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Conserved domains on  [gi|460381741|ref|XP_004236601|]
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short integuments 2, mitochondrial [Solanum lycopersicum]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YlqF cd01856
Circularly permuted YlqF GTPase; Proteins of the YlqF family contain all sequence motifs ...
 22-199 4.21e-62

Circularly permuted YlqF GTPase; Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The YlqF subfamily is represented in all eukaryotes as well as a phylogenetically diverse array of bacteria (including gram-positive bacteria, proteobacteria, Synechocystis, Borrelia, and Thermotoga).


:

Pssm-ID: 206749 [Multi-domain]  Cd Length: 171  Bit Score: 196.60  E-value: 4.21e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  22 WFPGHIDAANRAIRRRLKLSDFVIELRDARIPLSSANEDLQPMLCEKRRVIALNKKDLANPNIMHRWIRYFNSCKQECFP 101
Cdd:cd01856    1 WFPGHMAKALRQIKEKLKLVDVVIEVRDARIPLSSRNPDLDKILGNKPRLIVLNKADLADPAKTKKWLKYFKSQGEPVLF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 102 INAHSRSSVQKLLDIVEFKLKEVI------TREPTLLVMVVGVPNVGKSVLINSIHQIASSRfpvqekmrrstVGPLPGV 175
Cdd:cd01856   81 VNAKNGKGVKKLLKKAKKLLKENEklkakgLLPRPLRAMVVGIPNVGKSTLINRLRGKKVAK-----------VGNKPGV 149

                        170       180
                 ....*....|....*....|....
gi 460381741 176 TQDIAGYKIAhqPSIYVLDTPGVL 199
Cdd:cd01856  150 TRGQQWIRIG--PNIELLDTPGIL 171
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 135-265 5.70e-04

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.


The actual alignment was detected with superfamily member cd01881:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 167  Bit Score: 40.07  E-value: 5.70e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 135 VVGVPNVGKSVLINSIH----QIASSRFpvqekmrrSTVGPLPGVTQDIAGYKIAhqpsiyVLDTPGvLVPSiPDIETGL 210
Cdd:cd01881    2 LVGLPNVGKSTLLSALTsakvEIASYPF--------TTLEPNVGVFEFGDGVDIQ------IIDLPG-LLDG-ASEGRGL 65

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 460381741 211 KLALAGSIKDSvvgeDRIVQYLLAVLNTRGTPLHWRHLISRETEGLHHELDDKPE 265
Cdd:cd01881   66 GEQILAHLYRS----DLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFLKNKPE 116
 
Name Accession Description Interval E-value
YlqF cd01856
Circularly permuted YlqF GTPase; Proteins of the YlqF family contain all sequence motifs ...
 22-199 4.21e-62

Circularly permuted YlqF GTPase; Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The YlqF subfamily is represented in all eukaryotes as well as a phylogenetically diverse array of bacteria (including gram-positive bacteria, proteobacteria, Synechocystis, Borrelia, and Thermotoga).


Pssm-ID: 206749 [Multi-domain]  Cd Length: 171  Bit Score: 196.60  E-value: 4.21e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  22 WFPGHIDAANRAIRRRLKLSDFVIELRDARIPLSSANEDLQPMLCEKRRVIALNKKDLANPNIMHRWIRYFNSCKQECFP 101
Cdd:cd01856    1 WFPGHMAKALRQIKEKLKLVDVVIEVRDARIPLSSRNPDLDKILGNKPRLIVLNKADLADPAKTKKWLKYFKSQGEPVLF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 102 INAHSRSSVQKLLDIVEFKLKEVI------TREPTLLVMVVGVPNVGKSVLINSIHQIASSRfpvqekmrrstVGPLPGV 175
Cdd:cd01856   81 VNAKNGKGVKKLLKKAKKLLKENEklkakgLLPRPLRAMVVGIPNVGKSTLINRLRGKKVAK-----------VGNKPGV 149

                        170       180
                 ....*....|....*....|....
gi 460381741 176 TQDIAGYKIAhqPSIYVLDTPGVL 199
Cdd:cd01856  150 TRGQQWIRIG--PNIELLDTPGIL 171
RbgA COG1161
Ribosome biogenesis GTPase RbgA [Translation, ribosomal structure and biogenesis];
19-236 1.88e-61

Ribosome biogenesis GTPase RbgA [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440775 [Multi-domain]  Cd Length: 279  Bit Score: 198.79  E-value: 1.88e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  19 NINWFPGHIDAANRAIRRRLKLSDFVIELRDARIPLSSANEDLQPMLCEKRRVIALNKKDLANPNIMHRWIRYFNSCKQE 98
Cdd:COG1161    2 QIQWFPGHMAKARRQIKEILKLVDLVIEVVDARIPLSSRNPMLDELVGNKPRLLVLNKADLADPSVTKQWLKYFEKQGVD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  99 CFPINAHSRSSVQKLLDIVEFKLKEVITREPTLLVMVVGVPNVGKSVLINSIhqiaSSRfpvqekmRRSTVGPLPGVTQD 178
Cdd:COG1161   82 ALAISAKKGKGIKELIEAIRELAPEKGIKRRPIRVMIVGIPNVGKSTLINRL----AGK-------KVAKTGNKPGVTKG 150

