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Conserved domains on  [gi|1722117298|ref|WP_146438380|]
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S1 RNA-binding domain-containing protein [Crateriforma conspicua]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
953-1022 6.52e-20

Ribosomal protein S1-like RNA-binding domain;


:

Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 84.96  E-value: 6.52e-20
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298   953 KEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
Tex super family cl34417
Transcriptional accessory protein Tex/SPT6 [Transcription];
449-1027 1.92e-19

Transcriptional accessory protein Tex/SPT6 [Transcription];


The actual alignment was detected with superfamily member COG2183:

Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 94.32  E-value: 1.92e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  449 ELQEQASARLVGIAADNLRrsvnrggvD--------AKVVMSIDAvGPRTAA-TAIVSSDGRVLHHEDI-PCQlSKSLRS 518
Cdd:COG2183    288 ELKEKAEEEAIKVFAENLR--------DlllaapagGKVVLGLDP-GFRTGCkVAVVDETGKLLDTATIyPHP-PQNKWE 357

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  519 QAVLKMGELIHTYGVDLIVVSNGPARRASLAAIGDLIEQSpEQSIRWTLADRNGADAY-ASgPVADQE---MKATPRRfr 594
Cdd:COG2183    358 EAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKEL-DLKVQYVIVSEAGASVYsAS-ELAREEfpdLDVTVRG-- 433

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  595 AASwIAFSVVTPAQALAKVDPLKLRLGSFQRELSDDTLSGALRDVMISGASRGGIDANGAPVTWLSRLPGMNEAIAKAID 674
Cdd:COG2183    434 AVS-IARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIV 512

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  675 QRRREK-LFGSRTELteLDVwdslvsSR-------QALPFLRVFGSPQPLDGTMIHPDDYGLAEKLAKALelelppaepp 746
Cdd:COG2183    513 AYRDENgAFKSRKEL--LKV------PRlgpkafeQAAGFLRIRDGDNPLDNSAVHPESYPVVEKILKDL---------- 574

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  747 GYTAPSfddepseqpvepvetpVADDSLKVETFetvpdeKTENFAAkiesesdaapeaEATGEsePTADadspaeaadtp 826
Cdd:COG2183    575 GVSVKD----------------LIGNKELLKKL------DPEKYAD------------ELFGL--PTLR----------- 607

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  827 adpdaasesapeasadaeasdapppeasadagdDATAETsadadATPESDAEPDAEsdsaadaqpaTP-FRQalpepakv 905
Cdd:COG2183    608 ---------------------------------DILKEL-----EKPGRDPRPEFK----------TPtFRE-------- 631

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  906 dkcvkewqvgrhrshqivhwlcdpfgdsdpsGVSpavlntmpSLKSLKEGDEVIGVVVGVMPFGVFVelapDC----SGL 981
Cdd:COG2183    632 -------------------------------GVL--------KIEDLKPGMILEGTVTNVTDFGAFV----DIgvhqDGL 668

                          570       580       590       600
                   ....*....|....*....|....*....|....*....|....*.
gi 1722117298  982 IHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALSAISPQ 1027
Cdd:COG2183    669 VHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDD 714
Tex_N super family cl46305
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 25-189 2.04e-05

Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss:Q45388. This protein defines a novel family of prokaryotic transcriptional accessory factors.


The actual alignment was detected with superfamily member pfam09371:

Pssm-ID: 480645  Cd Length: 183  Bit Score: 46.63  E-value: 2.04e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298   25 LLEQGYTPPYLARYRRDELGDIDEASLWHLSHAVQSDLELQRRREELVQSWKTSELTDPALGKAVEKAASKRLLDRL--- 101
Cdd:pfam09371   18 LLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKAAIEAADTLTELEDLylp 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  102 ---ARRVKS----ELGekVDPstrLAARILNprkgdGDDIASIAGK----VDGIEAdqVEAAVAGLDNALAKRLCGDPRV 170
Cdd:pfam09371   98 ykpKRRTKAtiarEKG--LEP---LADAILA-----QPDPEEEAAKyinpEKGVAD--VEEALAGARDIIAERISEDAEL 165

                          170
                   ....*....|....*....
gi 1722117298  171 INAAVRWLTKNSRIhISQV 189
Cdd:pfam09371  166 RKKLRELLWREGVI-VSKV 183
CobT2 super family cl34772
Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]; ...
 804-906 2.85e-03

Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]; Cobalamin biosynthesis cobaltochelatase CobT subunit is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


The actual alignment was detected with superfamily member COG4547:

Pssm-ID: 443611 [Multi-domain]  Cd Length: 608  Bit Score: 41.70  E-value: 2.85e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  804 AEATGESEPTADADSPAEAADTPADPDAASESapeasaDAEASDAPPPEASADAGDDATAETSADADATPESDAEPDAES 883
Cdd:COG4547    208 AEELGEDEDEEDEDDEDDSGEQEEDEEDGEDE------DEESDEGAEAEDAEASGDDAEEGESEAAEAESDEMAEEAEGE 281

                           90       100
                   ....*....|....*....|...
gi 1722117298  884 DSAADAQPATPFRQALPEPAKVD 906
Cdd:COG4547    282 DSEEPGEPWRPNAPPPDDPADPD 304
 
Name Accession Description Interval E-value
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
953-1022 6.52e-20

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 84.96  E-value: 6.52e-20
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298   953 KEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 950-1022 9.26e-20

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 86.39  E-value: 9.26e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1722117298  950 KSLKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKrRRVALS 1022
Cdd:COG1098      1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDED-GKISLS 72
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
449-1027 1.92e-19

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 94.32  E-value: 1.92e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  449 ELQEQASARLVGIAADNLRrsvnrggvD--------AKVVMSIDAvGPRTAA-TAIVSSDGRVLHHEDI-PCQlSKSLRS 518
Cdd:COG2183    288 ELKEKAEEEAIKVFAENLR--------DlllaapagGKVVLGLDP-GFRTGCkVAVVDETGKLLDTATIyPHP-PQNKWE 357

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  519 QAVLKMGELIHTYGVDLIVVSNGPARRASLAAIGDLIEQSpEQSIRWTLADRNGADAY-ASgPVADQE---MKATPRRfr 594
Cdd:COG2183    358 EAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKEL-DLKVQYVIVSEAGASVYsAS-ELAREEfpdLDVTVRG-- 433

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  595 AASwIAFSVVTPAQALAKVDPLKLRLGSFQRELSDDTLSGALRDVMISGASRGGIDANGAPVTWLSRLPGMNEAIAKAID 674
Cdd:COG2183    434 AVS-IARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIV 512

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  675 QRRREK-LFGSRTELteLDVwdslvsSR-------QALPFLRVFGSPQPLDGTMIHPDDYGLAEKLAKALelelppaepp 746
Cdd:COG2183    513 AYRDENgAFKSRKEL--LKV------PRlgpkafeQAAGFLRIRDGDNPLDNSAVHPESYPVVEKILKDL---------- 574

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  747 GYTAPSfddepseqpvepvetpVADDSLKVETFetvpdeKTENFAAkiesesdaapeaEATGEsePTADadspaeaadtp 826
Cdd:COG2183    575 GVSVKD----------------LIGNKELLKKL------DPEKYAD------------ELFGL--PTLR----------- 607

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  827 adpdaasesapeasadaeasdapppeasadagdDATAETsadadATPESDAEPDAEsdsaadaqpaTP-FRQalpepakv 905
Cdd:COG2183    608 ---------------------------------DILKEL-----EKPGRDPRPEFK----------TPtFRE-------- 631

