Citrus Sinensis ID: 026232

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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-
Protein Sequence
MTLWCRTVQKVAHNSRTPFSRTTSYYHTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATKLENPEPAVM
Secondary Structure (PSIPRED)
ccccEEccEEccccccccccccccccEEEEEEEccccccHHHHHHHHcccccEEEEcccccccccccccccccEEEEEcHHHHHHHHHHcccccEEEEEEEEEEcccccEEEEEccccEEEEEEEEccccccEEEEEEEEEccccEEEEEEEEEEEEccccccEEEcEEEEEEEEEEEEEEEccccccEEEEEccccccccEEEEEcccccccEEEEEccccccEEEEEcccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHccccccHHHHHcccEEEEEEEccccccHHHHHHHHcccccEEEEcccccccccccccccccccEEEcHHHHHHHHHHcccccHEEEEEEEEEccccccccEEEEEEEEcHHccccccccccEEEEEEEEccccEEEEEEEEEEEccccccccccccEEEEEEEEEEEEEcHHHcccEEEEEccccccccEEEEcccccccccEEEEcccccEEEEEEcccccccccccc
Coil and Loop (DISEMBL)
MTLWCRTVQkvahnsrtpfsrttsyyhtiqaiprectgsrvsardrsqgripAVVFAQDlldkntdrrspsrkqILSTERKQIHSILKsvelpffcsttfplqiragsgssvlldsgkvlpikvhrdeetgRILNLVFVwaddgtelkvdVPVVfkgvescpglkkggyLKSIRTSLKylcpaehispkievdvsnldigdrvfmsdievhpswkllsknekmplckisatklenpepavm
Flexible Loop (DISEMBL)
mtlwcrtvqkvahnsrtpfsrttsyyhtiqaiprectgsrvsardrsqgripavvfaqdlldkntdrrspsrkqilsterKQIHSILKSVELPFFCSTTFPLQIRAGsgssvlldsgKVLPikvhrdeetgrILNLVFVWADDGTELKVDVPVVfkgvescpglkkggyLKSIRTSLKYLcpaehispkievdvsnLDIGDRVFMSDIEVhpswkllsknekmplckisatklenpepavm
Low Complexity Region (SEG)
MTLWCRTVQKVAHNSRTPFSRTTSYYHTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATKLENPEPAVM
Disordered region (IsUnstruct)
**LWCRTVQKVAHNSRTPFSRTTSYYHTIQAIPRECT*************IPAVVFAQD**********************QIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKN****LC***************
Disordered Region (DISOPRED)
****************************IQA**************RSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKI*************
Disordered Region (DISEMBL)
MTLWCRTVQKVAHNSRTPFSRTTSYYHTIQAIPRECTG*********QGRIPAVVFAQDLLDKNT**********LSTERKQIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATKLENPEPAVM
Disordered Region (DISPRO)
*********KVAHNSRTP***TTSYYHTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDK****RSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATK*********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTLWCRTVQKVAHNSRTPFSRTTSYYHTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATKLENPEPAVM
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	241	2.2.26 [Sep-21-2011]
Q3YT12	209	50S ribosomal protein L25	yes	no	0.755	0.870	0.288	1e-13
Q5HC84	208	50S ribosomal protein L25	yes	no	0.709	0.822	0.290	2e-12
Q5FFA2	208	50S ribosomal protein L25	yes	no	0.709	0.822	0.290	2e-12
Q2NAN1	229	50S ribosomal protein L25	yes	no	0.659	0.694	0.292	7e-12
Q2GHW3	210	50S ribosomal protein L25	yes	no	0.755	0.866	0.278	3e-11
B8EK41	227	50S ribosomal protein L25	yes	no	0.651	0.691	0.279	4e-11
Q1GSP2	212	50S ribosomal protein L25	yes	no	0.659	0.75	0.281	5e-11
Q7NNL2	211	50S ribosomal protein L25	yes	no	0.672	0.767	0.274	1e-10
A5CF34	207	50S ribosomal protein L25	yes	no	0.639	0.743	0.280	1e-10
Q4FVB4	224	50S ribosomal protein L25	yes	no	0.688	0.741	0.263	2e-10

>sp|Q3YT12|RL25_EHRCJ 50S ribosomal protein L25 OS=Ehrlichia canis (strain Jake) GN=rplY PE=3 SV=1

 Score = 77.0 bits (188), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 60/208 (28%), Positives = 95/208 (45%), Gaps = 26/208 (12%)

Query: 29  IQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSP--SRKQILSTERKQIHSI 86
           I A  RE  G+  +   R  G IPAVV+      KN D  S   S ++ LS  R      
Sbjct: 9   INASLRENVGTGPARAVRRNGGIPAVVYG-----KNRDSLSVFLSDREFLSKHRSA---- 59

Query: 87  LKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTE 146
                      +T  +++  G           VL   V +   T RI ++ F + D GTE
Sbjct: 60  ---------ALSTHLIELEIGDKKEY------VLMRDVQKHPVTDRIQHVDFQFIDYGTE 104

Query: 147 LKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMS 206
           +K++VP++F   + C G+K+GG L  +  +L   C    I   IE+D+S+L  G  + +S
Sbjct: 105 IKIEVPLIFTNEQKCIGVKRGGVLNILHRTLSIKCLPNAILQNIEIDLSDLTAGHSIHVS 164

Query: 207 DIEVHPSWKLLSKNEKMPLCKISATKLE 234
           D+ + P   ++ K     +  IS+T +E
Sbjct: 165 DLNLPPEINVVMKEHNPAIVTISSTSME 192

This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.
Ehrlichia canis (strain Jake) (taxid: 269484)

>sp|Q5HC84|RL25_EHRRW 50S ribosomal protein L25 OS=Ehrlichia ruminantium (strain Welgevonden) GN=rplY PE=3 SV=1

 Score = 73.2 bits (178), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/203 (29%), Positives = 89/203 (43%), Gaps = 32/203 (15%)

Query: 34  RECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSP-----SRKQILSTERKQIHSILK 88
           R   G+  S   R  G IPAVV+ +         RSP     S ++ LS  R        
Sbjct: 14  RNSVGTGPSRTLRRNGAIPAVVYGK--------HRSPLSIYLSDREFLSKYRSA------ 59

Query: 89  SVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELK 148
                    +T  +++  G           VL   + +   T RI ++ F + D GTE+K
Sbjct: 60  -------ALSTHLIELEIGEKKEY------VLMRDIQKHPVTDRIQHVDFQFIDHGTEIK 106

Query: 149 VDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDI 208
           ++VP+VF   + C G+KKGG L  +  +L   C    I   IEVD++NL IG  + +SD+
Sbjct: 107 IEVPLVFVNEQRCVGVKKGGVLNILHRTLHIKCLPNAILQSIEVDLANLTIGHSIHVSDL 166

Query: 209 EVHPSWKLLSKNEKMPLCKISAT 231
            +     ++ K     L  IS T
Sbjct: 167 NLPSEVTVVMKEHNPTLVTISGT 189

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

Ehrlichia ruminantium (strain Welgevonden) (taxid: 254945)

>sp|Q5FFA2|RL25_EHRRG 50S ribosomal protein L25 OS=Ehrlichia ruminantium (strain Gardel) GN=rplY PE=3 SV=2

 Score = 73.2 bits (178), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/203 (29%), Positives = 89/203 (43%), Gaps = 32/203 (15%)

Query: 34  RECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSP-----SRKQILSTERKQIHSILK 88
           R   G+  S   R  G IPAVV+ +         RSP     S ++ LS  R        
Sbjct: 14  RNSVGTGPSRTLRRNGAIPAVVYGK--------HRSPLSIYLSDREFLSKYRSA------ 59

Query: 89  SVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELK 148
                    +T  +++  G           VL   + +   T RI ++ F + D GTE+K
Sbjct: 60  -------ALSTHLIELEIGEKKEY------VLMRDIQKHPVTDRIQHVDFQFIDHGTEIK 106

Query: 149 VDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDI 208
           ++VP+VF   + C G+KKGG L  +  +L   C    I   IEVD++NL IG  + +SD+
Sbjct: 107 IEVPLVFVNEQRCVGVKKGGVLNILHRTLHIKCLPNAILQSIEVDLANLTIGHSIHVSDL 166

Query: 209 EVHPSWKLLSKNEKMPLCKISAT 231
            +     ++ K     L  IS T
Sbjct: 167 NLPSEVTVVMKEHNPTLVTISGT 189

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

Ehrlichia ruminantium (strain Gardel) (taxid: 302409)

>sp|Q2NAN1|RL25_ERYLH 50S ribosomal protein L25 OS=Erythrobacter litoralis (strain HTCC2594) GN=rplY PE=3 SV=1

 Score = 70.9 bits (172), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 89/181 (49%), Gaps = 22/181 (12%)

Query: 28  TIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSIL 87
           T+ A  RE  G   S   R +GR+PAV++          +  P+   ++  E K +   +
Sbjct: 6   TLPAEARERAGKGASRALRREGRVPAVIYGG--------KEEPT---MIHVEEKLL---I 51

Query: 88  KSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTEL 147
           K +    F ++   ++I    G +V     + LP  V     + R  +  F     G ++
Sbjct: 52  KQLMTGHFMNSIVEIEI---GGKTV-----RTLPKDVALHPVSDRPEHADFFRLAKGGKI 103

Query: 148 KVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSD 207
           +V VPVVF   E+ PGLKKGG L  +R  L+ +C  + I  +IE+DV+  ++GD + +S+
Sbjct: 104 EVSVPVVFMNEEASPGLKKGGVLNVVRHELELVCENDKIPGEIEIDVTGKEVGDSIHISE 163

Query: 208 I 208
           I
Sbjct: 164 I 164

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

Erythrobacter litoralis (strain HTCC2594) (taxid: 314225)

>sp|Q2GHW3|RL25_EHRCR 50S ribosomal protein L25 OS=Ehrlichia chaffeensis (strain Arkansas) GN=rplY PE=3 SV=1

 Score = 68.9 bits (167), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 97/208 (46%), Gaps = 26/208 (12%)

Query: 29  IQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILK 88
           I A  R+  G+  S   R  G IPAV++      K  D  S      +S   ++  S  +
Sbjct: 9   INASLRKNVGTGPSRALRLSGEIPAVIYG-----KGRDSLS------ISLSNREFVSKYR 57

Query: 89  SVELPFFCSTTFPLQIRAGSGSSVLLDSGK--VLPIKVHRDEETGRILNLVFVWADDGTE 146
           S  L     +T  +++         +D+ K  VL   V +   T RI ++ F + D GTE
Sbjct: 58  SAAL-----STHLIELE--------IDNKKEYVLMRDVQKHPVTDRIQHVDFQFIDYGTE 104

Query: 147 LKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMS 206
           +K++VP++F   + C G+K+GG L  +  +L   C  + I   IE+D+S L  G  + +S
Sbjct: 105 IKIEVPLIFTNEQKCIGIKRGGVLNILHRTLSIKCSPKAILQNIEIDLSGLTTGHSIHVS 164

Query: 207 DIEVHPSWKLLSKNEKMPLCKISATKLE 234
           D+++ P   +  K     +  IS+   E
Sbjct: 165 DLKLPPEVNVTMKEHNPAIVTISSASTE 192

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

Ehrlichia chaffeensis (strain Arkansas) (taxid: 205920)

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

 Score = 68.6 bits (166), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 50/179 (27%), Positives = 88/179 (49%), Gaps = 22/179 (12%)

Query: 28  TIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSIL 87
           T+ A  R  TG   +   R +GRIP V++         D   P     ++ + ++++ ++
Sbjct: 6   TLAAAARHGTGKGAARSVRREGRIPGVIYG------GGDPAEP-----ITLDYRELNKLI 54

Query: 88  KSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTEL 147
            +     F +T F + + AG+   V+    ++ PIK          L++ F+    G  L
Sbjct: 55  YAGH---FLTTLFEIDV-AGTKQRVIPRDYQLDPIK-------DLPLHVDFLRLKPGASL 103

