12 SRALRYLKSGYPVHLRGPAGTGKTTLAM----HVARKRDRPVMLINGD   55 (262)
T ss_pred             HHHHHHHhcCCeEEEEcCCCCCHHHHHH----HHHHHhCCCEEEEeCC
Confidence            4455556689999999999999997753    3333467777666543

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).

>PRK05973 replicative DNA helicase; Provisional

Probab=90.13  E-value=1.2  Score=43.17  Aligned_cols=53  Identities=17%  Similarity=0.128  Sum_probs=34.6

Q ss_pred             HHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHH
Q 042872          237 SVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQE  290 (381)
Q Consensus       237 iL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~  290 (381)
                      +-.|.=+++.+++|+|||.--+.-+.... ..|-+++++....+..+....+..
T Consensus        61 l~~Gsl~LIaG~PG~GKT~lalqfa~~~a-~~Ge~vlyfSlEes~~~i~~R~~s  113 (237)
T PRK05973         61 LKPGDLVLLGARPGHGKTLLGLELAVEAM-KSGRTGVFFTLEYTEQDVRDRLRA  113 (237)
T ss_pred             CCCCCEEEEEeCCCCCHHHHHHHHHHHHH-hcCCeEEEEEEeCCHHHHHHHHHH
Confidence            33566778899999999976543233332 348888888877776554444433

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=90.00  E-value=2  Score=40.61  Aligned_cols=50  Identities=16%  Similarity=0.204  Sum_probs=33.1

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQ  289 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~  289 (381)
                      .|.-+++.+|+|+|||.-.+.-+..-. ..|-+++.+....+..+..+.+.
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~-~~ge~~lyvs~ee~~~~i~~~~~   69 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGL-QMGEPGIYVALEEHPVQVRRNMA   69 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHH-HcCCcEEEEEeeCCHHHHHHHHH
Confidence            367889999999999975432222211 35888988887777665444333

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=89.97  E-value=1.6  Score=40.15  Aligned_cols=16  Identities=44%  Similarity=0.559  Sum_probs=13.4

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      +++++|||+|||-...
T Consensus         4 ilI~GptGSGKTTll~   19 (198)
T cd01131           4 VLVTGPTGSGKSTTLA   19 (198)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6789999999996653

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=89.94  E-value=0.82  Score=51.46  Aligned_cols=17  Identities=18%  Similarity=0.215  Sum_probs=15.3

Q ss_pred             CCEEEECCCCCCchhhH
Q 042872          241 QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF  257 (381)
                      .+.++++|+|.|||...
T Consensus       195 ~n~lL~G~pGvGKT~l~  211 (852)
T TIGR03346       195 NNPVLIGEPGVGKTAIV  211 (852)
T ss_pred             CceEEEcCCCCCHHHHH
Confidence            58999999999999775

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.

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=89.89  E-value=0.44  Score=54.46  Aligned_cols=36  Identities=17%  Similarity=0.151  Sum_probs=22.5

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      +.-++---||||||++-.--...|....+.+.+++.
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A~~l~~~~~~~~v~fv  309 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLARLLLELPKNPKVLFV  309 (962)
T ss_pred             CceEEEeecCCchHHHHHHHHHHHHhccCCCeEEEE
Confidence            458899999999998865222223323455555444

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=89.85  E-value=2.1  Score=45.44  Aligned_cols=32  Identities=22%  Similarity=0.320  Sum_probs=24.7

Q ss_pred             CcHHHHHHHHHHHcCCC--EEEECCCCCCchhhH
Q 042872          226 FRPLQHQACKASVAKQD--CFVLLPTGGGKSLCY  257 (381)
Q Consensus       226 fRpiQ~eAI~aiL~GrD--vLviaPTGsGKTLaF  257 (381)
                      +.+.|.+.+..++....  +++.+|||||||-+-
T Consensus       226 ~~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL  259 (486)
T TIGR02533       226 MSPELLSRFERLIRRPHGIILVTGPTGSGKTTTL  259 (486)
T ss_pred             CCHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH
Confidence            35778888888776543  678999999999554

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.

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=89.85  E-value=4.2  Score=37.30  Aligned_cols=39  Identities=10%  Similarity=0.107  Sum_probs=23.4

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcC------CcEEEEeCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFG------IPATFLNSQQ  279 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~g------I~a~~l~g~~  279 (381)
                      |+=+.+.+|+|+|||...+.-+.... ..+      .+++.+.+..
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~~~-~~~~~~g~~~~v~yi~~e~   63 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVEAQ-LPGELGGLEGKVVYIDTEG   63 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHHhh-cccccCCCcceEEEEecCC
Confidence            45578889999999976542222221 223      5666666544

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.

>PRK04195 replication factor C large subunit; Provisional

Probab=89.79  E-value=1.3  Score=46.31  Aligned_cols=35  Identities=26%  Similarity=0.311  Sum_probs=25.5

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      .+-+|+.+|+|+|||...    ..+...++..++.++..
T Consensus        39 ~~~lLL~GppG~GKTtla----~ala~el~~~~ielnas   73 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLA----HALANDYGWEVIELNAS   73 (482)
T ss_pred             CCeEEEECCCCCCHHHHH----HHHHHHcCCCEEEEccc
Confidence            467999999999999664    34444567777777653

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=89.79  E-value=1.5  Score=44.48  Aligned_cols=42  Identities=17%  Similarity=0.264  Sum_probs=27.5

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVS  282 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~  282 (381)
                      |+=+.+.+|+|+|||...+.-+.... ..|-+++++...-...
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~-~~g~~~vyId~E~~~~   96 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQ-KLGGTVAFIDAEHALD   96 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH-HcCCCEEEECccccHH
Confidence            56678999999999965542233332 4577888776554433

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=89.78  E-value=1  Score=44.91  Aligned_cols=37  Identities=24%  Similarity=0.248  Sum_probs=26.0

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ++.+++.+|+|.|||-...--...+. ..|+++.+++-
T Consensus       156 ~~gl~L~G~~G~GKThLa~Aia~~l~-~~g~~v~~~~~  192 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLAAIANELA-KKGVSSTLLHF  192 (306)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHH-HcCCCEEEEEH
Confidence            46799999999999955432344444 46888877753

>CHL00095 clpC Clp protease ATP binding subunit

Probab=89.77  E-value=0.91  Score=50.88  Aligned_cols=32  Identities=13%  Similarity=0.169  Sum_probs=23.8

Q ss_pred             cHHHHHHHHHHHcC---CCEEEECCCCCCchhhHH
Q 042872          227 RPLQHQACKASVAK---QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       227 RpiQ~eAI~aiL~G---rDvLviaPTGsGKTLaF~  258 (381)
                      |.-+.+-+-.+|..   +++++++|+|.|||.+..
T Consensus       184 r~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal~~  218 (821)
T CHL00095        184 REKEIERVIQILGRRTKNNPILIGEPGVGKTAIAE  218 (821)
T ss_pred             cHHHHHHHHHHHcccccCCeEEECCCCCCHHHHHH
Confidence            45555556666643   589999999999998863

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=89.75  E-value=0.72  Score=45.20  Aligned_cols=18  Identities=17%  Similarity=0.041  Sum_probs=15.6

Q ss_pred             CCCEEEECCCCCCchhhH
Q 042872          240 KQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF  257 (381)
                      +.++++.+|+|+|||.+.
T Consensus        58 ~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            458999999999999775

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.

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=89.64  E-value=0.65  Score=51.36  Aligned_cols=29  Identities=28%  Similarity=0.328  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHcCCCEEEECCCCCCchhh
Q 042872          228 PLQHQACKASVAKQDCFVLLPTGGGKSLC  256 (381)
Q Consensus       228 piQ~eAI~aiL~GrDvLviaPTGsGKTLa  256 (381)
                      ++-.+-+.++-...=+|+.+.||||||--
T Consensus       268 ~ykdell~av~e~QVLiI~GeTGSGKTTQ  296 (902)
T KOG0923|consen  268 PYKDELLKAVKEHQVLIIVGETGSGKTTQ  296 (902)
T ss_pred             hhHHHHHHHHHhCcEEEEEcCCCCCcccc
Confidence            34456666666677788889999999953

>TIGR02012 tigrfam_recA protein RecA

Probab=89.62  E-value=1.3  Score=44.87  Aligned_cols=42  Identities=19%  Similarity=0.240  Sum_probs=27.4

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTV  281 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~  281 (381)
                      .|+=+++.+|+|+|||...+.-+.... ..|-+++++...-..
T Consensus        54 ~G~iteI~G~~GsGKTtLaL~~~~~~~-~~g~~v~yId~E~~~   95 (321)
T TIGR02012        54 RGRIIEIYGPESSGKTTLALHAIAEAQ-KAGGTAAFIDAEHAL   95 (321)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH-HcCCcEEEEcccchh
Confidence            356678999999999966543233333 457778777654433

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.

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=89.53  E-value=3.9  Score=36.16  Aligned_cols=37  Identities=16%  Similarity=0.166  Sum_probs=25.6

Q ss_pred             EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCC
Q 042872          243 CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQT  280 (381)
Q Consensus       243 vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~  280 (381)
                      +++.+|+|+|||-....-...+. ..|.++.++..+.-
T Consensus         3 ~~~~G~~G~GKTt~~~~la~~~~-~~g~~v~~i~~D~~   39 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLK-KKGKKVLLVAADTY   39 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH-HCCCcEEEEEcCCC
Confidence            46789999999977654444454 34777777766543

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.

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=89.48  E-value=0.46  Score=52.71  Aligned_cols=33  Identities=21%  Similarity=0.150  Sum_probs=23.9

Q ss_pred             CcHHHHHHHHHHHc-----CCCEEEECCCCCCchhhHH
Q 042872          226 FRPLQHQACKASVA-----KQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       226 fRpiQ~eAI~aiL~-----GrDvLviaPTGsGKTLaF~  258 (381)
                      +-|+|..++.-++-     +.-.|+.---|-|||++-.
T Consensus       326 LmpHQkaal~Wl~wRE~q~~~GGILaddmGLGKTlsmi  363 (901)
T KOG4439|consen  326 LMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMI  363 (901)
T ss_pred             cchhhhhhhhhhcccccCCCCCcccccccccccchHHH
Confidence            34899999876652     3345677778999999654

>PRK10536 hypothetical protein; Provisional

Probab=89.47  E-value=0.39  Score=47.36  Aligned_cols=38  Identities=26%  Similarity=0.047  Sum_probs=31.8

Q ss_pred             hCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +++..-+..|...+.++..+.-+++.+|+|+|||....
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~   92 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISA   92 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHH
Confidence            45555668899999999988888999999999997654

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=89.38  E-value=0.84  Score=44.29  Aligned_cols=21  Identities=19%  Similarity=0.241  Sum_probs=17.7

Q ss_pred             HHcCCCEEEECCCCCCchhhH
Q 042872          237 SVAKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       237 iL~GrDvLviaPTGsGKTLaF  257 (381)
                      +-.|.-+++.+|.|.|||...
T Consensus        13 i~~Gqr~~I~G~~G~GKTTLl   33 (249)
T cd01128          13 IGKGQRGLIVAPPKAGKTTLL   33 (249)
T ss_pred             cCCCCEEEEECCCCCCHHHHH
Confidence            347899999999999999654

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=89.38  E-value=1.7  Score=44.62  Aligned_cols=44  Identities=18%  Similarity=0.128  Sum_probs=29.3

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQ  283 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e  283 (381)
                      .|.=+++.+++|.|||...+.....+. ..+-+++.+.+..+..+
T Consensus        81 ~GslvLI~G~pG~GKStLllq~a~~~a-~~g~~VlYvs~EEs~~q  124 (372)
T cd01121          81 PGSVILIGGDPGIGKSTLLLQVAARLA-KRGGKVLYVSGEESPEQ  124 (372)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHH-hcCCeEEEEECCcCHHH
Confidence            356678899999999976643333443 34567777777655443

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.

>PRK10436 hypothetical protein; Provisional

Probab=89.33  E-value=2.1  Score=45.27  Aligned_cols=32  Identities=25%  Similarity=0.391  Sum_probs=24.1

Q ss_pred             CcHHHHHHHHHHHcC--CCEEEECCCCCCchhhH
Q 042872          226 FRPLQHQACKASVAK--QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       226 fRpiQ~eAI~aiL~G--rDvLviaPTGsGKTLaF  257 (381)
                      +.+.|.+.+..++..  -=+|+.+|||||||-+.
T Consensus       202 ~~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL  235 (462)
T PRK10436        202 MTPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL  235 (462)
T ss_pred             cCHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH
Confidence            346688888877653  35889999999999653

>CHL00176 ftsH cell division protein; Validated

Probab=89.28  E-value=1  Score=49.43  Aligned_cols=71  Identities=11%  Similarity=0.203  Sum_probs=37.7

Q ss_pred             CCCCHHHHhhchHHHHHHHHHhCC-CCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          200 GTLSFEELQALDDMEFANVVIFGN-RAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       200 ~~~~fe~L~~l~~l~~~~~~~fG~-~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ...+|+.+..+++....+.....+ +.+..+  ..+. ....+.+|+.+|+|+|||...    +.+....+++.+.+.+
T Consensus       178 ~~~~f~dv~G~~~~k~~l~eiv~~lk~~~~~--~~~g-~~~p~gVLL~GPpGTGKT~LA----ralA~e~~~p~i~is~  249 (638)
T CHL00176        178 TGITFRDIAGIEEAKEEFEEVVSFLKKPERF--TAVG-AKIPKGVLLVGPPGTGKTLLA----KAIAGEAEVPFFSISG  249 (638)
T ss_pred             CCCCHHhccChHHHHHHHHHHHHHHhCHHHH--hhcc-CCCCceEEEECCCCCCHHHHH----HHHHHHhCCCeeeccH
Confidence            345677766665554444332211 111111  1111 112357999999999999875    3344445677655543

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=89.26  E-value=0.51  Score=42.89  Aligned_cols=35  Identities=26%  Similarity=0.352  Sum_probs=28.5

Q ss_pred             CCCCcHHHHHHHHHHHc-CCCEEEECCCCCCchhhH
Q 042872          223 NRAFRPLQHQACKASVA-KQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       223 ~~~fRpiQ~eAI~aiL~-GrDvLviaPTGsGKTLaF  257 (381)
                      ...+.+.|.+.+...+. |+.+++++|||+|||-.+
T Consensus         7 ~g~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll   42 (186)
T cd01130           7 QGTFSPLQAAYLWLAVEARKNILISGGTGSGKTTLL   42 (186)
T ss_pred             cCCCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            34577888888888765 678999999999999665

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.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=89.25  E-value=0.43  Score=47.29  Aligned_cols=33  Identities=21%  Similarity=0.313  Sum_probs=25.9

Q ss_pred             CCcHHHHHHHHHHHc-CCCEEEECCCCCCchhhH
Q 042872          225 AFRPLQHQACKASVA-KQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~-GrDvLviaPTGsGKTLaF  257 (381)
                      .+.+.|.+.+..++. ++++++++|||+|||-..
T Consensus       116 ~~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll  149 (299)
T TIGR02782       116 IMTAAQRDVLREAVLARKNILVVGGTGSGKTTLA  149 (299)
T ss_pred             CCCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH
Confidence            366777777777665 569999999999999553

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.

>PRK08760 replicative DNA helicase; Provisional

Probab=89.24  E-value=2.6  Score=44.55  Aligned_cols=47  Identities=15%  Similarity=0.007  Sum_probs=32.0

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      =+++.++||.|||.-.+..+.......|.+++++...++..+....+
T Consensus       231 LivIaarPg~GKTafal~iA~~~a~~~g~~V~~fSlEMs~~ql~~Rl  277 (476)
T PRK08760        231 LIILAARPAMGKTTFALNIAEYAAIKSKKGVAVFSMEMSASQLAMRL  277 (476)
T ss_pred             eEEEEeCCCCChhHHHHHHHHHHHHhcCCceEEEeccCCHHHHHHHH
Confidence            34667899999997665444444434577888888888876654443

>PRK09354 recA recombinase A; Provisional

Probab=89.19  E-value=2.2  Score=43.74  Aligned_cols=42  Identities=19%  Similarity=0.257  Sum_probs=27.4

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVS  282 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~  282 (381)
                      |+=+.+.+|+|+|||..-+.-+.... ..|-+++.+...-+..
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~-~~G~~~~yId~E~s~~  101 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQ-KAGGTAAFIDAEHALD  101 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH-HcCCcEEEECCccchH
Confidence            56678999999999965532222222 4577888876655444

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=89.08  E-value=1.2  Score=49.24  Aligned_cols=73  Identities=14%  Similarity=0.145  Sum_probs=40.6

Q ss_pred             CCCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          200 GTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       200 ~~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ...+|+.+..+++....+.....+.-..|...+.+ .+-.++.+++.+|+|+|||...    ..+....+.+.+.+++
T Consensus       173 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~-gi~~~~giLL~GppGtGKT~la----raia~~~~~~~i~i~~  245 (733)
T TIGR01243       173 PKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHL-GIEPPKGVLLYGPPGTGKTLLA----KAVANEAGAYFISING  245 (733)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhc-CCCCCceEEEECCCCCChHHHH----HHHHHHhCCeEEEEec
Confidence            45678888877776666555433221111111111 0123578999999999999664    2233334555555543

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.

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=89.04  E-value=3  Score=40.56  Aligned_cols=32  Identities=25%  Similarity=0.356  Sum_probs=24.0

Q ss_pred             CcHHHHHHHHHHHcC--CCEEEECCCCCCchhhH
Q 042872          226 FRPLQHQACKASVAK--QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       226 fRpiQ~eAI~aiL~G--rDvLviaPTGsGKTLaF  257 (381)
                      +.+.|.+.+..++..  .-+++.+|||+|||-..
T Consensus        64 ~~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l   97 (264)
T cd01129          64 LKPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL   97 (264)
T ss_pred             CCHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH
Confidence            356788888777653  35789999999999543

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.

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=89.00  E-value=1.1  Score=50.05  Aligned_cols=19  Identities=21%  Similarity=0.300  Sum_probs=16.4

Q ss_pred             CCCEEEECCCCCCchhhHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~  258 (381)
                      ..++|+++|+|+|||....
T Consensus       207 ~~n~LLvGppGvGKT~lae  225 (758)
T PRK11034        207 KNNPLLVGESGVGKTAIAE  225 (758)
T ss_pred             CCCeEEECCCCCCHHHHHH
Confidence            3599999999999998863

>PRK08116 hypothetical protein; Validated

Probab=88.99  E-value=2.5  Score=41.16  Aligned_cols=34  Identities=24%  Similarity=0.259  Sum_probs=23.2

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      -+++.+++|+|||....--...+.. .+.++++++
T Consensus       116 gl~l~G~~GtGKThLa~aia~~l~~-~~~~v~~~~  149 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAACIANELIE-KGVPVIFVN  149 (268)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHH-cCCeEEEEE
Confidence            4999999999999655423344442 377776665

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=88.97  E-value=1.4  Score=49.61  Aligned_cols=15  Identities=20%  Similarity=0.129  Sum_probs=12.8

Q ss_pred             EEEECCCCCCchhhH
Q 042872          243 CFVLLPTGGGKSLCY  257 (381)
Q Consensus       243 vLviaPTGsGKTLaF  257 (381)
                      +|+.+|.|.|||.+.
T Consensus        41 yLFtGPpGvGKTTlA   55 (830)
T PRK07003         41 YLFTGTRGVGKTTLS   55 (830)
T ss_pred             EEEECCCCCCHHHHH
Confidence            588999999999654

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=88.89  E-value=2.1  Score=46.15  Aligned_cols=31  Identities=29%  Similarity=0.384  Sum_probs=24.2

Q ss_pred             cHHHHHHHHHHHcC--CCEEEECCCCCCchhhH
Q 042872          227 RPLQHQACKASVAK--QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       227 RpiQ~eAI~aiL~G--rDvLviaPTGsGKTLaF  257 (381)
                      .|.|.+.+..++..  --+|+.+|||||||-+.
T Consensus       301 ~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl  333 (564)
T TIGR02538       301 EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL  333 (564)
T ss_pred             CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH
Confidence            47788888877654  35789999999999654

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.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=88.86  E-value=0.46  Score=47.68  Aligned_cols=31  Identities=32%  Similarity=0.403  Sum_probs=25.4

Q ss_pred             CcHHHHHHHHHHH-cCCCEEEECCCCCCchhh
Q 042872          226 FRPLQHQACKASV-AKQDCFVLLPTGGGKSLC  256 (381)
Q Consensus       226 fRpiQ~eAI~aiL-~GrDvLviaPTGsGKTLa  256 (381)
                      +.+.|.+.+..++ .+++++++++||+|||-.
T Consensus       133 ~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl  164 (319)
T PRK13894        133 MTAAQREAIIAAVRAHRNILVIGGTGSGKTTL  164 (319)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH
Confidence            6678888888765 567999999999999943

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=88.72  E-value=1.3  Score=45.16  Aligned_cols=37  Identities=14%  Similarity=0.069  Sum_probs=21.7

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhh-cCCcEEEEeC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLK-FGIPATFLNS  277 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~-~gI~a~~l~g  277 (381)
                      ..+++.+|+|+|||-.-.--...+... .+.+++.+++
T Consensus       137 n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~  174 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSS  174 (405)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEH
Confidence            357899999999996543122223221 2455655543

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).

>PRK11823 DNA repair protein RadA; Provisional

Probab=88.70  E-value=1.9  Score=45.16  Aligned_cols=44  Identities=18%  Similarity=0.145  Sum_probs=29.3

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQ  283 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e  283 (381)
                      .|.=+++.+++|+|||..-+.....+. ..|-+++.+.+..+..+
T Consensus        79 ~Gs~~lI~G~pG~GKTtL~lq~a~~~a-~~g~~vlYvs~Ees~~q  122 (446)
T PRK11823         79 PGSVVLIGGDPGIGKSTLLLQVAARLA-AAGGKVLYVSGEESASQ  122 (446)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHH-hcCCeEEEEEccccHHH
Confidence            356678999999999965532233333 34778888877655543

>CHL00181 cbbX CbbX; Provisional

Probab=88.69  E-value=0.99  Score=44.45  Aligned_cols=19  Identities=16%  Similarity=0.013  Sum_probs=15.8

Q ss_pred             CCCEEEECCCCCCchhhHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~  258 (381)
                      |-++++.+|+|+|||.+..
T Consensus        59 ~~~ill~G~pGtGKT~lAr   77 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVAL   77 (287)
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4468999999999997763

>PHA02542 41 41 helicase; Provisional

Probab=88.67  E-value=2.8  Score=44.42  Aligned_cols=45  Identities=16%  Similarity=0.110  Sum_probs=32.5

Q ss_pred             EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          243 CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       243 vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      +++.+++|.|||...+....... ..|-+++++...++..+....+
T Consensus       193 iiIaarPgmGKTtfalniA~~~a-~~g~~Vl~fSLEM~~~ql~~Rl  237 (473)
T PHA02542        193 NVLLAGVNVGKSLGLCSLAADYL-QQGYNVLYISMEMAEEVIAKRI  237 (473)
T ss_pred             EEEEcCCCccHHHHHHHHHHHHH-hcCCcEEEEeccCCHHHHHHHH
Confidence            56678999999977665554544 4688888888888877654444

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=88.65  E-value=0.73  Score=48.25  Aligned_cols=16  Identities=25%  Similarity=0.339  Sum_probs=13.3

Q ss_pred             CCEEEECCCCCCchhh
Q 042872          241 QDCFVLLPTGGGKSLC  256 (381)
Q Consensus       241 rDvLviaPTGsGKTLa  256 (381)
                      +.+++.+++|+|||-.
T Consensus       142 npl~i~G~~G~GKTHL  157 (450)
T PRK14087        142 NPLFIYGESGMGKTHL  157 (450)
T ss_pred             CceEEECCCCCcHHHH
Confidence            4588999999999943

>PRK09183 transposase/IS protein; Provisional

Probab=88.55  E-value=1.2  Score=43.03  Aligned_cols=39  Identities=21%  Similarity=0.198  Sum_probs=24.7

Q ss_pred             HHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          237 SVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       237 iL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      +-.|.++++.+|+|+|||-...--...+. ..|.++.++.
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al~~~a~-~~G~~v~~~~  137 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIALGYEAV-RAGIKVRFTT  137 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHHHHHHH-HcCCeEEEEe
Confidence            34678999999999999955421112222 3466666554

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.44  E-value=0.61  Score=50.28  Aligned_cols=16  Identities=25%  Similarity=0.306  Sum_probs=13.6

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      .|+.+|.|.|||.+..
T Consensus        41 ~Lf~Gp~G~GKTtlA~   56 (585)
T PRK14950         41 YLFTGPRGVGKTSTAR   56 (585)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5899999999997653

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=88.42  E-value=3.7  Score=39.00  Aligned_cols=48  Identities=19%  Similarity=0.226  Sum_probs=33.2

Q ss_pred             EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHH
Q 042872          243 CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQE  290 (381)
Q Consensus       243 vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~  290 (381)
                      +++.++||.|||...+.-+..+....|.++.++...++..+....+-.
T Consensus        22 ~vi~a~pg~GKT~~~l~ia~~~a~~~~~~vly~SlEm~~~~l~~R~la   69 (259)
T PF03796_consen   22 TVIAARPGVGKTAFALQIALNAALNGGYPVLYFSLEMSEEELAARLLA   69 (259)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTTSSEEEEEESSS-HHHHHHHHHH
T ss_pred             EEEEecccCCchHHHHHHHHHHHHhcCCeEEEEcCCCCHHHHHHHHHH
Confidence            566789999999776544555553446899999998887765544433

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=88.38  E-value=4.3  Score=38.48  Aligned_cols=50  Identities=16%  Similarity=0.134  Sum_probs=32.5

Q ss_pred             HcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          238 VAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       238 L~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      -.|.-+++.+|+|+|||...+.-+..+. +.|.+++.+....+..+....+
T Consensus        22 ~~g~~~~i~G~~G~GKTtl~~~~~~~~~-~~g~~~~yi~~e~~~~~~~~~~   71 (230)
T PRK08533         22 PAGSLILIEGDESTGKSILSQRLAYGFL-QNGYSVSYVSTQLTTTEFIKQM   71 (230)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHH-hCCCcEEEEeCCCCHHHHHHHH
Confidence            3477889999999999976432233333 3577787777666665543333

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=88.26  E-value=2.5  Score=47.43  Aligned_cols=34  Identities=26%  Similarity=0.325  Sum_probs=24.5

Q ss_pred             CCcHHHHHHHHHHH---cCC-------CEEEECCCCCCchhhHH
Q 042872          225 AFRPLQHQACKASV---AKQ-------DCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL---~Gr-------DvLviaPTGsGKTLaF~  258 (381)
                      ..||+|+|.+.-+-   .|.       -+|..=..|+|||+-..
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~I  281 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCI  281 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHH
Confidence            57899999998764   232       35566678999996543

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=88.21  E-value=3.7  Score=39.60  Aligned_cols=42  Identities=21%  Similarity=0.192  Sum_probs=27.4

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTV  281 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~  281 (381)
                      .|.=+++.+|+|+|||..-+.-+.... ..|-+++.+....+.
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a-~~Ge~vlyis~Ee~~   76 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQA-SRGNPVLFVTVESPA   76 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHH-hCCCcEEEEEecCCc
Confidence            466789999999999965432222222 357888877765443

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK09165 replicative DNA helicase; Provisional

Probab=88.14  E-value=3.2  Score=44.09  Aligned_cols=50  Identities=12%  Similarity=0.022  Sum_probs=31.9

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhh--------------cCCcEEEEeCCCCHHHHHHHHHH
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLK--------------FGIPATFLNSQQTVSQAAAVLQE  290 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~--------------~gI~a~~l~g~~~~~e~~~il~~  290 (381)
                      .=+++.++||.|||.-.+.........              .|.+++++...++..+....+-.
T Consensus       218 ~livIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSlEMs~~ql~~R~la  281 (497)
T PRK09165        218 DLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFSLEMSAEQLATRILS  281 (497)
T ss_pred             ceEEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEeCcCCHHHHHHHHHH
Confidence            335778999999996654333333222              25678888888887765544433

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=88.07  E-value=2.3  Score=44.04  Aligned_cols=71  Identities=8%  Similarity=0.039  Sum_probs=39.7

Q ss_pred             CCCCCHHHHhhchHHHHHHHHHhC--CCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          199 HGTLSFEELQALDDMEFANVVIFG--NRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       199 ~~~~~fe~L~~l~~l~~~~~~~fG--~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      .+..+|..+..++.....+....-  +..+.-++.--   +-..+.+|+.+|+|+|||+..    ..+....+.....+.
T Consensus       139 ~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~G---l~~pkgvLL~GppGTGKT~LA----kalA~~l~~~fi~i~  211 (398)
T PTZ00454        139 KPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIG---IDPPRGVLLYGPPGTGKTMLA----KAVAHHTTATFIRVV  211 (398)
T ss_pred             CCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcC---CCCCceEEEECCCCCCHHHHH----HHHHHhcCCCEEEEe
Confidence            345678888777765555544322  22221111111   113578999999999999875    333334455554443

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=88.00  E-value=0.75  Score=48.83  Aligned_cols=34  Identities=35%  Similarity=0.545  Sum_probs=25.0

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      ...++|+++|||+|||+..+    .|.+-++++.+++.
T Consensus       225 eKSNvLllGPtGsGKTllaq----TLAr~ldVPfaIcD  258 (564)
T KOG0745|consen  225 EKSNVLLLGPTGSGKTLLAQ----TLARVLDVPFAICD  258 (564)
T ss_pred             ecccEEEECCCCCchhHHHH----HHHHHhCCCeEEec
Confidence            34589999999999999874    34444577766654

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=87.97  E-value=1.5  Score=44.06  Aligned_cols=57  Identities=16%  Similarity=0.169  Sum_probs=31.3

Q ss_pred             CCCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhH
Q 042872          200 GTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       200 ~~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF  257 (381)
                      ....++.+..+++....+...+.+.-..|.-...+. +-..+.+++.+|+|+|||...
T Consensus       117 p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g-~~~p~gvLL~GppGtGKT~la  173 (364)
T TIGR01242       117 PNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVG-IEPPKGVLLYGPPGTGKTLLA  173 (364)
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcC-CCCCceEEEECCCCCCHHHHH
Confidence            455677777776655555443322111111111110 112356999999999999775

Many proteins may score above the trusted cutoff because an internal

>KOG1803 consensus DNA helicase [Replication, recombination and repair]

Probab=87.94  E-value=1.8  Score=47.29  Aligned_cols=50  Identities=20%  Similarity=0.201  Sum_probs=37.1

Q ss_pred             CCcHHHHHHHHHHHcCCCE-EEECCCCCCchhhHHHHHHHHHhhcCCcEEEE
Q 042872          225 AFRPLQHQACKASVAKQDC-FVLLPTGGGKSLCYQDQIITLNLKFGIPATFL  275 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDv-LviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l  275 (381)
                      .+-+-|.+|+..+++.+++ ++.+|.|+|||.+-.+-+..+- +.+-+++++
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlv-k~~k~VLVc  235 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLV-KQKKRVLVC  235 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHH-HcCCeEEEE
Confidence            4568899999999999776 5669999999988765555554 345555544

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=87.93  E-value=2.7  Score=37.42  Aligned_cols=54  Identities=19%  Similarity=0.142  Sum_probs=33.1

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhh---------cCCcEEEEeCCCCHHHHHHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLK---------FGIPATFLNSQQTVSQAAAVLQELR  292 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~---------~gI~a~~l~g~~~~~e~~~il~~lr  292 (381)
                      .|.=+++.+|+|+|||..-++.+..+...         .+.+++.+....+..+....+..+.
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~~~~~~~rl~~~~   93 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDSESQIARRLRALL   93 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS-HHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCCHHHHHHHHHHHh
Confidence            45558899999999997665444444321         3467888888887766666665544

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=87.87  E-value=1.2  Score=48.63  Aligned_cols=17  Identities=18%  Similarity=0.134  Sum_probs=14.4

Q ss_pred             CEEEECCCCCCchhhHH
Q 042872          242 DCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~  258 (381)
                      -.|+.+|.|.|||.+..
T Consensus        48 a~L~~Gp~GvGKTt~Ar   64 (598)
T PRK09111         48 AFMLTGVRGVGKTTTAR   64 (598)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            58999999999997653

>KOG1131 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription; Replication, recombination and repair]

Probab=87.85  E-value=2.3  Score=46.17  Aligned_cols=43  Identities=28%  Similarity=0.432  Sum_probs=33.6

Q ss_pred             HHhCCCCCcHHHHHHHHHHH----cCCCEEEECCCCCCchhhHHHHH
Q 042872          219 VIFGNRAFRPLQHQACKASV----AKQDCFVLLPTGGGKSLCYQDQI  261 (381)
Q Consensus       219 ~~fG~~~fRpiQ~eAI~aiL----~GrDvLviaPTGsGKTLaF~dQv  261 (381)
                      .+|.|....|-|.+=+..+-    ++-.+|+-||+|+|||++.+..+
T Consensus        10 v~FPY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli   56 (755)
T KOG1131|consen   10 VYFPYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLI   56 (755)
T ss_pred             EecCCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHH
Confidence            35889888999988766553    35689999999999998876333

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=87.79  E-value=1.2  Score=50.39  Aligned_cols=37  Identities=32%  Similarity=0.317  Sum_probs=30.0

Q ss_pred             hCCCCCcHHHHHHHHHHH----cCCCEEEECCCCCCchhhHH
Q 042872          221 FGNRAFRPLQHQACKASV----AKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL----~GrDvLviaPTGsGKTLaF~  258 (381)
                      |-| .|+|.|..-+..++    .+.+.++-.|||+||||+-+
T Consensus        18 fP~-qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLL   58 (945)
T KOG1132|consen   18 FPF-QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLL   58 (945)
T ss_pred             ccC-CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHH
Confidence            566 46889988877776    45689999999999998866

>PRK04328 hypothetical protein; Provisional

Probab=87.66  E-value=5.2  Score=38.31  Aligned_cols=50  Identities=18%  Similarity=0.298  Sum_probs=31.7

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQ  289 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~  289 (381)
                      .|.-+++.+|+|+|||.--+.-+.. ....|-+++.+.-..+..+....++
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~-~~~~ge~~lyis~ee~~~~i~~~~~   71 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWN-GLQMGEPGVYVALEEHPVQVRRNMR   71 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH-HHhcCCcEEEEEeeCCHHHHHHHHH
Confidence            4677899999999998543222222 1135888888877666665433333

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=87.66  E-value=2  Score=47.79  Aligned_cols=17  Identities=18%  Similarity=0.173  Sum_probs=14.3

Q ss_pred             CEEEECCCCCCchhhHH
Q 042872          242 DCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~  258 (381)
                      -+|+.+|.|.|||.+..
T Consensus        40 a~Lf~GP~GvGKTTlAr   56 (709)
T PRK08691         40 AYLLTGTRGVGKTTIAR   56 (709)
T ss_pred             EEEEECCCCCcHHHHHH
Confidence            47999999999997653

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=87.63  E-value=2.1  Score=47.00  Aligned_cols=50  Identities=18%  Similarity=0.085  Sum_probs=33.0

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQE  290 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~  290 (381)
                      .++++++++||+|||..+.--+.... ..|-.++++.+..+.+-...+...
T Consensus       176 ~~H~lv~G~TGsGKT~l~~~l~~q~i-~~g~~viv~DpKgD~~l~~~~~~~  225 (634)
T TIGR03743       176 VGHTLVLGTTGVGKTRLAELLITQDI-RRGDVVIVIDPKGDADLKRRMRAE  225 (634)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHH-HcCCeEEEEeCCCchHHHHHHHHH
Confidence            47999999999999988742233333 357778888776654433333333

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.

>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=87.63  E-value=1.7  Score=42.38  Aligned_cols=32  Identities=16%  Similarity=0.258  Sum_probs=20.5

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ++|..+|.|.|||-...    -+...++.....+.|
T Consensus        52 h~lf~GPPG~GKTTLA~----IIA~e~~~~~~~~sg   83 (233)
T PF05496_consen   52 HMLFYGPPGLGKTTLAR----IIANELGVNFKITSG   83 (233)
T ss_dssp             EEEEESSTTSSHHHHHH----HHHHHCT--EEEEEC
T ss_pred             eEEEECCCccchhHHHH----HHHhccCCCeEeccc
Confidence            58999999999995542    123346666666655

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.

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=87.59  E-value=0.55  Score=50.37  Aligned_cols=45  Identities=24%  Similarity=0.401  Sum_probs=35.8

Q ss_pred             CCCchhhHH------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          250 GGGKSLCYQ------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       250 GsGKTLaF~------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      -.||+++|.      +++...-...++++..++|+.+..+|..+|+.++.|
T Consensus       340 ~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG  390 (519)
T KOG0331|consen  340 SEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREG  390 (519)
T ss_pred             CCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccC
Confidence            458999998      444433334578999999999999999999998877

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=87.45  E-value=2.4  Score=40.66  Aligned_cols=20  Identities=20%  Similarity=0.192  Sum_probs=16.3

Q ss_pred             cCCC-EEEECCCCCCchhhHH
Q 042872          239 AKQD-CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       239 ~GrD-vLviaPTGsGKTLaF~  258 (381)
                      .+.. +|+.+|.|.|||.+..
T Consensus        22 ~~~halL~~Gp~G~Gktt~a~   42 (325)
T COG0470          22 RLPHALLFYGPPGVGKTTAAL   42 (325)
T ss_pred             CCCceeeeeCCCCCCHHHHHH
Confidence            3456 8999999999997764

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=87.43  E-value=1.3  Score=44.66  Aligned_cols=17  Identities=12%  Similarity=0.333  Sum_probs=15.3

Q ss_pred             CCEEEECCCCCCchhhH
Q 042872          241 QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF  257 (381)
                      .+++++++||-|||.+.
T Consensus        62 p~lLivG~snnGKT~Ii   78 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTMII   78 (302)
T ss_pred             CceEEecCCCCcHHHHH
Confidence            48999999999999875

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK05595 replicative DNA helicase; Provisional

Probab=87.39  E-value=3.8  Score=42.58  Aligned_cols=46  Identities=15%  Similarity=0.085  Sum_probs=32.1

Q ss_pred             EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          243 CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       243 vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      +++.|+||.|||...+..+..+....|-++.++...++..+....+
T Consensus       204 iviaarpg~GKT~~al~ia~~~a~~~g~~vl~fSlEms~~~l~~R~  249 (444)
T PRK05595        204 ILIAARPSMGKTTFALNIAEYAALREGKSVAIFSLEMSKEQLAYKL  249 (444)
T ss_pred             EEEEecCCCChHHHHHHHHHHHHHHcCCcEEEEecCCCHHHHHHHH
Confidence            4567899999997665445444434578888888888876654443

>PLN03025 replication factor C subunit; Provisional

Probab=87.29  E-value=3.4  Score=40.73  Aligned_cols=17  Identities=24%  Similarity=0.382  Sum_probs=14.2

Q ss_pred             CCEEEECCCCCCchhhH
Q 042872          241 QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF  257 (381)
                      ..+++.+|.|+|||-..
T Consensus        35 ~~lll~Gp~G~GKTtla   51 (319)
T PLN03025         35 PNLILSGPPGTGKTTSI   51 (319)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            36899999999999554

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=87.23  E-value=1  Score=46.33  Aligned_cols=18  Identities=33%  Similarity=0.648  Sum_probs=16.4

Q ss_pred             CCEEEECCCCCCchhhHH
Q 042872          241 QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~  258 (381)
                      .++++++|||||||..|.
T Consensus        45 ~h~lvig~tgSGKt~~~v   62 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFV   62 (469)
T ss_pred             eEEEEEeCCCCCccceee
Confidence            479999999999999886

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

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=87.21  E-value=2.1  Score=43.03  Aligned_cols=19  Identities=37%  Similarity=0.420  Sum_probs=15.8

Q ss_pred             cCCCEEEECCCCCCchhhH
Q 042872          239 AKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF  257 (381)
                      .+.-+++.+|||+|||-..
T Consensus       121 ~~g~ili~G~tGSGKTT~l  139 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL  139 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH
Confidence            3567899999999999665

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.

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=87.01  E-value=1.2  Score=52.03  Aligned_cols=30  Identities=17%  Similarity=0.150  Sum_probs=21.7

Q ss_pred             CcHHHHHHHHHHH----cCCCEEEECCCCCCchh
Q 042872          226 FRPLQHQACKASV----AKQDCFVLLPTGGGKSL  255 (381)
Q Consensus       226 fRpiQ~eAI~aiL----~GrDvLviaPTGsGKTL  255 (381)
                      +|.+|..-+.-+.    ++-|-|+.-.-|-|||+
T Consensus       616 LReYQkiGLdWLatLYeknlNGILADEmGLGKTI  649 (1958)
T KOG0391|consen  616 LREYQKIGLDWLATLYEKNLNGILADEMGLGKTI  649 (1958)
T ss_pred             HHHHHHhhHHHHHHHHHhcccceehhhhcccchh
Confidence            5678888776653    23366777789999994

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=87.00  E-value=2.3  Score=43.49  Aligned_cols=70  Identities=10%  Similarity=0.095  Sum_probs=36.8

Q ss_pred             CCCCHHHHhhchHHHHHHHHHhCC--CCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          200 GTLSFEELQALDDMEFANVVIFGN--RAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       200 ~~~~fe~L~~l~~l~~~~~~~fG~--~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      ...+++.+..+++....+....-+  ..+..++.--   +-.-+.+|+.+|+|+|||+..    ..+....+.+.+.+.
T Consensus       126 p~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g---~~~p~gvLL~GppGtGKT~lA----kaia~~~~~~~i~v~  197 (389)
T PRK03992        126 PNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVG---IEPPKGVLLYGPPGTGKTLLA----KAVAHETNATFIRVV  197 (389)
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcC---CCCCCceEEECCCCCChHHHH----HHHHHHhCCCEEEee
Confidence            356677777776655444433221  1111111000   011357999999999999775    233334455555443

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=86.96  E-value=1.6  Score=40.36  Aligned_cols=37  Identities=19%  Similarity=0.246  Sum_probs=22.5

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ++.+++.+|+|+|||-...--...+. ..+.++.++..
T Consensus        42 ~~~~~l~G~~G~GKT~La~ai~~~~~-~~~~~~~~i~~   78 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHLLQALVADAS-YGGRNARYLDA   78 (227)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHH-hCCCcEEEEeh
Confidence            35799999999999944321112222 34566666654

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=86.96  E-value=0.97  Score=48.67  Aligned_cols=16  Identities=25%  Similarity=0.318  Sum_probs=13.5

Q ss_pred             CEEEECCCCCCchhhH
Q 042872          242 DCFVLLPTGGGKSLCY  257 (381)
Q Consensus       242 DvLviaPTGsGKTLaF  257 (381)
                      -.|+.+|.|+|||.+.
T Consensus        40 ayLf~Gp~GtGKTt~A   55 (559)
T PRK05563         40 AYLFSGPRGTGKTSAA   55 (559)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3688999999999765

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=86.93  E-value=0.96  Score=41.88  Aligned_cols=39  Identities=21%  Similarity=0.180  Sum_probs=28.4

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      -++.+.|.+.||+|||-+-.-.+..+....+.+++++..
T Consensus        22 ~~~H~~I~G~TGsGKS~~~~~ll~~l~~~~~~~~ii~D~   60 (229)
T PF01935_consen   22 FNRHIAIFGTTGSGKSNTVKVLLEELLKKKGAKVIIFDP   60 (229)
T ss_pred             ccceEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEcC
Confidence            358999999999999977654455554346777777743

It contains several conserved aspartates and histidines that could be metal ligands.

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=86.89  E-value=5.3  Score=38.29  Aligned_cols=17  Identities=24%  Similarity=0.301  Sum_probs=14.6

Q ss_pred             CEEEECCCCCCchhhHH
Q 042872          242 DCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~  258 (381)
                      .+++.+|+|+|||.+..
T Consensus        40 ~~ll~G~~G~GKt~~~~   56 (319)
T PRK00440         40 HLLFAGPPGTGKTTAAL   56 (319)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            58999999999997753

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.75  E-value=2.3  Score=45.33  Aligned_cols=16  Identities=25%  Similarity=0.522  Sum_probs=13.9

Q ss_pred             CEEEECCCCCCchhhH
Q 042872          242 DCFVLLPTGGGKSLCY  257 (381)
Q Consensus       242 DvLviaPTGsGKTLaF  257 (381)
                      -.|..+|.|.|||-+.
T Consensus        37 a~Lf~Gp~G~GKTT~A   52 (491)
T PRK14964         37 SILLVGASGVGKTTCA   52 (491)
T ss_pred             eEEEECCCCccHHHHH
Confidence            5899999999999654

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.73  E-value=1.4  Score=44.53  Aligned_cols=16  Identities=19%  Similarity=0.162  Sum_probs=13.5

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      +|+.+|.|+|||....
T Consensus        41 ~L~~Gp~G~GKTtla~   56 (363)
T PRK14961         41 WLLSGTRGVGKTTIAR   56 (363)
T ss_pred             EEEecCCCCCHHHHHH
Confidence            5899999999997653

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=86.73  E-value=0.67  Score=47.51  Aligned_cols=35  Identities=14%  Similarity=0.096  Sum_probs=31.2

Q ss_pred             hCCCCCcHHHHHHHHHHHcCC-CEEEECCCCCCchh
Q 042872          221 FGNRAFRPLQHQACKASVAKQ-DCFVLLPTGGGKSL  255 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~Gr-DvLviaPTGsGKTL  255 (381)
                      ..|..+++-|.+.+-.+..++ ++|+.+.||||||-
T Consensus       153 i~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTT  188 (355)
T COG4962         153 IIFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTT  188 (355)
T ss_pred             HHcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHH
Confidence            566788999999999999886 99999999999993

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=86.70  E-value=2.4  Score=49.12  Aligned_cols=31  Identities=23%  Similarity=0.191  Sum_probs=22.8

Q ss_pred             HHHHHHHHHHHc--------CCCEEEECCCCCCchhhHH
Q 042872          228 PLQHQACKASVA--------KQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       228 piQ~eAI~aiL~--------GrDvLviaPTGsGKTLaF~  258 (381)
                      ..|-.|...+..        |-=++-.|-||+|||++=.
T Consensus       411 ~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNA  449 (1110)
T TIGR02562       411 RWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANA  449 (1110)
T ss_pred             chHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHH
Confidence            468888888764        2235666999999998744

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.

