Chromatin-remodeling ATPase INO80 [Caenorhabditis elegans]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| NtpE super family | cl34249 | Archaeal/vacuolar-type H+-ATPase subunit E/Vma4 [Energy production and conversion]; Archaeal ... |
473-626 | 7.88e-10 | ||||||
Archaeal/vacuolar-type H+-ATPase subunit E/Vma4 [Energy production and conversion]; Archaeal/vacuolar-type H+-ATPase subunit E/Vma4 is part of the Pathway/BioSystem: A/V-type ATP synthase The actual alignment was detected with superfamily member COG1390: Pssm-ID: 441000 [Multi-domain] Cd Length: 196 Bit Score: 59.19 E-value: 7.88e-10
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| Herpes_BLLF1 super family | cl37540 | Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
121-455 | 9.99e-05 | ||||||
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo. The actual alignment was detected with superfamily member pfam05109: Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 46.06 E-value: 9.99e-05
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| Name | Accession | Description | Interval | E-value | ||||||
| NtpE | COG1390 | Archaeal/vacuolar-type H+-ATPase subunit E/Vma4 [Energy production and conversion]; Archaeal ... |
473-626 | 7.88e-10 | ||||||
Archaeal/vacuolar-type H+-ATPase subunit E/Vma4 [Energy production and conversion]; Archaeal/vacuolar-type H+-ATPase subunit E/Vma4 is part of the Pathway/BioSystem: A/V-type ATP synthase Pssm-ID: 441000 [Multi-domain] Cd Length: 196 Bit Score: 59.19 E-value: 7.88e-10
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| ARGLU | pfam15346 | Arginine and glutamate-rich 1; ARGLU, arginine and glutamate-rich 1 protein family, is ... |
470-562 | 1.76e-09 | ||||||
Arginine and glutamate-rich 1; ARGLU, arginine and glutamate-rich 1 protein family, is required for the oestrogen-dependent expression of ESR1 target genes. It functions in cooperation with MED1. The family of proteins is found in eukaryotes. Pssm-ID: 405931 [Multi-domain] Cd Length: 151 Bit Score: 56.98 E-value: 1.76e-09
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
453-552 | 2.29e-07 | ||||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 53.70 E-value: 2.29e-07
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
473-582 | 5.99e-07 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 53.22 E-value: 5.99e-07
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| ATP-synt_Fo_b | cd06503 | F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex ... |
467-551 | 2.11e-06 | ||||||
F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens. Pssm-ID: 349951 [Multi-domain] Cd Length: 132 Bit Score: 47.43 E-value: 2.11e-06
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| Herpes_BLLF1 | pfam05109 | Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
121-455 | 9.99e-05 | ||||||
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo. Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 46.06 E-value: 9.99e-05
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| Name | Accession | Description | Interval | E-value | ||||||
| NtpE | COG1390 | Archaeal/vacuolar-type H+-ATPase subunit E/Vma4 [Energy production and conversion]; Archaeal ... |
473-626 | 7.88e-10 | ||||||
Archaeal/vacuolar-type H+-ATPase subunit E/Vma4 [Energy production and conversion]; Archaeal/vacuolar-type H+-ATPase subunit E/Vma4 is part of the Pathway/BioSystem: A/V-type ATP synthase Pssm-ID: 441000 [Multi-domain] Cd Length: 196 Bit Score: 59.19 E-value: 7.88e-10
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| ARGLU | pfam15346 | Arginine and glutamate-rich 1; ARGLU, arginine and glutamate-rich 1 protein family, is ... |
470-562 | 1.76e-09 | ||||||
Arginine and glutamate-rich 1; ARGLU, arginine and glutamate-rich 1 protein family, is required for the oestrogen-dependent expression of ESR1 target genes. It functions in cooperation with MED1. The family of proteins is found in eukaryotes. Pssm-ID: 405931 [Multi-domain] Cd Length: 151 Bit Score: 56.98 E-value: 1.76e-09
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
470-623 | 1.90e-07 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 54.94 E-value: 1.90e-07
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| MAP7 | pfam05672 | MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ... |
474-549 | 2.11e-07 | ||||||
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Pssm-ID: 461709 [Multi-domain] Cd Length: 153 Bit Score: 51.19 E-value: 2.11e-07
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
453-552 | 2.29e-07 | ||||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 53.70 E-value: 2.29e-07
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| DR0291 | COG1579 | Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ... |
470-566 | 4.15e-07 | ||||||
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only]; Pssm-ID: 441187 [Multi-domain] Cd Length: 236 Bit Score: 51.85 E-value: 4.15e-07
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
470-623 | 4.28e-07 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 53.79 E-value: 4.28e-07
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
473-582 | 5.99e-07 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 53.22 E-value: 5.99e-07
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
470-676 | 6.66e-07 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 53.02 E-value: 6.66e-07
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
466-642 | 1.02e-06 | ||||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 52.08 E-value: 1.02e-06
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
379-646 | 1.19e-06 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 52.45 E-value: 1.19e-06
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| NtpH | COG2811 | Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion]; Archaeal ... |
