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Conserved domains on  [gi|54607086|ref|NP_068756|]
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selenocysteine-specific elongation factor [Homo sapiens]

Protein Classification

selenocysteine-specific elongation factor( domain architecture ID 10112157)

selenocysteine-specific elongation factor is necessary for the incorporation of selenocysteine into proteins

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SelB_euk cd01889
SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ...
 8-209 1.07e-102

SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryotes, they do share a common feature. Unlike in E. coli, these SECIS elements are located in the 3' UTRs. This group contains eukaryotic SelBs and some from archaea.


:

Pssm-ID: 206676 [Multi-domain]  Cd Length: 192  Bit Score: 308.91  E-value: 1.07e-102
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   8 VNVGVLGHIDSGKTALARALSTTASTAAFDKQPQSRERGITLDLGFSCFSVPLPARLRSSL-PEFQaapeaepepgepLL 86
Cdd:cd01889   1 VNVGLLGHVDSGKTSLAKALSEIASTAAFDKNPQSQERGITLDLGFSSFEVDKPKHLEDNEnPQIE------------NY 68

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  87 QVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDLLPEGKRQAAIDKMTKK 166
Cdd:cd01889  69 QITLVDCPGHASLIRTIIGGAQIIDLMLLVVDAKKGIQTQTAECLVIGELLCKPLIVVLNKIDLIPEEERKRKIEKMKKR 148

                       170       180       190       200
                ....*....|....*....|....*....|....*....|...
gi 54607086 167 MQKTLENTKFRGAPIIPVAAKPGGPEApetEAPQGIPELIELL 209
Cdd:cd01889 149 LQKTLEKTRLKDSPIIPVSAKPGEGEA---ELGGELKNLIVLP 188
eSelB_III cd04094
Domain III of eukaryotic and archaeal elongation factor SelB; This model represents the domain ...
 311-450 1.16e-46

Domain III of eukaryotic and archaeal elongation factor SelB; This model represents the domain III of archaeal and eukaryotic selenocysteine (Sec)-specific eukaryotic elongation factor (eEFSec or eSelB), which is homologous to domain III of EF-Tu. SelB is a specialized translation elongation factor responsible for the co-translational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop, called Sec insertion sequence (SECIS) element.


:

Pssm-ID: 294009  Cd Length: 114  Bit Score: 159.79  E-value: 1.16e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 311 TVHAALISVEKIPYFRGPLQTKAKFHITVGHETVMGRLMFFSPAPDNFDQEPILDSFNfsqeylfqeqylskdltpavtd 390
Cdd:cd04094   1 TVTAAIALVCKISFFKGSIKSKSKFHITVGHQTVMARVTFFSDPGKDETEEDESAEFV---------------------- 58

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 391 ndeaDKKAGQATEGHCPRQQWALVEFEKPVTCPRLCLVIGSRLDADIHTNTCRLAFHGIL 450
Cdd:cd04094  59 ----EDEDESLEEAKPGSEQYALLEFEKPVAAPPGDLFIGSRLDTDPHSNTCRLAFYGRV 114
SelB_II cd03696
Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor ...
 224-306 3.71e-39

Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor SelB that is homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.


:

Pssm-ID: 293897 [Multi-domain]  Cd Length: 83  Bit Score: 138.04  E-value: 3.71e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 224 FLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLV 303
Cdd:cd03696   1 FRLPIDHVFSIKGAGTVVTGTVLSGKVKVGDELEIPPLGKEVRVRSIQVHDKPVEEAKAGDRVALNLTGVDAKELERGFV 80


                ...
gi 54607086 304 CAP 306
Cdd:cd03696  81 LSE 83
 
Name Accession Description Interval E-value
SelB_euk cd01889
SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ...
 8-209 1.07e-102

SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryotes, they do share a common feature. Unlike in E. coli, these SECIS elements are located in the 3' UTRs. This group contains eukaryotic SelBs and some from archaea.


Pssm-ID: 206676 [Multi-domain]  Cd Length: 192  Bit Score: 308.91  E-value: 1.07e-102
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   8 VNVGVLGHIDSGKTALARALSTTASTAAFDKQPQSRERGITLDLGFSCFSVPLPARLRSSL-PEFQaapeaepepgepLL 86
Cdd:cd01889   1 VNVGLLGHVDSGKTSLAKALSEIASTAAFDKNPQSQERGITLDLGFSSFEVDKPKHLEDNEnPQIE------------NY 68

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  87 QVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDLLPEGKRQAAIDKMTKK 166
Cdd:cd01889  69 QITLVDCPGHASLIRTIIGGAQIIDLMLLVVDAKKGIQTQTAECLVIGELLCKPLIVVLNKIDLIPEEERKRKIEKMKKR 148

                       170       180       190       200
                ....*....|....*....|....*....|....*....|...
gi 54607086 167 MQKTLENTKFRGAPIIPVAAKPGGPEApetEAPQGIPELIELL 209
Cdd:cd01889 149 LQKTLEKTRLKDSPIIPVSAKPGEGEA---ELGGELKNLIVLP 188
SelB COG3276
Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure ...
 8-351 2.14e-61

Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure and biogenesis]; Selenocysteine-specific translation elongation factor SelB is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 442507 [Multi-domain]  Cd Length: 630  Bit Score: 214.39  E-value: 2.14e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   8 VNVGVLGHIDSGKTALARALSTTAStaafDKQPQSRERGITLDLGFScfSVPLPARLRsslpefqaapeaepepgepllq 87
Cdd:COG3276   1 MIIGTAGHIDHGKTTLVKALTGIDT----DRLKEEKKRGITIDLGFA--YLPLPDGRR---------------------- 52

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  88 VTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIgqiaCQ-----KLVVVLNKIDLLPEgkrqAAIDK 162
Cdd:COG3276  53 LGFVDVPGHEKFIKNMLAGAGGIDLVLLVVAADEGVMPQTREHLAI----LDllgikRGIVVLTKADLVDE----EWLEL 124

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 163 MTKKMQKTLENTKFRGAPIIPVAAKPGgpeapeteapQGIPELIELLTSQI-SIPTRDPSGPFLMSVDHCFSIKGQGTVM 241
Cdd:COG3276 125 VEEEIRELLAGTFLEDAPIVPVSAVTG----------EGIDELRAALDALAaAVPARDADGPFRLPIDRVFSIKGFGTVV 194

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 242 TGTILSGSISLGDSVEI-PALKVVkKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERG-LVCAPESLHTVHAALISV 319
Cdd:COG3276 195 TGTLLSGTVRVGDELELlPSGKPV-RVRGIQVHGQPVEEAYAGQRVALNLAGVEKEEIERGdVLAAPGALRPTDRIDVRL 273

                       330       340       350
                ....*....|....*....|....*....|..
gi 54607086 320 EKIPYFRGPLQTKAKFHITVGHETVMGRLMFF 351
Cdd:COG3276 274 RLLPSAPRPLKHWQRVHLHHGTAEVLARVVLL 305
selB TIGR00475
selenocysteine-specific elongation factor SelB; In prokaryotes, the incorporation of ...
 8-348 5.18e-49

selenocysteine-specific elongation factor SelB; In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes. [Protein synthesis, Translation factors]


Pssm-ID: 129567 [Multi-domain]  Cd Length: 581  Bit Score: 179.68  E-value: 5.18e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086     8 VNVGVLGHIDSGKTALARALSTTAStaafDKQPQSRERGITLDLGFScfSVPLPARlrsslpefqaapeaepepgepllQ 87
Cdd:TIGR00475   1 MIIATAGHVDHGKTTLLKALTGIAA----DRLPEEKKRGMTIDLGFA--YFPLPDY-----------------------R 51

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    88 VTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECL-VIGQIACQKLVVVLNKIDLLPEgkrqAAIDKMTKK 166
Cdd:TIGR00475  52 LGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLaVLDLLGIPHTIVVITKADRVNE----EEIKRTEMF 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   167 MQKTLENTKF-RGAPIIPVAAKPGgpeapeteapQGIPELIELLTSQI-SIPTRDPSGPFLMSVDHCFSIKGQGTVMTGT 244
Cdd:TIGR00475 128 MKQILNSYIFlKNAKIFKTSAKTG----------QGIGELKKELKNLLeSLDIKRIQKPLRMAIDRAFKVKGAGTVVTGT 197

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   245 ILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLvCAPESLHTVHAalISVEKIPY 324
Cdd:TIGR00475 198 AFSGEVKVGDNLRLLPINHEVRVKAIQAQNQDVEIAYAGQRIALNLMDVEPESLKRGL-LILTPEDPKLR--VVVKFIAE 274

                         330       340
                  ....*....|....*....|....
gi 54607086   325 FrgPLQTKAKFHITVGHETVMGRL 348
Cdd:TIGR00475 275 V--PLLELQPYHIAHGMSVTTGKI 296
eSelB_III cd04094
Domain III of eukaryotic and archaeal elongation factor SelB; This model represents the domain ...
 311-450 1.16e-46

Domain III of eukaryotic and archaeal elongation factor SelB; This model represents the domain III of archaeal and eukaryotic selenocysteine (Sec)-specific eukaryotic elongation factor (eEFSec or eSelB), which is homologous to domain III of EF-Tu. SelB is a specialized translation elongation factor responsible for the co-translational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop, called Sec insertion sequence (SECIS) element.


Pssm-ID: 294009  Cd Length: 114  Bit Score: 159.79  E-value: 1.16e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 311 TVHAALISVEKIPYFRGPLQTKAKFHITVGHETVMGRLMFFSPAPDNFDQEPILDSFNfsqeylfqeqylskdltpavtd 390
Cdd:cd04094   1 TVTAAIALVCKISFFKGSIKSKSKFHITVGHQTVMARVTFFSDPGKDETEEDESAEFV---------------------- 58

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 391 ndeaDKKAGQATEGHCPRQQWALVEFEKPVTCPRLCLVIGSRLDADIHTNTCRLAFHGIL 450
Cdd:cd04094  59 ----EDEDESLEEAKPGSEQYALLEFEKPVAAPPGDLFIGSRLDTDPHSNTCRLAFYGRV 114
SelB_II cd03696
Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor ...
 224-306 3.71e-39

Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor SelB that is homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.


Pssm-ID: 293897 [Multi-domain]  Cd Length: 83  Bit Score: 138.04  E-value: 3.71e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 224 FLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLV 303
Cdd:cd03696   1 FRLPIDHVFSIKGAGTVVTGTVLSGKVKVGDELEIPPLGKEVRVRSIQVHDKPVEEAKAGDRVALNLTGVDAKELERGFV 80


                ...
gi 54607086 304 CAP 306
Cdd:cd03696  81 LSE 83
PRK12736 PRK12736
elongation factor Tu; Reviewed
 8-311 3.83e-38

elongation factor Tu; Reviewed


Pssm-ID: 237184 [Multi-domain]  Cd Length: 394  Bit Score: 145.09  E-value: 3.83e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    8 VNVGVLGHIDSGKTALARALSTTAST---------AAFDKQPQSRERGITLDlgfscfsvplparlrSSLPEFQAAPEae 78
Cdd:PRK12736  13 VNIGTIGHVDHGKTTLTAAITKVLAErglnqakdyDSIDAAPEEKERGITIN---------------TAHVEYETEKR-- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   79 pepgepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAE-CLVIGQIACQKLVVVLNKIDLL--PEgk 155
Cdd:PRK12736  76 --------HYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREhILLARQVGVPYLVVFLNKVDLVddEE-- 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  156 rqaAIDKMTKKMQKTLENTKFRG--APIIPVAAKPGGPEAPETEapQGIPELIELLTSQISIPTRDPSGPFLMSVDHCFS 233
Cdd:PRK12736 146 ---LLELVEMEVRELLSEYDFPGddIPVIRGSALKALEGDPKWE--DAIMELMDAVDEYIPTPERDTDKPFLMPVEDVFT 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  234 IKGQGTVMTGTILSGSISLGDSVEIPALKVVKK--VKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLV-CAPESL- 309
Cdd:PRK12736 221 ITGRGTVVTGRVERGTVKVGDEVEIVGIKETQKtvVTGVEMFRKLLDEGQAGDNVGVLLRGVDRDEVERGQVlAKPGSIk 300


                 ...
gi 54607086  310 -HT 311
Cdd:PRK12736 301 pHT 303
GTP_EFTU pfam00009
Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ...
 8-213 1.61e-23

Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in several other families such as pfam00071, pfam00025 and pfam00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.


