Conserved Domains in CDD Database Detected by RPS-BLAST and HHsearch
Conserved Domains in CDD Database Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
Original result of RPS-BLASTagainst CDD database part II
Identity Alignment graph Length
Definition
E-value
Target 74
50S ribosomal protein L31 [Candidatus Liberibacter asia
PRK00528 71
PRK00528, rpmE, 50S ribosomal protein L31; Reviewed
5e-27
TIGR00105 68
TIGR00105, L31, ribosomal protein L31
4e-23
COG0254 75
COG0254, RpmE, Ribosomal protein L31 [Translation, ribo
2e-14
PRK00019 72
PRK00019, rpmE, 50S ribosomal protein L31; Reviewed
2e-10
PRK01678 87
PRK01678, rpmE2, 50S ribosomal protein L31 type B; Revi
4e-09
PRK01397 78
PRK01397, PRK01397, 50S ribosomal protein L31; Provisio
1e-04
CHL00136 68
CHL00136, rpl31, ribosomal protein L31; Validated
9e-04
pfam01197 69
pfam01197, Ribosomal_L31, Ribosomal protein L31
3e-16
>gnl|CDD|179057 PRK00528, rpmE, 50S ribosomal protein L31; Reviewed
Back Show alignment and domain information
Score = 114 bits (288), Expect = 5e-27
Identities = 42/71 (59%), Positives = 55/71 (77%)
Query: 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ 60
MKK+IHP+ H I VVMTDGT+Y+TRSTW + G ++LDID +H AW GG QK+ D GG+
Sbjct: 1 MKKDIHPDYHPIKVVMTDGTEYETRSTWGKTGPELRLDIDSGNHPAWTGGTQKLLDTGGR 60
Query: 61 VSRFKKRFAGL 71
V++F K+F GL
Sbjct: 61 VAKFNKKFGGL 71
>gnl|CDD|129211 TIGR00105, L31, ribosomal protein L31
Back Show alignment and domain information
Score = 101 bits (254), Expect = 4e-23
Identities = 35/71 (49%), Positives = 45/71 (63%), Gaps = 3/71 (4%)
Query: 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ 60
MKK+IHP+ H ITV T G + TRSTW +E + LDI H + G+QKI D GG+
Sbjct: 1 MKKDIHPDYHEITVTCTCGNVFTTRSTWGKE--TLNLDICSKCHPFYT-GKQKIVDTGGR 57
Query: 61 VSRFKKRFAGL 71
V +F K+F GL
Sbjct: 58 VDKFNKKFGGL 68
This family consists exclusively of bacterial (and organellar) 50S ribosomal protein L31. In some species, such as Bacillus subtilis, this protein exists in two forms (RpmE and YtiA), one of which (RpmE) contains a pair of motifs, CXC and CXXC, for binding zinc. Length = 68
>gnl|CDD|30603 COG0254, RpmE, Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]
Back Show alignment and domain information
Score = 73.0 bits (179), Expect = 2e-14
Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 1 MKKNIHPETHLITVVMTD--GTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRG 58
MKK+IHPE + V + G ++ TRST + + LD+ H + G +QKI D
Sbjct: 1 MKKDIHPEYYRPVVFVCSSCGNEFTTRSTKGTD--EINLDVCSKCHPFYTG-KQKIVDTE 57
Query: 59 GQVSRFKKRFAGLS 72
G+V +F KRF G
Sbjct: 58 GRVEKFNKRFGGFK 71
>gnl|CDD|178797 PRK00019, rpmE, 50S ribosomal protein L31; Reviewed
Back Show alignment and domain information
Score = 59.6 bits (145), Expect = 2e-10
Identities = 28/69 (40%), Positives = 42/69 (60%), Gaps = 3/69 (4%)
Query: 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ 60
MKK+IHP+ +TV + G ++TRST ++ + +D+ H + G+QKI D GG+
Sbjct: 1 MKKDIHPKYEEVTVTCSCGNVFETRSTLGKD--EINVDVCSKCHPFYT-GKQKIVDTGGR 57
Query: 61 VSRFKKRFA 69
V RF KRF
Sbjct: 58 VERFNKRFG 66
>gnl|CDD|179318 PRK01678, rpmE2, 50S ribosomal protein L31 type B; Reviewed
Back Show alignment and domain information
Score = 55.3 bits (134), Expect = 4e-09
Identities = 29/83 (34%), Positives = 41/83 (49%), Gaps = 16/83 (19%)
Query: 1 MKKNIHPETHLITVV---MTDGTQYQTRSTWK-------EEG---AVMKLDIDPLSHFAW 47
MKK IHPE VV + G ++ T ST E+G ++K++I SH +
Sbjct: 1 MKKGIHPEYR--PVVFHDTSTGFKFLTGSTITTDETIEWEDGKTYPLVKVEISSASHPFY 58
Query: 48 IGGRQKITDRGGQVSRFKKRFAG 70
G +QK D G+V +F KRF
Sbjct: 59 TG-KQKFVDTEGRVEKFNKRFGR 80
