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Conserved domains on  [gi|2292844947|ref|WP_258863277|]
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hypothetical protein [Streptococcus pyogenes]

Protein Classification

P-loop NTPase family protein( domain architecture ID 1562424)

P-loop NTPase (nucleoside triphosphate hydrolase) family protein contains two conserved sequence signatures, the Walker A motif (the P-loop proper) and Walker B motif which bind, respectively, the beta and gamma phosphate moieties of the bound nucleotide (typically ATP or GTP), and a Mg(2+) cation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 91-182 4.30e-05

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member PRK12377:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 248  Bit Score: 42.51  E-value: 4.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2292844947  91 SATLKNYKEHSAVDTQALNYAKRITRDYVKGMeGNSLLQGPPGVGKSHLSMSIAkniNEMFKsynQSKSVIFVSVPLLSA 170
Cdd:PRK12377   70 KCSFANYQVQNDGQRYALSQAKSIADELMTGC-TNFVFSGKPGTGKNHLAAAIG---NRLLA---KGRSVIVVTVPDVMS 142

                          90
                  ....*....|..
gi 2292844947 171 LVKDTfdYDDKK 182
Cdd:PRK12377  143 RLHES--YDNGQ 152
 
Name Accession Description Interval E-value
PRK12377 PRK12377
putative replication protein; Provisional
 91-182 4.30e-05

putative replication protein; Provisional


Pssm-ID: 183482 [Multi-domain]  Cd Length: 248  Bit Score: 42.51  E-value: 4.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2292844947  91 SATLKNYKEHSAVDTQALNYAKRITRDYVKGMeGNSLLQGPPGVGKSHLSMSIAkniNEMFKsynQSKSVIFVSVPLLSA 170
Cdd:PRK12377   70 KCSFANYQVQNDGQRYALSQAKSIADELMTGC-TNFVFSGKPGTGKNHLAAAIG---NRLLA---KGRSVIVVTVPDVMS 142

                          90
                  ....*....|..
gi 2292844947 171 LVKDTfdYDDKK 182
Cdd:PRK12377  143 RLHES--YDNGQ 152
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 111-168 8.51e-05

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 40.98  E-value: 8.51e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2292844947 111 AKRITRDYVKGMEGNS-LLQGPPGVGKSHLSMSIAKNINEMfksynqSKSVIFVSVPLL 168
Cdd:cd00009     6 AIEALREALELPPPKNlLLYGPPGTGKTTLARAIANELFRP------GAPFLYLNASDL 58
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
117-168 3.04e-04

DNA replication protein DnaC [Replication, recombination and repair];


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 40.15  E-value: 3.04e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2292844947 117 DYVKGMEgNSLLQGPPGVGKSHLSMSIAkniNEMFKsynQSKSVIFVSVPLL 168
Cdd:COG1484    94 DFIERGE-NLILLGPPGTGKTHLAIALG---HEACR---AGYRVRFTTAPDL 138
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 125-168 1.26e-03

IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was built to hit full-length AAA+ ATPases of IS21 family IS (insertion sequence) elements.


Pssm-ID: 439516  Cd Length: 232  Bit Score: 38.22  E-value: 1.26e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2292844947 125 NSLLQGPPGVGKSHLSMSIAKNINEmfksynQSKSVIFVSVPLL 168
Cdd:NF038214   92 NVLLLGPPGTGKTHLAIALGYAACR------QGYRVRFTTAADL 129
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 127-164 1.35e-03

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 37.35  E-value: 1.35e-03
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 2292844947  127 LLQGPPGVGKSHLSMSIAKNINEmfksynQSKSVIFVS 164
Cdd:smart00382   6 LIVGPPGSGKTTLARALARELGP------PGGGVIYID 37
 
Name Accession Description Interval E-value
PRK12377 PRK12377
putative replication protein; Provisional
 91-182 4.30e-05

putative replication protein; Provisional


Pssm-ID: 183482 [Multi-domain]  Cd Length: 248  Bit Score: 42.51  E-value: 4.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2292844947  91 SATLKNYKEHSAVDTQALNYAKRITRDYVKGMeGNSLLQGPPGVGKSHLSMSIAkniNEMFKsynQSKSVIFVSVPLLSA 170
Cdd:PRK12377   70 KCSFANYQVQNDGQRYALSQAKSIADELMTGC-TNFVFSGKPGTGKNHLAAAIG---NRLLA---KGRSVIVVTVPDVMS 142

                          90
                  ....*....|..
gi 2292844947 171 LVKDTfdYDDKK 182
Cdd:PRK12377  143 RLHES--YDNGQ 152
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 111-168 8.51e-05

