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Conserved domains on  [gi|1747056208|gb|KAA5773186|]
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YihA family ribosome biogenesis GTP-binding protein [Klebsiella pneumoniae]

Protein Classification

GTP-binding protein( domain architecture ID 10785093)

GTP-binding protein similar to YsxC/EngB, a GTPase associated with ribosome biogenesis; belongs to the large superfamily of translation factor-related (TRAFAC) GTPases

CATH:  3.40.50.300
Gene Ontology:  GO:0046872|GO:0005525
PubMed:  16333325|11916378|11489118
SCOP:  4004043

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EngB COG0218
GTP-binding protein EngB required for normal cell division [Cell cycle control, cell division, ...
 5-197 9.40e-118

GTP-binding protein EngB required for normal cell division [Cell cycle control, cell division, chromosome partitioning];


:

Pssm-ID: 439988 [Multi-domain]  Cd Length: 194  Bit Score: 332.42  E-value: 9.40e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208   5 NYQLTHFVTSAPDIRHLPADTGIEVAFAGRSNAGKSSALNTLTNQKNLARTSKTPGRTQLINLFEVAEGKRLVDLPGYGY 84
Cdd:COG0218     2 KIKKAEFVTSAVKLEQLPPDDLPEIAFAGRSNVGKSSLINALTNRKKLARTSKTPGKTQLINFFLINDKFYLVDLPGYGY 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  85 AQVPEEMKIKWQRALGEYLEKRLCLKGLVVLMDIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKLASGARKAQVNMVRE 164
Cdd:COG0218    82 AKVSKAEKEKWQKLIEDYLEGRENLKGVVLLIDIRHPPKELDLEMLEWLDEAGIPFLIVLTKADKLKKSELAKQLKAIKK 161

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1747056208 165 AVLAFNGDVQVEPFSSLKKSGVDKLRQKLDSWF 197
Cdd:COG0218   162 ALGKDPAAPEVILFSSLKKEGIDELRAAIEEWL 194
 
Name Accession Description Interval E-value
EngB COG0218
GTP-binding protein EngB required for normal cell division [Cell cycle control, cell division, ...
 5-197 9.40e-118

GTP-binding protein EngB required for normal cell division [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 439988 [Multi-domain]  Cd Length: 194  Bit Score: 332.42  E-value: 9.40e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208   5 NYQLTHFVTSAPDIRHLPADTGIEVAFAGRSNAGKSSALNTLTNQKNLARTSKTPGRTQLINLFEVAEGKRLVDLPGYGY 84
Cdd:COG0218     2 KIKKAEFVTSAVKLEQLPPDDLPEIAFAGRSNVGKSSLINALTNRKKLARTSKTPGKTQLINFFLINDKFYLVDLPGYGY 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  85 AQVPEEMKIKWQRALGEYLEKRLCLKGLVVLMDIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKLASGARKAQVNMVRE 164
Cdd:COG0218    82 AKVSKAEKEKWQKLIEDYLEGRENLKGVVLLIDIRHPPKELDLEMLEWLDEAGIPFLIVLTKADKLKKSELAKQLKAIKK 161

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1747056208 165 AVLAFNGDVQVEPFSSLKKSGVDKLRQKLDSWF 197
Cdd:COG0218   162 ALGKDPAAPEVILFSSLKKEGIDELRAAIEEWL 194
GTPase_YsxC TIGR03598
ribosome biogenesis GTP-binding protein YsxC/EngB; Members of this protein family are a GTPase ...
 9-187 9.41e-113

ribosome biogenesis GTP-binding protein YsxC/EngB; Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes. [Protein synthesis, Other]


Pssm-ID: 274670 [Multi-domain]  Cd Length: 179  Bit Score: 319.42  E-value: 9.41e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208   9 THFVTSAPDIRHLPADTGIEVAFAGRSNAGKSSALNTLTNQKNLARTSKTPGRTQLINLFEVAEGKRLVDLPGYGYAQVP 88
Cdd:TIGR03598   1 AEFVKSAVKLKQLPPDDGPEIAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFEVNDGFRLVDLPGYGYAKVS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  89 EEMKIKWQRALGEYLEKRLCLKGLVVLMDIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKLASGARKAQVNMVREAVLA 168
Cdd:TIGR03598  81 KEEKEKWQKLIEEYLEKRENLKGVVLLMDIRHPLKELDLEMIEWLRERGIPVLIVLTKADKLKKSELNKQLKKIKKALKK 160

                         170
                  ....*....|....*....
gi 1747056208 169 FNGDVQVEPFSSLKKSGVD 187
Cdd:TIGR03598 161 DADDPSVQLFSSLKKTGID 179
YihA_EngB cd01876
YihA (EngB) GTPase family; The YihA (EngB) subfamily of GTPases is typified by the E. coli ...
 28-197 2.76e-93

YihA (EngB) GTPase family; The YihA (EngB) subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target.


