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Conserved domains on  [gi|2118808536|ref|XP_044317748|]
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uncharacterized protein LOC123038121 [Drosophila rhopaloa]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
457-671 1.55e-60

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.


The actual alignment was detected with superfamily member cd01644:

Pssm-ID: 477363  Cd Length: 213  Bit Score: 206.77  E-value: 1.55e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  457 LPHHAVFKEELHSIKQRIVFDASSRTsNGRSLNDILCIGPTLQNDMSSVILNWRKYRFVFTADIQKMYRCIDVHPEDAQY 536
Cdd:cd01644      4 LPHHAVIKPSKTTTKLRVVFDASARY-NGVSLNDMLLKGPDLLNSLFGVLLRFRQGKIAVSADIEKMFHQVKVRPEDRDV 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  537 QRILWRAADRA--INVFALSTLTFGTASAPFTAIRVIQQLAKDEQlsFPKAKEVLMNEIYVDDILSGGHTIEEAKDKRLQ 614
Cdd:cd01644     83 LRFLWRKDGDEpkPIEYRMTVVPFGAASAPFLANRALKQHAEDHP--HEAAAKIIKRNFYVDDILVSTDTLNEAVNVAKR 160
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2118808536  615 VSGAIKSARMELRKWASNDSRLLLSIPSEyhctQTLLSWDTTDPIKALGMYWLQNKD 671
Cdd:cd01644    161 LIALLKKGGFNLRKWASNSQEVLDDLPEE----RVLLDRDSDVTEKTLGLRWNPKTD 213
Peptidase_A17 pfam05380
Pao retrotransposon peptidase; Corresponds to Merops family A17. These proteins are homologous ...
686-859 1.78e-52

Pao retrotransposon peptidase; Corresponds to Merops family A17. These proteins are homologous to aspartic proteinases encoded by retroposons and retroviruses.


:

Pssm-ID: 461634  Cd Length: 162  Bit Score: 181.56  E-value: 1.78e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  686 TKRMILSSIARLFDPLGLIAPVIISGKLILKEVTMAKtkqadgtqtvLDWDDAVPDNIAERWRVFRDHLLRIGEISIDRW 765
Cdd:pfam05380    1 TKREVLSFIARIFDPLGLLSPVIVKGKILMQKLWQLK----------IDWDDPLPDELLEEWEKYRSELPELSTLTIPRQ 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  766 IhYTPSSISSVQMHAFCDGSSTSYAAAVYLRVEHQDGRCYTSLMAAKSKVTPTKPLTIPRTELSGAVLaikLVRWLTMAK 845
Cdd:pfam05380   71 L-TPPYDISSVELHGFSDASEKAYGAVVYLRSEDTDGTVTVKLLCAKSKVAPLKKLTIPRLELCGALL---LARLANYVI 146
                          170
                   ....*....|....*
gi 2118808536  846 FLSSLRVQTFY-WTD 859
Cdd:pfam05380  147 KELSLKISSVYaWSD 161
DUF1759 super family cl04160
Protein of unknown function (DUF1759); This is a family of proteins of unknown function. Most ...
109-230 9.74e-16

Protein of unknown function (DUF1759); This is a family of proteins of unknown function. Most of the members are gag-polyproteins.


The actual alignment was detected with superfamily member pfam03564:

Pssm-ID: 281552  Cd Length: 148  Bit Score: 75.95  E-value: 9.74e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  109 FSGACVDWPGYYDAFTSLIHNNNNLSNVQRLHFLKESLPISRDNDIRQMQLTDVNYAVAWGMMIKR-------------- 174
Cdd:pfam03564    1 FSGDYKEWPAFWDLFESTIHSKPHLPKVQKFNYLKSLLKGEAANVVAHLAITASNYESAWEALKKRydnprvikrsllne 80
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2118808536  175 ------LQKDSTDSLRSMLSTVNVCLAAFRRVQALGGESQHWLAHYIASKLPKETHNAWEHH 230
Cdd:pfam03564   81 fmklpsTNEDSVSQLRRFVDAANEIIRGLEALGENADQYDCILVHLLLQKLDEESRRKWISR 142
DUF5641 super family cl40017
Family of unknown function (DUF5641); This presumed domain is found in a range of ...
1364-1412 1.59e-13

Family of unknown function (DUF5641); This presumed domain is found in a range of retrotransposon polyproteins.


