Citrus Sinensis ID: 025088

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------26
Protein Sequence
MLIKITRSTLSKSLNLQLRCFSQAAAAILPDDPSAPLTYLDGLPRPDPRYDETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGRASDQKKSK
Secondary Structure (PSIPRED)
ccEEEccccccccHHHHHHHHHHHcccccccccccccccccccccccccccEEEEEEEccccccHHHHHHHHcccccEEEEccccccccccEEEEEEEcHHHHHHHHHHcccccEEEEEEEEEccccccccccEEEEEEEEcccccccccccEEEEEEEEcccccEEEEEEEEEEcccccccccccEEEEEEEEEEEEEEEccccccEEEEEccccccccEEEEEcccccccEEEEccccccEEEEEccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHcHHHHHHHHHHccHHHHHHcccccccccccccccccccccccEEEEEEEccccccHHHHHHHHcccccEEEEcccccccccccEEEEEcHHHHHHHHHHccccHHEEEEEEEEEccccccccEEEEEEEEHHHHccccccccEEEEEEEEEccccEEEEEEEEEEEccccccccccccEEEEEEEEEEEEEccHccccEEEEEccccccccEEEEEccEcccccEEEcccccEEEEEEccccccHHHcc
Coil and Loop (DISEMBL)
MLIKITRSTLSKSLNLQLRCFSQAAaailpddpsapltyldglprpdprydetilaipraspgtrvsvkerkagrvpsivfeqedgqhggnkrLISVQTNQIRKLVGHLGRSFFVSRLfdlevrsefgsgdliekVRVLprkvhlhsgtdaplnvtflrappeallkidvplvfrgddvspglrkggylnTIKRTVKflcpadivppyidvdlseLDVEQKILagdlkvhpalkllrskdepvckiaggrasdqkksk
Flexible Loop (DISEMBL)
mlikitrstlSKSLNLQLRCFSQAAAAILPDDPSAPLTYLDGLPRPDPRYDETIlaipraspgtrvsvkerkagrvpsivfeqedgqhggnkRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVrsefgsgdliekVRVLPRKVhlhsgtdaplnvtFLRAPPEAllkidvplvfrgddvspglrkggylnTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGdlkvhpalkllrskdepvckiaggrasdqkksk
Low Complexity Region (SEG)
MLIKITRSTLSKSLNLQLRCFSQAAAAILPDDPSAPLTYLDGLPRPDPRYDETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGRASDQKKSK
Disordered region (IsUnstruct)
*************LNLQLRCFSQAAAAILP******LTYLD************IL*************************************RLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRS********************
Disordered Region (DISOPRED)
*******STLSKSLNLQLRCFSQAAAAILPDDPSA*L*YL*GLPRPDPRYDETILAI**********VKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVC**************
Disordered Region (DISEMBL)
MLIKITRSTLSKSLNLQLRCFSQAAAAILPDDPSAPLTYLDGLPRPDPRYDETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIA***********
Disordered Region (DISPRO)
MLIKITRSTLSKSLNLQLRCFSQAAAAILPDDPSAPLTYLDGLPRPDPRYDETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGR********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLIKITRSTLSKSLNLQLRCFSQAAAAILPDDPSAPLTYLDGLPRPDPRYDETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGRASDQKKSK
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	258	2.2.26 [Sep-21-2011]
Q9AAV8	197	50S ribosomal protein L25	yes	no	0.709	0.928	0.299	3e-17
B8GZU9	197	50S ribosomal protein L25	yes	no	0.709	0.928	0.299	3e-17
B2IG64	221	50S ribosomal protein L25	yes	no	0.593	0.692	0.312	1e-16
Q2G6G9	204	50S ribosomal protein L25	yes	no	0.573	0.725	0.286	2e-16
Q1GSP2	212	50S ribosomal protein L25	yes	no	0.596	0.726	0.288	3e-16
A5CF34	207	50S ribosomal protein L25	yes	no	0.732	0.913	0.278	3e-16
B0T899	199	50S ribosomal protein L25	yes	no	0.709	0.919	0.308	3e-16
B8EK41	227	50S ribosomal protein L25	yes	no	0.589	0.669	0.310	6e-16
A5FZ47	217	50S ribosomal protein L25	yes	no	0.624	0.741	0.310	6e-16
A7HVD8	216	50S ribosomal protein L25	yes	no	0.546	0.652	0.317	1e-15

>sp|Q9AAV8|RL25_CAUCR 50S ribosomal protein L25 OS=Caulobacter crescentus (strain ATCC 19089 / CB15) GN=rplY PE=3 SV=1

 Score = 89.0 bits (219), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 61/204 (29%), Positives = 100/204 (49%), Gaps = 21/204 (10%)

Query: 52  ETILAIP-RASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKR--LISVQTNQIRKLVGH 108
           E IL +  R   GT  +   R+AG+VP +++       GG K    I+V+ N+ RK    
Sbjct: 3   EIILNVEVRDGAGTGNARATRRAGKVPGVLY-------GGGKAPVNIAVKANEFRK---- 51

Query: 109 LGRSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKI 168
              S +  +L    V  ++G     EK  V+ + V  H  TD P++    R     L+KI
Sbjct: 52  ---SLYTGKLLGHLVTLQYGE----EKQSVIAKAVQFHPVTDEPVHFDLYRVDEHQLIKI 104

Query: 169 DVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLK 228
           +VP+ F+  + S GL+KGG L  I+ TV+  CPAD +P  + +DL+  D+   I   ++K
Sbjct: 105 EVPVHFKNHETSVGLKKGGTLEVIRHTVELACPADKIPEELVIDLAGHDIGDVIRISEVK 164

Query: 229 VHPALKLLRSKDEPVCKIAGGRAS 252
           +   +K    +D  +  +    A+
Sbjct: 165 LPEGVKPAMDRDFVIANVKASSAA 188

This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.
Caulobacter crescentus (strain ATCC 19089 / CB15) (taxid: 190650)

>sp|B8GZU9|RL25_CAUCN 50S ribosomal protein L25 OS=Caulobacter crescentus (strain NA1000 / CB15N) GN=rplY PE=3 SV=1

 Score = 89.0 bits (219), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 61/204 (29%), Positives = 100/204 (49%), Gaps = 21/204 (10%)

Query: 52  ETILAIP-RASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKR--LISVQTNQIRKLVGH 108
           E IL +  R   GT  +   R+AG+VP +++       GG K    I+V+ N+ RK    
Sbjct: 3   EIILNVEVRDGAGTGNARATRRAGKVPGVLY-------GGGKAPVNIAVKANEFRK---- 51

Query: 109 LGRSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKI 168
              S +  +L    V  ++G     EK  V+ + V  H  TD P++    R     L+KI
Sbjct: 52  ---SLYTGKLLGHLVTLQYGE----EKQSVIAKAVQFHPVTDEPVHFDLYRVDEHQLIKI 104

Query: 169 DVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLK 228
           +VP+ F+  + S GL+KGG L  I+ TV+  CPAD +P  + +DL+  D+   I   ++K
Sbjct: 105 EVPVHFKNHETSVGLKKGGTLEVIRHTVELACPADKIPEELVIDLAGHDIGDVIRISEVK 164

Query: 229 VHPALKLLRSKDEPVCKIAGGRAS 252
           +   +K    +D  +  +    A+
Sbjct: 165 LPEGVKPAMDRDFVIANVKASSAA 188

This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.

Caulobacter crescentus (strain NA1000 / CB15N) (taxid: 565050)

>sp|B2IG64|RL25_BEII9 50S ribosomal protein L25 OS=Beijerinckia indica subsp. indica (strain ATCC 9039 / DSM 1715 / NCIB 8712) GN=rplY PE=3 SV=1

 Score = 86.7 bits (213), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 54/173 (31%), Positives = 87/173 (50%), Gaps = 20/173 (11%)

Query: 52  ETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLV--GHL 109
           +T+ A  R   G   +   R+ GR+P +++   D         I++   ++ KL+  GH 
Sbjct: 5   KTLAATVRGGTGKGAARSIRREGRIPGVIYGGGDAPEP-----ITLDYRELNKLIYAGH- 58

Query: 110 GRSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKID 169
               F++ +FD+EV           K RV+PR   L      PL+V FLR  P A LK+ 
Sbjct: 59  ----FLTTIFDIEVEGA--------KQRVVPRDYQLDPVKGQPLHVDFLRLKPGATLKVS 106

Query: 170 VPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKI 222
           VP+ F   D+ PGL+KGG LN ++  ++   PAD +P  +  DL  L++ + +
Sbjct: 107 VPIHFINADICPGLKKGGTLNIVRHAIELKVPADAMPDVLTADLHALEIAESM 159

This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.

Beijerinckia indica subsp. indica (strain ATCC 9039 / DSM 1715 / NCIB 8712) (taxid: 395963)

>sp|Q2G6G9|RL25_NOVAD 50S ribosomal protein L25 OS=Novosphingobium aromaticivorans (strain DSM 12444) GN=rplY PE=3 SV=1

 Score = 86.3 bits (212), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 47/164 (28%), Positives = 88/164 (53%), Gaps = 16/164 (9%)

Query: 71  RKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSG 130
           R+ GR P++++       GGN+  +++   + + LV  LG   F + + +L V  +    
Sbjct: 24  RREGRTPAVIY-------GGNEEPVAIHLEE-KALVKALGTGHFFNSVVELTVGGQ---- 71

Query: 131 DLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLN 190
                VR LP+ V  H  TD P +  FLR   ++++ ++VP++F  ++ SPGL+KGG LN
Sbjct: 72  ----TVRTLPKDVAFHPVTDRPEHADFLRVSKDSVVHVNVPVIFANEEKSPGLKKGGVLN 127

Query: 191 TIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALK 234
            ++  ++ +C  D +P  I +D++  +V   I    +K+   +K
Sbjct: 128 IVRHELELVCAPDAIPDDIVIDVAGYEVGDSIHISAVKLPAGVK 171

This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.

Novosphingobium aromaticivorans (strain DSM 12444) (taxid: 279238)

>sp|Q1GSP2|RL25_SPHAL 50S ribosomal protein L25 OS=Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256) GN=rplY PE=3 SV=1

 Score = 85.9 bits (211), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 49/170 (28%), Positives = 91/170 (53%), Gaps = 16/170 (9%)

Query: 53  TILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRS 112
           T+ A  R   G   S + R+ GRVP++V+       GG +  + +   + + L+  L   
Sbjct: 6   TLTAETRERGGKGASRELRRNGRVPAVVY-------GGKEEPLMIHVEE-KLLMKQLMTG 57

Query: 113 FFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPL 172
            F++ +  +EV  +        ++R LP+ V  H   D P++  FLR   +A +++ VP+
Sbjct: 58  HFMNSVVMIEVGGK--------QIRTLPKDVAFHPVKDRPIHADFLRIAKDATVQVAVPV 109

Query: 173 VFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKI 222
           VF+ ++ SPGL++GG LN ++  ++ +C AD +P  I +D++  D+   I
Sbjct: 110 VFQNEEKSPGLKRGGVLNIVRHELELVCDADNIPDEIAIDVTGFDIGDSI 159

This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.

Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256) (taxid: 317655)

>sp|A5CF34|RL25_ORITB 50S ribosomal protein L25 OS=Orientia tsutsugamushi (strain Boryong) GN=rplY PE=3 SV=1

 Score = 85.5 bits (210), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 102/208 (49%), Gaps = 19/208 (9%)

Query: 53  TILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRS 112
           T++   R+  GT  +   R+ G+VP ++++         K +  +    + K V  L R 
Sbjct: 6   TLVGQLRSDFGTSSARALRRQGKVPGVIYK---------KGITPIHVCTLEKEVAKLYRK 56

Query: 113 -FFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPE-ALLKIDV 170
            FF S +  L+V  +        + +VLP+ V LH  T+   ++ F+      ++ K+ V
Sbjct: 57  PFFSSTVIQLQVDDQ--------RFKVLPKAVQLHPVTEFMNHIDFILVEQNGSMQKVKV 108

Query: 171 PLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVH 230
           P+ F G + S G+++GGYLN +KR V  LCP D +P  I  D++ + V   I    L++ 
Sbjct: 109 PISFEGKEKSLGIKRGGYLNIVKRYVDLLCPVDKIPQCIKCDIANVSVGASIKISRLELP 168

Query: 231 PALKLLRSKDEPVCKIAGGRASDQKKSK 258
               L++S  + V     G++S Q K +
Sbjct: 169 EGCNLVKSTTDYVIASVIGKSSKQDKEE 196

This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.

Orientia tsutsugamushi (strain Boryong) (taxid: 357244)

>sp|B0T899|RL25_CAUSK 50S ribosomal protein L25 OS=Caulobacter sp. (strain K31) GN=rplY PE=3 SV=1

 Score = 85.5 bits (210), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 63/204 (30%), Positives = 102/204 (50%), Gaps = 21/204 (10%)

Query: 52  ETILAIP-RASPGTRVSVKERKAGRVPSIVFEQEDGQHGG--NKRLISVQTNQIRKLVGH 108
           E IL +  R   GT  S + R+ G+VP +++       GG      I+V+ N+ RK + H
Sbjct: 3   EIILNVEIRDRAGTGGSRETRRQGKVPGVLY-------GGPLAPVNIAVKGNEFRKAL-H 54

Query: 109 LGRSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKI 168
            G+   +  L  L+       GD  EK  V+ + V  H  TD PL+    R     L+KI
Sbjct: 55  TGK--LLGHLVTLQ------HGD--EKQSVIAKAVQFHPVTDEPLHFDLYRVDEHQLIKI 104

Query: 169 DVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLK 228
           ++P+ F+  D+S GL+KGG L  I+ TV+  CPAD +P  + +DL+  D+   I   ++K
Sbjct: 105 EIPVHFKNHDISVGLKKGGTLEIIRHTVELACPADKIPEELVIDLASHDIGDTIRISEIK 164

Query: 229 VHPALKLLRSKDEPVCKIAGGRAS 252
           +   ++    +D  +  +    AS
Sbjct: 165 LPEGVRPAMERDFVIANLKASAAS 188

This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.

Caulobacter sp. (strain K31) (taxid: 366602)

>sp|B8EK41|RL25_METSB 50S ribosomal protein L25 OS=Methylocella silvestris (strain BL2 / DSM 15510 / NCIMB 13906) GN=rplY PE=3 SV=1

 Score = 84.7 bits (208), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 54/174 (31%), Positives = 91/174 (52%), Gaps = 22/174 (12%)

Query: 52  ETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGN-KRLISVQTNQIRKLV--GH 108
           +T+ A  R   G   +   R+ GR+P +++       GG+    I++   ++ KL+  GH
Sbjct: 5   KTLAAAARHGTGKGAARSVRREGRIPGVIY------GGGDPAEPITLDYRELNKLIYAGH 58

Query: 109 LGRSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKI 168
                F++ LF+++V           K RV+PR   L    D PL+V FLR  P A LK+
Sbjct: 59  -----FLTTLFEIDVAGT--------KQRVIPRDYQLDPIKDLPLHVDFLRLKPGASLKV 105

Query: 169 DVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKI 222
           +VP+ F   +  PG++KGG +N ++ +++   PAD +P  I  DL EL++   +
Sbjct: 106 EVPVHFLNQETCPGVKKGGSVNIVRHSIELRVPADDIPEAITADLGELEINDSL 159

This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.

