chromosome segregation protein SMC [Mycoplasmoides genitalium]
Protein Classification
chromosome segregation protein SMC( domain architecture ID 11493846)
chromosome segregation protein SMC is required for chromosome condensation and partitioning
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||||||||||
| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
3-969 | 0e+00 | ||||||||||||||||
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: 884.01 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | ||||||||||||||||
| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
3-969 | 0e+00 | ||||||||||||||||
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: 884.01 E-value: 0e+00
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
2-978 | 3.10e-151 | ||||||||||||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 473.27 E-value: 3.10e-151
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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 ... |
3-963 | 2.93e-110 | ||||||||||||||||
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: 368.14 E-value: 2.93e-110
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| ABC_SMC_barmotin | cd03278 | ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ... |
863-963 | 4.41e-45 | ||||||||||||||||
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). Pssm-ID: 213245 [Multi-domain] Cd Length: 197 Bit Score: 161.09 E-value: 4.41e-45
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| SMC_hinge | smart00968 | SMC proteins Flexible Hinge Domain; This entry represents the hinge region of the SMC ... |
417-535 | 9.59e-31 | ||||||||||||||||
SMC proteins Flexible Hinge Domain; This entry represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction. Pssm-ID: 214944 [Multi-domain] Cd Length: 120 Bit Score: 117.33 E-value: 9.59e-31
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| PRK01156 | PRK01156 | chromosome segregation protein; Provisional |
4-940 | 2.99e-09 | ||||||||||||||||
chromosome segregation protein; Provisional Pssm-ID: 100796 [Multi-domain] Cd Length: 895 Bit Score: 61.07 E-value: 2.99e-09
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| Name | Accession | Description | Interval | E-value | ||||||||||||||||
| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
3-969 | 0e+00 | ||||||||||||||||
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: 884.01 E-value: 0e+00
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
2-978 | 3.10e-151 | ||||||||||||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 473.27 E-value: 3.10e-151
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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 ... |
3-963 | 2.93e-110 | ||||||||||||||||
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: 368.14 E-value: 2.93e-110
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
3-969 | 5.25e-80 | ||||||||||||||||
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: 283.11 E-value: 5.25e-80
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| ABC_SMC_barmotin | cd03278 | ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ... |
863-963 | 4.41e-45 | ||||||||||||||||
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). Pssm-ID: 213245 [Multi-domain] Cd Length: 197 Bit Score: 161.09 E-value: 4.41e-45
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| ABC_SMC_barmotin | cd03278 | ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ... |
4-92 | 6.77e-41 | ||||||||||||||||
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). Pssm-ID: 213245 [Multi-domain] Cd Length: 197 Bit Score: 149.15 E-value: 6.77e-41
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| SMC_hinge | smart00968 | SMC proteins Flexible Hinge Domain; This entry represents the hinge region of the SMC ... |
417-535 | 9.59e-31 | ||||||||||||||||
SMC proteins Flexible Hinge Domain; This entry represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction. Pssm-ID: 214944 [Multi-domain] Cd Length: 120 Bit Score: 117.33 E-value: 9.59e-31
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| ABC_SMC1_euk | cd03275 | ATP-binding cassette domain of eukaryotic SMC1 proteins; The structural maintenance of ... |
4-135 | 1.51e-24 | ||||||||||||||||
ATP-binding cassette domain of eukaryotic SMC1 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). Pssm-ID: 213242 [Multi-domain] Cd Length: 247 Bit Score: 103.81 E-value: 1.51e-24
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| SMC_hinge | pfam06470 | SMC proteins Flexible Hinge Domain; This family represents the hinge region of the SMC ... |
