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Conserved domains on  [gi|6320842|ref|NP_010921|]
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RNA-binding GTPase NUG1 [Saccharomyces cerevisiae S288C]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Nucleostemin_like cd04178
A circularly permuted subfamily of the Ras GTPases; Nucleostemin (NS) is a nucleolar protein ...
 177-340 1.64e-75

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: 235.55  E-value: 1.64e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  177 DVILYVLDARDPESTRSRKVEEAVLQS-QGKRLILILNKVDLIPPHVLEQWLNYLKSSFPTIPLRASSGAVNGTSFNRK- 254
Cdd:cd04178   1 DVILEVLDARDPLGCRCPQVERAVLVLgPNKKLVLVLNKIDLVPKENVEKWLKYLRNEFPTVAFKASTQQQKKNLSRKSk 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  255 ----------LSQTTTASALLESLKTYSNNSNLKRSIVVGVIGYPNVGKSSVINALLarrggQSKACPVGNEAGVTTSLR 324
Cdd:cd04178  81 kvkasddllsSSACLGADALLKLLKNYARNKGIKTSITVGVVGYPNVGKSSVINSLK-----RSRACNVGATPGVTKSMQ 155

                       170
                ....*....|....*.
gi 6320842  325 EIKIDNKLKILDSPGI 340
Cdd:cd04178 156 EVHLDKHVKLLDSPGV 171
GN3L_Grn1 pfam08701
GNL3L/Grn1 putative GTPase; Grn1 (yeast) and GNL3L (human) are putative GTPases which are ...
 13-89 3.66e-23

GNL3L/Grn1 putative GTPase; Grn1 (yeast) and GNL3L (human) are putative GTPases which are required for growth and play a role in processing of nucleolar pre-rRNA. This family contains a potential nuclear localization signal.


:

Pssm-ID: 462569 [Multi-domain]  Cd Length: 77  Bit Score: 92.98  E-value: 3.66e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6320842     13 TKLKEGIKKKASAHRKKEKKMAKKDVTWRSRSKKDPGIPSNFPYKAKILEEIEAKKMKDLEERELAKQQRLEARKAA 89
Cdd:pfam08701   1 LRKRYKIEKKVAEHHRKERKEAKKNPTWKSKKKKDPGIPNSFPFKEEILAEIEEKKRKKEEEKERRKEAKKAERAEA 77
MMR_HSR1 super family cl47706
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 138-214 1.44e-04

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.


The actual alignment was detected with superfamily member pfam01926:

Pssm-ID: 460387 [Multi-domain]  Cd Length: 113  Bit Score: 41.45  E-value: 1.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    138 LDVIDYNIDFYGEDVE-----GESELEKSRKAYDKIFKSVIDAsDVILYVLDARDPESTRSRKVEEaVLQSQGKRLILIL 212
Cdd:pfam01926  34 RDPNEGRLELKGKQIIlvdtpGLIEGASEGEGLGRAFLAIIEA-DLILFVVDSEEGITPLDEELLE-LLRENKKPIILVL 111


                  ..
gi 6320842    213 NK 214
Cdd:pfam01926 112 NK 113
 
Name Accession Description Interval E-value
Nucleostemin_like cd04178
A circularly permuted subfamily of the Ras GTPases; Nucleostemin (NS) is a nucleolar protein ...
 177-340 1.64e-75

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: 235.55  E-value: 1.64e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  177 DVILYVLDARDPESTRSRKVEEAVLQS-QGKRLILILNKVDLIPPHVLEQWLNYLKSSFPTIPLRASSGAVNGTSFNRK- 254
Cdd:cd04178   1 DVILEVLDARDPLGCRCPQVERAVLVLgPNKKLVLVLNKIDLVPKENVEKWLKYLRNEFPTVAFKASTQQQKKNLSRKSk 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  255 ----------LSQTTTASALLESLKTYSNNSNLKRSIVVGVIGYPNVGKSSVINALLarrggQSKACPVGNEAGVTTSLR 324
Cdd:cd04178  81 kvkasddllsSSACLGADALLKLLKNYARNKGIKTSITVGVVGYPNVGKSSVINSLK-----RSRACNVGATPGVTKSMQ 155

                       170
                ....*....|....*.
gi 6320842  325 EIKIDNKLKILDSPGI 340
Cdd:cd04178 156 EVHLDKHVKLLDSPGV 171
RbgA COG1161
Ribosome biogenesis GTPase RbgA [Translation, ribosomal structure and biogenesis];
163-453 1.24e-42

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


Pssm-ID: 440775 [Multi-domain]  Cd Length: 279  Bit Score: 152.95  E-value: 1.24e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  163 KAYDKIfKSVIDASDVILYVLDARDPESTRSRKVEEAVlqsQGKRLILILNKVDLIPPHVLEQWLNYLKS-SFPTIPLRA 241
Cdd:COG1161  12 KARRQI-KEILKLVDLVIEVVDARIPLSSRNPMLDELV---GNKPRLLVLNKADLADPSVTKQWLKYFEKqGVDALAISA 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  242 SSGAVngtsfnrklsqtttASALLESLKTYSNNSNLK-RSIVVGVIGYPNVGKSSVINALLARrggqsKACPVGNEAGVT 320
Cdd:COG1161  88 KKGKG--------------IKELIEAIRELAPEKGIKrRPIRVMIVGIPNVGKSTLINRLAGK-----KVAKTGNKPGVT 148

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  321 TSLREIKIDNKLKILDSPGICFPsenkkrsKVEHEAE---LALLNALPAKhIVDPYPAVLMLVKRLAKsdEMTESFKKLY 397
Cdd:COG1161 149 KGQQWIKLDDGLELLDTPGILWP-------KFEDPEVgykLAATGAIKDE-VLDLEEVALFLLGYLAR--RYPELLKERY 218

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 6320842  398 EIPPIPANDADtftkhFLIHVARKRGRLGKGGIPNLASAGLSVLNDWRDGKiLGWV 453
Cdd:COG1161 219 KLDELPRTKLE-----LLEAIGRKRGCLLSGGEVDLEKAAEILLTDFRSGK-LGRI 268
GTPase_YlqF TIGR03596
ribosome biogenesis GTP-binding protein YlqF; Members of this protein family are GTP-binding ...
 160-449 3.94e-39

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: 143.42  E-value: 3.94e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    160 KSRKAYDKIFKSVidasDVILYVLDARDPESTRSRKVEEAVlqsQGKRLILILNKVDLIPPHVLEQWLNYLKSS-FPTIP 238
Cdd:TIGR03596  10 KARREIKENLKLV----DVVIEVLDARIPLSSRNPMIDEIR---GNKPRLIVLNKADLADPAVTKQWLKYFEEKgIKALA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    239 LrassGAVNGTSFNrKLSQT--TTASALLESLKTysnNSNLKRSIVVGVIGYPNVGKSSVINALLARrggqsKACPVGNE 316
Cdd:TIGR03596  83 V----NAKKGAGVK-KIIKAakKLLKEKNEKLKA---KGLKNRPIRAMIVGIPNVGKSTLINRLAGK-----KVAKVGNR 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    317 AGVTTSLREIKIDNKLKILDSPGICFPsenkkrsKVEHE---AELALLNALPaKHIVDPYPAVLMLVKRLAKSDemTESF 393
Cdd:TIGR03596 150 PGVTKGQQWIKLSDNLELLDTPGILWP-------KFEDQevgLKLAATGAIK-DEALDLEDVALFLLEYLLEHY--PELL 219