470-560 | 1.55e-06 | ||||||
Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion]; Archaeal/vacuolar-type H+-ATPase subunit H is part of the Pathway/BioSystem: A/V-type ATP synthase Pssm-ID: 442060 [Multi-domain] Cd Length: 108 Bit Score: 47.22 E-value: 1.55e-06
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
470-647 | 2.07e-06 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 51.48 E-value: 2.07e-06
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| ATP-synt_Fo_b | cd06503 | F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex ... |
467-551 | 2.11e-06 | ||||||
F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens. Pssm-ID: 349951 [Multi-domain] Cd Length: 132 Bit Score: 47.43 E-value: 2.11e-06
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
469-540 | 2.12e-06 | ||||||
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain. Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 50.69 E-value: 2.12e-06
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
477-646 | 3.32e-06 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 50.91 E-value: 3.32e-06
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
469-581 | 3.54e-06 | ||||||
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain. Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 49.92 E-value: 3.54e-06
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| MAP7 | pfam05672 | MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ... |
470-548 | 3.76e-06 | ||||||
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Pssm-ID: 461709 [Multi-domain] Cd Length: 153 Bit Score: 47.34 E-value: 3.76e-06
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| AtpF | COG0711 | FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ... |
467-589 | 3.85e-06 | ||||||
FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ATP synthase, membrane subunit b or b' is part of the Pathway/BioSystem: FoF1-type ATP synthase Pssm-ID: 440475 [Multi-domain] Cd Length: 152 Bit Score: 47.47 E-value: 3.85e-06
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
468-568 | 4.53e-06 | ||||||
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain. Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 49.53 E-value: 4.53e-06
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
470-562 | 4.81e-06 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 50.32 E-value: 4.81e-06
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| MRP-S26 | pfam14943 | Mitochondrial ribosome subunit S26; This family of proteins corresponds to mitochondrial ... |
467-561 | 5.08e-06 | ||||||
Mitochondrial ribosome subunit S26; This family of proteins corresponds to mitochondrial ribosomal subunit S26 in eukaryotes Pssm-ID: 464391 [Multi-domain] Cd Length: 168 Bit Score: 47.24 E-value: 5.08e-06
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| Casc1_N | pfam15927 | Cancer susceptibility candidate 1 N-terminus; This presumed domain is functionally ... |
473-540 | 5.90e-06 | ||||||
Cancer susceptibility candidate 1 N-terminus; This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 200 amino acids in length. The family is found in association with pfam12366. There are two completely conserved residues (N and W) that may be functionally important. Pssm-ID: 464947 [Multi-domain] Cd Length: 201 Bit Score: 47.74 E-value: 5.90e-06
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| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
470-623 | 7.53e-06 | ||||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 49.27 E-value: 7.53e-06
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| NtpH | COG2811 | Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion]; Archaeal ... |
487-573 | 9.33e-06 | ||||||
Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion]; Archaeal/vacuolar-type H+-ATPase subunit H is part of the Pathway/BioSystem: A/V-type ATP synthase Pssm-ID: 442060 [Multi-domain] Cd Length: 108 Bit Score: 45.29 E-value: 9.33e-06
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
473-659 | 9.42e-06 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 49.37 E-value: 9.42e-06
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| ERM_helical | pfam20492 | Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ... |
468-566 | 1.26e-05 | ||||||
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins. Pssm-ID: 466641 [Multi-domain] Cd Length: 120 Bit Score: 44.91 E-value: 1.26e-05
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| PRK12704 | PRK12704 | phosphodiesterase; Provisional |
472-566 | 1.29e-05 | ||||||
phosphodiesterase; Provisional Pssm-ID: 237177 [Multi-domain] Cd Length: 520 Bit Score: 48.62 E-value: 1.29e-05
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| AtpF | COG0711 | FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ... |
470-557 | 1.34e-05 | ||||||
FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ATP synthase, membrane subunit b or b' is part of the Pathway/BioSystem: FoF1-type ATP synthase Pssm-ID: 440475 [Multi-domain] Cd Length: 152 Bit Score: 45.93 E-value: 1.34e-05
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
467-566 | 1.50e-05 | ||||||
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain. Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 47.99 E-value: 1.50e-05
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| CAF-1_p150 | pfam11600 | Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide ... |
470-541 | 1.65e-05 | ||||||
Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesized and acetylated histones H3/H4 into chromatin during DNA replication and repair. CAF-1_p150 includes the HP1 interaction site, the PEST, KER and ED interacting sites. CAF-1_p150 interacts directly with newly synthesized and acetylated histones through the acidic KER and ED domains. The PEST domain is associated with proteins that undergo rapid proteolysis. Pssm-ID: 402959 [Multi-domain] Cd Length: 164 Bit Score: 45.83 E-value: 1.65e-05