415-536 | 1.32e-22 | ||||||||||||||||
SMC proteins Flexible Hinge Domain; This family represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction. Pssm-ID: 461926 [Multi-domain] Cd Length: 116 Bit Score: 93.87 E-value: 1.32e-22
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| ABC_SMC1_euk | cd03275 | ATP-binding cassette domain of eukaryotic SMC1 proteins; The structural maintenance of ... |
868-953 | 3.15e-17 | ||||||||||||||||
ATP-binding cassette domain of eukaryotic SMC1 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). Pssm-ID: 213242 [Multi-domain] Cd Length: 247 Bit Score: 82.24 E-value: 3.15e-17
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| ABC_SMC_head | cd03239 | The SMC head domain belongs to the ATP-binding cassette superfamily; The structural ... |
4-92 | 3.60e-17 | ||||||||||||||||
The SMC head domain belongs to the ATP-binding cassette superfamily; The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression. Pssm-ID: 213206 [Multi-domain] Cd Length: 178 Bit Score: 80.43 E-value: 3.60e-17
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| ABC_SMC2_euk | cd03273 | ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of ... |
11-148 | 1.45e-16 | ||||||||||||||||
ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). Pssm-ID: 213240 [Multi-domain] Cd Length: 251 Bit Score: 80.42 E-value: 1.45e-16
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| ABC_SMC_head | cd03239 | The SMC head domain belongs to the ATP-binding cassette superfamily; The structural ... |
879-963 | 1.61e-16 | ||||||||||||||||
The SMC head domain belongs to the ATP-binding cassette superfamily; The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression. Pssm-ID: 213206 [Multi-domain] Cd Length: 178 Bit Score: 78.50 E-value: 1.61e-16
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| ABC_SMC3_euk | cd03272 | ATP-binding cassette domain of eukaryotic SMC3 proteins; The structural maintenance of ... |
4-162 | 5.82e-16 | ||||||||||||||||
ATP-binding cassette domain of eukaryotic SMC3 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). Pssm-ID: 213239 [Multi-domain] Cd Length: 243 Bit Score: 78.46 E-value: 5.82e-16
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| SbcC | COG0419 | DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; |
4-179 | 8.16e-15 | ||||||||||||||||
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]; Pssm-ID: 440188 [Multi-domain] Cd Length: 204 Bit Score: 74.28 E-value: 8.16e-15
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| ABC_SMC4_euk | cd03274 | ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of ... |
872-964 | 1.45e-13 | ||||||||||||||||
ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). Pssm-ID: 213241 [Multi-domain] Cd Length: 212 Bit Score: 70.79 E-value: 1.45e-13
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| ABC_SMC2_euk | cd03273 | ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of ... |
876-943 | 6.28e-13 | ||||||||||||||||
ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). Pssm-ID: 213240 [Multi-domain] Cd Length: 251 Bit Score: 69.63 E-value: 6.28e-13
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| ABC_SMC4_euk | cd03274 | ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of ... |
3-85 | 1.89e-12 | ||||||||||||||||
ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). Pssm-ID: 213241 [Multi-domain] Cd Length: 212 Bit Score: 67.32 E-value: 1.89e-12
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| ABC_Class2 | cd03227 | ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ... |
877-963 | 2.63e-12 | ||||||||||||||||
ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterized by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins. Pssm-ID: 213194 [Multi-domain] Cd Length: 162 Bit Score: 65.84 E-value: 2.63e-12
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| ABC_ATPase | cd00267 | ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large ... |
857-952 | 2.17e-11 | ||||||||||||||||
ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. Pssm-ID: 213179 [Multi-domain] Cd Length: 157 Bit Score: 63.03 E-value: 2.17e-11
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| ABC_SMC3_euk | cd03272 | ATP-binding cassette domain of eukaryotic SMC3 proteins; The structural maintenance of ... |
880-941 | 2.49e-11 | ||||||||||||||||
ATP-binding cassette domain of eukaryotic SMC3 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). Pssm-ID: 213239 [Multi-domain] Cd Length: 243 Bit Score: 64.97 E-value: 2.49e-11