Pssm-ID: 206665 [Multi-domain]  Cd Length: 170  Bit Score: 269.77  E-value: 2.76e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  28 EVAFAGRSNAGKSSALNTLTNQKNLARTSKTPGRTQLINLFEVAEGKRLVDLPGYGYAQVPEEMKIKWQRALGEYLEKRL 107
Cdd:cd01876     1 EVAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFNVGDKFRLVDLPGYGYAKVSKEVREKWGKLIEEYLENRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208 108 CLKGLVVLMDIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKLASGARKAQVNMVREAVLAFNGDVQVEPFSSLKKSGVD 187
Cdd:cd01876    81 NLKGVVLLIDARHGPTPIDLEMLEFLEELGIPFLIVLTKADKLKKSELAKVLKKIKEELNLFNILPPVILFSSKKGTGID 160

                         170
                  ....*....|
gi 1747056208 188 KLRQKLDSWF 197
Cdd:cd01876   161 ELRALIAEWL 170
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 28-146 4.27e-24

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: 91.91  E-value: 4.27e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  28 EVAFAGRSNAGKSSALNTLTNQKnlARTSKTPGRTQLINLFEVAEGKR---LVDLPGygyaqVPEEMKIKWQraLGEYLE 104
Cdd:pfam01926   1 RVALVGRPNVGKSTLINALTGAK--AIVSDYPGTTRDPNEGRLELKGKqiiLVDTPG-----LIEGASEGEG--LGRAFL 71

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1747056208 105 KRLCLKGLVVLMDIRHPLKDLDQQMIEWAVESDIQVLVLLTK 146
Cdd:pfam01926  72 AIIEADLILFVVDSEEGITPLDEELLELLRENKKPIILVLNK 113
era PRK00089
GTPase Era; Reviewed
 29-193 4.82e-13

GTPase Era; Reviewed


Pssm-ID: 234624 [Multi-domain]  Cd Length: 292  Bit Score: 66.22  E-value: 4.82e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  29 VAFAGRSNAGKSSALNTLTNQKnLARTSKTP-------------GRTQLInlfevaegkrLVDLPGYgyaqvpeemkIKW 95
Cdd:PRK00089    8 VAIVGRPNVGKSTLLNALVGQK-ISIVSPKPqttrhrirgivteDDAQII----------FVDTPGI----------HKP 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  96 QRALGEYLEK--RLCLKG--LVVLM-DIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKLASgarKAQVNMVREAVLAFN 170
Cdd:PRK00089   67 KRALNRAMNKaaWSSLKDvdLVLFVvDADEKIGPGDEFILEKLKKVKTPVILVLNKIDLVKD---KEELLPLLEELSELM 143

                         170       180
                  ....*....|....*....|...
gi 1747056208 171 GDVQVEPFSSLKKSGVDKLRQKL 193
Cdd:PRK00089  144 DFAEIVPISALKGDNVDELLDVI 166
 
Name Accession Description Interval E-value
EngB COG0218
GTP-binding protein EngB required for normal cell division [Cell cycle control, cell division, ...
 5-197 9.40e-118

GTP-binding protein EngB required for normal cell division [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 439988 [Multi-domain]  Cd Length: 194  Bit Score: 332.42  E-value: 9.40e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208   5 NYQLTHFVTSAPDIRHLPADTGIEVAFAGRSNAGKSSALNTLTNQKNLARTSKTPGRTQLINLFEVAEGKRLVDLPGYGY 84
Cdd:COG0218     2 KIKKAEFVTSAVKLEQLPPDDLPEIAFAGRSNVGKSSLINALTNRKKLARTSKTPGKTQLINFFLINDKFYLVDLPGYGY 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  85 AQVPEEMKIKWQRALGEYLEKRLCLKGLVVLMDIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKLASGARKAQVNMVRE 164
Cdd:COG0218    82 AKVSKAEKEKWQKLIEDYLEGRENLKGVVLLIDIRHPPKELDLEMLEWLDEAGIPFLIVLTKADKLKKSELAKQLKAIKK 161

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1747056208 165 AVLAFNGDVQVEPFSSLKKSGVDKLRQKLDSWF 197
Cdd:COG0218   162 ALGKDPAAPEVILFSSLKKEGIDELRAAIEEWL 194
GTPase_YsxC TIGR03598
ribosome biogenesis GTP-binding protein YsxC/EngB; Members of this protein family are a GTPase ...
 9-187 9.41e-113

ribosome biogenesis GTP-binding protein YsxC/EngB; Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes. [Protein synthesis, Other]


Pssm-ID: 274670 [Multi-domain]  Cd Length: 179  Bit Score: 319.42  E-value: 9.41e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208   9 THFVTSAPDIRHLPADTGIEVAFAGRSNAGKSSALNTLTNQKNLARTSKTPGRTQLINLFEVAEGKRLVDLPGYGYAQVP 88
Cdd:TIGR03598   1 AEFVKSAVKLKQLPPDDGPEIAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFEVNDGFRLVDLPGYGYAKVS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  89 EEMKIKWQRALGEYLEKRLCLKGLVVLMDIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKLASGARKAQVNMVREAVLA 168
Cdd:TIGR03598  81 KEEKEKWQKLIEEYLEKRENLKGVVLLMDIRHPLKELDLEMIEWLRERGIPVLIVLTKADKLKKSELNKQLKKIKKALKK 160

                         170
                  ....*....|....*....
gi 1747056208 169 FNGDVQVEPFSSLKKSGVD 187
Cdd:TIGR03598 161 DADDPSVQLFSSLKKTGID 179
YihA_EngB cd01876
YihA (EngB) GTPase family; The YihA (EngB) subfamily of GTPases is typified by the E. coli ...
 28-197 2.76e-93

YihA (EngB) GTPase family; The YihA (EngB) subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target.


