Domain of unknown function (DUF3854); A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This domain is likely to be related to the Toprim domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1531905251  148 IAHPSIPICITEGAKKAGALLSAGYVAIALPGINNGYRTPRDESGNRIGKSHLIPQLEKLAISGRQIYITFDQDSKPNTI 227
Cdd:pfam12965    1 LDHPNIPIIITEGAKKAAALLSQGYVAIALPGVNNGYRVPKDEFGKKIGKKRLIPDLEAFATPGREFYICFDQDTKPKTI 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1531905251  228 KSVNAAIRQLGYLFTQKSCQVKVITWRFEWGKGVDDFIANEGQK 271
Cdd:pfam12965   81 KNVNRAIVRLGELLEKRGCKVKVITWDPGLGKGVDDLIVAHGAD 124

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1531905251  312 IPNNAKLIGIKSPIGSGKTQVLENIVKEAI--ARKQKVLVIGHRIKLVEQLCQRF-----GLPYITEI-----KDNSRNE 379
Cdd:pfam04851   19 IKNGQKRGLIVMATGSGKTLTAAKLIARLFkkGPIKKVLFLVPRKDLLEQALEEFkkflpNYVEIGEIisgdkKDESVDD 98

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1531905251  380 CLGYGLCIDSLHENSSANFNLEDW-REALVIIDEVeqvlwHGLNSDTCKQnrvpILKCFKTLIQ 442
Cdd:pfam04851   99 NKIVVTTIQSLYKALELASLELLPdFFDVIIIDEA-----HRSGASSYRN----ILEYFKPAFL 153

Domain of unknown function (DUF3854); A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This domain is likely to be related to the Toprim domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1531905251  148 IAHPSIPICITEGAKKAGALLSAGYVAIALPGINNGYRTPRDESGNRIGKSHLIPQLEKLAISGRQIYITFDQDSKPNTI 227
Cdd:pfam12965    1 LDHPNIPIIITEGAKKAAALLSQGYVAIALPGVNNGYRVPKDEFGKKIGKKRLIPDLEAFATPGREFYICFDQDTKPKTI 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1531905251  228 KSVNAAIRQLGYLFTQKSCQVKVITWRFEWGKGVDDFIANEGQK 271
Cdd:pfam12965   81 KNVNRAIVRLGELLEKRGCKVKVITWDPGLGKGVDDLIVAHGAD 124

Type III restriction enzyme, res subunit;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1531905251  312 IPNNAKLIGIKSPIGSGKTQVLENIVKEAI--ARKQKVLVIGHRIKLVEQLCQRF-----GLPYITEI-----KDNSRNE 379
Cdd:pfam04851   19 IKNGQKRGLIVMATGSGKTLTAAKLIARLFkkGPIKKVLFLVPRKDLLEQALEEFkkflpNYVEIGEIisgdkKDESVDD 98

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1531905251  380 CLGYGLCIDSLHENSSANFNLEDW-REALVIIDEVeqvlwHGLNSDTCKQnrvpILKCFKTLIQ 442
Cdd:pfam04851   99 NKIVVTTIQSLYKALELASLELLPdFFDVIIIDEA-----HRSGASSYRN----ILEYFKPAFL 153

DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1531905251  319 IGIKSPIGSGKTQVLENIVKEAIA--RKQKVLVIGHRIKLVEQLCQRFGLPY----ITEIKDNSRNEcLGYGLC---IDS 389
Cdd:cd18032     23 ALLVMATGTGKTYTAAFLIKRLLEanRKKRILFLAHREELLEQAERSFKEVLpdgsFGNLKGGKKKP-DDARVVfatVQT 101

                           90       100
                   ....*....|....*....|....
gi 1531905251  390 LHENSSANfNLEDWREALVIIDEV 413
Cdd:cd18032    102 LNKRKRLE-KFPPDYFDLIIIDEA 124

Domain of unknown function (DUF3854); A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This domain is likely to be related to the Toprim domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1531905251  148 IAHPSIPICITEGAKKAGALLSAGYVAIALPGINNGYRTPRDESGNRIGKSHLIPQLEKLAISGRQIYITFDQDSKPNTI 227
Cdd:pfam12965    1 LDHPNIPIIITEGAKKAAALLSQGYVAIALPGVNNGYRVPKDEFGKKIGKKRLIPDLEAFATPGREFYICFDQDTKPKTI 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1531905251  228 KSVNAAIRQLGYLFTQKSCQVKVITWRFEWGKGVDDFIANEGQK 271
Cdd:pfam12965   81 KNVNRAIVRLGELLEKRGCKVKVITWDPGLGKGVDDLIVAHGAD 124

Type III restriction enzyme, res subunit;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1531905251  312 IPNNAKLIGIKSPIGSGKTQVLENIVKEAI--ARKQKVLVIGHRIKLVEQLCQRF-----GLPYITEI-----KDNSRNE 379
Cdd:pfam04851   19 IKNGQKRGLIVMATGSGKTLTAAKLIARLFkkGPIKKVLFLVPRKDLLEQALEEFkkflpNYVEIGEIisgdkKDESVDD 98

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1531905251  380 CLGYGLCIDSLHENSSANFNLEDW-REALVIIDEVeqvlwHGLNSDTCKQnrvpILKCFKTLIQ 442
Cdd:pfam04851   99 NKIVVTTIQSLYKALELASLELLPdFFDVIIIDEA-----HRSGASSYRN----ILEYFKPAFL 153

DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1531905251  319 IGIKSPIGSGKTQVLENIVKEAIA--RKQKVLVIGHRIKLVEQLCQRFGLPY----ITEIKDNSRNEcLGYGLC---IDS 389
Cdd:cd18032     23 ALLVMATGTGKTYTAAFLIKRLLEanRKKRILFLAHREELLEQAERSFKEVLpdgsFGNLKGGKKKP-DDARVVfatVQT 101

                           90       100
                   ....*....|....*....|....
gi 1531905251  390 LHENSSANfNLEDWREALVIIDEV 413
Cdd:cd18032    102 LNKRKRLE-KFPPDYFDLIIIDEA 124