Psyllid ID: psy8560

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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-----
Protein Sequence
MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIPVNTLESDNNSSIEKEKNNNS
Secondary Structure (PSIPRED)
cEEEEEEccccccHHHHHHHHcccccEEEEccccccEEEEEcHHHHHHHHHHccccEEEEEEEEccEEEEEEEEEEEccccccccEEEEEEEEccccEEEEEEEEEEEEccccccEEEcccEEEEEEEEEEEEEEccccccEEEEEccccccccEEEEcccccccccEEccccccccEEEEEEcccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEEEcccccHHHHHHHHHccEEEEEEEccccccEEEEEEHHHHHHHcccHHHHcccEEEEEccEEccEEEEEEEEccccccEEEEEEEEEccccEEEEEEEEEEEccccccccEcccEEEEEEEEEEEEEEcccccccEEEEEHcccccccEEEEccccccccEEEEEccccccEEEEEEccccccccccHHHHHccccccc
Coil and Loop (DISEMBL)
MKIIAFERkkkgtsfsrnlrkigkvpgiiyggnkdpvkisMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHAYKKLVLhadfqrvdtekkihvkvplhfinseispavklnSCIISNVISDLyisclpknlpKFIEINLEkmevntsihlsdiklprgvsvihsteedptiataiipvntlesdnnssiekeknnns
Flexible Loop (DISEMBL)
mkiiaferkkkgtsfsrnlrkigkvpgiiyggnKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLhfinseispavKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEedptiataiipvntlesdnnssiekeknnns
Low Complexity Region (SEG)
MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIPVNTLesdnnssiekeknnns
Disordered region (IsUnstruct)
*****************NLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIPV*******************
Disordered Region (DISOPRED)
MKIIAFE**********NLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATA***********************
Disordered Region (DISEMBL)
MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIPVNTLESD*************
Disordered Region (DISPRO)
MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIPV*******************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIPVNTLESDNNSSIEKEKNNNS
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	205	2.2.26 [Sep-21-2011]
A4G921	210	50S ribosomal protein L25	yes	N/A	0.926	0.904	0.649	3e-70
A6T2S2	214	50S ribosomal protein L25	yes	N/A	0.926	0.887	0.638	1e-69
Q1LRQ2	203	50S ribosomal protein L25	yes	N/A	0.970	0.980	0.542	3e-63
A0KAM6	201	50S ribosomal protein L25	yes	N/A	0.921	0.940	0.536	8e-63
B1JYQ0	201	50S ribosomal protein L25	yes	N/A	0.921	0.940	0.536	8e-63
Q1BTG5	201	50S ribosomal protein L25	yes	N/A	0.921	0.940	0.536	8e-63
Q0BBQ4	202	50S ribosomal protein L25	yes	N/A	0.921	0.935	0.536	2e-62
B1YN53	202	50S ribosomal protein L25	yes	N/A	0.921	0.935	0.536	2e-62
A9AEY7	201	50S ribosomal protein L25	yes	N/A	0.921	0.940	0.547	3e-62
Q39CT9	201	50S ribosomal protein L25	yes	N/A	0.921	0.940	0.536	5e-62

>sp|A4G921|RL25_HERAR 50S ribosomal protein L25 OS=Herminiimonas arsenicoxydans GN=rplY PE=3 SV=1

 Score =  264 bits (675), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 124/191 (64%), Positives = 154/191 (80%), Gaps = 1/191 (0%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK+IAF R   GT  SR  R  G  PGI+YGG   PV IS++HN +YHALKKE FHSSIL
Sbjct: 1   MKVIAFARNDLGTGASRRQRIAGLTPGIVYGGTAAPVNISLDHNALYHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ GKVE VLLR+FQ+HAYK+LVLHADFQRVD ++KIHVKVPLHFIN+EISPAVKL +
Sbjct: 61  DLEVDGKVEQVLLRDFQVHAYKQLVLHADFQRVDAKQKIHVKVPLHFINAEISPAVKLQA 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRG-VSVIHSTEEDPTI 179
            IIS+V ++L I+CLP NLP+F+E++L  +EV  SIHL+DIKLP+G V+VIH  E++PTI
Sbjct: 121 GIISHVATELDITCLPGNLPEFVEVDLATLEVGHSIHLADIKLPKGVVAVIHGGEDNPTI 180

Query: 180 ATAIIPVNTLE 190
           ATA +P   +E
Sbjct: 181 ATAAVPAGKVE 191

This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.
Herminiimonas arsenicoxydans (taxid: 204773)

>sp|A6T2S2|RL25_JANMA 50S ribosomal protein L25 OS=Janthinobacterium sp. (strain Marseille) GN=rplY PE=3 SV=1

 Score =  262 bits (669), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 122/191 (63%), Positives = 155/191 (81%), Gaps = 1/191 (0%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK+IAF RK+ GT  SR  R  G  PGI+YGG   PV IS++HN +YHALKKE FHSSIL
Sbjct: 1   MKVIAFARKELGTGASRRQRIAGLTPGIVYGGTAAPVNISLDHNALYHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ GKVE VLLR+FQ+HAYK+LVLHADFQRVD ++KIHVKVPLHF+N+E SPAVKL+ 
Sbjct: 61  DLEVDGKVEQVLLRDFQVHAYKQLVLHADFQRVDAKQKIHVKVPLHFVNAETSPAVKLHG 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGV-SVIHSTEEDPTI 179
            IIS+V S+L I+CLP +LP+F+E++L  ++V  SIHL+DIKLP+GV +VIH  E++PTI
Sbjct: 121 GIISHVASELDITCLPSDLPEFVEVDLANLDVGHSIHLADIKLPKGVAAVIHGGEDNPTI 180

Query: 180 ATAIIPVNTLE 190
           ATA +P   +E
Sbjct: 181 ATASVPAGKVE 191

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

Janthinobacterium sp. (strain Marseille) (taxid: 375286)

>sp|Q1LRQ2|RL25_RALME 50S ribosomal protein L25 OS=Ralstonia metallidurans (strain CH34 / ATCC 43123 / DSM 2839) GN=rplY PE=3 SV=1

 Score =  241 bits (615), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 108/199 (54%), Positives = 144/199 (72%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK++AFER  +GT  SR LR  GK PGIIYGG  +P  I ++HN ++HALKKE FHSSIL
Sbjct: 1   MKVVAFERSVQGTGASRRLRNSGKTPGIIYGGAAEPKMIELDHNALWHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ GK E  LLR FQ+H +K LVLH DFQRV   +KIHVKVPLHF+N E +P VKL  
Sbjct: 61  DLEVAGKSEKALLRAFQMHPFKPLVLHVDFQRVSATEKIHVKVPLHFMNQETAPGVKLGH 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIA 180
            I+S++++DL +SCLP +LP+FIE++L   E+N +IHLSD+KLP+GV+ I   +E+P IA
Sbjct: 121 GIVSHILNDLEVSCLPADLPEFIEVDLAAAELNQTIHLSDLKLPKGVTAITHGDENPAIA 180

Query: 181 TAIIPVNTLESDNNSSIEK 199
           +  +P     S+     E+
Sbjct: 181 SITLPAGAQSSEAAEGGEE 199

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

Ralstonia metallidurans (strain CH34 / ATCC 43123 / DSM 2839) (taxid: 266264)

>sp|A0KAM6|RL25_BURCH 50S ribosomal protein L25 OS=Burkholderia cenocepacia (strain HI2424) GN=rplY PE=3 SV=1

 Score =  239 bits (611), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 102/190 (53%), Positives = 145/190 (76%), Gaps = 1/190 (0%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK++AFER+++GT  SR LR  GK  GI+YGG   P KI ++HN ++HALKKE FHSSIL
Sbjct: 1   MKVVAFERQQQGTGASRRLRNAGKTTGIVYGGEAAPQKIELDHNALWHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ G+ + VLLR+ Q H +K+LVLH DFQRVD +KK+H K PLHF+N+E+SPAVKL+S
Sbjct: 61  DLEVAGQSQQVLLRDVQYHPFKQLVLHVDFQRVDAKKKLHTKAPLHFLNAEVSPAVKLSS 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVI-HSTEEDPTI 179
            I+S+V +++ I CLP +LP+F+E++L K+E   S+H  DI LP+GV+++ H   E+P I
Sbjct: 121 AIVSHVATEIEIECLPADLPEFLEVDLSKIEAGQSLHAKDIALPKGVALVAHVDAENPVI 180

Query: 180 ATAIIPVNTL 189
           A+A +P   +
Sbjct: 181 ASATVPAGAV 190

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

Burkholderia cenocepacia (strain HI2424) (taxid: 331272)

>sp|B1JYQ0|RL25_BURCC 50S ribosomal protein L25 OS=Burkholderia cenocepacia (strain MC0-3) GN=rplY PE=3 SV=1

