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Conserved domains on  [gi|403065183|gb|AFR13034|]
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DNA polymerase, partial [Mesoplodon densirostris herpesvirus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DNA_pol_B super family cl29029
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
1-230 6.64e-99

DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.


The actual alignment was detected with superfamily member pfam00136:

Pssm-ID: 395085  Cd Length: 439  Bit Score: 294.52  E-value: 6.64e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183    1 SIIQAHNLCFTTLSLDAASVAHLQPGKDYSEFEVGGKQLFFVHSHIRQSLLSVLLRDWLAMRKSIRARIPT-SSPEEAVL 79
Cdd:pfam00136  71 SIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEeTDPFERAI 150
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   80 LDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYLHDRWgtfdqltadfqeaetahaagtPYSVN 159
Cdd:pfam00136 151 LDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMY---------------------TYNFR 209
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 403065183  160 VIYGDTDSVFVKCTGLTYAGVCAIGEKMAQHVSQALFRPPVKLECEKTFAKLLLITKKKYIGII-----NGGKVLM 230
Cdd:pfam00136 210 VIYGDTDSVFIEFGGKDVEEAMKIGDELAEHVNQDLFKSPIKLEFEKVYKPLLLISKKKYAGLKytapsNFNKLDM 285
 
Name Accession Description Interval E-value
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
1-230 6.64e-99

DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.


Pssm-ID: 395085  Cd Length: 439  Bit Score: 294.52  E-value: 6.64e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183    1 SIIQAHNLCFTTLSLDAASVAHLQPGKDYSEFEVGGKQLFFVHSHIRQSLLSVLLRDWLAMRKSIRARIPT-SSPEEAVL 79
Cdd:pfam00136  71 SIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEeTDPFERAI 150
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   80 LDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYLHDRWgtfdqltadfqeaetahaagtPYSVN 159
Cdd:pfam00136 151 LDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMY---------------------TYNFR 209
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 403065183  160 VIYGDTDSVFVKCTGLTYAGVCAIGEKMAQHVSQALFRPPVKLECEKTFAKLLLITKKKYIGII-----NGGKVLM 230
Cdd:pfam00136 210 VIYGDTDSVFIEFGGKDVEEAMKIGDELAEHVNQDLFKSPIKLEFEKVYKPLLLISKKKYAGLKytapsNFNKLDM 285
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
1-174 1.55e-47

DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases


Pssm-ID: 214691 [Multi-domain]  Cd Length: 474  Bit Score: 162.70  E-value: 1.55e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183     1 SIIQAHNLCFTTLSLDAASVAHLQ---PGKDYSEFEVGGKQLFFVHSHIRQSLLSVLLRDWLAMRKSIRARIPTSSPE-- 75
Cdd:smart00486 314 SIIIAHNLCYSTLVGVGEVVIKGDliiPEDLLTIKYEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDEse 393
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183    76 -EAVLLDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYLHDRWGTFdqltadfqeaetahaagt 154
Cdd:smart00486 394 eLKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYPK------------------ 455
                          170       180
                   ....*....|....*....|
gi 403065183   155 pYSVNVIYGDTDSVFVKCTG 174
Cdd:smart00486 456 -PGFKVIYGDTDSIFVTKPG 474
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
1-221 4.72e-47

DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.


Pssm-ID: 99916  Cd Length: 393  Bit Score: 159.74  E-value: 4.72e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   1 SIIQAHNLCFTTLsLDAASVAHLQPgkdySEFEVGGKQLFFVHSHIRQSLLSVLLRDWLAMRKSIRARI--PTSSPEEAV 78
Cdd:cd05533   31 SIMMAHNLCYTTL-LNKNTAKKLPP----EDYIKTPNGDYFVKSSVRKGLLPEILEELLAARKRAKKDLkeETDPFKKAV 105
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  79 LlDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYLHDRWGTfdqltadfqeaetahAAGTPYSV 158
Cdd:cd05533  106 L-DGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEKYTK---------------ANGYSHDA 169
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 403065183 159 NVIYGDTDSVFVKCTGLTYAGVCAIGEKMAQHVSqALFRPPVKLECEKTFAKLLLITKKKYIG 221
Cdd:cd05533  170 KVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVS-KKFIKPIKLEFEKVYFPYLLINKKRYAG 231
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
1-222 8.24e-41