Pssm-ID: 425418 [Multi-domain]  Cd Length: 187  Bit Score: 97.98  E-value: 1.61e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086     8 VNVGVLGHIDSGKTALA------------RALSTTASTAAFDKQPQSRERGITLDLGFSCFSVPLParlrsslpefqaap 75
Cdd:pfam00009   4 RNIGIIGHVDHGKTTLTdrllyytgaiskRGEVKGEGEAGLDNLPEERERGITIKSAAVSFETKDY-------------- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    76 eaepepgepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAEclVIGQIACQ--KLVVVLNKIDLLPE 153
Cdd:pfam00009  70 -----------LINLIDTPGHVDFVKEVIRGLAQADGAILVVDAVEGVMPQTRE--HLRLARQLgvPIIVFINKMDRVDG 136

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 54607086   154 GKRQAAIDKMTKK-MQKTLENTKFRgaPIIPVAAKPGgpeapeteapQGIPELIELLTSQI 213
Cdd:pfam00009 137 AELEEVVEEVSRElLEKYGEDGEFV--PVVPGSALKG----------EGVQTLLDALDEYL 185
GTP_EFTU_D2 pfam03144
Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this ...
 238-305 1.74e-06

Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to pfam03143, and in fact has weak sequence matches to this domain.


Pssm-ID: 427163 [Multi-domain]  Cd Length: 73  Bit Score: 45.72  E-value: 1.74e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607086   238 GTVMTGTILSGSISLGDSVEIPALKVVKK-----VKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLVCA 305
Cdd:pfam03144   1 GTVATGRVESGTLKKGDKVRILPNGTGKKkivtrVTSLLMFHAPLREAVAGDNAGLILAGVGLEDIRVGDTLT 73
 
Name Accession Description Interval E-value
SelB_euk cd01889
SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ...
 8-209 1.07e-102

SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryotes, they do share a common feature. Unlike in E. coli, these SECIS elements are located in the 3' UTRs. This group contains eukaryotic SelBs and some from archaea.


Pssm-ID: 206676 [Multi-domain]  Cd Length: 192  Bit Score: 308.91  E-value: 1.07e-102
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   8 VNVGVLGHIDSGKTALARALSTTASTAAFDKQPQSRERGITLDLGFSCFSVPLPARLRSSL-PEFQaapeaepepgepLL 86
Cdd:cd01889   1 VNVGLLGHVDSGKTSLAKALSEIASTAAFDKNPQSQERGITLDLGFSSFEVDKPKHLEDNEnPQIE------------NY 68

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  87 QVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDLLPEGKRQAAIDKMTKK 166
Cdd:cd01889  69 QITLVDCPGHASLIRTIIGGAQIIDLMLLVVDAKKGIQTQTAECLVIGELLCKPLIVVLNKIDLIPEEERKRKIEKMKKR 148

                       170       180       190       200
                ....*....|....*....|....*....|....*....|...
gi 54607086 167 MQKTLENTKFRGAPIIPVAAKPGGPEApetEAPQGIPELIELL 209
Cdd:cd01889 149 LQKTLEKTRLKDSPIIPVSAKPGEGEA---ELGGELKNLIVLP 188
SelB COG3276
Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure ...
 8-351 2.14e-61

Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure and biogenesis]; Selenocysteine-specific translation elongation factor SelB is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 442507 [Multi-domain]  Cd Length: 630  Bit Score: 214.39  E-value: 2.14e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   8 VNVGVLGHIDSGKTALARALSTTAStaafDKQPQSRERGITLDLGFScfSVPLPARLRsslpefqaapeaepepgepllq 87
Cdd:COG3276   1 MIIGTAGHIDHGKTTLVKALTGIDT----DRLKEEKKRGITIDLGFA--YLPLPDGRR---------------------- 52

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  88 VTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIgqiaCQ-----KLVVVLNKIDLLPEgkrqAAIDK 162
Cdd:COG3276  53 LGFVDVPGHEKFIKNMLAGAGGIDLVLLVVAADEGVMPQTREHLAI----LDllgikRGIVVLTKADLVDE----EWLEL 124

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 163 MTKKMQKTLENTKFRGAPIIPVAAKPGgpeapeteapQGIPELIELLTSQI-SIPTRDPSGPFLMSVDHCFSIKGQGTVM 241
Cdd:COG3276 125 VEEEIRELLAGTFLEDAPIVPVSAVTG----------EGIDELRAALDALAaAVPARDADGPFRLPIDRVFSIKGFGTVV 194

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 242 TGTILSGSISLGDSVEI-PALKVVkKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERG-LVCAPESLHTVHAALISV 319
Cdd:COG3276 195 TGTLLSGTVRVGDELELlPSGKPV-RVRGIQVHGQPVEEAYAGQRVALNLAGVEKEEIERGdVLAAPGALRPTDRIDVRL 273

                       330       340       350
                ....*....|....*....|....*....|..
gi 54607086 320 EKIPYFRGPLQTKAKFHITVGHETVMGRLMFF 351
Cdd:COG3276 274 RLLPSAPRPLKHWQRVHLHHGTAEVLARVVLL 305
selB TIGR00475
selenocysteine-specific elongation factor SelB; In prokaryotes, the incorporation of ...
 8-348 5.18e-49

selenocysteine-specific elongation factor SelB; In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes. [Protein synthesis, Translation factors]


Pssm-ID: 129567 [Multi-domain]  Cd Length: 581  Bit Score: 179.68  E-value: 5.18e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086     8 VNVGVLGHIDSGKTALARALSTTAStaafDKQPQSRERGITLDLGFScfSVPLPARlrsslpefqaapeaepepgepllQ 87
Cdd:TIGR00475   1 MIIATAGHVDHGKTTLLKALTGIAA----DRLPEEKKRGMTIDLGFA--YFPLPDY-----------------------R 51

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    88 VTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECL-VIGQIACQKLVVVLNKIDLLPEgkrqAAIDKMTKK 166
Cdd:TIGR00475  52 LGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLaVLDLLGIPHTIVVITKADRVNE----EEIKRTEMF 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   167 MQKTLENTKF-RGAPIIPVAAKPGgpeapeteapQGIPELIELLTSQI-SIPTRDPSGPFLMSVDHCFSIKGQGTVMTGT 244
Cdd:TIGR00475 128 MKQILNSYIFlKNAKIFKTSAKTG----------QGIGELKKELKNLLeSLDIKRIQKPLRMAIDRAFKVKGAGTVVTGT 197

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   245 ILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLvCAPESLHTVHAalISVEKIPY 324
Cdd:TIGR00475 198 AFSGEVKVGDNLRLLPINHEVRVKAIQAQNQDVEIAYAGQRIALNLMDVEPESLKRGL-LILTPEDPKLR--VVVKFIAE 274

                         330       340
                  ....*....|....*....|....
gi 54607086   325 FrgPLQTKAKFHITVGHETVMGRL 348
Cdd:TIGR00475 275 V--PLLELQPYHIAHGMSVTTGKI 296
eSelB_III cd04094
Domain III of eukaryotic and archaeal elongation factor SelB; This model represents the domain ...
 311-450 1.16e-46

Domain III of eukaryotic and archaeal elongation factor SelB; This model represents the domain III of archaeal and eukaryotic selenocysteine (Sec)-specific eukaryotic elongation factor (eEFSec or eSelB), which is homologous to domain III of EF-Tu. SelB is a specialized translation elongation factor responsible for the co-translational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop, called Sec insertion sequence (SECIS) element.


Pssm-ID: 294009  Cd Length: 114  Bit Score: 159.79  E-value: 1.16e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 311 TVHAALISVEKIPYFRGPLQTKAKFHITVGHETVMGRLMFFSPAPDNFDQEPILDSFNfsqeylfqeqylskdltpavtd 390
Cdd:cd04094   1 TVTAAIALVCKISFFKGSIKSKSKFHITVGHQTVMARVTFFSDPGKDETEEDESAEFV---------------------- 58

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 391 ndeaDKKAGQATEGHCPRQQWALVEFEKPVTCPRLCLVIGSRLDADIHTNTCRLAFHGIL 450
Cdd:cd04094  59 ----EDEDESLEEAKPGSEQYALLEFEKPVAAPPGDLFIGSRLDTDPHSNTCRLAFYGRV 114
SelB_II cd03696
Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor ...
 224-306 3.71e-39

Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor SelB that is homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.


Pssm-ID: 293897 [Multi-domain]  Cd Length: 83  Bit Score: 138.04  E-value: 3.71e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 224 FLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLV 303
Cdd:cd03696   1 FRLPIDHVFSIKGAGTVVTGTVLSGKVKVGDELEIPPLGKEVRVRSIQVHDKPVEEAKAGDRVALNLTGVDAKELERGFV 80


                ...
gi 54607086 304 CAP 306
Cdd:cd03696  81 LSE 83
PRK12736 PRK12736
elongation factor Tu; Reviewed
 8-311 3.83e-38

elongation factor Tu; Reviewed


Pssm-ID: 237184 [Multi-domain]  Cd Length: 394  Bit Score: 145.09  E-value: 3.83e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    8 VNVGVLGHIDSGKTALARALSTTAST---------AAFDKQPQSRERGITLDlgfscfsvplparlrSSLPEFQAAPEae 78
Cdd:PRK12736  13 VNIGTIGHVDHGKTTLTAAITKVLAErglnqakdyDSIDAAPEEKERGITIN---------------TAHVEYETEKR-- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   79 pepgepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAE-CLVIGQIACQKLVVVLNKIDLL--PEgk 155
Cdd:PRK12736  76 --------HYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREhILLARQVGVPYLVVFLNKVDLVddEE-- 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  156 rqaAIDKMTKKMQKTLENTKFRG--APIIPVAAKPGGPEAPETEapQGIPELIELLTSQISIPTRDPSGPFLMSVDHCFS 233
Cdd:PRK12736 146 ---LLELVEMEVRELLSEYDFPGddIPVIRGSALKALEGDPKWE--DAIMELMDAVDEYIPTPERDTDKPFLMPVEDVFT 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  234 IKGQGTVMTGTILSGSISLGDSVEIPALKVVKK--VKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLV-CAPESL- 309
Cdd:PRK12736 221 ITGRGTVVTGRVERGTVKVGDEVEIVGIKETQKtvVTGVEMFRKLLDEGQAGDNVGVLLRGVDRDEVERGQVlAKPGSIk 300


                 ...
gi 54607086  310 -HT 311
Cdd:PRK12736 301 pHT 303
EF-Tu TIGR00485
translation elongation factor TU; This model models orthologs of translation elongation factor ...
 8-327 4.45e-37

translation elongation factor TU; This model models orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts, one of several GTP-binding translation factors found by the more general pfam model GTP_EFTU. The eukaryotic conterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this model. EF-Tu is one of the most abundant proteins in bacteria, as well as one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation. [Protein synthesis, Translation factors]


Pssm-ID: 129576 [Multi-domain]  Cd Length: 394  Bit Score: 142.22  E-value: 4.45e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086     8 VNVGVLGHIDSGKTALARALSTT------ASTAAF---DKQPQSRERGITLDlgfscfsvplparlrSSLPEFQAAPEae 78
Cdd:TIGR00485  13 VNVGTIGHVDHGKTTLTAAITTVlakeggAAARAYdqiDNAPEEKARGITIN---------------TAHVEYETETR-- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    79 pepgepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIG-QIACQKLVVVLNKIDLLPEgkrQ 157
Cdd:TIGR00485  76 --------HYAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGPMPQTREHILLArQVGVPYIVVFLNKCDMVDD---E 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   158 AAIDKMTKKMQKTLENTKFRG--APIIPVAAKPGGPEAPETEAPqgIPELIELLTSQISIPTRDPSGPFLMSVDHCFSIK 235
Cdd:TIGR00485 145 ELLELVEMEVRELLSQYDFPGddTPIIRGSALKALEGDAEWEAK--ILELMDAVDEYIPTPEREIDKPFLLPIEDVFSIT 222

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   236 GQGTVMTGTILSGSISLGDSVEIPALKVVKK--VKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLV-CAPESL--H 310
Cdd:TIGR00485 223 GRGTVVTGRVERGIIKVGEEVEIVGLKDTRKttVTGVEMFRKELDEGRAGDNVGLLLRGIKREEIERGMVlAKPGSIkpH 302

