NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1804145364|ref|WP_161799216|]
View 

MULTISPECIES: PIN/TRAM domain-containing protein [Staphylococcus]

Protein Classification

PIN/TRAM domain-containing protein( domain architecture ID 11471837)

PilT N terminus (PIN) domain and TRIF-related adaptor molecule (TRAM) domain-containing protein, where PIN domain is involved in growth inhibition by regulating translation and TRAM acts as a sorting adaptor for Toll-like receptors (TLRs)

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
COG4956 COG4956
Uncharacterized conserved protein YacL, contains PIN and TRAM domains [General function ...
 56-343 3.06e-124

Uncharacterized conserved protein YacL, contains PIN and TRAM domains [General function prediction only];


:

Pssm-ID: 443983 [Multi-domain]  Cd Length: 355  Bit Score: 361.01  E-value: 3.06e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364  56 KKVTYAFKELEQIIMRRSAVEILFATIGLIIGLFISVMVSFILELIGNSMLNHFIPIIITIILCYLGFQFGLKKRDEMLM 135
Cdd:COG4956    61 KYVVRLIRRLEKRLRKLPLSDLLAGTIGLILGLLIANLLSAPLSLLPIPIIGPLLPILLSILLGYLGISLGLKKREELLR 140

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364 136 FLPEN--MARSMSYNTRKAIPKIIDTSAIIDGRILDIIRCGFIDGDILIPQGVINELQVVADANDSVKREKGQRGLDILN 213
Cdd:COG4956   141 LFNPIsrEGKEAKGSLRKASPKILDTSVIIDGRIADIAKTGFLEGTLIVPRFVLEELQHIADSSDDLKRNRGRRGLDILN 220

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364 214 QLYDlDYPTRV-INPT--KSHNDIDTLLIKLAQHYHAHVITTDFNLNKVCHVQGIMALNVNDLSEAIKPNVHQGDHLNIL 290
Cdd:COG4956   221 RLQK-EPPIPVeIYEGdfEDIKEVDSKLVKLAKELNGKIVTNDYNLNKVAELQGVPVLNINELANALKPVVLPGEEMTVK 299

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1804145364 291 LTKMGKEPGQGVGYLDDGTMVVVDNAKKLVGQHVNLEVISLLQTSSGRIVFAK 343
Cdd:COG4956   300 IIKEGKEPGQGVGYLDDGTMVVVEGGRKYIGETVEVVVTSVLQTSAGRMIFAK 352
 
Name Accession Description Interval E-value
COG4956 COG4956
Uncharacterized conserved protein YacL, contains PIN and TRAM domains [General function ...
 56-343 3.06e-124

Uncharacterized conserved protein YacL, contains PIN and TRAM domains [General function prediction only];


Pssm-ID: 443983 [Multi-domain]  Cd Length: 355  Bit Score: 361.01  E-value: 3.06e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364  56 KKVTYAFKELEQIIMRRSAVEILFATIGLIIGLFISVMVSFILELIGNSMLNHFIPIIITIILCYLGFQFGLKKRDEMLM 135
Cdd:COG4956    61 KYVVRLIRRLEKRLRKLPLSDLLAGTIGLILGLLIANLLSAPLSLLPIPIIGPLLPILLSILLGYLGISLGLKKREELLR 140

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364 136 FLPEN--MARSMSYNTRKAIPKIIDTSAIIDGRILDIIRCGFIDGDILIPQGVINELQVVADANDSVKREKGQRGLDILN 213
Cdd:COG4956   141 LFNPIsrEGKEAKGSLRKASPKILDTSVIIDGRIADIAKTGFLEGTLIVPRFVLEELQHIADSSDDLKRNRGRRGLDILN 220

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364 214 QLYDlDYPTRV-INPT--KSHNDIDTLLIKLAQHYHAHVITTDFNLNKVCHVQGIMALNVNDLSEAIKPNVHQGDHLNIL 290
Cdd:COG4956   221 RLQK-EPPIPVeIYEGdfEDIKEVDSKLVKLAKELNGKIVTNDYNLNKVAELQGVPVLNINELANALKPVVLPGEEMTVK 299