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=86.66  E-value=4.8  Score=42.61  Aligned_cols=78  Identities=21%  Similarity=0.295  Sum_probs=48.7

Q ss_pred             EEEECCCCCCchhhHH--------------------------HHHHHHHhhcCCcEEEEeCCCC-HHHHHHHHHHHHhch
Q 042872          243 CFVLLPTGGGKSLCYQ--------------------------DQIITLNLKFGIPATFLNSQQT-VSQAAAVLQELRQGL  295 (381)
Q Consensus       243 vLviaPTGsGKTLaF~--------------------------dQv~~L~~~~gI~a~~l~g~~~-~~e~~~il~~lr~g~  295 (381)
                      ++.++=-|+|||-+-.                          +|+..|....++++.....+.+ .+-.++.++..+.  
T Consensus       103 ImmvGLQGsGKTTt~~KLA~~lkk~~~kvllVaaD~~RpAA~eQL~~La~q~~v~~f~~~~~~~Pv~Iak~al~~ak~--  180 (451)
T COG0541         103 ILMVGLQGSGKTTTAGKLAKYLKKKGKKVLLVAADTYRPAAIEQLKQLAEQVGVPFFGSGTEKDPVEIAKAALEKAKE--  180 (451)
T ss_pred             EEEEeccCCChHhHHHHHHHHHHHcCCceEEEecccCChHHHHHHHHHHHHcCCceecCCCCCCHHHHHHHHHHHHHH--
Confidence            5667778999995543                          7888887777777655533333 3333444444431  


Q ss_pred             hhhhhhhhhhhhhhhhhcccCCCCCccEEEE-CccccccCcchHHHHHHHH
Q 042872          296 VLSQHYFLHQLIFVLTCASRKDKPSCKLLYV-TPERIVGNQSFSEVLKCLH  345 (381)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~a-TPErL~~~~~f~~~L~~L~  345 (381)
                                             ..+++|++ |-+|+.-...+.+-+..++
T Consensus       181 -----------------------~~~DvvIvDTAGRl~ide~Lm~El~~Ik  208 (451)
T COG0541         181 -----------------------EGYDVVIVDTAGRLHIDEELMDELKEIK  208 (451)
T ss_pred             -----------------------cCCCEEEEeCCCcccccHHHHHHHHHHH
Confidence                                   24677766 9999986666655555444

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=86.57  E-value=2.4  Score=46.76  Aligned_cols=16  Identities=19%  Similarity=0.138  Sum_probs=13.3

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      .|+.+|.|.|||.+..
T Consensus        41 yLf~Gp~GvGKTTlAr   56 (647)
T PRK07994         41 YLFSGTRGVGKTTIAR   56 (647)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            4899999999996653

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=86.54  E-value=1.2  Score=47.14  Aligned_cols=34  Identities=18%  Similarity=0.317  Sum_probs=28.2

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      |++|..+|.|+|||+..    +.|..+.|+...+++||
T Consensus       385 RNilfyGPPGTGKTm~A----relAr~SGlDYA~mTGG  418 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMFA----RELARHSGLDYAIMTGG  418 (630)
T ss_pred             hheeeeCCCCCCchHHH----HHHHhhcCCceehhcCC
Confidence            79999999999999875    45666778888777776

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.53  E-value=1.3  Score=49.17  Aligned_cols=16  Identities=19%  Similarity=0.152  Sum_probs=13.4

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      .|+.+|.|.|||.+..
T Consensus        41 ~LFtGP~GvGKTTLAr   56 (700)
T PRK12323         41 YLFTGTRGVGKTTLSR   56 (700)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5889999999996653

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.34  E-value=1.4  Score=48.95  Aligned_cols=17  Identities=18%  Similarity=0.139  Sum_probs=13.8

Q ss_pred             CEEEECCCCCCchhhHH
Q 042872          242 DCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~  258 (381)
                      -+|+.+|.|.|||-+..
T Consensus        39 AyLF~GPpGvGKTTlAr   55 (702)
T PRK14960         39 AYLFTGTRGVGKTTIAR   55 (702)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            34899999999996653

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=86.32  E-value=0.82  Score=46.50  Aligned_cols=31  Identities=29%  Similarity=0.185  Sum_probs=21.3

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcE
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPA  272 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a  272 (381)
                      =+||.+|||||||-+-.-.+..+++.....+
T Consensus       127 LILVTGpTGSGKSTTlAamId~iN~~~~~HI  157 (353)
T COG2805         127 LILVTGPTGSGKSTTLAAMIDYINKHKAKHI  157 (353)
T ss_pred             eEEEeCCCCCcHHHHHHHHHHHHhccCCcce
Confidence            3788999999999776645665654443333

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=86.23  E-value=1  Score=46.95  Aligned_cols=34  Identities=21%  Similarity=0.122  Sum_probs=25.1

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      +=+++.+|.|+|||+..    +.+...+|+..+.+.++
T Consensus       149 lgllL~GPPGcGKTllA----raiA~elg~~~i~vsa~  182 (413)
T PLN00020        149 LILGIWGGKGQGKSFQC----ELVFKKMGIEPIVMSAG  182 (413)
T ss_pred             eEEEeeCCCCCCHHHHH----HHHHHHcCCCeEEEEHH
Confidence            34677899999999764    45555788888777654

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=86.20  E-value=5.7  Score=36.74  Aligned_cols=49  Identities=14%  Similarity=0.076  Sum_probs=30.2

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      .|.-+++.+++|+|||..-+.-+.... ..|-++..++-..+..+..+.+
T Consensus        15 ~g~~~li~G~~G~GKt~~~~~~~~~~~-~~g~~~~y~s~e~~~~~l~~~~   63 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSLQFLYQGL-KNGEKAMYISLEEREERILGYA   63 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH-hCCCeEEEEECCCCHHHHHHHH
Confidence            356788899999999854322222211 3477888887776665543333

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.

>PRK05642 DNA replication initiation factor; Validated

Probab=86.14  E-value=1.7  Score=41.28  Aligned_cols=35  Identities=23%  Similarity=0.332  Sum_probs=20.2

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      +.+++.+|+|+|||---+--...+. ..|.+++.+.
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~-~~~~~v~y~~   80 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFE-QRGEPAVYLP   80 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHH-hCCCcEEEee
Confidence            4578899999999944221122222 2355665554

>PRK13342 recombination factor protein RarA; Reviewed

Probab=86.13  E-value=2.6  Score=43.30  Aligned_cols=32  Identities=19%  Similarity=0.225  Sum_probs=20.8

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      .+++.+|+|+|||....    .+....+.....++.
T Consensus        38 ~ilL~GppGtGKTtLA~----~ia~~~~~~~~~l~a   69 (413)
T PRK13342         38 SMILWGPPGTGKTTLAR----IIAGATDAPFEALSA   69 (413)
T ss_pred             eEEEECCCCCCHHHHHH----HHHHHhCCCEEEEec
Confidence            68999999999997653    223234455544443

>PRK07004 replicative DNA helicase; Provisional

Probab=85.98  E-value=4.9  Score=42.32  Aligned_cols=49  Identities=14%  Similarity=0.137  Sum_probs=33.5

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      |.=+++.+.||.|||.-.+..+.......|.+++++.-.++..+....+
T Consensus       213 g~liviaarpg~GKT~~al~ia~~~a~~~~~~v~~fSlEM~~~ql~~R~  261 (460)
T PRK07004        213 GELIIVAGRPSMGKTAFSMNIGEYVAVEYGLPVAVFSMEMPGTQLAMRM  261 (460)
T ss_pred             CceEEEEeCCCCCccHHHHHHHHHHHHHcCCeEEEEeCCCCHHHHHHHH
Confidence            4446777899999997655444444434688888888888876654333

>TIGR03689 pup_AAA proteasome ATPase

Probab=85.89  E-value=2.5  Score=45.43  Aligned_cols=55  Identities=13%  Similarity=0.086  Sum_probs=29.9

Q ss_pred             CCCCHHHHhhchHHHHHHHHHhC--CCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhH
Q 042872          200 GTLSFEELQALDDMEFANVVIFG--NRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       200 ~~~~fe~L~~l~~l~~~~~~~fG--~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF  257 (381)
                      ...+|+.+..+++....+....-  +..+-.++.--+   -..+.+|+.+|+|+|||...
T Consensus       177 p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl---~~p~GILLyGPPGTGKT~LA  233 (512)
T TIGR03689       177 PDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYDL---KPPKGVLLYGPPGCGKTLIA  233 (512)
T ss_pred             CCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccC---CCCcceEEECCCCCcHHHHH
Confidence            35677777766654444433221  111111111111   12467999999999999875

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=85.88  E-value=4.1  Score=44.09  Aligned_cols=64  Identities=14%  Similarity=0.120  Sum_probs=42.7

Q ss_pred             CCcHHHHHHHHHHHc-CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHH
Q 042872          225 AFRPLQHQACKASVA-KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQE  290 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~-GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~  290 (381)
                      .+-|+|++-+...|+ |-.+|+.-.-|-|||+-.+- +..+ .....+.++++...-...++..+..
T Consensus       198 ~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAla-IA~y-yraEwplliVcPAsvrftWa~al~r  262 (689)
T KOG1000|consen  198 RLLPFQREGVIFALERGGRILLADEMGLGKTIQALA-IARY-YRAEWPLLIVCPASVRFTWAKALNR  262 (689)
T ss_pred             hhCchhhhhHHHHHhcCCeEEEecccccchHHHHHH-HHHH-HhhcCcEEEEecHHHhHHHHHHHHH
Confidence            455889999888774 67888888999999976541 1111 1334567777766555555555554

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=85.80  E-value=2.7  Score=45.04  Aligned_cols=17  Identities=18%  Similarity=0.151  Sum_probs=14.5

Q ss_pred             CEEEECCCCCCchhhHH
Q 042872          242 DCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~  258 (381)
                      -.|+.+|.|+|||-+..
T Consensus        45 a~Lf~Gp~G~GKTT~Ar   61 (507)
T PRK06645         45 GYLLTGIRGVGKTTSAR   61 (507)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            58999999999997653

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=85.78  E-value=3.1  Score=41.98  Aligned_cols=36  Identities=31%  Similarity=0.407  Sum_probs=27.8

Q ss_pred             CCCCcHHHHHHHHHHH----cCC---CEEEECCCCCCchhhHH
Q 042872          223 NRAFRPLQHQACKASV----AKQ---DCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       223 ~~~fRpiQ~eAI~aiL----~Gr---DvLviaPTGsGKTLaF~  258 (381)
                      +..+.|.|..++..+.    .||   -.|+.+|.|.||+....
T Consensus         2 ~~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~   44 (319)
T PRK08769          2 TSAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVAL   44 (319)
T ss_pred             CccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHH
Confidence            4568889999888876    344   47899999999986653

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=85.77  E-value=3  Score=46.10  Aligned_cols=33  Identities=18%  Similarity=0.275  Sum_probs=23.0

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      +-+|+.+|+|+|||+..    ..+....+.+.+.+.+
T Consensus       488 ~giLL~GppGtGKT~la----kalA~e~~~~fi~v~~  520 (733)
T TIGR01243       488 KGVLLFGPPGTGKTLLA----KAVATESGANFIAVRG  520 (733)
T ss_pred             ceEEEECCCCCCHHHHH----HHHHHhcCCCEEEEeh
Confidence            56899999999999775    3444445666655543

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.

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=85.73  E-value=2.4  Score=45.78  Aligned_cols=27  Identities=22%  Similarity=0.196  Sum_probs=19.9

Q ss_pred             HHHHHHHHHcCCCEEEECCCCCCchhh
Q 042872          230 QHQACKASVAKQDCFVLLPTGGGKSLC  256 (381)
Q Consensus       230 Q~eAI~aiL~GrDvLviaPTGsGKTLa  256 (381)
                      +.+-+..+++++-+++++.||+|||.-
T Consensus        52 k~~F~~~l~~nQ~~v~vGetgsGKttQ   78 (699)
T KOG0925|consen   52 KEEFLKLLLNNQIIVLVGETGSGKTTQ   78 (699)
T ss_pred             HHHHHHHHhcCceEEEEecCCCCcccc
Confidence            444555555667788899999999954

>PRK06321 replicative DNA helicase; Provisional

Probab=85.41  E-value=5  Score=42.52  Aligned_cols=50  Identities=12%  Similarity=0.091  Sum_probs=33.3

Q ss_pred             CCE-EEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHH
Q 042872          241 QDC-FVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQE  290 (381)
Q Consensus       241 rDv-LviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~  290 (381)
                      .++ ++.+.+|.|||.-.+..........|.++.++.-.++..+....+-.
T Consensus       226 G~LiiiaarPgmGKTafal~ia~~~a~~~g~~v~~fSLEMs~~ql~~Rlla  276 (472)
T PRK06321        226 SNLMILAARPAMGKTALALNIAENFCFQNRLPVGIFSLEMTVDQLIHRIIC  276 (472)
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHhcCCeEEEEeccCCHHHHHHHHHH
Confidence            455 66789999999665444444433457888888888887765544433

>PRK05636 replicative DNA helicase; Provisional

Probab=85.21  E-value=5.5  Score=42.59  Aligned_cols=47  Identities=17%  Similarity=0.149  Sum_probs=31.3

Q ss_pred             CCE-EEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHH
Q 042872          241 QDC-FVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAV  287 (381)
Q Consensus       241 rDv-LviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~i  287 (381)
                      .++ ++.+.||.|||.-.+..+.....+.|.+++++...++..+....
T Consensus       265 G~Liiiaarpg~GKT~~al~~a~~~a~~~g~~v~~fSlEMs~~ql~~R  312 (505)
T PRK05636        265 GQMIIVAARPGVGKSTLALDFMRSASIKHNKASVIFSLEMSKSEIVMR  312 (505)
T ss_pred             CceEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEEeeCCHHHHHHH
Confidence            455 66789999999655444444433457788888888877665433

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=85.08  E-value=3.9  Score=43.11  Aligned_cols=50  Identities=18%  Similarity=0.280  Sum_probs=33.5

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHH--HHHhhcCCcEEEEeCCCCHHHHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQII--TLNLKFGIPATFLNSQQTVSQAAAVLQE  290 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~--~L~~~~gI~a~~l~g~~~~~e~~~il~~  290 (381)
                      .|+-+++.+|+|+|||.-.+ |+.  .+. ..|-+++.+....+.++..+.+..
T Consensus        20 ~g~~~Li~G~pGsGKT~la~-qfl~~g~~-~~ge~~lyvs~eE~~~~l~~~~~~   71 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTLFSI-QFLYNGII-HFDEPGVFVTFEESPQDIIKNARS   71 (484)
T ss_pred             CCeEEEEEcCCCCCHHHHHH-HHHHHHHH-hCCCCEEEEEEecCHHHHHHHHHH
Confidence            46789999999999996553 332  222 347788888877666654444443

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.

>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=84.86  E-value=1.8  Score=43.24  Aligned_cols=35  Identities=17%  Similarity=0.145  Sum_probs=27.1

Q ss_pred             CCCCCcHHHHHHHHHHH-cCCCEEEECCCCCCchhh
Q 042872          222 GNRAFRPLQHQACKASV-AKQDCFVLLPTGGGKSLC  256 (381)
Q Consensus       222 G~~~fRpiQ~eAI~aiL-~GrDvLviaPTGsGKTLa  256 (381)
                      .+..+.+.|..-+-.++ .+++++++++||+|||-.
T Consensus       124 ~~gt~~~~~~ayL~~~ie~~~siii~G~t~sGKTt~  159 (312)
T COG0630         124 EYGTISPEQAAYLWLAIEARKSIIICGGTASGKTTL  159 (312)
T ss_pred             hcCCCCHHHHHHHHHHHHcCCcEEEECCCCCCHHHH
Confidence            45567777777665554 578999999999999944

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=84.80  E-value=1.4  Score=50.38  Aligned_cols=16  Identities=19%  Similarity=0.127  Sum_probs=13.5

Q ss_pred             CE-EEECCCCCCchhhH
Q 042872          242 DC-FVLLPTGGGKSLCY  257 (381)
Q Consensus       242 Dv-LviaPTGsGKTLaF  257 (381)
                      .. |+.+|.|.|||.+.
T Consensus        39 HAyLFtGPpGtGKTTLA   55 (944)
T PRK14949         39 HAYLFTGTRGVGKTSLA   55 (944)
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            44 89999999999765

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=84.79  E-value=4.4  Score=36.28  Aligned_cols=34  Identities=15%  Similarity=0.219  Sum_probs=24.6

Q ss_pred             EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          243 CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       243 vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      +.+++++|+|||.....-+..|. ..|.++.++..
T Consensus         2 i~i~G~~gsGKTtl~~~l~~~l~-~~G~~V~viK~   35 (155)
T TIGR00176         2 LQIVGPKNSGKTTLIERLVKALK-ARGYRVATIKH   35 (155)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH-hcCCeEEEEec
Confidence            35789999999976644455565 46888877754

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=84.65  E-value=2.9  Score=40.50  Aligned_cols=33  Identities=21%  Similarity=0.349  Sum_probs=19.2

Q ss_pred             CEEE-ECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          242 DCFV-LLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       242 DvLv-iaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      .+++ .+|+|+|||....    .+....+.....+++.
T Consensus        44 ~~lll~G~~G~GKT~la~----~l~~~~~~~~~~i~~~   77 (316)
T PHA02544         44 NMLLHSPSPGTGKTTVAK----ALCNEVGAEVLFVNGS   77 (316)
T ss_pred             eEEEeeCcCCCCHHHHHH----HHHHHhCccceEeccC
Confidence            4555 7999999996532    2222334444555544

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=84.60  E-value=3.8  Score=45.27  Aligned_cols=50  Identities=16%  Similarity=0.040  Sum_probs=34.3

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQE  290 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~  290 (381)
                      ..+++|+++||+|||..+..-+.... +.|-.++++....+.+-...+...
T Consensus       180 ~gHtlV~GtTGsGKT~l~~~li~q~i-~~g~~vi~fDpkgD~el~~~~~~~  229 (643)
T TIGR03754       180 VGHTLVLGTTRVGKTRLAELLITQDI-RRGDVVIVFDPKGDADLLKRMYAE  229 (643)
T ss_pred             cCceEEECCCCCCHHHHHHHHHHHHH-HcCCeEEEEeCCCCHHHHHHHHHH
Confidence            57899999999999977642233333 356778888877776555555544

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.

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=84.40  E-value=0.47  Score=51.75  Aligned_cols=37  Identities=11%  Similarity=-0.050  Sum_probs=34.1

Q ss_pred             CCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          222 GNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       222 G~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      -.+.+..+|.++|..+-+|+++++.-.|-+||++||+
T Consensus       283 ~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~  319 (1034)
T KOG4150|consen  283 TGESGIAISLELLKFASEGRADGGNEARQAGKGTCPT  319 (1034)
T ss_pred             cccchhhhhHHHHhhhhhcccccccchhhcCCccCcc
Confidence            4457889999999999999999999999999999998

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=84.31  E-value=5.1  Score=42.17  Aligned_cols=45  Identities=18%  Similarity=0.145  Sum_probs=29.9

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQA  284 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~  284 (381)
                      .|.-+++.+|+|+|||.... |+..-....|-+++.+....+.++.
T Consensus       272 ~g~~~li~G~~G~GKT~l~~-~~~~~~~~~g~~~~yis~e~~~~~i  316 (509)
T PRK09302        272 RGSIILVSGATGTGKTLLAS-KFAEAACRRGERCLLFAFEESRAQL  316 (509)
T ss_pred             CCcEEEEEcCCCCCHHHHHH-HHHHHHHhCCCcEEEEEecCCHHHH
Confidence            35677889999999996553 3222222467888888776665543

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=84.24  E-value=8.4  Score=39.52  Aligned_cols=49  Identities=16%  Similarity=0.137  Sum_probs=33.7

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      |.=+++.++||.|||..-+..+..+....|.++.++...++..+....+
T Consensus       194 g~liviag~pg~GKT~~al~ia~~~a~~~g~~v~~fSlEm~~~~l~~Rl  242 (421)
T TIGR03600       194 GDLIVIGARPSMGKTTLALNIAENVALREGKPVLFFSLEMSAEQLGERL  242 (421)
T ss_pred             CceEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEECCCCHHHHHHHH
Confidence            4456778999999996665444454434578888888888776654433

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>PRK07773 replicative DNA helicase; Validated

Probab=84.15  E-value=6.1  Score=44.88  Aligned_cols=47  Identities=13%  Similarity=0.075  Sum_probs=33.3

Q ss_pred             EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHH
Q 042872          243 CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQ  289 (381)
Q Consensus       243 vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~  289 (381)
                      +++.+++|.|||.-.+..+.......+.++.++.-.++..+....+-
T Consensus       220 ivIagrPg~GKT~fal~ia~~~a~~~~~~V~~fSlEms~~ql~~R~~  266 (886)
T PRK07773        220 IIVAARPSMGKTTFGLDFARNCAIRHRLAVAIFSLEMSKEQLVMRLL  266 (886)
T ss_pred             EEEEeCCCCCcHHHHHHHHHHHHHhcCCeEEEEecCCCHHHHHHHHH
Confidence            57789999999976655555554345788888888888776544443

>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=84.05  E-value=2.6  Score=39.64  Aligned_cols=14  Identities=36%  Similarity=0.527  Sum_probs=12.4

Q ss_pred             EEEECCCCCCchhh
Q 042872          243 CFVLLPTGGGKSLC  256 (381)
Q Consensus       243 vLviaPTGsGKTLa  256 (381)
                      +++.+|+|+|||--
T Consensus        37 l~l~G~~G~GKTHL   50 (219)
T PF00308_consen   37 LFLYGPSGLGKTHL   50 (219)
T ss_dssp             EEEEESTTSSHHHH
T ss_pred             eEEECCCCCCHHHH
Confidence            78999999999953

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.

>PRK08506 replicative DNA helicase; Provisional

Probab=84.03  E-value=6.9  Score=41.27  Aligned_cols=47  Identities=9%  Similarity=0.029  Sum_probs=32.5

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      .=+++.|+||.|||.-.+..+.... ..|.+++++...++..+....+
T Consensus       193 ~LivIaarpg~GKT~fal~ia~~~~-~~g~~V~~fSlEMs~~ql~~Rl  239 (472)
T PRK08506        193 DLIIIAARPSMGKTTLCLNMALKAL-NQDKGVAFFSLEMPAEQLMLRM  239 (472)
T ss_pred             ceEEEEcCCCCChHHHHHHHHHHHH-hcCCcEEEEeCcCCHHHHHHHH
Confidence            3456678999999976654444443 3578888888888876655444

>PRK05748 replicative DNA helicase; Provisional

Probab=83.95  E-value=8  Score=40.18  Aligned_cols=49  Identities=8%  Similarity=-0.008  Sum_probs=33.5

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      |.=+++.++||.|||.--+..+.......|.++.++.-.++..+....+
T Consensus       203 G~livIaarpg~GKT~~al~ia~~~a~~~g~~v~~fSlEms~~~l~~R~  251 (448)
T PRK05748        203 NDLIIVAARPSVGKTAFALNIAQNVATKTDKNVAIFSLEMGAESLVMRM  251 (448)
T ss_pred             CceEEEEeCCCCCchHHHHHHHHHHHHhCCCeEEEEeCCCCHHHHHHHH
Confidence            3446778999999996655444444434588888888888877654443

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=83.78  E-value=3.5  Score=43.04  Aligned_cols=37  Identities=16%  Similarity=0.113  Sum_probs=21.5

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHh-hcCCcEEEEeC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNL-KFGIPATFLNS  277 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~-~~gI~a~~l~g  277 (381)
                      ..+++.+|+|+|||-..+--...+.+ ..+.++..+++
T Consensus       131 n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~  168 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITS  168 (440)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH
Confidence            35899999999999654311222221 12455555543

>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=83.71  E-value=0.65  Score=45.43  Aligned_cols=25  Identities=20%  Similarity=0.361  Sum_probs=20.3

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIIT  263 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~  263 (381)
                      .++.+|+++|||+|||..-.+.+..
T Consensus        32 ~~~pvLl~G~~GtGKT~li~~~l~~   56 (272)
T PF12775_consen   32 NGRPVLLVGPSGTGKTSLIQNFLSS   56 (272)
T ss_dssp             CTEEEEEESSTTSSHHHHHHHHHHC
T ss_pred             cCCcEEEECCCCCchhHHHHhhhcc
Confidence            6789999999999999987544433

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=83.71  E-value=0.89  Score=45.88  Aligned_cols=17  Identities=29%  Similarity=0.583  Sum_probs=15.0

Q ss_pred             CEEEECCCCCCchhhHH
Q 042872          242 DCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~  258 (381)
                      ++++++|||+|||.+|.
T Consensus         1 H~lv~g~tGsGKt~~~v   17 (384)
T cd01126           1 HVLVFAPTRSGKGVGFV   17 (384)
T ss_pred             CeeEecCCCCCCccEEE
Confidence            47999999999998776

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.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=83.64  E-value=2.5  Score=43.27  Aligned_cols=16  Identities=19%  Similarity=0.100  Sum_probs=13.6

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      .|..+|.|.|||.+..
T Consensus        41 ~lf~Gp~G~GKtt~A~   56 (397)
T PRK14955         41 YIFSGLRGVGKTTAAR   56 (397)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            7889999999996653

>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold

Probab=83.61  E-value=0.98  Score=48.05  Aligned_cols=45  Identities=18%  Similarity=0.214  Sum_probs=33.8

Q ss_pred             HHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEE
Q 042872          230 QHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFL  275 (381)
Q Consensus       230 Q~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l  275 (381)
                      +...|+.-+.+|+-|+.+.||+|||.+-+--.+.|. ..|+++.+.
T Consensus         9 ~~v~l~~~~~NRHGLIaGATGTGKTvTLqvlAE~fS-~~GVPVfla   53 (502)
T PF05872_consen    9 APVYLPLKMANRHGLIAGATGTGKTVTLQVLAEQFS-DAGVPVFLA   53 (502)
T ss_pred             CceecChhhccccceeeccCCCCceehHHHHHHHhh-hcCCcEEEe
Confidence            445667778899999999999999999874445555 467776543

This family is restricted to bacterial proteins, none of which have currently been characterised.

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=83.53  E-value=1.4  Score=49.00  Aligned_cols=38  Identities=24%  Similarity=0.182  Sum_probs=29.5

Q ss_pred             hCCC-CCcHHHHHHHHHHH----cCCCEEEECCCCCCchhhHH
Q 042872          221 FGNR-AFRPLQHQACKASV----AKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       221 fG~~-~fRpiQ~eAI~aiL----~GrDvLviaPTGsGKTLaF~  258 (381)
                      |+|. +|+.||.+-+..+.    .|+=.|.-.|||+||||.-+
T Consensus        10 F~fPy~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLi   52 (821)
T KOG1133|consen   10 FPFPYTPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLI   52 (821)
T ss_pred             cCCCCCchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHH
Confidence            4443 57789998887764    58866888999999998765

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=83.31  E-value=0.69  Score=47.00  Aligned_cols=25  Identities=28%  Similarity=0.365  Sum_probs=18.6

Q ss_pred             HHHHHHH-cCCCEEEECCCCCCchhh
Q 042872          232 QACKASV-AKQDCFVLLPTGGGKSLC  256 (381)
Q Consensus       232 eAI~aiL-~GrDvLviaPTGsGKTLa  256 (381)
                      +.+..+. .++++++.+|||||||-.
T Consensus       153 ~~l~~~v~~~~nilI~G~tGSGKTTl  178 (344)
T PRK13851        153 AFLHACVVGRLTMLLCGPTGSGKTTM  178 (344)
T ss_pred             HHHHHHHHcCCeEEEECCCCccHHHH
Confidence            3344433 578999999999999944

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=83.27  E-value=1.2  Score=45.79  Aligned_cols=24  Identities=17%  Similarity=0.249  Sum_probs=19.7

Q ss_pred             HHHHHcCCCEEEECCCCCCchhhH
Q 042872          234 CKASVAKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       234 I~aiL~GrDvLviaPTGsGKTLaF  257 (381)
                      |+.-...++++++++||+|||.+.
T Consensus        36 ~~~~~~~~h~~i~g~tGsGKt~~i   59 (410)
T cd01127          36 FPKDAEEAHTMIIGTTGTGKTTQI   59 (410)
T ss_pred             CCcchhhccEEEEcCCCCCHHHHH
Confidence            455556789999999999999865

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.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=83.16  E-value=3.1  Score=45.59  Aligned_cols=33  Identities=18%  Similarity=0.303  Sum_probs=24.0

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      +.+++.+|+|+|||...    ..+....+++.+.+.+
T Consensus       186 ~gill~G~~G~GKt~~~----~~~a~~~~~~f~~is~  218 (644)
T PRK10733        186 KGVLMVGPPGTGKTLLA----KAIAGEAKVPFFTISG  218 (644)
T ss_pred             CcEEEECCCCCCHHHHH----HHHHHHcCCCEEEEeh
Confidence            56999999999999875    3344456777666654

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=83.12  E-value=2.3  Score=43.34  Aligned_cols=30  Identities=17%  Similarity=0.185  Sum_probs=21.3

Q ss_pred             HHHHHHHHHH---cCC---CEEEECCCCCCchhhHH
Q 042872          229 LQHQACKASV---AKQ---DCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       229 iQ~eAI~aiL---~Gr---DvLviaPTGsGKTLaF~  258 (381)
                      .|..++.+++   .++   ..|..+|.|+|||-+..
T Consensus        40 gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStal   75 (346)
T KOG0989|consen   40 GQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTAL   75 (346)
T ss_pred             chHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHH
Confidence            4766666654   233   57889999999996653

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=83.10  E-value=1.4  Score=43.16  Aligned_cols=35  Identities=26%  Similarity=0.355  Sum_probs=29.0

Q ss_pred             CccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccc
Q 042872          320 SCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH  379 (381)
Q Consensus       320 ~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAH  379 (381)
                      ..+|.|+||+||.          .|...+.+.++               .+.+||||=-|
T Consensus       177 ~~~i~vGTP~Rl~----------kLle~~~L~l~---------------~l~~ivlD~s~  211 (252)
T PF14617_consen  177 RVHIAVGTPGRLS----------KLLENGALSLS---------------NLKRIVLDWSY  211 (252)
T ss_pred             CceEEEeChHHHH----------HHHHcCCCCcc---------------cCeEEEEcCCc
Confidence            5789999999996          24577888888               99999999644

>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A

Probab=83.08  E-value=7.9  Score=37.21  Aligned_cols=36  Identities=22%  Similarity=0.237  Sum_probs=26.2

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      ..-..+.+|+|+|||-+    +..|...+|..+++++-..
T Consensus        32 ~~~~~~~GpagtGKtet----ik~La~~lG~~~~vfnc~~   67 (231)
T PF12774_consen   32 NLGGALSGPAGTGKTET----IKDLARALGRFVVVFNCSE   67 (231)
T ss_dssp             TTEEEEESSTTSSHHHH----HHHHHHCTT--EEEEETTS
T ss_pred             CCCCCCcCCCCCCchhH----HHHHHHHhCCeEEEecccc
Confidence            34567899999999966    5777777888888887543

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=82.95  E-value=2.5  Score=45.19  Aligned_cols=16  Identities=19%  Similarity=0.146  Sum_probs=13.4

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      .|+.+|.|.|||.+..
T Consensus        41 ~Lf~Gp~G~GKTt~A~   56 (527)
T PRK14969         41 YLFTGTRGVGKTTLAR   56 (527)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5899999999997653

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=82.27  E-value=0.89  Score=45.85  Aligned_cols=18  Identities=22%  Similarity=0.331  Sum_probs=15.7

Q ss_pred             HcCCCEEEECCCCCCchh
Q 042872          238 VAKQDCFVLLPTGGGKSL  255 (381)
Q Consensus       238 L~GrDvLviaPTGsGKTL  255 (381)
                      ..++++++++|||+|||-
T Consensus       158 ~~~~nili~G~tgSGKTT  175 (332)
T PRK13900        158 ISKKNIIISGGTSTGKTT  175 (332)
T ss_pred             HcCCcEEEECCCCCCHHH
Confidence            356899999999999993

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=82.13  E-value=3.1  Score=45.53  Aligned_cols=18  Identities=22%  Similarity=0.314  Sum_probs=14.5

Q ss_pred             CCEEEECCCCCCchhhHH
Q 042872          241 QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~  258 (381)
                      ..+|+.+|.|+|||....
T Consensus        39 ~a~Lf~Gp~G~GKttlA~   56 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSAR   56 (620)
T ss_pred             ceEEEECCCCCChHHHHH
Confidence            346899999999997653

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=82.12  E-value=2  Score=44.99  Aligned_cols=35  Identities=20%  Similarity=0.369  Sum_probs=21.0

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      +.+++.+|+|.|||-.-.--...+. ..+.+++.+.
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~-~~~~~v~yi~  176 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALR-ESGGKILYVR  176 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHH-HcCCCEEEee
Confidence            4589999999999954321122222 2355665554

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=82.08  E-value=9.2  Score=38.83  Aligned_cols=87  Identities=22%  Similarity=0.247  Sum_probs=51.1

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKP  319 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~  319 (381)
                      |+=+-+.+|+|+|||...+.-+..+. +.|-.++.+........  ..+..+  |.                       .
T Consensus        53 G~ivEi~G~~ssGKttLaL~~ia~~q-~~g~~~a~ID~e~~ld~--~~a~~l--Gv-----------------------d  104 (322)
T PF00154_consen   53 GRIVEIYGPESSGKTTLALHAIAEAQ-KQGGICAFIDAEHALDP--EYAESL--GV-----------------------D  104 (322)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHH-HTT-EEEEEESSS---H--HHHHHT--T-------------------------
T ss_pred             CceEEEeCCCCCchhhhHHHHHHhhh-cccceeEEecCcccchh--hHHHhc--Cc-----------------------c
Confidence            55567889999999977765455554 45777888876544322  112221  10                       0


Q ss_pred             CccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEec
Q 042872          320 SCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDE  377 (381)
Q Consensus       320 ~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDE  377 (381)
                      --+++|+.|+.-.   ...+....|.+.+                    .+.+||||=
T Consensus       105 l~rllv~~P~~~E---~al~~~e~lirsg--------------------~~~lVVvDS  139 (322)
T PF00154_consen  105 LDRLLVVQPDTGE---QALWIAEQLIRSG--------------------AVDLVVVDS  139 (322)
T ss_dssp             GGGEEEEE-SSHH---HHHHHHHHHHHTT--------------------SESEEEEE-
T ss_pred             ccceEEecCCcHH---HHHHHHHHHhhcc--------------------cccEEEEec
Confidence            1368898887642   3345666676676                    788899984

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>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=82.08  E-value=1.6  Score=35.92  Aligned_cols=29  Identities=28%  Similarity=0.418  Sum_probs=20.3

Q ss_pred             EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEE
Q 042872          243 CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFL  275 (381)
Q Consensus       243 vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l  275 (381)
                      +++.+|+|+|||-.-    ..|.+.+|++.+.+
T Consensus         2 I~I~G~~gsGKST~a----~~La~~~~~~~i~~   30 (121)
T PF13207_consen    2 IIISGPPGSGKSTLA----KELAERLGFPVISM   30 (121)
T ss_dssp             EEEEESTTSSHHHHH----HHHHHHHTCEEEEE
T ss_pred             EEEECCCCCCHHHHH----HHHHHHHCCeEEEe
Confidence            578899999999664    34454567765544

...

>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=82.00  E-value=4.7  Score=33.91  Aligned_cols=15  Identities=33%  Similarity=0.390  Sum_probs=12.4

Q ss_pred             EEEECCCCCCchhhH
Q 042872          243 CFVLLPTGGGKSLCY  257 (381)
Q Consensus       243 vLviaPTGsGKTLaF  257 (381)
                      +++++|+|+|||-..
T Consensus         2 ii~~G~pgsGKSt~a   16 (143)
T PF13671_consen    2 IILCGPPGSGKSTLA   16 (143)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            588999999999443

...

>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=81.81  E-value=1.6  Score=37.13  Aligned_cols=32  Identities=22%  Similarity=0.391  Sum_probs=20.5

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      +||+.+|+|+|||... .++   .+.++.+...+..
T Consensus         1 ~vlL~G~~G~GKt~l~-~~l---a~~~~~~~~~i~~   32 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLA-REL---AALLGRPVIRINC   32 (139)
T ss_dssp             EEEEEESSSSSHHHHH-HHH---HHHHTCEEEEEE-
T ss_pred             CEEEECCCCCCHHHHH-HHH---HHHhhcceEEEEe
Confidence            4899999999999775 233   3334555544443

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.

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=81.53  E-value=0.61  Score=49.40  Aligned_cols=54  Identities=22%  Similarity=0.450  Sum_probs=41.5

Q ss_pred             CchhhHHHH------HHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEE
Q 042872          252 GKSLCYQDQ------IITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLY  325 (381)
Q Consensus       252 GKTLaF~dQ------v~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~  325 (381)
                      |||++|.+.      ++-+-+.|||+.++++|..+..-|.-++.+...|                         -|+|||
T Consensus       269 gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG-------------------------~YdivI  323 (569)
T KOG0346|consen  269 GKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKG-------------------------LYDIVI  323 (569)
T ss_pred             CceEEEEechhhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCc-------------------------ceeEEE
Confidence            677777622      2222347999999999999988888888887766                         689999


Q ss_pred             ECccc
Q 042872          326 VTPER  330 (381)
Q Consensus       326 aTPEr  330 (381)
                      +|-+.
T Consensus       324 AtD~s  328 (569)
T KOG0346|consen  324 ATDDS  328 (569)
T ss_pred             EccCc
Confidence            99854

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=81.52  E-value=0.91  Score=40.95  Aligned_cols=23  Identities=22%  Similarity=0.179  Sum_probs=16.9

Q ss_pred             EEEECccccccCcchHHHHHHHH
Q 042872          323 LLYVTPERIVGNQSFSEVLKCLH  345 (381)
Q Consensus       323 IL~aTPErL~~~~~f~~~L~~L~  345 (381)
                      -+|=||+-...++.|...|....
T Consensus        39 ~~IDTPGEyiE~~~~y~aLi~ta   61 (143)
T PF10662_consen   39 NTIDTPGEYIENPRFYHALIVTA   61 (143)
T ss_pred             cEEECChhheeCHHHHHHHHHHH
Confidence            44778888888888877775543

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>PF13173 AAA_14: AAA domain

Probab=81.48  E-value=4.7  Score=34.19  Aligned_cols=18  Identities=22%  Similarity=0.290  Sum_probs=14.9

Q ss_pred             CCCEEEECCCCCCchhhH
Q 042872          240 KQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF  257 (381)
                      ++=+++.+|.|+|||-.-
T Consensus         2 ~~~~~l~G~R~vGKTtll   19 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLL   19 (128)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            456789999999999665

>PHA00350 putative assembly protein

Probab=81.42  E-value=2.5  Score=44.06  Aligned_cols=16  Identities=19%  Similarity=-0.027  Sum_probs=13.6

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      .|+.++.|||||+...
T Consensus         4 ~l~tG~pGSGKT~~aV   19 (399)
T PHA00350          4 YAIVGRPGSYKSYEAV   19 (399)
T ss_pred             EEEecCCCCchhHHHH
Confidence            4678999999998876

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=81.39  E-value=2.8  Score=46.38  Aligned_cols=18  Identities=28%  Similarity=0.433  Sum_probs=16.8

Q ss_pred             CCEEEECCCCCCchhhHH
Q 042872          241 QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~  258 (381)
                      +++++++|||+|||..|.
T Consensus       140 ~hvlviApTgSGKgvg~V  157 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVV  157 (670)
T ss_pred             ceEEEEecCCCCceeeeh
Confidence            589999999999999996

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

Probab=81.21  E-value=3.3  Score=46.80  Aligned_cols=37  Identities=16%  Similarity=0.124  Sum_probs=22.4

Q ss_pred             CCCE-EEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          240 KQDC-FVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       240 GrDv-LviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      .+.+ ++-+|.|+|||-+....+.......+.+++++.
T Consensus        48 ~~~V~vVRSpMGTGKTtaLi~wLk~~l~~~~~~VLvVS   85 (824)
T PF02399_consen   48 KRGVLVVRSPMGTGKTTALIRWLKDALKNPDKSVLVVS   85 (824)
T ss_pred             CCCeEEEECCCCCCcHHHHHHHHHHhccCCCCeEEEEE
Confidence            4554 666999999997765444433112345666653

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

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=81.20  E-value=5  Score=42.52  Aligned_cols=15  Identities=27%  Similarity=0.350  Sum_probs=13.1

Q ss_pred             EEEECCCCCCchhhH
Q 042872          243 CFVLLPTGGGKSLCY  257 (381)
Q Consensus       243 vLviaPTGsGKTLaF  257 (381)
                      +|+.+|.|+|||.+.
T Consensus        39 ~Lf~GPpGtGKTTlA   53 (472)
T PRK14962         39 YIFAGPRGTGKTTVA   53 (472)
T ss_pred             EEEECCCCCCHHHHH
Confidence            689999999999665

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=81.15  E-value=5.1  Score=43.66  Aligned_cols=16  Identities=25%  Similarity=0.328  Sum_probs=13.4

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      .|+.+|.|+|||-+..
T Consensus        38 ~Lf~Gp~G~GKTt~A~   53 (584)
T PRK14952         38 YLFSGPRGCGKTSSAR   53 (584)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5899999999996653

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=81.11  E-value=3.5  Score=46.48  Aligned_cols=60  Identities=17%  Similarity=0.191  Sum_probs=35.4

Q ss_pred             CcHHHHHHHHHHH----cCCCEEEECCCCCCchh---hHHHHHHHHHh--hcCCcEEEEeCCCCHHHHHHHH
Q 042872          226 FRPLQHQACKASV----AKQDCFVLLPTGGGKSL---CYQDQIITLNL--KFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       226 fRpiQ~eAI~aiL----~GrDvLviaPTGsGKTL---aF~dQv~~L~~--~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      +-|+|++.+.-+.    ++.--|+-=.-|-|||+   +|+   ..|-.  ++--++++++..+-..++..-+
T Consensus       206 Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFL---aaL~~S~k~~~paLIVCP~Tii~qW~~E~  274 (923)
T KOG0387|consen  206 LFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFL---AALHHSGKLTKPALIVCPATIIHQWMKEF  274 (923)
T ss_pred             hhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHH---HHHhhcccccCceEEEccHHHHHHHHHHH
Confidence            4588999998876    34455666678999994   454   22210  1223566666655444443333

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=80.86  E-value=2.2  Score=46.95  Aligned_cols=45  Identities=20%  Similarity=0.330  Sum_probs=33.4

Q ss_pred             CCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCC
Q 042872          224 RAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGI  270 (381)
Q Consensus       224 ~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI  270 (381)
                      ..++|-|++||...  ...++|+|..|||||.+....+..|-...|+
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i   47 (726)
T TIGR01073         3 AHLNPEQREAVKTT--EGPLLIMAGAGSGKTRVLTHRIAHLIAEKNV   47 (726)
T ss_pred             cccCHHHHHHHhCC--CCCEEEEeCCCCCHHHHHHHHHHHHHHcCCC
Confidence            35889999999753  4689999999999998876555555433343

Designed to identify pcrA members of the uvrD/rep subfamily.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=80.82  E-value=4.6  Score=44.32  Aligned_cols=16  Identities=19%  Similarity=0.183  Sum_probs=13.4

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      .|+.+|.|.|||.+..
T Consensus        41 ~Lf~Gp~GvGKTtlAr   56 (618)
T PRK14951         41 YLFTGTRGVGKTTVSR   56 (618)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            4899999999997653

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=80.63  E-value=5.6  Score=40.08  Aligned_cols=33  Identities=18%  Similarity=0.258  Sum_probs=25.1

Q ss_pred             CcHHHHHHHHHHHcC-C---CEEEECCCCCCchhhHH
Q 042872          226 FRPLQHQACKASVAK-Q---DCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       226 fRpiQ~eAI~aiL~G-r---DvLviaPTGsGKTLaF~  258 (381)
                      ..|+|...+..++.. |   -.|+.+|.|.||+....
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~   40 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAE   40 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHH
Confidence            357888888888754 2   47889999999996653

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=80.59  E-value=10  Score=40.00  Aligned_cols=52  Identities=15%  Similarity=0.215  Sum_probs=34.9

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQE  290 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~  290 (381)
                      .|+=+++.+++|+|||.-.+.-+.......|-+++.+....+.++....+..
T Consensus        30 ~Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyis~ee~~~~i~~~~~~   81 (509)
T PRK09302         30 KGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFVTFEESPEDIIRNVAS   81 (509)
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEEEccCCHHHHHHHHHH
Confidence            4677899999999999654322222222348889888888777765555444

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=80.48  E-value=6.2  Score=42.73  Aligned_cols=16  Identities=19%  Similarity=0.108  Sum_probs=13.5

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      .|+.+|.|+|||....
T Consensus        41 ~Lf~Gp~GvGKTTlAr   56 (546)
T PRK14957         41 YLFTGTRGVGKTTLGR   56 (546)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6889999999997653

>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=80.31  E-value=1.1  Score=42.70  Aligned_cols=30  Identities=20%  Similarity=0.309  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHH-cCCCEEEECCCCCCchhhH
Q 042872          228 PLQHQACKASV-AKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       228 piQ~eAI~aiL-~GrDvLviaPTGsGKTLaF  257 (381)
                      +...+.+...+ .+..+++.+|||||||-..
T Consensus       114 ~~~~~~l~~~v~~~~~ili~G~tGSGKTT~l  144 (270)
T PF00437_consen  114 EEIAEFLRSAVRGRGNILISGPTGSGKTTLL  144 (270)
T ss_dssp             HHHHHHHHHCHHTTEEEEEEESTTSSHHHHH
T ss_pred             HHHHHHHhhccccceEEEEECCCccccchHH
Confidence            34444555443 4679999999999999554

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 ....