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
468-566 | 1.94e-05 | ||||||
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain. Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 47.61 E-value: 1.94e-05
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
470-633 | 2.03e-05 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 48.39 E-value: 2.03e-05
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| CAF-1_p150 | pfam11600 | Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide ... |
470-562 | 2.52e-05 | ||||||
Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesized and acetylated histones H3/H4 into chromatin during DNA replication and repair. CAF-1_p150 includes the HP1 interaction site, the PEST, KER and ED interacting sites. CAF-1_p150 interacts directly with newly synthesized and acetylated histones through the acidic KER and ED domains. The PEST domain is associated with proteins that undergo rapid proteolysis. Pssm-ID: 402959 [Multi-domain] Cd Length: 164 Bit Score: 45.45 E-value: 2.52e-05
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
470-552 | 2.86e-05 | ||||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 47.15 E-value: 2.86e-05
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| UDM1_RNF168_RNF169-like | cd22249 | UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, ... |
488-552 | 2.93e-05 | ||||||
UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, RNF169 and similar proteins; This model represents the UDM1 (ubiquitin-dependent double-strand break [DSB] recruitment module 1) found in RING finger proteins, RNF168 and RNF169. RNF168 is an E3 ubiquitin-protein ligase that promotes non-canonical K27 ubiquitination to signal DNA damage. It functions, together with RNF8, as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates such as H2A and H2AX. With H2AK13/15 ubiquitylation, it facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. In addition, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to the regulation of DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin, independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. The UDM1 domain comprises LRM1 (LR motif 1), UMI (ubiquitin-interacting motif [UIM]- and MIU-related UBD) and MIU1 (motif interacting with ubiquitin 1). Mutations of Ub-interacting residues in UDM1 have little effect on the accumulation of RNF168 to DSB sites, suggesting that it may not be the main site of binding ubiquitylated and polyubiquitylated targets. Pssm-ID: 409016 [Multi-domain] Cd Length: 66 Bit Score: 42.26 E-value: 2.93e-05
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
470-551 | 3.26e-05 | ||||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 46.76 E-value: 3.26e-05
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
466-552 | 3.63e-05 | ||||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 46.76 E-value: 3.63e-05
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
470-646 | 3.70e-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: 47.36 E-value: 3.70e-05
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
470-646 | 4.79e-05 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 46.85 E-value: 4.79e-05
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| PRK03918 | PRK03918 | DNA double-strand break repair ATPase Rad50; |
468-579 | 5.66e-05 | ||||||
DNA double-strand break repair ATPase Rad50; Pssm-ID: 235175 [Multi-domain] Cd Length: 880 Bit Score: 46.60 E-value: 5.66e-05
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| APG6_N | pfam17675 | Apg6 coiled-coil region; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. ... |
470-555 | 5.92e-05 | ||||||
Apg6 coiled-coil region; In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway. Pssm-ID: 465452 [Multi-domain] Cd Length: 127 Bit Score: 43.35 E-value: 5.92e-05
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
473-562 | 6.56e-05 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 46.67 E-value: 6.56e-05
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| EnvC | COG4942 | Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ... |
468-596 | 7.61e-05 | ||||||
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: 45.91 E-value: 7.61e-05
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| PRK03918 | PRK03918 | DNA double-strand break repair ATPase Rad50; |
470-574 | 7.76e-05 | ||||||
DNA double-strand break repair ATPase Rad50; Pssm-ID: 235175 [Multi-domain] Cd Length: 880 Bit Score: 46.21 E-value: 7.76e-05
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
471-623 | 8.06e-05 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 46.08 E-value: 8.06e-05
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| Nop53 | pfam07767 | Nop53 (60S ribosomal biogenesis); This nucleolar family of proteins are involved in 60S ... |
470-577 | 8.68e-05 | ||||||
Nop53 (60S ribosomal biogenesis); This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Pssm-ID: 462259 [Multi-domain] Cd Length: 353 Bit Score: 45.36 E-value: 8.68e-05
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
470-537 | 9.69e-05 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 46.29 E-value: 9.69e-05
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| Herpes_BLLF1 | pfam05109 | Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
121-455 | 9.99e-05 | ||||||
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo. Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 46.06 E-value: 9.99e-05
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| tolA | PRK09510 | cell envelope integrity inner membrane protein TolA; Provisional |
468-541 | 1.27e-04 | ||||||
cell envelope integrity inner membrane protein TolA; Provisional Pssm-ID: 236545 [Multi-domain] Cd Length: 387 Bit Score: 45.18 E-value: 1.27e-04