                         330       340
                  ....*....|....*....|....
gi 54607086   311 TVHAALISVEK-------IPYFRG 327
Cdd:TIGR00485 303 TKFEAEVYVLSkeeggrhTPFFSG 326
TufA COG0050
Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis] ...
 8-311 9.85e-37

Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis]; Translation elongation factor EF-Tu, a GTPase is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 439820 [Multi-domain]  Cd Length: 396  Bit Score: 141.44  E-value: 9.85e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   8 VNVGVLGHIDSGKTALARALSTTASTA------AF---DKQPQSRERGITLDlgfscfsvplparlrSSLPEFQAAPEae 78
Cdd:COG0050  13 VNIGTIGHVDHGKTTLTAAITKVLAKKggakakAYdqiDKAPEEKERGITIN---------------TSHVEYETEKR-- 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  79 pepgepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIG-QIACQKLVVVLNKIDLL--PEgk 155
Cdd:COG0050  76 --------HYAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGPMPQTREHILLArQVGVPYIVVFLNKCDMVddEE-- 145

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 156 rqaAIDKMTKKMQKTLENTKFRG--APIIPVAAKPG--GPEAPETEAPqgIPELIELLTSQISIPTRDPSGPFLMSVDHC 231
Cdd:COG0050 146 ---LLELVEMEVRELLSKYGFPGddTPIIRGSALKAleGDPDPEWEKK--ILELMDAVDSYIPEPERDTDKPFLMPVEDV 220

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 232 FSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKK--VKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLV-CAPES 308
Cdd:COG0050 221 FSITGRGTVVTGRVERGIIKVGDEVEIVGIRDTQKtvVTGVEMFRKLLDEGEAGDNVGLLLRGIKREDVERGQVlAKPGS 300


                ....*
gi 54607086 309 L--HT 311
Cdd:COG0050 301 ItpHT 305
PRK12735 PRK12735
elongation factor Tu; Reviewed
 8-311 2.50e-35

elongation factor Tu; Reviewed


Pssm-ID: 183708 [Multi-domain]  Cd Length: 396  Bit Score: 137.28  E-value: 2.50e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    8 VNVGVLGHIDSGKTALARALSTTASTAAF---------DKQPQSRERGITLDlgfscfsvplparlrSSLPEFQAAPEae 78
Cdd:PRK12735  13 VNVGTIGHVDHGKTTLTAAITKVLAKKGGgeakaydqiDNAPEEKARGITIN---------------TSHVEYETANR-- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   79 pepgepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAE-CLVIGQIACQKLVVVLNKIDLL--PEgk 155
Cdd:PRK12735  76 --------HYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREhILLARQVGVPYIVVFLNKCDMVddEE-- 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  156 rqaAIDKMTKKMQKTLENTKFRG--APIIPVAAKPG--GPEAPETEAPqgIPELIELLTSQISIPTRDPSGPFLMSVDHC 231
Cdd:PRK12735 146 ---LLELVEMEVRELLSKYDFPGddTPIIRGSALKAleGDDDEEWEAK--ILELMDAVDSYIPEPERAIDKPFLMPIEDV 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  232 FSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKK--VKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLV-CAPES 308
Cdd:PRK12735 221 FSISGRGTVVTGRVERGIVKVGDEVEIVGIKETQKttVTGVEMFRKLLDEGQAGDNVGVLLRGTKREDVERGQVlAKPGS 300


                 ....*
gi 54607086  309 L--HT 311
Cdd:PRK12735 301 IkpHT 305
PRK00049 PRK00049
elongation factor Tu; Reviewed
 8-311 2.88e-35

elongation factor Tu; Reviewed


Pssm-ID: 234596 [Multi-domain]  Cd Length: 396  Bit Score: 137.24  E-value: 2.88e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    8 VNVGVLGHIDSGKTALARALSTTASTA------AF---DKQPQSRERGITLDlgfscfsvplparlrSSLPEFQAAPEae 78
Cdd:PRK00049  13 VNVGTIGHVDHGKTTLTAAITKVLAKKggaeakAYdqiDKAPEEKARGITIN---------------TAHVEYETEKR-- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   79 pepgepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAE-CLVIGQIACQKLVVVLNKIDLL--PEgk 155
Cdd:PRK00049  76 --------HYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREhILLARQVGVPYIVVFLNKCDMVddEE-- 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  156 rqaAIDKMTKKMQKTLENTKFRG--APIIPVAAKP---GGPEAPETEApqgIPELIELLTSQISIPTRDPSGPFLMSVDH 230
Cdd:PRK00049 146 ---LLELVEMEVRELLSKYDFPGddTPIIRGSALKaleGDDDEEWEKK---ILELMDAVDSYIPTPERAIDKPFLMPIED 219

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  231 CFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKK--VKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLV-CAPE 307
Cdd:PRK00049 220 VFSISGRGTVVTGRVERGIIKVGEEVEIVGIRDTQKttVTGVEMFRKLLDEGQAGDNVGALLRGIKREDVERGQVlAKPG 299


                 ....*.
gi 54607086  308 SL--HT 311
Cdd:PRK00049 300 SItpHT 305
PLN03127 PLN03127
Elongation factor Tu; Provisional
 8-311 5.79e-33

Elongation factor Tu; Provisional


Pssm-ID: 178673 [Multi-domain]  Cd Length: 447  Bit Score: 131.49  E-value: 5.79e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    8 VNVGVLGHIDSGKTALARALSTT------ASTAAF---DKQPQSRERGITLDlgfscfsvplparlrSSLPEFQAAPEae 78
Cdd:PLN03127  62 VNVGTIGHVDHGKTTLTAAITKVlaeegkAKAVAFdeiDKAPEEKARGITIA---------------TAHVEYETAKR-- 124

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   79 pepgepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAE-CLVIGQIACQKLVVVLNKIDLLPEgkrQ 157
Cdd:PLN03127 125 --------HYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEhILLARQVGVPSLVVFLNKVDVVDD---E 193

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  158 AAIDKMTKKMQKTLENTKFRG--APIIPVAAKPGGPEAPETEAPQGIPELIELLTSQISIPTRDPSGPFLMSVDHCFSIK 235
Cdd:PLN03127 194 ELLELVEMELRELLSFYKFPGdeIPIIRGSALSALQGTNDEIGKNAILKLMDAVDEYIPEPVRVLDKPFLMPIEDVFSIQ 273

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  236 GQGTVMTGTILSGSISLGDSVEIPALKVVKKVKS----MQMFHMPITSAMQGDRLGICVTQFDPKLLERGLV-CAPESLH 310
Cdd:PLN03127 274 GRGTVATGRVEQGTIKVGEEVEIVGLRPGGPLKTtvtgVEMFKKILDQGQAGDNVGLLLRGLKREDVQRGQViCKPGSIK 353


                 .
gi 54607086  311 T 311
Cdd:PLN03127 354 T 354
PLN03126 PLN03126
Elongation factor Tu; Provisional
 4-327 1.43e-32

Elongation factor Tu; Provisional


Pssm-ID: 215592 [Multi-domain]  Cd Length: 478  Bit Score: 130.89  E-value: 1.43e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    4 RRVNVNVGVLGHIDSGKT----ALARALSTTASTAA-----FDKQPQSRERGITLDlgfscfsvplparlrSSLPEFQAA 74
Cdd:PLN03126  78 KKPHVNIGTIGHVDHGKTtltaALTMALASMGGSAPkkydeIDAAPEERARGITIN---------------TATVEYETE 142

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   75 PEaepepgepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAE-CLVIGQIACQKLVVVLNKIDLLPE 153
Cdd:PLN03126 143 NR----------HYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEhILLAKQVGVPNMVVFLNKQDQVDD 212

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  154 GKRQAAIDKMTKKMqktLENTKFRG--APIIP------VAAKPGGPEAP--ETEAPQGIPELIELLTSQISIPTRDPSGP 223
Cdd:PLN03126 213 EELLELVELEVREL---LSSYEFPGddIPIISgsallaLEALMENPNIKrgDNKWVDKIYELMDAVDSYIPIPQRQTDLP 289

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  224 FLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKK--VKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERG 301
Cdd:PLN03126 290 FLLAVEDVFSITGRGTVATGRVERGTVKVGETVDIVGLRETRSttVTGVEMFQKILDEALAGDNVGLLLRGIQKADIQRG 369

                        330       340       350
                 ....*....|....*....|....*....|....*.
gi 54607086  302 LVCA-PESL--HTVHAALISVEK-------IPYFRG 327
Cdd:PLN03126 370 MVLAkPGSItpHTKFEAIVYVLKkeeggrhSPFFAG 405
tufA CHL00071
elongation factor Tu
 8-311 1.63e-32

elongation factor Tu


Pssm-ID: 177010 [Multi-domain]  Cd Length: 409  Bit Score: 129.69  E-value: 1.63e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    8 VNVGVLGHIDSGKTALARALSTTASTAA---------FDKQPQSRERGITLDlgfscfsvplparlrSSLPEFQAApeae 78
Cdd:CHL00071  13 VNIGTIGHVDHGKTTLTAAITMTLAAKGgakakkydeIDSAPEEKARGITIN---------------TAHVEYETE---- 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   79 pepgepLLQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIG-QIACQKLVVVLNKIDLLPEGKrq 157
Cdd:CHL00071  74 ------NRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTKEHILLAkQVGVPNIVVFLNKEDQVDDEE-- 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  158 aAIDKMTKKMQKTLENTKFRGA--PIIPVAA-------------KPGgpeapETEAPQGIPELIELLTSQISIPTRDPSG 222
Cdd:CHL00071 146 -LLELVELEVRELLSKYDFPGDdiPIVSGSAllalealtenpkiKRG-----ENKWVDKIYNLMDAVDSYIPTPERDTDK 219

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  223 PFLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVK--KVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLER 300
Cdd:CHL00071 220 PFLMAIEDVFSITGRGTVATGRIERGTVKVGDTVEIVGLRETKttTVTGLEMFQKTLDEGLAGDNVGILLRGIQKEDIER 299

                        330
                 ....*....|....
gi 54607086  301 GLVCA-PESL--HT 311
Cdd:CHL00071 300 GMVLAkPGTItpHT 313
PRK04000 PRK04000
translation initiation factor IF-2 subunit gamma; Validated
 8-297 4.90e-31

translation initiation factor IF-2 subunit gamma; Validated


Pssm-ID: 235194 [Multi-domain]  Cd Length: 411  Bit Score: 125.35  E-value: 4.90e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    8 VNVGVLGHIDSGKTALARALSTTAStaafDKQPQSRERGITLDLGFS------CFSVPLPARLRS--------SLPEFqa 73
Cdd:PRK04000  10 VNIGMVGHVDHGKTTLVQALTGVWT----DRHSEELKRGITIRLGYAdatirkCPDCEEPEAYTTepkcpncgSETEL-- 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   74 apeaepepgepLLQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGM-QTQSAECLV-IGQIACQKLVVVLNKIDLL 151
Cdd:PRK04000  84 -----------LRRVSFVDAPGHETLMATMLSGAALMDGAILVIAANEPCpQPQTKEHLMaLDIIGIKNIVIVQNKIDLV 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  152 PegkRQAAIDKMtKKMQKTLENTKFRGAPIIPVAAKpggpeapeteapQG--IPELIELLTSQISIPTRDPSGPFLMSVD 229
Cdd:PRK04000 153 S---KERALENY-EQIKEFVKGTVAENAPIIPVSAL------------HKvnIDALIEAIEEEIPTPERDLDKPPRMYVA 216

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  230 HCFSIKGQGT--------VMTGTILSGSISLGDSVEI-PALKVVKKVKS-MQMFHMPITSAMQGDR----------LGIc 289
Cdd:PRK04000 217 RSFDVNKPGTppeklkggVIGGSLIQGVLKVGDEIEIrPGIKVEEGGKTkWEPITTKIVSLRAGGEkveearpgglVGV- 295


                 ....*...
gi 54607086  290 VTQFDPKL 297
Cdd:PRK04000 296 GTKLDPSL 303
GTP_translation_factor cd00881
GTP translation factor family primarily contains translation initiation, elongation and ...
 9-216 3.19e-28

GTP translation factor family primarily contains translation initiation, elongation and release factors; The GTP translation factor family consists primarily of translation initiation, elongation, and release factors, which play specific roles in protein translation. In addition, the family includes Snu114p, a component of the U5 small nuclear riboprotein particle which is a component of the spliceosome and is involved in excision of introns, TetM, a tetracycline resistance gene that protects the ribosome from tetracycline binding, and the unusual subfamily CysN/ATPS, which has an unrelated function (ATP sulfurylase) acquired through lateral transfer of the EF1-alpha gene and development of a new function.


