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Conserved domains on  [gi|9625567|ref|NP_039820|]
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polyprotein [Commelina yellow mottle virus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1429-1612 8.31e-60

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: 203.60  E-value: 8.31e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1429 KVIRPSESKHRSTAFIVrsgteidpitgKEKKGKERMVFNYKLLNENTESDQYSLPGINTIISKVGRSKIYSKFDLKSGF 1508
Cdd:cd01647    1 GIIEPSSSPYASPVVVV-----------KKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1509 WQVAMEEESVPWTAFLAGNKLYEWLVMPFGLKNAPAIFQRKMDNVFKGT-EKFIAVYIDDILVFSETAEQHSQHLYTMLQ 1587
Cdd:cd01647   70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                        170       180
                 ....*....|....*....|....*
gi 9625567  1588 LCKENGLILSPTKMKIGTPEIDFLG 1612
Cdd:cd01647  150 RLREAGLKLNPEKCEFGVPEVEFLG 174
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 1193-1305 8.00e-30

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


:

Pssm-ID: 425454  Cd Length: 101  Bit Score: 114.77  E-value: 8.00e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1193 AEYNGLYNVKVGIKpdnmepyYINAIVDTGATACLIQISAIPENYYeDAKVTVNFRSVLGiGTSTQMIKAGRILIGEQYF 1272
Cdd:pfam00077    1 AEQRPLLTVKIGGK-------YFTALLDTGADDTVISQNDWPTNWP-KQKATTNIQGIGG-GINVRQSDQILILIGEDKF 71

                           90       100       110
                   ....*....|....*....|....*....|...
gi 9625567    1273 RMPVTYVMNMGLsPGIqmIIGCSFIRSLEGGLR 1305
Cdd:pfam00077   72 RGTVSPLILPTC-PVN--IIGRDLLQQLGGRLT 101
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1711-1838 1.13e-21

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


The actual alignment was detected with superfamily member cd09274:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 121  Bit Score: 92.17  E-value: 1.13e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1711 IIETDGCMTGWGAVckwkMSKHDPRSTERICAYASGSFNPIK---STIDAEIQAAIHGLDKFKiYYLDKKELIIRSDCEA 1787
Cdd:cd09274    1 ILETDASDYGIGAV----LSQEDDDGKERPIAFFSRKLTPAErnySTTEKELLAIVWALKKFR-HYLLGRPFTVYTDHKA 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9625567  1788 IIKFYNKTNENKpsRV-RWLTF-SDFltglgiTVTFEHIDGKHNGLADALSRM 1838
Cdd:cd09274   76 LKYLLTQKDLNG--RLaRWLLLlSEF------DFEIEYRPGKENVVADALSRL 120
ZnF_C2HC smart00343
zinc finger;
880-896 7.46e-05

zinc finger;


:

Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 41.27  E-value: 7.46e-05
                            10
                    ....*....|....*..
gi 9625567      880 KCYICGQEGHYANQCRN 896
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
BRcat_Rcat_RBR super family cl45895
BRcat (benign-catalytic) and Rcat (required-for-catalysis) domains, part of the RBR ...
 1029-1047 2.11e-04

BRcat (benign-catalytic) and Rcat (required-for-catalysis) domains, part of the RBR (RING1-BRcat-Rcat) domain; The RBR family of RING-type E3 ligases are characterized by containing an RBR (RING1-BRcat-Rcat) domain, which was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. It is composed of an extended RING domain (RING1) followed by an in-between RING (IBR) domain and the catalytic domain, which is structurally an IBR domain but is commonly designated as RING2. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBRs has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis), where the IBR and RING2 domains have been renamed as BRcat and Rcat domains, respectively. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. The BRcat domain adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes.


The actual alignment was detected with superfamily member cd20344:

Pssm-ID: 459240  Cd Length: 72  Bit Score: 41.15  E-value: 2.11e-04
                         10
                 ....*....|....*....
gi 9625567  1029 VQCHHCHAVYCFMCAEAYH 1047
Cdd:cd20344   31 VQCKRCKTSFCFKCGEDYH 49
Lebercilin super family cl25726
Ciliary protein causing Leber congenital amaurosis disease; Lebercilin is a family of ...
 1084-1161 3.34e-04

Ciliary protein causing Leber congenital amaurosis disease; Lebercilin is a family of eukaryotic ciliary proteins. Mutations in the gene, LCA5, are implicated in the disease Leber congenital amaurosis. In photoreceptors, lebercilin is uniquely localized at the cilium that bridges the inner and outer segments. Lebercilin functions as an integral element of selective protein transport through photoreceptor cilia. Lebercilin specifically interacts with the intraflagellar transport (IFT), and disruption of IFT can lead to Leber congenital amaurosis.


