254780713

254780713

16S rRNA-processing protein

GeneID in NCBI database:8209718Locus tag:CLIBASIA_03000
Protein GI in NCBI database:254780713Protein Accession:YP_003065126.1
Gene range:-(552403, 552975)Protein Length:190aa
Gene description:16S rRNA-processing protein
COG prediction:[J] RimM protein, required for 16S rRNA processing
KEGG prediction:rimM; 16S rRNA-processing protein; K02860 16S rRNA processing protein RimM
SEED prediction:16S rRNA processing protein RimM
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Ribosome biogenesis bacterial
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-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190
MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKILIDPIAAGLNNTTMKNPQYDCPLDSAGKKS
ccccHHEEEEEEEEccccEEEEEEEEEccccHHHHHHHcccccccEEEEEEEEEEEccEEEEEEcccccHHHHHHHcccEEEEcHHHccccccccccEEEEEEEccEEEEccccEEEEEEEEEEccccEEEEEEEccccEEEEEcHHHHccEEEccccEEEEEccccccccccccccccccccccccccc
cccccccEEEEEEEccccEEEEEEEEEccccHHHHHccEEEcccccEEEEEEEEEcccEEEEEEcccccHHHHHHHcccEEEEcHHHccccccccccEEHHHHccEEEEEccccEcEEEHHHcccccccEEEEEccccccEEEcccHHHHHHEcccccEEEEcccccccccccccccccccccccccccc
MVKLDKLVLMATIgtthglngevyidsyannpidlnryvlysndnRELRILKMYRKNKRFIATFsgidnihsasELRDLKLYAKRqdfkdeeleedeffnTDLEEMETFdrqgkywgqvcgvynfgagSILEIKNTMEKTFLIPFTKFAVLEVNLQENKilidpiaaglnnttmknpqydcpldsagkks
MVKLDKLVLMATIgtthglngevYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIAtfsgidnihsaselrDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKILIDPIAAglnnttmknpqydcpldsagkks
MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYAKRQdfkdeeleedeffntdleeMETFDRQGKYWGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKILIDPIAAGLNNTTMKNPQYDCPLDSAGKKS
****DKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKILIDPIAAGL*********************
MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKILIDPIAAGLNNTTMKNPQYDCPLDSAGKKS
****DKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKILIDPIAAGLN********************
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iiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKILIDPIAAGLNNTTMKNPQYDCPLDSAGKKS
MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKILIDPIAAGLNNTTMKNPQYDCPLDSAGKKS
MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKILIDPIAAGLNNTTMKNPQYDCPLDSAGKKS

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
Target190 16S rRNA-processing protein [Candidatus Liberibacter as
315121878190 16S rRNA-processing protein [Candidatus Liberibacter so 1 2e-62
222087527190 16S rRNA processing protein RimM [Agrobacterium radioba 1 5e-36
109893039188 RecName: Full=Ribosome maturation factor rimM Length = 1 8e-35
86359540217 16S rRNA-processing protein [Rhizobium etli CFN 42] Len 1 1e-34
190893807193 16S rRNA processing protein [Rhizobium etli CIAT 652] L 1 3e-34
209551324189 16S rRNA-processing protein RimM [Rhizobium leguminosar 1 9e-34
163757327202 16S rRNA-processing protein [Hoeflea phototrophica DFL- 1 1e-33
218513354206 16S rRNA-processing protein [Rhizobium etli 8C-3] Lengt 1 1e-33
222150103221 16S rRNA-processing protein RimM [Agrobacterium vitis S 1 3e-33
241206760189 16S rRNA-processing protein RimM [Rhizobium leguminosar 1 4e-33
>gi|315121878|ref|YP_004062367.1| 16S rRNA-processing protein [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 190 Back     alignment and organism information
 Score =  242 bits (617), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 126/187 (67%), Positives = 158/187 (84%)

Query: 1   MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRF 60
           MVK +KLVL+ATIGTTHGL GEVY++SYA+NP+DL+RY+LYS+D +E +IL +Y+ NKR 
Sbjct: 1   MVKSEKLVLIATIGTTHGLKGEVYVNSYASNPMDLSRYILYSDDAKEFKILDIYQNNKRL 60

Query: 61  IATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVC 120
           IATF GI +IHSA +LR LKLYA+RQDFKDEELEEDEFFN DLEE+ETFD QGKYWG++C
Sbjct: 61  IATFDGIYDIHSAEKLRHLKLYARRQDFKDEELEEDEFFNADLEELETFDLQGKYWGKIC 120

Query: 121 GVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKILIDPIAAGLNNTTMKNPQYD 180
           G+Y+FGAG++LE K++ EK FLIPFTK  VL VNL+ENKILID ++AGL+  T K+  ++
Sbjct: 121 GIYDFGAGAVLEFKDSKEKKFLIPFTKSTVLSVNLKENKILIDSVSAGLDCMTKKDKNHE 180

