dimerization/docking (D/D) domain found in adenylate kinase 7 and similar proteins; Adenylate kinase (AK7, EC2.7.4.3/EC 2.7.4.6), also called ATP-AMP transphosphorylase 7, is a nucleoside monophosphate (NMP) kinase that catalyzes the reversible transfer of the terminal phosphate group between nucleoside triphosphates and monophosphates. It has highest activity toward AMP, and weaker activity toward dAMP, CMP and dCMP. It also displays broad nucleoside diphosphate kinase activity. AK7 is involved in maintaining ciliary structure and function. This model corresponds to the C-terminal domain of AK7, which shows high sequence similarity to the dimerization/docking (D/D) domain of protein DPY-30/SDC1.

                          10        20        30
                  ....*....|....*....|....*....|...
gi 2462538762 587 PLRNYLMTYVMPTLIQGLNECCNVRPEDPVDFL 619
Cdd:cd22967     1 PLRNYLMKYVMPTLTEGLVEVCKVRPEDPVDFL 33

Nucleoside-diphosphate-sugar epimerase [Cell wall/membrane/envelope biogenesis];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462538762 168 DSEVPFTEED-------YRRRKshpnfldhINAEKMVLKFGKKaRKFAAYVVAAGLQYGAEG-GMLHTFFKMAWLGEipA 239
Cdd:COG0451   119 DGEGPIDEDTplrpvspYGASK--------LAAELLARAYARR-YGLPVTILRPGNVYGPGDrGVLPRLIRRALAGE--P 187

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2462538762 240 LPVFGDGTNVIPTIHVLDLAGVIQNVIDHVPKPH--YLVAVDESVhTLEDIVK 290
Cdd:COG0451   188 VPVFGDGDQRRDFIHVDDVARAIVLALEAPAAPGgvYNVGGGEPV-TLRELAE 239

dimerization/docking (D/D) domain found in adenylate kinase 7 and similar proteins; Adenylate kinase (AK7, EC2.7.4.3/EC 2.7.4.6), also called ATP-AMP transphosphorylase 7, is a nucleoside monophosphate (NMP) kinase that catalyzes the reversible transfer of the terminal phosphate group between nucleoside triphosphates and monophosphates. It has highest activity toward AMP, and weaker activity toward dAMP, CMP and dCMP. It also displays broad nucleoside diphosphate kinase activity. AK7 is involved in maintaining ciliary structure and function. This model corresponds to the C-terminal domain of AK7, which shows high sequence similarity to the dimerization/docking (D/D) domain of protein DPY-30/SDC1.

                          10        20        30
                  ....*....|....*....|....*....|...
gi 2462538762 587 PLRNYLMTYVMPTLIQGLNECCNVRPEDPVDFL 619
Cdd:cd22967     1 PLRNYLMKYVMPTLTEGLVEVCKVRPEDPVDFL 33

Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462538762 343 KICILGPPAVGKSSIAKELAKYYKLHHIQLKDVISEAIA-------KLEAIVAPNDVGEGEEEVEEEEEEENVEDAQE-- 413
Cdd:cd01428     1 RILLLGPPGSGKGTQAERLAKKYGLPHISTGDLLREEIAsgtelgkKAKEYIDSGKLVPDEIVIKLLKERLKKPDCKKgf 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2462538762 414 LLDGIKESMEQ------------NAEFVCALDASDEFLKERVINLPESIVAGTHY 456
Cdd:cd01428    81 ILDGFPRTVDQaealdelldegiKPDKVIELDVPDEVLIERILGRRICPVSGRVY 135

adenylate kinase 1; Provisional

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2462538762 335 QSRGlmPIKICILGPPAVGKSSIAKELAKYYKLHHIQLKDVISEAIAK 382
Cdd:PTZ00088    2 KLKG--PLKIVLFGAPGVGKGTFAEILSKKENLKHINMGNILREEIKA 47

atypical (a) SDRs, subgroup 1; Atypical SDRs in this subgroup are poorly defined and have been identified putatively as isoflavones reductase, sugar dehydratase, mRNA binding protein etc. Atypical SDRs are distinct from classical SDRs. Members of this subgroup retain the canonical active site triad (though not the upstream Asn found in most SDRs) but have an unusual putative glycine-rich NAD(P)-binding motif, GGXXXXG, in the usual location. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462538762 149 FILLSTVMtwARSKALDPEDSEVPFTEEDYRRRKSHPNF-LDHINAEKMVLKfgkkARKFAAYVVAAGLQYGAE--GGML 225
Cdd:cd05265    93 YIFISSAS--VYLKPGRVITESTPLREPDAVGLSDPWDYgRGKRAAEDVLIE----AAAFPYTIVRPPYIYGPGdyTGRL 166