The actual alignment was detected with superfamily member pfam15619:

Pssm-ID: 464776 [Multi-domain]  Cd Length: 193  Bit Score: 43.74  E-value: 3.34e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1084 ISQLQQENQRLQKQVERLQEE---LMKLHREKDEALKHSEKASRVFSTIQESDEAELNLIKEELRQFKEETRMAIAQLKE 1160
Cdd:pfam15619   13 IKELQNELAELQSKLEELRKEnrlLKRLQKRQEKALGKYEGTESELPQLIARHNEEVRVLRERLRRLQEKERDLERKLKE 92


                   .
gi 9625567    1161 A 1161
Cdd:pfam15619   93 K 93
AIR1 super family cl34894
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 863-904 3.19e-03

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


The actual alignment was detected with superfamily member COG5082:

Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 40.60  E-value: 3.19e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 9625567   863 AHDNH--IRVTKAKyqrkcKCYICGQEGHYANQCrNKHKDQQRV 904
Cdd:COG5082   85 SWDGHrsNHCPKPK-----KCYNCGETGHLSRDC-NPSKDQQKS 122
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1429-1612 8.31e-60

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: 203.60  E-value: 8.31e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1429 KVIRPSESKHRSTAFIVrsgteidpitgKEKKGKERMVFNYKLLNENTESDQYSLPGINTIISKVGRSKIYSKFDLKSGF 1508
Cdd:cd01647    1 GIIEPSSSPYASPVVVV-----------KKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1509 WQVAMEEESVPWTAFLAGNKLYEWLVMPFGLKNAPAIFQRKMDNVFKGT-EKFIAVYIDDILVFSETAEQHSQHLYTMLQ 1587
Cdd:cd01647   70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                        170       180
                 ....*....|....*....|....*
gi 9625567  1588 LCKENGLILSPTKMKIGTPEIDFLG 1612
Cdd:cd01647  150 RLREAGLKLNPEKCEFGVPEVEFLG 174
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1457-1612 4.86e-39

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 144.37  E-value: 4.86e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1457 KEKKGKERMV----FNYKLLNENT-------ESDQYSLPGINTIISKVGRSKIYSKFDLKSGFWQVAMEEESVPWTAF-- 1523
Cdd:pfam00078    3 KKGKGKYRPIsllsIDYKALNKIIvkrlkpeNLDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFtt 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1524 ---------LAGNKLYEWLVMPFGLKNAPAIFQRKMDNVF----KGTEKFIAVYIDDILVFSETAEQHSQHLYTMLQLCK 1590
Cdd:pfam00078   83 ppininwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLrplrKRAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLK 162

                          170       180
                   ....*....|....*....|....
gi 9625567    1591 ENGLILSPTKMKI--GTPEIDFLG 1612
Cdd:pfam00078  163 ESGLKINPEKTQFflKSKEVKYLG 186
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 1193-1305 8.00e-30

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 425454  Cd Length: 101  Bit Score: 114.77  E-value: 8.00e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1193 AEYNGLYNVKVGIKpdnmepyYINAIVDTGATACLIQISAIPENYYeDAKVTVNFRSVLGiGTSTQMIKAGRILIGEQYF 1272
Cdd:pfam00077    1 AEQRPLLTVKIGGK-------YFTALLDTGADDTVISQNDWPTNWP-KQKATTNIQGIGG-GINVRQSDQILILIGEDKF 71

                           90       100       110
                   ....*....|....*....|....*....|...
gi 9625567    1273 RMPVTYVMNMGLsPGIqmIIGCSFIRSLEGGLR 1305
Cdd:pfam00077   72 RGTVSPLILPTC-PVN--IIGRDLLQQLGGRLT 101
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1711-1838 1.13e-21

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 92.17  E-value: 1.13e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1711 IIETDGCMTGWGAVckwkMSKHDPRSTERICAYASGSFNPIK---STIDAEIQAAIHGLDKFKiYYLDKKELIIRSDCEA 1787
Cdd:cd09274    1 ILETDASDYGIGAV----LSQEDDDGKERPIAFFSRKLTPAErnySTTEKELLAIVWALKKFR-HYLLGRPFTVYTDHKA 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9625567  1788 IIKFYNKTNENKpsRV-RWLTF-SDFltglgiTVTFEHIDGKHNGLADALSRM 1838
Cdd:cd09274   76 LKYLLTQKDLNG--RLaRWLLLlSEF------DFEIEYRPGKENVVADALSRL 120
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1705-1806 2.31e-13

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 67.92  E-value: 2.31e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1705 PKDSFIIiETDGCMTGWGAVckwkMSKHDPRSTERICAYASGSFNPIK---STIDAEIQAAIHGLDKFKiYYLDKKELII 1781
Cdd:pfam17917    2 PSKPFIL-ETDASDYGIGAV----LSQKDEDGKERPIAYASRKLTPAErnySTTEKELLAIVWALKKFR-HYLLGRKFTV 75

                           90       100
                   ....*....|....*....|....*.
gi 9625567    1782 RSDCEAIIKFYNKTNENkpSRV-RWL 1806
Cdd:pfam17917   76 YTDHKPLKYLFTPKELN--GRLaRWA 99
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1710-1838 7.69e-06