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 6320842    394 KKLYEIPPIPANDADtftkhFLIHVARKRGRLGKGGIPNLASAGLSVLNDWRDGKI 449
Cdd:TIGR03596 220 KERYKLDELPEDPVE-----LLEAIAKKRGCLLKGGELDLDRAAEILLNDFRKGKL 270
GN3L_Grn1 pfam08701
GNL3L/Grn1 putative GTPase; Grn1 (yeast) and GNL3L (human) are putative GTPases which are ...
 13-89 3.66e-23

GNL3L/Grn1 putative GTPase; Grn1 (yeast) and GNL3L (human) are putative GTPases which are required for growth and play a role in processing of nucleolar pre-rRNA. This family contains a potential nuclear localization signal.


Pssm-ID: 462569 [Multi-domain]  Cd Length: 77  Bit Score: 92.98  E-value: 3.66e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6320842     13 TKLKEGIKKKASAHRKKEKKMAKKDVTWRSRSKKDPGIPSNFPYKAKILEEIEAKKMKDLEERELAKQQRLEARKAA 89
Cdd:pfam08701   1 LRKRYKIEKKVAEHHRKERKEAKKNPTWKSKKKKDPGIPNSFPFKEEILAEIEEKKRKKEEEKERRKEAKKAERAEA 77
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 283-371 3.13e-13

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: 66.10  E-value: 3.13e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    283 VGVIGYPNVGKSSVINALLARRggqskaCPVGNEAGVTTSLREIKI---DNKLKILDSPGICFPSENKK---RSKVEH-E 355
Cdd:pfam01926   2 VALVGRPNVGKSTLINALTGAK------AIVSDYPGTTRDPNEGRLelkGKQIILVDTPGLIEGASEGEglgRAFLAIiE 75

                          90
                  ....*....|....*.
gi 6320842    356 AELALlnalpakHIVD 371
Cdd:pfam01926  76 ADLIL-------FVVD 84
PRK00093 PRK00093
GTP-binding protein Der; Reviewed
 130-357 5.67e-11

GTP-binding protein Der; Reviewed


Pssm-ID: 234628 [Multi-domain]  Cd Length: 435  Bit Score: 64.69  E-value: 5.67e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842   130 DADVRDDELDVIDY-NIDFYGEDVEGESeLEKSRKAydkifksvIDASDVILYVLDARD---PEstrsrkvEEAV---LQ 202
Cdd:PRK00093  43 EAEWLGREFILIDTgGIEPDDDGFEKQI-REQAELA--------IEEADVILFVVDGRAgltPA-------DEEIakiLR 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842   203 SQGKRLILILNKVDliPPHVLEQWLNYLKSSFPT-IPLRASSGavNGTSfnrKLSQtttasALLESLKTYSNNSNLKRSI 281
Cdd:PRK00093 107 KSNKPVILVVNKVD--GPDEEADAYEFYSLGLGEpYPISAEHG--RGIG---DLLD-----AILEELPEEEEEDEEDEPI 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842   282 VVGVIGYPNVGKSSVINALLarrgGQSKACpVGNEAGvTTslR-----EIKIDNK-LKILDSPGIcfpsenKKRSKVEHE 355
Cdd:PRK00093 175 KIAIIGRPNVGKSSLINALL----GEERVI-VSDIAG-TT--RdsidtPFERDGQkYTLIDTAGI------RRKGKVTEG 240


                 ..
gi 6320842   356 AE 357
Cdd:PRK00093 241 VE 242
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 138-214 1.44e-04

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: 41.45  E-value: 1.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    138 LDVIDYNIDFYGEDVE-----GESELEKSRKAYDKIFKSVIDAsDVILYVLDARDPESTRSRKVEEaVLQSQGKRLILIL 212
Cdd:pfam01926  34 RDPNEGRLELKGKQIIlvdtpGLIEGASEGEGLGRAFLAIIEA-DLILFVVDSEEGITPLDEELLE-LLRENKKPIILVL 111


                  ..
gi 6320842    213 NK 214
Cdd:pfam01926 112 NK 113
 
Name Accession Description Interval E-value
Nucleostemin_like cd04178
A circularly permuted subfamily of the Ras GTPases; Nucleostemin (NS) is a nucleolar protein ...
 177-340 1.64e-75

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: 235.55  E-value: 1.64e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  177 DVILYVLDARDPESTRSRKVEEAVLQS-QGKRLILILNKVDLIPPHVLEQWLNYLKSSFPTIPLRASSGAVNGTSFNRK- 254
Cdd:cd04178   1 DVILEVLDARDPLGCRCPQVERAVLVLgPNKKLVLVLNKIDLVPKENVEKWLKYLRNEFPTVAFKASTQQQKKNLSRKSk 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  255 ----------LSQTTTASALLESLKTYSNNSNLKRSIVVGVIGYPNVGKSSVINALLarrggQSKACPVGNEAGVTTSLR 324
Cdd:cd04178  81 kvkasddllsSSACLGADALLKLLKNYARNKGIKTSITVGVVGYPNVGKSSVINSLK-----RSRACNVGATPGVTKSMQ 155

                       170
                ....*....|....*.
gi 6320842  325 EIKIDNKLKILDSPGI 340
Cdd:cd04178 156 EVHLDKHVKLLDSPGV 171
RbgA COG1161
Ribosome biogenesis GTPase RbgA [Translation, ribosomal structure and biogenesis];
163-453 1.24e-42

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


Pssm-ID: 440775 [Multi-domain]  Cd Length: 279  Bit Score: 152.95  E-value: 1.24e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  163 KAYDKIfKSVIDASDVILYVLDARDPESTRSRKVEEAVlqsQGKRLILILNKVDLIPPHVLEQWLNYLKS-SFPTIPLRA 241
Cdd:COG1161  12 KARRQI-KEILKLVDLVIEVVDARIPLSSRNPMLDELV---GNKPRLLVLNKADLADPSVTKQWLKYFEKqGVDALAISA 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  242 SSGAVngtsfnrklsqtttASALLESLKTYSNNSNLK-RSIVVGVIGYPNVGKSSVINALLARrggqsKACPVGNEAGVT 320
Cdd:COG1161  88 KKGKG--------------IKELIEAIRELAPEKGIKrRPIRVMIVGIPNVGKSTLINRLAGK-----KVAKTGNKPGVT 148