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1804145364 291 LTKMGKEPGQGVGYLDDGTMVVVDNAKKLVGQHVNLEVISLLQTSSGRIVFAK 343
Cdd:COG4956   300 IIKEGKEPGQGVGYLDDGTMVVVEGGRKYIGETVEVVVTSVLQTSAGRMIFAK 352
PIN_YacL-like cd09877
VapC-like PIN domain of Thermus Thermophilus Hb8, uncharacterized Bacillus subtilis YacL, and ...
 155-279 7.70e-56

VapC-like PIN domain of Thermus Thermophilus Hb8, uncharacterized Bacillus subtilis YacL, and other bacterial homologs; PIN (PilT N terminus) domain of the conserved membrane protein of unknown function of Thermus Thermophilus Hb8, Bacillus subtilis YacL and other similar homologs are included in this family. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Proteins in this group have a C-terminal TRAM domain whose function is unknown but predicted to be a RNA-binding domain common to tRNA uracil methylation and adenine thiolation enzymes.


Pssm-ID: 350225 [Multi-domain]  Cd Length: 127  Bit Score: 178.38  E-value: 7.70e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364 155 KIIDTSAIIDGRILDIIRCGFIDGDILIPQGVINELQVVADANDSVKREKGQRGLDILNQLYDLDYPTRVINPT--KSHN 232
Cdd:cd09877     1 KVLDTSVLIDGRIADIAKTGFLDGTLVVPRFVLDELQLLADSSDPLKRARGRRGLDVLKKLQKLPGLDVRIVDTdfPEIK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1804145364 233 DIDTLLIKLAQHYHAHVITTDFNLNKVCHVQGIMALNVNDLSEAIKP 279
Cdd:cd09877    81 EVDAKLVRLAKELGAKLLTNDFNLNKVAKLQGVKVLNINELANALKP 127
PRK13764 PRK13764
ATPase; Provisional
 156-265 7.59e-10

ATPase; Provisional


Pssm-ID: 184311 [Multi-domain]  Cd Length: 602  Bit Score: 60.24  E-value: 7.59e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364 156 IIDTSAIIDGRILDIIRCG-FIDGDILIPQGVINELQvvADANDsvKREKGQRGLDILNQLYDL------------DYPT 222
Cdd:PRK13764    4 VPDTSVVIDGRVSELIEKGeYIGGTIIIPEAVVAELE--AQANQ--GREIGFSGLEELKKLRELaeeglielefvgERPT 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1804145364 223 RVINPTKSHNDIDTLLIKLAQHYHAHVITTDFNLNKVCHVQGI 265
Cdd:PRK13764   80 LEQIKLAKGGEIDALIREVAKELGATLVTSDRVQAEVARAKGI 122
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 155-258 2.31e-05

Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.


Pssm-ID: 214771 [Multi-domain]  Cd Length: 111  Bit Score: 43.18  E-value: 2.31e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364  155 KIIDTSAIIDGRILDIIRCG-FIDGDILIPQGVINELQ---VVADANDSVKREKGQRGLDILNQLYDLDYPTRVINPTKS 230
Cdd:smart00670   3 VVLDTNVLIDGLIRDALEKLlEKKGEVYIPQTVLEELEylaLRSLKKLEELALEGKIILKVLKEERIEEEILERLSLKLE 82

                           90       100
                   ....*....|....*....|....*....
gi 1804145364  231 HNDIDTLLIKLAQHYHAHVI-TTDFNLNK 258
Cdd:smart00670  83 LLPNDALILATAKELGNVVLvTNDRDLRR 111
 
Name Accession Description Interval E-value
COG4956 COG4956
Uncharacterized conserved protein YacL, contains PIN and TRAM domains [General function ...
 56-343 3.06e-124

Uncharacterized conserved protein YacL, contains PIN and TRAM domains [General function prediction only];


