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Conserved domains on  [gi|556488211|ref|WP_023335944|]
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MULTISPECIES: lipopolysaccharide assembly protein LapB [Enterobacter]

Protein Classification

lipopolysaccharide assembly protein LapB( domain architecture ID 11485508)

lipopolysaccharide assembly protein LapB is a tetratricopeptide repeat (TPR) protein that modulates cellular lipopolysaccharide (LPS) levels by regulating LpxC, which is involved in lipid A biosynthesis

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11788 PRK11788
tetratricopeptide repeat protein; Provisional
 10-389 0e+00

tetratricopeptide repeat protein; Provisional


:

Pssm-ID: 236983 [Multi-domain]  Cd Length: 389  Bit Score: 644.94  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  10 PVAAAYGWYMGRRSAQQTKQDEANRLSRDYVAGVNFLLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAI 89
Cdd:PRK11788  10 PVAAAYGWYMGRRSARQDQQKESNRLSRDYFKGLNFLLNEQPDKAIDLFIEMLKVDPETVELHLALGNLFRRRGEVDRAI 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  90 RIHQTLMESASLTYDQRLLAVQQLGRDYMAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVK 169
Cdd:PRK11788  90 RIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLDRAEELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEK 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 170 LGKDKQRVEIAHFYCELALQQMGNDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIDQDKELVS 249
Cdd:PRK11788 170 LGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKALAADPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLS 249

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 250 ETLEMLQTCYQQLDKQEEWVAFLRRCVEENTGATAELMLSDVVEQYEGSDTAQVYITRQLQRHPTMRVFHKLMDYHLNDA 329
Cdd:PRK11788 250 EVLPKLMECYQALGDEAEGLEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLRGFHRLLDYHLAEA 329

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 330 EEGRAKESLMVLRDMVGEQVRSKPRYRCQKCGFTAYTLYWHCPSCRAWSTIKPIRGLDGQ 389
Cdd:PRK11788 330 EEGRAKESLLLLRDLVGEQLKRKPRYRCRNCGFTARTLYWHCPSCKAWETIKPIRGLDGE 389
 
Name Accession Description Interval E-value
PRK11788 PRK11788
tetratricopeptide repeat protein; Provisional
 10-389 0e+00

tetratricopeptide repeat protein; Provisional


Pssm-ID: 236983 [Multi-domain]  Cd Length: 389  Bit Score: 644.94  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  10 PVAAAYGWYMGRRSAQQTKQDEANRLSRDYVAGVNFLLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAI 89
Cdd:PRK11788  10 PVAAAYGWYMGRRSARQDQQKESNRLSRDYFKGLNFLLNEQPDKAIDLFIEMLKVDPETVELHLALGNLFRRRGEVDRAI 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  90 RIHQTLMESASLTYDQRLLAVQQLGRDYMAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVK 169
Cdd:PRK11788  90 RIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLDRAEELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEK 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 170 LGKDKQRVEIAHFYCELALQQMGNDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIDQDKELVS 249
Cdd:PRK11788 170 LGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKALAADPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLS 249

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 250 ETLEMLQTCYQQLDKQEEWVAFLRRCVEENTGATAELMLSDVVEQYEGSDTAQVYITRQLQRHPTMRVFHKLMDYHLNDA 329
Cdd:PRK11788 250 EVLPKLMECYQALGDEAEGLEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLRGFHRLLDYHLAEA 329

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 330 EEGRAKESLMVLRDMVGEQVRSKPRYRCQKCGFTAYTLYWHCPSCRAWSTIKPIRGLDGQ 389
Cdd:PRK11788 330 EEGRAKESLLLLRDLVGEQLKRKPRYRCRNCGFTARTLYWHCPSCKAWETIKPIRGLDGE 389
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 10-312 3.76e-84

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: 257.35  E-value: 3.76e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  10 PVAAAYGWYMgrrsaqqtkqdeanrlsrdyvAGVNFLLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAI 89
Cdd:COG2956    4 PVAAALGWYF---------------------KGLNYLLNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAI 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  90 RIHQTLMESAsltyDQRLLAVQQLGRDYMAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVK 169
Cdd:COG2956   63 RIHQKLLERD----PDRAEALLELAQDYLKAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLK 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 170 LGKDKqrveiAHFYCELALQQMGNDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIDQDKELVS 249
Cdd:COG2956  139 LGPEN-----AHAYCELAELYLEQGDYDEAIEALEKALKLDPDCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLP 213

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556488211 250 eTLEMLQTCYQQLDKQEEWVAFLRRCVEENTGATAELMLSDVVEQYEGSDTAQVYITRQLQRH 312
Cdd:COG2956  214 -ALPRLAELYEKLGDPEEALELLRKALELDPSDDLLLALADLLERKEGLEAALALLERQLRRH 275
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 21-355 2.47e-12

