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Conserved domains on  [gi|334182285|ref|NP_001184905|]
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Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNA14 super family cl34906
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 60-249 4.58e-11

Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification];


The actual alignment was detected with superfamily member COG5107:

Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 66.58  E-value: 4.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285  60 SATDNVAVTAPAAEHGDNTGSTLSTEEERLWNIVRANSLEFNAWTALIDETEriAQDNIAKIRKVYDAFLAEFPLCYGYW 139
Cdd:COG5107    2 SSSTTPDLLYPSADKVAEPSDNIHGDELRLRERIKDNPTNILSYFQLIQYLE--TQESMDAEREMYEQLSSPFPIMEHAW 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285 140 KKFADHEARVGAMDKVVEVYERAVLGVtYSVDIWLHYCTFA--INTYGDPE---TIRRLFERALVYVGTDFLSSPLWDKY 214
Cdd:COG5107   80 RLYMSGELARKDFRSVESLFGRCLKKS-LNLDLWMLYLEYIrrVNNLITGQkrfKIYEAYEFVLGCAIFEPQSENYWDEY 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 334182285 215 IEY-EYM--------QQDWSRVALIYTRILENPIQNLDRYFSSF 249
Cdd:COG5107  159 GLFlEYIeelgkweeQQRIDKIRNGYMRALQTPMGNLEKLWKDY 202
PEP_TPR_lipo super family cl37187
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 464-596 9.96e-04

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


The actual alignment was detected with superfamily member TIGR02917:

Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 42.76  E-value: 9.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285  464 GSADLAENALARATQVF---VKKQPEiHLFA----ARLKEQNGDIAGARAAYQLVhSEISPGLLEAVIKHANMEYRLGNL 536
Cdd:TIGR02917 472 GAIYLGKGDLAKAREAFekaLSIEPD-FFPAaanlARIDIQEGNPDDAIQRFEKV-LTIDPKNLRAILALAGLYLRTGNE 549

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285  537 DDAFSLYEQVIAVEKGKEHstiLPLLYAQYsrfsYLVSRDAEKARRIIVEALDhVQPSKP 596
Cdd:TIGR02917 550 EEAVAWLEKAAELNPQEIE---PALALAQY----YLGKGQLKKALAILNEAAD-AAPDSP 601
Suf super family cl37739
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 186-315 9.65e-03

Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilization and an important role of the GU-rich sequence for this regulation to occur.


The actual alignment was detected with superfamily member pfam05843:

Pssm-ID: 428647 [Multi-domain]  Cd Length: 291  Bit Score: 38.90  E-value: 9.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285  186 DPETIRRLFERALVYVGTDFLSSPLWDKYIEYEYMQQDWSRVALIYTRILE-----NPIQNL-DRYfsSFKELAET--RP 257
Cdd:pfam05843  85 DDNNARVLFERVLTRLAQEKEAKPLWKKFISYESTFGDLASILKLEKRMAElfpedPPLALFvDRY--SFMDLDPItvRE 162

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 334182285  258 LSELRSAEEsaaaavavagdaSESAASESGEKADEGRSQVDGSTEQSPKLESASSTEP 315
Cdd:pfam05843 163 LGSPTYQER------------PKAPLNPVIEQPSSLPPSPVPQAQNSPKRPLSSDDTD 208
 
Name Accession Description Interval E-value
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 60-249 4.58e-11

Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification];


Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 66.58  E-value: 4.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285  60 SATDNVAVTAPAAEHGDNTGSTLSTEEERLWNIVRANSLEFNAWTALIDETEriAQDNIAKIRKVYDAFLAEFPLCYGYW 139
Cdd:COG5107    2 SSSTTPDLLYPSADKVAEPSDNIHGDELRLRERIKDNPTNILSYFQLIQYLE--TQESMDAEREMYEQLSSPFPIMEHAW 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285 140 KKFADHEARVGAMDKVVEVYERAVLGVtYSVDIWLHYCTFA--INTYGDPE---TIRRLFERALVYVGTDFLSSPLWDKY 214
Cdd:COG5107   80 RLYMSGELARKDFRSVESLFGRCLKKS-LNLDLWMLYLEYIrrVNNLITGQkrfKIYEAYEFVLGCAIFEPQSENYWDEY 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 334182285 215 IEY-EYM--------QQDWSRVALIYTRILENPIQNLDRYFSSF 249
Cdd:COG5107  159 GLFlEYIeelgkweeQQRIDKIRNGYMRALQTPMGNLEKLWKDY 202
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 464-596 9.96e-04