Methylocella silvestris (strain BL2 / DSM 15510 / NCIMB 13906) (taxid: 395965)

>sp|A5FZ47|RL25_ACICJ 50S ribosomal protein L25 OS=Acidiphilium cryptum (strain JF-5) GN=rplY PE=3 SV=1

 Score = 84.7 bits (208), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 55/177 (31%), Positives = 90/177 (50%), Gaps = 16/177 (9%)

Query: 52  ETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGR 111
           ETI A  RA  G  V+   R+AG+VP++++        G K+  ++     R ++  + R
Sbjct: 5   ETIAAEDRARAGKGVARATRRAGKVPAVIY--------GAKQEPTLIALDPRIVLREMKR 56

Query: 112 SFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVP 171
             + SRL+++E  S         K R L R + LH  TD P +V F R      +++ V 
Sbjct: 57  GGWRSRLYEIETASG--------KARALMRDIQLHPVTDQPEHVDFQRLAAGEPVRVAVN 108

Query: 172 LVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLK 228
           + F  + +S G+++GG LN ++  V+ LC  D +P + + DL  LD+   I   DLK
Sbjct: 109 VNFLNELISVGMKRGGVLNVVRHAVEVLCDPDHIPDHFEADLGPLDINDNIRWSDLK 165

This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.

Acidiphilium cryptum (strain JF-5) (taxid: 349163)

>sp|A7HVD8|RL25_PARL1 50S ribosomal protein L25 OS=Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966) GN=rplY PE=3 SV=1

 Score = 84.0 bits (206), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 52/164 (31%), Positives = 88/164 (53%), Gaps = 23/164 (14%)

Query: 63  GTRVSVKE-RKAGRVPSIVFEQEDGQHGGNKR---LISVQTNQIRKLVGHLGRSFFVSRL 118
           G++ +V+  R+AGRVP++++        G+K+   LI+V    +  L        F+S +
Sbjct: 15  GSKGAVRSLRRAGRVPAVIY--------GDKQSPELIAVSYKDVSAL---YQTGTFMSHV 63

Query: 119 FDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDD 178
            D+E+      G   E  RV+PR V      D  ++V FLR    A + +DVP+ F   +
Sbjct: 64  LDVEI------GGKTE--RVIPRDVQFEPVRDFIIHVDFLRLGKNATVTVDVPVHFHNHE 115

Query: 179 VSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKI 222
            SPG++ GG LN ++  V+ +CPAD +P  +D+DL+  ++   I
Sbjct: 116 ASPGIKAGGVLNIVRHEVELVCPADAIPEQLDIDLTGFEMGSSI 159

This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.

Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966) (taxid: 402881)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	258
225426106	258	PREDICTED: 50S ribosomal protein L25 [Vi	0.992	0.992	0.746	1e-105
359476745	258	PREDICTED: 50S ribosomal protein L25-lik	0.992	0.992	0.746	1e-104
186701238	257	50S ribosomal protein [Capsella rubella]	0.961	0.964	0.733	1e-101
297799630	257	hypothetical protein ARALYDRAFT_492505 [	0.961	0.964	0.725	1e-100
15236554	264	ribosomal L25/TL5/CTC N-terminal 5S rRNA	0.961	0.939	0.730	1e-100
449437765	260	PREDICTED: 50S ribosomal protein L25-lik	0.988	0.980	0.727	1e-100
334186857	277	ribosomal L25/TL5/CTC N-terminal 5S rRNA	0.961	0.895	0.698	2e-98
356571771	257	PREDICTED: 50S ribosomal protein L25-lik	0.930	0.933	0.734	2e-96
356560821	257	PREDICTED: 50S ribosomal protein L25-lik	0.930	0.933	0.734	3e-96
145687759	251	ribosomal protein L25 [Nicotiana bentham	0.961	0.988	0.698	4e-96

>gi|225426106|ref|XP_002272347.1| PREDICTED: 50S ribosomal protein L25 [Vitis vinifera] gi|297742259|emb|CBI34408.3| unnamed protein product [Vitis vinifera]

 Score =  385 bits (989), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 194/260 (74%), Positives = 217/260 (83%), Gaps = 4/260 (1%)

Query: 1   MLIKITRSTLSKSLNLQLRCFSQAAAAILPDDP--SAPLTYLDGLPRPDPRYDETILAIP 58
           MLI   R  L+ +L+L  R FSQ+AAA +  DP    PLTYL+G PRPDP++ E I AIP
Sbjct: 1   MLIHRHRQILTNALHL--RHFSQSAAAAVLQDPLEPPPLTYLEGFPRPDPKFAEIIRAIP 58

Query: 59  RASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRL 118
           R   G  +S KERK GRVPSIVFEQEDGQHGGNKRLISV+TNQIRKLV HLGRSFF+SRL
Sbjct: 59  RTISGKNISAKERKVGRVPSIVFEQEDGQHGGNKRLISVKTNQIRKLVNHLGRSFFLSRL 118

Query: 119 FDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDD 178
           FDLEV   F S ++IEKVRVLPRK+HLH+GTDA LNVTF+RAP  ALLK+DVPLVFRG+D
Sbjct: 119 FDLEVGPHFESNEVIEKVRVLPRKLHLHAGTDAVLNVTFIRAPSHALLKVDVPLVFRGED 178

Query: 179 VSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRS 238
           VSPGL+KG YLNTIKRTVK+LCPADI+PPYIDVDLSELD  QKI+ GDLKVHPALKLLRS
Sbjct: 179 VSPGLKKGAYLNTIKRTVKYLCPADIIPPYIDVDLSELDAGQKIVMGDLKVHPALKLLRS 238

Query: 239 KDEPVCKIAGGRASDQKKSK 258
           KDEPVCKI G R SDQ+KSK
Sbjct: 239 KDEPVCKIMGTRVSDQRKSK 258

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359476745|ref|XP_002276349.2| PREDICTED: 50S ribosomal protein L25-like [Vitis vinifera] gi|297735240|emb|CBI17602.3| unnamed protein product [Vitis vinifera]

 Score =  385 bits (989), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 194/260 (74%), Positives = 218/260 (83%), Gaps = 4/260 (1%)

Query: 1   MLIKITRSTLSKSLNLQLRCFSQAAAAILPDDP--SAPLTYLDGLPRPDPRYDETILAIP 58
           MLI   R  L+ +L+L  R FSQ+AAA +  DP    PLTYL+G PRPDP++ E I AIP
Sbjct: 1   MLIHRHRQILTNALHL--RHFSQSAAAAVLQDPLEPPPLTYLEGFPRPDPKFAEIIRAIP 58

Query: 59  RASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRL 118
           R   G  +S KERK GRVPSIVFEQEDGQHGGNKRLISV+TNQIRKLV HLGRSFF+SRL
Sbjct: 59  RTISGKNISAKERKVGRVPSIVFEQEDGQHGGNKRLISVRTNQIRKLVNHLGRSFFLSRL 118

Query: 119 FDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDD 178
           FDLEV  +F S ++IEKVRVLPRK+HLH+GTDA LNVTF+RAP  ALLK+DVPLVFRG+D
Sbjct: 119 FDLEVGPDFESNEVIEKVRVLPRKLHLHAGTDAVLNVTFIRAPSHALLKVDVPLVFRGED 178

Query: 179 VSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRS 238
           VSPGL+KG YLNTIKRTVK+LCPADI+PPYIDVDLSELD  QKI+ GDLKVHPALKLLRS
Sbjct: 179 VSPGLKKGAYLNTIKRTVKYLCPADIIPPYIDVDLSELDAGQKIVMGDLKVHPALKLLRS 238

Query: 239 KDEPVCKIAGGRASDQKKSK 258
           KDEPVCKI G R SDQ+KSK
Sbjct: 239 KDEPVCKIMGTRVSDQRKSK 258

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|186701238|gb|ACC91264.1| 50S ribosomal protein [Capsella rubella]

 Score =  374 bits (960), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 184/251 (73%), Positives = 213/251 (84%), Gaps = 3/251 (1%)

Query: 8   STLSKSLNLQLRCFSQAAAAILPDDPS--APLTYLDGLPRPDPRYDETILAIPRASPGTR 65
           +TL K+L   LR FS AA A L  D S    LTYL G PRPDP+Y ETILA+PR+  G  
Sbjct: 7   TTLPKTLQ-NLRLFSPAATAALALDHSLDTQLTYLPGFPRPDPKYAETILAVPRSVSGKS 65

Query: 66  VSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRS 125
           +S KERKAGRVPSI+FEQEDGQHGGNKRL+SVQTNQIRKLV HLG SFF+SRLFD+EVR+
Sbjct: 66  ISAKERKAGRVPSIIFEQEDGQHGGNKRLVSVQTNQIRKLVTHLGYSFFLSRLFDVEVRA 125

Query: 126 EFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRK 185
           E GS ++IEKVR LPR +HLHSGTDAPLNVTF+RAPP ALLK+D+PLVF GDDVSPGL+K
Sbjct: 126 EIGSDEVIEKVRALPRAIHLHSGTDAPLNVTFIRAPPGALLKVDIPLVFIGDDVSPGLKK 185

Query: 186 GGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCK 245
           G  LNTIKRTVKFLCPA+I+PPYI+VDLS+LD+ QK++ GDLKVHPALKL++ KDEP+ K
Sbjct: 186 GASLNTIKRTVKFLCPAEIIPPYIEVDLSQLDIGQKLVMGDLKVHPALKLIKPKDEPIVK 245

Query: 246 IAGGRASDQKK 256
           IAGGR SDQ+K
Sbjct: 246 IAGGRVSDQQK 256

Source: Capsella rubella

Species: Capsella rubella

Genus: Capsella

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297799630|ref|XP_002867699.1| hypothetical protein ARALYDRAFT_492505 [Arabidopsis lyrata subsp. lyrata] gi|297313535|gb|EFH43958.1| hypothetical protein ARALYDRAFT_492505 [Arabidopsis lyrata subsp. lyrata]

 Score =  371 bits (953), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 182/251 (72%), Positives = 213/251 (84%), Gaps = 3/251 (1%)

Query: 8   STLSKSLNLQLRCFSQAAAAILPDDPS--APLTYLDGLPRPDPRYDETILAIPRASPGTR 65
           +TL K+L   LR FS AA A L  D +    LTYL G PRPDP++ ETILA+PR+  G  
Sbjct: 7   TTLPKTLQ-NLRLFSPAANAALSLDHTQETQLTYLPGFPRPDPKHAETILAVPRSVSGKS 65

Query: 66  VSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRS 125
           +S KERKAGRVPSI+FEQEDGQHGGNKRLISVQTNQIRKLV HLG SFF+SRLFD+EVR+
Sbjct: 66  ISAKERKAGRVPSIIFEQEDGQHGGNKRLISVQTNQIRKLVNHLGYSFFLSRLFDVEVRA 125

Query: 126 EFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRK 185
           E GS ++IEKVR LPR +HLHSGTDAPLNVTF+RAPP ALLK+D+PLVF GDDVSPGL+K
Sbjct: 126 EIGSDEVIEKVRALPRAIHLHSGTDAPLNVTFIRAPPGALLKVDIPLVFIGDDVSPGLKK 185

Query: 186 GGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCK 245
           G  LNTIKRTVKFLCPA+I+PPYI+VDLS+LD+ QK++ GDLKVHPALKL++SKDEP+ K
Sbjct: 186 GASLNTIKRTVKFLCPAEIIPPYIEVDLSQLDIGQKLVMGDLKVHPALKLIKSKDEPIVK 245

Query: 246 IAGGRASDQKK 256
           +AGGR SD +K
Sbjct: 246 VAGGRVSDTQK 256

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15236554|ref|NP_194093.1| ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain-containing protein [Arabidopsis thaliana] gi|4454031|emb|CAA23028.1| putative protein [Arabidopsis thaliana] gi|7269210|emb|CAB79317.1| putative protein [Arabidopsis thaliana] gi|18253005|gb|AAL62429.1| putative protein [Arabidopsis thaliana] gi|21389687|gb|AAM48042.1| putative protein [Arabidopsis thaliana] gi|21594031|gb|AAM65949.1| unknown [Arabidopsis thaliana] gi|332659385|gb|AEE84785.1| ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain-containing protein [Arabidopsis thaliana]

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 184/252 (73%), Positives = 213/252 (84%), Gaps = 4/252 (1%)

Query: 9   TLSKSLNLQLRCFSQAAAAILPDD--PSAPLTYLDGLPRPDPRYDETILAIPRASPGTRV 66
           TL K+L   LR FS AA A L  D      LTYL G PRPDP++ ETILA+PR+  G  +
Sbjct: 8   TLPKTLQ-NLRLFSPAANAALSLDHIQETQLTYLPGFPRPDPKHAETILAVPRSVSGKSI 66

Query: 67  SVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSE 126
           S KERKAGRVPSI+FEQEDGQHGGNKRLISVQTNQIRKLV HLG SFF+SRLFD+EVR+E
Sbjct: 67  SAKERKAGRVPSIIFEQEDGQHGGNKRLISVQTNQIRKLVNHLGYSFFLSRLFDVEVRAE 126

Query: 127 FGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKG 186
            GS ++IEKVR LPR +HLHSGTDAPLNVTF+RAPP ALLK+D+PLVF GDDVSPGL+KG
Sbjct: 127 IGSDEVIEKVRALPRAIHLHSGTDAPLNVTFIRAPPGALLKVDIPLVFIGDDVSPGLKKG 186

Query: 187 GYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKI 246
             LNTIKRTVKFLCPA+I+PPYI+VDLS+LD+ QK++ GDLKVHPALKL++SKDEP+ K+
Sbjct: 187 ASLNTIKRTVKFLCPAEIIPPYIEVDLSQLDIGQKLVMGDLKVHPALKLIKSKDEPIVKV 246

Query: 247 AGGRASD-QKKS 257
           AGGR +D QKKS
Sbjct: 247 AGGRVTDTQKKS 258

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449437765|ref|XP_004136661.1| PREDICTED: 50S ribosomal protein L25-like [Cucumis sativus] gi|449494761|ref|XP_004159639.1| PREDICTED: 50S ribosomal protein L25-like [Cucumis sativus]

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 187/257 (72%), Positives = 218/257 (84%), Gaps = 2/257 (0%)

Query: 2   LIKITRS-TLSKSLNLQLRCFSQAAAAILPDDPSAPL-TYLDGLPRPDPRYDETILAIPR 59
           +++  RS TLS+ L  +    +  A A   D  S PL +YL+G P+PDP+Y ETILAIPR
Sbjct: 1   MLRFYRSPTLSRVLLRRYSAATAPATAPAFDSVSEPLFSYLEGFPKPDPKYAETILAIPR 60

