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Conserved domains on  [gi|1079632716|emb|SCW28755|]
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N-terminal 7TM region of histidine kinase [Ruminococcaceae bacterium YRB3002]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HDGYP COG2206
HD-GYP domain, c-di-GMP phosphodiesterase class II (or its inactivated variant) [Signal ...
 336-563 5.09e-59

HD-GYP domain, c-di-GMP phosphodiesterase class II (or its inactivated variant) [Signal transduction mechanisms];


:

Pssm-ID: 441808 [Multi-domain]  Cd Length: 316  Bit Score: 199.43  E-value: 5.09e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 336 EIVDETEQVNYINELNFAGVRLKKEADRQTRRAENLQGSIILGMAAMIESRDNSTGGHINRTSACIQMFVDKIKNSGEFp 415
Cdd:COG2206    90 LLLLAALESLLAELFEELRLGLLEELKKLVEELDELLPDALLALLAALDAKDPYTYGHSVRVAVLALALARELGLSEEE- 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 416 MADIYWtnvinAAPLHDLGKIAVDDRILRKRDKLEPYEYEEMKKHAAVGAEIVQQVladvddkEFVRVASNVAHYHHEKY 495
Cdd:COG2206   169 LEDLGL-----AALLHDIGKIGIPDEILNKPGKLTDEEFEIIKKHPEYGYEILKKL-------PGLSEVAEIVLQHHERL 236

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1079632716 496 NGTGYPEGLKGDRIPLEARIMALADVFDALISRRYYKSRMSYDDAFNIIRRDMGSHFDPRLGRIFISM 563
Cdd:COG2206   237 DGSGYPRGLKGEEIPLLARILAVADVYDALTSDRPYRKALSPEEALEELRKGAGTQFDPELVEAFIKV 304
HisKA_7TM super family cl24076
N-terminal 7TM region of histidine kinase; HisKA_7TM is an N-terminal region consisting of ...
 9-223 5.43e-10

N-terminal 7TM region of histidine kinase; HisKA_7TM is an N-terminal region consisting of seven transmembrane domains found in Archaea and some bacteria. It is always found associated with histidine kinase.


The actual alignment was detected with superfamily member pfam16927:

Pssm-ID: 465318 [Multi-domain]  Cd Length: 221  Bit Score: 59.61  E-value: 5.43e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716   9 LASATLCALCTSYLIFNASKSIDPLYVLASFIITVSNVGYFLMSDCSSYDSLIIANGISYIGGVFLPFILMIMLAQFSGT 88
Cdd:pfam16927   1 LISALLSLLLAIYAWRRRSRPGARAFLLLMLAAAIWSLGYALELAATTLEAKLFWSKLEYLGIVFIPVLWLLFALEYTGR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716  89 --HLPNWFQITLTAVNIGIYTLVLLSYRFNIYYAGSYMDPQNVMKLVNTPGYGYYIRLVVLIVEVALSIFFTILALMGRK 166
Cdd:pfam16927  81 erWLTRRRLALLFIIPVLTLILVLTNPLHHLFYTSVSLVPGGFPVLVFTHGPLYWVHLAYSYLLLLAGVVLLIRALIRSS 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1079632716 167 KA-SWKTMWTFLAFMIATIV--VYALTSVL-HISHTIISFLFLAcdFALVFTTSRFQLYDI 223
Cdd:pfam16927 161 GLyRKQALLLLLGALIPWVAnlLYLLGLPPpGIDLTPISFALTG--LLFAWAIFRYRLFDI 219
 
Name Accession Description Interval E-value
HDGYP COG2206
HD-GYP domain, c-di-GMP phosphodiesterase class II (or its inactivated variant) [Signal ...
 336-563 5.09e-59

HD-GYP domain, c-di-GMP phosphodiesterase class II (or its inactivated variant) [Signal transduction mechanisms];


Pssm-ID: 441808 [Multi-domain]  Cd Length: 316  Bit Score: 199.43  E-value: 5.09e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 336 EIVDETEQVNYINELNFAGVRLKKEADRQTRRAENLQGSIILGMAAMIESRDNSTGGHINRTSACIQMFVDKIKNSGEFp 415
Cdd:COG2206    90 LLLLAALESLLAELFEELRLGLLEELKKLVEELDELLPDALLALLAALDAKDPYTYGHSVRVAVLALALARELGLSEEE- 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 416 MADIYWtnvinAAPLHDLGKIAVDDRILRKRDKLEPYEYEEMKKHAAVGAEIVQQVladvddkEFVRVASNVAHYHHEKY 495
Cdd:COG2206   169 LEDLGL-----AALLHDIGKIGIPDEILNKPGKLTDEEFEIIKKHPEYGYEILKKL-------PGLSEVAEIVLQHHERL 236