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  321 TSLREIKIDNKLKILDSPGICFPsenkkrsKVEHEAE---LALLNALPAKhIVDPYPAVLMLVKRLAKsdEMTESFKKLY 397
Cdd:COG1161 149 KGQQWIKLDDGLELLDTPGILWP-------KFEDPEVgykLAATGAIKDE-VLDLEEVALFLLGYLAR--RYPELLKERY 218

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 6320842  398 EIPPIPANDADtftkhFLIHVARKRGRLGKGGIPNLASAGLSVLNDWRDGKiLGWV 453
Cdd:COG1161 219 KLDELPRTKLE-----LLEAIGRKRGCLLSGGEVDLEKAAEILLTDFRSGK-LGRI 268
MJ1464 cd01859
An uncharacterized, circularly permuted subfamily of the Ras GTPases; This family represents ...
 167-340 1.04e-40

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: 144.00  E-value: 1.04e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  167 KIFKSVIDASDVILYVLDARDPESTRSRKVEEAVLqSQGKRLILILNKVDLIPPHVLEQWLNYLKSS-FPTIPLRAssga 245
Cdd:cd01859   3 RLVRRIIKEADVVLEVVDARDPELTRSRKLERMAL-ELGKKLIIVLNKADLVPREVLEKWKEVFESEgLPVVYVSA---- 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  246 vngtsfnRKLSQTTTasaLLESLKTYSNNsnlKRSIVVGVIGYPNVGKSSVINALLARRGGQSKacPVGNEAGVTTSLRE 325
Cdd:cd01859  78 -------RERLGTRI---LRRTIKELAID---GKPVIVGVVGYPKVGKSSIINALKGRHSASTS--PIPGSPGYTKGIQL 142

                       170
                ....*....|....*
gi 6320842  326 IKIDNKLKILDSPGI 340
Cdd:cd01859 143 VRIDSKIYLIDTPGV 157
NGP_1 cd01858
A novel nucleolar GTP-binding protein, circularly permuted subfamily of the Ras GTPases; ...
 172-340 2.14e-39

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: 140.51  E-value: 2.14e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  172 VIDASDVILYVLDARDPESTRSRKVEEAVL-QSQGKRLILILNKVDLIPPHVLEQWLNYLKSSFPTIPLRASsgaVNgTS 250
Cdd:cd01858   5 VIDSSDVIIQVLDARDPMGTRCKHVEKYLRkEKPHKHLIFVLNKCDLVPTWVTKRWVKVLSKEYPTLAFHAS---IT-NP 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  251 FNRklsqtttaSALLESLKTYSNNSNLKRSIVVGVIGYPNVGKSSVINALlarrgGQSKACPVGNEAGVTTSLREIKIDN 330
Cdd:cd01858  81 FGK--------GALINLLRQFAKLHSDKKQISVGFIGYPNVGKSSVINTL-----RSKKVCKVAPIPGETKVWQYITLMK 147

                       170
                ....*....|
gi 6320842  331 KLKILDSPGI 340
Cdd:cd01858 148 RIYLIDCPGV 157
GTPase_YlqF TIGR03596
ribosome biogenesis GTP-binding protein YlqF; Members of this protein family are GTP-binding ...
 160-449 3.94e-39

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: 143.42  E-value: 3.94e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    160 KSRKAYDKIFKSVidasDVILYVLDARDPESTRSRKVEEAVlqsQGKRLILILNKVDLIPPHVLEQWLNYLKSS-FPTIP 238
Cdd:TIGR03596  10 KARREIKENLKLV----DVVIEVLDARIPLSSRNPMIDEIR---GNKPRLIVLNKADLADPAVTKQWLKYFEEKgIKALA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    239 LrassGAVNGTSFNrKLSQT--TTASALLESLKTysnNSNLKRSIVVGVIGYPNVGKSSVINALLARrggqsKACPVGNE 316
Cdd:TIGR03596  83 V----NAKKGAGVK-KIIKAakKLLKEKNEKLKA---KGLKNRPIRAMIVGIPNVGKSTLINRLAGK-----KVAKVGNR 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    317 AGVTTSLREIKIDNKLKILDSPGICFPsenkkrsKVEHE---AELALLNALPaKHIVDPYPAVLMLVKRLAKSDemTESF 393
Cdd:TIGR03596 150 PGVTKGQQWIKLSDNLELLDTPGILWP-------KFEDQevgLKLAATGAIK-DEALDLEDVALFLLEYLLEHY--PELL 219

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 6320842    394 KKLYEIPPIPANDADtftkhFLIHVARKRGRLGKGGIPNLASAGLSVLNDWRDGKI 449
Cdd:TIGR03596 220 KERYKLDELPEDPVE-----LLEAIAKKRGCLLKGGELDLDRAAEILLNDFRKGKL 270
YlqF_related_GTPase cd01849
Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, ...
 177-340 1.45e-35

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: 129.81  E-value: 1.45e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  177 DVILYVLDARDPESTRSRKVEEAVlQSQGKRLILILNKVDLIPPHVLEQWLNYLKSSFPTIPLRASSGAVNGTsfnrkls 256
Cdd:cd01849   1 DVVVEVVDARDPLSSRNPDIEVLI-NEKNKKLIMVLNKADLVPKEVLRKWVAELSELYGTKTFFISATNGQGI------- 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  257 qtttaSALLESLKTYSNNSNLKRSIVVGVIGYPNVGKSSVINALLarrggQSKACPVGNEAGVTTSLREIKIDNKLKILD 336
Cdd:cd01849  73 -----LKLKAEITKQKLKLKYKKGIRVGVVGLPNVGKSSFINALL-----NKFKLKVGSIPGTTKLQQDVKLDKEIYLYD 142


                ....
gi 6320842  337 SPGI 340
Cdd:cd01849 143 TPGI 146
YlqF cd01856
Circularly permuted YlqF GTPase; Proteins of the YlqF family contain all sequence motifs ...
 160-340 3.56e-32

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: 121.10  E-value: 3.56e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  160 KSRKAYDKIFKSVidasDVILYVLDARDPESTRSRKVEEAVLQsqgKRLILILNKVDLIPPHVLEQWLNYLKSS-FPTIP 238
Cdd:cd01856   8 KALRQIKEKLKLV----DVVIEVRDARIPLSSRNPDLDKILGN---KPRLIVLNKADLADPAKTKKWLKYFKSQgEPVLF 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  239 LRASSGavNGTSFNRKLsqtttASALLESLKTYSNNSNLKRSIVVGVIGYPNVGKSSVINALLARrggqsKACPVGNEAG 318
Cdd:cd01856  81 VNAKNG--KGVKKLLKK-----AKKLLKENEKLKAKGLLPRPLRAMVVGIPNVGKSTLINRLRGK-----KVAKVGNKPG 148