Query: 181 CPLDSAG 187
           C   S G
Sbjct: 181 CQSSSPG 187


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222087527|ref|YP_002546064.1| 16S rRNA processing protein RimM [Agrobacterium radiobacter K84] Length = 190 Back     alignment and organism information
>gi|109893039|sp|Q2K381|RIMM_RHIEC RecName: Full=Ribosome maturation factor rimM Length = 188 Back     alignment and organism information
>gi|86359540|ref|YP_471432.1| 16S rRNA-processing protein [Rhizobium etli CFN 42] Length = 217 Back     alignment and organism information
>gi|190893807|ref|YP_001980349.1| 16S rRNA processing protein [Rhizobium etli CIAT 652] Length = 193 Back     alignment and organism information
>gi|209551324|ref|YP_002283241.1| 16S rRNA-processing protein RimM [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 189 Back     alignment and organism information
>gi|163757327|ref|ZP_02164416.1| 16S rRNA-processing protein [Hoeflea phototrophica DFL-43] Length = 202 Back     alignment and organism information
>gi|218513354|ref|ZP_03510194.1| 16S rRNA-processing protein [Rhizobium etli 8C-3] Length = 206 Back     alignment and organism information
>gi|222150103|ref|YP_002551060.1| 16S rRNA-processing protein RimM [Agrobacterium vitis S4] Length = 221 Back     alignment and organism information
>gi|241206760|ref|YP_002977856.1| 16S rRNA-processing protein RimM [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 189 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
Target190 16S rRNA-processing protein [Candidatus Liberibacter as
PRK00122172 PRK00122, rimM, 16S rRNA-processing protein RimM; Provi 2e-30
TIGR02273165 TIGR02273, 16S_RimM, 16S rRNA processing protein RimM 5e-29
PRK13828161 PRK13828, rimM, 16S rRNA-processing protein RimM; Provi 6e-23
PRK14592165 PRK14592, rimM, 16S rRNA-processing protein RimM; Provi 2e-16
PRK13829162 PRK13829, rimM, 16S rRNA-processing protein RimM; Provi 5e-05
PRK14591169 PRK14591, rimM, 16S rRNA-processing protein RimM; Provi 0.002
COG0806174 COG0806, RimM, RimM protein, required for 16S rRNA proc 6e-30
pfam0178284 pfam01782, RimM, RimM N-terminal domain 2e-10
pfam0523977 pfam05239, PRC, PRC-barrel domain 7e-06
PRK14590171 PRK14590, rimM, 16S rRNA-processing protein RimM; Provi 2e-05
>gnl|CDD|178881 PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>gnl|CDD|162792 TIGR02273, 16S_RimM, 16S rRNA processing protein RimM Back     alignment and domain information
>gnl|CDD|184351 PRK13828, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>gnl|CDD|173056 PRK14592, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>gnl|CDD|184352 PRK13829, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>gnl|CDD|173055 PRK14591, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>gnl|CDD|31149 COG0806, RimM, RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|145113 pfam01782, RimM, RimM N-terminal domain Back     alignment and domain information
>gnl|CDD|147440 pfam05239, PRC, PRC-barrel domain Back     alignment and domain information
>gnl|CDD|173054 PRK14590, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 190 16S rRNA-processing protein [Candidatus Liberibacter as
PRK13828177 rimM 16S rRNA-processing protein; Provisional 100.0
PRK00122168 rimM 16S rRNA-processing protein; Provisional 100.0
TIGR02273179 16S_RimM 16S rRNA processing protein RimM; InterPro: IP 100.0
COG0806174 RimM RimM protein, required for 16S rRNA processing [Tr 100.0
PRK13829177 rimM 16S rRNA-processing protein; Provisional 100.0
pfam0178284 RimM RimM N-terminal domain. The RimM protein is essent 99.76
pfam0523977 PRC PRC-barrel domain. The PRC-barrel is an all beta ba 98.91
COG187387 Protein implicated in RNA metabolism, contains PRC-barr 96.41
TIGR01150264 puhA photosynthetic reaction center H subunit; InterPro 94.97
cd00226246 PRCH Photosynthetic reaction center (RC) complex, subun 92.73
>PRK13828 rimM 16S rRNA-processing protein; Provisional Back     alignment and domain information
>PRK00122 rimM 16S rRNA-processing protein; Provisional Back     alignment and domain information
>TIGR02273 16S_RimM 16S rRNA processing protein RimM; InterPro: IPR011961 This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing Back     alignment and domain information
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK13829 rimM 16S rRNA-processing protein; Provisional Back     alignment and domain information
>pfam01782 RimM RimM N-terminal domain Back     alignment and domain information
>pfam05239 PRC PRC-barrel domain Back     alignment and domain information
>COG1873 Protein implicated in RNA metabolism, contains PRC-barrel domain [General function prediction only] Back     alignment and domain information
>TIGR01150 puhA photosynthetic reaction center H subunit; InterPro: IPR005652 The photosynthetic apparatus in non-oxygenic bacteria consists of light-harvesting (LH) protein-pigment complexes LH1 and LH2, which use carotenoid and bacteriochlorophyll as primary donors Back     alignment and domain information
>cd00226 PRCH Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce ATP by ATP synthase 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
Target190 16S rRNA-processing protein [Candidatus Liberibacter as
2f1l_A187 Crystal Structure Of A Putative 16s Ribosomal Rna P 2e-30
3h9n_A177 Crystal Structure Of The Ribosome Maturation Factor 4e-27
2qgg_A182 X-Ray Structure Of The Protein Q6f7i0 From Acinetob 1e-22
2dyi_A162 Crystal Structure Of 16s Ribosomal Rna Processing P 7e-19
>gi|90109245|pdb|2F1L|A Chain A, Crystal Structure Of A Putative 16s Ribosomal Rna Processing Protein Rimm (Pa3744) From Pseudomonas Aeruginosa At 2.46 A Resolution Length = 187 Back     alignment and structure
 Score =  136 bits (342), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 74/167 (44%), Gaps = 10/167 (5%)