 Score =  239 bits (611), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 102/190 (53%), Positives = 145/190 (76%), Gaps = 1/190 (0%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK++AFER+++GT  SR LR  GK  GI+YGG   P KI ++HN ++HALKKE FHSSIL
Sbjct: 1   MKVVAFERQQQGTGASRRLRNAGKTTGIVYGGEAAPQKIELDHNALWHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ G+ + VLLR+ Q H +K+LVLH DFQRVD +KK+H K PLHF+N+E+SPAVKL+S
Sbjct: 61  DLEVAGQSQQVLLRDVQYHPFKQLVLHVDFQRVDAKKKLHTKAPLHFLNAEVSPAVKLSS 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVI-HSTEEDPTI 179
            I+S+V +++ I CLP +LP+F+E++L K+E   S+H  DI LP+GV+++ H   E+P I
Sbjct: 121 AIVSHVATEIEIECLPADLPEFLEVDLSKIEAGQSLHAKDIALPKGVALVAHVDAENPVI 180

Query: 180 ATAIIPVNTL 189
           A+A +P   +
Sbjct: 181 ASATVPAGAV 190

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

Burkholderia cenocepacia (strain MC0-3) (taxid: 406425)

>sp|Q1BTG5|RL25_BURCA 50S ribosomal protein L25 OS=Burkholderia cenocepacia (strain AU 1054) GN=rplY PE=3 SV=1

 Score =  239 bits (611), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 102/190 (53%), Positives = 145/190 (76%), Gaps = 1/190 (0%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK++AFER+++GT  SR LR  GK  GI+YGG   P KI ++HN ++HALKKE FHSSIL
Sbjct: 1   MKVVAFERQQQGTGASRRLRNAGKTTGIVYGGEAAPQKIELDHNALWHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ G+ + VLLR+ Q H +K+LVLH DFQRVD +KK+H K PLHF+N+E+SPAVKL+S
Sbjct: 61  DLEVAGQSQQVLLRDVQYHPFKQLVLHVDFQRVDAKKKLHTKAPLHFLNAEVSPAVKLSS 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVI-HSTEEDPTI 179
            I+S+V +++ I CLP +LP+F+E++L K+E   S+H  DI LP+GV+++ H   E+P I
Sbjct: 121 AIVSHVATEIEIECLPADLPEFLEVDLSKIEAGQSLHAKDIALPKGVALVAHVDAENPVI 180

Query: 180 ATAIIPVNTL 189
           A+A +P   +
Sbjct: 181 ASATVPAGAV 190

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

Burkholderia cenocepacia (strain AU 1054) (taxid: 331271)

>sp|Q0BBQ4|RL25_BURCM 50S ribosomal protein L25 OS=Burkholderia ambifaria (strain ATCC BAA-244 / AMMD) GN=rplY PE=3 SV=1

 Score =  238 bits (607), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 102/190 (53%), Positives = 145/190 (76%), Gaps = 1/190 (0%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK++AFER+++GT  SR LR  GK  GI+YGG   P KI ++HN ++HALKKE FHSSIL
Sbjct: 1   MKVVAFERQEQGTGASRRLRNAGKTTGIVYGGEAAPQKIELDHNALWHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ G+ + VLLR+ Q H +K+LVLH DFQRVD +KK+H KVPLHF+N+E+SPAVKL+S
Sbjct: 61  DLEVAGQSQQVLLRDVQYHPFKQLVLHVDFQRVDAKKKLHTKVPLHFLNAEVSPAVKLSS 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVI-HSTEEDPTI 179
            ++S+V +++ I CLP  LP+F+E++L K+E   S+H  DI LP+GV+++ H   E+P +
Sbjct: 121 AVVSHVATEIEIECLPSALPEFLEVDLSKIEAGQSLHAKDIALPKGVALVAHIDAENPVV 180

Query: 180 ATAIIPVNTL 189
           A+A IP   +
Sbjct: 181 ASATIPAGAV 190

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

Burkholderia ambifaria (strain ATCC BAA-244 / AMMD) (taxid: 339670)

>sp|B1YN53|RL25_BURA4 50S ribosomal protein L25 OS=Burkholderia ambifaria (strain MC40-6) GN=rplY PE=3 SV=1

 Score =  238 bits (607), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 102/190 (53%), Positives = 145/190 (76%), Gaps = 1/190 (0%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK++AFER+++GT  SR LR  GK  GI+YGG   P KI ++HN ++HALKKE FHSSIL
Sbjct: 1   MKVVAFERQEQGTGASRRLRNAGKTTGIVYGGEAAPQKIELDHNALWHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ G+ + VLLR+ Q H +K+LVLH DFQRVD +KK+H KVPLHF+N+E+SPAVKL+S
Sbjct: 61  DLEVAGQSQQVLLRDVQYHPFKQLVLHVDFQRVDAKKKLHTKVPLHFLNAEVSPAVKLSS 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVI-HSTEEDPTI 179
            ++S+V +++ I CLP  LP+F+E++L K+E   S+H  DI LP+GV+++ H   E+P +
Sbjct: 121 AVVSHVATEIEIECLPSALPEFLEVDLSKIEAGQSLHAKDIALPKGVALVAHIDAENPVV 180

Query: 180 ATAIIPVNTL 189
           A+A IP   +
Sbjct: 181 ASATIPAGAV 190

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

Burkholderia ambifaria (strain MC40-6) (taxid: 398577)

>sp|A9AEY7|RL25_BURM1 50S ribosomal protein L25 OS=Burkholderia multivorans (strain ATCC 17616 / 249) GN=rplY PE=3 SV=1

 Score =  237 bits (605), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 104/190 (54%), Positives = 143/190 (75%), Gaps = 1/190 (0%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK++AFERK++GT  SR LR  GK  GI+YGG   P  I ++HN ++HALKKE FHSSIL
Sbjct: 1   MKVVAFERKEQGTGASRRLRNAGKTTGIVYGGEAAPQMIELDHNALWHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ G+ + VLLR+ Q H +K+LVLH DFQRVD +KK+H KVPLHF+N+E+SPAVKL+S
Sbjct: 61  DLEVAGQSQQVLLRDVQYHPFKQLVLHVDFQRVDAKKKLHTKVPLHFLNAEVSPAVKLSS 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVI-HSTEEDPTI 179
            I+S+V +++ + CLP  LP+F+E++L K+E   SIH  DI LP+GV++  H   E+P I
Sbjct: 121 AIVSHVATEIEVECLPAALPEFLEVDLSKIEAGQSIHAKDIALPKGVALTAHVDAENPVI 180

Query: 180 ATAIIPVNTL 189
           A+A IP   +
Sbjct: 181 ASATIPAGAV 190

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

Burkholderia multivorans (strain ATCC 17616 / 249) (taxid: 395019)

>sp|Q39CT9|RL25_BURS3 50S ribosomal protein L25 OS=Burkholderia sp. (strain 383) GN=rplY PE=3 SV=1

 Score =  237 bits (604), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 102/190 (53%), Positives = 144/190 (75%), Gaps = 1/190 (0%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK++AFER+++GT  SR LR  GK  GI+YGG   P KI ++HN ++HALKKE FHSSIL
Sbjct: 1   MKVVAFERQEQGTGASRRLRNAGKTTGIVYGGEAAPQKIELDHNALWHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ G+ + VLLR+ Q H +K+LVLH DFQRVD +KK+H K PLHF+N+EISPAVKL+S
Sbjct: 61  DLEVAGQSQQVLLRDVQYHPFKQLVLHVDFQRVDAKKKLHTKAPLHFLNAEISPAVKLSS 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVI-HSTEEDPTI 179
            I+S+V +++ I CLP +LP+F+E++L K+E   S+H  DI LP+GV ++ H   E+P +
Sbjct: 121 AIVSHVATEIEIECLPADLPEFLEVDLSKIEAGQSLHAKDITLPKGVVLVAHVDAENPVV 180

Query: 180 ATAIIPVNTL 189
           A+A +P   +
Sbjct: 181 ASATVPAGAV 190

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

Burkholderia sp. (strain 383) (taxid: 269483)

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	205
134096054	210	50S ribosomal protein L25 [Herminiimonas	0.926	0.904	0.649	1e-68
399019855	202	ribosomal protein L25, Ctc-form [Herbasp	0.931	0.945	0.611	4e-68
152980425	214	50S ribosomal protein L25 [Janthinobacte	0.926	0.887	0.638	8e-68
124483376	202	50S ribosomal subunit protein L25 [Herba	0.912	0.925	0.619	1e-67
415906029	202	50S ribosomal subunit protein L25 [Herba	0.902	0.915	0.614	2e-66
409407694	202	large subunit ribosomal protein L25 [Her	0.902	0.915	0.614	3e-66
340785804	208	50S ribosomal protein L25 [Collimonas fu	0.902	0.889	0.625	4e-66
398831927	201	ribosomal protein L25, Ctc-form [Herbasp	0.912	0.930	0.608	2e-65
430809763	203	50S ribosomal protein L25/general stress	0.970	0.980	0.547	9e-62
94309233	203	50S ribosomal protein L25/general stress	0.970	0.980	0.542	1e-61

>gi|134096054|ref|YP_001101129.1| 50S ribosomal protein L25 [Herminiimonas arsenicoxydans] gi|166223689|sp|A4G921.1|RL25_HERAR RecName: Full=50S ribosomal protein L25; AltName: Full=General stress protein CTC gi|133739957|emb|CAL63008.1| 50S ribosomal protein L25 (General stress protein CTC) [Herminiimonas arsenicoxydans]