The actual alignment was detected with superfamily member pfam18701:

Pssm-ID: 465838  Cd Length: 94  Bit Score: 67.52  E-value: 1.59e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2118808536 1364 LIQQtMIRHFWKAWSRDWLAHLQQRPKWCQETESFQLNDLVIIKDDRFP 1412
Cdd:pfam18701    5 LVQQ-LRQHFWKRWSSEYLPQLQQRSKWTSSKPNLKVGDLVLVKEDNLP 52
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
1081-1136 1.36e-10

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


:

Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 58.03  E-value: 1.36e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2118808536 1081 HHFTELVIRHSHCLTLHGGAQLTLAHARQRFWILTGRQAVRRVIRKCVRCFRTRPT 1136
Cdd:pfam17921    3 KSLRKEILKEAHDSGGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
 
Name Accession Description Interval E-value
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
457-671 1.55e-60

RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.


Pssm-ID: 238822  Cd Length: 213  Bit Score: 206.77  E-value: 1.55e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  457 LPHHAVFKEELHSIKQRIVFDASSRTsNGRSLNDILCIGPTLQNDMSSVILNWRKYRFVFTADIQKMYRCIDVHPEDAQY 536
Cdd:cd01644      4 LPHHAVIKPSKTTTKLRVVFDASARY-NGVSLNDMLLKGPDLLNSLFGVLLRFRQGKIAVSADIEKMFHQVKVRPEDRDV 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  537 QRILWRAADRA--INVFALSTLTFGTASAPFTAIRVIQQLAKDEQlsFPKAKEVLMNEIYVDDILSGGHTIEEAKDKRLQ 614
Cdd:cd01644     83 LRFLWRKDGDEpkPIEYRMTVVPFGAASAPFLANRALKQHAEDHP--HEAAAKIIKRNFYVDDILVSTDTLNEAVNVAKR 160
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2118808536  615 VSGAIKSARMELRKWASNDSRLLLSIPSEyhctQTLLSWDTTDPIKALGMYWLQNKD 671
Cdd:cd01644    161 LIALLKKGGFNLRKWASNSQEVLDDLPEE----RVLLDRDSDVTEKTLGLRWNPKTD 213
Peptidase_A17 pfam05380
Pao retrotransposon peptidase; Corresponds to Merops family A17. These proteins are homologous ...
686-859 1.78e-52

Pao retrotransposon peptidase; Corresponds to Merops family A17. These proteins are homologous to aspartic proteinases encoded by retroposons and retroviruses.


Pssm-ID: 461634  Cd Length: 162  Bit Score: 181.56  E-value: 1.78e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  686 TKRMILSSIARLFDPLGLIAPVIISGKLILKEVTMAKtkqadgtqtvLDWDDAVPDNIAERWRVFRDHLLRIGEISIDRW 765
Cdd:pfam05380    1 TKREVLSFIARIFDPLGLLSPVIVKGKILMQKLWQLK----------IDWDDPLPDELLEEWEKYRSELPELSTLTIPRQ 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  766 IhYTPSSISSVQMHAFCDGSSTSYAAAVYLRVEHQDGRCYTSLMAAKSKVTPTKPLTIPRTELSGAVLaikLVRWLTMAK 845
Cdd:pfam05380   71 L-TPPYDISSVELHGFSDASEKAYGAVVYLRSEDTDGTVTVKLLCAKSKVAPLKKLTIPRLELCGALL---LARLANYVI 146
                          170
                   ....*....|....*
gi 2118808536  846 FLSSLRVQTFY-WTD 859
Cdd:pfam05380  147 KELSLKISSVYaWSD 161
DUF1759 pfam03564
Protein of unknown function (DUF1759); This is a family of proteins of unknown function. Most ...
109-230 9.74e-16

Protein of unknown function (DUF1759); This is a family of proteins of unknown function. Most of the members are gag-polyproteins.


