RIMS-binding protein 2 isoform X8 [Homo sapiens]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| SH3_RIM-BP_1 | cd12014 | First Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs ... |
309-369 | 4.51e-37 | |||||
First Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. : Pssm-ID: 212947 Cd Length: 62 Bit Score: 132.86 E-value: 4.51e-37
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| Smc super family | cl34174 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
73-203 | 2.10e-06 | |||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; The actual alignment was detected with superfamily member COG1196: Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 51.48 E-value: 2.10e-06
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| FN3 super family | cl27307 | Fibronectin type 3 domain [General function prediction only]; |
419-685 | 1.02e-05 | |||||
Fibronectin type 3 domain [General function prediction only]; The actual alignment was detected with superfamily member COG3401: Pssm-ID: 442628 [Multi-domain] Cd Length: 603 Bit Score: 49.23 E-value: 1.02e-05
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| Name | Accession | Description | Interval | E-value | |||||
| SH3_RIM-BP_1 | cd12014 | First Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs ... |
309-369 | 4.51e-37 | |||||
First Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212947 Cd Length: 62 Bit Score: 132.86 E-value: 4.51e-37
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| SH3 | smart00326 | Src homology 3 domains; Src homology 3 (SH3) domains bind to target proteins through sequences ... |
306-367 | 8.84e-10 | |||||
Src homology 3 domains; Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations. Pssm-ID: 214620 [Multi-domain] Cd Length: 56 Bit Score: 55.24 E-value: 8.84e-10
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| SH3_9 | pfam14604 | Variant SH3 domain; |
312-368 | 8.45e-07 | |||||
Variant SH3 domain; Pssm-ID: 434066 [Multi-domain] Cd Length: 49 Bit Score: 46.46 E-value: 8.45e-07
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
73-203 | 2.10e-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: 2.10e-06
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| FN3 | COG3401 | Fibronectin type 3 domain [General function prediction only]; |
419-685 | 1.02e-05 | |||||
Fibronectin type 3 domain [General function prediction only]; Pssm-ID: 442628 [Multi-domain] Cd Length: 603 Bit Score: 49.23 E-value: 1.02e-05
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| fn3 | pfam00041 | Fibronectin type III domain; |
531-594 | 1.31e-05 | |||||
Fibronectin type III domain; Pssm-ID: 394996 [Multi-domain] Cd Length: 85 Bit Score: 44.33 E-value: 1.31e-05
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| FN3 | cd00063 | Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein ... |
625-711 | 3.00e-05 | |||||
Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases. Pssm-ID: 238020 [Multi-domain] Cd Length: 93 Bit Score: 43.25 E-value: 3.00e-05
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
76-198 | 8.29e-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: 46.59 E-value: 8.29e-05
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| mukB | PRK04863 | chromosome partition protein MukB; |
35-207 | 2.96e-04 | |||||
chromosome partition protein MukB; Pssm-ID: 235316 [Multi-domain] Cd Length: 1486 Bit Score: 44.56 E-value: 2.96e-04
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| Cast | pfam10174 | RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part ... |
92-300 | 3.24e-04 | |||||
RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains. Pssm-ID: 431111 [Multi-domain] Cd Length: 766 Bit Score: 44.43 E-value: 3.24e-04
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| FN3 | smart00060 | Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, ... |
438-515 | 3.28e-04 | |||||
Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins. Pssm-ID: 214495 [Multi-domain] Cd Length: 83 Bit Score: 40.29 E-value: 3.28e-04
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| SPEC | cd00176 | Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members ... |
58-206 | 1.42e-03 | |||||
Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here Pssm-ID: 238103 [Multi-domain] Cd Length: 213 Bit Score: 40.89 E-value: 1.42e-03
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| Name | Accession | Description | Interval | E-value | |||||
| SH3_RIM-BP_1 | cd12014 | First Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs ... |
309-369 | 4.51e-37 | |||||
First Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212947 Cd Length: 62 Bit Score: 132.86 E-value: 4.51e-37
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| SH3_RIM-BP | cd11851 | Src homology 3 domains of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding ... |