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1079632716 496 NGTGYPEGLKGDRIPLEARIMALADVFDALISRRYYKSRMSYDDAFNIIRRDMGSHFDPRLGRIFISM 563
Cdd:COG2206   237 DGSGYPRGLKGEEIPLLARILAVADVYDALTSDRPYRKALSPEEALEELRKGAGTQFDPELVEAFIKV 304
HDc cd00077
Metal dependent phosphohydrolases with conserved 'HD' motif
 389-534 3.08e-22

Metal dependent phosphohydrolases with conserved 'HD' motif


Pssm-ID: 238032 [Multi-domain]  Cd Length: 145  Bit Score: 93.17  E-value: 3.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 389 STGGHINRTSACIQMFVDKIKNSGEFPMAdiywtnVINAAPLHDLGKIAVDDRILRKrdklepyEYEEMKKHAAVGAEIV 468
Cdd:cd00077     2 HRFEHSLRVAQLARRLAEELGLSEEDIEL------LRLAALLHDIGKPGTPDAITEE-------ESELEKDHAIVGAEIL 68

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1079632716 469 QQVLADVDDKEFVRVASNVAHYHHEKYNGTGYPEGLKGDRIPLEARIMALADVFDALISRRYYKSR 534
Cdd:cd00077    69 RELLLEEVIKLIDELILAVDASHHERLDGLGYPDGLKGEEITLEARIVKLADRLDALRRDSREKRR 134
HD_5 pfam13487
HD domain; HD domains are metal dependent phosphohydrolases.
 447-516 5.24e-15

HD domain; HD domains are metal dependent phosphohydrolases.


Pssm-ID: 433249 [Multi-domain]  Cd Length: 64  Bit Score: 69.55  E-value: 5.24e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 447 DKLEPYEYEEMKKHAAVGAEIVQQVladvddKEFVRVASNVAHYHHEKYNGTGYPEGLKGDRIPLEARIM 516
Cdd:pfam13487   1 GTLTPEEREIINRHPEHTARLLSTL------PRLPKEVAEIIAQHHERLDGSGYPRGLKGEEIPLGARIL 64
HDc smart00471
Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic ...
 427-532 1.16e-13

Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic nucleotide phosphodiesterases (PDEc). This profile/HMM does not detect HD homologues in bacterial glycine aminoacyl-tRNA synthetases (beta subunit).


Pssm-ID: 214679 [Multi-domain]  Cd Length: 124  Bit Score: 67.71  E-value: 1.16e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716  427 AAPLHDLGKIAVDDRILRKrdklepyeYEEMKKHAAVGAEIVQQVLADVDDKEFVRVAsnvAHYHHEKYNGtgypegLKG 506
Cdd:smart00471  34 AALLHDIGKPGTPDSFLVK--------TSVLEDHHFIGAEILLEEEEPRILEEILRTA---ILSHHERPDG------LRG 96

                           90       100
                   ....*....|....*....|....*.
gi 1079632716  507 DRIPLEARIMALADVFDALISRRYYK 532
Cdd:smart00471  97 EPITLEARIVKVADRLDALRADRRYR 122
HisKA_7TM pfam16927
N-terminal 7TM region of histidine kinase; HisKA_7TM is an N-terminal region consisting of ...
 9-223 5.43e-10

N-terminal 7TM region of histidine kinase; HisKA_7TM is an N-terminal region consisting of seven transmembrane domains found in Archaea and some bacteria. It is always found associated with histidine kinase.