Pssm-ID: 443983 [Multi-domain]  Cd Length: 355  Bit Score: 361.01  E-value: 3.06e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364  56 KKVTYAFKELEQIIMRRSAVEILFATIGLIIGLFISVMVSFILELIGNSMLNHFIPIIITIILCYLGFQFGLKKRDEMLM 135
Cdd:COG4956    61 KYVVRLIRRLEKRLRKLPLSDLLAGTIGLILGLLIANLLSAPLSLLPIPIIGPLLPILLSILLGYLGISLGLKKREELLR 140

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364 136 FLPEN--MARSMSYNTRKAIPKIIDTSAIIDGRILDIIRCGFIDGDILIPQGVINELQVVADANDSVKREKGQRGLDILN 213
Cdd:COG4956   141 LFNPIsrEGKEAKGSLRKASPKILDTSVIIDGRIADIAKTGFLEGTLIVPRFVLEELQHIADSSDDLKRNRGRRGLDILN 220

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364 214 QLYDlDYPTRV-INPT--KSHNDIDTLLIKLAQHYHAHVITTDFNLNKVCHVQGIMALNVNDLSEAIKPNVHQGDHLNIL 290
Cdd:COG4956   221 RLQK-EPPIPVeIYEGdfEDIKEVDSKLVKLAKELNGKIVTNDYNLNKVAELQGVPVLNINELANALKPVVLPGEEMTVK 299

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1804145364 291 LTKMGKEPGQGVGYLDDGTMVVVDNAKKLVGQHVNLEVISLLQTSSGRIVFAK 343
Cdd:COG4956   300 IIKEGKEPGQGVGYLDDGTMVVVEGGRKYIGETVEVVVTSVLQTSAGRMIFAK 352
PIN_YacL-like cd09877
VapC-like PIN domain of Thermus Thermophilus Hb8, uncharacterized Bacillus subtilis YacL, and ...
 155-279 7.70e-56

VapC-like PIN domain of Thermus Thermophilus Hb8, uncharacterized Bacillus subtilis YacL, and other bacterial homologs; PIN (PilT N terminus) domain of the conserved membrane protein of unknown function of Thermus Thermophilus Hb8, Bacillus subtilis YacL and other similar homologs are included in this family. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Proteins in this group have a C-terminal TRAM domain whose function is unknown but predicted to be a RNA-binding domain common to tRNA uracil methylation and adenine thiolation enzymes.


Pssm-ID: 350225 [Multi-domain]  Cd Length: 127  Bit Score: 178.38  E-value: 7.70e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364 155 KIIDTSAIIDGRILDIIRCGFIDGDILIPQGVINELQVVADANDSVKREKGQRGLDILNQLYDLDYPTRVINPT--KSHN 232
Cdd:cd09877     1 KVLDTSVLIDGRIADIAKTGFLDGTLVVPRFVLDELQLLADSSDPLKRARGRRGLDVLKKLQKLPGLDVRIVDTdfPEIK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1804145364 233 DIDTLLIKLAQHYHAHVITTDFNLNKVCHVQGIMALNVNDLSEAIKP 279
Cdd:cd09877    81 EVDAKLVRLAKELGAKLLTNDFNLNKVAKLQGVKVLNINELANALKP 127
PIN_VapC_VirB11L-ATPase-like cd09878
VapC-like PIN domain of an uncharacterized AAA+, VirB11-like ATPase-, KH- and PIN-domain ...
 158-265 3.32e-14