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 47.15  E-value: 7.69e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1710 IIIETDG-CMT-----GWGAVCKWKmskhdprsteRICAYASGSFnPIKSTIDAEIQAAIHGLDKFKiyYLDKKELIIRS 1783
Cdd:COG0328    3 IEIYTDGaCRGnpgpgGWGAVIRYG----------GEEKELSGGL-GDTTNNRAELTALIAALEALK--ELGPCEVEIYT 69

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 9625567  1784 DCEAIIKFYNKTNENKPSR----VR----WLTFSDFLTglGITVTFEHIDGKH----NGLADALSRM 1838
Cdd:COG0328   70 DSQYVVNQITGWIHGWKKNgwkpVKnpdlWQRLDELLA--RHKVTFEWVKGHAghpgNERADALANK 134
ZnF_C2HC smart00343
zinc finger;
880-896 7.46e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 41.27  E-value: 7.46e-05
                            10
                    ....*....|....*..
gi 9625567      880 KCYICGQEGHYANQCRN 896
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
BRcat_RBR_TRIAD1 cd20344
BRcat domain found in two RING fingers and DRIL [double RING finger linked] 1 (TRIAD1); TRIAD1, ...
 1029-1047 2.11e-04

BRcat domain found in two RING fingers and DRIL [double RING finger linked] 1 (TRIAD1); TRIAD1, also called ariadne-2 (ARI-2), protein ariadne-2 homolog, Ariadne RBR E3 ubiquitin protein ligase 2 (ARIH2), or UbcM4-interacting protein 48, is an RBR-type E3 ubiquitin-protein ligase that catalyzes the formation of polyubiquitin chains linked via lysine-48 as well as lysine-63 residues. Its auto-ubiquitylation can be catalyzed by the E2 conjugating enzyme UBCH7. TRIAD1 has been implicated in hematopoiesis, specifically in myelopoiesis, as well as in embryogenesis. It functions as a regulator of endosomal transport, and is required for the proper function of multivesicular bodies. It also acts as a novel ubiquitination target for proteasome-dependent degradation by murine double minute 2 (MDM2). As a proapoptotic protein, TRIAD1 promotes p53 activation, and inhibits MDM2-mediated p53 ubiquitination and degradation. Furthermore, TRIAD1 can inhibit the ubiquitination and proteasomal degradation of growth factor independence 1 (Gfi1), a transcriptional repressor essential for the function and development of many different hematopoietic lineages. TRIAD1 contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of TRIAD1 that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity.


Pssm-ID: 439005  Cd Length: 72  Bit Score: 41.15  E-value: 2.11e-04
                         10
                 ....*....|....*....
gi 9625567  1029 VQCHHCHAVYCFMCAEAYH 1047
Cdd:cd20344   31 VQCKRCKTSFCFKCGEDYH 49
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 879-896 2.84e-04

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 39.43  E-value: 2.84e-04
                           10
                   ....*....|....*...
gi 9625567     879 CKCYICGQEGHYANQCRN 896
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
Lebercilin pfam15619
Ciliary protein causing Leber congenital amaurosis disease; Lebercilin is a family of ...
 1084-1161 3.34e-04

Ciliary protein causing Leber congenital amaurosis disease; Lebercilin is a family of eukaryotic ciliary proteins. Mutations in the gene, LCA5, are implicated in the disease Leber congenital amaurosis. In photoreceptors, lebercilin is uniquely localized at the cilium that bridges the inner and outer segments. Lebercilin functions as an integral element of selective protein transport through photoreceptor cilia. Lebercilin specifically interacts with the intraflagellar transport (IFT), and disruption of IFT can lead to Leber congenital amaurosis.


Pssm-ID: 464776 [Multi-domain]  Cd Length: 193  Bit Score: 43.74  E-value: 3.34e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1084 ISQLQQENQRLQKQVERLQEE---LMKLHREKDEALKHSEKASRVFSTIQESDEAELNLIKEELRQFKEETRMAIAQLKE 1160
Cdd:pfam15619   13 IKELQNELAELQSKLEELRKEnrlLKRLQKRQEKALGKYEGTESELPQLIARHNEEVRVLRERLRRLQEKERDLERKLKE 92


                   .
gi 9625567    1161 A 1161
Cdd:pfam15619   93 K 93
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
1084-1180 1.24e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 43.35  E-value: 1.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1084 ISQLQQENQRLQKQVERLQEELMKLHREKDEAlkhSEKASRVFSTIQESdEAELNLIKEELRQFKEEtrmaIAQLKEAII 1163
Cdd:COG4372  103 LESLQEEAEELQEELEELQKERQDLEQQRKQL---EAQIAELQSEIAER-EEELKELEEQLESLQEE----LAALEQELQ 174

                         90
                 ....*....|....*..
gi 9625567  1164 VQEEDTIEERCAMILEE 1180
Cdd:COG4372  175 ALSEAEAEQALDELLKE 191
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 863-904 3.19e-03