Query: 148 KVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMS 206
           KV+VPV F   E+CPG+KKGG +  +R S++   PA+ I   I  D+  L+I D + ++
Sbjct: 104 KVEVPVHFLNQETCPGVKKGGSVNIVRHSIELRVPADDIPEAITADLGELEINDSLHLT 162

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

 Score = 68.2 bits (165), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 51/181 (28%), Positives = 86/181 (47%), Gaps = 22/181 (12%)

Query: 28  TIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSIL 87
           T+ A  RE  G   S   R  GR+PAVV+          +  P    ++  E K +   +
Sbjct: 6   TLTAETRERGGKGASRELRRNGRVPAVVYGG--------KEEP---LMIHVEEKLL---M 51

Query: 88  KSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTEL 147
           K +    F ++   +++    G  +     + LP  V       R ++  F+       +
Sbjct: 52  KQLMTGHFMNSVVMIEV---GGKQI-----RTLPKDVAFHPVKDRPIHADFLRIAKDATV 103

Query: 148 KVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSD 207
           +V VPVVF+  E  PGLK+GG L  +R  L+ +C A++I  +I +DV+  DIGD + +S+
Sbjct: 104 QVAVPVVFQNEEKSPGLKRGGVLNIVRHELELVCDADNIPDEIAIDVTGFDIGDSIHISN 163

Query: 208 I 208
           +
Sbjct: 164 V 164

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|Q7NNL2|RL25_GLOVI 50S ribosomal protein L25 OS=Gloeobacter violaceus (strain PCC 7421) GN=rplY PE=3 SV=1

 Score = 67.0 bits (162), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 51/186 (27%), Positives = 90/186 (48%), Gaps = 24/186 (12%)

Query: 34  RECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELP 93
           +  TG++  A  R +GRIPAV++              ++   L  E++    +LK V + 
Sbjct: 9   QRATGAQPRAM-RREGRIPAVLYGH----------RGTQSLALELEQRTAEDLLKRVTI- 56

Query: 94  FFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPV 153
              +T  PL++  G        SG VL  +V  D   G++L+L F        + +D+P+
Sbjct: 57  --NNTILPLKVERGW-------SGDVLLREVQHDAVGGKLLHLSFFAVAGHGSITLDLPL 107

Query: 154 VFKGVESCPGLK-KGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHP 212
           VF G     G+K  GG L+ + T L    P   +   IEVD+S + +GD +++ D+ + P
Sbjct: 108 VFTG--EAVGVKMDGGLLEKVLTQLTVNTPPTDVPEAIEVDISTMQVGDMLYVKDLVLPP 165

Query: 213 SWKLLS 218
             ++++
Sbjct: 166 GIEVVN 171

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

Gloeobacter violaceus (strain PCC 7421) (taxid: 251221)

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

 Score = 66.6 bits (161), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 50/178 (28%), Positives = 88/178 (49%), Gaps = 24/178 (13%)

Query: 42  SARD-RSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTF 100
           SAR  R QG++P V++ + +        +P     + T  K++  + +    PFF ST  
Sbjct: 19  SARALRRQGKVPGVIYKKGI--------TPIH---VCTLEKEVAKLYRK---PFFSSTVI 64

Query: 101 PLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWAD-DGTELKVDVPVVFKGVE 159
            LQ+             KVLP  V     T  + ++ F+  + +G+  KV VP+ F+G E
Sbjct: 65  QLQVDD--------QRFKVLPKAVQLHPVTEFMNHIDFILVEQNGSMQKVKVPISFEGKE 116

Query: 160 SCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLL 217
              G+K+GGYL  ++  +  LCP + I   I+ D++N+ +G  + +S +E+     L+
Sbjct: 117 KSLGIKRGGYLNIVKRYVDLLCPVDKIPQCIKCDIANVSVGASIKISRLELPEGCNLV 174

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|Q4FVB4|RL25_PSYA2 50S ribosomal protein L25 OS=Psychrobacter arcticus (strain DSM 17307 / 273-4) GN=rplY PE=3 SV=1

 Score = 66.6 bits (161), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 50/190 (26%), Positives = 86/190 (45%), Gaps = 24/190 (12%)

Query: 23  TSYYHTIQAIPR--ECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTER 80
           T  +  + A+ R  E  G   S R R Q  +PA+++                +Q ++   
Sbjct: 2   TINHFALNAVDRSAEVQGKGASRRLRKQNLVPAIIYG-------------GGEQPIAISI 48

Query: 81  KQIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVW 140
           K I+ ++KS+E   F S    L +       V+ D        + R    G  ++  F  
Sbjct: 49  K-INELVKSLEFEAFFSHILTLNVDGEEHQVVIKD--------LQRHPAKGFPMHADFQR 99

Query: 141 ADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIG 200
              G ++ ++VPV F G E  PG K GG L ++ T ++ +C    +   +E+DVS ++IG
Sbjct: 100 VVKGQKINMNVPVHFSGREEAPGTKAGGILSTLVTDIEIVCIPSQLPEYLEIDVSGMEIG 159

Query: 201 DRVFMSDIEV 210
           D   +SDI++
Sbjct: 160 DLFRLSDIKL 169

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

Psychrobacter arcticus (strain DSM 17307 / 273-4) (taxid: 259536)

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	241
255562637	253	50S ribosomal protein L25, putative [Ric	0.975	0.928	0.740	9e-97
224096802	261	predicted protein [Populus trichocarpa]	0.908	0.839	0.753	3e-93
449461415	258	PREDICTED: 50S ribosomal protein L25-lik	0.900	0.841	0.737	5e-93
359497479	251	PREDICTED: 50S ribosomal protein L25-lik	0.892	0.856	0.75	5e-89
359480435	249	PREDICTED: 50S ribosomal protein L25 [Vi	0.892	0.863	0.75	7e-89
356511738	246	PREDICTED: 50S ribosomal protein L25-lik	0.954	0.934	0.695	7e-88
357518581	255	50S ribosomal protein L25 [Medicago trun	0.887	0.839	0.719	9e-87
15240108	249	Ribosomal protein L25/Gln-tRNA synthetas	0.983	0.951	0.640	2e-81
297794323	245	hypothetical protein ARALYDRAFT_920032 [	0.983	0.967	0.634	6e-81
388505558	195	unknown [Lotus japonicus]	0.792	0.979	0.685	1e-72

>gi|255562637|ref|XP_002522324.1| 50S ribosomal protein L25, putative [Ricinus communis] gi|223538402|gb|EEF40008.1| 50S ribosomal protein L25, putative [Ricinus communis]

 Score =  358 bits (920), Expect = 9e-97,   Method: Compositional matrix adjust.
 Identities = 174/235 (74%), Positives = 200/235 (85%)

Query: 1   MTLWCRTVQKVAHNSRTPFSRTTSYYHTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDL 60
           M  W R ++ V  +S    +  +S+YHTIQAIPRECTGSRV+ARDR+QGRIPAVVF+Q L
Sbjct: 1   MAKWLRGLKTVVQSSSPSLNSQSSFYHTIQAIPRECTGSRVAARDRAQGRIPAVVFSQSL 60

Query: 61  LDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVL 120
           LDKN + RS SRKQ+L+TERKQI SIL SVELPFFCSTTF LQIRAGSGSSVL++SG +L
Sbjct: 61  LDKNPNSRSISRKQLLTTERKQIQSILTSVELPFFCSTTFNLQIRAGSGSSVLIESGTIL 120

Query: 121 PIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYL 180
           PIKVHRDEETG+ILNLVFVWADDGTELKVDVP++FKG E CPGLKKGG L  IR SLK L
Sbjct: 121 PIKVHRDEETGKILNLVFVWADDGTELKVDVPLIFKGEEDCPGLKKGGKLNRIRKSLKVL 180

Query: 181 CPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATKLEN 235
           CPAEHI PK+EVDVS+LDIGD+V M D+EVHPS KLLSKNE +P+CKI +T LE+
Sbjct: 181 CPAEHIPPKLEVDVSSLDIGDKVSMGDVEVHPSLKLLSKNENIPICKIVSTDLES 235

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224096802|ref|XP_002310742.1| predicted protein [Populus trichocarpa] gi|222853645|gb|EEE91192.1| predicted protein [Populus trichocarpa]

 Score =  347 bits (889), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 165/219 (75%), Positives = 191/219 (87%)

Query: 23  TSYYHTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQ 82
           +S YHTIQAIPRE  GSRVSAR+R QGRIPAVVF+Q LLD N   R  SRK++L+TE+KQ
Sbjct: 27  SSRYHTIQAIPREVVGSRVSAREREQGRIPAVVFSQSLLDINPSNRYTSRKRLLTTEKKQ 86

Query: 83  IHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWAD 142
           I +ILKSVE+PFFCSTTFPLQIRAG+GSSVLL+SG VLPIK+HRDE+TG+ILNLVF WAD
Sbjct: 87  ILAILKSVEIPFFCSTTFPLQIRAGTGSSVLLESGTVLPIKIHRDEKTGKILNLVFAWAD 146

Query: 143 DGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDR 202
           +GTE+KVDVPVVFKG E+CPGLKKGG+LK +R++LKYLCPAEHI  KIEVD+SNLDI D 
Sbjct: 147 EGTEMKVDVPVVFKGEENCPGLKKGGHLKMMRSTLKYLCPAEHIPQKIEVDISNLDIEDG 206

Query: 203 VFMSDIEVHPSWKLLSKNEKMPLCKISATKLENPEPAVM 241
           +FM DIEVH S KLLSKNE MP+CKI AT L+ PEPA +
Sbjct: 207 LFMRDIEVHSSLKLLSKNENMPVCKIVATNLDTPEPAAL 245

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449461415|ref|XP_004148437.1| PREDICTED: 50S ribosomal protein L25-like [Cucumis sativus] gi|449515688|ref|XP_004164880.1| PREDICTED: 50S ribosomal protein L25-like [Cucumis sativus]

 Score =  346 bits (887), Expect = 5e-93,   Method: Compositional matrix adjust.
 Identities = 160/217 (73%), Positives = 189/217 (87%)

Query: 18  PFSRTTSYYHTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILS 77
           PFS   + YHTIQAIPREC+G ++S++DR+QGRIPAVVF+Q +L+KN+   SPSRK +L+
Sbjct: 26  PFSSFRAAYHTIQAIPRECSGRKISSKDRAQGRIPAVVFSQQILEKNSVHGSPSRKHLLT 85

Query: 78  TERKQIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLV 137
           TERKQIHSILKSVELPFFCST F LQIRAGSGSSVLL+SG +LPIK+HR+EETG+I N+V
Sbjct: 86  TERKQIHSILKSVELPFFCSTRFKLQIRAGSGSSVLLESGSILPIKIHRNEETGKIFNIV 145

Query: 138 FVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNL 197
           FVWAD+G+ELKVDVP+VFKG E+CPGL+KGG L  IRTSLKYLCPAEHI  KIEVDVSNL
Sbjct: 146 FVWADEGSELKVDVPIVFKGEEACPGLQKGGQLNKIRTSLKYLCPAEHIPSKIEVDVSNL 205

Query: 198 DIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATKLE 234
           DIGDR+F+ D++VH S KLLSKNE MP+CKI   K E
Sbjct: 206 DIGDRIFIRDVDVHSSMKLLSKNEVMPICKIVTIKSE 242

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359497479|ref|XP_003635532.1| PREDICTED: 50S ribosomal protein L25-like [Vitis vinifera]

 Score =  333 bits (853), Expect = 5e-89,   Method: Compositional matrix adjust.
 Identities = 162/216 (75%), Positives = 183/216 (84%), Gaps = 1/216 (0%)

Query: 23  TSYYHTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLL-DKNTDRRSPSRKQILSTERK 81
            + YHTIQAI RE TGS+VSARDR+QGRIPAVVFAQ LL   N + RS SRK++L+TERK
Sbjct: 30  AAAYHTIQAISREFTGSKVSARDRAQGRIPAVVFAQQLLTGGNMNGRSVSRKRLLTTERK 89