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: 68.57  E-value: 2.47e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211   21 RRSAQQTKQDEANRLSRDYVAGVNFLLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIRIHQTLMESAS 100
Cdd:TIGR02917 281 RETLQDALKSAPEYLPALLLAGASEYQLGNLEQAYQYLNQILKYAPNSHQARRLLASIQLRLGRVDEAIATLSPALGLDP 360

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  101 LtyDQRLLAVqqLGRDYMAAGLYDRAEDMFAQlVDETDFRIGALQ-QLLQIYQATSDWQKAIDTAERLVKLGKDKQRVEI 179
Cdd:TIGR02917 361 D--DPAALSL--LGEAYLALGDFEKAAEYLAK-ATELDPENAAARtQLGISKLSQGDPSEAIADLETAAQLDPELGRADL 435

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  180 AhfyceLALQQMGNDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIDQDKELVSETLEMLQTCY 259
Cdd:TIGR02917 436 L-----LILSYLRSGQFDKALAAAKKLEKKQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSIEPDFFPAAANLARIDI 510

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  260 QQlDKQEEWVAFLRRCVEEN-TGATAELMLSDVVEQYEGSDTAQVYITRQLQRHPTMRVFHK-LMDYHLndaEEGRAKES 337
Cdd:TIGR02917 511 QE-GNPDDAIQRFEKVLTIDpKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALaLAQYYL---GKGQLKKA 586

                         330
                  ....*....|....*...
gi 556488211  338 LMVLRDMVGEQvRSKPRY 355
Cdd:TIGR02917 587 LAILNEAADAA-PDSPEA 603
Rubredoxin_2 pfam18073
Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found ...
 355-382 8.27e-12

Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found in Interest in lipopolysaccharide (LPS) assembly protein B (LapB). Rubredoxin proteins form small non-heme iron binding sites that use four cysteine residues to coordinate a single metal ion in a tetrahedral environment. Rubredoxins are most commonly found in bacterial systems, but have also been found in eukaryotes. The key features of these rubredoxin-like domains are the extended loops or 'knuckles' and the tetracysteine mode of iron binding. Structural analysis of LapB from Escherichia coli show that the rubredoxin metal binding domain is intimately bound to the TPR motifs and that this association to the TPR motifs is essential to LPS regulation and growth in vivo. Other family members include RadA proteins which play a role in DNA damage repair. In E. coli, a protein known as RadA (or Sms) participates in the recombinational repair of radiation-damaged DNA in a process that uses an undamaged DNA strand in one DNA duplex to fill a DNA strand gap in a homologous sister DNA duplex. RadA carries a zinc finger at the N-terminal domain.


Pssm-ID: 436248 [Multi-domain]  Cd Length: 28  Bit Score: 59.09  E-value: 8.27e-12
                          10        20
                  ....*....|....*....|....*...
gi 556488211  355 YRCQKCGFTAYTLYWHCPSCRAWSTIKP 382
Cdd:pfam18073   1 YRCSQCGFESPQWFGRCPSCGSWGTLVE 28
 
Name Accession Description Interval E-value
PRK11788 PRK11788
tetratricopeptide repeat protein; Provisional
 10-389 0e+00

tetratricopeptide repeat protein; Provisional


Pssm-ID: 236983 [Multi-domain]  Cd Length: 389  Bit Score: 644.94  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  10 PVAAAYGWYMGRRSAQQTKQDEANRLSRDYVAGVNFLLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAI 89
Cdd:PRK11788  10 PVAAAYGWYMGRRSARQDQQKESNRLSRDYFKGLNFLLNEQPDKAIDLFIEMLKVDPETVELHLALGNLFRRRGEVDRAI 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  90 RIHQTLMESASLTYDQRLLAVQQLGRDYMAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVK 169
Cdd:PRK11788  90 RIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLDRAEELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEK 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 170 LGKDKQRVEIAHFYCELALQQMGNDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIDQDKELVS 249
Cdd:PRK11788 170 LGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKALAADPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLS 249

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 250 ETLEMLQTCYQQLDKQEEWVAFLRRCVEENTGATAELMLSDVVEQYEGSDTAQVYITRQLQRHPTMRVFHKLMDYHLNDA 329
Cdd:PRK11788 250 EVLPKLMECYQALGDEAEGLEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLRGFHRLLDYHLAEA 329

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 330 EEGRAKESLMVLRDMVGEQVRSKPRYRCQKCGFTAYTLYWHCPSCRAWSTIKPIRGLDGQ 389
Cdd:PRK11788 330 EEGRAKESLLLLRDLVGEQLKRKPRYRCRNCGFTARTLYWHCPSCKAWETIKPIRGLDGE 389
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 10-312 3.76e-84