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
482-559 | 1.29e-04 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 45.90 E-value: 1.29e-04
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
470-604 | 1.32e-04 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 45.70 E-value: 1.32e-04
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| CCDC47 | pfam07946 | PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of ... |
470-524 | 1.34e-04 | ||||||
PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway. Pssm-ID: 462322 Cd Length: 323 Bit Score: 44.87 E-value: 1.34e-04
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| AhaH | TIGR02926 | ATP synthase archaeal, H subunit; he A1/A0 ATP synthase is homologous to the V-type (V1/V0, ... |
467-540 | 1.37e-04 | ||||||
ATP synthase archaeal, H subunit; he A1/A0 ATP synthase is homologous to the V-type (V1/V0, vacuolar) ATPase, but functions in the ATP synthetic direction as does the F1/F0 ATPase of bacteria. The hydrophilic A1 "stalk" complex (AhaABCDEFG) is the site of ATP generation and is coupled to the membrane-embedded proton translocating A0 complex. It is unclear precisely where AhaH fits into these complexes. Pssm-ID: 131972 [Multi-domain] Cd Length: 85 Bit Score: 40.98 E-value: 1.37e-04
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
475-562 | 1.40e-04 | ||||||
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain. Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 44.91 E-value: 1.40e-04
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
473-564 | 1.57e-04 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 45.31 E-value: 1.57e-04
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| PRK00247 | PRK00247 | putative inner membrane protein translocase component YidC; Validated |
415-551 | 1.58e-04 | ||||||
putative inner membrane protein translocase component YidC; Validated Pssm-ID: 178945 [Multi-domain] Cd Length: 429 Bit Score: 44.84 E-value: 1.58e-04
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| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
468-610 | 1.60e-04 | ||||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 45.03 E-value: 1.60e-04
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| DUF6033 | pfam19498 | Protein of unknown function (DUF6033); This family of proteins is functionally uncharacterized. ... |
480-563 | 1.87e-04 | ||||||
Protein of unknown function (DUF6033); This family of proteins is functionally uncharacterized. This family of proteins is primarily found in Clostridia. Proteins in this family are typically between 212 and 271 amino acids in length. Pssm-ID: 437330 Cd Length: 204 Bit Score: 43.43 E-value: 1.87e-04
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| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
470-642 | 1.90e-04 | ||||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 44.65 E-value: 1.90e-04
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| UDM1_RNF168 | cd22265 | UDM1 (ubiquitin-dependent DSB recruitment module 1) domain found in RING finger protein 168; ... |
482-538 | 1.95e-04 | ||||||
UDM1 (ubiquitin-dependent DSB recruitment module 1) domain found in RING finger protein 168; RING finger protein 168 (RNF168) is an E3 ubiquitin-protein ligase that promotes noncanonical K27 ubiquitination to signal DNA damage. Together with RNF8, RNF168 functions as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates such as H2A and H2AX. With H2AK13/15 ubiquitylation, it facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. In addition, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. This model corresponds to the UDM1 (ubiquitin-dependent double-strand break [DSB] recruitment module 1) domain of RNF168, which comprises LRM1 (LR motif 1), UMI (ubiquitin-interacting motif [UIM]- and MIU-related UBD) and MIU1 (motif interacting with ubiquitin 1). Mutations of Ub-interacting residues in UDM1 have little effect on the accumulation of RNF168 to DSB sites, suggesting that it may not be the main site of binding ubiquitylated and polyubiquitylated targets. Pssm-ID: 409018 [Multi-domain] Cd Length: 73 Bit Score: 40.23 E-value: 1.95e-04
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
468-560 | 1.99e-04 | ||||||
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain. Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 44.14 E-value: 1.99e-04
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
470-563 | 2.09e-04 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 44.93 E-value: 2.09e-04
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
470-594 | 2.13e-04 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 45.13 E-value: 2.13e-04
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| YqiK | COG2268 | Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; |
471-619 | 2.27e-04 | ||||||
Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; Pssm-ID: 441869 [Multi-domain] Cd Length: 439 Bit Score: 44.48 E-value: 2.27e-04
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| UDM1_RNF168_RNF169-like | cd22249 | UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, ... |
477-535 | 2.31e-04 | ||||||
UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, RNF169 and similar proteins; This model represents the UDM1 (ubiquitin-dependent double-strand break [DSB] recruitment module 1) found in RING finger proteins, RNF168 and RNF169. RNF168 is an E3 ubiquitin-protein ligase that promotes non-canonical K27 ubiquitination to signal DNA damage. It functions, together with RNF8, as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates such as H2A and H2AX. With H2AK13/15 ubiquitylation, it facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. In addition, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to the regulation of DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin, independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. The UDM1 domain comprises LRM1 (LR motif 1), UMI (ubiquitin-interacting motif [UIM]- and MIU-related UBD) and MIU1 (motif interacting with ubiquitin 1). Mutations of Ub-interacting residues in UDM1 have little effect on the accumulation of RNF168 to DSB sites, suggesting that it may not be the main site of binding ubiquitylated and polyubiquitylated targets. Pssm-ID: 409016 [Multi-domain] Cd Length: 66 Bit Score: 39.94 E-value: 2.31e-04
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
468-566 | 2.64e-04 | ||||||
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: 2.64e-04
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| YqiK | COG2268 | Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; |
471-544 | 3.04e-04 | ||||||
Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; Pssm-ID: 441869 [Multi-domain] Cd Length: 439 Bit Score: 44.09 E-value: 3.04e-04
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| DUF3584 | pfam12128 | Protein of unknown function (DUF3584); This protein is found in bacteria and eukaryotes. ... |
456-662 | 3.17e-04 | ||||||
Protein of unknown function (DUF3584); This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication. Pssm-ID: 432349 [Multi-domain] Cd Length: 1191 Bit Score: 44.44 E-value: 3.17e-04
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| CAF-1_p150 | pfam11600 | Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide ... |
468-536 | 3.33e-04 | ||||||
Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesized and acetylated histones H3/H4 into chromatin during DNA replication and repair. CAF-1_p150 includes the HP1 interaction site, the PEST, KER and ED interacting sites. CAF-1_p150 interacts directly with newly synthesized and acetylated histones through the acidic KER and ED domains. The PEST domain is associated with proteins that undergo rapid proteolysis. Pssm-ID: 402959 [Multi-domain] Cd Length: 164 Bit Score: 41.98 E-value: 3.33e-04
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| YqiK | COG2268 | Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; |
471-558 | 3.38e-04 | ||||||
Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; Pssm-ID: 441869 [Multi-domain] Cd Length: 439 Bit Score: 43.71 E-value: 3.38e-04
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| SMC_N | pfam02463 | RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ... |
467-646 | 3.65e-04 | ||||||
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Pssm-ID: 426784 [Multi-domain] Cd Length: 1161 Bit Score: 44.19 E-value: 3.65e-04
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| ERM_helical | pfam20492 | Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ... |
471-560 | 3.94e-04 | ||||||
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins. Pssm-ID: 466641 [Multi-domain] Cd Length: 120 Bit Score: 40.67 E-value: 3.94e-04
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| PRK03918 | PRK03918 | DNA double-strand break repair ATPase Rad50; |
467-569 | 4.42e-04 | ||||||
DNA double-strand break repair ATPase Rad50; Pssm-ID: 235175 [Multi-domain] Cd Length: 880 Bit Score: 43.90 E-value: 4.42e-04
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
470-568 | 4.45e-04 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 43.98 E-value: 4.45e-04
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
467-562 | 5.12e-04 | ||||||
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain. Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 42.98 E-value: 5.12e-04
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| YqiK | COG2268 | Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; |
467-538 | 5.16e-04 | ||||||
Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; Pssm-ID: 441869 [Multi-domain] Cd Length: 439 Bit Score: 43.32 E-value: 5.16e-04
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| ERM_helical | pfam20492 | Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ... |
473-543 | 5.31e-04 | ||||||
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins. Pssm-ID: 466641 [Multi-domain] Cd Length: 120 Bit Score: 40.29 E-value: 5.31e-04
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| RNase_Y_N | pfam12072 | RNase Y N-terminal region; |
470-568 | 5.58e-04 | ||||||
RNase Y N-terminal region; Pssm-ID: 463456 [Multi-domain] Cd Length: 201 Bit Score: 41.80 E-value: 5.58e-04
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| YqiK | COG2268 | Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; |
470-541 | 5.62e-04 | ||||||
Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; Pssm-ID: 441869 [Multi-domain] Cd Length: 439 Bit Score: 42.94 E-value: 5.62e-04
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| CCDC47 | pfam07946 | PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of ... |
480-531 | 5.77e-04 | ||||||
PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway. Pssm-ID: 462322 Cd Length: 323 Bit Score: 42.94 E-value: 5.77e-04
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| PRK00409 | PRK00409 | recombination and DNA strand exchange inhibitor protein; Reviewed |
472-602 | 5.95e-04 | ||||||
recombination and DNA strand exchange inhibitor protein; Reviewed Pssm-ID: 234750 [Multi-domain] Cd Length: 782 Bit Score: 43.28 E-value: 5.95e-04
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| GBP_C | cd16269 | Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ... |
471-565 | 6.22e-04 | ||||||
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines. Pssm-ID: 293879 [Multi-domain] Cd Length: 291 Bit Score: 42.56 E-value: 6.22e-04
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
467-568 | 6.74e-04 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 43.59 E-value: 6.74e-04