 Score =  264 bits (675), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 124/191 (64%), Positives = 154/191 (80%), Gaps = 1/191 (0%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK+IAF R   GT  SR  R  G  PGI+YGG   PV IS++HN +YHALKKE FHSSIL
Sbjct: 1   MKVIAFARNDLGTGASRRQRIAGLTPGIVYGGTAAPVNISLDHNALYHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ GKVE VLLR+FQ+HAYK+LVLHADFQRVD ++KIHVKVPLHFIN+EISPAVKL +
Sbjct: 61  DLEVDGKVEQVLLRDFQVHAYKQLVLHADFQRVDAKQKIHVKVPLHFINAEISPAVKLQA 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRG-VSVIHSTEEDPTI 179
            IIS+V ++L I+CLP NLP+F+E++L  +EV  SIHL+DIKLP+G V+VIH  E++PTI
Sbjct: 121 GIISHVATELDITCLPGNLPEFVEVDLATLEVGHSIHLADIKLPKGVVAVIHGGEDNPTI 180

Query: 180 ATAIIPVNTLE 190
           ATA +P   +E
Sbjct: 181 ATAAVPAGKVE 191

Source: Herminiimonas arsenicoxydans

Species: Herminiimonas arsenicoxydans

Genus: Herminiimonas

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|399019855|ref|ZP_10721998.1| ribosomal protein L25, Ctc-form [Herbaspirillum sp. CF444] gi|398096874|gb|EJL87189.1| ribosomal protein L25, Ctc-form [Herbaspirillum sp. CF444]

 Score =  263 bits (671), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 118/193 (61%), Positives = 159/193 (82%), Gaps = 2/193 (1%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK+IAF RK++GT  SR LR  G+ P I+YGG   P+ I+++HN +YHALKKE FHSSIL
Sbjct: 1   MKVIAFPRKEQGTGASRRLRNAGQTPAIVYGGTAAPLNIALDHNALYHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LEI GKVE VLLR+FQ+HAYK+LVLH DFQRVD  +KIHVKVPLHF+N+E+SPAVKL+S
Sbjct: 61  DLEIDGKVEQVLLRDFQVHAYKQLVLHVDFQRVDASQKIHVKVPLHFVNAEVSPAVKLSS 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIA 180
            IIS+V++DL ISCLPK+LP+F+ ++L K+EV  SIHL+D++LP GV+ +  ++E+ T+A
Sbjct: 121 GIISHVMTDLDISCLPKDLPEFVSVDLSKLEVGHSIHLADLQLPSGVTAV--SQENLTVA 178

Query: 181 TAIIPVNTLESDN 193
           TA +P   +E+D+
Sbjct: 179 TASVPAGKVEADS 191

Source: Herbaspirillum sp. CF444

Species: Herbaspirillum sp. CF444

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|152980425|ref|YP_001354819.1| 50S ribosomal protein L25 [Janthinobacterium sp. Marseille] gi|166223690|sp|A6T2S2.1|RL25_JANMA RecName: Full=50S ribosomal protein L25; AltName: Full=General stress protein CTC gi|151280502|gb|ABR88912.1| large subunit ribosomal protein L25 [Janthinobacterium sp. Marseille]

 Score =  262 bits (669), Expect = 8e-68,   Method: Compositional matrix adjust.
 Identities = 122/191 (63%), Positives = 155/191 (81%), Gaps = 1/191 (0%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK+IAF RK+ GT  SR  R  G  PGI+YGG   PV IS++HN +YHALKKE FHSSIL
Sbjct: 1   MKVIAFARKELGTGASRRQRIAGLTPGIVYGGTAAPVNISLDHNALYHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ GKVE VLLR+FQ+HAYK+LVLHADFQRVD ++KIHVKVPLHF+N+E SPAVKL+ 
Sbjct: 61  DLEVDGKVEQVLLRDFQVHAYKQLVLHADFQRVDAKQKIHVKVPLHFVNAETSPAVKLHG 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGV-SVIHSTEEDPTI 179
            IIS+V S+L I+CLP +LP+F+E++L  ++V  SIHL+DIKLP+GV +VIH  E++PTI
Sbjct: 121 GIISHVASELDITCLPSDLPEFVEVDLANLDVGHSIHLADIKLPKGVAAVIHGGEDNPTI 180

Query: 180 ATAIIPVNTLE 190
           ATA +P   +E
Sbjct: 181 ATASVPAGKVE 191

Source: Janthinobacterium sp. Marseille

Species: Janthinobacterium sp. Marseille

Genus: Janthinobacterium

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|124483376|emb|CAM32561.1| 50S ribosomal subunit protein L25 [Herbaspirillum seropedicae]

 Score =  261 bits (667), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 117/189 (61%), Positives = 156/189 (82%), Gaps = 2/189 (1%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK+IAF RK++GT  SR LR+ G+ PGI+YGG   P+ I+++HN +YHALKKETFHSSIL
Sbjct: 1   MKVIAFPRKEQGTGASRRLRRAGQTPGIVYGGTAAPLNIAVDHNALYHALKKETFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LEI GKVE VLLR+FQ+HAYK+LVLH DFQRVD  +K+H KVPLHF+N+E+SPAVKL+ 
Sbjct: 61  DLEIEGKVEQVLLRDFQVHAYKQLVLHVDFQRVDASQKLHTKVPLHFVNAEVSPAVKLHG 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIA 180
            IIS+V ++L ++CLPKNLP+FIE++L K++V  SIHL+D+KLP GV+ +  T+E+ TIA
Sbjct: 121 GIISHVAAELDVTCLPKNLPEFIEVDLAKLDVGQSIHLADLKLPNGVTAV--TQENLTIA 178

Query: 181 TAIIPVNTL 189
           TA +P   +
Sbjct: 179 TATVPAGQV 187

Source: Herbaspirillum seropedicae

Species: Herbaspirillum seropedicae

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|415906029|ref|ZP_11552650.1| 50S ribosomal subunit protein L25 [Herbaspirillum frisingense GSF30] gi|407763203|gb|EKF71905.1| 50S ribosomal subunit protein L25 [Herbaspirillum frisingense GSF30]

 Score =  257 bits (657), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 115/187 (61%), Positives = 155/187 (82%), Gaps = 2/187 (1%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK+IAF R ++GT  SR LR+ G+ PGI+YGG   P+ I+++HN +YHALKKETFHSSIL
Sbjct: 1   MKVIAFPRNEQGTGASRRLRRAGQTPGIVYGGTAAPLNIAVDHNALYHALKKETFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LEI GKVE VLLR+FQ+HA+K+LVLH DFQRVD  +K+H KVPLHF+N+E+SPAVKL++
Sbjct: 61  DLEIDGKVEQVLLRDFQVHAFKQLVLHVDFQRVDASQKLHTKVPLHFVNAEVSPAVKLHA 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIA 180
            IIS+V ++L ++CLPKNLP+FIE++L K++V  SIHL+D+KLP GV+ +  T+E+ TIA
Sbjct: 121 GIISHVAAELDVTCLPKNLPEFIEVDLSKLDVGQSIHLADLKLPNGVTAV--TQENLTIA 178

Query: 181 TAIIPVN 187
           TA +P  
Sbjct: 179 TATVPAG 185

Source: Herbaspirillum frisingense GSF30

Species: Herbaspirillum frisingense

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|409407694|ref|ZP_11256145.1| large subunit ribosomal protein L25 [Herbaspirillum sp. GW103] gi|386433445|gb|EIJ46271.1| large subunit ribosomal protein L25 [Herbaspirillum sp. GW103]

 Score =  256 bits (655), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 115/187 (61%), Positives = 153/187 (81%), Gaps = 2/187 (1%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK+IAF R ++GT  SR LR+ G+ PGI+YGG   P  I+++HN +YHALKKETFHSSIL
Sbjct: 1   MKVIAFPRNEQGTGASRRLRRAGQTPGIVYGGTAAPTNIAVDHNALYHALKKETFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LEI GKVE VLLR+FQ+HA+K+LVLH DFQRVD  +K+H KVPLHF+N+E+SPAVKL+ 
Sbjct: 61  DLEIDGKVEQVLLRDFQVHAFKQLVLHVDFQRVDASQKLHTKVPLHFVNAEVSPAVKLHG 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIA 180
            IIS+V ++L ++CLPKNLP+FIE++L K++V  SIHL+D+KLP GV+ +  T+E+ TIA
Sbjct: 121 GIISHVAAELDVTCLPKNLPEFIEVDLAKLDVGQSIHLADLKLPNGVTAV--TQENLTIA 178

Query: 181 TAIIPVN 187
           TA +P  
Sbjct: 179 TATVPAG 185

Source: Herbaspirillum sp. GW103

Species: Herbaspirillum sp. GW103

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|340785804|ref|YP_004751269.1| 50S ribosomal protein L25 [Collimonas fungivorans Ter331] gi|340551071|gb|AEK60446.1| LSU ribosomal protein L25p [Collimonas fungivorans Ter331]