                       170       180
                ....*....|....*....|..
gi 6320842  319 VTTSLREIKIDNKLKILDSPGI 340
Cdd:cd01856 149 VTRGQQWIRIGPNIELLDTPGI 170
HSR1_MMR1 cd01857
A circularly permuted subfamily of the Ras GTPases; Human HSR1 is localized to the human MHC ...
 172-343 2.22e-27

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: 106.93  E-value: 2.22e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  172 VIDASDVILYVLDARDPESTRSRKVEEAVLQSQG-KRLILILNKVDLIPPHVLEQWLNYLKSSFPTIPLrassgavngts 250
Cdd:cd01857   8 VIERSDVVVQIVDARNPLFFRCPDLEKYVKEVDPsKENVLLLNKADLVTEEQRKAWARYFKKEGIVVLF----------- 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  251 fnrklsqtttASALLESlktysnnsnlkrsiVVGVIGYPNVGKSSVINALLarrgGQSKACpVGNEAGVTTSLREIKIDN 330
Cdd:cd01857  77 ----------FSALNEA--------------TIGLVGYPNVGKSSLINALV----GSKKVS-VSSTPGKTKHFQTIFLEP 127

                       170
                ....*....|...
gi 6320842  331 KLKILDSPGICFP 343
Cdd:cd01857 128 GITLCDCPGLVFP 140
GN3L_Grn1 pfam08701
GNL3L/Grn1 putative GTPase; Grn1 (yeast) and GNL3L (human) are putative GTPases which are ...
 13-89 3.66e-23

GNL3L/Grn1 putative GTPase; Grn1 (yeast) and GNL3L (human) are putative GTPases which are required for growth and play a role in processing of nucleolar pre-rRNA. This family contains a potential nuclear localization signal.


Pssm-ID: 462569 [Multi-domain]  Cd Length: 77  Bit Score: 92.98  E-value: 3.66e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6320842     13 TKLKEGIKKKASAHRKKEKKMAKKDVTWRSRSKKDPGIPSNFPYKAKILEEIEAKKMKDLEERELAKQQRLEARKAA 89
Cdd:pfam08701   1 LRKRYKIEKKVAEHHRKERKEAKKNPTWKSKKKKDPGIPNSFPFKEEILAEIEEKKRKKEEEKERRKEAKKAERAEA 77
YqeH cd01855
Circularly permuted YqeH GTPase; YqeH is an essential GTP-binding protein. Depletion of YqeH ...
 161-340 1.05e-20

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: 90.02  E-value: 1.05e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  161 SRKAYDKIFKSVIDASDVILYVLDARDPESTRSRKVEEAVlqsQGKRLILILNKVDLIPPHV----LEQWL-NYLKSSFP 235
Cdd:cd01855  19 PDEDFLEILSTLLNDNALVVHVVDIFDFPGSLIPGLAELI---GAKPVILVGNKIDLLPKDVkpnrLKQWVkKRLKIGGL 95

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  236 TIPLRASSGAVNGTSFNRKLSQtttasalLESLKTYSNNsnlkrsivVGVIGYPNVGKSSVINALLARRGGQSKACPVGN 315
Cdd:cd01855  96 KIKDVILVSAKKGWGVEELIEE-------IKKLAKYRGD--------VYVVGATNVGKSTLINALLKSNGGKVQAQALVQ 160

                       170       180       190
                ....*....|....*....|....*....|.
gi 6320842  316 EAGV-----TT-SLREIKIDNKLKILDSPGI 340
Cdd:cd01855 161 RLTVspipgTTlGLIKIPLGEGKKLYDTPGI 191
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 283-371 3.13e-13

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: 66.10  E-value: 3.13e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    283 VGVIGYPNVGKSSVINALLARRggqskaCPVGNEAGVTTSLREIKI---DNKLKILDSPGICFPSENKK---RSKVEH-E 355
Cdd:pfam01926   2 VALVGRPNVGKSTLINALTGAK------AIVSDYPGTTRDPNEGRLelkGKQIILVDTPGLIEGASEGEglgRAFLAIiE 75

                          90
                  ....*....|....*.
gi 6320842    356 AELALlnalpakHIVD 371
Cdd:pfam01926  76 ADLIL-------FVVD 84
PRK00093 PRK00093
GTP-binding protein Der; Reviewed
 130-357 5.67e-11

GTP-binding protein Der; Reviewed


Pssm-ID: 234628 [Multi-domain]  Cd Length: 435  Bit Score: 64.69  E-value: 5.67e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842   130 DADVRDDELDVIDY-NIDFYGEDVEGESeLEKSRKAydkifksvIDASDVILYVLDARD---PEstrsrkvEEAV---LQ 202
Cdd:PRK00093  43 EAEWLGREFILIDTgGIEPDDDGFEKQI-REQAELA--------IEEADVILFVVDGRAgltPA-------DEEIakiLR 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842   203 SQGKRLILILNKVDliPPHVLEQWLNYLKSSFPT-IPLRASSGavNGTSfnrKLSQtttasALLESLKTYSNNSNLKRSI 281
Cdd:PRK00093 107 KSNKPVILVVNKVD--GPDEEADAYEFYSLGLGEpYPISAEHG--RGIG---DLLD-----AILEELPEEEEEDEEDEPI 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842   282 VVGVIGYPNVGKSSVINALLarrgGQSKACpVGNEAGvTTslR-----EIKIDNK-LKILDSPGIcfpsenKKRSKVEHE 355
Cdd:PRK00093 175 KIAIIGRPNVGKSSLINALL----GEERVI-VSDIAG-TT--RdsidtPFERDGQkYTLIDTAGI------RRKGKVTEG 240


                 ..
gi 6320842   356 AE 357
Cdd:PRK00093 241 VE 242
Der COG1160
Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis];
173-357 9.84e-09

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


Pssm-ID: 440774 [Multi-domain]  Cd Length: 438  Bit Score: 57.34  E-value: 9.84e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  173 IDASDVILYVLDARD---PEstrsrkvEEAV---LQSQGKRLILILNKVDLI--PPHVLEQWlnylksSF---PTIPLRA 241
Cdd:COG1160  80 IEEADVILFVVDGRAgltPL-------DEEIaklLRRSGKPVILVVNKVDGPkrEADAAEFY------SLglgEPIPISA 146

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  242 SSGavNGTSfnrKLSQtttasALLESLKTYSNNSNLKRSIVVGVIGYPNVGKSSVINALLarrgGQSKACpVGNEAGvTT 321
Cdd:COG1160 147 EHG--RGVG---DLLD-----AVLELLPEEEEEEEEDDPIKIAIVGRPNVGKSSLINALL----GEERVI-VSDIAG-TT 210

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 6320842  322 slR-----EIKIDNKLKIL-DSPGIcfpsenKKRSKVEHEAE 357
Cdd:COG1160 211 --RdsidtPFERDGKKYTLiDTAGI------RRKGKVDEGIE 244
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 130-252 6.37e-08

