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Conserved domains on  [gi|1086009861|emb|SDU75869|]
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alginate biosynthesis protein Alg44 [Pseudomonas moraviensis]

Protein Classification

alginate biosynthesis protein Alg44( domain architecture ID 10537884)

alginate biosynthesis protein Alg44 is required for alginate biosynthesis; it binds bis-(3',5')-cyclic dimeric guanosine monophosphate (c-di-GMP) through its PilZ domain and regulates alginate secretion

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PilZ pfam07238
PilZ domain; PilZ is a c-di-GMP binding domain found in widespread cytoplasmic receptors, ...
 16-115 6.10e-13

PilZ domain; PilZ is a c-di-GMP binding domain found in widespread cytoplasmic receptors, which is involved in regulation of motility, biofilm formation and virulence of many bacterial pathogens. This domain binds c-di-GMP through RXXXR and [D/N]hSXXG motifs, however, some PilZ domains lack these motifs and do not bind c-di-GMP. Proteins which contain PilZ are known to interact with the flagellar switch-complex proteins FliG and FliM. This interaction results in a reduction of torque generation and induces CCW motor bias. This is the canonical PilZ domain whose structure consists of six beta-strands that form a beta barrel, followed by a long C-terminal alpha-helix.


:

Pssm-ID: 399904  Cd Length: 102  Bit Score: 64.44  E-value: 6.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1086009861  16 QRQHARVKIPAKLRFFGPDRTpLEARVLDLSAGGLAFNAGQMPLTIGEVYKARLQFVIDNLGLAMDVELQVRSFDRATGR 95
Cdd:pfam07238   2 RRRFPRVPVSLPVTLRDGGGE-YKGRLIDISLGGAAIRLPDEPLALGDRVELSLDLLDDGQELALPGRVVRIRPDEDGAR 80

                          90       100
                  ....*....|....*....|
gi 1086009861  96 AGCQFQNLEPQDISTLRHLI 115
Cdd:pfam07238  81 VGVQFLDLDEEQRRLLVRLL 100
EmrA super family cl34307
Multidrug resistance efflux pump EmrA [Defense mechanisms];
262-369 4.04e-10

Multidrug resistance efflux pump EmrA [Defense mechanisms];


The actual alignment was detected with superfamily member COG1566:

Pssm-ID: 441174 [Multi-domain]  Cd Length: 331  Bit Score: 60.45  E-value: 4.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1086009861 262 TLTSPCDCTVAQQLVADGQYASKGDVIFQLVPRNtQANVEARFSYRQFGDVRPGTPVSFQI-AGEDKTRTGKiVSSTSLK 340
Cdd:COG1566   209 TIRAPVDGVVTNLNVEPGEVVSAGQPLLTIVPLD-DLWVEAYVPETDLGRVKPGQPVEVRVdAYPDRVFEGK-VTSISPG 286

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1086009861 341 SADLSSD----------IRVQIQPDEPLDSSL-AGRPVEV 369
Cdd:COG1566   287 AGFTSPPknatgnvvqrYPVRIRLDNPDPEPLrPGMSATV 326
 
Name Accession Description Interval E-value
PilZ pfam07238
PilZ domain; PilZ is a c-di-GMP binding domain found in widespread cytoplasmic receptors, ...
 16-115 6.10e-13

PilZ domain; PilZ is a c-di-GMP binding domain found in widespread cytoplasmic receptors, which is involved in regulation of motility, biofilm formation and virulence of many bacterial pathogens. This domain binds c-di-GMP through RXXXR and [D/N]hSXXG motifs, however, some PilZ domains lack these motifs and do not bind c-di-GMP. Proteins which contain PilZ are known to interact with the flagellar switch-complex proteins FliG and FliM. This interaction results in a reduction of torque generation and induces CCW motor bias. This is the canonical PilZ domain whose structure consists of six beta-strands that form a beta barrel, followed by a long C-terminal alpha-helix.