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: 257.35  E-value: 3.76e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  10 PVAAAYGWYMgrrsaqqtkqdeanrlsrdyvAGVNFLLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAI 89
Cdd:COG2956    4 PVAAALGWYF---------------------KGLNYLLNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAI 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  90 RIHQTLMESAsltyDQRLLAVQQLGRDYMAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVK 169
Cdd:COG2956   63 RIHQKLLERD----PDRAEALLELAQDYLKAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLK 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 170 LGKDKqrveiAHFYCELALQQMGNDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIDQDKELVS 249
Cdd:COG2956  139 LGPEN-----AHAYCELAELYLEQGDYDEAIEALEKALKLDPDCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLP 213

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556488211 250 eTLEMLQTCYQQLDKQEEWVAFLRRCVEENTGATAELMLSDVVEQYEGSDTAQVYITRQLQRH 312
Cdd:COG2956  214 -ALPRLAELYEKLGDPEEALELLRKALELDPSDDLLLALADLLERKEGLEAALALLERQLRRH 275
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 21-355 2.47e-12

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: 68.57  E-value: 2.47e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211   21 RRSAQQTKQDEANRLSRDYVAGVNFLLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIRIHQTLMESAS 100
Cdd:TIGR02917 281 RETLQDALKSAPEYLPALLLAGASEYQLGNLEQAYQYLNQILKYAPNSHQARRLLASIQLRLGRVDEAIATLSPALGLDP 360

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  101 LtyDQRLLAVqqLGRDYMAAGLYDRAEDMFAQlVDETDFRIGALQ-QLLQIYQATSDWQKAIDTAERLVKLGKDKQRVEI 179
Cdd:TIGR02917 361 D--DPAALSL--LGEAYLALGDFEKAAEYLAK-ATELDPENAAARtQLGISKLSQGDPSEAIADLETAAQLDPELGRADL 435

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  180 AhfyceLALQQMGNDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIDQDKELVSETLEMLQTCY 259
Cdd:TIGR02917 436 L-----LILSYLRSGQFDKALAAAKKLEKKQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSIEPDFFPAAANLARIDI 510

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  260 QQlDKQEEWVAFLRRCVEEN-TGATAELMLSDVVEQYEGSDTAQVYITRQLQRHPTMRVFHK-LMDYHLndaEEGRAKES 337
Cdd:TIGR02917 511 QE-GNPDDAIQRFEKVLTIDpKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALaLAQYYL---GKGQLKKA 586

                         330
                  ....*....|....*...
gi 556488211  338 LMVLRDMVGEQvRSKPRY 355
Cdd:TIGR02917 587 LAILNEAADAA-PDSPEA 603
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 104-246 8.06e-12

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 62.52  E-value: 8.06e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 104 DQRLLAVQQLGRDYMAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLgkDKQRVEIAHFY 183
Cdd:COG4783    1 AACAEALYALAQALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALEL--DPDEPEARLNL 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556488211 184 CELALQQmgnDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIDQDKE 246
Cdd:COG4783   79 GLALLKA---GDYDEALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKALELDPD 138
Rubredoxin_2 pfam18073
Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found ...
 355-382 8.27e-12

Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found in Interest in lipopolysaccharide (LPS) assembly protein B (LapB). Rubredoxin proteins form small non-heme iron binding sites that use four cysteine residues to coordinate a single metal ion in a tetrahedral environment. Rubredoxins are most commonly found in bacterial systems, but have also been found in eukaryotes. The key features of these rubredoxin-like domains are the extended loops or 'knuckles' and the tetracysteine mode of iron binding. Structural analysis of LapB from Escherichia coli show that the rubredoxin metal binding domain is intimately bound to the TPR motifs and that this association to the TPR motifs is essential to LPS regulation and growth in vivo. Other family members include RadA proteins which play a role in DNA damage repair. In E. coli, a protein known as RadA (or Sms) participates in the recombinational repair of radiation-damaged DNA in a process that uses an undamaged DNA strand in one DNA duplex to fill a DNA strand gap in a homologous sister DNA duplex. RadA carries a zinc finger at the N-terminal domain.


Pssm-ID: 436248 [Multi-domain]  Cd Length: 28  Bit Score: 59.09  E-value: 8.27e-12
                          10        20
                  ....*....|....*....|....*...
gi 556488211  355 YRCQKCGFTAYTLYWHCPSCRAWSTIKP 382
Cdd:pfam18073   1 YRCSQCGFESPQWFGRCPSCGSWGTLVE 28
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
62-247 8.21e-10

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 58.86  E-value: 8.21e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  62 LKEDTGTVEAHLTLGNLFRSRGEVDRAIRIHQTLMESASLTYDqrllAVQQLGRDYMAAGLYDRAEDMFAQLVDETDFRI 141
Cdd:COG0457    1 LELDPDDAEAYNNLGLAYRRLGRYEEAIEDYEKALELDPDDAE----ALYNLGLAYLRLGRYEEALADYEQALELDPDDA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 142 GALQQLLQIYQATSDWQKAIDTAERLVKLGKDkqrVEIAHFYCELALQQMGndDMDKAMALLKKGAAADRNSARISIMMG 221
Cdd:COG0457   77 EALNNLGLALQALGRYEEALEDYDKALELDPD---DAEALYNLGLALLELG--RYDEAIEAYERALELDPDDADALYNLG 151