>gnl|CDD|179294 PRK01397, PRK01397, 50S ribosomal protein L31; Provisional
Back Show alignment and domain information
Score = 40.3 bits (94), Expect = 1e-04
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ 60
MK IHPE ++ ++T ST +M D+D H AW + ++ +
Sbjct: 1 MKSGIHPEYKKF-LIKVGSDVFETMSTHPTGEILM--DVDFRKHPAWNKDSGNVVNQSNK 57
Query: 61 -VSRFKKRFAGLS 72
VS F KRF+GLS
Sbjct: 58 SVSDFNKRFSGLS 70
>gnl|CDD|177058 CHL00136, rpl31, ribosomal protein L31; Validated
Back Show alignment and domain information
Score = 37.3 bits (87), Expect = 9e-04
Identities = 26/70 (37%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ 60
KKNIHP+ T V DG T + K E + +DI +H + G QKI D G+
Sbjct: 2 PKKNIHPQWFPETKVYCDGQLVMTVGSTKPE---LNVDIWSGNHPFYT-GSQKIIDTEGR 57
Query: 61 VSRFKKRFAG 70
V RF K++
Sbjct: 58 VERFMKKYGL 67
>gnl|CDD|144697 pfam01197, Ribosomal_L31, Ribosomal protein L31
Back Show alignment and domain information
Score = 79.1 bits (196), Expect = 3e-16
Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 1 MKKNIHPETHLITVVMT-DGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGG 59
MKK IHPE + + G + TRST + V+K+D+ H + G +QK+ D G
Sbjct: 1 MKKGIHPEYREVVFTCSSCGNVFVTRSTKEYP--VIKIDVCSACHPFYTG-KQKLVDTAG 57
Query: 60 QVSRFKKRFAG 70
+V +F KRF
Sbjct: 58 RVEKFNKRFGK 68
Conserved Domains in CDD Database Detected by HHsearch
Original result of HHsearch against CDD database
Identity Alignment graph Length
Definition
Probability
Target
74
50S ribosomal protein L31 [Candidatus Liberibacter asia
PRK00528 71
rpmE 50S ribosomal protein L31; Reviewed
99.97
PRK01678 86
rpmE2 50S ribosomal protein L31 type B; Reviewed
99.97
PRK00019 71
rpmE 50S ribosomal protein L31; Reviewed
99.96
COG0254 75
RpmE Ribosomal protein L31 [Translation, ribosomal stru
99.95
pfam01197 69
Ribosomal_L31 Ribosomal protein L31.
99.95
TIGR00105 77
L31 ribosomal protein L31; InterPro: IPR002150 Ribosome
99.94
PRK01397 78
50S ribosomal protein L31; Provisional
99.93
CHL00136 72
rpl31 ribosomal protein L31; Validated
99.93
>PRK00528 rpmE 50S ribosomal protein L31; Reviewed
Back Show alignment and domain information
Probab=99.97 E-value=2.2e-31 Score=207.14 Aligned_cols=71 Identities=63% Similarity=1.091 Sum_probs=68.0
Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCC
Q ss_conf 98878898407999987999799887654768869998548778971168178972136489999776026
Q gi|254780194|r 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGL 71 (74)
Q Consensus 1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~ 71 (74)
T Consensus 1 MKk~IHP~y~~~~v~~~~G~~~~t~st~G~~~~~i~vdi~s~~HPfyTgG~q~~~dt~GRV~kF~kryg~l 71 (71)
T PRK00528 1 MKKDIHPDYHPIKVVMTDGTEYETRSTWGKEGPELRLDIDSGNHPAWTGGTQKILDTGGRVAKFKKKFGGL 71 (71)
T ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCCCCCEECCCEEEECCCCCHHHHHHHHCCC
T ss_conf 98987999887899994999999867678778859998679888768589248971665699998770699
>PRK01678 rpmE2 50S ribosomal protein L31 type B; Reviewed
Back Show alignment and domain information
Probab=99.97 E-value=1.3e-30 Score=202.70 Aligned_cols=73 Identities=33% Similarity=0.549 Sum_probs=68.9
Q ss_pred CCCCCCCCCEEEEEE-ECCCCEEEEEEEE---------CCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHC
Q ss_conf 988788984079999-8799979988765---------476886999854877897116817897213648999977602
Q gi|254780194|r 1 MKKNIHPETHLITVV-MTDGTQYQTRSTW---------KEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAG 70 (74)
Q Consensus 1 MKk~IHP~y~~v~v~-~t~g~~~~t~sT~---------g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~ 70 (74)
T Consensus 1 MKk~IHP~Y~~v~f~d~s~g~~f~~~ST~~~~~t~~~eG~~yP~~~vdi~S~~HP-FyTG~qk~vdt~GRVekF~kRy~~ 79 (86)