Pssm-ID: 399904  Cd Length: 102  Bit Score: 64.44  E-value: 6.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1086009861  16 QRQHARVKIPAKLRFFGPDRTpLEARVLDLSAGGLAFNAGQMPLTIGEVYKARLQFVIDNLGLAMDVELQVRSFDRATGR 95
Cdd:pfam07238   2 RRRFPRVPVSLPVTLRDGGGE-YKGRLIDISLGGAAIRLPDEPLALGDRVELSLDLLDDGQELALPGRVVRIRPDEDGAR 80

                          90       100
                  ....*....|....*....|
gi 1086009861  96 AGCQFQNLEPQDISTLRHLI 115
Cdd:pfam07238  81 VGVQFLDLDEEQRRLLVRLL 100
YcgR COG5581
Cyclic di-GMP-binding flagellar brake protein FlgZ/YcgR, contains PilZNR(YcgR) and PilZ ...
 17-116 6.33e-12

Cyclic di-GMP-binding flagellar brake protein FlgZ/YcgR, contains PilZNR(YcgR) and PilZ domains [Cell motility];


Pssm-ID: 444320 [Multi-domain]  Cd Length: 205  Bit Score: 64.24  E-value: 6.33e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1086009861  17 RQHARVKIP--AKLRFFGPDR--TPLEARVLDLSAGGLAFNA-GQMPLTIGEVYkaRLQFVIDNLGLaMDVELQVRSFDR 91
Cdd:COG5581    89 REYFRVPVPldVPVRCLRPDGegEPLEGRLLDISGGGLALVLpEPPPLEVGDIL--ELRLDLPDEGE-IVVDAEVRRVVE 165

                          90       100       110
                  ....*....|....*....|....*....|
gi 1086009861  92 ATG-----RAGCQFQNLEPQDISTLRHLIT 116
Cdd:COG5581   166 VELgkgkyRLGCEFVDLSEADRRKIQRYIF 195
EmrA COG1566
Multidrug resistance efflux pump EmrA [Defense mechanisms];
262-369 4.04e-10

Multidrug resistance efflux pump EmrA [Defense mechanisms];


Pssm-ID: 441174 [Multi-domain]  Cd Length: 331  Bit Score: 60.45  E-value: 4.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1086009861 262 TLTSPCDCTVAQQLVADGQYASKGDVIFQLVPRNtQANVEARFSYRQFGDVRPGTPVSFQI-AGEDKTRTGKiVSSTSLK 340
Cdd:COG1566   209 TIRAPVDGVVTNLNVEPGEVVSAGQPLLTIVPLD-DLWVEAYVPETDLGRVKPGQPVEVRVdAYPDRVFEGK-VTSISPG 286

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1086009861 341 SADLSSD----------IRVQIQPDEPLDSSL-AGRPVEV 369
Cdd:COG1566   287 AGFTSPPknatgnvvqrYPVRIRLDNPDPEPLrPGMSATV 326
HlyD_3 pfam13437
HlyD family secretion protein; This is a family of largely bacterial haemolysin translocator ...
 262-364 2.18e-07

HlyD family secretion protein; This is a family of largely bacterial haemolysin translocator HlyD proteins.


Pssm-ID: 433206 [Multi-domain]  Cd Length: 104  Bit Score: 48.90  E-value: 2.18e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1086009861 262 TLTSPCDCTVAQQLVADGQYASKGDVIFQLVPRNTQAnVEARFSYRQFGDVRPGTPVSFQI-AGEDKTRTGKIVS-STSL 339
Cdd:pfam13437   1 TIRAPVDGVVAELNVEEGQVVQAGDPLATIVPPDRLL-VEAFVPAADLGSLKKGQKVTLKLdPGSDYTLEGKVVRiSPTV 79

                          90       100
                  ....*....|....*....|....*
gi 1086009861 340 KSADLSSDIRVQIQPDEPLDSSLAG 364
Cdd:pfam13437  80 DPDTGVIPVRVSIENPKTPIPLLPG 104
type_I_hlyD TIGR01843
type I secretion membrane fusion protein, HlyD family; Type I secretion is an ABC transport ...
 262-357 3.08e-04

type I secretion membrane fusion protein, HlyD family; Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins. [Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 130902 [Multi-domain]  Cd Length: 423  Bit Score: 42.69  E-value: 3.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1086009861 262 TLTSPCDCTVAQQLV-ADGQYASKGDVIFQLVPRNTQANVEARFSYRQFGDVRPGTPVSFQIAGEDKTRTGKIVSSTSLK 340
Cdd:TIGR01843 273 IIRSPVDGTVQSLKVhTVGGVVQPGETLMEIVPEDDPLEIEAKLSPKDIGFVHVGQPAEIKFSAFPYRRYGILNGKVKSI 352