Pssm-ID: 206665 [Multi-domain]  Cd Length: 170  Bit Score: 269.77  E-value: 2.76e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  28 EVAFAGRSNAGKSSALNTLTNQKNLARTSKTPGRTQLINLFEVAEGKRLVDLPGYGYAQVPEEMKIKWQRALGEYLEKRL 107
Cdd:cd01876     1 EVAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFNVGDKFRLVDLPGYGYAKVSKEVREKWGKLIEEYLENRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208 108 CLKGLVVLMDIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKLASGARKAQVNMVREAVLAFNGDVQVEPFSSLKKSGVD 187
Cdd:cd01876    81 NLKGVVLLIDARHGPTPIDLEMLEFLEELGIPFLIVLTKADKLKKSELAKVLKKIKEELNLFNILPPVILFSSKKGTGID 160

                         170
                  ....*....|
gi 1747056208 188 KLRQKLDSWF 197
Cdd:cd01876   161 ELRALIAEWL 170
Era_like cd00880
E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ...
 30-197 2.77e-25

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: 96.16  E-value: 2.77e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  30 AFAGRSNAGKSSALNTLTNQKNLArTSKTPGRTQLINLFEVAEGK----RLVDLPGYGYAQVPEEMKIkwQRALGEYLEK 105
Cdd:cd00880     1 AIFGRPNVGKSSLLNALLGQNVGI-VSPIPGTTRDPVRKEWELLPlgpvVLIDTPGLDEEGGLGRERV--EEARQVADRA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208 106 RLCLkgLVVlmDIRHPLKDLDQQmIEWAVESDIQVLVLLTKADKLASGARKAQvnmVREAVLAFNGDVQVEPFSSLKKSG 185
Cdd:cd00880    78 DLVL--LVV--DSDLTPVEEEAK-LGLLRERGKPVLLVLNKIDLVPESEEEEL---LRERKLELLPDLPVIAVSALPGEG 149

                         170
                  ....*....|..
gi 1747056208 186 VDKLRQKLDSWF 197
Cdd:cd00880   150 IDELRKKIAELL 161
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 28-146 4.27e-24

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: 91.91  E-value: 4.27e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  28 EVAFAGRSNAGKSSALNTLTNQKnlARTSKTPGRTQLINLFEVAEGKR---LVDLPGygyaqVPEEMKIKWQraLGEYLE 104
Cdd:pfam01926   1 RVALVGRPNVGKSTLINALTGAK--AIVSDYPGTTRDPNEGRLELKGKqiiLVDTPG-----LIEGASEGEG--LGRAFL 71

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1747056208 105 KRLCLKGLVVLMDIRHPLKDLDQQMIEWAVESDIQVLVLLTK 146
Cdd:pfam01926  72 AIIEADLILFVVDSEEGITPLDEELLELLRENKKPIILVLNK 113
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 30-193 2.21e-18

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


Pssm-ID: 206648 [Multi-domain]  Cd Length: 161  Bit Score: 78.27  E-value: 2.21e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  30 AFAGRSNAGKSSALNTLTNQkNLARTSKTPGRTQLINLFEVAEGK-----RLVDLPGYGYAQVPEEMKIKWQRALGeyle 104
Cdd:cd00882     1 VVVGRGGVGKSSLLNALLGG-EVGEVSDVPGTTRDPDVYVKELDKgkvklVLVDTPGLDEFGGLGREELARLLLRG---- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208 105 krlcLKGLVVLMDIRHPLKDLDQQ--MIEWAVESDIQVLVLLTKADKLasgARKAQVNMVREAVLAFNGDVQVEPFSSLK 182
Cdd:cd00882    76 ----ADLILLVVDSTDRESEEDAKllILRRLRKEGIPIILVGNKIDLL---EEREVEELLRLEELAKILGVPVFEVSAKT 148

                         170
                  ....*....|.
gi 1747056208 183 KSGVDKLRQKL 193
Cdd:cd00882   149 GEGVDELFEKL 159
Era cd04163
E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ...
 29-193 2.98e-13

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: 64.79  E-value: 2.98e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  29 VAFAGRSNAGKSSALNTLTNQKnLARTSKTP-------------GRTQLInlfevaegkrLVDLPGYgyaqvpeemkIKW 95
Cdd:cd04163     6 VAIIGRPNVGKSTLLNALVGQK-ISIVSPKPqttrnrirgiytdDDAQII----------FVDTPGI----------HKP 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  96 QRALGEYLeKRLCLKGL------VVLMDIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKLasgARKAQVNMVREAVLAF 169
Cdd:cd04163    65 KKKLGERM-VKAAWSALkdvdlvLFVVDASEWIGEGDEFILELLKKSKTPVILVLNKIDLV---KDKEDLLPLLEKLKEL 140