Pssm-ID: 465318 [Multi-domain]  Cd Length: 221  Bit Score: 59.61  E-value: 5.43e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716   9 LASATLCALCTSYLIFNASKSIDPLYVLASFIITVSNVGYFLMSDCSSYDSLIIANGISYIGGVFLPFILMIMLAQFSGT 88
Cdd:pfam16927   1 LISALLSLLLAIYAWRRRSRPGARAFLLLMLAAAIWSLGYALELAATTLEAKLFWSKLEYLGIVFIPVLWLLFALEYTGR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716  89 --HLPNWFQITLTAVNIGIYTLVLLSYRFNIYYAGSYMDPQNVMKLVNTPGYGYYIRLVVLIVEVALSIFFTILALMGRK 166
Cdd:pfam16927  81 erWLTRRRLALLFIIPVLTLILVLTNPLHHLFYTSVSLVPGGFPVLVFTHGPLYWVHLAYSYLLLLAGVVLLIRALIRSS 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1079632716 167 KA-SWKTMWTFLAFMIATIV--VYALTSVL-HISHTIISFLFLAcdFALVFTTSRFQLYDI 223
Cdd:pfam16927 161 GLyRKQALLLLLGALIPWVAnlLYLLGLPPpGIDLTPISFALTG--LLFAWAIFRYRLFDI 219
cas3_HD TIGR01596
CRISPR-associated endonuclease Cas3-HD; CRISPR/Cas systems are widespread, mobile systems for ...
 430-529 2.82e-03

CRISPR-associated endonuclease Cas3-HD; CRISPR/Cas systems are widespread, mobile systems for host defense against invasive elements such as phage. In these systems, Cas3 designates one of the core proteins shared widely by multiple types of CRISPR/Cas system. This model represents an HD-like endonuclease that occurs either separately or as the N-terminal region of Cas3, the helicase-containing CRISPR-associated protein.


Pssm-ID: 273711 [Multi-domain]  Cd Length: 176  Bit Score: 39.11  E-value: 2.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 430 LHDLGKIAVD--DRILRKRDKLEPYEYEemkkHAAVGAEIVQQVLAD-VDDKEFVRVASNVAHYHHEKYNGTGYPEGLKG 506
Cdd:TIGR01596  40 LHDLGKASPAfqKKLRKAEERGDRGEVR----HSTLSAALLYDLLEElGLEEELALLLALAIAGHHGGLIDDDDLEELLE 115

                          90       100
                  ....*....|....*....|....
gi 1079632716 507 DRIPLEARI-MALADVFDALISRR 529
Cdd:TIGR01596 116 LLERELEEAlGELLEELEELLDEV 139
 
Name Accession Description Interval E-value
HDGYP COG2206
HD-GYP domain, c-di-GMP phosphodiesterase class II (or its inactivated variant) [Signal ...
 336-563 5.09e-59

HD-GYP domain, c-di-GMP phosphodiesterase class II (or its inactivated variant) [Signal transduction mechanisms];


Pssm-ID: 441808 [Multi-domain]  Cd Length: 316  Bit Score: 199.43  E-value: 5.09e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 336 EIVDETEQVNYINELNFAGVRLKKEADRQTRRAENLQGSIILGMAAMIESRDNSTGGHINRTSACIQMFVDKIKNSGEFp 415
Cdd:COG2206    90 LLLLAALESLLAELFEELRLGLLEELKKLVEELDELLPDALLALLAALDAKDPYTYGHSVRVAVLALALARELGLSEEE- 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 416 MADIYWtnvinAAPLHDLGKIAVDDRILRKRDKLEPYEYEEMKKHAAVGAEIVQQVladvddkEFVRVASNVAHYHHEKY 495
Cdd:COG2206   169 LEDLGL-----AALLHDIGKIGIPDEILNKPGKLTDEEFEIIKKHPEYGYEILKKL-------PGLSEVAEIVLQHHERL 236

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1079632716 496 NGTGYPEGLKGDRIPLEARIMALADVFDALISRRYYKSRMSYDDAFNIIRRDMGSHFDPRLGRIFISM 563
Cdd:COG2206   237 DGSGYPRGLKGEEIPLLARILAVADVYDALTSDRPYRKALSPEEALEELRKGAGTQFDPELVEAFIKV 304
HDc cd00077
Metal dependent phosphohydrolases with conserved 'HD' motif
 389-534 3.08e-22

Metal dependent phosphohydrolases with conserved 'HD' motif


Pssm-ID: 238032 [Multi-domain]  Cd Length: 145  Bit Score: 93.17  E-value: 3.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 389 STGGHINRTSACIQMFVDKIKNSGEFPMAdiywtnVINAAPLHDLGKIAVDDRILRKrdklepyEYEEMKKHAAVGAEIV 468
Cdd:cd00077     2 HRFEHSLRVAQLARRLAEELGLSEEDIEL------LRLAALLHDIGKPGTPDAITEE-------ESELEKDHAIVGAEIL 68

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1079632716 469 QQVLADVDDKEFVRVASNVAHYHHEKYNGTGYPEGLKGDRIPLEARIMALADVFDALISRRYYKSR 534
Cdd:cd00077    69 RELLLEEVIKLIDELILAVDASHHERLDGLGYPDGLKGEEITLEARIVKLADRLDALRRDSREKRR 134
HD_5 pfam13487
HD domain; HD domains are metal dependent phosphohydrolases.
 447-516 5.24e-15

HD domain; HD domains are metal dependent phosphohydrolases.