                          90       100
                  ....*....|....*....|....
gi 1086009861 341 SADLSSDIR-------VQIQPDEP 357
Cdd:TIGR01843 353 SPDTFTDERgggpyyrVRISIDQN 376
 
Name Accession Description Interval E-value
PilZ pfam07238
PilZ domain; PilZ is a c-di-GMP binding domain found in widespread cytoplasmic receptors, ...
 16-115 6.10e-13

PilZ domain; PilZ is a c-di-GMP binding domain found in widespread cytoplasmic receptors, which is involved in regulation of motility, biofilm formation and virulence of many bacterial pathogens. This domain binds c-di-GMP through RXXXR and [D/N]hSXXG motifs, however, some PilZ domains lack these motifs and do not bind c-di-GMP. Proteins which contain PilZ are known to interact with the flagellar switch-complex proteins FliG and FliM. This interaction results in a reduction of torque generation and induces CCW motor bias. This is the canonical PilZ domain whose structure consists of six beta-strands that form a beta barrel, followed by a long C-terminal alpha-helix.


Pssm-ID: 399904  Cd Length: 102  Bit Score: 64.44  E-value: 6.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1086009861  16 QRQHARVKIPAKLRFFGPDRTpLEARVLDLSAGGLAFNAGQMPLTIGEVYKARLQFVIDNLGLAMDVELQVRSFDRATGR 95
Cdd:pfam07238   2 RRRFPRVPVSLPVTLRDGGGE-YKGRLIDISLGGAAIRLPDEPLALGDRVELSLDLLDDGQELALPGRVVRIRPDEDGAR 80

                          90       100
                  ....*....|....*....|
gi 1086009861  96 AGCQFQNLEPQDISTLRHLI 115
Cdd:pfam07238  81 VGVQFLDLDEEQRRLLVRLL 100
YcgR COG5581
Cyclic di-GMP-binding flagellar brake protein FlgZ/YcgR, contains PilZNR(YcgR) and PilZ ...
 17-116 6.33e-12

Cyclic di-GMP-binding flagellar brake protein FlgZ/YcgR, contains PilZNR(YcgR) and PilZ domains [Cell motility];


Pssm-ID: 444320 [Multi-domain]  Cd Length: 205  Bit Score: 64.24  E-value: 6.33e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1086009861  17 RQHARVKIP--AKLRFFGPDR--TPLEARVLDLSAGGLAFNA-GQMPLTIGEVYkaRLQFVIDNLGLaMDVELQVRSFDR 91
Cdd:COG5581    89 REYFRVPVPldVPVRCLRPDGegEPLEGRLLDISGGGLALVLpEPPPLEVGDIL--ELRLDLPDEGE-IVVDAEVRRVVE 165

                          90       100       110
                  ....*....|....*....|....*....|
gi 1086009861  92 ATG-----RAGCQFQNLEPQDISTLRHLIT 116
Cdd:COG5581   166 VELgkgkyRLGCEFVDLSEADRRKIQRYIF 195
EmrA COG1566
Multidrug resistance efflux pump EmrA [Defense mechanisms];
262-369 4.04e-10

Multidrug resistance efflux pump EmrA [Defense mechanisms];


Pssm-ID: 441174 [Multi-domain]  Cd Length: 331  Bit Score: 60.45  E-value: 4.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1086009861 262 TLTSPCDCTVAQQLVADGQYASKGDVIFQLVPRNtQANVEARFSYRQFGDVRPGTPVSFQI-AGEDKTRTGKiVSSTSLK 340
Cdd:COG1566   209 TIRAPVDGVVTNLNVEPGEVVSAGQPLLTIVPLD-DLWVEAYVPETDLGRVKPGQPVEVRVdAYPDRVFEGK-VTSISPG 286

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1086009861 341 SADLSSD----------IRVQIQPDEPLDSSL-AGRPVEV 369
Cdd:COG1566   287 AGFTSPPknatgnvvqrYPVRIRLDNPDPEPLrPGMSATV 326
HlyD_3 pfam13437
HlyD family secretion protein; This is a family of largely bacterial haemolysin translocator ...
 262-364 2.18e-07

HlyD family secretion protein; This is a family of largely bacterial haemolysin translocator HlyD proteins.