                         170       180
                  ....*....|....*....|....
gi 1747056208 170 NGDVQVEPFSSLKKSGVDKLRQKL 193
Cdd:cd04163   141 HPFAEIFPISALKGENVDELLEYI 164
era PRK00089
GTPase Era; Reviewed
 29-193 4.82e-13

GTPase Era; Reviewed


Pssm-ID: 234624 [Multi-domain]  Cd Length: 292  Bit Score: 66.22  E-value: 4.82e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  29 VAFAGRSNAGKSSALNTLTNQKnLARTSKTP-------------GRTQLInlfevaegkrLVDLPGYgyaqvpeemkIKW 95
Cdd:PRK00089    8 VAIVGRPNVGKSTLLNALVGQK-ISIVSPKPqttrhrirgivteDDAQII----------FVDTPGI----------HKP 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  96 QRALGEYLEK--RLCLKG--LVVLM-DIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKLASgarKAQVNMVREAVLAFN 170
Cdd:PRK00089   67 KRALNRAMNKaaWSSLKDvdLVLFVvDADEKIGPGDEFILEKLKKVKTPVILVLNKIDLVKD---KEELLPLLEELSELM 143

                         170       180
                  ....*....|....*....|...
gi 1747056208 171 GDVQVEPFSSLKKSGVDKLRQKL 193
Cdd:PRK00089  144 DFAEIVPISALKGDNVDELLDVI 166
Era COG1159
GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis];
29-193 7.78e-13

GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440773 [Multi-domain]  Cd Length: 290  Bit Score: 65.78  E-value: 7.78e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  29 VAFAGRSNAGKSSALNTLTNQKnLARTSKTP-------------GRTQLInlfevaegkrLVDLPGYgyaqvpeemkIKW 95
Cdd:COG1159     6 VAIVGRPNVGKSTLLNALVGQK-VSIVSPKPqttrhrirgivtrEDAQIV----------FVDTPGI----------HKP 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  96 QRALGEYLeKRLCLKGL----VVLM--DIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKLasgaRKAQVNMVREAVLAF 169
Cdd:COG1159    65 KRKLGRRM-NKAAWSALedvdVILFvvDATEKIGEGDEFILELLKKLKTPVILVINKIDLV----KKEELLPLLAEYSEL 139

                         170       180
                  ....*....|....*....|....
gi 1747056208 170 NGDVQVEPFSSLKKSGVDKLRQKL 193
Cdd:COG1159   140 LDFAEIVPISALKGDNVDELLDEI 163
PRK04213 PRK04213
GTP-binding protein EngB;
24-149 1.33e-12

GTP-binding protein EngB;


Pssm-ID: 179790 [Multi-domain]  Cd Length: 201  Bit Score: 63.78  E-value: 1.33e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  24 DTGIEVAFAGRSNAGKSSALNTLTNQKnlARTSKTPGRTQLINLFEVAEgKRLVDLPGYGY-AQVPEEMKIKWQRALGEY 102
Cdd:PRK04213    7 DRKPEIVFVGRSNVGKSTLVRELTGKK--VRVGKRPGVTRKPNHYDWGD-FILTDLPGFGFmSGVPKEVQEKIKDEIVRY 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1747056208 103 LE---KRLCLKGLVV----LMDI--RHPLKD---LDQQMIEWAVESDIQVLVLLTKADK 149
Cdd:PRK04213   84 IEdnaDRILAAVLVVdgksFIEIieRWEGRGeipIDVEMFDFLRELGIPPIVAVNKMDK 142
trmE cd04164
trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in ...
 25-193 5.56e-08

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: 50.19  E-value: 5.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  25 TGIEVAFAGRSNAGKSSALNTLTNqKNLARTSKTPGRT-----QLINL--FEVaegkRLVDLPGYGYAQVPEEmKIKWQR 97
Cdd:cd04164     2 EGIKVVIAGKPNVGKSSLLNALAG-RDRAIVSDIAGTTrdvieEEIDLggIPV----RLIDTAGLRETEDEIE-KIGIER 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  98 ALGEYLEKRLCLkglvVLMDIRHPLKDLDQQMIEWAveSDIQVLVLLTKADKLASGARKAQVNMvrEAVLAfngdvqvep 177
Cdd:cd04164    76 AREAIEEADLVL----LVVDASEGLDEEDLEILELP--AKKPVIVVLNKSDLLSDAEGISELNG--KPIIA--------- 138

                         170
                  ....*....|....*.
gi 1747056208 178 FSSLKKSGVDKLRQKL 193
Cdd:cd04164   139 ISAKTGEGIDELKEAL 154
YeeP COG3596
Predicted GTPase [General function prediction only];
28-205 8.94e-08

Predicted GTPase [General function prediction only];