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=80.21  E-value=5.6  Score=44.45  Aligned_cols=16  Identities=25%  Similarity=0.308  Sum_probs=14.2

Q ss_pred             CEEEECCCCCCchhhH
Q 042872          242 DCFVLLPTGGGKSLCY  257 (381)
Q Consensus       242 DvLviaPTGsGKTLaF  257 (381)
                      .+++.+|+|+|||...
T Consensus        54 slLL~GPpGtGKTTLA   69 (725)
T PRK13341         54 SLILYGPPGVGKTTLA   69 (725)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            7899999999999665

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	381
2v1x_A	591	Crystal Structure Of Human Recq-Like Dna Helicase L		4e-09
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		2e-08
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		2e-07

>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase Length = 591

Iteration: 1
 Score = 59.3 bits (142), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 46/182 (25%), Positives = 68/182 (37%), Gaps = 65/182 (35%)
Query: 220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ--------------------- 258
           +F    FRPLQ +    ++A ++ F+++PTGGGKSLCYQ                     
Sbjct: 39  VFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLISLME 98
Query: 259 DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDK 318
           DQ++ L  + GI AT LN+  +      V  E+                           
Sbjct: 99  DQLMVLK-QLGISATMLNASSSKEHVKWVHAEMVN-----------------------KN 134
Query: 319 PSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEA 378
              KL+YVTPE+I  ++ F   L+  +                      R+     VDE 
Sbjct: 135 SELKLIYVTPEKIAKSKMFMSRLEKAYE--------------------ARRFTRIAVDEV 174
Query: 379 HC 380
           HC
Sbjct: 175 HC 176

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 39/132 (29%), Positives = 54/132 (40%), Gaps = 45/132 (34%)
Query: 221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLN--------------- 265
           FG + FRP Q +     ++ +DC V++PTGGGKSLCYQ   + LN               
Sbjct: 21  FGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLISLMKD 80
Query: 266 -----LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPS 320
                   G+ A  LNS QT  Q   V+   R G +                        
Sbjct: 81  QVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQI------------------------ 116
Query: 321 CKLLYVTPERIV 332
            +LLY+ PER++
Sbjct: 117 -RLLYIAPERLM 127

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 39/131 (29%), Positives = 51/131 (38%), Gaps = 45/131 (34%)
Query: 221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLN--------------- 265
           FG + FRP Q +     ++ +DC V+ PTGGGKSLCYQ   + LN               
Sbjct: 21  FGYQQFRPGQEEIIDTVLSGRDCLVVXPTGGGKSLCYQIPALLLNGLTVVVSPLISLXKD 80
Query: 266 -----LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPS 320
                   G+ A  LNS QT  Q   V    R G +                        
Sbjct: 81  QVDQLQANGVAAACLNSTQTREQQLEVXTGCRTGQI------------------------ 116
Query: 321 CKLLYVTPERI 331
            +LLY+ PER+
Sbjct: 117 -RLLYIAPERL 126

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	381
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	2e-37
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	5e-28
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A* Length = 591

 Score =  141 bits (358), Expect = 2e-37
 Identities = 45/183 (24%), Positives = 67/183 (36%), Gaps = 65/183 (35%)

Query: 220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ--------------------- 258
           +F    FRPLQ +    ++A ++ F+++PTGGGKSLCYQ                     
Sbjct: 39  VFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLISLME 98

Query: 259 DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDK 318
           DQ++ L  + GI AT LN+  +      V  E+                           
Sbjct: 99  DQLMVLK-QLGISATMLNASSSKEHVKWVHAEMVNK-----------------------N 134

Query: 319 PSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEA 378
              KL+YVTPE+I  ++ F   L+  +                       +     VDE 
Sbjct: 135 SELKLIYVTPEKIAKSKMFMSRLEKAYEAR--------------------RFTRIAVDEV 174

Query: 379 HCV 381
           HC 
Sbjct: 175 HCC 177

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A* Length = 523

 Score =  114 bits (287), Expect = 5e-28
 Identities = 49/183 (26%), Positives = 66/183 (36%), Gaps = 72/183 (39%)

Query: 220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ--------------------- 258
            FG + FRP Q +     ++ +DC V++PTGGGKSLCYQ                     
Sbjct: 20  TFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLISLMK 79

Query: 259 DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDK 318
           DQ+  L    G+ A  LNS QT  Q   V+   R G +                      
Sbjct: 80  DQVDQLQA-NGVAAACLNSTQTREQQLEVMTGCRTGQI---------------------- 116

Query: 319 PSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEA 378
              +LLY+ PER++   +F E L                                 VDEA
Sbjct: 117 ---RLLYIAPERLM-LDNFLEHLA------------------------HWNPVLLAVDEA 148

Query: 379 HCV 381
           HC+
Sbjct: 149 HCI 151

>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 = 61.0 bits (147), Expect = 3e-10
 Identities = 38/364 (10%), Positives = 94/364 (25%), Gaps = 136/364 (37%)

Query: 29  KSLNRL-----ISLYGDDGQDFISVEHCGDDFIATLAETMQDSEE---------W----- 69
           ++L  L     + + G  G         G  ++A   +     +          W     
Sbjct: 142 QALLELRPAKNVLIDGVLG--------SGKTWVA--LDVCLSYKVQCKMDFKIFWLNLKN 191

Query: 70  ----DDLQAMESEACGALNNMFDKRVIDNNQANDNDNSREYIDILDDSPEPKRR------ 119
               + +  M       L  +     ID N  + +D+S      +       RR      
Sbjct: 192 CNSPETVLEM-------LQKLL--YQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKP 242

Query: 120 --PTLMELDSLSDTEDLD-FTIPKQKDAILNLSSCPDGRSQIFTPSSVKHSSKSVDCKSG 176
               L+ L ++ + +  + F +                                  CK  
Sbjct: 243 YENCLLVLLNVQNAKAWNAFNL---------------------------------SCKIL 269

Query: 177 VSTSSAS---SVSNKKRSSLISDNEHGTLSFEELQALDDMEFANVVIFGNRAFRPLQHQA 233
           ++T        +S    + +  D+   TL+ +E+++L        +   +   + L  + 
Sbjct: 270 LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL----LLKYL---DCRPQDLPREV 322

Query: 234 CKAS------VAK------------------------QDCFVLLPTGGGKSLCYQD-QII 262
              +      +A+                        +    +L     +   +    + 
Sbjct: 323 LTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK-MFDRLSVF 381

Query: 263 TLNLKFGIPATFLN---SQQTVSQAAAVLQELRQGLVLSQH-----YFLHQLIFVLTCAS 314
             +    IP   L+        S    V+ +L +  ++ +        +  +   L    
Sbjct: 382 PPSAH--IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKL 439

Query: 315 RKDK 318
             + 
Sbjct: 440 ENEY 443

>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 = 48.3 bits (114), Expect = 3e-06
 Identities = 60/430 (13%), Positives = 118/430 (27%), Gaps = 124/430 (28%)

Query: 4   HDFEFEKARLLSLALEFGFDQDSANKSLNRLISLYGDDGQDFISVE----HCGDDFIATL 59
                 +A L  L              L  L+ L   + Q+  +       C       L
Sbjct: 225 LRIHSIQAELRRL-----LKSKPYENCL--LV-L--LNVQNAKAWNAFNLSC-----KIL 269

Query: 60  AETMQDSEEWDDLQAMESEACGALNNMFDKRVIDNNQANDNDNSRE----YIDI-LDDSP 114
             T +  +  D L A                +  ++     D  +     Y+D    D P
Sbjct: 270 LTT-RFKQVTDFLSA---------ATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP 319

Query: 115 E--PKRRPTLMEL--DSLSDTED-----LDFTIPKQKDAI---LNLSSCPDGRSQ----- 157
                  P  + +  +S+ D              K    I   LN+    + R       
Sbjct: 320 REVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS 379

Query: 158 IFTPSSVKHSSKSVDCK--SGVSTSSASSVSNK--KRSSLISDNEHGTLSFEELQALDDM 213
           +F P S    +  +       V  S    V NK  K S +    +  T+S   +     +
Sbjct: 380 VF-PPSAHIPTI-LLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKV 437

Query: 214 EFANVVIFGNRAFRPLQHQACKASVAKQDCF----VLLPTGGGKSLCY---------QDQ 260
           +  N             H++          F    ++ P        +           +
Sbjct: 438 KLEN---------EYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPE 488

Query: 261 ------IITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCAS 314
                 ++ L+ +F +     +     + + ++L  L+Q L   + Y             
Sbjct: 489 RMTLFRMVFLDFRF-LEQKIRHDSTAWNASGSILNTLQQ-LKFYKPYI------------ 534

Query: 315 RKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLA--- 371
             + P         ER+V     + +L  L +           +++   +T   ++A   
Sbjct: 535 CDNDP-------KYERLV-----NAILDFLPKIE--------ENLICSKYTDLLRIALMA 574

Query: 372 --GFVVDEAH 379
               + +EAH
Sbjct: 575 EDEAIFEEAH 584

>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 = 45.6 bits (107), Expect = 2e-05
 Identities = 57/359 (15%), Positives = 109/359 (30%), Gaps = 94/359 (26%)

Query: 48  VEHCGDDFIATLAETMQDSEEWDDLQAMESEACGALNNMFDKRVIDN--NQANDNDNSRE 105
            ++   D ++   +   D+ +  D+Q M         ++  K  ID+     +    +  
Sbjct: 14  HQYQYKDILSVFEDAFVDNFDCKDVQDM-------PKSILSKEEIDHIIMSKDAVSGTLR 66

Query: 106 YIDILDDSPEP--KRRPTLMELDSLSDTEDLDF------TIPKQKDAILNL-SSCPD--- 153
               L    E   ++    +E + L    +  F      T  +Q   +  +     D   
Sbjct: 67  LFWTLLSKQEEMVQK---FVE-EVLRI--NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLY 120

Query: 154 GRSQIFTPSSVKHSSKSVDCKSGV-STSSASSV-------SNKKRSSLISDNEHGTLSFE 205
             +Q+F   +V      +  +  +     A +V       S K  + +  D         
Sbjct: 121 NDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK--TWVALD----VCLSY 174

Query: 206 ELQALDDMEFANVVIF----GNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQI 261
           ++Q    M+F    IF     N          C +    +    +L     + L YQ   
Sbjct: 175 KVQ--CKMDFK---IFWLNLKN----------CNSP---ETVLEML-----QKLLYQ--- 208

Query: 262 ITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVL--TCASRKDKP 319
           I  N          N +  +    A L+ L     L    + + L+ VL     ++    
Sbjct: 209 IDPNWTSR-SDHSSNIKLRIHSIQAELRRL-----LKSKPYENCLL-VLLNVQNAKAWNA 261

Query: 320 ---SCKLLYVTPER----IVGNQSFSEVLKCLHRKG-------SIRLKVLTTDVVVLPH 364
              SCK+L  T  +     +   + + +    H          S+ LK L      LP 
Sbjct: 262 FNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR 320

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	381
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.85
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.84
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.83
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.82
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.81
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.81
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.8
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.79
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.79
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.79
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.78
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.78
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.78
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.77
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.77
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.77
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.77
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.76
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.75
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.75
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.74
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.73
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.73
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.72
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.72
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.72
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.7
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.7
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.69
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.67
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.66
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.65
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.63
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.62
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.62
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.61
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.59
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.56
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.55
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.55
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.55
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.54
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.53
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.52
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.52
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.51
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.5
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.5
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.49
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.43
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.42
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.4
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.4
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.36
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.35
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.34
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.33
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.32
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.29
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.27
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.25
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.25
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.16
3h1t_A	590	Type I site-specific restriction-modification syst	99.05
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.04
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	98.98
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	98.96
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	98.94
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.94
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.88
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.84
1yks_A	440	Genome polyprotein [contains: flavivirin protease	98.82
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.74
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	98.66
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	98.63
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.6
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	98.57
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.57
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	98.53
3jux_A	822	Protein translocase subunit SECA; protein transloc	98.22
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	97.8
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.55
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	96.55
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	96.54
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	96.43
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.21
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	95.04
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	94.88
2chg_A	226	Replication factor C small subunit; DNA-binding pr	94.8
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	94.59
3bos_A	242	Putative DNA replication factor; P-loop containing	94.39
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	94.38
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	94.37
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	94.05
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	93.86
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	93.83
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	93.81
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	93.58
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	93.5
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	93.4
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	93.35
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	93.16
2r6a_A	454	DNAB helicase, replicative helicase; replication,	92.97
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	92.93
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	92.82
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	92.79
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	92.52
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	92.51
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	92.37
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	92.25
1u94_A	356	RECA protein, recombinase A; homologous recombinat	92.11
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	92.11
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	91.92
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	91.87
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	91.85
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	91.69
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	91.65
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	91.63
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	91.14
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	91.07
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	90.91
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	90.77
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	90.68
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	90.67
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	90.63
2cvh_A	220	DNA repair and recombination protein RADB; filamen	90.62
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	90.5
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	90.42
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	90.35
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	90.31
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	90.28
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	90.22
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	90.1
2xxa_A	433	Signal recognition particle protein; protein trans	90.1
1xp8_A	366	RECA protein, recombinase A; recombination, radior	90.06
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	90.03
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	90.02
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	89.56
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	89.56
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	89.5
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	89.42
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	89.26
2chq_A	319	Replication factor C small subunit; DNA-binding pr	89.26
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	89.23
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	89.17
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	89.1
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	89.07
3pvs_A	447	Replication-associated recombination protein A; ma	88.91
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	88.89
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	88.45
2z43_A	324	DNA repair and recombination protein RADA; archaea	88.25
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	88.19
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	88.12
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	88.12
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	88.1
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	87.86
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	87.81
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	87.72
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	87.63
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	87.53
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	87.4
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	87.39
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	87.23
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	86.64
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	86.34
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	85.68
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	84.97
3co5_A	143	Putative two-component system transcriptional RES	84.87
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	84.76
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	84.33
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	84.17
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	83.84
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	83.28
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	83.18
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	83.07
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	82.29
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	82.22
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	82.17
4a74_A	231	DNA repair and recombination protein RADA; hydrola	82.15
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	82.02
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	81.78
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	81.43
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	81.17
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	81.17
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	81.08
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	80.91
2bzb_A	62	Conserved domain protein; transferase, phosphatase	80.87
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	80.86
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	80.46
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	80.24

>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=99.85  E-value=1.3e-21  Score=204.27  Aligned_cols=126  Identities=36%  Similarity=0.624  Sum_probs=105.8

Q ss_pred             HHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------HHHHHHHhhcCC
Q 042872          212 DMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------DQIITLNLKFGI  270 (381)
Q Consensus       212 ~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------dQv~~L~~~~gI  270 (381)
                      .+...+.+.|||..|||+|.++|++++.|+|+|++||||+|||+||+                     +|+..|. .+|+
T Consensus        31 ~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~~g~~lVisP~~~L~~q~~~~l~-~~gi  109 (591)
T 2v1x_A           31 KVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLISLMEDQLMVLK-QLGI  109 (591)
T ss_dssp             HHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTSSSEEEEECSCHHHHHHHHHHHH-HHTC
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHcCCcEEEEeCHHHHHHHHHHHHH-hcCC
Confidence            35566777799999999999999999999999999999999999998                     6778887 5799


Q ss_pred             cEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCc
Q 042872          271 PATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSI  350 (381)
Q Consensus       271 ~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~  350 (381)
                      ++..++|+.+..++..++..+.                       ...+.++|||+|||+|..+..|...+......+  
T Consensus       110 ~~~~l~~~~~~~~~~~~~~~l~-----------------------~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~~~--  164 (591)
T 2v1x_A          110 SATMLNASSSKEHVKWVHAEMV-----------------------NKNSELKLIYVTPEKIAKSKMFMSRLEKAYEAR--  164 (591)
T ss_dssp             CEEECCSSCCHHHHHHHHHHHH-----------------------CTTCCCCEEEECHHHHHSCHHHHHHHHHHHHTT--
T ss_pred             cEEEEeCCCCHHHHHHHHHHhh-----------------------cccCCCCEEEEChhHhhccHHHHHHHHhhhhcc--
Confidence            9999999999888877777763                       223478999999999986567777766554333  


Q ss_pred             cccccccccccccccccCCccEEEEeccccC
Q 042872          351 RLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       351 ~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                        ++.+|||||||||
T Consensus       165 ------------------~i~~iViDEAH~i  177 (591)
T 2v1x_A          165 ------------------RFTRIAVDEVHCC  177 (591)
T ss_dssp             ------------------CEEEEEEETGGGG
T ss_pred             ------------------CCcEEEEECcccc
Confidence                              8999999999996

>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=99.84  E-value=1.9e-21  Score=199.29  Aligned_cols=127  Identities=40%  Similarity=0.635  Sum_probs=105.5

Q ss_pred             HHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------HHHH
Q 042872          204 FEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------DQII  262 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------dQv~  262 (381)
                      |+.+..-+++...+.+.|||..|||+|.++|+++++|+|+|++||||+|||+||+                     +|+.
T Consensus         4 fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~~g~~lvi~P~~aL~~q~~~   83 (523)
T 1oyw_A            4 AEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLISLMKDQVD   83 (523)
T ss_dssp             CCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHSSSEEEEECSCHHHHHHHHH
T ss_pred             hhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHhCCCEEEECChHHHHHHHHH
Confidence            3444445557777878899999999999999999999999999999999999998                     6788


Q ss_pred             HHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHH
Q 042872          263 TLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLK  342 (381)
Q Consensus       263 ~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~  342 (381)
                      .+. .+|+++..++++.+..++...+..+..|                         .++|+|+|||+|. +..|...+.
T Consensus        84 ~l~-~~gi~~~~l~~~~~~~~~~~~~~~~~~~-------------------------~~~ilv~Tpe~l~-~~~~~~~l~  136 (523)
T 1oyw_A           84 QLQ-ANGVAAACLNSTQTREQQLEVMTGCRTG-------------------------QIRLLYIAPERLM-LDNFLEHLA  136 (523)
T ss_dssp             HHH-HTTCCEEEECTTSCHHHHHHHHHHHHHT-------------------------CCSEEEECHHHHT-STTHHHHHT
T ss_pred             HHH-HcCCcEEEEeCCCCHHHHHHHHHHHhcC-------------------------CCCEEEECHHHHh-ChHHHHHHh
Confidence            887 5899999999999988887777777654                         6899999999997 455544432


Q ss_pred             HHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          343 CLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       343 ~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                          ..                    ++.+||||||||+
T Consensus       137 ----~~--------------------~~~~vViDEaH~i  151 (523)
T 1oyw_A          137 ----HW--------------------NPVLLAVDEAHCI  151 (523)
T ss_dssp             ----TS--------------------CEEEEEESSGGGG
T ss_pred             ----hC--------------------CCCEEEEeCcccc
Confidence                12                    7999999999996

>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=99.83  E-value=2e-20  Score=171.13  Aligned_cols=54  Identities=20%  Similarity=0.161  Sum_probs=43.8

Q ss_pred             HHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          204 FEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      |+.+..-+.+...+.+ +||..|||+|.++|+.++.|+|+++.+|||+|||++|+
T Consensus        31 f~~~~l~~~l~~~l~~-~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~   84 (242)
T 3fe2_A           31 FYEANFPANVMDVIAR-QNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYL   84 (242)
T ss_dssp             TTTTTCCHHHHHHHHT-TTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHH
T ss_pred             HhhcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHH
Confidence            3334333344444433 89999999999999999999999999999999999997

>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=99.82  E-value=5e-20  Score=166.03  Aligned_cols=145  Identities=23%  Similarity=0.262  Sum_probs=88.9

Q ss_pred             CCCHHH-HhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHH-HHHHH-------hhcCCc
Q 042872          201 TLSFEE-LQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQ-IITLN-------LKFGIP  271 (381)
Q Consensus       201 ~~~fe~-L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQ-v~~L~-------~~~gI~  271 (381)
                      ..+|+. +...+++..++.+ +||..|||+|.++|+.++.|+|+++.+|||+|||++|+-- +..+.       ...+.+
T Consensus        18 ~~~f~~~~~l~~~l~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~   96 (228)
T 3iuy_A           18 TCRFKDAFQQYPDLLKSIIR-VGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPG   96 (228)
T ss_dssp             CCSHHHHHTTCHHHHHHHHH-HTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------CCCS
T ss_pred             hhhHhhhhccCHHHHHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCc
Confidence            345777 5656666666655 7999999999999999999999999999999999999721 22221       124566


Q ss_pred             EEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhccc-C-------CCCCccEEEECccccccCcchHHHHHH
Q 042872          272 ATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASR-K-------DKPSCKLLYVTPERIVGNQSFSEVLKC  343 (381)
Q Consensus       272 a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~-~-------~~~~~~IL~aTPErL~~~~~f~~~L~~  343 (381)
                      ++++...  .+-..++.+.+++-        ....+......++ .       ....++|+|+|||+|..          
T Consensus        97 ~lil~Pt--~~L~~q~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~----------  156 (228)
T 3iuy_A           97 MLVLTPT--RELALHVEAECSKY--------SYKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLND----------  156 (228)
T ss_dssp             EEEECSS--HHHHHHHHHHHHHH--------CCTTCCEEEECC------CHHHHHSCCSEEEECHHHHHH----------
T ss_pred             EEEEeCC--HHHHHHHHHHHHHh--------cccCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHH----------
Confidence            7777643  32222233333210        0000000000000 0       01247999999999862          


Q ss_pred             HHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          344 LHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       344 L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      +...+.+.++               ++.+|||||||++
T Consensus       157 ~~~~~~~~~~---------------~~~~lViDEah~~  179 (228)
T 3iuy_A          157 LQMNNSVNLR---------------SITYLVIDEADKM  179 (228)
T ss_dssp             HHHTTCCCCT---------------TCCEEEECCHHHH
T ss_pred             HHHcCCcCcc---------------cceEEEEECHHHH
Confidence            1223334444               8999999999974

>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=99.81  E-value=6e-20  Score=162.03  Aligned_cols=54  Identities=20%  Similarity=0.300  Sum_probs=45.0

Q ss_pred             HHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          204 FEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      |+.+..-+++...+.. +||..|||+|.++|+.++.|+|+++.+|||+|||++|+
T Consensus         5 f~~~~l~~~l~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~   58 (206)
T 1vec_A            5 FEDYCLKRELLMGIFE-MGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYL   58 (206)
T ss_dssp             GGGSCCCHHHHHHHHT-TTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHH
T ss_pred             hhhcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHH
Confidence            4444444445555544 89999999999999999999999999999999999997

>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=99.81  E-value=1.2e-19  Score=168.05  Aligned_cols=55  Identities=24%  Similarity=0.247  Sum_probs=45.9

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +|+.+..-+.+...+. .+||..|||+|.++|+.++.|+|+++.+|||+|||++|+
T Consensus        44 ~f~~l~l~~~l~~~l~-~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~   98 (249)
T 3ber_A           44 TFKDLGVTDVLCEACD-QLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFA   98 (249)
T ss_dssp             CTGGGTCCHHHHHHHH-HTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH
T ss_pred             CHHHcCCCHHHHHHHH-HcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhH
Confidence            4555554455555554 389999999999999999999999999999999999997

>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=99.80  E-value=1.7e-19  Score=168.20  Aligned_cols=45  Identities=22%  Similarity=0.313  Sum_probs=40.2

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +...+.. +||..|||+|.++|+.++.|+|+++++|||+|||++|+
T Consensus        65 l~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~  109 (262)
T 3ly5_A           65 TLKAIKE-MGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFL  109 (262)
T ss_dssp             HHHHHHH-TTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHH
T ss_pred             HHHHHHH-CCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHH
Confidence            3444433 89999999999999999999999999999999999997

>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=99.79  E-value=1.8e-19  Score=163.49  Aligned_cols=56  Identities=21%  Similarity=0.177  Sum_probs=47.8

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .+|+.+..-+.+...+.+ +||..|||+|.++|+.++.|+|+++.+|||+|||++|+
T Consensus        24 ~~f~~l~l~~~l~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~   79 (230)
T 2oxc_A           24 ADFESLLLSRPVLEGLRA-AGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFS   79 (230)
T ss_dssp             CCGGGGTCCHHHHHHHHH-TTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH
T ss_pred             CCHhhcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHH
Confidence            456666655556666644 89999999999999999999999999999999999996

>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=99.79  E-value=2.5e-19  Score=160.39  Aligned_cols=75  Identities=13%  Similarity=0.207  Sum_probs=54.8

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHH-HHHHHh-hcCCcEEEEeC
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQ-IITLNL-KFGIPATFLNS  277 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~-~~gI~a~~l~g  277 (381)
                      .+|+.+..-+.+...+.. +||..|||+|.++|+.++.|+|+++.+|||+|||++|+-. +..+.. ..+.+++++..
T Consensus        14 ~~f~~l~l~~~l~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (224)
T 1qde_A           14 YKFDDMELDENLLRGVFG-YGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAP   90 (224)
T ss_dssp             CCGGGGTCCHHHHHHHHH-HTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECS
T ss_pred             CChhhcCCCHHHHHHHHH-CCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEEC
Confidence            456666655556655544 8999999999999999999999999999999999998621 222211 12345666654

>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=99.79  E-value=9.1e-19  Score=156.62  Aligned_cols=54  Identities=19%  Similarity=0.231  Sum_probs=43.1

Q ss_pred             HHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          204 FEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      |+.+..-+++...+.. +||..|||+|.++|+.+++|+|+++.+|||+|||++|+
T Consensus        16 f~~~~l~~~l~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~   69 (220)
T 1t6n_A           16 FRDFLLKPELLRAIVD-CGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFV   69 (220)
T ss_dssp             STTSCCCHHHHHHHHH-TTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH
T ss_pred             HhhcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhh
Confidence            3333333333344433 89999999999999999999999999999999999997

>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=99.78  E-value=2.2e-19  Score=164.01  Aligned_cols=150  Identities=16%  Similarity=0.173  Sum_probs=86.4

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHH-HHHh-hcCCcEEEEeCCC
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQII-TLNL-KFGIPATFLNSQQ  279 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~-~L~~-~~gI~a~~l~g~~  279 (381)
                      .+|+.+..-+++...+. .+||..|||+|.++|+.++.|+|+++.+|||+|||++|+-.+. .+.. ..+.+++++... 
T Consensus        30 ~~f~~l~l~~~l~~~l~-~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt-  107 (237)
T 3bor_A           30 DNFDDMNLKESLLRGIY-AYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPT-  107 (237)
T ss_dssp             CSGGGSCCCHHHHHHHH-HHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSS-
T ss_pred             CChhhcCCCHHHHHHHH-HCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEECc-
Confidence            45666665555555554 4899999999999999999999999999999999999972222 2211 134566666543 


Q ss_pred             CHHHHHHHHHHHHhchhhhhh-hhhhhhhhhhhh---cccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcccccc
Q 042872          280 TVSQAAAVLQELRQGLVLSQH-YFLHQLIFVLTC---ASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVL  355 (381)
Q Consensus       280 ~~~e~~~il~~lr~g~~~~~~-~~~~~~~~~~~~---~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~  355 (381)
                       .+-..++.+.+++  +.... ............   ........++|+|+||++|..          +..++.+.++  
T Consensus       108 -~~L~~q~~~~~~~--~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~----------~l~~~~~~~~--  172 (237)
T 3bor_A          108 -RELAQQIQKVILA--LGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFD----------MLNRRYLSPK--  172 (237)
T ss_dssp             -HHHHHHHHHHHHH--HTTTTTCCEEEECC-------------CCCSEEEECHHHHHH----------HHHTTSSCST--
T ss_pred             -HHHHHHHHHHHHH--HhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHH----------HHHhCCcCcc--
Confidence             2222223333321  00000 000000000000   001112248999999999862          1123333344  


Q ss_pred             ccccccccccccCCccEEEEeccccC
Q 042872          356 TTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       356 ~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                   .+.+|||||||++
T Consensus       173 -------------~~~~lViDEah~~  185 (237)
T 3bor_A          173 -------------WIKMFVLDEADEM  185 (237)
T ss_dssp             -------------TCCEEEEESHHHH
T ss_pred             -------------cCcEEEECCchHh
Confidence                         8999999999974

>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=99.78  E-value=3.8e-19  Score=176.73  Aligned_cols=149  Identities=17%  Similarity=0.174  Sum_probs=86.6

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHH-HHHHHhh------cCCcEEEE
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQ-IITLNLK------FGIPATFL  275 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~------~gI~a~~l  275 (381)
                      +|+.+..-+.+...+. .+||..|||+|.+|||.+++|+|+++++|||+|||++|+-. +..+...      .+.+++++
T Consensus        57 ~f~~~~l~~~l~~~l~-~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil  135 (434)
T 2db3_A           57 HFTSADLRDIIIDNVN-KSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIV  135 (434)
T ss_dssp             CGGGSCCCHHHHHHHH-HTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEE
T ss_pred             ChhhcCCCHHHHHHHH-HcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEE
Confidence            4555554444444443 38999999999999999999999999999999999999722 2233211      14466666


Q ss_pred             eCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhh---cccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccc
Q 042872          276 NSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTC---ASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRL  352 (381)
Q Consensus       276 ~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~---~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l  352 (381)
                      ...  ++-..++.+.+++-  ..........+.+...   .......+++|+|+||++|..          +..++.+.+
T Consensus       136 ~Pt--reLa~Q~~~~~~~~--~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~----------~l~~~~~~l  201 (434)
T 2db3_A          136 SPT--RELAIQIFNEARKF--AFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLD----------FVDRTFITF  201 (434)
T ss_dssp             CSS--HHHHHHHHHHHHHH--TTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHH----------HHHTTSCCC
T ss_pred             ecC--HHHHHHHHHHHHHH--hccCCcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHH----------HHHhCCccc
Confidence            543  33222333332210  0000000000000000   000012358999999999962          123344444


Q ss_pred             cccccccccccccccCCccEEEEeccccC
Q 042872          353 KVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       353 ~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      +               ++.+|||||||++
T Consensus       202 ~---------------~~~~lVlDEah~~  215 (434)
T 2db3_A          202 E---------------DTRFVVLDEADRM  215 (434)
T ss_dssp             T---------------TCCEEEEETHHHH
T ss_pred             c---------------cCCeEEEccHhhh
Confidence            5               8999999999973

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.78  E-value=9.5e-20  Score=163.56  Aligned_cols=148  Identities=16%  Similarity=0.062  Sum_probs=86.4

Q ss_pred             HHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHH-HHHHh-hcCCcEEEEeCCCCH
Q 042872          204 FEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQI-ITLNL-KFGIPATFLNSQQTV  281 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv-~~L~~-~~gI~a~~l~g~~~~  281 (381)
                      |+.+..-+.+..++.+ +||..|||+|.++|+.+++|+|+++.+|||+|||++|+--+ ..+.. ..+.+++++...  .
T Consensus         6 f~~~~l~~~l~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt--~   82 (219)
T 1q0u_A            6 FTRFPFQPFIIEAIKT-LRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPT--R   82 (219)
T ss_dssp             GGGSCCCHHHHHHHHH-TTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSS--H
T ss_pred             HhhCCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCc--H
Confidence            4444444445555543 89999999999999999999999999999999999997222 22211 124677777653  2


Q ss_pred             HHHHHHHHHHHhchhhhhhhhh-hhhh---h-h--hhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccc
Q 042872          282 SQAAAVLQELRQGLVLSQHYFL-HQLI---F-V--LTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKV  354 (381)
Q Consensus       282 ~e~~~il~~lr~g~~~~~~~~~-~~~~---~-~--~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~  354 (381)
                      +-..++.+.+++-  ....... .-.+   . .  ...........++|+|+|||++..          +..++.+.++ 
T Consensus        83 ~L~~q~~~~~~~~--~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~----------~l~~~~~~~~-  149 (219)
T 1q0u_A           83 ELATQIYHETLKI--TKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRIND----------FIREQALDVH-  149 (219)
T ss_dssp             HHHHHHHHHHHHH--HTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHH----------HHHTTCCCGG-
T ss_pred             HHHHHHHHHHHHH--hhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHH----------HHHcCCCCcC-
Confidence            2222233322210  0000000 0000   0 0  000011122367999999999962          1123334444 


Q ss_pred             cccccccccccccCCccEEEEeccccC
Q 042872          355 LTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       355 ~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                    ++.+|||||||++
T Consensus       150 --------------~~~~lViDEah~~  162 (219)
T 1q0u_A          150 --------------TAHILVVDEADLM  162 (219)
T ss_dssp             --------------GCCEEEECSHHHH
T ss_pred             --------------cceEEEEcCchHH
Confidence                          8999999999974

>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=99.77  E-value=1.1e-18  Score=153.79  Aligned_cols=141  Identities=23%  Similarity=0.211  Sum_probs=83.7

Q ss_pred             HHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHH-HHh----hcCCcEEEEeCC
Q 042872          204 FEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIIT-LNL----KFGIPATFLNSQ  278 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~-L~~----~~gI~a~~l~g~  278 (381)
                      |+.+..-+++...+.+ +||..|||+|.++|+.+++|+|+++.+|||+|||++|+-.+.. +..    ..+.+++++...
T Consensus         3 f~~~~l~~~l~~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~   81 (207)
T 2gxq_A            3 FKDFPLKPEILEALHG-RGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPT   81 (207)
T ss_dssp             GGGSCCCHHHHHHHHH-TTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSS
T ss_pred             hhhcCCCHHHHHHHHH-cCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECC
Confidence            4444444444444544 8999999999999999999999999999999999998732222 110    134566666543


Q ss_pred             CCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCC--------CCCccEEEECccccccCcchHHHHHHHHhcCCc
Q 042872          279 QTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKD--------KPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSI  350 (381)
Q Consensus       279 ~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~  350 (381)
                        ..-..++.+.+++-        ... .......++..        ...++|+|+||+++..      .+    .++.+
T Consensus        82 --~~L~~q~~~~~~~~--------~~~-~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~------~~----~~~~~  140 (207)
T 2gxq_A           82 --RELALQVASELTAV--------APH-LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALD------YL----RQGVL  140 (207)
T ss_dssp             --HHHHHHHHHHHHHH--------CTT-SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHH------HH----HHTSS
T ss_pred             --HHHHHHHHHHHHHH--------hhc-ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHH------HH----HcCCc
Confidence              22222233333210        000 00000000000        0247899999999862      11    22333


Q ss_pred             cccccccccccccccccCCccEEEEeccccC
Q 042872          351 RLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       351 ~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      .+.               ++.+|||||||++
T Consensus       141 ~~~---------------~~~~iViDEah~~  156 (207)
T 2gxq_A          141 DLS---------------RVEVAVLDEADEM  156 (207)
T ss_dssp             CCT---------------TCSEEEEESHHHH
T ss_pred             chh---------------hceEEEEEChhHh
Confidence            344               8999999999973

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.77  E-value=4.3e-19  Score=160.71  Aligned_cols=143  Identities=20%  Similarity=0.223  Sum_probs=85.1

Q ss_pred             HHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHH-HHHHHh-----hcCCcEEEEeC
Q 042872          204 FEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQ-IITLNL-----KFGIPATFLNS  277 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~-----~~gI~a~~l~g  277 (381)
                      |+.+...+.+...+.+ +||..|+|+|.++|+.++.|+|+++.+|||+|||++|+-- +..+..     ..+.+++++..
T Consensus        27 f~~~~l~~~l~~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~P  105 (236)
T 2pl3_A           27 FSDFPLSKKTLKGLQE-AQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISP  105 (236)
T ss_dssp             GGGSCCCHHHHHHHHH-TTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECS
T ss_pred             HhhcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEEeC
Confidence            4444444444444443 8999999999999999999999999999999999999722 222211     23567777764


Q ss_pred             CCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhc-cc-------CCCCCccEEEECccccccCcchHHHHHHHHhcCC
Q 042872          278 QQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCA-SR-------KDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGS  349 (381)
Q Consensus       278 ~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~-~~-------~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~  349 (381)
                      .  ..-..++.+.++.  +.....      ....+. ++       .....++|+|+||++|..         .+.....
T Consensus       106 t--~~L~~q~~~~~~~--~~~~~~------~~~~~~~g~~~~~~~~~~~~~~~iiv~Tp~~l~~---------~l~~~~~  166 (236)
T 2pl3_A          106 T--RELAYQTFEVLRK--VGKNHD------FSAGLIIGGKDLKHEAERINNINILVCTPGRLLQ---------HMDETVS  166 (236)
T ss_dssp             S--HHHHHHHHHHHHH--HTTTSS------CCEEEECCC--CHHHHHHHTTCSEEEECHHHHHH---------HHHHCSS
T ss_pred             C--HHHHHHHHHHHHH--HhCCCC------eeEEEEECCCCHHHHHHhCCCCCEEEECHHHHHH---------HHHhcCC
Confidence            3  2222223333321  000000      000000 00       001257999999999962         1222222


Q ss_pred             ccccccccccccccccccCCccEEEEeccccC
Q 042872          350 IRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       350 ~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      +.+.               ++.+|||||||++
T Consensus       167 ~~~~---------------~~~~lViDEah~~  183 (236)
T 2pl3_A          167 FHAT---------------DLQMLVLDEADRI  183 (236)
T ss_dssp             CCCT---------------TCCEEEETTHHHH
T ss_pred             cccc---------------cccEEEEeChHHH
Confidence            3333               8999999999974

>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=99.77  E-value=2.4e-18  Score=166.10  Aligned_cols=56  Identities=18%  Similarity=0.303  Sum_probs=48.3

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .+|+.+..-+++...+.. +||..|||+|.++|+.++.|+|+++.+|||+|||++|+
T Consensus        37 ~~f~~~~l~~~l~~~l~~-~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~   92 (410)
T 2j0s_A           37 PTFDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFS   92 (410)
T ss_dssp             CSGGGGCCCHHHHHHHHH-HTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH
T ss_pred             CCHhhcCCCHHHHHHHHH-cCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHH
Confidence            457777666666666644 89999999999999999999999999999999999997

>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=99.77  E-value=7.7e-19  Score=160.92  Aligned_cols=54  Identities=22%  Similarity=0.331  Sum_probs=43.2

Q ss_pred             HHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          204 FEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      |+.+..-+.+..++. .+||..|||+|.++|+.++.|+|+++.+|||+|||++|+
T Consensus        25 f~~l~l~~~l~~~l~-~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~   78 (253)
T 1wrb_A           25 FDELKLDPTIRNNIL-LASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFL   78 (253)
T ss_dssp             SGGGSCCCSTTTTTT-TTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH
T ss_pred             HhhCCCCHHHHHHHH-HCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHH
Confidence            444433333333332 289999999999999999999999999999999999997

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.76  E-value=1e-18  Score=170.26  Aligned_cols=119  Identities=16%  Similarity=0.138  Sum_probs=91.2

Q ss_pred             chHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-----------------------H-HHHHHH
Q 042872          210 LDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-----------------------D-QIITLN  265 (381)
Q Consensus       210 l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-----------------------d-Qv~~L~  265 (381)
                      ++++...+++.+|| +|+|+|.+||+.++.|+|+++.+|||+|||++|+                       . +...+.
T Consensus         7 ~~~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~   85 (414)
T 3oiy_A            7 YEDFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQ   85 (414)
T ss_dssp             HHHHHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhcCCCEEEEEECCHHHHHHHHHHHH
Confidence            44566677788999 6999999999999999999999999999999987                       2 233333


Q ss_pred             hh--cCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHH
Q 042872          266 LK--FGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKC  343 (381)
Q Consensus       266 ~~--~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~  343 (381)
                      ..  .++++..++|+.+..++...+..+..|                         .++|+|+||++|..  .    +..
T Consensus        86 ~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~-------------------------~~~Iiv~Tp~~l~~--~----l~~  134 (414)
T 3oiy_A           86 KLADEKVKIFGFYSSMKKEEKEKFEKSFEED-------------------------DYHILVFSTQFVSK--N----REK  134 (414)
T ss_dssp             HHCCSSCCEEECCTTSCHHHHHHHHHHHHHT-------------------------CCSEEEEEHHHHHH--C----HHH
T ss_pred             HHccCCceEEEEECCCChhhHHHHHHHhhcC-------------------------CCCEEEECHHHHHH--H----HHH
Confidence            21  477888888888877766667766643                         58999999999973  1    111


Q ss_pred             HHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          344 LHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       344 L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      +      .+.               ++.+||||||||+
T Consensus       135 ~------~~~---------------~~~~iViDEaH~~  151 (414)
T 3oiy_A          135 L------SQK---------------RFDFVFVDDVDAV  151 (414)
T ss_dssp             H------TTC---------------CCSEEEESCHHHH
T ss_pred             h------ccc---------------cccEEEEeChHhh
Confidence            1      122               8999999999974

>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=99.75  E-value=1.4e-18  Score=166.00  Aligned_cols=151  Identities=19%  Similarity=0.124  Sum_probs=91.2

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcC--CCEEEECCCCCCchhhHHH-HHHHHHh-hcCCcEEEEeC
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAK--QDCFVLLPTGGGKSLCYQD-QIITLNL-KFGIPATFLNS  277 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~G--rDvLviaPTGsGKTLaF~d-Qv~~L~~-~~gI~a~~l~g  277 (381)
                      .+|+.+..-+.+...+.. +||..|+|+|.+|||.++.|  +|+++.+|||+|||+||+- -+..+.. ..+.+++++..
T Consensus        92 ~~f~~l~l~~~l~~~l~~-~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~P  170 (300)
T 3fmo_B           92 KSFEELRLKPQLLQGVYA-MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSP  170 (300)
T ss_dssp             CCSGGGTCCHHHHHHHHH-TTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECS
T ss_pred             CCHhhcCCCHHHHHHHHH-cCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEcC
Confidence            346666655555555544 89999999999999999998  9999999999999999972 2222221 22446777765


Q ss_pred             CCCHHHHHHHHHHHHhchhhhhh-hhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccc
Q 042872          278 QQTVSQAAAVLQELRQGLVLSQH-YFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLT  356 (381)
Q Consensus       278 ~~~~~e~~~il~~lr~g~~~~~~-~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~  356 (381)
                      .  ++-..++.+.++.  +.... ....................++|||+||++|..         .+...+.+.++   
T Consensus       171 t--reLa~Q~~~~~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~TP~~l~~---------~l~~~~~~~l~---  234 (300)
T 3fmo_B          171 T--YELALQTGKVIEQ--MGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLD---------WCSKLKFIDPK---  234 (300)
T ss_dssp             S--HHHHHHHHHHHHH--HTTTSTTCCEEEESTTCCCCTTCCCCCSEEEECHHHHHH---------HHTTTCCCCGG---
T ss_pred             c--HHHHHHHHHHHHH--HHhhCCCcEEEEEeCCccHhhhhcCCCCEEEECHHHHHH---------HHHhcCCCChh---
Confidence            3  3332333222221  00000 000000000011112223467999999999962         23233445555   


Q ss_pred             cccccccccccCCccEEEEeccccC
Q 042872          357 TDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       357 ~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                  ++.+|||||||++
T Consensus       235 ------------~l~~lVlDEad~l  247 (300)
T 3fmo_B          235 ------------KIKVFVLDEADVM  247 (300)
T ss_dssp             ------------GCSEEEETTHHHH
T ss_pred             ------------hceEEEEeCHHHH
Confidence                        8999999999974

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.75  E-value=3e-18  Score=165.06  Aligned_cols=55  Identities=20%  Similarity=0.200  Sum_probs=45.5

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +|+.+..-+.+...+.. +||..|||+|.++|+.++.|+|+++.+|||+|||++|+
T Consensus        16 ~f~~~~l~~~l~~~l~~-~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~   70 (417)
T 2i4i_A           16 SFSDVEMGEIIMGNIEL-TRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFL   70 (417)
T ss_dssp             SGGGSCCCHHHHHHHHH-HTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH
T ss_pred             CHhhCCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHH
Confidence            35555544445555433 89999999999999999999999999999999999997

>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=99.74  E-value=1.6e-17  Score=151.14  Aligned_cols=152  Identities=22%  Similarity=0.329  Sum_probs=90.7

Q ss_pred             CCHHHH----hhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHH-HHHHHh--hcCCcEEE
Q 042872          202 LSFEEL----QALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQ-IITLNL--KFGIPATF  274 (381)
Q Consensus       202 ~~fe~L----~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~--~~gI~a~~  274 (381)
                      .+|+.+    ..-+.+...+.+ +||..|||+|.++|+.++.|+|+++.+|||+|||++|+-. +..+..  ..+.++++
T Consensus        25 ~~f~~l~~~~~l~~~l~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~li  103 (245)
T 3dkp_A           25 ATFQQLDQEYKINSRLLQNILD-AGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALI  103 (245)
T ss_dssp             SSHHHHHHHHCCCHHHHHHHHH-TTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCCSSSCCEEE
T ss_pred             cCHHHhhhccCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcccCCceEEE
Confidence            457766    344455555544 8999999999999999999999999999999999999732 233321  13567777


Q ss_pred             EeCCCCHHHHHHHHHHHHh---chhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhc-CCc
Q 042872          275 LNSQQTVSQAAAVLQELRQ---GLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRK-GSI  350 (381)
Q Consensus       275 l~g~~~~~e~~~il~~lr~---g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~-g~~  350 (381)
                      +...  .+-..++.+.++.   +.-...+ ..+................++|+|+||++|..      .   +... ..+
T Consensus       104 l~Pt--~~L~~q~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~------~---l~~~~~~~  171 (245)
T 3dkp_A          104 ISPT--RELASQIHRELIKISEGTGFRIH-MIHKAAVAAKKFGPKSSKKFDILVTTPNRLIY------L---LKQDPPGI  171 (245)
T ss_dssp             ECSS--HHHHHHHHHHHHHHTTTSCCCEE-CCCHHHHHHTTTSTTSCCCCCEEEECHHHHHH------H---HHSSSCSC
T ss_pred             EeCC--HHHHHHHHHHHHHHhcccCceEE-EEecCccHHHHhhhhhcCCCCEEEECHHHHHH------H---HHhCCCCc
Confidence            7653  3322233333321   0000000 00000000001112334578999999999962      1   1111 123


Q ss_pred             cccccccccccccccccCCccEEEEeccccC
Q 042872          351 RLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       351 ~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      .++               ++.+|||||||++
T Consensus       172 ~~~---------------~~~~lViDEah~~  187 (245)
T 3dkp_A          172 DLA---------------SVEWLVVDESDKL  187 (245)
T ss_dssp             CCT---------------TCCEEEESSHHHH
T ss_pred             ccc---------------cCcEEEEeChHHh
Confidence            444               8999999999974

>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=99.73  E-value=1.1e-17  Score=159.30  Aligned_cols=55  Identities=18%  Similarity=0.230  Sum_probs=46.6

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +|+.+..-+.+..++.. +||..|||+|.++|+.++.|+|+++.+|||+|||++|+
T Consensus         9 ~f~~~~l~~~l~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~   63 (391)
T 1xti_A            9 GFRDFLLKPELLRAIVD-CGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFV   63 (391)
T ss_dssp             CGGGGCCCHHHHHHHHH-HSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHH
T ss_pred             ChhhcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHH
Confidence            45665555555555544 89999999999999999999999999999999999996

>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=99.73  E-value=1.9e-17  Score=158.88  Aligned_cols=56  Identities=16%  Similarity=0.266  Sum_probs=47.6

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .+|+.+..-+.+...+.+ +||..|||+|.++|+.++.|+|+++.+|||+|||++|+
T Consensus        40 ~~f~~~~l~~~~~~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~   95 (414)
T 3eiq_A           40 DSFDDMNLSESLLRGIYA-YGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFA   95 (414)
T ss_dssp             CCGGGGCCCHHHHHHHHH-TTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHH
T ss_pred             cCHhhCCCCHHHHHHHHH-cCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHH
Confidence            456666655555555544 89999999999999999999999999999999999996

>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=99.72  E-value=1.9e-17  Score=154.04  Aligned_cols=45  Identities=24%  Similarity=0.340  Sum_probs=40.2

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +..++. .+||..|||+|.++|+.+++|+++++.+|||+|||++|+
T Consensus         5 i~~~l~-~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~   49 (337)
T 2z0m_A            5 IEQAIR-EMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYA   49 (337)
T ss_dssp             HHHHHH-HTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH
T ss_pred             HHHHHH-HcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHH
Confidence            334443 489999999999999999999999999999999999997

