NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|505266715|ref|WP_015453817|]
View 

hypothetical protein [Helicobacter cinaedi]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Cas10 super family cl34236
CRISPR/Cas system-associated protein Cas10, large subunit of type III CRISPR-Cas systems, ...
 53-224 4.38e-21

CRISPR/Cas system-associated protein Cas10, large subunit of type III CRISPR-Cas systems, contains HD superfamily nuclease domain [Defense mechanisms]; CRISPR/Cas system-associated protein Cas10, large subunit of type III CRISPR-Cas systems, contains HD superfamily nuclease domain is part of the Pathway/BioSystem: CRISPR-Cas system


The actual alignment was detected with superfamily member COG1353:

Pssm-ID: 440964 [Multi-domain]  Cd Length: 477  Bit Score: 94.05  E-value: 4.38e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505266715  53 KEMFDTSVNQKLQAFNEAVNKNKALAQDINAI----KNKKNKIAVIHIDGNGLGGIVRGLEKD---EMKTFSQKLDSATK 125
Cdd:COG1353  209 YLLNDGELLEERLLANYVPKKKLEEPKTLEELaeksGEGIPYLAVLKADGDNMGKIFSGEKEAtpsRHATLSRALSLFFK 288

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505266715 126 EAYKQTLEsiidsnpTYQNALRDIILGGDDVTLICNANIALDLSEKFLENFESNTQNIHkqSSLTACAGIAYCNEKFPFF 205
Cdd:COG1353  289 KAVNEIVE-------ELRHNGYVIYAGGDDVLAIGPWDEALEFARELREAFEEYTGNLN--PEITLSAGIVIAHPKYPLY 359

                        170
                 ....*....|....*....
gi 505266715 206 YAVKLAEDLCAYAKKDAKE 224
Cdd:COG1353  360 RALELAEELLKKAKKVSEK 378
 
Name Accession Description Interval E-value
Cas10 COG1353
CRISPR/Cas system-associated protein Cas10, large subunit of type III CRISPR-Cas systems, ...
 53-224 4.38e-21

CRISPR/Cas system-associated protein Cas10, large subunit of type III CRISPR-Cas systems, contains HD superfamily nuclease domain [Defense mechanisms]; CRISPR/Cas system-associated protein Cas10, large subunit of type III CRISPR-Cas systems, contains HD superfamily nuclease domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 440964 [Multi-domain]  Cd Length: 477  Bit Score: 94.05  E-value: 4.38e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505266715  53 KEMFDTSVNQKLQAFNEAVNKNKALAQDINAI----KNKKNKIAVIHIDGNGLGGIVRGLEKD---EMKTFSQKLDSATK 125
Cdd:COG1353  209 YLLNDGELLEERLLANYVPKKKLEEPKTLEELaeksGEGIPYLAVLKADGDNMGKIFSGEKEAtpsRHATLSRALSLFFK 288

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505266715 126 EAYKQTLEsiidsnpTYQNALRDIILGGDDVTLICNANIALDLSEKFLENFESNTQNIHkqSSLTACAGIAYCNEKFPFF 205
Cdd:COG1353  289 KAVNEIVE-------ELRHNGYVIYAGGDDVLAIGPWDEALEFARELREAFEEYTGNLN--PEITLSAGIVIAHPKYPLY 359

                        170
                 ....*....|....*....
gi 505266715 206 YAVKLAEDLCAYAKKDAKE 224
Cdd:COG1353  360 RALELAEELLKKAKKVSEK 378
cas_TM1794_Cmr2 TIGR02577
CRISPR-associated protein Cas10/Cmr2, subtype III-B; This model represent a Crm2 family of the ...
 81-220 4.56e-09

CRISPR-associated protein Cas10/Cmr2, subtype III-B; This model represent a Crm2 family of the CRISPR-associated RAMP module, a set of six genes recurring found together in prokaryotic genomes. This gene cluster is found only in species with CRISPR repeats, usually near the repeats themselves. Because most of the six (but not this family) contain RAMP domains, and because its appearance in a genome appears to depend on other CRISPR-associated Cas genes, the set is designated the CRISPR RAMP module. This protein, typified by TM1794 from Thermotoga maritima, is designated Crm2, for CRISPR RAMP Module protein 2.