Pssm-ID: 206647 [Multi-domain]  Cd Length: 183  Bit Score: 111.23  E-value: 3.19e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   9 NVGVLGHIDSGKTALARALST---------TASTAAFDKQPQSRERGITLDLGFSCFSVPLParlrsslpefqaapeaep 79
Cdd:cd00881   1 NVGVIGHVDHGKTTLTGSLLYqtgaidrrgTRKETFLDTLKEERERGITIKTGVVEFEWPKR------------------ 62

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  80 epgepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDLLPEGKRQAA 159
Cdd:cd00881  63 -------RINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGVEPQTREHLNIALAGGLPIIVAVNKIDRVGEEDFDEV 135

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 54607086 160 IDKMTKKMQKTLENT-KFRGAPIIPVAAKPGGpeapeteapqGIPELIELLTSQISIP 216
Cdd:cd00881 136 LREIKELLKLIGFTFlKGKDVPIIPISALTGE----------GIEELLDAIVEHLPPP 183
TEF1 COG5256
Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ...
 1-306 2.24e-26

Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]; Translation elongation factor EF-1alpha (GTPase) is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 444074 [Multi-domain]  Cd Length: 423  Bit Score: 111.95  E-value: 2.24e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   1 MAGRRVNVNVGVLGHIDSGKTAL------------ARALSTTASTA----------AF--DKQPQSRERGITLDLGFSCF 56
Cdd:COG5256   1 MASEKPHLNLVVIGHVDHGKSTLvgrllyetgaidEHIIEKYEEEAekkgkesfkfAWvmDRLKEERERGVTIDLAHKKF 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  57 SVPLparlrsslpefqaapeaepepgeplLQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAE------C 130
Cdd:COG5256  81 ETDK-------------------------YYFTIIDAPGHRDFVKNMITGASQADAAILVVSAKDGVMGQTREhaflarT 135

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 131 LVIGQIacqklVVVLNKIDLLP-EGKRQAAIDKMTKKMQKTLeNTKFRGAPIIPVAAKPGG---PEAPETEAPQGiPELI 206
Cdd:COG5256 136 LGINQL-----IVAVNKMDAVNySEKRYEEVKEEVSKLLKMV-GYKVDKIPFIPVSAWKGDnvvKKSDNMPWYNG-PTLL 208

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 207 ELLtSQISIPTRDPSGPFLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQGDRL 286
Cdd:COG5256 209 EAL-DNLKEPEKPVDKPLRIPIQDVYSISGIGTVPVGRVETGVLKVGDKVVFMPAGVVGEVKSIEMHHEELEQAEPGDNI 287

                       330       340
                ....*....|....*....|
gi 54607086 287 GICVTQFDPKLLERGLVCAP 306
Cdd:COG5256 288 GFNVRGVEKNDIKRGDVAGH 307
SelB cd04171
SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ...
 10-211 4.41e-25

SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryotes, they do share a common feature. Unlike in E. coli, these SECIS elements are located in the 3' UTRs. This group contains bacterial SelBs, as well as, one from archaea.


Pssm-ID: 206734 [Multi-domain]  Cd Length: 170  Bit Score: 101.91  E-value: 4.41e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  10 VGVLGHIDSGKTALARALSTTAStaafDKQPQSRERGITLDLGFSCFSVPLPARLrsslpefqaapeaepepgepllqvT 89
Cdd:cd04171   2 IGTAGHIDHGKTTLIKALTGIET----DRLPEEKKRGITIDLGFAYLDLPDGKRL------------------------G 53

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  90 LVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIGQI-ACQKLVVVLNKIDLLPEgkrqAAIDKMTKKMQ 168
Cdd:cd04171  54 FIDVPGHEKFVKNMLAGAGGIDAVLLVVAADEGIMPQTREHLEILELlGIKKGLVVLTKADLVDE----DRLELVEEEIL 129

                       170       180       190       200
                ....*....|....*....|....*....|....*....|...
gi 54607086 169 KTLENTKFRGAPIIPVAAKPGgpeapeteapQGIPELIELLTS 211
Cdd:cd04171 130 ELLAGTFLADAPIFPVSSVTG----------EGIEELKNYLDE 162
PRK12317 PRK12317
elongation factor 1-alpha; Reviewed
 8-306 3.55e-24

elongation factor 1-alpha; Reviewed


Pssm-ID: 237055 [Multi-domain]  Cd Length: 425  Bit Score: 105.39  E-value: 3.55e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    8 VNVGVLGHIDSGK-TALARALSTTAS-------------------TAAF----DKQPQSRERGITLDLGFSCFSVPLpar 63
Cdd:PRK12317   7 LNLAVIGHVDHGKsTLVGRLLYETGAidehiieelreeakekgkeSFKFawvmDRLKEERERGVTIDLAHKKFETDK--- 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   64 lrsslpefqaapeaepepgeplLQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGM----QTQS----AECLVIGQ 135
Cdd:PRK12317  84 ----------------------YYFTIVDCPGHRDFVKNMITGASQADAAVLVVAADDAGgvmpQTREhvflARTLGINQ 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  136 iacqkLVVVLNKIDLLP-EGKRQAAIDKMTKKMQKTLeNTKFRGAPIIPVAAKPGG---PEAPETEAPQGiPELIELLtS 211
Cdd:PRK12317 142 -----LIVAINKMDAVNyDEKRYEEVKEEVSKLLKMV-GYKPDDIPFIPVSAFEGDnvvKKSENMPWYNG-PTLLEAL-D 213

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  212 QISIPTRDPSGPFLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQGDRLGICVT 291
Cdd:PRK12317 214 NLKPPEKPTDKPLRIPIQDVYSISGVGTVPVGRVETGVLKVGDKVVFMPAGVVGEVKSIEMHHEELPQAEPGDNIGFNVR 293

                        330
                 ....*....|....*
gi 54607086  292 QFDPKLLERGLVCAP 306
Cdd:PRK12317 294 GVGKKDIKRGDVCGH 308
PRK10512 PRK10512
selenocysteinyl-tRNA-specific translation factor; Provisional
 14-288 4.10e-24

selenocysteinyl-tRNA-specific translation factor; Provisional


Pssm-ID: 182508 [Multi-domain]  Cd Length: 614  Bit Score: 106.67  E-value: 4.10e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   14 GHIDSGKTALARALsTTASTaafDKQPQSRERGITLDLGFSCFsvPLParlRSSLPEFqaapeaepepgepllqvtlVDC 93
Cdd:PRK10512   7 GHVDHGKTTLLQAI-TGVNA---DRLPEEKKRGMTIDLGYAYW--PQP---DGRVLGF-------------------IDV 58

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   94 PGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIGQIA-CQKLVVVLNKIDLLPEGKrqaaIDKMTKKMQKTLE 172
Cdd:PRK10512  59 PGHEKFLSNMLAGVGGIDHALLVVACDDGVMAQTREHLAILQLTgNPMLTVALTKADRVDEAR----IAEVRRQVKAVLR 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  173 NTKFRGAPIIPVAAKPGgpeapeteapQGIPELIELLtSQISIPTRDPSGPFLMSVDHCFSIKGQGTVMTGTILSGSISL 252
Cdd:PRK10512 135 EYGFAEAKLFVTAATEG----------RGIDALREHL-LQLPEREHAAQHRFRLAIDRAFTVKGAGLVVTGTALSGEVKV 203

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 54607086  253 GDSVEIPALKVVKKVKSMQMFHMPITSAMQGDRLGI 288
Cdd:PRK10512 204 GDTLWLTGVNKPMRVRGLHAQNQPTEQAQAGQRIAL 239
PTZ00327 PTZ00327
eukaryotic translation initiation factor 2 gamma subunit; Provisional
 4-258 4.87e-24

eukaryotic translation initiation factor 2 gamma subunit; Provisional


Pssm-ID: 240362 [Multi-domain]  Cd Length: 460  Bit Score: 105.47  E-value: 4.87e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    4 RRVNVNVGVLGHIDSGKTALARALSTTaSTAAFDkqpQSRERGITLDLG------FSCFSVPLPARLRS--SLPEFQAAP 75
Cdd:PTZ00327  31 RQATINIGTIGHVAHGKSTVVKALSGV-KTVRFK---REKVRNITIKLGyanakiYKCPKCPRPTCYQSygSSKPDNPPC 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   76 EAEPEPGEPLLQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGM-QTQSAECLVIGQIACQKLVVVL-NKIDLLpe 153
Cdd:PTZ00327 107 PGCGHKMTLKRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAANESCpQPQTSEHLAAVEIMKLKHIIILqNKIDLV-- 184

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  154 gKRQAAIDKMtKKMQKTLENTKFRGAPIIPVAAKPGgpeapeteapQGIPELIELLTSQISIPTRDPSGPFLMSVDHCFS 233
Cdd:PTZ00327 185 -KEAQAQDQY-EEIRNFVKGTIADNAPIIPISAQLK----------YNIDVVLEYICTQIPIPKRDLTSPPRMIVIRSFD 252

                        250       260       270
                 ....*....|....*....|....*....|...
gi 54607086  234 IKG--------QGTVMTGTILSGSISLGDSVEI 258
Cdd:PTZ00327 253 VNKpgedienlKGGVAGGSILQGVLKVGDEIEI 285
GTP_EFTU pfam00009
Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ...
 8-213 1.61e-23

Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in several other families such as pfam00071, pfam00025 and pfam00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.


Pssm-ID: 425418 [Multi-domain]  Cd Length: 187  Bit Score: 97.98  E-value: 1.61e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086     8 VNVGVLGHIDSGKTALA------------RALSTTASTAAFDKQPQSRERGITLDLGFSCFSVPLParlrsslpefqaap 75
Cdd:pfam00009   4 RNIGIIGHVDHGKTTLTdrllyytgaiskRGEVKGEGEAGLDNLPEERERGITIKSAAVSFETKDY-------------- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    76 eaepepgepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAEclVIGQIACQ--KLVVVLNKIDLLPE 153
Cdd:pfam00009  70 -----------LINLIDTPGHVDFVKEVIRGLAQADGAILVVDAVEGVMPQTRE--HLRLARQLgvPIIVFINKMDRVDG 136

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 54607086   154 GKRQAAIDKMTKK-MQKTLENTKFRgaPIIPVAAKPGgpeapeteapQGIPELIELLTSQI 213
Cdd:pfam00009 137 AELEEVVEEVSRElLEKYGEDGEFV--PVVPGSALKG----------EGVQTLLDALDEYL 185
eIF2_gamma cd01888
Gamma subunit of initiation factor 2 (eIF2 gamma); eIF2 is a heterotrimeric translation ...
 8-218 3.37e-23

Gamma subunit of initiation factor 2 (eIF2 gamma); eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits. The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome. The gamma subunit has no intrinsic GTPase activity, but is stimulated by the GTPase activating protein (GAP) eIF5, and GDP/GTP exchange is stimulated by the guanine nucleotide exchange factor (GEF) eIF2B. eIF2B is a heteropentamer, and the epsilon chain binds eIF2. Both eIF5 and eIF2B-epsilon are known to bind strongly to eIF2-beta, but have also been shown to bind directly to eIF2-gamma. It is possible that eIF2-beta serves simply as a high-affinity docking site for eIF5 and eIF2B-epsilon, or that eIF2-beta serves a regulatory role. eIF2-gamma is found only in eukaryotes and archaea. It is closely related to SelB, the selenocysteine-specific elongation factor from eubacteria. The translational factor components of the ternary complex, IF2 in eubacteria and eIF2 in eukaryotes are not the same protein (despite their unfortunately similar names). Both factors are GTPases; however, eubacterial IF-2 is a single polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is a member of the same family as eubacterial IF2, but the two proteins are only distantly related. This family includes translation initiation, elongation, and release factors.


