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Conserved domains on  [gi|971520639|dbj|GAQ77626|]
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chloroplast translation initiation factor IF-1 [Klebsormidium nitens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
infA CHL00010
translation initiation factor 1
 446-517 5.18e-39

translation initiation factor 1


:

Pssm-ID: 214332  Cd Length: 78  Bit Score: 137.05  E-value: 5.18e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 971520639 446 KKQSAMIEMEGEVQKALPNAMFQVALDNGCQVLAHISGKIRRNRIEIFQGDRVKVEISPYDLTRGRITHRNR 517
Cdd:CHL00010   1 MKKENKIEMEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLR 72
PRK11212 super family cl00756
7-cyano-7-deazaguanine/7-aminomethyl-7-deazaguanine transporter;
316-390 3.78e-03

7-cyano-7-deazaguanine/7-aminomethyl-7-deazaguanine transporter;


The actual alignment was detected with superfamily member PRK11212:

Pssm-ID: 469907  Cd Length: 210  Bit Score: 38.76  E-value: 3.78e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971520639 316 ALAYPALFLQTGILASEQGAERARQAALWSLPPALLVSSC---------FMGW-----------RVAAASAAAFLTAQLV 375
Cdd:PRK11212  46 AFSFPFIFLATDLTVRIFGAPLARRIIFAVMLPALLISYVisvlfyqgsWQGFaalaefnlfvaRIALASFMAYVLGQIL 125

                         90
                 ....*....|....*
gi 971520639 376 NVNVSERLPRASHWW 390
Cdd:PRK11212 126 DVHVFNRLRQSRAWW 140
 
Name Accession Description Interval E-value
infA CHL00010
translation initiation factor 1
 446-517 5.18e-39

translation initiation factor 1


Pssm-ID: 214332  Cd Length: 78  Bit Score: 137.05  E-value: 5.18e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 971520639 446 KKQSAMIEMEGEVQKALPNAMFQVALDNGCQVLAHISGKIRRNRIEIFQGDRVKVEISPYDLTRGRITHRNR 517
Cdd:CHL00010   1 MKKENKIEMEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLR 72
S1_IF1 cd04451
S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like ...
 452-515 4.10e-35

S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of the mRNA.


Pssm-ID: 239898  Cd Length: 64  Bit Score: 125.71  E-value: 4.10e-35
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 971520639 452 IEMEGEVQKALPNAMFQVALDNGCQVLAHISGKIRRNRIEIFQGDRVKVEISPYDLTRGRITHR 515
Cdd:cd04451    1 IEMEGVVTEALPNAMFRVELENGHEVLAHISGKMRMNYIRILPGDRVKVELSPYDLTKGRIVYR 64
infA TIGR00008
translation initiation factor IF-1; This family consists of translation initiation factor IF-1 ...
 452-515 8.71e-33

translation initiation factor IF-1; This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575). [Protein synthesis, Translation factors]


Pssm-ID: 188015  Cd Length: 69  Bit Score: 119.75  E-value: 8.71e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 971520639  452 IEMEGEVQKALPNAMFQVALDNGCQVLAHISGKIRRNRIEIFQGDRVKVEISPYDLTRGRITHR 515
Cdd:TIGR00008   5 IEMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDRVKVELSPYDLTRGRITYR 68
InfA COG0361
Translation initiation factor IF-1 [Translation, ribosomal structure and biogenesis]; ...
 452-515 1.25e-32

Translation initiation factor IF-1 [Translation, ribosomal structure and biogenesis]; Translation initiation factor IF-1 is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440130  Cd Length: 73  Bit Score: 119.44  E-value: 1.25e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 971520639 452 IEMEGEVQKALPNAMFQVALDNGCQVLAHISGKIRRNRIEIFQGDRVKVEISPYDLTRGRITHR 515
Cdd:COG0361    8 IEVEGVVEEVLPNARFRVRLENGHERLARISGKMRKNRIRILPGDRVLVEPSPYDLTKGRIVYR 71
eIF-1a pfam01176
Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation ...
 453-515 4.73e-26

Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.