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 460381741 179 IAGYKIAhqPSIYVLDTPGVLVPSIPDIETGLKLALAGSIKDSVVGEDRIVQYLLAVL 236
Cdd:COG1161  151 QQWIKLD--DGLELLDTPGILWPKFEDPEVGYKLAATGAIKDEVLDLEEVALFLLGYL 206
GTPase_YlqF TIGR03596
ribosome biogenesis GTP-binding protein YlqF; Members of this protein family are GTP-binding ...
 20-239 1.35e-58

ribosome biogenesis GTP-binding protein YlqF; Members of this protein family are GTP-binding proteins involved in ribosome biogenesis, including the essential YlqF protein of Bacillus subtilis, which is an essential protein. They are related to Era, EngA, and other GTPases of ribosome biogenesis, but are circularly permuted. This family is not universal, and is not present in Escherichia coli, and so is not as well studied as some other GTPases. This model is built for bacterial members. [Protein synthesis, Other]


Pssm-ID: 274669 [Multi-domain]  Cd Length: 276  Bit Score: 191.18  E-value: 1.35e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741   20 INWFPGHIDAANRAIRRRLKLSDFVIELRDARIPLSSANEDLQPMLCEKRRVIALNKKDLANPNIMHRWIRYFNSCKQEC 99
Cdd:TIGR03596   1 IQWFPGHMAKARREIKENLKLVDVVIEVLDARIPLSSRNPMIDEIRGNKPRLIVLNKADLADPAVTKQWLKYFEEKGIKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  100 FPINAHSRSSVQKLLDIVEFKLKEVITRE-------PTLLVMVVGVPNVGKSVLINSIHQiassrfpvqekmRRST-VGP 171
Cdd:TIGR03596  81 LAVNAKKGAGVKKIIKAAKKLLKEKNEKLkakglknRPIRAMIVGIPNVGKSTLINRLAG------------KKVAkVGN 148

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 460381741  172 LPGVTQDIAGYKIAhqPSIYVLDTPGVLVPSIPDIETGLKLALAGSIKDSVVGEDRIVQYLLAVLNTR 239
Cdd:TIGR03596 149 RPGVTKGQQWIKLS--DNLELLDTPGILWPKFEDQEVGLKLAATGAIKDEALDLEDVALFLLEYLLEH 214
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 133-243 2.03e-11

50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide.


Pssm-ID: 460387 [Multi-domain]  Cd Length: 113  Bit Score: 60.33  E-value: 2.03e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  133 VMVVGVPNVGKSVLINSIHQiassrfpvqekmRRSTVGPLPGVTQDIAGYKIAH-QPSIYVLDTPGVLvpSIPDIETGLK 211
Cdd:pfam01926   2 VALVGRPNVGKSTLINALTG------------AKAIVSDYPGTTRDPNEGRLELkGKQIILVDTPGLI--EGASEGEGLG 67

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 460381741  212 LALAGSIK--------DSVVGEDRIVQYLLAVLNTRGTPL 243
Cdd:pfam01926  68 RAFLAIIEadlilfvvDSEEGITPLDEELLELLRENKKPI 107
PRK09518 PRK09518
bifunctional cytidylate kinase/GTPase Der; Reviewed
 38-178 1.74e-05

bifunctional cytidylate kinase/GTPase Der; Reviewed


Pssm-ID: 236546 [Multi-domain]  Cd Length: 712  Bit Score: 46.71  E-value: 1.74e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  38 LKLSDFVIELRDARIPLSSANEDLQPML--CEKRRVIALNKKDlaNPNIMHRWIRYFNSCKQECFPINA-HSRSsVQKLL 114
Cdd:PRK09518 352 VSLADAVVFVVDGQVGLTSTDERIVRMLrrAGKPVVLAVNKID--DQASEYDAAEFWKLGLGEPYPISAmHGRG-VGDLL 428

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 115 DIVEFKLKE------VITREPTLLVMVVGVPNVGKSVLINsihQIASSrfpvqekmRRSTVGPLPGVTQD 178
Cdd:PRK09518 429 DEALDSLKVaektsgFLTPSGLRRVALVGRPNVGKSSLLN---QLTHE--------ERAVVNDLAGTTRD 487
Obg_like cd01881
Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; ...
 135-265 5.70e-04

Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; The Obg-like subfamily consists of five well-delimited, ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210, and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and Ygr210) are characterized by a distinct glycine-rich motif immediately following the Walker B motif (G3 box). Obg/CgtA is an essential gene that is involved in the initiation of sporulation and DNA replication in the bacteria Caulobacter and Bacillus, but its exact molecular role is unknown. Furthermore, several OBG family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. Nog1 is a nucleolar protein that might function in ribosome assembly. The DRG and Nog1 subfamilies are ubiquitous in archaea and eukaryotes, the Ygr210 subfamily is present in archaea and fungi, and the Obg and YyaF/YchF subfamilies are ubiquitous in bacteria and eukaryotes. The Obg/Nog1 and DRG subfamilies appear to form one major branch of the Obg family and the Ygr210 and YchF subfamilies form another branch. No GEFs, GAPs, or GDIs for Obg have been identified.


Pssm-ID: 206668 [Multi-domain]  Cd Length: 167  Bit Score: 40.07  E-value: 5.70e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 135 VVGVPNVGKSVLINSIH----QIASSRFpvqekmrrSTVGPLPGVTQDIAGYKIAhqpsiyVLDTPGvLVPSiPDIETGL 210
Cdd:cd01881    2 LVGLPNVGKSTLLSALTsakvEIASYPF--------TTLEPNVGVFEFGDGVDIQ------IIDLPG-LLDG-ASEGRGL 65

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 460381741 211 KLALAGSIKDSvvgeDRIVQYLLAVLNTRGTPLHWRHLISRETEGLHHELDDKPE 265
Cdd:cd01881   66 GEQILAHLYRS----DLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFLKNKPE 116
 
Name Accession Description Interval E-value
YlqF cd01856
Circularly permuted YlqF GTPase; Proteins of the YlqF family contain all sequence motifs ...
 22-199 4.21e-62

Circularly permuted YlqF GTPase; Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The YlqF subfamily is represented in all eukaryotes as well as a phylogenetically diverse array of bacteria (including gram-positive bacteria, proteobacteria, Synechocystis, Borrelia, and Thermotoga).


