NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|40807120|gb|AAH65259|]
View 

SMC4 protein, partial [Homo sapiens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 82-241 9.59e-73

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd03274:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 212  Bit Score: 227.18  E-value: 9.59e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  82 LMITHIVNQNFKSYAGEKILGPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQKIRSKKLSVLIHNSDEHKDIQSCTVE 161
Cdd:cd03274   1 LIITKLVLENFKSYAGEQVIGPFHKSFSAIVGPNGSGKSNVIDSMLFVFGFRASKMRQKKLSDLIHNSAGHPNLDSCSVE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 162 VHFQKIIDKEgddyevipnsnfyvsrtacrdntsvyhisgkkktfkdvgnLLRSHGIDLDHNRFLILQGEVEQIAMMkPK 241
Cdd:cd03274  81 VHFQEIIDKP----------------------------------------LLKSKGIDLDHNRFLILQGEVEQIAQM-PK 119
SMC_N super family cl47134
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 83-423 2.59e-72

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.


The actual alignment was detected with superfamily member pfam02463:

Pssm-ID: 481474 [Multi-domain]  Cd Length: 1161  Bit Score: 246.04  E-value: 2.59e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120     83 MITHIVNQNFKSYAgEKILGPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQK-IRSKKLSVLIHnSDEHKDIQSCTVE 161
Cdd:pfam02463    1 YLKRIEIEGFKSYA-KTVILPFSPGFTAIVGPNGSGKSNILDAILFVLGERSAKsLRSERLSDLIH-SKSGAFVNSAEVE 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    162 VHFqkiidKEGDDYEVIPNSNFYVSRTACRDNTSVYHISGKKKTFKDVGNLLRSHGIDLDHNRFLILQGEVEQIAMMKPK 241
Cdd:pfam02463   79 ITF-----DNEDHELPIDKEEVSIRRRVYRGGDSEYYINGKNVTKKEVAELLESQGISPEAYNFLVQGGKIEIIAMMKPE 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    242 GQTEHDEGMLEYLEDIIGCGRLNEPIKVLCRRVEILNEHRGEKLNRVKMVEKEKDALEGEKNIAIEFLTLENEIFRKKNH 321
Cdd:pfam02463  154 RRLEIEEEAAGSRLKRKKKEALKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEEYLLYLDYLK 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    322 VCQYYIYELQKRIAEMETQKEKIHEDTKEINEKSNILSNEMKAKNKDVKDTEKKLNKITKFIEENKEKFTQLDLEDVQVR 401
Cdd:pfam02463  234 LNEERIDLLQELLRDEQEEIESSKQEIEKEEEKLAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDE 313

                          330       340
                   ....*....|....*....|..
gi 40807120    402 EKLKHATSKAKKTGETTSKKKK 423
Cdd:pfam02463  314 EKLKESEKEKKKAEKELKKEKE 335
 
Name Accession Description Interval E-value
ABC_SMC4_euk cd03274
ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of ...
 82-241 9.59e-73

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: 227.18  E-value: 9.59e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  82 LMITHIVNQNFKSYAGEKILGPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQKIRSKKLSVLIHNSDEHKDIQSCTVE 161
Cdd:cd03274   1 LIITKLVLENFKSYAGEQVIGPFHKSFSAIVGPNGSGKSNVIDSMLFVFGFRASKMRQKKLSDLIHNSAGHPNLDSCSVE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 162 VHFQKIIDKEgddyevipnsnfyvsrtacrdntsvyhisgkkktfkdvgnLLRSHGIDLDHNRFLILQGEVEQIAMMkPK 241
Cdd:cd03274  81 VHFQEIIDKP----------------------------------------LLKSKGIDLDHNRFLILQGEVEQIAQM-PK 119
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 83-423 2.59e-72

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: 246.04  E-value: 2.59e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120     83 MITHIVNQNFKSYAgEKILGPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQK-IRSKKLSVLIHnSDEHKDIQSCTVE 161
Cdd:pfam02463    1 YLKRIEIEGFKSYA-KTVILPFSPGFTAIVGPNGSGKSNILDAILFVLGERSAKsLRSERLSDLIH-SKSGAFVNSAEVE 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    162 VHFqkiidKEGDDYEVIPNSNFYVSRTACRDNTSVYHISGKKKTFKDVGNLLRSHGIDLDHNRFLILQGEVEQIAMMKPK 241
Cdd:pfam02463   79 ITF-----DNEDHELPIDKEEVSIRRRVYRGGDSEYYINGKNVTKKEVAELLESQGISPEAYNFLVQGGKIEIIAMMKPE 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    242 GQTEHDEGMLEYLEDIIGCGRLNEPIKVLCRRVEILNEHRGEKLNRVKMVEKEKDALEGEKNIAIEFLTLENEIFRKKNH 321
Cdd:pfam02463  154 RRLEIEEEAAGSRLKRKKKEALKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEEYLLYLDYLK 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    322 VCQYYIYELQKRIAEMETQKEKIHEDTKEINEKSNILSNEMKAKNKDVKDTEKKLNKITKFIEENKEKFTQLDLEDVQVR 401
Cdd:pfam02463  234 LNEERIDLLQELLRDEQEEIESSKQEIEKEEEKLAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDE 313