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: 52.07  E-value: 6.37e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  130 DADVRDDELDVIDYNIDFYgeDVEGESELEKSRkaYDKIFKSVIDASDVILYVLDARDPESTRSRKVEEAV-LQSQGKRL 208
Cdd:cd00882  34 DPDVYVKELDKGKVKLVLV--DTPGLDEFGGLG--REELARLLLRGADLILLVVDSTDRESEEDAKLLILRrLRKEGIPI 109

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 6320842  209 ILILNKVDLIPPHVLEQWLNYLKSSF-PTIPLRASSgAVNGTSFN 252
Cdd:cd00882 110 ILVGNKIDLLEEREVEELLRLEELAKiLGVPVFEVS-AKTGEGVD 153
FeoB_N pfam02421
Ferrous iron transport protein B; Escherichia coli has an iron(II) transport system (feo) ...
 281-340 1.52e-07

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: 50.91  E-value: 1.52e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6320842    281 IVVGVIGYPNVGKSSVINALLarrGGQSKacpVGNEAGVTTSLREIKI---DNKLKILDSPGI 340
Cdd:pfam02421   1 ITIALVGNPNVGKTTLFNALT---GANQH---VGNWPGVTVEKKEGKFkykGYEIEIVDLPGI 57
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
120-235 2.34e-07

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 50.75  E-value: 2.34e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  120 AAEYEGTpsNDADVRDDELDVIDYNIDFYGEDVEGESELEKSRKAYDKIFKSvidaSDVILYVLDARDPESTRS-RKVEE 198
Cdd:COG1100  30 LEKYLST--NGVTIDKKELKLDGLDVDLVIWDTPGQDEFRETRQFYARQLTG----ASLYLFVVDGTREETLQSlYELLE 103

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 6320842  199 AVLQSQGK-RLILILNKVDLIPPHVLEQWlNYLKSSFP 235
Cdd:COG1100 104 SLRRLGKKsPIILVLNKIDLYDEEEIEDE-ERLKEALS 140
YjeQ_EngC cd01854
Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; ...
 177-340 2.45e-07

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: 51.24  E-value: 2.45e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  177 DVILYVLDARDPEsTRSRKVEE--AVLQSQGKRLILILNKVDLIPPHVLEQWLNYLKSS-FPTIPLRASSGavngtsfnr 253
Cdd:cd01854   4 DQVLIVFSLKEPF-FNLRLLDRylVAAEASGIEPVIVLNKADLVDDEELEELLEIYEKLgYPVLAVSAKTG--------- 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  254 klsqtttasALLESLKTYSNNsnlKRSIVVGVIGypnVGKSSVINALL---ARRGGQ-SKAcpvgNEAGV-TTSLRE-IK 327
Cdd:cd01854  74 ---------EGLDELRELLKG---KTSVLVGQSG---VGKSTLLNALLpelVLATGEiSEK----LGRGRhTTTHRElFP 134

                       170
                ....*....|...
gi 6320842  328 IDNKLKILDSPGI 340
Cdd:cd01854 135 LPGGGLIIDTPGF 147
Era_like cd00880
E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ...
 284-361 2.57e-07

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: 50.32  E-value: 2.57e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  284 GVIGYPNVGKSSVINALLarrgGQSKAcPVGNEAGVTTSLR----EIKIDNKLKILDSPGIcFPSENKKRSKVE------ 353
Cdd:cd00880   1 AIFGRPNVGKSSLLNALL----GQNVG-IVSPIPGTTRDPVrkewELLPLGPVVLIDTPGL-DEEGGLGRERVEearqva 74


                ....*...
gi 6320842  354 HEAELALL 361
Cdd:cd00880  75 DRADLVLL 82
Era COG1159
GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis];
170-244 2.82e-07

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


Pssm-ID: 440773 [Multi-domain]  Cd Length: 290  Bit Score: 52.30  E-value: 2.82e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6320842  170 KSVIDASDVILYVLDARDPESTRSRKVEEAvLQSQGKRLILILNKVDLIPPHVLEQWLNYLKSSFP---TIPLRASSG 244
Cdd:COG1159  77 WSALEDVDVILFVVDATEKIGEGDEFILEL-LKKLKTPVILVINKIDLVKKEELLPLLAEYSELLDfaeIVPISALKG 153
Era_like cd00880
E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ...
 145-244 5.96e-07

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: 49.17  E-value: 5.96e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  145 IDFYGEDVEGESELEKSRKAYDKIFKSvidasDVILYVLDardpeSTRSRKVEEAVLQS---QGKRLILILNKVDLIPPH 221
Cdd:cd00880  51 IDTPGLDEEGGLGRERVEEARQVADRA-----DLVLLVVD-----SDLTPVEEEAKLGLlreRGKPVLLVLNKIDLVPES 120

                        90       100
                ....*....|....*....|....*..
gi 6320842  222 VLEQWLNYLKSSF----PTIPLRASSG 244
Cdd:cd00880 121 EEEELLRERKLELlpdlPVIAVSALPG 147
YihA_EngB cd01876
YihA (EngB) GTPase family; The YihA (EngB) subfamily of GTPases is typified by the E. coli ...
 283-339 9.46e-07

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: 49.05  E-value: 9.46e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 6320842  283 VGVIGYPNVGKSSVINALLARRGgqsKAcPVGNEAGVTTSLREIKIDNKLKILDSPG 339
Cdd:cd01876   2 VAFAGRSNVGKSSLINALTNRKK---LA-RTSKTPGRTQLINFFNVGDKFRLVDLPG 54
Era cd04163
E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ...
 167-244 2.21e-06

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: 47.84  E-value: 2.21e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  167 KIFKSVIDASDVILYVLDARDPESTRSRKVEEaVLQSQGKRLILILNKVDLIPPH-VLEQWLNYLKSSFP---TIPLRAS 242
Cdd:cd04163  74 KAAWSALKDVDLVLFVVDASEWIGEGDEFILE-LLKKSKTPVILVLNKIDLVKDKeDLLPLLEKLKELHPfaeIFPISAL 152


                ..
gi 6320842  243 SG 244
Cdd:cd04163 153 KG 154
FeoB COG0370
Fe2+ transporter FeoB [Inorganic ion transport and metabolism];
278-340 2.35e-06

Fe2+ transporter FeoB [Inorganic ion transport and metabolism];


Pssm-ID: 440139 [Multi-domain]  Cd Length: 662  Bit Score: 50.12  E-value: 2.35e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6320842  278 KRSIVVGVIGYPNVGKSSVINALLarrGGQSKacpVGNEAGVTTSLRE--IKIDNK-LKILDSPGI 340
Cdd:COG0370   1 MKMITIALVGNPNVGKTTLFNALT---GSRQK---VGNWPGVTVEKKEgkFKLKGKeIELVDLPGT 60
era PRK00089
GTPase Era; Reviewed
 167-244 2.57e-06