>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=99.72  E-value=1.2e-17  Score=160.31  Aligned_cols=75  Identities=16%  Similarity=0.215  Sum_probs=54.9

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHH-HHh-hcCCcEEEEeC
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIIT-LNL-KFGIPATFLNS  277 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~-L~~-~~gI~a~~l~g  277 (381)
                      .+|+.+..-+++...+.+ +||..|||+|.++|+.++.|+++++.+|||+|||++|+-.+.. +.. ..+.+++++..
T Consensus        21 ~~f~~~~l~~~l~~~l~~-~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P   97 (400)
T 1s2m_A           21 NTFEDFYLKRELLMGIFE-AGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVP   97 (400)
T ss_dssp             CCGGGGCCCHHHHHHHHH-TTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECS
T ss_pred             CChhhcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcC
Confidence            456666655556555544 8999999999999999999999999999999999999722221 111 12446666654

>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=99.72  E-value=1.6e-17  Score=158.01  Aligned_cols=56  Identities=14%  Similarity=0.277  Sum_probs=46.6

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .+|+.+..-+.+...+.. +||..|||+|.++|+.++.|+|+++.+|||+|||++|+
T Consensus        21 ~~f~~~~l~~~l~~~l~~-~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~   76 (394)
T 1fuu_A           21 YKFDDMELDENLLRGVFG-YGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFS   76 (394)
T ss_dssp             CSSGGGCCCHHHHHHHHH-HTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHH
T ss_pred             CChhhcCCCHHHHHHHHH-cCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHH
Confidence            345666555555555544 89999999999999999999999999999999999986

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.70  E-value=5.6e-17  Score=166.44  Aligned_cols=78  Identities=15%  Similarity=0.226  Sum_probs=55.5

Q ss_pred             CCCCHHHHh----hchHHHHHHHHHhCCCCCcHHHHHHHHHHH--cCCCEEEECCCCCCchhhHHHH-HHHHHhh-----
Q 042872          200 GTLSFEELQ----ALDDMEFANVVIFGNRAFRPLQHQACKASV--AKQDCFVLLPTGGGKSLCYQDQ-IITLNLK-----  267 (381)
Q Consensus       200 ~~~~fe~L~----~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL--~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~-----  267 (381)
                      ..++++.+.    +-+++..++ +.+||..|||+|.++|+.++  .|+|+|+.||||+|||+||+-. +..+...     
T Consensus        15 ~~~~~~~l~~~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~   93 (579)
T 3sqw_A           15 KEVTLDSLLEEGVLDKEIHKAI-TRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQ   93 (579)
T ss_dssp             CCCCHHHHHHTTSSCHHHHHHH-HTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSST
T ss_pred             CCcCHHHHhhcCCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhcccccc
Confidence            345666665    334454555 44899999999999999999  7899999999999999999822 2222211     


Q ss_pred             cCCcEEEEeCC
Q 042872          268 FGIPATFLNSQ  278 (381)
Q Consensus       268 ~gI~a~~l~g~  278 (381)
                      .+.+++++...
T Consensus        94 ~~~~~lvl~Pt  104 (579)
T 3sqw_A           94 YMVKAVIVAPT  104 (579)
T ss_dssp             TSCCEEEECSS
T ss_pred             CCCeEEEEcch
Confidence            13567777653

>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=99.70  E-value=5.4e-17  Score=152.26  Aligned_cols=75  Identities=23%  Similarity=0.228  Sum_probs=54.7

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcC-CCEEEECCCCCCchhhHHHHHHHHH-hhcCCcEEEEeC
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAK-QDCFVLLPTGGGKSLCYQDQIITLN-LKFGIPATFLNS  277 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~G-rDvLviaPTGsGKTLaF~dQv~~L~-~~~gI~a~~l~g  277 (381)
                      ++|+.+...+.+...+.+ +||..|||+|.++|+.++.| +++++.+|||+|||++|+-.+..+. ...+.+++++..
T Consensus         6 ~~f~~~~l~~~~~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil~P   82 (367)
T 1hv8_A            6 MNFNELNLSDNILNAIRN-KGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTP   82 (367)
T ss_dssp             CCGGGSSCCHHHHHHHHH-HTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECS
T ss_pred             CchhhcCCCHHHHHHHHH-cCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEEcC
Confidence            456666655556555554 89999999999999999998 7999999999999999973322221 112456666654

>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=99.69  E-value=8e-17  Score=163.18  Aligned_cols=77  Identities=16%  Similarity=0.233  Sum_probs=54.0

Q ss_pred             CCCHHHHh----hchHHHHHHHHHhCCCCCcHHHHHHHHHHH--cCCCEEEECCCCCCchhhHHHH-HHHHHhh-----c
Q 042872          201 TLSFEELQ----ALDDMEFANVVIFGNRAFRPLQHQACKASV--AKQDCFVLLPTGGGKSLCYQDQ-IITLNLK-----F  268 (381)
Q Consensus       201 ~~~fe~L~----~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL--~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~-----~  268 (381)
                      ..+++.+.    .-+++..++ ..+||..|||+|.+||+.++  .|+|+|+.||||+|||+||+-. +..+...     .
T Consensus        67 ~~~~~~l~~~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~  145 (563)
T 3i5x_A           67 EVTLDSLLEEGVLDKEIHKAI-TRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQY  145 (563)
T ss_dssp             CCCHHHHHHTTSSCHHHHHHH-HTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTT
T ss_pred             CcCHHHHhhcCCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccC
Confidence            34566654    333444444 44899999999999999999  6789999999999999999822 2222211     1


Q ss_pred             CCcEEEEeCC
Q 042872          269 GIPATFLNSQ  278 (381)
Q Consensus       269 gI~a~~l~g~  278 (381)
                      +.+++++...
T Consensus       146 ~~~~lil~Pt  155 (563)
T 3i5x_A          146 MVKAVIVAPT  155 (563)
T ss_dssp             SCCEEEECSS
T ss_pred             CeeEEEEcCc
Confidence            3467777653

>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=99.67  E-value=1.4e-16  Score=152.40  Aligned_cols=150  Identities=19%  Similarity=0.130  Sum_probs=87.4

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcC--CCEEEECCCCCCchhhHHHHH-HHHHh-hcCCcEEEEeCC
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAK--QDCFVLLPTGGGKSLCYQDQI-ITLNL-KFGIPATFLNSQ  278 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~G--rDvLviaPTGsGKTLaF~dQv-~~L~~-~~gI~a~~l~g~  278 (381)
                      +|+.+..-+.+...+.+ +||..|||+|.++|+.++.|  +++++.+|||+|||++|+-.+ ..+.. ..+.+++++...
T Consensus        26 ~f~~~~l~~~l~~~l~~-~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  104 (412)
T 3fht_A           26 SFEELRLKPQLLQGVYA-MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT  104 (412)
T ss_dssp             CTGGGTCCHHHHHHHHH-TTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSS
T ss_pred             CHhhCCCCHHHHHHHHH-cCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEEECCC
Confidence            45555555555555544 89999999999999999997  999999999999999996222 22221 123467777553


Q ss_pred             CCHHHHHHHHHHHHhchhhhhhhhh-hhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcccccccc
Q 042872          279 QTVSQAAAVLQELRQGLVLSQHYFL-HQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTT  357 (381)
Q Consensus       279 ~~~~e~~~il~~lr~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~  357 (381)
                        ..-..++.+.+++  +....... .................++|+|+||++|..         .+...+.+.+.    
T Consensus       105 --~~L~~q~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivv~T~~~l~~---------~~~~~~~~~~~----  167 (412)
T 3fht_A          105 --YELALQTGKVIEQ--MGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLD---------WCSKLKFIDPK----  167 (412)
T ss_dssp             --HHHHHHHHHHHHH--HTTTSTTCCEEEECTTCCCCTTCCCCCSEEEECHHHHHH---------HHTTSCSSCGG----
T ss_pred             --HHHHHHHHHHHHH--HHhhcccceEEEeecCcchhhhhcCCCCEEEECchHHHH---------HHHhcCCcChh----
Confidence              2222222222220  00000000 000000000112223357999999999962         22223333444    


Q ss_pred             ccccccccccCCccEEEEeccccC
Q 042872          358 DVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       358 ~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                 ++.+|||||||++
T Consensus       168 -----------~~~~iViDEah~~  180 (412)
T 3fht_A          168 -----------KIKVFVLDEADVM  180 (412)
T ss_dssp             -----------GCCEEEEETHHHH
T ss_pred             -----------hCcEEEEeCHHHH
Confidence                       8999999999963

>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=99.66  E-value=9.9e-17  Score=151.95  Aligned_cols=139  Identities=18%  Similarity=0.229  Sum_probs=81.4

Q ss_pred             HHHHHHHHHhCCCCCcHHHHHHHHHHHcC--CCEEEECCCCCCchhhHHHHHHH-HHh-hcCCcEEEEeCCCCHHHHHHH
Q 042872          212 DMEFANVVIFGNRAFRPLQHQACKASVAK--QDCFVLLPTGGGKSLCYQDQIIT-LNL-KFGIPATFLNSQQTVSQAAAV  287 (381)
Q Consensus       212 ~l~~~~~~~fG~~~fRpiQ~eAI~aiL~G--rDvLviaPTGsGKTLaF~dQv~~-L~~-~~gI~a~~l~g~~~~~e~~~i  287 (381)
                      ++...+.+ +||..|||+|.++|+.++.|  +++++.+|||+|||++|+-.+.. +.. ..+.+++++...  ..-..++
T Consensus        15 ~l~~~l~~-~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~--~~L~~q~   91 (395)
T 3pey_A           15 ELLKGIYA-MKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPS--RELARQT   91 (395)
T ss_dssp             HHHHHHHH-TTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECSS--HHHHHHH
T ss_pred             HHHHHHHH-CCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECCC--HHHHHHH
Confidence            33334433 89999999999999999998  99999999999999999733222 111 134567777653  2222223


Q ss_pred             HHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcccccccccccccccccc
Q 042872          288 LQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQ  367 (381)
Q Consensus       288 l~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~  367 (381)
                      .+.++.  +........... ............++|+|+||++|..          +..++.+.+.              
T Consensus        92 ~~~~~~--~~~~~~~~~~~~-~~~~~~~~~~~~~~iiv~T~~~l~~----------~~~~~~~~~~--------------  144 (395)
T 3pey_A           92 LEVVQE--MGKFTKITSQLI-VPDSFEKNKQINAQVIVGTPGTVLD----------LMRRKLMQLQ--------------  144 (395)
T ss_dssp             HHHHHH--HTTTSCCCEEEE-STTSSCTTSCBCCSEEEECHHHHHH----------HHHTTCBCCT--------------
T ss_pred             HHHHHH--HhcccCeeEEEE-ecCchhhhccCCCCEEEEcHHHHHH----------HHHcCCcccc--------------
Confidence            333321  000000000000 0000112223368999999999962          1122333333              


Q ss_pred             CCccEEEEeccccC
Q 042872          368 RQLAGFVVDEAHCV  381 (381)
Q Consensus       368 ~~L~~lVIDEAHcI  381 (381)
                       ++.+|||||||++
T Consensus       145 -~~~~iIiDEah~~  157 (395)
T 3pey_A          145 -KIKIFVLDEADNM  157 (395)
T ss_dssp             -TCCEEEEETHHHH
T ss_pred             -cCCEEEEEChhhh
Confidence             8999999999973

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.65  E-value=2.2e-16  Score=163.56  Aligned_cols=58  Identities=17%  Similarity=0.179  Sum_probs=43.5

Q ss_pred             HhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhc----CCcEEEEeC
Q 042872          220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKF----GIPATFLNS  277 (381)
Q Consensus       220 ~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~----gI~a~~l~g  277 (381)
                      .+||..|||+|.++|+.++.|+|+|+++|||+|||++|+-.+.......    +.+++++..
T Consensus         8 ~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~P   69 (696)
T 2ykg_A            8 LYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFAN   69 (696)
T ss_dssp             TTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECS
T ss_pred             ccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEEC
Confidence            3899999999999999999999999999999999999983332221122    146666655

>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=99.63  E-value=5.5e-16  Score=154.32  Aligned_cols=148  Identities=18%  Similarity=0.168  Sum_probs=86.9

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcC--CCEEEECCCCCCchhhHHHHHH-HHHh-hcCCcEEEEeCC
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAK--QDCFVLLPTGGGKSLCYQDQII-TLNL-KFGIPATFLNSQ  278 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~G--rDvLviaPTGsGKTLaF~dQv~-~L~~-~~gI~a~~l~g~  278 (381)
                      +|+.+..-+++...+.. +||..|+|+|.+||+.++.|  +|+|+.+|||+|||++|+-.+. .+.. ..+.+++++...
T Consensus        93 ~f~~~~l~~~l~~~l~~-~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  171 (479)
T 3fmp_B           93 SFEELRLKPQLLQGVYA-MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT  171 (479)
T ss_dssp             CSGGGTCCHHHHHHHHH-TTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEECSS
T ss_pred             CHHHcCCCHHHHHHHHH-cCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEeCh
Confidence            45555555555555544 89999999999999999987  9999999999999999962221 1211 123367777653


Q ss_pred             CCHHHHHHH---HHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcccccc
Q 042872          279 QTVSQAAAV---LQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVL  355 (381)
Q Consensus       279 ~~~~e~~~i---l~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~  355 (381)
                        ..-..++   ++.+...  ..  .....................+|||+||++|..         .+...+.+.+.  
T Consensus       172 --~~La~Q~~~~~~~~~~~--~~--~~~~~~~~~~~~~~~~~~~~~~Ivv~Tp~~l~~---------~l~~~~~~~~~--  234 (479)
T 3fmp_B          172 --YELALQTGKVIEQMGKF--YP--ELKLAYAVRGNKLERGQKISEQIVIGTPGTVLD---------WCSKLKFIDPK--  234 (479)
T ss_dssp             --HHHHHHHHHHHHHHHTT--ST--TCCEEEESTTCCCCTTCCCCCSEEEECHHHHHH---------HHTTSCCCCGG--
T ss_pred             --HHHHHHHHHHHHHHHhh--CC--CceEEEEeCCccccccccCCCCEEEECchHHHH---------HHHhcCCcCcc--
Confidence              2222222   2222110  00  000000000000112223356899999999962         22233334444  


Q ss_pred             ccccccccccccCCccEEEEeccccC
Q 042872          356 TTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       356 ~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                   ++.+|||||||++
T Consensus       235 -------------~~~~iViDEah~~  247 (479)
T 3fmp_B          235 -------------KIKVFVLDEADVM  247 (479)
T ss_dssp             -------------GCCEEEECCHHHH
T ss_pred             -------------cCCEEEEECHHHH
Confidence                         8999999999963

>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=99.62  E-value=7.8e-16  Score=153.29  Aligned_cols=57  Identities=16%  Similarity=0.235  Sum_probs=41.0

Q ss_pred             CCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHH-HHhhc---CCcEEEEeCC
Q 042872          222 GNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIIT-LNLKF---GIPATFLNSQ  278 (381)
Q Consensus       222 G~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~-L~~~~---gI~a~~l~g~  278 (381)
                      +.-+|||+|.++|+.++.|+|+++.+|||+|||++|+--+.. +....   +.+++++...
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~   64 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATK   64 (556)
T ss_dssp             ----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSS
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCC
Confidence            344799999999999999999999999999999999733322 22111   5566666553

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.62  E-value=7.4e-16  Score=171.42  Aligned_cols=119  Identities=17%  Similarity=0.155  Sum_probs=89.2

Q ss_pred             chHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH------------------------HHHHHHH
Q 042872          210 LDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ------------------------DQIITLN  265 (381)
Q Consensus       210 l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~------------------------dQv~~L~  265 (381)
                      ..++...+...+|| +|+|+|.+||+.++.|+|++++||||+|||++|+                        ++...+.
T Consensus        64 ~~~~~~~~~~~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~~~~~~Lil~PtreLa~Q~~~~l~  142 (1104)
T 4ddu_A           64 YEDFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQ  142 (1104)
T ss_dssp             HHHHHHHHHHHSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHhcCCeEEEEechHHHHHHHHHHHH
Confidence            34455566677899 5999999999999999999999999999999886                        2233343


Q ss_pred             h--hcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHH
Q 042872          266 L--KFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKC  343 (381)
Q Consensus       266 ~--~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~  343 (381)
                      .  ..++++..++|+.+..++...++.+++|                         .++|||+||++|...      +..
T Consensus       143 ~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g-------------------------~~~IlV~Tp~rL~~~------l~~  191 (1104)
T 4ddu_A          143 KLADEKVKIFGFYSSMKKEEKEKFEKSFEED-------------------------DYHILVFSTQFVSKN------REK  191 (1104)
T ss_dssp             TTSCTTSCEEEECTTCCTTHHHHHHHHHHTS-------------------------CCSEEEEEHHHHHHS------HHH
T ss_pred             HhhCCCCeEEEEeCCCCHHHHHHHHHHHhCC-------------------------CCCEEEECHHHHHHH------HHh
Confidence            2  2467888888888776666666666643                         589999999999631      111


Q ss_pred             HHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          344 LHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       344 L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      +      .++               ++.+||||||||+
T Consensus       192 l------~~~---------------~l~~lViDEaH~l  208 (1104)
T 4ddu_A          192 L------SQK---------------RFDFVFVDDVDAV  208 (1104)
T ss_dssp             H------HTS---------------CCSEEEESCHHHH
T ss_pred             h------ccc---------------CcCEEEEeCCCcc
Confidence            1      122               8999999999973

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.61  E-value=9.5e-16  Score=151.95  Aligned_cols=54  Identities=19%  Similarity=0.116  Sum_probs=41.9

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHH-HHHhhc---CCcEEEEeCC
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQII-TLNLKF---GIPATFLNSQ  278 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~-~L~~~~---gI~a~~l~g~  278 (381)
                      +|||+|.++|+.++.|+|+++.+|||+|||++|+--+. .+....   +.+++++...
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~   61 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQ   61 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSS
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCC
Confidence            68999999999999999999999999999999983332 222111   5667777653

>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=99.59  E-value=2.4e-15  Score=160.52  Aligned_cols=58  Identities=16%  Similarity=0.269  Sum_probs=41.1

Q ss_pred             HhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHH-HHhhc---CCcEEEEeC
Q 042872          220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIIT-LNLKF---GIPATFLNS  277 (381)
Q Consensus       220 ~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~-L~~~~---gI~a~~l~g  277 (381)
                      .+|+..|||+|.++|+.++.|+|+|+.+|||+|||++|+--+.. +....   +.+++++..
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~P  304 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLAT  304 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECS
T ss_pred             hcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeC
Confidence            37899999999999999999999999999999999999833222 22111   556666654

>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=99.56  E-value=1.7e-15  Score=167.45  Aligned_cols=45  Identities=20%  Similarity=0.174  Sum_probs=39.8

Q ss_pred             hHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          211 DDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       211 ~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .++...+.+.+||. | |+|.++|+.++.|+|+++++|||+|||+ |+
T Consensus        44 ~~~~~~~~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~   88 (1054)
T 1gku_B           44 KEFVEFFRKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FG   88 (1054)
T ss_dssp             HHHHHHHHTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HH
T ss_pred             HHHHHHHHHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HH
Confidence            34556666779999 9 9999999999999999999999999998 55

>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=99.55  E-value=2.9e-15  Score=155.27  Aligned_cols=126  Identities=19%  Similarity=0.260  Sum_probs=72.7

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHH-HHhh----cCCcEEEEeCCCCH-HHH-HHHHHHHHhchhh
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIIT-LNLK----FGIPATFLNSQQTV-SQA-AAVLQELRQGLVL  297 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~-L~~~----~gI~a~~l~g~~~~-~e~-~~il~~lr~g~~~  297 (381)
                      .|||+|.++|+.++.|+|+|+.+|||+|||++|+--+.. +...    .+.+++++...... .++ ...++.+-.+   
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~---   83 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK---   83 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTT---
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCc---
Confidence            699999999999999999999999999999999832222 2111    12566666664422 222 3333332100   


Q ss_pred             hhhhhhhhhhhhhhhcccCC-------CCCccEEEECccccccCcchHHHHHHHH--hcCCccccccccccccccccccC
Q 042872          298 SQHYFLHQLIFVLTCASRKD-------KPSCKLLYVTPERIVGNQSFSEVLKCLH--RKGSIRLKVLTTDVVVLPHTCQR  368 (381)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~-------~~~~~IL~aTPErL~~~~~f~~~L~~L~--~~g~~~l~~~~~~~v~~~~~~~~  368 (381)
                            .-.+..+ ......       ...++|||+|||+|..      .+....  ..+.+.+.               
T Consensus        84 ------~~~v~~~-~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~------~l~~~~~~~~~~~~~~---------------  135 (699)
T 4gl2_A           84 ------WYRVIGL-SGDTQLKISFPEVVKSCDIIISTAQILEN------SLLNLENGEDAGVQLS---------------  135 (699)
T ss_dssp             ------TSCEEEE-C----CCCCHHHHHHSCSEEEEEHHHHHH------HTC--------CCCGG---------------
T ss_pred             ------CceEEEE-eCCcchhhHHHhhhcCCCEEEECHHHHHH------HHhccccccccceecc---------------
Confidence                  0000000 000000       1358999999999972      110000  12223333               


Q ss_pred             CccEEEEeccccC
Q 042872          369 QLAGFVVDEAHCV  381 (381)
Q Consensus       369 ~L~~lVIDEAHcI  381 (381)
                      .+.+||||||||+
T Consensus       136 ~~~lvViDEaH~~  148 (699)
T 4gl2_A          136 DFSLIIIDECHHT  148 (699)
T ss_dssp             GCSEEEEESGGGC
T ss_pred             cCcEEEEECcccc
Confidence            8999999999985

>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=99.55  E-value=2.4e-15  Score=132.24  Aligned_cols=58  Identities=17%  Similarity=0.175  Sum_probs=43.8

Q ss_pred             hCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHH-Hh----hcCCcEEEEeCC
Q 042872          221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITL-NL----KFGIPATFLNSQ  278 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L-~~----~~gI~a~~l~g~  278 (381)
                      .+...|||+|.++++.++.++++++.+|||+|||++|+--+..+ ..    ..+.+++++...
T Consensus        29 ~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~   91 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNK   91 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESS
T ss_pred             cCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECH
Confidence            34457999999999999999999999999999999997322221 11    125677777653

>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=99.55  E-value=2e-15  Score=158.57  Aligned_cols=143  Identities=17%  Similarity=0.168  Sum_probs=85.1

Q ss_pred             CHHHHh--hchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHH-HHHHHhhcCCcEEEEeCCC
Q 042872          203 SFEELQ--ALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQ-IITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       203 ~fe~L~--~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~~gI~a~~l~g~~  279 (381)
                      +|+.+.  .-+.+...+.+ +||+.|+|+|.++++.++.|+++++++|||+|||++|.-- +..+.  .+.+++++... 
T Consensus         2 ~f~~l~~~l~~~~~~~l~~-~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~--~~~~~l~i~P~-   77 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKE-EGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAI--KGGKSLYVVPL-   77 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHC-C---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHH--TTCCEEEEESS-
T ss_pred             chhhhhhccCHHHHHHHHh-CCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHH--hCCcEEEEeCc-
Confidence            456665  44445555544 8999999999999999999999999999999999999622 22332  25677777653 


Q ss_pred             CHHHHHHHHHHHHhchhhhhhhhhhhhhh---hhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccc
Q 042872          280 TVSQAAAVLQELRQGLVLSQHYFLHQLIF---VLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLT  356 (381)
Q Consensus       280 ~~~e~~~il~~lr~g~~~~~~~~~~~~~~---~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~  356 (381)
                       ..-..++.+.++.  +..    ....+.   +............+|+|+|||++..      .+    +++...++   
T Consensus        78 -r~La~q~~~~~~~--~~~----~g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~------~l----~~~~~~l~---  137 (702)
T 2p6r_A           78 -RALAGEKYESFKK--WEK----IGLRIGISTGDYESRDEHLGDCDIIVTTSEKADS------LI----RNRASWIK---  137 (702)
T ss_dssp             -HHHHHHHHHHHTT--TTT----TTCCEEEECSSCBCCSSCSTTCSEEEEEHHHHHH------HH----HTTCSGGG---
T ss_pred             -HHHHHHHHHHHHH--HHh----cCCEEEEEeCCCCcchhhccCCCEEEECHHHHHH------HH----HcChhHHh---
Confidence             3233333333320  000    000000   0000111223378999999999862      11    12222233   


Q ss_pred             cccccccccccCCccEEEEeccccC
Q 042872          357 TDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       357 ~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                  ++++|||||||++
T Consensus       138 ------------~~~~vIiDE~H~l  150 (702)
T 2p6r_A          138 ------------AVSCLVVDEIHLL  150 (702)
T ss_dssp             ------------GCCEEEETTGGGG
T ss_pred             ------------hcCEEEEeeeeec
Confidence                        8999999999984

>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=99.54  E-value=2.3e-15  Score=158.51  Aligned_cols=143  Identities=20%  Similarity=0.271  Sum_probs=83.3

Q ss_pred             HHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHH-HHcCCCEEEECCCCCCchhhHHHH-HHHHHhhcCCcEEEEeCCCCH
Q 042872          204 FEELQALDDMEFANVVIFGNRAFRPLQHQACKA-SVAKQDCFVLLPTGGGKSLCYQDQ-IITLNLKFGIPATFLNSQQTV  281 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~a-iL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~~gI~a~~l~g~~~~  281 (381)
                      |+.+..-+.+...+.. +||..|+|+|.++|+. ++.|+++++++|||+|||++|.-. +..+. ..|.+++++..-.. 
T Consensus         3 f~~l~l~~~~~~~l~~-~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~-~~~~~~l~i~P~ra-   79 (720)
T 2zj8_A            3 VDELRVDERIKSTLKE-RGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRIL-TQGGKAVYIVPLKA-   79 (720)
T ss_dssp             GGGCCSCHHHHHHHHH-TTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHH-HHCSEEEEECSSGG-
T ss_pred             HhhcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHH-hCCCEEEEEcCcHH-
Confidence            3344433334444433 8999999999999998 889999999999999999999522 23332 23667777765322 


Q ss_pred             HHHHHHHHHHHhchhhhhhhhhhhhhhhhhh---cccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccc
Q 042872          282 SQAAAVLQELRQGLVLSQHYFLHQLIFVLTC---ASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTD  358 (381)
Q Consensus       282 ~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~---~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~  358 (381)
                       -..++.+.++.  +..    ....+..++-   ........++|+|+|||++..      .+.    ++...++     
T Consensus        80 -La~q~~~~~~~--l~~----~g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~------~~~----~~~~~l~-----  137 (720)
T 2zj8_A           80 -LAEEKFQEFQD--WEK----IGLRVAMATGDYDSKDEWLGKYDIIIATAEKFDS------LLR----HGSSWIK-----  137 (720)
T ss_dssp             -GHHHHHHHTGG--GGG----GTCCEEEECSCSSCCCGGGGGCSEEEECHHHHHH------HHH----HTCTTGG-----
T ss_pred             -HHHHHHHHHHH--HHh----cCCEEEEecCCCCccccccCCCCEEEECHHHHHH------HHH----cChhhhh-----
Confidence             12222333220  000    0000000000   001112268999999999962      111    1222233     


Q ss_pred             cccccccccCCccEEEEeccccC
Q 042872          359 VVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       359 ~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                ++++|||||||++
T Consensus       138 ----------~~~~vIiDE~H~l  150 (720)
T 2zj8_A          138 ----------DVKILVADEIHLI  150 (720)
T ss_dssp             ----------GEEEEEEETGGGG
T ss_pred             ----------cCCEEEEECCccc
Confidence                      8999999999985

>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=99.53  E-value=2.2e-14  Score=154.78  Aligned_cols=110  Identities=21%  Similarity=0.214  Sum_probs=86.9

Q ss_pred             HHHHHhCCCCCcHHHHHHHHHHHcC------CCEEEECCCCCCchhhHH-----------------------HH-HHHHH
Q 042872          216 ANVVIFGNRAFRPLQHQACKASVAK------QDCFVLLPTGGGKSLCYQ-----------------------DQ-IITLN  265 (381)
Q Consensus       216 ~~~~~fG~~~fRpiQ~eAI~aiL~G------rDvLviaPTGsGKTLaF~-----------------------dQ-v~~L~  265 (381)
                      .+...+|| .+|++|.+||+.++.+      +++|+++|||+|||++|+                       .| ...+.
T Consensus       360 ~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~g~qvlvlaPtr~La~Q~~~~l~  438 (780)
T 1gm5_A          360 EFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTV  438 (780)
T ss_dssp             HHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHH
T ss_pred             HHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHH
Confidence            34456799 8999999999999875      699999999999999997                       22 33333


Q ss_pred             ---hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHH
Q 042872          266 ---LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLK  342 (381)
Q Consensus       266 ---~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~  342 (381)
                         ..+|+++..++|+.+..++...+..+..|                         .++|||+||+++..         
T Consensus       439 ~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g-------------------------~~~IvVgT~~ll~~---------  484 (780)
T 1gm5_A          439 ESFSKFNIHVALLIGATTPSEKEKIKSGLRNG-------------------------QIDVVIGTHALIQE---------  484 (780)
T ss_dssp             HHHTCSSCCEEECCSSSCHHHHHHHHHHHHSS-------------------------CCCEEEECTTHHHH---------
T ss_pred             HHhhhcCceEEEEeCCCCHHHHHHHHHHHhcC-------------------------CCCEEEECHHHHhh---------
Confidence               23478999999999988888888887755                         68999999987742         


Q ss_pred             HHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          343 CLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       343 ~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                            .+.+.               ++++|||||||++
T Consensus       485 ------~~~~~---------------~l~lVVIDEaHr~  502 (780)
T 1gm5_A          485 ------DVHFK---------------NLGLVIIDEQHRF  502 (780)
T ss_dssp             ------CCCCS---------------CCCEEEEESCCCC
T ss_pred             ------hhhcc---------------CCceEEecccchh
Confidence                  11222               8999999999984

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.52  E-value=6.5e-15  Score=154.52  Aligned_cols=145  Identities=18%  Similarity=0.181  Sum_probs=87.5

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHH-HHcCCCEEEECCCCCCchhhHHHH-HHHHHhhcCCcEEEEeCCC
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKA-SVAKQDCFVLLPTGGGKSLCYQDQ-IITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~a-iL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~~gI~a~~l~g~~  279 (381)
                      ++|+.+..-+.+...+.. +||+.|+|+|.++|+. ++.|+++++++|||+|||++|.-- +..+. ..|.+++++..- 
T Consensus         8 ~~~~~l~l~~~~~~~l~~-~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~-~~~~~il~i~P~-   84 (715)
T 2va8_A            8 MPIEDLKLPSNVIEIIKK-RGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLL-KNGGKAIYVTPL-   84 (715)
T ss_dssp             CBGGGSSSCHHHHHHHHT-TSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHH-HSCSEEEEECSC-
T ss_pred             CcHHHcCCCHHHHHHHHh-CCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHH-HCCCeEEEEeCc-
Confidence            456666544455555544 8999999999999999 788999999999999999999622 22333 246677776543 


Q ss_pred             CHHHHHHHHHHHHhchhhhhhhhhhhhhhhh---hhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccc
Q 042872          280 TVSQAAAVLQELRQGLVLSQHYFLHQLIFVL---TCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLT  356 (381)
Q Consensus       280 ~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~---~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~  356 (381)
                       ..-..++.+.++.  +..    +...+..+   ...........+|+|+|||++..      .+.    ++...++   
T Consensus        85 -r~La~q~~~~~~~--~~~----~g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~------~~~----~~~~~l~---  144 (715)
T 2va8_A           85 -RALTNEKYLTFKD--WEL----IGFKVAMTSGDYDTDDAWLKNYDIIITTYEKLDS------LWR----HRPEWLN---  144 (715)
T ss_dssp             -HHHHHHHHHHHGG--GGG----GTCCEEECCSCSSSCCGGGGGCSEEEECHHHHHH------HHH----HCCGGGG---
T ss_pred             -HHHHHHHHHHHHH--hhc----CCCEEEEEeCCCCCchhhcCCCCEEEEcHHHHHH------HHh----CChhHhh---
Confidence             3333333433320  000    00000000   00011111268999999999962      111    1222233   


Q ss_pred             cccccccccccCCccEEEEeccccC
Q 042872          357 TDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       357 ~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                  ++++|||||||++
T Consensus       145 ------------~~~~vIiDE~H~l  157 (715)
T 2va8_A          145 ------------EVNYFVLDELHYL  157 (715)
T ss_dssp             ------------GEEEEEECSGGGG
T ss_pred             ------------ccCEEEEechhhc
Confidence                        8999999999984

>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=99.52  E-value=2e-14  Score=157.00  Aligned_cols=38  Identities=18%  Similarity=0.433  Sum_probs=33.4

Q ss_pred             hCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      +|+..|||+|.++|+.++.|+|+|+.+|||+|||++|+
T Consensus       244 ~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~  281 (936)
T 4a2w_A          244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSI  281 (936)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHH
Confidence            67889999999999999999999999999999999997

>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=99.51  E-value=1.4e-14  Score=161.35  Aligned_cols=122  Identities=18%  Similarity=0.175  Sum_probs=79.9

Q ss_pred             hCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhh
Q 042872          221 FGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQH  300 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~  300 (381)
                      ++| .|+|+|.+||++++.|+|+|+++|||+|||++|+--+.... ..|.+++++...  ..-..++.+.+++       
T Consensus       181 ~~f-~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l-~~g~rvlvl~Pt--raLa~Q~~~~l~~-------  249 (1108)
T 3l9o_A          181 YPF-TLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSL-KNKQRVIYTSPI--KALSNQKYRELLA-------  249 (1108)
T ss_dssp             CSS-CCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHH-HTTCEEEEEESS--HHHHHHHHHHHHH-------
T ss_pred             CCC-CCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHH-hcCCeEEEEcCc--HHHHHHHHHHHHH-------
Confidence            444 69999999999999999999999999999999973332222 346677777653  2222233333331       


Q ss_pred             hhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          301 YFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       301 ~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                       .+.  ...+-......++.++|||+|||+|.+          +..++...+.               ++.+|||||||+
T Consensus       250 -~~~--~VglltGd~~~~~~~~IlV~Tpe~L~~----------~L~~~~~~l~---------------~l~lVVIDEaH~  301 (1108)
T 3l9o_A          250 -EFG--DVGLMTGDITINPDAGCLVMTTEILRS----------MLYRGSEVMR---------------EVAWVIFDEVHY  301 (1108)
T ss_dssp             -HTS--SEEEECSSCBCCCSCSEEEEEHHHHHH----------HHHHCSSHHH---------------HEEEEEEETGGG
T ss_pred             -HhC--CccEEeCccccCCCCCEEEeChHHHHH----------HHHcCccccc---------------cCCEEEEhhhhh
Confidence             000  011111233455679999999999962          1122333344               899999999998


Q ss_pred             C
Q 042872          381 V  381 (381)
Q Consensus       381 I  381 (381)
                      +
T Consensus       302 l  302 (1108)
T 3l9o_A          302 M  302 (1108)
T ss_dssp             T
T ss_pred             c
Confidence            5

>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=99.50  E-value=3.5e-14  Score=154.12  Aligned_cols=115  Identities=18%  Similarity=0.136  Sum_probs=84.5

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITLN  265 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L~  265 (381)
                      +..+..+.+|| .|+|+|..+||.++.|+  |+.|+||+|||++|.                           +++..|.
T Consensus        72 vrea~~r~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~g~~vlVltptreLA~qd~e~~~~l~  148 (844)
T 1tf5_A           72 VREASRRVTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIF  148 (844)
T ss_dssp             HHHHHHHHHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHH
Confidence            44456667999 99999999999999999  999999999999998                           4456666


Q ss_pred             hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHH
Q 042872          266 LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLH  345 (381)
Q Consensus       266 ~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~  345 (381)
                      ..+|+++.++.|+++...+...  .                             .++|+|+||++|.     ...|....
T Consensus       149 ~~lgl~v~~i~gg~~~~~r~~~--~-----------------------------~~dIv~gTpgrlg-----fD~L~D~m  192 (844)
T 1tf5_A          149 EFLGLTVGLNLNSMSKDEKREA--Y-----------------------------AADITYSTNNELG-----FDYLRDNM  192 (844)
T ss_dssp             HHTTCCEEECCTTSCHHHHHHH--H-----------------------------HSSEEEEEHHHHH-----HHHHHHTT
T ss_pred             hhcCCeEEEEeCCCCHHHHHHh--c-----------------------------CCCEEEECchhhh-----HHHHHHhh
Confidence            6678998888888876543221  1                             4799999999993     01222111


Q ss_pred             --hcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          346 --RKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       346 --~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                        ..+.+.               ++.+.++||||||.|
T Consensus       193 ~~~~~~l~---------------lr~~~~lVlDEaD~m  215 (844)
T 1tf5_A          193 VLYKEQMV---------------QRPLHFAVIDEVDSI  215 (844)
T ss_dssp             CSSGGGCC---------------CCCCCEEEEETHHHH
T ss_pred             hcchhhhc---------------ccCCCEEEECchhhh
Confidence              011122               238999999999964

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.50  E-value=1.4e-14  Score=159.64  Aligned_cols=126  Identities=16%  Similarity=0.229  Sum_probs=82.1

Q ss_pred             HHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhh
Q 042872          219 VIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLS  298 (381)
Q Consensus       219 ~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~  298 (381)
                      ..|+|+ ++|+|.++|+.++.|+|+|+++|||+|||+||+-.+..+. ..+.+++++.......  .++.+.+++-    
T Consensus        34 ~~~~f~-l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~-~~g~~vlvl~PtraLa--~Q~~~~l~~~----  105 (997)
T 4a4z_A           34 RSWPFE-LDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAH-RNMTKTIYTSPIKALS--NQKFRDFKET----  105 (997)
T ss_dssp             CCCSSC-CCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHH-HTTCEEEEEESCGGGH--HHHHHHHHTT----
T ss_pred             HhCCCC-CCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHH-hcCCeEEEEeCCHHHH--HHHHHHHHHH----
Confidence            347885 8999999999999999999999999999999875554443 3466777776643322  2233333310    


Q ss_pred             hhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEecc
Q 042872          299 QHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEA  378 (381)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEA  378 (381)
                          +.......-......++.++|+|+|||+|.+      .   + .++...+.               ++.+||||||
T Consensus       106 ----~~~~~v~~l~G~~~~~~~~~IlV~Tpe~L~~------~---l-~~~~~~l~---------------~l~lvViDEa  156 (997)
T 4a4z_A          106 ----FDDVNIGLITGDVQINPDANCLIMTTEILRS------M---L-YRGADLIR---------------DVEFVIFDEV  156 (997)
T ss_dssp             ----C--CCEEEECSSCEECTTSSEEEEEHHHHHH------H---H-HHTCSGGG---------------GEEEEEECCT
T ss_pred             ----cCCCeEEEEeCCCccCCCCCEEEECHHHHHH------H---H-HhCchhhc---------------CCCEEEEECc
Confidence                0000011111122344568999999999962      1   1 12323333               8999999999


Q ss_pred             ccC
Q 042872          379 HCV  381 (381)
Q Consensus       379 HcI  381 (381)
                      ||+
T Consensus       157 H~l  159 (997)
T 4a4z_A          157 HYV  159 (997)
T ss_dssp             TCC
T ss_pred             ccc
Confidence            996

>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=99.49  E-value=1.2e-13  Score=132.26  Aligned_cols=52  Identities=25%  Similarity=0.268  Sum_probs=39.7

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      .+||+|.++++.++.+ ++|+.+|||+|||++|+--+..+....+-+++++..
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P   60 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAP   60 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECS
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEEC
Confidence            6899999999999999 999999999999999973322222123556666654

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.43  E-value=8.6e-14  Score=153.65  Aligned_cols=123  Identities=19%  Similarity=0.190  Sum_probs=79.5

Q ss_pred             HhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhh
Q 042872          220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQ  299 (381)
Q Consensus       220 ~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~  299 (381)
                      .|+|+ |+|+|.+||++++.|+++|+++|||+|||++|.--+.... ..|.+++++...  ..-..++.+.++.      
T Consensus        82 ~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l-~~g~rvL~l~Pt--kaLa~Q~~~~l~~------  151 (1010)
T 2xgj_A           82 TYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSL-KNKQRVIYTSPI--KALSNQKYRELLA------  151 (1010)
T ss_dssp             CCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHH-HTTCEEEEEESS--HHHHHHHHHHHHH------
T ss_pred             hCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHh-ccCCeEEEECCh--HHHHHHHHHHHHH------
Confidence            37886 9999999999999999999999999999999963222221 346677777753  2222233333331      


Q ss_pred             hhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccc
Q 042872          300 HYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH  379 (381)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAH  379 (381)
                        .+. .+ .+-......++.++|+|+|||+|.+      .   + .++...+.               ++.+|||||||
T Consensus       152 --~~~-~v-glltGd~~~~~~~~IvV~Tpe~L~~------~---L-~~~~~~l~---------------~l~lVViDEaH  202 (1010)
T 2xgj_A          152 --EFG-DV-GLMTGDITINPDAGCLVMTTEILRS------M---L-YRGSEVMR---------------EVAWVIFDEVH  202 (1010)
T ss_dssp             --HHS-CE-EEECSSCEECTTCSEEEEEHHHHHH------H---H-HHTCTTGG---------------GEEEEEEETGG
T ss_pred             --HhC-CE-EEEeCCCccCCCCCEEEEcHHHHHH------H---H-HcCcchhh---------------cCCEEEEechh
Confidence              000 00 1111122334568999999999862      1   1 22333344               89999999999


Q ss_pred             cC
Q 042872          380 CV  381 (381)
Q Consensus       380 cI  381 (381)
                      ++
T Consensus       203 ~l  204 (1010)
T 2xgj_A          203 YM  204 (1010)
T ss_dssp             GG
T ss_pred             hh
Confidence            85

>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=99.40  E-value=2.9e-13  Score=147.60  Aligned_cols=115  Identities=16%  Similarity=0.122  Sum_probs=84.4

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITLN  265 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L~  265 (381)
                      +..+..+.+|+ .|+|+|..+|+.++.|+  |+.|+||+|||++|.                           +++..+.
T Consensus       100 vrEa~~R~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~g~~v~VvTpTreLA~Qdae~m~~l~  176 (922)
T 1nkt_A          100 AREAAWRVLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALAGNGVHIVTVNDYLAKRDSEWMGRVH  176 (922)
T ss_dssp             HHHHHHHHHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTTTSCEEEEESSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHhCCCeEEEeCCHHHHHHHHHHHHHHH
Confidence            44466678999 89999999999999999  999999999999997                           4456666


Q ss_pred             hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHH
Q 042872          266 LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLH  345 (381)
Q Consensus       266 ~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~  345 (381)
                      ..+|+++.++.|+++...+....                               .++|+|+||++|.     ...|....
T Consensus       177 ~~lGLsv~~i~gg~~~~~r~~~y-------------------------------~~DIvygTpgrlg-----fDyLrD~m  220 (922)
T 1nkt_A          177 RFLGLQVGVILATMTPDERRVAY-------------------------------NADITYGTNNEFG-----FDYLRDNM  220 (922)
T ss_dssp             HHTTCCEEECCTTCCHHHHHHHH-------------------------------HSSEEEEEHHHHH-----HHHHHHTT
T ss_pred             hhcCCeEEEEeCCCCHHHHHHhc-------------------------------CCCEEEECchHhh-----HHHHHhhh
Confidence            67889999988888765432111                               3799999999993     01222211


Q ss_pred             --hcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          346 --RKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       346 --~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                        ..+.+               .++.+.++||||||.|
T Consensus       221 ~~~~~~l---------------~lr~l~~lIVDEaDsm  243 (922)
T 1nkt_A          221 AHSLDDL---------------VQRGHHYAIVDEVDSI  243 (922)
T ss_dssp             CSSGGGC---------------CCCCCCEEEETTHHHH
T ss_pred             hccHhhh---------------ccCCCCEEEEeChHHH
Confidence              01112               2338999999999964

>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=99.40  E-value=3.8e-13  Score=146.02  Aligned_cols=114  Identities=18%  Similarity=0.132  Sum_probs=83.3

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITLN  265 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L~  265 (381)
                      +..+..+.+|. .|+|+|..+++.++.|+  ++.|+||+|||++|.                           +.+..+.
T Consensus        63 vrea~~R~lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~g~~vlVltPTreLA~Q~~e~~~~l~  139 (853)
T 2fsf_A           63 VREASKRVFGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALTGKGVHVVTVNDYLAQRDAENNRPLF  139 (853)
T ss_dssp             HHHHHHHHHSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTTSSCCEEEESSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHcCCcEEEEcCCHHHHHHHHHHHHHHH
Confidence            44556677897 79999999999999999  999999999999997                           3456666


Q ss_pred             hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECcccc-ccCcchHHHHHHH
Q 042872          266 LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERI-VGNQSFSEVLKCL  344 (381)
Q Consensus       266 ~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL-~~~~~f~~~L~~L  344 (381)
                      ..+|+++.+++|+++...+.     +..                          .++|+|+||++| +      ..|+.-
T Consensus       140 ~~lgl~v~~i~GG~~~~~r~-----~~~--------------------------~~dIvvgTpgrl~f------DyLrd~  182 (853)
T 2fsf_A          140 EFLGLTVGINLPGMPAPAKR-----EAY--------------------------AADITYGTNNEYGF------DYLRDN  182 (853)
T ss_dssp             HHTTCCEEECCTTCCHHHHH-----HHH--------------------------HSSEEEEEHHHHHH------HHHHHT
T ss_pred             HhcCCeEEEEeCCCCHHHHH-----Hhc--------------------------CCCEEEECCchhhH------HHHHhh
Confidence            67789999999888764321     111                          379999999998 3      122211


Q ss_pred             H--hcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          345 H--RKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       345 ~--~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      .  ..+.+               .++.+.++||||||.+
T Consensus       183 ~~~~~~~~---------------~~~~l~~lVlDEaD~m  206 (853)
T 2fsf_A          183 MAFSPEER---------------VQRKLHYALVDEVDSI  206 (853)
T ss_dssp             TCSSGGGC---------------CCCSCCEEEESCHHHH
T ss_pred             hhccHhHh---------------cccCCcEEEECchHHH
Confidence            1  01111               2338999999999953

>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=99.36  E-value=6.5e-13  Score=153.51  Aligned_cols=57  Identities=23%  Similarity=0.309  Sum_probs=41.8