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462538762 226 HTFFKMAWLGEipALPVFGDGTNVIPTIHVLDLAGVIQNVI--DHVPKPHYLVAVDEsVHTLEDIVK 290
Cdd:cd05265   167 AYFFDRLARGR--PILVPGDGHSLVQFIHVKDLARALLGAAgnPKAIGGIFNITGDE-AVTWDELLE 230

cytidylate kinase, putative; Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2462538762 342 IKICILGPPAVGKSSIAKELAKYYKLHHIQLKDVISEAIAK 382
Cdd:TIGR02173   1 MIITISGPPGSGKTTVAKILAEKLSLKLISAGDIFRELAAK 41

dimerization/docking (D/D) domain found in adenylate kinase 7 and similar proteins; Adenylate kinase (AK7, EC2.7.4.3/EC 2.7.4.6), also called ATP-AMP transphosphorylase 7, is a nucleoside monophosphate (NMP) kinase that catalyzes the reversible transfer of the terminal phosphate group between nucleoside triphosphates and monophosphates. It has highest activity toward AMP, and weaker activity toward dAMP, CMP and dCMP. It also displays broad nucleoside diphosphate kinase activity. AK7 is involved in maintaining ciliary structure and function. This model corresponds to the C-terminal domain of AK7, which shows high sequence similarity to the dimerization/docking (D/D) domain of protein DPY-30/SDC1.

                          10        20        30
                  ....*....|....*....|....*....|...
gi 2462538762 587 PLRNYLMTYVMPTLIQGLNECCNVRPEDPVDFL 619
Cdd:cd22967     1 PLRNYLMKYVMPTLTEGLVEVCKVRPEDPVDFL 33

Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462538762 343 KICILGPPAVGKSSIAKELAKYYKLHHIQLKDVISEAIA-------KLEAIVAPNDVGEGEEEVEEEEEEENVEDAQE-- 413
Cdd:cd01428     1 RILLLGPPGSGKGTQAERLAKKYGLPHISTGDLLREEIAsgtelgkKAKEYIDSGKLVPDEIVIKLLKERLKKPDCKKgf 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2462538762 414 LLDGIKESMEQ------------NAEFVCALDASDEFLKERVINLPESIVAGTHY 456
Cdd:cd01428    81 ILDGFPRTVDQaealdelldegiKPDKVIELDVPDEVLIERILGRRICPVSGRVY 135

dimerization/docking (D/D) domain found in the DPY30/SDC1 family; This family includes DPY30 from animals and its homologs, including SDC1 from yeast. DPY30, also called dumpy-30, was initially discovered in Caenorhabditis elegans as a key player in X chromosome dosage compensation. Human DPY30 plays a dual function in moderately allosterically regulating the methyltransferase activity of SET1/COMPASS (COMplex of Proteins ASsociated with Set1) enzymes and contributing to the recruitment of the complex to chromatin. DPY30 is the core component of several methyltransferase-containing complexes including MLL1/MLL, MLL2/3 (also named ASCOM complex) and MLL4/WBP7. As part of the MLL1/MLL complex, DPY30 is involved in the methylation of histone H3 at 'Lys-4', particularly trimethylation. Histone H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. In a teratocarcinoma cell, DPY30 plays a crucial role in retinoic acid-induced differentiation along the neural lineage, regulating gene induction and H3 'Lys-4' methylation at key developmental loci. It may also play an indirect or direct role in endosomal transport. Yeast SDC1, also called complex proteins associated with SET1 (COMPASS) protein SDC1, Set1C component SDC1, or suppressor of CDC25 protein 1, is the smallest subunit of COMPASS and interacts exclusively with Bre2 at the distal end of the catalytic module. It positively regulates the COMPASS catalytic module by stabilizing the non-canonical Bre2 SPRY domain. The COMPASS (Set1C) complex specifically mono-, di- and trimethylates histone H3 to form H3K4me1/2/3, which subsequently activates gene expression by regulating transcription elongation and plays a role in telomere length maintenance. This model corresponds to the C-terminal helical bundle domain of DPY30/SDC1, which is called dimerization/docking (D/D) domain. It forms a homodimer, which directly interacts with the Ash2L (Bre2 in yeast) subunit of COMPASS through its DPY30-binding motif (DBM).