Pssm-ID: 460099  Cd Length: 62  Bit Score: 100.54  E-value: 4.73e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 971520639  453 EMEGEVQKALPNAMFQVALDNGCQVLAHISGKIrRNRIEIFQGDRVKVEISPYDLTRGRITHR 515
Cdd:pfam01176   1 EVIGKVVEALGNNLFEVELDNGHTRLAHIPGKM-RNRIWIKRGDYVLVEPSPYDLTKGRIVYR 62
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
454-512 2.39e-07

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.98  E-value: 2.39e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 971520639   454 MEGEVQKALPNAMFqVALDNGCQVLAHIS----GKIRRNRIEIFQGDRVKVEISPYDLTRGRI 512
Cdd:smart00316   6 VEGTVTEITPGGAF-VDLGNGVEGLIPISelsdKRVKDPEEVLKVGDEVKVKVLSVDEEKGRI 67
PRK11212 PRK11212
7-cyano-7-deazaguanine/7-aminomethyl-7-deazaguanine transporter;
316-390 3.78e-03

7-cyano-7-deazaguanine/7-aminomethyl-7-deazaguanine transporter;


Pssm-ID: 183041  Cd Length: 210  Bit Score: 38.76  E-value: 3.78e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971520639 316 ALAYPALFLQTGILASEQGAERARQAALWSLPPALLVSSC---------FMGW-----------RVAAASAAAFLTAQLV 375
Cdd:PRK11212  46 AFSFPFIFLATDLTVRIFGAPLARRIIFAVMLPALLISYVisvlfyqgsWQGFaalaefnlfvaRIALASFMAYVLGQIL 125

                         90
                 ....*....|....*
gi 971520639 376 NVNVSERLPRASHWW 390
Cdd:PRK11212 126 DVHVFNRLRQSRAWW 140
 
Name Accession Description Interval E-value
infA CHL00010
translation initiation factor 1
 446-517 5.18e-39

translation initiation factor 1


Pssm-ID: 214332  Cd Length: 78  Bit Score: 137.05  E-value: 5.18e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 971520639 446 KKQSAMIEMEGEVQKALPNAMFQVALDNGCQVLAHISGKIRRNRIEIFQGDRVKVEISPYDLTRGRITHRNR 517
Cdd:CHL00010   1 MKKENKIEMEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLR 72
infA PRK00276
translation initiation factor IF-1; Validated
 450-517 1.29e-37

translation initiation factor IF-1; Validated


Pssm-ID: 178954  Cd Length: 72  Bit Score: 132.97  E-value: 1.29e-37
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 971520639 450 AMIEMEGEVQKALPNAMFQVALDNGCQVLAHISGKIRRNRIEIFQGDRVKVEISPYDLTRGRITHRNR 517
Cdd:PRK00276   5 DVIEMEGTVVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITYRHK 72
S1_IF1 cd04451
S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like ...
 452-515 4.10e-35

S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of the mRNA.


Pssm-ID: 239898  Cd Length: 64  Bit Score: 125.71  E-value: 4.10e-35
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 971520639 452 IEMEGEVQKALPNAMFQVALDNGCQVLAHISGKIRRNRIEIFQGDRVKVEISPYDLTRGRITHR 515
Cdd:cd04451    1 IEMEGVVTEALPNAMFRVELENGHEVLAHISGKMRMNYIRILPGDRVKVELSPYDLTKGRIVYR 64
infA TIGR00008
translation initiation factor IF-1; This family consists of translation initiation factor IF-1 ...
 452-515 8.71e-33

translation initiation factor IF-1; This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575). [Protein synthesis, Translation factors]


Pssm-ID: 188015  Cd Length: 69  Bit Score: 119.75  E-value: 8.71e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 971520639  452 IEMEGEVQKALPNAMFQVALDNGCQVLAHISGKIRRNRIEIFQGDRVKVEISPYDLTRGRITHR 515
Cdd:TIGR00008   5 IEMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDRVKVELSPYDLTRGRITYR 68
InfA COG0361
Translation initiation factor IF-1 [Translation, ribosomal structure and biogenesis]; ...
 452-515 1.25e-32