 Score =  256 bits (654), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 117/187 (62%), Positives = 155/187 (82%), Gaps = 2/187 (1%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK+IAF RK++GT  SR LR  G+ PGI+YGG+  PV IS++HN +YHALKKETFHSSIL
Sbjct: 1   MKVIAFVRKEQGTGASRRLRNAGQTPGIVYGGSDAPVNISLDHNALYHALKKETFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LEI G V+ VLLR+FQ+HAYK+LVLHADFQRVD ++ IHVKVPLHF+N+EI+PAVKL+ 
Sbjct: 61  DLEIDGAVQKVLLRDFQVHAYKQLVLHADFQRVDAKQAIHVKVPLHFVNAEIAPAVKLSG 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIA 180
            IIS+V ++L ++CLP +LP+FIE++L  +EV  SIHL+D+KLP+GV+ +  ++E+ TIA
Sbjct: 121 AIISHVFTELEVTCLPADLPEFIEVDLTNIEVGHSIHLADLKLPKGVAAV--SQENVTIA 178

Query: 181 TAIIPVN 187
           TA IP  
Sbjct: 179 TASIPAG 185

Source: Collimonas fungivorans Ter331

Species: Collimonas fungivorans

Genus: Collimonas

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|398831927|ref|ZP_10590096.1| ribosomal protein L25, Ctc-form [Herbaspirillum sp. YR522] gi|398224089|gb|EJN10414.1| ribosomal protein L25, Ctc-form [Herbaspirillum sp. YR522]

 Score =  254 bits (648), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 115/189 (60%), Positives = 153/189 (80%), Gaps = 2/189 (1%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MKII F RK++GT  SR LR  G+ PGI+YGG   PV I+++HN +YHALKKETFH+SIL
Sbjct: 1   MKIIGFPRKEQGTGASRRLRIAGQTPGIVYGGTAAPVNIALDHNALYHALKKETFHASIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LEI GKVE VLLR+FQ+HA+K+LVLH DFQRVD  +K+H KVPLHF+N+EISPAVKL+S
Sbjct: 61  DLEIEGKVEQVLLRDFQVHAFKQLVLHVDFQRVDASQKLHTKVPLHFVNAEISPAVKLSS 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIA 180
            I+S+V S+L + CLPKNLP+FIE++L  +++  SIHL+D+KLP GV+ +  ++E+ TIA
Sbjct: 121 GIVSHVQSELDVQCLPKNLPEFIEVDLANLQIGQSIHLADLKLPVGVTAV--SQENLTIA 178

Query: 181 TAIIPVNTL 189
           TA +P   +
Sbjct: 179 TATVPAGQV 187

Source: Herbaspirillum sp. YR522

Species: Herbaspirillum sp. YR522

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|430809763|ref|ZP_19436878.1| 50S ribosomal protein L25/general stress protein Ctc [Cupriavidus sp. HMR-1] gi|429497787|gb|EKZ96310.1| 50S ribosomal protein L25/general stress protein Ctc [Cupriavidus sp. HMR-1]

 Score =  241 bits (616), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 109/199 (54%), Positives = 144/199 (72%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK+IAFER  +GT  SR LR  GK PGIIYGG  +P  I ++HN ++HALKKE FHSSIL
Sbjct: 1   MKVIAFERSVQGTGASRRLRNSGKTPGIIYGGAAEPKMIELDHNALWHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ GK E  LLR FQ+H +K LVLH DFQRV   +KIHVKVPLHF+N E +P VKL  
Sbjct: 61  DLEVAGKSEKALLRAFQMHPFKPLVLHVDFQRVSASEKIHVKVPLHFMNQETAPGVKLGH 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIA 180
            I+S++++DL +SCLP +LP+FIE++L   E+N +IHLSD+KLP+GV+ I   +E+P IA
Sbjct: 121 GIVSHILNDLEVSCLPADLPEFIEVDLAAAELNQTIHLSDLKLPKGVTAITHGDENPAIA 180

Query: 181 TAIIPVNTLESDNNSSIEK 199
           +  +P     S+     E+
Sbjct: 181 SITLPAGAQSSEAAEGGEE 199

Source: Cupriavidus sp. HMR-1

Species: Cupriavidus sp. HMR-1

Genus: Cupriavidus

Family: Burkholderiaceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|94309233|ref|YP_582443.1| 50S ribosomal protein L25/general stress protein Ctc [Cupriavidus metallidurans CH34] gi|166223709|sp|Q1LRQ2.1|RL25_RALME RecName: Full=50S ribosomal protein L25; AltName: Full=General stress protein CTC gi|93353085|gb|ABF07174.1| 50S ribosomal protein L25 (General stress protein CTC) [Cupriavidus metallidurans CH34]

 Score =  241 bits (615), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 108/199 (54%), Positives = 144/199 (72%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           MK++AFER  +GT  SR LR  GK PGIIYGG  +P  I ++HN ++HALKKE FHSSIL
Sbjct: 1   MKVVAFERSVQGTGASRRLRNSGKTPGIIYGGAAEPKMIELDHNALWHALKKEAFHSSIL 60

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ GK E  LLR FQ+H +K LVLH DFQRV   +KIHVKVPLHF+N E +P VKL  
Sbjct: 61  DLEVAGKSEKALLRAFQMHPFKPLVLHVDFQRVSATEKIHVKVPLHFMNQETAPGVKLGH 120

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIA 180
            I+S++++DL +SCLP +LP+FIE++L   E+N +IHLSD+KLP+GV+ I   +E+P IA
Sbjct: 121 GIVSHILNDLEVSCLPADLPEFIEVDLAAAELNQTIHLSDLKLPKGVTAITHGDENPAIA 180

Query: 181 TAIIPVNTLESDNNSSIEK 199
           +  +P     S+     E+
Sbjct: 181 SITLPAGAQSSEAAEGGEE 199

Source: Cupriavidus metallidurans CH34

Species: Cupriavidus metallidurans

Genus: Cupriavidus

Family: Burkholderiaceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

---

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	205
TIGR_CMR|CPS_3558	211	CPS_3558 "ribosomal 5S rRNA E-	0.853	0.829	0.359	2.6e-31
TIGR_CMR|CBU_1840	244	CBU_1840 "ribosomal 5S rRNA E-	0.892	0.75	0.363	1e-29
TIGR_CMR|APH_1302	211	APH_1302 "ribosomal 5S rRNA E-	0.863	0.838	0.368	6.6e-26
TIGR_CMR|ECH_0142	210	ECH_0142 "ribosomal 5S rRNA E-	0.868	0.847	0.357	3.8e-23
TIGR_CMR|CHY_0195	197	CHY_0195 "ribosomal protein L2	0.834	0.868	0.362	1.3e-22
TIGR_CMR|GSU_0662	194	GSU_0662 "ribosoma protein L25	0.829	0.876	0.284	1.6e-17
TIGR_CMR|SPO_0812	207	SPO_0812 "ribosomal protein L2	0.878	0.869	0.266	1.6e-17
TIGR_CMR|NSE_0306	194	NSE_0306 "ribosomal 5S rRNA E-	0.804	0.850	0.310	3.2e-17
UNIPROTKB|P66121	215	rplY "50S ribosomal protein L2	0.756	0.720	0.256	1.3e-13
TIGR_CMR|SO_2112	95	SO_2112 "ribosomal protein L25	0.429	0.926	0.386	6.4e-12

TIGR_CMR|CPS_3558 CPS_3558 "ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 65/181 (35%), Positives = 110/181 (60%)

Query:     8 RKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGK 67
             R   G   SR LR   KVP I+YG N++P+ +++ H  ++ A ++E F+S +L L I GK
Sbjct:    12 RTDLGKGASRRLRHANKVPAILYGENEEPISLTLEHKNVFRAQQEEAFYSQVLTLNIAGK 71

Query:    68 VELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVI 127
                 L+++ Q H +K++V+H DF R+D +  +H   P+HF+N + +     N   IS+ +
Sbjct:    72 PVECLIKDMQRHPFKQVVMHLDFLRIDAKHAVHANAPIHFLNEDEAAKTGAN---ISHHM 128

Query:   128 SDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVS---VIHSTEEDPTIATAII 184
             +++ I+CLPK+LP+FI I+L  +E+  +IHLSD+  P GV+   +    + D  + +A  
Sbjct:   129 NEIAITCLPKDLPEFISIDLAGLELGQTIHLSDVTFPAGVTSDELAKGEDHDLAVVSANA 188

Query:   185 P 185
             P
Sbjct:   189 P 189

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

 Score = 329 (120.9 bits), Expect = 1.0e-29, P = 1.0e-29
 Identities = 68/187 (36%), Positives = 117/187 (62%)

Query:     2 KIIAFERKKKGTSFSRNLRKI-GKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
             ++IA  R+  G S +R +R+   KVPG +YG  K P  I++    +  AL+ E+  SSIL
Sbjct:     7 ELIAELREFTGKSAARRMRRFEDKVPGTVYGAGKAPQSITLLQKDLLKALESESTFSSIL 66

Query:    61 NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
              L++  K + V+L+  Q H  K  ++H DFQR+   +K+ + VPLHF+  +  P V+   
Sbjct:    67 TLKVGDKKQKVILKALQRHHTKPKIVHIDFQRIKASEKLIMNVPLHFLGEDDCPGVEAGG 126

Query:   121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEE--DPT 178
              ++S++ S++ I CLP +LP++IE++L  ++++ S+HLS++KLP GV +  + +E  D  
Sbjct:   127 -VVSHLQSEVEIRCLPADLPEYIEVDLSHLQLDESVHLSNLKLPAGVGLTSAVDEEHDSP 185