Pssm-ID: 281552  Cd Length: 148  Bit Score: 75.95  E-value: 9.74e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  109 FSGACVDWPGYYDAFTSLIHNNNNLSNVQRLHFLKESLPISRDNDIRQMQLTDVNYAVAWGMMIKR-------------- 174
Cdd:pfam03564    1 FSGDYKEWPAFWDLFESTIHSKPHLPKVQKFNYLKSLLKGEAANVVAHLAITASNYESAWEALKKRydnprvikrsllne 80
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2118808536  175 ------LQKDSTDSLRSMLSTVNVCLAAFRRVQALGGESQHWLAHYIASKLPKETHNAWEHH 230
Cdd:pfam03564   81 fmklpsTNEDSVSQLRRFVDAANEIIRGLEALGENADQYDCILVHLLLQKLDEESRRKWISR 142
DUF5641 pfam18701
Family of unknown function (DUF5641); This presumed domain is found in a range of ...
1364-1412 1.59e-13

Family of unknown function (DUF5641); This presumed domain is found in a range of retrotransposon polyproteins.


Pssm-ID: 465838  Cd Length: 94  Bit Score: 67.52  E-value: 1.59e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2118808536 1364 LIQQtMIRHFWKAWSRDWLAHLQQRPKWCQETESFQLNDLVIIKDDRFP 1412
Cdd:pfam18701    5 LVQQ-LRQHFWKRWSSEYLPQLQQRSKWTSSKPNLKVGDLVLVKEDNLP 52
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
1081-1136 1.36e-10

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 58.03  E-value: 1.36e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2118808536 1081 HHFTELVIRHSHCLTLHGGAQLTLAHARQRFWILTGRQAVRRVIRKCVRCFRTRPT 1136
Cdd:pfam17921    3 KSLRKEILKEAHDSGGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
 
Name Accession Description Interval E-value
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
457-671 1.55e-60

RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.


Pssm-ID: 238822  Cd Length: 213  Bit Score: 206.77  E-value: 1.55e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  457 LPHHAVFKEELHSIKQRIVFDASSRTsNGRSLNDILCIGPTLQNDMSSVILNWRKYRFVFTADIQKMYRCIDVHPEDAQY 536
Cdd:cd01644      4 LPHHAVIKPSKTTTKLRVVFDASARY-NGVSLNDMLLKGPDLLNSLFGVLLRFRQGKIAVSADIEKMFHQVKVRPEDRDV 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  537 QRILWRAADRA--INVFALSTLTFGTASAPFTAIRVIQQLAKDEQlsFPKAKEVLMNEIYVDDILSGGHTIEEAKDKRLQ 614
Cdd:cd01644     83 LRFLWRKDGDEpkPIEYRMTVVPFGAASAPFLANRALKQHAEDHP--HEAAAKIIKRNFYVDDILVSTDTLNEAVNVAKR 160
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2118808536  615 VSGAIKSARMELRKWASNDSRLLLSIPSEyhctQTLLSWDTTDPIKALGMYWLQNKD 671
Cdd:cd01644    161 LIALLKKGGFNLRKWASNSQEVLDDLPEE----RVLLDRDSDVTEKTLGLRWNPKTD 213
Peptidase_A17 pfam05380
Pao retrotransposon peptidase; Corresponds to Merops family A17. These proteins are homologous ...
686-859 1.78e-52

Pao retrotransposon peptidase; Corresponds to Merops family A17. These proteins are homologous to aspartic proteinases encoded by retroposons and retroviruses.


