Citrus Sinensis ID: 011462

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-----

MNNSRGRYPPGIGSGRGGVNASNPSFQSSRPQQQYVQRNFLQNHYHNQQFQQQQQQQQQQQWLRRNNFPGADSSIVDEVEKTVQSEAAVDPSSQDWKARLKIPPADTRYRTEDVTATKGNEFEDYFLKRELLMGIFEKGFERPSPIQEESIPIALTGSDILARAKNGTGKTAAFCIPALEKIDQDNNVIQVVILVPTRELALQTSQVCKELGKHLNIQVMVTTGGTSLKDDIMRLYQPVHLLVGTPGRILDLSKKGVCILKDCSMLVMDEADKLLSPEFQPSVEQLIRFLPANRQILMFSATFPVTVKDFKDKYLQKPYVINLMDELTLKGITQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNGACRNLVCTDLFTRGIDIQAVNVVINFDFPKNSETYLHRVCWIQLSFSLSLPNLQFMCSMLMYICFTDRLVDLEGLDTLD

cccccccccccccccccccccccccccccccHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHccccccccccHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHcccccccccEEEEEcccHHHHHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHcccccEEEcccHHHHHHHcccccccccccEEEEEccccccccccHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHHcccccEEEEccccccccEEEEEEEcccccHHHHHHHHHHHcccccEEEEEccHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHcccccEEEEccccccccccccccEEEEcccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccc

ccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccHcccccccccccccccHHHHccccccccccccccccccccccHHHccccHHHHHHHHHcccccccccHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHcccccccccEEEEcccHHHHHHHHHHHHHHcccccccEEEEcccccHHHHHHHHccccEEEEEcccHHHHHHHcccccccccEEEEEcHHHHHHccccHHHHHHHHHHccHHHcEEEEEccccHHHHHHHHHHccccEEEEEcccccccccEEEEEEEcHHHHHHHHHHHHHHccccEEEEEEccHHHHHHHHHHHHHccccEHHHcccccHHHHHHHHHHHHcccccEEEEHHHHHcccccccccEEEEEcccccHcHEEEEEcccccccEEEEccHHHHHHHHHHHHHHHcccccccccccc

mnnsrgryppgigsgrggvnasnpsfqssrpqqQYVQRNFLQNHYHNQQFQQQQQQQQQQQWLrrnnfpgadssivDEVEKTVqseaavdpssqdwkarlkippadtryrtedvtatkgnefedYFLKRELLMGIFEkgferpspiqeesipialtgsDILArakngtgktaafcipalekidqdnnvIQVVILVPTRELALQTSQVCKELGKHLNIQVMVTtggtslkddIMRLYQpvhllvgtpgrildlskkgvcilkdcsmlvmdeadkllspefqpSVEQLIRFLPANRQilmfsatfpvtvkdfkdkylqkpyviNLMDELTLKGITQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHrnrvfhdfrngacrnlvctdlftrgidiqaVNVVInfdfpknsetyLHRVCWIQLsfslslpnLQFMCSMLMYICFTDrlvdlegldtld

mnnsrgryppgigsgrggVNASNPSFQSSRPQQQYVQRNFLQNHYHNQQFQQQQQQQQQQQWLRRNNFPGADSSIVDEVEKTVQseaavdpssqdwkarlkippadtryrtedvtatkgnefedyFLKRELLMGIFEKGFERPSPIQEESIPIALTGSDILARAKNGTGKTAAFCIPAlekidqdnNVIQVVILVPTRELALQTSQVCKELGKHLNIQVMVTTGGTSLKDDIMRLYQPVHLLVGtpgrildlsKKGVCILKDCSMLVMDEADKLLSPEFQPSVEQLIRFLPANRQILMFSATFPVTVKDFKDKYLQKPYVINLMDELTLKGITQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNGACRNLVCTDLFTRGIDIQAVNVVINFDFPKNSETYLHRVCWIQLSFSLSLPNLQFMCSMLMYICFTDRLVDLEGLDTLD

MNNSRGRYPPGIGSGRGGVNASNPSFQSSRPQQQYVQRNFLQNHYHNqqfqqqqqqqqqqqWLRRNNFPGADSSIVDEVEKTVQSEAAVDPSSQDWKARLKIPPADTRYRTEDVTATKGNEFEDYFLKRELLMGIFEKGFERPSPIQEESIPIALTGSDILARAKNGTGKTAAFCIPALEKIDQDNNVIQVVILVPTRELALQTSQVCKELGKHLNIQVMVTTGGTSLKDDIMRLYQPVHLLVGTPGRILDLSKKGVCILKDCSMLVMDEADKLLSPEFQPSVEQLIRFLPANRQILMFSATFPVTVKDFKDKYLQKPYVINLMDELTLKGITQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNGACRNLVCTDLFTRGIDIQAVNVVINFDFPKNSETYLHRVCWIQLSFSLSLPNLQFMCSMLMYICFTDRLVDLEGLDTLD

*****************************************************************************************************************VTATKGNEFEDYFLKRELLMGIFEKGFER******ESIPIALTGSDILARAKNGTGKTAAFCIPALEKIDQDNNVIQVVILVPTRELALQTSQVCKELGKHLNIQVMVTTGGTSLKDDIMRLYQPVHLLVGTPGRILDLSKKGVCILKDCSMLVMDEADKLLSPEFQPSVEQLIRFLPANRQILMFSATFPVTVKDFKDKYLQKPYVINLMDELTLKGITQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNGACRNLVCTDLFTRGIDIQAVNVVINFDFPKNSETYLHRVCWIQLSFSLSLPNLQFMCSMLMYICFTDRLVDLEG*****

*******************************************************************************************************************ATKGNEFEDYFLKRELLMGIFEKGFERPSPIQEESIPIALTGSDILARAKNGTGKTAAFCIPALEKIDQDNNVIQVVILVPTRELALQTSQVCKELGKHLNIQVMVTTGGTSLKDDIMRLYQPVHLLVGTPGRILDLSKKGVCILKDCSMLVMDEADKLLSPEFQPSVEQLIRFLPANRQILMFSATFPVTVKDFKDKYLQKPYVINLMDELTLKGITQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNGACRNLVCTDLFTRGIDIQAVNVVINFDFPKNSETYLHRVCWIQLSFSLSLPNLQFMCSMLMYIC***************

MNNSRGRYPPGIGSGRGGVNAS**********QQYVQRNFLQNHYH*****************RRNNFPGADSSIVDEVEK**************WKARLKIPPADTRYRTEDVTATKGNEFEDYFLKRELLMGIFEKGFERPSPIQEESIPIALTGSDILARAKNGTGKTAAFCIPALEKIDQDNNVIQVVILVPTRELALQTSQVCKELGKHLNIQVMVTTGGTSLKDDIMRLYQPVHLLVGTPGRILDLSKKGVCILKDCSMLVMDEADKLLSPEFQPSVEQLIRFLPANRQILMFSATFPVTVKDFKDKYLQKPYVINLMDELTLKGITQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNGACRNLVCTDLFTRGIDIQAVNVVINFDFPKNSETYLHRVCWIQLSFSLSLPNLQFMCSMLMYICFTDRLVDLEGLDTLD

**************************************************************************************************************TEDVTATKGNEFEDYFLKRELLMGIFEKGFERPSPIQEESIPIALTGSDILARAKNGTGKTAAFCIPALEKIDQDNNVIQVVILVPTRELALQTSQVCKELGKHLNIQVMVTTGGTSLKDDIMRLYQPVHLLVGTPGRILDLSKKGVCILKDCSMLVMDEADKLLSPEFQPSVEQLIRFLPANRQILMFSATFPVTVKDFKDKYLQKPYVINLMDELTLKGITQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNGACRNLVCTDLFTRGIDIQAVNVVINFDFPKNSETYLHRVCWIQLSFSLSLPNLQFMCSMLMYICFTDRLVDLEG*****

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		485	2.2.26 [Sep-21-2011]
Q8RXK6		505	DEAD-box ATP-dependent RN	yes	no	0.909	0.873	0.844	0.0
Q7XMK8		498	DEAD-box ATP-dependent RN	no	no	0.901	0.877	0.803	0.0
Q6H7S2		508	DEAD-box ATP-dependent RN	yes	no	0.905	0.864	0.805	0.0
Q94BV4		528	DEAD-box ATP-dependent RN	no	no	0.901	0.827	0.758	0.0
Q9M2E0		498	DEAD-box ATP-dependent RN	no	no	0.913	0.889	0.793	0.0
Q109G2		521	DEAD-box ATP-dependent RN	no	no	0.789	0.735	0.885	0.0
Q54E49		423	Probable ATP-dependent RN	yes	no	0.723	0.829	0.786	1e-167
Q1E5R1		512	ATP-dependent RNA helicas	N/A	no	0.721	0.683	0.774	1e-166
Q0U7S9		522	ATP-dependent RNA helicas	N/A	no	0.767	0.712	0.739	1e-165
Q2U5A2		511	ATP-dependent RNA helicas	yes	no	0.760	0.722	0.733	1e-165

>sp\|Q8RXK6\|RH8_ARATH DEAD-box ATP-dependent RNA helicase 8 OS=Arabidopsis thaliana GN=RH8 PE=2 SV=1	Back alignment and function desciption

 Score =  749 bits (1935), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 386/457 (84%), Positives = 409/457 (89%), Gaps = 16/457 (3%)

Query: 3   NSRGRYPPGIGSGRGGVNASNPSFQS-----SRPQQQYVQR-NFLQNHYH------NQQF 50
           N+RGRYPPGIG+GRG  N  NP++QS       P  QYVQR N+ QNH        +Q  
Sbjct: 2   NNRGRYPPGIGAGRGAFNP-NPNYQSRSGYQQHPPPQYVQRGNYAQNHQQQFQQAPSQPH 60

Query: 51  QQQQQQQQQQQWLRRNNFPGADSS--IVDEVEKTVQSEAAVDPSSQDWKARLKIPPADTR 108
           Q QQQQQQQQQWLRR   PG +S+   V EVEKTVQSE  +DP+S+DWKARLK+P  DTR
Sbjct: 61  QYQQQQQQQQQWLRRGQIPGGNSNGDAVVEVEKTVQSEV-IDPNSEDWKARLKLPAPDTR 119

Query: 109 YRTEDVTATKGNEFEDYFLKRELLMGIFEKGFERPSPIQEESIPIALTGSDILARAKNGT 168
           YRTEDVTATKGNEFEDYFLKRELLMGI+EKGFERPSPIQEESIPIALTG DILARAKNGT
Sbjct: 120 YRTEDVTATKGNEFEDYFLKRELLMGIYEKGFERPSPIQEESIPIALTGRDILARAKNGT 179

Query: 169 GKTAAFCIPALEKIDQDNNVIQVVILVPTRELALQTSQVCKELGKHLNIQVMVTTGGTSL 228
           GKTAAFCIP LEKIDQDNNVIQ VI+VPTRELALQTSQVCKELGKHL IQVMVTTGGTSL
Sbjct: 180 GKTAAFCIPVLEKIDQDNNVIQAVIIVPTRELALQTSQVCKELGKHLKIQVMVTTGGTSL 239

Query: 229 KDDIMRLYQPVHLLVGTPGRILDLSKKGVCILKDCSMLVMDEADKLLSPEFQPSVEQLIR 288
           KDDIMRLYQPVHLLVGTPGRILDL+KKGVC+LKDCS+LVMDEADKLLS EFQPSVE LI 
Sbjct: 240 KDDIMRLYQPVHLLVGTPGRILDLTKKGVCVLKDCSVLVMDEADKLLSQEFQPSVEHLIS 299

Query: 289 FLPANRQILMFSATFPVTVKDFKDKYLQKPYVINLMDELTLKGITQYYAFVEERQKVHCL 348
           FLP +RQILMFSATFPVTVKDFKD++L  PYVINLMDELTLKGITQ+YAFVEERQK+HCL
Sbjct: 300 FLPESRQILMFSATFPVTVKDFKDRFLTNPYVINLMDELTLKGITQFYAFVEERQKIHCL 359

Query: 349 NTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNGAC 408
           NTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNGAC
Sbjct: 360 NTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNGAC 419

Query: 409 RNLVCTDLFTRGIDIQAVNVVINFDFPKNSETYLHRV 445
           RNLVCTDLFTRGIDIQAVNVVINFDFPKN+ETYLHRV
Sbjct: 420 RNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRV 456