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 148.25  E-value: 8.24e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183    1 SIIQAHNLCFTTLsLDAASVAHLQPgkdysEFEVGGKQ-LFFVHSHIRQSLLSVLLRDWLAMRKSIRARIP-TSSPEEAV 78
Cdd:PTZ00166  568 SIMIAHNLCYSTL-VPPNDANNYPE-----DTYVTTPTgDKFVKKEVRKGILPLIVEELIAARKKAKKEMKdEKDPLLKK 641
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   79 LLDKQQSAIKVVCNSVYGFTG-VANGLLPCLPVAATVTTIGRHMLLSTRQYLHDRWgtfdqltadfqeaetAHAAGTPYS 157
Cdd:PTZ00166  642 VLNGRQLALKISANSVYGYTGaQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKHY---------------TKANGYKHD 706
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 403065183  158 VNVIYGDTDSVFVKCtgltyaGVCAIGEKM------AQHVSQaLFRPPVKLECEKTFAKLLLITKKKYIGI 222
Cdd:PTZ00166  707 ATVIYGDTDSVMVKF------GTDDIQEAMdlgkeaAERISK-KFLKPIKLEFEKVYCPYLLMNKKRYAGL 770
PolB COG0417
DNA polymerase elongation subunit (family B) [Replication, recombination and repair];
1-226 1.61e-39

DNA polymerase elongation subunit (family B) [Replication, recombination and repair];


Pssm-ID: 223494 [Multi-domain]  Cd Length: 792  Bit Score: 144.49  E-value: 1.61e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   1 SIIQAHNLCFTTLSLDAASvahlqpgKDYSEFEVGgkqlfFVHSHIRQSLLSVLLRDWLAMRKSIRARIPT-SSPEEAVL 79
Cdd:COG0417  433 SIIIKYNISPDTLVEEDCS-------DDYSPPGVG-----HGFCKREKGFLPEILEELLDRRDEIKKKMKKeKDPSERKL 500
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  80 LDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYLHDRWGTfdqltadfqeaetahaagtpysvn 159
Cdd:COG0417  501 LDGRQLALKVLANSFYGYLGYSNSRFYCIECAESVTAFGREILRETKELAEEMGLR------------------------ 556
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 403065183 160 VIYGDTDSVFVKCTGLTYAGVCAIGEKMAQHVSQALfRPPVKLECEKTFAKLLLIT-KKKYIGIINGG 226
Cdd:COG0417  557 VIYGDTDSLFVTLPGATYEEAIKIGEELVEEVNERL-PSGIELEVEKVYKRFLLPTaKKRYAGLLEDG 623
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
1-222 4.21e-25

DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.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: 273159 [Multi-domain]  Cd Length: 1172  Bit Score: 102.83  E-value: 4.21e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183     1 SIIQAHNLCFTTLslDAASVAHLQPGKDYSEFEVGgkqlffvhshirqsLLSVLLRDWLAMRKSIRARIPTS-SPEEAVL 79
Cdd:TIGR00592  824 SIIQEFNICFTTV--QQKVDEDELPELPDSELEMG--------------ILPRELRKLVERRKEVKKLMKQDlNPDLRLQ 887
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183    80 LDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYLhdrwgtfdqltadfqeaetahaagTPYSVN 159
Cdd:TIGR00592  888 YDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLV------------------------EEMNLE 943
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 403065183   160 VIYGDTDSVFVKCTGLTYAGVCAIGEKMAQHVSQALfrPPVKLECEKTFAKLLLITKKKYIGI 222
Cdd:TIGR00592  944 VIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLY--KLLELDIDGVFKRLLLLKKKKYAAI 1004
 
Name Accession Description Interval E-value
DNA_pol_B pfam00136
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ...
1-230 6.64e-99

DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.


