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Conserved domains on  [gi|146134374|ref|NP_001078877|]
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endosome-associated-trafficking regulator 1 isoform 4 [Mus musculus]

Protein Classification

ClyA-like and alpha/beta hydrolases superfamily-containing protein( domain architecture ID 1903979)

ClyA-like and alpha/beta hydrolases superfamily-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SMC_prok_B super family cl37069
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 178-300 8.39e-05

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


The actual alignment was detected with superfamily member TIGR02168:

Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 44.66  E-value: 8.39e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146134374   178 AAHEESLGDRHLRTLQISYEALKDENSKLRRKLNEVQSFSETQTEMVRTLERKLE---AKMIKEESDFHDLESVVQQVEQ 254
Cdd:TIGR02168  251 AEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQilrERLANLERQLEELEAQLEELES 330

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 146134374   255 NLELMTKRAVKAENHVLKLKQEINLLQAQLSNLRRENEALRSGQGA 300
Cdd:TIGR02168  331 KLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEE 376
ClyA-like super family cl45899
family of the cytolysin A (ClyA) family alpha pore-forming toxins (alpha-PFT) including ...
 264-358 1.51e-03

family of the cytolysin A (ClyA) family alpha pore-forming toxins (alpha-PFT) including Bacillus cereus HblB, Aeromonas hydrophila AhlB, Bacillus thuringiensis Cry6Aa and similar proteins; This family belongs to the ClyA family of alpha-PFT bacterial toxins. PFTs form the major group of virulence factors in many pathogenic bacteria and in general are critical components of the molecular offensive and defensive machinery of cells in all kingdoms of life. Bacterial PFTs facilitate the takeover of host resources by puncturing holes in the membrane. PFTs can be classified as alpha-PFTs and beta-PFTs depending on the secondary structures of their membrane component. Alpha-PFTs use a ring of amphipathic helices while beta-PFTs use a beta-barrel to construct the pore. Members of this family include the toxins: Bacillus cereus hemolysin binding component B (HblB or HBL-B) of the diarrheal enterotoxin hemolysin BL, Aeromonas hydrophila hemolytic (Ahl) component B (AhlB) of the tripartite AhlABC toxin, Vibrio cholerae cytotoxin motility associated killing factor A (MakA) cytotoxin, Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA), Bacillus thuringiensis crystal 6Aa (Cry6Aa) parasporal crystal (Cry) toxin, and Bacillus cereus non-hemolytic enterotoxin (Nhe) component A (NheA) of the non-hemolytic enterotoxin Nhe, which, despite its name, is hemolytic, among others. In solution, ClyA proteins have an elongated, almost entirely alpha-helical structure, except for a short hydrophobic beta-hairpin known as the beta-tongue. Pore formation by ClyA requires circular oligomerization of the toxin by a sequential mechanism. This, in turn, concentrates the amphipathic helices in the center of the ring-like structure, forming a helical barrel that inserts into the membrane by a wedge-like mechanism. Compared with ClyA, NheA is almost entirely alpha-helical with an enlarged "head" domain, and an enlarged beta-tongue; it has been proposed that NheA could even form beta-barrel pores. Alpha-PFTs with similar structures are increasingly being found in eukaryotes, in particular as components of the immune systems of animals. This family may be distantly related to Escherichia coli alpha-PFT hemolysin E (HlyE, also known as ClyA or SheA).


The actual alignment was detected with superfamily member cd22657:

Pssm-ID: 459244 [Multi-domain]  Cd Length: 306  Bit Score: 39.88  E-value: 1.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146134374 264 VKAENhVLKLKQEINLLQAQLSNLRRENEALRsgqgASLSVVKQNtdvaLQNLHLVMNSAHASIKQLVsgaDTLNLV-AE 342
Cdd:cd22657  197 VKAEK-IRKERNELIAEREELIQKLKSKNRLL----GSLERLETD----LQDLDIRMIDAEVATKNLE---TVWNTIlTY 264

                         90
                 ....*....|....*.
gi 146134374 343 ILKSIDRISEVKDEVD 358
Cdd:cd22657  265 IDASAEELDKIDDALS 280
 
Name Accession Description Interval E-value
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 178-300 8.39e-05

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 44.66  E-value: 8.39e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146134374   178 AAHEESLGDRHLRTLQISYEALKDENSKLRRKLNEVQSFSETQTEMVRTLERKLE---AKMIKEESDFHDLESVVQQVEQ 254
Cdd:TIGR02168  251 AEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQilrERLANLERQLEELEAQLEELES 330