Query: 60  ASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLF 119
           +  G  +S KERKAGRVPSIVFEQEDGQHGGNKRLISV+TNQI KLV +LGRSFF+SRLF
Sbjct: 61  SISGKSISAKERKAGRVPSIVFEQEDGQHGGNKRLISVRTNQIVKLVKNLGRSFFLSRLF 120

Query: 120 DLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDV 179
           DLEV S+F SGD++EKVRVLPRK+HLH+GTDAPLNVTF+RAP  A+LK+DVPLVFRG+DV
Sbjct: 121 DLEVLSDFESGDIVEKVRVLPRKIHLHAGTDAPLNVTFIRAPSHAVLKVDVPLVFRGEDV 180

Query: 180 SPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSK 239
            PGLRKG YLNTIKRTVK+LCPADI+PPYIDVDLSELDV QK++ GDLKVHPALKL++SK
Sbjct: 181 CPGLRKGSYLNTIKRTVKYLCPADIIPPYIDVDLSELDVGQKLVMGDLKVHPALKLVKSK 240

Query: 240 DEPVCKIAGGRASDQKK 256
           DEPVCKIAG R SDQ+K
Sbjct: 241 DEPVCKIAGARVSDQQK 257

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334186857|ref|NP_001190814.1| ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain-containing protein [Arabidopsis thaliana] gi|332659386|gb|AEE84786.1| ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain-containing protein [Arabidopsis thaliana]

 Score =  364 bits (934), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 185/265 (69%), Positives = 214/265 (80%), Gaps = 17/265 (6%)

Query: 9   TLSKSLNLQLRCFSQAAAAILPDD--PSAPLTYLDGLPRPDPRYDETILAIPRASPGTRV 66
           TL K+L   LR FS AA A L  D      LTYL G PRPDP++ ETILA+PR+  G  +
Sbjct: 8   TLPKTLQ-NLRLFSPAANAALSLDHIQETQLTYLPGFPRPDPKHAETILAVPRSVSGKSI 66

Query: 67  SVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSE 126
           S KERKAGRVPSI+FEQEDGQHGGNKRLISVQTNQIRKLV HLG SFF+SRLFD+EVR+E
Sbjct: 67  SAKERKAGRVPSIIFEQEDGQHGGNKRLISVQTNQIRKLVNHLGYSFFLSRLFDVEVRAE 126

Query: 127 FGSGDLIEKVRVLPR-------------KVHLHSGTDAPLNVTFLRAPPEALLKIDVPLV 173
            GS ++IEKVR LPR             K+HLHSGTDAPLNVTF+RAPP ALLK+D+PLV
Sbjct: 127 IGSDEVIEKVRALPRAVKSPFLSLMKLIKIHLHSGTDAPLNVTFIRAPPGALLKVDIPLV 186

Query: 174 FRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPAL 233
           F GDDVSPGL+KG  LNTIKRTVKFLCPA+I+PPYI+VDLS+LD+ QK++ GDLKVHPAL
Sbjct: 187 FIGDDVSPGLKKGASLNTIKRTVKFLCPAEIIPPYIEVDLSQLDIGQKLVMGDLKVHPAL 246

Query: 234 KLLRSKDEPVCKIAGGRASD-QKKS 257
           KL++SKDEP+ K+AGGR +D QKKS
Sbjct: 247 KLIKSKDEPIVKVAGGRVTDTQKKS 271

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356571771|ref|XP_003554046.1| PREDICTED: 50S ribosomal protein L25-like [Glycine max]

 Score =  358 bits (918), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 177/241 (73%), Positives = 204/241 (84%), Gaps = 1/241 (0%)

Query: 19  RCFSQAAAAILPDDPSAPLTYLDGLPRPDPRYDETILAIPRASPGTRVSVKERKAGRVPS 78
           R FS +AAA+L      PLTYLDG PRPDP++DETILAIPRA  G  +S KER+AGR+PS
Sbjct: 17  RHFSHSAAAVLRPPGPEPLTYLDGFPRPDPKHDETILAIPRADSGKNISAKERRAGRLPS 76

Query: 79  IVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGS-GDLIEKVR 137
           IVFEQEDGQHGGNKRLISV+T+QIRKLV HLGRSFF+SRLF L+VR+ F S  D +E VR
Sbjct: 77  IVFEQEDGQHGGNKRLISVRTDQIRKLVNHLGRSFFLSRLFHLQVRAHFDSEDDFVETVR 136

Query: 138 VLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVK 197
           VLPR +HL +GTDAPLNVTF+RAP  ALLK+DVPLVFRG+DVSPGL+KG  LNTIKRTVK
Sbjct: 137 VLPRAIHLKAGTDAPLNVTFIRAPSNALLKVDVPLVFRGEDVSPGLKKGASLNTIKRTVK 196

Query: 198 FLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGRASDQKKS 257
           +LCPADI+PPYIDVDLSELDV QK++ GDLKVHPALKLL+S+DE V KI G R S+ +K 
Sbjct: 197 YLCPADIIPPYIDVDLSELDVGQKLVMGDLKVHPALKLLQSRDEAVVKIMGQRVSELQKK 256

Query: 258 K 258
           K
Sbjct: 257 K 257

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356560821|ref|XP_003548685.1| PREDICTED: 50S ribosomal protein L25-like isoform 1 [Glycine max]

 Score =  357 bits (915), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 177/241 (73%), Positives = 205/241 (85%), Gaps = 1/241 (0%)

Query: 19  RCFSQAAAAILPDDPSAPLTYLDGLPRPDPRYDETILAIPRASPGTRVSVKERKAGRVPS 78
           R FS +AAA+L      PLTYLDG PRPDP++DETILA+PRA  G  +S KER+AGR+PS
Sbjct: 17  RHFSHSAAAVLRPPEPEPLTYLDGFPRPDPKHDETILAVPRADSGKNISAKERRAGRLPS 76

Query: 79  IVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGS-GDLIEKVR 137
           IVFEQEDGQHGGNKRLISV+T+QIRKLV HLGRSFF+SRLF LEVRS F S  D++E VR
Sbjct: 77  IVFEQEDGQHGGNKRLISVRTDQIRKLVNHLGRSFFLSRLFLLEVRSGFDSENDVVETVR 136

Query: 138 VLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVK 197
           VLPR +HL +GTDAPLNVTF+RAP +ALLK+DVPLVFRG+DVSPGL+KG  LNTIKRTVK
Sbjct: 137 VLPRAIHLKAGTDAPLNVTFIRAPSDALLKVDVPLVFRGEDVSPGLKKGASLNTIKRTVK 196

Query: 198 FLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGRASDQKKS 257
           +LCPADI+PPYIDVDLSELDV QK++ GDLKVHPALKLL+ +DE V KI G R S+ +K 
Sbjct: 197 YLCPADIIPPYIDVDLSELDVGQKLVMGDLKVHPALKLLQPRDEAVVKIMGQRVSELQKK 256

Query: 258 K 258
           K
Sbjct: 257 K 257

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145687759|gb|ABP88855.1| ribosomal protein L25 [Nicotiana benthamiana]

 Score =  356 bits (914), Expect = 4e-96,   Method: Compositional matrix adjust.
 Identities = 178/255 (69%), Positives = 207/255 (81%), Gaps = 7/255 (2%)

Query: 5   ITRSTLSKSLN-LQLRCFSQAAAAILPDDPSAPLTYLDGLPRPDPRYDETILAIPRASPG 63
           I R  L+ SL+   LR FS +AAA++   P          P+PDP+YDETI AI RA  G
Sbjct: 3   IRRVALTASLHHYHLRFFSNSAAAVVLPYPEP------EFPKPDPKYDETIHAIARAKSG 56

Query: 64  TRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEV 123
             ++ KERKAGRVPSIVFEQEDGQHGGNKRLISVQ NQIRKLV HLGRS F+SRLFDLEV
Sbjct: 57  KNIAAKERKAGRVPSIVFEQEDGQHGGNKRLISVQANQIRKLVNHLGRSHFLSRLFDLEV 116

Query: 124 RSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGL 183
           R +F S +++EKVRVLPRKVHL +G+DAPLNVTF+RAP  ALLK+DVPL+FRG+DVSPGL
Sbjct: 117 RPDFDSVEVVEKVRVLPRKVHLEAGSDAPLNVTFIRAPSSALLKVDVPLIFRGEDVSPGL 176

Query: 184 RKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPV 243
           +KG YLN IKRTVK+LCPAD++PPYIDVDLSELDV QK++ GDLKVHPALKL++ KD PV
Sbjct: 177 KKGSYLNIIKRTVKYLCPADVIPPYIDVDLSELDVGQKLVMGDLKVHPALKLVQPKDHPV 236

Query: 244 CKIAGGRASDQKKSK 258
            KI G R SDQKK+K
Sbjct: 237 VKIMGARVSDQKKAK 251

Source: Nicotiana benthamiana

Species: Nicotiana benthamiana

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	258
TAIR|locus:2174979	249	AT5G66860 [Arabidopsis thalian	0.751	0.779	0.458	3.7e-39
TIGR_CMR|ECH_0142	210	ECH_0142 "ribosomal 5S rRNA E-	0.709	0.871	0.26	3.2e-12
TIGR_CMR|SPO_0812	207	SPO_0812 "ribosomal protein L2	0.689	0.859	0.276	3.9e-11
TIGR_CMR|APH_1302	211	APH_1302 "ribosomal 5S rRNA E-	0.689	0.843	0.24	2.6e-09
TIGR_CMR|CBU_1840	244	CBU_1840 "ribosomal 5S rRNA E-	0.457	0.483	0.320	1.1e-08
TIGR_CMR|NSE_0306	194	NSE_0306 "ribosomal 5S rRNA E-	0.426	0.567	0.333	1.5e-08
TIGR_CMR|GSU_0662	194	GSU_0662 "ribosoma protein L25	0.383	0.510	0.274	5.6e-05

TAIR|locus:2174979 AT5G66860 [Arabidopsis thaliana (taxid:3702)]

 Score = 418 (152.2 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 93/203 (45%), Positives = 128/203 (63%)

Query:    52 ETILAIPRASPGTRVSVKERKAGRVPSIVFEQE----DGQHGG--NKRLISVQTNQIRKL 105
             +TI AIPR + G  VS ++R  GR+P++VF Q     D    G   K+L++    QI+ +
Sbjct:    34 QTIQAIPREATGRGVSARDRTIGRIPAVVFPQSLLDTDASKRGVSRKQLLTADKKQIKSI 93

Query:   106 VGHLGRSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEAL 165
             +  +G  FF S  F L++R+  GS  L+E  RVLP KVH    T   LN+ F+ A     
Sbjct:    94 IDSVGLPFFCSTTFQLQIRAGQGSSTLVESGRVLPLKVHRDEETGKILNLVFVWADDGEK 153

Query:   166 LKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAG 225
             LK+DVP+VF+G D  PGL+KGG L TI+ T+K L PA+ +P  I+VD+S LD+E K+L  
Sbjct:   154 LKVDVPVVFKGLDHCPGLQKGGNLRTIRSTLKLLGPAEHIPSKIEVDVSNLDIEDKVLLQ 213

Query:   226 DLKVHPALKLLRSKDE--PVCKI 246
             D+  HP+LKLL SK+E  PVCKI
Sbjct:   214 DVVFHPSLKLL-SKNETMPVCKI 235

GO:0006412 "translation" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

TIGR_CMR|ECH_0142 ECH_0142 "ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 164 (62.8 bits), Expect = 3.2e-12, P = 3.2e-12
 Identities = 52/200 (26%), Positives = 92/200 (46%)

Query:    59 RASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRL 118
             R + GT  S   R +G +P++++       G  +  +S+  +  R+ V     +   + L
Sbjct:    14 RKNVGTGPSRALRLSGEIPAVIY-------GKGRDSLSISLSN-REFVSKYRSAALSTHL 65

Query:   119 FDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDD 178
              +LE+ ++        K  VL R V  H  TD   +V F        +KI+VPL+F  + 
Sbjct:    66 IELEIDNK--------KEYVLMRDVQKHPVTDRIQHVDFQFIDYGTEIKIEVPLIFTNEQ 117

Query:   179 VSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRS 238
                G+++GG LN + RT+   C    +   I++DLS L     I   DLK+ P + +   
Sbjct:   118 KCIGIKRGGVLNILHRTLSIKCSPKAILQNIEIDLSGLTTGHSIHVSDLKLPPEVNVTMK 177

Query:   239 KDEPVCKIAGGRASDQKKSK 258
             +  P   +    AS +K+++
Sbjct:   178 EHNPAI-VTISSASTEKEAE 196

GO:0000315 "organellar large ribosomal subunit" evidence=ISS

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0006950 "response to stress" evidence=ISS

GO:0008097 "5S rRNA binding" evidence=ISS

TIGR_CMR|SPO_0812 SPO_0812 "ribosomal protein L25" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 155 (59.6 bits), Expect = 3.9e-11, P = 3.9e-11
 Identities = 54/195 (27%), Positives = 92/195 (47%)

Query:    54 ILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRL-ISVQTNQIRKLVGHLGRS 112
             ++A+ R   G   + + R+ G VP IVF    G  G N+ L I +  N++ K++   GR 
Sbjct:     8 LVALERTGTGKGAARQARRDGMVPGIVF----G--GDNEPLPIQIPFNRLLKML-KAGR- 59

Query:   113 FFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPL 172
              F S LF+L+V          E VRV+ R V      D P ++  +R    + +K+ + +
Sbjct:    60 -FKSTLFNLKVEGH-------EDVRVICRDVQRDVVKDLPTHLDLMRLRRTSRIKLFIHV 111

Query:   173 VFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPA 232
              F     +PGL+KGG L  ++  V+    A  +P  I VDL+ L++   +    + +   
Sbjct:   112 DFVNHAAAPGLKKGGVLTVVRPEVELEVTAGDIPESITVDLTGLNIGDVVTISSVTLPAG 171

Query:   233 LKLLRSKDEPVCKIA 247
              K    +D  +  I+
Sbjct:   172 AKPTVERDFVIANIS 186

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0006950 "response to stress" evidence=ISS

GO:0008097 "5S rRNA binding" evidence=ISS

TIGR_CMR|APH_1302 APH_1302 "ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5" [Anaplasma phagocytophilum HZ (taxid:212042)]

 Score = 148 (57.2 bits), Expect = 2.6e-09, P = 2.6e-09
 Identities = 48/200 (24%), Positives = 102/200 (51%)

Query:    63 GTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFV-SRLFDL 121
             GT  +   R  G +P++++       G N+  I++  +Q+  L     R+F + S+L +L
Sbjct:    18 GTGSARALRARGLIPAVIY-------GKNRDPINISLSQVDFL--KKCRTFPIFSKLIEL 68

Query:   122 EVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSP 181
              +      G+  +K  V+ + +  H  + A  +V F     +A +K++VPLVF  +    
Sbjct:    69 CI------GE--KKEYVITKDIQKHPVSGAIAHVDFQFVDQDAEMKMEVPLVFLNEQKCV 120