ATP-dependent RNA helicase involved in mRNA turnover, and more specifically in mRNA decapping.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp\|Q7XMK8\|RH6_ORYSJ DEAD-box ATP-dependent RNA helicase 6 OS=Oryza sativa subsp. japonica GN=Os04g0533000 PE=2 SV=1	Back alignment and function description

>sp\|Q6H7S2\|RH8_ORYSJ DEAD-box ATP-dependent RNA helicase 8 OS=Oryza sativa subsp. japonica GN=Os02g0641800 PE=2 SV=2	Back alignment and function description

>sp\|Q94BV4\|RH6_ARATH DEAD-box ATP-dependent RNA helicase 6 OS=Arabidopsis thaliana GN=RH6 PE=2 SV=2	Back alignment and function description

>sp\|Q9M2E0\|RH12_ARATH DEAD-box ATP-dependent RNA helicase 12 OS=Arabidopsis thaliana GN=RH12 PE=2 SV=1	Back alignment and function description

>sp\|Q109G2\|RH12_ORYSJ DEAD-box ATP-dependent RNA helicase 12 OS=Oryza sativa subsp. japonica GN=Os10g0503700 PE=2 SV=2	Back alignment and function description

>sp\|Q54E49\|DDX6_DICDI Probable ATP-dependent RNA helicase ddx6 OS=Dictyostelium discoideum GN=ddx6 PE=3 SV=1	Back alignment and function description

>sp\|Q1E5R1\|DHH1_COCIM ATP-dependent RNA helicase DHH1 OS=Coccidioides immitis (strain RS) GN=DHH1 PE=3 SV=1	Back alignment and function description

>sp\|Q0U7S9\|DHH1_PHANO ATP-dependent RNA helicase DHH1 OS=Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) GN=DHH1 PE=3 SV=1	Back alignment and function description

>sp\|Q2U5A2\|DHH1_ASPOR ATP-dependent RNA helicase dhh1 OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) GN=dhh1 PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		485
255541534		507	dead box ATP-dependent RNA helicase, put	0.905	0.865	0.893	0.0
224064015		499	predicted protein [Populus trichocarpa]	0.911	0.885	0.9	0.0
449432163		492	PREDICTED: DEAD-box ATP-dependent RNA he	0.907	0.894	0.901	0.0
225426363		480	PREDICTED: DEAD-box ATP-dependent RNA he	0.880	0.889	0.874	0.0
225454138		491	PREDICTED: DEAD-box ATP-dependent RNA he	0.892	0.881	0.884	0.0
297745244		472	unnamed protein product [Vitis vinifera]	0.868	0.891	0.905	0.0
224127608		485	predicted protein [Populus trichocarpa]	0.872	0.872	0.894	0.0
356520426		500	PREDICTED: DEAD-box ATP-dependent RNA he	0.890	0.864	0.851	0.0
356520424		503	PREDICTED: DEAD-box ATP-dependent RNA he	0.894	0.862	0.871	0.0
356504657		502	PREDICTED: DEAD-box ATP-dependent RNA he	0.880	0.850	0.839	0.0

>gi\|255541534\|ref\|XP_002511831.1\| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi\|223549011\|gb\|EEF50500.1\| dead box ATP-dependent RNA helicase, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  796 bits (2055), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 402/450 (89%), Positives = 415/450 (92%), Gaps = 11/450 (2%)

Query: 5   RGRYPPGIGSGRGGVNASNPSFQSSRPQQQYVQRNFLQNHYHNQQFQQQQQQQQQQQ--- 61
           RGRYPPGIG+GRG    +NPSFQS  PQQQYVQRN +QNH+   Q QQ  Q   QQQ   
Sbjct: 11  RGRYPPGIGAGRGAGMNANPSFQSRVPQQQYVQRNMMQNHHQQFQHQQHHQHHLQQQQQQ 70

Query: 62  ------WLRRNNFPGADSSIVDEVEKTVQSEAAVDPSSQDWKARLKIPPADTRYRTEDVT 115
                 WLRR+  P ADSS VDEVEKTVQSEA VD +SQDWKARLKIPP DTRY+TEDVT
Sbjct: 71  QQQQQQWLRRSQLPPADSS-VDEVEKTVQSEA-VDSTSQDWKARLKIPPPDTRYKTEDVT 128

Query: 116 ATKGNEFEDYFLKRELLMGIFEKGFERPSPIQEESIPIALTGSDILARAKNGTGKTAAFC 175
           ATKGNEFEDYFLKRELLMGI+EKGFERPSPIQEESIPIALTGSDILARAKNGTGKTAAFC
Sbjct: 129 ATKGNEFEDYFLKRELLMGIYEKGFERPSPIQEESIPIALTGSDILARAKNGTGKTAAFC 188

Query: 176 IPALEKIDQDNNVIQVVILVPTRELALQTSQVCKELGKHLNIQVMVTTGGTSLKDDIMRL 235
           IPALEKIDQDNNVIQVVILVPTRELALQTSQVCKELGKHL IQVMVTTGGTSLKDDIMRL
Sbjct: 189 IPALEKIDQDNNVIQVVILVPTRELALQTSQVCKELGKHLKIQVMVTTGGTSLKDDIMRL 248

Query: 236 YQPVHLLVGTPGRILDLSKKGVCILKDCSMLVMDEADKLLSPEFQPSVEQLIRFLPANRQ 295
           YQPVHLLVGTPGRILDL+KKGVC+LKDCSMLVMDEADKLLSPEFQPSVEQLIRFLP  RQ
Sbjct: 249 YQPVHLLVGTPGRILDLAKKGVCVLKDCSMLVMDEADKLLSPEFQPSVEQLIRFLPPTRQ 308

Query: 296 ILMFSATFPVTVKDFKDKYLQKPYVINLMDELTLKGITQYYAFVEERQKVHCLNTLFSKL 355
           ILMFSATFPVTVKDFKD++LQKPYVINLMDELTLKGITQ+YAFVEERQKVHCLNTLFSKL
Sbjct: 309 ILMFSATFPVTVKDFKDRFLQKPYVINLMDELTLKGITQFYAFVEERQKVHCLNTLFSKL 368

Query: 356 QINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNGACRNLVCTD 415
           QINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNGACRNLVCTD
Sbjct: 369 QINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNGACRNLVCTD 428

Query: 416 LFTRGIDIQAVNVVINFDFPKNSETYLHRV 445
           LFTRGIDIQAVNVVINFDFPKNSETYLHRV
Sbjct: 429 LFTRGIDIQAVNVVINFDFPKNSETYLHRV 458

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224064015\|ref\|XP_002301349.1\| predicted protein [Populus trichocarpa] gi\|222843075\|gb\|EEE80622.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449432163\|ref\|XP_004133869.1\| PREDICTED: DEAD-box ATP-dependent RNA helicase 8-like [Cucumis sativus] gi\|449480172\|ref\|XP_004155819.1\| PREDICTED: DEAD-box ATP-dependent RNA helicase 8-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|225426363\|ref\|XP_002271357.1\| PREDICTED: DEAD-box ATP-dependent RNA helicase 8 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|225454138\|ref\|XP_002270379.1\| PREDICTED: DEAD-box ATP-dependent RNA helicase 8 [Vitis vinifera] gi\|147785187\|emb\|CAN75439.1\| hypothetical protein VITISV_000835 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297745244\|emb\|CBI40324.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224127608\|ref\|XP_002320116.1\| predicted protein [Populus trichocarpa] gi\|222860889\|gb\|EEE98431.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356520426\|ref\|XP_003528863.1\| PREDICTED: DEAD-box ATP-dependent RNA helicase 8-like [Glycine max]	Back alignment and taxonomy information

>gi\|356520424\|ref\|XP_003528862.1\| PREDICTED: DEAD-box ATP-dependent RNA helicase 8-like [Glycine max]	Back alignment and taxonomy information

>gi\|356504657\|ref\|XP_003521112.1\| PREDICTED: DEAD-box ATP-dependent RNA helicase 8-like [Glycine max]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		485
TAIR\|locus:2127043		505	RH8 "RNAhelicase-like 8" [Arab	0.911	0.875	0.821	1.6e-196
TAIR\|locus:2098886		498	AT3G61240 [Arabidopsis thalian	0.913	0.889	0.778	1.9e-186
TAIR\|locus:2050715		528	AT2G45810 [Arabidopsis thalian	0.868	0.797	0.800	4.2e-182
DICTYBASE\|DDB_G0291804		423	ddx6 "DEAD/DEAH box helicase"	0.723	0.829	0.786	3.3e-150
POMBASE\|SPBC776.09		485	ste13 "ATP-dependent RNA helic	0.725	0.725	0.764	3.1e-147
ASPGD\|ASPL0000036135		498	AN10417 [Emericella nidulans (	0.721	0.702	0.765	3.5e-146
UNIPROTKB\|A4R715		535	DHH1 "ATP-dependent RNA helica	0.758	0.687	0.727	4e-145
GENEDB_PFALCIPARUM\|PFC0915w		433	PFC0915w "ATP-dependent RNA he	0.725	0.812	0.767	1.4e-144
ZFIN\|ZDB-GENE-030131-6611		483	wu:fk48d07 "wu:fk48d07" [Danio	0.777	0.780	0.698	1.1e-140
FB\|FBgn0004419		459	me31B "maternal expression at	0.721	0.762	0.728	2.4e-140

TAIR\|locus:2127043 RH8 "RNAhelicase-like 8" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1903 (674.9 bits), Expect = 1.6e-196, P = 1.6e-196
 Identities = 377/459 (82%), Positives = 398/459 (86%)

Query:     1 MNNSRGRYPPGIGSGRGGVNASNPSFQS-----SRPQQQYVQR-NFLQNHYHNXXXXXXX 54
             MNN RGRYPPGIG+GRG  N  NP++QS       P  QYVQR N+ QNH          
Sbjct:     1 MNN-RGRYPPGIGAGRGAFNP-NPNYQSRSGYQQHPPPQYVQRGNYAQNHQQQFQQAPSQ 58

Query:    55 ------XXXXXXXWLRRNNFPGADSS--IVDEVEKTVQSEAAVDPSSQDWKARLKIPPAD 106
                          WLRR   PG +S+   V EVEKTVQSE  +DP+S+DWKARLK+P  D
Sbjct:    59 PHQYQQQQQQQQQWLRRGQIPGGNSNGDAVVEVEKTVQSEV-IDPNSEDWKARLKLPAPD 117

Query:   107 TRYRTEDVTATKGNEFEDYFLKRELLMGIFEKGFERPSPIQEESIPIALTGSDILARAKN 166
             TRYRTEDVTATKGNEFEDYFLKRELLMGI+EKGFERPSPIQEESIPIALTG DILARAKN
Sbjct:   118 TRYRTEDVTATKGNEFEDYFLKRELLMGIYEKGFERPSPIQEESIPIALTGRDILARAKN 177

Query:   167 GTGKTAAFCIPALEKIDQDNNVIQVVILVPTRELALQTSQVCKELGKHLNIQVMVTTGGT 226
             GTGKTAAFCIP LEKIDQDNNVIQ VI+VPTRELALQTSQVCKELGKHL IQVMVTTGGT
Sbjct:   178 GTGKTAAFCIPVLEKIDQDNNVIQAVIIVPTRELALQTSQVCKELGKHLKIQVMVTTGGT 237

Query:   227 SLKDDIMRLYQPVHLLVGTPGRILDLSKKGVCILKDCSMLVMDEADKLLSPEFQPSVEQL 286
             SLKDDIMRLYQPVHLLVGTPGRILDL+KKGVC+LKDCS+LVMDEADKLLS EFQPSVE L
Sbjct:   238 SLKDDIMRLYQPVHLLVGTPGRILDLTKKGVCVLKDCSVLVMDEADKLLSQEFQPSVEHL 297

Query:   287 IRFLPANRQILMFSATFPVTVKDFKDKYLQKPYVINLMDELTLKGITQYYAFVEERQKVH 346
             I FLP +RQILMFSATFPVTVKDFKD++L  PYVINLMDELTLKGITQ+YAFVEERQK+H
Sbjct:   298 ISFLPESRQILMFSATFPVTVKDFKDRFLTNPYVINLMDELTLKGITQFYAFVEERQKIH 357

Query:   347 CLNTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNG 406
             CLNTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNG
Sbjct:   358 CLNTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNG 417

Query:   407 ACRNLVCTDLFTRGIDIQAVNVVINFDFPKNSETYLHRV 445
             ACRNLVCTDLFTRGIDIQAVNVVINFDFPKN+ETYLHRV
Sbjct:   418 ACRNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRV 456

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0016032 "viral reproduction" evidence=IMP