Pssm-ID: 433249 [Multi-domain]  Cd Length: 64  Bit Score: 69.55  E-value: 5.24e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 447 DKLEPYEYEEMKKHAAVGAEIVQQVladvddKEFVRVASNVAHYHHEKYNGTGYPEGLKGDRIPLEARIM 516
Cdd:pfam13487   1 GTLTPEEREIINRHPEHTARLLSTL------PRLPKEVAEIIAQHHERLDGSGYPRGLKGEEIPLGARIL 64
HDc smart00471
Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic ...
 427-532 1.16e-13

Metal dependent phosphohydrolases with conserved 'HD' motif; Includes eukaryotic cyclic nucleotide phosphodiesterases (PDEc). This profile/HMM does not detect HD homologues in bacterial glycine aminoacyl-tRNA synthetases (beta subunit).


Pssm-ID: 214679 [Multi-domain]  Cd Length: 124  Bit Score: 67.71  E-value: 1.16e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716  427 AAPLHDLGKIAVDDRILRKrdklepyeYEEMKKHAAVGAEIVQQVLADVDDKEFVRVAsnvAHYHHEKYNGtgypegLKG 506
Cdd:smart00471  34 AALLHDIGKPGTPDSFLVK--------TSVLEDHHFIGAEILLEEEEPRILEEILRTA---ILSHHERPDG------LRG 96

                           90       100
                   ....*....|....*....|....*.
gi 1079632716  507 DRIPLEARIMALADVFDALISRRYYK 532
Cdd:smart00471  97 EPITLEARIVKVADRLDALRADRRYR 122
HD pfam01966
HD domain; HD domains are metal dependent phosphohydrolases.
 427-525 1.61e-13

HD domain; HD domains are metal dependent phosphohydrolases.


Pssm-ID: 460398 [Multi-domain]  Cd Length: 110  Bit Score: 66.88  E-value: 1.61e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 427 AAPLHDLGKIAVDDRILrkrdklepyEYEEMKKHAAVGAEIVQQVLADvddkEFVRVASNVAHYHHEKYNGTGYPEglkg 506
Cdd:pfam01966  30 AALLHDIGKGPFGDEKP---------EFEIFLGHAVVGAEILRELEKR----LGLEDVLKLILEHHESWEGAGYPE---- 92

                          90
                  ....*....|....*....
gi 1079632716 507 dRIPLEARIMALADVFDAL 525
Cdd:pfam01966  93 -EISLEARIVKLADRLDAL 110
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 426-545 2.51e-13

Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains [Signal transduction mechanisms];


Pssm-ID: 442663 [Multi-domain]  Cd Length: 224  Bit Score: 69.42  E-value: 2.51e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 426 NAAPLHDLGKIAVDDRILRKRDKLEPYEYEEMKKHAAVGAEIVQqvladvdDKEFVRVASNVahyhHEKYNGTGypeglk 505
Cdd:COG3437   142 LAAPLHDIGKIGIPDAILLKPGKLTPEEWEITHAHIGAEILSGS-------LLPLLQLAAEI----HERWDGSG------ 204

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1079632716 506 gdripLEARimaladvfDALISRRyyksrmsYDDAFNIIR 545
Cdd:COG3437   205 -----LSAR--------DALTSKK-------LEEALEEIR 224
HisKA_7TM pfam16927
N-terminal 7TM region of histidine kinase; HisKA_7TM is an N-terminal region consisting of ...
 9-223 5.43e-10

N-terminal 7TM region of histidine kinase; HisKA_7TM is an N-terminal region consisting of seven transmembrane domains found in Archaea and some bacteria. It is always found associated with histidine kinase.