                        170       180
                 ....*....|....*....|....*.
gi 556488211 222 RVFMANGDYAKAVESLLRVIDQDKEL 247
Cdd:COG0457  152 IALEKLGRYEEALELLEKLEAAALAA 177
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 32-170 1.88e-09

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 55.58  E-value: 1.88e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  32 ANRLSRDYVAGVNFLLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIRihqtLMESASLTYDQRLLAVQ 111
Cdd:COG4783    1 AACAEALYALAQALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIV----LLHEALELDPDEPEARL 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 556488211 112 QLGRDYMAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKL 170
Cdd:COG4783   77 NLGLALLKAGDYDEALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKALEL 135
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 143-279 4.16e-09

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 54.43  E-value: 4.16e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 143 ALQQLLQIYQATSDWQKAIDTAERLVKLGKDKqrveiAHFYCELALQQMGNDDMDKAMALLKKGAAADRNSARISIMMGR 222
Cdd:COG4783    6 ALYALAQALLLAGDYDEAEALLEKALELDPDN-----PEAFALLGEILLQLGDLDEAIVLLHEALELDPDEPEARLNLGL 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 556488211 223 VFMANGDYAKAVESLLRVIDQDKELVsETLEMLQTCYQQLDKQEEWVAFLRRCVEEN 279
Cdd:COG4783   81 ALLKAGDYDEALALLEKALKLDPEHP-EAYLRLARAYRALGRPDEAIAALEKALELD 136
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 29-311 9.43e-09

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


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 57.31  E-value: 9.43e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  29 QDEANRLSRDYVAGVNFLLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIRIHqtLMESASLTYDQRLL 108
Cdd:COG3914    2 AAAALLALAALAAAALLAAAAAAELALAAELEAAALAAALGLALLLLAALAEAAAAALLALAAG--EAAAAAAALLLLAA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 109 AVQQLGRDYMAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLGKDkqrveIAHFYCELAL 188
Cdd:COG3914   80 LLELAALLLQALGRYEEALALYRRALALNPDNAEALFNLGNLLLALGRLEEALAALRRALALNPD-----FAEAYLNLGE 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 189 QQMGNDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIdqdkELVSETLEMLQTCYQQLDKQEEW 268
Cdd:COG3914  155 ALRRLGRLEEAIAALRRALELDPDNAEALNNLGNALQDLGRLEEAIAAYRRAL----ELDPDNADAHSNLLFALRQACDW 230

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 556488211 269 VAFLRRCVEENTGATAELMLSDVVEQYEGSDTAQVYitRQLQR 311
Cdd:COG3914  231 EVYDRFEELLAALARGPSELSPFALLYLPDDDPAEL--LALAR 271
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 46-234 2.41e-08

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: 55.86  E-value: 2.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211   46 LLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIrihqTLMESASLTYDQRLLAVQQLGRDYMAAGLYDR 125
Cdd:TIGR02917 544 LRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKAL----AILNEAADAAPDSPEAWLMLGRAQLAAGDLNK 619

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  126 AEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLGKDKQRVEIAhfyceLALQQMGNDDMDKAMALLKK 205
Cdd:TIGR02917 620 AVSSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALELKPDNTEAQIG-----LAQLLLAAKRTESAKKIAKS 694

                         170       180
                  ....*....|....*....|....*....
gi 556488211  206 GAAADRNSARISIMMGRVFMANGDYAKAV 234
Cdd:TIGR02917 695 LQKQHPKAALGFELEGDLYLRQKDYPAAI 723
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 12-214 4.64e-08

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


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 55.00  E-value: 4.64e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  12 AAAYGWYMGRRSAQQTKQDEANRLSRDYVAGVNFLLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIRI 91
Cdd:COG3914   55 AAAALLALAAGEAAAAAAALLLLAALLELAALLLQALGRYEEALALYRRALALNPDNAEALFNLGNLLLALGRLEEALAA 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  92 HQTLMESASltydQRLLAVQQLGRDYMAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLg 171
Cdd:COG3914  135 LRRALALNP----DFAEAYLNLGEALRRLGRLEEAIAALRRALELDPDNAEALNNLGNALQDLGRLEEAIAAYRRALEL- 209

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 556488211 172 kDKQRVEIAHFYCELALQQMGNDDMDKAMALLKKGAAADRNSA 214
Cdd:COG3914  210 -DPDNADAHSNLLFALRQACDWEVYDRFEELLAALARGPSELS 251
HemYx COG3071
Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to ...
 82-289 5.97e-08

Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to protoporphyrinogen oxidase HemY) [Function unknown];


Pssm-ID: 442305 [Multi-domain]  Cd Length: 323  Bit Score: 53.76  E-value: 5.97e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  82 RGEVDRAirihQTLMESASLTYDQRLLAVQQL-GRDYMAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKA 160
Cdd:COG3071   63 LGDYERR----DEYLAQALELAPEAELAVLLTrAELLLDQGQAEQALATLEALRAGAPRHPQVLRLLLQAYRQLGDWEEL 138

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 161 IDTAERLVK---LGKDKQRVEIAHFYCELALQQMgnDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESL 237
Cdd:COG3071  139 LELLPALRKhkaLSAEEAQALERRAYLGLLRQAA--RDAEALKALWKALPRAERRDPELAAAYARALIALGDHDEAERLL 216

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 556488211 238 LRVIDQ--DKELVsetlEMLQTCyqQLDKQEEWVAFLRRCVEENtGATAELMLS 289
Cdd:COG3071  217 REALKRqwDPRLV----RLYGRL--QGGDPAKQLKRAEKWLKKH-PNDPDLLLA 263
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
143-350 1.66e-07

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 51.93  E-value: 1.66e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 143 ALQQLLQIYQATSDWQKAIDTAERLVKLGKDkqrVEIAHFYCELALQQMGndDMDKAMALLKKGAAADRNSARISIMMGR 222
Cdd:COG0457   10 AYNNLGLAYRRLGRYEEAIEDYEKALELDPD---DAEALYNLGLAYLRLG--RYEEALADYEQALELDPDDAEALNNLGL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 223 VFMANGDYAKAVESLLRVIDQDKELvSETLEMLQTCYQQLDKQEEWVAFLRRCVEENTG-ATAELMLSDVVEQYEGSDTA 301
Cdd:COG0457   85 ALQALGRYEEALEDYDKALELDPDD-AEALYNLGLALLELGRYDEAIEAYERALELDPDdADALYNLGIALEKLGRYEEA 163

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 556488211 302 QVYITRQLQRHPTMRVFHKLMDYHLNDAEEGRAKESLMVLRDMVGEQVR 350
Cdd:COG0457  164 LELLEKLEAAALAALLAAALGEAALALAAAEVLLALLLALEQALRKKLA 212
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
49-215 4.46e-06

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 47.69  E-value: 4.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  49 NQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIRIHQTLMESASltydQRLLAVQQLGRDYMAAGLYDRAED 128
Cdd:COG0457   22 GRYEEAIEDYEKALELDPDDAEALYNLGLAYLRLGRYEEALADYEQALELDP----DDAEALNNLGLALQALGRYEEALE 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 129 MFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLGKDkqrveIAHFYCELALQQMGNDDMDKAMALLKKGAA 208
Cdd:COG0457   98 DYDKALELDPDDAEALYNLGLALLELGRYDEAIEAYERALELDPD-----DADALYNLGIALEKLGRYEEALELLEKLEA 172


                 ....*..
gi 556488211 209 ADRNSAR 215
Cdd:COG0457  173 AALAALL 179
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 42-244 7.11e-06

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: 48.16  E-value: 7.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211   42 GVNFLLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIRIHQTLMESasltYDQRLLAVQQLGRDYMAAG 121
Cdd:TIGR02917 404 GISKLSQGDPSEAIADLETAAQLDPELGRADLLLILSYLRSGQFDKALAAAKKLEKK----QPDNASLHNLLGAIYLGKG 479

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  122 LYDRAEDMFAQ-LVDETDFrIGALQQLLQIYQATSDWQKAIDTAERLVK------------------------------- 169
Cdd:TIGR02917 480 DLAKAREAFEKaLSIEPDF-FPAAANLARIDIQEGNPDDAIQRFEKVLTidpknlrailalaglylrtgneeeavawlek 558

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556488211  170 -LGKDKQRVEIAhfyceLALQQ--MGNDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIDQD 244
Cdd:TIGR02917 559 aAELNPQEIEPA-----LALAQyyLGKGQLKKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ 631
CpoB COG1729
Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane ...
 115-205 7.47e-06

Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane constriction [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441335 [Multi-domain]  Cd Length: 113  Bit Score: 44.60  E-value: 7.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 115 RDYMAAGLYDRAEDMFAQLVD---ETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLGKDKQRVEIAHFYCELALQQM 191
Cdd:COG1729    1 KALLKAGDYDEAIAAFKAFLKrypNSPLAPDALYWLGEAYYALGDYDEAAEAFEKLLKRYPDSPKAPDALLKLGLSYLEL 80

                         90
                 ....*....|....
gi 556488211 192 GndDMDKAMALLKK 205
Cdd:COG1729   81 G--DYDKARATLEE 92
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 106-245 8.36e-06