GO:0019048 "virus-host interaction" evidence=IPI

TAIR\|locus:2098886 AT3G61240 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2050715 AT2G45810 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0291804 ddx6 "DEAD/DEAH box helicase" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

POMBASE\|SPBC776.09 ste13 "ATP-dependent RNA helicase Ste13" [Schizosaccharomyces pombe (taxid:4896)]	Back alignment and assigned GO terms

ASPGD\|ASPL0000036135 AN10417 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

UNIPROTKB\|A4R715 DHH1 "ATP-dependent RNA helicase DHH1" [Magnaporthe oryzae 70-15 (taxid:242507)]	Back alignment and assigned GO terms

GENEDB_PFALCIPARUM\|PFC0915w PFC0915w "ATP-dependent RNA helicase, putative" [Plasmodium falciparum (taxid:5833)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-6611 wu:fk48d07 "wu:fk48d07" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

FB\|FBgn0004419 me31B "maternal expression at 31B" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q0CBE1	DHH1_ASPTN	3, ., 6, ., 4, ., 1, 3	0.7627	0.7298	0.6954	N/A	no
Q1E5R1	DHH1_COCIM	3, ., 6, ., 4, ., 1, 3	0.7742	0.7216	0.6835	N/A	no
A3LWX3	DHH1_PICST	3, ., 6, ., 4, ., 1, 3	0.7344	0.7298	0.6954	yes	no
P54824	DDX6_XENLA	3, ., 6, ., 4, ., 1, 3	0.7187	0.7237	0.7297	N/A	no
Q75BS4	DHH1_ASHGO	3, ., 6, ., 4, ., 1, 3	0.7280	0.7278	0.7293	yes	no
Q54E49	DDX6_DICDI	3, ., 6, ., 4, ., 1, 3	0.7863	0.7237	0.8297	yes	no
P23128	DDX6_DROME	3, ., 6, ., 4, ., 1, 3	0.7285	0.7216	0.7625	yes	no
Q4WWD3	DHH1_ASPFU	3, ., 6, ., 4, ., 1, 3	0.7685	0.7216	0.6903	yes	no
Q0U7S9	DHH1_PHANO	3, ., 6, ., 4, ., 1, 3	0.7399	0.7670	0.7126	N/A	no
Q6FQU5	DHH1_CANGA	3, ., 6, ., 4, ., 1, 3	0.7142	0.7216	0.6903	yes	no
Q94BV4	RH6_ARATH	3, ., 6, ., 4, ., 1, 3	0.7584	0.9010	0.8276	no	no
Q0IHV9	DDX6_XENTR	3, ., 6, ., 4, ., 1, 3	0.7187	0.7237	0.7297	yes	no
Q2U5A2	DHH1_ASPOR	3, ., 6, ., 4, ., 1, 3	0.7338	0.7608	0.7221	yes	no
Q6C0X2	DHH1_YARLI	3, ., 6, ., 4, ., 1, 3	0.7578	0.7237	0.6724	yes	no
Q95YF3	CGH1_CAEEL	3, ., 6, ., 4, ., 1, 3	0.6977	0.7298	0.8232	yes	no
Q9WTM2	DDX6_CAVPO	3, ., 6, ., 4, ., 1, 3	0.6818	0.7690	0.7902	yes	no
A4R715	DHH1_MAGO7	3, ., 6, ., 4, ., 1, 3	0.7277	0.7587	0.6878	N/A	no
Q8RXK6	RH8_ARATH	3, ., 6, ., 4, ., 1, 3	0.8446	0.9092	0.8732	yes	no
Q6H7S2	RH8_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.8051	0.9051	0.8641	yes	no
Q6BJX6	DHH1_DEBHA	3, ., 6, ., 4, ., 1, 3	0.7090	0.7298	0.6860	yes	no
A1CJ18	DHH1_ASPCL	3, ., 6, ., 4, ., 1, 3	0.7338	0.7608	0.7335	N/A	no
A5DIP0	DHH1_PICGU	3, ., 6, ., 4, ., 1, 3	0.7195	0.7278	0.6453	N/A	no
Q5RFQ5	DDX6_PONAB	3, ., 6, ., 4, ., 1, 3	0.6818	0.7690	0.7722	yes	no
P26196	DDX6_HUMAN	3, ., 6, ., 4, ., 1, 3	0.6844	0.7690	0.7722	yes	no
Q5AAW3	DHH1_CANAL	3, ., 6, ., 4, ., 1, 3	0.7175	0.7298	0.6448	N/A	no
Q6CSZ7	DHH1_KLULA	3, ., 6, ., 4, ., 1, 3	0.7033	0.7298	0.6887	yes	no
Q7S5D9	DHH1_NEUCR	3, ., 6, ., 4, ., 1, 3	0.7381	0.7402	0.7108	N/A	no
Q5ZKB9	DDX6_CHICK	3, ., 6, ., 4, ., 1, 3	0.6844	0.7690	0.7722	yes	no
Q4HW67	DHH1_GIBZE	3, ., 6, ., 4, ., 1, 3	0.7592	0.7278	0.7263	yes	no
P54823	DDX6_MOUSE	3, ., 6, ., 4, ., 1, 3	0.6925	0.7690	0.7722	yes	no
Q9M2E0	RH12_ARATH	3, ., 6, ., 4, ., 1, 3	0.7937	0.9134	0.8895	no	no
P0CQ80	DHH1_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.7301	0.7237	0.5616	yes	no
Q09181	DHH1_SCHPO	3, ., 6, ., 4, ., 1, 3	0.7642	0.7257	0.7257	yes	no
A7TGU7	DHH1_VANPO	3, ., 6, ., 4, ., 1, 3	0.7187	0.7257	0.7272	N/A	no
P39517	DHH1_YEAST	3, ., 6, ., 4, ., 1, 3	0.7159	0.7257	0.6956	yes	no
A6RY31	DHH1_BOTFB	3, ., 6, ., 4, ., 1, 3	0.7419	0.7649	0.6895	N/A	no
A1D8G1	DHH1_NEOFI	3, ., 6, ., 4, ., 1, 3	0.7311	0.7608	0.7278	N/A	no
A2QY39	DHH1_ASPNC	3, ., 6, ., 4, ., 1, 3	0.7284	0.7608	0.7306	yes	no
Q7XMK8	RH6_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.8039	0.9010	0.8775	no	no
A6ZXG9	DHH1_YEAS7	3, ., 6, ., 4, ., 1, 3	0.7159	0.7257	0.6956	N/A	no
Q2GQ93	DHH1_CHAGB	3, ., 6, ., 4, ., 1, 3	0.7807	0.6865	0.6503	N/A	no

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	3.6.4.13	0.979
3rd Layer	3.6.4	0.983

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	fgenesh4_pg.C_LG_II001453	hypothetical protein (499 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		485
COG0513		513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-125
cd00268		203	cd00268, DEADc, DEAD-box helicases	6e-95
PTZ00424		401	PTZ00424, PTZ00424, helicase 45; Provisional	1e-94
PRK11776		460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	6e-80
PRK10590		456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	5e-67
PRK11192		434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	5e-64
PTZ00110		545	PTZ00110, PTZ00110, helicase; Provisional	9e-63
pfam00270		169	pfam00270, DEAD, DEAD/DEAH box helicase	7e-62
PRK11634		629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	5e-60
PRK01297		475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	9e-55
smart00487		201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-51
PLN00206		518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	9e-48
PRK04537		572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	4e-46
PRK04837		423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	9e-41
cd00046		144	cd00046, DEXDc, DEAD-like helicases superfamily	5e-40
cd00079		131	cd00079, HELICc, Helicase superfamily c-terminal d	1e-32
pfam00271		78	pfam00271, Helicase_C, Helicase conserved C-termin	1e-23
smart00490		82	smart00490, HELICc, helicase superfamily c-termina	2e-22
COG1201		814	COG1201, Lhr, Lhr-like helicases [General function	6e-16
COG0514		590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	4e-12
COG1061		442	COG1061, SSL2, DNA or RNA helicases of superfamily	2e-11
TIGR01389		591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	3e-11
COG1204		766	COG1204, COG1204, Superfamily II helicase [General	5e-11
TIGR00614		470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	4e-10
COG1202		830	COG1202, COG1202, Superfamily II helicase, archaea	5e-10
PRK11057		607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	5e-09
TIGR00643		630	TIGR00643, recG, ATP-dependent DNA helicase RecG	8e-07
PRK00254		720	PRK00254, PRK00254, ski2-like helicase; Provisiona	3e-06
cd09639		353	cd09639, Cas3_I, CRISPR/Cas system-associated prot	4e-06
COG1205		851	COG1205, COG1205, Distinct helicase family with a	5e-06
COG1203		733	COG1203, COG1203, CRISPR-associated helicase Cas3	1e-05
TIGR01587		358	TIGR01587, cas3_core, CRISPR-associated helicase C	2e-05
COG1111		542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	4e-05
PRK13767		876	PRK13767, PRK13767, ATP-dependent helicase; Provis	4e-04
TIGR00580		926	TIGR00580, mfd, transcription-repair coupling fact	0.002
COG1197		1139	COG1197, Mfd, Transcription-repair coupling factor	0.003

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

 Score =  374 bits (963), Expect = e-125
 Identities = 132/342 (38%), Positives = 199/342 (58%), Gaps = 7/342 (2%)

Query: 111 TEDVTATKGNEFEDYFLKRELLMGIFEKGFERPSPIQEESIPIALTGSDILARAKNGTGK 170
                     EF    L  ELL  + + GFE P+PIQ  +IP+ L G D+L +A+ GTGK
Sbjct: 20  LSRGEEKTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGK 79

Query: 171 TAAFCIPALEKIDQ--DNNVIQVVILVPTRELALQTSQVCKELGKHL-NIQVMVTTGGTS 227
           TAAF +P L+KI +  +   +  +IL PTRELA+Q ++  ++LGK+L  ++V V  GG S
Sbjct: 80  TAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVS 139

Query: 228 LKDDIMRLYQPVHLLVGTPGRILDLSKKGVCILKDCSMLVMDEADKLLSPEFQPSVEQLI 287
           ++  I  L + V ++V TPGR+LDL K+G   L     LV+DEAD++L   F   +E+++
Sbjct: 140 IRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKIL 199

Query: 288 RFLPANRQILMFSATFPVTVKDFKDKYLQKPYVINL---MDELTLKGITQYYAFVE-ERQ 343
           + LP +RQ L+FSAT P  +++   +YL  P  I +     E TLK I Q+Y  VE E +
Sbjct: 200 KALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEE 259

Query: 344 KVHCLNTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDF 403
           K+  L  L       + I+F  +   VE LA+ + + G+    +H  + Q+ R+R    F
Sbjct: 260 KLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKF 319

Query: 404 RNGACRNLVCTDLFTRGIDIQAVNVVINFDFPKNSETYLHRV 445
           ++G  R LV TD+  RG+DI  V+ VIN+D P + E Y+HR+
Sbjct: 320 KDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRI 361

Length = 513

>gnl\|CDD\|238167 cd00268, DEADc, DEAD-box helicases	Back alignment and domain information

>gnl\|CDD\|185609 PTZ00424, PTZ00424, helicase 45; Provisional	Back alignment and domain information

>gnl\|CDD\|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional	Back alignment and domain information

>gnl\|CDD\|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional	Back alignment and domain information

>gnl\|CDD\|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional	Back alignment and domain information

>gnl\|CDD\|240273 PTZ00110, PTZ00110, helicase; Provisional	Back alignment and domain information

>gnl\|CDD\|215832 pfam00270, DEAD, DEAD/DEAH box helicase	Back alignment and domain information

>gnl\|CDD\|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional	Back alignment and domain information

>gnl\|CDD\|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>gnl\|CDD\|214692 smart00487, DEXDc, DEAD-like helicases superfamily	Back alignment and domain information

>gnl\|CDD\|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase; Provisional	Back alignment and domain information

>gnl\|CDD\|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>gnl\|CDD\|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>gnl\|CDD\|238005 cd00046, DEXDc, DEAD-like helicases superfamily	Back alignment and domain information

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

Back alignment and domain information

>gnl\|CDD\|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain	Back alignment and domain information

>gnl\|CDD\|197757 smart00490, HELICc, helicase superfamily c-terminal domain	Back alignment and domain information

>gnl\|CDD\|224122 COG1201, Lhr, Lhr-like helicases [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication, recombination, and repair]	Back alignment and domain information

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

>gnl\|CDD\|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ	Back alignment and domain information

>gnl\|CDD\|224125 COG1204, COG1204, Superfamily II helicase [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family	Back alignment and domain information