GTPase Era; Reviewed


Pssm-ID: 234624 [Multi-domain]  Cd Length: 292  Bit Score: 49.28  E-value: 2.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842   167 KIFKSVIDASDVILYVLDARDPESTRSRKVEEAvLQSQGKRLILILNKVDLIPPH-VLEQWLNYLKSSFP---TIPLRAS 242
Cdd:PRK00089  76 KAAWSSLKDVDLVLFVVDADEKIGPGDEFILEK-LKKVKTPVILVLNKIDLVKDKeELLPLLEELSELMDfaeIVPISAL 154


                 ..
gi 6320842   243 SG 244
Cdd:PRK00089 155 KG 156
trmE cd04164
trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in ...
 153-245 2.99e-06

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: 47.10  E-value: 2.99e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  153 EGESELEKS--RKAYDKIFKSvidasDVILYVLDARDPESTrsrKVEEAVLQSQGKRLILILNKVDLIPphvlEQWLNYL 230
Cdd:cd04164  63 ETEDEIEKIgiERAREAIEEA-----DLVLLVVDASEGLDE---EDLEILELPAKKPVIVVLNKSDLLS----DAEGISE 130

                        90
                ....*....|....*
gi 6320842  231 KSSFPTIPLRASSGA 245
Cdd:cd04164 131 LNGKPIIAISAKTGE 145
FeoB cd01879
Ferrous iron transport protein B (FeoB) family; Ferrous iron transport protein B (FeoB) ...
 285-340 4.90e-06

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: 46.68  E-value: 4.90e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 6320842  285 VIGYPNVGKSSVINALLarrGGQSKacpVGNEAGVTTSLREIKI---DNKLKILDSPGI 340
Cdd:cd01879   2 LVGNPNVGKTTLFNALT---GARQK---VGNWPGVTVEKKEGEFklgGKEIEIVDLPGT 54
EngA2 cd01895
EngA2 GTPase contains the second domain of EngA; This EngA2 subfamily CD represents the second ...
 280-366 5.42e-06

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: 46.66  E-value: 5.42e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  280 SIVVGVIGYPNVGKSSVINALLarrggQSKACPVGNEAGVTtslR-----EIKIDN-KLKILDSPGIcfpsenKKRSKVE 353
Cdd:cd01895   2 PIKIAIIGRPNVGKSSLLNALL-----GEERVIVSDIAGTT---RdsidvPFEYDGqKYTLIDTAGI------RKKGKVT 67

                        90
                ....*....|....
gi 6320842  354 HEAE-LALLNALPA 366
Cdd:cd01895  68 EGIEkYSVLRTLKA 81
RsgA COG1162
Ribosome biogenesis GTPase RsgA [Translation, ribosomal structure and biogenesis];
161-340 5.67e-06

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


Pssm-ID: 440776 [Multi-domain]  Cd Length: 300  Bit Score: 48.19  E-value: 5.67e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  161 SRKAYDKIFKSVIDAS-DVILYVLDARDPEsTRSRKVEE--AVLQSQGKRLILILNKVDLIPPHVLEQWLNYLKSS-FPT 236
Cdd:COG1162  68 VRPAVGRDKEQVIAANiDQVLIVVALAEPD-FNLRLLDRylVAAEAAGIEPVIVLNKADLADDEELEELLAIYEALgYPV 146

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  237 IPLRASSGavngtsfnrklsqtTTASALLESLKTysnnsnlKRSIVVGVIGypnVGKSSVINALLarrGGQSKAcpVG-- 314
Cdd:COG1162 147 LAVSAKTG--------------EGLDELRELLKG-------KTSVLVGQSG---VGKSTLINALL---PDADLA--TGei 197

                       170       180       190
                ....*....|....*....|....*....|.
gi 6320842  315 NEA---GV-TTSLRE-IKIDNKLKILDSPGI 340
Cdd:COG1162 198 SEKlgrGRhTTTHAElYPLPGGGWLIDTPGF 228
HflX cd01878
HflX GTPase family; HflX subfamily. A distinct conserved domain with a glycine-rich segment ...
 169-245 1.14e-05

HflX GTPase family; HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.


Pssm-ID: 206666 [Multi-domain]  Cd Length: 204  Bit Score: 46.30  E-value: 1.14e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  169 FKS----VIDAsDVILYVLDARDPESTRSRKVEEAVLQS---QGKRLILILNKVDLIPPHVLEQWLnyLKSSFPTIPLRA 241
Cdd:cd01878 111 FRStleeVAEA-DLLLHVVDASDPDREEQIETVEEVLKElgaDDIPIILVLNKIDLLDDEELEERL--RAGRPDAVFISA 187


                ....
gi 6320842  242 SSGA 245
Cdd:cd01878 188 KTGE 191
YeeP COG3596
Predicted GTPase [General function prediction only];
278-370 1.59e-05

Predicted GTPase [General function prediction only];


Pssm-ID: 442815 [Multi-domain]  Cd Length: 318  Bit Score: 47.07  E-value: 1.59e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  278 KRSIVVGVIGYPNVGKSSVINALLarrggQSKACPVGNEAGVTTSLREIKIDNK----LKILDSPGIcfpsenkKRSKVE 353
Cdd:COG3596  37 LPPPVIALVGKTGAGKSSLINALF-----GAEVAEVGVGRPCTREIQRYRLESDglpgLVLLDTPGL-------GEVNER 104

                        90
                ....*....|....*..
gi 6320842  354 HEAELALLNALPAKHIV 370
Cdd:COG3596 105 DREYRELRELLPEADLI 121
MnmE COG0486
tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal ...
 159-224 1.90e-05

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: 46.98  E-value: 1.90e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6320842  159 EKSRKAydkifksvIDASDVILYVLDARDPESTRSRKVEEAVlqsQGKRLILILNKVDLIPPHVLE 224
Cdd:COG0486 284 ERAREA--------IEEADLVLLLLDASEPLTEEDEEILEKL---KDKPVIVVLNKIDLPSEADGE 338
EngA2 cd01895
EngA2 GTPase contains the second domain of EngA; This EngA2 subfamily CD represents the second ...
 141-237 1.98e-05

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: 45.12  E-value: 1.98e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  141 IDYNIDFYGedvegeseLEKSRKAydkifksvIDASDVILYVLDARDPESTRSRKVEEAVLQSqGKRLILILNKVDLIP- 219
Cdd:cd01895  66 VTEGIEKYS--------VLRTLKA--------IERADVVLLVLDASEGITEQDLRIAGLILEE-GKALIIVVNKWDLVEk 128

                        90
                ....*....|....*....
gi 6320842  220 -PHVLEQWLNYLKSSFPTI 237
Cdd:cd01895 129 dEKTMKEFEKELRRKLPFL 147
trmE PRK05291
tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE;
159-245 2.07e-05

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


Pssm-ID: 235392 [Multi-domain]  Cd Length: 449  Bit Score: 47.03  E-value: 2.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842   159 EKSRKAydkifksvIDASDVILYVLDARDPESTrsrKVEEAVLQSQGKRLILILNKVDLIPPHVLEQWLNYlkssfPTIP 238
Cdd:PRK05291 286 ERSREA--------IEEADLVLLVLDASEPLTE---EDDEILEELKDKPVIVVLNKADLTGEIDLEEENGK-----PVIR 349


