match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	cd09178	134	133	99.2	4.8E-11	[---------                                        ]	PLDc_N_Snf2_like	N-terminal putative catalytic domain of uncharacterized HKD family nucleases fused to putative helicases from the Snf2-like family. N-terminal putative catalytic domain of uncharacterized archaeal and prokaryotic HKD family nucleases fused to putative helicases from the Snf2-like family, which belong to the DNA/RNA helicase superfamily II (SF2). Although Snf2-like family enzymes do not possess helicase activity, they contain a helicase-like region, where seven helicase-related sequence motifs are found, similar to those in DEAD/DEAH box helicases, which represent the biggest family within the SF2 superfamily. In addition to the helicase-like region, members of this family also contain an N-terminal putative catalytic domain with one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), and have been classified as members of the phospholipase D (PLD, EC 3.1.4.4) superfamily.
2	cd00079	131	93	98.3	5.4E-06	[                                  -----          ]	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
3	pfam00271	78	46	97.9	8.1E-06	[                                     --          ]	Helicase_C	Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
4	COG0553	866	130	97.1	0.17	[                                  -------        ]	HepA	Superfamily II DNA or RNA helicase, SNF2 family
5	pfam00176	286	148	96.3	0.0015	[            -------                              ]	SNF2_N	SNF2 family N-terminal domain. This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1).
6	COG0513	513	119	93.3	0.26	[                                  ------         ]	SrmB	Superfamily II DNA and RNA helicase
7	COG1111	542	123	92.6	0.47	[                                 ------          ]	MPH1	ERCC4-related helicase
8	pfam13091	129	50	92.4	0.17	[      ---                                        ]	PLDc_2	PLD-like domain.
9	PRK04914	956	98	90.3	0.13	[                                  -----          ]	PRK04914	ATP-dependent helicase HepA; Validated
10	PRK04537	572	72	77.4	2.1	[                                    ----         ]	PRK04537	ATP-dependent RNA helicase RhlB; Provisional
11	PRK11192	434	86	66.3	3.5	[                                   -----         ]	PRK11192	ATP-dependent RNA helicase SrmB; Provisional
12	PRK13766	773	126	66.1	17	[                                 ------          ]	PRK13766	Hef nuclease; Provisional
13	PRK04837	423	76	64.7	7.9	[                                    ----         ]	PRK04837	ATP-dependent RNA helicase RhlB; Provisional
14	PRK11776	460	72	57.2	3.7	[                                    ----         ]	PRK11776	ATP-dependent RNA helicase DbpA; Provisional
15	PRK04914	956	111	52.2	4.1	[            ------                               ]	PRK04914	ATP-dependent helicase HepA; Validated
16	cd00046	144	46	49.8	5.3	[            --                                   ]	DEXDc	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
17	PRK11634	629	82	49.0	13	[                                     ----        ]	PRK11634	ATP-dependent RNA helicase DeaD; Provisional
18	COG1061	442	117	37.4	22	[                                  ------         ]	SSL2	Superfamily II DNA or RNA helicase
19	pfam04851	103	48	30.1	7.8	[            ---                                  ]	ResIII	Type III restriction enzyme, res subunit.
20	pfam01125	143	86	28.3	78	[                 -----                           ]	G10	G10 protein.
21	COG1200	677	112	27.4	61	[                                    -----        ]	RecG	RecG-like helicase
22	PRK01297	475	58	27.3	41	[                                     ---         ]	PRK01297	ATP-dependent RNA helicase RhlB; Provisional
23	PRK10590	456	108	25.5	52	[                                 ------          ]	PRK10590	ATP-dependent RNA helicase RhlE; Provisional
24	pfam13680	227	108	23.9	55	[                    -----                        ]	DUF4152	Protein of unknown function (DUF4152). This family of proteins is functionally uncharacterized. This family of proteins is found in archaea. Proteins in this family are approximately 230 amino acids in length. The structure of PF2046 from pyrococcus furiosus has been solved. It shows an RNaseH like fold that conserves critical catalytic residues. This suggests that these proteins may cleave nucleic acid.
25	TIGR04095	451	53	23.4	36	[                                     --          ]	dnd_restrict_1	DNA phosphorothioation system restriction enzyme. The DNA phosphorothioate modification system dnd (DNA instability during electrophoresis) recently has been shown to provide a modification essential to a restriction system. This protein family was detected by Partial Phylogenetic Profiling as linked to dnd, and its members usually are clustered with the dndABCDE genes.
26	TIGR00643	630	111	22.3	45	[                                     -----       ]	recG	ATP-dependent DNA helicase RecG.