>gnl\|CDD\|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional	Back alignment and domain information

>gnl\|CDD\|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG	Back alignment and domain information

>gnl\|CDD\|234702 PRK00254, PRK00254, ski2-like helicase; Provisional	Back alignment and domain information

>gnl\|CDD\|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3	Back alignment and domain information

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

>gnl\|CDD\|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	Back alignment and domain information

>gnl\|CDD\|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3	Back alignment and domain information

>gnl\|CDD\|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional	Back alignment and domain information

>gnl\|CDD\|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd)	Back alignment and domain information

>gnl\|CDD\|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		485
KOG0326		459	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0331		519	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0330		476	consensus ATP-dependent RNA helicase [RNA processi	100.0
COG0513		513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
PTZ00110		545	helicase; Provisional	100.0
KOG0328		400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
PRK11776		460	ATP-dependent RNA helicase DbpA; Provisional	100.0
KOG0333		673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
PRK10590		456	ATP-dependent RNA helicase RhlE; Provisional	100.0
PRK04837		423	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0338		691	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0342		543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
PRK11634		629	ATP-dependent RNA helicase DeaD; Provisional	100.0
KOG0345		567	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK04537		572	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0343		758	consensus RNA Helicase [RNA processing and modific	100.0
PRK11192		434	ATP-dependent RNA helicase SrmB; Provisional	100.0
PLN00206		518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
KOG0340		442	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0336		629	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK01297		475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0335		482	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00424		401	helicase 45; Provisional	100.0
KOG0341		610	consensus DEAD-box protein abstrakt [RNA processin	100.0
KOG0347		731	consensus RNA helicase [RNA processing and modific	100.0
KOG0348		708	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0339		731	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0346		569	consensus RNA helicase [RNA processing and modific	100.0
KOG0332		477	consensus ATP-dependent RNA helicase [RNA processi	100.0
TIGR03817		742	DECH_helic helicase/secretion neighborhood putativ	100.0
KOG4284		980	consensus DEAD box protein [Transcription]	100.0
PLN03137		1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
KOG0327		397	consensus Translation initiation factor 4F, helica	100.0
KOG0334		997	consensus RNA helicase [RNA processing and modific	100.0
TIGR00614		470	recQ_fam ATP-dependent DNA helicase, RecQ family.	100.0
KOG0337		529	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0350		620	consensus DEAD-box ATP-dependent RNA helicase [RNA	100.0
PRK11057		607	ATP-dependent DNA helicase RecQ; Provisional	100.0
TIGR01389		591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	100.0
COG0514		590	RecQ Superfamily II DNA helicase [DNA replication,	100.0
PRK02362		737	ski2-like helicase; Provisional	100.0
PRK13767		876	ATP-dependent helicase; Provisional	100.0
PRK00254		720	ski2-like helicase; Provisional	100.0
TIGR02621		844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	100.0
KOG0329		387	consensus ATP-dependent RNA helicase [RNA processi	100.0
COG1201		814	Lhr Lhr-like helicases [General function predictio	100.0
KOG0344		593	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK01172		674	ski2-like helicase; Provisional	100.0
TIGR01970		819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	100.0
TIGR00580		926	mfd transcription-repair coupling factor (mfd). Al	100.0
PRK11664		812	ATP-dependent RNA helicase HrpB; Provisional	100.0
PRK10689		1147	transcription-repair coupling factor; Provisional	100.0
PHA02653		675	RNA helicase NPH-II; Provisional	100.0
PRK09751		1490	putative ATP-dependent helicase Lhr; Provisional	100.0
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	100.0
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	100.0
KOG0353		695	consensus ATP-dependent DNA helicase [General func	100.0
KOG0351		941	consensus ATP-dependent DNA helicase [Replication,	100.0
PRK09401		1176	reverse gyrase; Reviewed	100.0
PRK14701		1638	reverse gyrase; Provisional	100.0
KOG0352		641	consensus ATP-dependent DNA helicase [Replication,	100.0
PRK11131		1294	ATP-dependent RNA helicase HrpA; Provisional	100.0
TIGR01587		358	cas3_core CRISPR-associated helicase Cas3. This mo	100.0
COG1111		542	MPH1 ERCC4-like helicases [DNA replication, recomb	100.0
PRK12898		656	secA preprotein translocase subunit SecA; Reviewed	100.0
PHA02558		501	uvsW UvsW helicase; Provisional	100.0
COG1205		851	Distinct helicase family with a unique C-terminal	100.0
COG1202		830	Superfamily II helicase, archaea-specific [General	100.0
KOG0922		674	consensus DEAH-box RNA helicase [RNA processing an	100.0
KOG0923		902	consensus mRNA splicing factor ATP-dependent RNA h	100.0
COG1204		766	Superfamily II helicase [General function predicti	100.0
TIGR03158		357	cas3_cyano CRISPR-associated helicase, Cyano-type.	100.0
TIGR01967		1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	100.0
KOG0349		725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	100.0
PRK09200		790	preprotein translocase subunit SecA; Reviewed	100.0
COG1643		845	HrpA HrpA-like helicases [DNA replication, recombi	100.0
TIGR03714		762	secA2 accessory Sec system translocase SecA2. Memb	100.0
TIGR01054		1171	rgy reverse gyrase. Generally, these gyrases are e	100.0
TIGR00963		745	secA preprotein translocase, SecA subunit. The pro	100.0
PRK13766		773	Hef nuclease; Provisional	100.0
KOG0924		1042	consensus mRNA splicing factor ATP-dependent RNA h	100.0
KOG0920		924	consensus ATP-dependent RNA helicase A [RNA proces	100.0
KOG0354		746	consensus DEAD-box like helicase [General function	100.0
TIGR00603		732	rad25 DNA repair helicase rad25. All proteins in t	100.0
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	100.0
PRK09694		878	helicase Cas3; Provisional	100.0
cd00268		203	DEADc DEAD-box helicases. A diverse family of prot	100.0
PRK04914		956	ATP-dependent helicase HepA; Validated	99.98
PRK05580		679	primosome assembly protein PriA; Validated	99.97
KOG0947		1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.97
KOG0926		1172	consensus DEAH-box RNA helicase [RNA processing an	99.97
COG1061		442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.97
KOG0948		1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.97
PRK13104		896	secA preprotein translocase subunit SecA; Reviewed	99.97
COG4581		1041	Superfamily II RNA helicase [DNA replication, reco	99.97
COG1197		1139	Mfd Transcription-repair coupling factor (superfam	99.97
KOG0925		699	consensus mRNA splicing factor ATP-dependent RNA h	99.97
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.97
COG1200		677	RecG RecG-like helicase [DNA replication, recombin	99.97
COG4098		441	comFA Superfamily II DNA/RNA helicase required for	99.96
PRK12904		830	preprotein translocase subunit SecA; Reviewed	99.96
TIGR00595		505	priA primosomal protein N'. All proteins in this f	99.96
PRK12899		970	secA preprotein translocase subunit SecA; Reviewed	99.96
PRK12906		796	secA preprotein translocase subunit SecA; Reviewed	99.96
PRK11448		1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.96
PLN03142		1033	Probable chromatin-remodeling complex ATPase chain	99.95
PF00270		169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.95
KOG0950		1008	consensus DNA polymerase theta/eta, DEAD-box super	99.94
PRK13107		908	preprotein translocase subunit SecA; Reviewed	99.94
COG1203		733	CRISPR-associated helicase Cas3 [Defense mechanism	99.93
KOG0385		971	consensus Chromatin remodeling complex WSTF-ISWI,	99.92
KOG0384		1373	consensus Chromodomain-helicase DNA-binding protei	99.9
COG1110		1187	Reverse gyrase [DNA replication, recombination, an	99.89
PRK12326		764	preprotein translocase subunit SecA; Reviewed	99.88
PRK12900		1025	secA preprotein translocase subunit SecA; Reviewed	99.88
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	99.88
TIGR00348		667	hsdR type I site-specific deoxyribonuclease, HsdR	99.87
KOG0387		923	consensus Transcription-coupled repair protein CSB	99.87
COG4096		875	HsdR Type I site-specific restriction-modification	99.87
COG1198		730	PriA Primosomal protein N' (replication factor Y)	99.86
smart00487		201	DEXDc DEAD-like helicases superfamily.	99.86
TIGR00631		655	uvrb excinuclease ABC, B subunit. This family is b	99.86
KOG0949		1330	consensus Predicted helicase, DEAD-box superfamily	99.85
PRK13103		913	secA preprotein translocase subunit SecA; Reviewed	99.85
KOG1123		776	consensus RNA polymerase II transcription initiati	99.84
COG0556		663	UvrB Helicase subunit of the DNA excision repair c	99.83
PRK12903		925	secA preprotein translocase subunit SecA; Reviewed	99.83
KOG0390		776	consensus DNA repair protein, SNF2 family [Replica	99.82
KOG4150		1034	consensus Predicted ATP-dependent RNA helicase [RN	99.8
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.8
PRK05298		652	excinuclease ABC subunit B; Provisional	99.79
KOG0389		941	consensus SNF2 family DNA-dependent ATPase [Chroma	99.79
KOG1000		689	consensus Chromatin remodeling protein HARP/SMARCA	99.78
CHL00122		870	secA preprotein translocase subunit SecA; Validate	99.78
KOG0392		1549	consensus SNF2 family DNA-dependent ATPase domain-	99.77
KOG0953		700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	99.77
KOG0921		1282	consensus Dosage compensation complex, subunit MLE	99.77
PF00271		78	Helicase_C: Helicase conserved C-terminal domain;	99.76
cd00079		131	HELICc Helicase superfamily c-terminal domain; ass	99.75
cd00046		144	DEXDc DEAD-like helicases superfamily. A diverse f	99.75
COG4889		1518	Predicted helicase [General function prediction on	99.74
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.73
TIGR03117		636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.72
TIGR02562		1110	cas3_yersinia CRISPR-associated helicase Cas3. The	99.69
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.69
PRK12902		939	secA preprotein translocase subunit SecA; Reviewed	99.69
PF04851		184	ResIII: Type III restriction enzyme, res subunit;	99.66
KOG0386		1157	consensus Chromatin remodeling complex SWI/SNF, co	99.65
smart00490		82	HELICc helicase superfamily c-terminal domain.	99.63
PRK12901		1112	secA preprotein translocase subunit SecA; Reviewed	99.61
KOG0391		1958	consensus SNF2 family DNA-dependent ATPase [Genera	99.6
KOG1002		791	consensus Nucleotide excision repair protein RAD16	99.57
KOG0388		1185	consensus SNF2 family DNA-dependent ATPase [Replic	99.55
PF02399		824	Herpes_ori_bp: Origin of replication binding prote	99.55
PRK11747		697	dinG ATP-dependent DNA helicase DinG; Provisional	99.54
COG1199		654	DinG Rad3-related DNA helicases [Transcription / D	99.53
TIGR00604		705	rad3 DNA repair helicase (rad3). All proteins in t	99.51
PRK14873		665	primosome assembly protein PriA; Provisional	99.5