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 42.76  E-value: 9.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285  464 GSADLAENALARATQVF---VKKQPEiHLFA----ARLKEQNGDIAGARAAYQLVhSEISPGLLEAVIKHANMEYRLGNL 536
Cdd:TIGR02917 472 GAIYLGKGDLAKAREAFekaLSIEPD-FFPAaanlARIDIQEGNPDDAIQRFEKV-LTIDPKNLRAILALAGLYLRTGNE 549

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285  537 DDAFSLYEQVIAVEKGKEHstiLPLLYAQYsrfsYLVSRDAEKARRIIVEALDhVQPSKP 596
Cdd:TIGR02917 550 EEAVAWLEKAAELNPQEIE---PALALAQY----YLGKGQLKKALAILNEAAD-AAPDSP 601
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 460-589 1.33e-03

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 42.29  E-value: 1.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285 460 MEASGSADLAENALARATQVFVKKQPEIHLFAARLKEQnGDIAGARAAYQLVHsEISPGLLEAVIKHANMEYRLGNLDDA 539
Cdd:COG3914   88 LQALGRYEEALALYRRALALNPDNAEALFNLGNLLLAL-GRLEEALAALRRAL-ALNPDFAEAYLNLGEALRRLGRLEEA 165

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 334182285 540 FSLYEQVIAVEKGkehstiLPLLYAQYSRFsYLVSRDAEKARRIIVEALD 589
Cdd:COG3914  166 IAALRRALELDPD------NAEALNNLGNA-LQDLGRLEEAIAAYRRALE 208
HAT smart00386
HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and ...
 185-218 1.68e-03

HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.


Pssm-ID: 214642 [Multi-domain]  Cd Length: 33  Bit Score: 36.76  E-value: 1.68e-03
                           10        20        30
                   ....*....|....*....|....*....|....
gi 334182285   185 GDPETIRRLFERALVYVGtdfLSSPLWDKYIEYE 218
Cdd:smart00386   1 GDIERARKIYERALEKFP---KSVELWLKYAEFE 31
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 186-315 9.65e-03

Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilization and an important role of the GU-rich sequence for this regulation to occur.


Pssm-ID: 428647 [Multi-domain]  Cd Length: 291  Bit Score: 38.90  E-value: 9.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285  186 DPETIRRLFERALVYVGTDFLSSPLWDKYIEYEYMQQDWSRVALIYTRILE-----NPIQNL-DRYfsSFKELAET--RP 257
Cdd:pfam05843  85 DDNNARVLFERVLTRLAQEKEAKPLWKKFISYESTFGDLASILKLEKRMAElfpedPPLALFvDRY--SFMDLDPItvRE 162

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 334182285  258 LSELRSAEEsaaaavavagdaSESAASESGEKADEGRSQVDGSTEQSPKLESASSTEP 315
Cdd:pfam05843 163 LGSPTYQER------------PKAPLNPVIEQPSSLPPSPVPQAQNSPKRPLSSDDTD 208
 
Name Accession Description Interval E-value
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 60-249 4.58e-11

Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification];


Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 66.58  E-value: 4.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285  60 SATDNVAVTAPAAEHGDNTGSTLSTEEERLWNIVRANSLEFNAWTALIDETEriAQDNIAKIRKVYDAFLAEFPLCYGYW 139
Cdd:COG5107    2 SSSTTPDLLYPSADKVAEPSDNIHGDELRLRERIKDNPTNILSYFQLIQYLE--TQESMDAEREMYEQLSSPFPIMEHAW 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285 140 KKFADHEARVGAMDKVVEVYERAVLGVtYSVDIWLHYCTFA--INTYGDPE---TIRRLFERALVYVGTDFLSSPLWDKY 214
Cdd:COG5107   80 RLYMSGELARKDFRSVESLFGRCLKKS-LNLDLWMLYLEYIrrVNNLITGQkrfKIYEAYEFVLGCAIFEPQSENYWDEY 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 334182285 215 IEY-EYM--------QQDWSRVALIYTRILENPIQNLDRYFSSF 249
Cdd:COG5107  159 GLFlEYIeelgkweeQQRIDKIRNGYMRALQTPMGNLEKLWKDY 202
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 464-596 9.96e-04