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 146134374   255 NLELMTKRAVKAENHVLKLKQEINLLQAQLSNLRRENEALRSGQGA 300
Cdd:TIGR02168  331 KLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEE 376
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 220-347 2.17e-04

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 42.83  E-value: 2.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146134374 220 QTEMVRTLERKLEA--KMIKE-ESDFHDLESVVQQVEQNLELMTKRAVKAENHVLKLKQEINLLQAQLSNLRRENEALRS 296
Cdd:COG4942   18 QADAAAEAEAELEQlqQEIAElEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEIAELRA 97

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 146134374 297 gqgaslSVVKQNTDVALQNLHLVMNSAHASIKQLVSGADTLNLV--AEILKSI 347
Cdd:COG4942   98 ------ELEAQKEELAELLRALYRLGRQPPLALLLSPEDFLDAVrrLQYLKYL 144
ClyA_XaxA-like cd22657
Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA) and Yersinia enterocolitica YaxA, and ...
 264-358 1.51e-03

Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA) and Yersinia enterocolitica YaxA, and similar proteins; This model includes Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA) and Yersinia enterocolitica YaxA, both parts of two-component alpha-helical pore-forming toxins (alpha-PFTs). The xaxAB genes encoding the XaxAB toxin have also been also identified in various plant and human pathogens. XaxAB triggers necrosis and apoptosis in both insect hemocytes and mammalian cells. Structure studies show that component A binds to component B's back, forming a subunit; twelve to fifteen of these subunits then conjoin as the pore-forming toxin. Component A stabilizes each subunit on the membrane and activates component B, which then punctures the membrane by swinging out its lower end. Similarly, Yersinia enterocolitica YaxA, encoded by the yaxAB gene, forms a pore predominantly composed of decamers of YaxA-YaxB heterodimers. Although both subunits bear membrane-active moieties, only YaxA is capable of binding to membranes by itself and YaxB is subsequently recruited to membrane-associated YaxA and induced to present its lytic transmembrane helices; pore formation then progresses by further oligomerization of YaxA-YaxB dimers. YaxAB has been found to be strongly upregulated by the Yersinia master regulator RovA, a transcriptional activator of Yersinia outer membrane protein invasion which is involved in bacterial attachment and invasion across the intestinal epithelium.


Pssm-ID: 439155 [Multi-domain]  Cd Length: 306  Bit Score: 39.88  E-value: 1.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146134374 264 VKAENhVLKLKQEINLLQAQLSNLRRENEALRsgqgASLSVVKQNtdvaLQNLHLVMNSAHASIKQLVsgaDTLNLV-AE 342
Cdd:cd22657  197 VKAEK-IRKERNELIAEREELIQKLKSKNRLL----GSLERLETD----LQDLDIRMIDAEVATKNLE---TVWNTIlTY 264

                         90
                 ....*....|....*.
gi 146134374 343 ILKSIDRISEVKDEVD 358
Cdd:cd22657  265 IDASAEELDKIDDALS 280
 
Name Accession Description Interval E-value
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 178-300 8.39e-05

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 44.66  E-value: 8.39e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146134374   178 AAHEESLGDRHLRTLQISYEALKDENSKLRRKLNEVQSFSETQTEMVRTLERKLE---AKMIKEESDFHDLESVVQQVEQ 254
Cdd:TIGR02168  251 AEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQilrERLANLERQLEELEAQLEELES 330

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 146134374   255 NLELMTKRAVKAENHVLKLKQEINLLQAQLSNLRRENEALRSGQGA 300
Cdd:TIGR02168  331 KLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEE 376
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 220-347 2.17e-04

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 42.83  E-value: 2.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146134374 220 QTEMVRTLERKLEA--KMIKE-ESDFHDLESVVQQVEQNLELMTKRAVKAENHVLKLKQEINLLQAQLSNLRRENEALRS 296
Cdd:COG4942   18 QADAAAEAEAELEQlqQEIAElEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEIAELRA 97

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 146134374 297 gqgaslSVVKQNTDVALQNLHLVMNSAHASIKQLVSGADTLNLV--AEILKSI 347
Cdd:COG4942   98 ------ELEAQKEELAELLRALYRLGRQPPLALLLSPEDFLDAVrrLQYLKYL 144
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 197-311 3.01e-04