KOG4439		901	consensus RNA polymerase II transcription terminat	99.43
COG0553		866	HepA Superfamily II DNA/RNA helicases, SNF2 family	99.42
KOG1015		1567	consensus Transcription regulator XNP/ATRX, DEAD-b	99.41
COG0653		822	SecA Preprotein translocase subunit SecA (ATPase,	99.38
PF06862		442	DUF1253: Protein of unknown function (DUF1253); In	99.36
PF07652		148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.31
PF00176		299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.28
COG0610		962	Type I site-specific restriction-modification syst	99.2
KOG2340		698	consensus Uncharacterized conserved protein [Funct	99.12
smart00489		289	DEXDc3 DEAD-like helicases superfamily.	99.07
smart00488		289	DEXDc2 DEAD-like helicases superfamily.	99.07
PF07517		266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	98.92
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	98.89
KOG1016		1387	consensus Predicted DNA helicase, DEAD-box superfa	98.88
PRK15483		986	type III restriction-modification system StyLTI en	98.68
COG3587		985	Restriction endonuclease [Defense mechanisms]	98.65
TIGR00596		814	rad1 DNA repair protein (rad1). This family is bas	98.6
PF13086		236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.58
PF13604		196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.57
PF02562		205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.54
PF13872		303	AAA_34: P-loop containing NTP hydrolase pore-1	98.39
PRK10536		262	hypothetical protein; Provisional	98.35
KOG1001		674	consensus Helicase-like transcription factor HLTF/	98.32
TIGR01447		586	recD exodeoxyribonuclease V, alpha subunit. This f	98.24
PRK10875		615	recD exonuclease V subunit alpha; Provisional	98.19
TIGR01448		720	recD_rel helicase, putative, RecD/TraA family. Thi	98.17
KOG1803		649	consensus DNA helicase [Replication, recombination	98.16
PF09848		352	DUF2075: Uncharacterized conserved protein (DUF207	98.16
KOG1802		935	consensus RNA helicase nonsense mRNA reducing fact	98.07
PF13307		167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.05
PF12340		229	DUF3638: Protein of unknown function (DUF3638); In	98.05
PF13245		76	AAA_19: Part of AAA domain	97.99
KOG0383		696	consensus Predicted helicase [General function pre	97.96
TIGR00376		637	DNA helicase, putative. The gene product may repre	97.91
COG1875		436	NYN ribonuclease and ATPase of PhoH family domains	97.9
PRK12723		388	flagellar biosynthesis regulator FlhF; Provisional	97.84
PRK13889		988	conjugal transfer relaxase TraA; Provisional	97.72
TIGR02768		744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.7
KOG1132		945	consensus Helicase of the DEAD superfamily [Replic	97.69
PF00448		196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.69
PF13401		131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.6
PRK04296		190	thymidine kinase; Provisional	97.56
cd00009		151	AAA The AAA+ (ATPases Associated with a wide varie	97.5
PF00580		315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.5
PRK13826		1102	Dtr system oriT relaxase; Provisional	97.5
KOG1805		1100	consensus DNA replication helicase [Replication, r	97.43
PRK14722		374	flhF flagellar biosynthesis regulator FlhF; Provis	97.41
PRK05703		424	flhF flagellar biosynthesis regulator FlhF; Valida	97.38
PRK14974		336	cell division protein FtsY; Provisional	97.36
COG1419		407	FlhF Flagellar GTP-binding protein [Cell motility	97.34
PRK11889		436	flhF flagellar biosynthesis regulator FlhF; Provis	97.33
PRK06526		254	transposase; Provisional	97.3
smart00382		148	AAA ATPases associated with a variety of cellular	97.26
PRK08181		269	transposase; Validated	97.21
TIGR02760		1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.19
KOG1131		755	consensus RNA polymerase II transcription initiati	97.18
PF05970		364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.16
PRK12727		559	flagellar biosynthesis regulator FlhF; Provisional	97.15
PRK07764		824	DNA polymerase III subunits gamma and tau; Validat	97.09
PF05127		177	Helicase_RecD: Helicase; InterPro: IPR007807 This	97.08
PRK14956		484	DNA polymerase III subunits gamma and tau; Provisi	97.06
PF14617		252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.03
PRK07003		830	DNA polymerase III subunits gamma and tau; Validat	96.99
KOG0989		346	consensus Replication factor C, subunit RFC4 [Repl	96.98
PRK12323		700	DNA polymerase III subunits gamma and tau; Provisi	96.96
PRK00771		437	signal recognition particle protein Srp54; Provisi	96.93
PRK08116		268	hypothetical protein; Validated	96.81
PRK14087		450	dnaA chromosomal replication initiation protein; P	96.79
PRK05642		234	DNA replication initiation factor; Validated	96.78
PF13871		278	Helicase_C_4: Helicase_C-like	96.78
smart00492		141	HELICc3 helicase superfamily c-terminal domain.	96.77
PRK14960		702	DNA polymerase III subunits gamma and tau; Provisi	96.77
PRK06893		229	DNA replication initiation factor; Validated	96.75
KOG0701		1606	consensus dsRNA-specific nuclease Dicer and relate	96.75
PRK12726		407	flagellar biosynthesis regulator FlhF; Provisional	96.72
PRK11331		459	5-methylcytosine-specific restriction enzyme subun	96.7
PRK14949		944	DNA polymerase III subunits gamma and tau; Provisi	96.7
PRK14723		767	flhF flagellar biosynthesis regulator FlhF; Provis	96.7
COG1444		758	Predicted P-loop ATPase fused to an acetyltransfer	96.7
PRK14951		618	DNA polymerase III subunits gamma and tau; Provisi	96.68
PRK07994		647	DNA polymerase III subunits gamma and tau; Validat	96.68
PRK14964		491	DNA polymerase III subunits gamma and tau; Provisi	96.68
KOG0298		1394	consensus DEAD box-containing helicase-like transc	96.66
COG3421		812	Uncharacterized protein conserved in bacteria [Fun	96.65
PRK14958		509	DNA polymerase III subunits gamma and tau; Provisi	96.65
TIGR03420		226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.64
PRK08727		233	hypothetical protein; Validated	96.64
PRK12377		248	putative replication protein; Provisional	96.61
cd01120		165	RecA-like_NTPases RecA-like NTPases. This family i	96.6
PRK07952		244	DNA replication protein DnaC; Validated	96.6
PRK14712		1623	conjugal transfer nickase/helicase TraI; Provision	96.59
smart00491		142	HELICc2 helicase superfamily c-terminal domain.	96.58
PRK00149		450	dnaA chromosomal replication initiation protein; R	96.57
PRK08084		235	DNA replication initiation factor; Provisional	96.57
PHA02533		534	17 large terminase protein; Provisional	96.56
PHA02544		316	44 clamp loader, small subunit; Provisional	96.54
COG2805		353	PilT Tfp pilus assembly protein, pilus retraction	96.53
PRK13709		1747	conjugal transfer nickase/helicase TraI; Provision	96.52
PRK14952		584	DNA polymerase III subunits gamma and tau; Provisi	96.45
TIGR01547		396	phage_term_2 phage terminase, large subunit, PBSX	96.45
TIGR01425		429	SRP54_euk signal recognition particle protein SRP5	96.45
PRK06921		266	hypothetical protein; Provisional	96.45
PF03354		477	Terminase_1: Phage Terminase ; InterPro: IPR005021	96.44
cd01124		187	KaiC KaiC is a circadian clock protein primarily f	96.43
PRK00411		394	cdc6 cell division control protein 6; Reviewed	96.42
PRK09111		598	DNA polymerase III subunits gamma and tau; Validat	96.42
PRK08691		709	DNA polymerase III subunits gamma and tau; Validat	96.4
PRK05707		328	DNA polymerase III subunit delta'; Validated	96.4
PRK14965		576	DNA polymerase III subunits gamma and tau; Provisi	96.38
PRK06731		270	flhF flagellar biosynthesis regulator FlhF; Valida	96.37
PF00308		219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	96.37
TIGR02881		261	spore_V_K stage V sporulation protein K. Members o	96.36
PF13177		162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.35
PRK06835		329	DNA replication protein DnaC; Validated	96.34
PRK06645		507	DNA polymerase III subunits gamma and tau; Validat	96.32
TIGR00362		405	DnaA chromosomal replication initiator protein Dna	96.32
PTZ00293		211	thymidine kinase; Provisional	96.3
PRK14721		420	flhF flagellar biosynthesis regulator FlhF; Provis	96.29
TIGR00064		272	ftsY signal recognition particle-docking protein F	96.28
PRK06995		484	flhF flagellar biosynthesis regulator FlhF; Valida	96.27
PRK10919		672	ATP-dependent DNA helicase Rep; Provisional	96.25
COG2256		436	MGS1 ATPase related to the helicase subunit of the	96.23
PRK11054		684	helD DNA helicase IV; Provisional	96.21
PRK14961		363	DNA polymerase III subunits gamma and tau; Provisi	96.2
PRK08903		227	DnaA regulatory inactivator Hda; Validated	96.18
PRK14959		624	DNA polymerase III subunits gamma and tau; Provisi	96.17
PF13173		128	AAA_14: AAA domain	96.17
COG2909		894	MalT ATP-dependent transcriptional regulator [Tran	96.15
PLN03025		319	replication factor C subunit; Provisional	96.14
PRK14969		527	DNA polymerase III subunits gamma and tau; Provisi	96.13
PRK10867		433	signal recognition particle protein; Provisional	96.08
PRK05563		559	DNA polymerase III subunits gamma and tau; Validat	96.01
PRK12402		337	replication factor C small subunit 2; Reviewed	95.99
PRK12724		432	flagellar biosynthesis regulator FlhF; Provisional	95.99
PTZ00112		1164	origin recognition complex 1 protein; Provisional	95.98
KOG2028		554	consensus ATPase related to the helicase subunit o	95.96
TIGR03499		282	FlhF flagellar biosynthetic protein FlhF.	95.95
PRK14962		472	DNA polymerase III subunits gamma and tau; Provisi	95.94
PRK07471		365	DNA polymerase III subunit delta'; Validated	95.94
cd03115		173	SRP The signal recognition particle (SRP) mediates	95.93
PHA03333		752	putative ATPase subunit of terminase; Provisional	95.92
PF05876		557	Terminase_GpA: Phage terminase large subunit (GpA)	95.91
PRK14088		440	dnaA chromosomal replication initiation protein; P	95.9
PRK08769		319	DNA polymerase III subunit delta'; Validated	95.87
PRK13833		323	conjugal transfer protein TrbB; Provisional	95.85
PRK14086		617	dnaA chromosomal replication initiation protein; P	95.84
PRK14955		397	DNA polymerase III subunits gamma and tau; Provisi	95.84
PRK04195		482	replication factor C large subunit; Provisional	95.8
TIGR02785		1232	addA_Gpos recombination helicase AddA, Firmicutes	95.79
TIGR01075		715	uvrD DNA helicase II. Designed to identify uvrD me	95.77
PRK14957		546	DNA polymerase III subunits gamma and tau; Provisi	95.75
PRK09183		259	transposase/IS protein; Provisional	95.75
TIGR01074		664	rep ATP-dependent DNA helicase Rep. Designed to id	95.74
PF05496		233	RuvB_N: Holliday junction DNA helicase ruvB N-term	95.73
CHL00181		287	cbbX CbbX; Provisional	95.73
PRK05896		605	DNA polymerase III subunits gamma and tau; Validat	95.72
COG3973		747	Superfamily I DNA and RNA helicases [General funct	95.7
cd00561		159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.69
KOG0058		716	consensus Peptide exporter, ABC superfamily [Intra	95.69
TIGR02525		372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	95.66
TIGR00959		428	ffh signal recognition particle protein. This mode	95.66
PRK08451		535	DNA polymerase III subunits gamma and tau; Validat	95.66
TIGR02760		1960	TraI_TIGR conjugative transfer relaxase protein Tr	95.66
PRK11773		721	uvrD DNA-dependent helicase II; Provisional	95.66
KOG0991		333	consensus Replication factor C, subunit RFC2 [Repl	95.64
TIGR00678		188	holB DNA polymerase III, delta' subunit. At positi	95.63
COG1110		1187	Reverse gyrase [DNA replication, recombination, an	95.63
PF00004		132	AAA: ATPase family associated with various cellula	95.63
PRK14963		504	DNA polymerase III subunits gamma and tau; Provisi	95.63
COG1484		254	DnaC DNA replication protein [DNA replication, rec	95.62
PRK12422		445	chromosomal replication initiation protein; Provis	95.61