309-369 | 5.10e-29 | |||||
Src homology 3 domains of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212785 Cd Length: 62 Bit Score: 110.10 E-value: 5.10e-29
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| SH3_RIM-BP_3 | cd12013 | Third Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs ... |
311-367 | 1.14e-20 | |||||
Third Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212946 Cd Length: 61 Bit Score: 86.28 E-value: 1.14e-20
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| SH3_RIM-BP_2 | cd12012 | Second Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs ... |
311-367 | 2.31e-14 | |||||
Second Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212945 Cd Length: 62 Bit Score: 68.09 E-value: 2.31e-14
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| SH3 | smart00326 | Src homology 3 domains; Src homology 3 (SH3) domains bind to target proteins through sequences ... |
306-367 | 8.84e-10 | |||||
Src homology 3 domains; Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations. Pssm-ID: 214620 [Multi-domain] Cd Length: 56 Bit Score: 55.24 E-value: 8.84e-10
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| SH3 | cd00174 | Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction ... |
310-366 | 4.97e-08 | |||||
Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction. Pssm-ID: 212690 [Multi-domain] Cd Length: 51 Bit Score: 49.77 E-value: 4.97e-08
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| SH3_9 | pfam14604 | Variant SH3 domain; |
312-368 | 8.45e-07 | |||||
Variant SH3 domain; Pssm-ID: 434066 [Multi-domain] Cd Length: 49 Bit Score: 46.46 E-value: 8.45e-07
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
73-203 | 2.10e-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: 2.10e-06
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| MukB | COG3096 | Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell ... |
35-207 | 2.54e-06 | |||||
Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 442330 [Multi-domain] Cd Length: 1470 Bit Score: 51.49 E-value: 2.54e-06
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
49-215 | 2.62e-06 | |||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 51.31 E-value: 2.62e-06
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| SH3_CD2AP-like_2 | cd11874 | Second Src Homology 3 domain (SH3B) of CD2-associated protein and similar proteins; This ... |
310-367 | 9.54e-06 | |||||
Second Src Homology 3 domain (SH3B) of CD2-associated protein and similar proteins; This subfamily is composed of the second SH3 domain (SH3B) of CD2AP, CIN85 (Cbl-interacting protein of 85 kDa), and similar domains. CD2AP and CIN85 are adaptor proteins that bind to protein partners and assemble complexes that have been implicated in T cell activation, kidney function, and apoptosis of neuronal cells. They also associate with endocytic proteins, actin cytoskeleton components, and other adaptor proteins involved in receptor tyrosine kinase (RTK) signaling. CD2AP and the main isoform of CIN85 contain three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CD2AP and CIN85 to bind various protein partners and assemble complexes that have been implicated in many different functions. SH3B of both proteins have been shown to bind to Cbl. In the case of CD2AP, its SH3B binds to Cbl at a site distinct from the c-Cbl/SH3A binding site. The CIN85 SH3B also binds ubiquitin. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212807 [Multi-domain] Cd Length: 53 Bit Score: 43.48 E-value: 9.54e-06
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| FN3 | COG3401 | Fibronectin type 3 domain [General function prediction only]; |
419-685 | 1.02e-05 | |||||
Fibronectin type 3 domain [General function prediction only]; Pssm-ID: 442628 [Multi-domain] Cd Length: 603 Bit Score: 49.23 E-value: 1.02e-05
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| fn3 | pfam00041 | Fibronectin type III domain; |
531-594 | 1.31e-05 | |||||
Fibronectin type III domain; Pssm-ID: 394996 [Multi-domain] Cd Length: 85 Bit Score: 44.33 E-value: 1.31e-05
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| SH3_Nostrin | cd11823 | Src homology 3 domain of Nitric Oxide Synthase TRaffic INducer; Nostrin is expressed in ... |
310-368 | 1.43e-05 | |||||
Src homology 3 domain of Nitric Oxide Synthase TRaffic INducer; Nostrin is expressed in endothelial and epithelial cells and is involved in the regulation, trafficking and targeting of endothelial NOS (eNOS). It facilitates the endocytosis of eNOS by coordinating the functions of dynamin and the Wiskott-Aldrich syndrome protein (WASP). Increased expression of Nostrin may be correlated to preeclampsia. Nostrin contains an N-terminal F-BAR domain and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212757 [Multi-domain] Cd Length: 53 Bit Score: 43.10 E-value: 1.43e-05