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 42.75  E-value: 3.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146134374   197 EALKDENSKLRRKLNEVQSFSETQTEMVRTLERKL---EAKMIKEESDFHDLESVVQQVEQNLELMTKRAVKAENHVLKL 273
Cdd:TIGR02169  395 EKLKREINELKRELDRLQEELQRLSEELADLNAAIagiEAKINELEEEKEDKALEIKKQEWKLEQLAADLSKYEQELYDL 474

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 146134374   274 KQEINLLQAQLSNLRRENEALRSGQGASLSVVKQNTDV 311
Cdd:TIGR02169  475 KEEYDRVEKELSKLQRELAEAEAQARASEERVRGGRAV 512
ClyA_XaxA-like cd22657
Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA) and Yersinia enterocolitica YaxA, and ...
 264-358 1.51e-03

Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA) and Yersinia enterocolitica YaxA, and similar proteins; This model includes Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA) and Yersinia enterocolitica YaxA, both parts of two-component alpha-helical pore-forming toxins (alpha-PFTs). The xaxAB genes encoding the XaxAB toxin have also been also identified in various plant and human pathogens. XaxAB triggers necrosis and apoptosis in both insect hemocytes and mammalian cells. Structure studies show that component A binds to component B's back, forming a subunit; twelve to fifteen of these subunits then conjoin as the pore-forming toxin. Component A stabilizes each subunit on the membrane and activates component B, which then punctures the membrane by swinging out its lower end. Similarly, Yersinia enterocolitica YaxA, encoded by the yaxAB gene, forms a pore predominantly composed of decamers of YaxA-YaxB heterodimers. Although both subunits bear membrane-active moieties, only YaxA is capable of binding to membranes by itself and YaxB is subsequently recruited to membrane-associated YaxA and induced to present its lytic transmembrane helices; pore formation then progresses by further oligomerization of YaxA-YaxB dimers. YaxAB has been found to be strongly upregulated by the Yersinia master regulator RovA, a transcriptional activator of Yersinia outer membrane protein invasion which is involved in bacterial attachment and invasion across the intestinal epithelium.


Pssm-ID: 439155 [Multi-domain]  Cd Length: 306  Bit Score: 39.88  E-value: 1.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146134374 264 VKAENhVLKLKQEINLLQAQLSNLRRENEALRsgqgASLSVVKQNtdvaLQNLHLVMNSAHASIKQLVsgaDTLNLV-AE 342
Cdd:cd22657  197 VKAEK-IRKERNELIAEREELIQKLKSKNRLL----GSLERLETD----LQDLDIRMIDAEVATKNLE---TVWNTIlTY 264

                         90
                 ....*....|....*.
gi 146134374 343 ILKSIDRISEVKDEVD 358
Cdd:cd22657  265 IDASAEELDKIDDALS 280
DivIVA COG3599
Cell division septum initiation protein DivIVA, interacts with FtsZ and MinD [Cell cycle ...
 186-290 3.12e-03

Cell division septum initiation protein DivIVA, interacts with FtsZ and MinD [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 442818 [Multi-domain]  Cd Length: 125  Bit Score: 37.14  E-value: 3.12e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146134374 186 DRHLRTLQISYEALKDENSKLRRKLN----EVQSFSETQTEMVRTLerkleaKMIKEESdfhdlESVVQQVEQNLELMTK 261
Cdd:COG3599   26 DEFLDEVAEDYERLIRENKELKEKLEeleeELEEYRELEETLQKTL------VVAQETA-----EEVKENAEKEAELIIK 94

                         90       100       110
                 ....*....|....*....|....*....|
gi 146134374 262 RA-VKAENHVLKLKQEINLLQAQLSNLRRE 290
Cdd:COG3599   95 EAeLEAEKIIEEAQEKARKIVREIEELKRQ 124
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
186-292 3.56e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 39.37  E-value: 3.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 146134374 186 DRHLRTLQISYEALKDENSKLRRKLNEVQSFSETQTEMVRTLERKLEAKMIKEESDFHDLESVVQQVEQNLELMTKRAVK 265
Cdd:COG4717  138 EAELAELPERLEELEERLEELRELEEELEELEAELAELQEELEELLEQLSLATEEELQDLAEELEELQQRLAELEEELEE 217

                         90       100
                 ....*....|....*....|....*..
gi 146134374 266 AENHVLKLKQEINLLQAQLSNLRRENE 292
Cdd:COG4717  218 AQEELEELEEELEQLENELEAAALEER 244
 
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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