Pssm-ID: 206675 [Multi-domain]  Cd Length: 197  Bit Score: 97.34  E-value: 3.37e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   8 VNVGVLGHIDSGKTALARALSTTAStaafDKQPQSRERGITLDLGFS------CFSVPLParlrSSLPEFQAAPEAEPEP 81
Cdd:cd01888   1 INIGTIGHVAHGKTTLVKALSGVWT----VRHKEELKRNITIKLGYAnakiykCPNCGCP----RPYDTPECECPGCGGE 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  82 GEPLLQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGM-QTQSAECLV-IGQIACQKLVVVLNKIDLLpegKRQAA 159
Cdd:cd01888  73 TKLVRHVSFVDCPGHEILMATMLSGAAVMDGALLLIAANEPCpQPQTSEHLAaLEIMGLKHIIILQNKIDLV---KEEQA 149

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 54607086 160 IDKMtKKMQKTLENTKFRGAPIIPVAAKPGgpeapeteapQGIPELIELLTSQISIPTR 218
Cdd:cd01888 150 LENY-EQIKEFVKGTIAENAPIIPISAQLK----------YNIDVLCEYIVKKIPTPPR 197
PTZ00141 PTZ00141
elongation factor 1- alpha; Provisional
 1-305 1.97e-20

elongation factor 1- alpha; Provisional


Pssm-ID: 185474 [Multi-domain]  Cd Length: 446  Bit Score: 94.43  E-value: 1.97e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    1 MAGRRVNVNVGVLGHIDSGKTALARAL------------------STTASTAAF------DKQPQSRERGITLDLgfscf 56
Cdd:PTZ00141   1 MGKEKTHINLVVIGHVDSGKSTTTGHLiykcggidkrtiekfekeAAEMGKGSFkyawvlDKLKAERERGITIDI----- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   57 svplparlrsSLPEFQAAPEAepepgepllqVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKG-------MQTQSAE 129
Cdd:PTZ00141  76 ----------ALWKFETPKYY----------FTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGefeagisKDGQTRE 135

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  130 -CLVIGQIACQKLVVVLNKIDLLPEGKRQAAIDKMTKKMQKTLENTKFRGA--PIIPVAAKPGG---PEAPETEAPQGiP 203
Cdd:PTZ00141 136 hALLAFTLGVKQMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVGYNPEkvPFIPISGWQGDnmiEKSDNMPWYKG-P 214

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  204 ELIELLtSQISIPTRDPSGPFLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQG 283
Cdd:PTZ00141 215 TLLEAL-DTLEPPKRPVDKPLRLPLQDVYKIGGIGTVPVGRVETGILKPGMVVTFAPSGVTTEVKSVEMHHEQLAEAVPG 293

                        330       340
                 ....*....|....*....|..
gi 54607086  284 DRLGICVTQFDPKLLERGLVCA 305
Cdd:PTZ00141 294 DNVGFNVKNVSVKDIKRGYVAS 315
PLN00043 PLN00043
elongation factor 1-alpha; Provisional
 1-305 1.48e-19

elongation factor 1-alpha; Provisional


Pssm-ID: 165621 [Multi-domain]  Cd Length: 447  Bit Score: 91.69  E-value: 1.48e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    1 MAGRRVNVNVGVLGHIDSGKTALA------------RALSTTASTAA------------FDKQPQSRERGITLDLgfscf 56
Cdd:PLN00043   1 MGKEKVHINIVVIGHVDSGKSTTTghliyklggidkRVIERFEKEAAemnkrsfkyawvLDKLKAERERGITIDI----- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   57 svplparlrsSLPEFQAAPeaepepgeplLQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKG-------MQTQSAE 129
Cdd:PLN00043  76 ----------ALWKFETTK----------YYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGgfeagisKDGQTRE 135

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  130 -CLVIGQIACQKLVVVLNKIDLLPEGKRQAAIDKMTKKMQKTLENTKFR--GAPIIPVAAKPGG---PEAPETEAPQGiP 203
Cdd:PLN00043 136 hALLAFTLGVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVGYNpdKIPFVPISGFEGDnmiERSTNLDWYKG-P 214

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  204 ELIELLtSQISIPTRDPSGPFLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQG 283
Cdd:PLN00043 215 TLLEAL-DQINEPKRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFGPTGLTTEVKSVEMHHESLQEALPG 293

                        330       340
                 ....*....|....*....|..
gi 54607086  284 DRLGICVTQFDPKLLERGLVCA 305
Cdd:PLN00043 294 DNVGFNVKNVAVKDLKRGYVAS 315
EFTU_II cd03697
Domain II of elongation factor Tu; Elongation factors Tu (EF-Tu) are three-domain GTPases with ...
 224-306 1.06e-15

Domain II of elongation factor Tu; Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven alpha helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Both non-catalytic domains are composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA; and an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher affinity for GDP than for GTP.


Pssm-ID: 293898 [Multi-domain]  Cd Length: 87  Bit Score: 72.55  E-value: 1.06e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 224 FLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKKVK--SMQMFHMPITSAMQGDRLGICVTQFDPKLLERG 301
Cdd:cd03697   1 FLMPIEDVFSIPGRGTVVTGRIERGVIKVGDEVEIVGFKETLKTTvtGIEMFRKTLDEAEAGDNVGVLLRGVKKEDVERG 80


                ....*.
gi 54607086 302 LV-CAP 306
Cdd:cd03697  81 MVlAKP 86
IF2_eIF5B cd01887
Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B ...
 10-209 1.07e-15

Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases, IF2/IF5B undergoes conformational changes between its GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess three characteristic segments, including a divergent N-terminal region followed by conserved central and C-terminal segments. This core region is conserved among all known eukaryotic and archaeal IF2/eIF5Bs and eubacterial IF2s.


Pssm-ID: 206674 [Multi-domain]  Cd Length: 169  Bit Score: 74.82  E-value: 1.07e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  10 VGVLGHIDSGKTALARALSTTastaafdkQPQSRE-RGITLDLGfsCFSVPLPARLRSslpefqaapeaepepgepllqV 88
Cdd:cd01887   3 VTVMGHVDHGKTTLLDKIRKT--------NVAAGEaGGITQHIG--AYQVPIDVKIPG---------------------I 51

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  89 TLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDLLPEgkRQAAIDKMTKKMQ 168
Cdd:cd01887  52 TFIDTPGHEAFTNMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAANVPIIVAINKIDKPYG--TEADPERVKNELS 129

                       170       180       190       200
                ....*....|....*....|....*....|....*....|...
gi 54607086 169 KTLENTK-FRG-APIIPVAAKPGgpeapeteapQGIPELIELL 209
Cdd:cd01887 130 ELGLVGEeWGGdVSIVPISAKTG----------EGIDDLLEAI 162
EF_Tu cd01884
Elongation Factor Tu (EF-Tu) GTP-binding proteins; EF-Tu subfamily. This subfamily includes ...
 7-216 7.20e-15

Elongation Factor Tu (EF-Tu) GTP-binding proteins; EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors. The eukaryotic counterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this family. EF-Tu is one of the most abundant proteins in bacteria, as well as, one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation.


Pssm-ID: 206671 [Multi-domain]  Cd Length: 195  Bit Score: 73.39  E-value: 7.20e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   7 NVNVGVLGHIDSGKTALARALSTTASTA---------AFDKQPQSRERGITLDLgfSCFSVPLPARLRSSlpefqaapea 77
Cdd:cd01884   2 HVNVGTIGHVDHGKTTLTAAITKVLAKKggakakkydEIDKAPEEKARGITINT--AHVEYETANRHYAH---------- 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  78 epepgepllqvtlVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIG-QIACQKLVVVLNKIDLLPEgkr 156
Cdd:cd01884  70 -------------VDCPGHADYIKNMITGAAQMDGAILVVSATDGPMPQTREHLLLArQVGVPYIVVFLNKADMVDD--- 133

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607086 157 QAAIDKMTKKMQKTLENTKFRG--APIIPVAAKPGGPEAPETEAPQGIPELIELLTSQISIP 216
Cdd:cd01884 134 EELLELVEMEVRELLSKYGFDGddTPIVRGSALKALEGDDPNKWVDKILELLDALDSYIPTP 195
GTPBP_II cd03694
Domain II of the GTPBP family of GTP binding proteins; This group includes proteins similar to ...
 224-303 8.28e-13

Domain II of the GTPBP family of GTP binding proteins; This group includes proteins similar to GTPBP1 and GTPBP2. GTPBP1 is structurally related to elongation factor 1 alpha, a key component of the protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.


Pssm-ID: 293895 [Multi-domain]  Cd Length: 87  Bit Score: 64.16  E-value: 8.28e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 224 FLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVK----KVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLE 299
Cdd:cd03694   1 FEFQIDDIYSVPGVGTVVSGTVSKGVIREGDTLLLGPDADGKfrpvTVKSIHRNRQPVDRARAGQSASFALKKIKRESLR 80


                ....
gi 54607086 300 RGLV 303
Cdd:cd03694  81 KGMV 84
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 11-211 6.77e-11

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: 60.93  E-value: 6.77e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  11 GVLGHIDSGKTALARALSTTASTAAfdkqpqSRERGITLDLGFSCFSVPLPARlrsslpefqaapeaepepgepllQVTL 90
Cdd:cd00882   1 VVVGRGGVGKSSLLNALLGGEVGEV------SDVPGTTRDPDVYVKELDKGKV-----------------------KLVL 51

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  91 VDCPGH--------ASLIRTIIGGAqiiDLMMLVIDVTKGMQTQSAECLVIGQIACQK--LVVVLNKIDLLPEGKRQAAI 160
Cdd:cd00882  52 VDTPGLdefgglgrEELARLLLRGA---DLILLVVDSTDRESEEDAKLLILRRLRKEGipIILVGNKIDLLEEREVEELL 128

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 54607086 161 DKMTKKmqktlentKFRGAPIIPVAAKPGgpeapeteapQGIPELIELLTS 211
Cdd:cd00882 129 RLEELA--------KILGVPVFEVSAKTG----------EGVDELFEKLIE 161
EF1_alpha cd01883
Elongation Factor 1-alpha (EF1-alpha) protein family; EF1 is responsible for the GTP-dependent ...
 9-186 1.03e-10

Elongation Factor 1-alpha (EF1-alpha) protein family; EF1 is responsible for the GTP-dependent binding of aminoacyl-tRNAs to the ribosomes. EF1 is composed of four subunits: the alpha chain which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This subfamily is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha interacts with the actin of the eukaryotic cytoskeleton and may thereby play a role in cellular transformation and apoptosis. EF-Tu can have no such role in bacteria. In humans, the isoform eEF1A2 is overexpressed in 2/3 of breast cancers and has been identified as a putative oncogene. This subfamily also includes Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation in yeast, and to associate with Dom34. It has been speculated that yeast Hbs1 and Dom34 proteins may function as part of a complex with a role in gene expression.


Pssm-ID: 206670 [Multi-domain]  Cd Length: 219  Bit Score: 61.74  E-value: 1.03e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   9 NVGVLGHIDSGKTAL------------ARAL------STTASTAAF------DKQPQSRERGITLDLGFSCFSVPlpaRL 64
Cdd:cd01883   1 NLVVIGHVDAGKSTLtghllyklggvdKRTIekyekeAKEMGKESFkyawvlDKLKEERERGVTIDVGLAKFETE---KY 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  65 RsslpefqaapeaepepgepllqVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKG-------MQTQSAE-CLVIGQI 136
Cdd:cd01883  78 R----------------------FTIIDAPGHRDFVKNMITGASQADVAVLVVSARKGefeagfeKGGQTREhALLARTL 135

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|..
gi 54607086 137 ACQKLVVVLNKIDLLPEGKRQAAIDKMTKKMQKTLENTKFRGA--PIIPVAA 186
Cdd:cd01883 136 GVKQLIVAVNKMDDVTVNWSQERYDEIKKKVSPFLKKVGYNPKdvPFIPISG 187
infB CHL00189
translation initiation factor 2; Provisional
 10-258 8.66e-10

translation initiation factor 2; Provisional


Pssm-ID: 177089 [Multi-domain]  Cd Length: 742  Bit Score: 61.77  E-value: 8.66e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   10 VGVLGHIDSGKTALARALSTTASTaafdkqpQSRERGITLDLGfsCFSVplparlrsslpEFQAAPEAEpepgepllQVT 89
Cdd:CHL00189 247 VTILGHVDHGKTTLLDKIRKTQIA-------QKEAGGITQKIG--AYEV-----------EFEYKDENQ--------KIV 298

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   90 LVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDllpegKRQAAIDKMTKKMQK 169
Cdd:CHL00189 299 FLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVPIIVAINKID-----KANANTERIKQQLAK 373

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  170 -TLENTKFRG-APIIPVAAKPGgpeapeteapQGIPELIE--LLTSQI----SIPTRDPSGPFLMS-VDhcfsiKGQGTV 240
Cdd:CHL00189 374 yNLIPEKWGGdTPMIPISASQG----------TNIDKLLEtiLLLAEIedlkADPTQLAQGIILEAhLD-----KTKGPV 438

                        250
                 ....*....|....*...
gi 54607086  241 MTGTILSGSISLGDSVEI 258
Cdd:CHL00189 439 ATILVQNGTLHIGDIIVI 456
EF1_alpha_II cd03693
Domain II of elongation factor 1-alpha; This family represents domain II of elongation factor ...
 222-304 1.38e-09

Domain II of elongation factor 1-alpha; This family represents domain II of elongation factor 1-alpha (EF-1A) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF-1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF-1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.