Pssm-ID: 395085  Cd Length: 439  Bit Score: 294.52  E-value: 6.64e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183    1 SIIQAHNLCFTTLSLDAASVAHLQPGKDYSEFEVGGKQLFFVHSHIRQSLLSVLLRDWLAMRKSIRARIPT-SSPEEAVL 79
Cdd:pfam00136  71 SIIQAHNLCYTTLVRSVDEANNLPPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAIKKLLKEeTDPFERAI 150
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   80 LDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYLHDRWgtfdqltadfqeaetahaagtPYSVN 159
Cdd:pfam00136 151 LDKQQLALKITANSVYGFTGFANGRLPCLPIAASVTAIGREMLENTKDLVEGMY---------------------TYNFR 209
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 403065183  160 VIYGDTDSVFVKCTGLTYAGVCAIGEKMAQHVSQALFRPPVKLECEKTFAKLLLITKKKYIGII-----NGGKVLM 230
Cdd:pfam00136 210 VIYGDTDSVFIEFGGKDVEEAMKIGDELAEHVNQDLFKSPIKLEFEKVYKPLLLISKKKYAGLKytapsNFNKLDM 285
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
1-174 1.55e-47

DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases


Pssm-ID: 214691 [Multi-domain]  Cd Length: 474  Bit Score: 162.70  E-value: 1.55e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183     1 SIIQAHNLCFTTLSLDAASVAHLQ---PGKDYSEFEVGGKQLFFVHSHIRQSLLSVLLRDWLAMRKSIRARIPTSSPE-- 75
Cdd:smart00486 314 SIIIAHNLCYSTLVGVGEVVIKGDliiPEDLLTIKYEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDEse 393
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183    76 -EAVLLDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYLHDRWGTFdqltadfqeaetahaagt 154
Cdd:smart00486 394 eLKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKELIEENGYPK------------------ 455
                          170       180
                   ....*....|....*....|
gi 403065183   155 pYSVNVIYGDTDSVFVKCTG 174
Cdd:smart00486 456 -PGFKVIYGDTDSIFVTKPG 474
POLBc_delta cd05533
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
1-221 4.72e-47

DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.


Pssm-ID: 99916  Cd Length: 393  Bit Score: 159.74  E-value: 4.72e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   1 SIIQAHNLCFTTLsLDAASVAHLQPgkdySEFEVGGKQLFFVHSHIRQSLLSVLLRDWLAMRKSIRARI--PTSSPEEAV 78
Cdd:cd05533   31 SIMMAHNLCYTTL-LNKNTAKKLPP----EDYIKTPNGDYFVKSSVRKGLLPEILEELLAARKRAKKDLkeETDPFKKAV 105
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  79 LlDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYLHDRWGTfdqltadfqeaetahAAGTPYSV 158
Cdd:cd05533  106 L-DGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEKYTK---------------ANGYSHDA 169
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 403065183 159 NVIYGDTDSVFVKCTGLTYAGVCAIGEKMAQHVSqALFRPPVKLECEKTFAKLLLITKKKYIG 221
Cdd:cd05533  170 KVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVS-KKFIKPIKLEFEKVYFPYLLINKKRYAG 231
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
1-222 8.24e-41

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 148.25  E-value: 8.24e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183    1 SIIQAHNLCFTTLsLDAASVAHLQPgkdysEFEVGGKQ-LFFVHSHIRQSLLSVLLRDWLAMRKSIRARIP-TSSPEEAV 78
Cdd:PTZ00166  568 SIMIAHNLCYSTL-VPPNDANNYPE-----DTYVTTPTgDKFVKKEVRKGILPLIVEELIAARKKAKKEMKdEKDPLLKK 641
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   79 LLDKQQSAIKVVCNSVYGFTG-VANGLLPCLPVAATVTTIGRHMLLSTRQYLHDRWgtfdqltadfqeaetAHAAGTPYS 157
Cdd:PTZ00166  642 VLNGRQLALKISANSVYGYTGaQVGGQLPCLEVSTSITSFGRQMIDKTKELVEKHY---------------TKANGYKHD 706
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 403065183  158 VNVIYGDTDSVFVKCtgltyaGVCAIGEKM------AQHVSQaLFRPPVKLECEKTFAKLLLITKKKYIGI 222
Cdd:PTZ00166  707 ATVIYGDTDSVMVKF------GTDDIQEAMdlgkeaAERISK-KFLKPIKLEFEKVYCPYLLMNKKRYAGL 770
PolB COG0417
DNA polymerase elongation subunit (family B) [Replication, recombination and repair];
1-226 1.61e-39