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| YqiK | COG2268 | Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; |
470-542 | 6.98e-04 | ||||||
Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; Pssm-ID: 441869 [Multi-domain] Cd Length: 439 Bit Score: 42.94 E-value: 6.98e-04
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| DR0291 | COG1579 | Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ... |
470-566 | 7.37e-04 | ||||||
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only]; Pssm-ID: 441187 [Multi-domain] Cd Length: 236 Bit Score: 41.83 E-value: 7.37e-04
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| MAP7 | pfam05672 | MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ... |
473-543 | 7.54e-04 | ||||||
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Pssm-ID: 461709 [Multi-domain] Cd Length: 153 Bit Score: 40.79 E-value: 7.54e-04
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| SMC_N | pfam02463 | RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ... |
473-646 | 8.83e-04 | ||||||
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Pssm-ID: 426784 [Multi-domain] Cd Length: 1161 Bit Score: 43.04 E-value: 8.83e-04
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| ATP-synt_Fo_b | cd06503 | F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex ... |
483-561 | 9.29e-04 | ||||||
F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens. Pssm-ID: 349951 [Multi-domain] Cd Length: 132 Bit Score: 40.11 E-value: 9.29e-04
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| DUF4670 | pfam15709 | Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ... |
471-535 | 9.66e-04 | ||||||
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length. Pssm-ID: 464815 [Multi-domain] Cd Length: 522 Bit Score: 42.63 E-value: 9.66e-04
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| PRK12705 | PRK12705 | hypothetical protein; Provisional |
471-609 | 1.15e-03 | ||||||
hypothetical protein; Provisional Pssm-ID: 237178 [Multi-domain] Cd Length: 508 Bit Score: 42.39 E-value: 1.15e-03
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| PRK03963 | PRK03963 | V-type ATP synthase subunit E; Provisional |
483-561 | 1.19e-03 | ||||||
V-type ATP synthase subunit E; Provisional Pssm-ID: 167649 [Multi-domain] Cd Length: 198 Bit Score: 40.89 E-value: 1.19e-03
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| ERM_helical | pfam20492 | Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ... |
470-548 | 1.22e-03 | ||||||
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins. Pssm-ID: 466641 [Multi-domain] Cd Length: 120 Bit Score: 39.52 E-value: 1.22e-03
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| tolA | PRK09510 | cell envelope integrity inner membrane protein TolA; Provisional |
468-550 | 1.24e-03 | ||||||
cell envelope integrity inner membrane protein TolA; Provisional Pssm-ID: 236545 [Multi-domain] Cd Length: 387 Bit Score: 42.10 E-value: 1.24e-03
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
467-613 | 1.31e-03 | ||||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 41.75 E-value: 1.31e-03
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| MAP7 | pfam05672 | MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ... |
471-528 | 1.32e-03 | ||||||
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Pssm-ID: 461709 [Multi-domain] Cd Length: 153 Bit Score: 40.02 E-value: 1.32e-03
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| PRK12704 | PRK12704 | phosphodiesterase; Provisional |
470-609 | 1.36e-03 | ||||||
phosphodiesterase; Provisional Pssm-ID: 237177 [Multi-domain] Cd Length: 520 Bit Score: 42.07 E-value: 1.36e-03
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| PRK12705 | PRK12705 | hypothetical protein; Provisional |
479-647 | 1.41e-03 | ||||||
hypothetical protein; Provisional Pssm-ID: 237178 [Multi-domain] Cd Length: 508 Bit Score: 42.00 E-value: 1.41e-03
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| DR0291 | COG1579 | Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ... |
470-563 | 1.44e-03 | ||||||
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only]; Pssm-ID: 441187 [Multi-domain] Cd Length: 236 Bit Score: 41.06 E-value: 1.44e-03
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| PRK02292 | PRK02292 | V-type ATP synthase subunit E; Provisional |
473-569 | 1.52e-03 | ||||||
V-type ATP synthase subunit E; Provisional Pssm-ID: 235026 [Multi-domain] Cd Length: 188 Bit Score: 40.37 E-value: 1.52e-03
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| vATP-synt_E | pfam01991 | ATP synthase (E/31 kDa) subunit; This family includes the vacuolar ATP synthase E subunit, as ... |
482-602 | 1.52e-03 | ||||||
ATP synthase (E/31 kDa) subunit; This family includes the vacuolar ATP synthase E subunit, as well as the archaebacterial ATP synthase E subunit. Pssm-ID: 396537 [Multi-domain] Cd Length: 199 Bit Score: 40.44 E-value: 1.52e-03
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| DUF5401 | pfam17380 | Family of unknown function (DUF5401); This is a family of unknown function found in ... |
456-548 | 1.66e-03 | ||||||
Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea. Pssm-ID: 375164 [Multi-domain] Cd Length: 722 Bit Score: 42.03 E-value: 1.66e-03
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| SPFH_HflK | cd03404 | High frequency of lysogenization K (HflK) family; SPFH (stomatin, prohibitin, flotillin, and ... |
468-536 | 1.77e-03 | ||||||