                 ....*..
gi 6320842   239 LRASSGA 245
Cdd:PRK05291 350 ISAKTGE 356
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 284-340 2.11e-05

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: 44.75  E-value: 2.11e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6320842  284 GVIGYPNVGKSSVINALLarrggQSKACPVGNEAGVTT-----SLREIKIDNKLKILDSPGI 340
Cdd:cd00882   1 VVVGRGGVGKSSLLNALL-----GGEVGEVSDVPGTTRdpdvyVKELDKGKVKLVLVDTPGL 57
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 138-214 1.44e-04

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: 41.45  E-value: 1.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    138 LDVIDYNIDFYGEDVE-----GESELEKSRKAYDKIFKSVIDAsDVILYVLDARDPESTRSRKVEEaVLQSQGKRLILIL 212
Cdd:pfam01926  34 RDPNEGRLELKGKQIIlvdtpGLIEGASEGEGLGRAFLAIIEA-DLILFVVDSEEGITPLDEELLE-LLRENKKPIILVL 111


                  ..
gi 6320842    213 NK 214
Cdd:pfam01926 112 NK 113
feoB TIGR00437
ferrous iron transporter FeoB; FeoB (773 amino acids in E. coli), a cytoplasmic membrane ...
 287-340 1.51e-04

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: 44.35  E-value: 1.51e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 6320842    287 GYPNVGKSSVINALlarRGGQSKacpVGNEAGVTTSLREIKI---DNKLKILDSPGI 340
Cdd:TIGR00437   1 GNPNVGKSTLFNAL---TGANQT---VGNWPGVTVEKKEGKLgfqGEDIEIVDLPGI 51
DLP_2 cd09912
Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The ...
 166-234 2.07e-04

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: 42.15  E-value: 2.07e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6320842  166 DKIFKSVIDASDVILYVLDARDPESTRSRKVEEAVLQSQGKRLILILNKVDLIPPHVLEQWLNYLKSSF 234
Cdd:cd09912  64 TEITESFLPRADAVIFVLSADQPLTESEREFLKEILKWSGKKIFFVLNKIDLLSEEELEEVLEYSREEL 132
MnmE_helical pfam12631
MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An ...
 159-220 2.30e-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: 43.24  E-value: 2.30e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6320842    159 EKSRKAydkifksvIDASDVILYVLDARDPESTRSRKVEEavLQSQGKRLILILNKVDLIPP 220
Cdd:pfam12631 165 ERAREA--------IEEADLVLLVLDASRPLDEEDLEILE--LLKDKKPIIVVLNKSDLLGE 216
Era cd04163
E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ...
 278-348 5.73e-04

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: 40.91  E-value: 5.73e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6320842  278 KRSIVVGVIGYPNVGKSSVINALLarrgGQsKACPVGNEAGvTT--SLREIKIDNKLKI--LDSPGIcFPSENKK 348
Cdd:cd04163   1 FKSGFVAIIGRPNVGKSTLLNALV----GQ-KISIVSPKPQ-TTrnRIRGIYTDDDAQIifVDTPGI-HKPKKKL 68
TIGR00157 TIGR00157
ribosome small subunit-dependent GTPase A; Members of this protein were designated YjeQ and ...
 149-398 6.62e-04

ribosome small subunit-dependent GTPase A; Members of this protein were designated YjeQ and are now designated RsgA (ribosome small subunit-dependent GTPase A). The strongest motif in the alignment of these proteins is GXSGVGKS[ST], a classic P-loop for nucleotide binding. This protein has been shown to cleave GTP and remain bound to GDP. A role as a regulator of translation has been suggested. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option). [Protein synthesis, Translation factors]


Pssm-ID: 272934 [Multi-domain]  Cd Length: 245  Bit Score: 41.63  E-value: 6.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    149 GEDVEGESELEKSRKayDKIFKSVIDASDVILYVLDARDPestrsrKVEEAVL-------QSQGKRLILILNKVDLIPPH 221
Cdd:TIGR00157  12 GNPVKVYGGAIAERK--NELTRPIVANIDQIVIVSSAVLP------ELSLNQLdrflvvaEAQNIEPIIVLNKIDLLDDE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    222 -VLEQWLNYLKSsfptiplrassgavngtsFNRKLSQTTTASA-LLESLKTYSNNsnlKRSIVVGVIGypnVGKSSVINA 299
Cdd:TIGR00157  84 dMEKEQLDIYRN------------------IGYQVLMTSSKNQdGLKELIEALQN---RISVFAGQSG---VGKSSLINA 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    300 LLARRGGQSKACPVGNEAG--VTTSLREIKIDNKLkILDSPGI------CFPSENKKRSKVEHEAELALLNALPAKHIVD 371
Cdd:TIGR00157 140 LDPSVKQQVNDISSKLGLGkhTTTHVELFHFHGGL-IADTPGFnefglwHLEPEQLTQGFVEFRDYLGLCKFRDCLHQSE 218

                         250       260
                  ....*....|....*....|....*..
gi 6320842    372 PYPAVLMLVKRLAKSDEMTESFKKLYE 398
Cdd:TIGR00157 219 PGCAVRQAVEQGEISEWRYENYLKLIE 245
RsgA_GTPase pfam03193
RsgA GTPase; RsgA (also known as EngC and YjeQ) represents a protein family whose members are ...
 177-340 7.67e-04

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: 40.60  E-value: 7.67e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    177 DVILYVLDARDPEsTRSRKVEE--AVLQSQGKRLILILNKVDLIPPH-VLEQWLN-YLKSSFPTIPLRASSGAVngtsfn 252
Cdd:pfam03193  24 DQAVIVFSLKEPD-FNLNLLDRflVLAEASGIEPVIVLNKIDLLDEEeELEELLKiYRAIGYPVLFVSAKTGEG------ 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842    253 rklsqtttasalLESLKTYsnnsnLKRSIVVgVIGYPNVGKSSVINALL----ARRGGQSKACPVGNEagVTTSLREIKI 328
Cdd:pfam03193  97 ------------IEALKEL-----LKGKTTV-LAGQSGVGKSTLLNALLpeldLRTGEISEKLGRGRH--TTTHVELFPL 156

                         170
                  ....*....|..
gi 6320842    329 DNKLKILDSPGI 340
Cdd:pfam03193 157 PGGGLLIDTPGF 168
Der COG1160
Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis];
282-360 8.40e-04

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


Pssm-ID: 440774 [Multi-domain]  Cd Length: 438  Bit Score: 41.93  E-value: 8.40e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  282 VVGVIGYPNVGKSSVINALLARRggqsKACpVGNEAGVTtslR-----EIKIDNK-LKILDSPGICFPSENKKRSKVEHE 355
Cdd:COG1160   4 VVAIVGRPNVGKSTLFNRLTGRR----DAI-VDDTPGVT---RdriygEAEWGGReFTLIDTGGIEPDDDDGLEAEIREQ 75