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| FN3 | cd00063 | Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein ... |
625-711 | 3.00e-05 | |||||
Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases. Pssm-ID: 238020 [Multi-domain] Cd Length: 93 Bit Score: 43.25 E-value: 3.00e-05
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
76-198 | 8.29e-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: 46.59 E-value: 8.29e-05
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| SH3_2 | pfam07653 | Variant SH3 domain; SH3 (Src homology 3) domains are often indicative of a protein involved in ... |
323-367 | 1.09e-04 | |||||
Variant SH3 domain; SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organization. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel. Pssm-ID: 429575 [Multi-domain] Cd Length: 54 Bit Score: 40.66 E-value: 1.09e-04
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| SH3_PACSIN3 | cd11997 | Src homology 3 domain of Protein kinase C and Casein kinase Substrate in Neurons 3 (PACSIN3); ... |
329-368 | 1.41e-04 | |||||
Src homology 3 domain of Protein kinase C and Casein kinase Substrate in Neurons 3 (PACSIN3); PACSIN 3 or Syndapin III (Synaptic dynamin-associated protein III) is expressed ubiquitously and regulates glucose uptake in adipocytes through its role in GLUT1 trafficking. It also modulates the subcellular localization and stimulus-specific function of the cation channel TRPV4. PACSINs act as regulators of cytoskeletal and membrane dynamics. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSINs contain an N-terminal F-BAR domain and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212930 [Multi-domain] Cd Length: 56 Bit Score: 40.33 E-value: 1.41e-04
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| FN3 | cd00063 | Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein ... |
531-595 | 2.13e-04 | |||||
Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases. Pssm-ID: 238020 [Multi-domain] Cd Length: 93 Bit Score: 40.94 E-value: 2.13e-04
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| mukB | PRK04863 | chromosome partition protein MukB; |
35-207 | 2.96e-04 | |||||
chromosome partition protein MukB; Pssm-ID: 235316 [Multi-domain] Cd Length: 1486 Bit Score: 44.56 E-value: 2.96e-04
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| Cast | pfam10174 | RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part ... |
92-300 | 3.24e-04 | |||||
RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains. Pssm-ID: 431111 [Multi-domain] Cd Length: 766 Bit Score: 44.43 E-value: 3.24e-04
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| FN3 | smart00060 | Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, ... |
438-515 | 3.28e-04 | |||||
Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins. Pssm-ID: 214495 [Multi-domain] Cd Length: 83 Bit Score: 40.29 E-value: 3.28e-04
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
50-207 | 3.41e-04 | |||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 44.54 E-value: 3.41e-04
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| FN3 | cd00063 | Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein ... |
438-519 | 3.58e-04 | |||||
Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases. Pssm-ID: 238020 [Multi-domain] Cd Length: 93 Bit Score: 40.56 E-value: 3.58e-04
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| SH3_CIN85_2 | cd12055 | Second Src Homology 3 domain (SH3B) of Cbl-interacting protein of 85 kDa; CIN85, also called ... |
310-367 | 3.62e-04 | |||||
Second Src Homology 3 domain (SH3B) of Cbl-interacting protein of 85 kDa; CIN85, also called SH3 domain-containing kinase-binding protein 1 (SH3KBP1) or CD2-binding protein 3 (CD2BP3) or Ruk, is an adaptor protein that is involved in the downregulation of receptor tyrosine kinases by facilitating endocytosis through interaction with endophilin-associated ubiquitin ligase Cbl proteins. It is also important in many other cellular processes including vesicle-mediated transport, cytoskeletal remodelling, apoptosis, cell adhesion and migration, and viral infection, among others. CIN85 exists as multiple variants from alternative splicing; the main variant contains three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CIN85 to bind various protein partners and assemble complexes that have been implicated in many different functions. This alignment model represents the second SH3 domain (SH3B) of CIN85. SH3B has been shown to bind Cbl proline-rich peptides and ubiquitin. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212988 [Multi-domain] Cd Length: 53 Bit Score: 39.21 E-value: 3.62e-04