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  906 dkcvkewqvgrhrshqivhwlcdpfgdsdpsGVSpavlntmpSLKSLKEGDEVIGVVVGVMPFGVFVelapDC----SGL 981
Cdd:COG2183    632 -------------------------------GVL--------KIEDLKPGMILEGTVTNVTDFGAFV----DIgvhqDGL 668

                          570       580       590       600
                   ....*....|....*....|....*....|....*....|....*.
gi 1722117298  982 IHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALSAISPQ 1027
Cdd:COG2183    669 VHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDD 714
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 955-1022 7.22e-17

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 76.12  E-value: 7.22e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1722117298  955 GDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:cd05685      1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
PRK08059 PRK08059
general stress protein 13; Validated
 952-1022 1.96e-15

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 73.93  E-value: 1.96e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1722117298  952 LKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK08059     5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLS 75
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 952-1022 1.27e-12

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 64.23  E-value: 1.27e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1722117298  952 LKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILS 71
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 949-1022 2.38e-12

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 70.92  E-value: 2.38e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1722117298  949 LKSLKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRIS-EGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:TIGR00717  267 EKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLG 341
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 751-889 5.74e-09

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 60.69  E-value: 5.74e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  751 PSFDDEPSEqpVEPV-----ETPVAD---DSLKVETFETVPDEKTENFAAKIESESDAAPEAEATGESEPTADADSPAEA 822
Cdd:NF033609   545 PEQPDEPGE--IEPIpedsdSDPGSDsgsDSSNSDSGSDSGSDSTSDSGSDSASDSDSASDSDSASDSDSASDSDSASDS 622

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1722117298  823 -----ADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPESDAEPDAESDSAADA 889
Cdd:NF033609   623 dsasdSDSASDSDSASDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 694
Tex_YqgF pfam16921
Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which ...
 479-586 1.51e-08

Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which is involved in transcriptional processes.


Pssm-ID: 465314  Cd Length: 125  Bit Score: 54.33  E-value: 1.51e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  479 VVMSIDAvGPRTAA-TAIVSSDGRVLHHEDIPCQLSKSLRSQAVLKMGELIHTYGVDLIVVSNGPARRASLAAIGDLIEQ 557
Cdd:pfam16921    1 VVLGLDP-GYRTGCkLAVVDETGKVLDTAVIYPHPPQNKVEEAKKKLKKLIKKYGVELIAIGNGTASRETEQFVAELIKE 79

                           90       100
                   ....*....|....*....|....*....
gi 1722117298  558 SPEQsIRWTLADRNGADAYASGPVADQEM 586
Cdd:pfam16921   80 LPLK-VKYVIVSEAGASVYSASELAREEF 107
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-890 2.11e-07

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 55.69  E-value: 2.11e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   701 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 779

                           90
                   ....*....|....*.
gi 1722117298  875 SDAEPDAESDSAADAQ 890
Cdd:NF033609   780 SDSDSDSDSDSDSDSD 795
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 755-890 2.61e-07

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 55.30  E-value: 2.61e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  755 DEP--SEQPVEPVET-PVADDSlkvetfETVPDEKTENFAAKIESESDAAPEAEATGESEPTADADSpAEAADTPADPDA 831
Cdd:NF033609   540 DKPvvPEQPDEPGEIePIPEDS------DSDPGSDSGSDSSNSDSGSDSGSDSTSDSGSDSASDSDS-ASDSDSASDSDS 612

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1722117298  832 ASESapeasadaeasdapppEASADAGDDATAETSADADATPESDAEPDAESDSAADAQ 890
Cdd:NF033609   613 ASDS----------------DSASDSDSASDSDSASDSDSASDSDSDSDSDSDSDSDSD 655
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-889 2.87e-07

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 55.30  E-value: 2.87e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEA-ADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATP 873
Cdd:NF033609   703 DSDSDSDSDSDSDSDSDSDSDSDSDSDSdSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 782

                           90
                   ....*....|....*.
gi 1722117298  874 ESDAEPDAESDSAADA 889
Cdd:NF033609   783 DSDSDSDSDSDSDSDS 798
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 770-889 3.61e-07

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 54.92  E-value: 3.61e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  770 ADDSLKVETFETVPDEKTENfAAKIESESDAAPEAEATGESEPTADADSPAEA-ADTPADPDAASESAPEASADAEASDA 848
Cdd:NF033609   607 ASDSDSASDSDSASDSDSAS-DSDSASDSDSASDSDSDSDSDSDSDSDSDSDSdSDSDSDSDSDSDSDSDSDSDSDSDSD 685

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1722117298  849 PPPEASADAGDDATAETSADADATPESDAEPDAESDSAADA 889
Cdd:NF033609   686 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 726
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-889 4.13e-07

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 54.53  E-value: 4.13e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEA-ADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATP 873
Cdd:NF033609   691 DSDSDSDSDSDSDSDSDSDSDSDSDSDSdSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 770

                           90
                   ....*....|....*.
gi 1722117298  874 ESDAEPDAESDSAADA 889
Cdd:NF033609   771 DSDSDSDSDSDSDSDS 786
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-889 5.80e-07

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 54.14  E-value: 5.80e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   643 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 721

                           90
                   ....*....|....*
gi 1722117298  875 SDAEPDAESDSAADA 889
Cdd:NF033609   722 SDSDSDSDSDSDSDS 736
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-889 1.10e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 53.37  E-value: 1.10e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEaADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   689 DSDSDSDSDSDSDSDSDSDSDSDSDSD-SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 767

                           90
                   ....*....|....*
gi 1722117298  875 SDAEPDAESDSAADA 889
Cdd:NF033609   768 SDSDSDSDSDSDSDS 782
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-889 1.40e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 52.99  E-value: 1.40e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   739 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 817

                           90
                   ....*....|....*
gi 1722117298  875 SDAEPDAESDSAADA 889
Cdd:NF033609   818 SDSDSDSDSDSDSDS 832
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-893 1.49e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 52.60  E-value: 1.49e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   649 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 727

                           90
                   ....*....|....*....
gi 1722117298  875 SDAEPDAESDSAADAQPAT 893
Cdd:NF033609   728 SDSDSDSDSDSDSDSDSDS 746
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-889 2.81e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 51.83  E-value: 2.81e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   745 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 823

                           90
                   ....*....|....*
gi 1722117298  875 SDAEPDAESDSAADA 889
Cdd:NF033609   824 SDSDSDSDSDSDSDS 838
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-893 3.06e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 51.83  E-value: 3.06e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   661 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 739

                           90
                   ....*....|....*....
gi 1722117298  875 SDAEPDAESDSAADAQPAT 893
Cdd:NF033609   740 SDSDSDSDSDSDSDSDSDS 758
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-893 3.59e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 51.45  E-value: 3.59e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAeAADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   725 DSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 803

                           90
                   ....*....|....*....
gi 1722117298  875 SDAEPDAESDSAADAQPAT 893
Cdd:NF033609   804 SDSDSDSDSDSDSDSDSDS 822
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-893 4.40e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 51.06  E-value: 4.40e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   731 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 809

                           90
                   ....*....|....*....
gi 1722117298  875 SDAEPDAESDSAADAQPAT 893
Cdd:NF033609   810 SDSDSDSDSDSDSDSDSDS 828
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-893 6.96e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 50.68  E-value: 6.96e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   751 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 829

                           90
                   ....*....|....*....
gi 1722117298  875 SDAEPDAESDSAADAQPAT 893
Cdd:NF033609   830 SDSDSDSDSDSDSDSDSDS 848
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 791-893 1.04e-05

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 49.91  E-value: 1.04e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  791 AAKIESESDAAPEAEATGESEPTADADSPAEA-ADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADA 869
Cdd:NF033609   649 DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSdSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 728

                           90       100
                   ....*....|....*....|....
gi 1722117298  870 DATPESDAEPDAESDSAADAQPAT 893
Cdd:NF033609   729 DSDSDSDSDSDSDSDSDSDSDSDS 752
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 25-189 2.04e-05

Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss:Q45388. This protein defines a novel family of prokaryotic transcriptional accessory factors.