Query: 5   DKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLY----SNDNRELRILKMYRKNKRF 60
           D LV++  I + +G+ GEV + S+ +   +L  Y  +      + R+  +++     K  
Sbjct: 18  DDLVVIGKIVSVYGIRGEVKVYSFTDPLDNLLDYRRWTLRRDGEIRQAELVRGRLHGKVL 77

Query: 61  IATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVC 120
            A   G+D+   A      ++   R +     LEE E++   LE ++  D+  +  G + 
Sbjct: 78  AAKLKGLDDREEARTFTGYEICIPRSELPS--LEEGEYYWHQLEGLKVIDQGRQLLGVID 135

Query: 121 GVYNFGAGSILEIKNT----MEKTFLIPFTKFAVLEVNLQENKILID 163
            +   GA  +  +K       ++  L+P+T   VL ++L   +  +D
Sbjct: 136 HLLETGANDVXVVKPCAGSLDDRERLLPYTGQCVLSIDLAAGEXRVD 182


>gi|237824061|pdb|3H9N|A Chain A, Crystal Structure Of The Ribosome Maturation Factor Rimm (Hi0203) From H.Influenzae. Northeast Structural Genomics Consortium Target Ir66 Length = 177 Back     alignment and structure
>gi|152149496|pdb|2QGG|A Chain A, X-Ray Structure Of The Protein Q6f7i0 From Acinetobacter Calcoaceticus Amms 248. Northeast Structural Genomics Consortium Target Asr73 Length = 182 Back     alignment and structure
gi|145579204|pdb|2DYI|A Chain A, Crystal Structure Of 16s Ribosomal Rna Processing Protein Rimm From Thermus Thermophilus Hb8 Length = 162 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target190 16S rRNA-processing protein [Candidatus Liberibacter as
2f1l_A187 16S rRNA processing protein; 9949912, structural genomi 3e-22
2qgg_A182 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR73, s 2e-21
3h9n_A177 Ribosome maturation factor RIMM; structural genomics, P 2e-20
2dyi_A162 Probable 16S rRNA-processing protein RIMM; ribosomal pr 4e-20
>2f1l_A 16S rRNA processing protein; 9949912, structural genomics, PSI, protein structure initiative, joint center for structural genomics, JCSG; HET: UNL; 2.46A {Pseudomonas aeruginosa} SCOP: b.41.1.4 b.43.3.4 Length = 187 Back     alignment and structure
 Score =  100 bits (249), Expect = 3e-22
 Identities = 36/168 (21%), Positives = 76/168 (45%), Gaps = 10/168 (5%)

Query: 5   DKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRY----VLYSNDNRELRILKMYRKNKRF 60
           D LV++  I + +G+ GEV + S+ +   +L  Y    +    + R+  +++     K  
Sbjct: 18  DDLVVIGKIVSVYGIRGEVKVYSFTDPLDNLLDYRRWTLRRDGEIRQAELVRGRLHGKVL 77

Query: 61  IATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVC 120
            A   G+D+   A      ++   R +     LEE E++   LE ++  D+  +  G + 
Sbjct: 78  AAKLKGLDDREEARTFTGYEICIPRSEL--PSLEEGEYYWHQLEGLKVIDQGRQLLGVID 135

Query: 121 GVYNFGAGSILEIKNTM----EKTFLIPFTKFAVLEVNLQENKILIDP 164
            +   GA  ++ +K       ++  L+P+T   VL ++L   ++ +D 
Sbjct: 136 HLLETGANDVMVVKPCAGSLDDRERLLPYTGQCVLSIDLAAGEMRVDW 183