Pssm-ID: 293894 [Multi-domain]  Cd Length: 91  Bit Score: 55.27  E-value: 1.38e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 222 GPFLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERG 301
Cdd:cd03693   3 KPLRLPIQDVYKIGGIGTVPVGRVETGILKPGMVVTFAPAGVTGEVKSVEMHHEPLEEAIPGDNVGFNVKGVSVKDIKRG 82


                ...
gi 54607086 302 LVC 304
Cdd:cd03693  83 DVA 85
CysN_ATPS cd04166
CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; CysN_ATPS ...
 43-189 4.12e-09

CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; CysN_ATPS subfamily. CysN, together with protein CysD, form the ATP sulfurylase (ATPS) complex in some bacteria and lower eukaryotes. ATPS catalyzes the production of ATP sulfurylase (APS) and pyrophosphate (PPi) from ATP and sulfate. CysD, which catalyzes ATP hydrolysis, is a member of the ATP pyrophosphatase (ATP PPase) family. CysN hydrolysis of GTP is required for CysD hydrolysis of ATP; however, CysN hydrolysis of GTP is not dependent on CysD hydrolysis of ATP. CysN is an example of lateral gene transfer followed by acquisition of new function. In many organisms, an ATPS exists which is not GTP-dependent and shares no sequence or structural similarity to CysN.


Pssm-ID: 206729 [Multi-domain]  Cd Length: 209  Bit Score: 56.81  E-value: 4.12e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  43 RERGITLDLGFSCFSvpLPARlrsslpEFqaapeaepepgepllqvTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKG 122
Cdd:cd04166  60 REQGITIDVAYRYFS--TPKR------KF-----------------IIADTPGHEQYTRNMVTGASTADLAILLVDARKG 114

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607086 123 MQTQS------AECLVIGQIacqklVVVLNKIDLLpeGKRQAAIDKMTKKMQKTLENTKFRGAPIIPVAAKPG 189
Cdd:cd04166 115 VLEQTrrhsyiASLLGIRHV-----VVAVNKMDLV--DYDEEVFEEIKADYLAFAASLGIEDITFIPISALEG 180
Era_like cd00880
E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ...
 87-212 7.88e-09

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: 54.94  E-value: 7.88e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  87 QVTLVDCPG----------HASLIRTIIGGAqiiDLMMLVIDVTkgmQTQSAECLVIGQIACQK--LVVVLNKIDLLPEG 154
Cdd:cd00880  47 PVVLIDTPGldeegglgreRVEEARQVADRA---DLVLLVVDSD---LTPVEEEAKLGLLRERGkpVLLVLNKIDLVPES 120

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 54607086 155 KRQAAIDKMTKKmqktlentKFRGAPIIPVAAKPGgpeapeteapQGIPELIELLTSQ 212
Cdd:cd00880 121 EEEELLRERKLE--------LLPDLPVIAVSALPG----------EGIDELRKKIAEL 160
LepA cd01890
LepA also known as Elongation Factor 4 (EF4); LepA (also known as elongation factor 4, EF4) ...
 9-216 1.35e-08

LepA also known as Elongation Factor 4 (EF4); LepA (also known as elongation factor 4, EF4) belongs to the GTPase family and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and eukaryota (e.g. yeast GUF1p), but is missing from archaea. This pattern of phyletic distribution suggests that LepA evolved through a duplication of the EF-G gene in bacteria, followed by early transfer into the eukaryotic lineage, most likely from the promitochondrial endosymbiont. Yeast GUF1p is not essential and mutant cells did not reveal any marked phenotype.


Pssm-ID: 206677 [Multi-domain]  Cd Length: 179  Bit Score: 54.85  E-value: 1.35e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   9 NVGVLGHIDSGKTALA-RALSTTASTAAFDKQPQ-------SRERGITLDLgfscfsvplparlrsslpefQAAPEAEPE 80
Cdd:cd01890   2 NFSIIAHIDHGKSTLAdRLLELTGTVSEREMKEQvldsmdlERERGITIKA--------------------QAVRLFYKA 61

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  81 PGEPLLQVTLVDCPGHA--------SLIRTiiGGAqiidlmMLVIDVTKGMQTQS-AEClvigQIACQ---KLVVVLNKI 148
Cdd:cd01890  62 KDGEEYLLNLIDTPGHVdfsyevsrSLAAC--EGA------LLVVDATQGVEAQTlANF----YLALEnnlEIIPVINKI 129

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 54607086 149 DLLpegkrQAAIDKMTKKMQKTLentkfrGAP---IIPVAAKPGgpeapeteapQGIPELIELLTSQISIP 216
Cdd:cd01890 130 DLP-----AADPDRVKQEIEDVL------GLDaseAILVSAKTG----------LGVEDLLEAIVERIPPP 179
PRK04004 PRK04004
translation initiation factor IF-2; Validated
 10-272 1.65e-08

translation initiation factor IF-2; Validated


Pssm-ID: 235195 [Multi-domain]  Cd Length: 586  Bit Score: 57.50  E-value: 1.65e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   10 VGVLGHIDSGKTALaraLSTTASTAAFDKQPQsrerGITLDLGFScfSVPL------------PARLRSSLPefqaapea 77
Cdd:PRK04004   9 VVVLGHVDHGKTTL---LDKIRGTAVAAKEAG----GITQHIGAT--EVPIdviekiagplkkPLPIKLKIP-------- 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   78 epepgePLLqvtLVDCPGHA---SLIRTiiGGAqIIDLMMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDLLPeG 154
Cdd:PRK04004  72 ------GLL---FIDTPGHEaftNLRKR--GGA-LADIAILVVDINEGFQPQTIEAINILKRRKTPFVVAANKIDRIP-G 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  155 KR-------QAAIDKMTKKMQKTLEN----------------------TKF-RGAPIIPVAAKPGgpeapeteapQGIPE 204
Cdd:PRK04004 139 WKstedapfLESIEKQSQRVQQELEEklyeligqlselgfsadrfdrvKDFtKTVAIVPVSAKTG----------EGIPD 208

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607086  205 LIELL--------TSQISIPTRDPSGPFLMSVDhcfSIKGQGTVMTGTILSGSISLGDSVEIPALK--VVKKVKSMQM 272
Cdd:PRK04004 209 LLMVLaglaqrylEERLKIDVEGPGKGTVLEVK---EERGLGTTIDVILYDGTLRKGDTIVVGGKDgpIVTKVRALLK 283
Translation_Factor_II_like cd01342
Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of ...
 224-305 2.73e-08

Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of three structural domains. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought to be involved in binding of E. coli IF-2 to 30S subunits.


Pssm-ID: 293888 [Multi-domain]  Cd Length: 80  Bit Score: 51.11  E-value: 2.73e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 224 FLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQGDRLGICVTqfDPKLLERGLV 303
Cdd:cd01342   1 LVMQVFKVFYIPGRGRVAGGRVESGTLKVGDEIRILPKGITGRVTSIERFHEEVDEAKAGDIVGIGIL--GVKDILTGDT 78


                ..
gi 54607086 304 CA 305
Cdd:cd01342  79 LT 80
EF-G_bact cd04170
Elongation factor G (EF-G) family; Translocation is mediated by EF-G (also called translocase). ...
 9-184 1.73e-07

Elongation factor G (EF-G) family; Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group contains only bacterial members.


Pssm-ID: 206733 [Multi-domain]  Cd Length: 268  Bit Score: 52.98  E-value: 1.73e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   9 NVGVLGHIDSGKTALARALSTTAS-----------TAAFDKQPQSRERGITLDLGFSCFsvplparlrsslpEFQAApea 77
Cdd:cd04170   1 NIALVGHSGSGKTTLAEALLYATGaidrlgrvedgNTVSDYDPEEKKRKMSIETSVAPL-------------EWNGH--- 64

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  78 epepgepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAecLVIGQIACQKL--VVVLNKIDllpegK 155
Cdd:cd04170  65 ---------KINLIDTPGYADFVGETLSALRAVDAALIVVEAQSGVEVGTE--KVWEFLDDAKLprIIFINKMD-----R 128

                       170       180
                ....*....|....*....|....*....
gi 54607086 156 RQAAIDKMTKKMQKTLentkfrGAPIIPV 184
Cdd:cd04170 129 ARADFDKTLAALREAF------GRPVVPI 151
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
5-214 4.16e-07

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 50.36  E-value: 4.16e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   5 RVNVNVGVLGHIDSGKTALARALSTtastAAFDKQPQSRERGITLDlgfscfsvplpaRLRSSLPEFQaapeaepepgep 84
Cdd:COG1100   1 MGEKKIVVVGTGGVGKTSLVNRLVG----DIFSLEKYLSTNGVTID------------KKELKLDGLD------------ 52

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  85 lLQVTLVDCPG-------HASLIRTIIGgaqiIDLMMLVIDVTKGMQTQSAE---CLVIGQIACQKLVVVLNKIDLLPEG 154
Cdd:COG1100  53 -VDLVIWDTPGqdefretRQFYARQLTG----ASLYLFVVDGTREETLQSLYellESLRRLGKKSPIILVLNKIDLYDEE 127

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 155 KRQAAidkmtKKMQKTLENTKFrgAPIIPVAAKPGgpeapeteapQGIPELIELLTSQIS 214
Cdd:COG1100 128 EIEDE-----ERLKEALSEDNI--VEVVATSAKTG----------EGVEELFAALAEILR 170
era PRK00089
GTPase Era; Reviewed
 87-225 6.98e-07

GTPase Era; Reviewed


Pssm-ID: 234624 [Multi-domain]  Cd Length: 292  Bit Score: 51.20  E-value: 6.98e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   87 QVTLVDCPG-HA-------SLIRTIIGGAQIIDLMMLVIDVTKGMQTQsaECLVIGQIACQK--LVVVLNKIDLLpegKR 156
Cdd:PRK00089  54 QIIFVDTPGiHKpkralnrAMNKAAWSSLKDVDLVLFVVDADEKIGPG--DEFILEKLKKVKtpVILVLNKIDLV---KD 128

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 54607086  157 QAAIDKMTKKMQKTLENtkfrgAPIIPVAAKPGgpeapeteapQGIPELIELLTSQIsiptrdPSGPFL 225
Cdd:PRK00089 129 KEELLPLLEELSELMDF-----AEIVPISALKG----------DNVDELLDVIAKYL------PEGPPY 176
EF2 cd01885
Elongation Factor 2 (EF2) in archaea and eukarya; Translocation requires hydrolysis of a ...
 9-151 9.24e-07

Elongation Factor 2 (EF2) in archaea and eukarya; Translocation requires hydrolysis of a molecule of GTP and is mediated by EF-G in bacteria and by eEF2 in eukaryotes. The eukaryotic elongation factor eEF2 is a GTPase involved in the translocation of the peptidyl-tRNA from the A site to the P site on the ribosome. The 95-kDa protein is highly conserved, with 60% amino acid sequence identity between the human and yeast proteins. Two major mechanisms are known to regulate protein elongation and both involve eEF2. First, eEF2 can be modulated by reversible phosphorylation. Increased levels of phosphorylated eEF2 reduce elongation rates presumably because phosphorylated eEF2 fails to bind the ribosomes. Treatment of mammalian cells with agents that raise the cytoplasmic Ca2+ and cAMP levels reduce elongation rates by activating the kinase responsible for phosphorylating eEF2. In contrast, treatment of cells with insulin increases elongation rates by promoting eEF2 dephosphorylation. Second, the protein can be post-translationally modified by ADP-ribosylation. Various bacterial toxins perform this reaction after modification of a specific histidine residue to diphthamide, but there is evidence for endogenous ADP ribosylase activity. Similar to the bacterial toxins, it is presumed that modification by the endogenous enzyme also inhibits eEF2 activity.


