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 1039780161 1485 DKRLFVLSVLGLQSSGKSTLLNALFGLQ--FTVSAG--RCTKGAYMQLLKVEETFTEELGfnyVLVIDTEGLRAPELNNK 1560
Cdd:cd01851      4 GFPVVVVSVFGSQSSGKSFLLNHLFGTSdgFDVMDTsqQTTKGIWMWSDPFKDTDGKKHA---VLLLDTEGTDGRERGEF 80

                   ..
gi 1039780161 1561 SQ 1562
Cdd:cd01851     81 EN 82

Guanylate-binding protein (GBP) family (N-terminal domain); Guanylate-binding protein (GBP), N-terminal domain. Guanylate-binding proteins (GBPs) define a group of proteins that are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. Furthermore, two unique regions around the base and the phosphate-binding areas, the guanine and the phosphate caps, respectively, give the nucleotide-binding site a unique appearance not found in the canonical GTP-binding proteins. The phosphate cap, which constitutes the region analogous to switch I, completely shields the phosphate-binding site from solvent such that a potential GTPase-activating protein (GAP) cannot approach.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039780161 1485 DKRLFVLSVLGLQSSGKSTLLNALFGLQ--FTVSAG--RCTKGAYMQLLKVEETFTEELGfnyVLVIDTEGLRAPELNNK 1560
Cdd:cd01851      4 GFPVVVVSVFGSQSSGKSFLLNHLFGTSdgFDVMDTsqQTTKGIWMWSDPFKDTDGKKHA---VLLLDTEGTDGRERGEF 80

                   ..
gi 1039780161 1561 SQ 1562
Cdd:cd01851     81 EN 82

putative inner membrane protein translocase component YidC; Validated

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039780161   72 KRALEK--LLDFSQPNSVAELQETPREMKKNRQRQAGQALQALKALQSEGKHREEEAVRRKEAELRQAME 139
Cdd:PRK00247   305 LWTLRRnrLRMIITPWRAPELHAENAEIKKTRTAEKNEAKARKKEIAQKRRAAEREINREARQERAAAMA 374

Guanylate-binding protein (GBP) family (N-terminal domain); Guanylate-binding protein (GBP), N-terminal domain. Guanylate-binding proteins (GBPs) define a group of proteins that are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. Furthermore, two unique regions around the base and the phosphate-binding areas, the guanine and the phosphate caps, respectively, give the nucleotide-binding site a unique appearance not found in the canonical GTP-binding proteins. The phosphate cap, which constitutes the region analogous to switch I, completely shields the phosphate-binding site from solvent such that a potential GTPase-activating protein (GAP) cannot approach.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039780161 1485 DKRLFVLSVLGLQSSGKSTLLNALFGLQ--FTVSAG--RCTKGAYMQLLKVEETFTEELGfnyVLVIDTEGLRAPELNNK 1560
Cdd:cd01851      4 GFPVVVVSVFGSQSSGKSFLLNHLFGTSdgFDVMDTsqQTTKGIWMWSDPFKDTDGKKHA---VLLLDTEGTDGRERGEF 80

                   ..
gi 1039780161 1561 SQ 1562
Cdd:cd01851     81 EN 82

Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039780161 1493 VLGLQSSGKSTLLNALFGLQFTVSAGR--CTKGAymqllkVEETFTEELGFNYVLVIDTEGLRapelnNKSQNWDHELAT 1570
Cdd:cd00882      2 VVGRGGVGKSSLLNALLGGEVGEVSDVpgTTRDP------DVYVKELDKGKVKLVLVDTPGLD-----EFGGLGREELAR 70

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1039780161 1571 LVIGLGNLTLINIFGENPSDIQDILQISVQAFLRMK 1606
Cdd:cd00882     71 LLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEG 106