Pssm-ID: 206749 [Multi-domain]  Cd Length: 171  Bit Score: 196.60  E-value: 4.21e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  22 WFPGHIDAANRAIRRRLKLSDFVIELRDARIPLSSANEDLQPMLCEKRRVIALNKKDLANPNIMHRWIRYFNSCKQECFP 101
Cdd:cd01856    1 WFPGHMAKALRQIKEKLKLVDVVIEVRDARIPLSSRNPDLDKILGNKPRLIVLNKADLADPAKTKKWLKYFKSQGEPVLF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 102 INAHSRSSVQKLLDIVEFKLKEVI------TREPTLLVMVVGVPNVGKSVLINSIHQIASSRfpvqekmrrstVGPLPGV 175
Cdd:cd01856   81 VNAKNGKGVKKLLKKAKKLLKENEklkakgLLPRPLRAMVVGIPNVGKSTLINRLRGKKVAK-----------VGNKPGV 149

                        170       180
                 ....*....|....*....|....
gi 460381741 176 TQDIAGYKIAhqPSIYVLDTPGVL 199
Cdd:cd01856  150 TRGQQWIRIG--PNIELLDTPGIL 171
RbgA COG1161
Ribosome biogenesis GTPase RbgA [Translation, ribosomal structure and biogenesis];
19-236 1.88e-61

Ribosome biogenesis GTPase RbgA [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440775 [Multi-domain]  Cd Length: 279  Bit Score: 198.79  E-value: 1.88e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  19 NINWFPGHIDAANRAIRRRLKLSDFVIELRDARIPLSSANEDLQPMLCEKRRVIALNKKDLANPNIMHRWIRYFNSCKQE 98
Cdd:COG1161    2 QIQWFPGHMAKARRQIKEILKLVDLVIEVVDARIPLSSRNPMLDELVGNKPRLLVLNKADLADPSVTKQWLKYFEKQGVD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  99 CFPINAHSRSSVQKLLDIVEFKLKEVITREPTLLVMVVGVPNVGKSVLINSIhqiaSSRfpvqekmRRSTVGPLPGVTQD 178
Cdd:COG1161   82 ALAISAKKGKGIKELIEAIRELAPEKGIKRRPIRVMIVGIPNVGKSTLINRL----AGK-------KVAKTGNKPGVTKG 150

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 460381741 179 IAGYKIAhqPSIYVLDTPGVLVPSIPDIETGLKLALAGSIKDSVVGEDRIVQYLLAVL 236
Cdd:COG1161  151 QQWIKLD--DGLELLDTPGILWPKFEDPEVGYKLAATGAIKDEVLDLEEVALFLLGYL 206
GTPase_YlqF TIGR03596
ribosome biogenesis GTP-binding protein YlqF; Members of this protein family are GTP-binding ...
 20-239 1.35e-58

ribosome biogenesis GTP-binding protein YlqF; Members of this protein family are GTP-binding proteins involved in ribosome biogenesis, including the essential YlqF protein of Bacillus subtilis, which is an essential protein. They are related to Era, EngA, and other GTPases of ribosome biogenesis, but are circularly permuted. This family is not universal, and is not present in Escherichia coli, and so is not as well studied as some other GTPases. This model is built for bacterial members. [Protein synthesis, Other]


Pssm-ID: 274669 [Multi-domain]  Cd Length: 276  Bit Score: 191.18  E-value: 1.35e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741   20 INWFPGHIDAANRAIRRRLKLSDFVIELRDARIPLSSANEDLQPMLCEKRRVIALNKKDLANPNIMHRWIRYFNSCKQEC 99
Cdd:TIGR03596   1 IQWFPGHMAKARREIKENLKLVDVVIEVLDARIPLSSRNPMIDEIRGNKPRLIVLNKADLADPAVTKQWLKYFEEKGIKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  100 FPINAHSRSSVQKLLDIVEFKLKEVITRE-------PTLLVMVVGVPNVGKSVLINSIHQiassrfpvqekmRRST-VGP 171
Cdd:TIGR03596  81 LAVNAKKGAGVKKIIKAAKKLLKEKNEKLkakglknRPIRAMIVGIPNVGKSTLINRLAG------------KKVAkVGN 148

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 460381741  172 LPGVTQDIAGYKIAhqPSIYVLDTPGVLVPSIPDIETGLKLALAGSIKDSVVGEDRIVQYLLAVLNTR 239
Cdd:TIGR03596 149 RPGVTKGQQWIKLS--DNLELLDTPGILWPKFEDQEVGLKLAATGAIKDEALDLEDVALFLLEYLLEH 214
MJ1464 cd01859
An uncharacterized, circularly permuted subfamily of the Ras GTPases; This family represents ...
 32-198 1.22e-24

An uncharacterized, circularly permuted subfamily of the Ras GTPases; This family represents archaeal GTPase typified by the protein MJ1464 from Methanococcus jannaschii. The members of this family show a circular permutation of the GTPase signature motifs so that C-terminal strands 5, 6, and 7 (strands 6 contain the NKxD motif) are relocated to the N terminus.