High frequency of lysogenization K (HflK) family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; This model characterizes proteins similar to prokaryotic HflK (High frequency of lysogenization K). Although many members of the SPFH (or band 7) superfamily are lipid raft associated, prokaryote plasma membranes lack cholesterol and are unlikely to have lipid raft domains. Individual proteins of this SPFH domain superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Escherichia coli HflK is an integral membrane protein which may localize to the plasma membrane. HflK associates with another SPFH superfamily member (HflC) to form an HflKC complex. HflKC interacts with FtsH in a large complex termed the FtsH holo-enzyme. FtsH is an AAA ATP-dependent protease which exerts progressive proteolysis against membrane-embedded and soluble substrate proteins. HflKC can modulate the activity of FtsH. HflKC plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Pssm-ID: 259802 [Multi-domain] Cd Length: 266 Bit Score: 40.96 E-value: 1.77e-03
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| GBP_C | cd16269 | Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ... |
470-566 | 1.85e-03 | ||||||
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines. Pssm-ID: 293879 [Multi-domain] Cd Length: 291 Bit Score: 41.02 E-value: 1.85e-03
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| DivIVA | COG3599 | Cell division septum initiation protein DivIVA, interacts with FtsZ and MinD [Cell cycle ... |
470-536 | 1.92e-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: 39.07 E-value: 1.92e-03
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| UDM1_RNF168_RNF169-like | cd22249 | UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, ... |
471-519 | 1.93e-03 | ||||||
UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, RNF169 and similar proteins; This model represents the UDM1 (ubiquitin-dependent double-strand break [DSB] recruitment module 1) found in RING finger proteins, RNF168 and RNF169. RNF168 is an E3 ubiquitin-protein ligase that promotes non-canonical K27 ubiquitination to signal DNA damage. It functions, together with RNF8, as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates such as H2A and H2AX. With H2AK13/15 ubiquitylation, it facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. In addition, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to the regulation of DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin, independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. The UDM1 domain comprises LRM1 (LR motif 1), UMI (ubiquitin-interacting motif [UIM]- and MIU-related UBD) and MIU1 (motif interacting with ubiquitin 1). Mutations of Ub-interacting residues in UDM1 have little effect on the accumulation of RNF168 to DSB sites, suggesting that it may not be the main site of binding ubiquitylated and polyubiquitylated targets. Pssm-ID: 409016 [Multi-domain] Cd Length: 66 Bit Score: 37.25 E-value: 1.93e-03
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
471-646 | 2.01e-03 | ||||||
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: 41.59 E-value: 2.01e-03
|
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
470-643 | 2.02e-03 | ||||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 41.04 E-value: 2.02e-03
|
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| NtpH | COG2811 | Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion]; Archaeal ... |
483-566 | 2.13e-03 | ||||||
Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion]; Archaeal/vacuolar-type H+-ATPase subunit H is part of the Pathway/BioSystem: A/V-type ATP synthase Pssm-ID: 442060 [Multi-domain] Cd Length: 108 Bit Score: 38.36 E-value: 2.13e-03
|
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
470-562 | 2.17e-03 | ||||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 41.04 E-value: 2.17e-03
|
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| PRK03918 | PRK03918 | DNA double-strand break repair ATPase Rad50; |
472-567 | 2.33e-03 | ||||||
DNA double-strand break repair ATPase Rad50; Pssm-ID: 235175 [Multi-domain] Cd Length: 880 Bit Score: 41.59 E-value: 2.33e-03
|
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
470-568 | 2.46e-03 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 41.67 E-value: 2.46e-03
|
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
470-561 | 2.57e-03 | ||||||
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: 41.58 E-value: 2.57e-03
|
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
473-560 | 2.69e-03 | ||||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 40.60 E-value: 2.69e-03
|
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| PRK03918 | PRK03918 | DNA double-strand break repair ATPase Rad50; |
471-565 | 2.81e-03 | ||||||
DNA double-strand break repair ATPase Rad50; Pssm-ID: 235175 [Multi-domain] Cd Length: 880 Bit Score: 41.20 E-value: 2.81e-03
|
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
470-568 | 2.87e-03 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 41.28 E-value: 2.87e-03
|
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| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
470-541 | 2.88e-03 | ||||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 40.79 E-value: 2.88e-03
|
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
468-560 | 2.92e-03 | ||||||
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain. Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 40.67 E-value: 2.92e-03
|
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
470-646 | 2.94e-03 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 41.28 E-value: 2.94e-03
|
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| HflC | COG0330 | Regulator of protease activity HflC, stomatin/prohibitin superfamily [Posttranslational ... |
466-558 | 3.15e-03 | ||||||
Regulator of protease activity HflC, stomatin/prohibitin superfamily [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440099 [Multi-domain] Cd Length: 279 Bit Score: 40.21 E-value: 3.15e-03
|
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| PRK05759 | PRK05759 | F0F1 ATP synthase subunit B; Validated |