Pssm-ID: 442815 [Multi-domain]  Cd Length: 318  Bit Score: 51.31  E-value: 8.94e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  28 EVAFAGRSNAGKSSALNTLTNQkNLARTSKTPGRTQLINLFEVAEGK----RLVDLPGYGYAQVPEEmkikWQRALGEYL 103
Cdd:COG3596    41 VIALVGKTGAGKSSLINALFGA-EVAEVGVGRPCTREIQRYRLESDGlpglVLLDTPGLGEVNERDR----EYRELRELL 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208 104 EkrlCLKGLVVLMDIRHPLKDLD----QQMIEWAveSDIQVLVLLTKADKL---------ASGARKAQVNMVREAVLAFN 170
Cdd:COG3596   116 P---EADLILWVVKADDRALATDeeflQALRAQY--PDPPVLVVLTQVDRLeperewdppYNWPSPPKEQNIRRALEAIA 190

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1747056208 171 GDVQVE-----PFSSLKK---SGVDKLRQKLdswFNEIPPQEA 205
Cdd:COG3596   191 EQLGVPidrviPVSAAEDrtgYGLEELVDAL---AEALPEAKR 230
EngA2 cd01895
EngA2 GTPase contains the second domain of EngA; This EngA2 subfamily CD represents the second ...
 26-189 2.34e-07

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: 48.97  E-value: 2.34e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  26 GIEVAFAGRSNAGKSSALNTLTNQKnlaR--TSKTPGRTQ--LINLFEVaEGKR--LVDLPGygyaqvpeemkIKWQRAL 99
Cdd:cd01895     2 PIKIAIIGRPNVGKSSLLNALLGEE---RviVSDIAGTTRdsIDVPFEY-DGQKytLIDTAG-----------IRKKGKV 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208 100 GEYLEKRLCLKGL---------VVLMDIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKL--ASGARKAQVNMVREaVLA 168
Cdd:cd01895    67 TEGIEKYSVLRTLkaieradvvLLVLDASEGITEQDLRIAGLILEEGKALIIVVNKWDLVekDEKTMKEFEKELRR-KLP 145

                         170       180
                  ....*....|....*....|.
gi 1747056208 169 FNGDVQVEPFSSLKKSGVDKL 189
Cdd:cd01895   146 FLDYAPIVFISALTGQGVDKL 166
PRK00093 PRK00093
GTP-binding protein Der; Reviewed
 22-189 4.35e-07

GTP-binding protein Der; Reviewed


Pssm-ID: 234628 [Multi-domain]  Cd Length: 435  Bit Score: 49.28  E-value: 4.35e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  22 PADTGIEVAFAGRSNAGKSSALNTLTNQKnlaR--TSKTPGRTQ-LIN-LFEVaEGK--RLVDLPGygyaqvpeeM---- 91
Cdd:PRK00093  169 EEDEPIKIAIIGRPNVGKSSLINALLGEE---RviVSDIAGTTRdSIDtPFER-DGQkyTLIDTAG---------Irrkg 235

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  92 KIKwqralgEYLEKRLCLKGL---------VVLMDIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKLASGARKAQVNMV 162
Cdd:PRK00093  236 KVT------EGVEKYSVIRTLkaieradvvLLVIDATEGITEQDLRIAGLALEAGRALVIVVNKWDLVDEKTMEEFKKEL 309

                         170       180
                  ....*....|....*....|....*..
gi 1747056208 163 REAvLAFNGDVQVEPFSSLKKSGVDKL 189
Cdd:PRK00093  310 RRR-LPFLDYAPIVFISALTGQGVDKL 335
YqeH cd01855
Circularly permuted YqeH GTPase; YqeH is an essential GTP-binding protein. Depletion of YqeH ...
 31-82 2.45e-06

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: 46.10  E-value: 2.45e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1747056208  31 FAGRSNAGKSSALNTL----------TNQKNLARTSKTPGRTQLINLFEVAEGKRLVDLPGY 82
Cdd:cd01855   130 VVGATNVGKSTLINALlksnggkvqaQALVQRLTVSPIPGTTLGLIKIPLGEGKKLYDTPGI 191
DLP_2 cd09912
Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The ...
 29-165 2.97e-06

Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The dynamin family of large mechanochemical GTPases includes the classical dynamins and dynamin-like proteins (DLPs) that are found throughout the Eukarya. This family also includes bacterial DLPs. These proteins catalyze membrane fission during clathrin-mediated endocytosis. Dynamin consists of five domains; an N-terminal G domain that binds and hydrolyzes GTP, a middle domain (MD) involved in self-assembly and oligomerization, a pleckstrin homology (PH) domain responsible for interactions with the plasma membrane, GED, which is also involved in self-assembly, and a proline arginine rich domain (PRD) that interacts with SH3 domains on accessory proteins. To date, three vertebrate dynamin genes have been identified; dynamin 1, which is brain specific, mediates uptake of synaptic vesicles in presynaptic terminals; dynamin-2 is expressed ubiquitously and similarly participates in membrane fission; mutations in the MD, PH and GED domains of dynamin 2 have been linked to human diseases such as Charcot-Marie-Tooth peripheral neuropathy and rare forms of centronuclear myopathy. Dynamin 3 participates in megakaryocyte progenitor amplification, and is also involved in cytoplasmic enlargement and the formation of the demarcation membrane system. This family also includes mitofusins (MFN1 and MFN2 in mammals) that are involved in mitochondrial fusion. Dynamin oligomerizes into helical structures around the neck of budding vesicles in a GTP hydrolysis-dependent manner.