>2qgg_A 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR73, structural genomics, PSI-2, protein structure initiative; 2.40A {Acinetobacter calcoaceticus} Length = 182 Back     alignment and structure
>3h9n_A Ribosome maturation factor RIMM; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.70A {Haemophilus influenzae} Length = 177 Back     alignment and structure
>2dyi_A Probable 16S rRNA-processing protein RIMM; ribosomal protein S19, PRC-barrel, structural genomics, NPPSFA; 2.00A {Thermus thermophilus HB8} PDB: 2dog_A Length = 162 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target190 16S rRNA-processing protein [Candidatus Liberibacter as
2f1l_A187 16S rRNA processing protein; structural genomics, joint 100.0
3h9n_A177 Ribosome maturation factor RIMM; structural genomics, P 100.0
2qgg_A182 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR73, s 100.0
2dyi_A162 Probable 16S rRNA-processing protein RIMM; ribosomal pr 100.0
1eys_H259 Photosynthetic reaction center; membrane protein comple 96.99
1rzh_H260 Reaction center protein H chain; bacterial photosynthes 96.73
1pm3_A97 MTH1895; unknown function, structural genomics, PSI, pr 96.47
3htr_A120 Uncharacterized PRC-barrel domain protein; beta-barrel, 95.92
2wjn_H258 Reaction center protein H chain; bacteriochlorophyll, l 95.1
>2f1l_A 16S rRNA processing protein; structural genomics, joint CENT structural genomics, JCSG, protein structure initiative, PS unknown function; HET: UNL; 2.46A {Pseudomonas aeruginosa} SCOP: b.41.1.4 b.43.3.4 Back     alignment and structure
Probab=100.00  E-value=0  Score=295.78  Aligned_cols=164  Identities=23%  Similarity=0.388  Sum_probs=150.3

Q ss_pred             CCCCEEEEEEEECCCEEEEEEEEEECCCCHHHHHHCCEEC----CCCEEEEEEEEEEECCEEEEEECCCCCHHHHHHHCC
Q ss_conf             8200799999944630505999994189977876301020----798379999999739979999638778455676349
Q gi|254780713|r    3 KLDKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYS----NDNRELRILKMYRKNKRFIATFSGIDNIHSASELRD   78 (190)
Q Consensus         3 k~~~~i~iGkI~k~hGlkGevki~~~td~~~~~~~~~~~~----~~~~~~~i~~~~~~~~~~iikf~gi~s~~~A~~l~g   78 (190)
                      +.++|+.||+|++|||+|||++|+++|++++++.++..+.    ....++.+++++.+++.++++|++++||++|+.|+|
T Consensus        16 ~~dd~i~iG~I~~~hGlkGevkv~~~td~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~~~~l~k~~gi~~re~Ae~L~g   95 (187)
T 2f1l_A           16 PADDLVVIGKIVSVYGIRGEVKVYSFTDPLDNLLDYRRWTLRRDGEIRQAELVRGRLHGKVLAAKLKGLDDREEARTFTG   95 (187)
T ss_dssp             ---CEEEEEEEEEEETTTTEEEEEECSSSGGGGGGCCEEEEEETTEEEEEEEEEEEEETTEEEEEETTCCSHHHHHTTTT
T ss_pred             CCCCEEEEEEEECCEEECEEEEEEECCCCHHHHHCCCEEEEEECCCEEEEEEEEEEECCCEEEEEECCCCCHHHHHHHCC
T ss_conf             97887999999298953779999998789799617776999608958899999998427589998469699899997449


Q ss_pred             CEEEECHHHCCCCCCCCCCCCHHHHHCCEEEEECCCEEEEEEEEEECCCCEEEEEECC----CCCEEEEECHHHHCCEEE
Q ss_conf             6877417778865564100214524011367525843119988665799508999749----982899875031001056
Q gi|254780713|r   79 LKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNT----MEKTFLIPFTKFAVLEVN  154 (190)
Q Consensus        79 ~~i~i~~~~lp~~~l~~~e~Y~~dLiG~~V~d~~~~~iG~V~~v~~~~a~dil~V~~~----~~ke~lIP~v~~~I~~ID  154 (190)
                      +.||+++++||  +|+++||||+|||||+|++.+++.+|+|.+++++||||+|+|+..    ++||+||||+++||.+||
T Consensus        96 ~~l~i~~~~lp--~l~e~E~y~~dLiG~~V~~~~~~~lG~V~~v~~~ga~dll~I~~~~~~~~~ke~LIPf~~~~V~~VD  173 (187)
T 2f1l_A           96 YEICIPRSELP--SLEEGEYYWHQLEGLKVIDQGRQLLGVIDHLLETGANDVMVVKPCAGSLDDRERLLPYTGQCVLSID  173 (187)
T ss_dssp             CEEEEEGGGSC--C-----CCHHHHTTCEEEETTSCEEEEEEEEECCSSSCEEEEECCTTSSSSCCEEEECSTTTEEEEE
T ss_pred             CEEEECHHHCC--CCCCCCEEHHHHCCCEEEECCCCEEEEEEEEECCCCCEEEEEEECCCCCCCCEEEEECCHHHCCEEE
T ss_conf             87995054588--7778824345635819997899788999999568993499998578888982999866731138897