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 40.60  E-value: 3.19e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 9625567   863 AHDNH--IRVTKAKyqrkcKCYICGQEGHYANQCrNKHKDQQRV 904
Cdd:COG5082   85 SWDGHrsNHCPKPK-----KCYNCGETGHLSRDC-NPSKDQQKS 122
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1429-1612 8.31e-60

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: 203.60  E-value: 8.31e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1429 KVIRPSESKHRSTAFIVrsgteidpitgKEKKGKERMVFNYKLLNENTESDQYSLPGINTIISKVGRSKIYSKFDLKSGF 1508
Cdd:cd01647    1 GIIEPSSSPYASPVVVV-----------KKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1509 WQVAMEEESVPWTAFLAGNKLYEWLVMPFGLKNAPAIFQRKMDNVFKGT-EKFIAVYIDDILVFSETAEQHSQHLYTMLQ 1587
Cdd:cd01647   70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                        170       180
                 ....*....|....*....|....*
gi 9625567  1588 LCKENGLILSPTKMKIGTPEIDFLG 1612
Cdd:cd01647  150 RLREAGLKLNPEKCEFGVPEVEFLG 174
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1457-1612 4.86e-39

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 144.37  E-value: 4.86e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1457 KEKKGKERMV----FNYKLLNENT-------ESDQYSLPGINTIISKVGRSKIYSKFDLKSGFWQVAMEEESVPWTAF-- 1523
Cdd:pfam00078    3 KKGKGKYRPIsllsIDYKALNKIIvkrlkpeNLDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFtt 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1524 ---------LAGNKLYEWLVMPFGLKNAPAIFQRKMDNVF----KGTEKFIAVYIDDILVFSETAEQHSQHLYTMLQLCK 1590
Cdd:pfam00078   83 ppininwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLrplrKRAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLK 162

                          170       180
                   ....*....|....*....|....
gi 9625567    1591 ENGLILSPTKMKI--GTPEIDFLG 1612
Cdd:pfam00078  163 ESGLKINPEKTQFflKSKEVKYLG 186
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 1193-1305 8.00e-30

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 425454  Cd Length: 101  Bit Score: 114.77  E-value: 8.00e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1193 AEYNGLYNVKVGIKpdnmepyYINAIVDTGATACLIQISAIPENYYeDAKVTVNFRSVLGiGTSTQMIKAGRILIGEQYF 1272
Cdd:pfam00077    1 AEQRPLLTVKIGGK-------YFTALLDTGADDTVISQNDWPTNWP-KQKATTNIQGIGG-GINVRQSDQILILIGEDKF 71

                           90       100       110
                   ....*....|....*....|....*....|...
gi 9625567    1273 RMPVTYVMNMGLsPGIqmIIGCSFIRSLEGGLR 1305
Cdd:pfam00077   72 RGTVSPLILPTC-PVN--IIGRDLLQQLGGRLT 101
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 1410-1612 6.86e-22

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.


Pssm-ID: 239685 [Multi-domain]  Cd Length: 210  Bit Score: 95.88  E-value: 6.86e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1410 VTPGDEEAMTRQINLLLQMKVIRPSESKHRSTAFIVRsgteidpitgKEKKGKERMVFNYKLLNENTESDQYSLPGINTI 1489
Cdd:cd03715    9 LPREAREGITPHIQELLEAGILVPCQSPWNTPILPVK----------KPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1490 ISKVGR-SKIYSKFDLKSGFWQVAMEEESVPWTAFLAGNKLYEWLVMPFGLKNAPAIF----QRKMDNVFKGTEKFIAV- 1563
Cdd:cd03715   79 LSLLPPkHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFhealARDLAPFPLEHEGTILLq 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 9625567  1564 YIDDILVFSETAEQHSQHLYTMLQLCKENGLILSPTKMKIGTPEIDFLG 1612
Cdd:cd03715  159 YVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLG 207
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1711-1838 1.13e-21

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 92.17  E-value: 1.13e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1711 IIETDGCMTGWGAVckwkMSKHDPRSTERICAYASGSFNPIK---STIDAEIQAAIHGLDKFKiYYLDKKELIIRSDCEA 1787
Cdd:cd09274    1 ILETDASDYGIGAV----LSQEDDDGKERPIAFFSRKLTPAErnySTTEKELLAIVWALKKFR-HYLLGRPFTVYTDHKA 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9625567  1788 IIKFYNKTNENKpsRV-RWLTF-SDFltglgiTVTFEHIDGKHNGLADALSRM 1838
Cdd:cd09274   76 LKYLLTQKDLNG--RLaRWLLLlSEF------DFEIEYRPGKENVVADALSRL 120
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 1416-1612 2.00e-14