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| SH3_PACSIN1-2 | cd11998 | Src homology 3 domain of Protein kinase C and Casein kinase Substrate in Neurons 1 (PACSIN1) ... |
312-368 | 4.07e-04 | |||||
Src homology 3 domain of Protein kinase C and Casein kinase Substrate in Neurons 1 (PACSIN1) and PACSIN 2; PACSIN 1 or Syndapin I (Synaptic dynamin-associated protein I) is expressed specifically in the brain and is localized in neurites and synaptic boutons. It binds the brain-specific proteins dynamin I, synaptojanin, synapsin I, and neural Wiskott-Aldrich syndrome protein (nWASP), and functions as a link between the cytoskeletal machinery and synaptic vesicle endocytosis. PACSIN 1 interacts with huntingtin and may be implicated in the neuropathology of Huntington's disease. PACSIN 2 or Syndapin II is expressed ubiquitously and is involved in the regulation of tubulin polymerization. It associates with Golgi membranes and forms a complex with dynamin II which is crucial in promoting vesicle formation from the trans-Golgi network. PACSINs act as regulators of cytoskeletal and membrane dynamics. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSINs contain an N-terminal F-BAR domain and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212931 [Multi-domain] Cd Length: 56 Bit Score: 39.16 E-value: 4.07e-04
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| SH3_D21-like | cd12142 | Src Homology 3 domain of SH3 domain-containing protein 21 (SH3D21) and similar proteins; ... |
310-367 | 4.72e-04 | |||||
Src Homology 3 domain of SH3 domain-containing protein 21 (SH3D21) and similar proteins; N-terminal SH3 domain of the uncharacterized protein SH3 domain-containing protein 21, and similar uncharacterized domains, it belongs to the CD2AP-like_3 subfamily of proteins. The CD2AP-like_3 subfamily is composed of the third SH3 domain (SH3C) of CD2AP, CIN85 (Cbl-interacting protein of 85 kDa), and similar domains. CD2AP and CIN85 are adaptor proteins that bind to protein partners and assemble complexes that have been implicated in T cell activation, kidney function, and apoptosis of neuronal cells. They also associate with endocytic proteins, actin cytoskeleton components, and other adaptor proteins involved in receptor tyrosine kinase (RTK) signaling. CD2AP and the main isoform of CIN85 contain three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CD2AP and CIN85 to bind various protein partners and assemble complexes that have been implicated in many different functions. SH3C of both proteins have been shown to bind to ubiquitin. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 213018 [Multi-domain] Cd Length: 55 Bit Score: 38.99 E-value: 4.72e-04
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| SH3_SNX9_like | cd11763 | Src Homology 3 domain of Sorting Nexin 9 and similar proteins; Sorting nexins (SNXs) are Phox ... |
326-367 | 4.80e-04 | |||||
Src Homology 3 domain of Sorting Nexin 9 and similar proteins; Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. This subfamily consists of SH3 domain containing SNXs including SNX9, SNX18, SNX33, and similar proteins. SNX9 is localized to plasma membrane endocytic sites and acts primarily in clathrin-mediated endocytosis, while SNX18 is localized to peripheral endosomal structures, and acts in a trafficking pathway that is clathrin-independent but relies on AP-1 and PACS1. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212697 [Multi-domain] Cd Length: 55 Bit Score: 38.85 E-value: 4.80e-04
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
96-198 | 5.09e-04 | |||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 43.77 E-value: 5.09e-04
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| FN3 | smart00060 | Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, ... |
625-711 | 5.74e-04 | |||||
Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins. Pssm-ID: 214495 [Multi-domain] Cd Length: 83 Bit Score: 39.52 E-value: 5.74e-04
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
43-200 | 5.79e-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: 43.89 E-value: 5.79e-04
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| DR0291 | COG1579 | Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ... |
106-181 | 7.00e-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: 42.22 E-value: 7.00e-04
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| RNase_Y_N | pfam12072 | RNase Y N-terminal region; |
44-187 | 7.90e-04 | |||||
RNase Y N-terminal region; Pssm-ID: 463456 [Multi-domain] Cd Length: 201 Bit Score: 41.41 E-value: 7.90e-04
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| DUF4659 | pfam15558 | Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins ... |