                          10        20        30
                  ....*....|....*....|....*....|..
gi 2462538762 588 LRNYLMTYVMPTLIQGLNECCNVRPEDPVDFL 619
Cdd:cd22965     1 TRQYLDKTVVPVLLEGLKELAKERPEDPLEFL 32

dimerization/docking (D/D) domain found in nucleoside diphosphate kinase homolog 5 (NDKH5)-like family; The NDKH5 family includes NDKH5, Chlamydomonas reinhardtii flagellar radial spoke protein 23 (RSP23) and similar proteins. NDKH5, also called NME5, NDP kinase homolog 5, inhibitor of p53-induced apoptosis-beta (IPIA-beta), testis-specific nm23 homolog, or nm23-H5, is specifically expressed in testis germinal cells. It may not have NDK kinase activity. It confers protection from cell death by Bax and alters the cellular levels of several antioxidant enzymes including Gpx5. It may play a role in spermiogenesis by increasing the ability of late-stage spermatids to eliminate reactive oxygen species. RSP23, also called p61, is a functional Ca2+/calmodulin-regulated nucleoside diphosphate kinase (NDK) from the flagella of Chlamydomonas that is present in the radial spoke stalk. It binds calmodulin in a calcium-dependent manner. Members of this family contain a C-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domain of protein DPY-30/SDC1.

                          10        20        30
                  ....*....|....*....|....*....|.
gi 2462538762 589 RNYLMTYVMPTLIQGLNECCNVRPEDPVDFL 619
Cdd:cd22970     6 KDYLSKHVNPTLLKGLTELCKEKPADPVTWL 36

dimerization/docking (D/D) domain found in the DPY30 domain-containing protein (DYDC)-like family; The DYDC-like family includes DYDC1 and DYDC2, as well as Chlamydomonas reinhardtii flagellar radial spoke protein 2 (RSP2) and similar proteins. DYDC1 plays a crucial role during acrosome biogenesis. RSP2 is a calmodulin binding spoke stalk protein required for motility in Chlamydomonas reinhardtii. It binds calmodulin in a calcium-dependent manner. Members of this family contain an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domain of protein DPY-30/SDC1.

                          10        20
                  ....*....|....*....|....*....
gi 2462538762 591 YLMTYVMPTLIQGLNECCNVRPEDPVDFL 619
Cdd:cd22966     4 YLKETVGDVLTKALAEVALKRPADPIEFL 32

Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase is part of the Pathway/BioSystem: NAD biosynthesis

                          10        20
                  ....*....|....*....|....*..
gi 2462538762 340 MPIKICILGPPAVGKSSIAKELAKYYK 366
Cdd:COG3172     7 FVKKIVLLGAESTGKTTLARALAAHYN 33

TIGR01777 family protein; This model represents a clade of proteins of unknown function including the E. coli yfcH protein. [Hypothetical proteins, Conserved]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462538762  82 LSKPDSPRPDFAVETYSAISREDLLMrLLECDVII----YNITES--SQQMEEAIW-----AVSALSEEVSHFEKR-KLF 149
Cdd:TIGR01777  28 LTRSPPPGANTKWEGYKPWAGEDADS-LEGADAVInlagEPIADKrwTEERKQEIRdsridTTRLLVEAIAAAEQKpKVF 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462538762 150 ILLSTVmtwarskALDPEDSEVPFTEEDyrrRKSHPNFLDHInaekmVLKFGKKARKFAAY---VVAA--GLQYGAEGGM 224
Cdd:TIGR01777 107 ISASAV-------GYYGPSEDREYTEED---SPAGDDFLAEL-----CRDWEEAAQAAEDLgtrVVLLrtGIVLGPKGGA 171

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2462538762 225 LHT---FFKMAWLGEipalpvFGDGTNVIPTIHVLDLAGVIQNVIDH 268
Cdd:TIGR01777 172 LAKmllPFRLGLGGP------LGSGRQWFSWIHIEDLVQLILFALEN 212

NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; This subgroup of extended SDR-like proteins are atypical SDRs. They have a glycine-rich NAD(P)-binding motif similar to the typical SDRs, GXXGXXG, and have the YXXXK active site motif (though not the other residues of the SDR tetrad). Members identified include NDUFA9 (mitochondrial) and putative nucleoside-diphosphate-sugar epimerase. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462538762 218 YGAEGGMLHTFFKMAWLGeiPALPVFGDGTNVIPTIHVLDLAGVIQNVI---DHVPKPHYLVAVDesVHTLEDIVK 290
Cdd:cd05271   153 FGREDRFLNRFAKLLAFL--PFPPLIGGGQTKFQPVYVGDVAEAIARALkdpETEGKTYELVGPK--VYTLAELVE 224

Cytidylate kinase [Nucleotide transport and metabolism];

                          10        20
                  ....*....|....*....|....*....
gi 2462538762 342 IKICILGPPAVGKSSIAKELAKYYKLHHI 370
Cdd:COG0283     1 PVIAIDGPAGSGKSTVAKALAKRLGYHYL 29