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 74.24  E-value: 2.00e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1416 EAMTRQINLLLQMKVIRPSESKHRSTAFIVrsgteidpitgKEKKGKERMVFNYKLLNENTE---SDQYSLPGINTIisK 1492
Cdd:cd01645   15 EALTELVTEQLKEGHIEPSTSPWNTPVFVI-----------KKKSGKWRLLHDLRAVNAQTQdmgALQPGLPHPAAL--P 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1493 VGRSKIYskFDLKSGFWQVAMEEESVPWTAF-------LAGNKLYEWLVMPFGLKNAPAIFQRKMDNVFKGT-EKF---- 1560
Cdd:cd01645   82 KGWPLIV--LDLKDCFFSIPLHPDDRERFAFtvpsinnKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFrKQYpdiv 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 9625567  1561 IAVYIDDILVFSETAEQHSQHLYTMLQLCKENGLILSPTKMKIGTPeIDFLG 1612
Cdd:cd01645  160 IYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPP-FQYLG 210
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1705-1806 2.31e-13

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 67.92  E-value: 2.31e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1705 PKDSFIIiETDGCMTGWGAVckwkMSKHDPRSTERICAYASGSFNPIK---STIDAEIQAAIHGLDKFKiYYLDKKELII 1781
Cdd:pfam17917    2 PSKPFIL-ETDASDYGIGAV----LSQKDEDGKERPIAYASRKLTPAErnySTTEKELLAIVWALKKFR-HYLLGRKFTV 75

                           90       100
                   ....*....|....*....|....*.
gi 9625567    1782 RSDCEAIIKFYNKTNENkpSRV-RWL 1806
Cdd:pfam17917   76 YTDHKPLKYLFTPKELN--GRLaRWA 99
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
1688-1781 3.28e-12

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 64.44  E-value: 3.28e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1688 VRQIKEKVKNLPDLQLPPKDSFIIIETDGCMTGWGAVckwkMSKHDPRSTERICAYASGSFNPIK---STIDAEIQAAIH 1764
Cdd:pfam17919    9 FEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAV----LSQEDDDGGERPIAYASRKLSPAErnySTTEKELLAIVF 84

                           90
                   ....*....|....*..
gi 9625567    1765 GLDKFKiYYLDKKELII 1781
Cdd:pfam17919   85 ALKKFR-HYLLGRKFTV 100
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 1502-1612 2.85e-09

RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.


Pssm-ID: 239684 [Multi-domain]  Cd Length: 119  Bit Score: 56.58  E-value: 2.85e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1502 FDLKSGFWQVAMEEESVPWTAFLAGNKLYEWLVMPFGLKNAPAIFQRkmdnVFKGTEKF-------IAVYIDDILVFSET 1574
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTK----VVEALLAPlrllgvrIFSYLDDLLIIASS 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 9625567  1575 A---EQHSQHLYTMlqLCKENGLILSPTKMKIG-TPEIDFLG 1612
Cdd:cd03714   77 IktsEAVLRHLRAT--LLANLGFTLNLEKSKLGpTQRITFLG 116
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1712-1837 6.07e-07

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 50.01  E-value: 6.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1712 IETDGCMT------GWGAVCKwkmskhdPRSTERICAYASGsfNPIKSTIDAEIQAAIHGLDKFKIYYLdkKELIIRSDC 1785
Cdd:cd06222    1 INVDGSCRgnpgpaGIGGVLR-------DHEGGWLGGFALK--IGAPTALEAELLALLLALELALDLGY--LKVIIESDS 69

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 9625567  1786 EAIIKFYNKTNENKPSRVRWLTFSDFLTGLGITVTFEHIDGKHNGLADALSR 1837
Cdd:cd06222   70 KYVVDLINSGSFKWSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 1502-1612 1.45e-06

RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 48.12  E-value: 1.45e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1502 FDLKSGFWQVAMeeesvpwtaflagnklyewlvmPFGLKNAPAIFQRKMDNVFKGTEK-----FIAVYIDDILVFSeTAE 1576
Cdd:cd00304    1 FDVKSFFTSIPL----------------------PQGSPLSPALANLYMEKLEAPILKqlldiTLIRYVDDLVVIA-KSE 57

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 9625567  1577 QHSQHLYTMLQLCKENGLILSPTKMK--IGTPEIDFLG 1612
Cdd:cd00304   58 QQAVKKRELEEFLARLGLNLSDEKTQftEKEKKFKFLG 95
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1710-1838 7.69e-06

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 47.15  E-value: 7.69e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1710 IIIETDG-CMT-----GWGAVCKWKmskhdprsteRICAYASGSFnPIKSTIDAEIQAAIHGLDKFKiyYLDKKELIIRS 1783
Cdd:COG0328    3 IEIYTDGaCRGnpgpgGWGAVIRYG----------GEEKELSGGL-GDTTNNRAELTALIAALEALK--ELGPCEVEIYT 69

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 9625567  1784 DCEAIIKFYNKTNENKPSR----VR----WLTFSDFLTglGITVTFEHIDGKH----NGLADALSRM 1838
Cdd:COG0328   70 DSQYVVNQITGWIHGWKKNgwkpVKnpdlWQRLDELLA--RHKVTFEWVKGHAghpgNERADALANK 134
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1711-1837 4.00e-05

DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260007  Cd Length: 120  Bit Score: 44.97  E-value: 4.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1711 IIETDGCMTGWGAVCkwkmskhdprSTERICAYAsgSFNPIKSTIDA-EIQAAIHGLDKFKiYYLDKKELIIRSDCEAII 1789
Cdd:cd09275    1 VLFTDASLSGWGAYL----------LNSRAHGPW--SADERNKHINLlELKAVLLALQHFA-AELKNRKILIRTDNTTAV 67

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 9625567  1790 KFYNKTNENKPSRVRWLTfSDFLTG---LGITVTFEHIDGKHNGLADALSR 1837
Cdd:cd09275   68 AYINKQGGTSSPPLLALA-RQILLWceqRNIWLRASHIPGVLNTEADRLSR 117
ZnF_C2HC smart00343
zinc finger;
880-896 7.46e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 41.27  E-value: 7.46e-05
                            10
                    ....*....|....*..
gi 9625567      880 KCYICGQEGHYANQCRN 896
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
BRcat_RBR_TRIAD1 cd20344
BRcat domain found in two RING fingers and DRIL [double RING finger linked] 1 (TRIAD1); TRIAD1, ...
 1029-1047 2.11e-04

BRcat domain found in two RING fingers and DRIL [double RING finger linked] 1 (TRIAD1); TRIAD1, also called ariadne-2 (ARI-2), protein ariadne-2 homolog, Ariadne RBR E3 ubiquitin protein ligase 2 (ARIH2), or UbcM4-interacting protein 48, is an RBR-type E3 ubiquitin-protein ligase that catalyzes the formation of polyubiquitin chains linked via lysine-48 as well as lysine-63 residues. Its auto-ubiquitylation can be catalyzed by the E2 conjugating enzyme UBCH7. TRIAD1 has been implicated in hematopoiesis, specifically in myelopoiesis, as well as in embryogenesis. It functions as a regulator of endosomal transport, and is required for the proper function of multivesicular bodies. It also acts as a novel ubiquitination target for proteasome-dependent degradation by murine double minute 2 (MDM2). As a proapoptotic protein, TRIAD1 promotes p53 activation, and inhibits MDM2-mediated p53 ubiquitination and degradation. Furthermore, TRIAD1 can inhibit the ubiquitination and proteasomal degradation of growth factor independence 1 (Gfi1), a transcriptional repressor essential for the function and development of many different hematopoietic lineages. TRIAD1 contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of TRIAD1 that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity.


Pssm-ID: 439005  Cd Length: 72  Bit Score: 41.15  E-value: 2.11e-04
                         10
                 ....*....|....*....
gi 9625567  1029 VQCHHCHAVYCFMCAEAYH 1047
Cdd:cd20344   31 VQCKRCKTSFCFKCGEDYH 49
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 879-896 2.84e-04

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 39.43  E-value: 2.84e-04
                           10
                   ....*....|....*...
gi 9625567     879 CKCYICGQEGHYANQCRN 896
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 1714-1838 3.23e-04

non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260008 [Multi-domain]  Cd Length: 131  Bit Score: 42.59  E-value: 3.23e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1714 TDGCM----TGWGAVCkwkmskhdPRSTERIcayaSGSFN-PIKSTI-DAEIQAAIHGLDKFKIYYLDKKELIIRSDCEA 1787
Cdd:cd09276    4 TDGSKlegsVGAGFVI--------YRGGEVI----SRSYRlGTHASVfDAELEAILEALELALATARRARKVTIFTDSQS 71

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 9625567  1788 IIKFYNKTNENKPS--RVRWLTFSDFLTGLGITVTFE----H--IDGkhNGLADALSRM 1838
Cdd:cd09276   72 ALQALRNPRRSSGQviLIRILRLLRLLKAKGVKVRLRwvpgHvgIEG--NEAADRLAKE 128
Lebercilin pfam15619
Ciliary protein causing Leber congenital amaurosis disease; Lebercilin is a family of ...
 1084-1161 3.34e-04

Ciliary protein causing Leber congenital amaurosis disease; Lebercilin is a family of eukaryotic ciliary proteins. Mutations in the gene, LCA5, are implicated in the disease Leber congenital amaurosis. In photoreceptors, lebercilin is uniquely localized at the cilium that bridges the inner and outer segments. Lebercilin functions as an integral element of selective protein transport through photoreceptor cilia. Lebercilin specifically interacts with the intraflagellar transport (IFT), and disruption of IFT can lead to Leber congenital amaurosis.


Pssm-ID: 464776 [Multi-domain]  Cd Length: 193  Bit Score: 43.74  E-value: 3.34e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1084 ISQLQQENQRLQKQVERLQEE---LMKLHREKDEALKHSEKASRVFSTIQESDEAELNLIKEELRQFKEETRMAIAQLKE 1160
Cdd:pfam15619   13 IKELQNELAELQSKLEELRKEnrlLKRLQKRQEKALGKYEGTESELPQLIARHNEEVRVLRERLRRLQEKERDLERKLKE 92


                   .
gi 9625567    1161 A 1161
Cdd:pfam15619   93 K 93
GAS pfam13851
Growth-arrest specific micro-tubule binding; This family is the highly conserved central ...
 1083-1180 6.72e-04

Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells.