Query: 82  QIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWA 141
           QI +ILKSVE  F CSTTFPLQIRAGSGSSVLL+SG VLP+K+HRDE TG++LNLVF WA
Sbjct: 90  QIQAILKSVEPEFICSTTFPLQIRAGSGSSVLLESGTVLPLKIHRDEATGKVLNLVFAWA 149

Query: 142 DDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGD 201
           D+G+ELKVDVP+VFKG + CPGLKKGGYL  IR SLK+LCPAEHI  KIEVDVSNLDIGD
Sbjct: 150 DEGSELKVDVPLVFKGEDVCPGLKKGGYLNRIRPSLKFLCPAEHIPSKIEVDVSNLDIGD 209

Query: 202 RVFMSDIEVHPSWKLLSKNEKMPLCKISATKLENPE 237
           R+ M D+EVHPS KLLSKNE MP+CKI A KLE  E
Sbjct: 210 RILMHDVEVHPSLKLLSKNETMPVCKIVAAKLERAE 245

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359480435|ref|XP_002263685.2| PREDICTED: 50S ribosomal protein L25 [Vitis vinifera] gi|302144151|emb|CBI23278.3| unnamed protein product [Vitis vinifera]

 Score =  332 bits (852), Expect = 7e-89,   Method: Compositional matrix adjust.
 Identities = 162/216 (75%), Positives = 183/216 (84%), Gaps = 1/216 (0%)

Query: 23  TSYYHTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLL-DKNTDRRSPSRKQILSTERK 81
            + YHTIQAI RE TGS+VSARDR+QGRIPAVVFAQ LL   N + RS SRK++L+TERK
Sbjct: 30  AAAYHTIQAISREFTGSKVSARDRAQGRIPAVVFAQQLLTGGNINGRSVSRKRLLTTERK 89

Query: 82  QIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWA 141
           QI +ILKSVE  F CSTTFPLQIRAGSGSSVLL+SG VLP+K+HRDE TG++LNLVF WA
Sbjct: 90  QIQAILKSVEPEFICSTTFPLQIRAGSGSSVLLESGTVLPLKIHRDEATGKVLNLVFAWA 149

Query: 142 DDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGD 201
           D+G+ELKVDVP+VFKG + CPGLKKGGYL  IR SLK+LCPAEHI  KIEVDVSNLDIGD
Sbjct: 150 DEGSELKVDVPLVFKGEDVCPGLKKGGYLNRIRPSLKFLCPAEHIPSKIEVDVSNLDIGD 209

Query: 202 RVFMSDIEVHPSWKLLSKNEKMPLCKISATKLENPE 237
           R+ M D+EVHPS KLLSKNE MP+CKI A KLE  E
Sbjct: 210 RILMHDVEVHPSLKLLSKNETMPVCKIVAAKLERAE 245

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356511738|ref|XP_003524580.1| PREDICTED: 50S ribosomal protein L25-like [Glycine max]

 Score =  329 bits (843), Expect = 7e-88,   Method: Compositional matrix adjust.
 Identities = 162/233 (69%), Positives = 190/233 (81%), Gaps = 3/233 (1%)

Query: 6   RTVQKVAHNSRTPFSRTTSYYHTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNT 65
           RTV      S + F R+T  YHTIQAIPREC+GS+VSARDR+QGRIP VVF Q+LL+KN 
Sbjct: 14  RTVA-AGRGSLSGFQRST--YHTIQAIPRECSGSKVSARDRTQGRIPCVVFLQNLLEKNP 70

Query: 66  DRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVH 125
           D RS S+K +L+ E+KQI +IL S + PFFCST FPLQIRAGSGSS LL+SG VLPIK+H
Sbjct: 71  DARSESKKHLLTVEKKQIKAILDSADAPFFCSTRFPLQIRAGSGSSHLLESGTVLPIKIH 130

Query: 126 RDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEH 185
           RDEE+G+ILNLVFVWA+DG +LKVDVPVVF+G ++CPG++KGG L  IR SLK+LCP+EH
Sbjct: 131 RDEESGKILNLVFVWAEDGMKLKVDVPVVFEGEDACPGVQKGGILNKIRPSLKFLCPSEH 190

Query: 186 ISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATKLENPEP 238
           I  KI VDVSNLDI DR+FM DIEVHPS KLLSKNE MP+CKI  T L N EP
Sbjct: 191 IPSKIVVDVSNLDIEDRIFMRDIEVHPSLKLLSKNESMPICKIVPTSLGNKEP 243

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357518581|ref|XP_003629579.1| 50S ribosomal protein L25 [Medicago truncatula] gi|355523601|gb|AET04055.1| 50S ribosomal protein L25 [Medicago truncatula]

 Score =  325 bits (834), Expect = 9e-87,   Method: Compositional matrix adjust.
 Identities = 154/214 (71%), Positives = 180/214 (84%)

Query: 24  SYYHTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQI 83
           ++YHTIQAIPRE TGSRV+ARDR QGRIPAVVF QDLL+K+ + RS SRKQ+L+ E++QI
Sbjct: 28  NHYHTIQAIPREITGSRVAARDRKQGRIPAVVFFQDLLEKSPEARSTSRKQLLTVEKRQI 87

Query: 84  HSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADD 143
            ++L S+E PFFCST FPLQIRAGSGS+ LL+SG VLPIK+HRDEE+G ILNLVFVWA+D
Sbjct: 88  KAVLNSIEAPFFCSTRFPLQIRAGSGSTHLLESGTVLPIKIHRDEESGNILNLVFVWAED 147

Query: 144 GTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRV 203
           G  LKVDVPVV KG + CPGLKKGG+L  IRTSL+YL P+EHI  KIEVD+SNLDI DR+
Sbjct: 148 GMNLKVDVPVVIKGEDVCPGLKKGGFLNKIRTSLRYLGPSEHIPSKIEVDISNLDIEDRI 207

Query: 204 FMSDIEVHPSWKLLSKNEKMPLCKISATKLENPE 237
           FM DIEVHPS KLL+KNE MP+CKI  T L   E
Sbjct: 208 FMRDIEVHPSLKLLNKNENMPICKIVPTSLGKQE 241

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15240108|ref|NP_201487.1| Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain protein [Arabidopsis thaliana] gi|9758136|dbj|BAB08628.1| unnamed protein product [Arabidopsis thaliana] gi|15450930|gb|AAK96736.1| Unknown protein [Arabidopsis thaliana] gi|17978763|gb|AAL47375.1| unknown protein [Arabidopsis thaliana] gi|332010889|gb|AED98272.1| Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain protein [Arabidopsis thaliana]

 Score =  307 bits (786), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 157/245 (64%), Positives = 187/245 (76%), Gaps = 8/245 (3%)

Query: 1   MTLWCRTVQKV-AHNSRTPFS------RTTSYYHTIQAIPRECTGSRVSARDRSQGRIPA 53
           M  W R ++ V A  +  P S      R    Y TIQAIPRE TG  VSARDR+ GRIPA
Sbjct: 1   MAKWWRGLRSVTAEVADLPASSFGRSIRCIHQYQTIQAIPREATGRGVSARDRTIGRIPA 60

Query: 54  VVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAGSGSSVL 113
           VVF Q LLD +  +R  SRKQ+L+ ++KQI SI+ SV LPFFCSTTF LQIRAG GSS L
Sbjct: 61  VVFPQSLLDTDASKRGVSRKQLLTADKKQIKSIIDSVGLPFFCSTTFQLQIRAGQGSSTL 120

Query: 114 LDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSI 173
           ++SG+VLP+KVHRDEETG+ILNLVFVWADDG +LKVDVPVVFKG++ CPGL+KGG L++I
Sbjct: 121 VESGRVLPLKVHRDEETGKILNLVFVWADDGEKLKVDVPVVFKGLDHCPGLQKGGNLRTI 180

Query: 174 RTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATK- 232
           R++LK L PAEHI  KIEVDVSNLDI D+V + D+  HPS KLLSKNE MP+CKI AT  
Sbjct: 181 RSTLKLLGPAEHIPSKIEVDVSNLDIEDKVLLQDVVFHPSLKLLSKNETMPVCKIVATSP 240

Query: 233 LENPE 237
           ++ PE
Sbjct: 241 VKEPE 245

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297794323|ref|XP_002865046.1| hypothetical protein ARALYDRAFT_920032 [Arabidopsis lyrata subsp. lyrata] gi|297310881|gb|EFH41305.1| hypothetical protein ARALYDRAFT_920032 [Arabidopsis lyrata subsp. lyrata]

 Score =  306 bits (783), Expect = 6e-81,   Method: Compositional matrix adjust.
 Identities = 153/241 (63%), Positives = 184/241 (76%), Gaps = 4/241 (1%)

Query: 1   MTLWCRTVQKVAHNSRTPFS---RTTSYYHTIQAIPRECTGSRVSARDRSQGRIPAVVFA 57
           M  W R ++ VA+   + F    R    Y TIQAIPRE TG  VSARDR+ GRIPAVVF 
Sbjct: 1   MAKWWRGLRSVANLPASSFGGSIRRIHQYQTIQAIPREATGRGVSARDRTIGRIPAVVFP 60

Query: 58  QDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAGSGSSVLLDSG 117
           Q LL+ +  +R  SRKQ+L+ + KQI SI+ SV LPFFCSTTF LQIRAG GSS L++SG
Sbjct: 61  QSLLETDASKRGVSRKQLLTADNKQIKSIIDSVGLPFFCSTTFQLQIRAGQGSSTLVESG 120

Query: 118 KVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSL 177
           +VLP+K+HRDEE G+ILNLVFVWADDG +LKVDVPVVF G+++CPGLKKGG L+SIR++L
Sbjct: 121 RVLPLKIHRDEENGKILNLVFVWADDGEKLKVDVPVVFNGLDNCPGLKKGGNLRSIRSTL 180

Query: 178 KYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATK-LENP 236
           K L PAEHI  KIEVDVS LDI D+V + D+  HPS KLLSKNE MP+CKI AT  ++ P
Sbjct: 181 KLLGPAEHIPSKIEVDVSELDIEDKVLLQDVVFHPSLKLLSKNETMPVCKIVATSPVKEP 240

Query: 237 E 237
           E
Sbjct: 241 E 241

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388505558|gb|AFK40845.1| unknown [Lotus japonicus]

 Score =  278 bits (711), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 131/191 (68%), Positives = 155/191 (81%)

Query: 48  QGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAG 107
           QGRIPA VF QDLL K+   RS ++K +L+ E+KQI +IL SV+  FFCST FPLQIRAG
Sbjct: 2   QGRIPAAVFLQDLLSKDAGNRSAAKKHLLTVEKKQIKAILNSVQTSFFCSTRFPLQIRAG 61

Query: 108 SGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKG 167
           SGSS L++SG VLP+K+H D+E+G+ILNLVFVWA+ G  LKVDVPVVFKG + CPGL+KG
Sbjct: 62  SGSSHLVESGTVLPVKIHMDQESGQILNLVFVWAEGGMNLKVDVPVVFKGEDVCPGLQKG 121

Query: 168 GYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCK 227
           G+L  IRTSLK+LCP+EHI  KIEVDVSNLDI DR+FM DIEVHPS KLLSKNE MP+CK
Sbjct: 122 GFLNKIRTSLKFLCPSEHIPSKIEVDVSNLDIEDRIFMRDIEVHPSLKLLSKNENMPICK 181

Query: 228 ISATKLENPEP 238
           +  T L N  P
Sbjct: 182 VVPTSLGNQAP 192

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

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	241
TAIR|locus:2174979	249	AT5G66860 [Arabidopsis thalian	0.983	0.951	0.640	1.3e-75
TIGR_CMR|ECH_0142	210	ECH_0142 "ribosomal 5S rRNA E-	0.502	0.576	0.317	7.7e-17
TIGR_CMR|APH_1302	211	APH_1302 "ribosomal 5S rRNA E-	0.468	0.535	0.274	4.2e-14
TIGR_CMR|GSU_0662	194	GSU_0662 "ribosoma protein L25	0.526	0.654	0.313	1.6e-07
TIGR_CMR|CHY_0195	197	CHY_0195 "ribosomal protein L2	0.464	0.568	0.278	8.1e-06
TIGR_CMR|NSE_0306	194	NSE_0306 "ribosomal 5S rRNA E-	0.443	0.551	0.276	3.6e-05
TIGR_CMR|SPO_0812	207	SPO_0812 "ribosomal protein L2	0.568	0.661	0.268	6.2e-05
TIGR_CMR|CJE_0356	178	CJE_0356 "ribosomal protein L2	0.373	0.505	0.336	6.9e-05
TIGR_CMR|CBU_1840	244	CBU_1840 "ribosomal 5S rRNA E-	0.381	0.377	0.276	0.00011