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| ABC_Rad50 | cd03240 | ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ... |
4-105 | 4.44e-10 | ||||||||||||||||
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence. Pssm-ID: 213207 [Multi-domain] Cd Length: 204 Bit Score: 60.31 E-value: 4.44e-10
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| YbjD | COG3593 | Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ... |
3-98 | 5.74e-10 | ||||||||||||||||
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains [Replication, recombination and repair]; Pssm-ID: 442812 [Multi-domain] Cd Length: 359 Bit Score: 62.33 E-value: 5.74e-10
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| ABC_Class2 | cd03227 | ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ... |
11-60 | 1.33e-09 | ||||||||||||||||
ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterized by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins. Pssm-ID: 213194 [Multi-domain] Cd Length: 162 Bit Score: 58.14 E-value: 1.33e-09
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| ABC_RecN | cd03241 | ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC ... |
17-162 | 2.31e-09 | ||||||||||||||||
ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. Pssm-ID: 213208 [Multi-domain] Cd Length: 276 Bit Score: 59.52 E-value: 2.31e-09
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| COG4637 | COG4637 | Predicted ATPase [General function prediction only]; |
4-89 | 2.78e-09 | ||||||||||||||||
Predicted ATPase [General function prediction only]; Pssm-ID: 443675 [Multi-domain] Cd Length: 371 Bit Score: 60.33 E-value: 2.78e-09
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| ABCC_MRP_Like | cd03228 | ATP-binding cassette domain of multidrug resistance protein-like transporters; The MRP ... |
879-949 | 2.90e-09 | ||||||||||||||||
ATP-binding cassette domain of multidrug resistance protein-like transporters; The MRP (Multidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. Pssm-ID: 213195 [Multi-domain] Cd Length: 171 Bit Score: 57.01 E-value: 2.90e-09
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| PRK01156 | PRK01156 | chromosome segregation protein; Provisional |
4-940 | 2.99e-09 | ||||||||||||||||
chromosome segregation protein; Provisional Pssm-ID: 100796 [Multi-domain] Cd Length: 895 Bit Score: 61.07 E-value: 2.99e-09
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| RecF | COG1195 | Recombinational DNA repair ATPase RecF [Replication, recombination and repair]; |
3-161 | 5.43e-09 | ||||||||||||||||
Recombinational DNA repair ATPase RecF [Replication, recombination and repair]; Pssm-ID: 440808 [Multi-domain] Cd Length: 352 Bit Score: 59.01 E-value: 5.43e-09
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| sbcc | TIGR00618 | exonuclease SbcC; All proteins in this family for which functions are known are part of an ... |
6-398 | 1.20e-08 | ||||||||||||||||
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: 59.21 E-value: 1.20e-08
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| AAA_23 | pfam13476 | AAA domain; |
11-193 | 1.50e-08 | ||||||||||||||||
AAA domain; Pssm-ID: 463890 [Multi-domain] Cd Length: 190 Bit Score: 55.58 E-value: 1.50e-08
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| ABC_cobalt_CbiO_domain1 | cd03225 | First domain of the ATP-binding cassette component of cobalt transport system; Domain I of the ... |
880-941 | 1.44e-07 | ||||||||||||||||
First domain of the ATP-binding cassette component of cobalt transport system; Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems. Pssm-ID: 213192 [Multi-domain] Cd Length: 211 Bit Score: 53.24 E-value: 1.44e-07
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| EcfA2 | COG1122 | Energy-coupling factor transporter ATP-binding protein EcfA2 [Inorganic ion transport and ... |
880-940 | 2.74e-07 | ||||||||||||||||
Energy-coupling factor transporter ATP-binding protein EcfA2 [Inorganic ion transport and metabolism, General function prediction only]; Pssm-ID: 440739 [Multi-domain] Cd Length: 230 Bit Score: 52.72 E-value: 2.74e-07
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| PRK10869 | PRK10869 | recombination and repair protein; Provisional |
18-126 | 1.23e-06 | ||||||||||||||||
recombination and repair protein; Provisional Pssm-ID: 236781 [Multi-domain] Cd Length: 553 Bit Score: 52.24 E-value: 1.23e-06
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| RecN | COG0497 | DNA repair ATPase RecN [Replication, recombination and repair]; |