T PRK01678 1 MKKGIHPEYRPVVFHDTSTGFKFLTGSTITTDETIEWEGKTYPLVKVEVSSASHP-FYTGKQKFVDTEGRVEKFNKRFGR 79 (86)
T ss_pred CCCCCCCCCEEEEEEECCCCCEEEECCCCCCCCEEEECCEECCEEEEEECCCCCC-CEECCEEEEECCHHHHHHHHHHHH
T ss_conf 9898799980688898879999982754367840667786777698610688885-481876786143129999988731
Q ss_pred CCCC
Q ss_conf 6789
Q gi|254780194|r 71 LSIE 74 (74)
Q Consensus 71 ~~~k 74 (74)
T Consensus 80 ~~~~ 83 (86)
T PRK01678 80 FASK 83 (86)
T ss_pred HCCC
T ss_conf 0223
>PRK00019 rpmE 50S ribosomal protein L31; Reviewed
Back Show alignment and domain information
Probab=99.96 E-value=2.7e-29 Score=194.78 Aligned_cols=70 Identities=40% Similarity=0.656 Sum_probs=66.1
Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCCCCC
Q ss_conf 98878898407999987999799887654768869998548778971168178972136489999776026789
Q gi|254780194|r 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGLSIE 74 (74)
Q Consensus 1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~~~k 74 (74)
T Consensus 1 MKk~IHP~y~~v~~~cscg~~f~~~ST~~~~---~~vdi~s~~HP-FyTG~q~~~dt~GRVekF~kry~~~~~~ 70 (71)
T PRK00019 1 MKKDIHPKYEEVTVTCSCGNVFKTRSTKGKD---INIDVCSKCHP-FYTGKQKIVDTGGRVERFNKRFGKPGAK 70 (71)
T ss_pred CCCCCCCCCEEEEEEECCCCEEEECCCCCCC---EEEEECCCCCC-CEECCEEEEECCCCHHHHHHHHCCCCCC
T ss_conf 9887799988899998889989851324753---88887689876-1848777871467699999877023468
>COG0254 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]
Back Show alignment and domain information
Probab=99.95 E-value=7.1e-28 Score=186.41 Aligned_cols=70 Identities=40% Similarity=0.645 Sum_probs=65.3
Q ss_pred CCCCCCCCC-EEEEEEEC-CCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCCCC
Q ss_conf 988788984-07999987-99979988765476886999854877897116817897213648999977602678
Q gi|254780194|r 1 MKKNIHPET-HLITVVMT-DGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGLSI 73 (74)
Q Consensus 1 MKk~IHP~y-~~v~v~~t-~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~~~ 73 (74)
T Consensus 1 MKk~IHP~y~~~v~~~~~s~g~~f~~~ST~~~~--~i~vdV~s~~HP-FyTG~qk~~d~~GRv~kF~kRf~~~~~ 72 (75)
T COG0254 1 MKKDIHPEYYRPVVFVCSSCGNEFTTRSTKGTD--EINLDVCSKCHP-FYTGKQKIVDTEGRVEKFNKRFGGFKG 72 (75)
T ss_pred CCCCCCCCCCCEEEEEECCCCCEEEEEECCCCC--EEEEEECCCCCC-CCCCCEEEECCCCCHHHHHHHHCCCCC
T ss_conf 988769876324899967899789977516886--089986799877-693854576065539999877634344
>pfam01197 Ribosomal_L31 Ribosomal protein L31
Back Show alignment and domain information
Probab=99.95 E-value=1.2e-27 Score=185.18 Aligned_cols=67 Identities=40% Similarity=0.625 Sum_probs=63.3
Q ss_pred CCCCCCCCCEEEEEEEC-CCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHC
Q ss_conf 98878898407999987-99979988765476886999854877897116817897213648999977602
Q gi|254780194|r 1 MKKNIHPETHLITVVMT-DGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAG 70 (74)
Q Consensus 1 MKk~IHP~y~~v~v~~t-~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~ 70 (74)
T Consensus 1 MKk~IHP~y~~v~~~c~~cg~~f~t~ST~--~~~~i~vdi~s~cHP-fyTG~~~~~dt~GRVeKF~kkf~~ 68 (69)
T pfam01197 1 MKKGIHPEYREVVFTCSSCGNVFVTRSTK--EYPVIKIDVCSACHP-FYTGKQKLVDTAGRVEKFNKRFGK 68 (69)
T ss_pred CCCCCCCCCEEEEEEECCCCCEEEEEECC--CCCCEEEEECCCCCC-EECCCEEEECCCHHHHHHHHHHCC
T ss_conf 98877998735689999999799973703--586099986489888-481987885142359999888746
>TIGR00105 L31 ribosomal protein L31; InterPro: IPR002150 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms
Back Show alignment and domain information
Probab=99.94 E-value=5e-27 Score=181.42 Aligned_cols=67 Identities=37% Similarity=0.561 Sum_probs=63.2
Q ss_pred CCCCCCCCCEEEEEEEC-CCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHC
Q ss_conf 98878898407999987-99979988765476886999854877897116817897213648999977602
Q gi|254780194|r 1 MKKNIHPETHLITVVMT-DGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAG 70 (74)
Q Consensus 1 MKk~IHP~y~~v~v~~t-~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~ 70 (74)
T Consensus 2 MK~~IHP~y~~~~~~~~~C~~~~~~~s~~~k--~e~~~dics~CHP-FYtG~~~~~~t~GRVerf~~kf~~ 69 (77)
T TIGR00105 2 MKKGIHPEYQEIPAACVSCNNGFEIESTSTK--KEINIDICSKCHP-FYTGKQKIVDTGGRVERFNKKFNL 69 (77)
T ss_pred CCCCCCCCCCCEECEEEEECCCEEEEECCCC--CEEEEEECCCCCC-CEECCEEEEECCCCHHHHHHHCCC
T ss_conf 8887898953010106662597787552777--3146886489889-420440367426641311213288
The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
>PRK01397 50S ribosomal protein L31; Provisional
Back Show alignment and domain information
Probab=99.93 E-value=2.8e-26 Score=177.01 Aligned_cols=71 Identities=32% Similarity=0.519 Sum_probs=67.0
Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCH-HHHHHHHHHCCCCC
Q ss_conf 988788984079999879997998876547688699985487789711681789721364-89999776026789
Q gi|254780194|r 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ-VSRFKKRFAGLSIE 74 (74)
Q Consensus 1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~Gr-veKF~kkfg~~~~k 74 (74)
T Consensus 1 MKkdIHPdYh~I~V~~~-G~~f~trST~--~gd~l~LDIDp~~HPAWTGg~~~lld~ggrqVskFnKrf~gL~f~ 72 (78)
T PRK01397 1 MKSGIHPEYKKFLIKVG-SDVFETMSTH--PTGEILMDVDFRKHPAWNKDSGNVVNQSNKSVSDFNKRFSGLSFG 72 (78)
T ss_pred CCCCCCCCCEEEEEEEC-CCEEEEEECC--CCCEEEEECCCCCCCCEECCCCEEEECCCCCHHHHHHHCCCCCCC
T ss_conf 98776888748999968-9778876024--797689823898887446786267806896547754013566657
>CHL00136 rpl31 ribosomal protein L31; Validated
Back Show alignment and domain information
Probab=99.93 E-value=3.3e-26 Score=176.54 Aligned_cols=67 Identities=33% Similarity=0.356 Sum_probs=57.7
Q ss_pred CCCCCCCCCEE-EEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCCC
Q ss_conf 98878898407-9999879997998876547688699985487789711681789721364899997760267
Q gi|254780194|r 1 MKKNIHPETHL-ITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGLS 72 (74)
Q Consensus 1 MKk~IHP~y~~-v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~~ 72 (74)
T Consensus 2 ~Kk~IHP~y~~~~~v~c~g~~~~~~~st----~~~~~vdIcS~cHP-FyTG~Qr~vdt~GRVekF~kryg~~~ 69 (72)
T CHL00136 2 PKKNIHPTWYPDAKVYCDGQLVMTIGST----KPELHVDIWSGNHP-FYTGSQKIIDTEGRVERFMRKYGLNS 69 (72)
T ss_pred CCCCCCCCCEEEEEEECCCCCEEEECCC----CCCEEEEECCCCCC-CCCCCEEEEECCCCHHHHHHHHCCCC
T ss_conf 8887898763148999389858986655----77589888689988-58487678714756999977547876
Homologous Domains in SCOP and MMDB Database Detected by RPS-BLAST and HHsearch
Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
Identity Alignment graph Length
Definition
E-value
Target
74
50S ribosomal protein L31 [Candidatus Liberibacter asia
d1vs6z1 70
d.325.1.2 (Z:1-70) Ribosomal protein L31p {Escherichia
1e-18
d2j0141 50
d.325.1.2 (4:1-50) Ribosomal protein L31p {Thermus ther
8e-11
>d1vs6z1 d.325.1.2 (Z:1-70) Ribosomal protein L31p {Escherichia coli [TaxId: 562]} Length = 70
Back Hide information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L31p
domain: Ribosomal protein L31p
species: Escherichia coli [TaxId: 562]
Score = 85.2 bits (211), Expect = 1e-18
Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 4/72 (5%)
Query: 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ 60
MKK+IHP+ IT + G + RST + + LD+ H + G Q+ GG+
Sbjct: 1 MKKDIHPKYEEITASCSCGNVMKIRSTVGHD---LNLDVCSKCHPFFTGK-QRDVATGGR 56
Query: 61 VSRFKKRFAGLS 72
V RF KRF
Sbjct: 57 VDRFNKRFNIPG 68
