partition proteins ParAB family; ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in Rhizobium etli symbiotic plasmid. This operon is involved in the plasmid replication and partition.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292825607   3 KIICVANRKGGVGKTTLATNLAVALNNKGKSIL-IDADEQQSAFKWAnqrddiecitihsdllekleqldkeYEYILIDV 81
Cdd:cd02042    1 KVIAVANQKGGVGKTTLAVNLAAALALRGKRVLlIDLDPQGSLTSWL-------------------------YDYILIDT 55

ParA-like ATPase involved in chromosome/plasmid partitioning or cellulose biosynthesis protein BcsQ [Cell cycle control, cell division, chromosome partitioning, Cell motility];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292825607   2 AKIICVANRKGGVGKTTLATNLAVALNNKGKSIL-IDADEQ---------------QSAFKWANQRDDIECITIHSD--- 62
Cdd:COG1192    1 MKVIAVANQKGGVGKTTTAVNLAAALARRGKRVLlIDLDPQgnltsglgldpddldPTLYDLLLDDAPLEDAIVPTEipg 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 292825607  63 --------------------------LLEKLEQLDKEYEYILID 80
Cdd:COG1192   81 ldlipanidlagaeielvsrpgrelrLKRALAPLADDYDYILID 124

cell division ATPase MinD, archaeal; This model represents the archaeal branch of the MinD family. MinD, a weak ATPase, works in bacteria with MinC as a generalized cell division inhibitor and, through interaction with MinE, prevents septum placement inappropriate sites. Often several members of this family are found in archaeal genomes, and the function is uncharacterized. More distantly related proteins ParA chromosome partitioning proteins. The exact roles of the various archaeal MinD homologs are unknown.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 292825607    3 KIICVANRKGGVGKTTLATNLAVALNNKGKSIL-IDAD 39
Cdd:TIGR01969   1 RIITIASGKGGTGKTTITANLGVALAKLGKKVLaLDAD 38

partition proteins ParAB family; ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in Rhizobium etli symbiotic plasmid. This operon is involved in the plasmid replication and partition.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292825607   3 KIICVANRKGGVGKTTLATNLAVALNNKGKSIL-IDADEQQSAFKWAnqrddiecitihsdllekleqldkeYEYILIDV 81
Cdd:cd02042    1 KVIAVANQKGGVGKTTLAVNLAAALALRGKRVLlIDLDPQGSLTSWL-------------------------YDYILIDT 55

ParA-like ATPase involved in chromosome/plasmid partitioning or cellulose biosynthesis protein BcsQ [Cell cycle control, cell division, chromosome partitioning, Cell motility];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292825607   2 AKIICVANRKGGVGKTTLATNLAVALNNKGKSIL-IDADEQ---------------QSAFKWANQRDDIECITIHSD--- 62
Cdd:COG1192    1 MKVIAVANQKGGVGKTTTAVNLAAALARRGKRVLlIDLDPQgnltsglgldpddldPTLYDLLLDDAPLEDAIVPTEipg 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 292825607  63 --------------------------LLEKLEQLDKEYEYILID 80
Cdd:COG1192   81 ldlipanidlagaeielvsrpgrelrLKRALAPLADDYDYILID 124

Mrp/NBP35 ATP-binding protein family; Mrp/NBP35 ATP-binding family protein are typically iron-sulfur (FeS) cluster scaffolds that function to assemble nascent FeS clusters for transfer to FeS-requiring enzymes. Members include the eukaryotic nucleotide-binding protein 1 (NUBP1) which is a component of the cytosolic iron-sulfur (Fe/S) protein assembly (CIA) machinery and the archael [NiFe] hydrogenase maturation protein HypB which is required for nickel insertion into [NiFe] hydrogenase.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 292825607   3 KIICVANRKGGVGKTTLATNLAVALNNKGKSI-LIDAD 39
Cdd:cd02037    1 HIIAVLSGKGGVGKSTVAVNLALALAKKGYKVgLLDAD 38

CobQ/CobB/MinD/ParA nucleotide binding domain; This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from S.typhimurium, and CobQ from R. capsulatus. These amidases catalyze amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 292825607    5 ICVANRKGGVGKTTLATNLAVALNNKGKSIL-IDADEQQSAFKWANQRDDIECI 57
Cdd:pfam01656   1 IAIAGTKGGVGKTTLAANLARALARRGLRVLlIDLDPQSNNSSVEGLEGDIAPA 54