Q ss_pred             hCCCCCcHHHHHHHHHHHcC-CCEEEECCCCCCchhhHHH-HHHHHHhhcCCcEEEEeC
Q 042872          221 FGNRAFRPLQHQACKASVAK-QDCFVLLPTGGGKSLCYQD-QIITLNLKFGIPATFLNS  277 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~G-rDvLviaPTGsGKTLaF~d-Qv~~L~~~~gI~a~~l~g  277 (381)
                      .+|+.|+|+|.+|++.++.+ +++++.||||||||++|.- -+..|...-+.+++++.+
T Consensus       922 ~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~~~~kavyi~P  980 (1724)
T 4f92_B          922 DKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITP  980 (1724)
T ss_dssp             TTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCTTCCEEEECS
T ss_pred             hcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCCCCEEEEEcC
Confidence            47899999999999999865 6899999999999999961 122333222445555543

>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=99.35  E-value=2.5e-12  Score=143.64  Aligned_cols=109  Identities=21%  Similarity=0.247  Sum_probs=81.7

Q ss_pred             HHHHhCCCCCcHHHHHHHHHHHc----CC--CEEEECCCCCCchhhHH-----------------------HH-HHHHHh
Q 042872          217 NVVIFGNRAFRPLQHQACKASVA----KQ--DCFVLLPTGGGKSLCYQ-----------------------DQ-IITLNL  266 (381)
Q Consensus       217 ~~~~fG~~~fRpiQ~eAI~aiL~----Gr--DvLviaPTGsGKTLaF~-----------------------dQ-v~~L~~  266 (381)
                      +...|||+ +||+|.+||+.++.    |+  |+|+++|||+|||++|+                       .| ...+..
T Consensus       596 ~~~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~g~~vlvlvPt~~La~Q~~~~~~~  674 (1151)
T 2eyq_A          596 FCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRD  674 (1151)
T ss_dssp             HHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHH
T ss_pred             HHHhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHhCCeEEEEechHHHHHHHHHHHHH
Confidence            44568886 69999999999997    66  99999999999998875                       22 333332


Q ss_pred             ---hcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHH
Q 042872          267 ---KFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKC  343 (381)
Q Consensus       267 ---~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~  343 (381)
                         .+++++..+++..+..++...++.+..|                         .++|||+||+.+..          
T Consensus       675 ~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g-------------------------~~dIvV~T~~ll~~----------  719 (1151)
T 2eyq_A          675 RFANWPVRIEMISRFRSAKEQTQILAEVAEG-------------------------KIDILIGTHKLLQS----------  719 (1151)
T ss_dssp             HSTTTTCCEEEESTTSCHHHHHHHHHHHHTT-------------------------CCSEEEECTHHHHS----------
T ss_pred             HhhcCCCeEEEEeCCCCHHHHHHHHHHHhcC-------------------------CCCEEEECHHHHhC----------
Confidence               2357777777777777777777776644                         68999999987642          


Q ss_pred             HHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          344 LHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       344 L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                           .+.++               ++++|||||||++
T Consensus       720 -----~~~~~---------------~l~lvIiDEaH~~  737 (1151)
T 2eyq_A          720 -----DVKFK---------------DLGLLIVDEEHRF  737 (1151)
T ss_dssp             -----CCCCS---------------SEEEEEEESGGGS
T ss_pred             -----Ccccc---------------ccceEEEechHhc
Confidence                 12222               8999999999983

>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=99.34  E-value=3.5e-12  Score=119.10  Aligned_cols=121  Identities=14%  Similarity=0.096  Sum_probs=72.5

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhh
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLH  304 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~  304 (381)
                      ++||+|.++++.++.+++.++.+|||+|||++|+--+..+....+.+++++...  ..-..+..+.+++  +...   ..
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~~lil~Pt--~~L~~q~~~~l~~--~~~~---~~  185 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPT--TALTTQMADDFVD--YRLF---SH  185 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSS--HHHHHHHHHHHHH--HTSC---CG
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcCCCeEEEEECC--HHHHHHHHHHHHH--hccc---cc
Confidence            689999999999999999999999999999999733333222223467777543  2222223333321  0000   00


Q ss_pred             hhhhhhhhcccCC----CCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          305 QLIFVLTCASRKD----KPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       305 ~~~~~~~~~~~~~----~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                      ..+..+. .+...    ....+|+|+||+++.....             ..+.               ++.+|||||||+
T Consensus       186 ~~~~~~~-~~~~~~~~~~~~~~I~v~T~~~l~~~~~-------------~~~~---------------~~~~vIiDEaH~  236 (282)
T 1rif_A          186 AMIKKIG-GGASKDDKYKNDAPVVVGTWQTVVKQPK-------------EWFS---------------QFGMMMNDECHL  236 (282)
T ss_dssp             GGEEECS-TTCSSTTCCCTTCSEEEECHHHHTTSCG-------------GGGG---------------GEEEEEEETGGG
T ss_pred             ceEEEEe-CCCcchhhhccCCcEEEEchHHHHhhHH-------------HHHh---------------hCCEEEEECCcc
Confidence            0000000 01111    1568999999999874211             0111               789999999998


Q ss_pred             C
Q 042872          381 V  381 (381)
Q Consensus       381 I  381 (381)
                      +
T Consensus       237 ~  237 (282)
T 1rif_A          237 A  237 (282)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.33  E-value=8.5e-13  Score=152.54  Aligned_cols=37  Identities=22%  Similarity=0.425  Sum_probs=34.8

Q ss_pred             CCCCCcHHHHHHHHHHHc-CCCEEEECCCCCCchhhHH
Q 042872          222 GNRAFRPLQHQACKASVA-KQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       222 G~~~fRpiQ~eAI~aiL~-GrDvLviaPTGsGKTLaF~  258 (381)
                      ||++|+++|.+++|.++. ++|+|++||||+|||++|.
T Consensus        76 g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~  113 (1724)
T 4f92_B           76 GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVAL  113 (1724)
T ss_dssp             TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHH
Confidence            899999999999999985 6899999999999999986

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.32  E-value=3.4e-12  Score=139.54  Aligned_cols=85  Identities=14%  Similarity=0.152  Sum_probs=70.0

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITLN  265 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L~  265 (381)
                      +..+..+.+|+ .|+|+|..+|+.++.|+  ++.|+||+|||++|.                           +.+..|.
T Consensus        68 vREAs~R~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~G~qv~VvTPTreLA~Qdae~m~~l~  144 (997)
T 2ipc_A           68 TRESAKRYLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALTGKGVHVVTVNDYLARRDAEWMGPVY  144 (997)
T ss_dssp             HHHHHHHHTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTTCSCCEEEESSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHHHHHHHHH
Confidence            55577778999 89999999999999999  999999999999997                           3456666


Q ss_pred             hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECcccc
Q 042872          266 LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERI  331 (381)
Q Consensus       266 ~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL  331 (381)
                      ..+|+++.+++|+++...+....                               .++|+|+||++|
T Consensus       145 ~~lGLsv~~i~Gg~~~~~r~~ay-------------------------------~~DIvyGTpgrl  179 (997)
T 2ipc_A          145 RGLGLSVGVIQHASTPAERRKAY-------------------------------LADVTYVTNSEL  179 (997)
T ss_dssp             HTTTCCEEECCTTCCHHHHHHHH-------------------------------TSSEEEEEHHHH
T ss_pred             HhcCCeEEEEeCCCCHHHHHHHc-------------------------------CCCEEEECchhh
Confidence            67799999999888754432211                               479999999999

>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=99.29  E-value=2e-12  Score=128.18  Aligned_cols=112  Identities=20%  Similarity=0.183  Sum_probs=73.4

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhh
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLH  304 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~  304 (381)
                      .+||+|.+||+.++.++++++.+|||+|||++|+--+..    .+.+++++...  ..-..+..+.+++         +.
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~----~~~~~Lvl~P~--~~L~~Q~~~~~~~---------~~  157 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINE----LSTPTLIVVPT--LALAEQWKERLGI---------FG  157 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHH----HCSCEEEEESS--HHHHHHHHHHGGG---------GC
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHH----cCCCEEEEECC--HHHHHHHHHHHHh---------CC
Confidence            689999999999999999999999999999999633322    36788888764  2222223333331         00


Q ss_pred             hhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          305 QLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       305 ~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                        +.......+......+|+|+||+++...      +..+  .                    .++.+|||||||++
T Consensus       158 --~~~v~~~~g~~~~~~~Ivv~T~~~l~~~------~~~~--~--------------------~~~~liIvDEaH~~  204 (472)
T 2fwr_A          158 --EEYVGEFSGRIKELKPLTVSTYDSAYVN------AEKL--G--------------------NRFMLLIFDEVHHL  204 (472)
T ss_dssp             --GGGEEEBSSSCBCCCSEEEEEHHHHHHT------HHHH--T--------------------TTCSEEEEETGGGT
T ss_pred             --CcceEEECCCcCCcCCEEEEEcHHHHHH------HHHh--c--------------------CCCCEEEEECCcCC
Confidence              0001112233334578999999998631      1111  0                    16899999999985

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.27  E-value=1.2e-11  Score=123.65  Aligned_cols=122  Identities=15%  Similarity=0.117  Sum_probs=74.2

Q ss_pred             CCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhh
Q 042872          224 RAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFL  303 (381)
Q Consensus       224 ~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~  303 (381)
                      ..+||+|.+||+.++.++++++.+|||+|||++|+--+..+....+-+++++.....  -..+..+.+++  +.   .+.
T Consensus       112 ~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~vlvl~P~~~--L~~Q~~~~~~~--~~---~~~  184 (510)
T 2oca_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTA--LTTQMADDFVD--YR---LFS  184 (510)
T ss_dssp             ECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHCSSEEEEEESSHH--HHHHHHHHHHH--TT---SSC
T ss_pred             CCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCCCCeEEEEECcHH--HHHHHHHHHHH--hh---cCC
Confidence            379999999999999999999999999999999973333322223347777776422  22223333321  00   000


Q ss_pred             hhhhhhhhhcccCC----CCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccc
Q 042872          304 HQLIFVLTCASRKD----KPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH  379 (381)
Q Consensus       304 ~~~~~~~~~~~~~~----~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAH  379 (381)
                      ...+..+ ..+...    .+..+|+|+||+.|.....             ..++               ++.+|||||||
T Consensus       185 ~~~v~~~-~~~~~~~~~~~~~~~I~i~T~~~l~~~~~-------------~~~~---------------~~~liIiDE~H  235 (510)
T 2oca_A          185 HAMIKKI-GGGASKDDKYKNDAPVVVGTWQTVVKQPK-------------EWFS---------------QFGMMMNDECH  235 (510)
T ss_dssp             GGGEEEC-GGGCCTTGGGCTTCSEEEEEHHHHTTSCG-------------GGGG---------------GEEEEEEETGG
T ss_pred             ccceEEE-ecCCccccccccCCcEEEEeHHHHhhchh-------------hhhh---------------cCCEEEEECCc
Confidence            0000000 011111    1578999999999874211             1111               78999999999


Q ss_pred             cC
Q 042872          380 CV  381 (381)
Q Consensus       380 cI  381 (381)
                      ++
T Consensus       236 ~~  237 (510)
T 2oca_A          236 LA  237 (510)
T ss_dssp             GC
T ss_pred             CC
Confidence            85

>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=99.25  E-value=1.1e-11  Score=113.21  Aligned_cols=122  Identities=13%  Similarity=0.092  Sum_probs=70.2

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHH-HHHHh---hcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhh
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQI-ITLNL---KFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQH  300 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv-~~L~~---~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~  300 (381)
                      .++++|.++|+.+..|+++++++|||+|||.+|.-.+ ..+..   ..++.++++..  ......++.+.+....    .
T Consensus        61 p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p--~~~la~q~~~~~~~~~----~  134 (235)
T 3llm_A           61 PVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQP--RRISAVSVAERVAFER----G  134 (235)
T ss_dssp             GGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEES--SHHHHHHHHHHHHHTT----T
T ss_pred             ChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEecc--chHHHHHHHHHHHHHh----c
Confidence            4678999999999999999999999999998775221 11111   11345555544  3333333333332110    0


Q ss_pred             hhhhhhhhh-hhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccc
Q 042872          301 YFLHQLIFV-LTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH  379 (381)
Q Consensus       301 ~~~~~~~~~-~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAH  379 (381)
                      ......+.. .........+..+|+|+||++|..      .+..       .++               ++++|||||||
T Consensus       135 ~~~~~~~g~~~~~~~~~~~~~~~Ivv~Tpg~l~~------~l~~-------~l~---------------~~~~lVlDEah  186 (235)
T 3llm_A          135 EEPGKSCGYSVRFESILPRPHASIMFCTVGVLLR------KLEA-------GIR---------------GISHVIVDEIH  186 (235)
T ss_dssp             CCTTSSEEEEETTEEECCCSSSEEEEEEHHHHHH------HHHH-------CCT---------------TCCEEEECCTT
T ss_pred             cccCceEEEeechhhccCCCCCeEEEECHHHHHH------HHHh-------hhc---------------CCcEEEEECCc
Confidence            000000000 000111223568899999999972      1211       123               89999999999


Q ss_pred             c
Q 042872          380 C  380 (381)
Q Consensus       380 c  380 (381)
                      .
T Consensus       187 ~  187 (235)
T 3llm_A          187 E  187 (235)
T ss_dssp             S
T ss_pred             c
Confidence            6

>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=99.25  E-value=1.1e-11  Score=114.53  Aligned_cols=112  Identities=20%  Similarity=0.187  Sum_probs=72.2

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhh
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLH  304 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~  304 (381)
                      .+||+|.+++..++.++++++++|||+|||++++--+.    ..+-+++++...  ..-..+..+.++.         +.
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~----~~~~~~liv~P~--~~L~~q~~~~~~~---------~~  157 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAIN----ELSTPTLIVVPT--LALAEQWKERLGI---------FG  157 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHH----HSCSCEEEEESS--HHHHHHHHHHHGG---------GC
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHH----HcCCCEEEEeCC--HHHHHHHHHHHHh---------CC
Confidence            68999999999999999999999999999999863222    246677777653  2222223333321         00


Q ss_pred             hhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          305 QLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       305 ~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                        +.......+......+|+|+||+++...      +..+  ..                    ++.+|||||||++
T Consensus       158 --~~~v~~~~g~~~~~~~i~v~T~~~l~~~------~~~~--~~--------------------~~~llIiDEaH~l  204 (237)
T 2fz4_A          158 --EEYVGEFSGRIKELKPLTVSTYDSAYVN------AEKL--GN--------------------RFMLLIFDEVHHL  204 (237)
T ss_dssp             --GGGEEEESSSCBCCCSEEEEEHHHHHHT------HHHH--TT--------------------TCSEEEEECSSCC
T ss_pred             --CCeEEEEeCCCCCcCCEEEEeHHHHHhh------HHHh--cc--------------------cCCEEEEECCccC
Confidence              0001112223334678999999998631      1111  11                    6899999999985

>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=99.16  E-value=1.7e-11  Score=123.04  Aligned_cols=119  Identities=20%  Similarity=0.120  Sum_probs=74.3

Q ss_pred             CCCCCcHHHHHHHHHHHcCCCE-EEECCCCCCchhhHHHHH-HHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhh
Q 042872          222 GNRAFRPLQHQACKASVAKQDC-FVLLPTGGGKSLCYQDQI-ITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQ  299 (381)
Q Consensus       222 G~~~fRpiQ~eAI~aiL~GrDv-LviaPTGsGKTLaF~dQv-~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~  299 (381)
                      |+..++|+|+ +||.++.|+|+ ++.+|||+|||++|+-.+ ..+. ..+.+++++...  ..-..++.+.++ |.    
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~-~~~~~~lvl~Pt--r~La~Q~~~~l~-g~----   71 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREAL-LRRLRTLILAPT--RVVAAEMEEALR-GL----   71 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHH-HTTCCEEEEESS--HHHHHHHHHHTT-TS----
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHH-hcCCcEEEECCC--HHHHHHHHHHhc-Cc----
Confidence            7888999985 89999999988 888999999999987443 3333 357788888753  332222333321 10    


Q ss_pred             hhhhhhhhhhhhh-cccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEecc
Q 042872          300 HYFLHQLIFVLTC-ASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEA  378 (381)
Q Consensus       300 ~~~~~~~~~~~~~-~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEA  378 (381)
                            .+..... ......+...|.++||+.+..         .+...  ..+.               ++++||||||
T Consensus        72 ------~v~~~~~~~~~~~~~~~~i~~~t~~~l~~---------~l~~~--~~l~---------------~~~~iViDEa  119 (451)
T 2jlq_A           72 ------PIRYQTPAVKSDHTGREIVDLMCHATFTT---------RLLSS--TRVP---------------NYNLIVMDEA  119 (451)
T ss_dssp             ------CEEECCTTCSCCCCSSCCEEEEEHHHHHH---------HHHHC--SCCC---------------CCSEEEEETT
T ss_pred             ------eeeeeeccccccCCCCceEEEEChHHHHH---------HhhCc--cccc---------------CCCEEEEeCC
Confidence                  0000000 111234456788999988751         12111  1223               8999999999


Q ss_pred             ccC
Q 042872          379 HCV  381 (381)
Q Consensus       379 HcI  381 (381)
                      |++
T Consensus       120 h~~  122 (451)
T 2jlq_A          120 HFT  122 (451)
T ss_dssp             TCC
T ss_pred             ccC
Confidence            984

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.05  E-value=9.7e-11  Score=120.07  Aligned_cols=123  Identities=15%  Similarity=0.098  Sum_probs=66.2

Q ss_pred             CCcHHHHHHHHHHHc----C-CCEEEECCCCCCchhhHHHHHHHHHhh--------cCCcEEEEeCCCCHHHHHHHH-HH
Q 042872          225 AFRPLQHQACKASVA----K-QDCFVLLPTGGGKSLCYQDQIITLNLK--------FGIPATFLNSQQTVSQAAAVL-QE  290 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~----G-rDvLviaPTGsGKTLaF~dQv~~L~~~--------~gI~a~~l~g~~~~~e~~~il-~~  290 (381)
                      .+||+|.+||+.++.    | +++++++|||+|||++++.-+..+...        .+-+++++........|  .. +.
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q--~~~~~  255 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDD--PKDKT  255 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-------------C
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHH--HHHHH
Confidence            699999999999986    5 569999999999999986444444322        34677777764322111  11 11


Q ss_pred             HHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCc
Q 042872          291 LRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQL  370 (381)
Q Consensus       291 lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L  370 (381)
                      ++        .+ ...+  ............+|+|+||++|.....      .-.....+..               ..+
T Consensus       256 ~~--------~~-~~~~--~~~~~~~~~~~~~I~v~T~~~l~~~~~------~~~~~~~~~~---------------~~~  303 (590)
T 3h1t_A          256 FT--------PF-GDAR--HKIEGGKVVKSREIYFAIYQSIASDER------RPGLYKEFPQ---------------DFF  303 (590)
T ss_dssp             CT--------TT-CSSE--EECCC--CCSSCSEEEEEGGGC------------CCGGGGSCT---------------TSC
T ss_pred             HH--------hc-chhh--hhhhccCCCCCCcEEEEEhhhhccccc------cccccccCCC---------------Ccc
Confidence            10        00 0000  001123344578999999999973200      0000011111               178


Q ss_pred             cEEEEeccccC
Q 042872          371 AGFVVDEAHCV  381 (381)
Q Consensus       371 ~~lVIDEAHcI  381 (381)
                      .+|||||||++
T Consensus       304 ~lvIiDEaH~~  314 (590)
T 3h1t_A          304 DLIIIDECHRG  314 (590)
T ss_dssp             SEEEESCCC--
T ss_pred             CEEEEECCccc
Confidence            99999999985

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.04  E-value=6.7e-11  Score=125.67  Aligned_cols=52  Identities=15%  Similarity=0.126  Sum_probs=40.0

Q ss_pred             CCcHHHH-----HHHHHHH------cCCCEEEECCCCCCchhhHHHHH-HHHHhhcCCcEEEEeC
Q 042872          225 AFRPLQH-----QACKASV------AKQDCFVLLPTGGGKSLCYQDQI-ITLNLKFGIPATFLNS  277 (381)
Q Consensus       225 ~fRpiQ~-----eAI~aiL------~GrDvLviaPTGsGKTLaF~dQv-~~L~~~~gI~a~~l~g  277 (381)
                      .|+|+|.     ++|+.++      .|+|+|+++|||+|||++|+-.+ ..+. ..+.+++++..
T Consensus       215 ~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~-~~~~~~lilaP  278 (673)
T 2wv9_A          215 YVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAI-QKRLRTAVLAP  278 (673)
T ss_dssp             EEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHH-HTTCCEEEEES
T ss_pred             ccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHH-hCCCcEEEEcc
Confidence            8899999     9999998      89999999999999999997333 3333 35678888875

>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=98.98  E-value=3e-10  Score=119.41  Aligned_cols=54  Identities=17%  Similarity=0.044  Sum_probs=44.1

Q ss_pred             CCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHH-HHHHHhhcCCcEEEEeC
Q 042872          223 NRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQ-IITLNLKFGIPATFLNS  277 (381)
Q Consensus       223 ~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~~gI~a~~l~g  277 (381)
                      ...++|+|+.+|+.+++|+|+|+.+|||+|||++|+-+ +..+. ..+.+++++..
T Consensus       169 ~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~-~~~~~vLvl~P  223 (618)
T 2whx_A          169 ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREAL-KRRLRTLILAP  223 (618)
T ss_dssp             CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHH-HTTCCEEEEES
T ss_pred             cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHH-hCCCeEEEEcC
Confidence            47788998889999999999999999999999999633 33443 35778888875

>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=98.96  E-value=4.3e-11  Score=127.44  Aligned_cols=113  Identities=16%  Similarity=0.099  Sum_probs=68.6

Q ss_pred             CcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhh
Q 042872          226 FRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQ  305 (381)
Q Consensus       226 fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~  305 (381)
                      ++++|.++++.+..++|+++++|||+|||++|.-   .+. ..+.+++++..-  +.-..++.+.+..        .+..
T Consensus       218 ~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l---~ll-~~g~~vLVl~PT--ReLA~Qia~~l~~--------~~g~  283 (666)
T 3o8b_A          218 VFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPA---AYA-AQGYKVLVLNPS--VAATLGFGAYMSK--------AHGI  283 (666)
T ss_dssp             SCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHH---HHH-HTTCCEEEEESC--HHHHHHHHHHHHH--------HHSC
T ss_pred             cHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHH---HHH-HCCCeEEEEcch--HHHHHHHHHHHHH--------HhCC
Confidence            3455666666666889999999999999999962   222 246678888763  3222222222210        0000


Q ss_pred             hhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          306 LIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       306 ~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      . ..............+|+|+|||+|+.             ++.+.++               ++++|||||||++
T Consensus       284 ~-vg~~vG~~~~~~~~~IlV~TPGrLl~-------------~~~l~l~---------------~l~~lVlDEAH~l  330 (666)
T 3o8b_A          284 D-PNIRTGVRTITTGAPVTYSTYGKFLA-------------DGGCSGG---------------AYDIIICDECHST  330 (666)
T ss_dssp             C-CEEECSSCEECCCCSEEEEEHHHHHH-------------TTSCCTT---------------SCSEEEETTTTCC
T ss_pred             C-eeEEECcEeccCCCCEEEECcHHHHh-------------CCCcccC---------------cccEEEEccchhc
Confidence            0 01111122234578999999999852             2233333               8999999999985

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=98.94  E-value=1e-09  Score=112.83  Aligned_cols=36  Identities=22%  Similarity=0.134  Sum_probs=31.4

Q ss_pred             CCCCCcHHHHHHHHHH----HcCCCEEEECCCCCCchhhHH
Q 042872          222 GNRAFRPLQHQACKAS----VAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       222 G~~~fRpiQ~eAI~ai----L~GrDvLviaPTGsGKTLaF~  258 (381)
                      || +|||.|.+.+.++    ..|+|+++.||||+|||++|+
T Consensus         1 ~~-~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l   40 (551)
T 3crv_A            1 MV-KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSL   40 (551)
T ss_dssp             CC-SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHH
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHH
Confidence            45 6999999977754    578999999999999999997

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.94  E-value=4.7e-10  Score=115.38  Aligned_cols=37  Identities=14%  Similarity=0.116  Sum_probs=28.8

Q ss_pred             hCCCCCcHHHHHHHHH----HHcCCCEEEECCCCCCchhhHH
Q 042872          221 FGNRAFRPLQHQACKA----SVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~a----iL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .|| .|||+|.+++.+    +..|+++++.||||+|||++|+
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l   44 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVE   44 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHH
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHH
Confidence            678 899999998654    4578999999999999999998

>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=98.88  E-value=3.3e-09  Score=105.82  Aligned_cols=120  Identities=15%  Similarity=0.126  Sum_probs=74.5

Q ss_pred             CCcHHHHHHHHHHH----cCCCEEEECCCCCCchhhHHHHHHHHHhh-cCCcEEEEeCCCCHHHHHHHHHHHHhchhhhh
Q 042872          225 AFRPLQHQACKASV----AKQDCFVLLPTGGGKSLCYQDQIITLNLK-FGIPATFLNSQQTVSQAAAVLQELRQGLVLSQ  299 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL----~GrDvLviaPTGsGKTLaF~dQv~~L~~~-~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~  299 (381)
                      .+||+|.+++..++    .|+++|+..+||+|||++++--+..+... ..-+++++....-..++...++..-.+.   .
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~~~~~~~~~~LIv~P~~l~~qw~~e~~~~~~~~---~  113 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICPLSVLKNWEEELSKFAPHL---R  113 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEECSTTHHHHHHHHHHHCTTS---C
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHHHhcCCCCCEEEEccHHHHHHHHHHHHHHCCCc---e
Confidence            69999999998764    57899999999999999876444444321 2357778877555555544444321000   0


Q ss_pred             hhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccc
Q 042872          300 HYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH  379 (381)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAH  379 (381)
                      ....+.      .........++|+|+||+++.....       +. ..                    ...+|||||||
T Consensus       114 v~~~~g------~~~~~~~~~~~ivi~t~~~l~~~~~-------l~-~~--------------------~~~~vIvDEaH  159 (500)
T 1z63_A          114 FAVFHE------DRSKIKLEDYDIILTTYAVLLRDTR-------LK-EV--------------------EWKYIVIDEAQ  159 (500)
T ss_dssp             EEECSS------STTSCCGGGSSEEEEEHHHHTTCHH-------HH-TC--------------------CEEEEEEETGG
T ss_pred             EEEEec------CchhccccCCcEEEeeHHHHhccch-------hc-CC--------------------CcCEEEEeCcc
Confidence            000000      0011222367899999999974311       11 11                    68899999999


Q ss_pred             cC
Q 042872          380 CV  381 (381)
Q Consensus       380 cI  381 (381)
                      ++
T Consensus       160 ~~  161 (500)
T 1z63_A          160 NI  161 (500)
T ss_dssp             GG
T ss_pred             cc
Confidence            85

>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=98.84  E-value=8.3e-10  Score=121.23  Aligned_cols=129  Identities=14%  Similarity=0.033  Sum_probs=77.0

Q ss_pred             CCcHHHHHHHHHHHcC--CCEEEECCCCCCchhhHHHHHHHHHhhcCC--cEEEEeCCCCHHHHHHHHHHHHhchhhhhh
Q 042872          225 AFRPLQHQACKASVAK--QDCFVLLPTGGGKSLCYQDQIITLNLKFGI--PATFLNSQQTVSQAAAVLQELRQGLVLSQH  300 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~G--rDvLviaPTGsGKTLaF~dQv~~L~~~~gI--~a~~l~g~~~~~e~~~il~~lr~g~~~~~~  300 (381)
                      +++|+|.+++..++..  ..+|+.++||+|||+++.--+..+. ..|-  +++++....-..++...+...- |  ....
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~-~~g~~~rvLIVvP~sLl~Qw~~E~~~~f-~--l~v~  228 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQL-LSGAAERVLIIVPETLQHQWLVEMLRRF-N--LRFA  228 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHH-HTSSCCCEEEECCTTTHHHHHHHHHHHS-C--CCCE
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHH-HhCCCCeEEEEeCHHHHHHHHHHHHHHh-C--CCEE
Confidence            5889999999998874  5889999999999999864444433 2333  6777777655544443332210 0  0001


Q ss_pred             hhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          301 YFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       301 ~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                      .+..................++|+|+|++.+..+......+.    ..                    .+.+|||||||+
T Consensus       229 v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~----~~--------------------~~dlVIvDEAH~  284 (968)
T 3dmq_A          229 LFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLC----EA--------------------EWDLLVVDEAHH  284 (968)
T ss_dssp             ECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHH----TS--------------------CCCEEEECCSSC
T ss_pred             EEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhh----hc--------------------CCCEEEehhhHh
Confidence            111111000001112333467999999999975544332222    11                    789999999998


Q ss_pred             C
Q 042872          381 V  381 (381)
Q Consensus       381 I  381 (381)
                      +
T Consensus       285 ~  285 (968)
T 3dmq_A          285 L  285 (968)
T ss_dssp             C
T ss_pred             h
Confidence            5

>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=98.82  E-value=4.8e-09  Score=105.15  Aligned_cols=41  Identities=12%  Similarity=0.123  Sum_probs=31.0

Q ss_pred             HHHcCCCEEEECCCCCCchhhHHHH-HHHHHhhcCCcEEEEeC
Q 042872          236 ASVAKQDCFVLLPTGGGKSLCYQDQ-IITLNLKFGIPATFLNS  277 (381)
Q Consensus       236 aiL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~~gI~a~~l~g  277 (381)
                      ++++|+|+|+++|||||||++|+-. +..+. ..+.+++++..
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~-~~~~~~lil~P   45 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECA-RRRLRTLVLAP   45 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHH-HTTCCEEEEES
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHH-hcCCeEEEEcc
Confidence            3578999999999999999999633 33333 34678888875

>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=98.74  E-value=1.3e-08  Score=113.19  Aligned_cols=53  Identities=21%  Similarity=0.200  Sum_probs=38.9

Q ss_pred             CCcHHHHHHHHHHHc--------------CCCEEEECCCCCCchhhHHHHHHHHHhh-cCCcEEEEeC
Q 042872          225 AFRPLQHQACKASVA--------------KQDCFVLLPTGGGKSLCYQDQIITLNLK-FGIPATFLNS  277 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~--------------GrDvLviaPTGsGKTLaF~dQv~~L~~~-~gI~a~~l~g  277 (381)
                      .+||+|.+||+.++.              ++++++.+|||+|||++++.-+..+... ..-+++++..
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~~~l~~ll~~~~~~~rvLvlvp  338 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTSFKAARLATELDFIDKVFFVVD  338 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHHHHHHHHHTTCTTCCEEEEEEC
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHHHHHHHHHHhcCCCceEEEEeC
Confidence            599999999999986              3799999999999999985333322211 1236777765

>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=98.66  E-value=3.5e-08  Score=99.23  Aligned_cols=43  Identities=19%  Similarity=0.091  Sum_probs=31.7

Q ss_pred             HHHHHcCCCEEEECCCCCCchhhHHHH-HHHHHhhcCCcEEEEeC
Q 042872          234 CKASVAKQDCFVLLPTGGGKSLCYQDQ-IITLNLKFGIPATFLNS  277 (381)
Q Consensus       234 I~aiL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~~gI~a~~l~g  277 (381)
                      ...+..|+++++.+|||+|||++|+-. +..+. ..+.+++++..
T Consensus        15 ~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~-~~~~~~lvl~P   58 (459)
T 2z83_A           15 PNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAI-QQRLRTAVLAP   58 (459)
T ss_dssp             CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHH-HTTCCEEEEEC
T ss_pred             HHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHH-hCCCcEEEECc
Confidence            444567899999999999999999733 33333 35778888875

>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=98.63  E-value=5.9e-08  Score=104.46  Aligned_cols=125  Identities=16%  Similarity=0.089  Sum_probs=68.5

Q ss_pred             hCCCCCcHHHHHHHHHHHcC-CCEEEECCCCCCchhhHHHHHHHH-H--hhcCCcEEEEeCCCCHHHHHHHHHHHHhchh
Q 042872          221 FGNRAFRPLQHQACKASVAK-QDCFVLLPTGGGKSLCYQDQIITL-N--LKFGIPATFLNSQQTVSQAAAVLQELRQGLV  296 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~G-rDvLviaPTGsGKTLaF~dQv~~L-~--~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~  296 (381)
                      .| ..|+++|+++|+.++.+ +++++++|||+|||+.. .++... .  ...|..++++..  ...-..++.+.+.... 
T Consensus        90 r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTtll-p~ll~~~~~~~~~g~~ilvl~P--~r~La~q~~~~l~~~~-  164 (773)
T 2xau_A           90 RR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQI-PQFVLFDEMPHLENTQVACTQP--RRVAAMSVAQRVAEEM-  164 (773)
T ss_dssp             HT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHH-HHHHHHHHCGGGGTCEEEEEES--CHHHHHHHHHHHHHHT-
T ss_pred             hh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHHHH-HHHHHHhccccCCCceEEecCc--hHHHHHHHHHHHHHHh-
Confidence            45 67889999999999865 67999999999999943 333111 1  111455655543  2222222222221100 


Q ss_pred             hhhhhhhhhhhhhhhh-cccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEE
Q 042872          297 LSQHYFLHQLIFVLTC-ASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVV  375 (381)
Q Consensus       297 ~~~~~~~~~~~~~~~~-~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVI  375 (381)
                         .......+ +... .........+|+|+|||++..         .+...  ..+.               ++.+|||
T Consensus       165 ---~~~v~~~v-G~~i~~~~~~~~~~~I~v~T~G~l~r---------~l~~~--~~l~---------------~~~~lIl  214 (773)
T 2xau_A          165 ---DVKLGEEV-GYSIRFENKTSNKTILKYMTDGMLLR---------EAMED--HDLS---------------RYSCIIL  214 (773)
T ss_dssp             ---TCCBTTTE-EEEETTEEECCTTCSEEEEEHHHHHH---------HHHHS--TTCT---------------TEEEEEE
T ss_pred             ---CCchhhee-cceeccccccCCCCCEEEECHHHHHH---------HHhhC--cccc---------------CCCEEEe
Confidence               00000000 0000 011223467899999999862         11111  1222               8999999


Q ss_pred             ecccc
Q 042872          376 DEAHC  380 (381)
Q Consensus       376 DEAHc  380 (381)
                      ||||+
T Consensus       215 DEah~  219 (773)
T 2xau_A          215 DEAHE  219 (773)
T ss_dssp             CSGGG
T ss_pred             cCccc
Confidence            99995

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.60  E-value=1e-07  Score=102.30  Aligned_cols=128  Identities=18%  Similarity=0.123  Sum_probs=74.6

Q ss_pred             CCcHHHHHHHHHHH----cCCCEEEECCCCCCchhhHHHHHHHHH--hhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhh
Q 042872          225 AFRPLQHQACKASV----AKQDCFVLLPTGGGKSLCYQDQIITLN--LKFGIPATFLNSQQTVSQAAAVLQELRQGLVLS  298 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL----~GrDvLviaPTGsGKTLaF~dQv~~L~--~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~  298 (381)
                      .+||+|.+++..++    .++.+|+..+||.|||+..+--+..+.  ....-+++++.......++...+...--+.  .
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P~sll~qW~~E~~~~~p~~--~  313 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVPLSTMPAWLDTFEKWAPDL--N  313 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECCTTTHHHHHHHHHHHSTTC--C
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEECchHHHHHHHHHHHHCCCc--e
Confidence            68999999998776    789999999999999987653333221  123456677776655555555554421000  0


Q ss_pred             hhhhh-----hhhhhhhh-----hcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccC
Q 042872          299 QHYFL-----HQLIFVLT-----CASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQR  368 (381)
Q Consensus       299 ~~~~~-----~~~~~~~~-----~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~  368 (381)
                      ...+.     ...+....     .........++|+|+|++.+.....   .+.    .-                    
T Consensus       314 v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~---~l~----~~--------------------  366 (800)
T 3mwy_W          314 CICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRA---ELG----SI--------------------  366 (800)
T ss_dssp             EEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHH---HHH----TS--------------------
T ss_pred             EEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHH---HHh----cC--------------------
Confidence            00000     00000000     0111344578999999999974211   111    11                    


Q ss_pred             CccEEEEeccccC
Q 042872          369 QLAGFVVDEAHCV  381 (381)
Q Consensus       369 ~L~~lVIDEAHcI  381 (381)
                      ...+|||||||++
T Consensus       367 ~w~~vIvDEaH~l  379 (800)
T 3mwy_W          367 KWQFMAVDEAHRL  379 (800)
T ss_dssp             EEEEEEETTGGGG
T ss_pred             Ccceeehhhhhhh
Confidence            5789999999975

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=98.57  E-value=2.2e-07  Score=92.75  Aligned_cols=39  Identities=18%  Similarity=0.151  Sum_probs=28.9

Q ss_pred             cCCCEEEECCCCCCchhhHHHH-HHHHHhhcCCcEEEEeCC
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQ-IITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~~gI~a~~l~g~  278 (381)
                      .|+++|+++|||+|||++|+-. +..+. ..|.+++++...
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~-~~g~~~lvl~Pt   40 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAV-KKRLRTVILAPT   40 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHH-HTTCCEEEEESS
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHH-hCCCCEEEECcH
Confidence            4789999999999999999633 32333 457788888753

>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=98.57  E-value=7e-08  Score=101.25  Aligned_cols=40  Identities=30%  Similarity=0.335  Sum_probs=31.9

Q ss_pred             CCcHHHHHHHHHHH---------cCCCEEEECCCCCCchhhHHHHHHHH
Q 042872          225 AFRPLQHQACKASV---------AKQDCFVLLPTGGGKSLCYQDQIITL  264 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL---------~GrDvLviaPTGsGKTLaF~dQv~~L  264 (381)
                      .+||+|.+++..++         .++.+|+..+||.|||+..+--+..+
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l  103 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTL  103 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHH
Confidence            68999999999875         34679999999999998876334333

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=98.53  E-value=1.3e-08  Score=108.46  Aligned_cols=24  Identities=21%  Similarity=0.207  Sum_probs=20.2

Q ss_pred             HHHHHcCCCEEEECCCCCCchhhH
Q 042872          234 CKASVAKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       234 I~aiL~GrDvLviaPTGsGKTLaF  257 (381)
                      ....+.|+++++++|||+|||+..
T Consensus       149 ~ar~l~rk~vlv~apTGSGKT~~a  172 (677)
T 3rc3_A          149 DARAMQRKIIFHSGPTNSGKTYHA  172 (677)
T ss_dssp             HHHTSCCEEEEEECCTTSSHHHHH
T ss_pred             HHHhcCCCEEEEEcCCCCCHHHHH
Confidence            345578999999999999999854

>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=98.22  E-value=2.5e-06  Score=92.35  Aligned_cols=62  Identities=23%  Similarity=0.153  Sum_probs=51.0

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHHH
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITLN  265 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L~  265 (381)
                      +..+..+.+|+. ++++|.-....+..|+  |+.|.||.|||++|.                           +++..+.
T Consensus        64 vREAa~R~lg~r-~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~G~~vhVvT~ndyLA~rdae~m~~l~  140 (822)
T 3jux_A           64 VREAARRTLGMR-PFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALIGKGVHLVTVNDYLARRDALWMGPVY  140 (822)
T ss_dssp             HHHHHHHHTSCC-CCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTTSSCEEEEESSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCC-CcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhcCCceEEEeccHHHHHhHHHHHHHHH
Confidence            445677789995 7799999999999998  999999999999986                           4566666


Q ss_pred             hhcCCcEEEEeC
Q 042872          266 LKFGIPATFLNS  277 (381)
Q Consensus       266 ~~~gI~a~~l~g  277 (381)
                      ..+|+.+.++.+
T Consensus       141 ~~Lglsvg~i~~  152 (822)
T 3jux_A          141 LFLGLRVGVINS  152 (822)
T ss_dssp             HHTTCCEEEEET
T ss_pred             HHhCCEEEEEcC
Confidence            677888877776

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=97.80  E-value=3.7e-05  Score=80.74  Aligned_cols=64  Identities=23%  Similarity=0.222  Sum_probs=40.9

Q ss_pred             CCcHHHHHHHHH----HHcCCCEEEECCCCCCchhhHHHH-HHHHHhhcCCcEEEEeCCCCHHHHHHHHHHH
Q 042872          225 AFRPLQHQACKA----SVAKQDCFVLLPTGGGKSLCYQDQ-IITLNLKFGIPATFLNSQQTVSQAAAVLQEL  291 (381)
Q Consensus       225 ~fRpiQ~eAI~a----iL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~~gI~a~~l~g~~~~~e~~~il~~l  291 (381)
                      +|||.|.+.+.+    +..|+++++.||||+|||++|+-- +..+. ..+.++++++.  +...+.++.+.+
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~-~~~~kvli~t~--T~~l~~Qi~~el   71 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSS-ERKLKVLYLVR--TNSQEEQVIKEL   71 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHH-HHTCEEEEEES--SHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhh-hcCCeEEEECC--CHHHHHHHHHHH
Confidence            579999998864    458999999999999999999721 22222 23455655554  333444444443

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=97.55  E-value=0.00017  Score=75.49  Aligned_cols=49  Identities=12%  Similarity=0.064  Sum_probs=36.6

Q ss_pred             cHHHHHHHHHHHcCCCEEEECCCCCCch--hhHHHHHHHHHh---hcCCcEEEEeC
Q 042872          227 RPLQHQACKASVAKQDCFVLLPTGGGKS--LCYQDQIITLNL---KFGIPATFLNS  277 (381)
Q Consensus       227 RpiQ~eAI~aiL~GrDvLviaPTGsGKT--LaF~dQv~~L~~---~~gI~a~~l~g  277 (381)
                      .+.|++||+.++.++.+++.+|+|+|||  ++++  +..|..   ..+.++.++..
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~l--l~~l~~~~~~~~~~vll~AP  204 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKL--LAALIQMADGERCRIRLAAP  204 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHH--HHHHHHTCSSCCCCEEEEBS
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHH--HHHHHHhhhcCCCeEEEEeC
Confidence            6899999999999999999999999999  5554  333331   23556666543

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=96.55  E-value=0.0085  Score=58.40  Aligned_cols=53  Identities=6%  Similarity=-0.055  Sum_probs=32.9

Q ss_pred             cHHHHHHHHHHH-------cCCCEEEECCCCCCchhhHHHHHHHHHhhc------CCcEEEEeCCC
Q 042872          227 RPLQHQACKASV-------AKQDCFVLLPTGGGKSLCYQDQIITLNLKF------GIPATFLNSQQ  279 (381)
Q Consensus       227 RpiQ~eAI~aiL-------~GrDvLviaPTGsGKTLaF~dQv~~L~~~~------gI~a~~l~g~~  279 (381)
                      |.-|.+.|...+       .+..+++.+|+|+|||.+...-+..|....      .+..+.+++..
T Consensus        25 Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~   90 (318)
T 3te6_A           25 QVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALE   90 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTC
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccc
Confidence            444555555433       346899999999999988753444454211      34566677543

>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=96.54  E-value=0.0056  Score=63.80  Aligned_cols=52  Identities=12%  Similarity=0.061  Sum_probs=39.9

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      .+++.|++|+..++.++-+++.+|.|+|||.+...-+..+. ..|.++.++..
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~~l~~~l~-~~g~~Vl~~Ap  240 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAVADLAE-SLGLEVGLCAP  240 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHHHHHHHHHH-HTTCCEEEEES
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHHHHHHHHHH-hcCCeEEEecC
Confidence            57899999999999999999999999999976543344444 45677766543

>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=96.43  E-value=0.0057  Score=61.22  Aligned_cols=55  Identities=15%  Similarity=0.055  Sum_probs=39.2

Q ss_pred             hCCCCCcHHHHHHHHHHHcC----C-CEEEECCCCCCchhhHHHHHHHHHhhcCC-cEEEEe
Q 042872          221 FGNRAFRPLQHQACKASVAK----Q-DCFVLLPTGGGKSLCYQDQIITLNLKFGI-PATFLN  276 (381)
Q Consensus       221 fG~~~fRpiQ~eAI~aiL~G----r-DvLviaPTGsGKTLaF~dQv~~L~~~~gI-~a~~l~  276 (381)
                      +.|..+++.|++|+..++..    + .+++.+|.|+|||.+...-+..|. ..+. .+.++.
T Consensus        21 ~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~~~~~~l~-~~~~~~il~~a   81 (459)
T 3upu_A           21 MTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTKFIIEALI-STGETGIILAA   81 (459)
T ss_dssp             CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHHHHHHHHH-HTTCCCEEEEE
T ss_pred             CccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHHHHHHHHHH-hcCCceEEEec
Confidence            56778999999999987643    3 889999999999976543344554 3344 444443

>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=96.21  E-value=0.015  Score=49.98  Aligned_cols=49  Identities=18%  Similarity=0.127  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHH---------cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          228 PLQHQACKASV---------AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       228 piQ~eAI~aiL---------~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      +.|.+++..+.         .|+.+++.+|+|+|||....--...+....|..+..+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~   74 (180)
T 3ec2_A           17 VSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFD   74 (180)
T ss_dssp             HHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEE
T ss_pred             HHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEE
Confidence            46777776654         37889999999999997663222233223465555544

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=95.04  E-value=0.033  Score=52.28  Aligned_cols=39  Identities=15%  Similarity=0.250  Sum_probs=24.2

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhh-----cCCcEEEEeCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLK-----FGIPATFLNSQ  278 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~-----~gI~a~~l~g~  278 (381)
                      ++.+++.+|+|+|||.....-...+...     .+...+.++..
T Consensus        44 ~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~   87 (387)
T 2v1u_A           44 PSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNAR   87 (387)
T ss_dssp             CCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETT
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECC
Confidence            4689999999999997754222223211     15566666643

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=94.88  E-value=0.14  Score=42.43  Aligned_cols=31  Identities=13%  Similarity=0.115  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHc---CCCEEEECCCCCCchhhHH
Q 042872          228 PLQHQACKASVA---KQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       228 piQ~eAI~aiL~---GrDvLviaPTGsGKTLaF~  258 (381)
                      .-+.+.+-..+.   ++.+++.+|+|+|||....
T Consensus        28 ~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~   61 (195)
T 1jbk_A           28 DEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVE   61 (195)
T ss_dssp             HHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHH
T ss_pred             hHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHH
Confidence            334444444442   3579999999999997653

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=94.80  E-value=0.12  Score=43.89  Aligned_cols=17  Identities=24%  Similarity=0.294  Sum_probs=14.6

Q ss_pred             CCEEEECCCCCCchhhH
Q 042872          241 QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF  257 (381)
                      ..+++.+|+|+|||...
T Consensus        39 ~~~ll~G~~G~GKT~l~   55 (226)
T 2chg_A           39 PHLLFSGPPGTGKTATA   55 (226)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            36999999999999765

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=94.59  E-value=0.11  Score=54.12  Aligned_cols=64  Identities=16%  Similarity=0.241  Sum_probs=44.2