PF05621		302	TniB: Bacterial TniB protein; InterPro: IPR008868	95.59
COG1435		201	Tdk Thymidine kinase [Nucleotide transport and met	95.58
PRK08699		325	DNA polymerase III subunit delta'; Validated	95.58
PRK14954		620	DNA polymerase III subunits gamma and tau; Provisi	95.57
COG0470		325	HolB ATPase involved in DNA replication [DNA repli	95.54
COG2804		500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	95.53
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	95.45
PHA03368		738	DNA packaging terminase subunit 1; Provisional	95.45
PRK13341		725	recombination factor protein RarA/unknown domain f	95.44
PRK05986		191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	95.44
TIGR02928		365	orc1/cdc6 family replication initiation protein. M	95.43
TIGR02782		299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.41
PRK13894		319	conjugal transfer ATPase TrbB; Provisional	95.41
TIGR02880		284	cbbX_cfxQ probable Rubsico expression protein CbbX	95.38
cd01122		271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.37
TIGR02524		358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	95.37
PRK10416		318	signal recognition particle-docking protein FtsY;	95.34
PF01443		234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	95.31
COG4962		355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	95.24
PRK08533		230	flagellar accessory protein FlaH; Reviewed	95.24
PRK14950		585	DNA polymerase III subunits gamma and tau; Provisi	95.24
PRK13342		413	recombination factor protein RarA; Reviewed	95.23
PF06745		226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.2
PRK00440		319	rfc replication factor C small subunit; Reviewed	95.2
COG0593		408	DnaA ATPase involved in DNA replication initiation	95.15
COG2109		198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	95.14
PRK04841		903	transcriptional regulator MalT; Provisional	95.09
PRK11823		446	DNA repair protein RadA; Provisional	95.09
PRK09112		351	DNA polymerase III subunit delta'; Validated	95.06
PF05729		166	NACHT: NACHT domain	95.02
TIGR00708		173	cobA cob(I)alamin adenosyltransferase. Alternate n	94.98
PRK05580		679	primosome assembly protein PriA; Validated	94.92
TIGR03015		269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	94.91
PHA00729		226	NTP-binding motif containing protein	94.88
COG4626		546	Phage terminase-like protein, large subunit [Gener	94.84
PRK14948		620	DNA polymerase III subunits gamma and tau; Provisi	94.83
COG1474		366	CDC6 Cdc6-related protein, AAA superfamily ATPase	94.75
PRK06647		563	DNA polymerase III subunits gamma and tau; Validat	94.72
COG3972		660	Superfamily I DNA and RNA helicases [General funct	94.72
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	94.71
KOG1513		1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	94.71
PRK07940		394	DNA polymerase III subunit delta'; Validated	94.7
PRK06620		214	hypothetical protein; Validated	94.63
cd00984		242	DnaB_C DnaB helicase C terminal domain. The hexame	94.62
TIGR03881		229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	94.59
COG0552		340	FtsY Signal recognition particle GTPase [Intracell	94.53
TIGR00595		505	priA primosomal protein N'. All proteins in this f	94.53
PRK14971		614	DNA polymerase III subunits gamma and tau; Provisi	94.52
PRK06305		451	DNA polymerase III subunits gamma and tau; Validat	94.52
cd01121		372	Sms Sms (bacterial radA) DNA repair protein. This	94.48
PRK06871		325	DNA polymerase III subunit delta'; Validated	94.46
PRK06964		342	DNA polymerase III subunit delta'; Validated	94.4
TIGR01073		726	pcrA ATP-dependent DNA helicase PcrA. Designed to	94.4
COG1132		567	MdlB ABC-type multidrug transport system, ATPase a	94.35
PRK08939		306	primosomal protein DnaI; Reviewed	94.28
PRK14953		486	DNA polymerase III subunits gamma and tau; Provisi	94.16
TIGR02397		355	dnaX_nterm DNA polymerase III, subunit gamma and t	94.12
COG1618		179	Predicted nucleotide kinase [Nucleotide transport	94.11
PRK07133		725	DNA polymerase III subunits gamma and tau; Validat	94.1
PRK13851		344	type IV secretion system protein VirB11; Provision	94.07
PF03266		168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	93.99
TIGR00767		415	rho transcription termination factor Rho. Members	93.97
PHA00350		399	putative assembly protein	93.93
PRK13900		332	type IV secretion system ATPase VirB11; Provisiona	93.92
PF00265		176	TK: Thymidine kinase; InterPro: IPR001267 Thymidin	93.92
PRK10436		462	hypothetical protein; Provisional	93.91
PRK06090		319	DNA polymerase III subunit delta'; Validated	93.9
PF03969		362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	93.86
PF02572		172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	93.85
TIGR00580		926	mfd transcription-repair coupling factor (mfd). Al	93.84
COG5008		375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	93.81
KOG0738		491	consensus AAA+-type ATPase [Posttranslational modi	93.77
TIGR02639		731	ClpA ATP-dependent Clp protease ATP-binding subuni	93.69
TIGR01420		343	pilT_fam pilus retraction protein PilT. This model	93.69
TIGR00635		305	ruvB Holliday junction DNA helicase, RuvB subunit.	93.67
TIGR02868		529	CydC thiol reductant ABC exporter, CydC subunit. T	93.65
PRK06067		234	flagellar accessory protein FlaH; Validated	93.64
KOG0742		630	consensus AAA+-type ATPase [Posttranslational modi	93.52
PRK07993		334	DNA polymerase III subunit delta'; Validated	93.46
COG1222		406	RPT1 ATP-dependent 26S proteasome regulatory subun	93.44
PRK14873		665	primosome assembly protein PriA; Provisional	93.38
PRK11034		758	clpA ATP-dependent Clp protease ATP-binding subuni	93.28
cd01129		264	PulE-GspE PulE/GspE The type II secretory pathway	93.28
COG1219		408	ClpX ATP-dependent protease Clp, ATPase subunit [P	93.17
KOG1133		821	consensus Helicase of the DEAD superfamily [Replic	93.15
COG2255		332	RuvB Holliday junction resolvasome, helicase subun	93.15
TIGR02237		209	recomb_radB DNA repair and recombination protein R	93.1
TIGR03877		237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	93.06
cd01131		198	PilT Pilus retraction ATPase PilT. PilT is a nucle	93.01
TIGR02533		486	type_II_gspE general secretory pathway protein E.	93.01
PF03237		384	Terminase_6: Terminase-like family; InterPro: IPR0	92.97
PRK10689		1147	transcription-repair coupling factor; Provisional	92.92
PRK07414		178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	92.92
PF00437		270	T2SE: Type II/IV secretion system protein; InterPr	92.88
KOG1133		821	consensus Helicase of the DEAD superfamily [Replic	92.86
PRK07413		382	hypothetical protein; Validated	92.82
PRK09087		226	hypothetical protein; Validated	92.8
PRK00080		328	ruvB Holliday junction DNA helicase RuvB; Reviewed	92.77
KOG0739		439	consensus AAA+-type ATPase [Posttranslational modi	92.72
TIGR02538		564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	92.72
TIGR02655		484	circ_KaiC circadian clock protein KaiC. Members of	92.72
TIGR00763		775	lon ATP-dependent protease La. This protein is ind	92.64
PRK05973		237	replicative DNA helicase; Provisional	92.62
cd01128		249	rho_factor Transcription termination factor rho is	92.61
cd01126		384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	92.6
PRK14970		367	DNA polymerase III subunits gamma and tau; Provisi	92.55
PRK09376		416	rho transcription termination factor Rho; Provisio	92.5
KOG0741		744	consensus AAA+-type ATPase [Posttranslational modi	92.5
COG0541		451	Ffh Signal recognition particle GTPase [Intracellu	92.41
COG0513		513	SrmB Superfamily II DNA and RNA helicases [DNA rep	92.36
PRK13764		602	ATPase; Provisional	92.3
PF01695		178	IstB_IS21: IstB-like ATP binding protein; InterPro	92.29
PRK07399		314	DNA polymerase III subunit delta'; Validated	92.1
TIGR03346		852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	92.03
PRK08058		329	DNA polymerase III subunit delta'; Validated	92.0
PF02534		469	T4SS-DNA_transf: Type IV secretory system Conjugat	91.99
cd03239		178	ABC_SMC_head The structural maintenance of chromos	91.74
PRK09354		349	recA recombinase A; Provisional	91.74
cd03221		144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	91.66
PHA00012		361	I assembly protein	91.64
cd01130		186	VirB11-like_ATPase Type IV secretory pathway compo	91.57
COG1855		604	ATPase (PilT family) [General function prediction	91.54
PRK10865		857	protein disaggregation chaperone; Provisional	91.53
TIGR00416		454	sms DNA repair protein RadA. The gene protuct code	91.51
TIGR03878		259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	91.46
PRK13897		606	type IV secretion system component VirD4; Provisio	91.44
TIGR02858		270	spore_III_AA stage III sporulation protein AA. Mem	91.43
PHA03372		668	DNA packaging terminase subunit 1; Provisional	91.42
PF12846		304	AAA_10: AAA-like domain	91.39
TIGR01243		733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	91.33
TIGR00602		637	rad24 checkpoint protein rad24. This family is bas	91.12
cd03247		178	ABCC_cytochrome_bd The CYD subfamily implicated in	91.1
CHL00095		821	clpC Clp protease ATP binding subunit	91.05
PRK13695		174	putative NTPase; Provisional	91.04
cd01393		226	recA_like RecA is a bacterial enzyme which has rol	90.95
COG2812		515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	90.92
PRK14701		1638	reverse gyrase; Provisional	90.9
TIGR02688		449	conserved hypothetical protein TIGR02688. Members	90.87
PF02606		326	LpxK: Tetraacyldisaccharide-1-P 4'-kinase; InterPr	90.87
COG2874		235	FlaH Predicted ATPases involved in biogenesis of a	90.85
TIGR03600		421	phage_DnaB phage replicative helicase, DnaB family	90.81
KOG0737		386	consensus AAA+-type ATPase [Posttranslational modi	90.81
cd03276		198	ABC_SMC6_euk Eukaryotic SMC6 proteins; SMC protein	90.78
PRK04328		249	hypothetical protein; Provisional	90.78
PF03796		259	DnaB_C: DnaB-like helicase C terminal domain; Inte	90.6
TIGR02640		262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	90.51
PF01637		234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	90.5
PRK13850		670	type IV secretion system protein VirD4; Provisiona	90.45
PRK11634		629	ATP-dependent RNA helicase DeaD; Provisional	90.36
cd03228		171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	90.32
PLN00020		413	ribulose bisphosphate carboxylase/oxygenase activa	90.29
PF08423		256	Rad51: Rad51; InterPro: IPR013632 This domain is f	90.23
KOG0780		483	consensus Signal recognition particle, subunit Srp	90.19
KOG0744		423	consensus AAA+-type ATPase [Posttranslational modi	90.16
PF13555		62	AAA_29: P-loop containing region of AAA domain	90.11
cd01125		239	repA Hexameric Replicative Helicase RepA. RepA is	89.95
CHL00176		638	ftsH cell division protein; Validated	89.92
TIGR02788		308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	89.89
KOG2227		529	consensus Pre-initiation complex, subunit CDC6, AA	89.84
cd03238		176	ABC_UvrA The excision repair protein UvrA; Nucleot	89.79
PF06733		174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	89.73
COG1200		677	RecG RecG-like helicase [DNA replication, recombin	89.72
KOG1513		1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	89.64
COG1198		730	PriA Primosomal protein N' (replication factor Y)	89.61
COG0630		312	VirB11 Type IV secretory pathway, VirB11 component	89.59
PF12775		272	AAA_7: P-loop containing dynein motor region D3; P	89.56
cd00268		203	DEADc DEAD-box helicases. A diverse family of prot	89.53
KOG0734		752	consensus AAA+-type ATPase containing the peptidas	89.49
PRK10787		784	DNA-binding ATP-dependent protease La; Provisional	89.45
TIGR03819		340	heli_sec_ATPase helicase/secretion neighborhood AT	89.31
TIGR02203		571	MsbA_lipidA lipid A export permease/ATP-binding pr	89.31