17-133 | 1.44e-06 | ||||||||||||||||
DNA repair ATPase RecN [Replication, recombination and repair]; Pssm-ID: 440263 [Multi-domain] Cd Length: 555 Bit Score: 52.00 E-value: 1.44e-06
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| ABC_sbcCD | cd03279 | ATP-binding cassette domain of sbcCD; SbcCD and other Mre11/Rad50 (MR) complexes are ... |
11-91 | 2.10e-06 | ||||||||||||||||
ATP-binding cassette domain of sbcCD; SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini. Pssm-ID: 213246 [Multi-domain] Cd Length: 213 Bit Score: 49.57 E-value: 2.10e-06
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| PRK13657 | PRK13657 | glucan ABC transporter ATP-binding protein/ permease; |
880-952 | 4.08e-06 | ||||||||||||||||
glucan ABC transporter ATP-binding protein/ permease; Pssm-ID: 184214 [Multi-domain] Cd Length: 588 Bit Score: 50.73 E-value: 4.08e-06
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
212-835 | 4.14e-06 | ||||||||||||||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 51.07 E-value: 4.14e-06
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| ABCC_MRP_domain2 | cd03244 | ATP-binding cassette domain 2 of multidrug resistance-associated protein; The ABC subfamily C ... |
880-952 | 4.25e-06 | ||||||||||||||||
ATP-binding cassette domain 2 of multidrug resistance-associated protein; The ABC subfamily C is also known as MRP (multidrug resistance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate. Pssm-ID: 213211 [Multi-domain] Cd Length: 221 Bit Score: 49.03 E-value: 4.25e-06
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| ABCC_ATM1_transporter | cd03253 | ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; ATM1 is an ABC ... |
880-952 | 4.37e-06 | ||||||||||||||||
ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; ATM1 is an ABC transporter that is expressed in the mitochondria. Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. Pssm-ID: 213220 [Multi-domain] Cd Length: 236 Bit Score: 49.15 E-value: 4.37e-06
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| PRK03918 | PRK03918 | DNA double-strand break repair ATPase Rad50; |
4-841 | 4.92e-06 | ||||||||||||||||
DNA double-strand break repair ATPase Rad50; Pssm-ID: 235175 [Multi-domain] Cd Length: 880 Bit Score: 50.45 E-value: 4.92e-06
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| ABC_cobalt_CbiO_domain2 | cd03226 | Second domain of the ATP-binding cassette component of cobalt transport system; Domain II of ... |
880-948 | 5.32e-06 | ||||||||||||||||
Second domain of the ATP-binding cassette component of cobalt transport system; Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems. Pssm-ID: 213193 [Multi-domain] Cd Length: 205 Bit Score: 48.41 E-value: 5.32e-06
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| COG1106 | COG1106 | ATPase/GTPase, AAA15 family [General function prediction only]; |
3-91 | 6.99e-06 | ||||||||||||||||
ATPase/GTPase, AAA15 family [General function prediction only]; Pssm-ID: 440723 [Multi-domain] Cd Length: 330 Bit Score: 49.27 E-value: 6.99e-06
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| recF | PRK00064 | recombination protein F; Reviewed |
2-161 | 8.56e-06 | ||||||||||||||||
recombination protein F; Reviewed Pssm-ID: 234608 [Multi-domain] Cd Length: 361 Bit Score: 49.00 E-value: 8.56e-06
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| YbjD | COG3593 | Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ... |
804-940 | 1.07e-05 | ||||||||||||||||
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains [Replication, recombination and repair]; Pssm-ID: 442812 [Multi-domain] Cd Length: 359 Bit Score: 48.85 E-value: 1.07e-05
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| COG3950 | COG3950 | Predicted ATP-binding protein involved in virulence [General function prediction only]; |
3-99 | 1.17e-05 | ||||||||||||||||
Predicted ATP-binding protein involved in virulence [General function prediction only]; Pssm-ID: 443150 [Multi-domain] Cd Length: 276 Bit Score: 48.07 E-value: 1.17e-05
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| CcmA | COG4133 | ABC-type transport system involved in cytochrome c biogenesis, ATPase component ... |
880-940 | 1.26e-05 | ||||||||||||||||
ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 443308 [Multi-domain] Cd Length: 206 Bit Score: 47.09 E-value: 1.26e-05
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| CydD | COG4988 | ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease ... |
880-949 | 1.36e-05 | ||||||||||||||||
ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 444012 [Multi-domain] Cd Length: 563 Bit Score: 48.99 E-value: 1.36e-05
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| AAA_21 | pfam13304 | AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ... |
865-940 | 1.46e-05 | ||||||||||||||||
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being of the abortive phage resistance system, in which case the family would be acting as the toxin for a type IV toxin-antitoxin resistance system. Pssm-ID: 433102 [Multi-domain] Cd Length: 303 Bit Score: 48.15 E-value: 1.46e-05
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
591-942 | 1.86e-05 | ||||||||||||||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 48.61 E-value: 1.86e-05
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| SunT | COG2274 | ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase ... |
880-952 | 2.02e-05 | ||||||||||||||||
ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Pssm-ID: 441875 [Multi-domain] Cd Length: 711 Bit Score: 48.68 E-value: 2.02e-05
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| ABC_Carb_Monos_I | cd03216 | First domain of the ATP-binding cassette component of monosaccharide transport system; This ... |
880-941 | 2.22e-05 | ||||||||||||||||
First domain of the ATP-binding cassette component of monosaccharide transport system; This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter. Pssm-ID: 213183 [Multi-domain] Cd Length: 163 Bit Score: 45.88 E-value: 2.22e-05
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| ATM1 | COG5265 | ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components ... |
880-952 | 3.32e-05 | ||||||||||||||||
ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 444078 [Multi-domain] Cd Length: 605 Bit Score: 47.89 E-value: 3.32e-05
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| PRK00409 | PRK00409 | recombination and DNA strand exchange inhibitor protein; Reviewed |
572-698 | 1.34e-04 | ||||||||||||||||
recombination and DNA strand exchange inhibitor protein; Reviewed Pssm-ID: 234750 [Multi-domain] Cd Length: 782 Bit Score: 45.97 E-value: 1.34e-04
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| COG4637 | COG4637 | Predicted ATPase [General function prediction only]; |
880-940 | 1.36e-04 | ||||||||||||||||
Predicted ATPase [General function prediction only]; Pssm-ID: 443675 [Multi-domain] Cd Length: 371 Bit Score: 45.31 E-value: 1.36e-04
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| CydD | TIGR02857 | thiol reductant ABC exporter, CydD subunit; The gene pair cydCD encodes an ABC-family ... |
880-949 | 1.62e-04 | ||||||||||||||||
thiol reductant ABC exporter, CydD subunit; The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex. Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD Pssm-ID: 274323 [Multi-domain] Cd Length: 529 Bit Score: 45.36 E-value: 1.62e-04
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| YddA | COG4178 | ABC-type uncharacterized transport system, permease and ATPase components [General function ... |
879-941 | 1.81e-04 | ||||||||||||||||
ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Pssm-ID: 443337 [Multi-domain] Cd Length: 571 Bit Score: 45.18 E-value: 1.81e-04
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| EnvC | COG4942 | Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ... |
238-422 | 1.98e-04 | ||||||||||||||||
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 44.75 E-value: 1.98e-04
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| PRK11176 | PRK11176 | lipid A ABC transporter ATP-binding protein/permease MsbA; |
876-952 | 2.06e-04 | ||||||||||||||||
lipid A ABC transporter ATP-binding protein/permease MsbA; Pssm-ID: 183016 [Multi-domain] Cd Length: 582 Bit Score: 45.01 E-value: 2.06e-04
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| ABCD_peroxisomal_ALDP | cd03223 | ATP-binding cassette domain of peroxisomal transporter, subfamily D; Peroxisomal ATP-binding ... |
880-942 | 2.69e-04 | ||||||||||||||||
ATP-binding cassette domain of peroxisomal transporter, subfamily D; Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asymptomatic). Pssm-ID: 213190 [Multi-domain] Cd Length: 166 Bit Score: 42.53 E-value: 2.69e-04
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| ABCC_TAP | cd03248 | ATP-binding cassette domain of the Transporter Associated with Antigen Processing, subfamily C; ... |
879-952 | 3.41e-04 | ||||||||||||||||