Pssm-ID: 462777  Cd Length: 183  Bit Score: 46.63  E-value: 2.04e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298   25 LLEQGYTPPYLARYRRDELGDIDEASLWHLSHAVQSDLELQRRREELVQSWKTSELTDPALGKAVEKAASKRLLDRL--- 101
Cdd:pfam09371   18 LLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKAAIEAADTLTELEDLylp 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  102 ---ARRVKS----ELGekVDPstrLAARILNprkgdGDDIASIAGK----VDGIEAdqVEAAVAGLDNALAKRLCGDPRV 170
Cdd:pfam09371   98 ykpKRRTKAtiarEKG--LEP---LADAILA-----QPDPEEEAAKyinpEKGVAD--VEEALAGARDIIAERISEDAEL 165

                          170
                   ....*....|....*....
gi 1722117298  171 INAAVRWLTKNSRIhISQV 189
Cdd:pfam09371  166 RKKLRELLWREGVI-VSKV 183
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 742-903 6.57e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 47.29  E-value: 6.57e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  742 PAEPPGYTAPSfDDEPSEQPVEPVETPVADDSLKVETFETVPDEKTENFAAKIESESDAAPEAEATGESEPTADADSPAE 821
Cdd:PRK07764   615 PAAPAAPAAPA-APAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAP 693

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  822 AADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPESDAEPDAESDSAADAQPATPFRQALPE 901
Cdd:PRK07764   694 AGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAA 773


                   ..
gi 1722117298  902 PA 903
Cdd:PRK07764   774 PP 775
SepH NF040712
septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces ...
 770-896 3.42e-04

septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces venezuelae, and homologs were identified in Mycobacterium smegmatis. SepH contains a N-terminal DUF3071 domain and a conserved C-terminal region. It binds directly to cell division protein FtsZ to stimulate the assembly of FtsZ protofilaments.


Pssm-ID: 468676 [Multi-domain]  Cd Length: 346  Bit Score: 44.37  E-value: 3.42e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  770 ADDSLKVETFETVPDEKTENFAAKIESESDAAPEAEATGESEPTADADSPAEAA---------DTPADPDAASESAPEAS 840
Cdd:NF040712   190 PDFGRPLRPLATVPRLAREPADARPEEVEPAPAAEGAPATDSDPAEAGTPDDLAsarrrragvEQPEDEPVGPGAAPAAE 269

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1722117298  841 ADAEASDAPPPEASADAGDDATAETSADADATPESDAEPDAESDSAADAQPATPFR 896
Cdd:NF040712   270 PDEATRDAGEPPAPGAAETPEAAEPPAPAPAAPAAPAAPEAEEPARPEPPPAPKPK 325
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-891 9.83e-04

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 43.74  E-value: 9.83e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSpaeaaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   783 DSDSDSDSDSDSDSDSDSDSDSDS-----DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSE 857

                           90
                   ....*....|....*..
gi 1722117298  875 SDAEPDAESDSAADAQP 891
Cdd:NF033609   858 SDSNSDSESGSNNNVVP 874
CobT2 COG4547
Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]; ...
 804-906 2.85e-03

Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]; Cobalamin biosynthesis cobaltochelatase CobT subunit is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


Pssm-ID: 443611 [Multi-domain]  Cd Length: 608  Bit Score: 41.70  E-value: 2.85e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  804 AEATGESEPTADADSPAEAADTPADPDAASESapeasaDAEASDAPPPEASADAGDDATAETSADADATPESDAEPDAES 883
Cdd:COG4547    208 AEELGEDEDEEDEDDEDDSGEQEEDEEDGEDE------DEESDEGAEAEDAEASGDDAEEGESEAAEAESDEMAEEAEGE 281

                           90       100
                   ....*....|....*....|...
gi 1722117298  884 DSAADAQPATPFRQALPEPAKVD 906
Cdd:COG4547    282 DSEEPGEPWRPNAPPPDDPADPD 304
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 806-906 3.05e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.90  E-value: 3.05e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  806 ATGESEPTADADSPAEAADTPADPDAASesAPEASADAEASDAPPPEASADAGDDATAETSADADATPESDAEPDAESDS 885
Cdd:PRK07764   388 AGGAGAPAAAAPSAAAAAPAAAPAPAAA--APAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQ 465

                           90       100
                   ....*....|....*....|.
gi 1722117298  886 AADAQPATPFRQALPEPAKVD 906
Cdd:PRK07764   466 PAPAPAAAPEPTAAPAPAPPA 486
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-894 3.16e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 41.82  E-value: 3.16e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEaADTPADPDAASESapeasadaeasdapppEASADAGDDATAETSADADATPE 874
Cdd:NF033609   793 DSDSDSDSDSDSDSDSDSDSDSDSDSD-SDSDSDSDSDSDS----------------DSDSDSDSDSDSDSDSDSDSDSD 855

                           90       100
                   ....*....|....*....|
gi 1722117298  875 SDAEPDAESDSAADAQPATP 894
Cdd:NF033609   856 SESDSNSDSESGSNNNVVPP 875
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 808-893 6.90e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 40.66  E-value: 6.90e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  808 GESEPT---ADADSPAEAADTPADPDAASESAPeasadaeasdapppEASADAGDDATAETSADADATPESDAEPDAESD 884
Cdd:NF033609   552 GEIEPIpedSDSDPGSDSGSDSSNSDSGSDSGS--------------DSTSDSGSDSASDSDSASDSDSASDSDSASDSD 617


                   ....*....
gi 1722117298  885 SAADAQPAT 893
Cdd:NF033609   618 SASDSDSAS 626
 
Name Accession Description Interval E-value
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
953-1022 6.52e-20

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 84.96  E-value: 6.52e-20
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298   953 KEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 950-1022 9.26e-20

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 86.39  E-value: 9.26e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1722117298  950 KSLKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKrRRVALS 1022
Cdd:COG1098      1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDED-GKISLS 72
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
449-1027 1.92e-19

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 94.32  E-value: 1.92e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  449 ELQEQASARLVGIAADNLRrsvnrggvD--------AKVVMSIDAvGPRTAA-TAIVSSDGRVLHHEDI-PCQlSKSLRS 518
Cdd:COG2183    288 ELKEKAEEEAIKVFAENLR--------DlllaapagGKVVLGLDP-GFRTGCkVAVVDETGKLLDTATIyPHP-PQNKWE 357

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  519 QAVLKMGELIHTYGVDLIVVSNGPARRASLAAIGDLIEQSpEQSIRWTLADRNGADAY-ASgPVADQE---MKATPRRfr 594
Cdd:COG2183    358 EAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKEL-DLKVQYVIVSEAGASVYsAS-ELAREEfpdLDVTVRG-- 433

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  595 AASwIAFSVVTPAQALAKVDPLKLRLGSFQRELSDDTLSGALRDVMISGASRGGIDANGAPVTWLSRLPGMNEAIAKAID 674
Cdd:COG2183    434 AVS-IARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIV 512

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  675 QRRREK-LFGSRTELteLDVwdslvsSR-------QALPFLRVFGSPQPLDGTMIHPDDYGLAEKLAKALelelppaepp 746
Cdd:COG2183    513 AYRDENgAFKSRKEL--LKV------PRlgpkafeQAAGFLRIRDGDNPLDNSAVHPESYPVVEKILKDL---------- 574