Pssm-ID: 274208 [Multi-domain]  Cd Length: 483  Bit Score: 57.84  E-value: 4.56e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505266715   81 INAIKNKKNK-IAVIHIDGNGLGGIVRGLEKDEMKT--FSQKLDSATKEAYKQTLESIIdsNPTYQNALRDII------- 150
Cdd:TIGR02577 333 RKKERKNPRPyYAILKADGDRMGKLLRGEIRPEEKEriHPKKVKNLTTPAAHVAFSRAL--AEFSLKAVKIVVnehygel 410

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 505266715  151 --LGGDDVTLICNANIALDLSEKFLENF-ESNTQNIHKQSSLTACAGIAYCNEKFPFFYAVKLAEDLCAYAKK 220
Cdd:TIGR02577 411 vyAGGDDVLALLPVDTALDVAKELRKEFrESLEKSLGGERGPTMSAGLLIVHHKEPLYDALELARRLLKRAKE 483
Cas10_III cd09679
CRISPR/Cas system-associated protein Cas10; CRISPR (Clustered Regularly Interspaced Short ...
 73-224 4.28e-08

CRISPR/Cas system-associated protein Cas10; 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; Multidomain protein with permuted HD nuclease domain, palm domain and Zn-ribbon; MTH326-like has inactivated polymerase catalytic domain; alr1562 and slr7011 - predicted only on the basis of size, presence of HD domain, and location with RAMPs in one operon; signature gene for type III; also known as Crm2 family


Pssm-ID: 187810 [Multi-domain]  Cd Length: 475  Bit Score: 54.76  E-value: 4.28e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505266715  73 KNKALAQDINAIKNKKNK---IAVIHIDGNGLGGIVRGLEKDEM--------KTFSQKLDSATKEAYKQTLEsiidsnpt 141
Cdd:cd09679  306 LEKEPEIVYLFIKAKKNPgpyYALLMADGDNMGKWLSGEKLPEKrlitpeyhRAISRALSNFALKAVKIVVE-------- 377

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505266715 142 yQNALRDIILGGDDVTLICNANIALD----LSEKFLENFESNtQNIHKQSSLTACAGIAYCNEKFPFFYAVKLAEDLCAY 217
Cdd:cd09679  378 -EHRGKLVYAGGDDVLALLPVDKALDcakkLRKAFSGILNKE-IGEDMGEGPTMSAGIVIAHHKEPLQDALELARRAEKR 455


                 ....*..
gi 505266715 218 AKKDAKE 224
Cdd:cd09679  456 AKKEGRN 462
 
Name Accession Description Interval E-value
Cas10 COG1353
CRISPR/Cas system-associated protein Cas10, large subunit of type III CRISPR-Cas systems, ...
 53-224 4.38e-21

CRISPR/Cas system-associated protein Cas10, large subunit of type III CRISPR-Cas systems, contains HD superfamily nuclease domain [Defense mechanisms]; CRISPR/Cas system-associated protein Cas10, large subunit of type III CRISPR-Cas systems, contains HD superfamily nuclease domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 440964 [Multi-domain]  Cd Length: 477  Bit Score: 94.05  E-value: 4.38e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505266715  53 KEMFDTSVNQKLQAFNEAVNKNKALAQDINAI----KNKKNKIAVIHIDGNGLGGIVRGLEKD---EMKTFSQKLDSATK 125
Cdd:COG1353  209 YLLNDGELLEERLLANYVPKKKLEEPKTLEELaeksGEGIPYLAVLKADGDNMGKIFSGEKEAtpsRHATLSRALSLFFK 288

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505266715 126 EAYKQTLEsiidsnpTYQNALRDIILGGDDVTLICNANIALDLSEKFLENFESNTQNIHkqSSLTACAGIAYCNEKFPFF 205
Cdd:COG1353  289 KAVNEIVE-------ELRHNGYVIYAGGDDVLAIGPWDEALEFARELREAFEEYTGNLN--PEITLSAGIVIAHPKYPLY 359

                        170
                 ....*....|....*....
gi 505266715 206 YAVKLAEDLCAYAKKDAKE 224
Cdd:COG1353  360 RALELAEELLKKAKKVSEK 378
cas_TM1794_Cmr2 TIGR02577
CRISPR-associated protein Cas10/Cmr2, subtype III-B; This model represent a Crm2 family of the ...
 81-220 4.56e-09

CRISPR-associated protein Cas10/Cmr2, subtype III-B; This model represent a Crm2 family of the CRISPR-associated RAMP module, a set of six genes recurring found together in prokaryotic genomes. This gene cluster is found only in species with CRISPR repeats, usually near the repeats themselves. Because most of the six (but not this family) contain RAMP domains, and because its appearance in a genome appears to depend on other CRISPR-associated Cas genes, the set is designated the CRISPR RAMP module. This protein, typified by TM1794 from Thermotoga maritima, is designated Crm2, for CRISPR RAMP Module protein 2.