>KOG0326 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

Probab=100.00  E-value=5.2e-77  Score=530.22  Aligned_cols=389  Identities=77%  Similarity=1.166  Sum_probs=377.1

Q ss_pred             CCCCchhHhhhcCCCCCCCCccccccccCCCCcccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhcCCCEEEEccCCC
Q 011462           89 VDPSSQDWKARLKIPPADTRYRTEDVTATKGNEFEDYFLKRELLMGIFEKGFERPSPIQEESIPIALTGSDILARAKNGT  168 (485)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~ii~~~TGs  168 (485)
                      .+....+|+...+.|+.+.++.++++...+..+|+++.|.++++..++++||+.|.|+|.++||.++.|+|+++.|..|+
T Consensus        54 ~~~~~~dwk~~l~lpp~d~R~~t~DVt~TkG~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGT  133 (459)
T KOG0326|consen   54 EEANGKDWKATLKLPPKDTRYKTEDVTATKGNEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGT  133 (459)
T ss_pred             ccccchhhHHhccCCCCCccccccccccccCccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCC
Confidence            33478899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhHHhHHHHHhhhhccCCceEEEEEcCcHHHHHHHHHHHHHHhccCCceEEEEECCCChHHHHHHhcCCCeEEEEcchH
Q 011462          169 GKTAAFCIPALEKIDQDNNVIQVVILVPTRELALQTSQVCKELGKHLNIQVMVTTGGTSLKDDIMRLYQPVHLLVGTPGR  248 (485)
Q Consensus       169 GKT~~~~~~~l~~l~~~~~~~~~lil~P~~~la~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~Ili~Tp~~  248 (485)
                      |||.+|.+|+++.+....+..+++|++|+|+||.|+.+.++++.+.+++.++..+||++.++++.++.+..+++|+|||+
T Consensus       134 GKT~a~~IP~Lekid~~~~~IQ~~ilVPtrelALQtSqvc~~lskh~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGR  213 (459)
T KOG0326|consen  134 GKTAAYCIPVLEKIDPKKNVIQAIILVPTRELALQTSQVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGR  213 (459)
T ss_pred             CCccceechhhhhcCccccceeEEEEeecchhhHHHHHHHHHHhcccCeEEEEecCCcccccceeeecCceEEEEcCChh
Confidence            99999999999999998888999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhcCccccCCcceEEeeccccccCCCCHHHHHHHHHhCCCCCcEEEEecccchHHHHHHHHhcCCCeEEeeccccc
Q 011462          249 ILDLSKKGVCILKDCSMLVMDEADKLLSPEFQPSVEQLIRFLPANRQILMFSATFPVTVKDFKDKYLQKPYVINLMDELT  328 (485)
Q Consensus       249 l~~~~~~~~~~l~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SATl~~~~~~~~~~~~~~~~~~~~~~~~~  328 (485)
                      ++++..++...++++.++|+||||.+++.+|.+.+..++..+|+++|++++|||+|..+..|..+++.+|+.+++.++..
T Consensus       214 IlDL~~KgVa~ls~c~~lV~DEADKlLs~~F~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM~eLt  293 (459)
T KOG0326|consen  214 ILDLAKKGVADLSDCVILVMDEADKLLSVDFQPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLMEELT  293 (459)
T ss_pred             HHHHHhcccccchhceEEEechhhhhhchhhhhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceeehhhhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccceEEEEeehhhhhHHHHHHHHHhcCCCcEEEEecChhHHHHHHHHHHHcCCeEEEEcCCCCHHHHHHHHHHHhcCCc
Q 011462          329 LKGITQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSVNRVELLAKKITELGYSCFYIHAKMLQDHRNRVFHDFRNGAC  408 (485)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~i~~~f~~g~~  408 (485)
                      ..++.+||.++.+..|..+|..++.+..-.+.|||||+...+|.+++.+.++|+.+.++|+.|.++.|.++|+.|++|.+
T Consensus       294 l~GvtQyYafV~e~qKvhCLntLfskLqINQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~c  373 (459)
T KOG0326|consen  294 LKGVTQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKC  373 (459)
T ss_pred             hcchhhheeeechhhhhhhHHHHHHHhcccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhcccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEccccccCCCCCCCCEEEEcCCCCChHHHHHHhhhccccCcccccc-------hHHHHHHHHHhhccccccC
Q 011462          409 RNLVCTDLFTRGIDIQAVNVVINFDFPKNSETYLHRVCWIQLSFSLSLPN-------LQFMCSMLMYICFTDRLVD  477 (485)
Q Consensus       409 ~vlvaT~~~~~Gidi~~v~~VI~~~~p~s~~~~~Qr~GRagR~g~~~~~~-------~~~~~~~~~~~~~~~~~~~  477 (485)
                      +.||||+.+.||||+++|++||+||+|++.++|.||+||+||.|++|.+-       ...+..++..+..+++.++
T Consensus       374 rnLVctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFGhlGlAInLityedrf~L~~IE~eLGtEI~pip  449 (459)
T KOG0326|consen  374 RNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYEDRFNLYRIEQELGTEIKPIP  449 (459)
T ss_pred             ceeeehhhhhcccccceeeEEEecCCCCCHHHHHHHccCCccCCCcceEEEEEehhhhhhHHHHHHHhccccccCC
Confidence            99999999999999999999999999999999999999999999999874       3356778888988888776

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0330 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

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

>PTZ00110 helicase; Provisional	Back alignment and domain information

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

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional	Back alignment and domain information

>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]	Back alignment and domain information

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional	Back alignment and domain information

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>KOG0338 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]	Back alignment and domain information

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional	Back alignment and domain information

>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>KOG0343 consensus RNA Helicase [RNA processing and modification]	Back alignment and domain information

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional	Back alignment and domain information

>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional	Back alignment and domain information

>KOG0340 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>PTZ00424 helicase 45; Provisional	Back alignment and domain information

>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]	Back alignment and domain information

>KOG0347 consensus RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0348 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0346 consensus RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0332 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase	Back alignment and domain information

>KOG4284 consensus DEAD box protein [Transcription]	Back alignment and domain information

>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional	Back alignment and domain information

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

>KOG0334 consensus RNA helicase [RNA processing and modification]	Back alignment and domain information

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family	Back alignment and domain information

>KOG0337 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0350 consensus DEAD-box ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional	Back alignment and domain information

>TIGR01389 recQ ATP-dependent DNA helicase RecQ	Back alignment and domain information

>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK02362 ski2-like helicase; Provisional	Back alignment and domain information

>PRK13767 ATP-dependent helicase; Provisional	Back alignment and domain information

>PRK00254 ski2-like helicase; Provisional	Back alignment and domain information

>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype	Back alignment and domain information

>KOG0329 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>COG1201 Lhr Lhr-like helicases [General function prediction only]	Back alignment and domain information

>KOG0344 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>PRK01172 ski2-like helicase; Provisional	Back alignment and domain information

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB	Back alignment and domain information

>TIGR00580 mfd transcription-repair coupling factor (mfd)	Back alignment and domain information

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional	Back alignment and domain information

>PRK10689 transcription-repair coupling factor; Provisional	Back alignment and domain information

>PHA02653 RNA helicase NPH-II; Provisional	Back alignment and domain information

>PRK09751 putative ATP-dependent helicase Lhr; Provisional	Back alignment and domain information

>PRK10917 ATP-dependent DNA helicase RecG; Provisional	Back alignment and domain information

>TIGR00643 recG ATP-dependent DNA helicase RecG	Back alignment and domain information

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]	Back alignment and domain information

>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]	Back alignment and domain information

>PRK09401 reverse gyrase; Reviewed	Back alignment and domain information

>PRK14701 reverse gyrase; Provisional	Back alignment and domain information

>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]	Back alignment and domain information

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional	Back alignment and domain information

>TIGR01587 cas3_core CRISPR-associated helicase Cas3	Back alignment and domain information

>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK12898 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PHA02558 uvsW UvsW helicase; Provisional	Back alignment and domain information

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

>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]	Back alignment and domain information

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>COG1204 Superfamily II helicase [General function prediction only]	Back alignment and domain information

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type	Back alignment and domain information

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA	Back alignment and domain information

>KOG0349 consensus Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]	Back alignment and domain information

>PRK09200 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]	Back alignment and domain information

>TIGR03714 secA2 accessory Sec system translocase SecA2	Back alignment and domain information

>TIGR01054 rgy reverse gyrase	Back alignment and domain information

>TIGR00963 secA preprotein translocase, SecA subunit	Back alignment and domain information

>PRK13766 Hef nuclease; Provisional	Back alignment and domain information

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]	Back alignment and domain information

>KOG0354 consensus DEAD-box like helicase [General function prediction only]	Back alignment and domain information

>TIGR00603 rad25 DNA repair helicase rad25	Back alignment and domain information

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

>PRK09694 helicase Cas3; Provisional	Back alignment and domain information

>cd00268 DEADc DEAD-box helicases	Back alignment and domain information

>PRK04914 ATP-dependent helicase HepA; Validated	Back alignment and domain information

>PRK05580 primosome assembly protein PriA; Validated	Back alignment and domain information

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

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

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

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

>PRK13104 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]	Back alignment and domain information

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

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

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

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

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

>PRK12904 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>TIGR00595 priA primosomal protein N'	Back alignment and domain information

>PRK12899 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PRK12906 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional	Back alignment and domain information

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional	Back alignment and domain information

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

>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]	Back alignment and domain information

>PRK13107 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]	Back alignment and domain information

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]	Back alignment and domain information

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]	Back alignment and domain information

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK12326 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PRK12900 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative	Back alignment and domain information

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family	Back alignment and domain information

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]	Back alignment and domain information

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

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

>smart00487 DEXDc DEAD-like helicases superfamily	Back alignment and domain information

>TIGR00631 uvrb excinuclease ABC, B subunit	Back alignment and domain information

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]	Back alignment and domain information

>PRK13103 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

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

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK12903 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]	Back alignment and domain information

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK05298 excinuclease ABC subunit B; Provisional	Back alignment and domain information

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]	Back alignment and domain information

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]	Back alignment and domain information

>CHL00122 secA preprotein translocase subunit SecA; Validated	Back alignment and domain information

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]	Back alignment and domain information

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]	Back alignment and domain information

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]	Back alignment and domain information

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins	Back alignment and domain information

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

Back alignment and domain information

>cd00046 DEXDc DEAD-like helicases superfamily	Back alignment and domain information

>COG4889 Predicted helicase [General function prediction only]	Back alignment and domain information

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

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4	Back alignment and domain information

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3	Back alignment and domain information

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK12902 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>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	Back alignment and domain information

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]	Back alignment and domain information

>smart00490 HELICc helicase superfamily c-terminal domain	Back alignment and domain information

>PRK12901 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]	Back alignment and domain information

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]	Back alignment and domain information

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]	Back alignment and domain information

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein	Back alignment and domain information

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional	Back alignment and domain information

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

>TIGR00604 rad3 DNA repair helicase (rad3)	Back alignment and domain information

>PRK14873 primosome assembly protein PriA; Provisional	Back alignment and domain information

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]	Back alignment and domain information

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]	Back alignment and domain information

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]	Back alignment and domain information

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]	Back alignment and domain information

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain	Back alignment and domain information

>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	Back alignment and domain information

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]	Back alignment and domain information

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>smart00489 DEXDc3 DEAD-like helicases superfamily	Back alignment and domain information

>smart00488 DEXDc2 DEAD-like helicases superfamily	Back alignment and domain information

>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	Back alignment and domain information

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

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]	Back alignment and domain information

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional	Back alignment and domain information

>COG3587 Restriction endonuclease [Defense mechanisms]	Back alignment and domain information

>TIGR00596 rad1 DNA repair protein (rad1)	Back alignment and domain information

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

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A	Back alignment and domain information

>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 []	Back alignment and domain information

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1	Back alignment and domain information

>PRK10536 hypothetical protein; Provisional	Back alignment and domain information

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]	Back alignment and domain information

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit	Back alignment and domain information

>PRK10875 recD exonuclease V subunit alpha; Provisional	Back alignment and domain information

>TIGR01448 recD_rel helicase, putative, RecD/TraA family	Back alignment and domain information

>KOG1803 consensus DNA helicase [Replication, recombination and repair]	Back alignment and domain information

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function	Back alignment and domain information

>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]	Back alignment and domain information

>PF13307 Helicase_C_2: Helicase C-terminal domain; PDB: 4A15_A 2VSF_A 3CRV_A 3CRW_1 2VL7_A	Back alignment and domain information

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length	Back alignment and domain information

>PF13245 AAA_19: Part of AAA domain	Back alignment and domain information

>KOG0383 consensus Predicted helicase [General function prediction only]	Back alignment and domain information

>TIGR00376 DNA helicase, putative	Back alignment and domain information

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]	Back alignment and domain information

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

>PRK13889 conjugal transfer relaxase TraA; Provisional	Back alignment and domain information

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA	Back alignment and domain information

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]	Back alignment and domain information

>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 [, ]	Back alignment and domain information

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B	Back alignment and domain information

>PRK04296 thymidine kinase; Provisional	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>PRK13826 Dtr system oriT relaxase; Provisional	Back alignment and domain information

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]	Back alignment and domain information

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated	Back alignment and domain information

>PRK14974 cell division protein FtsY; Provisional	Back alignment and domain information

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]	Back alignment and domain information

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

>PRK06526 transposase; Provisional	Back alignment and domain information

>smart00382 AAA ATPases associated with a variety of cellular activities	Back alignment and domain information

>PRK08181 transposase; Validated	Back alignment and domain information

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI	Back alignment and domain information

>KOG1131 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription; Replication, recombination and repair]	Back alignment and domain information

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins	Back alignment and domain information

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

>PRK07764 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase	Back alignment and domain information

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit	Back alignment and domain information

>PRK07003 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]	Back alignment and domain information

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK00771 signal recognition particle protein Srp54; Provisional	Back alignment and domain information

>PRK08116 hypothetical protein; Validated	Back alignment and domain information

>PRK14087 dnaA chromosomal replication initiation protein; Provisional	Back alignment and domain information

>PRK05642 DNA replication initiation factor; Validated	Back alignment and domain information

>PF13871 Helicase_C_4: Helicase_C-like	Back alignment and domain information

>smart00492 HELICc3 helicase superfamily c-terminal domain	Back alignment and domain information

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK06893 DNA replication initiation factor; Validated	Back alignment and domain information

>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]	Back alignment and domain information

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional	Back alignment and domain information

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]	Back alignment and domain information