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 42.76  E-value: 9.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285  464 GSADLAENALARATQVF---VKKQPEiHLFA----ARLKEQNGDIAGARAAYQLVhSEISPGLLEAVIKHANMEYRLGNL 536
Cdd:TIGR02917 472 GAIYLGKGDLAKAREAFekaLSIEPD-FFPAaanlARIDIQEGNPDDAIQRFEKV-LTIDPKNLRAILALAGLYLRTGNE 549

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285  537 DDAFSLYEQVIAVEKGKEHstiLPLLYAQYsrfsYLVSRDAEKARRIIVEALDhVQPSKP 596
Cdd:TIGR02917 550 EEAVAWLEKAAELNPQEIE---PALALAQY----YLGKGQLKKALAILNEAAD-AAPDSP 601
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 460-589 1.33e-03

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 42.29  E-value: 1.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285 460 MEASGSADLAENALARATQVFVKKQPEIHLFAARLKEQnGDIAGARAAYQLVHsEISPGLLEAVIKHANMEYRLGNLDDA 539
Cdd:COG3914   88 LQALGRYEEALALYRRALALNPDNAEALFNLGNLLLAL-GRLEEALAALRRAL-ALNPDFAEAYLNLGEALRRLGRLEEA 165

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 334182285 540 FSLYEQVIAVEKGkehstiLPLLYAQYSRFsYLVSRDAEKARRIIVEALD 589
Cdd:COG3914  166 IAALRRALELDPD------NAEALNNLGNA-LQDLGRLEEAIAAYRRALE 208
HAT smart00386
HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and ...
 185-218 1.68e-03

HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.


Pssm-ID: 214642 [Multi-domain]  Cd Length: 33  Bit Score: 36.76  E-value: 1.68e-03
                           10        20        30
                   ....*....|....*....|....*....|....
gi 334182285   185 GDPETIRRLFERALVYVGtdfLSSPLWDKYIEYE 218
Cdd:smart00386   1 GDIERARKIYERALEKFP---KSVELWLKYAEFE 31
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 448-549 2.41e-03

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 38.83  E-value: 2.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285 448 NYPEYWIRYVTNMEASGSADLAENALARATQvFVKKQPEIHLFAARLKEQNGDIAGARAAYQLVHsEISPGLLEAVIKHA 527
Cdd:COG4235   15 NDAEGWLLLGRAYLRLGRYDEALAAYEKALR-LDPDNADALLDLAEALLAAGDTEEAEELLERAL-ALDPDNPEALYLLG 92

                         90       100
                 ....*....|....*....|..
gi 334182285 528 NMEYRLGNLDDAFSLYEQVIAV 549
Cdd:COG4235   93 LAAFQQGDYAEAIAAWQKLLAL 114
HAT smart00386
HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and ...
 117-146 2.42e-03

HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.


Pssm-ID: 214642 [Multi-domain]  Cd Length: 33  Bit Score: 35.99  E-value: 2.42e-03
                           10        20        30
                   ....*....|....*....|....*....|
gi 334182285   117 NIAKIRKVYDAFLAEFPLCYGYWKKFADHE 146
Cdd:smart00386   2 DIERARKIYERALEKFPKSVELWLKYAEFE 31
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 464-596 3.52e-03

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 40.10  E-value: 3.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285 464 GSADLAENALARATQVFVK------KQPEIHLFAARLKEQNGDIAGARAAYQLVHsEISPGLLEAVIKHANMEYRLGNLD 537
Cdd:COG2956   15 GLNYLLNGQPDKAIDLLEEaleldpETVEAHLALGNLYRRRGEYDRAIRIHQKLL-ERDPDRAEALLELAQDYLKAGLLD 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 334182285 538 DAFSLYEQviAVEKGKEHSTILPLLYAQYSRfsylvSRDAEKARRiIVEALDHVQPSKP 596
Cdd:COG2956   94 RAEELLEK--LLELDPDDAEALRLLAEIYEQ-----EGDWEKAIE-VLERLLKLGPENA 144
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 462-551 5.44e-03