                          330       340
                   ....*....|....*....|..
gi 40807120    402 EKLKHATSKAKKTGETTSKKKK 423
Cdd:pfam02463  314 EKLKESEKEKKKAEKELKKEKE 335
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 84-410 1.10e-28

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: 119.02  E-value: 1.10e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120     84 ITHIVNQNFKSYAGEKILgPFHKRFSCIIGPNGSGKSNVIDSMLFVFGY-RAQKIRSKKLSVLIHNSDEHKDIQSCTVEV 162
Cdd:TIGR02169    2 IERIELENFKSFGKKKVI-PFSKGFTVISGPNGSGKSNIGDAILFALGLsSSKAMRAERLSDLISNGKNGQSGNEAYVTV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    163 HFQKIIDKEGDDYEVIpnsnfyVSRTACRDN-TSVYHISGKKKTFKDVGNLLRSHGIDLDHNRFlILQGEVEQIAMMKPK 241
Cdd:TIGR02169   81 TFKNDDGKFPDELEVV------RRLKVTDDGkYSYYYLNGQRVRLSEIHDFLAAAGIYPEGYNV-VLQGDVTDFISMSPV 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    242 GQTehdegmlEYLEDIIGCGRLNEPIKVLCRRVEILnehrGEKLNRVKMVEKEK----DALEGEKNIAIEFLTLENEIFr 317
Cdd:TIGR02169  154 ERR-------KIIDEIAGVAEFDRKKEKALEELEEV----EENIERLDLIIDEKrqqlERLRREREKAERYQALLKEKR- 221

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    318 kknhvcQYYIYELQKRIAEMETQKEKIHEDTKEINEKSNILSNEMKAKNKDVKDTEKKLNKITKFIEENKEKftqldlED 397
Cdd:TIGR02169  222 ------EYEGYELLKEKEALERQKEAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGEE------EQ 289

                          330
                   ....*....|...
gi 40807120    398 VQVREKLKHATSK 410
Cdd:TIGR02169  290 LRVKEKIGELEAE 302
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 84-412 3.06e-24

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 105.79  E-value: 3.06e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  84 ITHIVNQNFKSYAGEKILgPFHKRFSCIIGPNGSGKSNVIDSMLFVFG---YRAqkIRSKKLSVLIHN-SDEHKDIQSCT 159
Cdd:COG1196   3 LKRLELAGFKSFADPTTI-PFEPGITAIVGPNGSGKSNIVDAIRWVLGeqsAKS--LRGGKMEDVIFAgSSSRKPLGRAE 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 160 VEVHF---QKIIDkeGDDYEVIpnsnfyVSRTACRDNTSVYHISGKKKTFKDVGNLLRSHGIDLD-HNrfLILQGEVEQI 235
Cdd:COG1196  80 VSLTFdnsDGTLP--IDYDEVT------ITRRLYRSGESEYYINGKPCRLKDIQDLFLDTGLGPEsYS--IIGQGMIDRI 149

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 236 AMMKPkgqtehdEGMLEYLEDIIGCGRLNEpikvlcRRVEILNEHRG--EKLNRVK--MVEKEK--DALEGEKNIAIEFL 309
Cdd:COG1196 150 IEAKP-------EERRAIIEEAAGISKYKE------RKEEAERKLEAteENLERLEdiLGELERqlEPLERQAEKAERYR 216

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 310 TLENEIFRKKNhvcQYYIYELQKRIAEMETQKEKIHEDTKEINEksniLSNEMKAKNKDVKDTEKKLNKITKFIEENKEK 389
Cdd:COG1196 217 ELKEELKELEA---ELLLLKLRELEAELEELEAELEELEAELEE----LEAELAELEAELEELRLELEELELELEEAQAE 289

                       330       340
                ....*....|....*....|...
gi 40807120 390 FTQLDLEDVQVREKLKHATSKAK 412
Cdd:COG1196 290 EYELLAELARLEQDIARLEERRR 312
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
83-178 4.26e-09

DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 56.17  E-value: 4.26e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  83 MITHIVNQNFKSYAGEKILgPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQKiRSKKLSVLIHNSDEhkdiqSCTVEV 162
Cdd:COG0419   1 KLLRLRLENFRSYRDTETI-DFDDGLNLIVGPNGAGKSTILEAIRYALYGKARS-RSKLRSDLINVGSE-----EASVEL 73

                        90
                ....*....|....*.
gi 40807120 163 HFQkiidKEGDDYEVI 178
Cdd:COG0419  74 EFE----HGGKRYRIE 85
AAA_23 pfam13476
AAA domain;
90-258 7.23e-05