Septum site-determining ATPase MinD [Cell cycle control, cell division, chromosome partitioning];

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 292825607   1 MAKIICVANRKGGVGKTTLATNLAVALNNKGKS-ILIDAD 39
Cdd:COG2894    1 MGKVIVVTSGKGGVGKTTTTANLGTALALLGKKvVLIDAD 40

MinD-like ATPase FlhG; FlhG is a member of the SIMIBI superfamily. FlhG (also known as YlxH) is a major determinant for a variety of flagellation patterns. It effects location and number of bacterial flagella during C-ring assembly.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 292825607   3 KIICVANRKGGVGKTTLATNLAVALNNKGKS-ILIDAD 39
Cdd:cd02038    1 RIIAVTSGKGGVGKTNVSANLALALSKLGKRvLLLDAD 38

cell division ATPase MinD, archaeal; This model represents the archaeal branch of the MinD family. MinD, a weak ATPase, works in bacteria with MinC as a generalized cell division inhibitor and, through interaction with MinE, prevents septum placement inappropriate sites. Often several members of this family are found in archaeal genomes, and the function is uncharacterized. More distantly related proteins ParA chromosome partitioning proteins. The exact roles of the various archaeal MinD homologs are unknown.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 292825607    3 KIICVANRKGGVGKTTLATNLAVALNNKGKSIL-IDAD 39
Cdd:TIGR01969   1 RIITIASGKGGTGKTTITANLGVALAKLGKKVLaLDAD 38

ATPase MipZ; MipZ is an ATPase that forms a complex with the chromosome partitioning protein ParB near the chromosomal origin of replication. It is responsible for the temporal and spatial regulation of FtsZ ring formation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292825607    4 IICVANRKGGVGKTTLATNLAVALNNKGKSI-LIDADEQQSAF--------KWANQR----------------------- 51
Cdd:pfam09140   2 VIVVGNEKGGSGKSTTAVHVAVALLYKGARVaAIDLDLRQRTFhryfenrsATADRTglslptpehlnlpdndvaevpdg 81

                          90       100
                  ....*....|....*....|....*....
gi 292825607   52 DDIECitihSDLLEKLEQLDKEYEYILID 80
Cdd:pfam09140  82 ENIDD----ARLEEAFADLEARCDFIVID 106

CO dehydrogenase nickel-insertion accessory protein CooC1 [Posttranslational modification, protein turnover, chaperones];

                         10        20        30
                 ....*....|....*....|....*....|
gi 292825607  11 KGGVGKTTLATNLAVALNNKGKSIL-IDAD 39
Cdd:COG3640    8 KGGVGKTTLSALLARYLAEKGKPVLaVDAD 37

SIMIBI (signal recognition particle, MinD and BioD)-class NTPases; SIMIBI (after signal recognition particle, MinD, and BioD), consists of signal recognition particle (SRP) GTPases, the assemblage of MinD-like ATPases, which are involved in protein localization, chromosome partitioning, and membrane transport, and a group of metabolic enzymes with kinase or related phosphate transferase activity. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 292825607   3 KIICVANRKGGVGKTTLATNLAVALNNKGKSIL-IDADE 40
Cdd:cd01983    1 RVIAVTGGKGGVGKTTLAAALAVALAAKGYKVLlIDLDD 39

pilus assembly ATPase CpaE; This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains 7 genes: pilA, cpaA, cpaB, cpaC, cpaD, cpaE and cpaF. These genes are clustered together on chromosome.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 292825607   3 KIICVANRKGGVGKTTLATNLAVALN--NKGKSILIDADEQQSAfkwANQRDDIECITIHSDLLEKLEQLDKEY 74
Cdd:cd03111    1 RVVAVVGAKGGVGASTLAVNLAQELAqrAKDKVLLIDLDLPFGD---LGLYLNLRPDYDLADVIQNLDRLDRTL 71

septum site-determining protein MinD; This model describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model. [Cellular processes, Cell division]

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 292825607    2 AKIICVANRKGGVGKTTLATNLAVALNNKG-KSILIDAD 39
Cdd:TIGR01968   1 ARVIVITSGKGGVGKTTTTANLGTALARLGkKVVLIDAD 39

Anion-transporting ATPase, ArsA/GET3 family [Inorganic ion transport and metabolism];

                         10        20
                 ....*....|....*....|....*.
gi 292825607  11 KGGVGKTTLATNLAVALNNKGKSILI 36
Cdd:COG0003   11 KGGVGKTTVAAATALALAERGKRTLL 36

arsenical pump-driving ATPase; The broader family (TIGR00345) to which the current family belongs consists of transport-energizing ATPases, including to TRC40/GET3 family involved in post-translational insertion of protein C-terminal transmembrane anchors into membranes from the cyotosolic face. This family, however, is restricted to ATPases that energize pumps that export arsenite (or antimonite).