Q ss_pred             CCCCEEEEECCCCC
Q ss_conf             33979999528100
Q gi|254780713|r  155 LQENKILIDPIAAG  168 (190)
Q Consensus       155 ~~~k~I~v~~p~Gl  168 (190)
                      +++|+|+||+|+++
T Consensus       174 ~~~k~I~Vdw~~d~  187 (187)
T 2f1l_A          174 LAAGEMRVDWDADF  187 (187)
T ss_dssp             TTTTEEEECCCTTC
T ss_pred             CCCCEEEEECCCCC
T ss_conf             88999999589999



>3h9n_A Ribosome maturation factor RIMM; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.70A {Haemophilus influenzae} Back     alignment and structure
>2qgg_A 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR73, structural genomics, PSI-2, protein structure initiative; 2.40A {Acinetobacter calcoaceticus} Back     alignment and structure
>2dyi_A Probable 16S rRNA-processing protein RIMM; ribosomal protein S19, PRC-barrel, structural genomics, NPPSFA; 2.00A {Thermus thermophilus HB8} PDB: 3a1p_A 2dog_A Back     alignment and structure
>1eys_H Photosynthetic reaction center; membrane protein complex, electron transport; HET: BGL BCL BPH MQ8 HEM CRT LDA PEF; 2.20A {Thermochromatium tepidum} SCOP: b.41.1.1 f.23.10.1 Back     alignment and structure
>1rzh_H Reaction center protein H chain; bacterial photosynthesis, proton transfer pathway, revertant, X-RAY crystallography; HET: BCL BPH BPB U10 SPO LDA HTO CDL; 1.80A {Rhodobacter sphaeroides} SCOP: b.41.1.1 f.23.10.1 PDB: 1e14_H* 1f6n_H* 1fnp_H* 1fnq_H* 1jgw_H* 1jgx_H* 1jgy_H* 1jgz_H* 1jh0_H* 1k6l_H* 1k6n_H* 1kby_H* 1l9b_H* 1l9j_H* 1m3x_H* 1mps_H* 1pcr_H* 1e6d_H* 1rg5_H* 1rgn_H* ... Back     alignment and structure
>1pm3_A MTH1895; unknown function, structural genomics, PSI, protein structure initiative; 3.15A {Methanothermobacterthermautotrophicus} SCOP: b.41.1.2 Back     alignment and structure
>3htr_A Uncharacterized PRC-barrel domain protein; beta-barrel, photo-reaction-center domain, structural genomics, PSI-2; HET: MSE; 2.06A {Rhodopseudomonas palustris} Back     alignment and structure
>2wjn_H Reaction center protein H chain; bacteriochlorophyll, lipidic-sponge phase, photosynthesis, electron transport, cell membrane; HET: HEM FME BCB BPB MPG MQ7 NS5; 1.86A {Rhodopseudomonas viridis} PDB: 1prc_H* 1r2c_H* 1vrn_H* 1dxr_H* 2jbl_H* 2prc_H* 2i5n_H* 2wjm_H* 2x5u_H* 2x5v_H* 3d38_H* 3prc_H* 5prc_H* 6prc_H* 7prc_H* 3g7f_H* 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 190 16S rRNA-processing protein [Candidatus Liberibacter as
d2f1la289 b.43.3.4 (A:7-95) 16S rRNA processing protein RimM, N-t 1e-11
d2f1la175 b.41.1.4 (A:101-175) 16S rRNA processing protein RimM, 2e-11
>d2f1la2 b.43.3.4 (A:7-95) 16S rRNA processing protein RimM, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 89 Back     information, alignment and structure

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: RimM N-terminal domain-like
domain: 16S rRNA processing protein RimM, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]
 Score = 63.8 bits (155), Expect = 1e-11
 Identities = 17/86 (19%), Positives = 37/86 (43%), Gaps = 4/86 (4%)

Query: 7  LVLMATIGTTHGLNGEVYIDSYANNPIDLNRY----VLYSNDNRELRILKMYRKNKRFIA 62
          LV++  I + +G+ GEV + S+ +   +L  Y    +    + R+  +++     K   A
Sbjct: 2  LVVIGKIVSVYGIRGEVKVYSFTDPLDNLLDYRRWTLRRDGEIRQAELVRGRLHGKVLAA 61