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 43.25  E-value: 7.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    90 QNFKSYAGEKIlgPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQKIRSKKLSVLIHNS--DEHKDIQSCTVEVHFQKI 167
Cdd:pfam13476   4 ENFRSFRDQTI--DFSKGLTLITGPNGSGKTTILDAIKLALYGKTSRLKRKSGGGFVKGDirIGLEGKGKAYVEITFENN 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120   168 IDKEGDDYEVIPNSNFYVSRTACRDNTSVYHISGKKKTFKDvgnllrSHGIDLDHNRFLILQGEvEQIAMMKPKGQTEHD 247
Cdd:pfam13476  82 DGRYTYAIERSRELSKKKGKTKKKEILEILEIDELQQFISE------LLKSDKIILPLLVFLGQ-EREEEFERKEKKERL 154

                         170
                  ....*....|.
gi 40807120   248 EGMLEYLEDII 258
Cdd:pfam13476 155 EELEKALEEKE 165
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
90-423 1.18e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 44.67  E-value: 1.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120   90 QNFKSYAGEKIlgPFHKRFSCIIGPNGSGKSNVIDSmLFVFGYRAQKIRSKKLSvlihNSDEHKDIQSCT-VEVHFqkii 168
Cdd:PRK03918   9 KNFRSHKSSVV--EFDDGINLIIGQNGSGKSSILEA-ILVGLYWGHGSKPKGLK----KDDFTRIGGSGTeIELKF---- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  169 DKEGDDYEVIPNSNFYVSRTACRDNTSVYHiSGKKKTFKDVGNLLRSHgidLDHNRFLILQGEVEQIammkpkgqTEHDE 248
Cdd:PRK03918  78 EKNGRKYRIVRSFNRGESYLKYLDGSEVLE-EGDSSVREWVERLIPYH---VFLNAIYIRQGEIDAI--------LESDE 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  249 GMLEYLEDIIGCGR-------LNEPIKVLCRRVEILNE---HRGEKLNRVKMVEKEKDALEGE-KNIAIEFLTLENEIFR 317
Cdd:PRK03918 146 SREKVVRQILGLDDyenayknLGEVIKEIKRRIERLEKfikRTENIEELIKEKEKELEEVLREiNEISSELPELREELEK 225

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  318 KKNHVCQYYiyELQKRIAEMETQKEKIHEDTKEINEKSNILS---NEMKAKNKDVKDTEKKLNKI----------TKFIE 384
Cdd:PRK03918 226 LEKEVKELE--ELKEEIEELEKELESLEGSKRKLEEKIRELEeriEELKKEIEELEEKVKELKELkekaeeyiklSEFYE 303

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*.
gi 40807120  385 ENKEKFTQLDLEDVQ-------VREKLKHATSKAKKTGETTSKKKK 423
Cdd:PRK03918 304 EYLDELREIEKRLSRleeeingIEERIKELEEKEERLEELKKKLKE 349
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 84-166 1.18e-03

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: 40.80  E-value: 1.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    84 ITHIVNQNFKSYAGEKIlgPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQkiRSKKLSVLIHNSDEHkdiqsCTVEVH 163
Cdd:TIGR00611   3 LSRLELTDFRNYDAVDL--ELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSH--RTSRDKPLIRFGAEA-----FVIEGR 73


                  ...
gi 40807120   164 FQK 166
Cdd:TIGR00611  74 VSK 76
 
Name Accession Description Interval E-value
ABC_SMC4_euk cd03274
ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of ...
 82-241 9.59e-73

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: 227.18  E-value: 9.59e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  82 LMITHIVNQNFKSYAGEKILGPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQKIRSKKLSVLIHNSDEHKDIQSCTVE 161
Cdd:cd03274   1 LIITKLVLENFKSYAGEQVIGPFHKSFSAIVGPNGSGKSNVIDSMLFVFGFRASKMRQKKLSDLIHNSAGHPNLDSCSVE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 162 VHFQKIIDKEgddyevipnsnfyvsrtacrdntsvyhisgkkktfkdvgnLLRSHGIDLDHNRFLILQGEVEQIAMMkPK 241
Cdd:cd03274  81 VHFQEIIDKP----------------------------------------LLKSKGIDLDHNRFLILQGEVEQIAQM-PK 119
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 83-423 2.59e-72

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: 246.04  E-value: 2.59e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120     83 MITHIVNQNFKSYAgEKILGPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQK-IRSKKLSVLIHnSDEHKDIQSCTVE 161
Cdd:pfam02463    1 YLKRIEIEGFKSYA-KTVILPFSPGFTAIVGPNGSGKSNILDAILFVLGERSAKsLRSERLSDLIH-SKSGAFVNSAEVE 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    162 VHFqkiidKEGDDYEVIPNSNFYVSRTACRDNTSVYHISGKKKTFKDVGNLLRSHGIDLDHNRFLILQGEVEQIAMMKPK 241
Cdd:pfam02463   79 ITF-----DNEDHELPIDKEEVSIRRRVYRGGDSEYYINGKNVTKKEVAELLESQGISPEAYNFLVQGGKIEIIAMMKPE 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    242 GQTEHDEGMLEYLEDIIGCGRLNEPIKVLCRRVEILNEHRGEKLNRVKMVEKEKDALEGEKNIAIEFLTLENEIFRKKNH 321
Cdd:pfam02463  154 RRLEIEEEAAGSRLKRKKKEALKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEEYLLYLDYLK 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    322 VCQYYIYELQKRIAEMETQKEKIHEDTKEINEKSNILSNEMKAKNKDVKDTEKKLNKITKFIEENKEKFTQLDLEDVQVR 401
Cdd:pfam02463  234 LNEERIDLLQELLRDEQEEIESSKQEIEKEEEKLAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDE 313