                          10        20
                  ....*....|....*....|....*.
gi 292825607   11 KGGVGKTTLATNLAVALNNKGKSILI 36
Cdd:TIGR04291 329 KGGVGKTTVAAAIAVRLANKGLDVHL 354

protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 292825607   1 MAKIICVANrKGGVGKTTLATNLAVALNNKGKSIL 35
Cdd:PRK13185   1 MALVLAVYG-KGGIGKSTTSSNLSAAFAKLGKKVL 34

accessory protein CooC1; The accessory protein CooC1, a nickel-binding ATPase, participates in the incorporation of nickel into the complex active site ([Ni-4Fe-4S]) cluster of Ni,Fe-dependent carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.

                         10        20        30
                 ....*....|....*....|....*....|.
gi 292825607  11 KGGVGKTTLATNLAVALNNKGKSIL-IDADE 40
Cdd:cd02034    8 KGGVGKTTIAALLIRYLAKKGGKVLaVDADP 38

plasmid partitioning protein RepA; Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error. [Mobile and extrachromosomal element functions, Plasmid functions]

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 292825607    4 IICVANRKGGVGKTTLATNLAVALNNKGKSIL-IDADEQQS 43
Cdd:TIGR03453 106 VIAVTNFKGGSGKTTTAAHLAQYLALRGYRVLaIDLDPQAS 146

arsenical pump-driving ATPase; The broader family (TIGR00345) to which the current family belongs consists of transport-energizing ATPases, including to TRC40/GET3 family involved in post-translational insertion of protein C-terminal transmembrane anchors into membranes from the cyotosolic face. This family, however, is restricted to ATPases that energize pumps that export arsenite (or antimonite).

                          10        20
                  ....*....|....*....|....*.
gi 292825607   11 KGGVGKTTLATNLAVALNNKGKSILI 36
Cdd:TIGR04291  11 KGGVGKTSIACATAINLADQGKRVLL 36

nitrogenase component II NifH; NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.

                         10        20
                 ....*....|....*....|....*.
gi 292825607  11 KGGVGKTTLATNLAVALNNKGKSILI 36
Cdd:cd02040    8 KGGIGKSTTASNLSAALAEMGKKVLH 33

NifH family; This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase, and the BchX subunit of the Chlorophyllide reductase. Members of this family use energy from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for substrate reduction

                         10        20        30
                 ....*....|....*....|....*....|..
gi 292825607   5 ICVANRKGGVGKTTLATNLAVALNNKGKSILI 36
Cdd:cd02117    2 SIVVYGKGGIGKSTTASNLSAALAEGGKKVLH 33

Cellulose biosynthesis protein BcsQ; This is a family of bacterial proteins involved in cellulose biosynthesis. (Roemling U. and Galperin M.Y. "Bacterial cellulose biosynthesis. Diversity of operons and subunits" (manuscript in preparation)). A second component of the extracellular matrix of the multicellular morphotype (rdar) of Salmonella typhimurium and Escherichia coli is cellulose. The family does contain a P-loop sequence motif suggesting a nucleotide binding function, but this has not been confirmed.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 292825607    3 KIICVANRKGGVGKTTLATNLAVALNNKGKSIL-IDA 38
Cdd:pfam06564   2 KILALQGVRGGVGTTSILAALAWALQRLGERVLlIDL 38

pilus assembly protein TadZ; Pilus assembly protein TadZ is involved in the production of a variant of type IV pili. It is part of the SIMIBI superfamily which contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

                         10        20        30
                 ....*....|....*....|....*....|...
gi 292825607   3 KIICVANRKGGVGKTTLATNLAVALNNKGKSIL 35
Cdd:cd17869    4 SVITFHSPCGGSGKSTVAAACAYTLAEKGKKTL 36