Query:   182 GLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDE 241
             G+++GG +N + R++   C    +P  ++VDL ++ +   +   DLK+   + ++  +++
Sbjct:   121 GVKRGGVINILHRSLIIRCSPHHIPKSLEVDLIDVAIGHSLHVSDLKLPSTINVVMKEED 180

Query:   242 PVCK--IA--GGRASDQKKS 257
             PV    +A  GG + D +++
Sbjct:   181 PVIATVVASGGGISEDAEEA 200

GO:0000315 "organellar large ribosomal subunit" evidence=ISS

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0006950 "response to stress" evidence=ISS

GO:0008097 "5S rRNA binding" evidence=ISS

TIGR_CMR|CBU_1840 CBU_1840 "ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 148 (57.2 bits), Expect = 1.1e-08, P = 1.1e-08
 Identities = 41/128 (32%), Positives = 68/128 (53%)

Query:   121 LEVRSEFGS------GDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVF 174
             LE  S F S      GD  +K +V+ + +  H      +++ F R      L ++VPL F
Sbjct:    56 LESESTFSSILTLKVGD--KKQKVILKALQRHHTKPKIVHIDFQRIKASEKLIMNVPLHF 113

Query:   175 RGDDVSPGLRKGGYLNTIKRTVKFLC-PADIVPPYIDVDLSELDVEQKILAGDLKVHPAL 233
              G+D  PG+  GG ++ ++  V+  C PAD+ P YI+VDLS L +++ +   +LK+   +
Sbjct:   114 LGEDDCPGVEAGGVVSHLQSEVEIRCLPADL-PEYIEVDLSHLQLDESVHLSNLKLPAGV 172

Query:   234 KLLRSKDE 241
              L  + DE
Sbjct:   173 GLTSAVDE 180

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0006950 "response to stress" evidence=ISS

GO:0008097 "5S rRNA binding" evidence=ISS

TIGR_CMR|NSE_0306 NSE_0306 "ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5" [Neorickettsia sennetsu str. Miyayama (taxid:222891)]

 Score = 125 (49.1 bits), Expect = 1.5e-08, Sum P(2) = 1.5e-08
 Identities = 38/114 (33%), Positives = 52/114 (45%)

Query:   137 RVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTV 196
             +V+P+   LH  +   L++ F+ A   A  K  VPL F     S  +R G  LN +KRTV
Sbjct:    71 KVVPKAYELHPVSSVVLHLDFVFAGEHAS-KFQVPLNFVNSGKSEAIRLGAMLNIVKRTV 129

Query:   197 KFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHP--ALKLLRSKDEPVCKIAG 248
                C A  +P  I VD+    V   I   DL V P   + L R  +  V  + G
Sbjct:   130 LVRCTAANLPKSIPVDIENAKVGDSIKFSDL-VFPDGVVPLARDANSVVATVVG 182

GO:0000315 "organellar large ribosomal subunit" evidence=ISS

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0006950 "response to stress" evidence=ISS

GO:0008097 "5S rRNA binding" evidence=ISS

TIGR_CMR|GSU_0662 GSU_0662 "ribosoma protein L25" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 115 (45.5 bits), Expect = 5.6e-05, P = 5.6e-05
 Identities = 28/102 (27%), Positives = 54/102 (52%)

Query:   153 LNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVD 212
             L+V F R   +  +K+ VPLV  G   + G+++GG L+ +  ++   C    +P  I+VD
Sbjct:    91 LHVDFHRISLDEKVKVHVPLVMVG--TAAGVKEGGMLDVVTYSLDVECLPTAIPEAINVD 148

Query:   213 LSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGRASDQ 254
             ++ L +   I   +L +   +K+L   + P+  I G +A ++
Sbjct:   149 VTNLAIGHSIHVSELVLPAGIKVLNDPETPIVSIHG-KAKEE 189


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.319   0.139   0.402    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      258       258   0.00087  114 3  11 22  0.47    33
                                                     32  0.48    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  7
  No. of states in DFA:  563 (60 KB)
  Total size of DFA:  156 KB (2094 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  22.09u 0.09s 22.18t   Elapsed:  00:00:01
  Total cpu time:  22.09u 0.09s 22.18t   Elapsed:  00:00:01
  Start:  Thu May  9 15:10:13 2013   End:  Thu May  9 15:10:14 2013

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0006950 "response to stress" evidence=ISS

GO:0008097 "5S rRNA binding" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00002517001	SubName- Full=Chromosome chr2 scaffold_132, whole genome shotgun sequence; (258 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00018977001	RecName- Full=Ribose-phosphate pyrophosphokinase; EC=2.7.6.1; (322 aa)	•						•		0.649
	GSVIVG00015830001	RecName- Full=Ribose-phosphate pyrophosphokinase; EC=2.7.6.1; (321 aa)	•						•		0.646
	GSVIVG00017644001	SubName- Full=Chromosome chr17 scaffold_16, whole genome shotgun sequence; (252 aa)	•								0.586
	GSVIVG00024798001	SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (217 aa)	•								0.575
	GSVIVG00025769001	SubName- Full=Chromosome chr19 scaffold_35, whole genome shotgun sequence; (365 aa)	•								0.460
	GSVIVG00038245001	SubName- Full=Chromosome chr14 scaffold_9, whole genome shotgun sequence; (246 aa)	•								0.449

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	258
PRK05618	197	PRK05618, PRK05618, 50S ribosomal protein L25/gene	3e-33
TIGR00731	176	TIGR00731, ctc_TL5, ribosomal protein L25, Ctc-for	5e-13
cd00495	90	cd00495, Ribosomal_L25_TL5_CTC, Ribosomal L25/TL5/	6e-11
COG1825	93	COG1825, RplY, Ribosomal protein L25 (general stre	2e-04
pfam01386	87	pfam01386, Ribosomal_L25p, Ribosomal L25p family	3e-04

>gnl|CDD|235534 PRK05618, PRK05618, 50S ribosomal protein L25/general stress protein Ctc; Reviewed

 Score =  119 bits (300), Expect = 3e-33
 Identities = 62/201 (30%), Positives = 99/201 (49%), Gaps = 20/201 (9%)

Query: 53  TILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNK--RLISVQTNQIRKLVGHLG 110
           T+ A  R   G   + + R+AG+VP++++       G  K    ISV   ++ K    L 
Sbjct: 5   TLEAEVREEFGKGAARRLRRAGKVPAVIY-------GKGKEPVSISVDEKELIKA---LK 54

Query: 111 RSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDV 170
           +  F+S L DLEV  +        K +VL + V  H   D  L+V FLR      +K++V
Sbjct: 55  KGAFLSTLLDLEVGGK--------KQKVLVKDVQRHPVKDFILHVDFLRVDAGEKVKVEV 106

Query: 171 PLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVH 230
           P+ F G+    G++ GG LN +   ++  C  + +P +I+VD+S L++   I   DLK+ 
Sbjct: 107 PVHFVGEAKGVGVKLGGVLNQVLHELEVECLPEDIPEFIEVDVSGLEIGDSIHVSDLKLP 166

Query: 231 PALKLLRSKDEPVCKIAGGRA 251
             +KLL   DE V  +   R 
Sbjct: 167 EGVKLLDDPDEVVATVVAPRG 187

Length = 197

>gnl|CDD|233106 TIGR00731, ctc_TL5, ribosomal protein L25, Ctc-form

 Score = 65.1 bits (159), Expect = 5e-13
 Identities = 42/190 (22%), Positives = 86/190 (45%), Gaps = 19/190 (10%)

Query: 59  RASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRL 118
           R S G   + + RK GR+P++V+       G     + +++ +  K +     S     +
Sbjct: 6   RTSFGKSAARRIRKEGRIPAVVYG-----KGKENVNLELKSKEFIKYLRKGATS----TV 56

Query: 119 FDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDD 178
             LE+  +        + +VL +    +  T+  ++V FL       LK++VP+   G  
Sbjct: 57  LTLEIGGK--------EFKVLVKDYQYNPVTNEVIHVDFLEVVEGVKLKVEVPIKLIGTP 108

Query: 179 VSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRS 238
           +  G++ GG L  +KR ++  C    +P ++++D+S L V + +   DL++   +  +  
Sbjct: 109 I--GVKNGGILTQVKRRIEVECKPKDIPDFLELDVSSLGVGESLKLSDLELPAGVSFITD 166

Query: 239 KDEPVCKIAG 248
            DE V  +  
Sbjct: 167 DDEVVVTVIK 176

This model models a family of proteins with full-length homology to the general stress protein Ctc of Bacillus subtilis, a mesophile, and ribosomal protein TL5 of Thermus thermophilus, a thermophile. Ribosomal protein L25 of Escherichia coli and H. influenzae appear to be orthologous but consist only of the N-terminal half of Ctc and TL5. Both short (L25-like) and full-length (CTC-like) members of this family bind the E-loop of bacterial 5S rRNA. This protein appears to be restricted to bacteria and organelles, and consists of at most one copy per prokaryotic genome.Ctc of Bacillus subtilis has now been localized to ribosomes and can be viewed as the long form, or Ctc form, of L25. The C-terminal domain of sll1824, an apparent L25 of Synechocystis PCC6803, matches the N-terminal domain of this family. Examples of L25 and Ctc are not separated by a UPGMA tree built on the region of shared homology [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 176

>gnl|CDD|198379 cd00495, Ribosomal_L25_TL5_CTC, Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain

 Score = 57.1 bits (139), Expect = 6e-11
 Identities = 28/107 (26%), Positives = 47/107 (43%), Gaps = 17/107 (15%)

Query: 53  TILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRS 112
           T+ A  R   G   + + R+ G+VP++++       G     ISV   ++ KL+   G  
Sbjct: 1   TLKAEKREETGKGAARRLRREGKVPAVIY-----GKGEEPIPISVDAKELEKLLRKEGE- 54

Query: 113 FFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLR 159
              + + +LE+          +K  VL + V  H   D  L+V FLR
Sbjct: 55  ---NTVIELEIDG--------KKENVLIKDVQRHPVKDEILHVDFLR 90

L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had impaired protein synthesis capability. In Bacillus subtilis, CTC is induced under stress conditions and located in the ribosome; it has been proposed that CTC may be necessary for accurate translation under stress conditions. Ribosomal_L25_TL5_CTC is mostly found in bacteria, with a few exceptions such as plants or stramenopiles. Due to its limited taxonomic diversity and the viability of cells deleted for L25, this protein is not believed to be necessary for ribosomal assembly. Eukaryotes contain a protein called L25, which is not homologous to bacterial L25, but rather to bacterial L23. Length = 90

>gnl|CDD|224738 COG1825, RplY, Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis]

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 28/103 (27%), Positives = 49/103 (47%), Gaps = 21/103 (20%)

Query: 59  RASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQ--TNQIRKLVGHLGRSFFVS 116
           R S G   S + R+AG++P++V+       GG K  +++    ++  K +  LG S    
Sbjct: 9   RTSQGKGASRRLRRAGKIPAVVY-------GGGKEPVNIALDHHEFAKALRKLGYST--- 58

Query: 117 RLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLR 159
            +  LEV          ++++VL + V  H  TD   ++ FLR
Sbjct: 59  -VITLEVDG--------KEIKVLVKDVQRHPLTDEVQHIDFLR 92

Length = 93

>gnl|CDD|216471 pfam01386, Ribosomal_L25p, Ribosomal L25p family

 Score = 38.2 bits (90), Expect = 3e-04
 Identities = 24/104 (23%), Positives = 44/104 (42%), Gaps = 21/104 (20%)

Query: 56  AIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQ--TNQIRKLVGHLGRSF 113
           A  R   G   S + R+ G+VP++++       G  K  +S+     ++ KL+    R  
Sbjct: 3   AEKREETGKGASRRLRREGKVPAVIY-------GKGKEPVSISVDEKELEKLL----REA 51

Query: 114 FVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTF 157
             + + +L++          +K  VL + V  H   D  L+V F
Sbjct: 52  GENTVIELKIDG--------KKENVLIKDVQRHPVKDKILHVDF 87

Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis, which is induced by stress. Length = 87

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	258
TIGR00731	176	ctc_TL5 ribosomal protein L25, Ctc-form. The C-ter	100.0
PRK05618	197	50S ribosomal protein L25/general stress protein C	100.0
PRK05943	94	50S ribosomal protein L25; Reviewed	99.96
PF14693	88	Ribosomal_TL5_C: Ribosomal protein TL5, C-terminal	99.95
cd00495	91	Ribosomal_L25_TL5_CTC Ribosomal_L25_TL5_CTC: Ribos	99.95
PF01386	88	Ribosomal_L25p: Ribosomal L25p family; InterPro: I	99.95
COG1825	93	RplY Ribosomal protein L25 (general stress protein	99.92

>TIGR00731 ctc_TL5 ribosomal protein L25, Ctc-form

Probab=100.00  E-value=8e-56  Score=381.40  Aligned_cols=175  Identities=24%  Similarity=0.490  Sum_probs=166.8

Q ss_pred             EEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECCccCCCCcc
Q 025088           54 ILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDLI  133 (258)
Q Consensus        54 L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g~~~~~~~~  133 (258)
                      |+|++|+.+||+++|+||++|+|||||||+     |.++++|++++++|.+++++.+.    +++|+|+++|+       
T Consensus         1 l~a~~R~~~gk~~~r~LR~~G~VPaVvYG~-----~~~~~~i~v~~~el~k~l~~~~~----~~~i~L~v~g~-------   64 (176)
T TIGR00731         1 LEVKSRTSFGKSAARRIRKEGRIPAVVYGK-----GKENVNLELKSKEFIKYLRKGAT----STVLTLEIGGK-------   64 (176)
T ss_pred             CeEEEeCCCCChHHHHHHHCCCccEEEECC-----CCCCEEEEECHHHHHHHHhccCC----cEEEEEEECCE-------
Confidence            579999999999999999999999999998     45799999999999999987653    79999999974       


Q ss_pred             ceEeEEEeeeeeccCCCCceEEEEEEeCCCCeEEEEEeEEEEecCCCcccccCeEEEEEeeEEEEEeeCCCCCCeEEEEc
Q 025088          134 EKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDL  213 (258)
Q Consensus       134 ~~~~vliKeVQ~hpvt~~ilHVDF~~v~~~~~v~v~VPV~~~Ge~~s~Gvk~GG~L~~~~~~V~V~~~p~~IPe~IeVDv  213 (258)
                       +++|++||+|+||++++++|||||+++++++|+++|||+|+|+  ++|+|+||+|++.+++|+|+|+|++||++|+|||
T Consensus        65 -~~~vlikevQ~~pv~~~i~HvDF~~v~~~~~v~v~VPv~~~G~--~~gvk~GG~l~~~~~~v~v~~~p~~IPe~I~VDv  141 (176)
T TIGR00731        65 -EFKVLVKDYQYNPVTNEVIHVDFLEVVEGVKLKVEVPIKLIGT--PIGVKNGGILTQVKRRIEVECKPKDIPDFLELDV  141 (176)
T ss_pred             -EEEEEEehhhhccCCCCeEEEEeEEeCCCCEEEEEeeEEEecc--cccccCCcEEEEEEEEEEEEECHHHCCccEEEEC
Confidence             6799999999999999999999999999999999999999998  6899999999999999999999999999999999


Q ss_pred             CCCCCCCeEEEeccCCCCCeEEecCCCccEEEEE
Q 025088          214 SELDVEQKILAGDLKVHPALKLLRSKDEPVCKIA  247 (258)
Q Consensus       214 S~L~iGd~I~v~DL~lp~gv~ll~d~e~vVvsV~  247 (258)
                      |+|++||+||++||++|+|+++++|+|++||+|.
T Consensus       142 s~L~iGd~i~v~Dl~lp~gv~~~~d~~~~v~~V~  175 (176)
T TIGR00731       142 SSLGVGESLKLSDLELPAGVSFITDDDEVVVTVI  175 (176)
T ss_pred             ccCCCCCEEEEeeccCCCCcEEccCCCcEEEEEe
Confidence            9999999999999999999999999999999985

The C-terminal domain of sll1824, an apparent L25 of Synechocystis PCC6803, matches the N-terminal domain of this family. Examples of L25 and Ctc are not separated by a UPGMA tree built on the region of shared homology.