Translation initiation factor IF-1 [Translation, ribosomal structure and biogenesis]; Translation initiation factor IF-1 is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440130  Cd Length: 73  Bit Score: 119.44  E-value: 1.25e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 971520639 452 IEMEGEVQKALPNAMFQVALDNGCQVLAHISGKIRRNRIEIFQGDRVKVEISPYDLTRGRITHR 515
Cdd:COG0361    8 IEVEGVVEEVLPNARFRVRLENGHERLARISGKMRKNRIRILPGDRVLVEPSPYDLTKGRIVYR 71
eIF-1a pfam01176
Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation ...
 453-515 4.73e-26

Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.


Pssm-ID: 460099  Cd Length: 62  Bit Score: 100.54  E-value: 4.73e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 971520639  453 EMEGEVQKALPNAMFQVALDNGCQVLAHISGKIrRNRIEIFQGDRVKVEISPYDLTRGRITHR 515
Cdd:pfam01176   1 EVIGKVVEALGNNLFEVELDNGHTRLAHIPGKM-RNRIWIKRGDYVLVEPSPYDLTKGRIVYR 62
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
454-512 2.39e-07

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.98  E-value: 2.39e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 971520639   454 MEGEVQKALPNAMFqVALDNGCQVLAHIS----GKIRRNRIEIFQGDRVKVEISPYDLTRGRI 512
Cdd:smart00316   6 VEGTVTEITPGGAF-VDLGNGVEGLIPISelsdKRVKDPEEVLKVGDEVKVKVLSVDEEKGRI 67
S1_IF1A cd05793
S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A ...
 453-515 5.67e-06

S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.


Pssm-ID: 240219  Cd Length: 77  Bit Score: 44.44  E-value: 5.67e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 971520639 453 EMEGEVQKALPNAMFQVALDNGCQVLAHISGKIRRnRIEIFQGDRVKVEISPYDLTRGRITHR 515
Cdd:cd05793    1 EEYGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMRK-RVWINEGDIVLVAPWDFQDDKADIIYK 62
eIF1a smart00652
eukaryotic translation initiation factor 1A;
453-518 3.12e-05

eukaryotic translation initiation factor 1A;


Pssm-ID: 128900  Cd Length: 83  Bit Score: 42.24  E-value: 3.12e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 971520639   453 EMEGEVQKALPNAMFQVALDNGCQVLAHISGKIrRNRIEIFQGDRVKVEISPYDLTRGRITHRNRR 518
Cdd:smart00652   6 QEIAQVVKMLGNGRLEVMCADGKERLARIPGKM-RKKVWIRRGDIVLVDPWDFQDVKADIIYKYTK 70
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 455-512 1.20e-04

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 40.06  E-value: 1.20e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 971520639 455 EGEVQKALPNAMFqVALDNGCQVLAHIS----GKIRRNRIEIFQGDRVKVEISPYDLTRGRI 512
Cdd:cd00164    2 TGKVVSITKFGVF-VELEDGVEGLVHISelsdKFVKDPSEVFKVGDEVEVKVLEVDPEKGRI 62
PRK11212 PRK11212
7-cyano-7-deazaguanine/7-aminomethyl-7-deazaguanine transporter;
316-390 3.78e-03

7-cyano-7-deazaguanine/7-aminomethyl-7-deazaguanine transporter;


Pssm-ID: 183041  Cd Length: 210  Bit Score: 38.76  E-value: 3.78e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971520639 316 ALAYPALFLQTGILASEQGAERARQAALWSLPPALLVSSC---------FMGW-----------RVAAASAAAFLTAQLV 375
Cdd:PRK11212  46 AFSFPFIFLATDLTVRIFGAPLARRIIFAVMLPALLISYVisvlfyqgsWQGFaalaefnlfvaRIALASFMAYVLGQIL 125

                         90
                 ....*....|....*
gi 971520639 376 NVNVSERLPRASHWW 390
Cdd:PRK11212 126 DVHVFNRLRQSRAWW 140
 
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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