>d2j0141 d.325.1.2 (4:1-50) Ribosomal protein L31p {Thermus thermophilus [TaxId: 274]} Length = 50
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L31p
domain: Ribosomal protein L31p
species: Thermus thermophilus [TaxId: 274]
Score = 59.3 bits (144), Expect = 8e-11
Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKI 54
MK+ IHP+ ++ G +T ST E + +++ H + G+Q+
Sbjct: 1 MKEGIHPKLVPARIICGCGNVIETYSTKPE----IYVEVCSKCHPFYT-GQQRF 49
Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
Identity Alignment graph Length
Definition
Probability
Target 74
50S ribosomal protein L31 [Candidatus Liberibacter asia
d1vs6z1 70
Ribosomal protein L31p {Escherichia coli [TaxId: 562]}
99.94
d2j0141 50
Ribosomal protein L31p {Thermus thermophilus [TaxId: 27
99.7
>d1vs6z1 d.325.1.2 (Z:1-70) Ribosomal protein L31p {Escherichia coli [TaxId: 562]}
Back Hide information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L31p
domain: Ribosomal protein L31p
species: Escherichia coli [TaxId: 562]
Probab=99.94 E-value=6.5e-30 Score=195.78 Aligned_cols=70 Identities=36% Similarity=0.529 Sum_probs=66.7
Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCCCCC
Q ss_conf 98878898407999987999799887654768869998548778971168178972136489999776026789
Q gi|254780194|r 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGLSIE 74 (74)
Q Consensus 1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~~~k 74 (74)
||+||||+|++|++.|+||++|.++||++.+ +.|||||+||| ||||+|+++|++|||||||+|||.+++|
T Consensus 1 MKk~IHP~y~~v~~~~s~g~~f~~~sT~~~e---~~vdi~s~~HP-fyTG~q~~~dt~GRVekF~krf~~~~~K 70 (70)
T d1vs6z1 1 MKKDIHPKYEEITASCSCGNVMKIRSTVGHD---LNLDVCSKCHP-FFTGKQRDVATGGRVDRFNKRFNIPGSK 70 (70)
T ss_dssp CCCTTSCCCCCCBCCCCSSCCCCCBCCCCCC---CCCBCCSSSCC-BCCCCCTTTTTHHHHSCSSTTTTTTSCC
T ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEECCC---EEEEECCCCCC-CCCCCEEEEECCCCHHHHHHHHCCCCCC
T ss_conf 9798799998699997899999973684773---88875788887-5929787861467499998766553579
>d2j0141 d.325.1.2 (4:1-50) Ribosomal protein L31p {Thermus thermophilus [TaxId: 274]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L31p
domain: Ribosomal protein L31p
species: Thermus thermophilus [TaxId: 274]
Probab=99.70 E-value=1.5e-20 Score=140.34 Aligned_cols=50 Identities=24% Similarity=0.341 Sum_probs=46.4
Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEE
Q ss_conf 9887889840799998799979988765476886999854877897116817897
Q gi|254780194|r 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKIT 55 (74)
Q Consensus 1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~ 55 (74)
|||||||+|++++|.|+||++|.++||. ++++|||||+||| ||||+|+++
T Consensus 1 MKk~IHP~y~~v~~~cscg~~f~~~ST~----~~~~vdIcs~cHP-FyTG~qk~v 50 (50)
T d2j0141 1 MKEGIHPKLVPARIICGCGNVIETYSTK----PEIYVEVCSKCHP-FYTGQQRFV 50 (50)
T ss_dssp CCGGGCCCCTTTTTCTTSCGGGSCSSSS----CCSSCCSCCCCCS-SSCCCSCC-
T ss_pred CCCCCCCCCEEEEEEECCCCEEEECCCC----CCEEEEECCCCCC-CCCCEEEEC
T ss_conf 9887799888899998999999943058----7688888999978-697809839
Homologous Domains in MMDB70 Database Detected by RPS-BLAST
Original result of RPS-BLAST against MMDB70 database
Identity Alignment graph Length
Definition
E-value
Target
74
50S ribosomal protein L31 [Candidatus Liberibacter
2j01_4_ 71
(4:) 50S ribosomal protein L31; ribosome, tRNA, pa
2e-19
3f1f_4_ 97
(4:) 50S ribosomal protein L31; RF2, ribosome, ter
2e-17
3bbo_1_ 144
(1:) Ribosomal protein L31; large ribosomal subuni
2e-16
1nkw_Y_1-56 56
(Y:1-56) 50S ribosomal protein L31; ribosome, larg
4e-14
1vs6_Z_1-28 28
(Z:1-28) 50S ribosomal protein L31; ribosome, kasu
9e-08
1vs6_Z_29-70 42
(Z:29-70) 50S ribosomal protein L31; ribosome, kas
2e-07
>2j01_4 (4:) 50S ribosomal protein L31; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus}Length = 71
Back Hide alignment and structure
Score = 88.6 bits (220), Expect = 2e-19
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ 60
MK+ IHP+ ++ G +T ST E + +++ H + G+Q+ D G+
Sbjct: 1 MKEGIHPKLVPARIICGCGNVIETYSTKPE----IYVEVCSKCHPFYT-GQQRFVDTEGR 55
Query: 61 VSRFKKRFAGLS 72
V RF++R+
Sbjct: 56 VERFQRRYGDSY 67
>3f1f_4 (4:) 50S ribosomal protein L31; RF2, ribosome, termination, tRNA; 3.00A {Thermus thermophilus} PDB: 3d5d_4 3d5b_4 3f1h_4Length = 97
Back Show alignment and structure
Score = 82.2 bits (203), Expect = 2e-17
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ 60
+K+ IHP+ ++ G +T ST E + +++ H + G+Q+ D G+
Sbjct: 27 VKEGIHPKLVPARIICGCGNVIETYSTKPE----IYVEVCSKCHPFYT-GQQRFVDTEGR 81
Query: 61 VSRFKKRFAGLS 72
V RF++R+
Sbjct: 82 VERFQRRYGDSY 93
>3bbo_1 (1:) Ribosomal protein L31; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Arabidopsis thaliana}Length = 144
Back Show alignment and structure
Score = 79.3 bits (195), Expect = 2e-16
Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 1 MKKNIHPETH-LITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGG 59
KK +HPE H V T T KE +D+ +H ++G R +
Sbjct: 49 RKKELHPEFHEDAKVYCNGELVMTTGGTKKE----YVVDVWSGNHPFYLGNRSALMVDAD 104
Query: 60 QVSRFKKRFAGLS 72
QV +F+KRFAGLS
Sbjct: 105 QVEKFRKRFAGLS 117
>1nkw_Y (Y:1-56) 50S ribosomal protein L31; ribosome, large subunit, X- RAY structure, peptidyl-transferase, peptide bond formation; 3.10A {Deinococcus radiodurans}Length = 56
Back Show alignment and structure
Score = 71.6 bits (176), Expect = 4e-14
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQ 60
M+K++HP+ ++ +T ST E + +D+ H W G ++ D G+
Sbjct: 1 MQKDLHPKAVPCKIIYQGQVVMETMSTRPE----IHVDVWSGVHPFWT-GEERFLDTEGR 55
Query: 61 V 61
V
Sbjct: 56 V 56
>1vs6_Z (Z:1-28) 50S ribosomal protein L31; ribosome, kasugamycin; 3.46A {Escherichia coli}Length = 28
Back Show alignment and structure
Score = 50.4 bits (121), Expect = 9e-08
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 1 MKKNIHPETHLITVVMTDGTQYQTRST 27
MKK+IHP+ IT + G + RST
Sbjct: 1 MKKDIHPKYEEITASCSCGNVMKIRST 27
>1vs6_Z (Z:29-70) 50S ribosomal protein L31; ribosome, kasugamycin; 3.46A {Escherichia coli}Length = 42
Back Show alignment and structure
Score = 48.8 bits (117), Expect = 2e-07
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 32 GAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGLS 72
G + LD+ H + G Q+ GG+V RF KRF
Sbjct: 1 GHDLNLDVCSKCHPFFTGK-QRDVATGGRVDRFNKRFNIPG 40
Homologous Domains in MMDB70 Database Detected by HHsearch
Original result of HHsearch against MMDB70 database
Identity Alignment graph Length
Definition
Probability
Target 74
50S ribosomal protein L31 [Candidatus Liberibacter asia
3f1f_4_ 97
50S ribosomal protein L31; RF2, ribosome, terminat
99.93
2j01_4_ 71
50S ribosomal protein L31; ribosome, tRNA, paromom
99.93
1nkw_Y_1-56 56
50S ribosomal protein L31; ribosome, large subunit
99.89
3bbo_1_ 144
Ribosomal protein L31; large ribosomal subunit, sp
99.86
1vs6_Z_29-70 42
50S ribosomal protein L31; ribosome, kasugamycin;
99.52
1vs6_Z_1-28 28
50S ribosomal protein L31; ribosome, kasugamycin;
98.77
3f1f_4_ 97
50S ribosomal protein L31; RF2, ribosome, terminat
96.82
>3f1f_4 (4:) 50S ribosomal protein L31; RF2, ribosome, termination, tRNA; 3.00A {Thermus thermophilus} PDB: 3d5d_4 3d5b_4 3f1h_4
Back Hide alignment and structure
Probab=99.93 E-value=1.2e-27 Score=184.71 Aligned_cols=69 Identities=25% Similarity=0.410 Sum_probs=64.3
Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCCCCC
Q ss_conf 98878898407999987999799887654768869998548778971168178972136489999776026789
Q gi|254780194|r 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGLSIE 74 (74)
Q Consensus 1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~~~k 74 (74)
||++|||+|+++++.|+||++|++.||. |++.|||||+||| ||||+|+++|++|||||||+||+.+..+
T Consensus 27 MKk~IHP~y~~~~v~c~cg~~~~~~sT~----~~i~vdVcs~cHP-FyTG~q~~~dt~GRVekF~krf~~~~~~ 95 (97)
T 3f1f_4 27 VKEGIHPKLVPARIICGCGNVIETYSTK----PEIYVEVCSKCHP-FYTGQQRFVDTEGRVERFQRRYGDSYRK 95 (97)
T ss_dssp ---------CCCEEEETTEEEEECCCSS----CCEEESSCTTC-------------------------------
T ss_pred CCCCCCCCCEEEEEEECCCCEEEEEECC----CCEEEEECCCCCC-CCCCCEEEEECCCCHHHHHHHHCCCCCC
T ss_conf 5667898878899997899999973525----6589887689877-4818787871567399999987232324
>2j01_4 (4:) 50S ribosomal protein L31; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus}
Back Show alignment and structure
Probab=99.93 E-value=7.5e-29 Score=191.82 Aligned_cols=69 Identities=26% Similarity=0.423 Sum_probs=64.9
Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCCCCC
Q ss_conf 98878898407999987999799887654768869998548778971168178972136489999776026789
Q gi|254780194|r 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGLSIE 74 (74)
Q Consensus 1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~~~k 74 (74)
||+||||+|++++|.|+||++|+++||. |+|.|||||+||| ||||+|+++|++|||||||+||+.+..+
T Consensus 1 MKk~IHP~y~~v~~~ct~g~~f~~~ST~----~~i~vdv~s~~HP-fyTG~q~~~~~~GRv~kF~krf~~~~~~ 69 (71)
T 2j01_4 1 MKEGIHPKLVPARIICGCGNVIETYSTK----PEIYVEVCSKCHP-FYTGQQRFVDTEGRVERFQRRYGDSYRK 69 (71)
T ss_dssp CCGGGCCCCTTTTTCTTSCGGGSCSSSS----CCSSCCSCCCCCS-SSCCCSCC--------------------
T ss_pred CCCCCCCCCEEEEEEECCCCEEEECCCC----CEEEEEECCCCCC-CCCCCEEEEECCCCHHHHHHHHCCCCCC
T ss_conf 9887799878899998999889953026----1299987689877-4828788882467599999877253425
>1nkw_Y (Y:1-56) 50S ribosomal protein L31; ribosome, large subunit, X- RAY structure, peptidyl-transferase, peptide bond formation; 3.10A {Deinococcus radiodurans}
Back Show alignment and structure
Probab=99.89 E-value=2.1e-23 Score=159.61 Aligned_cols=56 Identities=23% Similarity=0.378 Sum_probs=53.8
Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEECCCHH
Q ss_conf 9887889840799998799979988765476886999854877897116817897213648
Q gi|254780194|r 1 MKKNIHPETHLITVVMTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDRGGQV 61 (74)
Q Consensus 1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt~Grv 61 (74)
|||+|||+|+++.|.|+||++|.++||. ++++|||||+||| ||||+|+++|++|||
T Consensus 1 MKk~IHP~y~~v~v~c~cg~~~~~~ST~----~~~~vdvcs~cHP-FyTG~q~~vdt~GRV 56 (56)
T 1nkw_Y 1 MQKDLHPKAVPCKIIYQGQVVMETMSTR----PEIHVDVWSGVHP-FWTGEERFLDTEGRV 56 (56)
T ss_pred CCCCCCCCCEEEEEEECCCCEEEECCCC----CCEEEEECCCCCC-CEECCEEEEECCCCH
T ss_conf 9887799988899998999899966345----4589988689877-282888887247549
>3bbo_1 (1:) Ribosomal protein L31; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Arabidopsis thaliana}
Back Show alignment and structure
Probab=99.86 E-value=1.7e-25 Score=171.97 Aligned_cols=68 Identities=32% Similarity=0.334 Sum_probs=60.8
Q ss_pred CCCCCCCCCEEEEEE-ECCCCEEEEEEEECCCCCEEEEEECCCCCCCEECCCEEEEEC-CCHHHHHHHHHHCCCC
Q ss_conf 988788984079999-879997998876547688699985487789711681789721-3648999977602678
Q gi|254780194|r 1 MKKNIHPETHLITVV-MTDGTQYQTRSTWKEEGAVMKLDIDPLSHFAWIGGRQKITDR-GGQVSRFKKRFAGLSI 73 (74)
Q Consensus 1 MKk~IHP~y~~v~v~-~t~g~~~~t~sT~g~~~~~~~vdi~s~~HP~fytgkq~~~dt-~GrveKF~kkfg~~~~ 73 (74)
||++|||+|++++++ |+||++|.++||. |+|+|||||.||| ||||+|+.+++ +||||||++|||++..
T Consensus 49 mKk~IHP~y~~~~~v~~s~g~~f~~~ST~----~~i~idv~s~~HP-fytG~~~~~~~~aGRv~kF~kRf~~~~~ 118 (144)
T 3bbo_1 49 RKKELHPEFHEDAKVYCNGELVMTTGGTK----KEYVVDVWSGNHP-FYLGNRSALMVDADQVEKFRKRFAGLSE 118 (144)
T ss_dssp -CTTTCCCCCHHHHHCSSSCTTTSCSSCS----CSSSCCSSCCCCC-SSSSSSSCCCCCCCCCCCSSCCCCCCSS
T ss_pred CCCCCCCCCCCCEEEECCCCCEEEEEECC----CCEEEEECCCCCC-EEECCEEEEECCCCHHHHHHHHHCCCCH
T ss_conf 45777989825539987999789972457----7368877389875-0767704885355339999988615001
>1vs6_Z (Z:29-70) 50S ribosomal protein L31; ribosome, kasugamycin; 3.46A {Escherichia coli}
Back Show alignment and structure
Probab=99.52 E-value=1.7e-16 Score=118.82 Aligned_cols=41 Identities=32% Similarity=0.502 Sum_probs=38.4
Q ss_pred CEEEEEECCCCCCCEECCCEEEEECCCHHHHHHHHHHCCCCC
Q ss_conf 869998548778971168178972136489999776026789
Q gi|254780194|r 33 AVMKLDIDPLSHFAWIGGRQKITDRGGQVSRFKKRFAGLSIE 74 (74)
Q Consensus 33 ~~~~vdi~s~~HP~fytgkq~~~dt~GrveKF~kkfg~~~~k 74 (74)
.+|.|||||+||| ||||+|+++|++||||||++||+.++.|
T Consensus 2 ~~~~vdv~s~~HP-fyTG~q~~~d~~GrV~kF~kky~~~~~k 42 (42)
T 1vs6_Z 2 HDLNLDVCSKCHP-FFTGKQRDVATGGRVDRFNKRFNIPGSK 42 (42)
T ss_dssp CCCCCBCCSSSCC-BCCCCCTTTTTHHHHSCSSTTTTTTSCC
T ss_pred CCEEEEECCCCCC-CCCCCEEEEECCCCHHHHHHHHCCCCCC
T ss_conf 7289987799887-4918787871467599998766553579
>1vs6_Z (Z:1-28) 50S ribosomal protein L31; ribosome, kasugamycin; 3.46A {Escherichia coli}
Back Show alignment and structure
Probab=98.77 E-value=4.9e-10 Score=80.54 Aligned_cols=28 Identities=43% Similarity=0.519 Sum_probs=27.1
Q ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEE
Q ss_conf 9887889840799998799979988765
Q gi|254780194|r 1 MKKNIHPETHLITVVMTDGTQYQTRSTW 28 (74)
Q Consensus 1 MKk~IHP~y~~v~v~~t~g~~~~t~sT~ 28 (74)
||+||||+|+++.|.|+||++|+|+||+
T Consensus 1 MK~~IHP~Y~~~~v~CsCGn~f~TrST~ 28 (28)
T 1vs6_Z 1 MKKDIHPKYEEITASCSCGNVMKIRSTV 28 (28)
T ss_dssp CCCTTSCCCCCCBCCCCSSCCCCCBCCC
T ss_pred CCCCCCCCCEEEEEEECCCCEEEEEEEE
T ss_conf 9798799998799997899999981695
>3f1f_4 (4:) 50S ribosomal protein L31; RF2, ribosome, termination, tRNA; 3.00A {Thermus thermophilus} PDB: 3d5d_4 3d5b_4 3f1h_4
Back Show alignment and structure
Probab=96.82 E-value=0.00022 Score=47.14 Aligned_cols=27 Identities=15% Similarity=0.147 Sum_probs=22.6
Q ss_pred CCCCCCCCCEEEEEEE-CCCCEEEEEEE
Q ss_conf 9887889840799998-79997998876
Q gi|254780194|r 1 MKKNIHPETHLITVVM-TDGTQYQTRST 27 (74)
Q Consensus 1 MKk~IHP~y~~v~v~~-t~g~~~~t~sT 27 (74)
||+||||+|++|++.. +++..|.+...
T Consensus 1 mk~~ihP~y~~v~f~d~~~~~~~~~~MK 28 (97)
T 3f1f_4 1 MPLGVHPLYTKRWLAHGQDRAKKEANVK 28 (97)
T ss_dssp ----------------------------
T ss_pred CCCCCCCCHHHHHHHCCCCCCCCCCCCC
T ss_conf 9877686131556523754442345656