Pssm-ID: 465318 [Multi-domain]  Cd Length: 221  Bit Score: 59.61  E-value: 5.43e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716   9 LASATLCALCTSYLIFNASKSIDPLYVLASFIITVSNVGYFLMSDCSSYDSLIIANGISYIGGVFLPFILMIMLAQFSGT 88
Cdd:pfam16927   1 LISALLSLLLAIYAWRRRSRPGARAFLLLMLAAAIWSLGYALELAATTLEAKLFWSKLEYLGIVFIPVLWLLFALEYTGR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716  89 --HLPNWFQITLTAVNIGIYTLVLLSYRFNIYYAGSYMDPQNVMKLVNTPGYGYYIRLVVLIVEVALSIFFTILALMGRK 166
Cdd:pfam16927  81 erWLTRRRLALLFIIPVLTLILVLTNPLHHLFYTSVSLVPGGFPVLVFTHGPLYWVHLAYSYLLLLAGVVLLIRALIRSS 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1079632716 167 KA-SWKTMWTFLAFMIATIV--VYALTSVL-HISHTIISFLFLAcdFALVFTTSRFQLYDI 223
Cdd:pfam16927 161 GLyRKQALLLLLGALIPWVAnlLYLLGLPPpGIDLTPISFALTG--LLFAWAIFRYRLFDI 219
PalH pfam08733
PalH/RIM21; PalH (also known as RIM21) is a transmembrane protein required for proteolytic ...
 60-213 5.07e-04

PalH/RIM21; PalH (also known as RIM21) is a transmembrane protein required for proteolytic cleavage of Rim101/PacC transcription factors which are activated by C terminal proteolytic processing. Rim101/PacC family proteins play a key role in pH-dependent responses and PalH has been implicated as a pH sensor.


Pssm-ID: 400879  Cd Length: 335  Bit Score: 42.58  E-value: 5.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716  60 LIIANGISYIGGVFLPFILMIMLAQFsgtHLPNWFQIT--LTAVNIGIYTLVLLSYRFNIYYAGSYMDPQNVMKLVNTpg 137
Cdd:pfam08733  75 ILFSLSASCVITWMLTLLLFLLPSTK---GSPWLLKLAtlLAAISLTIFLARSTKEVAEQQYYGGYQDAIELLDLINN-- 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 138 yGYYIRLVVLIVEVALSI--FFTILALMGRKKASWKTMWTFLAFMIATIVVYALTSVLHISH-----TIISFLFLACDFA 210
Cdd:pfam08733 150 -SLAYRVLDLISVFLLQLaqVQIIIRLFPRQKEKRIIFWVGLILIILDTILWAINLFSYNTRpdsflDILPAFVYLFRLA 228


                  ...
gi 1079632716 211 LVF 213
Cdd:pfam08733 229 LST 231
cas3_HD TIGR01596
CRISPR-associated endonuclease Cas3-HD; CRISPR/Cas systems are widespread, mobile systems for ...
 430-529 2.82e-03

CRISPR-associated endonuclease Cas3-HD; CRISPR/Cas systems are widespread, mobile systems for host defense against invasive elements such as phage. In these systems, Cas3 designates one of the core proteins shared widely by multiple types of CRISPR/Cas system. This model represents an HD-like endonuclease that occurs either separately or as the N-terminal region of Cas3, the helicase-containing CRISPR-associated protein.


Pssm-ID: 273711 [Multi-domain]  Cd Length: 176  Bit Score: 39.11  E-value: 2.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079632716 430 LHDLGKIAVD--DRILRKRDKLEPYEYEemkkHAAVGAEIVQQVLAD-VDDKEFVRVASNVAHYHHEKYNGTGYPEGLKG 506
Cdd:TIGR01596  40 LHDLGKASPAfqKKLRKAEERGDRGEVR----HSTLSAALLYDLLEElGLEEELALLLALAIAGHHGGLIDDDDLEELLE 115

                          90       100
                  ....*....|....*....|....
gi 1079632716 507 DRIPLEARI-MALADVFDALISRR 529
Cdd:TIGR01596 116 LLERELEEAlGELLEELEELLDEV 139
Cas3''_I cd09641
CRISPR/Cas system-associated protein Cas3''; CRISPR (Clustered Regularly Interspaced Short ...
 430-492 2.98e-03

CRISPR/Cas system-associated protein Cas3''; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; HD-like nuclease, specifically digesting double-stranded oligonucleotides and preferably cleaving at G:C pairs; signature gene for Type I


Pssm-ID: 193608 [Multi-domain]  Cd Length: 200  Bit Score: 39.18  E-value: 2.98e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1079632716 430 LHDLGKIAVD--DRILRKRDKLEPYEYEEmKKHAAVGAEIVQQVLADV-DDKEFVRVASNVAHYHH 492
Cdd:cd09641    48 LHDLGKATPAfqKYLRGGKEALREGKRKE-VRHSLLGALLLYELLKELgLDEELALLLAYAIAGHH 112
 
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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