Query:   179 IATAIIP 185
             IA+  +P
Sbjct:   186 IASVHMP 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

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

 Score = 293 (108.2 bits), Expect = 6.6e-26, P = 6.6e-26
 Identities = 69/187 (36%), Positives = 109/187 (58%)

Query:     1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKK-ETF--HS 57
             +K+ A  R++ GT  +R LR  G +P +IYG N+DP+ IS++       LKK  TF   S
Sbjct:     7 IKVDASVRERCGTGSARALRARGLIPAVIYGKNRDPINISLSQ---VDFLKKCRTFPIFS 63

Query:    58 SILNLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVK 117
              ++ L I  K E V+ ++ Q H     + H DFQ VD + ++ ++VPL F+N +    VK
Sbjct:    64 KLIELCIGEKKEYVITKDIQKHPVSGAIAHVDFQFVDQDAEMKMEVPLVFLNEQKCVGVK 123

Query:   118 LNSCIISNVIS-DLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEED 176
                 I  N++   L I C P ++PK +E++L  + +  S+H+SD+KLP  ++V+   EED
Sbjct:   124 RGGVI--NILHRSLIIRCSPHHIPKSLEVDLIDVAIGHSLHVSDLKLPSTINVVMK-EED 180

Query:   177 PTIATAI 183
             P IAT +
Sbjct:   181 PVIATVV 187

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

 Score = 267 (99.0 bits), Expect = 3.8e-23, P = 3.8e-23
 Identities = 65/182 (35%), Positives = 98/182 (53%)

Query:     1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
             +KI A  RK  GT  SR LR  G++P +IYG  +D + IS+++       +     + ++
Sbjct:     7 VKINASLRKNVGTGPSRALRLSGEIPAVIYGKGRDSLSISLSNREFVSKYRSAALSTHLI 66

Query:    61 NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
              LEI  K E VL+R+ Q H     + H DFQ +D   +I ++VPL F N +    +K   
Sbjct:    67 ELEIDNKKEYVLMRDVQKHPVTDRIQHVDFQFIDYGTEIKIEVPLIFTNEQKCIGIKRGG 126

Query:   121 CIISNVIS-DLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTI 179
              +  N++   L I C PK + + IEI+L  +    SIH+SD+KLP  V+V    E +P I
Sbjct:   127 VL--NILHRTLSIKCSPKAILQNIEIDLSGLTTGHSIHVSDLKLPPEVNVTMK-EHNPAI 183

Query:   180 AT 181
              T
Sbjct:   184 VT 185

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

 Score = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 67/185 (36%), Positives = 105/185 (56%)

Query:     2 KIIAFERKKKGTSFSRN-LRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
             KI A  R KK T   RN L K GKVPG++YG N +PV +++N   +   +++      + 
Sbjct:     3 KITASVRLKK-TRGERNRLLKEGKVPGVMYGKNIEPVAVAVNARELESLVERGL---KLF 58

Query:    61 NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPA-VKLN 119
              L + GK + VL++  Q H     ++H DFQ V++ +KI   VP+        PA VK  
Sbjct:    59 ELSVEGKTQRVLVKELQHHPVTGKLIHVDFQVVESGRKIRQLVPVELYGE---PAGVKAG 115

Query:   120 SCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTI 179
               I+ + +S++ + CLP++LP+FIE ++ K+EV   + + D++LP GV VI    EDP  
Sbjct:   116 G-ILEHGLSEVTVECLPEDLPEFIEADVSKLEVGDCLRVKDLELPPGVRVI----EDPES 170

Query:   180 ATAII 184
               A+I
Sbjct:   171 IIALI 175

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 = 214 (80.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 50/176 (28%), Positives = 94/176 (53%)

Query:     2 KIIAFE-RKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
             K ++ E R+K G   +R LR    VPG++YG   +PV + +    +   +  E   +S++
Sbjct:     4 KTMSIELREKNGKGVARKLRAQDVVPGVVYGKGIEPVSVKVAAKDLAATIAGEGGLNSLI 63

Query:    61 NLEIYGKVE--LVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKL 118
              L   G +   +V++ + Q +  K  +LH DF R+  ++K+ V VPL  + +  +  VK 
Sbjct:    64 TLSGGGSLNGNIVIVADMQRNPLKGDILHVDFHRISLDEKVKVHVPLVMVGT--AAGVKE 121

Query:   119 NSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTE 174
                ++  V   L + CLP  +P+ I +++  + +  SIH+S++ LP G+ V++  E
Sbjct:   122 GG-MLDVVTYSLDVECLPTAIPEAINVDVTNLAIGHSIHVSELVLPAGIKVLNDPE 176

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

 Score = 214 (80.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 49/184 (26%), Positives = 93/184 (50%)

Query:     3 IIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNL 62
             ++A ER   G   +R  R+ G VPGI++GG+ +P+ I +  N +   LK   F S++ NL
Sbjct:     8 LVALERTGTGKGAARQARRDGMVPGIVFGGDNEPLPIQIPFNRLLKMLKAGRFKSTLFNL 67

Query:    63 EIYGKVEL-VLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSC 121
             ++ G  ++ V+ R+ Q    K L  H D  R+    +I + + + F+N   +P +K    
Sbjct:    68 KVEGHEDVRVICRDVQRDVVKDLPTHLDLMRLRRTSRIKLFIHVDFVNHAAAPGLKKGG- 126

Query:   122 IISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIAT 181
             +++ V  ++ +     ++P+ I ++L  + +   + +S + LP G     + E D  IA 
Sbjct:   127 VLTVVRPEVELEVTAGDIPESITVDLTGLNIGDVVTISSVTLPAGAKP--TVERDFVIAN 184

Query:   182 AIIP 185
                P
Sbjct:   185 ISAP 188

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 = 211 (79.3 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 55/177 (31%), Positives = 95/177 (53%)

Query:    13 TSFSRN----LRKIGKVPGIIYGGNKDPVKISMN-HNMIYHALKKETFHSSILNLEIYGK 67
             TSF RN    LR+ G VP +IYG  ++ + ++++  ++  H        S ++ L   GK
Sbjct:    11 TSFGRNSANVLRRSGFVPAVIYGKERENINVAISVRDVSKHFAVLSG--SGVVELSCEGK 68

Query:    68 VELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVI 127
             V  V+ + ++LH    +VLH DF     E     +VPL+F+NS  S A++L + +  N++
Sbjct:    69 VYKVVPKAYELHPVSSVVLHLDFVFAG-EHASKFQVPLNFVNSGKSEAIRLGAML--NIV 125

Query:   128 S-DLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAI 183
                + + C   NLPK I +++E  +V  SI  SD+  P GV  + + + +  +AT +
Sbjct:   126 KRTVLVRCTAANLPKSIPVDIENAKVGDSIKFSDLVFPDGVVPL-ARDANSVVATVV 181

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

UNIPROTKB|P66121 rplY "50S ribosomal protein L25" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 177 (67.4 bits), Expect = 1.3e-13, P = 1.3e-13
 Identities = 42/164 (25%), Positives = 84/164 (51%)

Query:     8 RKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISM-NHNMIYHALKKETFHSSILNLEIYG 66
             R + G   SR  R+ GK+P ++YG   +P  + +  H+  Y A+ + +  +++L L+I G
Sbjct:    14 RTETGKGASRRARRAGKIPAVLYGHGAEPQHLELPGHD--YAAVLRHSGTNAVLTLDIAG 71

Query:    67 KVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNV 126
             K +L L +   +H  ++ + HAD   V   +K+ V+V +  +  +  P       +++  
Sbjct:    72 KEQLALTKALHIHPIRRTIQHADLLVVRRGEKVVVEVSV-VVEGQAGP-----DTLVTQE 125

Query:   127 ISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVI 170
              + + I     ++P+ + +++E  E  T +    I LP GVS+I
Sbjct:   126 TNSIEIEAEALSIPEQLTVSIEGAEPGTQLTAGQIALPAGVSLI 169

GO:0005829 "cytosol" evidence=IDA

TIGR_CMR|SO_2112 SO_2112 "ribosomal protein L25" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 34/88 (38%), Positives = 50/88 (56%)

Query:     3 IIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNL 62
             I A  R + G   SR LR  GKVP +IYG  K+PV I  +H  I +A   + F++S++ +
Sbjct:     5 ITAQTRTEIGKGSSRRLRHAGKVPAVIYGAGKEPVSIVFDHKDIINAQANDDFYTSVVTI 64

Query:    63 EIYGKVELVLLRNFQLHAYKKLVLHADF 90
              + GK   V  +  Q HA+K ++ H DF
Sbjct:    65 VLDGKEVGVRAQAMQRHAFKPIIEHVDF 92