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

 Score = 762 (273.3 bits), Expect = 1.3e-75, P = 1.3e-75
 Identities = 157/245 (64%), Positives = 187/245 (76%)

Query:     1 MTLWCRTVQKV-AHNSRTPFS------RTTSYYHTIQAIPRECTGSRVSARDRSQGRIPA 53
             M  W R ++ V A  +  P S      R    Y TIQAIPRE TG  VSARDR+ GRIPA
Sbjct:     1 MAKWWRGLRSVTAEVADLPASSFGRSIRCIHQYQTIQAIPREATGRGVSARDRTIGRIPA 60

Query:    54 VVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAGSGSSVL 113
             VVF Q LLD +  +R  SRKQ+L+ ++KQI SI+ SV LPFFCSTTF LQIRAG GSS L
Sbjct:    61 VVFPQSLLDTDASKRGVSRKQLLTADKKQIKSIIDSVGLPFFCSTTFQLQIRAGQGSSTL 120

Query:   114 LDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSI 173
             ++SG+VLP+KVHRDEETG+ILNLVFVWADDG +LKVDVPVVFKG++ CPGL+KGG L++I
Sbjct:   121 VESGRVLPLKVHRDEETGKILNLVFVWADDGEKLKVDVPVVFKGLDHCPGLQKGGNLRTI 180

Query:   174 RTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATK- 232
             R++LK L PAEHI  KIEVDVSNLDI D+V + D+  HPS KLLSKNE MP+CKI AT  
Sbjct:   181 RSTLKLLGPAEHIPSKIEVDVSNLDIEDKVLLQDVVFHPSLKLLSKNETMPVCKIVATSP 240

Query:   233 LENPE 237
             ++ PE
Sbjct:   241 VKEPE 245

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 = 176 (67.0 bits), Expect = 7.7e-17, Sum P(2) = 7.7e-17
 Identities = 39/123 (31%), Positives = 66/123 (53%)

Query:   114 LDSGK--VLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLK 171
             +D+ K  VL   V +   T RI ++ F + D GTE+K++VP++F   + C G+K+GG L 
Sbjct:    70 IDNKKEYVLMRDVQKHPVTDRIQHVDFQFIDYGTEIKIEVPLIFTNEQKCIGIKRGGVLN 129

Query:   172 SIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISAT 231
              +  +L   C  + I   IE+D+S L  G  + +SD+++ P   +  K     +  IS+ 
Sbjct:   130 ILHRTLSIKCSPKAILQNIEIDLSGLTTGHSIHVSDLKLPPEVNVTMKEHNPAIVTISSA 189

Query:   232 KLE 234
               E
Sbjct:   190 STE 192

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

 Score = 154 (59.3 bits), Expect = 4.2e-14, Sum P(2) = 4.2e-14
 Identities = 31/113 (27%), Positives = 62/113 (54%)

Query:   119 VLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLK 178
             V+   + +   +G I ++ F + D   E+K++VP+VF   + C G+K+GG +  +  SL 
Sbjct:    77 VITKDIQKHPVSGAIAHVDFQFVDQDAEMKMEVPLVFLNEQKCVGVKRGGVINILHRSLI 136

Query:   179 YLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISAT 231
               C   HI   +EVD+ ++ IG  + +SD+++  +  ++ K E   +  + A+
Sbjct:   137 IRCSPHHIPKSLEVDLIDVAIGHSLHVSDLKLPSTINVVMKEEDPVIATVVAS 189

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 = 122 (48.0 bits), Expect = 1.6e-07, Sum P(2) = 1.6e-07
 Identities = 42/134 (31%), Positives = 66/134 (49%)

Query:   106 AGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLK 165
             +G GS   L+   V+   + R+   G IL++ F       ++KV VP+V  G  +  G+K
Sbjct:    66 SGGGS---LNGNIVIVADMQRNPLKGDILHVDFHRISLDEKVKVHVPLVMVGTAA--GVK 120

Query:   166 KGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPL 225
             +GG L  +  SL   C    I   I VDV+NL IG  + +S++ +    K+L+  E  P+
Sbjct:   121 EGGMLDVVTYSLDVECLPTAIPEAINVDVTNLAIGHSIHVSELVLPAGIKVLNDPET-PI 179

Query:   226 CKISATKLENPEPA 239
               I   K +   PA
Sbjct:   180 VSIHG-KAKEEAPA 192

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

TIGR_CMR|CHY_0195 CHY_0195 "ribosomal protein L25" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 121 (47.7 bits), Expect = 8.1e-06, P = 8.1e-06
 Identities = 32/115 (27%), Positives = 62/115 (53%)

Query:   118 KVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSL 177
             +VL  ++     TG+++++ F   + G +++  VPV   G  +  G+K GG L+   + +
Sbjct:    68 RVLVKELQHHPVTGKLIHVDFQVVESGRKIRQLVPVELYGEPA--GVKAGGILEHGLSEV 125

Query:   178 KYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATK 232
                C  E +   IE DVS L++GD + + D+E+ P  +++   E + +  ISA +
Sbjct:   126 TVECLPEDLPEFIEADVSKLEVGDCLRVKDLELPPGVRVIEDPESI-IALISAPR 179

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 = 102 (41.0 bits), Expect = 3.6e-05, Sum P(2) = 3.6e-05
 Identities = 31/112 (27%), Positives = 52/112 (46%)

Query:   104 IRAGSGSSVLLDSGKVLPI--KVHRDEETGRI-LNLVFVWADDGTELKVDVPVVFKGVES 160
             + +GSG   L   GKV  +  K +       + L+L FV+A +    K  VP+ F     
Sbjct:    54 VLSGSGVVELSCEGKVYKVVPKAYELHPVSSVVLHLDFVFAGEHAS-KFQVPLNFVNSGK 112

Query:   161 CPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHP 212
                ++ G  L  ++ ++   C A ++   I VD+ N  +GD +  SD+ V P
Sbjct:   113 SEAIRLGAMLNIVKRTVLVRCTAANLPKSIPVDIENAKVGDSIKFSDL-VFP 163

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 = 100 (40.3 bits), Expect = 6.2e-05, Sum P(2) = 6.2e-05
 Identities = 39/145 (26%), Positives = 66/145 (45%)

Query:    86 ILKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGT 145
             +LK ++   F ST F L++          +  +V+   V RD       +L  +     +
Sbjct:    51 LLKMLKAGRFKSTLFNLKVEGH-------EDVRVICRDVQRDVVKDLPTHLDLMRLRRTS 103

Query:   146 ELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFM 205
              +K+ + V F    + PGLKKGG L  +R  ++    A  I   I VD++ L+IGD V +
Sbjct:   104 RIKLFIHVDFVNHAAAPGLKKGGVLTVVRPEVELEVTAGDIPESITVDLTGLNIGDVVTI 163

Query:   206 SDIEVHPSWKLLSKNEKMPLCKISA 230
             S + + P+    +      +  ISA
Sbjct:   164 SSVTL-PAGAKPTVERDFVIANISA 187

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|CJE_0356 CJE_0356 "ribosomal protein L25" [Campylobacter jejuni RM1221 (taxid:195099)]

 Score = 112 (44.5 bits), Expect = 6.9e-05, P = 6.9e-05
 Identities = 31/92 (33%), Positives = 45/92 (48%)

Query:   119 VLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLK 178
             V+ +   +D  T  + ++    A  G   K  VPV   G  +  GLK  G L   +  LK
Sbjct:    68 VVVVDYQKDPVTAELKHVDLKVAQKGVISKYMVPVKITG--TAIGLKNKGVLIQSKRRLK 125

Query:   179 YLCPAEHISPKIEVDVSNLDIGDRVFMSDIEV 210
               C AE++    E+DVS LD+GD + + DI V
Sbjct:   126 VKCAAENLPNFFELDVSKLDVGDALLVRDIVV 157

GO:0003735 "structural constituent of ribosome" 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 = 115 (45.5 bits), Expect = 0.00011, P = 0.00011
 Identities = 26/94 (27%), Positives = 56/94 (59%)

Query:   118 KVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSL 177
             KV+   + R     +I+++ F       +L ++VP+ F G + CPG++ GG +  +++ +
Sbjct:    76 KVILKALQRHHTKPKIVHIDFQRIKASEKLIMNVPLHFLGEDDCPGVEAGGVVSHLQSEV 135

Query:   178 KYLC-PAEHISPKIEVDVSNLDIGDRVFMSDIEV 210
             +  C PA+ +   IEVD+S+L + + V +S++++
Sbjct:   136 EIRCLPAD-LPEYIEVDLSHLQLDESVHLSNLKL 168


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   0.134   0.398    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      241       241   0.00094  113 3  11 22  0.43    33
                                                     32  0.44    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:  9
  No. of states in DFA:  608 (65 KB)
  Total size of DFA:  185 KB (2106 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:  21.01u 0.14s 21.15t   Elapsed:  00:00:01
  Total cpu time:  21.01u 0.14s 21.15t   Elapsed:  00:00:01
  Start:  Fri May 10 04:00:20 2013   End:  Fri May 10 04:00:21 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

---

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: estExt_fgenesh4_pg.C_LG_VII0918 hypothetical protein (261 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	241
PRK05618	197	PRK05618, PRK05618, 50S ribosomal protein L25/gene	7e-32
TIGR00731	176	TIGR00731, ctc_TL5, ribosomal protein L25, Ctc-for	3e-16
cd00495	90	cd00495, Ribosomal_L25_TL5_CTC, Ribosomal L25/TL5/	7e-06

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

 Score =  115 bits (290), Expect = 7e-32
 Identities = 66/213 (30%), Positives = 99/213 (46%), Gaps = 23/213 (10%)

Query: 27  HTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSI 86
            T++A  RE  G   + R R  G++PAV++      K  +  S      +S + K++   
Sbjct: 4   ITLEAEVREEFGKGAARRLRRAGKVPAVIYG-----KGKEPVS------ISVDEKELIKA 52

Query: 87  LKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTE 146
           LK      F ST   L++    G        KVL   V R      IL++ F+  D G +
Sbjct: 53  LKK---GAFLSTLLDLEV---GGKKQ-----KVLVKDVQRHPVKDFILHVDFLRVDAGEK 101

Query: 147 LKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMS 206
           +KV+VPV F G     G+K GG L  +   L+  C  E I   IEVDVS L+IGD + +S
Sbjct: 102 VKVEVPVHFVGEAKGVGVKLGGVLNQVLHELEVECLPEDIPEFIEVDVSGLEIGDSIHVS 161

Query: 207 DIEVHPSWKLLSKNEKMPLCKISATKLENPEPA 239
           D+++    KLL  +    +  + A + E  E  
Sbjct: 162 DLKLPEGVKLLD-DPDEVVATVVAPRGEEEEEE 193

Length = 197

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

 Score = 73.5 bits (181), Expect = 3e-16
 Identities = 47/188 (25%), Positives = 85/188 (45%), Gaps = 25/188 (13%)

Query: 34  RECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELP 93
           R   G   + R R +GRIPAVV+ +   + N           L  + K+    L+     
Sbjct: 6   RTSFGKSAARRIRKEGRIPAVVYGKGKENVN-----------LELKSKEFIKYLRK---- 50

Query: 94  FFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPV 153
              ST   L+I    G        KVL      +  T  ++++ F+   +G +LKV+VP+
Sbjct: 51  GATSTVLTLEI---GGKEF-----KVLVKDYQYNPVTNEVIHVDFLEVVEGVKLKVEVPI 102