>PRK05618 50S ribosomal protein L25/general stress protein Ctc; Reviewed

Probab=100.00  E-value=4.5e-55  Score=382.57  Aligned_cols=189  Identities=32%  Similarity=0.518  Sum_probs=175.1

Q ss_pred             CCceeEEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECCccC
Q 025088           49 RYDETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFG  128 (258)
Q Consensus        49 m~~~~L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g~~~  128 (258)
                      |...+|+|++|+.+||+++|+||++|+|||||||+     |.++++|+++.++|.+++++..   +.+++|+|+++|+  
T Consensus         1 m~~~~l~a~~R~~~gk~~~r~lR~~G~VPaViYG~-----~~~~~~i~v~~~~l~k~l~~~~---~~~~~i~L~i~g~--   70 (197)
T PRK05618          1 METITLEAEVREEFGKGAARRLRRAGKVPAVIYGK-----GKEPVSISVDEKELIKALKKGA---FLSTLLDLEVGGK--   70 (197)
T ss_pred             CCeEEEEEEEcCcCCChHHHHHHHCCCCcEEEECC-----CCCCEEEEECHHHHHHHHhcCC---ceeEEEEEEECCE--
Confidence            55689999999999999999999999999999998     3579999999999999995321   3488999999763  


Q ss_pred             CCCccceEeEEEeeeeeccCCCCceEEEEEEeCCCCeEEEEEeEEEEecCCCcccccCeEEEEEeeEEEEEeeCCCCCCe
Q 025088          129 SGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPY  208 (258)
Q Consensus       129 ~~~~~~~~~vliKeVQ~hpvt~~ilHVDF~~v~~~~~v~v~VPV~~~Ge~~s~Gvk~GG~L~~~~~~V~V~~~p~~IPe~  208 (258)
                            +++|++||||+||++++++|||||+++++++|+++|||.|+|++.+++.|+||+|++.+++|+|+|+|++||++
T Consensus        71 ------~~~vlikevQ~~pv~~~i~HvDF~~v~~~~~v~v~VPv~~~G~~~~~~~k~GG~l~~~~~~v~v~~~p~~IP~~  144 (197)
T PRK05618         71 ------KQKVLVKDVQRHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVKLGGVLNQVLHELEVECLPEDIPEF  144 (197)
T ss_pred             ------EEEEEEeeeeeccCCCCEEeEEEEEeCCCCEEEEEeeEEEEcCCCCcccccceEEEEEEEEEEEEEcHHHCCcc
Confidence                  78999999999999999999999999999999999999999998766677799999999999999999999999


Q ss_pred             EEEEcCCCCCCCeEEEeccCCCCCeEEecCCCccEEEEEcccccc
Q 025088          209 IDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGRASD  253 (258)
Q Consensus       209 IeVDvS~L~iGd~I~v~DL~lp~gv~ll~d~e~vVvsV~~~r~~~  253 (258)
                      |+||||+|++||+|+++||++|+|+++++|+|++||+|.+++.+.
T Consensus       145 I~VDVs~L~~Gd~i~v~Dl~lp~~v~i~~~~~~~v~~V~~~~~~~  189 (197)
T PRK05618        145 IEVDVSGLEIGDSIHVSDLKLPEGVKLLDDPDEVVATVVAPRGEE  189 (197)
T ss_pred             EEEEcccCCCCCEEEeeeecCCCCcEEcCCCCcEEEEEEcCCccc
Confidence            999999999999999999999999999999999999999998653

>PRK05943 50S ribosomal protein L25; Reviewed

Probab=99.96  E-value=1.8e-28  Score=191.64  Aligned_cols=93  Identities=24%  Similarity=0.334  Sum_probs=84.5

Q ss_pred             eeEEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECCccCCCC
Q 025088           52 ETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGD  131 (258)
Q Consensus        52 ~~L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g~~~~~~  131 (258)
                      .+|+|++|+.+||+++|+||++|+|||||||+     |.++++|++++++|.+++++.+   +.+++|+|+++|+     
T Consensus         2 ~~l~a~~R~~~gk~~~r~lR~~G~vPaViYG~-----~~~~~~i~v~~~el~k~l~~~~---~~~~~i~L~v~g~-----   68 (94)
T PRK05943          2 FTINAEVRPEQGKGASRRLRRAGKFPAIIYGG-----NEAPVSIVLDHKDVINLQAKAE---FYKEVITLVIDGK-----   68 (94)
T ss_pred             eEEEEEEeCcCCChHHHHHHHCCCCCEEEECC-----CCCcEEEEEcHHHHHHHHhcCC---CcceEEEEEECCE-----
Confidence            46899999999999999999999999999998     4578999999999999998644   3478999999874     


Q ss_pred             ccceEeEEEeeeeeccCCCCceEEEEEEe
Q 025088          132 LIEKVRVLPRKVHLHSGTDAPLNVTFLRA  160 (258)
Q Consensus       132 ~~~~~~vliKeVQ~hpvt~~ilHVDF~~v  160 (258)
                         +++|++||||+||+|++++|||||+|
T Consensus        69 ---~~~v~ikevQ~~pv~~~i~HvDF~~v   94 (94)
T PRK05943         69 ---EVKVKVQAVQRHPFKPKLEHIDFVRA   94 (94)
T ss_pred             ---EEEEEEeeeecCcCCCCeEeEeeeeC
Confidence               67999999999999999999999986

>PF14693 Ribosomal_TL5_C: Ribosomal protein TL5, C-terminal domain; PDB: 1FEU_D 2HGQ_Y 2HGJ_Y 2Y19_Z 2WRL_Z 3KIT_Z 2WH2_Z 2WDN_Z 3V25_Z 3HUZ_Z

Probab=99.95  E-value=7.6e-28  Score=186.04  Aligned_cols=88  Identities=32%  Similarity=0.620  Sum_probs=78.3

Q ss_pred             CeEEEEEeEEEEecCCCcccccCeEEEEEeeEEEEEeeCCCCCCeEEEEcCCCCCCCeEEEeccCCCCCeEEecCCCccE
Q 025088          164 ALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPV  243 (258)
Q Consensus       164 ~~v~v~VPV~~~Ge~~s~Gvk~GG~L~~~~~~V~V~~~p~~IPe~IeVDvS~L~iGd~I~v~DL~lp~gv~ll~d~e~vV  243 (258)
                      ++|+++|||+|+|+  |+|+|+||+|++.+++|+|+|+|++||++|+||||+|++||+|+++||++|+|+++++|+|++|
T Consensus         1 e~v~~~VPv~~~G~--~~gvk~Gg~l~~~~~~v~V~~~p~~iPe~I~vDvs~l~~g~~i~v~Dl~lp~gv~~~~d~~~vV   78 (88)
T PF14693_consen    1 EKVKVEVPVHFVGE--SPGVKKGGILQQVLREVEVECLPADIPESIEVDVSGLEIGDSIHVSDLKLPEGVEILDDPETVV   78 (88)
T ss_dssp             S-EEEEEEEEEESS--SHHHCTTSEEEESTSEEEEEE-TTS--SSEEEETTTSSTTCEEEGCCSB-STTEEESS-TTSEE
T ss_pred             CeEEEEEeEEEEcc--cccCcCCcEEEEEEeEEEEEEcHHHCCccEEEECccCcCCCEEEEeeccCCCCcEEcCCCCcEE
Confidence            58999999999997  7999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcccccc
Q 025088          244 CKIAGGRASD  253 (258)
Q Consensus       244 vsV~~~r~~~  253 (258)
                      |+|.++|+++
T Consensus        79 ~~v~~~~~ee   88 (88)
T PF14693_consen   79 ASVVAPRVEE   88 (88)
T ss_dssp             EEEE-SCSS-
T ss_pred             EEEeccccCC
Confidence            9999999874

...

>cd00495 Ribosomal_L25_TL5_CTC Ribosomal_L25_TL5_CTC: Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain

Probab=99.95  E-value=2.9e-27  Score=183.33  Aligned_cols=90  Identities=36%  Similarity=0.560  Sum_probs=83.5

Q ss_pred             eEEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECCccCCCCc
Q 025088           53 TILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDL  132 (258)
Q Consensus        53 ~L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g~~~~~~~  132 (258)
                      +|+|.+|+.+||+++|+||++|+|||||||+     |.++++|++++++|.+++++.|.    +++|+|+++|+      
T Consensus         2 ~l~a~~R~~~gk~~~r~lR~~G~iPavvYG~-----~~~~~~i~v~~~~l~k~l~~~~~----~~~~~L~i~g~------   66 (91)
T cd00495           2 TLKAEKREETGKGASRRLRRAGKVPAVIYGK-----GKEPISISVDEKELEKLLRKEGR----STLIELNIDGK------   66 (91)
T ss_pred             eEEEEEcccCCChHHHHHHHCCCCCEEEECC-----CCCCEEEEEcHHHHHHHHhhcCC----ceEEEEEECCE------
Confidence            6899999999999999999999999999997     35799999999999999998774    79999999864      


Q ss_pred             cceEeEEEeeeeeccCCCCceEEEEEE
Q 025088          133 IEKVRVLPRKVHLHSGTDAPLNVTFLR  159 (258)
Q Consensus       133 ~~~~~vliKeVQ~hpvt~~ilHVDF~~  159 (258)
                        +++|++||||+||++++++||||++
T Consensus        67 --~~~~~ikevQ~~pv~~~i~HvDF~~   91 (91)
T cd00495          67 --KENVLIKDVQRHPVKDKILHVDFLR   91 (91)
T ss_pred             --EEEEEEehhhhccCCCCEEEEeccC
Confidence              7899999999999999999999984

L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC, which each contain two domains. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had impaired protein synthesis capability. In Bacillus subtilis, CTC is induced under stress conditions and located in the ribosome; it has been proposed that CTC may be necessary for accurate translation under stress conditions. Ribosomal_L25_TL5_CTC is found only in bacteria and some plastids. Due to its limited taxonomic diversity and the viability of cells deleted for L25, this protein is not believed to be necessary for ribosomal assembly. Eukaryotes contain a protein called L25, which is not homologous to bacterial L

>PF01386 Ribosomal_L25p: Ribosomal L25p family; InterPro: IPR020055 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.95  E-value=3.1e-27  Score=182.47  Aligned_cols=87  Identities=26%  Similarity=0.494  Sum_probs=80.9

Q ss_pred             EEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHH-hhcCcccceeEEEEEEECCccCCCCc
Q 025088           54 ILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLV-GHLGRSFFVSRLFDLEVRSEFGSGDL  132 (258)
Q Consensus        54 L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l-~~~g~~~f~s~l~~L~v~g~~~~~~~  132 (258)
                      |+|++|+.+||+++|+||++|+|||||||+     |.++++|+|+.++|.+++ +..+.    +++|+|+++|+      
T Consensus         1 L~a~~R~~~gk~~~r~LR~~G~iPaviYG~-----~~~~~~i~v~~~~l~k~~~~~~~~----~~~i~L~i~g~------   65 (88)
T PF01386_consen    1 LKAEKREETGKSAARRLRREGKIPAVIYGK-----GKESIPISVDEKELEKLLRRKHGE----NSVIELNIDGK------   65 (88)
T ss_dssp             EEEEESSSTSSSHHHHHHHTTEEEEEEEES-----SEEEEEEEEEHHHHHHHHTHHHTT----TSEEEEEETTE------
T ss_pred             CeEEEcCcCCCHHHHHHHHcCCceEEEECC-----CCCCEEEEEeHHHHHHHHHhcCCc----eEEEEEEECCE------
Confidence            689999999999999999999999999998     457899999999999999 55554    79999999984      


Q ss_pred             cceEeEEEeeeeeccCCCCceEEEE
Q 025088          133 IEKVRVLPRKVHLHSGTDAPLNVTF  157 (258)
Q Consensus       133 ~~~~~vliKeVQ~hpvt~~ilHVDF  157 (258)
                        +++|++||||+||++++++||||
T Consensus        66 --~~~vlikevQ~~p~~~~i~HvDF   88 (88)
T PF01386_consen   66 --KYNVLIKEVQRDPVTDKILHVDF   88 (88)
T ss_dssp             --EEEEEEEEEEEESSSSSEEEEEE
T ss_pred             --EEEEEEEeeeeCCCCCCeEeccC
Confidence              89999999999999999999999

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 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 [, ]. This entry models the short-form of the ribosomal L25 protein. The long-form has homology to the general stress protein Ctc of Bacillus subtilis, a mesophile, and ribosomal protein TL5 of Thermus thermophilus, a thermophile. Ribosomal protein L25 of Escherichia coli and Haemophilus influenzae appear to be orthologous but consist only of the N-terminal half of Ctc and TL5. Both short (L25-like) and full-length (CTC-like) members of this family bind the E-loop of bacterial 5S rRNA.; GO: 0003735 structural constituent of ribosome, 0008097 5S rRNA binding, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2HGQ_Y 2HGJ_Y 2Y19_Z 2WRL_Z 3KIT_Z 2WH2_Z 2WDN_Z 3V25_Z 3HUZ_Z 3KIY_Z ....