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

GO:0006412 "translation" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
B2UER5	RL25_RALPJ	No assigned EC number	0.5265	0.9121	0.8990	yes	N/A
Q5P723	RL25_AROAE	No assigned EC number	0.5135	0.8926	0.9104	yes	N/A
Q12E00	RL25_POLSJ	No assigned EC number	0.5113	0.8585	0.7753	yes	N/A
A0KAM6	RL25_BURCH	No assigned EC number	0.5368	0.9219	0.9402	yes	N/A
A6T2S2	RL25_JANMA	No assigned EC number	0.6387	0.9268	0.8878	yes	N/A
B9ME47	RL25_ACIET	No assigned EC number	0.4623	0.9024	0.8894	yes	N/A
Q476G0	RL25_CUPPJ	No assigned EC number	0.5567	0.9024	0.9113	yes	N/A
A1UZN7	RL25_BURMS	No assigned EC number	0.5174	0.9707	0.9754	yes	N/A
Q3SLR4	RL25_THIDA	No assigned EC number	0.4921	0.9268	0.9452	yes	N/A
Q2T1B8	RL25_BURTA	No assigned EC number	0.5074	0.9707	0.9567	yes	N/A
B2JCN8	RL25_BURP8	No assigned EC number	0.525	0.9658	0.9753	yes	N/A
A9BP18	RL25_DELAS	No assigned EC number	0.4569	0.9024	0.8851	yes	N/A
Q21XW2	RL25_RHOFD	No assigned EC number	0.4619	0.8975	0.8251	yes	N/A
B1YN53	RL25_BURA4	No assigned EC number	0.5368	0.9219	0.9356	yes	N/A
Q145X3	RL25_BURXL	No assigned EC number	0.5430	0.9024	0.8937	yes	N/A
A1TT74	RL25_ACIAC	No assigned EC number	0.5588	0.8292	0.8095	yes	N/A
A9I6W5	RL25_BORPD	No assigned EC number	0.5405	0.8975	0.8888	yes	N/A
Q1LRQ2	RL25_RALME	No assigned EC number	0.5427	0.9707	0.9802	yes	N/A
Q2KYA2	RL25_BORA1	No assigned EC number	0.4972	0.8926	0.9242	yes	N/A
A1K3G6	RL25_AZOSB	No assigned EC number	0.5168	0.8682	0.89	yes	N/A
A4G921	RL25_HERAR	No assigned EC number	0.6492	0.9268	0.9047	yes	N/A
Q39CT9	RL25_BURS3	No assigned EC number	0.5368	0.9219	0.9402	yes	N/A
Q7VUH2	RL25_BORPE	No assigned EC number	0.5430	0.8975	0.8846	yes	N/A
A3MQB4	RL25_BURM7	No assigned EC number	0.5174	0.9707	0.9754	yes	N/A
Q62FC2	RL25_BURMA	No assigned EC number	0.5174	0.9707	0.9754	yes	N/A
Q479M1	RL25_DECAR	No assigned EC number	0.5348	0.8390	0.8472	yes	N/A
Q1H3J2	RL25_METFK	No assigned EC number	0.4835	0.8829	0.8743	yes	N/A
A4JHZ6	RL25_BURVG	No assigned EC number	0.5315	0.9219	0.9402	yes	N/A
A1W4G1	RL25_ACISJ	No assigned EC number	0.4623	0.9024	0.8894	yes	N/A
Q8Y2E2	RL25_RALSO	No assigned EC number	0.5319	0.9121	0.9077	yes	N/A
Q3JW87	RL25_BURP1	No assigned EC number	0.5174	0.9707	0.9567	yes	N/A
A3N5K0	RL25_BURP6	No assigned EC number	0.5174	0.9707	0.9754	yes	N/A
Q0BBQ4	RL25_BURCM	No assigned EC number	0.5368	0.9219	0.9356	yes	N/A
B2AGT7	RL25_CUPTR	No assigned EC number	0.5396	0.9219	0.9219	yes	N/A
Q1BTG5	RL25_BURCA	No assigned EC number	0.5368	0.9219	0.9402	yes	N/A
A4T069	RL25_POLSQ	No assigned EC number	0.5240	0.9073	0.8732	yes	N/A
A1WGH1	RL25_VEREI	No assigned EC number	0.5235	0.8292	0.7234	yes	N/A
Q63XL9	RL25_BURPS	No assigned EC number	0.5174	0.9707	0.9567	yes	N/A
A2SKU2	RL25_METPP	No assigned EC number	0.4619	0.8926	0.8551	yes	N/A
Q2YBH3	RL25_NITMU	No assigned EC number	0.4892	0.9024	0.8114	yes	N/A
B1JYQ0	RL25_BURCC	No assigned EC number	0.5368	0.9219	0.9402	yes	N/A
A9AEY7	RL25_BURM1	No assigned EC number	0.5473	0.9219	0.9402	yes	N/A
Q0KEP9	RL25_CUPNH	No assigned EC number	0.5502	0.9219	0.9219	yes	N/A
B1Y3Q0	RL25_LEPCP	No assigned EC number	0.4946	0.9024	0.8894	yes	N/A
C5CYZ6	RL25_VARPS	No assigned EC number	0.4892	0.9073	0.8303	yes	N/A
Q7WNY3	RL25_BORBR	No assigned EC number	0.5537	0.8975	0.9019	yes	N/A
B2SXG4	RL25_BURPP	No assigned EC number	0.5430	0.9024	0.8980	yes	N/A
A1VKN7	RL25_POLNA	No assigned EC number	0.4419	0.8829	0.8302	yes	N/A
B1XS65	RL25_POLNS	No assigned EC number	0.5376	0.9024	0.8644	yes	N/A
Q7W180	RL25_BORPA	No assigned EC number	0.5537	0.8975	0.9019	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	205
PRK05618	197	PRK05618, PRK05618, 50S ribosomal protein L25/gene	2e-69
TIGR00731	176	TIGR00731, ctc_TL5, ribosomal protein L25, Ctc-for	2e-34
cd00495	90	cd00495, Ribosomal_L25_TL5_CTC, Ribosomal L25/TL5/	2e-27
pfam01386	87	pfam01386, Ribosomal_L25p, Ribosomal L25p family	2e-25
COG1825	93	COG1825, RplY, Ribosomal protein L25 (general stre	3e-24
PRK05943	94	PRK05943, PRK05943, 50S ribosomal protein L25; Rev	6e-24

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

 Score =  210 bits (536), Expect = 2e-69
 Identities = 74/185 (40%), Positives = 121/185 (65%), Gaps = 3/185 (1%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           + + A  R++ G   +R LR+ GKVP +IYG  K+PV IS++   +  ALKK  F S++L
Sbjct: 4   ITLEAEVREEFGKGAARRLRRAGKVPAVIYGKGKEPVSISVDEKELIKALKKGAFLSTLL 63

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
           +LE+ GK + VL+++ Q H  K  +LH DF RVD  +K+ V+VP+HF+       VKL  
Sbjct: 64  DLEVGGKKQKVLVKDVQRHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVKLG- 122

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIA 180
            +++ V+ +L + CLP+++P+FIE+++  +E+  SIH+SD+KLP GV ++   + D  +A
Sbjct: 123 GVLNQVLHELEVECLPEDIPEFIEVDVSGLEIGDSIHVSDLKLPEGVKLL--DDPDEVVA 180

Query: 181 TAIIP 185
           T + P
Sbjct: 181 TVVAP 185

Length = 197

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

 Score =  119 bits (301), Expect = 2e-34
 Identities = 58/169 (34%), Positives = 95/169 (56%), Gaps = 4/169 (2%)

Query: 7   ERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYG 66
            R   G S +R +RK G++P ++YG  K+ V + +        L+K    S++L LEI G
Sbjct: 5   SRTSFGKSAARRIRKEGRIPAVVYGKGKENVNLELKSKEFIKYLRKGA-TSTVLTLEIGG 63

Query: 67  KVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNV 126
           K   VL++++Q +     V+H DF  V    K+ V+VP+  I + I   VK N  I++ V
Sbjct: 64  KEFKVLVKDYQYNPVTNEVIHVDFLEVVEGVKLKVEVPIKLIGTPI--GVK-NGGILTQV 120

Query: 127 ISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEE 175
              + + C PK++P F+E+++  + V  S+ LSD++LP GVS I   +E
Sbjct: 121 KRRIEVECKPKDIPDFLELDVSSLGVGESLKLSDLELPAGVSFITDDDE 169

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 = 99.5 bits (249), Expect = 2e-27
 Identities = 35/91 (38%), Positives = 57/91 (62%), Gaps = 1/91 (1%)

Query: 2  KIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILN 61
           + A +R++ G   +R LR+ GKVP +IYG  ++P+ IS++   +   L+KE   ++++ 
Sbjct: 1  TLKAEKREETGKGAARRLRREGKVPAVIYGKGEEPIPISVDAKELEKLLRKEGE-NTVIE 59

Query: 62 LEIYGKVELVLLRNFQLHAYKKLVLHADFQR 92
          LEI GK E VL+++ Q H  K  +LH DF R
Sbjct: 60 LEIDGKKENVLIKDVQRHPVKDEILHVDFLR 90

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

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

 Score = 94.1 bits (235), Expect = 2e-25
 Identities = 35/88 (39%), Positives = 55/88 (62%), Gaps = 1/88 (1%)

Query: 3  IIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNL 62
          + A +R++ G   SR LR+ GKVP +IYG  K+PV IS++   +   L +E   ++++ L
Sbjct: 1  LKAEKREETGKGASRRLRREGKVPAVIYGKGKEPVSISVDEKELEKLL-REAGENTVIEL 59