DNA polymerase elongation subunit (family B) [Replication, recombination and repair];


Pssm-ID: 223494 [Multi-domain]  Cd Length: 792  Bit Score: 144.49  E-value: 1.61e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   1 SIIQAHNLCFTTLSLDAASvahlqpgKDYSEFEVGgkqlfFVHSHIRQSLLSVLLRDWLAMRKSIRARIPT-SSPEEAVL 79
Cdd:COG0417  433 SIIIKYNISPDTLVEEDCS-------DDYSPPGVG-----HGFCKREKGFLPEILEELLDRRDEIKKKMKKeKDPSERKL 500
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  80 LDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYLHDRWGTfdqltadfqeaetahaagtpysvn 159
Cdd:COG0417  501 LDGRQLALKVLANSFYGYLGYSNSRFYCIECAESVTAFGREILRETKELAEEMGLR------------------------ 556
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 403065183 160 VIYGDTDSVFVKCTGLTYAGVCAIGEKMAQHVSQALfRPPVKLECEKTFAKLLLIT-KKKYIGIINGG 226
Cdd:COG0417  557 VIYGDTDSLFVTLPGATYEEAIKIGEELVEEVNERL-PSGIELEVEKVYKRFLLPTaKKRYAGLLEDG 623
POLBc cd00145
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ...
1-223 8.61e-33

DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis.


Pssm-ID: 99912  Cd Length: 323  Bit Score: 120.55  E-value: 8.61e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   1 SIIQAHNLCFTTLSLDAASVAHlqpgkdYSEFEVGgkqlfFVHSHIRQSLLSVLLRDWLAMRKSI--RARIPTSSPEEAV 78
Cdd:cd00145   30 SIIITYNLSPTTLVGNGEIAAP------EDYIGVG-----FRSPKDRKGLLPRILEELLNFRDEAkkRMKAAKLAPEERV 98
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  79 LLDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYLHDRWGTfdqltadfqeaetahaagtpysv 158
Cdd:cd00145   99 LYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGAR----------------------- 155
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 403065183 159 nVIYGDTDSVFVKCTG-LTYAGVCAIGEKMAQHVSQAlfrPPVKLECEKTFAKLLLITKKKYIGII 223
Cdd:cd00145  156 -VIYGDTDSIFVSLPKmGTKEDAIKEGREILQELADE---HLLELEFEKVYLPFFLGKKKRYAGLD 217
POLBc_zeta cd05534
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ...
1-221 4.94e-32

DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.


Pssm-ID: 99917  Cd Length: 451  Bit Score: 120.78  E-value: 4.94e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   1 SIIQAHNLCFTTLsldaasVAHLQPGKDYSEFEVGGKQLF-----------------------FVHSHIRQSLLSVLLRD 57
Cdd:cd05534   64 SIMIAYNYCYSTC------LGRVEELNGGGKFGFLGVKLYlppppldllllkddvtispngvmFVKKSVRKGILPKMLEE 137
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  58 WLAMRKSIRARI--PTSSPEEAVLLDKQQSAIKVVCNSVYGFTGvAN--GLLPCLPVAATVTTIGRHMLLSTRQYLH--D 131
Cdd:cd05534  138 ILDTRIMVKKAMkkYKDDKKLQRILDARQLALKLLANVTYGYTA-ASfsGRMPCVEIADSIVQTGRETLERAIELIEstP 216
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183 132 RWGtfdqltadfqeAEtahaagtpysvnVIYGDTDSVFVKCTGLTYAGVCAIGEKMAQHVSqALFRPPVKLECEKTFAKL 211
Cdd:cd05534  217 KWG-----------AK------------VVYGDTDSLFVLLPGRTKEEAFKIGKEIAEAVT-AANPSPIKLKFEKVYHPC 272
                        250
                 ....*....|
gi 403065183 212 LLITKKKYIG 221
Cdd:cd05534  273 VLVTKKRYVG 282
POLBc_alpha cd05532
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
1-223 1.00e-25

DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.