>COG1825 RplY Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis]

Probab=99.92  E-value=6e-25  Score=171.71  Aligned_cols=92  Identities=30%  Similarity=0.498  Sum_probs=86.2

Q ss_pred             eeEEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECCccCCCC
Q 025088           52 ETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGD  131 (258)
Q Consensus        52 ~~L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g~~~~~~  131 (258)
                      .+|+|+.|+..||+++|+||++|+|||||||.     |.++++|+++.++|.+++++.+.    +++|+|+++|+     
T Consensus         2 ~~l~~~~R~~~Gkg~~RrlR~~G~iPAviYG~-----g~~~v~i~l~~~~~~k~~~~~~~----~~v~~l~v~g~-----   67 (93)
T COG1825           2 RELEAEVRTSQGKGASRRLRRAGKIPAVVYGG-----GKEPVNIALDHHEFAKALRKLGY----STVITLEVDGK-----   67 (93)
T ss_pred             ceeceeEecccCcchhHhHHhcCCCCEEEECC-----CCCCceEEEcHHHHHHHHhhccc----ceEEEEEECCe-----
Confidence            56899999999999999999999999999997     56889999999999999998774    89999999984     


Q ss_pred             ccceEeEEEeeeeeccCCCCceEEEEEEe
Q 025088          132 LIEKVRVLPRKVHLHSGTDAPLNVTFLRA  160 (258)
Q Consensus       132 ~~~~~~vliKeVQ~hpvt~~ilHVDF~~v  160 (258)
                         +..|++|++|+||+++.++|+||+++
T Consensus        68 ---~~~Vlvkd~Q~~p~~~~~~HvDf~~v   93 (93)
T COG1825          68 ---EIKVLVKDVQRHPLTDEVQHIDFLRV   93 (93)
T ss_pred             ---EEEEEehhhhhCcccCceeecccccC
Confidence               78999999999999999999999975

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	258
3tve_V	175	Crystal Structure Analysis Of Ribosomal Decoding. T		3e-05
2j01_Z	206	Structure Of The Thermus Thermophilus 70s Ribosome		3e-05
3tvh_V	179	Crystal Structure Analysis Of Ribosomal Decoding. T		3e-05
1feu_A	206	Crystal Structure Of Ribosomal Protein Tl5, One Of		3e-05
3fin_Z	177	T. Thermophilus 70s Ribosome In Complex With Mrna,		3e-05
3pyo_V	188	Crystal Structure Of A Complex Containing Domain 3		3e-05

>pdb|3TVE|V Chain V, Crystal Structure Analysis Of Ribosomal Decoding. This Entry Contains The 50s Ribosomal Subunit Of The First 70s Molecule In The Asymmetric Unit For The Cognate Trna-Leu Complex Length = 175

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 34/109 (31%), Positives = 55/109 (50%), Gaps = 3/109 (2%)
Query: 139 LPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKF 198
           L R+V+L      P +V F     E + ++ VPL F G     G+R GG L  I R +  
Sbjct: 70  LVRQVNLDKRRRRPEHVDFFVLSDEPV-EMYVPLRFVG--TPAGVRAGGVLQEIHRDILV 126
Query: 199 LCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIA 247
                 +P +I+VD+S L++   + A DLK+ P ++L  S +E +  + 
Sbjct: 127 KVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVV 175

>pdb|2J01|Z Chain Z, Structure Of The Thermus Thermophilus 70s Ribosome Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4). This File Contains The 50s Subunit From Molecule I. Length = 206

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 34/109 (31%), Positives = 55/109 (50%), Gaps = 3/109 (2%)
Query: 139 LPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKF 198
           L R+V+L      P +V F     E + ++ VPL F G     G+R GG L  I R +  
Sbjct: 70  LVRQVNLDKRRRRPEHVDFFVLSDEPV-EMYVPLRFVG--TPAGVRAGGVLQEIHRDILV 126
Query: 199 LCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIA 247
                 +P +I+VD+S L++   + A DLK+ P ++L  S +E +  + 
Sbjct: 127 KVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVV 175

>pdb|3TVH|V Chain V, Crystal Structure Analysis Of Ribosomal Decoding. This Entry Contains The 50s Ribosomal Subunit Of The Second 70s Molecule In The Asymmetric Unit For The Cognate Trna-Leu Complex Length = 179

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 34/109 (31%), Positives = 55/109 (50%), Gaps = 3/109 (2%)
Query: 139 LPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKF 198
           L R+V+L      P +V F     E + ++ VPL F G     G+R GG L  I R +  
Sbjct: 70  LVRQVNLDKRRRRPEHVDFFVLSDEPV-EMYVPLRFVG--TPAGVRAGGVLQEIHRDILV 126
Query: 199 LCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIA 247
                 +P +I+VD+S L++   + A DLK+ P ++L  S +E +  + 
Sbjct: 127 KVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVV 175

>pdb|1FEU|A Chain A, Crystal Structure Of Ribosomal Protein Tl5, One Of The Ctc Family Proteins, Complexed With A Fragment Of 5s Rrna. Length = 206

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 34/109 (31%), Positives = 55/109 (50%), Gaps = 3/109 (2%)
Query: 139 LPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKF 198
           L R+V+L      P +V F     E + ++ VPL F G     G+R GG L  I R +  
Sbjct: 70  LVRQVNLDKRRRRPEHVDFFVLSDEPV-EMYVPLRFVG--TPAGVRAGGVLQEIHRDILV 126
Query: 199 LCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIA 247
                 +P +I+VD+S L++   + A DLK+ P ++L  S +E +  + 
Sbjct: 127 KVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVV 175

>pdb|3FIN|Z Chain Z, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A 6.4 A Cryo-Em Map. This File Contains The 50s Subunit Length = 177

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 34/109 (31%), Positives = 55/109 (50%), Gaps = 3/109 (2%)
Query: 139 LPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKF 198
           L R+V+L      P +V F     E + ++ VPL F G     G+R GG L  I R +  
Sbjct: 68  LVRQVNLDKRRRRPEHVDFFVLSDEPV-EMYVPLRFVG--TPAGVRAGGVLQEIHRDILV 124
Query: 199 LCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIA 247
                 +P +I+VD+S L++   + A DLK+ P ++L  S +E +  + 
Sbjct: 125 KVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVV 173

>pdb|3PYO|V Chain V, Crystal Structure Of A Complex Containing Domain 3 From The Psiv Igr Ires Rna Bound To The 70s Ribosome. This File Contains The 50s Subunit Of The First 70s Ribosome. Length = 188

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 34/109 (31%), Positives = 55/109 (50%), Gaps = 3/109 (2%)
Query: 139 LPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKF 198
           L R+V+L      P +V F     E + ++ VPL F G     G+R GG L  I R +  
Sbjct: 68  LVRQVNLDKRRRRPEHVDFFVLSDEPV-EMYVPLRFVG--TPAGVRAGGVLQEIHRDILV 124
Query: 199 LCPADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIA 247
                 +P +I+VD+S L++   + A DLK+ P ++L  S +E +  + 
Sbjct: 125 KVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVV 173

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	258
2zjr_S	237	50S ribosomal protein L25; ribosome, large ribosom	2e-26
1feu_A	206	50S ribosomal protein L25; general stress protein	3e-26
1b75_A	94	Protein (50S ribosomal protein L25); RNA-binding p	4e-09

>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S* 3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W ... Length = 237

 Score =  102 bits (255), Expect = 2e-26
 Identities = 34/198 (17%), Positives = 77/198 (38%), Gaps = 22/198 (11%)

Query: 59  RASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRL 118
             +   R   ++     + ++ + +E+          ++      +      R    + L
Sbjct: 2   ELTAKPRTPKQKLDESMIAAVAYNKENNVS------FALDRKAFDRAF----RQQSTTGL 51

Query: 119 FDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDD 178
           FD+ V       +  E    L + V +     AP++V F        +++ VP+   G  
Sbjct: 52  FDITV-------EGGETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGR- 103

Query: 179 VSPGLRKGGYLNTIKRTVKFLC--PADIVPPYIDVDLSELDVEQKILAGDLKVHPALKLL 236
            S G  +GG ++ +   ++ +   P  I P  + VD++++++   I AGD+K+     L 
Sbjct: 104 -SQGEVQGGLVDIVVHNLQIVAPGPRRI-PQELVVDVTKMNIGDHITAGDIKLPEGCTLA 161

Query: 237 RSKDEPVCKIAGGRASDQ 254
              +  V  +   R + +
Sbjct: 162 ADPELTVVSVLPPRLTAE 179

>1feu_A 50S ribosomal protein L25; general stress protein CTC, 5S rRNA-protein complex, cadmium IONS, ribosome; 2.30A {Thermus thermophilus} SCOP: b.53.1.1 PDB: 2j01_Z 1vsp_T 2hgj_Y 2hgq_Y 2hgu_Y 1vsa_T 2j03_Z 2jl6_Z 2jl8_Z 2v47_Z 2v49_Z 2wdi_Z 2wdj_Z 2wdl_Z 2wdn_Z 2wh2_Z 2wh4_Z 2wrj_Z 2wrl_Z 2wro_Z ... Length = 206

 Score =  100 bits (252), Expect = 3e-26
 Identities = 43/202 (21%), Positives = 80/202 (39%), Gaps = 23/202 (11%)

Query: 53  TILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRS 112
            + A  R           R+AG++P +++      +    R + V   +  K+       
Sbjct: 4   RLKAYYREGEKPS---ALRRAGKLPGLMY------NRHLNRKVYVDLVEFDKVFRQAS-- 52

Query: 113 FFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPL 172
                +       +         +  L R+V+L      P +V F     E + ++ VPL
Sbjct: 53  -IHHVIVLELPDGQ--------SLPTLVRQVNLDKRRRRPEHVDFFVLSDEPV-EMYVPL 102

Query: 173 VFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPA 232
            F G     G+R GG L  I R +        +P +I+VD+S L++   + A DLK+ P 
Sbjct: 103 RFVGT--PAGVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPG 160

Query: 233 LKLLRSKDEPVCKIAGGRASDQ 254
           ++L  S +E +  +      ++
Sbjct: 161 VELAVSPEETIAAVVPPEDVEK 182

>1b75_A Protein (50S ribosomal protein L25); RNA-binding protein, RNA binding protein; NMR {Escherichia coli} SCOP: b.53.1.1 PDB: 1d6k_A 1dfu_P 1giy_V 1ml5_v* 1p85_T 1p86_T 1vs6_V 1vs8_V 1vt2_V 2aw4_V 2awb_V 2gya_T 2gyc_T 2i2t_V 2i2v_V 2j28_V 2qam_V* 2qao_V* 2qba_V* 2qbc_V* ... Length = 94

 Score = 51.8 bits (125), Expect = 4e-09
 Identities = 23/110 (20%), Positives = 44/110 (40%), Gaps = 20/110 (18%)

Query: 53  TILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNK--RLISVQTNQIRKLVGHLG 110
           TI A  R   G   S + R A + P+I++       GG +    I +  +++  +     
Sbjct: 3   TINAEVRKEQGKGASRRLRAANKFPAIIY-------GGKEAPLAIELDHDKVMNMQAKAE 55

Query: 111 RSFFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRA 160
              F S +  + V      G   ++++V  + V  H       ++ F+RA
Sbjct: 56  ---FYSEVLTIVV-----DG---KEIKVKAQDVQRHPYKPKLQHIDFVRA 94

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	258
1feu_A	206	50S ribosomal protein L25; general stress protein	100.0
2zjr_S	237	50S ribosomal protein L25; ribosome, large ribosom	100.0
1b75_A	94	Protein (50S ribosomal protein L25); RNA-binding p	99.95
3lyw_A	90	YBBR family protein; structural genomics, PSI-2, p	94.98
2l3u_A	98	YBBR family protein; beta strand, figure eight, fi	92.42
2kq1_A	119	BH0266 protein; solution NESG, structural genomics	86.76

>1feu_A 50S ribosomal protein L25; general stress protein CTC, 5S rRNA-protein complex, cadmium IONS, ribosome; 2.30A {Thermus thermophilus} SCOP: b.53.1.1 PDB: 2j01_Z 1vsp_T 2hgj_Y 2hgq_Y 2hgu_Y 1vsa_T 2j03_Z 2jl6_Z 2jl8_Z 2v47_Z 2v49_Z 2wdi_Z 2wdj_Z 2wdl_Z 2wdn_Z 2wh2_Z 2wh4_Z 2wrj_Z 2wrl_Z 2wro_Z ...

Probab=100.00  E-value=4.9e-54  Score=377.28  Aligned_cols=176  Identities=26%  Similarity=0.436  Sum_probs=167.0

Q ss_pred             eeEEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEE-CCccCCC
Q 025088           52 ETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEV-RSEFGSG  130 (258)
Q Consensus        52 ~~L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v-~g~~~~~  130 (258)
                      .+|+|+.|+   |+++|+|||+|+|||||||+     |.+ ++|+++.++|.+++++.+.    +++|+|++ +|+    
T Consensus         3 ~~l~a~~R~---k~aarrLRr~G~VPaVvYG~-----~~e-~~i~v~~~el~~~l~~~~~----~~vi~L~i~~G~----   65 (206)
T 1feu_A            3 YRLKAYYRE---GEKPSALRRAGKLPGLMYNR-----HLN-RKVYVDLVEFDKVFRQASI----HHVIVLELPDGQ----   65 (206)
T ss_dssp             EEEECEECS---SSCHHHHHHTTEEEEEEECS-----SCE-EEEEEEHHHHHHHHHHHTT----TSEEEEECTTSC----
T ss_pred             eEEEEEEeC---ChHHHHHHHCCCceEEEEcC-----Cce-EEEEEcHHHHHHHHhhcCC----cEEEEEEEcCCC----
Confidence            689999999   78899999999999999997     457 9999999999999987553    78999999 874    


Q ss_pred             CccceEeEEEeeeeeccCCCCceEEEEEEeCCCCeEEEEEeEEEEecCCCcccccCeEEEEEeeEEEEEeeCCCCCCeEE
Q 025088          131 DLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYID  210 (258)
Q Consensus       131 ~~~~~~~vliKeVQ~hpvt~~ilHVDF~~v~~~~~v~v~VPV~~~Ge~~s~Gvk~GG~L~~~~~~V~V~~~p~~IPe~Ie  210 (258)
                          +++|++||||+||+++.++|||||++++ ++|+++|||+|+|+  |+|+|+||+|++.+++|+|+|+|.+||++|+
T Consensus        66 ----~~~vlikdvQ~hpv~~~i~HvDF~~v~~-~~v~v~VPv~~~G~--~~gvk~GG~l~~~~~~v~V~~~p~~IPe~I~  138 (206)
T 1feu_A           66 ----SLPTLVRQVNLDKRRRRPEHVDFFVLSD-EPVEMYVPLRFVGT--PAGVRAGGVLQEIHRDILVKVSPRNIPEFIE  138 (206)
T ss_dssp             ----EEEEEEEEEEECSSSSCEEEEEEEECCS-SCEEEEEEEEEESC--CHHHHTTCEEEECCSEEEEEECGGGCCSCEE
T ss_pred             ----EEEEEEEEeEeCCCCCCeEEEEEEEECC-EEEEEEeeEEEEcC--cccccCceEEEEEEeEEEEEEcHHHCCccEE
Confidence                6799999999999999999999999999 99999999999998  7999999999999999999999999999999


Q ss_pred             EEcCCCCCCCeEEEeccCCCCCeEEecCCCccEEEEEcccc
Q 025088          211 VDLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGRA  251 (258)
Q Consensus       211 VDvS~L~iGd~I~v~DL~lp~gv~ll~d~e~vVvsV~~~r~  251 (258)
                      ||||+|++||+||++||++|+|+++++|+|++||+|.+|++
T Consensus       139 VDvs~L~iGdsi~v~Dl~lP~gv~~~~d~d~~V~~V~~~~~  179 (206)
T 1feu_A          139 VDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVVPPED  179 (206)
T ss_dssp             EECTTCCTTEEEEGGGSCCCTTCEESSCTTCEEEEEECSSS
T ss_pred             EEcccCCCCCEEEEeeccCCCCcEEcCCCCcEEEEEeCCCc
Confidence            99999999999999999999999999999999999999984

>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S* 3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W ...