102-203 | 8.26e-04 | |||||
Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins in this family are typically between 427 and 674 amino acids in length. There are two completely conserved residues (D and I) that may be functionally important. Pssm-ID: 464768 [Multi-domain] Cd Length: 374 Bit Score: 42.72 E-value: 8.26e-04
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| HMMR_N | pfam15905 | Hyaluronan mediated motility receptor N-terminal; HMMR_N is the N-terminal region of ... |
74-199 | 1.03e-03 | |||||
Hyaluronan mediated motility receptor N-terminal; HMMR_N is the N-terminal region of eukaryotic hyaluronan-mediated motility receptor proteins. The protein is functionally associated with BRCA1 and thus predicted to be a common, low-penetrance breast cancer candidate. Pssm-ID: 464932 [Multi-domain] Cd Length: 329 Bit Score: 42.11 E-value: 1.03e-03
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
75-201 | 1.04e-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: 42.74 E-value: 1.04e-03
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| FN3 | smart00060 | Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, ... |
531-595 | 1.12e-03 | |||||
Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins. Pssm-ID: 214495 [Multi-domain] Cd Length: 83 Bit Score: 38.75 E-value: 1.12e-03
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| DR0291 | COG1579 | Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ... |
96-218 | 1.22e-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: 41.45 E-value: 1.22e-03
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| SH3_SH3RF2_3 | cd11784 | Third Src Homology 3 domain of SH3 domain containing ring finger 2; SH3RF2 is also called ... |
309-367 | 1.30e-03 | |||||
Third Src Homology 3 domain of SH3 domain containing ring finger 2; SH3RF2 is also called POSHER (POSH-eliminating RING protein) or HEPP1 (heart protein phosphatase 1-binding protein). It acts as an anti-apoptotic regulator of the JNK pathway by binding to and promoting the degradation of SH3RF1 (or POSH), a scaffold protein that is required for pro-apoptotic JNK activation. It may also play a role in cardiac functions together with protein phosphatase 1. SH3RF2 contains an N-terminal RING finger domain and three SH3 domains. This model represents the third SH3 domain, located in the middle, of SH3RF2. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212718 Cd Length: 55 Bit Score: 37.83 E-value: 1.30e-03
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| Jnk-SapK_ap_N | pfam09744 | JNK_SAPK-associated protein-1; This is the N-terminal 200 residues of a set of proteins ... |
112-207 | 1.35e-03 | |||||
JNK_SAPK-associated protein-1; This is the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have an RhoGEF pfam00621 domain at their C-terminal end. Pssm-ID: 462875 [Multi-domain] Cd Length: 150 Bit Score: 39.91 E-value: 1.35e-03
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| SPEC | cd00176 | Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members ... |
58-206 | 1.42e-03 | |||||
Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here Pssm-ID: 238103 [Multi-domain] Cd Length: 213 Bit Score: 40.89 E-value: 1.42e-03
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| SH3_Endophilin_A | cd11803 | Src homology 3 domain of Endophilin-A; Endophilins play roles in synaptic vesicle formation, ... |
310-370 | 1.51e-03 | |||||
Src homology 3 domain of Endophilin-A; Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. They are classified into two types, A and B. Vertebrates contain three endophilin-A isoforms (A1, A2, and A3). Endophilin-A proteins are enriched in the brain and play multiple roles in receptor-mediated endocytosis. They tubulate membranes and regulate calcium influx into neurons to trigger the activation of the endocytic machinery. They are also involved in the sorting of plasma membrane proteins, actin filament assembly, and the uncoating of clathrin-coated vesicles for fusion with endosomes. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212737 [Multi-domain] Cd Length: 55 Bit Score: 37.24 E-value: 1.51e-03
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
68-203 | 1.59e-03 | |||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 42.21 E-value: 1.59e-03
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| SH3_1 | pfam00018 | SH3 domain; SH3 (Src homology 3) domains are often indicative of a protein involved in signal ... |
311-364 | 1.59e-03 | |||||
SH3 domain; SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organization. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel. Pssm-ID: 394975 [Multi-domain] Cd Length: 47 Bit Score: 37.18 E-value: 1.59e-03