Pssm-ID: 206739 [Multi-domain]  Cd Length: 180  Bit Score: 45.62  E-value: 2.97e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  29 VAFAGRSNAGKSSALNTLTNQKNLArTSKTPgRTQLINL--FEVAEGKRLVDLPGYGYAQVPEEMKIKwqralgEYLEKr 106
Cdd:cd09912     3 LAVVGEFSAGKSTLLNALLGEEVLP-TGVTP-TTAVITVlrYGLLKGVVLVDTPGLNSTIEHHTEITE------SFLPR- 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208 107 lcLKGLVVLMDIRHPLKDLDQQ-MIEWAVESDIQVLVLLTKADKLASGARKAQVNMVREA 165
Cdd:cd09912    74 --ADAVIFVLSADQPLTESEREfLKEILKWSGKKIFFVLNKIDLLSEEELEEVLEYSREE 131
HSR1_MMR1 cd01857
A circularly permuted subfamily of the Ras GTPases; Human HSR1 is localized to the human MHC ...
 29-81 4.07e-06

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: 44.92  E-value: 4.07e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1747056208  29 VAFAGRSNAGKSSALNTLTNQKnLARTSKTPGRTQLINLFEVAEGKRLVDLPG 81
Cdd:cd01857    85 IGLVGYPNVGKSSLINALVGSK-KVSVSSTPGKTKHFQTIFLEPGITLCDCPG 136
MnmE COG0486
tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal ...
 26-199 8.34e-06

tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal structure and biogenesis]; tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440253 [Multi-domain]  Cd Length: 448  Bit Score: 45.44  E-value: 8.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  26 GIEVAFAGRSNAGKSSALNTLTNQkNLARTSKTPGRT-----QLINLfevaEGK--RLVDLpgygyA-------QVpEEM 91
Cdd:COG0486   213 GIKVVIVGRPNVGKSSLLNALLGE-ERAIVTDIAGTTrdvieERINI----GGIpvRLIDT-----AglretedEV-EKI 281

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  92 KIKwqRALGEylekrlcLKG--LVVLM-DIRHPLKDLDQQMIEWAveSDIQVLVLLTKADkLASGArkaqvnmvrEAVLA 168
Cdd:COG0486   282 GIE--RAREA-------IEEadLVLLLlDASEPLTEEDEEILEKL--KDKPVIVVLNKID-LPSEA---------DGELK 340

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1747056208 169 FNGDVQVEPFSSLKKSGVDKLRQKLDSWFNE 199
Cdd:COG0486   341 SLPGEPVIAISAKTGEGIDELKEAILELVGE 371
trmE PRK05291
tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE;
26-199 1.66e-05

tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE;


Pssm-ID: 235392 [Multi-domain]  Cd Length: 449  Bit Score: 44.72  E-value: 1.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  26 GIEVAFAGRSNAGKSSALNTLTNqKNLARTSKTPGRT-----QLINLfevaEGK--RLVDLPGYGYAQVPEEmKIKWQRA 98
Cdd:PRK05291  215 GLKVVIAGRPNVGKSSLLNALLG-EERAIVTDIAGTTrdvieEHINL----DGIplRLIDTAGIRETDDEVE-KIGIERS 288

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  99 LGEylekrlcLKG--LVVLM-DIRHPLKDLDQQmiEWAVESDIQVLVLLTKADkLASGARKAQVNmvreavlaFNGDVQV 175
Cdd:PRK05291  289 REA-------IEEadLVLLVlDASEPLTEEDDE--ILEELKDKPVIVVLNKAD-LTGEIDLEEEN--------GKPVIRI 350

                         170       180
                  ....*....|....*....|....
gi 1747056208 176 epfSSLKKSGVDKLRQKLDSWFNE 199
Cdd:PRK05291  351 ---SAKTGEGIDELREAIKELAFG 371
Der COG1160
Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis];
22-201 6.32e-05

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


Pssm-ID: 440774 [Multi-domain]  Cd Length: 438  Bit Score: 43.09  E-value: 6.32e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  22 PADTGIEVAFAGRSNAGKSSALNTLTNQKnlaR--TSKTPGRTQ-LIN-LFEVaEGK--RLVDLPGygyaqvpeeM---- 91
Cdd:COG1160   171 EEDDPIKIAIVGRPNVGKSSLINALLGEE---RviVSDIAGTTRdSIDtPFER-DGKkyTLIDTAG---------Irrkg 237