Pssm-ID: 464001 [Multi-domain]  Cd Length: 200  Bit Score: 42.97  E-value: 6.72e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1083 LISQLQQENQRLQKQVERLQEELMKLHREKDEALKHSEKASRVfstiqesdEAELNLIKEELRQFKEETRMAIAQLKEai 1162
Cdd:pfam13851   48 LMSEIQQENKRLTEPLQKAQEEVEELRKQLENYEKDKQSLKNL--------KARLKVLEKELKDLKWEHEVLEQRFEK-- 117

                           90
                   ....*....|....*...
gi 9625567    1163 IVQEEDTIEERCAMILEE 1180
Cdd:pfam13851  118 VERERDELYDKFEAAIQD 135
HMMR_N pfam15905
Hyaluronan mediated motility receptor N-terminal; HMMR_N is the N-terminal region of ...
 1095-1194 6.90e-04

Hyaluronan mediated motility receptor N-terminal; HMMR_N is the N-terminal region of eukaryotic hyaluronan-mediated motility receptor proteins. The protein is functionally associated with BRCA1 and thus predicted to be a common, low-penetrance breast cancer candidate.


Pssm-ID: 464932 [Multi-domain]  Cd Length: 329  Bit Score: 44.03  E-value: 6.90e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1095 QKQVERLQEELMKLHREKdealkhsEKASRVFSTIQESDEAELNLIKEELRQFKEEtrmaIAQLKEAIIVQEEDTIEERC 1174
Cdd:pfam15905  151 QKKMSSLSMELMKLRNKL-------EAKMKEVMAKQEGMEGKLQVTQKNLEHSKGK----VAQLEEKLVSTEKEKIEEKS 219

                           90       100
                   ....*....|....*....|
gi 9625567    1175 AMILEEKHTENIYSATAKAE 1194
Cdd:pfam15905  220 ETEKLLEYITELSCVSEQVE 239
Peptidase_A3 pfam02160
Cauliflower mosaic virus peptidase (A3);
1201-1338 7.42e-04

Cauliflower mosaic virus peptidase (A3);


Pssm-ID: 280345  Cd Length: 208  Bit Score: 42.78  E-value: 7.42e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567    1201 VKVGIKPDNMEPYYINAIVDTGATACLIQISAIPENYYEDAKVTVNFRSVLGIG-TSTQMIKAGRILIGEQYFRMPVTYV 1279
Cdd:pfam02160    7 IKGRIGFKGFKAIELHCFIDTGASLCFAKKFIIPEEHWEIAEQPIEIIIADGSKhTIREACKDIDLIIAGEEFLIPIIYL 86

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9625567    1280 MNmglsPGIQMIIGCSFIRSLEGGL-RIEKDIITFYKLVTSIETSR-TTQVANSIEELELS 1338
Cdd:pfam02160   87 HD----SGIDFIIGNNFCKLYEPFIqFLDRIEFRKKKLNNPKEIAKiSRAILTGNEGFKES 143
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
1084-1180 1.24e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 43.35  E-value: 1.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1084 ISQLQQENQRLQKQVERLQEELMKLHREKDEAlkhSEKASRVFSTIQESdEAELNLIKEELRQFKEEtrmaIAQLKEAII 1163
Cdd:COG4372  103 LESLQEEAEELQEELEELQKERQDLEQQRKQL---EAQIAELQSEIAER-EEELKELEEQLESLQEE----LAALEQELQ 174

                         90
                 ....*....|....*..
gi 9625567  1164 VQEEDTIEERCAMILEE 1180
Cdd:COG4372  175 ALSEAEAEQALDELLKE 191
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 1084-1173 1.73e-03

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 43.39  E-value: 1.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1084 ISQLQQENQRLQKQVERLQEELMKLHREKDEALKHSEKASRVFSTIQE---SDEAELNLIKEELRQFKEETRMAIAQLKE 1160
Cdd:COG1196  297 LARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEeleEAEEELEEAEAELAEAEEALLEAEAELAE 376

                         90
                 ....*....|...
gi 9625567  1161 AIIVQEEDTIEER 1173
Cdd:COG1196  377 AEEELEELAEELL 389
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 863-904 3.19e-03

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 40.60  E-value: 3.19e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 9625567   863 AHDNH--IRVTKAKyqrkcKCYICGQEGHYANQCrNKHKDQQRV 904
Cdd:COG5082   85 SWDGHrsNHCPKPK-----KCYNCGETGHLSRDC-NPSKDQQKS 122
Cep57_CLD_2 pfam14197
Centrosome localization domain of PPC89; The N-terminal region of the fission yeast spindle ...
 1083-1145 4.67e-03

Centrosome localization domain of PPC89; The N-terminal region of the fission yeast spindle pole body protein PPC89 has low similarity to the human Cep57 protein. The CLD or centrosome localization domain of Cep57 and PPC89 is found at the N-terminus. This region localizes to the centrosome internally to gamma-tubulin, suggesting that it is either on both centrioles or on a centromatrix component. This N-terminal region can also multimerize with the N-terminus of other Cep57 molecules. The C-terminal part, Family Cep57_MT_bd, pfam06657, is the microtubule-binding region of Cep57 and PPC89.