Query: 63 TFSGIDNIHSASELRDLKLYAKRQDF 88
             G+D+   A      ++   R + 
Sbjct: 62 KLKGLDDREEARTFTGYEICIPRSEL 87


>d2f1la1 b.41.1.4 (A:101-175) 16S rRNA processing protein RimM, C-terminal domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 75 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target190 16S rRNA-processing protein [Candidatus Liberibacter as
d2f1la289 16S rRNA processing protein RimM, N-terminal domain {Ps 99.84
d2f1la175 16S rRNA processing protein RimM, C-terminal domain {Ps 99.84
d1eysh1201 Photosynthetic reaction centre {Thermochromatium tepidu 96.98
d1rzhh1213 Photosynthetic reaction centre {Rhodobacter sphaeroides 96.82
d2i5nh1222 Photosynthetic reaction centre {Rhodopseudomonas viridi 95.48
d1pm3a_78 MTH1895 {Archaeon Methanobacterium thermoautotrophicum 91.26
>d2f1la2 b.43.3.4 (A:7-95) 16S rRNA processing protein RimM, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: RimM N-terminal domain-like
domain: 16S rRNA processing protein RimM, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]
Probab=99.84  E-value=3.6e-21  Score=136.41  Aligned_cols=85  Identities=20%  Similarity=0.367  Sum_probs=76.2

Q ss_pred             CEEEEEEEECCCEEEEEEEEEECCCCHHHHHHCCEEC----CCCEEEEEEEEEEECCEEEEEECCCCCHHHHHHHCCCEE
Q ss_conf             0799999944630505999994189977876301020----798379999999739979999638778455676349687
Q gi|254780713|r    6 KLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYS----NDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDLKL   81 (190)
Q Consensus         6 ~~i~iGkI~k~hGlkGevki~~~td~~~~~~~~~~~~----~~~~~~~i~~~~~~~~~~iikf~gi~s~~~A~~l~g~~i   81 (190)
                      |++.||+|++|||+|||++|++||++++.+..+..+.    ....++.+++.+.++++++++|+|++||++|++|+|+.|
T Consensus         1 d~i~iGki~~~hGlkG~vki~~~t~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~vk~~~i~~r~~Ae~l~g~~i   80 (89)
T d2f1la2           1 DLVVIGKIVSVYGIRGEVKVYSFTDPLDNLLDYRRWTLRRDGEIRQAELVRGRLHGKVLAAKLKGLDDREEARTFTGYEI   80 (89)
T ss_dssp             CEEEEEEEEEEETTTTEEEEEECSSSGGGGGGCCEEEEEETTEEEEEEEEEEEEETTEEEEEETTCCSHHHHHTTTTCEE
T ss_pred             CEEEEEEEECCEEEEEEEEEEECCCCHHHHHCCCEEEEECCCEEEEEEEEEEEECCCEEEEEECCCCCHHHHHHHCCCEE
T ss_conf             97999999088700189999987889889837884998009958999999988406279999908899899997579999


Q ss_pred             EECHHHCCC
Q ss_conf             741777886
Q gi|254780713|r   82 YAKRQDFKD   90 (190)
Q Consensus        82 ~i~~~~lp~   90 (190)
                      |+++++||.
T Consensus        81 ~i~~~~LPs   89 (89)
T d2f1la2          81 CIPRSELPS   89 (89)
T ss_dssp             EEEGGGSCC
T ss_pred             EEEHHHCCC
T ss_conf             999999999



>d2f1la1 b.41.1.4 (A:101-175) 16S rRNA processing protein RimM, C-terminal domain {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1eysh1 b.41.1.1 (H:59-259) Photosynthetic reaction centre {Thermochromatium tepidum [TaxId: 1050]} Back     information, alignment and structure
>d1rzhh1 b.41.1.1 (H:36-248) Photosynthetic reaction centre {Rhodobacter sphaeroides [TaxId: 1063]} Back     information, alignment and structure
>d2i5nh1 b.41.1.1 (H:37-258) Photosynthetic reaction centre {Rhodopseudomonas viridis [TaxId: 1079]} Back     information, alignment and structure
>d1pm3a_ b.41.1.2 (A:) MTH1895 {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 190 16S rRNA-processing protein [Candidatus Liberibact
2f1l_A_1-111111 (A:1-111) 16S rRNA processing protein; 9949912, st 8e-14
2qgg_A_1-102102 (A:1-102) 16S rRNA-processing protein RIMM; X-RAY, 9e-14
3h9n_A_1-9393 (A:1-93) Ribosome maturation factor RIMM; structur 2e-12
2dyi_A_1-8787 (A:1-87) Probable 16S rRNA-processing protein RIMM 2e-12
2f1l_A_112-18776 (A:112-187) 16S rRNA processing protein; 9949912, 3e-12
3h9n_A_94-17784 (A:94-177) Ribosome maturation factor RIMM; struct 3e-11
2qgg_A_103-18280 (A:103-182) 16S rRNA-processing protein RIMM; X-RA 5e-11
2dyi_A_88-16275 (A:88-162) Probable 16S rRNA-processing protein RI 1e-10
>2f1l_A (A:1-111) 16S rRNA processing protein; 9949912, structural genomics, PSI, protein structure initiative, joint center for structural genomics, JCSG; HET: UNL; 2.46A {Pseudomonas aeruginosa}Length = 111 Back     alignment and structure
 Score = 71.4 bits (175), Expect = 8e-14
 Identities = 20/99 (20%), Positives = 40/99 (40%), Gaps = 6/99 (6%)