Q ss_pred             CCcHHHHHHHHHHHcCCCE-EEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHH
Q 042872          225 AFRPLQHQACKASVAKQDC-FVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQEL  291 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDv-LviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~l  291 (381)
                      .+.+-|.+||..+|..+++ |+.+|.|+|||.+-..-+..+. ..|-++.++..  +......++.++
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~-~~~~~ILv~a~--TN~AvD~i~erL  253 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAV-KQGLKVLCCAP--SNIAVDNLVERL  253 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHH-HTTCCEEEEES--SHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHH-hCCCeEEEEcC--chHHHHHHHHHH
Confidence            4568899999999988875 7789999999977665555555 35666655543  333344445444

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=94.39  E-value=0.031  Score=48.70  Aligned_cols=37  Identities=11%  Similarity=0.197  Sum_probs=23.3

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      .++.+++.+|+|+|||.....-...+. ..+.++..+.
T Consensus        51 ~~~~~ll~G~~G~GKT~la~~l~~~~~-~~~~~~~~~~   87 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLIHAACARAN-ELERRSFYIP   87 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHHHHHHHHHH-HTTCCEEEEE
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHH-HcCCeEEEEE
Confidence            357899999999999976532223333 2345555544

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=94.38  E-value=0.081  Score=44.01  Aligned_cols=19  Identities=26%  Similarity=0.312  Sum_probs=15.7

Q ss_pred             CCCEEEECCCCCCchhhHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~  258 (381)
                      .+.+++.+|+|+|||....
T Consensus        43 ~~~vll~G~~G~GKT~la~   61 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVE   61 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHH
Confidence            4579999999999997653

>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=94.37  E-value=0.084  Score=49.73  Aligned_cols=35  Identities=14%  Similarity=0.157  Sum_probs=22.9

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhc-CCcEEEEeC
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKF-GIPATFLNS  277 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~-gI~a~~l~g  277 (381)
                      .+++.+|+|+|||.....-...+. .. +..++.++.
T Consensus        46 ~~li~G~~G~GKTtl~~~l~~~~~-~~~~~~~~~i~~   81 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLRKLWELYK-DKTTARFVYING   81 (389)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHT-TSCCCEEEEEET
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHh-hhcCeeEEEEeC
Confidence            699999999999977632222232 22 566666664

>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=94.05  E-value=0.24  Score=50.41  Aligned_cols=38  Identities=16%  Similarity=0.080  Sum_probs=26.3

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCC
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQT  280 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~  280 (381)
                      =+++++++|+|||-+...-...|. ..|.++.++..+.-
T Consensus       102 vIlivG~~G~GKTTt~~kLA~~l~-~~G~kVllv~~D~~  139 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTVAKLARYFQ-KRGYKVGVVCSDTW  139 (443)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH-TTTCCEEEEECCCS
T ss_pred             EEEEECcCCCCHHHHHHHHHHHHH-HCCCeEEEEeCCCc
Confidence            467889999999977654444444 45777777766554

>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=93.86  E-value=0.21  Score=47.19  Aligned_cols=18  Identities=28%  Similarity=0.305  Sum_probs=15.3

Q ss_pred             CCEEEECCCCCCchhhHH
Q 042872          241 QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~  258 (381)
                      +.+++.+|+|+|||....
T Consensus        46 ~~vll~G~~G~GKT~la~   63 (384)
T 2qby_B           46 FSNLFLGLTGTGKTFVSK   63 (384)
T ss_dssp             CEEEEEECTTSSHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            469999999999997653

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=93.83  E-value=0.17  Score=46.63  Aligned_cols=17  Identities=18%  Similarity=0.042  Sum_probs=15.0

Q ss_pred             CCEEEECCCCCCchhhH
Q 042872          241 QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF  257 (381)
                      ..+|+.+|+|+|||.+.
T Consensus        68 ~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           68 LHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CEEEEEECTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            46999999999999775

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=93.81  E-value=0.13  Score=49.92  Aligned_cols=35  Identities=11%  Similarity=0.193  Sum_probs=24.8

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      .+.+|+.+|+|+|||.+.    ..+....+.+.+.++..
T Consensus       148 ~~~vLL~GppGtGKT~la----~aia~~~~~~~~~v~~~  182 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLA----KAVAAESNATFFNISAA  182 (389)
T ss_dssp             CSEEEEESSTTSCHHHHH----HHHHHHTTCEEEEECSC
T ss_pred             CceEEEECCCCCCHHHHH----HHHHHhhcCcEEEeeHH
Confidence            478999999999999775    23344456666666543

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=93.58  E-value=0.12  Score=44.76  Aligned_cols=35  Identities=14%  Similarity=0.142  Sum_probs=23.2

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      +.+++.+|+|+|||....--...+. ..+.++..++
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~-~~~~~~~~~~   89 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELA-KRNVSSLIVY   89 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHH-TTTCCEEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHH-HcCCeEEEEE
Confidence            6899999999999976532223333 3466666554

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=93.50  E-value=0.18  Score=45.08  Aligned_cols=34  Identities=21%  Similarity=0.361  Sum_probs=23.4

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      .+.+++.+|+|+|||....    .+....+.+.+.+.+
T Consensus        39 ~~~vll~G~~GtGKT~la~----~la~~~~~~~~~~~~   72 (262)
T 2qz4_A           39 PKGALLLGPPGCGKTLLAK----AVATEAQVPFLAMAG   72 (262)
T ss_dssp             CCEEEEESCTTSSHHHHHH----HHHHHHTCCEEEEET
T ss_pred             CceEEEECCCCCCHHHHHH----HHHHHhCCCEEEech
Confidence            4679999999999997652    333345666666554

>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=93.40  E-value=0.19  Score=47.12  Aligned_cols=37  Identities=19%  Similarity=0.184  Sum_probs=23.9

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ++.+++.+|+|+|||....--...+. ..+.+++.++.
T Consensus        37 ~~~lll~G~~GtGKT~la~~i~~~~~-~~~~~~~~i~~   73 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQAAGNEAK-KRGYRVIYSSA   73 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHHHHHHHHH-HTTCCEEEEEH
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHH-HCCCEEEEEEH
Confidence            36899999999999976532222232 22666666653

>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=93.35  E-value=0.13  Score=53.66  Aligned_cols=54  Identities=17%  Similarity=0.130  Sum_probs=39.7

Q ss_pred             CCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          223 NRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       223 ~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      +..+.+.|.+|+..++.+.-+++.+|+|+|||.+...-+..+....+-++.++.
T Consensus       178 ~~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~~i~~l~~~~~~~ilv~a  231 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCA  231 (624)
T ss_dssp             SCCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHHHHHHHHTSSSCCEEEEE
T ss_pred             cCCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEe
Confidence            446789999999999987778999999999998765445455422345555544

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=93.16  E-value=0.72  Score=45.86  Aligned_cols=49  Identities=12%  Similarity=0.036  Sum_probs=32.4

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      |.=+++.+++|+|||...+.-+.......|.+++++...++..+....+
T Consensus       200 G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~slE~~~~~l~~R~  248 (444)
T 2q6t_A          200 GSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSLEMPAAQLTLRM  248 (444)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEESSSCHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEECCCCHHHHHHHH
Confidence            4456888999999995543333333323478899988888876544433

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=92.97  E-value=0.74  Score=45.93  Aligned_cols=49  Identities=10%  Similarity=-0.004  Sum_probs=32.7

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAV  287 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~i  287 (381)
                      .|.=+++.+++|+|||.....-+..+....|.+++++....+..+....
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~E~s~~~l~~r  250 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMR  250 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEESSSCHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEECCCCHHHHHHH
Confidence            3456788899999999655433333433357888888888776554433

>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=92.93  E-value=0.056  Score=46.25  Aligned_cols=16  Identities=19%  Similarity=0.084  Sum_probs=13.9

Q ss_pred             CEEEECCCCCCchhhH
Q 042872          242 DCFVLLPTGGGKSLCY  257 (381)
Q Consensus       242 DvLviaPTGsGKTLaF  257 (381)
                      -+++.+|+|+|||...
T Consensus        47 ~~ll~G~~G~GKT~l~   62 (250)
T 1njg_A           47 AYLFSGTRGVGKTSIA   62 (250)
T ss_dssp             EEEEECSTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5899999999999665

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=92.82  E-value=0.22  Score=47.00  Aligned_cols=19  Identities=16%  Similarity=0.191  Sum_probs=16.0

Q ss_pred             CCCEEEECCCCCCchhhHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~  258 (381)
                      ++.+|+.+|+|+|||....
T Consensus        70 ~~~vLl~GppGtGKT~la~   88 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIAM   88 (368)
T ss_dssp             TCEEEEEESTTSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            3579999999999998763

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=92.79  E-value=0.33  Score=52.61  Aligned_cols=67  Identities=12%  Similarity=0.091  Sum_probs=44.8

Q ss_pred             CCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHH
Q 042872          223 NRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQEL  291 (381)
Q Consensus       223 ~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~l  291 (381)
                      +..+.+.|.+|+..++.+.-+++.+|.|+|||.+...-+..+....+-++.++..  +......+.+++
T Consensus       358 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i~~l~~~~~~~ILv~a~--tn~A~d~l~~rL  424 (802)
T 2xzl_A          358 FAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAP--SNVAVDHLAAKL  424 (802)
T ss_dssp             SCCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEES--SHHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhCCCCeEEEEcC--cHHHHHHHHHHH
Confidence            3457799999999999877789999999999977654444444223556655543  333333444444

>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=92.52  E-value=0.11  Score=48.05  Aligned_cols=39  Identities=13%  Similarity=0.048  Sum_probs=28.0

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      |.=+++.+|+|+|||...+..+.++. ..|.++.++.+..
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~-~~g~kVli~~~~~   50 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLE-YADVKYLVFKPKI   50 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHH-HTTCCEEEEEECC
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHH-hcCCEEEEEEecc
Confidence            44567789999999987755555555 4578888886554

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=92.51  E-value=0.29  Score=44.92  Aligned_cols=34  Identities=15%  Similarity=0.237  Sum_probs=23.5

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ++.+++.+|+|+|||...    ..+....+.+.+.+++
T Consensus        54 ~~~vll~Gp~GtGKT~la----~~la~~~~~~~~~i~~   87 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLA----RAVATECSATFLNISA   87 (297)
T ss_dssp             CSEEEEESSSSSCHHHHH----HHHHHHTTCEEEEEES
T ss_pred             CCeEEEECcCCCCHHHHH----HHHHHHhCCCeEEeeH
Confidence            578999999999999775    2333345555555543

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=92.37  E-value=0.18  Score=45.95  Aligned_cols=34  Identities=15%  Similarity=0.152  Sum_probs=23.1

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      .++.+|+.+|+|+|||...    ..+....+.+.+.+.
T Consensus        50 ~~~~~ll~G~~GtGKT~la----~~la~~~~~~~~~v~   83 (285)
T 3h4m_A           50 PPKGILLYGPPGTGKTLLA----KAVATETNATFIRVV   83 (285)
T ss_dssp             CCSEEEEESSSSSSHHHHH----HHHHHHTTCEEEEEE
T ss_pred             CCCeEEEECCCCCcHHHHH----HHHHHHhCCCEEEEe
Confidence            3568999999999999765    333434555555443

>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=92.25  E-value=0.11  Score=48.45  Aligned_cols=37  Identities=24%  Similarity=0.377  Sum_probs=23.8

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhc--CCcEEEEe
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKF--GIPATFLN  276 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~--gI~a~~l~  276 (381)
                      ++.+++.+|+|+|||.....-...+....  +..++.++
T Consensus        45 ~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~   83 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYIN   83 (386)
T ss_dssp             CCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEE
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEE
Confidence            56899999999999977532223333222  56666665

>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=92.11  E-value=0.48  Score=46.46  Aligned_cols=49  Identities=12%  Similarity=0.215  Sum_probs=32.6

Q ss_pred             HHHHHHHc------CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCH
Q 042872          232 QACKASVA------KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTV  281 (381)
Q Consensus       232 eAI~aiL~------GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~  281 (381)
                      ..+..+|.      |+-+++.+|.|+|||...+.-+..+. ..|-+++++....+.
T Consensus        49 ~~LD~~Lg~GGl~~G~ii~I~G~pGsGKTtLal~la~~~~-~~g~~vlyid~E~s~  103 (356)
T 1u94_A           49 LSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQ-REGKTCAFIDAEHAL  103 (356)
T ss_dssp             HHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHH-HTTCCEEEEESSCCC
T ss_pred             HHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHH-HCCCeEEEEeCCCCc
Confidence            34666664      45688999999999966543333333 457788888776543

>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=92.11  E-value=0.29  Score=47.24  Aligned_cols=33  Identities=15%  Similarity=0.158  Sum_probs=22.5

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      .+.+|+.+|+|+|||....    .+....+.+.+.+.
T Consensus        84 ~~~iLL~GppGtGKT~la~----ala~~~~~~~~~v~  116 (355)
T 2qp9_X           84 TSGILLYGPPGTGKSYLAK----AVATEANSTFFSVS  116 (355)
T ss_dssp             CCCEEEECSTTSCHHHHHH----HHHHHHTCEEEEEE
T ss_pred             CceEEEECCCCCcHHHHHH----HHHHHhCCCEEEee
Confidence            3579999999999997752    33334455555554

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=91.92  E-value=0.77  Score=40.29  Aligned_cols=45  Identities=18%  Similarity=0.240  Sum_probs=31.0

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQA  284 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~  284 (381)
                      .|.=+++.+|+|+|||.....-+..+. ..+-+++.+....+..+.
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~-~~~~~v~~~~~e~~~~~~   66 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGL-KMGEPGIYVALEEHPVQV   66 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHH-HTTCCEEEEESSSCHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHH-hcCCeEEEEEccCCHHHH
Confidence            466789999999999976532233333 457788888877765543

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=91.87  E-value=0.42  Score=45.51  Aligned_cols=17  Identities=29%  Similarity=0.460  Sum_probs=15.2

Q ss_pred             CCEEEECCCCCCchhhH
Q 042872          241 QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF  257 (381)
                      +.+|+.+|+|+|||...
T Consensus        46 ~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A           46 RGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             SEEEEESSSSSCHHHHH
T ss_pred             ceEEEECCCCccHHHHH
Confidence            67999999999999775

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=91.85  E-value=0.63  Score=43.48  Aligned_cols=33  Identities=12%  Similarity=0.147  Sum_probs=22.9

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ..+++.+|+|+|||....    .+....+.+.+.+++
T Consensus        56 ~~vll~G~~GtGKT~la~----~ia~~~~~~~~~~~~   88 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLAN----IISYEMSANIKTTAA   88 (338)
T ss_dssp             CCEEEECSTTSSHHHHHH----HHHHHTTCCEEEEEG
T ss_pred             CeEEEECcCCCCHHHHHH----HHHHHhCCCeEEecc
Confidence            589999999999998752    333345556555554

>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=91.69  E-value=0.57  Score=47.46  Aligned_cols=39  Identities=13%  Similarity=0.069  Sum_probs=26.6

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCH
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTV  281 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~  281 (381)
                      =+++++|+|+|||-+...-...+. ..|.++.++..+.-+
T Consensus        99 vI~lvG~~GsGKTTt~~kLA~~l~-~~G~kVllv~~D~~r  137 (433)
T 3kl4_A           99 IIMLVGVQGSGKTTTAGKLAYFYK-KRGYKVGLVAADVYR  137 (433)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHH-HTTCCEEEEEECCSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH-HcCCeEEEEecCccc
Confidence            467789999999977653344444 457777777666543

>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=91.65  E-value=0.55  Score=50.87  Aligned_cols=54  Identities=17%  Similarity=0.130  Sum_probs=39.9

Q ss_pred             CCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          223 NRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       223 ~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      ...+.+.|.+|+..++.+.-+++.+|.|+|||.+...-+..+....+-++.++.
T Consensus       354 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~~~i~~l~~~~~~~ilv~a  407 (800)
T 2wjy_A          354 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCA  407 (800)
T ss_dssp             SCCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHHHHHHHHHTTCSSCEEEEE
T ss_pred             ccCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHHHHHHHHHHcCCCcEEEEc
Confidence            345789999999999987778999999999998765445555432345555554

>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=91.63  E-value=1.1  Score=45.18  Aligned_cols=38  Identities=13%  Similarity=0.150  Sum_probs=22.6

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      +=+++++|+|+|||-+...-...+. ..|-++.++..+.
T Consensus        99 ~vi~i~G~~GsGKTT~~~~LA~~l~-~~g~~Vllvd~D~  136 (425)
T 2ffh_A           99 NLWFLVGLQGSGKTTTAAKLALYYK-GKGRRPLLVAADT  136 (425)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH-TTTCCEEEEECCS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH-HcCCeEEEeeccc
Confidence            3466779999999966542233333 3355555555443

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=91.14  E-value=0.42  Score=44.54  Aligned_cols=34  Identities=18%  Similarity=0.196  Sum_probs=22.0

Q ss_pred             CE-EEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          242 DC-FVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       242 Dv-LviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      .+ |+.+|+|+|||...    ..+....+.+...+++..
T Consensus        49 ~~~L~~G~~G~GKT~la----~~la~~l~~~~~~i~~~~   83 (324)
T 3u61_B           49 HIILHSPSPGTGKTTVA----KALCHDVNADMMFVNGSD   83 (324)
T ss_dssp             SEEEECSSTTSSHHHHH----HHHHHHTTEEEEEEETTT
T ss_pred             eEEEeeCcCCCCHHHHH----HHHHHHhCCCEEEEcccc
Confidence            45 55566999999775    334445566777776543

>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=91.07  E-value=0.5  Score=43.23  Aligned_cols=17  Identities=24%  Similarity=0.258  Sum_probs=14.7

Q ss_pred             CEEEECCCCCCchhhHH
Q 042872          242 DCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~  258 (381)
                      .+++.+|+|+|||....
T Consensus        48 ~~ll~G~~G~GKT~la~   64 (327)
T 1iqp_A           48 HLLFAGPPGVGKTTAAL   64 (327)
T ss_dssp             EEEEESCTTSSHHHHHH
T ss_pred             eEEEECcCCCCHHHHHH
Confidence            69999999999997653

>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=90.91  E-value=1.2  Score=42.34  Aligned_cols=37  Identities=14%  Similarity=0.123  Sum_probs=23.5

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      =+++++++|+|||-....-...+. ..|-++.++..+.
T Consensus       100 vi~i~G~~G~GKTT~~~~la~~~~-~~g~~v~l~~~D~  136 (297)
T 1j8m_F          100 VIMLVGVQGTGKTTTAGKLAYFYK-KKGFKVGLVGADV  136 (297)
T ss_dssp             EEEEECSSCSSTTHHHHHHHHHHH-HTTCCEEEEECCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH-HCCCeEEEEecCC
Confidence            466789999999976643333333 3466666665553

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=90.77  E-value=0.69  Score=48.77  Aligned_cols=64  Identities=30%  Similarity=0.285  Sum_probs=40.9

Q ss_pred             CCCCCcHHHHHHHHHHHc----C-CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHH
Q 042872          222 GNRAFRPLQHQACKASVA----K-QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELR  292 (381)
Q Consensus       222 G~~~fRpiQ~eAI~aiL~----G-rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr  292 (381)
                      +| .|++.|.++|..++.    | +..++.+.||||||+++..-+..+    +-+++++...  .....+....++
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~~~~~~----~~~~lvv~~~--~~~A~ql~~el~   74 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVIEAL----GRPALVLAPN--KILAAQLAAEFR   74 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHH----TCCEEEEESS--HHHHHHHHHHHH
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHHHHHHh----CCCEEEEecC--HHHHHHHHHHHH
Confidence            45 788999999988764    3 246788999999999886333322    3456666543  333333444443

>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=90.68  E-value=0.94  Score=43.45  Aligned_cols=38  Identities=13%  Similarity=0.072  Sum_probs=23.4

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      +=+++++|+|+|||-....-...+. ..|-++.++..+.
T Consensus       105 ~vi~ivG~~GsGKTTl~~~LA~~l~-~~g~kV~lv~~D~  142 (306)
T 1vma_A          105 FVIMVVGVNGTGKTTSCGKLAKMFV-DEGKSVVLAAADT  142 (306)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH-HTTCCEEEEEECT
T ss_pred             eEEEEEcCCCChHHHHHHHHHHHHH-hcCCEEEEEcccc
Confidence            3467889999999966543333333 3455666555544

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=90.67  E-value=0.12  Score=46.61  Aligned_cols=16  Identities=31%  Similarity=0.603  Sum_probs=13.6

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      +++.++.|+|||....
T Consensus         8 ~l~tG~pGsGKT~~a~   23 (199)
T 2r2a_A            8 CLITGTPGSGKTLKMV   23 (199)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEEeCCCCCHHHHHH
Confidence            5789999999998654

>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=90.63  E-value=0.24  Score=46.49  Aligned_cols=15  Identities=20%  Similarity=0.096  Sum_probs=13.4

Q ss_pred             EEEECCCCCCchhhH
Q 042872          243 CFVLLPTGGGKSLCY  257 (381)
Q Consensus       243 vLviaPTGsGKTLaF  257 (381)
                      +++.+|.|+|||...
T Consensus        41 ~ll~G~~G~GKT~la   55 (373)
T 1jr3_A           41 YLFSGTRGVGKTSIA   55 (373)
T ss_dssp             EEEESCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            789999999999765

>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=90.62  E-value=1  Score=38.91  Aligned_cols=36  Identities=17%  Similarity=0.053  Sum_probs=24.9

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      |.=+++.+|+|+|||... .++..   ..+-+++.+....
T Consensus        20 G~~~~i~G~~GsGKTtl~-~~l~~---~~~~~v~~i~~~~   55 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLA-LQTGL---LSGKKVAYVDTEG   55 (220)
T ss_dssp             TSEEEEECSTTSSHHHHH-HHHHH---HHCSEEEEEESSC
T ss_pred             CEEEEEECCCCCCHHHHH-HHHHH---HcCCcEEEEECCC
Confidence            556788999999999665 33333   3466777777654

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=90.50  E-value=0.7  Score=43.85  Aligned_cols=18  Identities=17%  Similarity=0.133  Sum_probs=14.2

Q ss_pred             CCEEE--ECCCCCCchhhHH
Q 042872          241 QDCFV--LLPTGGGKSLCYQ  258 (381)
Q Consensus       241 rDvLv--iaPTGsGKTLaF~  258 (381)
                      +.+++  .+|.|+|||....
T Consensus        51 ~~~li~i~G~~G~GKT~L~~   70 (412)
T 1w5s_A           51 VNMIYGSIGRVGIGKTTLAK   70 (412)
T ss_dssp             EEEEEECTTCCSSSHHHHHH
T ss_pred             CEEEEeCcCcCCCCHHHHHH
Confidence            35677  7999999997754

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=90.42  E-value=0.68  Score=45.31  Aligned_cols=48  Identities=8%  Similarity=-0.021  Sum_probs=33.2

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      |.=+++.+++|.|||...+.-+..+. ..|.++.++...++..+....+
T Consensus        46 G~LiiIaG~pG~GKTt~al~ia~~~a-~~g~~Vl~fSlEms~~ql~~Rl   93 (338)
T 4a1f_A           46 GSLVIIGARPSMGKTSLMMNMVLSAL-NDDRGVAVFSLEMSAEQLALRA   93 (338)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHH-HTTCEEEEEESSSCHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHH-HcCCeEEEEeCCCCHHHHHHHH
Confidence            34467789999999965543333333 3688899999888877655444

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=90.35  E-value=1.4  Score=45.29  Aligned_cols=37  Identities=11%  Similarity=0.127  Sum_probs=25.6

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      -+++++++|+|||-....-...+. ..|.++.++..+.
T Consensus       103 vI~ivG~~GvGKTTl~~kLA~~l~-~~G~kVllVd~D~  139 (504)
T 2j37_W          103 VIMFVGLQGSGKTTTCSKLAYYYQ-RKGWKTCLICADT  139 (504)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH-HTTCCEEEEEECC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH-hCCCeEEEEeccc
Confidence            477889999999977754444454 3477777776644

>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=90.31  E-value=0.29  Score=45.24  Aligned_cols=33  Identities=15%  Similarity=0.312  Sum_probs=22.2

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      +.+++.+|+|+|||....    .+....+.+...+++
T Consensus        39 ~~vll~G~~GtGKT~la~----~i~~~~~~~~~~~~~   71 (324)
T 1hqc_A           39 EHLLLFGPPGLGKTTLAH----VIAHELGVNLRVTSG   71 (324)
T ss_dssp             CCCEEECCTTCCCHHHHH----HHHHHHTCCEEEECT
T ss_pred             CcEEEECCCCCCHHHHHH----HHHHHhCCCEEEEec
Confidence            689999999999997752    222234555555543

>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=90.28  E-value=0.37  Score=45.52  Aligned_cols=33  Identities=15%  Similarity=0.158  Sum_probs=22.3

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      .+.+|+.+|+|+|||....    .+....+.+.+.++
T Consensus        51 ~~~vLl~GppGtGKT~la~----aia~~~~~~~~~v~   83 (322)
T 3eie_A           51 TSGILLYGPPGTGKSYLAK----AVATEANSTFFSVS   83 (322)
T ss_dssp             CCEEEEECSSSSCHHHHHH----HHHHHHTCEEEEEE
T ss_pred             CCeEEEECCCCCcHHHHHH----HHHHHHCCCEEEEc
Confidence            3579999999999997752    33333455555554

>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=90.22  E-value=0.5  Score=45.01  Aligned_cols=32  Identities=16%  Similarity=0.130  Sum_probs=22.7

Q ss_pred             cHHHHHHHHHHH----cCC--C-EEEECCCCCCchhhHH
Q 042872          227 RPLQHQACKASV----AKQ--D-CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       227 RpiQ~eAI~aiL----~Gr--D-vLviaPTGsGKTLaF~  258 (381)
                      .|.|.+++..+.    .|+  . +|+.+|.|+|||.+..
T Consensus         4 ~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~   42 (334)
T 1a5t_A            4 YPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIY   42 (334)
T ss_dssp             CGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHH
T ss_pred             CCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHH
Confidence            466777665554    444  3 7999999999997653

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=90.10  E-value=1.6  Score=37.52  Aligned_cols=44  Identities=16%  Similarity=0.206  Sum_probs=28.1

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQ  283 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e  283 (381)
                      .|.-+++++|+|+|||... .++.......+-++..+....+..+
T Consensus        22 ~G~~~~i~G~~GsGKTtl~-~~l~~~~~~~~~~v~~~~~~~~~~~   65 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFS-LHFIAKGLRDGDPCIYVTTEESRDS   65 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHH-HHHHHHHHHHTCCEEEEESSSCHHH
T ss_pred             CCCEEEEEcCCCCCHHHHH-HHHHHHHHHCCCeEEEEEcccCHHH
Confidence            3667888999999999554 2333222234667777776665443

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=90.10  E-value=0.98  Score=45.45  Aligned_cols=38  Identities=13%  Similarity=0.010  Sum_probs=27.6

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      -+++++++|+|||-+-..-...|....|.++.++..+.
T Consensus       102 vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D~  139 (433)
T 2xxa_A          102 VVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADV  139 (433)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecCC
Confidence            46777999999997765555556532288888887765

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=90.06  E-value=0.62  Score=45.89  Aligned_cols=49  Identities=14%  Similarity=0.240  Sum_probs=31.7

Q ss_pred             HHHHHHc------CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHH
Q 042872          233 ACKASVA------KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVS  282 (381)
Q Consensus       233 AI~aiL~------GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~  282 (381)
                      .+..+|.      |+=+++.+|+|+|||...+.-+..+. ..|-+++++....+..
T Consensus        61 ~LD~~Lg~GGl~~G~li~I~G~pGsGKTtlal~la~~~~-~~g~~vlyi~~E~s~~  115 (366)
T 1xp8_A           61 SLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQ-KAGGTCAFIDAEHALD  115 (366)
T ss_dssp             HHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH-HTTCCEEEEESSCCCC
T ss_pred             HHHHHhCCCCccCCcEEEEEcCCCCChHHHHHHHHHHHH-HCCCeEEEEECCCChh
Confidence            4555554      45678889999999965533333333 3567888887665543

>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=90.03  E-value=0.34  Score=45.39  Aligned_cols=34  Identities=15%  Similarity=0.171  Sum_probs=23.2

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      .++.+++.+|+|+|||...    +.+....+.+.+.+.
T Consensus        48 ~~~~vLL~Gp~GtGKT~la----~ala~~~~~~~i~v~   81 (301)
T 3cf0_A           48 PSKGVLFYGPPGCGKTLLA----KAIANECQANFISIK   81 (301)
T ss_dssp             CCSEEEEECSSSSSHHHHH----HHHHHHTTCEEEEEC
T ss_pred             CCceEEEECCCCcCHHHHH----HHHHHHhCCCEEEEE
Confidence            3577999999999999775    233334455555554

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=90.02  E-value=0.68  Score=40.68  Aligned_cols=39  Identities=8%  Similarity=-0.030  Sum_probs=26.5

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      .|+=.++.+|.|+|||...+..+..+. ..|.++.++...
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll~~~~~~~-~~g~~v~~~~~~   40 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELLSFVEIYK-LGKKKVAVFKPK   40 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHH-HTTCEEEEEEEC
T ss_pred             ccEEEEEECCCCCCHHHHHHHHHHHHH-HCCCeEEEEeec
Confidence            345567889999999988755555554 346677666544

>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=89.56  E-value=0.35  Score=46.60  Aligned_cols=34  Identities=18%  Similarity=0.278  Sum_probs=23.4

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      .+.+|+.+|+|+|||....    .+....+.+.+.++.
T Consensus       117 ~~~vLl~GppGtGKT~la~----aia~~~~~~~~~i~~  150 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIGK----CIASQSGATFFSISA  150 (357)
T ss_dssp             CSEEEEESSTTSSHHHHHH----HHHHHTTCEEEEEEG
T ss_pred             CceEEEECCCCCCHHHHHH----HHHHHcCCeEEEEeh
Confidence            4689999999999997752    333345666555543

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=89.56  E-value=0.39  Score=45.05  Aligned_cols=33  Identities=21%  Similarity=0.146  Sum_probs=23.1

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      +-+|+.+|+|+|||...    ..+...+|.+.+.+..
T Consensus        37 ~~lLl~GppGtGKT~la----~aiA~~l~~~~i~v~~   69 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQC----ELVFRKMGINPIMMSA   69 (293)
T ss_dssp             SEEEEEECTTSCHHHHH----HHHHHHHTCCCEEEEH
T ss_pred             eEEEEECCCCCCHHHHH----HHHHHHhCCCEEEEeH
Confidence            45788899999999765    3344455777766653

>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=89.50  E-value=0.31  Score=46.76  Aligned_cols=33  Identities=33%  Similarity=0.540  Sum_probs=23.5

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      ...+++.+|+|+|||...    ..+...++.+.+.+.
T Consensus        72 ~~~ill~Gp~GtGKT~la----~~la~~l~~~~~~~~  104 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMA----QTLAKHLDIPIAISD  104 (376)
T ss_dssp             CCCEEEECCTTSSHHHHH----HHHHHHTTCCEEEEE
T ss_pred             CCCEEEECCCCCCHHHHH----HHHHHHhCCCEEEec
Confidence            468999999999999775    233434566666554

>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=89.42  E-value=0.72  Score=44.89  Aligned_cols=41  Identities=15%  Similarity=0.216  Sum_probs=27.5

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTV  281 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~  281 (381)
                      |+=+++.+|.|+|||...+.-+..+. ..|-+++++....+.
T Consensus        61 G~iv~I~G~pGsGKTtLal~la~~~~-~~g~~vlyi~~E~~~  101 (349)
T 2zr9_A           61 GRVIEIYGPESSGKTTVALHAVANAQ-AAGGIAAFIDAEHAL  101 (349)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHH-HTTCCEEEEESSCCC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH-hCCCeEEEEECCCCc
Confidence            56688999999999966532233333 457788888766543

>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=89.26  E-value=1.1  Score=40.99  Aligned_cols=16  Identities=19%  Similarity=0.125  Sum_probs=14.1

Q ss_pred             CEEEECCCCCCchhhH
Q 042872          242 DCFVLLPTGGGKSLCY  257 (381)
Q Consensus       242 DvLviaPTGsGKTLaF  257 (381)
                      .+++.+|+|+|||...
T Consensus        44 ~~ll~G~~G~GKt~la   59 (323)
T 1sxj_B           44 HMIISGMPGIGKTTSV   59 (323)
T ss_dssp             CEEEECSTTSSHHHHH
T ss_pred             eEEEECcCCCCHHHHH
Confidence            4999999999999665

>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=89.26  E-value=0.68  Score=42.19  Aligned_cols=16  Identities=25%  Similarity=0.316  Sum_probs=14.2

Q ss_pred             CEEEECCCCCCchhhH
Q 042872          242 DCFVLLPTGGGKSLCY  257 (381)
Q Consensus       242 DvLviaPTGsGKTLaF  257 (381)
                      .+++.+|+|+|||...
T Consensus        40 ~~ll~G~~G~GKt~la   55 (319)
T 2chq_A           40 HLLFSGPPGTGKTATA   55 (319)
T ss_dssp             CEEEESSSSSSHHHHH
T ss_pred             eEEEECcCCcCHHHHH
Confidence            5999999999999665

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.23  E-value=0.45  Score=48.01  Aligned_cols=71  Identities=8%  Similarity=0.047  Sum_probs=42.2

Q ss_pred             CCCCHHHHhhchHHHHHHHHHhCC--CCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          200 GTLSFEELQALDDMEFANVVIFGN--RAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       200 ~~~~fe~L~~l~~l~~~~~~~fG~--~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      +..+|+.+..+++....++...-+  ..|--++.--+   --.+-+|+.+|.|+|||+..    .++....+.+.+.+.+
T Consensus       143 p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi---~~prGvLL~GPPGTGKTllA----kAiA~e~~~~f~~v~~  215 (405)
T 4b4t_J          143 PDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGI---AQPKGVILYGPPGTGKTLLA----RAVAHHTDCKFIRVSG  215 (405)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTC---CCCCCEEEESCSSSSHHHHH----HHHHHHHTCEEEEEEG
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCceEEeCCCCCCHHHHH----HHHHHhhCCCceEEEh
Confidence            356788887777766666543221  11111111111   12378999999999999875    4455456777666654

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=89.17  E-value=1.7  Score=41.26  Aligned_cols=51  Identities=8%  Similarity=-0.035  Sum_probs=33.0

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQEL  291 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~l  291 (381)
                      |.=+++.+++|+|||...+.-..... ..|.+++++....+..+....+...
T Consensus        68 G~l~li~G~pG~GKTtl~l~ia~~~a-~~g~~vl~~slE~s~~~l~~R~~~~  118 (315)
T 3bh0_A           68 RNFVLIAARPSMGKTAFALKQAKNMS-DNDDVVNLHSLEMGKKENIKRLIVT  118 (315)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHH-TTTCEEEEEESSSCHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHH-HcCCeEEEEECCCCHHHHHHHHHHH
Confidence            45578889999999954432222333 3467888888888876655544443

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=89.10  E-value=0.49  Score=40.46  Aligned_cols=44  Identities=23%  Similarity=0.395  Sum_probs=32.7

Q ss_pred             CCchhhHH------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          251 GGKSLCYQ------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       251 sGKTLaF~------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      .||+++|.      +.+...-...|+.+..++|+++..++..+++.+++|
T Consensus        34 ~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g   83 (175)
T 2rb4_A           34 IGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDG   83 (175)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTT
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcC
Confidence            45777765      222222225689999999999999999999998866

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=89.07  E-value=0.52  Score=39.89  Aligned_cols=28  Identities=18%  Similarity=0.414  Sum_probs=25.3

Q ss_pred             hcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          267 KFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       267 ~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      ..|+++..++|+++..++..+++.+++|
T Consensus        57 ~~~~~~~~~hg~~~~~~r~~~~~~f~~g   84 (163)
T 2hjv_A           57 DLGYPCDKIHGGMIQEDRFDVMNEFKRG   84 (163)
T ss_dssp             HTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             HcCCcEEEEeCCCCHHHHHHHHHHHHcC
Confidence            5689999999999999999999998866

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=88.91  E-value=1.5  Score=43.99  Aligned_cols=33  Identities=12%  Similarity=0.165  Sum_probs=21.8

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ..+|+.+|+|+|||....    .+....+.+...++.
T Consensus        51 ~~vLL~GppGtGKTtlAr----~ia~~~~~~f~~l~a   83 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLAE----VIARYANADVERISA   83 (447)
T ss_dssp             CEEEEECSTTSSHHHHHH----HHHHHTTCEEEEEET
T ss_pred             cEEEEECCCCCcHHHHHH----HHHHHhCCCeEEEEe
Confidence            368999999999997752    233334555555543

>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=88.89  E-value=1.4  Score=38.60  Aligned_cols=40  Identities=10%  Similarity=0.027  Sum_probs=24.6

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHH-Hhh-----cCCcEEEEeCCC
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITL-NLK-----FGIPATFLNSQQ  279 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L-~~~-----~gI~a~~l~g~~  279 (381)
                      .|.=+++++|+|+|||.... ++... ...     .+-.++.+.+..
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~-~l~~~~~~~~~~g~~~~~~~~i~~~~   68 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICH-TLAVTCQLPIDRGGGEGKAMYIDTEG   68 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHH-HHHHHTTSCGGGTCCSSEEEEEESSS
T ss_pred             CCeEEEEECCCCCcHHHHHH-HHHHHHhCchhcCCCCCeEEEEECCC
Confidence            45678899999999996653 33221 101     144566776655

>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=88.45  E-value=1.2  Score=41.25  Aligned_cols=18  Identities=22%  Similarity=0.309  Sum_probs=15.2

Q ss_pred             CCEEEECCCCCCchhhHH
Q 042872          241 QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~  258 (381)
                      ..+++.+|+|+|||....
T Consensus        59 ~~~ll~G~~G~GKT~la~   76 (353)
T 1sxj_D           59 PHMLFYGPPGTGKTSTIL   76 (353)
T ss_dssp             CCEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            469999999999997653

>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=88.25  E-value=1.1  Score=42.65  Aligned_cols=48  Identities=15%  Similarity=0.209  Sum_probs=28.7

Q ss_pred             HHHHHH-----cCCCEEEECCCCCCchhhHHHHHHHHHhh-----cCCcEEEEeCCCC
Q 042872          233 ACKASV-----AKQDCFVLLPTGGGKSLCYQDQIITLNLK-----FGIPATFLNSQQT  280 (381)
Q Consensus       233 AI~aiL-----~GrDvLviaPTGsGKTLaF~dQv~~L~~~-----~gI~a~~l~g~~~  280 (381)
                      .+..+|     .|+=+++.+|+|+|||.....-+......     .+-+++.+....+
T Consensus        95 ~LD~~L~GGl~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~  152 (324)
T 2z43_A           95 ALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGT  152 (324)
T ss_dssp             HHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSC
T ss_pred             hHHHhcCCCCCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCC
Confidence            345555     35678999999999996553222221111     1557777776654

>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=88.19  E-value=0.72  Score=49.75  Aligned_cols=17  Identities=18%  Similarity=0.215  Sum_probs=15.1

Q ss_pred             CCEEEECCCCCCchhhH
Q 042872          241 QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF  257 (381)
                      +++++++|+|+|||...
T Consensus       192 ~~vlL~G~pG~GKT~la  208 (854)
T 1qvr_A          192 NNPVLIGEPGVGKTAIV  208 (854)
T ss_dssp             CCCEEEECTTSCHHHHH
T ss_pred             CceEEEcCCCCCHHHHH
Confidence            47999999999999765

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=88.12  E-value=0.55  Score=41.85  Aligned_cols=28  Identities=32%  Similarity=0.536  Sum_probs=25.4

Q ss_pred             hcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          267 KFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       267 ~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      ..|+.+..++|+++..++..+++.+++|
T Consensus        53 ~~~~~~~~lhg~~~~~~r~~~~~~f~~g   80 (212)
T 3eaq_A           53 RLGHPAQALHGDLSQGERERVLGAFRQG   80 (212)
T ss_dssp             HHTCCEEEECSSSCHHHHHHHHHHHHSS
T ss_pred             HcCCCEEEEECCCCHHHHHHHHHHHHCC
Confidence            5689999999999999999999998866

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=88.12  E-value=1.4  Score=38.60  Aligned_cols=49  Identities=16%  Similarity=0.203  Sum_probs=31.7

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAV  287 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~i  287 (381)
                      .|.=+++.+++|+|||.-.+.-+.+.....+-++.++....+..+....
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~E~~~~~~~~~   77 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLEERARDLRRE   77 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEESSSCHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeecccCCHHHHHHH
Confidence            3566899999999999544322222222457788888877776654333

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=88.10  E-value=0.89  Score=41.47  Aligned_cols=38  Identities=16%  Similarity=0.051  Sum_probs=23.6

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      |+=.++.+|.|+|||.-.+.-+..+. ..+.++.++.+.
T Consensus        20 g~l~fiyG~MgsGKTt~Ll~~i~n~~-~~~~kvl~~kp~   57 (195)
T 1w4r_A           20 GQIQVILGPMFSGKSTELMRRVRRFQ-IAQYKCLVIKYA   57 (195)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHH-HTTCCEEEEEET
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHH-HcCCeEEEEccc
Confidence            55567889999999955433343333 235566666544

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=87.86  E-value=1  Score=44.92  Aligned_cols=34  Identities=18%  Similarity=0.182  Sum_probs=22.3

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhc-CCcEEEEeC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKF-GIPATFLNS  277 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~-gI~a~~l~g  277 (381)
                      .+.+|+.+|+|+|||....    .+.... +.+.+.+.+
T Consensus       167 ~~~vLL~GppGtGKT~lA~----aia~~~~~~~~~~v~~  201 (444)
T 2zan_A          167 WRGILLFGPPGTGKSYLAK----AVATEANNSTFFSISS  201 (444)
T ss_dssp             CSEEEEECSTTSSHHHHHH----HHHHHCCSSEEEEECC
T ss_pred             CceEEEECCCCCCHHHHHH----HHHHHcCCCCEEEEeH
Confidence            3679999999999997752    333333 445544443

>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=87.81  E-value=0.96  Score=45.09  Aligned_cols=38  Identities=16%  Similarity=0.088  Sum_probs=23.5

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhh-cCCcEEEEeC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLK-FGIPATFLNS  277 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~-~gI~a~~l~g  277 (381)
                      +..+++.+|+|+|||....--...+... .+.+++.+++
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~  168 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITS  168 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeH
Confidence            3579999999999997653112222211 1566666654

>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=87.72  E-value=0.47  Score=48.52  Aligned_cols=51  Identities=20%  Similarity=0.194  Sum_probs=37.1

Q ss_pred             CCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCC---cEEEEe
Q 042872          224 RAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGI---PATFLN  276 (381)
Q Consensus       224 ~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI---~a~~l~  276 (381)
                      ..+++.|.+||..  ....++|+|+.|||||.+-..-+..+....++   ++.+++
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~lt   61 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVT   61 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEE
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEe
Confidence            4688999999983  35789999999999998876556555543343   455554

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=87.63  E-value=0.73  Score=39.60  Aligned_cols=28  Identities=11%  Similarity=0.139  Sum_probs=25.3

Q ss_pred             hcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          267 KFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       267 ~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      ..|+++..++|+++..++..+++.+++|
T Consensus        53 ~~~~~~~~~hg~~~~~~r~~~~~~f~~g   80 (172)
T 1t5i_A           53 EQNFPAIAIHRGMPQEERLSRYQQFKDF   80 (172)
T ss_dssp             HTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             hcCCCEEEEECCCCHHHHHHHHHHHHCC
Confidence            5689999999999999999999998866

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=87.53  E-value=0.83  Score=46.69  Aligned_cols=33  Identities=18%  Similarity=0.357  Sum_probs=23.0

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      +.+++.+|+|+|||....    .+....+.+.+.+++
T Consensus        50 ~gvLL~GppGtGKT~Lar----aia~~~~~~f~~is~   82 (476)
T 2ce7_A           50 KGILLVGPPGTGKTLLAR----AVAGEANVPFFHISG   82 (476)
T ss_dssp             SEEEEECCTTSSHHHHHH----HHHHHHTCCEEEEEG
T ss_pred             CeEEEECCCCCCHHHHHH----HHHHHcCCCeeeCCH
Confidence            569999999999998752    333345666665553

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=87.40  E-value=1.3  Score=44.39  Aligned_cols=49  Identities=8%  Similarity=-0.046  Sum_probs=33.0

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQ  289 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~  289 (381)
                      |.=+++.+++|.|||...+.-+..... .|.+++++...++..+....+.
T Consensus       197 G~liiIaG~pG~GKTtlal~ia~~~a~-~g~~vl~fSlEms~~ql~~R~~  245 (444)
T 3bgw_A          197 RNFVLIAARPSMGKTAFALKQAKNMSD-NDDVVNLHSLEMGKKENIKRLI  245 (444)
T ss_dssp             SCEEEEEECSSSSHHHHHHHHHHHHHH-TTCEEEEECSSSCTTHHHHHHH
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHH-cCCEEEEEECCCCHHHHHHHHH
Confidence            445788899999999665433444442 3888988888877665544433

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=87.39  E-value=2.6  Score=42.37  Aligned_cols=50  Identities=16%  Similarity=0.112  Sum_probs=33.9

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHH
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVL  288 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il  288 (381)
                      .|.=+++.+++|+|||...+.-+..+....|.+++++....+..+....+
T Consensus       241 ~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~E~s~~~l~~r~  290 (503)
T 1q57_A          241 GGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDL  290 (503)
T ss_dssp             TTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEESSSCHHHHHHHH
T ss_pred             CCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEeccCCHHHHHHHH
Confidence            34557888999999996654334444433378899998888876544333

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=87.23  E-value=0.66  Score=39.25  Aligned_cols=28  Identities=14%  Similarity=0.278  Sum_probs=25.1

Q ss_pred             hcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          267 KFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       267 ~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      ..|+.+..++|+++..++..+++.+++|
T Consensus        52 ~~~~~~~~~~~~~~~~~r~~~~~~f~~g   79 (165)
T 1fuk_A           52 NDKFTVSAIYSDLPQQERDTIMKEFRSG   79 (165)
T ss_dssp             HTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             HcCCCEEEEECCCCHHHHHHHHHHHHcC
Confidence            5689999999999999999999998866

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=86.64  E-value=0.74  Score=40.54  Aligned_cols=28  Identities=14%  Similarity=0.340  Sum_probs=25.3

Q ss_pred             hcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          267 KFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       267 ~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      ..|+++..++|+++..++..+++.+++|
T Consensus        76 ~~g~~~~~lhg~~~~~~R~~~l~~F~~g  103 (191)
T 2p6n_A           76 LKGVEAVAIHGGKDQEERTKAIEAFREG  103 (191)
T ss_dssp             HHTCCEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             HcCCcEEEEeCCCCHHHHHHHHHHHhcC
Confidence            5699999999999999999999998866