Query: 154 VFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPS 213
              G      +K GG L  ++  ++  C  + I   +E+DVS+L +G+ + +SD+E+   
Sbjct: 103 KLIGTPIG--VKNGGILTQVKRRIEVECKPKDIPDFLELDVSSLGVGESLKLSDLELPAG 160

Query: 214 WKLLSKNE 221
              ++ ++
Sbjct: 161 VSFITDDD 168

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 = 42.8 bits (102), Expect = 7e-06
 Identities = 26/111 (23%), Positives = 45/111 (40%), Gaps = 23/111 (20%)

Query: 28  TIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSIL 87
           T++A  RE TG   + R R +G++PAV++      K  +         +S + K++  +L
Sbjct: 1   TLKAEKREETGKGAARRLRREGKVPAVIY-----GKGEEPIP------ISVDAKELEKLL 49

Query: 88  KSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVF 138
           +        +T   L+I              VL   V R      IL++ F
Sbjct: 50  RKEGE----NTVIELEIDG--------KKENVLIKDVQRHPVKDEILHVDF 88

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	241
PRK05618	197	50S ribosomal protein L25/general stress protein C	100.0
TIGR00731	176	ctc_TL5 ribosomal protein L25, Ctc-form. The C-ter	100.0
PRK05943	94	50S ribosomal protein L25; Reviewed	99.96
PF01386	88	Ribosomal_L25p: Ribosomal L25p family; InterPro: I	99.95
cd00495	91	Ribosomal_L25_TL5_CTC Ribosomal_L25_TL5_CTC: Ribos	99.95
PF14693	88	Ribosomal_TL5_C: Ribosomal protein TL5, C-terminal	99.95
COG1825	93	RplY Ribosomal protein L25 (general stress protein	99.92

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

Probab=100.00  E-value=2.2e-55  Score=379.56  Aligned_cols=192  Identities=33%  Similarity=0.487  Sum_probs=174.9

Q ss_pred             CCcceEEEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEE
Q 026232           23 TSYYHTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPL  102 (241)
Q Consensus        23 ms~~~~L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L  102 (241)
                      |. ..+|+|.+|+..||+++||||++|+|||||||++           .++++++++.++|.+++++..   +.+++|+|
T Consensus         1 m~-~~~l~a~~R~~~gk~~~r~lR~~G~VPaViYG~~-----------~~~~~i~v~~~~l~k~l~~~~---~~~~~i~L   65 (197)
T PRK05618          1 ME-TITLEAEVREEFGKGAARRLRRAGKVPAVIYGKG-----------KEPVSISVDEKELIKALKKGA---FLSTLLDL   65 (197)
T ss_pred             CC-eEEEEEEEcCcCCChHHHHHHHCCCCcEEEECCC-----------CCCEEEEECHHHHHHHHhcCC---ceeEEEEE
Confidence            44 4789999999999999999999999999999993           469999999999999995432   24789999


Q ss_pred             EEcCCCCccccccceeeeeeeeeeccCCCceeEEEEEEeCCCCEEEEEEeEEEEecCCCCccccCeEEEEEecEEEEEee
Q 026232          103 QIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCP  182 (241)
Q Consensus       103 ~i~~g~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~v~~~~~V~v~VPI~l~G~~~s~Gvk~GG~L~~~~~~I~V~~l  182 (241)
                      +++ |       +++.||+||+|+||++++++|+|||+++++++|+++|||+|+|++.+++.|+||+|++.+++|+|+|+
T Consensus        66 ~i~-g-------~~~~vlikevQ~~pv~~~i~HvDF~~v~~~~~v~v~VPv~~~G~~~~~~~k~GG~l~~~~~~v~v~~~  137 (197)
T PRK05618         66 EVG-G-------KKQKVLVKDVQRHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVKLGGVLNQVLHELEVECL  137 (197)
T ss_pred             EEC-C-------EEEEEEEeeeeeccCCCCEEeEEEEEeCCCCEEEEEeeEEEEcCCCCcccccceEEEEEEEEEEEEEc
Confidence            996 6       57899999999999999999999999999999999999999999865666669999999999999999


Q ss_pred             cCCCCCeEEEEccCCCCCCeEEEeccCCCCCeEEeecCCCccEEEEEcCCCCCCCC
Q 026232          183 AEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATKLENPEP  238 (241)
Q Consensus       183 P~~IPe~I~VDVs~L~iGd~i~V~DL~lp~gv~il~~~~~~vV~~V~~~~~e~~~~  238 (241)
                      |.+||++|+||||+|++||+|+|+||++|+|+++++ +++.+||+|.+|+.++++.
T Consensus       138 p~~IP~~I~VDVs~L~~Gd~i~v~Dl~lp~~v~i~~-~~~~~v~~V~~~~~~~~~e  192 (197)
T PRK05618        138 PEDIPEFIEVDVSGLEIGDSIHVSDLKLPEGVKLLD-DPDEVVATVVAPRGEEEEE  192 (197)
T ss_pred             HHHCCccEEEEcccCCCCCEEEeeeecCCCCcEEcC-CCCcEEEEEEcCCcccccc
Confidence            999999999999999999999999999999999985 8899999999988865554

>TIGR00731 ctc_TL5 ribosomal protein L25, Ctc-form

Probab=100.00  E-value=1e-55  Score=375.77  Aligned_cols=175  Identities=27%  Similarity=0.467  Sum_probs=165.0

Q ss_pred             EEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEEEEcCCC
Q 026232           29 IQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAGS  108 (241)
Q Consensus        29 L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i~~g~  108 (241)
                      |+|++|+.+||+++|||||+|+||||+||++           .++++++++.++|.+++++.+.    +++|+|+++ | 
T Consensus         1 l~a~~R~~~gk~~~r~LR~~G~VPaVvYG~~-----------~~~~~i~v~~~el~k~l~~~~~----~~~i~L~v~-g-   63 (176)
T TIGR00731         1 LEVKSRTSFGKSAARRIRKEGRIPAVVYGKG-----------KENVNLELKSKEFIKYLRKGAT----STVLTLEIG-G-   63 (176)
T ss_pred             CeEEEeCCCCChHHHHHHHCCCccEEEECCC-----------CCCEEEEECHHHHHHHHhccCC----cEEEEEEEC-C-
Confidence            5799999999999999999999999999993           4699999999999999987653    689999998 6 


Q ss_pred             CccccccceeeeeeeeeeccCCCceeEEEEEEeCCCCEEEEEEeEEEEecCCCCccccCeEEEEEecEEEEEeecCCCCC
Q 026232          109 GSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISP  188 (241)
Q Consensus       109 ~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~v~~~~~V~v~VPI~l~G~~~s~Gvk~GG~L~~~~~~I~V~~lP~~IPe  188 (241)
                            ++++||+||+|+||++++++|+|||+++++++|+++|||+|+|+  ++|+|+||+|++.+++|+|+|+|.+||+
T Consensus        64 ------~~~~vlikevQ~~pv~~~i~HvDF~~v~~~~~v~v~VPv~~~G~--~~gvk~GG~l~~~~~~v~v~~~p~~IPe  135 (176)
T TIGR00731        64 ------KEFKVLVKDYQYNPVTNEVIHVDFLEVVEGVKLKVEVPIKLIGT--PIGVKNGGILTQVKRRIEVECKPKDIPD  135 (176)
T ss_pred             ------EEEEEEEehhhhccCCCCeEEEEeEEeCCCCEEEEEeeEEEecc--cccccCCcEEEEEEEEEEEEECHHHCCc
Confidence                  46799999999999999999999999999999999999999998  5799999999999999999999999999


Q ss_pred             eEEEEccCCCCCCeEEEeccCCCCCeEEeecCCCccEEEEE
Q 026232          189 KIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKIS  229 (241)
Q Consensus       189 ~I~VDVs~L~iGd~i~V~DL~lp~gv~il~~~~~~vV~~V~  229 (241)
                      +|+||||+|++||+||++||++|+|+++++ +++.+||+|.
T Consensus       136 ~I~VDvs~L~iGd~i~v~Dl~lp~gv~~~~-d~~~~v~~V~  175 (176)
T TIGR00731       136 FLELDVSSLGVGESLKLSDLELPAGVSFIT-DDDEVVVTVI  175 (176)
T ss_pred             cEEEECccCCCCCEEEEeeccCCCCcEEcc-CCCcEEEEEe
Confidence            999999999999999999999999999985 8889999984

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.

>PRK05943 50S ribosomal protein L25; Reviewed

Probab=99.96  E-value=2.9e-29  Score=193.42  Aligned_cols=93  Identities=26%  Similarity=0.356  Sum_probs=84.1

Q ss_pred             eEEEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEEEEcC
Q 026232           27 HTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRA  106 (241)
Q Consensus        27 ~~L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i~~  106 (241)
                      ++|+|++|+..||+++|+||++|+|||||||++           .++++++++.++|.+++++.+   +.+++|+|+++ 
T Consensus         2 ~~l~a~~R~~~gk~~~r~lR~~G~vPaViYG~~-----------~~~~~i~v~~~el~k~l~~~~---~~~~~i~L~v~-   66 (94)
T PRK05943          2 FTINAEVRPEQGKGASRRLRRAGKFPAIIYGGN-----------EAPVSIVLDHKDVINLQAKAE---FYKEVITLVID-   66 (94)
T ss_pred             eEEEEEEeCcCCChHHHHHHHCCCCCEEEECCC-----------CCcEEEEEcHHHHHHHHhcCC---CcceEEEEEEC-
Confidence            579999999999999999999999999999993           468999999999999998654   23689999998 


Q ss_pred             CCCccccccceeeeeeeeeeccCCCceeEEEEEEe
Q 026232          107 GSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWA  141 (241)
Q Consensus       107 g~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~v  141 (241)
                      |       ++++||+||+|+||++++++|||||+|
T Consensus        67 g-------~~~~v~ikevQ~~pv~~~i~HvDF~~v   94 (94)
T PRK05943         67 G-------KEVKVKVQAVQRHPFKPKLEHIDFVRA   94 (94)
T ss_pred             C-------EEEEEEEeeeecCcCCCCeEeEeeeeC
Confidence            6       467999999999999999999999985

>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=9.9e-28  Score=182.74  Aligned_cols=87  Identities=31%  Similarity=0.498  Sum_probs=80.4

Q ss_pred             EEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHH-HhcCCCceeeeEEEEEEcCC
Q 026232           29 IQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSIL-KSVELPFFCSTTFPLQIRAG  107 (241)
Q Consensus        29 L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll-~~~g~~~~~~~v~~L~i~~g  107 (241)
                      |+|++|+.+||+++|+||++|+|||||||++           .++++|+++.++|.+++ +..+.    +++|+|+++ |
T Consensus         1 L~a~~R~~~gk~~~r~LR~~G~iPaviYG~~-----------~~~~~i~v~~~~l~k~~~~~~~~----~~~i~L~i~-g   64 (88)
T PF01386_consen    1 LKAEKREETGKSAARRLRREGKIPAVIYGKG-----------KESIPISVDEKELEKLLRRKHGE----NSVIELNID-G   64 (88)
T ss_dssp             EEEEESSSTSSSHHHHHHHTTEEEEEEEESS-----------EEEEEEEEEHHHHHHHHTHHHTT----TSEEEEEET-T
T ss_pred             CeEEEcCcCCCHHHHHHHHcCCceEEEECCC-----------CCCEEEEEeHHHHHHHHHhcCCc----eEEEEEEEC-C
Confidence            7899999999999999999999999999993           46899999999999999 55554    689999998 6


Q ss_pred             CCccccccceeeeeeeeeeccCCCceeEEEE
Q 026232          108 SGSSVLLDSGKVLPIKVHRDEETGRILNLVF  138 (241)
Q Consensus       108 ~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF  138 (241)
                             +++.||+||+|+||++++++||||
T Consensus        65 -------~~~~vlikevQ~~p~~~~i~HvDF   88 (88)
T PF01386_consen   65 -------KKYNVLIKEVQRDPVTDKILHVDF   88 (88)
T ss_dssp             -------EEEEEEEEEEEEESSSSSEEEEEE
T ss_pred             -------EEEEEEEEeeeeCCCCCCeEeccC
Confidence                   578999999999999999999999

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 ....