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK07994 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]	Back alignment and domain information

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]	Back alignment and domain information

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda	Back alignment and domain information

>PRK08727 hypothetical protein; Validated	Back alignment and domain information

>PRK12377 putative replication protein; Provisional	Back alignment and domain information

>cd01120 RecA-like_NTPases RecA-like NTPases	Back alignment and domain information

>PRK07952 DNA replication protein DnaC; Validated	Back alignment and domain information

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional	Back alignment and domain information

>smart00491 HELICc2 helicase superfamily c-terminal domain	Back alignment and domain information

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed	Back alignment and domain information

>PRK08084 DNA replication initiation factor; Provisional	Back alignment and domain information

>PHA02533 17 large terminase protein; Provisional	Back alignment and domain information

>PHA02544 44 clamp loader, small subunit; Provisional	Back alignment and domain information

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]	Back alignment and domain information

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional	Back alignment and domain information

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family	Back alignment and domain information

>TIGR01425 SRP54_euk signal recognition particle protein SRP54	Back alignment and domain information

>PRK06921 hypothetical protein; Provisional	Back alignment and domain information

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)	Back alignment and domain information

>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	Back alignment and domain information

>PRK00411 cdc6 cell division control protein 6; Reviewed	Back alignment and domain information

>PRK09111 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>PRK08691 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>PRK05707 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated	Back alignment and domain information

>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	Back alignment and domain information

>TIGR02881 spore_V_K stage V sporulation protein K	Back alignment and domain information

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A	Back alignment and domain information

>PRK06835 DNA replication protein DnaC; Validated	Back alignment and domain information

>PRK06645 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>TIGR00362 DnaA chromosomal replication initiator protein DnaA	Back alignment and domain information

>PTZ00293 thymidine kinase; Provisional	Back alignment and domain information

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

>TIGR00064 ftsY signal recognition particle-docking protein FtsY	Back alignment and domain information

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated	Back alignment and domain information

>PRK10919 ATP-dependent DNA helicase Rep; Provisional	Back alignment and domain information

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK11054 helD DNA helicase IV; Provisional	Back alignment and domain information

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK08903 DnaA regulatory inactivator Hda; Validated	Back alignment and domain information

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PF13173 AAA_14: AAA domain	Back alignment and domain information

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]	Back alignment and domain information

>PLN03025 replication factor C subunit; Provisional	Back alignment and domain information

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK10867 signal recognition particle protein; Provisional	Back alignment and domain information

>PRK05563 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>PRK12402 replication factor C small subunit 2; Reviewed	Back alignment and domain information

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

>PTZ00112 origin recognition complex 1 protein; Provisional	Back alignment and domain information

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]	Back alignment and domain information

>TIGR03499 FlhF flagellar biosynthetic protein FlhF	Back alignment and domain information

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK07471 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes	Back alignment and domain information

>PHA03333 putative ATPase subunit of terminase; Provisional	Back alignment and domain information

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA	Back alignment and domain information

>PRK14088 dnaA chromosomal replication initiation protein; Provisional	Back alignment and domain information

>PRK08769 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PRK13833 conjugal transfer protein TrbB; Provisional	Back alignment and domain information

>PRK14086 dnaA chromosomal replication initiation protein; Provisional	Back alignment and domain information

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK04195 replication factor C large subunit; Provisional	Back alignment and domain information

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type	Back alignment and domain information

>TIGR01075 uvrD DNA helicase II	Back alignment and domain information

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK09183 transposase/IS protein; Provisional	Back alignment and domain information

>TIGR01074 rep ATP-dependent DNA helicase Rep	Back alignment and domain information

>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	Back alignment and domain information

>CHL00181 cbbX CbbX; Provisional	Back alignment and domain information

>PRK05896 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]	Back alignment and domain information

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP	Back alignment and domain information

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ	Back alignment and domain information

>TIGR00959 ffh signal recognition particle protein	Back alignment and domain information

>PRK08451 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI	Back alignment and domain information

>PRK11773 uvrD DNA-dependent helicase II; Provisional	Back alignment and domain information

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]	Back alignment and domain information

>TIGR00678 holB DNA polymerase III, delta' subunit	Back alignment and domain information

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]	Back alignment and domain information

>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	Back alignment and domain information

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK12422 chromosomal replication initiation protein; Provisional	Back alignment and domain information

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins	Back alignment and domain information

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]	Back alignment and domain information

>PRK08699 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]	Back alignment and domain information

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]	Back alignment and domain information

>PRK10917 ATP-dependent DNA helicase RecG; Provisional	Back alignment and domain information

>PHA03368 DNA packaging terminase subunit 1; Provisional	Back alignment and domain information

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed	Back alignment and domain information

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated	Back alignment and domain information

>TIGR02928 orc1/cdc6 family replication initiation protein	Back alignment and domain information

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB	Back alignment and domain information

>PRK13894 conjugal transfer ATPase TrbB; Provisional	Back alignment and domain information

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX	Back alignment and domain information

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases	Back alignment and domain information

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB	Back alignment and domain information

>PRK10416 signal recognition particle-docking protein FtsY; Provisional	Back alignment and domain information

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases	Back alignment and domain information

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]	Back alignment and domain information

>PRK08533 flagellar accessory protein FlaH; Reviewed	Back alignment and domain information

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK13342 recombination factor protein RarA; Reviewed	Back alignment and domain information

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical	Back alignment and domain information

>PRK00440 rfc replication factor C small subunit; Reviewed	Back alignment and domain information

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]	Back alignment and domain information

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]	Back alignment and domain information

>PRK04841 transcriptional regulator MalT; Provisional	Back alignment and domain information

>PRK11823 DNA repair protein RadA; Provisional	Back alignment and domain information

>PRK09112 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PF05729 NACHT: NACHT domain	Back alignment and domain information

>TIGR00708 cobA cob(I)alamin adenosyltransferase	Back alignment and domain information

>PRK05580 primosome assembly protein PriA; Validated	Back alignment and domain information

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily	Back alignment and domain information

>PHA00729 NTP-binding motif containing protein	Back alignment and domain information

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]	Back alignment and domain information

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK06647 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]	Back alignment and domain information

>TIGR00643 recG ATP-dependent DNA helicase RecG	Back alignment and domain information

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]	Back alignment and domain information

>PRK07940 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PRK06620 hypothetical protein; Validated	Back alignment and domain information

>cd00984 DnaB_C DnaB helicase C terminal domain	Back alignment and domain information

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family	Back alignment and domain information

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]	Back alignment and domain information

>TIGR00595 priA primosomal protein N'	Back alignment and domain information

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK06305 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>cd01121 Sms Sms (bacterial radA) DNA repair protein	Back alignment and domain information

>PRK06871 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PRK06964 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA	Back alignment and domain information

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	Back alignment and domain information

>PRK08939 primosomal protein DnaI; Reviewed	Back alignment and domain information

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau	Back alignment and domain information

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]	Back alignment and domain information

>PRK07133 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>PRK13851 type IV secretion system protein VirB11; Provisional	Back alignment and domain information

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []	Back alignment and domain information

>TIGR00767 rho transcription termination factor Rho	Back alignment and domain information

>PHA00350 putative assembly protein	Back alignment and domain information

>PRK13900 type IV secretion system ATPase VirB11; Provisional	Back alignment and domain information

>PF00265 TK: Thymidine kinase; InterPro: IPR001267 Thymidine kinase (TK) (2	Back alignment and domain information

>PRK10436 hypothetical protein; Provisional	Back alignment and domain information

>PRK06090 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP	Back alignment and domain information

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2	Back alignment and domain information

>TIGR00580 mfd transcription-repair coupling factor (mfd)	Back alignment and domain information

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]	Back alignment and domain information

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA	Back alignment and domain information

>TIGR01420 pilT_fam pilus retraction protein PilT	Back alignment and domain information

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit	Back alignment and domain information

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit	Back alignment and domain information

>PRK06067 flagellar accessory protein FlaH; Validated	Back alignment and domain information

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK07993 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK14873 primosome assembly protein PriA; Provisional	Back alignment and domain information

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional	Back alignment and domain information

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)	Back alignment and domain information

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]	Back alignment and domain information

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]	Back alignment and domain information

>TIGR02237 recomb_radB DNA repair and recombination protein RadB	Back alignment and domain information

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family	Back alignment and domain information

>cd01131 PilT Pilus retraction ATPase PilT	Back alignment and domain information

>TIGR02533 type_II_gspE general secretory pathway protein E	Back alignment and domain information

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []	Back alignment and domain information

>PRK10689 transcription-repair coupling factor; Provisional	Back alignment and domain information

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated	Back alignment and domain information

>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 [, ]	Back alignment and domain information

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]	Back alignment and domain information

>PRK07413 hypothetical protein; Validated	Back alignment and domain information

>PRK09087 hypothetical protein; Validated	Back alignment and domain information

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed	Back alignment and domain information

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB	Back alignment and domain information

>TIGR02655 circ_KaiC circadian clock protein KaiC	Back alignment and domain information

>TIGR00763 lon ATP-dependent protease La	Back alignment and domain information

>PRK05973 replicative DNA helicase; Provisional	Back alignment and domain information

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase	Back alignment and domain information

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion	Back alignment and domain information

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK09376 rho transcription termination factor Rho; Provisional	Back alignment and domain information

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]	Back alignment and domain information

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

>PRK13764 ATPase; Provisional	Back alignment and domain information

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif	Back alignment and domain information

>PRK07399 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB	Back alignment and domain information

>PRK08058 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues	Back alignment and domain information

>cd03239 ABC_SMC_head The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms	Back alignment and domain information

>PRK09354 recA recombinase A; Provisional	Back alignment and domain information

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth	Back alignment and domain information

>PHA00012 I assembly protein	Back alignment and domain information

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases	Back alignment and domain information

>COG1855 ATPase (PilT family) [General function prediction only]	Back alignment and domain information

>PRK10865 protein disaggregation chaperone; Provisional	Back alignment and domain information

>TIGR00416 sms DNA repair protein RadA	Back alignment and domain information

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family	Back alignment and domain information

>PRK13897 type IV secretion system component VirD4; Provisional	Back alignment and domain information

>TIGR02858 spore_III_AA stage III sporulation protein AA	Back alignment and domain information

>PHA03372 DNA packaging terminase subunit 1; Provisional	Back alignment and domain information

>PF12846 AAA_10: AAA-like domain	Back alignment and domain information

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily	Back alignment and domain information

>TIGR00602 rad24 checkpoint protein rad24	Back alignment and domain information

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis	Back alignment and domain information

>CHL00095 clpC Clp protease ATP binding subunit	Back alignment and domain information

>PRK13695 putative NTPase; Provisional	Back alignment and domain information

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response	Back alignment and domain information

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK14701 reverse gyrase; Provisional	Back alignment and domain information

>TIGR02688 conserved hypothetical protein TIGR02688	Back alignment and domain information

>PF02606 LpxK: Tetraacyldisaccharide-1-P 4'-kinase; InterPro: IPR003758 Tetraacyldisaccharide 4'-kinase phosphorylates the 4'-position of a tetraacyldisaccharide 1-phosphate precursor (DS-1-P) of lipid A, but the enzyme has not yet been purified because of instability []	Back alignment and domain information

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]	Back alignment and domain information

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily	Back alignment and domain information

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>cd03276 ABC_SMC6_euk Eukaryotic SMC6 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains	Back alignment and domain information

>PRK04328 hypothetical protein; Provisional	Back alignment and domain information

>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	Back alignment and domain information

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN	Back alignment and domain information

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP	Back alignment and domain information

>PRK13850 type IV secretion system protein VirD4; Provisional	Back alignment and domain information

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional	Back alignment and domain information

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export	Back alignment and domain information

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional	Back alignment and domain information

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51	Back alignment and domain information

>KOG0780 consensus Signal recognition particle, subunit Srp54 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF13555 AAA_29: P-loop containing region of AAA domain	Back alignment and domain information

>cd01125 repA Hexameric Replicative Helicase RepA	Back alignment and domain information

>CHL00176 ftsH cell division protein; Validated	Back alignment and domain information

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11	Back alignment and domain information

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion	Back alignment and domain information

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin	Back alignment and domain information

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

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]	Back alignment and domain information

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

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]	Back alignment and domain information

>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	Back alignment and domain information

>cd00268 DEADc DEAD-box helicases	Back alignment and domain information

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK10787 DNA-binding ATP-dependent protease La; Provisional	Back alignment and domain information

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase	Back alignment and domain information

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA	Back alignment and domain information

Homologous Structure Templates