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: 45.34  E-value: 8.36e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 106 RLLAVQQLGRDYMAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLGKDKqrveiAHFYCE 185
Cdd:COG5010   19 KLRTLVEKYEAALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYNKLGDFEESLALLEQALQLDPNN-----PELYYN 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 186 LALQQMGNDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIDQDK 245
Cdd:COG5010   94 LALLYSRSGDKDEAKEYYEKALALSPDNPNAYSNLAALLLSLGQDDEAKAALQRALGTSP 153
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 49-338 4.66e-05

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: 45.46  E-value: 4.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211   49 NQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIRIHQTLMESASLTYDQRLLAVQQLgrdyMAAGLYDRAED 128
Cdd:TIGR02917 173 NRFDEARALIDEVLTADPGNVDALLLKGDLLLSLGNIELALAAYRKAIALRPNNIAVLLALATIL----IEAGEFEEAEK 248

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  129 MFAQLVDETDFRIGA--LQQLLQiYQAtSDWQKAIDTAERLVKLGKD----KQRVEIAHFYCE----------------- 185
Cdd:TIGR02917 249 HADALLKKAPNSPLAhyLKALVD-FQK-KNYEDARETLQDALKSAPEylpaLLLAGASEYQLGnleqayqylnqilkyap 326

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  186 --------LALQQMGNDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIDQDKELVSETLEMLQT 257
Cdd:TIGR02917 327 nshqarrlLASIQLRLGRVDEAIATLSPALGLDPDDPAALSLLGEAYLALGDFEKAAEYLAKATELDPENAAARTQLGIS 406

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  258 CYQQLDKqEEWVAFLRRCVE-ENTGATAELMLSDVVEQYEGSDTAQVYITRQLQRHPTMRVFHKLMDY-HLNDAEEGRAK 335
Cdd:TIGR02917 407 KLSQGDP-SEAIADLETAAQlDPELGRADLLLILSYLRSGQFDKALAAAKKLEKKQPDNASLHNLLGAiYLGKGDLAKAR 485


                  ...
gi 556488211  336 ESL 338
Cdd:TIGR02917 486 EAF 488
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 30-243 5.49e-05

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: 45.46  E-value: 5.49e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211   30 DEANRLSRDYVAGVNFLLSNQ-----QDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIRIHQtlmesASLTYD 104
Cdd:TIGR02917 591 NEAADAAPDSPEAWLMLGRAQlaagdLNKAVSSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLK-----RALELK 665

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  105 QRLLAVQQ-LGRDYMAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLGKDKQRVeiahfy 183
Cdd:TIGR02917 666 PDNTEAQIgLAQLLLAAKRTESAKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNA------ 739

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  184 CELALQQMGNDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVeSLLRVIDQ 243
Cdd:TIGR02917 740 IKLHRALLASGNTAEAVKTLEAWLKTHPNDAVLRTALAELYLAQKDYDKAI-KHYQTVVK 798
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 112-205 5.64e-05

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: 42.69  E-value: 5.64e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 112 QLGRDYMAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLGKDKQRveiAHFYceLALQQM 191
Cdd:COG4235   22 LLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERALALDPDNPE---ALYL--LGLAAF 96

                         90
                 ....*....|....
gi 556488211 192 GNDDMDKAMALLKK 205
Cdd:COG4235   97 QQGDYAEAIAAWQK 110
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 183-294 9.58e-05

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: 41.92  E-value: 9.58e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 183 YCELALQQMGNDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIDQDKELVsETLEMLQTCYQQL 262
Cdd:COG4235   20 WLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERALALDPDNP-EALYLLGLAAFQQ 98

                         90       100       110
                 ....*....|....*....|....*....|..
gi 556488211 263 DKQEEWVAFLRRCVEENTGATAELMLSDVVEQ 294
Cdd:COG4235   99 GDYAEAIAAWQKLLALLPADAPARLLEASIAE 130
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
52-216 1.54e-04

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 43.07  E-value: 1.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  52 DKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIRIHQTLMESASLTYDqrllAVQQLGRDYMAAGLYDRAEDMFA 131
Cdd:COG0457   59 EEALADYEQALELDPDDAEALNNLGLALQALGRYEEALEDYDKALELDPDDAE----ALYNLGLALLELGRYDEAIEAYE 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 132 QLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLGKDKQRVEIAHFYCELALQQMGNDDMDKAMALLKKGAAADR 211
Cdd:COG0457  135 RALELDPDDADALYNLGIALEKLGRYEEALELLEKLEAAALAALLAAALGEAALALAAAEVLLALLLALEQALRKKLAIL 214


                 ....*
gi 556488211 212 NSARI 216
Cdd:COG0457  215 TLAAL 219
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
150-247 1.92e-04