Pssm-ID: 274208 [Multi-domain]  Cd Length: 483  Bit Score: 57.84  E-value: 4.56e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505266715   81 INAIKNKKNK-IAVIHIDGNGLGGIVRGLEKDEMKT--FSQKLDSATKEAYKQTLESIIdsNPTYQNALRDII------- 150
Cdd:TIGR02577 333 RKKERKNPRPyYAILKADGDRMGKLLRGEIRPEEKEriHPKKVKNLTTPAAHVAFSRAL--AEFSLKAVKIVVnehygel 410

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 505266715  151 --LGGDDVTLICNANIALDLSEKFLENF-ESNTQNIHKQSSLTACAGIAYCNEKFPFFYAVKLAEDLCAYAKK 220
Cdd:TIGR02577 411 vyAGGDDVLALLPVDTALDVAKELRKEFrESLEKSLGGERGPTMSAGLLIVHHKEPLYDALELARRLLKRAKE 483
Cas10_III cd09679
CRISPR/Cas system-associated protein Cas10; CRISPR (Clustered Regularly Interspaced Short ...
 73-224 4.28e-08

CRISPR/Cas system-associated protein Cas10; 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; Multidomain protein with permuted HD nuclease domain, palm domain and Zn-ribbon; MTH326-like has inactivated polymerase catalytic domain; alr1562 and slr7011 - predicted only on the basis of size, presence of HD domain, and location with RAMPs in one operon; signature gene for type III; also known as Crm2 family


Pssm-ID: 187810 [Multi-domain]  Cd Length: 475  Bit Score: 54.76  E-value: 4.28e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505266715  73 KNKALAQDINAIKNKKNK---IAVIHIDGNGLGGIVRGLEKDEM--------KTFSQKLDSATKEAYKQTLEsiidsnpt 141
Cdd:cd09679  306 LEKEPEIVYLFIKAKKNPgpyYALLMADGDNMGKWLSGEKLPEKrlitpeyhRAISRALSNFALKAVKIVVE-------- 377

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505266715 142 yQNALRDIILGGDDVTLICNANIALD----LSEKFLENFESNtQNIHKQSSLTACAGIAYCNEKFPFFYAVKLAEDLCAY 217
Cdd:cd09679  378 -EHRGKLVYAGGDDVLALLPVDKALDcakkLRKAFSGILNKE-IGEDMGEGPTMSAGIVIAHHKEPLQDALELARRAEKR 455


                 ....*..
gi 505266715 218 AKKDAKE 224
Cdd:cd09679  456 AKKEGRN 462
Cas10_III cd09680
CRISPR/Cas system-associated protein Cas10; CRISPR (Clustered Regularly Interspaced Short ...
 88-220 9.73e-05

CRISPR/Cas system-associated protein Cas10; 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; Multidomain protein with permuted HD nuclease domain, palm domain and Zn-ribbon; signature gene for type III; also known as Csm1 family


Pssm-ID: 187811 [Multi-domain]  Cd Length: 650  Bit Score: 44.24  E-value: 9.73e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505266715  88 KNKIAVIHIDGNGLGGI-VRGLEKDE-----MKTFSQKLDSAtkeaYKQTLESIIDSNPTY--QNALRDIIL---GGDDV 156
Cdd:cd09680  516 IKRLGVLKADVDNLGEIfASGFKEEKrtlsrLATLSRQLSLF----FKGYVNYLAKNGEAGlkPERKRNIYIvysGGDDL 591

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 505266715 157 TLICNANIALDLSEKFLENFESNTQNihkqsSLTACAGIAYCNEKFPFFYAVKLAEDLCAYAKK 220
Cdd:cd09680  592 FIVGAWDDIIELALDIREAFARFTGG-----KLTLSAGIGLFPPKYPISRMARIAEELEEAAKE 650
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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