                          330       340
                   ....*....|....*....|..
gi 40807120    402 EKLKHATSKAKKTGETTSKKKK 423
Cdd:pfam02463  314 EKLKESEKEKKKAEKELKKEKE 335
ABC_SMC1_euk cd03275
ATP-binding cassette domain of eukaryotic SMC1 proteins; The structural maintenance of ...
 90-242 6.51e-33

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: 124.22  E-value: 6.51e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  90 QNFKSYAGEKILGPFhKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQKIRSKKLSVLIHN-SDEHKDIQSCTVEVHFQkii 168
Cdd:cd03275   7 ENFKSYKGRHVIGPF-DRFTCIIGPNGSGKSNLMDAISFVLGEKSSHLRSKNLKDLIYRaRVGKPDSNSAYVTAVYE--- 82

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 40807120 169 dkegDDYEVIPnsnfyVSRTACRDNTSVYHISGKKKTFKDVGNLLRSHGIDLDHNRFLILQGEVEQIAMMKPKG 242
Cdd:cd03275  83 ----DDDGEEK-----TFRRIITGGSSSYRINGKVVSLKEYNEELEKINILVKARNFLVFQGDVESIASKNPPG 147
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 84-410 1.10e-28

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: 119.02  E-value: 1.10e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120     84 ITHIVNQNFKSYAGEKILgPFHKRFSCIIGPNGSGKSNVIDSMLFVFGY-RAQKIRSKKLSVLIHNSDEHKDIQSCTVEV 162
Cdd:TIGR02169    2 IERIELENFKSFGKKKVI-PFSKGFTVISGPNGSGKSNIGDAILFALGLsSSKAMRAERLSDLISNGKNGQSGNEAYVTV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    163 HFQKIIDKEGDDYEVIpnsnfyVSRTACRDN-TSVYHISGKKKTFKDVGNLLRSHGIDLDHNRFlILQGEVEQIAMMKPK 241
Cdd:TIGR02169   81 TFKNDDGKFPDELEVV------RRLKVTDDGkYSYYYLNGQRVRLSEIHDFLAAAGIYPEGYNV-VLQGDVTDFISMSPV 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    242 GQTehdegmlEYLEDIIGCGRLNEPIKVLCRRVEILnehrGEKLNRVKMVEKEK----DALEGEKNIAIEFLTLENEIFr 317
Cdd:TIGR02169  154 ERR-------KIIDEIAGVAEFDRKKEKALEELEEV----EENIERLDLIIDEKrqqlERLRREREKAERYQALLKEKR- 221

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    318 kknhvcQYYIYELQKRIAEMETQKEKIHEDTKEINEKSNILSNEMKAKNKDVKDTEKKLNKITKFIEENKEKftqldlED 397
Cdd:TIGR02169  222 ------EYEGYELLKEKEALERQKEAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGEE------EQ 289

                          330
                   ....*....|...
gi 40807120    398 VQVREKLKHATSK 410
Cdd:TIGR02169  290 LRVKEKIGELEAE 302
ABC_SMC_head cd03239
The SMC head domain belongs to the ATP-binding cassette superfamily; The structural ...
 84-167 1.44e-28

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: 110.48  E-value: 1.44e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  84 ITHIVNQNFKSYAGEKILGPFHkRFSCIIGPNGSGKSNVIDSMLFVFGYRAQKIRSKKLSVLIHnSDEHKDIQSCTVEVH 163
Cdd:cd03239   1 IKQITLKNFKSYRDETVVGGSN-SFNAIVGPNGSGKSNIVDAICFVLGGKAAKLRRGSLLFLAG-GGVKAGINSASVEIT 78


                ....
gi 40807120 164 FQKI 167
Cdd:cd03239  79 FDKS 82
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 84-412 3.06e-24

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 105.79  E-value: 3.06e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  84 ITHIVNQNFKSYAGEKILgPFHKRFSCIIGPNGSGKSNVIDSMLFVFG---YRAqkIRSKKLSVLIHN-SDEHKDIQSCT 159
Cdd:COG1196   3 LKRLELAGFKSFADPTTI-PFEPGITAIVGPNGSGKSNIVDAIRWVLGeqsAKS--LRGGKMEDVIFAgSSSRKPLGRAE 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 160 VEVHF---QKIIDkeGDDYEVIpnsnfyVSRTACRDNTSVYHISGKKKTFKDVGNLLRSHGIDLD-HNrfLILQGEVEQI 235
Cdd:COG1196  80 VSLTFdnsDGTLP--IDYDEVT------ITRRLYRSGESEYYINGKPCRLKDIQDLFLDTGLGPEsYS--IIGQGMIDRI 149