Pssm-ID: 206752 [Multi-domain]  Cd Length: 157  Bit Score: 98.16  E-value: 1.22e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  32 RAIRRRLKLSDFVIELRDARIPLSSANEDLQPMLCE--KRRVIALNKKDLANPNIMHRWIRYFNSCKQECFPINAHSRSS 109
Cdd:cd01859    3 RLVRRIIKEADVVLEVVDARDPELTRSRKLERMALElgKKLIIVLNKADLVPREVLEKWKEVFESEGLPVVYVSARERLG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 110 VQKLLDivefKLKEVITREPTLLVMVVGVPNVGKSVLINSI---HQIASSRFPVQekmrrstvgplPGVTQDIAGYKIAh 186
Cdd:cd01859   83 TRILRR----TIKELAIDGKPVIVGVVGYPKVGKSSIINALkgrHSASTSPIPGS-----------PGYTKGIQLVRID- 146

                        170
                 ....*....|..
gi 460381741 187 qPSIYVLDTPGV 198
Cdd:cd01859  147 -SKIYLIDTPGV 157
YlqF_related_GTPase cd01849
Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, ...
 42-198 3.38e-17

Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, and archaea. They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases.


Pssm-ID: 206746 [Multi-domain]  Cd Length: 146  Bit Score: 77.42  E-value: 3.38e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  42 DFVIELRDARIPLSSANEDLQPM--LCEKRRVIALNKKDLANPNIMHRWIRY-FNSCKQECFPINAHSRSSVQKLLD-IV 117
Cdd:cd01849    1 DVVVEVVDARDPLSSRNPDIEVLinEKNKKLIMVLNKADLVPKEVLRKWVAElSELYGTKTFFISATNGQGILKLKAeIT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 118 EFKLKEVITREPTLLVmvVGVPNVGKSVLINSIhqiassrfpvqEKMRRSTVGPLPGVTQDIAGYKIAHQpsIYVLDTPG 197
Cdd:cd01849   81 KQKLKLKYKKGIRVGV--VGLPNVGKSSFINAL-----------LNKFKLKVGSIPGTTKLQQDVKLDKE--IYLYDTPG 145


                 .
gi 460381741 198 V 198
Cdd:cd01849  146 I 146
YqeH cd01855
Circularly permuted YqeH GTPase; YqeH is an essential GTP-binding protein. Depletion of YqeH ...
 67-198 2.25e-14

Circularly permuted YqeH GTPase; YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases.


Pssm-ID: 206748 [Multi-domain]  Cd Length: 191  Bit Score: 70.76  E-value: 2.25e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  67 EKRRVIALNKKDL----ANPNIMHRWIRyfNSCKQECFPIN------AHSRSSVQKLLDivefKLKEviTREPTLLVMVV 136
Cdd:cd01855   60 AKPVILVGNKIDLlpkdVKPNRLKQWVK--KRLKIGGLKIKdvilvsAKKGWGVEELIE----EIKK--LAKYRGDVYVV 131

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 460381741 137 GVPNVGKSVLINSIHQIASSRFPVQEKMRRSTVGPLPGVTQDIAGYKIAHQPSIYvlDTPGV 198
Cdd:cd01855  132 GATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLGLIKIPLGEGKKLY--DTPGI 191
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 133-243 2.03e-11

50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide.


Pssm-ID: 460387 [Multi-domain]  Cd Length: 113  Bit Score: 60.33  E-value: 2.03e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  133 VMVVGVPNVGKSVLINSIHQiassrfpvqekmRRSTVGPLPGVTQDIAGYKIAH-QPSIYVLDTPGVLvpSIPDIETGLK 211
Cdd:pfam01926   2 VALVGRPNVGKSTLINALTG------------AKAIVSDYPGTTRDPNEGRLELkGKQIILVDTPGLI--EGASEGEGLG 67

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 460381741  212 LALAGSIK--------DSVVGEDRIVQYLLAVLNTRGTPL 243
Cdd:pfam01926  68 RAFLAIIEadlilfvvDSEEGITPLDEELLELLRENKKPI 107
HSR1_MMR1 cd01857
A circularly permuted subfamily of the Ras GTPases; Human HSR1 is localized to the human MHC ...
 36-201 5.02e-11

A circularly permuted subfamily of the Ras GTPases; Human HSR1 is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with sequence NKXD) are relocated to the N-terminus.


Pssm-ID: 206750 [Multi-domain]  Cd Length: 140  Bit Score: 59.94  E-value: 5.02e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  36 RRLKLSDFVIELRDARIPLSSANEDL----QPMLCEKRRVIALNKKDLANPNIMHRWIRYFNSckqecfpiNAHSrssvq 111
Cdd:cd01857    7 RVIERSDVVVQIVDARNPLFFRCPDLekyvKEVDPSKENVLLLNKADLVTEEQRKAWARYFKK--------EGIV----- 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 112 klLDIVEFKLKEVITreptllvmVVGVPNVGKSVLINSIhqiassrfpVQEKmrRSTVGPLPGVTQDIAGYKIahQPSIY 191
Cdd:cd01857   74 --VLFFSALNEATIG--------LVGYPNVGKSSLINAL---------VGSK--KVSVSSTPGKTKHFQTIFL--EPGIT 130

                        170
                 ....*....|
gi 460381741 192 VLDTPGVLVP 201
Cdd:cd01857  131 LCDCPGLVFP 140
Nucleostemin_like cd04178
A circularly permuted subfamily of the Ras GTPases; Nucleostemin (NS) is a nucleolar protein ...
 42-198 3.43e-10