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  747 GYTAPSfddepseqpvepvetpVADDSLKVETFetvpdeKTENFAAkiesesdaapeaEATGEsePTADadspaeaadtp 826
Cdd:COG2183    575 GVSVKD----------------LIGNKELLKKL------DPEKYAD------------ELFGL--PTLR----------- 607

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  827 adpdaasesapeasadaeasdapppeasadagdDATAETsadadATPESDAEPDAEsdsaadaqpaTP-FRQalpepakv 905
Cdd:COG2183    608 ---------------------------------DILKEL-----EKPGRDPRPEFK----------TPtFRE-------- 631

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  906 dkcvkewqvgrhrshqivhwlcdpfgdsdpsGVSpavlntmpSLKSLKEGDEVIGVVVGVMPFGVFVelapDC----SGL 981
Cdd:COG2183    632 -------------------------------GVL--------KIEDLKPGMILEGTVTNVTDFGAFV----DIgvhqDGL 668

                          570       580       590       600
                   ....*....|....*....|....*....|....*....|....*.
gi 1722117298  982 IHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALSAISPQ 1027
Cdd:COG2183    669 VHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDD 714
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 955-1022 7.22e-17

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 76.12  E-value: 7.22e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1722117298  955 GDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:cd05685      1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 958-1022 3.21e-16

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 73.95  E-value: 3.21e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1722117298  958 VIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:cd00164      1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 952-1022 1.00e-15

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 80.09  E-value: 1.00e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1722117298  952 LKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEG-FVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:COG0539    272 YPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSWTkRVAHPSDVVKVGDEVEVKVLDIDPEERRISLS 343
PRK08059 PRK08059
general stress protein 13; Validated
 952-1022 1.96e-15

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 73.93  E-value: 1.96e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1722117298  952 LKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK08059     5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLS 75
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 955-1022 1.99e-14

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 69.24  E-value: 1.99e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1722117298  955 GDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEkRRRVALS 1022
Cdd:cd05692      1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLS 67
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 955-1022 6.00e-14

S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 67.57  E-value: 6.00e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1722117298  955 GDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDeKRRRVALS 1022
Cdd:cd04472      1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLS 67
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 949-1022 1.29e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 75.20  E-value: 1.29e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1722117298  949 LKSLKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK06299   455 AKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLS 528
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
953-1022 2.42e-13

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 74.60  E-value: 2.42e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  953 KEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK00087   561 PVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLS 630
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 949-1022 8.50e-13

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 71.23  E-value: 8.50e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1722117298  949 LKSLKEGDEVIGVVVGVMPFGVFVELAP-DcsGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:COG0539    184 LEKLEEGDVVEGTVKNITDFGAFVDLGGvD--GLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLS 256
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 952-1022 1.27e-12

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 64.23  E-value: 1.27e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1722117298  952 LKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILS 71
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
952-1040 1.29e-12

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 65.88  E-value: 1.29e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  952 LKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALSAispqRVIE 1031
Cdd:PRK07252     1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSL----RTLE 76


                   ....*....
gi 1722117298 1032 LDQERQQQH 1040
Cdd:PRK07252    77 EEKQHFPHR 85
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 953-1022 1.64e-12

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 71.96  E-value: 1.64e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  953 KEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDeKRRRVALS 1022
Cdd:COG1185    615 EVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEID-DQGRIKLS 683
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 944-1022 2.08e-12

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 63.76  E-value: 2.08e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  944 NTMPSLKS-LKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:cd04461      3 GTLPTNFSdLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS 82
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 949-1022 2.38e-12

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 70.92  E-value: 2.38e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1722117298  949 LKSLKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRIS-EGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:TIGR00717  267 EKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLG 341
rpsA PRK13806
30S ribosomal protein S1; Provisional
 949-1023 4.92e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 69.75  E-value: 4.92e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1722117298  949 LKSLKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDE----KRRRVALSA 1023
Cdd:PRK13806   197 METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERakkgKGLRISLSI 275
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 953-1022 9.82e-12

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 61.58  E-value: 9.82e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1722117298  953 KEGDEVIGVVVGVMPFGVFVEL-APDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:cd05708      1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLG 71
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 952-1022 1.32e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 67.98  E-value: 1.32e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1722117298  952 LKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK06676   275 LPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLS 345
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 953-1022 2.58e-11

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 68.15  E-value: 2.58e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  953 KEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDeKRRRVALS 1022
Cdd:PRK11824   620 EVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLS 688
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 953-1022 4.11e-11

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 67.07  E-value: 4.11e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  953 KEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:TIGR00717  445 KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLS 514
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
949-1022 1.03e-10

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 66.12  E-value: 1.03e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1722117298  949 LKSLKEGDEVIGVVVGVMPFGVFVELApDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK00087   472 WNSLEEGDVVEGEVKRLTDFGAFVDIG-GVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLS 544
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 949-1022 1.36e-10

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 64.90  E-value: 1.36e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1722117298  949 LKSLKEGDEVIGVVVGVMPFGVFVELApDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK06676   187 LSSLKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLS 259
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 954-1022 1.65e-10

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 58.02  E-value: 1.65e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1722117298  954 EGDEVIGVVVGVMPFGVFVELApDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:cd05688      1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
rpsA PRK13806
30S ribosomal protein S1; Provisional
 952-1022 6.90e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 63.20  E-value: 6.90e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1722117298  952 LKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEG-FVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK13806   290 LKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTrRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLS 361
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 949-1022 1.30e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 62.49  E-value: 1.30e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1722117298  949 LKSLKEGDEVIGVVVGVMPFGVFVELAP-DcsGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK06299   196 LENLEEGQVVEGVVKNITDYGAFVDLGGvD--GLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLG 268
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 950-1022 1.54e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 62.10  E-value: 1.54e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1722117298  950 KSLKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISegFVEDL-H--EAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK06299   282 KKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMS--WTKKNkHpsKVVSVGQEVEVMVLEIDEEKRRISLG 355
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 948-1022 1.71e-09

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 61.67  E-value: 1.71e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1722117298  948 SLKSLKEGDEVIGVVVGVMPFGVFVELApDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:TIGR00717  181 LLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLS 254
PRK08582 PRK08582
RNA-binding protein S1;
951-1022 2.96e-09

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 56.58  E-value: 2.96e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1722117298  951 SLKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIdEKRRRVALS 1022
Cdd:PRK08582     2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNV-EDDGKIGLS 72
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 751-889 5.74e-09

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 60.69  E-value: 5.74e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  751 PSFDDEPSEqpVEPV-----ETPVAD---DSLKVETFETVPDEKTENFAAKIESESDAAPEAEATGESEPTADADSPAEA 822
Cdd:NF033609   545 PEQPDEPGE--IEPIpedsdSDPGSDsgsDSSNSDSGSDSGSDSTSDSGSDSASDSDSASDSDSASDSDSASDSDSASDS 622

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1722117298  823 -----ADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPESDAEPDAESDSAADA 889
Cdd:NF033609   623 dsasdSDSASDSDSASDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 694
Tex_YqgF pfam16921
Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which ...
 479-586 1.51e-08

Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which is involved in transcriptional processes.