Probab=100.00  E-value=1.9e-52  Score=373.21  Aligned_cols=174  Identities=18%  Similarity=0.339  Sum_probs=163.8

Q ss_pred             EcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECC-ccCCCCccceE
Q 025088           58 PRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRS-EFGSGDLIEKV  136 (258)
Q Consensus        58 ~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g-~~~~~~~~~~~  136 (258)
                      +|+.+||+++||| |+|+||||||| +     .++++|+++.++|.+++++.+.    +++|+|+++| +        ++
T Consensus         2 ~R~~~GKgaaRrL-r~G~VPaVvYG-g-----~e~v~i~v~~~el~k~l~~~~~----~~li~L~IdG~~--------~~   62 (237)
T 2zjr_S            2 ELTAKPRTPKQKL-DESMIAAVAYN-K-----ENNVSFALDRKAFDRAFRQQST----TGLFDITVEGGE--------TF   62 (237)
T ss_dssp             CCCBCCSCCHHHH-SSSCCCEEEES-S-----SCCCCCBCCHHHHHHHHHHHTT----SCCCBCCCTTCC--------CC
T ss_pred             cccccCcHHHHHH-hCCCCCEEEeC-C-----CCCEEEEECHHHHHHHHHhcCC----cEEEEEEECCce--------eE
Confidence            6999999999999 99999999998 4     4789999999999999987442    7999999998 5        56


Q ss_pred             eEEEeeeeeccCCCCceEEEEEEeCCCCeEEEEEeEEEEecCCCcccccCeEEEEEeeEEEEEe-eCCCCCCeEEEEcCC
Q 025088          137 RVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLC-PADIVPPYIDVDLSE  215 (258)
Q Consensus       137 ~vliKeVQ~hpvt~~ilHVDF~~v~~~~~v~v~VPV~~~Ge~~s~Gvk~GG~L~~~~~~V~V~~-~p~~IPe~IeVDvS~  215 (258)
                      +||+|+||+||+|++++|||||+++++++|+++|||+|+|+  |+|+|+||+|++.+++|+|+| +|.+||++|+||||+
T Consensus        63 ~vliKdvQ~hPvk~~ilHVDF~~V~~~ekV~v~VPV~~vGe--~~GvK~GGvL~~~~~eveV~~~lP~~IPe~IeVDVs~  140 (237)
T 2zjr_S           63 PALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGR--SQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTK  140 (237)
T ss_dssp             BCCEEEEEECSSSCCEEEEEEECCCSSCCCEEEEECEEESC--CTTTTTTSEEECSCSEEEEECCCTTCCCSCCEEECTT
T ss_pred             EEEEEEEEecCCCCCeEEEEEEEECCCCEEEEEEeEEEecC--CccccCCcEEEEEEeEEEEEEeCHHHCCccEEEEccc
Confidence            89999999999999999999999999999999999999997  799999999999999999999 999999999999999


Q ss_pred             CCCCCeEEEeccCCCCCeEEecCCCccEEEEEccccc
Q 025088          216 LDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGRAS  252 (258)
Q Consensus       216 L~iGd~I~v~DL~lp~gv~ll~d~e~vVvsV~~~r~~  252 (258)
                      |++||+||++||++|+|+++++|+|++||+|..|+.+
T Consensus       141 LeiGdsI~v~DL~LPeGv~l~~d~d~vVvsV~~p~~~  177 (237)
T 2zjr_S          141 MNIGDHITAGDIKLPEGCTLAADPELTVVSVLPPRLT  177 (237)
T ss_dssp             CCSSCEEETTTSCCSTTCCCCSCTTCEEEEEECCC--
T ss_pred             CCCCCEEEeeeccCCCCcEEcCCCCcEEEEEEcCCCC
Confidence            9999999999999999999999999999999999853

>1b75_A Protein (50S ribosomal protein L25); RNA-binding protein, RNA binding protein; NMR {Escherichia coli} SCOP: b.53.1.1 PDB: 1d6k_A 1dfu_P 1giy_V 1ml5_v* 1p85_T 1p86_T 1vs6_V 1vs8_V 1vt2_V 2aw4_V 2awb_V 2gya_T 2gyc_T 2i2t_V 2i2v_V 2j28_V 2qam_V* 2qao_V* 2qba_V* 2qbc_V* ...

Probab=99.95  E-value=4.2e-29  Score=194.03  Aligned_cols=93  Identities=22%  Similarity=0.331  Sum_probs=84.2

Q ss_pred             eeEEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECCccCCCC
Q 025088           52 ETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGD  131 (258)
Q Consensus        52 ~~L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g~~~~~~  131 (258)
                      ++|+|++|+.+||+++|+||++|+|||||||+     |.++++|+++.++|.+++++.+   |.+++|+|+++|+     
T Consensus         2 ~~l~a~~R~~~Gk~~arrLRr~G~vPaVvYG~-----~~e~~~i~v~~~~~~~~l~~~~---~~~~~i~L~i~G~-----   68 (94)
T 1b75_A            2 FTINAEVRKEQGKGASRRLRAANKFPAIIYGG-----KEAPLAIELDHDKVMNMQAKAE---FYSEVLTIVVDGK-----   68 (94)
T ss_dssp             CCEEECSSCCSSSSSSSSTTTTTBCCEEEECS-----SSCCEEECCBSHHHHHHHTTTH---HHHTCEEEEESSC-----
T ss_pred             eEEEEEEecccCChHHHHHHHCCCceEEEECC-----CCCCEEEEECHHHHHHHHhccC---cceEEEEEEECCE-----
Confidence            57899999999999999999999999999997     4589999999999999997533   5578999999984     


Q ss_pred             ccceEeEEEeeeeeccCCCCceEEEEEEe
Q 025088          132 LIEKVRVLPRKVHLHSGTDAPLNVTFLRA  160 (258)
Q Consensus       132 ~~~~~~vliKeVQ~hpvt~~ilHVDF~~v  160 (258)
                         +++|++||||+||++++++||||++|
T Consensus        69 ---~~~vlikdvQ~hp~~~~i~HvDF~~v   94 (94)
T 1b75_A           69 ---EIKVKAQDVQRHPYKPKLQHIDFVRA   94 (94)
T ss_dssp             ---EEEECCSEEECCSSSCCCCEEEEEBC
T ss_pred             ---EEEEEEEEEEeCCCCCCeEEEEEEEC
Confidence               67899999999999999999999985

>3lyw_A YBBR family protein; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 1.90A {Desulfitobacterium hafniense} PDB: 2kpu_A 2l5n_A

Probab=94.98  E-value=0.15  Score=38.70  Aligned_cols=73  Identities=14%  Similarity=0.181  Sum_probs=49.0

Q ss_pred             EEEEeEEEEecCCCcccccCeEEEEEeeEEEEEeeC-CCCCC----eEEEEcCCCCCCCe-EEEeccCCCCCeEEec-CC
Q 025088          167 KIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPA-DIVPP----YIDVDLSELDVEQK-ILAGDLKVHPALKLLR-SK  239 (258)
Q Consensus       167 ~v~VPV~~~Ge~~s~Gvk~GG~L~~~~~~V~V~~~p-~~IPe----~IeVDvS~L~iGd~-I~v~DL~lp~gv~ll~-d~  239 (258)
                      +.+|||.+.|.+      .|-.+.....+|+|+... .....    +..||+|++..|+. +.|+ +.+|.|+++.. +|
T Consensus         4 tytVPv~~~Nlp------~~~~v~~~~~tV~V~v~G~r~~~~~~di~A~VDLsg~~~G~~~~~V~-v~~P~G~~lv~vsP   76 (90)
T 3lyw_A            4 TLTLSLIAKNTP------ANSMIMTKLPSVRVKTEGYNPSINVNELFAYVDLSGSEPGEHDYEVK-VEPIPNIKIVEISP   76 (90)
T ss_dssp             EEEEEEEEESCC------TTEEECSCCCEEEEEEEECCTTCCSTTCEEEEECTTCCSEEEEEECE-ECCCTTEEEEEEES
T ss_pred             eEEeeEEEeeCC------CCcEEecCCCEEEEEEEecCcCCChHHEEEEEECcCCCCCcEeEEEE-EECCCCCEEEEEcc
Confidence            579999999974      233333333566665542 11111    46899999999984 4455 89999999987 77


Q ss_pred             CccEEEE
Q 025088          240 DEPVCKI  246 (258)
Q Consensus       240 e~vVvsV  246 (258)
                      +.+-...
T Consensus        77 ~~V~~~~   83 (90)
T 3lyw_A           77 RVVTLQL   83 (90)
T ss_dssp             SEEEEEE
T ss_pred             ceEEEEe
Confidence            7766554

>2l3u_A YBBR family protein; beta strand, figure eight, figure 8, structural genomics, PS biology, protein structure initiative; NMR {Desulfitobacterium hafniense}

Probab=92.42  E-value=0.048  Score=41.42  Aligned_cols=79  Identities=13%  Similarity=0.118  Sum_probs=50.6

Q ss_pred             EEEeEEEEecCCCcccccCeEEEEEeeEEEEEee--CC---CC-CC--eEEEEcCCCCCCCeEEEeccCCCCCeEEec-C
Q 025088          168 IDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCP--AD---IV-PP--YIDVDLSELDVEQKILAGDLKVHPALKLLR-S  238 (258)
Q Consensus       168 v~VPV~~~Ge~~s~Gvk~GG~L~~~~~~V~V~~~--p~---~I-Pe--~IeVDvS~L~iGd~I~v~DL~lp~gv~ll~-d  238 (258)
                      .+|||.+.|.+  .++    .+...-.+|+|.+.  ..   .+ ++  .+.+|+|++..|..-.-=.+.+|+|+++.. +
T Consensus         5 ~~VPV~v~n~~--~~~----~v~~~p~~V~V~v~G~~~~l~~l~~~di~~~vDls~l~~G~~~v~v~v~~P~~~~~v~i~   78 (98)
T 2l3u_A            5 YDLPIVLRNLP--EDL----VLEKPLPEVSVTIRAYPEILNNLTKEQISLWIDATGKAVGEHTVKIYWQLPAGIEMVSIP   78 (98)
T ss_dssp             CCCSCEEESCC--TTE----EESSCCCCCCCEEECCHHHHTTCCGGGCBCEEECSSCCSBCCEECCCCBCSSSCEEEECC
T ss_pred             EecCEEEEeCC--Cce----EEEcCCCEEEEEEEECHHHhhhCChhhEEEEEEecCCcCceEEEeEEEECCCCcEEEEeC
Confidence            36899999963  333    33333344444443  21   11 11  567899999999744333578999999875 8


Q ss_pred             CCccEEEEEccccc
Q 025088          239 KDEPVCKIAGGRAS  252 (258)
Q Consensus       239 ~e~vVvsV~~~r~~  252 (258)
                      |..+-++|..-..|
T Consensus        79 P~~V~V~i~e~~~E   92 (98)
T 2l3u_A           79 DVTYTLKAKEDPLE   92 (98)
T ss_dssp             CEECCEEECCCSSC
T ss_pred             CCEEEEEEeccccc
Confidence            88888888655443

>2kq1_A BH0266 protein; solution NESG, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Bacillus halodurans}

Probab=86.76  E-value=2.8  Score=32.44  Aligned_cols=80  Identities=14%  Similarity=0.046  Sum_probs=53.0

Q ss_pred             CeEEEEEeEEEEecCCCcccccCeEEEEEeeEEEEEeeCC-----CC---CC--eEEEEcCCCCCCC-eEEEeccCCCCC
Q 025088          164 ALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPAD-----IV---PP--YIDVDLSELDVEQ-KILAGDLKVHPA  232 (258)
Q Consensus       164 ~~v~v~VPV~~~Ge~~s~Gvk~GG~L~~~~~~V~V~~~p~-----~I---Pe--~IeVDvS~L~iGd-~I~v~DL~lp~g  232 (258)
                      ...-.+|||.+.+.+      .|-.+.-.-.+|+|.....     .+   ++  ...+|+|+|..|. .+.+.=-.+|+|
T Consensus         8 ~~~~~~VPV~v~~~~------~~~~v~~~p~~V~V~l~G~~~~l~~~~~~~~~i~~~vDLs~l~~G~~~vpv~v~~lp~~   81 (119)
T 2kq1_A            8 NLSLGELELTVLYDE------ERYDIVEQTETVQVDLEGPRGVLTVFRFARPSYEVFVDLTEAGEGSHTVDVEHRGFPGD   81 (119)
T ss_dssp             EEEEEEEEEEEECCT------TTCEEEECCCEEEEEEEECHHHHHHHTTSCCCCEEEEECTTCCBEEEEEECEEESSCTT
T ss_pred             eEEEEEeeEEEEECC------CCEEEECCCCEEEEEEEECHHHhhhccccccCEEEEEECccCCCCeEEEEEEEecCCCC
Confidence            455678999999853      3445554455666665532     11   23  5689999999997 333332248999


Q ss_pred             eEEecCCCccEEEEEcc
Q 025088          233 LKLLRSKDEPVCKIAGG  249 (258)
Q Consensus       233 v~ll~d~e~vVvsV~~~  249 (258)
                      +++-.+|+.+-++|...
T Consensus        82 v~v~v~P~~V~V~i~~~   98 (119)
T 2kq1_A           82 LAVTVEPRMARVQLEER   98 (119)
T ss_dssp             SEEEESCCEEEEEEESC
T ss_pred             eEEEEcCCEEEEEEEEE
Confidence            99666999988888543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	258
d2zjrs1	175	b.53.1.1 (S:1-175) Ribosomal protein TL5 (general	1e-18
d1feua_	185	b.53.1.1 (A:) Ribosomal protein TL5 (general stres	2e-16
d1dfup_	94	b.53.1.1 (P:) Ribosomal protein L25 {Escherichia c	3e-07

>d2zjrs1 b.53.1.1 (S:1-175) Ribosomal protein TL5 (general stress protein CTC) {Deinococcus radiodurans [TaxId: 1299]} Length = 175

class: All beta proteins
fold: Ribosomal protein L25-like
superfamily: Ribosomal protein L25-like
family: Ribosomal protein L25-like
domain: Ribosomal protein TL5 (general stress protein CTC)
species: Deinococcus radiodurans [TaxId: 1299]