Pssm-ID: 206672 [Multi-domain]  Cd Length: 218  Bit Score: 49.92  E-value: 9.24e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   9 NVGVLGHIDSGKTALARAL--------STTASTAAF-DKQPQSRERGITLDLGfscfSVPLparlrsslpEFQAAPEAEP 79
Cdd:cd01885   2 NICIIAHVDHGKTTLSDSLlasagiisEKLAGKARYlDTREDEQERGITIKSS----AISL---------YFEYEEEKMD 68

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607086  80 EPGEPLlqvTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLvigQIACQ---KLVVVLNKIDLL 151
Cdd:cd01885  69 GNDYLI---NLIDSPGHVDFSSEVTAALRLTDGALVVVDAVEGVCVQTETVL---RQALEervKPVLVINKIDRL 137
FusA COG0480
Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]; ...
 9-184 1.02e-06

Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]; Translation elongation factor EF-G, a GTPase is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440248 [Multi-domain]  Cd Length: 693  Bit Score: 51.59  E-value: 1.02e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   9 NVGVLGHIDSGKTALARAL-----------STTASTAAFDKQPQSRERGITLDLgfSCFSVplparlrsslpEFQAApea 77
Cdd:COG0480  11 NIGIVAHIDAGKTTLTERIlfytgaihrigEVHDGNTVMDWMPEEQERGITITS--AATTC-----------EWKGH--- 74

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  78 epepgepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAecLVIGQIACQKL--VVVLNKIDllpegK 155
Cdd:COG0480  75 ---------KINIIDTPGHVDFTGEVERSLRVLDGAVVVFDAVAGVEPQTE--TVWRQADKYGVprIVFVNKMD-----R 138

                       170       180
                ....*....|....*....|....*....
gi 54607086 156 RQAAIDKMTKKMQKTLentkfrGAPIIPV 184
Cdd:COG0480 139 EGADFDRVLEQLKERL------GANPVPL 161
PRK13351 PRK13351
elongation factor G-like protein;
9-149 1.02e-06

elongation factor G-like protein;


Pssm-ID: 237358 [Multi-domain]  Cd Length: 687  Bit Score: 51.88  E-value: 1.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    9 NVGVLGHIDSGKTALA-RALSTTASTAAF----------DKQPQSRERGITLDLGF-SCFsvplparlrsslpeFQAape 76
Cdd:PRK13351  10 NIGILAHIDAGKTTLTeRILFYTGKIHKMgevedgttvtDWMPQEQERGITIESAAtSCD--------------WDN--- 72

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 54607086   77 aepepgeplLQVTLVDCPGH----ASLIRTIIGgaqiIDLMMLVIDVTKGMQTQSAecLVIGQIACQKL--VVVLNKID 149
Cdd:PRK13351  73 ---------HRINLIDTPGHidftGEVERSLRV----LDGAVVVFDAVTGVQPQTE--TVWRQADRYGIprLIFINKMD 136
Era COG1159
GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis];
87-225 1.21e-06

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


Pssm-ID: 440773 [Multi-domain]  Cd Length: 290  Bit Score: 50.37  E-value: 1.21e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  87 QVTLVDCPG--------HASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAEclVIGQIACQK--LVVVLNKIDLLPEGKR 156
Cdd:COG1159  52 QIVFVDTPGihkpkrklGRRMNKAAWSALEDVDVILFVVDATEKIGEGDEF--ILELLKKLKtpVILVINKIDLVKKEEL 129

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 54607086 157 QAAIDKMTKKMqktlentKFrgAPIIPVAAKPGgpeapeteapQGIPELIELLTSQIsiptrdPSGPFL 225
Cdd:COG1159 130 LPLLAEYSELL-------DF--AEIVPISALKG----------DNVDELLDEIAKLL------PEGPPY 173
PRK12740 PRK12740
elongation factor G-like protein EF-G2;
13-184 1.38e-06

elongation factor G-like protein EF-G2;


Pssm-ID: 237186 [Multi-domain]  Cd Length: 668  Bit Score: 51.28  E-value: 1.38e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   13 LGHIDSGKTALARAL-----------STTASTAAFDKQPQSRERGITLDLgfSCFSVplparlrsslpEFQAApeaepep 81
Cdd:PRK12740   1 VGHSGAGKTTLTEAIlfytgaihrigEVEDGTTTMDFMPEERERGISITS--AATTC-----------EWKGH------- 60

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   82 gepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAecLVIGQIACQKL--VVVLNKIDllpegkRQAA 159
Cdd:PRK12740  61 -----KINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEPQTE--TVWRQAEKYGVprIIFVNKMD------RAGA 127

                        170       180
                 ....*....|....*....|....*.
gi 54607086  160 -IDKMTKKMQKTLentkfrGAPIIPV 184
Cdd:PRK12740 128 dFFRVLAQLQEKL------GAPVVPL 147
GTP_EFTU_D2 pfam03144
Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this ...
 238-305 1.74e-06

Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to pfam03143, and in fact has weak sequence matches to this domain.


Pssm-ID: 427163 [Multi-domain]  Cd Length: 73  Bit Score: 45.72  E-value: 1.74e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607086   238 GTVMTGTILSGSISLGDSVEIPALKVVKK-----VKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLVCA 305
Cdd:pfam03144   1 GTVATGRVESGTLKKGDKVRILPNGTGKKkivtrVTSLLMFHAPLREAVAGDNAGLILAGVGLEDIRVGDTLT 73
Snu114p cd04167
Snu114p, a spliceosome protein, is a GTPase; Snu114p subfamily. Snu114p is one of several ...
 9-151 5.81e-06

Snu114p, a spliceosome protein, is a GTPase; Snu114p subfamily. Snu114p is one of several proteins that make up the U5 small nuclear ribonucleoprotein (snRNP) particle. U5 is a component of the spliceosome, which catalyzes the splicing of pre-mRNA to remove introns. Snu114p is homologous to EF-2, but typically contains an additional N-terminal domain not found in Ef-2. This protein is part of the GTP translation factor family and the Ras superfamily, characterized by five G-box motifs.


Pssm-ID: 206730 [Multi-domain]  Cd Length: 213  Bit Score: 47.65  E-value: 5.81e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   9 NVGVLGHIDSGKTAL-------ARALSTTAS-----TAAFDKQPQSRERGITLDLgfSCFSVPLP-ARLRSSLpefqaap 75
Cdd:cd04167   2 NVCIAGHLHHGKTSLldmlieqTHKRTPSVKlgwkpLRYTDTRKDEQERGISIKS--NPISLVLEdSKGKSYL------- 72

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607086  76 eaepepgepllqVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAEclVIGQIACQKL--VVVLNKIDLL 151
Cdd:cd04167  73 ------------INIIDTPGHVNFMDEVAAALRLCDGVVLVVDVVEGLTSVTER--LIRHAIQEGLpmVLVINKIDRL 136
cysN PRK05124
sulfate adenylyltransferase subunit 1; Provisional
 92-319 7.82e-06

sulfate adenylyltransferase subunit 1; Provisional


Pssm-ID: 235349 [Multi-domain]  Cd Length: 474  Bit Score: 48.76  E-value: 7.82e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   92 DCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQS------AECLVIGQiacqkLVVVLNKIDLLpeGKRQAAIDKMT- 164
Cdd:PRK05124 113 DTPGHEQYTRNMATGASTCDLAILLIDARKGVLDQTrrhsfiATLLGIKH-----LVVAVNKMDLV--DYSEEVFERIRe 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  165 --KKMQKTL-ENTKFRgapIIPVAAKPGGPEAPETEA-P--QGiPELIELLTSqISIPTRDPSGPFLMSVDHC----FSI 234
Cdd:PRK05124 186 dyLTFAEQLpGNLDIR---FVPLSALEGDNVVSQSESmPwySG-PTLLEVLET-VDIQRVVDAQPFRFPVQYVnrpnLDF 260

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  235 KGqgtvMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQGDrlGICVTQFDPKLLERG--LVCAPESLHTV 312
Cdd:PRK05124 261 RG----YAGTLASGVVKVGDRVKVLPSGKESNVARIVTFDGDLEEAFAGE--AITLVLEDEIDISRGdlLVAADEALQAV 334


                 ....*..
gi 54607086  313 HAALISV 319
Cdd:PRK05124 335 QHASADV 341
Der COG1160
Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis];
98-208 9.69e-06

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


Pssm-ID: 440774 [Multi-domain]  Cd Length: 438  Bit Score: 48.10  E-value: 9.69e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  98 SLIRTIiggaQII---DLMMLVIDVTKGMQTQSAEclVIGQIACQK--LVVVLNKIDLLPegKRQAAIDKMTKKMQKTLe 172
Cdd:COG1160 247 SVLRTL----RAIeraDVVLLVIDATEGITEQDLK--IAGLALEAGkaLVIVVNKWDLVE--KDRKTREELEKEIRRRL- 317

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 54607086 173 ntKF-RGAPIIPVAAKPGgpeapeteapQGIPELIEL 208
Cdd:COG1160 318 --PFlDYAPIVFISALTG----------QGVDKLLEA 342
PRK10218 PRK10218
translational GTPase TypA;
9-258 1.35e-05

translational GTPase TypA;


Pssm-ID: 104396 [Multi-domain]  Cd Length: 607  Bit Score: 48.17  E-value: 1.35e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    9 NVGVLGHIDSGKTALARALSTTASTaaFDKQPQSRER-----GITLDLGFSCFSVPLPARLRSslpefqaapeaepepge 83
Cdd:PRK10218   7 NIAIIAHVDHGKTTLVDKLLQQSGT--FDSRAETQERvmdsnDLEKERGITILAKNTAIKWND----------------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   84 plLQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDlLPEGKRQAAIDKM 163
Cdd:PRK10218  68 --YRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPIVVINKVD-RPGARPDWVVDQV 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  164 TK---KMQKTLENTKFrgaPIIPVAAKPGGPEAPETEAPQGIPELIELLTSQISIPTRDPSGPFLMSVDHCFSIKGQGTV 240
Cdd:PRK10218 145 FDlfvNLDATDEQLDF---PIVYASALNGIAGLDHEDMAEDMTPLYQAIVDHVPAPDVDLDGPFQMQISQLDYNSYVGVI 221

                        250
                 ....*....|....*...
gi 54607086  241 MTGTILSGSISLGDSVEI 258
Cdd:PRK10218 222 GIGRIKRGKVKPNQQVTI 239
Era cd04163
E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ...
 87-212 1.37e-05

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: 45.53  E-value: 1.37e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  87 QVTLVDCPG-HAS-------LIRTIIGGAQIIDLMMLVIDVTKGMQTQsaECLVIGQIACQKL--VVVLNKIDLL-PEGK 155
Cdd:cd04163  52 QIIFVDTPGiHKPkkklgerMVKAAWSALKDVDLVLFVVDASEWIGEG--DEFILELLKKSKTpvILVLNKIDLVkDKED 129

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 54607086 156 RQAAIDKMTKKMQktlentkfrGAPIIPVAAKPGgpeapeteapQGIPELIELLTSQ 212
Cdd:cd04163 130 LLPLLEKLKELHP---------FAEIFPISALKG----------ENVDELLEYIVEY 167
PRK05506 PRK05506
bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
 43-307 2.46e-05

bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional


Pssm-ID: 180120 [Multi-domain]  Cd Length: 632  Bit Score: 47.23  E-value: 2.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   43 RERGITLDLGFSCFSVPlpARlrsslpefqaapeaepepgepllQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKG 122
Cdd:PRK05506  86 REQGITIDVAYRYFATP--KR-----------------------KFIVADTPGHEQYTRNMVTGASTADLAIILVDARKG 140

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  123 MQTQS------AECLVIGQIacqklVVVLNKIDLLpeGKRQAAIDKMTKKMQKTLENTKFRGAPIIPVAAKPG------G 190
Cdd:PRK05506 141 VLTQTrrhsfiASLLGIRHV-----VLAVNKMDLV--DYDQEVFDEIVADYRAFAAKLGLHDVTFIPISALKGdnvvtrS 213

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  191 PEAPETEAPQgipeLIELLTSqISIPTRDPSGPFLMSV--------DHcfsiKGqgtvMTGTILSGSISLGDsvEIPALK 262
Cdd:PRK05506 214 ARMPWYEGPS----LLEHLET-VEIASDRNLKDFRFPVqyvnrpnlDF----RG----FAGTVASGVVRPGD--EVVVLP 278