473-536 | 3.40e-03 | ||||||
F0F1 ATP synthase subunit B; Validated Pssm-ID: 180240 [Multi-domain] Cd Length: 156 Bit Score: 38.99 E-value: 3.40e-03
|
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
467-569 | 3.46e-03 | ||||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 41.05 E-value: 3.46e-03
|
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
464-569 | 3.64e-03 | ||||||
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: 40.82 E-value: 3.64e-03
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| DUF5401 | pfam17380 | Family of unknown function (DUF5401); This is a family of unknown function found in ... |
468-646 | 4.06e-03 | ||||||
Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea. Pssm-ID: 375164 [Multi-domain] Cd Length: 722 Bit Score: 40.49 E-value: 4.06e-03
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
469-612 | 4.50e-03 | ||||||
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: 40.81 E-value: 4.50e-03
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
470-646 | 4.65e-03 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 40.51 E-value: 4.65e-03
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
467-606 | 4.66e-03 | ||||||
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: 40.43 E-value: 4.66e-03
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| EnvC | COG4942 | Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ... |
470-552 | 5.27e-03 | ||||||
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: 39.75 E-value: 5.27e-03
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| CwlO1 | COG3883 | Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ... |
467-621 | 5.66e-03 | ||||||
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown]; Pssm-ID: 443091 [Multi-domain] Cd Length: 379 Bit Score: 39.81 E-value: 5.66e-03
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| ARGLU | pfam15346 | Arginine and glutamate-rich 1; ARGLU, arginine and glutamate-rich 1 protein family, is ... |
473-516 | 5.73e-03 | ||||||
Arginine and glutamate-rich 1; ARGLU, arginine and glutamate-rich 1 protein family, is required for the oestrogen-dependent expression of ESR1 target genes. It functions in cooperation with MED1. The family of proteins is found in eukaryotes. Pssm-ID: 405931 [Multi-domain] Cd Length: 151 Bit Score: 38.11 E-value: 5.73e-03
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| EnvC | COG4942 | Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ... |
467-565 | 6.11e-03 | ||||||
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: 39.75 E-value: 6.11e-03
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| PRK06231 | PRK06231 | F0F1 ATP synthase subunit B; Validated |
470-558 | 6.38e-03 | ||||||
F0F1 ATP synthase subunit B; Validated Pssm-ID: 180481 [Multi-domain] Cd Length: 205 Bit Score: 38.67 E-value: 6.38e-03
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
470-568 | 6.47e-03 | ||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 40.12 E-value: 6.47e-03
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| ATP-synt_Fo_b | cd06503 | F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex ... |
472-542 | 6.75e-03 | ||||||
F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens. Pssm-ID: 349951 [Multi-domain] Cd Length: 132 Bit Score: 37.42 E-value: 6.75e-03
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
467-581 | 7.19e-03 | ||||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 39.90 E-value: 7.19e-03
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| DUF4670 | pfam15709 | Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ... |
470-543 | 7.66e-03 | ||||||
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length. Pssm-ID: 464815 [Multi-domain] Cd Length: 522 Bit Score: 39.55 E-value: 7.66e-03
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| SPFH_prohibitin | cd03401 | Prohibitin family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; This model ... |
487-535 | 8.06e-03 | ||||||
Prohibitin family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; This model characterizes proteins similar to prohibitin (a lipid raft-associated integral membrane protein). Individual proteins of the SPFH (band 7) domain superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. These microdomains, in addition to being stable scaffolds, may also be dynamic units with their own regulatory functions. Prohibitin is a mitochondrial inner-membrane protein which may act as a chaperone for the stabilization of mitochondrial proteins. Human prohibitin forms a hetero-oligomeric complex with Bap-37 (prohibitin 2, an SPFH domain carrying homolog). This complex may protect non-assembled membrane proteins against proteolysis by the m-AAA protease. Prohibitin and Bap-37 yeast homologs have been implicated in yeast longevity and in the maintenance of mitochondrial morphology. Pssm-ID: 259799 [Multi-domain] Cd Length: 195 Bit Score: 38.26 E-value: 8.06e-03
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| ClpA | COG0542 | ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ... |
471-551 | 8.18e-03 | ||||||
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440308 [Multi-domain] Cd Length: 836 Bit Score: 39.68 E-value: 8.18e-03
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| mukB | PRK04863 | chromosome partition protein MukB; |
467-598 | 8.85e-03 | ||||||
chromosome partition protein MukB; Pssm-ID: 235316 [Multi-domain] Cd Length: 1486 Bit Score: 39.56 E-value: 8.85e-03
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| PRK02224 | PRK02224 | DNA double-strand break repair Rad50 ATPase; |
470-567 | 9.81e-03 | ||||||
DNA double-strand break repair Rad50 ATPase; Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 39.64 E-value: 9.81e-03
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