Pssm-ID: 465314  Cd Length: 125  Bit Score: 54.33  E-value: 1.51e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  479 VVMSIDAvGPRTAA-TAIVSSDGRVLHHEDIPCQLSKSLRSQAVLKMGELIHTYGVDLIVVSNGPARRASLAAIGDLIEQ 557
Cdd:pfam16921    1 VVLGLDP-GYRTGCkLAVVDETGKVLDTAVIYPHPPQNKVEEAKKKLKKLIKKYGVELIAIGNGTASRETEQFVAELIKE 79

                           90       100
                   ....*....|....*....|....*....
gi 1722117298  558 SPEQsIRWTLADRNGADAYASGPVADQEM 586
Cdd:pfam16921   80 LPLK-VKYVIVSEAGASVYSASELAREEF 107
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 949-1012 1.56e-08

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 55.75  E-value: 1.56e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1722117298  949 LKSLKEGDEVIGVVVGVMPFGVFV----------ELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGI 1012
Cdd:PRK09521    59 PPLLKKGDIVYGRVVDVKEQRALVrivsiegserELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISY 132
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 955-1022 1.63e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 58.52  E-value: 1.63e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1722117298  955 GDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK07899   294 GQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLS 361
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 953-1022 3.54e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 57.87  E-value: 3.54e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1722117298  953 KEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRIS-EGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK06299   372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLG 442
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 955-1019 8.40e-08

S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.


Pssm-ID: 239917 [Multi-domain]  Cd Length: 83  Bit Score: 50.86  E-value: 8.40e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1722117298  955 GDEVIGVVVGVMPFGVFVELaPD--CSGLIHVSRISEG---FVEDLHEAV--------QVGDVITGWVTGIDEKRRRV 1019
Cdd:cd04471      2 GEEFDGVISGVTSFGLFVEL-DNltVEGLVHVSTLGDDyyeFDEENHALVgertgkvfRLGDKVKVRVVRVDLDRRKI 78
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-890 2.11e-07

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 55.69  E-value: 2.11e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   701 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 779

                           90
                   ....*....|....*.
gi 1722117298  875 SDAEPDAESDSAADAQ 890
Cdd:NF033609   780 SDSDSDSDSDSDSDSD 795
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 755-890 2.61e-07

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 55.30  E-value: 2.61e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  755 DEP--SEQPVEPVET-PVADDSlkvetfETVPDEKTENFAAKIESESDAAPEAEATGESEPTADADSpAEAADTPADPDA 831
Cdd:NF033609   540 DKPvvPEQPDEPGEIePIPEDS------DSDPGSDSGSDSSNSDSGSDSGSDSTSDSGSDSASDSDS-ASDSDSASDSDS 612

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1722117298  832 ASESapeasadaeasdapppEASADAGDDATAETSADADATPESDAEPDAESDSAADAQ 890
Cdd:NF033609   613 ASDS----------------DSASDSDSASDSDSASDSDSASDSDSDSDSDSDSDSDSD 655
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-889 2.87e-07

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 55.30  E-value: 2.87e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEA-ADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATP 873
Cdd:NF033609   703 DSDSDSDSDSDSDSDSDSDSDSDSDSDSdSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 782

                           90
                   ....*....|....*.
gi 1722117298  874 ESDAEPDAESDSAADA 889
Cdd:NF033609   783 DSDSDSDSDSDSDSDS 798
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 953-1022 2.97e-07

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 49.12  E-value: 2.97e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1722117298  953 KEGDEVIGVVVGVMPFGVFVELA--PDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:cd04452      2 EEGELVVVTVKSIADMGAYVSLLeyGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLS 73
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 954-1021 3.16e-07

S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 48.73  E-value: 3.16e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  954 EGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRIsEGFVEDLHEA--VQVGDVITGWVTGIDEKRRRVAL 1021
Cdd:cd05689      3 EGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEM-DWTNKNIHPSkvVSLGDEVEVMVLDIDEERRRISL 71
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 770-889 3.61e-07

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 54.92  E-value: 3.61e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  770 ADDSLKVETFETVPDEKTENfAAKIESESDAAPEAEATGESEPTADADSPAEA-ADTPADPDAASESAPEASADAEASDA 848
Cdd:NF033609   607 ASDSDSASDSDSASDSDSAS-DSDSASDSDSASDSDSDSDSDSDSDSDSDSDSdSDSDSDSDSDSDSDSDSDSDSDSDSD 685

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1722117298  849 PPPEASADAGDDATAETSADADATPESDAEPDAESDSAADA 889
Cdd:NF033609   686 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 726
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-889 4.13e-07

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 54.53  E-value: 4.13e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEA-ADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATP 873
Cdd:NF033609   691 DSDSDSDSDSDSDSDSDSDSDSDSDSDSdSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 770

                           90
                   ....*....|....*.
gi 1722117298  874 ESDAEPDAESDSAADA 889
Cdd:NF033609   771 DSDSDSDSDSDSDSDS 786
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-889 5.80e-07

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 54.14  E-value: 5.80e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   643 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 721

                           90
                   ....*....|....*
gi 1722117298  875 SDAEPDAESDSAADA 889
Cdd:NF033609   722 SDSDSDSDSDSDSDS 736
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 955-1022 5.87e-07

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 48.04  E-value: 5.87e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1722117298  955 GDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:cd05691      1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLS 68
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 955-1021 7.03e-07

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 47.87  E-value: 7.03e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  955 GDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISegFVEDLHEAVQV---GDVITGWVTGIDEKRRRVAL 1021
Cdd:cd05690      1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDIS--WTQRVRHPSEIykkGQEVEAVVLNIDVERERISL 68
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 954-1022 8.54e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 51.75  E-value: 8.54e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1722117298  954 EGDEVIGVVVGVMPFGVFVELA--PDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK03987     8 EGELVVGTVKEVKDFGAFVTLDeyPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLS 78
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 960-1022 9.43e-07

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 47.62  E-value: 9.43e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1722117298  960 GVVVGVMPFGVFVEL---APDCSGLIHVSRIS-EGFVEDLHEAVQVGDVItgWVTGIDEKRRRVALS 1022
Cdd:cd05684      6 GKVTSIMDFGCFVQLeglKGRKEGLVHISQLSfEGRVANPSDVVKRGQKV--KVKVISIQNGKISLS 70
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-889 1.10e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 53.37  E-value: 1.10e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEaADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   689 DSDSDSDSDSDSDSDSDSDSDSDSDSD-SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 767

                           90
                   ....*....|....*
gi 1722117298  875 SDAEPDAESDSAADA 889
Cdd:NF033609   768 SDSDSDSDSDSDSDS 782
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-889 1.40e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 52.99  E-value: 1.40e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   739 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 817

                           90
                   ....*....|....*
gi 1722117298  875 SDAEPDAESDSAADA 889
Cdd:NF033609   818 SDSDSDSDSDSDSDS 832
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-893 1.49e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 52.60  E-value: 1.49e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   649 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 727

                           90
                   ....*....|....*....
gi 1722117298  875 SDAEPDAESDSAADAQPAT 893
Cdd:NF033609   728 SDSDSDSDSDSDSDSDSDS 746
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 955-1022 2.20e-06

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 46.13  E-value: 2.20e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1722117298  955 GDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:cd05707      1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 955-1022 2.41e-06

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 46.06  E-value: 2.41e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1722117298  955 GDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLS 68
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-889 2.81e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 51.83  E-value: 2.81e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   745 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 823

                           90
                   ....*....|....*
gi 1722117298  875 SDAEPDAESDSAADA 889
Cdd:NF033609   824 SDSDSDSDSDSDSDS 838
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-893 3.06e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 51.83  E-value: 3.06e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   661 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 739

                           90
                   ....*....|....*....
gi 1722117298  875 SDAEPDAESDSAADAQPAT 893
Cdd:NF033609   740 SDSDSDSDSDSDSDSDSDS 758
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-893 3.59e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 51.45  E-value: 3.59e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAeAADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   725 DSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 803