Pssm-ID: 99915  Cd Length: 400  Bit Score: 103.04  E-value: 1.00e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   1 SIIQAHNLCFTTLSLDAASVahlqpgkdysefeVGGKQLFFVHSHIRQSLLSVLLRDWLAMRKSIRARIPT-SSPEEAVL 79
Cdd:cd05532   36 SIIQEYNICFTTVDRADPDD-------------EDDEEPPLPPSDQEKGILPRIIRKLVERRRQVKKLMKSeKDPDKKAQ 102
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  80 LDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRqylhdrwgtfdqltaDFQEAEtahaagtpySVN 159
Cdd:cd05532  103 LDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTK---------------DLVEKM---------NLE 158
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 403065183 160 VIYGDTDSVFVkCTGLT-YAGVCAIGEKMAQHVSQaLFRpPVKLECEKTFAKLLLITKKKYIGII 223
Cdd:cd05532  159 VIYGDTDSIMI-NTGTTdYEEAKKLGNKIKKEVNK-SYK-KLEIDIDGVFKRLLLLKKKKYAALK 220
pol2 TIGR00592
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ...
1-222 4.21e-25

DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.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: 273159 [Multi-domain]  Cd Length: 1172  Bit Score: 102.83  E-value: 4.21e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183     1 SIIQAHNLCFTTLslDAASVAHLQPGKDYSEFEVGgkqlffvhshirqsLLSVLLRDWLAMRKSIRARIPTS-SPEEAVL 79
Cdd:TIGR00592  824 SIIQEFNICFTTV--QQKVDEDELPELPDSELEMG--------------ILPRELRKLVERRKEVKKLMKQDlNPDLRLQ 887
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183    80 LDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYLhdrwgtfdqltadfqeaetahaagTPYSVN 159
Cdd:TIGR00592  888 YDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTRQLV------------------------EEMNLE 943
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 403065183   160 VIYGDTDSVFVKCTGLTYAGVCAIGEKMAQHVSQALfrPPVKLECEKTFAKLLLITKKKYIGI 222
Cdd:TIGR00592  944 VIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLY--KLLELDIDGVFKRLLLLKKKKYAAI 1004
POLBc_B3 cd05536
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ...
54-230 3.30e-22

DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.


Pssm-ID: 99919  Cd Length: 371  Bit Score: 93.16  E-value: 3.30e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  54 LLRDWLAMRKSIRARIPTSSPE--EAVLLDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYlhd 131
Cdd:cd05536   72 VLEDLLEERRRIKEKMKKLDPEseEYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKI--- 148
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183 132 rwgtfdqltadfqeaetAHAAGtpysVNVIYGDTDSVFVKctgltYAGVCAIGEKMAQHVSQALFRPPVKLECEKTFAKL 211
Cdd:cd05536  149 -----------------AEEKG----FKVIYGDTDSLFVK-----IDGADAVKKKVKKLLKYINEELPLELEIEKFYKRG 202
                        170
                 ....*....|....*....
gi 403065183 212 LLITKKKYIGIINGGKVLM 230
Cdd:cd05536  203 FFVTKKRYAGLTEDGKIDV 221
PRK05761 PRK05761
DNA-directed DNA polymerase I;
1-228 5.18e-18

DNA-directed DNA polymerase I;