ATP-binding cassette domain of the Transporter Associated with Antigen Processing, subfamily C; TAP (Transporter Associated with Antigen Processing) is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules. Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes. Pssm-ID: 213215 [Multi-domain] Cd Length: 226 Bit Score: 43.23 E-value: 3.41e-04
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| ABC_RecF | cd03242 | ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ... |
4-187 | 3.48e-04 | ||||||||||||||||
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication fork, allowing it to resume and complete its task. This CD represents the nucleotide binding domain of RecF. RecF belongs to a large superfamily of ABC transporters involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases with a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. Pssm-ID: 213209 [Multi-domain] Cd Length: 270 Bit Score: 43.44 E-value: 3.48e-04
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| CydC | COG4987 | ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease ... |
880-941 | 3.50e-04 | ||||||||||||||||
ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 444011 [Multi-domain] Cd Length: 569 Bit Score: 44.37 E-value: 3.50e-04
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| CwlO1 | COG3883 | Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ... |
573-720 | 3.59e-04 | ||||||||||||||||
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown]; Pssm-ID: 443091 [Multi-domain] Cd Length: 379 Bit Score: 44.05 E-value: 3.59e-04
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| EnvC | COG4942 | Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ... |
579-734 | 4.11e-04 | ||||||||||||||||
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 43.98 E-value: 4.11e-04
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| recf | TIGR00611 | recF protein; All proteins in this family for which functions are known are DNA binding ... |
3-59 | 5.77e-04 | ||||||||||||||||
recF protein; All proteins in this family for which functions are known are DNA binding proteins that assist the filamentation of RecA onto DNA for the initiation of recombination or recombinational repair. 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: 273173 [Multi-domain] Cd Length: 365 Bit Score: 43.50 E-value: 5.77e-04
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| ABCC_Protease_Secretion | cd03246 | ATP-binding cassette domain of PrtD, subfamily C; This family represents the ABC component of ... |
858-952 | 6.27e-04 | ||||||||||||||||
ATP-binding cassette domain of PrtD, subfamily C; This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain. They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substrates ranges from inorganic ions, nutrients such as amino acids, sugars, or peptides, hydrophobic drugs, to large polypeptides, such as HlyA. Pssm-ID: 213213 [Multi-domain] Cd Length: 173 Bit Score: 41.82 E-value: 6.27e-04
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| PRK13539 | PRK13539 | cytochrome c biogenesis protein CcmA; Provisional |
880-928 | 6.85e-04 | ||||||||||||||||
cytochrome c biogenesis protein CcmA; Provisional Pssm-ID: 237421 [Multi-domain] Cd Length: 207 Bit Score: 42.17 E-value: 6.85e-04
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| MdlB | COG1132 | ABC-type multidrug transport system, ATPase and permease component [Defense mechanisms]; |
880-949 | 8.16e-04 | ||||||||||||||||
ABC-type multidrug transport system, ATPase and permease component [Defense mechanisms]; Pssm-ID: 440747 [Multi-domain] Cd Length: 579 Bit Score: 43.23 E-value: 8.16e-04
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| AAA_21 | pfam13304 | AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ... |
27-96 | 8.54e-04 | ||||||||||||||||
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being of the abortive phage resistance system, in which case the family would be acting as the toxin for a type IV toxin-antitoxin resistance system. Pssm-ID: 433102 [Multi-domain] Cd Length: 303 Bit Score: 42.38 E-value: 8.54e-04
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| ABCC_NFT1 | cd03369 | ATP-binding cassette domain 2 of NFT1, subfamily C; Domain 2 of NFT1 (New full-length MRP-type ... |
880-952 | 1.09e-03 | ||||||||||||||||
ATP-binding cassette domain 2 of NFT1, subfamily C; Domain 2 of NFT1 (New full-length MRP-type transporter 1). NFT1 belongs to the MRP (multidrug resistance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate. Pssm-ID: 213269 [Multi-domain] Cd Length: 207 Bit Score: 41.63 E-value: 1.09e-03