                ....*
gi 6320842  356 AELAL 360
Cdd:COG1160  76 AELAI 80
PRK00093 PRK00093
GTP-binding protein Der; Reviewed
 162-235 1.58e-03

GTP-binding protein Der; Reviewed


Pssm-ID: 234628 [Multi-domain]  Cd Length: 435  Bit Score: 40.80  E-value: 1.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842   162 RKA--YDKIFK-SVIDA------SDVILYVLDARDPestrsrkVEEAVL------QSQGKRLILILNKVDLIPPHVLEQW 226
Cdd:PRK00093 233 RKGkvTEGVEKySVIRTlkaierADVVLLVIDATEG-------ITEQDLriaglaLEAGRALVIVVNKWDLVDEKTMEEF 305


                 ....*....
gi 6320842   227 LNYLKSSFP 235
Cdd:PRK00093 306 KKELRRRLP 314
Obg_like cd01881
Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; ...
 284-372 2.16e-03

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: 38.91  E-value: 2.16e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  284 GVIGYPNVGKSSVINALlarrggqSKACP-VGNEAGVTTSLR----EIKIDNKLKILDSPGIcfpSENKKRSKVEHEAEL 358
Cdd:cd01881   1 GLVGLPNVGKSTLLSAL-------TSAKVeIASYPFTTLEPNvgvfEFGDGVDIQIIDLPGL---LDGASEGRGLGEQIL 70

                        90
                ....*....|....*.
gi 6320842  359 ALL--NALPAkHIVDP 372
Cdd:cd01881  71 AHLyrSDLIL-HVIDA 85
YejR COG0523
Zinc metallochaperone YeiR/ZagA and related GTPases, G3E family [General function prediction ...
 177-247 2.52e-03

Zinc metallochaperone YeiR/ZagA and related GTPases, G3E family [General function prediction only];


Pssm-ID: 440289 [Multi-domain]  Cd Length: 318  Bit Score: 40.16  E-value: 2.52e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6320842  177 DVILYVLDARDPESTRSRKVEEAVLQSQgkrL----ILILNKVDLIPPHVLEQWLNYLKSSFPTIP-LRASSGAVN 247
Cdd:COG0523 119 DGVVTVVDARNLLDDLADRTLHELLVDQ---IafadVIVLNKTDLVDEEELAALEARLRALNPGAPiVRTSHGEVD 191
PRK12288 PRK12288
small ribosomal subunit biogenesis GTPase RsgA;
209-301 3.30e-03

small ribosomal subunit biogenesis GTPase RsgA;


Pssm-ID: 237039 [Multi-domain]  Cd Length: 347  Bit Score: 39.84  E-value: 3.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842   209 ILILNKVDLIPPHV---LEQWLN-YLKSSFPTipLRASSGAVNGtsfnrklsqtttasalLESLKTYSNNsnlKRSIVVG 284
Cdd:PRK12288 154 LIVLNKIDLLDDEGrafVNEQLDiYRNIGYRV--LMVSSHTGEG----------------LEELEAALTG---RISIFVG 212

                         90
                 ....*....|....*..
gi 6320842   285 VIGypnVGKSSVINALL 301
Cdd:PRK12288 213 QSG---VGKSSLINALL 226
feoB PRK09554
Fe(2+) transporter permease subunit FeoB;
283-340 3.41e-03

Fe(2+) transporter permease subunit FeoB;


Pssm-ID: 236563 [Multi-domain]  Cd Length: 772  Bit Score: 40.09  E-value: 3.41e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6320842   283 VGVIGYPNVGKSSVINALLARRggQSkacpVGNEAGVTTSLRE---IKIDNKLKILDSPGI 340
Cdd:PRK09554   6 IGLIGNPNSGKTTLFNQLTGAR--QR----VGNWAGVTVERKEgqfSTTDHQVTLVDLPGT 60
trmE cd04164
trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in ...
 281-340 5.05e-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: 37.86  E-value: 5.05e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6320842  281 IVVGVIGYPNVGKSSVINALLarrgGQSKACpVGNEAGvTT--SLRE-IKIDN-KLKILDSPGI 340
Cdd:cd04164   4 IKVVIAGKPNVGKSSLLNALA----GRDRAI-VSDIAG-TTrdVIEEeIDLGGiPVRLIDTAGL 61
DLP_2 cd09912
Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The ...
 283-340 5.28e-03

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: 37.91  E-value: 5.28e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320842  283 VGVIGYPNVGKSSVINALLarrggQSKACPVGN--EAGVTTSLReIKIDNKLKILDSPGI 340
Cdd:cd09912   3 LAVVGEFSAGKSTLLNALL-----GEEVLPTGVtpTTAVITVLR-YGLLKGVVLVDTPGL 56
PRK03003 PRK03003
GTP-binding protein Der; Reviewed
 282-304 6.28e-03

GTP-binding protein Der; Reviewed


Pssm-ID: 179525 [Multi-domain]  Cd Length: 472  Bit Score: 39.18  E-value: 6.28e-03
                         10        20
                 ....*....|....*....|...
gi 6320842   282 VVGVIGYPNVGKSSVINALLARR 304
Cdd:PRK03003  40 VVAVVGRPNVGKSTLVNRILGRR 62
Obg cd01898
Obg GTPase; The Obg nucleotide binding protein subfamily has been implicated in stress ...
 283-300 7.79e-03

Obg GTPase; The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis. Members of the subfamily contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain.


Pssm-ID: 206685 [Multi-domain]  Cd Length: 170  Bit Score: 37.40  E-value: 7.79e-03
                        10
                ....*....|....*...
gi 6320842  283 VGVIGYPNVGKSSVINAL 300
Cdd:cd01898   3 VGLVGLPNAGKSTLLSAI 20
YeeP COG3596
Predicted GTPase [General function prediction only];
172-233 9.17e-03

Predicted GTPase [General function prediction only];


Pssm-ID: 442815 [Multi-domain]  Cd Length: 318  Bit Score: 38.21  E-value: 9.17e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6320842  172 VIDASDVILYVLDARDpestRSRKVEEAVLQS-----QGKRLILILNKVDLIPPHVLEQWLNYLKSS 233
Cdd:COG3596 114 LLPEADLILWVVKADD----RALATDEEFLQAlraqyPDPPVLVVLTQVDRLEPEREWDPPYNWPSP 176
GTPase_YsxC TIGR03598
ribosome biogenesis GTP-binding protein YsxC/EngB; Members of this protein family are a GTPase ...
 286-305 9.97e-03

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: 37.07  E-value: 9.97e-03
                          10        20
                  ....*....|....*....|
gi 6320842    286 IGYPNVGKSSVINALLARRG 305
Cdd:TIGR03598  24 AGRSNVGKSSLINALTNRKK 43
 
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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