Pssm-ID: 235594 [Multi-domain]  Cd Length: 787  Bit Score: 82.04  E-value: 5.18e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   1 SIIQAHNLCFTTLSLDaasvaHLQPGKDYSEFEVGgkqlffvHS--HIRQSLLSVL---LRDwlaMRKSI---RARIPTS 72
Cdd:PRK05761 434 SIIVKWNLSPETVRIP-----ECKCHYDDEVPELG-------HSvcDDRPGLTSVLvglLRD---FRVKIykkKAKDPNL 498
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  73 SPEEAVLLDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYlhdrwgtfdqltadfqeaetAHAA 152
Cdd:PRK05761 499 DEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGREILLSTKKK--------------------AEEL 558
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 403065183 153 GtpysVNVIYGDTDSVFVkcTGLTYAGVcaigEKMAQHVSQALfrpPVKLECEKTFaKLLLIT--KKKYIGIINGGKV 228
Cdd:PRK05761 559 G----LKVLYGDTDSLFV--WGPTKESL----EELIKEIEERT---GIDLEVDKTY-DWVAFSglKKNYFGVLKDGKV 622
POLBc_B1 cd05530
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ...
49-228 8.26e-16

DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.


Pssm-ID: 99913  Cd Length: 372  Bit Score: 75.08  E-value: 8.26e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  49 SLLSVLLRDWLAMRKSIRARIPTSSPEEAVLLDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQY 128
Cdd:cd05530   80 SQIIGLLRDLRVKIYKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITSTIKK 159
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183 129 lhdrwgtfdqltadfqeaetAHAAGtpysVNVIYGDTDSVFVKctGLTYAGVcaigEKMAQHVSQALfrpPVKLECEKTF 208
Cdd:cd05530  160 --------------------ARELG----LKVLYGDTDSLFLW--NPPQEQL----EDLVEWVEKEL---GLDLELDKEY 206
                        170       180
                 ....*....|....*....|..
gi 403065183 209 aKLLLIT--KKKYIGIINGGKV 228
Cdd:cd05530  207 -RYVVFSglKKNYLGVTKDGSV 227
PHA03036 PHA03036
DNA polymerase; Provisional
54-222 7.31e-14

DNA polymerase; Provisional


Pssm-ID: 222962 [Multi-domain]  Cd Length: 1004  Bit Score: 70.05  E-value: 7.31e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   54 LLRDWLAMRKSIRARI-PTSSPEEAVLLDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQYLHDR 132
Cdd:PHA03036  628 LLKTFLEERARYKKLLkEATSSVEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTAIGRNMIKYLNSVLNGS 707
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  133 WGTFDQLT-ADFQE---AETAHAAGTPYSVNV----------IYGDTDSVFV----KCTGLTYAGVCAIGEKMAQHVSQA 194
Cdd:PHA03036  708 KLINGKLIlANCPInpfFKDDRSIDTNYDTNLpveynftfrsVYGDTDSVFLeintKDVDKSIKIAKELERIINEKVLFD 787
                         170       180
                  ....*....|....*....|....*...
gi 403065183  195 LFrppvKLECEKTFAKLLLITKKKYIGI 222
Cdd:PHA03036  788 NF----KIEFEAVYKNLIMQSKKKYTTL 811
PRK05762 PRK05762
DNA polymerase II; Reviewed
1-223 2.39e-11

DNA polymerase II; Reviewed


Pssm-ID: 235595 [Multi-domain]  Cd Length: 786  Bit Score: 62.56  E-value: 2.39e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   1 SIIQAHNLCFTTLSldaasVAHLQPGKDYSEFEVGGKqlFFVHSHIRQSLLSVLLRDwlamRKSIRARiptsspeeavlL 80
Cdd:PRK05762 428 SIIRTFNIDPDGLV-----EGLAQPPEESVAGFLGAR--FSREKHFLPEIVERLWEG----RDEAKRE-----------M 485
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  81 DK--QQsAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRqylhdrwgtfdqltadfqeaETAHAAGtpYSV 158
Cdd:PRK05762 486 NKplSQ-AIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTR--------------------ELIEAQG--YQV 542
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183 159 nvIYGDTDSVFVKCTGLTYAGVC-AIGEKMAQHVSQ---ALFRPPVKLEC------EKTFAKLLLIT--------KKKYI 220
Cdd:PRK05762 543 --IYGDTDSTFVWLGGAHDEEDAaKIGRALVQEINQwwqEHLQQEFGLESalelefEKHYRRFFMPTirgaeegsKKRYA 620

                 ...
gi 403065183 221 GII 223
Cdd:PRK05762 621 GLI 623
POLBc_Pol_II cd05537
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
86-227 8.32e-07

DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.