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 38.40  E-value: 5.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285 462 ASGSADLAENALARATQVFvKKQPEIHLFAARLKEQNGDIAGARAAYQLVHsEISPGLLEAVIKHANMEYRLGNLDDAFS 541
Cdd:COG5010   66 KLGDFEESLALLEQALQLD-PNNPELYYNLALLYSRSGDKDEAKEYYEKAL-ALSPDNPNAYSNLAALLLSLGQDDEAKA 143

                         90
                 ....*....|
gi 334182285 542 LYEQVIAVEK 551
Cdd:COG5010  144 ALQRALGTSP 153
HAT smart00386
HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and ...
 150-182 6.29e-03

HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.


Pssm-ID: 214642 [Multi-domain]  Cd Length: 33  Bit Score: 34.83  E-value: 6.29e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 334182285   150 GAMDKVVEVYERAVLGVTYSVDIWLHYCTFAIN 182
Cdd:smart00386   1 GDIERARKIYERALEKFPKSVELWLKYAEFEER 33
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 459-635 7.11e-03

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 40.07  E-value: 7.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285  459 NMEASGSADLAEnALARATQVFVKKQPEIHLFAARLKEQNGDIAGARAAYQLVhSEISPGLLEAVIKHANMEYRLGNLDD 538
Cdd:TIGR02917 576 YYLGKGQLKKAL-AILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKL-LALQPDSALALLLLADAYAVMKNYAK 653

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285  539 AFSLYEQviAVEKgKEHSTILPLLYAQYsrfsYLVSRDAEKARRII--VEALDHVQPSKPLMEALIHFEAIQPPPREIDY 616
Cdd:TIGR02917 654 AITSLKR--ALEL-KPDNTEAQIGLAQL----LLAAKRTESAKKIAksLQKQHPKAALGFELEGDLYLRQKDYPAAIQAY 726

                         170
                  ....*....|....*....
gi 334182285  617 leplvEKVIKPDADAQNIA 635
Cdd:TIGR02917 727 -----RKALKRAPSSQNAI 740
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 462-623 7.95e-03

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 38.94  E-value: 7.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285 462 ASGSADLAENALARATQVfVKKQPEIHLFAARLKEQNGDIAGARAAYQLVhSEISPGLLEAVIKHANMEYRLGNLDDAFS 541
Cdd:COG2956   88 KAGLLDRAEELLEKLLEL-DPDDAEALRLLAEIYEQEGDWEKAIEVLERL-LKLGPENAHAYCELAELYLEQGDYDEAIE 165

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285 542 LYEQVIAVEKGKEHSTilpLLYAQYsrfsYLVSRDAEKARRIIVEALDHVQPSKPLMEALIH-FEAIQPPPREIDYLEPL 620
Cdd:COG2956  166 ALEKALKLDPDCARAL---LLLAEL----YLEQGDYEEAIAALERALEQDPDYLPALPRLAElYEKLGDPEEALELLRKA 238


                 ...
gi 334182285 621 VEK 623
Cdd:COG2956  239 LEL 241
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 186-315 9.65e-03

Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilization and an important role of the GU-rich sequence for this regulation to occur.


Pssm-ID: 428647 [Multi-domain]  Cd Length: 291  Bit Score: 38.90  E-value: 9.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334182285  186 DPETIRRLFERALVYVGTDFLSSPLWDKYIEYEYMQQDWSRVALIYTRILE-----NPIQNL-DRYfsSFKELAET--RP 257
Cdd:pfam05843  85 DDNNARVLFERVLTRLAQEKEAKPLWKKFISYESTFGDLASILKLEKRMAElfpedPPLALFvDRY--SFMDLDPItvRE 162

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 334182285  258 LSELRSAEEsaaaavavagdaSESAASESGEKADEGRSQVDGSTEQSPKLESASSTEP 315
Cdd:pfam05843 163 LGSPTYQER------------PKAPLNPVIEQPSSLPPSPVPQAQNSPKRPLSSDDTD 208
 
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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