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| ABCC_Glucan_exporter_like | cd03254 | ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Glucan ... |
859-952 | 1.16e-03 | ||||||||||||||||
ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virulence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. Pssm-ID: 213221 [Multi-domain] Cd Length: 229 Bit Score: 41.44 E-value: 1.16e-03
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| ABC_Rad50 | cd03240 | ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ... |
880-940 | 1.22e-03 | ||||||||||||||||
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence. Pssm-ID: 213207 [Multi-domain] Cd Length: 204 Bit Score: 41.05 E-value: 1.22e-03
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| 235kDa-fam | TIGR01612 | reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in ... |
354-827 | 1.24e-03 | ||||||||||||||||
reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii. Pssm-ID: 130673 [Multi-domain] Cd Length: 2757 Bit Score: 43.12 E-value: 1.24e-03
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| ABC_FeS_Assembly | cd03217 | ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Biosynthesis of ... |
880-942 | 1.48e-03 | ||||||||||||||||
ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Biosynthesis of iron-sulfur clusters (Fe-S) depends on multi-protein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet. Pssm-ID: 213184 [Multi-domain] Cd Length: 200 Bit Score: 40.97 E-value: 1.48e-03
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| Mplasa_alph_rch | TIGR04523 | helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ... |
579-834 | 1.52e-03 | ||||||||||||||||
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown. Pssm-ID: 275316 [Multi-domain] Cd Length: 745 Bit Score: 42.31 E-value: 1.52e-03
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| Myosin_tail_1 | pfam01576 | Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ... |
586-823 | 1.60e-03 | ||||||||||||||||
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament. Pssm-ID: 460256 [Multi-domain] Cd Length: 1081 Bit Score: 42.47 E-value: 1.60e-03
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| PRK02224 | PRK02224 | DNA double-strand break repair Rad50 ATPase; |
4-97 | 1.90e-03 | ||||||||||||||||
DNA double-strand break repair Rad50 ATPase; Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 42.33 E-value: 1.90e-03
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| ABC_SMC5_euk | cd03277 | ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of ... |
6-91 | 3.46e-03 | ||||||||||||||||
ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). Pssm-ID: 213244 [Multi-domain] Cd Length: 213 Bit Score: 39.89 E-value: 3.46e-03
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| ABCC_MsbA | cd03251 | ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; ... |
880-952 | 4.05e-03 | ||||||||||||||||
ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. Pssm-ID: 213218 [Multi-domain] Cd Length: 234 Bit Score: 39.91 E-value: 4.05e-03
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| EnvC | COG4942 | Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ... |
581-835 | 4.43e-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: 40.52 E-value: 4.43e-03
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| ABC_DR_subfamily_A | cd03230 | ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily ... |
857-940 | 4.96e-03 | ||||||||||||||||
ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; This family of ATP-binding proteins belongs to a multi-subunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryotic systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. Pssm-ID: 213197 [Multi-domain] Cd Length: 173 Bit Score: 38.92 E-value: 4.96e-03
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| ccmA | TIGR01189 | heme ABC exporter, ATP-binding protein CcmA; This model describes the cyt c biogenesis protein ... |
880-926 | 5.01e-03 | ||||||||||||||||
heme ABC exporter, ATP-binding protein CcmA; This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c. [Protein fate, Protein and peptide secretion and trafficking, Transport and binding proteins, Other] Pssm-ID: 273491 [Multi-domain] Cd Length: 198 Bit Score: 39.26 E-value: 5.01e-03
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| COG1340 | COG1340 | Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; |
583-834 | 5.64e-03 | ||||||||||||||||
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Pssm-ID: 440951 [Multi-domain] Cd Length: 297 Bit Score: 39.89 E-value: 5.64e-03