VapC-like PIN domain of an uncharacterized AAA+, VirB11-like ATPase-, KH- and PIN-domain containing protein MJ1533 from Methanocaldococcus jannaschii DSM 2661, and other similar archaeal homologs; PIN (PilT N terminus) domain present N-terminal of AAA+, VirB11-like ATPases. Several members of this subfamily possess an AAA+, VirB11-like ATPase domain, flanked by PIN and KH nucleic acid-binding domains. VirB11-ATPase is a type IV secretory pathway component required for T-pilus biogenesis and virulence. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. PIN domains within this subgroup contain four of these highly conserved residues which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350226 [Multi-domain]  Cd Length: 125  Bit Score: 68.29  E-value: 3.32e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364 158 DTSAIIDGRILDIIRCGFI-DGDILIPQGVINELQvvADANDsvKREKGQRGLDILNQLYDL------------DYPTRV 224
Cdd:cd09878     4 DTSVIIDGRISKLIEEGELkGGEIIIPEAVVAELE--HQANK--GREIGFAGLEELKKLRELakeggiklefvgERPTLE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1804145364 225 INPTKSHNDIDTLLIKLAQHYHAHVITTDFNLNKVCHVQGI 265
Cdd:cd09878    80 EIKLAKSGEIDALIRDVAREEGATLVTSDRVQAEVAEAEGI 120
PRK13764 PRK13764
ATPase; Provisional
 156-265 7.59e-10

ATPase; Provisional


Pssm-ID: 184311 [Multi-domain]  Cd Length: 602  Bit Score: 60.24  E-value: 7.59e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364 156 IIDTSAIIDGRILDIIRCG-FIDGDILIPQGVINELQvvADANDsvKREKGQRGLDILNQLYDL------------DYPT 222
Cdd:PRK13764    4 VPDTSVVIDGRVSELIEKGeYIGGTIIIPEAVVAELE--AQANQ--GREIGFSGLEELKKLRELaeeglielefvgERPT 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1804145364 223 RVINPTKSHNDIDTLLIKLAQHYHAHVITTDFNLNKVCHVQGI 265
Cdd:PRK13764   80 LEQIKLAKGGEIDALIREVAKELGATLVTSDRVQAEVARAKGI 122
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 155-258 2.31e-05

Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.


Pssm-ID: 214771 [Multi-domain]  Cd Length: 111  Bit Score: 43.18  E-value: 2.31e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364  155 KIIDTSAIIDGRILDIIRCG-FIDGDILIPQGVINELQ---VVADANDSVKREKGQRGLDILNQLYDLDYPTRVINPTKS 230
Cdd:smart00670   3 VVLDTNVLIDGLIRDALEKLlEKKGEVYIPQTVLEELEylaLRSLKKLEELALEGKIILKVLKEERIEEEILERLSLKLE 82

                           90       100
                   ....*....|....*....|....*....
gi 1804145364  231 HNDIDTLLIKLAQHYHAHVI-TTDFNLNK 258
Cdd:smart00670  83 LLPNDALILATAKELGNVVLvTNDRDLRR 111
PIN_Nob1-like cd09876
VapC-like PIN domain of eukaryotic ribosome assembly factor Nob1 and archaeal UPF0129 protein ...
 155-265 3.22e-03

VapC-like PIN domain of eukaryotic ribosome assembly factor Nob1 and archaeal UPF0129 protein Ta0041-like homologs; PIN (PilT N terminus) domain of the Saccharomyces cerevisiae ribosome assembly factor, Nob1 (Nin one binding) protein, the Thermoplasma acidophilum DSM 1728, UPF0129 protein Ta0041, and similar eukaryotic and archaeal homologs are included in this family. The Nob1 PIN domain binds the single-stranded cleavage site D at the 3-prime end of 18S rRNA. Recombinant Nob1 binds as a tetramer to pre-18S rRNA fragments containing cleavage site D and believed to cleave at this site. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_6.


Pssm-ID: 350224  Cd Length: 112  Bit Score: 36.72  E-value: 3.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804145364 155 KIIDTSAIIDGRILDIIRCGFIdgdilIPQGVINElqvvadandsVKREKGQRGLDILnqLYDLdyptRVINPTK----- 229
Cdd:cd09876     1 LVLDTSAFISGAPLDGLAEKLY-----TTPEVLEE----------IRDKKSRLRLELL--PGKL----KVREPSEesika 59

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1804145364 230 --------------SHNDIDtlLIKLAQHYHAHVITTDFNLNKVCHVQGI 265
Cdd:cd09876    60 vkefakktgdygslSATDIK--VLALALELEAEIVTDDYAIQNVAKHLGI 107
 
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