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 236 AMMKPkgqtehdEGMLEYLEDIIGCGRLNEpikvlcRRVEILNEHRG--EKLNRVK--MVEKEK--DALEGEKNIAIEFL 309
Cdd:COG1196 150 IEAKP-------EERRAIIEEAAGISKYKE------RKEEAERKLEAteENLERLEdiLGELERqlEPLERQAEKAERYR 216

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 310 TLENEIFRKKNhvcQYYIYELQKRIAEMETQKEKIHEDTKEINEksniLSNEMKAKNKDVKDTEKKLNKITKFIEENKEK 389
Cdd:COG1196 217 ELKEELKELEA---ELLLLKLRELEAELEELEAELEELEAELEE----LEAELAELEAELEELRLELEELELELEEAQAE 289

                       330       340
                ....*....|....*....|...
gi 40807120 390 FTQLDLEDVQVREKLKHATSKAK 412
Cdd:COG1196 290 EYELLAELARLEQDIARLEERRR 312
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 92-423 1.54e-18

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: 88.19  E-value: 1.54e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120     92 FKSYAgEKILGPFHKRFSCIIGPNGSGKSNVIDSMLFVFG-YRAQKIRSKKLSVLIHN-SDEHKDIQSCTVEVHFqkiiD 169
Cdd:TIGR02168   10 FKSFA-DPTTINFDKGITGIVGPNGCGKSNIVDAIRWVLGeQSAKALRGGKMEDVIFNgSETRKPLSLAEVELVF----D 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    170 KE-----GDDYEVIPnsnfyVSRTACRDNTSVYHISGKKKTFKDVGNLL-------RSHGIdldhnrflILQGEVEQIAM 237
Cdd:TIGR02168   85 NSdgllpGADYSEIS-----ITRRLYRDGESEYFINGQPCRLKDIQDLFldtglgkRSYSI--------IEQGKISEIIE 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    238 MKPkgqtehdEGMLEYLEDIIGCGRLNEpikvlcRRVEILN--EHRGEKLNRV----KMVEKEKDALEGEKNIAIEFLTL 311
Cdd:TIGR02168  152 AKP-------EERRAIFEEAAGISKYKE------RRKETERklERTRENLDRLedilNELERQLKSLERQAEKAERYKEL 218

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    312 ENEI--------------FRKKNHVCQYYIYELQKRIAEMETQKEKIHEDTKEINEKSNILSNEMKAKNKDVKDTEKKLN 377
Cdd:TIGR02168  219 KAELrelelallvlrleeLREELEELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEIS 298

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 40807120    378 KITKFIEENKEKFTQLDLEDVQVREKLKHATSKAKKTGETTSKKKK 423
Cdd:TIGR02168  299 RLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEE 344
ABC_SMC_barmotin cd03278
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ...
 84-164 4.48e-17

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: 79.05  E-value: 4.48e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  84 ITHIVNQNFKSYAGEKILgPFHKRFSCIIGPNGSGKSNVIDSMLFVFG-YRAQKIRSKKLSVLIHNSDEHKDIQS-CTVE 161
Cdd:cd03278   1 LKKLELKGFKSFADKTTI-PFPPGLTAIVGPNGSGKSNIIDAIRWVLGeQSAKSLRGEKMSDVIFAGSETRKPANfAEVT 79


                ...
gi 40807120 162 VHF 164
Cdd:cd03278  80 LTF 82
ABC_SMC2_euk cd03273
ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of ...
 84-238 2.32e-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: 78.11  E-value: 2.32e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  84 ITHIVNQNFKSYAGEKILGPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRA-QKIRSKKLSVLIHNSDEhKDIQSCTVEV 162
Cdd:cd03273   3 IKEIILDGFKSYATRTVISGFDPQFNAITGLNGSGKSNILDAICFVLGITNlSTVRASNLQDLIYKRGQ-AGITKASVTI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 163 HFqKIIDKEG-----DDYEVIPnsnfyVSRTACRDNTSVYHISGKKKTFKDVGNLLRSHGIDLDHNRFLILQGEVEQIAM 237
Cdd:cd03273  82 VF-DNSDKSQspigfENYPEIT-----VTRQIVLGGTNKYLINGHRAQQQRVQDLFQSVQLNVNNPHFLIMQGRITKVLN 155


                .
gi 40807120 238 M 238
Cdd:cd03273 156 M 156
ABC_Class2 cd03227
ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ...
 86-170 2.09e-15

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: 73.55  E-value: 2.09e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  86 HIVNQNFKSYAGEKILGPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQKIRSKklsvlihnSDEHKDIQSCTVEVHFQ 165
Cdd:cd03227   1 KIVLGRFPSYFVPNDVTFGEGSLTIITGPNGSGKSTILDAIGLALGGAQSATRRR--------SGVKAGCIVAAVSAELI 72