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  92 KIKwqralgEYLEKRLCLKGL---------VVLMDIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKLA--SGARKAQVN 160
Cdd:COG1160   238 KVD------EGIEKYSVLRTLraieradvvLLVIDATEGITEQDLKIAGLALEAGKALVIVVNKWDLVEkdRKTREELEK 311

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1747056208 161 MVREAvLAFNGDVQVEPFSSLKKSGVDKLRQKLD----SWFNEIP 201
Cdd:COG1160   312 EIRRR-LPFLDYAPIVFISALTGQGVDKLLEAVDevyeSANKRIS 355
YlqF_related_GTPase cd01849
Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, ...
 24-81 8.48e-05

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: 41.22  E-value: 8.48e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1747056208  24 DTGIEVAFAGRSNAGKSSALNTLTNQKNLaRTSKTPGRTQLINLFEVAEGKRLVDLPG 81
Cdd:cd01849    89 KKGIRVGVVGLPNVGKSSFINALLNKFKL-KVGSIPGTTKLQQDVKLDKEIYLYDTPG 145
MnmE_helical pfam12631
MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An ...
 26-193 1.48e-04

MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An N-terminal domain, a helical domain and a GTPase domain which is nested within the helical domain. This family represents the helical domain.


Pssm-ID: 463649 [Multi-domain]  Cd Length: 326  Bit Score: 41.70  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  26 GIEVAFAGRSNAGKSSALNTLTNQkNLARTSKTPGRT-----QLINLfevaEGK--RLVDLPG--YGYAQVpEEMKIKwq 96
Cdd:pfam12631  94 GIKVVIVGKPNVGKSSLLNALLGE-ERAIVTDIPGTTrdvieETINI----GGIplRLIDTAGirETDDEV-EKIGIE-- 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  97 RALgEYLEKrlclKGLVVLM-DIRHPLKDLDQQMIEwAVESDIQVLVLLTKADKLAsgarkaqvnmvREAVLAFNGDVQV 175
Cdd:pfam12631 166 RAR-EAIEE----ADLVLLVlDASRPLDEEDLEILE-LLKDKKPIIVVLNKSDLLG-----------EIDELEELKGKPV 228

                         170
                  ....*....|....*...
gi 1747056208 176 EPFSSLKKSGVDKLRQKL 193
Cdd:pfam12631 229 LAISAKTGEGLDELEEAI 246
YfjP cd11383
YfjP GTPase; The Era (E. coli Ras-like protein)-like YfjP subfamily includes several ...
 30-193 1.74e-04

YfjP GTPase; The Era (E. coli Ras-like protein)-like YfjP subfamily includes several uncharacterized bacterial GTPases that are similar to Era. They 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. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain.


Pssm-ID: 206743 [Multi-domain]  Cd Length: 140  Bit Score: 40.02  E-value: 1.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  30 AFAGRSNAGKSSALNTLTnQKNLARTSKTPGRTQLINLFEVA---EGKRLVDLPGYGYAQVPEEmkikWQRALgeylekr 106
Cdd:cd11383     1 GLMGKTGAGKSSLCNALF-GTEVAAVGDRRPTTRAAQAYVWQtggDGLVLLDLPGVGERGRRDR----EYEEL------- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208 107 lclkglvvlmdIRHPLKDLDqqmiewavesdiqVLVLLTKADKLASGA----RKAQVNMVREAVLAFNGDV-QVEPFSSL 181
Cdd:cd11383    69 -----------YRRLLPEAD-------------LVLWLLDADDRALAAdhdfYLLPLAGHDAPLLFVLNQVdPVLAVSAR 124

                         170
                  ....*....|..
gi 1747056208 182 KKSGVDKLRQKL 193
Cdd:cd11383   125 TGWGLDELAEAL 136
CobW-like cd03112
cobalamin synthesis protein CobW; The function of this protein family is unknown. The amino ...
 101-175 2.79e-04

cobalamin synthesis protein CobW; The function of this protein family is unknown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K.


Pssm-ID: 349766  Cd Length: 198  Bit Score: 40.20  E-value: 2.79e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1747056208 101 EYLEKRLCLKGLVVLMDIRHPLKDLDQQMIEWAVESDIQV--LVLLTKADKLASgarkAQVNMVREAVLAFNGDVQV 175
Cdd:cd03112   109 EELESRLRLDGVVTVVDAKNFLKQLDEEDVSDLAVDQIAFadVIVLNKTDLVDE----EELEALRARIRALNPGAKI 181
YlqF cd01856
Circularly permuted YlqF GTPase; Proteins of the YlqF family contain all sequence motifs ...
 36-81 4.07e-04

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: 39.43  E-value: 4.07e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1747056208  36 NAGKSSALNTLTNqKNLARTSKTPGRTQLINLFEVAEGKRLVDLPG 81
Cdd:cd01856   125 NVGKSTLINRLRG-KKVAKVGNKPGVTRGQQWIRIGPNIELLDTPG 169
PRK12289 PRK12289
small ribosomal subunit biogenesis GTPase RsgA;
31-91 7.70e-04

small ribosomal subunit biogenesis GTPase RsgA;