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

Probab=99.95  E-value=1.9e-27  Score=181.85  Aligned_cols=90  Identities=31%  Similarity=0.474  Sum_probs=83.0

Q ss_pred             EEEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEEEEcCC
Q 026232           28 TIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAG  107 (241)
Q Consensus        28 ~L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i~~g  107 (241)
                      +|+|.+|+.+||+++|+||++|+|||||||++           .++++|+++.++|.+++++.+.    +++|+|+++ |
T Consensus         2 ~l~a~~R~~~gk~~~r~lR~~G~iPavvYG~~-----------~~~~~i~v~~~~l~k~l~~~~~----~~~~~L~i~-g   65 (91)
T cd00495           2 TLKAEKREETGKGASRRLRRAGKVPAVIYGKG-----------KEPISISVDEKELEKLLRKEGR----STLIELNID-G   65 (91)
T ss_pred             eEEEEEcccCCChHHHHHHHCCCCCEEEECCC-----------CCCEEEEEcHHHHHHHHhhcCC----ceEEEEEEC-C
Confidence            68999999999999999999999999999992           4799999999999999988763    689999998 6


Q ss_pred             CCccccccceeeeeeeeeeccCCCceeEEEEEE
Q 026232          108 SGSSVLLDSGKVLPIKVHRDEETGRILNLVFVW  140 (241)
Q Consensus       108 ~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~  140 (241)
                             +++.|++||+|+||++++++||||++
T Consensus        66 -------~~~~~~ikevQ~~pv~~~i~HvDF~~   91 (91)
T cd00495          66 -------KKENVLIKDVQRHPVKDKILHVDFLR   91 (91)
T ss_pred             -------EEEEEEEehhhhccCCCCEEEEeccC
Confidence                   56799999999999999999999984

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

>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=1.5e-27  Score=181.89  Aligned_cols=88  Identities=35%  Similarity=0.649  Sum_probs=77.6

Q ss_pred             CEEEEEEeEEEEecCCCCccccCeEEEEEecEEEEEeecCCCCCeEEEEccCCCCCCeEEEeccCCCCCeEEeecCCCcc
Q 026232          145 TELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMP  224 (241)
Q Consensus       145 ~~V~v~VPI~l~G~~~s~Gvk~GG~L~~~~~~I~V~~lP~~IPe~I~VDVs~L~iGd~i~V~DL~lp~gv~il~~~~~~v  224 (241)
                      |+|+++|||+|+|+  |+|+|+||+|++.+++|+|+|+|.+||++|+||||+|++||+||++||++|+|++++ +|++.+
T Consensus         1 e~v~~~VPv~~~G~--~~gvk~Gg~l~~~~~~v~V~~~p~~iPe~I~vDvs~l~~g~~i~v~Dl~lp~gv~~~-~d~~~v   77 (88)
T PF14693_consen    1 EKVKVEVPVHFVGE--SPGVKKGGILQQVLREVEVECLPADIPESIEVDVSGLEIGDSIHVSDLKLPEGVEIL-DDPETV   77 (88)
T ss_dssp             S-EEEEEEEEEESS--SHHHCTTSEEEESTSEEEEEE-TTS--SSEEEETTTSSTTCEEEGCCSB-STTEEES-S-TTSE
T ss_pred             CeEEEEEeEEEEcc--cccCcCCcEEEEEEeEEEEEEcHHHCCccEEEECccCcCCCEEEEeeccCCCCcEEc-CCCCcE
Confidence            68999999999998  689999999999999999999999999999999999999999999999999999999 489999


Q ss_pred             EEEEEcCCCCC
Q 026232          225 LCKISATKLEN  235 (241)
Q Consensus       225 V~~V~~~~~e~  235 (241)
                      ||+|.++|+|+
T Consensus        78 V~~v~~~~~ee   88 (88)
T PF14693_consen   78 VASVVAPRVEE   88 (88)
T ss_dssp             EEEEE-SCSS-
T ss_pred             EEEEeccccCC
Confidence            99999999875

...

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

Probab=99.92  E-value=3.2e-25  Score=170.71  Aligned_cols=92  Identities=26%  Similarity=0.392  Sum_probs=85.5

Q ss_pred             eEEEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEEEEcC
Q 026232           27 HTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRA  106 (241)
Q Consensus        27 ~~L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i~~  106 (241)
                      .+|+++.|+..||+++|+||++|+||||+||.           +.++++++++.++|.+.+++.+.    +++|+|+++ 
T Consensus         2 ~~l~~~~R~~~Gkg~~RrlR~~G~iPAviYG~-----------g~~~v~i~l~~~~~~k~~~~~~~----~~v~~l~v~-   65 (93)
T COG1825           2 RELEAEVRTSQGKGASRRLRRAGKIPAVVYGG-----------GKEPVNIALDHHEFAKALRKLGY----STVITLEVD-   65 (93)
T ss_pred             ceeceeEecccCcchhHhHHhcCCCCEEEECC-----------CCCCceEEEcHHHHHHHHhhccc----ceEEEEEEC-
Confidence            47999999999999999999999999999999           35789999999999999998773    799999998 


Q ss_pred             CCCccccccceeeeeeeeeeccCCCceeEEEEEEe
Q 026232          107 GSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWA  141 (241)
Q Consensus       107 g~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~v  141 (241)
                      |       ++..||+|++|+||+++.++|+||+++
T Consensus        66 g-------~~~~Vlvkd~Q~~p~~~~~~HvDf~~v   93 (93)
T COG1825          66 G-------KEIKVLVKDVQRHPLTDEVQHIDFLRV   93 (93)
T ss_pred             C-------eEEEEEehhhhhCcccCceeecccccC
Confidence            6       578999999999999999999999975

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	241
3fin_Z	177	T. Thermophilus 70s Ribosome In Complex With Mrna,		5e-05
3tvh_V	179	Crystal Structure Analysis Of Ribosomal Decoding. T		5e-05
3pyo_V	188	Crystal Structure Of A Complex Containing Domain 3		5e-05
3tve_V	175	Crystal Structure Analysis Of Ribosomal Decoding. T		6e-05
1feu_A	206	Crystal Structure Of Ribosomal Protein Tl5, One Of		7e-05
2j01_Z	206	Structure Of The Thermus Thermophilus 70s Ribosome		7e-05

>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 = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 46/85 (54%), Gaps = 4/85 (4%)
Query: 138 FVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNL 197
           FV +D+  E+ V  P+ F G  +  G++ GG L+ I   +       +I   IEVDVS L
Sbjct: 87  FVLSDEPVEMYV--PLRFVGTPA--GVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGL 142
Query: 198 DIGDRVFMSDIEVHPSWKLLSKNEK 222
           +IGD +  SD+++ P  +L    E+
Sbjct: 143 EIGDSLHASDLKLPPGVELAVSPEE 167

>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 = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 46/85 (54%), Gaps = 4/85 (4%)
Query: 138 FVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNL 197
           FV +D+  E+ V  P+ F G  +  G++ GG L+ I   +       +I   IEVDVS L
Sbjct: 89  FVLSDEPVEMYV--PLRFVGTPA--GVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGL 144
Query: 198 DIGDRVFMSDIEVHPSWKLLSKNEK 222
           +IGD +  SD+++ P  +L    E+
Sbjct: 145 EIGDSLHASDLKLPPGVELAVSPEE 169

>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 = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 46/85 (54%), Gaps = 4/85 (4%)
Query: 138 FVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNL 197
           FV +D+  E+ V  P+ F G  +  G++ GG L+ I   +       +I   IEVDVS L
Sbjct: 87  FVLSDEPVEMYV--PLRFVGTPA--GVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGL 142
Query: 198 DIGDRVFMSDIEVHPSWKLLSKNEK 222
           +IGD +  SD+++ P  +L    E+
Sbjct: 143 EIGDSLHASDLKLPPGVELAVSPEE 167

>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 = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 46/85 (54%), Gaps = 4/85 (4%)
Query: 138 FVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNL 197
           FV +D+  E+ V  P+ F G  +  G++ GG L+ I   +       +I   IEVDVS L
Sbjct: 89  FVLSDEPVEMYV--PLRFVGTPA--GVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGL 144
Query: 198 DIGDRVFMSDIEVHPSWKLLSKNEK 222
           +IGD +  SD+++ P  +L    E+
Sbjct: 145 EIGDSLHASDLKLPPGVELAVSPEE 169

>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 = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 138 FVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNL 197
           FV +D+  E+ V  P+ F G  +  G++ GG L+ I   +       +I   IEVDVS L
Sbjct: 89  FVLSDEPVEMYV--PLRFVGTPA--GVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGL 144
Query: 198 DIGDRVFMSDIEVHPSWKL 216
           +IGD +  SD+++ P  +L
Sbjct: 145 EIGDSLHASDLKLPPGVEL 163

>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 = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 138 FVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNL 197
           FV +D+  E+ V  P+ F G  +  G++ GG L+ I   +       +I   IEVDVS L
Sbjct: 89  FVLSDEPVEMYV--PLRFVGTPA--GVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGL 144
Query: 198 DIGDRVFMSDIEVHPSWKL 216
           +IGD +  SD+++ P  +L
Sbjct: 145 EIGDSLHASDLKLPPGVEL 163

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	241
1feu_A	206	50S ribosomal protein L25; general stress protein	9e-23
2zjr_S	237	50S ribosomal protein L25; ribosome, large ribosom	6e-20

>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 = 90.9 bits (226), Expect = 9e-23
 Identities = 39/213 (18%), Positives = 81/213 (38%), Gaps = 30/213 (14%)

Query: 27  HTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSI 86
           + ++A  RE          R  G++P +++ +               + +  +  +   +
Sbjct: 3   YRLKAYYREGEKPS---ALRRAGKLPGLMYNRH------------LNRKVYVDLVEFDKV 47

Query: 87  LKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTE 146
            +   +         L++  G        S   L  +V+ D+   R  ++ F        
Sbjct: 48  FRQASI----HHVIVLELPDG-------QSLPTLVRQVNLDKRRRRPEHVDFF-VLSDEP 95

Query: 147 LKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMS 206
           +++ VP+ F G  +  G++ GG L+ I   +       +I   IEVDVS L+IGD +  S
Sbjct: 96  VEMYVPLRFVG--TPAGVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHAS 153

Query: 207 DIEVHPSWKLLSKNEKMPLCKISATKLENPEPA 239
           D+++ P  +L    E   +  +   +       
Sbjct: 154 DLKLPPGVELAVSPE-ETIAAVVPPEDVEKLAE 185

>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 = 84.0 bits (208), Expect = 6e-20
 Identities = 37/204 (18%), Positives = 75/204 (36%), Gaps = 27/204 (13%)

Query: 37  TGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFC 96
              R   +   +  I AV + +   + N            + +RK      +        
Sbjct: 5   AKPRTPKQKLDESMIAAVAYNK---ENN---------VSFALDRKAFDRAFRQQ----ST 48

Query: 97  STTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFK 156
           +  F + +  G       ++   L   V  D+     +++ F     G  ++V VPV   
Sbjct: 49  TGLFDITVEGG-------ETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTT 101

Query: 157 GVESCPGLKKGGYLKSIRTSLKYLCPA-EHISPKIEVDVSNLDIGDRVFMSDIEVHPSWK 215
           G     G  +GG +  +  +L+ + P    I  ++ VDV+ ++IGD +   DI++     
Sbjct: 102 GR--SQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCT 159

Query: 216 LLSKNEKMPLCKISATKLENPEPA 239
           L +  E + +  +   +L   E  
Sbjct: 160 LAADPE-LTVVSVLPPRLTAEELE 182

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	241
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	93.46

>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=1.6e-54  Score=375.26  Aligned_cols=176  Identities=22%  Similarity=0.380  Sum_probs=165.6