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 40.15  E-value: 1.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 150 IYQATSDWQKAIDTAERLVKLGKDkqrveIAHFYCELALQQMGNDDMDKAMALlKKGAAADRNSARISIMMGRVFMANGD 229
Cdd:COG3063    1 LYLKLGDLEEAEEYYEKALELDPD-----NADALNNLGLLLLEQGRYDEAIAL-EKALKLDPNNAEALLNLAELLLELGD 74

                         90
                 ....*....|....*...
gi 556488211 230 YAKAVESLLRVIDQDKEL 247
Cdd:COG3063   75 YDEALAYLERALELDPSA 92
COG4700 COG4700
Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown];
102-195 2.78e-04

Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown];


Pssm-ID: 443735 [Multi-domain]  Cd Length: 249  Bit Score: 42.18  E-value: 2.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 102 TYDQRLlavqQLGRDYMAAGLYDRAEDMFAQ-LVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLGKDKQRVEiA 180
Cdd:COG4700   88 TVQNRV----RLADALLELGRYDEAIELYEEaLTGIFADDPHILLGLAQALFELGRYAEALETLEKLIAKNPDFKSSD-A 162

                         90
                 ....*....|....*
gi 556488211 181 HFYCELALQQMGNDD 195
Cdd:COG4700  163 HLLYARALEALGDLE 177
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 53-170 3.22e-04

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: 40.37  E-value: 3.22e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  53 KAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIRIHQTLMESAsltyDQRLLAVQQLGRDYMAAGLYDRAEDMFAQ 132
Cdd:COG4235    1 EAIARLRQALAANPNDAEGWLLLGRAYLRLGRYDEALAAYEKALRLD----PDNADALLDLAEALLAAGDTEEAEELLER 76

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 556488211 133 LVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKL 170
Cdd:COG4235   77 ALALDPDNPEALYLLGLAAFQQGDYAEAIAAWQKLLAL 114
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 24-256 3.81e-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: 3.81e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211   24 AQQTKQDeANRLSRDYVAGVnFLLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIRihqtLMESASLTY 103
Cdd:TIGR02917 456 KLEKKQP-DNASLHNLLGAI-YLGKGDLAKAREAFEKALSIEPDFFPAAANLARIDIQEGNPDDAIQ----RFEKVLTID 529

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  104 DQRLLAVQQLGRDYMAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLGKDKQRveiahFY 183
Cdd:TIGR02917 530 PKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADAAPDSPE-----AW 604

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556488211  184 CELALQQMGNDDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIDQDKELVSETLEMLQ 256
Cdd:TIGR02917 605 LMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALELKPDNTEAQIGLAQ 677
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 131-279 4.88e-04

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: 40.33  E-value: 4.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 131 AQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLGKDKQRVEIAHFYCELALQQMGndDMDKAMALLKKGAAAD 210
Cdd:COG5010    7 FDRLPLYLLLLTKLRTLVEKYEAALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYNKLG--DFEESLALLEQALQLD 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556488211 211 RNSARISIMMGRVFMANGDYAKAVESLLRVIDQDKELvSETLEMLQTCYQQLDKQEEWVAFLRRCVEEN 279
Cdd:COG5010   85 PNNPELYYNLALLYSRSGDKDEAKEYYEKALALSPDN-PNAYSNLAALLLSLGQDDEAKAALQRALGTS 152
TPR_hemY_coli TIGR00540
heme biosynthesis-associated TPR protein; Members of this protein family are uncharacterized ...
 118-239 5.40e-04

heme biosynthesis-associated TPR protein; Members of this protein family are uncharacterized tetratricopeptide repeat (TPR) proteins invariably found in heme biosynthesis gene clusters. The absence of any invariant residues other than Ala argues against this protein serving as an enzyme per se. The gene symbol hemY assigned in E. coli is unfortunate in that an unrelated protein, protoporphyrinogen oxidase (HemG in E. coli) is designated HemY in Bacillus subtilis. [Unknown function, General]


Pssm-ID: 273126 [Multi-domain]  Cd Length: 367  Bit Score: 41.89  E-value: 5.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  118 MAAGLYDRAEDMFAQLVDETDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLG--KDKQRVEIAHFYCELALQQMGNDD 195
Cdd:TIGR00540 145 LDQRDYEAALAALDSLQAQAPRHTAVLRLALRAYQRSGNWDALLKLLPALRKAKalSPEEAARLEQQAYIGLLDEAREED 224

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 556488211  196 MDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAvESLLR 239
Cdd:TIGR00540 225 ADALKTWWKQLPRAERQEPELAVAAAEALIQLGDHDEA-EKLIE 267
Sms COG1066
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and ...
 350-380 6.35e-04

DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and repair];