A circularly permuted subfamily of the Ras GTPases; Nucleostemin (NS) is a nucleolar protein that functions as a regulator of cell growth and proliferation in stem cells and in several types of cancer cells, but is not expressed in the differentiated cells of most mammalian adult tissues. NS shuttles between the nucleolus and nucleoplasm bidirectionally at a rate that is fast and independent of cell type. Lowering GTP levels decreases the nucleolar retention of NS, and expression of NS is abruptly down-regulated during differentiation prior to terminal cell division. Found only in eukaryotes, NS consists of an N-terminal basic domain, a coiled-coil domain, a GTP-binding domain, an intermediate domain, and a C-terminal acidic domain. Experimental evidence indicates that NS uses its GTP-binding property as a molecular switch to control the transition between the nucleolus and nucleoplasm, and this process involves interaction between the basic, GTP-binding, and intermediate domains of the protein.


Pssm-ID: 206753 [Multi-domain]  Cd Length: 171  Bit Score: 58.36  E-value: 3.43e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  42 DFVIELRDARIPLSSANEDLQPMLC----EKRRVIALNKKDLANPNIMHRWIRYFnsckQECFPI----------NAH-S 106
Cdd:cd04178    1 DVILEVLDARDPLGCRCPQVERAVLvlgpNKKLVLVLNKIDLVPKENVEKWLKYL----RNEFPTvafkastqqqKKNlS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 107 RSSVQKLLDIVEFKLKEVITREpTLL-----------------VMVVGVPNVGKSVLINSIhqiassrfpvqeKMRRS-T 168
Cdd:cd04178   77 RKSKKVKASDDLLSSSACLGAD-ALLkllknyarnkgiktsitVGVVGYPNVGKSSVINSL------------KRSRAcN 143

                        170       180       190
                 ....*....|....*....|....*....|
gi 460381741 169 VGPLPGVTQDIAGYKIAHQpsIYVLDTPGV 198
Cdd:cd04178  144 VGATPGVTKSMQEVHLDKH--VKLLDSPGV 171
NGP_1 cd01858
A novel nucleolar GTP-binding protein, circularly permuted subfamily of the Ras GTPases; ...
 41-198 2.91e-08

A novel nucleolar GTP-binding protein, circularly permuted subfamily of the Ras GTPases; Autoantigen NGP-1 (Nucleolar G-protein gene 1) has been shown to localize in the nucleolus and nucleolar organizers in all cell types analyzed, which is indicative of a function in ribosomal assembly. NGP-1 and its homologs show a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with NKXD motif) are relocated to the N terminus.


Pssm-ID: 206751 [Multi-domain]  Cd Length: 157  Bit Score: 52.69  E-value: 2.91e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  41 SDFVIELRDARIPLSSANEDLQPMLCEKRR----VIALNKKDLANPNIMHRWIRYFNsckqECFPINAHsRSSVQK---- 112
Cdd:cd01858    9 SDVIIQVLDARDPMGTRCKHVEKYLRKEKPhkhlIFVLNKCDLVPTWVTKRWVKVLS----KEYPTLAF-HASITNpfgk 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 113 --LLDIVEfKLKEVITREPTLLVMVVGVPNVGKSVLINSIhqiassrfpvqEKMRRSTVGPLPGVTQdIAGYkIAHQPSI 190
Cdd:cd01858   84 gaLINLLR-QFAKLHSDKKQISVGFIGYPNVGKSSVINTL-----------RSKKVCKVAPIPGETK-VWQY-ITLMKRI 149


                 ....*...
gi 460381741 191 YVLDTPGV 198
Cdd:cd01858  150 YLIDCPGV 157
Der COG1160
Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis];
98-198 2.38e-06

Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440774 [Multi-domain]  Cd Length: 438  Bit Score: 49.25  E-value: 2.38e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  98 ECFPINAHSRSSVQKLLDIVEFKLKEVITREPTLLVM---VVGVPNVGKSVLINSIhqiassrfpVQEKmrRSTVGPLPG 174
Cdd:COG1160  140 EPIPISAEHGRGVGDLLDAVLELLPEEEEEEEEDDPIkiaIVGRPNVGKSSLINAL---------LGEE--RVIVSDIAG 208

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 460381741 175 VTQDiagykiahqpSIYVL-----------DTPGV 198
Cdd:COG1160  209 TTRD----------SIDTPferdgkkytliDTAGI 233
GTPase_YqeH TIGR03597
ribosome biogenesis GTPase YqeH; This family describes YqeH, a member of a larger family of ...
 75-199 2.83e-06

ribosome biogenesis GTPase YqeH; This family describes YqeH, a member of a larger family of GTPases involved in ribosome biogenesis. Like YqlF, it shows a cyclical permutation relative to GTPases EngA (in which the GTPase domain is duplicated), Era, and others. Members of this protein family are found in a relatively small number of bacterial species, including Bacillus subtilis but not Escherichia coli. [Protein synthesis, Other]


Pssm-ID: 213834 [Multi-domain]  Cd Length: 360  Bit Score: 48.77  E-value: 2.83e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741   75 NKKDL----ANPNIMHRWIR-YFNS---CKQECFPINAHSRSSVQKLLDIVEfKLKEVITreptllVMVVGVPNVGKSVL 146
Cdd:TIGR03597  98 NKIDLlpksVNLSKIKEWMKkRAKElglKPVDIILVSAKKGNGIDELLDKIK-KARNKKD------VYVVGVTNVGKSSL 170

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 460381741  147 INSIHQIASsrfpVQEKMrrSTVGPLPGVTQDIAgyKIAHQPSIYVLDTPGVL 199
Cdd:TIGR03597 171 INKLLKQNN----GDKDV--ITTSPFPGTTLDLI--EIPLDDGHSLYDTPGII 215
Era_like cd00880
E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ...
 135-199 3.36e-06

E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngB), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family.