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| PRK12704 | PRK12704 | phosphodiesterase; Provisional |
585-698 | 6.65e-03 | ||||||||||||||||
phosphodiesterase; Provisional Pssm-ID: 237177 [Multi-domain] Cd Length: 520 Bit Score: 40.15 E-value: 6.65e-03
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| DR0291 | COG1579 | Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ... |
242-382 | 6.85e-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: 39.14 E-value: 6.85e-03
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| AAA_29 | pfam13555 | P-loop containing region of AAA domain; |
15-49 | 7.00e-03 | ||||||||||||||||
P-loop containing region of AAA domain; Pssm-ID: 433304 [Multi-domain] Cd Length: 61 Bit Score: 36.04 E-value: 7.00e-03
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| CwlO1 | COG3883 | Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ... |
658-835 | 7.60e-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: 7.60e-03
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| COG1340 | COG1340 | Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; |
573-834 | 7.88e-03 | ||||||||||||||||
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Pssm-ID: 440951 [Multi-domain] Cd Length: 297 Bit Score: 39.51 E-value: 7.88e-03
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| EzrA | pfam06160 | Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like ... |
563-829 | 8.66e-03 | ||||||||||||||||
Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation. The structure contains 5 spectrin like alpha helical repeats. Pssm-ID: 428797 [Multi-domain] Cd Length: 542 Bit Score: 39.84 E-value: 8.66e-03
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| ABC_CcmA_heme_exporter | cd03231 | Cytochrome c biogenesis ATP-binding export protein; CcmA, the ATP-binding component of the ... |
880-923 | 8.82e-03 | ||||||||||||||||
Cytochrome c biogenesis ATP-binding export protein; CcmA, the ATP-binding component of the bacterial CcmAB transporter. The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH). CcmE is a periplasmic heme chaperon that binds heme covalently and transfers it onto apocytochrome c in the presence of CcmF, CcmG, and CcmH. The CcmAB proteins represent an ABC transporter and the CcmCD proteins participate in heme transfer to CcmE. Pssm-ID: 213198 [Multi-domain] Cd Length: 201 Bit Score: 38.63 E-value: 8.82e-03
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| 235kDa-fam | TIGR01612 | reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in ... |
157-420 | 9.22e-03 | ||||||||||||||||
reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii. Pssm-ID: 130673 [Multi-domain] Cd Length: 2757 Bit Score: 40.03 E-value: 9.22e-03
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| cbiO | PRK13640 | energy-coupling factor transporter ATPase; |
880-940 | 9.37e-03 | ||||||||||||||||
energy-coupling factor transporter ATPase; Pssm-ID: 184200 [Multi-domain] Cd Length: 282 Bit Score: 39.01 E-value: 9.37e-03
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| SbcC_Walker_B | pfam13558 | SbcC/RAD50-like, Walker B motif; This entry represents the Walker B domain of RAD50 from ... |
880-928 | 9.61e-03 | ||||||||||||||||
SbcC/RAD50-like, Walker B motif; This entry represents the Walker B domain of RAD50 from eukaryotes and the prokaryotic homolog SbcCD complex subunit C. RAD50-ATPase forms a complex with Mre11-nuclease that detects and processes diverse and obstructed DNA ends. This domain is separated of the Walker A domain by a long coiled-coil domain and forms the nucleotide-binding domain (NBD) when the coiled coils fold back on themselves and bring together Walker A and B domains. Two RAD50-NBDs forms heterotetramers with a Mre11 nuclease dimer that assemble as catalytic head module that binds and cleaves DNA in an ATP-dependent reaction. Through secondary structural analysis, it has been suggested that there is a wide structural conservation in the Rad50/SMC protein family as seen in structural similarities between RAD50's hook and ABC-ATPase MukB's elbow region. Pssm-ID: 463921 [Multi-domain] Cd Length: 90 Bit Score: 36.44 E-value: 9.61e-03
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| Mplasa_alph_rch | TIGR04523 | helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ... |
249-411 | 9.66e-03 | ||||||||||||||||
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown. Pssm-ID: 275316 [Multi-domain] Cd Length: 745 Bit Score: 40.00 E-value: 9.66e-03
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