Query: 63 EIYGKVELVLLRNFQLHAYKKLVLHADF 90
          +I GK E VL+++ Q H  K  +LH DF
Sbjct: 60 KIDGKKENVLIKDVQRHPVKDKILHVDF 87

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

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

 Score = 91.2 bits (227), Expect = 3e-24
 Identities = 36/93 (38%), Positives = 57/93 (61%), Gaps = 1/93 (1%)

Query: 1  MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
           ++ A  R  +G   SR LR+ GK+P ++YGG K+PV I+++H+    AL+K   +S+++
Sbjct: 2  RELEAEVRTSQGKGASRRLRRAGKIPAVVYGGGKEPVNIALDHHEFAKALRKLG-YSTVI 60

Query: 61 NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRV 93
           LE+ GK   VL+++ Q H     V H DF RV
Sbjct: 61 TLEVDGKEIKVLVKDVQRHPLTDEVQHIDFLRV 93

Length = 93

>gnl|CDD|180318 PRK05943, PRK05943, 50S ribosomal protein L25; Reviewed

 Score = 90.3 bits (225), Expect = 6e-24
 Identities = 35/93 (37%), Positives = 50/93 (53%)

Query: 1  MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
            I A  R ++G   SR LR+ GK P IIYGGN+ PV I ++H  + +   K  F+  ++
Sbjct: 2  FTINAEVRPEQGKGASRRLRRAGKFPAIIYGGNEAPVSIVLDHKDVINLQAKAEFYKEVI 61

Query: 61 NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRV 93
           L I GK   V ++  Q H +K  + H DF R 
Sbjct: 62 TLVIDGKEVKVKVQAVQRHPFKPKLEHIDFVRA 94

Length = 94

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	205
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	100.0
PF01386	88	Ribosomal_L25p: Ribosomal L25p family; InterPro: I	99.97
cd00495	91	Ribosomal_L25_TL5_CTC Ribosomal_L25_TL5_CTC: Ribos	99.97
COG1825	93	RplY Ribosomal protein L25 (general stress protein	99.96
PF14693	88	Ribosomal_TL5_C: Ribosomal protein TL5, C-terminal	99.95

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

Probab=100.00  E-value=5.5e-60  Score=395.60  Aligned_cols=191  Identities=39%  Similarity=0.724  Sum_probs=178.4

Q ss_pred             CEEEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecc
Q psy8560           1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHA   80 (205)
Q Consensus         1 ~~l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~p   80 (205)
                      ++|+|++|+.+||+++||||++|+||||+||++.+|++++++.++|.+++++..+.+++|+|+++|++++||+|++|+||
T Consensus         4 ~~l~a~~R~~~gk~~~r~lR~~G~VPaViYG~~~~~~~i~v~~~~l~k~l~~~~~~~~~i~L~i~g~~~~vlikevQ~~p   83 (197)
T PRK05618          4 ITLEAEVREEFGKGAARRLRRAGKVPAVIYGKGKEPVSISVDEKELIKALKKGAFLSTLLDLEVGGKKQKVLVKDVQRHP   83 (197)
T ss_pred             EEEEEEEcCcCCChHHHHHHHCCCCcEEEECCCCCCEEEEECHHHHHHHHhcCCceeEEEEEEECCEEEEEEEeeeeecc
Confidence            37999999999999999999999999999999999999999999999999765556889999999999999999999999


Q ss_pred             cCCceeEEEEEEeCCCCeEEEEEeEEEEecCCCcceeeCCeEEEEEecEEEEEEeCCCCCceEEEeccCCCCCCeEEEec
Q psy8560          81 YKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSD  160 (205)
Q Consensus        81 v~~~i~HvDF~~v~~~~~v~v~VPI~~~Ge~~~~gvk~~GG~l~~~~~~i~V~~~p~~IPe~I~vDvs~L~iGd~i~v~D  160 (205)
                      ++++++|+|||+++++++|+++|||+|+|++.+++.| .||+|++.+++|+|+|+|.+||++|+||||+|++||+|||+|
T Consensus        84 v~~~i~HvDF~~v~~~~~v~v~VPv~~~G~~~~~~~k-~GG~l~~~~~~v~v~~~p~~IP~~I~VDVs~L~~Gd~i~v~D  162 (197)
T PRK05618         84 VKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVK-LGGVLNQVLHELEVECLPEDIPEFIEVDVSGLEIGDSIHVSD  162 (197)
T ss_pred             CCCCEEeEEEEEeCCCCEEEEEeeEEEEcCCCCcccc-cceEEEEEEEEEEEEEcHHHCCccEEEEcccCCCCCEEEeee
Confidence            9999999999999999999999999999988777766 599999999999999999999999999999999999999999


Q ss_pred             cCCCCCeEEeccCCCCceEEEEECccccccCCCC
Q psy8560         161 IKLPRGVSVIHSTEEDPTIATAIIPVNTLESDNN  194 (205)
Q Consensus       161 l~lp~gv~~~~~~d~~~vV~sv~~~~~~~~~~~~  194 (205)
                      |++|+|+++..  +++++||+|.+|+.+++++++
T Consensus       163 l~lp~~v~i~~--~~~~~v~~V~~~~~~~~~e~~  194 (197)
T PRK05618        163 LKLPEGVKLLD--DPDEVVATVVAPRGEEEEEEE  194 (197)
T ss_pred             ecCCCCcEEcC--CCCcEEEEEEcCCcccccccc
Confidence            99999999763  899999999999876655443

>TIGR00731 ctc_TL5 ribosomal protein L25, Ctc-form

Probab=100.00  E-value=1.5e-59  Score=386.86  Aligned_cols=175  Identities=34%  Similarity=0.618  Sum_probs=168.0

Q ss_pred             EEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecccC
Q psy8560           3 IIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHAYK   82 (205)
Q Consensus         3 l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~pv~   82 (205)
                      |+|+.|+.+||+++|||||+|+||||+||++.+++++++++++|.+++++.+ .+++|+|+++|++++||+||+|+||++
T Consensus         1 l~a~~R~~~gk~~~r~LR~~G~VPaVvYG~~~~~~~i~v~~~el~k~l~~~~-~~~~i~L~v~g~~~~vlikevQ~~pv~   79 (176)
T TIGR00731         1 LEVKSRTSFGKSAARRIRKEGRIPAVVYGKGKENVNLELKSKEFIKYLRKGA-TSTVLTLEIGGKEFKVLVKDYQYNPVT   79 (176)
T ss_pred             CeEEEeCCCCChHHHHHHHCCCccEEEECCCCCCEEEEECHHHHHHHHhccC-CcEEEEEEECCEEEEEEEehhhhccCC
Confidence            5799999999999999999999999999999999999999999999998765 588999999999999999999999999


Q ss_pred             CceeEEEEEEeCCCCeEEEEEeEEEEecCCCcceeeCCeEEEEEecEEEEEEeCCCCCceEEEeccCCCCCCeEEEeccC
Q psy8560          83 KLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIK  162 (205)
Q Consensus        83 ~~i~HvDF~~v~~~~~v~v~VPI~~~Ge~~~~gvk~~GG~l~~~~~~i~V~~~p~~IPe~I~vDvs~L~iGd~i~v~Dl~  162 (205)
                      ++++|+|||+++++++|+++|||+|+|+  ++|+| .||+|++.+++|+|+|+|.+||++|+||||+|++||+||++||+
T Consensus        80 ~~i~HvDF~~v~~~~~v~v~VPv~~~G~--~~gvk-~GG~l~~~~~~v~v~~~p~~IPe~I~VDvs~L~iGd~i~v~Dl~  156 (176)
T TIGR00731        80 NEVIHVDFLEVVEGVKLKVEVPIKLIGT--PIGVK-NGGILTQVKRRIEVECKPKDIPDFLELDVSSLGVGESLKLSDLE  156 (176)
T ss_pred             CCeEEEEeEEeCCCCEEEEEeeEEEecc--ccccc-CCcEEEEEEEEEEEEECHHHCCccEEEECccCCCCCEEEEeecc
Confidence            9999999999999999999999999996  57999 89999999999999999999999999999999999999999999


Q ss_pred             CCCCeEEeccCCCCceEEEEE
Q psy8560         163 LPRGVSVIHSTEEDPTIATAI  183 (205)
Q Consensus       163 lp~gv~~~~~~d~~~vV~sv~  183 (205)
                      +|+|+++..  +++++||+|.
T Consensus       157 lp~gv~~~~--d~~~~v~~V~  175 (176)
T TIGR00731       157 LPAGVSFIT--DDDEVVVTVI  175 (176)
T ss_pred             CCCCcEEcc--CCCcEEEEEe
Confidence            999999763  8999999984

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=100.00  E-value=1.8e-33  Score=210.11  Aligned_cols=93  Identities=38%  Similarity=0.580  Sum_probs=88.7