Pssm-ID: 206646 [Multi-domain]  Cd Length: 161  Bit Score: 46.47  E-value: 3.36e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 460381741 135 VVGVPNVGKSVLINSIHqiassrfpvqeKMRRSTVGPLPGVTQDIAGYKIAHQP--SIYVLDTPGVL 199
Cdd:cd00880    2 IFGRPNVGKSSLLNALL-----------GQNVGIVSPIPGTTRDPVRKEWELLPlgPVVLIDTPGLD 57
PRK09518 PRK09518
bifunctional cytidylate kinase/GTPase Der; Reviewed
 38-178 1.74e-05

bifunctional cytidylate kinase/GTPase Der; Reviewed


Pssm-ID: 236546 [Multi-domain]  Cd Length: 712  Bit Score: 46.71  E-value: 1.74e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  38 LKLSDFVIELRDARIPLSSANEDLQPML--CEKRRVIALNKKDlaNPNIMHRWIRYFNSCKQECFPINA-HSRSsVQKLL 114
Cdd:PRK09518 352 VSLADAVVFVVDGQVGLTSTDERIVRMLrrAGKPVVLAVNKID--DQASEYDAAEFWKLGLGEPYPISAmHGRG-VGDLL 428

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 115 DIVEFKLKE------VITREPTLLVMVVGVPNVGKSVLINsihQIASSrfpvqekmRRSTVGPLPGVTQD 178
Cdd:PRK09518 429 DEALDSLKVaektsgFLTPSGLRRVALVGRPNVGKSSLLN---QLTHE--------ERAVVNDLAGTTRD 487
PRK00093 PRK00093
GTP-binding protein Der; Reviewed
 43-198 5.13e-05

GTP-binding protein Der; Reviewed


Pssm-ID: 234628 [Multi-domain]  Cd Length: 435  Bit Score: 45.04  E-value: 5.13e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  43 FVIelrDARIPLSSANEDLQPML--CEKRRVIALNKKDlaNPNIMHRWIRYFNSCKQECFPINAHSRSSVQKLLDIVEFK 120
Cdd:PRK00093  86 FVV---DGRAGLTPADEEIAKILrkSNKPVILVVNKVD--GPDEEADAYEFYSLGLGEPYPISAEHGRGIGDLLDAILEE 160

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 121 L---KEVITREPTLLVMVVGVPNVGKSVLINSIhqiassrfpVQEKmrRSTVGPLPGVTQDiagykiahqpSIYVL---- 193
Cdd:PRK00093 161 LpeeEEEDEEDEPIKIAIIGRPNVGKSSLINAL---------LGEE--RVIVSDIAGTTRD----------SIDTPferd 219

                        170
                 ....*....|..
gi 460381741 194 -------DTPGV 198
Cdd:PRK00093 220 gqkytliDTAGI 231
YjeQ_EngC cd01854
Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; ...
 71-150 1.19e-04

Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; YjeQ (YloQ in Bacillus subtilis) is a ribosomal small subunit-dependent GTPase; hence also known as RsgA. YjeQ is a late-stage ribosomal biogenesis factor involved in the 30S subunit maturation, and it represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain.


Pssm-ID: 206747 [Multi-domain]  Cd Length: 211  Bit Score: 42.77  E-value: 1.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  71 VIALNKKDLANPNIMHRWIRYFNSCKQECFPINAHSRSSVQKLLDIVEFKlkevitreptlLVMVVGVPNVGKSVLINSI 150
Cdd:cd01854   37 VIVLNKADLVDDEELEELLEIYEKLGYPVLAVSAKTGEGLDELRELLKGK-----------TSVLVGQSGVGKSTLLNAL 105
Nog1 COG1084
GTP-binding protein, GTP1/Obg family [General function prediction only];
120-199 1.96e-04

GTP-binding protein, GTP1/Obg family [General function prediction only];


Pssm-ID: 440701 [Multi-domain]  Cd Length: 330  Bit Score: 42.90  E-value: 1.96e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 120 KLKEVITREPTllVMVVGVPNVGKSVLINSI----HQIASsrFPVQEKmrrstvgplpGVtqdIAGYKIAHQPSIYVLDT 195
Cdd:COG1084  152 KLPDIDPDLPT--IVVAGYPNVGKSSLVSKVtsakPEIAS--YPFTTK----------GI---IVGHFERGHGRYQVIDT 214


                 ....
gi 460381741 196 PGVL 199
Cdd:COG1084  215 PGLL 218
FeoB cd01879
Ferrous iron transport protein B (FeoB) family; Ferrous iron transport protein B (FeoB) ...
 135-205 2.07e-04

Ferrous iron transport protein B (FeoB) family; Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.