Query: 1   MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDL----NRYVLYSNDNRELRILKMYRK 56
               D LV++  I + +G+ GEV + S+ +   +L       +    + R+  +++    
Sbjct: 14  PTPADDLVVIGKIVSVYGIRGEVKVYSFTDPLDNLLDYRRWTLRRDGEIRQAELVRGRLH 73

Query: 57  NKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEE 95
            K   A   G+D+   A      ++   R +     LEE
Sbjct: 74  GKVLAAKLKGLDDREEARTFTGYEICIPRSEL--PSLEE 110


>2qgg_A (A:1-102) 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR73, structural genomics, PSI-2, protein structure initiative; 2.40A {Acinetobacter calcoaceticus}Length = 102 Back     alignment and structure
>3h9n_A (A:1-93) Ribosome maturation factor RIMM; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.70A {Haemophilus influenzae}Length = 93 Back     alignment and structure
>2dyi_A (A:1-87) Probable 16S rRNA-processing protein RIMM; ribosomal protein S19, PRC-barrel, structural genomics, NPPSFA; 2.00A {Thermus thermophilus HB8} PDB: 2dog_ALength = 87 Back     alignment and structure
>2f1l_A (A:112-187) 16S rRNA processing protein; 9949912, structural genomics, PSI, protein structure initiative, joint center for structural genomics, JCSG; HET: UNL; 2.46A {Pseudomonas aeruginosa}Length = 76 Back     alignment and structure
>3h9n_A (A:94-177) Ribosome maturation factor RIMM; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.70A {Haemophilus influenzae}Length = 84 Back     alignment and structure
>2qgg_A (A:103-182) 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR73, structural genomics, PSI-2, protein structure initiative; 2.40A {Acinetobacter calcoaceticus}Length = 80 Back     alignment and structure
>2dyi_A (A:88-162) Probable 16S rRNA-processing protein RIMM; ribosomal protein S19, PRC-barrel, structural genomics, NPPSFA; 2.00A {Thermus thermophilus HB8} PDB: 2dog_ALength = 75 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target190 16S rRNA-processing protein [Candidatus Liberibacter as
3h9n_A_94-17784 Ribosome maturation factor RIMM; structural genomi 99.9
2f1l_A_112-18776 16S rRNA processing protein; 9949912, structural g 99.88
2qgg_A_103-18280 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR 99.87
2dyi_A_88-16275 Probable 16S rRNA-processing protein RIMM; ribosom 99.82
1rzh_H_116-260145 Reaction center protein H chain; bacterial photosy 96.84
1pm3_A_97 MTH1895; unknown function, structural genomics, PS 96.05
1eys_H_118-259142 Photosynthetic reaction center; membrane protein c 96.04
2wjn_H_113-258146 Reaction center protein H chain; bacteriochlorophy 95.6
3htr_A_20-120101 Uncharacterized PRC-barrel domain protein; beta-ba 95.53
2f1l_A_1-111111 16S rRNA processing protein; 9949912, structural g 99.89
2qgg_A_1-102102 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR 99.89
3h9n_A_1-9393 Ribosome maturation factor RIMM; structural genomi 99.85
2dyi_A_1-8787 Probable 16S rRNA-processing protein RIMM; ribosom 99.84
>3h9n_A (A:94-177) Ribosome maturation factor RIMM; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.70A {Haemophilus influenzae} Back     alignment and structure
Probab=99.90  E-value=2.2e-23  Score=151.06  Aligned_cols=78  Identities=24%  Similarity=0.298  Sum_probs=72.6