                ....*
gi 40807120 166 KIIDK 170
Cdd:cd03227  73 FTRLQ 77
ABC_SMC3_euk cd03272
ATP-binding cassette domain of eukaryotic SMC3 proteins; The structural maintenance of ...
 84-245 1.17e-13

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: 70.37  E-value: 1.17e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  84 ITHIVNQNFKSYAGEKILGPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQKIRSKKLSVLIHNSDEHKDIqSCTVEVH 163
Cdd:cd03272   1 IKQVIIQGFKSYKDQTVIEPFSPKHNVVVGRNGSGKSNFFAAIRFVLSDEYTHLREEQRQALLHEGSGPSVM-SAYVEII 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 164 FQKIidkegDDYEVIPNSNFYVSRT--ACRDNtsvYHISGKKKTFKDVGNLLRSHGIDLDHNRFLILQGEVEQIAMMKPK 241
Cdd:cd03272  80 FDNS-----DNRFPIDKEEVRLRRTigLKKDE---YFLDKKNVTKNDVMNLLESAGFSRSNPYYIVPQGKINSLTNMKQD 151


                ....
gi 40807120 242 GQTE 245
Cdd:cd03272 152 EQQE 155
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
83-178 4.26e-09

DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 56.17  E-value: 4.26e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  83 MITHIVNQNFKSYAGEKILgPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQKiRSKKLSVLIHNSDEhkdiqSCTVEV 162
Cdd:COG0419   1 KLLRLRLENFRSYRDTETI-DFDDGLNLIVGPNGAGKSTILEAIRYALYGKARS-RSKLRSDLINVGSE-----EASVEL 73

                        90
                ....*....|....*.
gi 40807120 163 HFQkiidKEGDDYEVI 178
Cdd:COG0419  74 EFE----HGGKRYRIE 85
COG4637 COG4637
Predicted ATPase [General function prediction only];
83-129 1.14e-08

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 56.48  E-value: 1.14e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 40807120  83 MITHIVNQNFKSYAGEKI-LGPFHkrfsCIIGPNGSGKSNVIDSMLFV 129
Cdd:COG4637   1 MITRIRIKNFKSLRDLELpLGPLT----VLIGANGSGKSNLLDALRFL 44
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 84-170 1.75e-06

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: 49.62  E-value: 1.75e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  84 ITHIVNQNFKSYAGEKIlgPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRaqkiRSKKLSVL-IHNSDEHKDIqSCTVEV 162
Cdd:COG3593   3 LEKIKIKNFRSIKDLSI--ELSDDLTVLVGENNSGKSSILEALRLLLGPS----SSRKFDEEdFYLGDDPDLP-EIEIEL 75


                ....*...
gi 40807120 163 HFQKIIDK 170
Cdd:COG3593  76 TFGSLLSR 83
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
84-125 3.22e-05

Recombinational DNA repair ATPase RecF [Replication, recombination and repair];


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 45.53  E-value: 3.22e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 40807120  84 ITHIVNQNFKSYAGEKIlgPFHKRFSCIIGPNGSGKSNVIDS 125
Cdd:COG1195   2 LKRLSLTNFRNYESLEL--EFSPGINVLVGPNGQGKTNLLEA 41
AAA_23 pfam13476
AAA domain;
90-258 7.23e-05

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 43.25  E-value: 7.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    90 QNFKSYAGEKIlgPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQKIRSKKLSVLIHNS--DEHKDIQSCTVEVHFQKI 167
Cdd:pfam13476   4 ENFRSFRDQTI--DFSKGLTLITGPNGSGKTTILDAIKLALYGKTSRLKRKSGGGFVKGDirIGLEGKGKAYVEITFENN 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120   168 IDKEGDDYEVIPNSNFYVSRTACRDNTSVYHISGKKKTFKDvgnllrSHGIDLDHNRFLILQGEvEQIAMMKPKGQTEHD 247
Cdd:pfam13476  82 DGRYTYAIERSRELSKKKGKTKKKEILEILEIDELQQFISE------LLKSDKIILPLLVFLGQ-EREEEFERKEKKERL 154

                         170
                  ....*....|.
gi 40807120   248 EGMLEYLEDII 258
Cdd:pfam13476 155 EELEKALEEKE 165
ABC_RecN cd03241
ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC ...
 104-238 7.31e-05

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: 44.12  E-value: 7.31e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 104 FHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQK--IRSKKLSVLIH----NSDEHKdiqsctvevHFQKIIDKEGDDYEV 177
Cdd:cd03241  19 FEEGLTVLTGETGAGKSILLDALSLLLGGRASAdlIRSGAEKAVVEgvfdISDEEE---------AKALLLELGIEDDDD 89