Pssm-ID: 206667 [Multi-domain]  Cd Length: 159  Bit Score: 41.29  E-value: 2.07e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 460381741 135 VVGVPNVGKSVLINsihQIASSRFpvqekmrrsTVGPLPGVTQDIA-GYKIAHQPSIYVLDTPGV--LVPSIPD 205
Cdd:cd01879    2 LVGNPNVGKTTLFN---ALTGARQ---------KVGNWPGVTVEKKeGEFKLGGKEIEIVDLPGTysLTPYSED 63
YeeP COG3596
Predicted GTPase [General function prediction only];
113-198 5.24e-04

Predicted GTPase [General function prediction only];


Pssm-ID: 442815 [Multi-domain]  Cd Length: 318  Bit Score: 41.68  E-value: 5.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 113 LLDIVEFKLKEVITREPTLLVMVVGVPNVGKSVLINSIhqiassrfpVQEKmrRSTVGPLPGVTQDIAGYKIAHQ--PSI 190
Cdd:COG3596   22 LRELLAEALERLLVELPPPVIALVGKTGAGKSSLINAL---------FGAE--VAEVGVGRPCTREIQRYRLESDglPGL 90


                 ....*...
gi 460381741 191 YVLDTPGV 198
Cdd:COG3596   91 VLLDTPGL 98
Obg_like cd01881
Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; ...
 135-265 5.70e-04

Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; The Obg-like subfamily consists of five well-delimited, ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210, and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and Ygr210) are characterized by a distinct glycine-rich motif immediately following the Walker B motif (G3 box). Obg/CgtA is an essential gene that is involved in the initiation of sporulation and DNA replication in the bacteria Caulobacter and Bacillus, but its exact molecular role is unknown. Furthermore, several OBG family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. Nog1 is a nucleolar protein that might function in ribosome assembly. The DRG and Nog1 subfamilies are ubiquitous in archaea and eukaryotes, the Ygr210 subfamily is present in archaea and fungi, and the Obg and YyaF/YchF subfamilies are ubiquitous in bacteria and eukaryotes. The Obg/Nog1 and DRG subfamilies appear to form one major branch of the Obg family and the Ygr210 and YchF subfamilies form another branch. No GEFs, GAPs, or GDIs for Obg have been identified.


Pssm-ID: 206668 [Multi-domain]  Cd Length: 167  Bit Score: 40.07  E-value: 5.70e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 135 VVGVPNVGKSVLINSIH----QIASSRFpvqekmrrSTVGPLPGVTQDIAGYKIAhqpsiyVLDTPGvLVPSiPDIETGL 210
Cdd:cd01881    2 LVGLPNVGKSTLLSALTsakvEIASYPF--------TTLEPNVGVFEFGDGVDIQ------IIDLPG-LLDG-ASEGRGL 65

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 460381741 211 KLALAGSIKDSvvgeDRIVQYLLAVLNTRGTPLHWRHLISRETEGLHHELDDKPE 265
Cdd:cd01881   66 GEQILAHLYRS----DLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFLKNKPE 116
PRK03003 PRK03003
GTP-binding protein Der; Reviewed
 114-182 1.13e-03

GTP-binding protein Der; Reviewed


Pssm-ID: 179525 [Multi-domain]  Cd Length: 472  Bit Score: 40.72  E-value: 1.13e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 460381741 114 LDIVEFKLKEVITREPTLLVMVVGVPNVGKSVLINSIhqiaSSRfpvqekmRRSTVGPLPGVTQDIAGY 182
Cdd:PRK03003  22 LDDEDLAELEAAEGGPLPVVAVVGRPNVGKSTLVNRI----LGR-------REAVVEDVPGVTRDRVSY 79
FeoB_N pfam02421
Ferrous iron transport protein B; Escherichia coli has an iron(II) transport system (feo) ...
 133-198 1.24e-03

Ferrous iron transport protein B; Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.


Pssm-ID: 460552 [Multi-domain]  Cd Length: 156  Bit Score: 38.97  E-value: 1.24e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 460381741  133 VMVVGVPNVGKSVLINsihQIASSrfpvqekmrRSTVGPLPGVTQDIA-GYKIAHQPSIYVLDTPGV 198
Cdd:pfam02421   3 IALVGNPNVGKTTLFN---ALTGA---------NQHVGNWPGVTVEKKeGKFKYKGYEIEIVDLPGI 57
era TIGR00436
GTP-binding protein Era; Era is an essential GTPase in Escherichia coli and many other ...
 133-197 1.27e-03

GTP-binding protein Era; Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein. [Protein synthesis, Other]


Pssm-ID: 129528 [Multi-domain]  Cd Length: 270  Bit Score: 40.06  E-value: 1.27e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 460381741  133 VMVVGVPNVGKSVLINSIHqiassrfpvqeKMRRSTVGPLPGVTQD-IAGYKIAHQPSIYVLDTPG 197
Cdd:TIGR00436   3 VAILGRPNVGKSTLLNQLH-----------GQKISITSPKAQTTRNrISGIHTTGASQIIFIDTPG 57
trmE cd04164
trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in ...
 32-115 1.60e-03

trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance.


Pssm-ID: 206727 [Multi-domain]  Cd Length: 159  Bit Score: 38.63  E-value: 1.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  32 RAiRRRLKLSDFVIELRDARIPLSSANEDLQPMLCEKRRVIALNKKDLANPNIMHRwiryfNSCKQECFPINAHSRSSVQ 111
Cdd:cd04164   75 RA-REAIEEADLVLLVVDASEGLDEEDLEILELPAKKPVIVVLNKSDLLSDAEGIS-----ELNGKPIIAISAKTGEGID 148


                 ....
gi 460381741 112 KLLD 115
Cdd:cd04164  149 ELKE 152
EngA2 cd01895
EngA2 GTPase contains the second domain of EngA; This EngA2 subfamily CD represents the second ...
 135-178 1.60e-03

EngA2 GTPase contains the second domain of EngA; This EngA2 subfamily CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.