Pssm-ID: 99920  Cd Length: 371  Bit Score: 48.80  E-value: 8.32e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  86 AIKVVCNSVYGFTGvANGllpCL----PVAATVTTIGRHMLLSTRQYLHDrwgtfdqltADFQeaetahaagtpysvnVI 161
Cdd:cd05537   95 AIKIIMNSFYGVLG-STG---CRffdpRLASSITLRGHEIMKQTRAWIEQ---------QGYQ---------------VI 146
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183 162 YGDTDSVFVKC-TGLTYAGVCAIGEKMAQHVSQ---ALFRPPVKLEC------EKTFAKLLLIT--------KKKYIGII 223
Cdd:cd05537  147 YGDTDSTFVWLgEELDAAEAQAIGKELASQINQwwaQKLKEEFGLESfleiefETHYSRFFMPTirgsdegsKKRYAGLK 226

                 ....
gi 403065183 224 NGGK 227
Cdd:cd05537  227 STDG 230
POLBc_B2 cd05531
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ...
47-187 1.27e-06

DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.


Pssm-ID: 99914  Cd Length: 352  Bit Score: 48.11  E-value: 1.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  47 RQSLLSVLLRDWLAMRKSIRARIPTSSPEEAVlldkqQSAIK---VVCnsvYGFTGVANGLLPCLPVAATVTTIGRHMLL 123
Cdd:cd05531   65 RRGFLPEVLEPLLERRLEYKRLKKEEDPYAGR-----QKALKwilVTS---FGYLGYKNAKFGRIEVHEAITAYGRKILL 136
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 403065183 124 STRqylhdrwgtfdqltadfqeaETAHAAGtpysVNVIYGDTDSVFVKCTGLtYAGVCA-IGEKM 187
Cdd:cd05531  137 RAK--------------------EIAEEMG----FRVLHGIVDSLWIQGRGD-IEELAReIEERT 176
PHA03334 PHA03334
putative DNA polymerase catalytic subunit; Provisional
55-172 1.46e-06

putative DNA polymerase catalytic subunit; Provisional


Pssm-ID: 223049 [Multi-domain]  Cd Length: 1545  Bit Score: 48.70  E-value: 1.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183   55 LRDWLAMRKSIRARIPTSS-PEEAVLLDKQQSAIKVVCNSVYgftGVANGLLPCLpvaatVTTIGRHMLLSTRQYLHDRW 133
Cdd:PHA03334  732 LNHYLSMRTEYKGAMKQAKdPKLKSYHNQLQNEMKICANSHY---GVAPHACQHL-----ITTLGRHKIKLVEEFIKKEP 803
                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 403065183  134 GTFdqltadfqeaetahaagtpysvnVIYGDTDSVFVKC 172
Cdd:PHA03334  804 GMT-----------------------VNYGDTDSVMFQL 819
POLBc_Pol_II_B cd05538
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ...
49-230 1.35e-05

DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.


Pssm-ID: 99921  Cd Length: 347  Bit Score: 45.17  E-value: 1.35e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183  49 SLLSVLLRDWLAMRKSIRAripTSSPEEAVLLDKQQSAIKVVCNSVYGFTGVANGLLPCLPVAATVTTIGRHMLLSTRQY 128
Cdd:cd05538   49 ALLKYLVELRLAAKESARA---AARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRW 125
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403065183 129 LHDRwgtfdqltadfqeaetahaAGTPYSVnviygDTDSVFVkctgLTYAGVCAIGEK--MAQHVSQALfrPP-VKLECE 205
Cdd:cd05538  126 LRRR-------------------GATPVEV-----DTDGIYF----IPPNGVDTEDEEeeLVRELSSTL--PKgITVEFD 175
                        170       180
                 ....*....|....*....|....*
gi 403065183 206 KTFAKLLLITKKKYIGIINGGKVLM 230
Cdd:cd05538  176 GRYRAMFSYKIKNYALLDYDGKLIV 200
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.19
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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