Q ss_pred             CCCHHHHHCCEEEEECCCEEEEEEEEEECCCCEEEEEEC-----CCCCEEEEECHH-HHCCEEECCCCEEEEECCCCCCC
Q ss_conf             021452401136752584311998866579950899974-----998289987503-10010563397999952810038
Q gi|254780713|r   97 EFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKN-----TMEKTFLIPFTK-FAVLEVNLQENKILIDPIAAGLN  170 (190)
Q Consensus        97 e~Y~~dLiG~~V~d~~~~~iG~V~~v~~~~a~dil~V~~-----~~~ke~lIP~v~-~~I~~ID~~~k~I~v~~p~Glld  170 (190)
                      ||||+||+||+|++.+|+.+|+|.+|+++||||+|+|++     .++|++||||++ .||++||.++|+|.|+||+||||
T Consensus         1 Efy~~dLiG~~V~d~~g~~iG~V~~v~~~~a~dll~I~~~~~~~~~gke~liPfv~e~~V~~iD~e~~~I~v~~p~Glld   80 (84)
T 3h9n_A            1 DYYWHDLIGCTVVNLEGYTXGTVTEXXETGSNDVLVVKANTKDAFGKQERLIPFLYEQVVKRVDLTTKTIEVDWDAGFLE   80 (84)
T ss_dssp             CGGGGGTTTCEEEETTCCEEEEEEEEEESSSCEEEEEECCTTCTTCCSEEEEECCBTTTEEEEEGGGTEEEECCCSSTTC
T ss_pred             CEEHHHHEEEEEEEECCCCCEEEEEECCCCCCEEEEEEECCCCCCCCCEEEEECCCCCCCEEEECCCCEEEEECCCCHHH
T ss_conf             20221010008997079624799398106992599998288667798289974376467517967899999988812644


Q ss_pred             CCCC
Q ss_conf             8865
Q gi|254780713|r  171 NTTM  174 (190)
Q Consensus       171 ~~~~  174 (190)
                      ++.+
T Consensus        81 ~~~e   84 (84)
T 3h9n_A           81 HHHH   84 (84)
T ss_dssp             CCCC
T ss_pred             CCCC
T ss_conf             4489



>2f1l_A (A:112-187) 16S rRNA processing protein; 9949912, structural genomics, PSI, protein structure initiative, joint center for structural genomics, JCSG; HET: UNL; 2.46A {Pseudomonas aeruginosa} Back     alignment and structure
>2qgg_A (A:103-182) 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR73, structural genomics, PSI-2, protein structure initiative; 2.40A {Acinetobacter calcoaceticus} Back     alignment and structure
>2dyi_A (A:88-162) Probable 16S rRNA-processing protein RIMM; ribosomal protein S19, PRC-barrel, structural genomics, NPPSFA; 2.00A {Thermus thermophilus HB8} PDB: 2dog_A Back     alignment and structure
>1rzh_H (H:116-260) Reaction center protein H chain; bacterial photosynthesis, proton transfer pathway, revertant, X-RAY crystallography; HET: BCL BPH BPB U10 SPO LDA HTO CDL; 1.80A {Rhodobacter sphaeroides} Back     alignment and structure
>1pm3_A (A:) MTH1895; unknown function, structural genomics, PSI, protein structure initiative; 3.15A {Methanothermobacterthermautotrophicus} Back     alignment and structure
>1eys_H (H:118-259) Photosynthetic reaction center; membrane protein complex, electron transport; HET: BGL BCL BPH MQ8 HEM CRT LDA PEF; 2.20A {Thermochromatium tepidum} Back     alignment and structure
>2wjn_H (H:113-258) Reaction center protein H chain; bacteriochlorophyll, lipidic-sponge phase, photosynthesis, electron transport, cell membrane; HET: HEM FME BCB BPB MPG MQ7 NS5; 1.86A {Rhodopseudomonas viridis} PDB: 1prc_H* 1r2c_H* 1vrn_H* 1dxr_H* 2jbl_H* 2prc_H* 2i5n_H* 2wjm_H* 3d38_H* 3prc_H* 5prc_H* 6prc_H* 7prc_H* 3g7f_H* Back     alignment and structure
>3htr_A (A:20-120) Uncharacterized PRC-barrel domain protein; beta-barrel, photo-reaction-center domain, structural genomics, PSI-2; HET: MSE; 2.06A {Rhodopseudomonas palustris} Back     alignment and structure
>2f1l_A (A:1-111) 16S rRNA processing protein; 9949912, structural genomics, PSI, protein structure initiative, joint center for structural genomics, JCSG; HET: UNL; 2.46A {Pseudomonas aeruginosa} Back     alignment and structure
>2qgg_A (A:1-102) 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR73, structural genomics, PSI-2, protein structure initiative; 2.40A {Acinetobacter calcoaceticus} Back     alignment and structure
>3h9n_A (A:1-93) Ribosome maturation factor RIMM; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.70A {Haemophilus influenzae} Back     alignment and structure
>2dyi_A (A:1-87) Probable 16S rRNA-processing protein RIMM; ribosomal protein S19, PRC-barrel, structural genomics, NPPSFA; 2.00A {Thermus thermophilus HB8} PDB: 2dog_A Back     alignment and structure