Pssm-ID: 206682 [Multi-domain]  Cd Length: 174  Bit Score: 38.95  E-value: 1.60e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 460381741 135 VVGVPNVGKSVLINSIhqiassrfpVQEKmrRSTVGPLPGVTQD 178
Cdd:cd01895    7 IIGRPNVGKSSLLNAL---------LGEE--RVIVSDIAGTTRD 39
RsgA COG1162
Ribosome biogenesis GTPase RsgA [Translation, ribosomal structure and biogenesis];
71-150 1.80e-03

Ribosome biogenesis GTPase RsgA [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440776 [Multi-domain]  Cd Length: 300  Bit Score: 39.71  E-value: 1.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  71 VIALNKKDLANPNIMHRWIRYFNSCKQECFPINAHSRSSVQKLLDIVEFKLkevitreptllVMVVGVPNVGKSVLINSI 150
Cdd:COG1162  118 VIVLNKADLADDEELEELLAIYEALGYPVLAVSAKTGEGLDELRELLKGKT-----------SVLVGQSGVGKSTLINAL 186
Rbg1 COG1163
Ribosome-interacting GTPase RBG1 [Translation, ribosomal structure and biogenesis];
133-199 2.09e-03

Ribosome-interacting GTPase RBG1 [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440777 [Multi-domain]  Cd Length: 368  Bit Score: 39.78  E-value: 2.09e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 460381741 133 VMVVGVPNVGKSVLINSI----HQIASSRFpvqekmrrSTVGPLPGVTQdiagYKIAHqpsIYVLDTPGVL 199
Cdd:COG1163   66 VVLVGFPSVGKSTLLNKLtnakSEVGAYEF--------TTLDVVPGMLE----YKGAK---IQILDVPGLI 121
PRK03003 PRK03003
GTP-binding protein Der; Reviewed
 98-178 2.76e-03

GTP-binding protein Der; Reviewed


Pssm-ID: 179525 [Multi-domain]  Cd Length: 472  Bit Score: 39.57  E-value: 2.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741  98 ECFPINA-HSRSSVQkLLDIVEFKLKEViTREPTLL-----VMVVGVPNVGKSVLINsihQIASSrfpvqekmRRSTVGP 171
Cdd:PRK03003 175 EPHPVSAlHGRGVGD-LLDAVLAALPEV-PRVGSASggprrVALVGKPNVGKSSLLN---KLAGE--------ERSVVDD 241


                 ....*..
gi 460381741 172 LPGVTQD 178
Cdd:PRK03003 242 VAGTTVD 248
EngA1 cd01894
EngA1 GTPase contains the first domain of EngA; This EngA1 subfamily CD represents the first ...
 136-198 3.53e-03

EngA1 GTPase contains the first domain of EngA; This EngA1 subfamily CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.


Pssm-ID: 206681 [Multi-domain]  Cd Length: 157  Bit Score: 37.80  E-value: 3.53e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 460381741 136 VGVPNVGKSVLINSIhqiassrfpVQEkmRRSTVGPLPGVTQD-IAGYKIAHQPSIYVLDTPGV 198
Cdd:cd01894    3 VGRPNVGKSTLFNRL---------TGR--RDAIVSDTPGVTRDrKYGEAEWGGREFILIDTGGI 55
feoB TIGR00437
ferrous iron transporter FeoB; FeoB (773 amino acids in E. coli), a cytoplasmic membrane ...
 137-198 4.03e-03

ferrous iron transporter FeoB; FeoB (773 amino acids in E. coli), a cytoplasmic membrane protein required for iron(II) update, is encoded in an operon with FeoA (75 amino acids), which is also required, and is regulated by Fur. There appear to be two copies in Archaeoglobus fulgidus and Clostridium acetobutylicum. [Transport and binding proteins, Cations and iron carrying compounds]


Pssm-ID: 273077 [Multi-domain]  Cd Length: 591  Bit Score: 39.34  E-value: 4.03e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 460381741  137 GVPNVGKSVLINsihQIASSRFpvqekmrrsTVGPLPGVTQDIA-GYKIAHQPSIYVLDTPGV 198
Cdd:TIGR00437   1 GNPNVGKSTLFN---ALTGANQ---------TVGNWPGVTVEKKeGKLGFQGEDIEIVDLPGI 51
PRK09518 PRK09518
bifunctional cytidylate kinase/GTPase Der; Reviewed
 126-182 6.13e-03

bifunctional cytidylate kinase/GTPase Der; Reviewed


Pssm-ID: 236546 [Multi-domain]  Cd Length: 712  Bit Score: 38.62  E-value: 6.13e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 460381741 126 TREPTLLVMVVGVPNVGKSVLINSIhqiaSSRfpvqekmRRSTVGPLPGVTQDIAGY 182
Cdd:PRK09518 271 GPKAVGVVAIVGRPNVGKSTLVNRI----LGR-------REAVVEDTPGVTRDRVSY 316
Era cd04163
E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ...
 133-198 6.85e-03

E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.


Pssm-ID: 206726 [Multi-domain]  Cd Length: 168  Bit Score: 37.06  E-value: 6.85e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 460381741 133 VMVVGVPNVGKSVLINSIhqiassrfpVQEKMrrSTVGPLPGVT-QDIAGykIAHQPS---IYVlDTPGV 198
Cdd:cd04163    6 VAIIGRPNVGKSTLLNAL---------VGQKI--SIVSPKPQTTrNRIRG--IYTDDDaqiIFV-DTPGI 61
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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