                           90
                   ....*....|....*....
gi 1722117298  875 SDAEPDAESDSAADAQPAT 893
Cdd:NF033609   804 SDSDSDSDSDSDSDSDSDS 822
PRK05807 PRK05807
RNA-binding protein S1;
951-1038 4.15e-06

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 47.43  E-value: 4.15e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  951 SLKEGDEVIGVVVGVMPFGVFVELAPDcSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKrRRVALS---AISPQ 1027
Cdd:PRK05807     2 TLKAGSILEGTVVNITNFGAFVEVEGK-TGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDN-GKISLSikqAMKQK 79

                           90
                   ....*....|....
gi 1722117298 1028 ---RVIELDQERQQ 1038
Cdd:PRK05807    80 ksvKPAEIDWQKEK 93
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-893 4.40e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 51.06  E-value: 4.40e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   731 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 809

                           90
                   ....*....|....*....
gi 1722117298  875 SDAEPDAESDSAADAQPAT 893
Cdd:NF033609   810 SDSDSDSDSDSDSDSDSDS 828
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 952-1022 5.25e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 49.80  E-value: 5.25e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1722117298  952 LKEGDEVIGVVVGVMPFGVFVELApDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK07400   194 LEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLS 263
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 957-1024 5.74e-06

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 48.28  E-value: 5.74e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  957 EVI-GVVVGVMPFGVFVELAP-DcsGLIHVSRISEGFV-----------EDLHEAVQVGDVITGWVTGIDEKRRRVALSA 1023
Cdd:PRK08563    83 EVVeGEVVEVVEFGAFVRIGPvD--GLLHISQIMDDYIsydpkngrligKESKRVLKVGDVVRARIVAVSLKERRPRGSK 160


                   .
gi 1722117298 1024 I 1024
Cdd:PRK08563   161 I 161
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-893 6.96e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 50.68  E-value: 6.96e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEAaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   751 DSDSDSDSDSDSDSDSDSDSDSDSDSDS-DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 829

                           90
                   ....*....|....*....
gi 1722117298  875 SDAEPDAESDSAADAQPAT 893
Cdd:NF033609   830 SDSDSDSDSDSDSDSDSDS 848
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
950-1033 9.77e-06

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 49.95  E-value: 9.77e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  950 KSLKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALSAISPQRV 1029
Cdd:PRK00087   298 KQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADRE 377


                   ....
gi 1722117298 1030 IELD 1033
Cdd:PRK00087   378 KAWK 381
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 791-893 1.04e-05

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 49.91  E-value: 1.04e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  791 AAKIESESDAAPEAEATGESEPTADADSPAEA-ADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADA 869
Cdd:NF033609   649 DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSdSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 728

                           90       100
                   ....*....|....*....|....
gi 1722117298  870 DATPESDAEPDAESDSAADAQPAT 893
Cdd:NF033609   729 DSDSDSDSDSDSDSDSDSDSDSDS 752
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 949-1022 1.59e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 48.89  E-value: 1.59e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1722117298  949 LKSLKEGDEVIGVVVGVMPFGVFVELApDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:PRK07899   203 LNQLQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLS 275
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 25-189 2.04e-05

Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss:Q45388. This protein defines a novel family of prokaryotic transcriptional accessory factors.


Pssm-ID: 462777  Cd Length: 183  Bit Score: 46.63  E-value: 2.04e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298   25 LLEQGYTPPYLARYRRDELGDIDEASLWHLSHAVQSDLELQRRREELVQSWKTSELTDPALGKAVEKAASKRLLDRL--- 101
Cdd:pfam09371   18 LLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKAAIEAADTLTELEDLylp 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  102 ---ARRVKS----ELGekVDPstrLAARILNprkgdGDDIASIAGK----VDGIEAdqVEAAVAGLDNALAKRLCGDPRV 170
Cdd:pfam09371   98 ykpKRRTKAtiarEKG--LEP---LADAILA-----QPDPEEEAAKyinpEKGVAD--VEEALAGARDIIAERISEDAEL 165

                          170
                   ....*....|....*....
gi 1722117298  171 INAAVRWLTKNSRIhISQV 189
Cdd:pfam09371  166 RKKLRELLWREGVI-VSKV 183
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 957-1024 2.10e-05

S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.


Pssm-ID: 239907 [Multi-domain]  Cd Length: 99  Bit Score: 44.59  E-value: 2.10e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  957 EVI-GVVVGVMPFGVFVELAPdCSGLIHVSRISEGFVEDLHEA-----------VQVGDVITGWVTGIDEKRRRVALSAI 1024
Cdd:cd04460      1 EVVeGEVVEVVDFGAFVRIGP-VDGLLHISQIMDDYISYDPKNkrligeetkrvLKVGDVVRARIVAVSLKERRPRESKI 79
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 960-1022 2.30e-05

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 43.62  E-value: 2.30e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1722117298  960 GVVVGVMPFGVFVELaPDC--SGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKrRRVALS 1022
Cdd:cd05686      9 GEVASVTEYGAFVKI-PGCrkQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLS 71
rpsA PRK13806
30S ribosomal protein S1; Provisional
 955-1038 3.68e-05

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 47.80  E-value: 3.68e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  955 GDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALSAISPQRVIELDQ 1034
Cdd:PRK13806   380 GTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPAGAAGSGADDD 459


                   ....
gi 1722117298 1035 ERQQ 1038
Cdd:PRK13806   460 DWKQ 463
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 742-903 6.57e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 47.29  E-value: 6.57e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  742 PAEPPGYTAPSfDDEPSEQPVEPVETPVADDSLKVETFETVPDEKTENFAAKIESESDAAPEAEATGESEPTADADSPAE 821
Cdd:PRK07764   615 PAAPAAPAAPA-APAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAP 693

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  822 AADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPESDAEPDAESDSAADAQPATPFRQALPE 901
Cdd:PRK07764   694 AGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAA 773


                   ..
gi 1722117298  902 PA 903
Cdd:PRK07764   774 PP 775
VacB COG0557
Exoribonuclease R [Transcription];
953-1028 7.59e-05

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 47.02  E-value: 7.59e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  953 KEGDEVIGVVVGVMPFGVFVELaPD--CSGLIHVSRISEG---FVEDLHEAV--------QVGDVITGWVTGIDEKRRRV 1019
Cdd:COG0557    621 RVGEEFEGVISGVTSFGLFVEL-DElgVEGLVHVSSLGDDyyeYDERRQALVgertgkryRLGDRVEVRVVRVDLDRRQI 699


                   ....*....
gi 1722117298 1020 ALSAISPQR 1028
Cdd:COG0557    700 DFELVEGGS 708
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 965-1038 7.76e-05

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 47.20  E-value: 7.76e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1722117298  965 VMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEK-RRRVALSAISPQRVIELDQERQQ 1038
Cdd:PLN00207   765 IAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKgQLRLSRRALLPEANSEKSSQKQQ 839
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 942-1016 1.13e-04

S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.


Pssm-ID: 239919 [Multi-domain]  Cd Length: 77  Bit Score: 41.82  E-value: 1.13e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1722117298  942 VLNTMPSLKSLKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSrisegfveDLHEAVQVGDVITGWVTGIDEKR 1016
Cdd:cd04473      4 VLDPACTMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRS--------NLLRDYEVGDEVIVQVTDIPENG 70
PRK13108 PRK13108
prolipoprotein diacylglyceryl transferase; Reviewed
 742-889 1.28e-04

prolipoprotein diacylglyceryl transferase; Reviewed


Pssm-ID: 237284 [Multi-domain]  Cd Length: 460  Bit Score: 46.13  E-value: 1.28e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  742 PAEPPGYTAPSFDDEPSEQPVEPVETPVADDSLKVETFETvPDEKTENFAAKIESESDAApEAEATGESEPTADADSPAE 821
Cdd:PRK13108   323 PNQPDDVAEAVKAEVAEVTDEVAAESVVQVADRDGESTPA-VEETSEADIEREQPGDLAG-QAPAAHQVDAEAASAAPEE 400

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1722117298  822 AADTPA-DPDAASESAPEASAdaeasdappPEASADAGDDATAETSADADATPESDAEPDAESDSAADA 889
Cdd:PRK13108   401 PAALASeAHDETEPEVPEKAA---------PIPDPAKPDELAVAGPGDDPAEPDGIRRQDDFSSRRRRW 460
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 648-690 1.64e-04

Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 40.93  E-value: 1.64e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1722117298  648 GIDANGAPVTWLSRLPGMNEAIAKAIdQRRREKL--FGSRTELTE 690
Cdd:pfam12836    3 GVDINTASAELLSRVPGLGPKLAKNI-VEYREENgpFRSREDLLK 46
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 955-1023 1.87e-04

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 45.50  E-value: 1.87e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  955 GDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRIS-EGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALSA 1023
Cdd:TIGR00717  360 GDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGV 429
PRK13108 PRK13108
prolipoprotein diacylglyceryl transferase; Reviewed
 780-903 2.22e-04

prolipoprotein diacylglyceryl transferase; Reviewed


Pssm-ID: 237284 [Multi-domain]  Cd Length: 460  Bit Score: 45.35  E-value: 2.22e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  780 ETVPDEKTENFAAKIESESDAAPEAEA--TGESEPTADADSPAEAADTPADPDA--ASESAPEASADAEASDAPPPEAS- 854
Cdd:PRK13108   289 EYVVDEALEREPAELAAAAVASAASAVgpVGPGEPNQPDDVAEAVKAEVAEVTDevAAESVVQVADRDGESTPAVEETSe 368

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1722117298  855 ADAGDDATAETSADADATPESDAEPDAESDSAADAQPATPFRQALPEPA 903
Cdd:PRK13108   369 ADIEREQPGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEPEVP 417
SepH NF040712
septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces ...
 770-896 3.42e-04

septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces venezuelae, and homologs were identified in Mycobacterium smegmatis. SepH contains a N-terminal DUF3071 domain and a conserved C-terminal region. It binds directly to cell division protein FtsZ to stimulate the assembly of FtsZ protofilaments.


Pssm-ID: 468676 [Multi-domain]  Cd Length: 346  Bit Score: 44.37  E-value: 3.42e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  770 ADDSLKVETFETVPDEKTENFAAKIESESDAAPEAEATGESEPTADADSPAEAA---------DTPADPDAASESAPEAS 840
Cdd:NF040712   190 PDFGRPLRPLATVPRLAREPADARPEEVEPAPAAEGAPATDSDPAEAGTPDDLAsarrrragvEQPEDEPVGPGAAPAAE 269

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1722117298  841 ADAEASDAPPPEASADAGDDATAETSADADATPESDAEPDAESDSAADAQPATPFR 896
Cdd:NF040712   270 PDEATRDAGEPPAPGAAETPEAAEPPAPAPAAPAAPAAPEAEEPARPEPPPAPKPK 325
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 952-1023 4.58e-04

S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 39.93  E-value: 4.58e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1722117298  952 LKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALSA 1023
Cdd:cd05706      1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSL 72
PRK04163 PRK04163
exosome complex protein Rrp4;
953-1017 5.43e-04

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 42.96  E-value: 5.43e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1722117298  953 KEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFV----EDLHEAVQVGDVITGWVTGIDEKRR 1017
Cdd:PRK04163    62 KVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVnvegTDLRKYLDIGDYIIAKVKDVDRTRD 130
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 800-903 5.82e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 44.21  E-value: 5.82e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  800 AAPEAEATGESEPTADA-DSPAEAADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPESDAE 878
Cdd:PRK07764   598 EGPPAPASSGPPEEAARpAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAA 677

                           90       100
                   ....*....|....*....|....*
gi 1722117298  879 PDAESDSAADAQPATPFRQALPEPA 903
Cdd:PRK07764   678 PAAPPPAPAPAAPAAPAGAAPAQPA 702
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
791-903 5.87e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 44.07  E-value: 5.87e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  791 AAKIESESDAAPEAEATGESEPTADADSPAEAADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADAD 870
Cdd:PRK07003   428 AAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAV 507

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1722117298  871 ATPESDAEPDAESDSAADAQPATpfRQALPEPA 903
Cdd:PRK07003   508 PDARAPAAASREDAPAAAAPPAP--EARPPTPA 538
HHH_9 pfam17674
HHH domain;
714-740 6.87e-04

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 39.44  E-value: 6.87e-04
                           10        20
                   ....*....|....*....|....*..
gi 1722117298  714 QPLDGTMIHPDDYGLAEKLAKALELEL 740
Cdd:pfam17674    1 NPLDNTAIHPESYPLAEKILKDLGLDL 27
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 955-1022 8.01e-04

S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 39.05  E-value: 8.01e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1722117298  955 GDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:cd05687      1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLS 68
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-891 9.83e-04

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 43.74  E-value: 9.83e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSpaeaaDTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE 874
Cdd:NF033609   783 DSDSDSDSDSDSDSDSDSDSDSDS-----DSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSE 857

                           90
                   ....*....|....*..
gi 1722117298  875 SDAEPDAESDSAADAQP 891
Cdd:NF033609   858 SDSNSDSESGSNNNVVP 874
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 800-894 1.10e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 43.44  E-value: 1.10e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  800 AAPEAEATGESEPTADADSPAEAADTPADPDAASESAPEASADAEASDAPPPEASADAGDD--ATAETSADADATPESDA 877
Cdd:PRK07764   404 AAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAqpAPAPAAAPEPTAAPAPA 483

                           90
                   ....*....|....*..
gi 1722117298  878 EPDAESDSAADAQPATP 894
Cdd:PRK07764   484 PPAAPAPAAAPAAPAAP 500
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 800-901 1.28e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 43.05  E-value: 1.28e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  800 AAPEAEATGESEPTADADSPAEAADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPESDAEP 879
Cdd:PRK07764   415 AAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAP 494

                           90       100
                   ....*....|....*....|....
gi 1722117298  880 DAESDSAA--DAQPATPFRQALPE 901
Cdd:PRK07764   495 AAPAAPAApaGADDAATLRERWPE 518
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
741-903 1.32e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 42.91  E-value: 1.32e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  741 PPAEPPGYTAPSFDDEPSEQPVePVETPVADDSLKVETFETVPDEKTENFAAKIESESDAAPEAEATGESEPTADADSPA 820
Cdd:PRK07003   422 RAEAPPAAPAPPATADRGDDAA-DGDAPVPAKANARASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPS 500

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  821 EAADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPE----------SDAEPDAESDSAADAQ 890
Cdd:PRK07003   501 AATPAAVPDARAPAAASREDAPAAAAPPAPEARPPTPAAAAPAARAGGAAAALDvlrnagmrvsSDRGARAAAAAKPAAA 580

                          170
                   ....*....|...
gi 1722117298  891 PATPFRQALPEPA 903
Cdd:PRK07003   581 PAAAPKPAAPRVA 593
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
729-889 1.64e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 42.91  E-value: 1.64e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  729 AEKLAKALELELPPAEPPGYTAPSFDDEPSEQPVEPVETPVADDSlkvetfeTVPDEKTENFAAKIESESDAAPEAEATG 808
Cdd:PRK07003   395 AVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATADRG-------DDAADGDAPVPAKANARASADSRCDERD 467