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 40807120 178 IpnsnfYVSRTACRDNTSVYHISGK---KKTFKDVGNLL------RSHGIDLDHNRFL-ILQGEVEQIAMM 238
Cdd:cd03241  90 L-----IIRREISRKGRSRYFINGQsvtLKLLRELGSLLvdihgqHDHQNLLNPERQLdLLDGGLDDVEFL 155
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
90-423 1.18e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 44.67  E-value: 1.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120   90 QNFKSYAGEKIlgPFHKRFSCIIGPNGSGKSNVIDSmLFVFGYRAQKIRSKKLSvlihNSDEHKDIQSCT-VEVHFqkii 168
Cdd:PRK03918   9 KNFRSHKSSVV--EFDDGINLIIGQNGSGKSSILEA-ILVGLYWGHGSKPKGLK----KDDFTRIGGSGTeIELKF---- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  169 DKEGDDYEVIPNSNFYVSRTACRDNTSVYHiSGKKKTFKDVGNLLRSHgidLDHNRFLILQGEVEQIammkpkgqTEHDE 248
Cdd:PRK03918  78 EKNGRKYRIVRSFNRGESYLKYLDGSEVLE-EGDSSVREWVERLIPYH---VFLNAIYIRQGEIDAI--------LESDE 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  249 GMLEYLEDIIGCGR-------LNEPIKVLCRRVEILNE---HRGEKLNRVKMVEKEKDALEGE-KNIAIEFLTLENEIFR 317
Cdd:PRK03918 146 SREKVVRQILGLDDyenayknLGEVIKEIKRRIERLEKfikRTENIEELIKEKEKELEEVLREiNEISSELPELREELEK 225

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  318 KKNHVCQYYiyELQKRIAEMETQKEKIHEDTKEINEKSNILS---NEMKAKNKDVKDTEKKLNKI----------TKFIE 384
Cdd:PRK03918 226 LEKEVKELE--ELKEEIEELEKELESLEGSKRKLEEKIRELEeriEELKKEIEELEEKVKELKELkekaeeyiklSEFYE 303

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*.
gi 40807120  385 ENKEKFTQLDLEDVQ-------VREKLKHATSKAKKTGETTSKKKK 423
Cdd:PRK03918 304 EYLDELREIEKRLSRleeeingIEERIKELEEKEERLEELKKKLKE 349
CwlO1 COG3883
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ...
 327-419 1.87e-04

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];


Pssm-ID: 443091 [Multi-domain]  Cd Length: 379  Bit Score: 43.28  E-value: 1.87e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 327 IYELQKRIAEMETQKEKIHEDTKEINEksnilsnEMKAKNKDVKDTEKKLNKITKFIEENKEKFTQLDLEDVQVREKLKH 406
Cdd:COG3883  18 IQAKQKELSELQAELEAAQAELDALQA-------ELEELNEEYNELQAELEALQAEIDKLQAEIAEAEAEIEERREELGE 90

                        90
                ....*....|...
gi 40807120 407 ATSKAKKTGETTS 419
Cdd:COG3883  91 RARALYRSGGSVS 103
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
83-129 2.04e-04

ATPase/GTPase, AAA15 family [General function prediction only];


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 43.11  E-value: 2.04e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 40807120  83 MITHIVNQNFKSYAGEKIL-----GPFHKRFSCIIGPNGSGKSNVIDSMLFV 129
Cdd:COG1106   1 MLISFSIENFRSFKDELTLsmvasGLRLLRVNLIYGANASGKSNLLEALYFL 52
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
83-154 2.69e-04

Predicted ATP-binding protein involved in virulence [General function prediction only];


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 42.68  E-value: 2.69e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 40807120  83 MITHIVNQNFKSYAGEKILGPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQKIRSKKLSVLIHNSDEHKD 154
Cdd:COG3950   2 RIKSLTIENFRGFEDLEIDFDNPPRLTVLVGENGSGKTTLLEAIALALSGLLSRLDDVKFRKLLIRNGEFGD 73
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 329-416 3.23e-04

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


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 42.44  E-value: 3.23e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 329 ELQKRIAEMETQKEKIHEDTKEINEKSNILSNEMKAKNKDVKDTEKKLNKITKFIEENKEKFTQLDLEDVQVREKLKHAT 408
Cdd:COG4942  31 QLQQEIAELEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEIAELRAELEAQKEELAELL 110


                ....*...
gi 40807120 409 SKAKKTGE 416
Cdd:COG4942 111 RALYRLGR 118
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 108-140 1.09e-03

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: 40.84  E-value: 1.09e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 40807120   108 FSCIIGPNGSGKSNVIDSMLFVFGYRAQKIRSK 140
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFDALVIGLT 33
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 84-166 1.18e-03

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: 40.80  E-value: 1.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    84 ITHIVNQNFKSYAGEKIlgPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQkiRSKKLSVLIHNSDEHkdiqsCTVEVH 163
Cdd:TIGR00611   3 LSRLELTDFRNYDAVDL--ELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSH--RTSRDKPLIRFGAEA-----FVIEGR 73


                  ...
gi 40807120   164 FQK 166
Cdd:TIGR00611  74 VSK 76
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 84-128 1.48e-03