>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=86.34  E-value=1.4  Score=43.34  Aligned_cols=40  Identities=18%  Similarity=0.179  Sum_probs=26.7

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQT  280 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~  280 (381)
                      |+=+++.+|+|+|||... -++.......|-+++.+.+...
T Consensus        61 G~i~~I~GppGsGKSTLa-l~la~~~~~~gg~VlyId~E~s  100 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLA-LHAIAEAQKMGGVAAFIDAEHA  100 (356)
T ss_dssp             TEEEEEEESTTSSHHHHH-HHHHHHHHHTTCCEEEEESSCC
T ss_pred             CcEEEEECCCCCCHHHHH-HHHHHHHHhcCCeEEEEecccc
Confidence            556788999999999554 3433332245677777776554

>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=85.68  E-value=5.9  Score=40.90  Aligned_cols=66  Identities=18%  Similarity=0.091  Sum_probs=41.0

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHH-HHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHH
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQ-IITLNLKFGIPATFLNSQQTVSQAAAVLQELR  292 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQ-v~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr  292 (381)
                      .++|+|...+..+-..+-+++..|-|.|||.+..-. +-.+....+..+.++  ..+..+...++..++
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~~~~i~~v--a~t~~qA~~~~~~i~  229 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGIL--AHKGSMSAEVLDRTK  229 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTSSSCEEEEE--ESSHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhCCCCeEEEE--ECCHHHHHHHHHHHH
Confidence            367999999988755678999999999999876521 111221223333333  335555555555544

>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=84.97  E-value=5.2  Score=37.86  Aligned_cols=40  Identities=15%  Similarity=0.162  Sum_probs=27.1

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      |+-+++++|+|+|||-+...-...+....|-++.++..+.
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~D~  144 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTDT  144 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEECCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEecCc
Confidence            4567888999999997664333344423577777776654

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=84.87  E-value=0.55  Score=39.06  Aligned_cols=21  Identities=10%  Similarity=0.009  Sum_probs=17.5

Q ss_pred             HHcCCCEEEECCCCCCchhhH
Q 042872          237 SVAKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       237 iL~GrDvLviaPTGsGKTLaF  257 (381)
                      +-.+..+++.+|+|+|||.+.
T Consensus        24 ~~~~~~vll~G~~GtGKt~lA   44 (143)
T 3co5_A           24 AKRTSPVFLTGEAGSPFETVA   44 (143)
T ss_dssp             HTCSSCEEEEEETTCCHHHHH
T ss_pred             hCCCCcEEEECCCCccHHHHH
Confidence            345689999999999999764

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=84.76  E-value=0.62  Score=38.72  Aligned_cols=20  Identities=10%  Similarity=0.107  Sum_probs=17.4

Q ss_pred             HcCCCEEEECCCCCCchhhH
Q 042872          238 VAKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       238 L~GrDvLviaPTGsGKTLaF  257 (381)
                      ..+..+++.+|+|+|||...
T Consensus        22 ~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHH
Confidence            35679999999999999876

>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=84.33  E-value=3.7  Score=40.82  Aligned_cols=66  Identities=18%  Similarity=0.125  Sum_probs=41.1

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHH-HHhhcCCcEEEEeCCCCHHHHHHHHHHHH
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIIT-LNLKFGIPATFLNSQQTVSQAAAVLQELR  292 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~-L~~~~gI~a~~l~g~~~~~e~~~il~~lr  292 (381)
                      .++|+|...+..+-..|-+++..+-+.|||.+..-.+.. +....|..+.++  ..+..+...+++.++
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~~g~~v~~v--A~t~~qA~~vf~~i~  229 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGIL--AHKGSMSAEVLDRTK  229 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSSSSCEEEEE--ESSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhCCCCeEEEE--eCCHHHHHHHHHHHH
Confidence            568999999987755567899999999999876522221 111123344333  345555555565543

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=84.17  E-value=1  Score=45.90  Aligned_cols=33  Identities=21%  Similarity=0.267  Sum_probs=23.7

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      .+.+|+.+|+|+|||++.    +.+....+.+.+.++
T Consensus       238 ~~~vLL~GppGtGKT~lA----raia~~~~~~fv~vn  270 (489)
T 3hu3_A          238 PRGILLYGPPGTGKTLIA----RAVANETGAFFFLIN  270 (489)
T ss_dssp             CCEEEEECSTTSSHHHHH----HHHHHHCSSEEEEEE
T ss_pred             CCcEEEECcCCCCHHHHH----HHHHHHhCCCEEEEE
Confidence            367999999999999875    334444566666665

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=83.84  E-value=1.4  Score=46.36  Aligned_cols=18  Identities=22%  Similarity=0.285  Sum_probs=15.9

Q ss_pred             CCCEEEECCCCCCchhhH
Q 042872          240 KQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF  257 (381)
                      ++++++++|+|+|||.+.
T Consensus       207 ~~~vlL~G~~GtGKT~la  224 (758)
T 1r6b_X          207 KNNPLLVGESGVGKTAIA  224 (758)
T ss_dssp             SCEEEEECCTTSSHHHHH
T ss_pred             CCCeEEEcCCCCCHHHHH
Confidence            468999999999999775

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=83.28  E-value=1.6  Score=44.91  Aligned_cols=71  Identities=11%  Similarity=0.140  Sum_probs=40.1

Q ss_pred             CCCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHH--HcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          200 GTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKAS--VAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       200 ~~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~ai--L~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      +..+|+.+..+++....+++..-+.-..|   +....+  ---|-+|+.+|.|+|||+..    .++....+.+.+.+.+
T Consensus       204 P~vt~~DIgGl~~~k~~L~e~V~~pl~~p---e~f~~~Gi~pprGILLyGPPGTGKTlLA----kAiA~e~~~~fi~vs~  276 (467)
T 4b4t_H          204 PDVTYSDVGGCKDQIEKLREVVELPLLSP---ERFATLGIDPPKGILLYGPPGTGKTLCA----RAVANRTDATFIRVIG  276 (467)
T ss_dssp             CSCCCSSCTTCHHHHHHHHHHTHHHHHCH---HHHHHHTCCCCSEEEECSCTTSSHHHHH----HHHHHHHTCEEEEEEG
T ss_pred             CCCCHHHhccHHHHHHHHHHHHHHHhcCH---HHHHHCCCCCCCceEeeCCCCCcHHHHH----HHHHhccCCCeEEEEh
Confidence            34667777777766665554321110001   111111  12478999999999999875    4455456666666553

>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=83.18  E-value=3  Score=39.27  Aligned_cols=15  Identities=27%  Similarity=0.388  Sum_probs=13.5

Q ss_pred             EEEECCCCCCchhhH
Q 042872          243 CFVLLPTGGGKSLCY  257 (381)
Q Consensus       243 vLviaPTGsGKTLaF  257 (381)
                      +++.+|.|+|||...
T Consensus        49 ~ll~Gp~G~GKTtla   63 (340)
T 1sxj_C           49 LLFYGPPGTGKTSTI   63 (340)
T ss_dssp             EEEECSSSSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            899999999999665

>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=83.07  E-value=0.73  Score=47.96  Aligned_cols=50  Identities=26%  Similarity=0.359  Sum_probs=35.6

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCC---cEEEEe
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGI---PATFLN  276 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI---~a~~l~  276 (381)
                      .++|-|++||..  .+..++|.|+.|||||.+-..-+..|....|+   ++.+++
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lT   54 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVT   54 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEE
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEe
Confidence            478999999986  36789999999999998876555555433333   345553

>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=82.29  E-value=0.98  Score=44.18  Aligned_cols=19  Identities=32%  Similarity=0.324  Sum_probs=16.9

Q ss_pred             cCCCEEEECCCCCCchhhH
Q 042872          239 AKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF  257 (381)
                      ...++++++|||+|||...
T Consensus        52 ~~~h~~i~G~tGsGKs~~~   70 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL   70 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH
T ss_pred             CcceEEEECCCCCCHHHHH
Confidence            4689999999999999876

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=82.22  E-value=4.3  Score=48.55  Aligned_cols=45  Identities=13%  Similarity=0.220  Sum_probs=31.9

Q ss_pred             HHHHHHc------CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          233 ACKASVA------KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       233 AI~aiL~------GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      .+..+|.      |+.+++.+|+|+|||.....-+.... ..|-++.++.-.
T Consensus      1414 ~LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~ea~-~~G~~v~Fi~~e 1464 (2050)
T 3cmu_A         1414 SLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQ-REGKTCAFIDAE 1464 (2050)
T ss_dssp             HHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHH-TTTCCEEEECTT
T ss_pred             HHHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHHHH-HcCCcEEEEEcc
Confidence            3677776      78999999999999976532233333 467888888643

>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=82.17  E-value=1.9  Score=43.29  Aligned_cols=36  Identities=14%  Similarity=0.207  Sum_probs=24.5

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      -+++++++|+|||-....-...+. ..|.++.++..+
T Consensus       101 vI~ivG~~GvGKTTla~~La~~l~-~~G~kVllv~~D  136 (432)
T 2v3c_C          101 VILLVGIQGSGKTTTAAKLARYIQ-KRGLKPALIAAD  136 (432)
T ss_dssp             CEEEECCSSSSTTHHHHHHHHHHH-HHHCCEEEECCS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH-HcCCeEEEEecc
Confidence            678899999999976643344444 346677666554

>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=82.15  E-value=5.5  Score=34.35  Aligned_cols=19  Identities=21%  Similarity=0.090  Sum_probs=15.2

Q ss_pred             cCCCEEEECCCCCCchhhH
Q 042872          239 AKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF  257 (381)
                      .|.=+.+++|+|+|||...
T Consensus        24 ~G~~~~l~G~nGsGKSTll   42 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLA   42 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            3556788899999999665

>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=82.02  E-value=3.2  Score=39.35  Aligned_cols=34  Identities=12%  Similarity=0.161  Sum_probs=22.4

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      ..+++.+|+|+|||....    .+...++.......|.
T Consensus        52 ~~~ll~Gp~G~GKTTLa~----~ia~~l~~~~~~~sg~   85 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLAH----IIASELQTNIHVTSGP   85 (334)
T ss_dssp             CCEEEESSTTSSHHHHHH----HHHHHHTCCEEEEETT
T ss_pred             CeEEEECCCCCcHHHHHH----HHHHHhCCCEEEEech
Confidence            578999999999997652    2232345555555554

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=81.78  E-value=4.6  Score=38.71  Aligned_cols=47  Identities=11%  Similarity=0.011  Sum_probs=28.6

Q ss_pred             HHHHHHc-----CCCEEEECCCCCCchhhHHHHHHHHHhh------cCCcEEEEeCCCC
Q 042872          233 ACKASVA-----KQDCFVLLPTGGGKSLCYQDQIITLNLK------FGIPATFLNSQQT  280 (381)
Q Consensus       233 AI~aiL~-----GrDvLviaPTGsGKTLaF~dQv~~L~~~------~gI~a~~l~g~~~  280 (381)
                      .+..+|.     |+=+++.+|+|+|||.... ++..-...      .+-+++.+....+
T Consensus       110 ~LD~~LgGGl~~G~i~~I~G~~GsGKTtla~-~la~~~~~~~~~gg~~~~vlyi~~E~~  167 (343)
T 1v5w_A          110 EFDKLLGGGIESMAITEAFGEFRTGKTQLSH-TLCVTAQLPGAGGYPGGKIIFIDTENT  167 (343)
T ss_dssp             HHHHHTTSSBCSSEEEEEECCTTCTHHHHHH-HHHHHTTSCBTTTBCCCEEEEEESSSC
T ss_pred             hHHHHhcCCCCCCeEEEEECCCCCCHHHHHH-HHHHHHhcccccCCCCCeEEEEECCCC
Confidence            3556663     4567899999999996543 32221111      2556777776654

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=81.43  E-value=4.7  Score=43.99  Aligned_cols=33  Identities=21%  Similarity=0.277  Sum_probs=25.6

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      +-+|+.+|.|+|||+..    +.+....|.+...+.+
T Consensus       239 ~GILL~GPPGTGKT~LA----raiA~elg~~~~~v~~  271 (806)
T 3cf2_A          239 RGILLYGPPGTGKTLIA----RAVANETGAFFFLING  271 (806)
T ss_dssp             CEEEEECCTTSCHHHHH----HHHHTTTTCEEEEEEH
T ss_pred             CeEEEECCCCCCHHHHH----HHHHHHhCCeEEEEEh
Confidence            67999999999999874    4556567777776653

>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=81.17  E-value=1.4  Score=46.71  Aligned_cols=51  Identities=14%  Similarity=0.202  Sum_probs=36.6

Q ss_pred             CCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCC---cEEEEe
Q 042872          224 RAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGI---PATFLN  276 (381)
Q Consensus       224 ~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI---~a~~l~  276 (381)
                      ..++|.|++||..  ....++|.|+.|||||.+-..-+..|....|+   ++.+++
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vT   63 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAIT   63 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEE
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEe
Confidence            4688999999986  35789999999999998776555555433343   344554

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=81.17  E-value=5.7  Score=36.99  Aligned_cols=39  Identities=13%  Similarity=0.097  Sum_probs=28.0

Q ss_pred             cCC-CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          239 AKQ-DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       239 ~Gr-DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      .|+ .+++.++.|.|||-+.+.....+. ..|.++.++.-+
T Consensus         4 ~g~l~I~~~~kgGvGKTt~a~~la~~l~-~~G~~V~v~d~D   43 (228)
T 2r8r_A            4 RGRLKVFLGAAPGVGKTYAMLQAAHAQL-RQGVRVMAGVVE   43 (228)
T ss_dssp             CCCEEEEEESSTTSSHHHHHHHHHHHHH-HTTCCEEEEECC
T ss_pred             CceEEEEEECCCCCcHHHHHHHHHHHHH-HCCCCEEEEEeC
Confidence            344 689999999999988765555555 468887666543

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=81.08  E-value=3.2  Score=38.95  Aligned_cols=18  Identities=17%  Similarity=0.008  Sum_probs=14.8

Q ss_pred             CCCEEEECCCCCCchhhH
Q 042872          240 KQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF  257 (381)
                      |+=+++.+|+|+|||...
T Consensus        98 g~i~~i~G~~gsGKT~la  115 (322)
T 2i1q_A           98 QSVTEFAGVFGSGKTQIM  115 (322)
T ss_dssp             TEEEEEEESTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            466899999999999554

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=80.91  E-value=1.5  Score=41.88  Aligned_cols=28  Identities=29%  Similarity=0.529  Sum_probs=25.5

Q ss_pred             hcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          267 KFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       267 ~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      ..|+.+..++|+++..++..+++.+++|
T Consensus        50 ~~g~~~~~lhg~l~~~~r~~~~~~f~~g   77 (300)
T 3i32_A           50 RLGHPAQALHGDMSQGERERVMGAFRQG   77 (300)
T ss_dssp             TTTCCEEEECSCCCTHHHHHHHHHHHHT
T ss_pred             hCCCCEEEEeCCCCHHHHHHHHHHhhcC
Confidence            5689999999999999999999998876

>2bzb_A Conserved domain protein; transferase, phosphatase, phosphorylation, sporulation, antithetical, negative, regulator, spine; NMR {Bacillus anthracis} SCOP: a.30.7.1

Probab=80.87  E-value=1.8  Score=32.81  Aligned_cols=46  Identities=26%  Similarity=0.395  Sum_probs=38.0

Q ss_pred             hhhHHHHHHHHHHHhhCCChHHHHHH---HHHHHhhhcCCCCceeEeee
Q 042872            5 DFEFEKARLLSLALEFGFDQDSANKS---LNRLISLYGDDGQDFISVEH   50 (381)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~   50 (381)
                      ..|..|..|+.||.++||.-..+-+|   ||+||..|=.=-.+-.++||
T Consensus         9 ~IE~kR~eL~~l~~k~Gl~~~~vI~~SQeLD~LIn~Y~k~~~~~~~~~~   57 (62)
T 2bzb_A            9 KIENKKKELIQLVARHGLDHDKVLLFSRDLDKLINKFMNVKDKVHKLEH   57 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHTCCCCCCCCSS
T ss_pred             HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHhcccchhhh
Confidence            46778889999999999998887766   99999999776666666665

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=80.86  E-value=0.87  Score=39.72  Aligned_cols=28  Identities=18%  Similarity=0.364  Sum_probs=17.4

Q ss_pred             hcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          267 KFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       267 ~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      ..|+++..+.|+++..++..+++.+++|
T Consensus        68 ~~g~~~~~lhg~~~~~~r~~~~~~f~~g   95 (185)
T 2jgn_A           68 HEGYACTSIHGDRSQRDREEALHQFRSG   95 (185)
T ss_dssp             HTTCCEEEEC--------CHHHHHHHHT
T ss_pred             HcCCceEEEeCCCCHHHHHHHHHHHHcC
Confidence            5689999999999999999999998866

>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=80.46  E-value=2.8  Score=39.13  Aligned_cols=16  Identities=25%  Similarity=0.372  Sum_probs=14.1

Q ss_pred             CEEEECCCCCCchhhH
Q 042872          242 DCFVLLPTGGGKSLCY  257 (381)
Q Consensus       242 DvLviaPTGsGKTLaF  257 (381)
                      .+++.+|.|+|||...
T Consensus        38 ~~ll~Gp~G~GKTtl~   53 (354)
T 1sxj_E           38 HLLLYGPNGTGKKTRC   53 (354)
T ss_dssp             CEEEECSTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4999999999999765

>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=80.24  E-value=7.2  Score=36.73  Aligned_cols=38  Identities=13%  Similarity=0.174  Sum_probs=22.0

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      |+=+.+++++|+|||-....-...+. ..|-++.++..+
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~~~-~~~~~v~l~~~d  135 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALYYK-GKGRRPLLVAAD  135 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHHH-HTTCCEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH-HcCCeEEEecCC
Confidence            44566779999999966542222222 335555555444

---

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	381
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	7e-06
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	2e-04
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	7e-04

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 44.2 bits (103), Expect = 7e-06
 Identities = 20/42 (47%), Positives = 27/42 (64%)

Query: 220 IFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQI 261
            FG + FRP Q +     ++ +DC V++PTGGGKSLCYQ   
Sbjct: 20  TFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPA 61

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 39.9 bits (92), Expect = 2e-04
 Identities = 21/135 (15%), Positives = 43/135 (31%), Gaps = 4/135 (2%)

Query: 214 EFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPAT 273
           EF           R +Q    K  + K+      PTG GK+       + L LK      
Sbjct: 32  EFVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGKRCYV 91

Query: 274 FLNSQQTVSQAAAVLQELRQGL----VLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPE 329
              +   V QAA  +++  +           Y+  ++         ++  + K++  T +
Sbjct: 92  IFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQ 151

Query: 330 RIVGNQSFSEVLKCL 344
            +  +         +
Sbjct: 152 FLSKHYRELGHFDFI 166

>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 = 38.0 bits (87), Expect = 7e-04
 Identities = 14/93 (15%), Positives = 37/93 (39%), Gaps = 1/93 (1%)

Query: 202 LSFEEL-QALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQ 260
           +  EEL +++       +   G     P Q +A +   + ++  + +PT  GK+L  +  
Sbjct: 1   MKVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMA 60

Query: 261 IITLNLKFGIPATFLNSQQTVSQAAAVLQELRQ 293
           ++   +K G     +  +    +     ++  +
Sbjct: 61  MVREAIKGGKSLYVVPLRALAGEKYESFKKWEK 93

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	381
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.88
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.86
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.85
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.84
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.84
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.84
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.81
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.8
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.8
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.8
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.69
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.54
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.51
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.11
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.07
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.01
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	98.98
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.87
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	98.82
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.47
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.3
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.16
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.08
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	97.93
d1okkd2	207	GTPase domain of the signal recognition particle r	97.13
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.03
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.95
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.73
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	96.02
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.01
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	94.71
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	94.61
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	93.92
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	93.58
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.27
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	92.48
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	92.33
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	92.12
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	92.06
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	91.89
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	91.71
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	91.31
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	91.06
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	90.89
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	90.83
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	90.33
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	90.3
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	90.13
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	89.9
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	89.36
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	89.34
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	89.3
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	88.94
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	88.72
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	88.21
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	87.95
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	87.89
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	87.76
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	87.69
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	87.34
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	87.2
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	87.13
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	86.73
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	86.71
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	86.5
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	86.46
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	86.35
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	85.9
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	85.83
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	85.31
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	84.88
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	83.95
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	83.57
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	83.54
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	81.82
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	81.45
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	80.69
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	80.48

>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=99.88  E-value=6.9e-23  Score=187.92  Aligned_cols=127  Identities=19%  Similarity=0.275  Sum_probs=101.1

Q ss_pred             CCCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------
Q 042872          200 GTLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------  258 (381)
Q Consensus       200 ~~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------  258 (381)
                      ...+|+.|..-+++..++.+ .||+.|+|+|.+|||.+++|+|+++.+|||||||+||+                     
T Consensus        15 ~~~sF~~l~L~~~l~~~L~~-~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~P   93 (222)
T d2j0sa1          15 VTPTFDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAP   93 (222)
T ss_dssp             CCCSGGGGCCCHHHHHHHHH-HTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECS
T ss_pred             CCCCHHHCCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccccCceeEEecc
Confidence            34568888777777777755 89999999999999999999999999999999999998                     


Q ss_pred             ---------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECcc
Q 042872          259 ---------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPE  329 (381)
Q Consensus       259 ---------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPE  329 (381)
                               +.+..+....++++..+.|+.....+...++.                             +++|||+||+
T Consensus        94 treLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~-----------------------------~~~Ilv~TPg  144 (222)
T d2j0sa1          94 TRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-----------------------------GQHVVAGTPG  144 (222)
T ss_dssp             SHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHH-----------------------------CCSEEEECHH
T ss_pred             hHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhcc-----------------------------CCeEEeCCCC
Confidence                     33455555567888888888887765544433                             5799999999


Q ss_pred             ccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          330 RIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       330 rL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      ||..          +...+.+.++               ++.+|||||||++
T Consensus       145 rl~~----------~~~~~~~~~~---------------~l~~lVlDEaD~l  171 (222)
T d2j0sa1         145 RVFD----------MIRRRSLRTR---------------AIKMLVLDEADEM  171 (222)
T ss_dssp             HHHH----------HHHTTSSCCT---------------TCCEEEEETHHHH
T ss_pred             cHHh----------cccccccccc---------------cceeeeecchhHh
Confidence            9962          3345556666               9999999999963

>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=99.86  E-value=4e-22  Score=178.55  Aligned_cols=124  Identities=20%  Similarity=0.316  Sum_probs=93.7

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH------------------------
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ------------------------  258 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~------------------------  258 (381)
                      +|+.|..-+++..++.+ .||..|||+|.+|||.++.|+|+++.+|||+|||++|+                        
T Consensus         2 sF~~l~L~~~l~~~L~~-~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~   80 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFE-AGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRE   80 (206)
T ss_dssp             CGGGGCCCHHHHHHHHH-TTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             ChHHcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccccccccceeeccchh
Confidence            45666666666666655 79999999999999999999999999999999999997                        


Q ss_pred             ------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccc
Q 042872          259 ------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIV  332 (381)
Q Consensus       259 ------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~  332 (381)
                            .....+....++++..+.|+.....+...+                             ...++|||+||++|.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l-----------------------------~~~~~Ili~TP~~l~  131 (206)
T d1s2ma1          81 LALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRL-----------------------------NETVHILVGTPGRVL  131 (206)
T ss_dssp             HHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHT-----------------------------TSCCSEEEECHHHHH
T ss_pred             hhhhhhhhhhhcccccCeeEEeecCccchhhHHHHh-----------------------------cccceEEEECCcccc
Confidence                  222333444577777777777665443322                             126899999999996


Q ss_pred             cCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          333 GNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       333 ~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      .          +.+.+.++|+               ++.+|||||||.+
T Consensus       132 ~----------~l~~~~~~l~---------------~l~~lV~DEaD~l  155 (206)
T d1s2ma1         132 D----------LASRKVADLS---------------DCSLFIMDEADKM  155 (206)
T ss_dssp             H----------HHHTTCSCCT---------------TCCEEEEESHHHH
T ss_pred             c----------ccccceeecc---------------cceEEEeechhhh
Confidence            2          2345566666               9999999999963

>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=99.85  E-value=8.7e-22  Score=177.34  Aligned_cols=149  Identities=21%  Similarity=0.193  Sum_probs=86.6

Q ss_pred             CHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHH-HHHHH-hhcCCcEEEEeCCCC
Q 042872          203 SFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQ-IITLN-LKFGIPATFLNSQQT  280 (381)
Q Consensus       203 ~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQ-v~~L~-~~~gI~a~~l~g~~~  280 (381)
                      +|+.+..-+++..++.+ +||+.|||+|.+|||.+++|+|+++.+|||+|||+||+-. +.++. ...+..++++...  
T Consensus         4 ~F~~l~L~~~l~~~l~~-~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt--   80 (206)
T d1veca_           4 EFEDYCLKRELLMGIFE-MGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPT--   80 (206)
T ss_dssp             SGGGSCCCHHHHHHHHT-TTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSC--
T ss_pred             ChhccCcCHHHHHHHHH-CCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccccCcceEEEeec--
Confidence            45556555555555544 8999999999999999999999999999999999999811 11111 1223445444432  


Q ss_pred             HHHHHHHHHHHHhchhhhhhhhhhhhhh-h---hhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccc
Q 042872          281 VSQAAAVLQELRQGLVLSQHYFLHQLIF-V---LTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLT  356 (381)
Q Consensus       281 ~~e~~~il~~lr~g~~~~~~~~~~~~~~-~---~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~  356 (381)
                      .+...++.+.+++-  ........-... +   ...........++|||+||+||..          +...+.++++   
T Consensus        81 ~el~~q~~~~~~~~--~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~----------~~~~~~~~~~---  145 (206)
T d1veca_          81 RELALQVSQICIQV--SKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILD----------LIKKGVAKVD---  145 (206)
T ss_dssp             HHHHHHHHHHHHHH--TTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHH----------HHHTTCSCCT---
T ss_pred             chhhHHHHHHHHHH--hhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccc----------cccchhcccc---
Confidence            22211121111100  000000000000 0   000001113368999999999962          2345556666   


Q ss_pred             cccccccccccCCccEEEEeccccC
Q 042872          357 TDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       357 ~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                  ++.+|||||||.+
T Consensus       146 ------------~l~~lVlDEaD~l  158 (206)
T d1veca_         146 ------------HVQMIVLDEADKL  158 (206)
T ss_dssp             ------------TCCEEEEETHHHH
T ss_pred             ------------ccceEEEeccccc
Confidence                        9999999999963

>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=99.84  E-value=3e-21  Score=173.93  Aligned_cols=123  Identities=20%  Similarity=0.290  Sum_probs=85.2

Q ss_pred             HHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-------------------------
Q 042872          204 FEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-------------------------  258 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-------------------------  258 (381)
                      |+.|..-+++..++.+ .||+.|+|+|.+|||.+++|+|+++.+|||+|||+||+                         
T Consensus         3 F~dl~L~~~l~~~l~~-~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~PtreL   81 (207)
T d1t6na_           3 FRDFLLKPELLRAIVD-CGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTREL   81 (207)
T ss_dssp             STTSCCCHHHHHHHHH-TTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHH
T ss_pred             ccccCcCHHHHHHHHH-CCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccchh
Confidence            3344444444444444 79999999999999999999999999999999999998                         


Q ss_pred             -HH----HHHHHhhc-CCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccc
Q 042872          259 -DQ----IITLNLKF-GIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIV  332 (381)
Q Consensus       259 -dQ----v~~L~~~~-gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~  332 (381)
                       .|    +..+.... .++...+.|+.+...+...+..                            ..++|||+||+++.
T Consensus        82 ~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~----------------------------~~~~ilI~TP~rl~  133 (207)
T d1t6na_          82 AFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKK----------------------------NCPHIVVGTPGRIL  133 (207)
T ss_dssp             HHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHH----------------------------SCCSEEEECHHHHH
T ss_pred             hHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHh----------------------------cCCCEEEeCcchhh
Confidence             22    22222111 2345555565554443222211                            15899999999996


Q ss_pred             cCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEecccc
Q 042872          333 GNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       333 ~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                      .          +.+.+.++++               ++.+|||||||.
T Consensus       134 ~----------~~~~~~~~l~---------------~l~~lVlDEaD~  156 (207)
T d1t6na_         134 A----------LARNKSLNLK---------------HIKHFILDECDK  156 (207)
T ss_dssp             H----------HHHTTSSCCT---------------TCCEEEEESHHH
T ss_pred             h----------hccCCceecc---------------ccceeehhhhhh
Confidence            2          2345566666               999999999995

>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=99.84  E-value=2.3e-21  Score=174.34  Aligned_cols=124  Identities=21%  Similarity=0.302  Sum_probs=93.2

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCC-CEEEECCCCCCchhhHH----------------------
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQ-DCFVLLPTGGGKSLCYQ----------------------  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~Gr-DvLviaPTGsGKTLaF~----------------------  258 (381)
                      ++|+.|+.-+++..++.+ +||.+|+|+|.++||.++.|+ |+++.+|||+|||++|.                      
T Consensus         4 msf~~l~l~~~l~~~l~~-~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~~~~~~lil~pt~   82 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRN-KGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTR   82 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHH-HTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCH
T ss_pred             cCHHHcCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccccCcceEEEeecc
Confidence            567777766667777655 899999999999999999985 99999999999999997                      


Q ss_pred             -------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECcccc
Q 042872          259 -------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERI  331 (381)
Q Consensus       259 -------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL  331 (381)
                             +.+..+....++++..+.|+.+..++..   .++                           +++|||+|||+|
T Consensus        83 ~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~---~l~---------------------------~~~IlV~TP~~l  132 (208)
T d1hv8a1          83 ELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIK---ALK---------------------------NANIVVGTPGRI  132 (208)
T ss_dssp             HHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHH---HHH---------------------------TCSEEEECHHHH
T ss_pred             ccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHH---hcC---------------------------CCCEEEEChHHH
Confidence                   2234444344566666666665554322   222                           479999999998


Q ss_pred             ccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          332 VGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       332 ~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      ..          +.+++.++++               ++.+|||||||++
T Consensus       133 ~~----------~l~~~~~~~~---------------~l~~lViDEad~l  157 (208)
T d1hv8a1         133 LD----------HINRGTLNLK---------------NVKYFILDEADEM  157 (208)
T ss_dssp             HH----------HHHTTCSCTT---------------SCCEEEEETHHHH
T ss_pred             HH----------HHHcCCCCcc---------------cCcEEEEEChHHh
Confidence            62          3345666666               9999999999963

>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=99.84  E-value=2e-21  Score=176.10  Aligned_cols=152  Identities=14%  Similarity=0.187  Sum_probs=93.1

Q ss_pred             CCCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-HHHHHHH-hhcCCcEEEEeCC
Q 042872          201 TLSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-DQIITLN-LKFGIPATFLNSQ  278 (381)
Q Consensus       201 ~~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-dQv~~L~-~~~gI~a~~l~g~  278 (381)
                      -.+|+.|+.-+++..++.+ +||++|+|+|.+|||.++.|+|+++.+|||+|||++|+ .-+.++. ...+..++++...
T Consensus         9 ~~sF~~l~l~~~l~~~L~~-~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~pt   87 (212)
T d1qdea_           9 VYKFDDMELDENLLRGVFG-YGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPT   87 (212)
T ss_dssp             CCCGGGGTCCHHHHHHHHH-HTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSS
T ss_pred             ccChhhCCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEEEccc
Confidence            4568888777777777765 89999999999999999999999999999999999998 2222222 1234556665542


Q ss_pred             CCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhh-cccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcccccccc
Q 042872          279 QTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTC-ASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTT  357 (381)
Q Consensus       279 ~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~-~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~  357 (381)
                        .+...+....+... ................. .......+++|||+||+++..          +...+.++|+    
T Consensus        88 --~el~~q~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvI~TP~~l~~----------~~~~~~~~l~----  150 (212)
T d1qdea_          88 --RELALQIQKVVMAL-AFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFD----------NIQRRRFRTD----  150 (212)
T ss_dssp             --HHHHHHHHHHHHHH-TTTSCCCEEEECC----------CTTCSEEEECHHHHHH----------HHHTTSSCCT----
T ss_pred             --HHHhhhhhhhhccc-ccccccceeeEeeccchhHHHHHhcCCcEEEECCCcccc----------ccccCceecC----
Confidence              22222222222100 00000000000000000 011222367999999999862          3456667777    


Q ss_pred             ccccccccccCCccEEEEeccccC
Q 042872          358 DVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       358 ~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                 ++++|||||||++
T Consensus       151 -----------~l~~lVlDEad~l  163 (212)
T d1qdea_         151 -----------KIKMFILDEADEM  163 (212)
T ss_dssp             -----------TCCEEEEETHHHH
T ss_pred             -----------cceEEeehhhhhh
Confidence                       9999999999974

>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=99.81  E-value=2e-20  Score=172.23  Aligned_cols=56  Identities=21%  Similarity=0.302  Sum_probs=47.5

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      .+|+.+...+++..++.+ .||+.|+|+|.+|||.+++|+|+++.+|||+|||+||+
T Consensus        21 ~~F~~l~l~~~l~~~L~~-~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayl   76 (238)
T d1wrba1          21 ENFDELKLDPTIRNNILL-ASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFL   76 (238)
T ss_dssp             CSSGGGSCCCSTTTTTTT-TTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH
T ss_pred             CCHHHCCCCHHHHHHHHH-CCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeH
Confidence            356666655555555543 89999999999999999999999999999999999998

>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=99.80  E-value=2.8e-21  Score=171.55  Aligned_cols=54  Identities=15%  Similarity=0.063  Sum_probs=45.1

Q ss_pred             HHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH
Q 042872          204 FEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       204 fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~  258 (381)
                      |+.+..-+++..++.+ +||++|+|+|.+|||.+++|+|+++++|||+|||+||+
T Consensus         3 F~~l~L~~~l~~~l~~-~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayl   56 (209)
T d1q0ua_           3 FTRFPFQPFIIEAIKT-LRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYL   56 (209)
T ss_dssp             GGGSCCCHHHHHHHHH-TTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHH
T ss_pred             cccCCcCHHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeee
Confidence            4444444445555544 89999999999999999999999999999999999997

>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=99.80  E-value=2.9e-20  Score=169.24  Aligned_cols=149  Identities=14%  Similarity=0.137  Sum_probs=93.9

Q ss_pred             CCHHHHhhchHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH-HHHHHHH-hhcCCcEEEEeCCC
Q 042872          202 LSFEELQALDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ-DQIITLN-LKFGIPATFLNSQQ  279 (381)
Q Consensus       202 ~~fe~L~~l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~-dQv~~L~-~~~gI~a~~l~g~~  279 (381)
                      .+|+.+..-+.+..++.+ +||+.|+|+|.+|||.++.|+|+++.+|||+|||++|+ .-+..+. ...+.+++++... 
T Consensus        12 ~sF~~l~L~~~l~~~L~~-~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil~Pt-   89 (218)
T d2g9na1          12 DSFDDMNLSESLLRGIYA-YGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPT-   89 (218)
T ss_dssp             CCGGGSCCCHHHHHHHHH-HTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSS-
T ss_pred             CCHHHCCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCccEEEEccc-
Confidence            467777766667777754 89999999999999999999999999999999999998 2222222 1235667777653 


Q ss_pred             CHHHHHHHHHHHHhchhhhhhhhhhhhh-hh-hh---hcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccc
Q 042872          280 TVSQAAAVLQELRQGLVLSQHYFLHQLI-FV-LT---CASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKV  354 (381)
Q Consensus       280 ~~~e~~~il~~lr~g~~~~~~~~~~~~~-~~-~~---~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~  354 (381)
                       .+-..++.+.+++.   .......... .. ..   .........++|||+||+++..          +..++.+.++ 
T Consensus        90 -~eL~~Q~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~----------~l~~~~~~~~-  154 (218)
T d2g9na1          90 -RELAQQIQKVVMAL---GDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFD----------MLNRRYLSPK-  154 (218)
T ss_dssp             -HHHHHHHHHHHHHH---HTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHH----------HHHTTSSCST-
T ss_pred             -chhhhhHHHHHhhh---ccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHH----------HHhcCCcccc-
Confidence             33333333332210   0000000000 00 00   0112223468999999999962          2234545555 


Q ss_pred             cccccccccccccCCccEEEEeccccC
Q 042872          355 LTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       355 ~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                    ++.+|||||||.+
T Consensus       155 --------------~l~~lVlDEaD~l  167 (218)
T d2g9na1         155 --------------YIKMFVLDEADEM  167 (218)
T ss_dssp             --------------TCCEEEEESHHHH
T ss_pred             --------------cceEEEeeecchh
Confidence                          8999999999963

>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=2.3e-20  Score=164.97  Aligned_cols=118  Identities=41%  Similarity=0.671  Sum_probs=85.8

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------HHHHHHHhhcCCc
Q 042872          213 MEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------DQIITLNLKFGIP  271 (381)
Q Consensus       213 l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------dQv~~L~~~~gI~  271 (381)
                      ....++..|||+.|||+|.+||+++++|+|+++++|||+|||+||+                     ++...+. .++..
T Consensus        13 ~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~~~~~~~v~P~~~L~~q~~~~l~-~~~~~   91 (206)
T d1oywa2          13 AKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLISLMKDQVDQLQ-ANGVA   91 (206)
T ss_dssp             HHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHSSSEEEEECSCHHHHHHHHHHHH-HTTCC
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhccCceEEeccchhhhhhHHHHHH-hhccc
Confidence            4556667899999999999999999999999999999999999997                     3444554 45666


Q ss_pred             EEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCcc
Q 042872          272 ATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIR  351 (381)
Q Consensus       272 a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~  351 (381)
                      ......................+                         ..++++.||+++... ....    ....    
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~-------------------------~~~i~~~t~~~~~~~-~~~~----~~~~----  137 (206)
T d1oywa2          92 AACLNSTQTREQQLEVMTGCRTG-------------------------QIRLLYIAPERLMLD-NFLE----HLAH----  137 (206)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHT-------------------------CCSEEEECHHHHTST-THHH----HHTT----
T ss_pred             ccccccccccccchhHHHHHhcC-------------------------CceEEEEechhhhch-hhcc----cchh----
Confidence            66665555555444444443322                         578999999998742 2211    1111    


Q ss_pred             ccccccccccccccccCCccEEEEeccccC
Q 042872          352 LKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       352 l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                                      ..+.++|||||||+
T Consensus       138 ----------------~~v~~lviDEaH~~  151 (206)
T d1oywa2         138 ----------------WNPVLLAVDEAHCI  151 (206)
T ss_dssp             ----------------SCEEEEEESSGGGG
T ss_pred             ----------------heeeeeeeeeeeee
Confidence                            17999999999985

>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=99.69  E-value=9.5e-18  Score=151.50  Aligned_cols=66  Identities=18%  Similarity=0.044  Sum_probs=49.4

Q ss_pred             chHHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          210 LDDMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       210 l~~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      ++++...+++  ++.+|+++|+++|+.++.|+|++++||||+|||++|+-.+..+. ..|-+++++...
T Consensus        30 ~~~~~~~~~~--~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~-~~~~rvliv~Pt   95 (237)
T d1gkub1          30 LKEFVEFFRK--CVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLA-LKGKRCYVIFPT   95 (237)
T ss_dssp             HHHHHHHHHT--TTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHH-TTSCCEEEEESC
T ss_pred             HHHHHHHHHh--ccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHH-HhcCeEEEEecc
Confidence            3444444444  66689999999999999999999999999999999873333333 346677777653

>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=99.54  E-value=9.6e-15  Score=126.82  Aligned_cols=53  Identities=25%  Similarity=0.270  Sum_probs=38.6

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      +||++|.+++..++ ++++|+++|||+|||++|+--+.......+-+++++...
T Consensus         9 ~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P~   61 (200)
T d1wp9a1           9 QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPT   61 (200)
T ss_dssp             CCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSS
T ss_pred             CCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcCc
Confidence            79999999999875 568999999999999988622222222345566666543

>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=99.51  E-value=2e-15  Score=132.98  Aligned_cols=131  Identities=17%  Similarity=0.175  Sum_probs=76.9

Q ss_pred             HHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHH-HHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhh
Q 042872          219 VIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQD-QIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVL  297 (381)
Q Consensus       219 ~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~d-Qv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~  297 (381)
                      +..||.+++|+|.+||+.+++|+|+++++|||+|||.+|+- -+..+.  .+-+++++....  .-..+..+.+++  +.
T Consensus        19 ~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~--~~~~vl~l~P~~--~L~~q~~~~~~~--~~   92 (202)
T d2p6ra3          19 KEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAI--KGGKSLYVVPLR--ALAGEKYESFKK--WE   92 (202)
T ss_dssp             HCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHH--TTCCEEEEESSH--HHHHHHHHHHTT--TT
T ss_pred             HHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhh--ccCcceeecccH--HHHHHHHHHHHH--Hh
Confidence            34899999999999999999999999999999999999852 233333  345777776542  222233333331  00


Q ss_pred             hhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEec
Q 042872          298 SQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDE  377 (381)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDE  377 (381)
                      ......... .............+.++++||..+..          +...+...+.               .+.+||+||
T Consensus        93 ~~~~~v~~~-~~~~~~~~~~~~~~~ii~~~~~~~~~----------~~~~~~~~~~---------------~~~~ii~DE  146 (202)
T d2p6ra3          93 KIGLRIGIS-TGDYESRDEHLGDCDIIVTTSEKADS----------LIRNRASWIK---------------AVSCLVVDE  146 (202)
T ss_dssp             TTTCCEEEE-CSSCBCCSSCSTTCSEEEEEHHHHHH----------HHHTTCSGGG---------------GCCEEEETT
T ss_pred             hccccceee-ccCcccccccccccceeeeccHHHHH----------HHhccchhhh---------------hhhhccccH
Confidence            000000000 00001122333467899999998861          1122222233               789999999


Q ss_pred             cccC
Q 042872          378 AHCV  381 (381)
Q Consensus       378 AHcI  381 (381)
                      ||++
T Consensus       147 ~h~~  150 (202)
T d2p6ra3         147 IHLL  150 (202)
T ss_dssp             GGGG
T ss_pred             HHHh
Confidence            9974

>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=99.11  E-value=5.5e-11  Score=105.45  Aligned_cols=50  Identities=22%  Similarity=0.363  Sum_probs=41.0

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      .+||+|.+|+..+++++..++.+|||+|||++.+.-+    ..++-+++++...
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~----~~~~~~~Liv~p~  119 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAI----NELSTPTLIVVPT  119 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHH----HHSCSCEEEEESS
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHH----HHhcCceeEEEcc
Confidence            5899999999999999999999999999999875322    2456788877753

>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=99.07  E-value=9.8e-11  Score=106.23  Aligned_cols=107  Identities=21%  Similarity=0.183  Sum_probs=59.6

Q ss_pred             HHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccC
Q 042872          237 SVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRK  316 (381)
Q Consensus       237 iL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~  316 (381)
                      +.+|+++|+.||||+|||++|+..+.......|.+++++..  ...-..++.+.++.-.+        ..  ........
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~lvi~P--tr~La~q~~~~l~~~~~--------~~--~~~~~~~~   73 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAP--TRVVAAEMEEALRGLPI--------RY--QTPAIRAE   73 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHHTCCEEEEES--SHHHHHHHHHHTTTSCC--------BC--CC------
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhcCCEEEEEcc--HHHHHHHHHHHHhcCCc--------ce--eeeEEeec
Confidence            34789999999999999999973332222235778888865  33333333333321000        00  00001122


Q ss_pred             CCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          317 DKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       317 ~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      ..+...++++||+.|..         .+  .....+               .++++|||||||++
T Consensus        74 ~~~~~~i~~~t~~~l~~---------~~--~~~~~~---------------~~~~~vViDE~H~~  112 (305)
T d2bmfa2          74 HTGREIVDLMCHATFTM---------RL--LSPIRV---------------PNYNLIIMDEAHFT  112 (305)
T ss_dssp             --CCCSEEEEEHHHHHH---------HH--TSSSCC---------------CCCSEEEEESTTCC
T ss_pred             ccCccccccCCcHHHHH---------HH--hcCccc---------------cceeEEEeeeeeec
Confidence            23456789999987741         11  111122               28999999999985

>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=99.01  E-value=5.5e-10  Score=104.32  Aligned_cols=54  Identities=15%  Similarity=0.051  Sum_probs=42.7

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      .+|++|.+|+..++.++..++++|||+|||++..--+..+....+-+++++...
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~~~~~~~~~k~Liivp~  166 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPT  166 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSS
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHHHhhhcccceEEEEEcC
Confidence            689999999999999999999999999999886533434433455677777654

>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=98.98  E-value=1.6e-09  Score=101.44  Aligned_cols=86  Identities=19%  Similarity=0.153  Sum_probs=70.2

Q ss_pred             HHHHhCCCCCcHHHHHHHHHHHc----C--CCEEEECCCCCCchhhHH-----------------------HH-HHHHHh
Q 042872          217 NVVIFGNRAFRPLQHQACKASVA----K--QDCFVLLPTGGGKSLCYQ-----------------------DQ-IITLNL  266 (381)
Q Consensus       217 ~~~~fG~~~fRpiQ~eAI~aiL~----G--rDvLviaPTGsGKTLaF~-----------------------dQ-v~~L~~  266 (381)
                      +.+.+.| ++|+-|.+||..+..    +  .+.|+.+-||||||.+|+                       .| ...+..
T Consensus        76 f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh~~~~~~  154 (264)
T d1gm5a3          76 FIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVE  154 (264)
T ss_dssp             HHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHH
T ss_pred             HHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhcccceeEEeehHhhhHHHHHHHHH
Confidence            3445777 599999999999863    3  478999999999999987                       33 444444


Q ss_pred             h---cCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECc
Q 042872          267 K---FGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTP  328 (381)
Q Consensus       267 ~---~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTP  328 (381)
                      .   +|+.+.+++|+.+..++..++..++.|                         .++|||+|=
T Consensus       155 ~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g-------------------------~~~iiIGTh  194 (264)
T d1gm5a3         155 SFSKFNIHVALLIGATTPSEKEKIKSGLRNG-------------------------QIDVVIGTH  194 (264)
T ss_dssp             HHTCSSCCEEECCSSSCHHHHHHHHHHHHSS-------------------------CCCEEEECT
T ss_pred             hhhhccccceeeccccchHHHHHHHHHHHCC-------------------------CCCEEEeeh
Confidence            4   489999999999999999999999877                         789999984

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=98.87  E-value=2.6e-09  Score=85.18  Aligned_cols=40  Identities=15%  Similarity=0.176  Sum_probs=29.2

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      .|+++++.||||+|||+++...+.......+.+++++...
T Consensus         6 ~~~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~~p~   45 (140)
T d1yksa1           6 KGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPT   45 (140)
T ss_dssp             TTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESS
T ss_pred             cCCcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeeeecc
Confidence            5899999999999999888644333333567777777653