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| FN3 | COG3401 | Fibronectin type 3 domain [General function prediction only]; |
624-723 | 1.78e-03 | |||||
Fibronectin type 3 domain [General function prediction only]; Pssm-ID: 442628 [Multi-domain] Cd Length: 603 Bit Score: 41.91 E-value: 1.78e-03
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| CwlO1 | COG3883 | Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ... |
111-271 | 2.11e-03 | |||||
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown]; Pssm-ID: 443091 [Multi-domain] Cd Length: 379 Bit Score: 41.35 E-value: 2.11e-03
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
44-201 | 2.49e-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: 2.49e-03
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| TPH | pfam13868 | Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ... |
96-188 | 2.66e-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: 41.06 E-value: 2.66e-03
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| DUF4659 | pfam15558 | Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins ... |
98-189 | 2.76e-03 | |||||
Domain of unknown function (DUF4659); This family of proteins is found in eukaryotes. Proteins in this family are typically between 427 and 674 amino acids in length. There are two completely conserved residues (D and I) that may be functionally important. Pssm-ID: 464768 [Multi-domain] Cd Length: 374 Bit Score: 41.18 E-value: 2.76e-03
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| Mod_r | pfam07200 | Modifier of rudimentary (Mod(r)) protein; This family represents a conserved region ... |
76-199 | 2.84e-03 | |||||
Modifier of rudimentary (Mod(r)) protein; This family represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic, and both of these regions are represented in this family. Members of this family include the Vps37 subunit of the endosomal sorting complex ESCRT-I, a complex involved in recruiting transport machinery for protein sorting at the multivesicular body (MVB). The yeast ESCRT-I complex consists of three proteins (Vps23, Vps28 and Vps37). The mammalian homolog of Vps37 interacts with Tsg101 (Pfam: PF05743) through its mod(r) domain and its function is essential for lysosomal sorting of EGF receptors. Pssm-ID: 462117 [Multi-domain] Cd Length: 146 Bit Score: 39.14 E-value: 2.84e-03
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
103-202 | 2.88e-03 | |||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 41.44 E-value: 2.88e-03
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| SH3_Bem1p_1 | cd11878 | First Src Homology 3 domain of Bud emergence protein 1 and similar domains; Members of this ... |
312-366 | 3.06e-03 | |||||
First Src Homology 3 domain of Bud emergence protein 1 and similar domains; Members of this subfamily bear similarity to Saccharomyces cerevisiae Bem1p, containing two Src Homology 3 (SH3) domains at the N-terminus, a central PX domain, and a C-terminal PB1 domain. Bem1p is a scaffolding protein that is critical for proper Cdc42p activation during bud formation in yeast. During budding and mating, Bem1p migrates to the plasma membrane where it can serve as an adaptor for Cdc42p and some other proteins. Bem1p also functions as an effector of the G1 cyclin Cln3p and the cyclin-dependent kinase Cdc28p in promoting vacuolar fusion. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. Pssm-ID: 212811 [Multi-domain] Cd Length: 54 Bit Score: 36.50 E-value: 3.06e-03
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
74-204 | 3.27e-03 | |||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 41.44 E-value: 3.27e-03
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
101-204 | 3.49e-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: 41.21 E-value: 3.49e-03
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
96-209 | 3.51e-03 | |||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 40.91 E-value: 3.51e-03
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
96-201 | 3.53e-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: 3.53e-03
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| PRK12704 | PRK12704 | phosphodiesterase; Provisional |
96-188 | 3.65e-03 | |||||
phosphodiesterase; Provisional Pssm-ID: 237177 [Multi-domain] Cd Length: 520 Bit Score: 40.92 E-value: 3.65e-03
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| SH3_Pex13p_fungal | cd11771 | Src Homology 3 domain of fungal peroxisomal membrane protein Pex13p; Pex13p, located in the ... |
310-367 | 3.74e-03 | |||||