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 54607086  263 VVK--KVKSMQMFHMPITSAMQGDrlGICVTQFDPKLLERG-LVCAPE 307
Cdd:PRK05506 279 SGKtsRVKRIVTPDGDLDEAFAGQ--AVTLTLADEIDISRGdMLARAD 324
MnmE COG0486
tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal ...
 111-230 8.88e-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: 45.05  E-value: 8.88e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 111 DLMMLVIDVTKGMQTQSAEclVIGQIACQKLVVVLNKIDLLPEgkrqaaidkmtkkmqKTLENTKFRGAPIIPVAAKPGg 190
Cdd:COG0486 294 DLVLLLLDASEPLTEEDEE--ILEKLKDKPVIVVLNKIDLPSE---------------ADGELKSLPGEPVIAISAKTG- 355

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 54607086 191 peapeteapQGIPELIELLTSQISIPTRDPSGPFLMSVDH 230
Cdd:COG0486 356 ---------EGIDELKEAILELVGEGALEGEGVLLTNARH 386
EngA2 cd01895
EngA2 GTPase contains the second domain of EngA; This EngA2 subfamily CD represents the second ...
 98-208 1.04e-04

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: 43.19  E-value: 1.04e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  98 SLIRTIiggaQII---DLMMLVIDVTKGMQTQSAEclVIGQIACQK--LVVVLNKIDLLPegKRQAAIDKMTKKMQKTLe 172
Cdd:cd01895  74 SVLRTL----KAIeraDVVLLVLDASEGITEQDLR--IAGLILEEGkaLIIVVNKWDLVE--KDEKTMKEFEKELRRKL- 144

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 54607086 173 nTKFRGAPIIPVAAKPGgpeapeteapQGIPELIEL 208
Cdd:cd01895 145 -PFLDYAPIVFISALTG----------QGVDKLFDA 169
PRK00093 PRK00093
GTP-binding protein Der; Reviewed
 98-208 3.18e-04

GTP-binding protein Der; Reviewed


Pssm-ID: 234628 [Multi-domain]  Cd Length: 435  Bit Score: 43.50  E-value: 3.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   98 SLIRTIiggaQII---DLMMLVIDVTKGMQTQSAecLVIGQIACQK--LVVVLNKIDLLPEGKRQAAIDKMTKKMQktle 172
Cdd:PRK00093 245 SVIRTL----KAIeraDVVLLVIDATEGITEQDL--RIAGLALEAGraLVIVVNKWDLVDEKTMEEFKKELRRRLP---- 314

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 54607086  173 ntKFRGAPIIPVAAKPGgpeapeteapQGIPELIEL 208
Cdd:PRK00093 315 --FLDYAPIVFISALTG----------QGVDKLLEA 338
HBS1-like_II cd16267
Domain II of Hbs1-like proteins; S. cerevisiae Hbs1 is closely related to the eukaryotic class ...
 223-295 3.47e-04

Domain II of Hbs1-like proteins; S. cerevisiae Hbs1 is closely related to the eukaryotic class II release factor (eRF3). Hbs1, together with Dom34 (pelota), plays an important role in termination and recycling, but in contrast to eRF3/eRF1, Hbs1, together with Dom34 (pelota), functions on mRNA-bound ribosomes in a codon-independent manner and promotes subunit splitting on completely empty ribosomes.


Pssm-ID: 293912 [Multi-domain]  Cd Length: 84  Bit Score: 39.42  E-value: 3.47e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607086 223 PFLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQGDRLGICVTQFDP 295
Cdd:cd16267   1 PFRLSVSDVFKGQGSGFTVSGRIEAGSVQVGDKVLVMPSNETATVKSIEIDDEPVDWAVAGDNVTLTLTGIDP 73
trmE cd04164
trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in ...
 111-211 3.84e-04

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: 41.33  E-value: 3.84e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 111 DLMMLVIDVTKGMQTQSAEclVIGQIACQKLVVVLNKIDLLPEGKRQAAIDkmtkkmqktlentkfrGAPIIPVAAKPGg 190
Cdd:cd04164  84 DLVLLVVDASEGLDEEDLE--ILELPAKKPVIVVLNKSDLLSDAEGISELN----------------GKPIIAISAKTG- 144

                        90       100
                ....*....|....*....|.
gi 54607086 191 peapeteapQGIPELIELLTS 211
Cdd:cd04164 145 ---------EGIDELKEALLE 156
PTZ00416 PTZ00416
elongation factor 2; Provisional
 9-149 4.64e-04

elongation factor 2; Provisional


Pssm-ID: 240409 [Multi-domain]  Cd Length: 836  Bit Score: 43.11  E-value: 4.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    9 NVGVLGHIDSGKTALARAL--------STTASTAAF-DKQPQSRERGITL-DLGFSCF---SVPLPARLRSSLpefqaap 75
Cdd:PTZ00416  21 NMSVIAHVDHGKSTLTDSLvckagiisSKNAGDARFtDTRADEQERGITIkSTGISLYyehDLEDGDDKQPFL------- 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 54607086   76 eaepepgepllqVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKG--MQTQSaeclVIGQiACQ---KLVVVLNKID 149
Cdd:PTZ00416  94 ------------INLIDSPGHVDFSSEVTAALRVTDGALVVVDCVEGvcVQTET----VLRQ-ALQeriRPVLFINKVD 155
MnmE_helical pfam12631
MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An ...
 111-230 7.75e-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: 42.08  E-value: 7.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086   111 DLMMLVIDVTKGmQTQSAECLVIGQIACQKLVVVLNKIDLLPEGKrqaaidkmtkkmqktlENTKFRGAPIIPVAAKPGg 190
Cdd:pfam12631 175 DLVLLVLDASRP-LDEEDLEILELLKDKKPIIVVLNKSDLLGEID----------------ELEELKGKPVLAISAKTG- 236

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 54607086   191 peapeteapQGIPELIELLTSQISIPTRDPSGPFLMSVDH 230
Cdd:pfam12631 237 ---------EGLDELEEAIKELFLAGEIASDGPIITNARH 267
cobW pfam02492
CobW/HypB/UreG, nucleotide-binding domain; This domain is found in HypB, a hydrogenase ...
 110-183 1.35e-03

CobW/HypB/UreG, nucleotide-binding domain; This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif. HypB has GTPase activity and is a guanine nucleotide binding protein. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression. UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins. This family of domains also contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans.


Pssm-ID: 396860  Cd Length: 179  Bit Score: 39.93  E-value: 1.35e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 54607086   110 IDLMMLVIDVTKGMQTQSAECLVIGQIACQKLVVvLNKIDLLPEGKRQAAIDKMTKKMQktlentkfRGAPIIP 183
Cdd:pfam02492 115 LDGVITVVDAANEADGEKIPRKAGDQIAFADLIV-LNKTDLAPEVALLEVLEEDLRRLN--------PGAPVVP 179
DLP_2 cd09912
Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The ...
 88-213 2.10e-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: 39.45  E-value: 2.10e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  88 VTLVDCPG-------HASLIRTIIGGAqiiDLMMLVIDVTKGMqTQSaECLVIGQIA---CQKLVVVLNKIDLLpegkRQ 157
Cdd:cd09912  48 VVLVDTPGlnstiehHTEITESFLPRA---DAVIFVLSADQPL-TES-EREFLKEILkwsGKKIFFVLNKIDLL----SE 118

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607086 158 AAIDKMTKKMQKTLENTKFRGA--PIIPVAAKPG----GPEAPETEAPQGIPELIELLTSQI 213
Cdd:cd09912 119 EELEEVLEYSREELGVLELGGGepRIFPVSAKEAlearLQGDEELLEQSGFEELEEHLEEFL 180
Translation_Factor_II cd16265
Proteins related to domain II of EF-Tu and related translation factors; Elongation factor Tu ...
 238-288 4.09e-03

Proteins related to domain II of EF-Tu and related translation factors; Elongation factor Tu consists of three structural domains; this family represents single domain proteins that are related to the second domain of EF-Tu. Domain II of EF-Tu adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is also found in other proteins such as elongation factor G and translation initiation factor IF-2.


Pssm-ID: 293910 [Multi-domain]  Cd Length: 80  Bit Score: 36.50  E-value: 4.09e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 54607086 238 GTVMTGTILSGSISLGDSVEIPALkvVKKVKSMQMFHMPITSAMQGDRLGI 288
Cdd:cd16265  14 RQVLTGEVESGVIYVGYKVKGDKG--VALIRAIEREHRKVDFAVAGDEVAL 62
InfB COG0532
Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; ...
 87-270 4.42e-03

Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; Translation initiation factor IF-2, a GTPase is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440298 [Multi-domain]  Cd Length: 502  Bit Score: 40.00  E-value: 4.42e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  87 QVTLVDCPGHASL----IRtiigGAQIIDLMMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDllpegKRQAAIDK 162
Cdd:COG0532  52 KITFLDTPGHEAFtamrAR----GAQVTDIVILVVAADDGVMPQTIEAINHAKAAGVPIIVAINKID-----KPGANPDR 122

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086 163 MtkkMQKTLE----------NTKFrgapiIPVAAKPGgpeapeteapQGIPELIE--LLTSQI----SIPTRDPSGPFL- 225
Cdd:COG0532 123 V---KQELAEhglvpeewggDTIF-----VPVSAKTG----------EGIDELLEmiLLQAEVlelkANPDRPARGTVIe 184

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*....
gi 54607086 226 MSVDhcfsiKGQGTVMTGTILSGSISLGDSVeipalkVVK----KVKSM 270
Cdd:COG0532 185 AKLD-----KGRGPVATVLVQNGTLKVGDIV------VAGtaygRVRAM 222
trmE PRK05291
tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE;
111-211 7.03e-03

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


Pssm-ID: 235392 [Multi-domain]  Cd Length: 449  Bit Score: 39.32  E-value: 7.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086  111 DLMMLVIDVTKGMQTQSAEclVIGQIACQKLVVVLNKIDLLPEgkrqaaidkmtkkmqktLENTKFRGAPIIPVAAKPGg 190
Cdd:PRK05291 296 DLVLLVLDASEPLTEEDDE--ILEELKDKPVIVVLNKADLTGE-----------------IDLEEENGKPVIRISAKTG- 355

                         90       100
                 ....*....|....*....|.
gi 54607086  191 peapeteapQGIPELIELLTS 211
Cdd:PRK05291 356 ---------EGIDELREAIKE 367
PLN00116 PLN00116
translation elongation factor EF-2 subunit; Provisional
 9-149 7.58e-03

translation elongation factor EF-2 subunit; Provisional


Pssm-ID: 177730 [Multi-domain]  Cd Length: 843  Bit Score: 39.32  E-value: 7.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    9 NVGVLGHIDSGKTALARALSTTASTAAFDKQPQSR---------ERGITL-DLGFSCFSVPLPARLRSSLPEFQAAPEAe 78
Cdd:PLN00116  21 NMSVIAHVDHGKSTLTDSLVAAAGIIAQEVAGDVRmtdtradeaERGITIkSTGISLYYEMTDESLKDFKGERDGNEYL- 99

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607086   79 pepgepllqVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKG--MQTQSaeclVIGQIACQKL--VVVLNKID 149
Cdd:PLN00116 100 ---------INLIDSPGHVDFSSEVTAALRITDGALVVVDCIEGvcVQTET----VLRQALGERIrpVLTVNKMD 161
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 87-147 7.80e-03

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: 36.44  E-value: 7.80e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607086    87 QVTLVDCPGhasLIRTIIGGAQII---------DLMMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNK 147
Cdd:pfam01926  47 QIILVDTPG---LIEGASEGEGLGraflaiieaDLILFVVDSEEGITPLDEELLELLRENKKPIILVLNK 113
RsgA_GTPase pfam03193
RsgA GTPase; RsgA (also known as EngC and YjeQ) represents a protein family whose members are ...
 140-215 8.99e-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: 37.52  E-value: 8.99e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 54607086   140 KLVVVLNKIDLLPEgkrqaaiDKMTKKMQKTLENTkfrGAPIIPVAAKPGgpeapeteapQGIPELIELLTSQISI 215
Cdd:pfam03193  55 EPVIVLNKIDLLDE-------EEELEELLKIYRAI---GYPVLFVSAKTG----------EGIEALKELLKGKTTV 110
 
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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