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: 40.36  E-value: 1.48e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 40807120  84 ITHIVNQNFKSYAGEKIlgPFHKRFSCIIGPNGSGKSNVIDSMLF 128
Cdd:cd03242   1 LKSLELRNFRNYAELEL--EFEPGVTVLVGENAQGKTNLLEAISL 43
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
261-374 3.33e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 39.66  E-value: 3.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  261 GRLNEPIKVLCRRVEILNEHR---GEKLNRVKMVEKEKDALEGEKNIAIEFLTLENEIFRKKNHVCQYYIYELQKRIAEM 337
Cdd:PRK03918 317 SRLEEEINGIEERIKELEEKEerlEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGLTPEKLEKELEEL 396

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 40807120  338 ETQKEKIHEDTKEINEKSNILSNEMKAKNKDVKDTEK 374
Cdd:PRK03918 397 EKAKEEIEEEISKITARIGELKKEIKELKKAIEELKK 433
ABC_sbcCD cd03279
ATP-binding cassette domain of sbcCD; SbcCD and other Mre11/Rad50 (MR) complexes are ...
 90-176 4.88e-03

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: 38.02  E-value: 4.88e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  90 QNFKSYAGEKILG--PFHKR-FSCIIGPNGSGKSNVIDSMLF-VFGYRAQKIRSKKLSVLIHNSDehkdiqsCTVEVHFQ 165
Cdd:cd03279   9 KNFGPFREEQVIDftGLDNNgLFLICGPTGAGKSTILDAITYaLYGKTPRYGRQENLRSVFAPGE-------DTAEVSFT 81

                        90
                ....*....|....*....
gi 40807120 166 --------KIIDKEGDDYE 176
Cdd:cd03279  82 fqlggkkyRVERSRGLDYD 100
SCP-1 pfam05483
Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major ...
 263-412 6.05e-03

Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.


Pssm-ID: 114219 [Multi-domain]  Cd Length: 787  Bit Score: 38.93  E-value: 6.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120   263 LNEPIKVLCRRVEILNEHrgeklnrvKMVEKEKDALEGEKNIAIEFL-TLENEIFRKKNHVC------QYYIYELQKRIA 335
Cdd:pfam05483 407 LEELKKILAEDEKLLDEK--------KQFEKIAEELKGKEQELIFLLqAREKEIHDLEIQLTaiktseEHYLKEVEDLKT 478

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120   336 EMETQKEKIHE----------DTKEINEKSNILSNEMKAKNKDVKDTEKKLNKITKFIEENKEKFTQLDLEDVQVREKLK 405
Cdd:pfam05483 479 ELEKEKLKNIEltahcdklllENKELTQEASDMTLELKKHQEDIINCKKQEERMLKQIENLEEKEMNLRDELESVREEFI 558


                  ....*..
gi 40807120   406 HATSKAK 412
Cdd:pfam05483 559 QKGDEVK 565
ABC_SMC5_euk cd03277
ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of ...
 84-151 6.87e-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: 37.58  E-value: 6.87e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120  84 ITHIVNQNFKSYagEKILGPFHKRFSCIIGPNGSGKSNVIDSMLFVFGYRAQKI-RSKKL-SVLIHNSDE 151
Cdd:cd03277   3 IVRIKLENFVTY--DETEFRPGPSLNMIIGPNGSGKSSIVCAICLGLGGKPKLLgRAKKVgEFVKRGCDE 70
AAA_29 pfam13555
P-loop containing region of AAA domain;
111-130 8.38e-03

P-loop containing region of AAA domain;


Pssm-ID: 433304 [Multi-domain]  Cd Length: 61  Bit Score: 34.50  E-value: 8.38e-03
                          10        20
                  ....*....|....*....|
gi 40807120   111 IIGPNGSGKSNVIDSMLFVF 130
Cdd:pfam13555  27 LTGPSGSGKSTLLDAIQTLL 46
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 265-404 9.85e-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: 38.51  E-value: 9.85e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120    265 EPIKVLCRRVEILNEHRGEKLNRVKMVEKEKDALEGEKNIaiefltLENEIFRKKNHV--CQYYIYELQKRIAEMETQKE 342
Cdd:TIGR02169  791 SRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEY------LEKEIQELQEQRidLKEQIKSIEKEIENLNGKKE 864

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 40807120    343 KIHEDTKEINEKSNILSNEMKAKNKDVKDTEKKLNKITKFIEENKEKFTQLDLEDVQVREKL 404
Cdd:TIGR02169  865 ELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQIEKKRKRLSELKAKL 926
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
 279-413 9.86e-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: 37.60  E-value: 9.86e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40807120 279 EHRGEKLN-RVKMVEKEKDALEGE-KNIAIEFLTLENEIFRKKNHVCQyyiyeLQKRIAEMETQKEKIhEDTKEINeksn 356
Cdd:COG1579  23 EHRLKELPaELAELEDELAALEARlEAAKTELEDLEKEIKRLELEIEE-----VEARIKKYEEQLGNV-RNNKEYE---- 92

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 40807120 357 ILSNEMKAKNKDVKDTEKKLNKITKFIEENKEKFTQLDLEDVQVREKLKHATSKAKK 413
Cdd:COG1579  93 ALQKEIESLKRRISDLEDEILELMERIEELEEELAELEAELAELEAELEEKKAELDE 149
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH