254780584

254780584

50S ribosomal protein L28

GeneID in NCBI database:8209581Locus tag:CLIBASIA_02355
Protein GI in NCBI database:254780584Protein Accession:YP_003064997.1
Gene range:-(698718, 699011)Protein Length:97aa
Gene description:50S ribosomal protein L28
COG prediction:[J] Ribosomal protein L28
KEGG prediction:rpmB; 50S ribosomal protein L28; K02902 large subunit ribosomal protein L28
SEED prediction:hypothetical protein
Pathway involved in KEGG:Ribosome [PATH:las03010]
Subsystem involved in SEED:- none -
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------
MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQGGLDRFLSNSKKENLSARMRTLRSQILKKMSEKSS
cccEEEccccccccccccHHHHHHccccccccEEEEEEEEcccccEEEEEEEHHHHHHHHHcccHHHHHHHHcHHHHcHHHHHHHHHHHHHHHHHcc
cccEEEEccccccccccccHHHHHHHHcccccccccEEEEHHcccEEEEEEEHHHHHEHHccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHcc
msrvceltkktvmsgnkvshannktrrrflPNLCRITLISDIMEQKYQLRISKCALRsverqggldrflsnsKKENLSARMRTLRSQILKKMSEKSS
msrvceltkktvmsgnkvshannktrrrflpNLCRITLISDIMEQKYQLRISKCALRSverqggldrflsnskkenlsarmrtlrsqilkkmsekss
MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQGGLDRFLSNSKKENLSARMRTLRSQILKKMSEKSS
MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQGGLDRFLSNSKKENLSARMRTLRSQILKKM*****
MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQGGLDRFLSNSKKENLSARMRTLRSQI*********
*SRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQGGLDRFLSNSKKENLSARMRTLRSQILKKMS****
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MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQGGLDRFLSNSKKENLSARMRTLRSQILKKMSEKSS
MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQGGLDRFLSNSKKENLSARMRTLRSQILKKMSEKSS
MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQGGLDRFLSNSKKENLSARMRTLRSQILKKMSEKSS

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target97 50S ribosomal protein L28 [Candidatus Liberibacter asia
315121776103 50S ribosomal protein L28 [Candidatus Liberibacter sola 1 1e-38
8635939998 50S ribosomal protein L28 [Rhizobium etli CFN 42] Lengt 1 3e-29
114706269100 50S ribosomal protein L28 [Fulvimarina pelagi HTCC2506] 1 3e-29
20955116299 50S ribosomal protein L28 [Rhizobium leguminosarum bv. 1 4e-29
19089365499 50S ribosomal protein L28 [Rhizobium etli CIAT 652] Len 1 4e-29
21868299598 50S ribosomal protein L28 [Rhizobium etli CIAT 894] Len 1 5e-29
9042022398 50S ribosomal protein L28 [Aurantimonas manganoxydans S 1 1e-28
12160243298 50S ribosomal protein L28 [Bartonella bacilliformis KC5 1 1e-28
240851331105 50S ribosomal protein L28 [Bartonella grahamii as4aup] 1 1e-28
4947624697 50S ribosomal protein L28 [Bartonella henselae str. Hou 1 2e-28
>gi|315121776|ref|YP_004062265.1| 50S ribosomal protein L28 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 103 Back     alignment and organism information
 Score =  162 bits (411), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 82/97 (84%), Positives = 90/97 (92%)

Query: 1  MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVE 60
          MSRVCELT+KTVMSGNKVS +NNKT+RRFLPNLCRITLISDIM Q+YQLRISK ALRSVE
Sbjct: 1  MSRVCELTRKTVMSGNKVSRSNNKTKRRFLPNLCRITLISDIMGQQYQLRISKHALRSVE 60

Query: 61 RQGGLDRFLSNSKKENLSARMRTLRSQILKKMSEKSS 97
          RQGGLD+FL +SKKENLS R R LRSQI+KK+SEKSS
Sbjct: 61 RQGGLDQFLLHSKKENLSDRTRLLRSQIIKKISEKSS 97


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|86359399|ref|YP_471291.1| 50S ribosomal protein L28 [Rhizobium etli CFN 42] Length = 98 Back     alignment and organism information
>gi|114706269|ref|ZP_01439171.1| 50S ribosomal protein L28 [Fulvimarina pelagi HTCC2506] Length = 100 Back     alignment and organism information
>gi|209551162|ref|YP_002283079.1| 50S ribosomal protein L28 [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 99 Back     alignment and organism information
>gi|190893654|ref|YP_001980196.1| 50S ribosomal protein L28 [Rhizobium etli CIAT 652] Length = 99 Back     alignment and organism information
>gi|218682995|ref|ZP_03530596.1| 50S ribosomal protein L28 [Rhizobium etli CIAT 894] Length = 98 Back     alignment and organism information
>gi|90420223|ref|ZP_01228131.1| 50S ribosomal protein L28 [Aurantimonas manganoxydans SI85-9A1] Length = 98 Back     alignment and organism information
>gi|121602432|ref|YP_988415.1| 50S ribosomal protein L28 [Bartonella bacilliformis KC583] Length = 98 Back     alignment and organism information
>gi|240851331|ref|YP_002972734.1| 50S ribosomal protein L28 [Bartonella grahamii as4aup] Length = 105 Back     alignment and organism information
>gi|49476246|ref|YP_034287.1| 50S ribosomal protein L28 [Bartonella henselae str. Houston-1] Length = 97 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target97 50S ribosomal protein L28 [Candidatus Liberibacter asia
PRK0035976 PRK00359, rpmB, 50S ribosomal protein L28; Reviewed 2e-17
pfam0083061 pfam00830, Ribosomal_L28, Ribosomal L28 family 5e-14
TIGR0000956 TIGR00009, L28, ribosomal protein L28 6e-11
KOG3278215 KOG3278, KOG3278, KOG3278, Mitochondrial/chloroplast ri 7e-07
COG022777 COG0227, RpmB, Ribosomal protein L28 [Translation, ribo 5e-14
>gnl|CDD|178987 PRK00359, rpmB, 50S ribosomal protein L28; Reviewed Back     alignment and domain information
>gnl|CDD|144429 pfam00830, Ribosomal_L28, Ribosomal L28 family Back     alignment and domain information
>gnl|CDD|129121 TIGR00009, L28, ribosomal protein L28 Back     alignment and domain information
>gnl|CDD|38488 KOG3278, KOG3278, KOG3278, Mitochondrial/chloroplast ribosomal protein L28 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|30576 COG0227, RpmB, Ribosomal protein L28 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 97 50S ribosomal protein L28 [Candidatus Liberibacter asia
PRK0035978 rpmB 50S ribosomal protein L28; Reviewed 99.95
CHL0011270 rpl28 ribosomal protein L28; Provisional 99.94
COG022777 RpmB Ribosomal protein L28 [Translation, ribosomal stru 99.94
TIGR0000970 L28 ribosomal protein L28; InterPro: IPR001383 Ribosome 99.9
pfam0083061 Ribosomal_L28 Ribosomal L28 family. The ribosomal 28 fa 99.89
KOG3278215 consensus 99.84
KOG3279 283 consensus 99.25
>PRK00359 rpmB 50S ribosomal protein L28; Reviewed Back     alignment and domain information
>CHL00112 rpl28 ribosomal protein L28; Provisional Back     alignment and domain information
>COG0227 RpmB Ribosomal protein L28 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00009 L28 ribosomal protein L28; InterPro: IPR001383 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>pfam00830 Ribosomal_L28 Ribosomal L28 family Back     alignment and domain information
>KOG3278 consensus Back     alignment and domain information
>KOG3279 consensus Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target97 50S ribosomal protein L28 [Candidatus Liberibacter asia
2qov_Z78 Crystal Structure Of The Bacterial Ribosome From Es 7e-17
2i2t_X77 Crystal Structure Of Ribosome With Messenger Rna An 7e-16
3bbo_Y151 Homology Model For The Spinach Chloroplast 50s Subu 2e-12
2jz6_A77 Solution Structure Of 50s Ribosomal Protein L28 Fro 3e-10
gi|157836074|pdb|2QOV|Z Chain Z, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Spectinomycin. This File Contains The 50s Subunit Of The First 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes. Length = 78 Back     alignment and structure
 Score = 90.5 bits (224), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 28/75 (37%), Positives = 45/75 (60%), Gaps = 1/75 (1%)

Query: 1  MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVE 60
          MSRVC++T K  ++GN  SHA N T+RRFLPNL       +  ++   LR+S   +R ++
Sbjct: 1  MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVID 60

Query: 61 RQGGLDRFLSNSKKE 75
          ++G +D  L+  +  
Sbjct: 61 KKG-IDTVLAELRAR 74


>gi|118138114|pdb|2I2T|X Chain X, Crystal Structure Of Ribosome With Messenger Rna And The Anticodon Stem-Loop Of P-Site Trna. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. Length = 77 Back     alignment and structure
gi|189096147|pdb|3BBO|Y Chain Y, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 151 Back     alignment and structure
>gi|166235356|pdb|2JZ6|A Chain A, Solution Structure Of 50s Ribosomal Protein L28 From Thermotoga Maritima. Northeast Structural Genomics Consortium Target Vr97 Length = 77 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target97 50S ribosomal protein L28 [Candidatus Liberibacter asia
3bbo_Y151 Ribosomal protein L28; large ribosomal subunit, spinach 9e-17
3ofq_X77 50S ribosomal protein L28; protein biosynthesis, riboso 7e-16
3i1n_X78 50S ribosomal protein L28; ribosome structure, protein- 8e-16
2jz6_A77 50S ribosomal protein L28; structure, NESG, ribonucleop 8e-14
2jl6_189 50S ribosomal protein L28, 50S ribosomal protein L25; m 2e-10
2j01_198 50S ribosomal protein L28; ribosome, tRNA, paromomycin, 6e-10
2zjr_U81 50S ribosomal protein L28; ribosome, large ribosomal su 4e-09
>3bbo_Y Ribosomal protein L28; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Nicotiana tabacum} Length = 151 Back     alignment and structure
 Score = 80.3 bits (198), Expect = 9e-17
 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 2/80 (2%)

Query: 1   MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVE 60
             R+C  T K     NKVSH+N+KT++    NL    +  +  ++  +LR+S  A++++E
Sbjct: 74  ARRICPFTGKKSNRANKVSHSNHKTKKLQFVNLQYKRIWWEAGKRYVKLRLSTKAIKTIE 133

Query: 61  RQGGLDRFLSNSKKENLSAR 80
           +  GLD         +LS +
Sbjct: 134 K-NGLDAVA-KKAGIDLSKK 151


>3ofq_X 50S ribosomal protein L28; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 2i2v_X 2wwq_0* 3fik_X 2i2t_X 3ofr_X* 3i1n_X 1vt2_X* 2qao_Z* 2qba_Z* 2qbc_Z* 2qbe_Z 2qbg_Z 2qbi_Z* 2qbk_Z* 2qov_Z 2qox_Z 2qoz_Z* 2qp1_Z* 2z4l_Z* 2z4n_Z* ... Length = 77 Back     alignment and structure
>3i1n_X 50S ribosomal protein L28; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 2qao_Z* 2qba_Z* 2qbc_Z* 2qbe_Z 2qbg_Z 2qbi_Z* 2qbk_Z* 2qov_Z 2qox_Z 2qoz_Z* 2qp1_Z* 2z4l_Z* 2z4n_Z* 3df2_Z 3df4_Z 2qam_Z 3i1p_X 3i1r_X 3i1t_X 3i20_X ... Length = 78 Back     alignment and structure
>2jz6_A 50S ribosomal protein L28; structure, NESG, ribonucleoprotein, structural genomics, PSI-2, protein structure initiative; NMR {Thermotoga maritima MSB8} SCOP: d.325.1.1 Length = 77 Back     alignment and structure
>2j01_1 50S ribosomal protein L28; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: d.325.1.1 PDB: 2j03_1 2v47_1 2v49_1 2wdi_1 2wdj_1 2wdl_1 2wdn_1 2wh2_1 2wh4_1 3hux_1 3huz_1 3f1f_1 1vsp_V 1vsa_V 3d5d_1 3d5b_1 3f1h_1 3fin_1 Length = 98 Back     alignment and structure
>2zjr_U 50S ribosomal protein L28; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.325.1.1 PDB: 2zjp_U 2zjq_U 3cf5_U* 3dll_U* Length = 81 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target97 50S ribosomal protein L28 [Candidatus Liberibacter asia
3ofq_X77 50S ribosomal protein L28; protein biosynthesis, riboso 99.94
3bbo_Y151 Ribosomal protein L28; large ribosomal subunit, spinach 99.94
2jz6_A77 50S ribosomal protein L28; structure, NESG, ribonucleop 99.91
2j01_198 50S ribosomal protein L28; ribosome, tRNA, paromomycin, 99.87
2zjr_U81 50S ribosomal protein L28; ribosome, large ribosomal su 99.83
2jl6_189 50S ribosomal protein L28, 50S ribosomal protein L25; m 99.82
>3ofq_X 50S ribosomal protein L28; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 2i2v_X 2wwq_0* 3fik_X 2i2t_X 3ofr_X* 3i1n_X 1vt2_X* 2qao_Z* 2qba_Z* 2qbc_Z* 2qbe_Z 2qbg_Z 2qbi_Z* 2qbk_Z* 2qov_Z 2qox_Z 2qoz_Z* 2qp1_Z* 2z4l_Z* 2z4n_Z* ... Back     alignment and structure
Probab=99.94  E-value=1.1e-28  Score=191.19  Aligned_cols=73  Identities=37%  Similarity=0.596  Sum_probs=69.9

Q ss_pred             CCCCCCCCCCCCCCCCCCHHHCCCCCEECCCEEEEEEEECCCCCEEEEEEEHHHHHHHHHCCCHHHHHHHCCHH
Q ss_conf             85410117855367722332302374255524899998557786899999724530236418877999729844
Q gi|254780584|r    2 SRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQGGLDRFLSNSKKE   75 (97)
Q Consensus         2 sr~C~itGk~~~~Gn~vshs~~kTkR~~~PNlq~~~~~s~~l~~~v~l~vst~~lrtI~K~GGlD~yLl~~~~~   75 (97)
                      ||+||||||+|++||+||||+++|+|+|.||||++++|+|+++++|+|+|||+|||||+| +|||+||++++++
T Consensus         1 Sr~C~itGK~~~~Gn~vShs~~kTkR~~~pNlq~kr~~~~~~~~~v~lkvst~~LRtI~K-~Gld~~l~~~~~~   73 (77)
T 3ofq_X            1 SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDK-KGIDTVLAELRAR   73 (77)
T ss_dssp             CCCCSSSCCCCCCCBCCCSTTCCCBCCCCCCCCCEEEECSSSCSEEEECCCTTTTTHHHH-TCHHHHHHHHHTT
T ss_pred             CCCCCCCCCCCCCCCEECCCCCCCCCEECCCEEEEEEEECCCCEEEEEEEEHHHEEEEHH-CCHHHHHHHHHHC
T ss_conf             988700897445586101025644655526538999998679979999999142316203-4999999998870



>3bbo_Y Ribosomal protein L28; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Nicotiana tabacum} Back     alignment and structure
>2jz6_A 50S ribosomal protein L28; structure, NESG, ribonucleoprotein, structural genomics, PSI-2, protein structure initiative; NMR {Thermotoga maritima MSB8} SCOP: d.325.1.1 Back     alignment and structure
>2j01_1 50S ribosomal protein L28; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: d.325.1.1 PDB: 2j03_1 2v47_1 2v49_1 2wdi_1 2wdj_1 2wdl_1 2wdn_1 2wh2_1 2wh4_1 2wrj_1 2wrl_1 2wro_1 2wrr_1 2x9s_1 2x9u_1 3hux_1 3huz_1 3i8f_Z 3i8i_Z 3i9c_Z ... Back     alignment and structure
>2zjr_U 50S ribosomal protein L28; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.325.1.1 PDB: 2zjp_U 2zjq_U 3cf5_U* 3dll_U* Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 97 50S ribosomal protein L28 [Candidatus Liberibacter asia
d2qamz177 d.325.1.1 (Z:2-78) Ribosomal protein L28 (L28p) {Escher 5e-16
d2jz6a170 d.325.1.1 (A:6-75) Ribosomal protein L28 (L28p) {Thermo 7e-14
d2zjru172 d.325.1.1 (U:8-79) Ribosomal protein L28 (L28p) {Deinoc 1e-10
d2j011189 d.325.1.1 (1:8-96) Ribosomal protein L28 (L28p) {Thermu 3e-09
>d2qamz1 d.325.1.1 (Z:2-78) Ribosomal protein L28 (L28p) {Escherichia coli [TaxId: 562]} Length = 77 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L28
domain: Ribosomal protein L28 (L28p)
species: Escherichia coli [TaxId: 562]
 Score = 76.6 bits (189), Expect = 5e-16
 Identities = 27/75 (36%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 2  SRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVER 61
          SRVC++T K  ++GN  SHA N T+RRFLPNL       +  ++   LR+S   +R +++
Sbjct: 1  SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDK 60

Query: 62 QGGLDRFLSNSKKEN 76
            G+D  L+  +   
Sbjct: 61 -KGIDTVLAELRARG 74


>d2jz6a1 d.325.1.1 (A:6-75) Ribosomal protein L28 (L28p) {Thermotoga maritima [TaxId: 2336]} Length = 70 Back     information, alignment and structure
>d2zjru1 d.325.1.1 (U:8-79) Ribosomal protein L28 (L28p) {Deinococcus radiodurans [TaxId: 1299]} Length = 72 Back     information, alignment and structure
>d2j0111 d.325.1.1 (1:8-96) Ribosomal protein L28 (L28p) {Thermus thermophilus [TaxId: 274]} Length = 89 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target97 50S ribosomal protein L28 [Candidatus Liberibacter asia
d2qamz177 Ribosomal protein L28 (L28p) {Escherichia coli [TaxId: 99.95
d2jz6a170 Ribosomal protein L28 (L28p) {Thermotoga maritima [TaxI 99.91
d2j011189 Ribosomal protein L28 (L28p) {Thermus thermophilus [Tax 99.78
d2zjru172 Ribosomal protein L28 (L28p) {Deinococcus radiodurans [ 99.76
>d2qamz1 d.325.1.1 (Z:2-78) Ribosomal protein L28 (L28p) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L28
domain: Ribosomal protein L28 (L28p)
species: Escherichia coli [TaxId: 562]
Probab=99.95  E-value=2.7e-29  Score=193.33  Aligned_cols=74  Identities=36%  Similarity=0.590  Sum_probs=71.4

Q ss_pred             CCCCCCCCCCCCCCCCCCHHHCCCCCEECCCEEEEEEEECCCCCEEEEEEEHHHHHHHHHCCCHHHHHHHCCHHH
Q ss_conf             854101178553677223323023742555248999985577868999997245302364188779997298445
Q gi|254780584|r    2 SRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVERQGGLDRFLSNSKKEN   76 (97)
Q Consensus         2 sr~C~itGk~~~~Gn~vshs~~kTkR~~~PNlq~~~~~s~~l~~~v~l~vst~~lrtI~K~GGlD~yLl~~~~~~   76 (97)
                      ||+||||||+|++||+||||+++|+|+|.||||++++|||+++++|+|+|||+|||||+| ||||+||++++++.
T Consensus         1 Sr~C~itGK~~~~Gn~vShs~~kTkR~~~pNlq~kr~~~~~~~~~v~lkvstk~LRtI~K-~Gld~~l~k~~~~g   74 (77)
T d2qamz1           1 SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDK-KGIDTVLAELRARG   74 (77)
T ss_dssp             CCCCSSSCCCCCCCBCCBGGGBCCBCCCCCCCCCEECCCSTTCCCCEECCCTTHHHHHTT-SCHHHHHHTTTTTT
T ss_pred             CCCCCCCCCCCCCCCEEEECCCCCCCEECCCEEEEEEEECCCCEEEEEEEEHHHEEEEHH-CCHHHHHHHHHHCC
T ss_conf             988601898545686220036644756646438999998578979999998053324113-79999999999735



>d2jz6a1 d.325.1.1 (A:6-75) Ribosomal protein L28 (L28p) {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2j0111 d.325.1.1 (1:8-96) Ribosomal protein L28 (L28p) {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2zjru1 d.325.1.1 (U:8-79) Ribosomal protein L28 (L28p) {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 97 50S ribosomal protein L28 [Candidatus Liberibacter
3bbo_Y_151 (Y:) Ribosomal protein L28; large ribosomal subuni 9e-15
2jz6_A_77 (A:) 50S ribosomal protein L28; structure, NESG, r 1e-14
2jl6_1_89 (1:) 50S ribosomal protein L28, 50S ribosomal prot 5e-14
3i1n_X_1-3333 (X:1-33) 50S ribosomal protein L28; ribosome struc 5e-10
2zjr_U_1-4747 (U:1-47) 50S ribosomal protein L28; ribosome, larg 5e-06
>3bbo_Y (Y:) Ribosomal protein L28; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Nicotiana tabacum}Length = 151 Back     alignment and structure
 Score = 73.4 bits (180), Expect = 9e-15
 Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 1   MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVE 60
             R+C  T K     NKVSH+N+KT++    NL    +  +  ++  +LR+S  A++++E
Sbjct: 74  ARRICPFTGKKSNRANKVSHSNHKTKKLQFVNLQYKRIWWEAGKRYVKLRLSTKAIKTIE 133

Query: 61  RQGGLDRFLSNSKKENLS 78
           +  GLD     +  +   
Sbjct: 134 K-NGLDAVAKKAGIDLSK 150


>2jz6_A (A:) 50S ribosomal protein L28; structure, NESG, ribonucleoprotein, structural genomics, PSI-2, protein structure initiative; NMR {Thermotoga maritima MSB8}Length = 77 Back     alignment and structure
>3i1n_X (X:1-33) 50S ribosomal protein L28; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 2qao_Z* 2qba_Z* 2qbc_Z* 2qbe_Z 2qbg_Z 2qbi_Z* 2qbk_Z* 2qov_Z 2qox_Z 2qoz_Z* 2qp1_Z* 2z4l_Z* 2z4n_Z* 3df2_Z 3df4_Z 2qam_Z 3i1p_X 3i1r_X 3i1t_X 3i20_X ...Length = 33 Back     alignment and structure
>2zjr_U (U:1-47) 50S ribosomal protein L28; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans}Length = 47 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target97 50S ribosomal protein L28 [Candidatus Liberibacter asia
2jl6_1_89 50S ribosomal protein L28, 50S ribosomal protein L 99.92
3bbo_Y_151 Ribosomal protein L28; large ribosomal subunit, sp 99.91
2jz6_A_77 50S ribosomal protein L28; structure, NESG, ribonu 99.91
3i1n_X_1-3333 50S ribosomal protein L28; ribosome structure, pro 99.43
2zjr_U_1-4747 50S ribosomal protein L28; ribosome, large ribosom 99.2
2j01_1_1-4646 50S ribosomal protein L28; ribosome, tRNA, paromom 98.34
3i1n_X_34-7845 50S ribosomal protein L28; ribosome structure, pro 98.57
>3bbo_Y (Y:) Ribosomal protein L28; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Nicotiana tabacum} Back     alignment and structure
>2jz6_A (A:) 50S ribosomal protein L28; structure, NESG, ribonucleoprotein, structural genomics, PSI-2, protein structure initiative; NMR {Thermotoga maritima MSB8} Back     alignment and structure
>3i1n_X (X:1-33) 50S ribosomal protein L28; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 2qao_Z* 2qba_Z* 2qbc_Z* 2qbe_Z 2qbg_Z 2qbi_Z* 2qbk_Z* 2qov_Z 2qox_Z 2qoz_Z* 2qp1_Z* 2z4l_Z* 2z4n_Z* 3df2_Z 3df4_Z 2qam_Z 3i1p_X 3i1r_X 3i1t_X 3i20_X ... Back     alignment and structure
>2zjr_U (U:1-47) 50S ribosomal protein L28; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} Back     alignment and structure
>2j01_1 (1:1-46) 50S ribosomal protein L28; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} Back     alignment and structure
>3i1n_X (X:34-78) 50S ribosomal protein L28; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 2qao_Z* 2qba_Z* 2qbc_Z* 2qbe_Z 2qbg_Z 2qbi_Z* 2qbk_Z* 2qov_Z 2qox_Z 2qoz_Z* 2qp1_Z* 2z4l_Z* 2z4n_Z* 3df2_Z 3df4_Z 2qam_Z 3i1p_X 3i1r_X 3i1t_X 3i20_X ... Back     alignment and structure