Pssm-ID: 433206 [Multi-domain]  Cd Length: 104  Bit Score: 48.90  E-value: 2.18e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1086009861 262 TLTSPCDCTVAQQLVADGQYASKGDVIFQLVPRNTQAnVEARFSYRQFGDVRPGTPVSFQI-AGEDKTRTGKIVS-STSL 339
Cdd:pfam13437   1 TIRAPVDGVVAELNVEEGQVVQAGDPLATIVPPDRLL-VEAFVPAADLGSLKKGQKVTLKLdPGSDYTLEGKVVRiSPTV 79

                          90       100
                  ....*....|....*....|....*
gi 1086009861 340 KSADLSSDIRVQIQPDEPLDSSLAG 364
Cdd:pfam13437  80 DPDTGVIPVRVSIENPKTPIPLLPG 104
AcrA COG0845
Multidrug efflux pump subunit AcrA (membrane-fusion protein) [Cell wall/membrane/envelope ...
 262-335 2.12e-05

Multidrug efflux pump subunit AcrA (membrane-fusion protein) [Cell wall/membrane/envelope biogenesis, Defense mechanisms];


Pssm-ID: 440606 [Multi-domain]  Cd Length: 324  Bit Score: 46.09  E-value: 2.12e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1086009861 262 TLTSPCDCTVAQQLVADGQYASKGDVIFQLVpRNTQANVEARFSYRQFGDVRPGTPVSFQI-AGEDKTRTGKIVS 335
Cdd:COG0845   133 TIRAPFDGVVGERNVEPGQLVSAGTPLFTIA-DLDPLEVEFDVPESDLARLKVGQPVTVTLdAGPGKTFEGKVTF 206
type_I_hlyD TIGR01843
type I secretion membrane fusion protein, HlyD family; Type I secretion is an ABC transport ...
 262-357 3.08e-04

type I secretion membrane fusion protein, HlyD family; Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins. [Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 130902 [Multi-domain]  Cd Length: 423  Bit Score: 42.69  E-value: 3.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1086009861 262 TLTSPCDCTVAQQLV-ADGQYASKGDVIFQLVPRNTQANVEARFSYRQFGDVRPGTPVSFQIAGEDKTRTGKIVSSTSLK 340
Cdd:TIGR01843 273 IIRSPVDGTVQSLKVhTVGGVVQPGETLMEIVPEDDPLEIEAKLSPKDIGFVHVGQPAEIKFSAFPYRRYGILNGKVKSI 352

                          90       100
                  ....*....|....*....|....
gi 1086009861 341 SADLSSDIR-------VQIQPDEP 357
Cdd:TIGR01843 353 SPDTFTDERgggpyyrVRISIDQN 376
HlyD_D23 pfam16576
Barrel-sandwich domain of CusB or HlyD membrane-fusion; HlyD_D23 is the combined domains 2 and ...
 262-333 9.69e-04

Barrel-sandwich domain of CusB or HlyD membrane-fusion; HlyD_D23 is the combined domains 2 and 3 of the membrane-fusion proteins CusB and HlyD, which forms a barrel-sandwich. CusB and HlyD proteins are membrane fusion proteins of the CusCFBA copper efflux system in E.coli and related bacteria. The whole molecule hinges between D2 and D3. Efflux systems of this resistance-nodulation-division group - RND - have been developed to excrete poisonous metal ions, and in E.coli the only one that deals with silver and copper is the CusA transporter. The transporter CusA works in conjunction with a periplasmic component that is a membrane fusion protein, eg CusB, and an outer-membrane channel component CusC in a CusABC complex driven by import of protons.


Pssm-ID: 435440 [Multi-domain]  Cd Length: 214  Bit Score: 40.18  E-value: 9.69e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1086009861 262 TLTSPCDCTVAQQLVADGQYASKGDVIFQLVPRNT---QANV-EarfsyRQFGDVRPGTPVSFQI-AGEDKTRTGKI 333
Cdd:pfam16576 110 TVYAPISGVVTELNVREGMYVQPGDTLFTIADLSTvwvEADVpE-----QDLALVKVGQPAEVTLpALPGKTFEGKV 181
 
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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