Src Homology 3 domain of fungal peroxisomal membrane protein Pex13p; Pex13p, located in the peroxisomal membrane, contains two transmembrane regions and a C-terminal SH3 domain. It binds to the peroxisomal targeting type I (PTS1) receptor Pex5p and the docking factor Pex14p through its SH3 domain. It is essential for both PTS1 and PTS2 protein import pathways into the peroxisomal matrix. Pex13p binds Pex14p, which contains a PxxP motif, in a classical fashion to the proline-rich ligand binding site of its SH3 domain. It binds the WxxxF/Y motif of Pex5p in a novel site that does not compete with Pex14p binding. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212705 [Multi-domain] Cd Length: 60 Bit Score: 36.49 E-value: 3.74e-03
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
91-206 | 3.93e-03 | |||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 40.66 E-value: 3.93e-03
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| fn3 | pfam00041 | Fibronectin type III domain; |
436-517 | 4.03e-03 | |||||
Fibronectin type III domain; Pssm-ID: 394996 [Multi-domain] Cd Length: 85 Bit Score: 37.01 E-value: 4.03e-03
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| DUF4200 | pfam13863 | Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil ... |
145-206 | 4.75e-03 | |||||
Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil domain of unknwon function. Pssm-ID: 464003 [Multi-domain] Cd Length: 119 Bit Score: 37.93 E-value: 4.75e-03
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
44-168 | 4.98e-03 | |||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 40.52 E-value: 4.98e-03
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| SH3_CD2AP_1 | cd12053 | First Src Homology 3 domain (SH3A) of CD2-associated protein; CD2AP, also called CMS (Cas ... |
327-371 | 5.31e-03 | |||||
First Src Homology 3 domain (SH3A) of CD2-associated protein; CD2AP, also called CMS (Cas ligand with Multiple SH3 domains) or METS1 (Mesenchyme-to-Epithelium Transition protein with SH3 domains), is a cytosolic adaptor protein that plays a role in regulating the cytoskeleton. It is critical in cell-to-cell union necessary for kidney function. It also stabilizes the contact between a T cell and antigen-presenting cells. It is primarily expressed in podocytes at the cytoplasmic face of the slit diaphragm and serves as a linker anchoring podocin and nephrin to the actin cytoskeleton. CD2AP contains three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CD2AP to bind various protein partners and assemble complexes that have been implicated in many different functions. This alignment model represents the first SH3 domain (SH3A) of CD2AP. SH3A binds to the PXXXPR motif present in c-Cbl and the cytoplasmic domain of cell adhesion protein CD2. Its interaction with CD2 anchors CD2 at sites of cell contact. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212986 Cd Length: 56 Bit Score: 35.97 E-value: 5.31e-03
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| SH3_SH3RF_C | cd11785 | C-terminal (Fourth) Src Homology 3 domain of SH3 domain containing ring finger 1 (SH3RF1), ... |
325-368 | 5.59e-03 | |||||
C-terminal (Fourth) Src Homology 3 domain of SH3 domain containing ring finger 1 (SH3RF1), SH3RF3, and similar domains; SH3RF1 (or POSH) and SH3RF3 (or POSH2) are scaffold proteins that function as E3 ubiquitin-protein ligases. They contain an N-terminal RING finger domain and four SH3 domains. This model represents the fourth SH3 domain, located at the C-terminus of SH3RF1 and SH3RF3, and similar domains. SH3RF1 plays a role in calcium homeostasis through the control of the ubiquitin domain protein Herp. It may also have a role in regulating death receptor mediated and JNK mediated apoptosis. SH3RF3 interacts with p21-activated kinase 2 (PAK2) and GTP-loaded Rac1. It may play a role in regulating JNK mediated apoptosis in certain conditions. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212719 Cd Length: 55 Bit Score: 35.90 E-value: 5.59e-03
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| ERM_helical | pfam20492 | Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ... |
96-187 | 5.65e-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: 37.59 E-value: 5.65e-03
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| sbcc | TIGR00618 | exonuclease SbcC; All proteins in this family for which functions are known are part of an ... |
70-206 | 5.94e-03 | |||||
exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 129705 [Multi-domain] Cd Length: 1042 Bit Score: 40.34 E-value: 5.94e-03
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| COG1340 | COG1340 | Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; |
83-201 | 5.94e-03 | |||||
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Pssm-ID: 440951 [Multi-domain] Cd Length: 297 Bit Score: 39.51 E-value: 5.94e-03
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| SH3_ephexin1_like | cd11793 | Src homology 3 domain of ephexin-1-like SH3 domain containing Rho guanine nucleotide exchange ... |
329-369 | 6.82e-03 | |||||