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 40.98  E-value: 8.51e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2292844947 111 AKRITRDYVKGMEGNS-LLQGPPGVGKSHLSMSIAKNINEMfksynqSKSVIFVSVPLL 168
Cdd:cd00009     6 AIEALREALELPPPKNlLLYGPPGTGKTTLARAIANELFRP------GAPFLYLNASDL 58
PRK08116 PRK08116
hypothetical protein; Validated
 81-176 2.50e-04

hypothetical protein; Validated


Pssm-ID: 236153 [Multi-domain]  Cd Length: 268  Bit Score: 40.39  E-value: 2.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2292844947  81 KESVLSKEIASATLKNYKeHSAVDTQALNYAKRitrdYVKG---MEGNS---LLQGPPGVGKSHLSMSIAkniNEMFKsy 154
Cdd:PRK08116   71 SNSLLDEKFRNSTFENFL-FDKGSEKAYKIARK----YVKKfeeMKKENvglLLWGSVGTGKTYLAACIA---NELIE-- 140

                          90       100
                  ....*....|....*....|..
gi 2292844947 155 nQSKSVIFVSVPLLSALVKDTF 176
Cdd:PRK08116  141 -KGVPVIFVNFPQLLNRIKSTY 161
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
117-168 3.04e-04

DNA replication protein DnaC [Replication, recombination and repair];


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 40.15  E-value: 3.04e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2292844947 117 DYVKGMEgNSLLQGPPGVGKSHLSMSIAkniNEMFKsynQSKSVIFVSVPLL 168
Cdd:COG1484    94 DFIERGE-NLILLGPPGTGKTHLAIALG---HEACR---AGYRVRFTTAPDL 138
PRK07952 PRK07952
DNA replication protein DnaC; Validated
 96-176 4.08e-04

DNA replication protein DnaC; Validated


Pssm-ID: 181180 [Multi-domain]  Cd Length: 244  Bit Score: 39.75  E-value: 4.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2292844947  96 NYKEHSAVDTQALNYAKRitrdYVKGMEGNS---LLQGPPGVGKSHLSMSIAkniNEMFksyNQSKSVIFVSVPLLSALV 172
Cdd:PRK07952   73 NYRVECEGQMNALSKARQ----YVEEFDGNIasfIFSGKPGTGKNHLAAAIC---NELL---LRGKSVLIITVADIMSAM 142


                  ....
gi 2292844947 173 KDTF 176
Cdd:PRK07952  143 KDTF 146
McrB COG1401
5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB ...
 76-165 1.02e-03

5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB [Defense mechanisms];


Pssm-ID: 441011 [Multi-domain]  Cd Length: 477  Bit Score: 38.98  E-value: 1.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2292844947  76 YNVFYKESVLSKEIASATLKNYKEHSAVDTQALNYAKRITRDYVKGME--GNSLLQGPPGVGKSHLsmsiAKNINEMFKS 153
Cdd:COG1401   172 LSADALAAELSAAEELYSEDLESEDDYLKDLLREKFEETLEAFLAALKtkKNVILAGPPGTGKTYL----ARRLAEALGG 247

                          90
                  ....*....|..
gi 2292844947 154 YNQSKsVIFVSV 165
Cdd:COG1401   248 EDNGR-IEFVQF 258
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 125-168 1.26e-03

IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was built to hit full-length AAA+ ATPases of IS21 family IS (insertion sequence) elements.


Pssm-ID: 439516  Cd Length: 232  Bit Score: 38.22  E-value: 1.26e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2292844947 125 NSLLQGPPGVGKSHLSMSIAKNINEmfksynQSKSVIFVSVPLL 168
Cdd:NF038214   92 NVLLLGPPGTGKTHLAIALGYAACR------QGYRVRFTTAADL 129
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 127-164 1.35e-03

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 37.35  E-value: 1.35e-03
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 2292844947  127 LLQGPPGVGKSHLSMSIAKNINEmfksynQSKSVIFVS 164
Cdd:smart00382   6 LIVGPPGSGKTTLARALARELGP------PGGGVIYID 37
PRK06921 PRK06921
hypothetical protein; Provisional
 107-147 3.66e-03

hypothetical protein; Provisional


Pssm-ID: 180750 [Multi-domain]  Cd Length: 266  Bit Score: 37.07  E-value: 3.66e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2292844947 107 ALNYAKRITRdyVKGMEGNSL-LQGPPGVGKSHLSMSIAKNI 147
Cdd:PRK06921  102 AVEYVKDFEK--IQESRKNSIaLLGQPGSGKTHLLTAAANEL 141
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 126-149 9.41e-03

EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350694 [Multi-domain]  Cd Length: 178  Bit Score: 35.21  E-value: 9.41e-03
                          10        20
                  ....*....|....*....|....
gi 2292844947 126 SLLQGPPGVGKSHLSMSIAKNINE 149
Cdd:cd17936    19 ALIQGPPGTGKTFLGVKLVRALLQ 42
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 119-161 9.70e-03

DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438712 [Multi-domain]  Cd Length: 218  Bit Score: 35.65  E-value: 9.70e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2292844947 119 VKGMEGNSLLQGPPGVGKSHLSMSIAK-NINEMFKSYNQSKSVI 161
Cdd:cd18042    13 LQNSPGITLIQGPPGTGKTKTIVGILSvLLAGKYRKYYEKVKKK 56
 
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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