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  809 ESEPTADADSPAEAADTPadPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADATPESDAEPDAESDSAAD 888
Cdd:PRK07003   468 AQPPADSGSASAPASDAP--PDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPPTPAAAAPAAR 545


                   .
gi 1722117298  889 A 889
Cdd:PRK07003   546 A 546
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 948-1022 1.92e-03

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 41.95  E-value: 1.92e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1722117298  948 SLKSLKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEgfvEDLHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:COG0539     12 SLKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSD---EPGELEVKVGDEVEVYVEKVEDGEGEIVLS 83
PHA03247 PHA03247
large tegument protein UL36; Provisional
 741-900 2.37e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 42.62  E-value: 2.37e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  741 PPAEPP--GYTAPSFDDEPSEQPVEPVETPVADDS---LKVETFETVPDEKTENFAAKIESESDAAPEAEATGESEP-TA 814
Cdd:PHA03247  2685 RRAARPtvGSLTSLADPPPPPPTPEPAPHALVSATplpPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPtTA 2764

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  815 DADSPAEAADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSA-DADATPESDAEPDAESDSAADAQPAT 893
Cdd:PHA03247  2765 GPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAAlPPAASPAGPLPPPTSAQPTAPPPPPG 2844


                   ....*..
gi 1722117298  894 PFRQALP 900
Cdd:PHA03247  2845 PPPPSLP 2851
CobT2 COG4547
Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]; ...
 804-906 2.85e-03

Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]; Cobalamin biosynthesis cobaltochelatase CobT subunit is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


Pssm-ID: 443611 [Multi-domain]  Cd Length: 608  Bit Score: 41.70  E-value: 2.85e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  804 AEATGESEPTADADSPAEAADTPADPDAASESapeasaDAEASDAPPPEASADAGDDATAETSADADATPESDAEPDAES 883
Cdd:COG4547    208 AEELGEDEDEEDEDDEDDSGEQEEDEEDGEDE------DEESDEGAEAEDAEASGDDAEEGESEAAEAESDEMAEEAEGE 281

                           90       100
                   ....*....|....*....|...
gi 1722117298  884 DSAADAQPATPFRQALPEPAKVD 906
Cdd:COG4547    282 DSEEPGEPWRPNAPPPDDPADPD 304
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 806-906 3.05e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.90  E-value: 3.05e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  806 ATGESEPTADADSPAEAADTPADPDAASesAPEASADAEASDAPPPEASADAGDDATAETSADADATPESDAEPDAESDS 885
Cdd:PRK07764   388 AGGAGAPAAAAPSAAAAAPAAAPAPAAA--APAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQ 465

                           90       100
                   ....*....|....*....|.
gi 1722117298  886 AADAQPATPFRQALPEPAKVD 906
Cdd:PRK07764   466 PAPAPAAAPEPTAAPAPAPPA 486
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 795-894 3.16e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 41.82  E-value: 3.16e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  795 ESESDAAPEAEATGESEPTADADSPAEaADTPADPDAASESapeasadaeasdapppEASADAGDDATAETSADADATPE 874
Cdd:NF033609   793 DSDSDSDSDSDSDSDSDSDSDSDSDSD-SDSDSDSDSDSDS----------------DSDSDSDSDSDSDSDSDSDSDSD 855

                           90       100
                   ....*....|....*....|
gi 1722117298  875 SDAEPDAESDSAADAQPATP 894
Cdd:NF033609   856 SESDSNSDSESGSNNNVVPP 875
PRK13108 PRK13108
prolipoprotein diacylglyceryl transferase; Reviewed
 742-897 5.66e-03

prolipoprotein diacylglyceryl transferase; Reviewed


Pssm-ID: 237284 [Multi-domain]  Cd Length: 460  Bit Score: 40.73  E-value: 5.66e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  742 PAEPPGYTAPSFDDEPSEQPVEPVE--TPVADDSLKVETFETVPDEKTENFAAKIESESDaaPEAEATGESEPTADADSP 819
Cdd:PRK13108   295 ALEREPAELAAAAVASAASAVGPVGpgEPNQPDDVAEAVKAEVAEVTDEVAAESVVQVAD--RDGESTPAVEETSEADIE 372

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  820 AEAadtPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSADADAtPESDA----EPDAESDSAADAQPATPF 895
Cdd:PRK13108   373 REQ---PGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEPEVPEKAA-PIPDPakpdELAVAGPGDDPAEPDGIR 448


                   ..
gi 1722117298  896 RQ 897
Cdd:PRK13108   449 RQ 450
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 950-1039 6.83e-03

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 40.41  E-value: 6.83e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  950 KSLKEGDEVIGVVVGVMPFGVFVelapDCSGL---IHVSRISEGFVEDLheAVQVGDVITGWVTGIDEKRRRVALSaisp 1026
Cdd:COG0539     98 EAFENGEPVEGKVKGVVKGGLIV----DIGGVrafLPASQVDVRPVRDL--DEYVGKTLEFKIIKLDRKRNNVVVS---- 167

                           90
                   ....*....|...
gi 1722117298 1027 QRVIeLDQERQQQ 1039
Cdd:COG0539    168 RRAV-LEEEREEK 179
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 808-893 6.90e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 40.66  E-value: 6.90e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  808 GESEPT---ADADSPAEAADTPADPDAASESAPeasadaeasdapppEASADAGDDATAETSADADATPESDAEPDAESD 884
Cdd:NF033609   552 GEIEPIpedSDSDPGSDSGSDSSNSDSGSDSGS--------------DSTSDSGSDSASDSDSASDSDSASDSDSASDSD 617


                   ....*....
gi 1722117298  885 SAADAQPAT 893
Cdd:NF033609   618 SASDSDSAS 626
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 952-1022 6.92e-03

S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 36.61  E-value: 6.92e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1722117298  952 LKEGDEVIGVVVGVMPFGVFVELAPDCSGLIHVSRISEGFVED---LHEAVQVGDVITGWVTGIDEKRRRVALS 1022
Cdd:cd05705      1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDpslYNKYLPEGKLLTAKVLSVNSEKNLVELS 74
PRK12495 PRK12495
hypothetical protein; Provisional
 807-902 7.22e-03

hypothetical protein; Provisional


Pssm-ID: 183558 [Multi-domain]  Cd Length: 226  Bit Score: 39.47  E-value: 7.22e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  807 TGESEPTADADSPAEAADTPadpDAASESAPEASADAEASDAPPPEASADagDDATAETSADADATPESDAEPDAESDSA 886
Cdd:PRK12495    63 TCQQPVTEDGAAGDDAGDGA---EATAPSDAGSQASPDDDAQPAAEAEAA--DQSAPPEASSTSATDEAATDPPATAAAR 137

                           90
                   ....*....|....*.
gi 1722117298  887 ADAQPATPFRQALPEP 902
Cdd:PRK12495   138 DGPTPDPTAQPATPDE 153
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 790-903 8.87e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 40.35  E-value: 8.87e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722117298  790 FAAKIESESDAAPEAEATGESEPTA--DADSPAEAADTPADPDAASESAPEASADAEASDAPPPEASADAGDDATAETSA 867
Cdd:PRK07764   374 LLARLERLERRLGVAGGAGAPAAAApsAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGA 453

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1722117298  868 DADATPESDAEPDAESDSAADAQPATPFRQALPEPA 903
Cdd:PRK07764   454 PSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPA 489
 
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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