Src homology 3 domain of ephexin-1-like SH3 domain containing Rho guanine nucleotide exchange factors; Members of this family contain RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), and C-terminal SH3 domains. They include the Rho guanine nucleotide exchange factors ARHGEF5, ARHGEF16, ARHGEF19, ARHGEF26, ARHGEF27 (also called ephexin-1), and similar proteins, and are also called ephexins because they interact directly with ephrin A receptors. GEFs interact with Rho GTPases via their DH domains to catalyze nucleotide exchange by stabilizing the nucleotide-free GTPase intermediate. They play important roles in neuronal development. The SH3 domains of ARHGEFs play an autoinhibitory role through intramolecular interactions with a proline-rich region N-terminal to the DH domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212727 [Multi-domain] Cd Length: 55 Bit Score: 35.77 E-value: 6.82e-03
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| SH3_GRAF-like | cd11882 | Src Homology 3 domain of GTPase Regulator Associated with Focal adhesion kinase and similar ... |
345-369 | 6.99e-03 | |||||
Src Homology 3 domain of GTPase Regulator Associated with Focal adhesion kinase and similar proteins; This subfamily is composed of Rho GTPase activating proteins (GAPs) with similarity to GRAF. Members contain an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. Although vertebrates harbor four Rho GAPs in the GRAF subfamily including GRAF, GRAF2, GRAF3, and Oligophrenin-1 (OPHN1), only three are included in this model. OPHN1 contains the BAR, PH and GAP domains, but not the C-terminal SH3 domain. GRAF and GRAF2 show GAP activity towards RhoA and Cdc42. GRAF influences Rho-mediated cytoskeletal rearrangements and binds focal adhesion kinase. GRAF2 regulates caspase-activated p21-activated protein kinase-2. The SH3 domain of GRAF and GRAF2 binds PKNbeta, a target of the small GTPase Rho. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. Pssm-ID: 212815 [Multi-domain] Cd Length: 54 Bit Score: 35.35 E-value: 6.99e-03
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| SH3_CD2AP-like_3 | cd11875 | Third Src Homology 3 domain (SH3C) of CD2-associated protein and similar proteins; This ... |
310-367 | 7.98e-03 | |||||
Third Src Homology 3 domain (SH3C) of CD2-associated protein and similar proteins; This subfamily is composed of the third SH3 domain (SH3C) of CD2AP, CIN85 (Cbl-interacting protein of 85 kDa), and similar domains. CD2AP and CIN85 are adaptor proteins that bind to protein partners and assemble complexes that have been implicated in T cell activation, kidney function, and apoptosis of neuronal cells. They also associate with endocytic proteins, actin cytoskeleton components, and other adaptor proteins involved in receptor tyrosine kinase (RTK) signaling. CD2AP and the main isoform of CIN85 contain three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CD2AP and CIN85 to bind various protein partners and assemble complexes that have been implicated in many different functions. SH3C of both proteins have been shown to bind to ubiquitin. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212808 [Multi-domain] Cd Length: 55 Bit Score: 35.40 E-value: 7.98e-03
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
103-181 | 8.58e-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: 39.44 E-value: 8.58e-03
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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 ... |
97-198 | 9.05e-03 | |||||
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: 39.95 E-value: 9.05e-03
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| SH3_Abi | cd11826 | Src homology 3 domain of Abl Interactor proteins; Abl interactor (Abi) proteins are adaptor ... |
311-368 | 9.48e-03 | |||||
Src homology 3 domain of Abl Interactor proteins; Abl interactor (Abi) proteins are adaptor proteins serving as binding partners and substrates of Abl tyrosine kinases. They are involved in regulating actin cytoskeletal reorganization and play important roles in membrane-ruffling, endocytosis, cell motility, and cell migration. They localize to sites of actin polymerization in epithelial adherens junction and immune synapses, as well as to the leading edge of lamellipodia. Vertebrates contain two Abi proteins, Abi1 and Abi2. Abi1 displays a wide expression pattern while Abi2 is highly expressed in the eye and brain. Abi proteins contain a homeobox homology domain, a proline-rich region, and a SH3 domain. The SH3 domain of Abi binds to a PxxP motif in Abl. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. Pssm-ID: 212760 [Multi-domain] Cd Length: 52 Bit Score: 34.99 E-value: 9.48e-03
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