 Score = 78.6 bits (193), Expect = 1e-18
 Identities = 25/185 (13%), Positives = 64/185 (34%), Gaps = 20/185 (10%)

Query: 64  TRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEV 123
            R   ++     + ++ + +E+          ++      +       +       +   
Sbjct: 7   PRTPKQKLDESMIAAVAYNKENNVS------FALDRKAFDRAFRQQSTTGLFDITVEGG- 59

Query: 124 RSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGL 183
                     E    L + V +     AP++V F          ++V +       S G 
Sbjct: 60  ----------ETFPALVKAVQMDKRKRAPIHVDFYMVTYGE--PVEVSVPVHTTGRSQGE 107

Query: 184 RKGGYLNTIKRTVKFLCPA-DIVPPYIDVDLSELDVEQKILAGDLKVHPALKLLRSKDEP 242
            +GG ++ +   ++ + P    +P  + VD++++++   I AGD+K+     L    +  
Sbjct: 108 VQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELT 167

Query: 243 VCKIA 247
           V  + 
Sbjct: 168 VVSVL 172

>d1feua_ b.53.1.1 (A:) Ribosomal protein TL5 (general stress protein CTC) {Thermus thermophilus [TaxId: 274]} Length = 185

class: All beta proteins
fold: Ribosomal protein L25-like
superfamily: Ribosomal protein L25-like
family: Ribosomal protein L25-like
domain: Ribosomal protein TL5 (general stress protein CTC)
species: Thermus thermophilus [TaxId: 274]

 Score = 72.9 bits (178), Expect = 2e-16
 Identities = 38/199 (19%), Positives = 77/199 (38%), Gaps = 23/199 (11%)

Query: 53  TILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRS 112
            + A  R           R+AG++P +++ +   +       + V   +  K+     ++
Sbjct: 4   RLKAYYREGEKPSAL---RRAGKLPGLMYNRHLNRK------VYVDLVEFDKV---FRQA 51

Query: 113 FFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPL 172
                +               + +  L R+V+L      P +V F     E    +++ +
Sbjct: 52  SIHHVIVLELPD--------GQSLPTLVRQVNLDKRRRRPEHVDFFVLSDE---PVEMYV 100

Query: 173 VFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDVDLSELDVEQKILAGDLKVHPA 232
             R      G+R GG L  I R +        +P +I+VD+S L++   + A DLK+ P 
Sbjct: 101 PLRFVGTPAGVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPG 160

Query: 233 LKLLRSKDEPVCKIAGGRA 251
           ++L  S +E +  +     
Sbjct: 161 VELAVSPEETIAAVVPPED 179

>d1dfup_ b.53.1.1 (P:) Ribosomal protein L25 {Escherichia coli [TaxId: 562]} Length = 94

class: All beta proteins
fold: Ribosomal protein L25-like
superfamily: Ribosomal protein L25-like
family: Ribosomal protein L25-like
domain: Ribosomal protein L25
species: Escherichia coli [TaxId: 562]

 Score = 45.3 bits (107), Expect = 3e-07
 Identities = 22/108 (20%), Positives = 47/108 (43%), Gaps = 16/108 (14%)

Query: 53  TILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRS 112
           TI A  R   G   S + R A + P+I+       +GG +  ++++ +   K++    ++
Sbjct: 3   TINAEVRKEQGKGASRRLRAANKFPAII-------YGGKEAPLAIELDH-DKVMNMQAKA 54

Query: 113 FFVSRLFDLEVRSEFGSGDLIEKVRVLPRKVHLHSGTDAPLNVTFLRA 160
            F S +  + V  +        +++V  + V  H       ++ F+RA
Sbjct: 55  EFYSEVLTIVVDGK--------EIKVKAQDVQRHPYKPKLQHIDFVRA 94

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	258
d1feua_	185	Ribosomal protein TL5 (general stress protein CTC)	100.0
d2zjrs1	175	Ribosomal protein TL5 (general stress protein CTC)	100.0
d1dfup_	94	Ribosomal protein L25 {Escherichia coli [TaxId: 56	99.95

>d1feua_ b.53.1.1 (A:) Ribosomal protein TL5 (general stress protein CTC) {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: Ribosomal protein L25-like
superfamily: Ribosomal protein L25-like
family: Ribosomal protein L25-like
domain: Ribosomal protein TL5 (general stress protein CTC)
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=1.2e-52  Score=360.78  Aligned_cols=180  Identities=24%  Similarity=0.434  Sum_probs=165.0

Q ss_pred             eeEEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECCccCCCC
Q 025088           52 ETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGD  131 (258)
Q Consensus        52 ~~L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g~~~~~~  131 (258)
                      .+|+|+.|+..|+   ++|||+|+|||||||+     | .+.+|+++.++|.++++..+.    ++++.|++.++     
T Consensus         3 ~~l~a~~Re~~~~---~~LRr~G~VPaViYG~-----~-~~~~i~v~~~e~~k~~~~~~~----~~~i~l~~~dg-----   64 (185)
T d1feua_           3 YRLKAYYREGEKP---SALRRAGKLPGLMYNR-----H-LNRKVYVDLVEFDKVFRQASI----HHVIVLELPDG-----   64 (185)
T ss_dssp             EEEECEECSSSCH---HHHHHTTEEEEEEECS-----S-CEEEEEEEHHHHHHHHHHHTT----TSEEEEECTTS-----
T ss_pred             EEEEEEEecCCCc---hHHHhCCCceEEEECC-----C-CCcCEEecchHHHhHhhhhhc----cceEEEEeecc-----
Confidence            6899999996654   4699999999999986     2 358999999999999998775    57788888433     


Q ss_pred             ccceEeEEEeeeeeccCCCCceEEEEEEeCCCCeEEEEEeEEEEecCCCcccccCeEEEEEeeEEEEEeeCCCCCCeEEE
Q 025088          132 LIEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCPADIVPPYIDV  211 (258)
Q Consensus       132 ~~~~~~vliKeVQ~hpvt~~ilHVDF~~v~~~~~v~v~VPV~~~Ge~~s~Gvk~GG~L~~~~~~V~V~~~p~~IPe~IeV  211 (258)
                        ++++||+||||+||++++++|||||+++ +++|+++|||+|+|+  |+|+|+||+|++.+++|+|+|+|++||++|+|
T Consensus        65 --~~~~vlikevQ~~pv~~~i~HvDF~~v~-~~~v~v~VPv~~~G~--~~gvk~GG~l~~~~~~i~v~~~p~~IPe~i~V  139 (185)
T d1feua_          65 --QSLPTLVRQVNLDKRRRRPEHVDFFVLS-DEPVEMYVPLRFVGT--PAGVRAGGVLQEIHRDILVKVSPRNIPEFIEV  139 (185)
T ss_dssp             --CEEEEEEEEEEECSSSSCEEEEEEEECC-SSCEEEEEEEEEESC--CHHHHTTCEEEECCSEEEEEECGGGCCSCEEE
T ss_pred             --hhhhheeeeeEecccccceeEEEEeecc-CceEEEEeceEEeec--ccccccccEEEEEEeeeEEEeeccCCCeEEEE
Confidence              3789999999999999999999999986 999999999999997  79999999999999999999999999999999


Q ss_pred             EcCCCCCCCeEEEeccCCCCCeEEecCCCccEEEEEccccccc
Q 025088          212 DLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGRASDQ  254 (258)
Q Consensus       212 DvS~L~iGd~I~v~DL~lp~gv~ll~d~e~vVvsV~~~r~~~~  254 (258)
                      |||+|++||+|+++||++|+|++++.|+|++||+|.+|+.++.
T Consensus       140 Dvs~L~igd~i~v~Dl~lp~gv~~~~d~~~~vv~v~~p~~~ee  182 (185)
T d1feua_         140 DVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVVPPEDVEK  182 (185)
T ss_dssp             ECTTCCTTEEEEGGGSCCCTTCEESSCTTCEEEEEECSSSSSC
T ss_pred             EcccCCCCCeEEEEeecCCCCcEEccCCCCeEEEEeCCCcccc
Confidence            9999999999999999999999999999999999999997654

>d2zjrs1 b.53.1.1 (S:1-175) Ribosomal protein TL5 (general stress protein CTC) {Deinococcus radiodurans [TaxId: 1299]}

class: All beta proteins
fold: Ribosomal protein L25-like
superfamily: Ribosomal protein L25-like
family: Ribosomal protein L25-like
domain: Ribosomal protein TL5 (general stress protein CTC)
species: Deinococcus radiodurans [TaxId: 1299]

Probab=100.00  E-value=1.6e-52  Score=357.20  Aligned_cols=173  Identities=20%  Similarity=0.396  Sum_probs=161.5

Q ss_pred             eEEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECCccCCCCc
Q 025088           53 TILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGDL  132 (258)
Q Consensus        53 ~L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g~~~~~~~  132 (258)
                      +|+|++|+      +|++|++|+||||+||+     + +++++++++++|.+++++.|.    +++|+|+++|+      
T Consensus         2 ~l~a~~r~------~k~~R~~G~VPaViYG~-----~-~~~~i~v~~~~l~k~l~~~~~----~~li~l~i~g~------   59 (175)
T d2zjrs1           2 ELTAKPRT------PKQKLDESMIAAVAYNK-----E-NNVSFALDRKAFDRAFRQQST----TGLFDITVEGG------   59 (175)
T ss_dssp             CCCBCCSC------CHHHHSSSCCCEEEESS-----S-CCCCCBCCHHHHHHHHHHHTT----SCCCBCCCTTC------
T ss_pred             eeEeccch------HHHHhhCCCCCEEEECC-----C-CCEEEEEcHHHHHHHHHhcCc----ceEEEEEecCC------
Confidence            46677773      58999999999999985     3 689999999999999998775    78999999875      


Q ss_pred             cceEeEEEeeeeeccCCCCceEEEEEEeCCCCeEEEEEeEEEEecCCCcccccCeEEEEEeeEEEEEee-CCCCCCeEEE
Q 025088          133 IEKVRVLPRKVHLHSGTDAPLNVTFLRAPPEALLKIDVPLVFRGDDVSPGLRKGGYLNTIKRTVKFLCP-ADIVPPYIDV  211 (258)
Q Consensus       133 ~~~~~vliKeVQ~hpvt~~ilHVDF~~v~~~~~v~v~VPV~~~Ge~~s~Gvk~GG~L~~~~~~V~V~~~-p~~IPe~IeV  211 (258)
                       ++++||+||+|+||++++++|+|||+++++++|+++|||+|+|+  |+|+|+||+|++.+++|++.|+ |++||++|+|
T Consensus        60 -~~~~vlikevQ~~pv~~~i~HvDF~~v~~~~~i~v~VPi~~~G~--~~gvk~Gg~l~~~~~~i~v~~~~P~~IP~~i~v  136 (175)
T d2zjrs1          60 -ETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGR--SQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVV  136 (175)
T ss_dssp             -CCCBCCEEEEEECSSSCCEEEEEEECCCSSCCCEEEEECEEESC--CTTTTTTSEEECSCSEEEEECCCTTCCCSCCEE
T ss_pred             -ceEEEEehhhhhhhccCceeEEEEEecCCCcEEEEEEEEEeecc--cccccccceeeeeehhhhhhccChhhCCceEEe
Confidence             36789999999999999999999999999999999999999997  7999999999999999999996 9999999999


Q ss_pred             EcCCCCCCCeEEEeccCCCCCeEEecCCCccEEEEEccc
Q 025088          212 DLSELDVEQKILAGDLKVHPALKLLRSKDEPVCKIAGGR  250 (258)
Q Consensus       212 DvS~L~iGd~I~v~DL~lp~gv~ll~d~e~vVvsV~~~r  250 (258)
                      |||+|++||+|+++||++|+|+++++|+|++||+|.+||
T Consensus       137 Dvs~L~iGd~i~v~Dl~lp~gv~~~~d~~~~v~~V~~pr  175 (175)
T d2zjrs1         137 DVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVLPPR  175 (175)
T ss_dssp             ECTTCCSSCEEETTTSCCSTTCCCCSCTTCEEEEEECCC
T ss_pred             cchhccCCCeEEEEeecCCCCcEEccCCCcEEEEEeCCC
Confidence            999999999999999999999999999999999999986

>d1dfup_ b.53.1.1 (P:) Ribosomal protein L25 {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: Ribosomal protein L25-like
superfamily: Ribosomal protein L25-like
family: Ribosomal protein L25-like
domain: Ribosomal protein L25
species: Escherichia coli [TaxId: 562]

Probab=99.95  E-value=6.3e-29  Score=191.33  Aligned_cols=93  Identities=22%  Similarity=0.331  Sum_probs=85.0

Q ss_pred             eeEEEEEcCCCCchHhHHHHHcCCccEEEecCcCCCCCCceeEEEEeHHHHHHHHhhcCcccceeEEEEEEECCccCCCC
Q 025088           52 ETILAIPRASPGTRVSVKERKAGRVPSIVFEQEDGQHGGNKRLISVQTNQIRKLVGHLGRSFFVSRLFDLEVRSEFGSGD  131 (258)
Q Consensus        52 ~~L~a~~R~~~Gk~~arkLRr~G~VPaVIYG~~~g~~G~~~~~I~v~~~el~k~l~~~g~~~f~s~l~~L~v~g~~~~~~  131 (258)
                      .+|+|++|+.+||+++|+||++|+|||||||+     |.++++|+++.++|.+++++.+   |.+.+++|+++|+     
T Consensus         2 ~~L~a~~R~~~Gk~~~r~lRr~G~vPaViYG~-----~~~~~~i~v~~~~l~~~l~~~~---~~~~~i~l~~~g~-----   68 (94)
T d1dfup_           2 FTINAEVRKEQGKGASRRLRAANKFPAIIYGG-----KEAPLAIELDHDKVMNMQAKAE---FYSEVLTIVVDGK-----   68 (94)
T ss_dssp             CEEECEECSCCSHHHHHHHHHTTEEEEEEECS-----SSCCEEEEEEHHHHHHHTTSGG---GGTSCBEEEETTE-----
T ss_pred             eEEEEEEeccCCcHHHHHHHHcCCccEEEECC-----CCCCcEEEecHHHHhhhhcccc---cccceEEEEECCe-----
Confidence            47999999999999999999999999999997     4689999999999999998644   4588999999984     


Q ss_pred             ccceEeEEEeeeeeccCCCCceEEEEEEe
Q 025088          132 LIEKVRVLPRKVHLHSGTDAPLNVTFLRA  160 (258)
Q Consensus       132 ~~~~~~vliKeVQ~hpvt~~ilHVDF~~v  160 (258)
                         +++|++||||+||++++++||||+|.
T Consensus        69 ---~~~vlikevQ~~pv~~~i~HvDF~r~   94 (94)
T d1dfup_          69 ---EIKVKAQDVQRHPYKPKLQHIDFVRA   94 (94)
T ss_dssp             ---ECCEEEEEEEECSSSSCEEEEEEEEC
T ss_pred             ---EEEeeheeeeecCCCCCEEEEeeecC
Confidence               67899999999999999999999984