Pssm-ID: 372959 [Multi-domain]  Cd Length: 67  Bit Score: 37.26  E-value: 4.67e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 9625567    1083 LISQLQQENQRLQKQVERLQEELMKLHREKDEALKhseKASRVFSTIQESdEAELNLIKEELR 1145
Cdd:pfam14197    4 ENLTLQNRLDSLTRKVAVHEIELKRLRRERDSAVR---QLGVAYLEIQEL-KAENEALRKELK 62
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 1084-1168 4.84e-03

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


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 41.29  E-value: 4.84e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1084 ISQLQQENQRLQKQVERLQEELMKLHREKDEALK----HSEKASRVFSTIQESdEAELNLIKEELRQFKEEtrmaIAQLK 1159
Cdd:COG4942   22 AAEAEAELEQLQQEIAELEKELAALKKEEKALLKqlaaLERRIAALARRIRAL-EQELAALEAELAELEKE----IAELR 96


                 ....*....
gi 9625567  1160 EAIIVQEED 1168
Cdd:COG4942   97 AELEAQKEE 105
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 1757-1838 4.84e-03

Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many of which are uncharacterized. Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication.


Pssm-ID: 260014 [Multi-domain]  Cd Length: 153  Bit Score: 39.49  E-value: 4.84e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1757 AEIQAAIHGLDKFKIYYLDKKE----LIIRSDCEAIIK-----FYN-KTNENKPSRVR-------WLTFSDFLTGL---G 1816
Cdd:cd13934   49 AELRAAIAALRFRSWIIDPDGEglktVVIATDSEYVVKgatewIPKwKRNGWRTSKGKpvknrdlFELLLDEIEDLeegG 128

                         90       100
                 ....*....|....*....|..
gi 9625567  1817 ITVTFEHIDGKHNGLADALSRM 1838
Cdd:cd13934  129 VEVQFWHVPRELNKEADRLAKA 150
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
1084-1173 6.20e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 41.04  E-value: 6.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1084 ISQLQQENQRLQKQVERLQEELMKLHREKDEALKHSEKASRVFSTIQEsdeaELNLIKEELRQFKEETRMAIAQLKEAIi 1163
Cdd:COG4372   47 LEQLREELEQAREELEQLEEELEQARSELEQLEEELEELNEQLQAAQA----ELAQAQEELESLQEEAEELQEELEELQ- 121

                         90
                 ....*....|
gi 9625567  1164 vQEEDTIEER 1173
Cdd:COG4372  122 -KERQDLEQQ 130
ADIP pfam11559
Afadin- and alpha -actinin-Binding; This family is found in mammals where it is localized at ...
 1084-1159 8.16e-03

Afadin- and alpha -actinin-Binding; This family is found in mammals where it is localized at cell-cell adherens junctions, and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins localized at Cell-Cell Adherens Junctions.


Pssm-ID: 463295 [Multi-domain]  Cd Length: 151  Bit Score: 38.84  E-value: 8.16e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 9625567    1084 ISQLQQENQRLQKQVERLQEELMKLHREKD---EALKHSEKAsrvfstiQESDEAELNLIKEELRQfkeeTRMAIAQLK 1159
Cdd:pfam11559   61 IRTLEAEIERLQSKIERLKTQLEDLERELAllqAKERQLEKK-------LKTLEQKLKNEKEELQR----LKNALQQIK 128
COG2433 COG2433
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
1084-1160 8.21e-03

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 41.00  E-value: 8.21e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1084 ISQLQQENQRLQKQVERLQEELMKLH---REKDEALKHSE-KASRVFSTIQES--DEAELNLIKEELRQFK---EETRMA 1154
Cdd:COG2433  408 LTEEEEEIRRLEEQVERLEAEVEELEaelEEKDERIERLErELSEARSEERREirKDREISRLDREIERLErelEEERER 487


                 ....*.
gi 9625567  1155 IAQLKE 1160
Cdd:COG2433  488 IEELKR 493
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 1084-1181 9.31e-03

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 41.08  E-value: 9.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9625567  1084 ISQLQQENQRLQKQVERLQEELMKLHREKDEALKHSEKASRVFSTIQESDEAELNLIKEELRQFKEETRMAIAQLKEAI- 1162
Cdd:COG1196  318 LEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAe 397

                         90
                 ....*....|....*....
gi 9625567  1163 IVQEEDTIEERCAMILEEK 1181
Cdd:COG1196  398 LAAQLEELEEAEEALLERL 416
 
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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