Q ss_pred             eEEEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEEEE-c
Q 026232           27 HTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQI-R  105 (241)
Q Consensus        27 ~~L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i-~  105 (241)
                      ++|+|+.|+   |+++|||||+|+|||||||++           .+ ++|+++.++|.+++++.+.    +++|+|++ +
T Consensus         3 ~~l~a~~R~---k~aarrLRr~G~VPaVvYG~~-----------~e-~~i~v~~~el~~~l~~~~~----~~vi~L~i~~   63 (206)
T 1feu_A            3 YRLKAYYRE---GEKPSALRRAGKLPGLMYNRH-----------LN-RKVYVDLVEFDKVFRQASI----HHVIVLELPD   63 (206)
T ss_dssp             EEEECEECS---SSCHHHHHHTTEEEEEEECSS-----------CE-EEEEEEHHHHHHHHHHHTT----TSEEEEECTT
T ss_pred             eEEEEEEeC---ChHHHHHHHCCCceEEEEcCC-----------ce-EEEEEcHHHHHHHHhhcCC----cEEEEEEEcC
Confidence            589999999   888999999999999999982           46 9999999999999987653    68999999 7


Q ss_pred             CCCCccccccceeeeeeeeeeccCCCceeEEEEEEeCCCCEEEEEEeEEEEecCCCCccccCeEEEEEecEEEEEeecCC
Q 026232          106 AGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEH  185 (241)
Q Consensus       106 ~g~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~v~~~~~V~v~VPI~l~G~~~s~Gvk~GG~L~~~~~~I~V~~lP~~  185 (241)
                       |       ++++||+||+|+||++++++|+|||++++ ++|+++|||+|+|+  |+|+|+||+|++.+++|+|+|+|.+
T Consensus        64 -G-------~~~~vlikdvQ~hpv~~~i~HvDF~~v~~-~~v~v~VPv~~~G~--~~gvk~GG~l~~~~~~v~V~~~p~~  132 (206)
T 1feu_A           64 -G-------QSLPTLVRQVNLDKRRRRPEHVDFFVLSD-EPVEMYVPLRFVGT--PAGVRAGGVLQEIHRDILVKVSPRN  132 (206)
T ss_dssp             -S-------CEEEEEEEEEEECSSSSCEEEEEEEECCS-SCEEEEEEEEEESC--CHHHHTTCEEEECCSEEEEEECGGG
T ss_pred             -C-------CEEEEEEEEeEeCCCCCCeEEEEEEEECC-EEEEEEeeEEEEcC--cccccCceEEEEEEeEEEEEEcHHH
Confidence             6       46789999999999999999999999999 99999999999999  6899999999999999999999999


Q ss_pred             CCCeEEEEccCCCCCCeEEEeccCCCCCeEEeecCCCccEEEEEcCCC
Q 026232          186 ISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATKL  233 (241)
Q Consensus       186 IPe~I~VDVs~L~iGd~i~V~DL~lp~gv~il~~~~~~vV~~V~~~~~  233 (241)
                      ||++|+||||+|++||+||++||++|+|+++++ +++.+||+|.+|++
T Consensus       133 IPe~I~VDvs~L~iGdsi~v~Dl~lP~gv~~~~-d~d~~V~~V~~~~~  179 (206)
T 1feu_A          133 IPEFIEVDVSGLEIGDSLHASDLKLPPGVELAV-SPEETIAAVVPPED  179 (206)
T ss_dssp             CCSCEEEECTTCCTTEEEEGGGSCCCTTCEESS-CTTCEEEEEECSSS
T ss_pred             CCccEEEEcccCCCCCEEEEeeccCCCCcEEcC-CCCcEEEEEeCCCc
Confidence            999999999999999999999999999999985 88999999999984

>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=6.4e-53  Score=370.99  Aligned_cols=179  Identities=18%  Similarity=0.325  Sum_probs=162.4

Q ss_pred             EcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEEEEcCCCCccc
Q 026232           33 PRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAGSGSSV  112 (241)
Q Consensus        33 ~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i~~g~~~~~  112 (241)
                      +|+.+||+++||| |+|+||||||| +           .++++|+++.++|.+++++.+.    +++|+|+++ |.    
T Consensus         2 ~R~~~GKgaaRrL-r~G~VPaVvYG-g-----------~e~v~i~v~~~el~k~l~~~~~----~~li~L~Id-G~----   59 (237)
T 2zjr_S            2 ELTAKPRTPKQKL-DESMIAAVAYN-K-----------ENNVSFALDRKAFDRAFRQQST----TGLFDITVE-GG----   59 (237)
T ss_dssp             CCCBCCSCCHHHH-SSSCCCEEEES-S-----------SCCCCCBCCHHHHHHHHHHHTT----SCCCBCCCT-TC----
T ss_pred             cccccCcHHHHHH-hCCCCCEEEeC-C-----------CCCEEEEECHHHHHHHHHhcCC----cEEEEEEEC-Cc----
Confidence            5999999999999 99999999999 5           3689999999999999987542    689999998 61    


Q ss_pred             cccceeeeeeeeeeccCCCceeEEEEEEeCCCCEEEEEEeEEEEecCCCCccccCeEEEEEecEEEEEe-ecCCCCCeEE
Q 026232          113 LLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLC-PAEHISPKIE  191 (241)
Q Consensus       113 ~~~~~~vlikevQ~hpv~~~ilHvDF~~v~~~~~V~v~VPI~l~G~~~s~Gvk~GG~L~~~~~~I~V~~-lP~~IPe~I~  191 (241)
                        ++++||+||+|+||++++++|+|||+++++++|+++|||+|+|+  |+|+|+||+|++.+++|+|+| +|.+||++|+
T Consensus        60 --~~~~vliKdvQ~hPvk~~ilHVDF~~V~~~ekV~v~VPV~~vGe--~~GvK~GGvL~~~~~eveV~~~lP~~IPe~Ie  135 (237)
T 2zjr_S           60 --ETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGR--SQGEVQGGLVDIVVHNLQIVAPGPRRIPQELV  135 (237)
T ss_dssp             --CCCBCCEEEEEECSSSCCEEEEEEECCCSSCCCEEEEECEEESC--CTTTTTTSEEECSCSEEEEECCCTTCCCSCCE
T ss_pred             --eeEEEEEEEEEecCCCCCeEEEEEEEECCCCEEEEEEeEEEecC--CccccCCcEEEEEEeEEEEEEeCHHHCCccEE
Confidence              25689999999999999999999999999999999999999998  689999999999999999999 9999999999


Q ss_pred             EEccCCCCCCeEEEeccCCCCCeEEeecCCCccEEEEEcCCCCCCCC
Q 026232          192 VDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATKLENPEP  238 (241)
Q Consensus       192 VDVs~L~iGd~i~V~DL~lp~gv~il~~~~~~vV~~V~~~~~e~~~~  238 (241)
                      ||||+|++||+||++||++|+|+++++ +++.+||+|..|+.+.+|+
T Consensus       136 VDVs~LeiGdsI~v~DL~LPeGv~l~~-d~d~vVvsV~~p~~~~ee~  181 (237)
T 2zjr_S          136 VDVTKMNIGDHITAGDIKLPEGCTLAA-DPELTVVSVLPPRLTAEEL  181 (237)
T ss_dssp             EECTTCCSSCEEETTTSCCSTTCCCCS-CTTCEEEEEECCC------
T ss_pred             EEcccCCCCCEEEeeeccCCCCcEEcC-CCCcEEEEEEcCCCCCCcc
Confidence            999999999999999999999999985 8899999999998764443

>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=1.1e-29  Score=194.58  Aligned_cols=93  Identities=23%  Similarity=0.359  Sum_probs=83.7

Q ss_pred             eEEEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEEEEcC
Q 026232           27 HTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRA  106 (241)
Q Consensus        27 ~~L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i~~  106 (241)
                      ++|+|++|+.+||+++|||||+|+|||||||++           .++++++++.++|.+++++.+   +.+++|+|+++ 
T Consensus         2 ~~l~a~~R~~~Gk~~arrLRr~G~vPaVvYG~~-----------~e~~~i~v~~~~~~~~l~~~~---~~~~~i~L~i~-   66 (94)
T 1b75_A            2 FTINAEVRKEQGKGASRRLRAANKFPAIIYGGK-----------EAPLAIELDHDKVMNMQAKAE---FYSEVLTIVVD-   66 (94)
T ss_dssp             CCEEECSSCCSSSSSSSSTTTTTBCCEEEECSS-----------SCCEEECCBSHHHHHHHTTTH---HHHTCEEEEES-
T ss_pred             eEEEEEEecccCChHHHHHHHCCCceEEEECCC-----------CCCEEEEECHHHHHHHHhccC---cceEEEEEEEC-
Confidence            469999999999999999999999999999982           479999999999999997643   44688999998 


Q ss_pred             CCCccccccceeeeeeeeeeccCCCceeEEEEEEe
Q 026232          107 GSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWA  141 (241)
Q Consensus       107 g~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~v  141 (241)
                      |       +++.|++||+|+||++++++|+||++|
T Consensus        67 G-------~~~~vlikdvQ~hp~~~~i~HvDF~~v   94 (94)
T 1b75_A           67 G-------KEIKVKAQDVQRHPYKPKLQHIDFVRA   94 (94)
T ss_dssp             S-------CEEEECCSEEECCSSSCCCCEEEEEBC
T ss_pred             C-------EEEEEEEEEEEeCCCCCCeEEEEEEEC
Confidence            6       467899999999999999999999975

>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=93.46  E-value=0.4  Score=35.72  Aligned_cols=74  Identities=14%  Similarity=0.178  Sum_probs=49.1

Q ss_pred             EEEEeEEEEecCCCCccccCeEEEEEecEEEEE--eecCCCC-C--eEEEEccCCCCCCe-EEEeccCCCCCeEEeecCC
Q 026232          148 KVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYL--CPAEHIS-P--KIEVDVSNLDIGDR-VFMSDIEVHPSWKLLSKNE  221 (241)
Q Consensus       148 ~v~VPI~l~G~~~s~Gvk~GG~L~~~~~~I~V~--~lP~~IP-e--~I~VDVs~L~iGd~-i~V~DL~lp~gv~il~~~~  221 (241)
                      +++|||.+.|.+.  +.    .+.....+++|+  +....+- +  +..||+|++..|+. +.|+ +.+|.|+++..-.|
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 TLTLSLIAKNTPA--NS----MIMTKLPSVRVKTEGYNPSINVNELFAYVDLSGSEPGEHDYEVK-VEPIPNIKIVEISP   76 (90)
T ss_dssp             EEEEEEEEESCCT--TE----EECSCCCEEEEEEEECCTTCCSTTCEEEEECTTCCSEEEEEECE-ECCCTTEEEEEEES
T ss_pred             eEEeeEEEeeCCC--Cc----EEecCCCEEEEEEEecCcCCChHHEEEEEECcCCCCCcEeEEEE-EECCCCCEEEEEcc
Confidence            6799999999862  32    333333455544  4332221 1  46799999999974 4455 89999999997677


Q ss_pred             CccEEEE
Q 026232          222 KMPLCKI  228 (241)
Q Consensus       222 ~~vV~~V  228 (241)
                      +.+-..+
T Consensus        77 ~~V~~~~   83 (90)
T 3lyw_A           77 RVVTLQL   83 (90)
T ss_dssp             SEEEEEE
T ss_pred             ceEEEEe
Confidence            7665554

---

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	241
d2zjrs1	175	b.53.1.1 (S:1-175) Ribosomal protein TL5 (general	7e-16
d1feua_	185	b.53.1.1 (A:) Ribosomal protein TL5 (general stres	2e-14
d1dfup_	94	b.53.1.1 (P:) Ribosomal protein L25 {Escherichia c	0.001

>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 = 70.9 bits (173), Expect = 7e-16
 Identities = 34/194 (17%), Positives = 72/194 (37%), Gaps = 27/194 (13%)

Query: 40  RVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTT 99
           R   +   +  I AV + ++                 + +RK      +        +  
Sbjct: 8   RTPKQKLDESMIAAVAYNKE------------NNVSFALDRKAFDRAFRQQ----STTGL 51

Query: 100 FPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVE 159
           F + +  G       ++   L   V  D+     +++ F     G  ++V VPV   G  
Sbjct: 52  FDITVEGG-------ETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGR- 103