Pssm-ID: 461634  Cd Length: 162  Bit Score: 181.56  E-value: 1.78e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  686 TKRMILSSIARLFDPLGLIAPVIISGKLILKEVTMAKtkqadgtqtvLDWDDAVPDNIAERWRVFRDHLLRIGEISIDRW 765
Cdd:pfam05380    1 TKREVLSFIARIFDPLGLLSPVIVKGKILMQKLWQLK----------IDWDDPLPDELLEEWEKYRSELPELSTLTIPRQ 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  766 IhYTPSSISSVQMHAFCDGSSTSYAAAVYLRVEHQDGRCYTSLMAAKSKVTPTKPLTIPRTELSGAVLaikLVRWLTMAK 845
Cdd:pfam05380   71 L-TPPYDISSVELHGFSDASEKAYGAVVYLRSEDTDGTVTVKLLCAKSKVAPLKKLTIPRLELCGALL---LARLANYVI 146
                          170
                   ....*....|....*
gi 2118808536  846 FLSSLRVQTFY-WTD 859
Cdd:pfam05380  147 KELSLKISSVYaWSD 161
DUF1759 pfam03564
Protein of unknown function (DUF1759); This is a family of proteins of unknown function. Most ...
109-230 9.74e-16

Protein of unknown function (DUF1759); This is a family of proteins of unknown function. Most of the members are gag-polyproteins.


Pssm-ID: 281552  Cd Length: 148  Bit Score: 75.95  E-value: 9.74e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  109 FSGACVDWPGYYDAFTSLIHNNNNLSNVQRLHFLKESLPISRDNDIRQMQLTDVNYAVAWGMMIKR-------------- 174
Cdd:pfam03564    1 FSGDYKEWPAFWDLFESTIHSKPHLPKVQKFNYLKSLLKGEAANVVAHLAITASNYESAWEALKKRydnprvikrsllne 80
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2118808536  175 ------LQKDSTDSLRSMLSTVNVCLAAFRRVQALGGESQHWLAHYIASKLPKETHNAWEHH 230
Cdd:pfam03564   81 fmklpsTNEDSVSQLRRFVDAANEIIRGLEALGENADQYDCILVHLLLQKLDEESRRKWISR 142
DUF5641 pfam18701
Family of unknown function (DUF5641); This presumed domain is found in a range of ...
1364-1412 1.59e-13

Family of unknown function (DUF5641); This presumed domain is found in a range of retrotransposon polyproteins.


Pssm-ID: 465838  Cd Length: 94  Bit Score: 67.52  E-value: 1.59e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2118808536 1364 LIQQtMIRHFWKAWSRDWLAHLQQRPKWCQETESFQLNDLVIIKDDRFP 1412
Cdd:pfam18701    5 LVQQ-LRQHFWKRWSSEYLPQLQQRSKWTSSKPNLKVGDLVLVKEDNLP 52
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
1081-1136 1.36e-10

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 58.03  E-value: 1.36e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2118808536 1081 HHFTELVIRHSHCLTLHGGAQLTLAHARQRFWILTGRQAVRRVIRKCVRCFRTRPT 1136
Cdd:pfam17921    3 KSLRKEILKEAHDSGGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
471-607 2.57e-03

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 40.27  E-value: 2.57e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118808536  471 KQRIVFDAssrtsngRSLND--ILCIGPTLQNDMSSVILNWRKYrfvFTA-DIQKMYRCIDVHPEDAQYQrilwraadrA 547
Cdd:cd01647     23 KLRLCVDY-------RKLNKvtIKDRYPLPTIDELLEELAGAKV---FSKlDLRSGYHQIPLAEESRPKT---------A 83
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2118808536  548 INV----FALSTLTFGTASAPFTAIRVIQQLAKDEQLSFpkakevlmNEIYVDDILSGGHTIEE 607
Cdd:cd01647     84 FRTpfglYEYTRMPFGLKNAPATFQRLMNKILGDLLGDF--------VEVYLDDILVYSKTEEE 139
 
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.
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