Pssm-ID: 237040 [Multi-domain]  Cd Length: 352  Bit Score: 39.61  E-value: 7.70e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1747056208  31 FAGRSNAGKSSALNTLTNQKNLaRTSKTPGR-------TQLINLFEVAEGKRLVDLPGYGYAQV---PEEM 91
Cdd:PRK12289  177 VAGPSGVGKSSLINRLIPDVEL-RVGKVSGKlgrgrhtTRHVELFELPNGGLLADTPGFNQPDLdcsPREL 246
FeoB cd01879
Ferrous iron transport protein B (FeoB) family; Ferrous iron transport protein B (FeoB) ...
 30-196 1.10e-03

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: 38.21  E-value: 1.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  30 AFAGRSNAGKSSALNTLTNQKnlARTSKTPGRTqlinlFEVAEGK--------RLVDLPG----YGYAqvPEEmKIKwqr 97
Cdd:cd01879     1 ALVGNPNVGKTTLFNALTGAR--QKVGNWPGVT-----VEKKEGEfklggkeiEIVDLPGtyslTPYS--EDE-KVA--- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  98 algeyleKRLCLKG----LVVLMDIRHPLKDL--DQQMIEWavesDIQVLVLLTKADKlasgARKAQVnMVREAVLAFNG 171
Cdd:cd01879    68 -------RDFLLGEepdlIVNVVDATNLERNLylTLQLLEL----GLPVVVALNMIDE----AEKRGI-KIDLDKLSELL 131

                         170       180
                  ....*....|....*....|....*
gi 1747056208 172 DVQVEPFSSLKKSGVDKLRQKLDSW 196
Cdd:cd01879   132 GVPVVPTSARKGEGIDELLDAIAKL 156
MJ1464 cd01859
An uncharacterized, circularly permuted subfamily of the Ras GTPases; This family represents ...
 29-81 1.90e-03

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: 37.30  E-value: 1.90e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1747056208  29 VAFAGRSNAGKSSALNTLTNQKNlARTSKTPGR---TQLINLFEVAEGKRLVDLPG 81
Cdd:cd01859   102 VGVVGYPKVGKSSIINALKGRHS-ASTSPIPGSpgyTKGIQLVRIDSKIYLIDTPG 156
RsgA_GTPase pfam03193
RsgA GTPase; RsgA (also known as EngC and YjeQ) represents a protein family whose members are ...
 2-81 7.04e-03

RsgA GTPase; RsgA (also known as EngC and YjeQ) represents a protein family whose members are broadly conserved in bacteria and are indispensable for growth. The GTPase domain of RsgA is very similar to several P-loop GTPases, but differs in having a circular permutation of the GTPase structure described by a G4-G1-G3 pattern.


Pssm-ID: 427191 [Multi-domain]  Cd Length: 174  Bit Score: 35.98  E-value: 7.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208   2 TNWNYQLthFVTSA------PDIR-HLPADTgieVAFAGRSNAGKSSALNTLTNQKNLA--RTSKTPGR----TQLINLF 68
Cdd:pfam03193  80 RAIGYPV--LFVSAktgegiEALKeLLKGKT---TVLAGQSGVGKSTLLNALLPELDLRtgEISEKLGRgrhtTTHVELF 154

                          90
                  ....*....|...
gi 1747056208  69 EVAEGKRLVDLPG 81
Cdd:pfam03193 155 PLPGGGLLIDTPG 167
NGP_1 cd01858
A novel nucleolar GTP-binding protein, circularly permuted subfamily of the Ras GTPases; ...
 27-81 8.80e-03

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: 35.35  E-value: 8.80e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  27 IEVAFAGRSNAGKSSALNTLTNQKnLARTSKTPGRT---QLINLFevaegKR--LVDLPG 81
Cdd:cd01858   103 ISVGFIGYPNVGKSSVINTLRSKK-VCKVAPIPGETkvwQYITLM-----KRiyLIDCPG 156
EngA1 cd01894
EngA1 GTPase contains the first domain of EngA; This EngA1 subfamily CD represents the first ...
 33-193 9.97e-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: 35.49  E-value: 9.97e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208  33 GRSNAGKSSALNTLTNQKnLARTSKTPGRTQLInLFEVAE--GKR--LVDLPGYGYAQVP--EEMKIKWQRALGEylekr 106
Cdd:cd01894     4 GRPNVGKSTLFNRLTGRR-DAIVSDTPGVTRDR-KYGEAEwgGREfiLIDTGGIEPDDEGisKEIREQAEIAIEE----- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1747056208 107 lclKGLVV-LMDIRHPLKDLDQQMIEWAVESDIQVLVLLTKADKLASGARKAQvnmvreavlaFN----GDVQvePFSSL 181
Cdd:cd01894    77 ---ADVILfVVDGREGLTPADEEIAKYLRKSKKPVILVVNKIDNIKEEEEAAE----------FYslgfGEPI--PISAE 141

                         170
                  ....*....|..
gi 1747056208 182 KKSGVDKLRQKL 193
Cdd:cd01894   142 HGRGIGDLLDAI 153
 
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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