Query: 160 SCPGLKKGGYLKSIRTSLKYLCPA-EHISPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLS 218
              G  +GG +  +  +L+ + P    I  ++ VDV+ ++IGD +   DI++     L +
Sbjct: 104 -SQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAA 162

Query: 219 KNEKMPLCKISATK 232
             E + +  +   +
Sbjct: 163 DPE-LTVVSVLPPR 175

>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 = 67.1 bits (163), Expect = 2e-14
 Identities = 36/206 (17%), Positives = 78/206 (37%), Gaps = 30/206 (14%)

Query: 27  HTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSI 86
           + ++A  RE          R  G++P +++ + L ++          ++          +
Sbjct: 3   YRLKAYYREGEKPSAL---RRAGKLPGLMYNRHL-NRKVYVDLVEFDKVFRQASIHHVIV 58

Query: 87  LKSVELPFFCSTTFPLQIRAGSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTE 146
           L+  +     +                         +V+ D+   R  ++ F +      
Sbjct: 59  LELPDGQSLPTL----------------------VRQVNLDKRRRRPEHVDF-FVLSDEP 95

Query: 147 LKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHISPKIEVDVSNLDIGDRVFMS 206
           +++ VP+ F    +  G++ GG L+ I   +       +I   IEVDVS L+IGD +  S
Sbjct: 96  VEMYVPLRFV--GTPAGVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHAS 153

Query: 207 DIEVHPSWKLLSKNEKMPLCKISATK 232
           D+++ P  +L    E   +  +   +
Sbjct: 154 DLKLPPGVELAVSPE-ETIAAVVPPE 178

>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 = 34.9 bits (80), Expect = 0.001
 Identities = 10/29 (34%), Positives = 16/29 (55%)

Query: 28 TIQAIPRECTGSRVSARDRSQGRIPAVVF 56
          TI A  R+  G   S R R+  + PA+++
Sbjct: 3  TINAEVRKEQGKGASRRLRAANKFPAIIY 31

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	241
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	99.96

>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=3.2e-53  Score=359.61  Aligned_cols=182  Identities=21%  Similarity=0.347  Sum_probs=165.8

Q ss_pred             eEEEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEEEEcC
Q 026232           27 HTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRA  106 (241)
Q Consensus        27 ~~L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i~~  106 (241)
                      ++|+|+.|+..|+   ++|||+|+|||||||++            .+.+++++.++|.++++..+.    ++++.|++.+
T Consensus         3 ~~l~a~~Re~~~~---~~LRr~G~VPaViYG~~------------~~~~i~v~~~e~~k~~~~~~~----~~~i~l~~~d   63 (185)
T d1feua_           3 YRLKAYYREGEKP---SALRRAGKLPGLMYNRH------------LNRKVYVDLVEFDKVFRQASI----HHVIVLELPD   63 (185)
T ss_dssp             EEEECEECSSSCH---HHHHHTTEEEEEEECSS------------CEEEEEEEHHHHHHHHHHHTT----TSEEEEECTT
T ss_pred             EEEEEEEecCCCc---hHHHhCCCceEEEECCC------------CCcCEEecchHHHhHhhhhhc----cceEEEEeec
Confidence            5799999996654   46999999999999982            357999999999999998875    4788898853


Q ss_pred             CCCccccccceeeeeeeeeeccCCCceeEEEEEEeCCCCEEEEEEeEEEEecCCCCccccCeEEEEEecEEEEEeecCCC
Q 026232          107 GSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCPAEHI  186 (241)
Q Consensus       107 g~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~v~~~~~V~v~VPI~l~G~~~s~Gvk~GG~L~~~~~~I~V~~lP~~I  186 (241)
                      |       +++.||+||+|+||++++++|+|||+++ +++|+++|||+|+|+  |+|+|+||+|++.+++|+|+|+|.+|
T Consensus        64 g-------~~~~vlikevQ~~pv~~~i~HvDF~~v~-~~~v~v~VPv~~~G~--~~gvk~GG~l~~~~~~i~v~~~p~~I  133 (185)
T d1feua_          64 G-------QSLPTLVRQVNLDKRRRRPEHVDFFVLS-DEPVEMYVPLRFVGT--PAGVRAGGVLQEIHRDILVKVSPRNI  133 (185)
T ss_dssp             S-------CEEEEEEEEEEECSSSSCEEEEEEEECC-SSCEEEEEEEEEESC--CHHHHTTCEEEECCSEEEEEECGGGC
T ss_pred             c-------hhhhheeeeeEecccccceeEEEEeecc-CceEEEEeceEEeec--ccccccccEEEEEEeeeEEEeeccCC
Confidence            5       5789999999999999999999999986 999999999999997  68999999999999999999999999


Q ss_pred             CCeEEEEccCCCCCCeEEEeccCCCCCeEEeecCCCccEEEEEcCCCCCCCC
Q 026232          187 SPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATKLENPEP  238 (241)
Q Consensus       187 Pe~I~VDVs~L~iGd~i~V~DL~lp~gv~il~~~~~~vV~~V~~~~~e~~~~  238 (241)
                      |++|+||||+|++||+|+++||++|+|++++. +++.+|++|.+|+.+++++
T Consensus       134 Pe~i~VDvs~L~igd~i~v~Dl~lp~gv~~~~-d~~~~vv~v~~p~~~ee~~  184 (185)
T d1feua_         134 PEFIEVDVSGLEIGDSLHASDLKLPPGVELAV-SPEETIAAVVPPEDVEKLA  184 (185)
T ss_dssp             CSCEEEECTTCCTTEEEEGGGSCCCTTCEESS-CTTCEEEEEECSSSSSCCC
T ss_pred             CeEEEEEcccCCCCCeEEEEeecCCCCcEEcc-CCCCeEEEEeCCCcccccC
Confidence            99999999999999999999999999999995 8899999999999876554

>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=1.4e-52  Score=352.99  Aligned_cols=173  Identities=20%  Similarity=0.390  Sum_probs=160.1

Q ss_pred             EEEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEEEEcCC
Q 026232           28 TIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRAG  107 (241)
Q Consensus        28 ~L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i~~g  107 (241)
                      .|+|++|+      +|++|++|+||||+||+            .+++++++++++|.+++++.+.    +++|+|+++ |
T Consensus         2 ~l~a~~r~------~k~~R~~G~VPaViYG~------------~~~~~i~v~~~~l~k~l~~~~~----~~li~l~i~-g   58 (175)
T d2zjrs1           2 ELTAKPRT------PKQKLDESMIAAVAYNK------------ENNVSFALDRKAFDRAFRQQST----TGLFDITVE-G   58 (175)
T ss_dssp             CCCBCCSC------CHHHHSSSCCCEEEESS------------SCCCCCBCCHHHHHHHHHHHTT----SCCCBCCCT-T
T ss_pred             eeEeccch------HHHHhhCCCCCEEEECC------------CCCEEEEEcHHHHHHHHHhcCc----ceEEEEEec-C
Confidence            46677773      68999999999999998            2588999999999999998775    689999998 4


Q ss_pred             CCccccccceeeeeeeeeeccCCCceeEEEEEEeCCCCEEEEEEeEEEEecCCCCccccCeEEEEEecEEEEEee-cCCC
Q 026232          108 SGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWADDGTELKVDVPVVFKGVESCPGLKKGGYLKSIRTSLKYLCP-AEHI  186 (241)
Q Consensus       108 ~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~v~~~~~V~v~VPI~l~G~~~s~Gvk~GG~L~~~~~~I~V~~l-P~~I  186 (241)
                      .      ++++||+||+|+||++++++|+|||+++.+++|+++|||+|+|+  |+|+|+||+|++.+++|+++|+ |++|
T Consensus        59 ~------~~~~vlikevQ~~pv~~~i~HvDF~~v~~~~~i~v~VPi~~~G~--~~gvk~Gg~l~~~~~~i~v~~~~P~~I  130 (175)
T d2zjrs1          59 G------ETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGR--SQGEVQGGLVDIVVHNLQIVAPGPRRI  130 (175)
T ss_dssp             C------CCCBCCEEEEEECSSSCCEEEEEEECCCSSCCCEEEEECEEESC--CTTTTTTSEEECSCSEEEEECCCTTCC
T ss_pred             C------ceEEEEehhhhhhhccCceeEEEEEecCCCcEEEEEEEEEeecc--cccccccceeeeeehhhhhhccChhhC
Confidence            2      56799999999999999999999999999999999999999998  6899999999999999999995 9999


Q ss_pred             CCeEEEEccCCCCCCeEEEeccCCCCCeEEeecCCCccEEEEEcCC
Q 026232          187 SPKIEVDVSNLDIGDRVFMSDIEVHPSWKLLSKNEKMPLCKISATK  232 (241)
Q Consensus       187 Pe~I~VDVs~L~iGd~i~V~DL~lp~gv~il~~~~~~vV~~V~~~~  232 (241)
                      |++|+||||+|++||+|+|+||++|+|+++++ |++.+||+|.+||
T Consensus       131 P~~i~vDvs~L~iGd~i~v~Dl~lp~gv~~~~-d~~~~v~~V~~pr  175 (175)
T d2zjrs1         131 PQELVVDVTKMNIGDHITAGDIKLPEGCTLAA-DPELTVVSVLPPR  175 (175)
T ss_dssp             CSCCEEECTTCCSSCEEETTTSCCSTTCCCCS-CTTCEEEEEECCC
T ss_pred             CceEEecchhccCCCeEEEEeecCCCCcEEcc-CCCcEEEEEeCCC
Confidence            99999999999999999999999999999995 8999999999987

>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=99.96  E-value=2.2e-29  Score=191.26  Aligned_cols=93  Identities=23%  Similarity=0.355  Sum_probs=84.2

Q ss_pred             eEEEEEEcCCCCChHHHHHHHCCCccEEEeCCCcCCcCCCCCCCCCceEEEEeHHHHHHHHHhcCCCceeeeEEEEEEcC
Q 026232           27 HTIQAIPRECTGSRVSARDRSQGRIPAVVFAQDLLDKNTDRRSPSRKQILSTERKQIHSILKSVELPFFCSTTFPLQIRA  106 (241)
Q Consensus        27 ~~L~a~~R~~~Gk~~~rrLRr~G~VPaViYG~~~~~~~~~~~~~~~~~~v~v~~~~l~kll~~~g~~~~~~~v~~L~i~~  106 (241)
                      .+|+|++|+.+||+++|+||++|+|||||||+           +.++++++++.++|.+++++.+   +.+.+++|+++ 
T Consensus         2 ~~L~a~~R~~~Gk~~~r~lRr~G~vPaViYG~-----------~~~~~~i~v~~~~l~~~l~~~~---~~~~~i~l~~~-   66 (94)
T d1dfup_           2 FTINAEVRKEQGKGASRRLRAANKFPAIIYGG-----------KEAPLAIELDHDKVMNMQAKAE---FYSEVLTIVVD-   66 (94)
T ss_dssp             CEEECEECSCCSHHHHHHHHHTTEEEEEEECS-----------SSCCEEEEEEHHHHHHHTTSGG---GGTSCBEEEET-
T ss_pred             eEEEEEEeccCCcHHHHHHHHcCCccEEEECC-----------CCCCcEEEecHHHHhhhhcccc---cccceEEEEEC-
Confidence            57999999999999999999999999999998           2579999999999999998754   33689999998 


Q ss_pred             CCCccccccceeeeeeeeeeccCCCceeEEEEEEe
Q 026232          107 GSGSSVLLDSGKVLPIKVHRDEETGRILNLVFVWA  141 (241)
Q Consensus       107 g~~~~~~~~~~~vlikevQ~hpv~~~ilHvDF~~v  141 (241)
                      |       +++.||+||+|+||++++++||||++.
T Consensus        67 g-------~~~~vlikevQ~~pv~~~i~HvDF~r~   94 (94)
T d1dfup_          67 G-------KEIKVKAQDVQRHPYKPKLQHIDFVRA   94 (94)
T ss_dssp             T-------EECCEEEEEEEECSSSSCEEEEEEEEC
T ss_pred             C-------eEEEeeheeeeecCCCCCEEEEeeecC
Confidence            6       567899999999999999999999973