>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=98.82  E-value=1.2e-08  Score=93.68  Aligned_cols=106  Identities=22%  Similarity=0.264  Sum_probs=81.7

Q ss_pred             HHhCCCCCcHHHHHHHHHHHc----C--CCEEEECCCCCCchhhHH-----------------------HH-HHHHHh--
Q 042872          219 VIFGNRAFRPLQHQACKASVA----K--QDCFVLLPTGGGKSLCYQ-----------------------DQ-IITLNL--  266 (381)
Q Consensus       219 ~~fG~~~fRpiQ~eAI~aiL~----G--rDvLviaPTGsGKTLaF~-----------------------dQ-v~~L~~--  266 (381)
                      ..|.| .+|+-|..|+..+.+    +  .+.|+++.||||||.+|+                       .| ...+.+  
T Consensus        50 ~~lP~-~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~La~Q~~~~~~~~~  128 (233)
T d2eyqa3          50 DSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRF  128 (233)
T ss_dssp             HTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHS
T ss_pred             hcccc-ccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHHHhHHHHHHHHHHHH
Confidence            34666 588999999988863    3  378999999999999998                       34 444543  


Q ss_pred             -hcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHH
Q 042872          267 -KFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLH  345 (381)
Q Consensus       267 -~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~  345 (381)
                       .+++.+..+++..+..++..++..+..|                         ..+|||+|==.+..            
T Consensus       129 ~~~~~~v~~l~~~~~~~~~~~~~~~~~~g-------------------------~~~iviGths~l~~------------  171 (233)
T d2eyqa3         129 ANWPVRIEMISRFRSAKEQTQILAEVAEG-------------------------KIDILIGTHKLLQS------------  171 (233)
T ss_dssp             TTTTCCEEEESTTSCHHHHHHHHHHHHTT-------------------------CCSEEEECTHHHHS------------
T ss_pred             hhCCCEEEeccCcccchhHHHHHHHHhCC-------------------------CCCEEEeehhhhcc------------
Confidence             4678999999999999999999999877                         78999998333321            


Q ss_pred             hcCCccccccccccccccccccCCccEEEEecccc
Q 042872          346 RKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHC  380 (381)
Q Consensus       346 ~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHc  380 (381)
                         .+.+.               +|++|||||=|.
T Consensus       172 ---~~~f~---------------~LgLiIiDEeH~  188 (233)
T d2eyqa3         172 ---DVKFK---------------DLGLLIVDEEHR  188 (233)
T ss_dssp             ---CCCCS---------------SEEEEEEESGGG
T ss_pred             ---CCccc---------------cccceeeechhh
Confidence               11111               899999999995

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=98.47  E-value=4.4e-08  Score=79.84  Aligned_cols=34  Identities=29%  Similarity=0.312  Sum_probs=24.7

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      +..++.+|||+|||+.+.   ..+. ..|-+++++..-
T Consensus         9 ~~~ll~apTGsGKT~~~~---~~~~-~~~~~vli~~P~   42 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVP---AAYA-AQGYKVLVLNPS   42 (136)
T ss_dssp             EEEEEECCTTSCTTTHHH---HHHH-TTTCCEEEEESC
T ss_pred             CEEEEEeCCCCCHHHHHH---HHHH-HcCCcEEEEcCh
Confidence            567999999999998763   2222 567788777653

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=98.30  E-value=1.9e-06  Score=80.74  Aligned_cols=118  Identities=17%  Similarity=0.120  Sum_probs=86.8

Q ss_pred             HHHHHHHHHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHH---------------------------HHHHHH
Q 042872          212 DMEFANVVIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQ---------------------------DQIITL  264 (381)
Q Consensus       212 ~l~~~~~~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~---------------------------dQv~~L  264 (381)
                      -+..+..+.+|.. +.++|.-..-.+..|+  |+.|.||=||||+..                           ++...+
T Consensus        68 lVREAakRtlG~R-hyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al~g~~vhvvTvNdyLA~RDae~m~~i  144 (273)
T d1tf5a3          68 VVREASRRVTGMF-PFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKI  144 (273)
T ss_dssp             HHHHHHHHHHSCC-CCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhceE-EehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhcCCCceEEecCccccchhhhHHhHH
Confidence            3566778889994 6699999999998886  999999999998764                           456666


Q ss_pred             HhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHH
Q 042872          265 NLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCL  344 (381)
Q Consensus       265 ~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L  344 (381)
                      -+.+|+.+.++....+..+++...                               .++|+|+|...+.     ...|+.-
T Consensus       145 y~~lGlsvg~~~~~~~~~~r~~~Y-------------------------------~~di~Ygt~~e~~-----fDyLrd~  188 (273)
T d1tf5a3         145 FEFLGLTVGLNLNSMSKDEKREAY-------------------------------AADITYSTNNELG-----FDYLRDN  188 (273)
T ss_dssp             HHHTTCCEEECCTTSCHHHHHHHH-------------------------------HSSEEEEEHHHHH-----HHHHHHT
T ss_pred             HHHcCCCccccccccCHHHHHHHh-------------------------------hCCceecchhhhh-----hhhcchh
Confidence            667899998888888877765544                               4689999987774     1233321


Q ss_pred             HhcCCccccccccccccccccccCCccEEEEeccccC
Q 042872          345 HRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAHCV  381 (381)
Q Consensus       345 ~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAHcI  381 (381)
                      .   ..+          .....|+.+.+.|||||+.|
T Consensus       189 ~---~~~----------~~~~~~r~~~~aIvDEvDsi  212 (273)
T d1tf5a3         189 M---VLY----------KEQMVQRPLHFAVIDEVDSI  212 (273)
T ss_dssp             T---CSS----------GGGCCCCCCCEEEEETHHHH
T ss_pred             h---hcC----------hhhhccCCCCEEEEEcchhh
Confidence            1   001          22345678999999999854

>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=98.16  E-value=2.8e-06  Score=74.96  Aligned_cols=120  Identities=13%  Similarity=0.087  Sum_probs=71.2

Q ss_pred             CCcHHHHHHHHHHH----cCCCEEEECCCCCCchhhHHHHHHHHHhhcC-CcEEEEeCCCCHHHHHHHHHHHHhchhhhh
Q 042872          225 AFRPLQHQACKASV----AKQDCFVLLPTGGGKSLCYQDQIITLNLKFG-IPATFLNSQQTVSQAAAVLQELRQGLVLSQ  299 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL----~GrDvLviaPTGsGKTLaF~dQv~~L~~~~g-I~a~~l~g~~~~~e~~~il~~lr~g~~~~~  299 (381)
                      +++|+|.+++.-+.    .+..+|+.-++|.|||+..+--+..+..... -++.++....-.......+...-..   ..
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~~~~~~~~~~~~~LIv~p~~l~~~W~~e~~~~~~~---~~   88 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICPLSVLKNWEEELSKFAPH---LR   88 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEECSTTHHHHHHHHHHHCTT---SC
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhhhhhhhcccccccceecchhhhhHHHHHHHhhccc---cc
Confidence            58899999997543    3456888889999999876533444433223 3567777665555554444432110   00


Q ss_pred             hhhhhhhhhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEeccc
Q 042872          300 HYFLHQLIFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDEAH  379 (381)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDEAH  379 (381)
                      ..      .............++|+++|.+.+.....       +.. .                    ...++|+||||
T Consensus        89 ~~------~~~~~~~~~~~~~~~vvi~~~~~~~~~~~-------l~~-~--------------------~~~~vI~DEah  134 (230)
T d1z63a1          89 FA------VFHEDRSKIKLEDYDIILTTYAVLLRDTR-------LKE-V--------------------EWKYIVIDEAQ  134 (230)
T ss_dssp             EE------ECSSSTTSCCGGGSSEEEEEHHHHTTCHH-------HHT-C--------------------CEEEEEEETGG
T ss_pred             ce------eeccccchhhccCcCEEEeeHHHHHhHHH-------Hhc-c--------------------cceEEEEEhhh
Confidence            00      00111222334467899999998864211       111 1                    57789999999


Q ss_pred             cC
Q 042872          380 CV  381 (381)
Q Consensus       380 cI  381 (381)
                      .+
T Consensus       135 ~~  136 (230)
T d1z63a1         135 NI  136 (230)
T ss_dssp             GG
T ss_pred             cc
Confidence            75

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=97.93  E-value=7.4e-06  Score=75.16  Aligned_cols=33  Identities=27%  Similarity=0.353  Sum_probs=25.6

Q ss_pred             CCcHHHHHHHHHHH---------cCCCEEEECCCCCCchhhH
Q 042872          225 AFRPLQHQACKASV---------AKQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL---------~GrDvLviaPTGsGKTLaF  257 (381)
                      .+||+|.++|.-+.         .+.-+|+.-..|.|||+.-
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qa   96 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQC   96 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHH
Confidence            58999999998653         2345788889999999643

>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=97.13  E-value=0.00079  Score=59.82  Aligned_cols=18  Identities=22%  Similarity=0.224  Sum_probs=14.3

Q ss_pred             CCEEEECCCCCCchhhHH
Q 042872          241 QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~  258 (381)
                      +=+++++|||+|||-+-.
T Consensus         7 ~vi~lvGptGvGKTTTia   24 (207)
T d1okkd2           7 RVVLVVGVNGVGKTTTIA   24 (207)
T ss_dssp             SEEEEECSTTSSHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHH
Confidence            346779999999997755

>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=97.03  E-value=0.0011  Score=59.08  Aligned_cols=16  Identities=19%  Similarity=0.204  Sum_probs=13.1

Q ss_pred             EEEECCCCCCchhhHH
Q 042872          243 CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       243 vLviaPTGsGKTLaF~  258 (381)
                      +++++|||+|||-+-.
T Consensus        12 i~lvGptGvGKTTTiA   27 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIG   27 (211)
T ss_dssp             EEEECCTTSCHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            4568999999996655

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=96.95  E-value=0.0011  Score=59.15  Aligned_cols=37  Identities=14%  Similarity=0.103  Sum_probs=21.4

Q ss_pred             EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCC
Q 042872          243 CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQT  280 (381)
Q Consensus       243 vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~  280 (381)
                      +++++|||+|||-+-..-...+. ..|.++.+++.++-
T Consensus        14 i~lvGptGvGKTTTiAKLAa~~~-~~~~kV~lit~Dt~   50 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLAKMFV-DEGKSVVLAAADTF   50 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHH-HTTCCEEEEEECTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH-HCCCceEEEeeccc
Confidence            46789999999977552222232 23445544444443

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=96.73  E-value=0.0041  Score=54.90  Aligned_cols=19  Identities=21%  Similarity=0.364  Sum_probs=14.0

Q ss_pred             CCCE-EEECCCCCCchhhHH
Q 042872          240 KQDC-FVLLPTGGGKSLCYQ  258 (381)
Q Consensus       240 GrDv-LviaPTGsGKTLaF~  258 (381)
                      .+.+ ++++|||+|||-+-.
T Consensus         9 ~~~vi~lvGp~GvGKTTTia   28 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAA   28 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            3555 558999999996544

>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=96.02  E-value=0.011  Score=55.95  Aligned_cols=58  Identities=12%  Similarity=0.036  Sum_probs=40.2

Q ss_pred             HHhCCCCCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHh---hcCCcEEEEe
Q 042872          219 VIFGNRAFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNL---KFGIPATFLN  276 (381)
Q Consensus       219 ~~fG~~~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~---~~gI~a~~l~  276 (381)
                      +.|.-....+.|.+|+..++.++=+++.+|.|+|||.+-..-+..+..   ..+.++.++.
T Consensus       142 ~~~~~~~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~A  202 (359)
T d1w36d1         142 KLFPVSDEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAA  202 (359)
T ss_dssp             TTCCCTTSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEB
T ss_pred             HhccCcccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEec
Confidence            335555566889999999999988899999999999765322333332   2345555554

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=96.01  E-value=0.012  Score=52.17  Aligned_cols=37  Identities=14%  Similarity=0.128  Sum_probs=17.9

Q ss_pred             EEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCC
Q 042872          243 CFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQT  280 (381)
Q Consensus       243 vLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~  280 (381)
                      ++.++|||+|||-+-..-...+. ..|.++.+++.+.-
T Consensus        15 i~lvGptGvGKTTTiAKLA~~~~-~~g~kV~lit~Dt~   51 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAYFYK-KKGFKVGLVGADVY   51 (211)
T ss_dssp             EEEECSCCC----HHHHHHHHHH-HTTCCEEEEECCCS
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH-HCCCceEEEEeecc
Confidence            45689999999966543233333 23445555554443

>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=94.71  E-value=0.035  Score=46.99  Aligned_cols=37  Identities=16%  Similarity=0.145  Sum_probs=23.7

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      ..+++.+|+|+|||.+.---...+....+.+.+.+..
T Consensus        44 ~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~   80 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYING   80 (276)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEET
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecc
Confidence            5799999999999977532233443334555555543

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=94.61  E-value=0.11  Score=45.28  Aligned_cols=51  Identities=20%  Similarity=0.183  Sum_probs=34.8

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQE  290 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~  290 (381)
                      |.=+++.++||+|||..-...+..+....|.++.++....+..+....+-.
T Consensus        35 G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~E~~~~~~~~r~~~   85 (277)
T d1cr2a_          35 GEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIG   85 (277)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEESSSCHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeeeccchhhHHhHHHH
Confidence            555678899999999544333444544578999999888887665444433

>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=93.92  E-value=0.031  Score=48.85  Aligned_cols=51  Identities=25%  Similarity=0.334  Sum_probs=34.7

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCC---cEEEEeC
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGI---PATFLNS  277 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI---~a~~l~g  277 (381)
                      +++|-|.+||..  ....++|.+|.|||||-+.+.-+..+....+.   ++.+++-
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~   54 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTF   54 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEES
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeC
Confidence            367899999975  34569999999999998766444444333333   4555543

>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=93.58  E-value=0.16  Score=48.00  Aligned_cols=33  Identities=24%  Similarity=0.366  Sum_probs=26.4

Q ss_pred             CcHHHHHHHHHHHcCCC--EEEECCCCCCchhhHH
Q 042872          226 FRPLQHQACKASVAKQD--CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       226 fRpiQ~eAI~aiL~GrD--vLviaPTGsGKTLaF~  258 (381)
                      +.+.|.+.+..++....  +|+.+|||||||-+..
T Consensus       142 ~~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl~  176 (401)
T d1p9ra_         142 MTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLY  176 (401)
T ss_dssp             CCHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHH
T ss_pred             ccHHHHHHHHHHHhhhhceEEEEcCCCCCccHHHH
Confidence            34789999998887654  6788999999997655

>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=93.27  E-value=0.029  Score=54.48  Aligned_cols=34  Identities=21%  Similarity=0.213  Sum_probs=27.2

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      ..+++|+++|||+|||+..    ++|.+..++|.+.+.
T Consensus        48 ~ksNILliGPTGvGKTlLA----r~LAk~l~VPFv~~d   81 (443)
T d1g41a_          48 TPKNILMIGPTGVGKTEIA----RRLAKLANAPFIKVE   81 (443)
T ss_dssp             CCCCEEEECCTTSSHHHHH----HHHHHHTTCCEEEEE
T ss_pred             ccccEEEECCCCCCHHHHH----HHHHHHhCCCEEEee
Confidence            3579999999999999886    466666788877764

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=92.48  E-value=0.16  Score=44.19  Aligned_cols=32  Identities=13%  Similarity=0.155  Sum_probs=22.5

Q ss_pred             cHHHHHHHHHHHcC---CCEEEECCCCCCchhhHH
Q 042872          227 RPLQHQACKASVAK---QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       227 RpiQ~eAI~aiL~G---rDvLviaPTGsGKTLaF~  258 (381)
                      |.-..+-+-.+|..   .++++++|.|.|||..-.
T Consensus        27 Rd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~   61 (195)
T d1jbka_          27 RDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVE   61 (195)
T ss_dssp             CHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHH
T ss_pred             cHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHH
Confidence            44445445555542   489999999999997753

>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=92.33  E-value=0.16  Score=43.14  Aligned_cols=35  Identities=11%  Similarity=0.110  Sum_probs=26.0

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQ  279 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~  279 (381)
                      ..+|+.+|+|+|||.+.    ..+...++.....+++..
T Consensus        36 ~~~L~~GPpGtGKT~lA----~~la~~~~~~~~~~~~~~   70 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLA----HIIASELQTNIHVTSGPV   70 (238)
T ss_dssp             CCEEEESSTTSSHHHHH----HHHHHHHTCCEEEEETTT
T ss_pred             CeEEEECCCCCcHHHHH----HHHHhccCCCcccccCcc
Confidence            47999999999999765    345556677777776543

>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=92.12  E-value=0.073  Score=45.62  Aligned_cols=34  Identities=15%  Similarity=0.152  Sum_probs=25.1

Q ss_pred             CCcHHHHHHHHHHH----cCC--C-EEEECCCCCCchhhHH
Q 042872          225 AFRPLQHQACKASV----AKQ--D-CFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL----~Gr--D-vLviaPTGsGKTLaF~  258 (381)
                      .|.|+|..++..+.    .++  . +|+.+|.|+|||....
T Consensus         2 ~~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~   42 (207)
T d1a5ta2           2 RWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIY   42 (207)
T ss_dssp             CCCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHH
T ss_pred             CCCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHH
Confidence            35588877777664    344  3 8999999999997654

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=92.06  E-value=0.08  Score=45.40  Aligned_cols=51  Identities=20%  Similarity=0.404  Sum_probs=36.0

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      .|+.+|+..+|   |--|  +.+...-...|+++..++|+++..++..+++.+++|
T Consensus        30 ~g~r~lvfc~t---~~~~--~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G   80 (174)
T d1c4oa2          30 RGERTLVTVLT---VRMA--EELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLG   80 (174)
T ss_dssp             TTCEEEEECSS---HHHH--HHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTT
T ss_pred             cCCcEEEEEcc---hhHH--HHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCC
Confidence            45555555544   1111  344333336899999999999999999999999987

>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=91.89  E-value=0.1  Score=46.00  Aligned_cols=51  Identities=14%  Similarity=0.187  Sum_probs=35.2

Q ss_pred             CCcHHHHHHHHHHHcCCCEEEECCCCCCchhhHHHHHHHHHhhcCC---cEEEEeC
Q 042872          225 AFRPLQHQACKASVAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGI---PATFLNS  277 (381)
Q Consensus       225 ~fRpiQ~eAI~aiL~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI---~a~~l~g  277 (381)
                      .+++-|.++|..  .+..++|.++.|||||.+.+.-+..|....++   ++.++..
T Consensus        11 ~L~~eQ~~~v~~--~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~   64 (318)
T d1pjra1          11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITF   64 (318)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEES
T ss_pred             hCCHHHHHHHhC--CCCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEec
Confidence            377899999985  34579999999999998876544444433333   3455543

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=91.71  E-value=0.29  Score=44.35  Aligned_cols=31  Identities=13%  Similarity=0.161  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHc---CCCEEEECCCCCCchhhHH
Q 042872          228 PLQHQACKASVA---KQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       228 piQ~eAI~aiL~---GrDvLviaPTGsGKTLaF~  258 (381)
                      .--.+-+-.+|.   ..++++++|.|.|||..-.
T Consensus        24 d~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~   57 (268)
T d1r6bx2          24 EKELERAIQVLCRRRKNNPLLVGESGVGKTAIAE   57 (268)
T ss_dssp             HHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHH
T ss_pred             HHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHH
Confidence            333444444553   2589999999999997753

>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=91.31  E-value=0.46  Score=39.86  Aligned_cols=44  Identities=16%  Similarity=0.073  Sum_probs=30.9

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHH
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQA  284 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~  284 (381)
                      |.=+++.+|+|+|||..-+.-+.... +.+-++..+....+....
T Consensus        26 gsl~li~G~pGsGKT~l~~qia~~~~-~~~~~~~~is~e~~~~~~   69 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRFVENAC-ANKERAILFAYEESRAQL   69 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHH-TTTCCEEEEESSSCHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHH-HhccccceeeccCCHHHH
Confidence            56688999999999976643344433 457778888777666553

>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=91.06  E-value=0.1  Score=47.47  Aligned_cols=34  Identities=21%  Similarity=0.213  Sum_probs=24.5

Q ss_pred             cCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          239 AKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       239 ~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      ..+.+|.++|||+|||...    +.+.+.++.+.+.+.
T Consensus        48 ~~~~iLl~GPpG~GKT~lA----kalA~~~~~~~~~i~   81 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIA----RRLAKLANAPFIKVE   81 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHH----HHHHHHHTCCEEEEE
T ss_pred             CCceEEEECCCCCCHHHHH----HHHhhccccchhccc
Confidence            3589999999999999886    233334566666554

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=90.89  E-value=0.13  Score=43.62  Aligned_cols=15  Identities=20%  Similarity=0.029  Sum_probs=12.2

Q ss_pred             EEECCCCCCchhhHH
Q 042872          244 FVLLPTGGGKSLCYQ  258 (381)
Q Consensus       244 LviaPTGsGKTLaF~  258 (381)
                      ++.+|+|+|||.+-.
T Consensus        50 ~l~GppGtGKT~l~~   64 (287)
T d1w5sa2          50 GSIGRVGIGKTTLAK   64 (287)
T ss_dssp             ECTTCCSSSHHHHHH
T ss_pred             EeECCCCCCHHHHHH
Confidence            456999999998764

>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=90.83  E-value=0.48  Score=40.64  Aligned_cols=34  Identities=21%  Similarity=0.203  Sum_probs=20.5

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      -+++.+|+|+|||---+--...+. ..+..++.+.
T Consensus        38 ~l~l~G~~G~GKTHLl~A~~~~~~-~~~~~~~~~~   71 (213)
T d1l8qa2          38 PIFIYGSVGTGKTHLLQAAGNEAK-KRGYRVIYSS   71 (213)
T ss_dssp             SEEEECSSSSSHHHHHHHHHHHHH-HTTCCEEEEE
T ss_pred             cEEEECCCCCcHHHHHHHHHHHhc-cCccceEEec
Confidence            388999999999944331122233 3455555554

>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=90.33  E-value=0.28  Score=42.19  Aligned_cols=15  Identities=20%  Similarity=0.096  Sum_probs=13.1

Q ss_pred             EEEECCCCCCchhhH
Q 042872          243 CFVLLPTGGGKSLCY  257 (381)
Q Consensus       243 vLviaPTGsGKTLaF  257 (381)
                      +|+.+|.|+|||.+.
T Consensus        37 ~Ll~Gp~G~GKtt~a   51 (239)
T d1njfa_          37 YLFSGTRGVGKTSIA   51 (239)
T ss_dssp             EEEECSTTSSHHHHH
T ss_pred             EEEECCCCCcHHHHH
Confidence            788999999999654

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=90.30  E-value=0.14  Score=43.54  Aligned_cols=36  Identities=19%  Similarity=0.415  Sum_probs=30.1

Q ss_pred             HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          259 DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       259 dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      +.+..+-...|+++..++|+++..++..+++.+++|
T Consensus        45 ~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g   80 (181)
T d1t5la2          45 EDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLG   80 (181)
T ss_dssp             HHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCC
Confidence            334444447899999999999999999999999988

>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=90.13  E-value=0.22  Score=42.19  Aligned_cols=16  Identities=25%  Similarity=0.372  Sum_probs=14.1

Q ss_pred             CEEEECCCCCCchhhH
Q 042872          242 DCFVLLPTGGGKSLCY  257 (381)
Q Consensus       242 DvLviaPTGsGKTLaF  257 (381)
                      .+|+.+|.|+|||...
T Consensus        35 ~lll~Gp~G~GKTt~~   50 (252)
T d1sxje2          35 HLLLYGPNGTGKKTRC   50 (252)
T ss_dssp             CEEEECSTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            5899999999999765

>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=89.90  E-value=0.41  Score=40.82  Aligned_cols=28  Identities=7%  Similarity=-0.168  Sum_probs=21.3

Q ss_pred             HHHHHHHHHc---CCCEEEECCCCCCchhhH
Q 042872          230 QHQACKASVA---KQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       230 Q~eAI~aiL~---GrDvLviaPTGsGKTLaF  257 (381)
                      |.+.+..+..   +..+|..+|.|+|||-..
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a   32 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVS   32 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHH
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHH
Confidence            6677777764   347899999999998554

>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=89.36  E-value=0.22  Score=42.01  Aligned_cols=18  Identities=22%  Similarity=0.241  Sum_probs=15.1

Q ss_pred             CCEEEECCCCCCchhhHH
Q 042872          241 QDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~  258 (381)
                      .++|+.+|+|+|||.+..
T Consensus        46 ~~lll~Gp~G~GKTtla~   63 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTAAL   63 (231)
T ss_dssp             CEEEEESCTTSSHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHH
Confidence            468999999999997653

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.34  E-value=0.21  Score=41.41  Aligned_cols=44  Identities=9%  Similarity=0.095  Sum_probs=33.4

Q ss_pred             CCchhhHH------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          251 GGKSLCYQ------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       251 sGKTLaF~------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      .+|+++|.      +.+..+-...|+++..++|+++..++...++..+.|
T Consensus        27 ~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g   76 (168)
T d1t5ia_          27 FNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDF   76 (168)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             CCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccc
Confidence            34666665      344433336799999999999999999999998866

>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=89.30  E-value=0.36  Score=43.31  Aligned_cols=87  Identities=21%  Similarity=0.285  Sum_probs=52.4

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKP  319 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~  319 (381)
                      |+=+.+.+|+|+|||-.-+.-+... ++.|..++.+.........  .++.+  |.                      + 
T Consensus        54 g~itei~G~~gsGKTtl~l~~~~~~-q~~g~~~vyidtE~~~~~~--~a~~~--Gv----------------------d-  105 (263)
T d1u94a1          54 GRIVEIYGPESSGKTTLTLQVIAAA-QREGKTCAFIDAEHALDPI--YARKL--GV----------------------D-  105 (263)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHH-HHTTCCEEEEESSCCCCHH--HHHHT--TC----------------------C-
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHH-HcCCCEEEEEccccccCHH--HHHHh--CC----------------------C-
Confidence            3567889999999995543222222 3568888888765443321  12221  20                      0 


Q ss_pred             CccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEec
Q 042872          320 SCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDE  377 (381)
Q Consensus       320 ~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDE  377 (381)
                      .-+++|.-|..+.   .+.+.+..|.+.+                    .+.+||||=
T Consensus       106 ~d~v~~~~~~~~E---~~~~~i~~l~~~~--------------------~~~liViDS  140 (263)
T d1u94a1         106 IDNLLCSQPDTGE---QALEICDALARSG--------------------AVDVIVVDS  140 (263)
T ss_dssp             GGGCEEECCSSHH---HHHHHHHHHHHHT--------------------CCSEEEEEC
T ss_pred             HHHEEEecCCCHH---HHHHHHHHHHhcC--------------------CCCEEEEEC
Confidence            1257787776553   4556666666666                    778899984

>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=88.94  E-value=0.11  Score=41.24  Aligned_cols=36  Identities=22%  Similarity=0.207  Sum_probs=27.7

Q ss_pred             HcCCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          238 VAKQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       238 L~GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      |.|+=+++.+|+|+|||-+.    ..|.+.+|++.+.+.+
T Consensus         2 ~~g~iI~l~G~~GsGKSTia----~~La~~lg~~~~~~~~   37 (176)
T d1zp6a1           2 LGGNILLLSGHPGSGKSTIA----EALANLPGVPKVHFHS   37 (176)
T ss_dssp             CTTEEEEEEECTTSCHHHHH----HHHHTCSSSCEEEECT
T ss_pred             CCCeEEEEECCCCCCHHHHH----HHHHHHhCCCEEEecH
Confidence            35677889999999999753    5566677888887765

>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=88.72  E-value=0.58  Score=39.10  Aligned_cols=16  Identities=25%  Similarity=0.372  Sum_probs=13.8

Q ss_pred             CEEEECCCCCCchhhH
Q 042872          242 DCFVLLPTGGGKSLCY  257 (381)
Q Consensus       242 DvLviaPTGsGKTLaF  257 (381)
                      .+|+.+|+|+|||.+.
T Consensus        37 ~lLl~Gp~G~GKttl~   52 (227)
T d1sxjc2          37 HLLFYGPPGTGKTSTI   52 (227)
T ss_dssp             CEEEECSSSSSHHHHH
T ss_pred             eEEEECCCCCChhHHH
Confidence            5899999999999554

>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=88.21  E-value=0.15  Score=47.14  Aligned_cols=34  Identities=21%  Similarity=0.151  Sum_probs=25.1

Q ss_pred             CCCCcHHHHHHHHHHH-cCCCEEEECCCCCCchhh
Q 042872          223 NRAFRPLQHQACKASV-AKQDCFVLLPTGGGKSLC  256 (381)
Q Consensus       223 ~~~fRpiQ~eAI~aiL-~GrDvLviaPTGsGKTLa  256 (381)
                      +..+.+.+.+.+..++ .++++++++|||||||-.
T Consensus       148 ~~~~~~~~~~~l~~~v~~~~nili~G~tgSGKTT~  182 (323)
T d1g6oa_         148 LLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTY  182 (323)
T ss_dssp             TCSSHHHHHHHHHHHHHHTCCEEEEESTTSSHHHH
T ss_pred             ccccHHHHHHHHHHHHHhCCCEEEEeeccccchHH
Confidence            3344566666666665 568999999999999954

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=87.95  E-value=0.9  Score=42.88  Aligned_cols=31  Identities=16%  Similarity=0.133  Sum_probs=20.8

Q ss_pred             cHHHHHHHHHHHc---CCCEEEECCCCCCchhhH
Q 042872          227 RPLQHQACKASVA---KQDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       227 RpiQ~eAI~aiL~---GrDvLviaPTGsGKTLaF  257 (381)
                      |.--.+-+-.+|.   ..++++++|.|.|||.+-
T Consensus        27 r~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv   60 (387)
T d1qvra2          27 RDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIV   60 (387)
T ss_dssp             CHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHH
T ss_pred             cHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHH
Confidence            4433444444443   247999999999999775

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=87.89  E-value=0.55  Score=42.38  Aligned_cols=87  Identities=21%  Similarity=0.269  Sum_probs=54.2

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhhhhhhhhcccCCCC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQLIFVLTCASRKDKP  319 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~~~~~~~~~~~~~~  319 (381)
                      |+=+.+.+|.|+|||-.-+ |+..-.+..|..++.+.........  .++++  |.                      + 
T Consensus        60 g~i~e~~G~~~~GKT~l~l-~~~~~~q~~g~~~vyIDtE~~~~~e--~a~~~--Gv----------------------D-  111 (269)
T d1mo6a1          60 GRVIEIYGPESSGKTTVAL-HAVANAQAAGGVAAFIDAEHALDPD--YAKKL--GV----------------------D-  111 (269)
T ss_dssp             SSEEEEECSSSSSHHHHHH-HHHHHHHHTTCEEEEEESSCCCCHH--HHHHH--TC----------------------C-
T ss_pred             ceeEEEecCCCcHHHHHHH-HHHHHHhcCCCEEEEEECCccCCHH--HHHHh--CC----------------------C-
Confidence            5667889999999995543 2322233567888888765543211  12332  21                      1 


Q ss_pred             CccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEec
Q 042872          320 SCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDE  377 (381)
Q Consensus       320 ~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDE  377 (381)
                      .-+|+|..|+...   ...+.+..|...+                    .+.+||||=
T Consensus       112 ~d~il~~~~~~~E---~~~~~~~~l~~~~--------------------~~~liIiDS  146 (269)
T d1mo6a1         112 TDSLLVSQPDTGE---QALEIADMLIRSG--------------------ALDIVVIDS  146 (269)
T ss_dssp             GGGCEEECCSSHH---HHHHHHHHHHHTT--------------------CEEEEEEEC
T ss_pred             HHHeEEecCCCHH---HHHHHHHHHHhcC--------------------CCCEEEEec
Confidence            1368888887763   4556677776666                    788899984

>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=87.76  E-value=0.2  Score=42.59  Aligned_cols=34  Identities=15%  Similarity=0.267  Sum_probs=23.9

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCC
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQ  278 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~  278 (381)
                      ..+|+.+|+|+|||.+.    ..+...++.....+++.
T Consensus        36 ~~~Ll~GPpG~GKTtla----~~la~~~~~~~~~~~~~   69 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLA----HVIAHELGVNLRVTSGP   69 (239)
T ss_dssp             CCEEEECCTTSCHHHHH----HHHHHHHTCCEEEEETT
T ss_pred             CeEEEECCCCCCHHHHH----HHHHHHhCCCeEeccCC
Confidence            47999999999999665    23344456666666544

>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=87.69  E-value=0.35  Score=40.72  Aligned_cols=16  Identities=19%  Similarity=0.125  Sum_probs=14.2

Q ss_pred             CEEEECCCCCCchhhH
Q 042872          242 DCFVLLPTGGGKSLCY  257 (381)
Q Consensus       242 DvLviaPTGsGKTLaF  257 (381)
                      .+|+.+|.|+|||.+.
T Consensus        38 ~~ll~Gp~G~GKTt~a   53 (224)
T d1sxjb2          38 HMIISGMPGIGKTTSV   53 (224)
T ss_dssp             CEEEECSTTSSHHHHH
T ss_pred             eEEEECCCCCCchhhH
Confidence            6899999999999765

>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=87.34  E-value=0.2  Score=46.18  Aligned_cols=21  Identities=29%  Similarity=0.319  Sum_probs=17.6

Q ss_pred             HcCCCEEEECCCCCCchhhHH
Q 042872          238 VAKQDCFVLLPTGGGKSLCYQ  258 (381)
Q Consensus       238 L~GrDvLviaPTGsGKTLaF~  258 (381)
                      ...++++++++||+|||.++.
T Consensus        48 ~~~~H~~I~G~tGsGKT~~l~   68 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVLLR   68 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHHHH
T ss_pred             cccceEEEEeCCCCcHHHHHH
Confidence            446899999999999997653

>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=87.13  E-value=0.13  Score=40.34  Aligned_cols=29  Identities=21%  Similarity=0.267  Sum_probs=22.0

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEE
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPAT  273 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~  273 (381)
                      |.+++.+|+|+|||-.    +..|.+.+|.+.+
T Consensus         8 K~I~i~G~~GsGKTTl----a~~La~~~~~~~i   36 (192)
T d1lw7a2           8 KTVAILGGESSGKSVL----VNKLAAVFNTTSA   36 (192)
T ss_dssp             EEEEEECCTTSHHHHH----HHHHHHHTTCEEE
T ss_pred             eEEEEECCCCCCHHHH----HHHHHHHhCCCeE
Confidence            6799999999999954    4566666776544

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=86.73  E-value=0.37  Score=39.03  Aligned_cols=43  Identities=16%  Similarity=0.230  Sum_probs=33.5

Q ss_pred             CchhhHH------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          252 GKSLCYQ------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       252 GKTLaF~------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      +|+++|.      +.+..+-...|+.+..++++.+..++..+++.++.|
T Consensus        29 ~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~   77 (155)
T d1hv8a2          29 FYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQK   77 (155)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTT
T ss_pred             CCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcc
Confidence            5677775      334333336899999999999999999999999876

>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=86.71  E-value=0.61  Score=41.20  Aligned_cols=33  Identities=15%  Similarity=0.173  Sum_probs=25.3

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEe
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLN  276 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~  276 (381)
                      .+-+|+.+|.|+|||...    ..+...+|++.+.+.
T Consensus        41 ~~giLL~Gp~GtGKT~l~----~ala~~~~~~~~~~~   73 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLLA----KAIANECQANFISIK   73 (265)
T ss_dssp             CCEEEEBCCTTSSHHHHH----HHHHHHTTCEEEEEC
T ss_pred             CCeEEEECCCCCcchhHH----HHHHHHhCCcEEEEE
Confidence            367999999999999774    455656788876664

>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=86.50  E-value=0.27  Score=37.56  Aligned_cols=30  Identities=27%  Similarity=0.369  Sum_probs=22.3

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEE
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPAT  273 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~  273 (381)
                      .|.+++++|.|+|||-+.    +.|.+.+|.+.+
T Consensus         2 ~k~I~l~G~~GsGKSTva----k~La~~L~~~~i   31 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIG----RQLAQQLNMEFY   31 (169)
T ss_dssp             CCCEEEECCTTSCHHHHH----HHHHHHTTCEEE
T ss_pred             CCeEEEECCCCCCHHHHH----HHHHHHhCCCeE
Confidence            478999999999999665    345555666653

>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=86.46  E-value=0.8  Score=40.54  Aligned_cols=34  Identities=18%  Similarity=0.289  Sum_probs=26.1

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      .+-+|+.+|+|+|||...    +.+....+++.+.+.+
T Consensus        45 ~~~iLL~GppGtGKT~la----~~iA~~~~~~~~~i~~   78 (256)
T d1lv7a_          45 PKGVLMVGPPGTGKTLLA----KAIAGEAKVPFFTISG   78 (256)
T ss_dssp             CCEEEEECCTTSCHHHHH----HHHHHHHTCCEEEECS
T ss_pred             CCeEEeeCCCCCCccHHH----HHHHHHcCCCEEEEEh
Confidence            367999999999999874    3445567888877765

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.90  E-value=0.38  Score=37.57  Aligned_cols=31  Identities=26%  Similarity=0.411  Sum_probs=21.5

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcE
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPA  272 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a  272 (381)
                      |.+++.+|.|+|||-....-+..|.. .|..+
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~-~~~~v   32 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKS-SGVPV   32 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHH-TTCCC
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHH-CCCEE
Confidence            78999999999999755434555543 34433

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=85.83  E-value=0.48  Score=44.00  Aligned_cols=17  Identities=18%  Similarity=0.073  Sum_probs=13.5

Q ss_pred             CCE-EEECCCCCCchhhH
Q 042872          241 QDC-FVLLPTGGGKSLCY  257 (381)
Q Consensus       241 rDv-LviaPTGsGKTLaF  257 (381)
                      +.+ |+.+|.|+|||+..
T Consensus       123 ~g~~l~~G~pG~GKT~la  140 (321)
T d1w44a_         123 SGMVIVTGKGNSGKTPLV  140 (321)
T ss_dssp             SEEEEEECSSSSCHHHHH
T ss_pred             CceEEEECCCCccHHHHH
Confidence            444 55799999999886

>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=85.31  E-value=0.21  Score=46.87  Aligned_cols=17  Identities=35%  Similarity=0.643  Sum_probs=15.3

Q ss_pred             CCEEEECCCCCCchhhH
Q 042872          241 QDCFVLLPTGGGKSLCY  257 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF  257 (381)
                      .++|.++|||.|||.+.
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            57999999999999775

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=84.88  E-value=0.45  Score=39.13  Aligned_cols=43  Identities=12%  Similarity=0.234  Sum_probs=32.4

Q ss_pred             CchhhHH------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          252 GKSLCYQ------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       252 GKTLaF~------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      .|+++|.      +++...-...|+++..++|+++..++..+++.++.|
T Consensus        28 ~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~   76 (162)
T d1fuka_          28 TQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSG   76 (162)
T ss_dssp             SCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             CcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhc
Confidence            4555554      343333336799999999999999999999998866

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.95  E-value=0.61  Score=38.31  Aligned_cols=43  Identities=14%  Similarity=0.335  Sum_probs=32.0

Q ss_pred             CCchhhHH------HH-HHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          251 GGKSLCYQ------DQ-IITLNLKFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       251 sGKTLaF~------dQ-v~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      .+|+++|.      +. ...|. ..|+.+..++|+.+..++..+++..+.|
T Consensus        32 ~~k~iVF~~~~~~~~~l~~~L~-~~g~~~~~~h~~~~~~~r~~~~~~f~~~   81 (171)
T d1s2ma2          32 INQAIIFCNSTNRVELLAKKIT-DLGYSCYYSHARMKQQERNKVFHEFRQG   81 (171)
T ss_dssp             CSEEEEECSSHHHHHHHHHHHH-HHTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             CCceEEEEeeeehhhHhHHhhh-cccccccccccccchhhhhhhhhhcccC
Confidence            45666665      22 22333 5699999999999999999999998866

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=83.57  E-value=1  Score=40.43  Aligned_cols=94  Identities=21%  Similarity=0.323  Sum_probs=57.0

Q ss_pred             HHHHHHc------CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhchhhhhhhhhhhh
Q 042872          233 ACKASVA------KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQGLVLSQHYFLHQL  306 (381)
Q Consensus       233 AI~aiL~------GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g~~~~~~~~~~~~  306 (381)
                      ++..+|.      |+=+.+.+|.|+|||..-+ |+..-.++.|..++.+....+....  .++.+  |.           
T Consensus        44 ~lD~~Lg~GGip~g~itei~G~~~sGKT~l~l-~~~~~aqk~g~~v~yiDtE~~~~~~--~a~~~--Gv-----------  107 (268)
T d1xp8a1          44 SLDLALGVGGIPRGRITEIYGPESGGKTTLAL-AIVAQAQKAGGTCAFIDAEHALDPV--YARAL--GV-----------  107 (268)
T ss_dssp             HHHHHTSSSSEETTSEEEEEESTTSSHHHHHH-HHHHHHHHTTCCEEEEESSCCCCHH--HHHHT--TC-----------
T ss_pred             HHHHHhcCCCccCceEEEEecCCccchHHHHH-HHHHHHHhCCCEEEEEECCccCCHH--HHHHh--CC-----------
Confidence            5555553      3456778999999995443 3333333568888888765443321  22221  20           


Q ss_pred             hhhhhhcccCCCCCccEEEECccccccCcchHHHHHHHHhcCCccccccccccccccccccCCccEEEEec
Q 042872          307 IFVLTCASRKDKPSCKLLYVTPERIVGNQSFSEVLKCLHRKGSIRLKVLTTDVVVLPHTCQRQLAGFVVDE  377 (381)
Q Consensus       307 ~~~~~~~~~~~~~~~~IL~aTPErL~~~~~f~~~L~~L~~~g~~~l~~~~~~~v~~~~~~~~~L~~lVIDE  377 (381)
                                 + .-+++|+.|....   ...+.+..|...+                    .+.+||||=
T Consensus       108 -----------d-~d~i~~~~~~~~E---~~~~~~~~l~~~~--------------------~~~liIiDS  143 (268)
T d1xp8a1         108 -----------N-TDELLVSQPDNGE---QALEIMELLVRSG--------------------AIDVVVVDS  143 (268)
T ss_dssp             -----------C-GGGCEEECCSSHH---HHHHHHHHHHTTT--------------------CCSEEEEEC
T ss_pred             -----------C-chhEEEEcCCCHH---HHHHHHHHHHhcC--------------------CCcEEEEec
Confidence                       1 1267888887653   3456677676555                    688899984

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=83.54  E-value=0.62  Score=39.80  Aligned_cols=28  Identities=18%  Similarity=0.200  Sum_probs=25.8

Q ss_pred             hcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          267 KFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       267 ~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      ..|+.+..++|+.+..++..+++.+++|
T Consensus        52 ~~~~~~~~~h~~~~~~~r~~~~~~f~~g   79 (200)
T d1oywa3          52 SKGISAAAYHAGLENNVRADVQEKFQRD   79 (200)
T ss_dssp             HTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             cCCceeEEecCCCcHHHHHHHHHHHhcc
Confidence            6799999999999999999999998876

>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=81.82  E-value=0.5  Score=39.88  Aligned_cols=32  Identities=9%  Similarity=0.008  Sum_probs=22.7

Q ss_pred             CEEEECCCCCCchhhHHHHHHHHHhhcCCcEEEEeC
Q 042872          242 DCFVLLPTGGGKSLCYQDQIITLNLKFGIPATFLNS  277 (381)
Q Consensus       242 DvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~l~g  277 (381)
                      -+|+.+|+|+|||...    ..+...++...+.+++
T Consensus        34 ~ilL~GpPGtGKT~la----~~la~~~~~~~~~i~~   65 (273)
T d1gvnb_          34 AFLLGGQPGSGKTSLR----SAIFEETQGNVIVIDN   65 (273)
T ss_dssp             EEEEECCTTSCTHHHH----HHHHHHTTTCCEEECT
T ss_pred             EEEEECCCCCCHHHHH----HHHHHHhhcceEEEec
Confidence            3899999999999764    3444455666666654

>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=81.45  E-value=0.48  Score=38.67  Aligned_cols=31  Identities=23%  Similarity=0.218  Sum_probs=22.5

Q ss_pred             CCCEEEECCCCCCchhhHHHHHHHHHhhcCCcEEE
Q 042872          240 KQDCFVLLPTGGGKSLCYQDQIITLNLKFGIPATF  274 (381)
Q Consensus       240 GrDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~~  274 (381)
                      |-.+++++|+|||||-.    ...|.+++|+..+.
T Consensus         3 ~~riil~G~pGSGKsT~----a~~La~~~g~~~i~   33 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQ----APKLAKNFCVCHLA   33 (190)
T ss_dssp             CCEEEEECCTTSSHHHH----HHHHHHHHTCEEEE
T ss_pred             ccEEEEECCCCCCHHHH----HHHHHHHhCCeEEe
Confidence            55688899999999954    35566677776543

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=80.69  E-value=0.53  Score=36.73  Aligned_cols=29  Identities=21%  Similarity=0.149  Sum_probs=20.0

Q ss_pred             CCEEEECCCCCCchhhHHHHHHHHHhhcCCcEE
Q 042872          241 QDCFVLLPTGGGKSLCYQDQIITLNLKFGIPAT  273 (381)
Q Consensus       241 rDvLviaPTGsGKTLaF~dQv~~L~~~~gI~a~  273 (381)
                      -.+++.+|.|+|||-.-    ..|.+++|++.+
T Consensus         5 ~~I~i~G~pGsGKTTia----~~La~~l~~~~i   33 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLG----KELASKSGLKYI   33 (173)
T ss_dssp             CCEEEECSTTSSHHHHH----HHHHHHHCCEEE
T ss_pred             CEEEEECCCCCCHHHHH----HHHHHHHCCcEE
Confidence            46889999999999654    344445566543

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.48  E-value=0.81  Score=37.76  Aligned_cols=43  Identities=9%  Similarity=0.245  Sum_probs=32.4

Q ss_pred             CchhhHH------HHHHHHHhhcCCcEEEEeCCCCHHHHHHHHHHHHhc
Q 042872          252 GKSLCYQ------DQIITLNLKFGIPATFLNSQQTVSQAAAVLQELRQG  294 (381)
Q Consensus       252 GKTLaF~------dQv~~L~~~~gI~a~~l~g~~~~~e~~~il~~lr~g  294 (381)
                      .|+++|.      +.+...-...|+.+..++|+.+..++...++.++.|
T Consensus        35 ~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~g   83 (168)
T d2j0sa2          35 TQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG   83 (168)
T ss_dssp             SEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHT
T ss_pred             CceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhcC
Confidence            3555554      333333336799999999999999999999999877