Pssm-ID: 440685 [Multi-domain]  Cd Length: 453  Bit Score: 41.57  E-value: 6.35e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 556488211 350 RSKPRYRCQKCGFTayTLYWH--CPSCRAWSTI 380
Cdd:COG1066    3 KTKTVYVCQECGYE--SPKWLgrCPECGAWNTL 33
PRK11447 PRK11447
cellulose synthase subunit BcsC; Provisional
 104-313 1.86e-03

cellulose synthase subunit BcsC; Provisional


Pssm-ID: 183140 [Multi-domain]  Cd Length: 1157  Bit Score: 40.45  E-value: 1.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  104 DQRLLAVQQLGRDymAAGLYDRAEDMFAQLVDE--TDFRIGALQQLLQIYQATSDWQKAIDTAERLVKLGKD---KQRVE 178
Cdd:PRK11447  198 DEGFAVLEQMAKS--PAGRDAAAQLWYGQIKDMpvSDASVAALQKYLQVFSDGDSVAAARSQLAEQQKQLADpafRARAQ 275

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  179 iahfycELALQQMGNDDmdKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAV-------------------ESLLR 239
Cdd:PRK11447  276 ------GLAAVDSGQGG--KAIPELQQAVRANPKDSEALGALGQAYSQQGDRARAVaqfekalaldphssnrdkwESLLK 347

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  240 V------IDQ-DKELVSETLEMLQTCYQQLDKQEewvaflrrcveeNTGATAELMLSDVVEQYEGSDTAQVYITRQLQRH 312
Cdd:PRK11447  348 VnrywllIQQgDAALKANNLAQAERLYQQARQVD------------NTDSYAVLGLGDVAMARKDYAAAERYYQQALRMD 415


                  .
gi 556488211  313 P 313
Cdd:PRK11447  416 P 416
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
45-135 3.25e-03

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 36.69  E-value: 3.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  45 FLLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIRIHQTLMESASLTYdqrllAVQQLGRDYMAAGLYD 124
Cdd:COG3063    2 YLKLGDLEEAEEYYEKALELDPDNADALNNLGLLLLEQGRYDEAIALEKALKLDPNNAE-----ALLNLAELLLELGDYD 76

                         90
                 ....*....|.
gi 556488211 125 RAEDMFAQLVD 135
Cdd:COG3063   77 EALAYLERALE 87
CpoB COG1729
Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane ...
 43-136 3.25e-03

Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane constriction [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441335 [Multi-domain]  Cd Length: 113  Bit Score: 36.89  E-value: 3.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211  43 VNFLLSNQQDKAVDLFLDMLK---EDTGTVEAHLTLGNLFRSRGEVDRAIRIHQTLMESASlTYDQRLLAVQQLGRDYMA 119
Cdd:COG1729    1 KALLKAGDYDEAIAAFKAFLKrypNSPLAPDALYWLGEAYYALGDYDEAAEAFEKLLKRYP-DSPKAPDALLKLGLSYLE 79

                         90
                 ....*....|....*..
gi 556488211 120 AGLYDRAEDMFAQLVDE 136
Cdd:COG1729   80 LGDYDKARATLEELIKK 96
TPR_19 pfam14559
Tetratricopeptide repeat;
195-246 4.00e-03

Tetratricopeptide repeat;


Pssm-ID: 434038 [Multi-domain]  Cd Length: 65  Bit Score: 35.64  E-value: 4.00e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 556488211  195 DMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVESLLRVIDQDKE 246
Cdd:pfam14559   3 DYAEALELLEQALAEDPDNAEARLGLAEALLALGRLDEAEALLAALPAADPD 54
CpoB COG1729
Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane ...
 193-302 4.27e-03

Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane constriction [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441335 [Multi-domain]  Cd Length: 113  Bit Score: 36.89  E-value: 4.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 193 NDDMDKAMALLKKGAAADRNS---ARISIMMGRVFMANGDYAKAVESLLRVIDQ--DKELVSETLEMLQTCYQQLDKQEE 267
Cdd:COG1729    6 AGDYDEAIAAFKAFLKRYPNSplaPDALYWLGEAYYALGDYDEAAEAFEKLLKRypDSPKAPDALLKLGLSYLELGDYDK 85

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 556488211 268 wvaflrrcveentgatAELMLSDVVEQYEGSDTAQ 302
Cdd:COG1729   86 ----------------ARATLEELIKKYPDSEAAK 104
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
187-279 9.79e-03

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 35.15  E-value: 9.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556488211 187 ALQQMGndDMDKAMALLKKGAAADRNSARISIMMGRVFMANGDYAKAVEsLLRVIDQDKELVsETLEMLQTCYQQLDKQE 266
Cdd:COG3063    1 LYLKLG--DLEEAEEYYEKALELDPDNADALNNLGLLLLEQGRYDEAIA-LEKALKLDPNNA-EALLNLAELLLELGDYD 76

                         90
                 ....*....|...
gi 556488211 267 EWVAFLRRCVEEN 279
Cdd:COG3063   77 EALAYLERALELD 89
 
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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