DNA polymerase III, alpha chain, Gram-positive type; This model describes a polypeptide chain of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model. [DNA metabolism, DNA replication, recombination, and repair]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707236892    1 NAQDLMEVAHAPRKDYAPEgeKRVELHMHSNMSTMDATNKVGDLVAQAGKWGHKAIAITDHGGAQAFPDAHAAGKKAGVK 80
Cdd:TIGR01405   84 IIKDIEEIPYAERKDNAKE--KRVELHFHTKMSQMDAITSVQEYVKQAKKWGHKAIAITDHGVVQAFPEAYKAAKKDGIK 161

                           90       100
                   ....*....|....*....|..
gi 1707236892   81 ILYGVEANIVDDGVPIAYNEEH 102
Cdd:TIGR01405  162 IIYGMEANLVDDRVPIVYNPDD 183

DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family of hypothetical proteins

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707236892   25 ELHMHSNMSTMDATNKVGDLVAQAGKWGHKAIAITDHGGAQAFPDAHAAGKKAGVKILYGVEANIVD 91
Cdd:smart00481   1 DLHVHSDYSLLDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIGLEANIVD 67

DNA polymerase III, alpha subunit [Replication, recombination and repair];

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1707236892   24 VELHMHSNMSTMDATNKVGDLVAQAGKWGHKAIAITDHGGAQAFPDAHAAGKKAGVKILYGVEANIVDDGVPIAY 98
Cdd:COG0587      6 VHLHVHSEYSLLDGASRPEELVARAAELGMPALAITDHGNLFGAVRFYKAAKKAGIKPIIGCELYVAPGSRDDAG 80

DNA polymerase III, alpha chain, Gram-positive type; This model describes a polypeptide chain of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model. [DNA metabolism, DNA replication, recombination, and repair]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707236892    1 NAQDLMEVAHAPRKDYAPEgeKRVELHMHSNMSTMDATNKVGDLVAQAGKWGHKAIAITDHGGAQAFPDAHAAGKKAGVK 80
Cdd:TIGR01405   84 IIKDIEEIPYAERKDNAKE--KRVELHFHTKMSQMDAITSVQEYVKQAKKWGHKAIAITDHGVVQAFPEAYKAAKKDGIK 161

                           90       100
                   ....*....|....*....|..
gi 1707236892   81 ILYGVEANIVDDGVPIAYNEEH 102
Cdd:TIGR01405  162 IIYGMEANLVDDRVPIVYNPDD 183

DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family of hypothetical proteins

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707236892   25 ELHMHSNMSTMDATNKVGDLVAQAGKWGHKAIAITDHGGAQAFPDAHAAGKKAGVKILYGVEANIVD 91
Cdd:smart00481   1 DLHVHSDYSLLDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIGLEANIVD 67

Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that is responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. The PolIIIA PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination, and like other PHP structures, exhibits a distorted (beta/alpha) 7 barrel and coordinates up to 3 metals. Initially, it was proposed that PHP region might be involved in pyrophosphate hydrolysis, but such activity has not been found. It has been shown that the PHP domain of PolIIIA has a trinuclear metal complex and is capable of proofreading activity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707236892  24 VELHMHSNMSTMDATNKVGDLVAQAGKWGHKAIAITDHGGAQAFPDAHAAGKKAGVKILYGVEANIVDDGVP-----IAY 98
Cdd:cd07431     1 AHLHVHSSYSLLDSAIRPEDLVARAKELGYSALALTDRNVLYGAVRFYKACKKAGIKPIIGLELTVEGDGEPyplllLAK 80

                  ...
gi 1707236892  99 NEE 101
Cdd:cd07431    81 NNE 83

Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PHP in polymerases has trinuclear zinc/magnesium dependent proofreading activity. It has also been shown that the PHP domain functions in DNA repair. The PHP structures have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707236892  24 VELHMHSNMSTMDATnKVGDLVAQAGKWGHKAIAITDHGGAQAFPDAH--------AAGKKAGVKILYGVEANIVDDGVP 95
Cdd:cd07309     1 VDLHTHTVFSDGDHA-KLTELVDKAKELGPDALAITDHGNLRGLAEFNtagk*nhiKAAEAAGIKIIIGSEVNLTVLAHP 79

                  ....
gi 1707236892  96 IAYN 99
Cdd:cd07309    80 VVAT 83

Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that is responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. The PolIIIA PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination, and like other PHP structures, the PolIIIA PHP exhibits a distorted (beta/alpha) 7 barrel and coordinates up to 3 metals. Initially, it was proposed that PHP region might be involved in pyrophosphate hydrolysis, but such an activity has not been found. It has been shown that the PHP of PolIIIA has a trinuclear metal complex and is capable of proofreading activity. Bacterial genome replication and DNA repair mechanisms is related to the GC content of its genomes. There is a correlation between GC content variations and the dimeric combinations of PolIIIA subunits. Eubacteria can be grouped into different GC variable groups: the full-spectrum or dnaE1 group, the high-GC or dnaE2-dnaE1 group, and the low GC or polC-dnaE3 group.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1707236892  24 VELHMHSNMSTMDATNKVGDLVAQAGKWGHKAIAITDHG---GAQAFpdaHAAGKKAGVKILYGVEANIVDD 92
Cdd:cd12113     3 VHLHVHTEYSLLDGAIRIKDLVKRAKELGMPALAITDHGnmfGAIEF---YKAAKKAGIKPIIGCEVYVAPG 71

Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce histidinol. HisPPase can be classified into two types: the bifunctional HisPPase found in proteobacteria that belongs to the DDDD superfamily and the monofunctional Bacillus subtilis type that is a member of the PHP family. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707236892  24 VELHMHSNMSTmDATNKVGDLVAQAGKWGHKAIAITDHGGAQAFPDAHAAGKKAGVKILYGVEANIV 90
Cdd:cd07432     1 ADLHIHSVFSP-DSDMTPEEIVERAIELGLDGIAITDHNTIDGAEEALKEAYKDGLLVIPGVEVTLV 66

5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism];

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1707236892  23 RVELHMHSNMStmDATNKVGDLVAQAGKWGHKAIAITDHGGAQAFPDAHAAGKKAGVKILYGVEANIVDDGVPI 96
Cdd:COG0613     3 KIDLHVHTTAS--DGSLSPEELVARAKAAGLDVLAITDHDTVAGYEEAAEAAKELGLLVIPGVEISTRWEGREV 74

Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and metabolism, General function prediction only]; Histidinol phosphatase or related hydrolase of the PHP family is part of the Pathway/BioSystem: Histidine biosynthesis

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707236892  23 RVELHMHSNMStmDATNKVGDLVAQAGKWGHKAIAITDHggAQAFPDAH----------------AAGKKAGVKILYGVE 86
Cdd:COG1387     2 RGDLHTHTTYS--DGEGTIEEMVEAAIELGLEYIAITDH--SPSLFVANglseerlleyleeieeLNEKYPDIKILKGIE 77

                  ....*..
gi 1707236892  87 ANIVDDG 93
Cdd:COG1387    78 VDILPDG 84

error-prone DNA polymerase; Validated

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1707236892   25 ELHMHSNMSTMDATNKVGDLVAQAGKWGHKAIAITDHGGAQAFPDAHAAGKKAGVKILYGVE 86
Cdd:PRK05672     7 ELHCHSNFSFLDGASHPEELVERAARLGLRALAITDECGLAGVVRAAEAAKELGLRLVIGAE 68

Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; The bacterial/archaeal X-family DNA polymerases (PolXs) have a PHP domain at their C-terminus. The bacterial/archaeal PolX core domain and PHP domain interact with each other and together are involved in metal dependent 3'-5' exonuclease activity. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PolX is found in all kingdoms, however bacterial PolXs have a completely different domain structure from eukaryotic PolXs. Bacterial PolX has an extended conformation in contrast to the common closed 'right hand' conformation for DNA polymerases. This extended conformation is stabilized by the PHP domain. The PHP domain of PolX is structurally homologous to other members of the PHP family that has a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707236892  26 LHMHSNMStmDATNKVGDLVAQAGKWGHKAIAITDHGGAQAFpdAH----------------AAGKKAGVKILYGVEANI 89
Cdd:cd07436     9 LHVHTTWS--DGRNSIEEMAEAARALGYEYIAITDHSKSLRV--ANglseerlreqieeidaLNEKLPGIRILKGIEVDI 84

                  ....
gi 1707236892  90 VDDG 93
Cdd:cd07436    85 LPDG 88

DNA polymerase III subunit alpha; Validated

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707236892   24 VELHMHSNMSTMDATNKVGDLVAQAGKWGHKAIAITDHGGAQAFPDAHAAGKKAGVKILYGVEANIV----DDGVPIAYN 99
Cdd:PRK07374     4 VPLHNHSDYSLLDGASQLPKMVERAKELGMPAIALTDHGVMYGAIELLKLCKGKGIKPIIGNEMYVIngsiDDPQPKKEK 83

                   ...
gi 1707236892  100 EEH 102
Cdd:PRK07374    84 RYH 86

Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. PolIIIA core enzyme catalyzes the reaction for polymerizing both DNA strands. dnaE1 is the longest compared to dnaE2 and dnaE3. A unique motif was also identified in dnaE1 and dnaE3 genes.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707236892  24 VELHMHSNMSTMDATNKVGDLVAQAGKWGHKAIAITDHG---GAQAFPDahaAGKKAGVKILYGVEANIVDDGVPIAY 98
Cdd:cd07433     3 VHLRVHSEYSLLDGAVRIKKLVKLAKEDGMPALAITDLSnlfGAVKFYK---AASKAGIKPIIGADLNVANPDDADEP 77

CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is found in several partially characterized metallohydrolases, including McbA and CehA. Both were studied as hydrolases of carbaryl, a xenobiotic compound that does not contain a phosphate group, suggesting that presuming members of this family to be phosphoesterases (like many PHP domain-containing proteins) may be incorrect.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1707236892  23 RVELHMHSNMStmDATNKVGDLVAQAGKWGHKAIAITDHGGAQAFPDAHAA-GKKAGVKILYGVE 86
Cdd:NF038032    4 SGDLHIHTNHS--DGPTTPEELARAALAEGLDVIALTDHNTISGRAYFAELlASERGLLVIPGME 66