Q ss_pred             CEEEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecc
Q psy8560           1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHA   80 (205)
Q Consensus         1 ~~l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~p   80 (205)
                      ++|+|++|+.+||+++|+||++|+|||||||++.+|++++++.++|.+++++.++.+++|+|+++|++++|++||+|+||
T Consensus         2 ~~l~a~~R~~~gk~~~r~lR~~G~vPaViYG~~~~~~~i~v~~~el~k~l~~~~~~~~~i~L~v~g~~~~v~ikevQ~~p   81 (94)
T PRK05943          2 FTINAEVRPEQGKGASRRLRRAGKFPAIIYGGNEAPVSIVLDHKDVINLQAKAEFYKEVITLVIDGKEVKVKVQAVQRHP   81 (94)
T ss_pred             eEEEEEEeCcCCChHHHHHHHCCCCCEEEECCCCCcEEEEEcHHHHHHHHhcCCCcceEEEEEECCEEEEEEEeeeecCc
Confidence            47999999999999999999999999999999999999999999999999877656789999999999999999999999


Q ss_pred             cCCceeEEEEEEe
Q psy8560          81 YKKLVLHADFQRV   93 (205)
Q Consensus        81 v~~~i~HvDF~~v   93 (205)
                      +|++++|||||+|
T Consensus        82 v~~~i~HvDF~~v   94 (94)
T PRK05943         82 FKPKLEHIDFVRA   94 (94)
T ss_pred             CCCCeEeEeeeeC
Confidence            9999999999985

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

Probab=99.97  E-value=1.6e-31  Score=197.34  Aligned_cols=88  Identities=33%  Similarity=0.567  Sum_probs=83.3

Q ss_pred             EEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecccC
Q psy8560           3 IIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHAYK   82 (205)
Q Consensus         3 l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~pv~   82 (205)
                      |+|++|+.+||+++|+||++|+|||||||++.+|++|+++.++|.+++++..+.+++|+|+++|++++||+||+|+||++
T Consensus         1 L~a~~R~~~gk~~~r~LR~~G~iPaviYG~~~~~~~i~v~~~~l~k~~~~~~~~~~~i~L~i~g~~~~vlikevQ~~p~~   80 (88)
T PF01386_consen    1 LKAEKREETGKSAARRLRREGKIPAVIYGKGKESIPISVDEKELEKLLRRKHGENSVIELNIDGKKYNVLIKEVQRDPVT   80 (88)
T ss_dssp             EEEEESSSTSSSHHHHHHHTTEEEEEEEESSEEEEEEEEEHHHHHHHHTHHHTTTSEEEEEETTEEEEEEEEEEEEESSS
T ss_pred             CeEEEcCcCCCHHHHHHHHcCCceEEEECCCCCCEEEEEeHHHHHHHHHhcCCceEEEEEEECCEEEEEEEEeeeeCCCC
Confidence            78999999999999999999999999999999999999999999999953334578999999999999999999999999


Q ss_pred             CceeEEEE
Q psy8560          83 KLVLHADF   90 (205)
Q Consensus        83 ~~i~HvDF   90 (205)
                      ++++||||
T Consensus        81 ~~i~HvDF   88 (88)
T PF01386_consen   81 DKILHVDF   88 (88)
T ss_dssp             SSEEEEEE
T ss_pred             CCeEeccC
Confidence            99999999

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=99.97  E-value=6.1e-31  Score=195.11  Aligned_cols=91  Identities=41%  Similarity=0.693  Sum_probs=87.0

Q ss_pred             CEEEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecc
Q psy8560           1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHA   80 (205)
Q Consensus         1 ~~l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~p   80 (205)
                      .+|+|.+|+.+||+++|+||++|+|||||||++.+|++|+++.++|.+++++.+ .+++|+|+++|+++.|++||+|+||
T Consensus         1 ~~l~a~~R~~~gk~~~r~lR~~G~iPavvYG~~~~~~~i~v~~~~l~k~l~~~~-~~~~~~L~i~g~~~~~~ikevQ~~p   79 (91)
T cd00495           1 LTLKAEKREETGKGASRRLRRAGKVPAVIYGKGKEPISISVDEKELEKLLRKEG-RSTLIELNIDGKKENVLIKDVQRHP   79 (91)
T ss_pred             CeEEEEEcccCCChHHHHHHHCCCCCEEEECCCCCCEEEEEcHHHHHHHHhhcC-CceEEEEEECCEEEEEEEehhhhcc
Confidence            479999999999999999999999999999999999999999999999998776 5789999999999999999999999


Q ss_pred             cCCceeEEEEEE
Q psy8560          81 YKKLVLHADFQR   92 (205)
Q Consensus        81 v~~~i~HvDF~~   92 (205)
                      ++++++|||||+
T Consensus        80 v~~~i~HvDF~~   91 (91)
T cd00495          80 VKDKILHVDFLR   91 (91)
T ss_pred             CCCCEEEEeccC
Confidence            999999999985

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

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

Probab=99.96  E-value=3.2e-29  Score=186.85  Aligned_cols=92  Identities=39%  Similarity=0.643  Sum_probs=89.0

Q ss_pred             CEEEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecc
Q psy8560           1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHA   80 (205)
Q Consensus         1 ~~l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~p   80 (205)
                      +.|+|+.|+..||+++|+||++|++|||+||++.+|+++++++++|.+++++.+ .|++|+|+++|++..|++|++|+||
T Consensus         2 ~~l~~~~R~~~Gkg~~RrlR~~G~iPAviYG~g~~~v~i~l~~~~~~k~~~~~~-~~~v~~l~v~g~~~~Vlvkd~Q~~p   80 (93)
T COG1825           2 RELEAEVRTSQGKGASRRLRRAGKIPAVVYGGGKEPVNIALDHHEFAKALRKLG-YSTVITLEVDGKEIKVLVKDVQRHP   80 (93)
T ss_pred             ceeceeEecccCcchhHhHHhcCCCCEEEECCCCCCceEEEcHHHHHHHHhhcc-cceEEEEEECCeEEEEEehhhhhCc
Confidence            578999999999999999999999999999999999999999999999999887 7899999999999999999999999


Q ss_pred             cCCceeEEEEEEe
Q psy8560          81 YKKLVLHADFQRV   93 (205)
Q Consensus        81 v~~~i~HvDF~~v   93 (205)
                      +++.++|+||+++
T Consensus        81 ~~~~~~HvDf~~v   93 (93)
T COG1825          81 LTDEVQHIDFLRV   93 (93)
T ss_pred             ccCceeecccccC
Confidence            9999999999975

>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=1.2e-27  Score=176.84  Aligned_cols=88  Identities=35%  Similarity=0.776  Sum_probs=76.6

Q ss_pred             CeEEEEEeEEEEecCCCcceeeCCeEEEEEecEEEEEEeCCCCCceEEEeccCCCCCCeEEEeccCCCCCeEEeccCCCC
Q psy8560          97 KKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEED  176 (205)
Q Consensus        97 ~~v~v~VPI~~~Ge~~~~gvk~~GG~l~~~~~~i~V~~~p~~IPe~I~vDvs~L~iGd~i~v~Dl~lp~gv~~~~~~d~~  176 (205)
                      ++|+++|||+|+|+  ++|+| .||+|++.+++|+|+|+|++||++|++|||+|++||+||++||++|+|+++..  |+|
T Consensus         1 e~v~~~VPv~~~G~--~~gvk-~Gg~l~~~~~~v~V~~~p~~iPe~I~vDvs~l~~g~~i~v~Dl~lp~gv~~~~--d~~   75 (88)
T PF14693_consen    1 EKVKVEVPVHFVGE--SPGVK-KGGILQQVLREVEVECLPADIPESIEVDVSGLEIGDSIHVSDLKLPEGVEILD--DPE   75 (88)
T ss_dssp             S-EEEEEEEEEESS--SHHHC-TTSEEEESTSEEEEEE-TTS--SSEEEETTTSSTTCEEEGCCSB-STTEEESS---TT
T ss_pred             CeEEEEEeEEEEcc--cccCc-CCcEEEEEEeEEEEEEcHHHCCccEEEECccCcCCCEEEEeeccCCCCcEEcC--CCC
Confidence            68999999999996  79999 89999999999999999999999999999999999999999999999999874  899


Q ss_pred             ceEEEEECccccc
Q psy8560         177 PTIATAIIPVNTL  189 (205)
Q Consensus       177 ~vV~sv~~~~~~~  189 (205)
                      ++||+|..|++++
T Consensus        76 ~vV~~v~~~~~ee   88 (88)
T PF14693_consen   76 TVVASVVAPRVEE   88 (88)
T ss_dssp             SEEEEEE-SCSS-
T ss_pred             cEEEEEeccccCC
Confidence            9999999999764

...

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	205
3fin_Z	177	T. Thermophilus 70s Ribosome In Complex With Mrna,		3e-14
3tvh_V	179	Crystal Structure Analysis Of Ribosomal Decoding. T		3e-14
2j01_Z	206	Structure Of The Thermus Thermophilus 70s Ribosome		3e-14
3pyo_V	188	Crystal Structure Of A Complex Containing Domain 3		3e-14
1feu_A	206	Crystal Structure Of Ribosomal Protein Tl5, One Of		4e-14
3tve_V	175	Crystal Structure Analysis Of Ribosomal Decoding. T		1e-13
1b75_A	94	Solution Structure Of Ribosomal Protein L25 From Es		4e-11
1d6k_A	94	Nmr Solution Structure Of The 5s Rrna E-LoopL25 COM		4e-11
1pnu_T	173	Crystal Structure Of A Streptomycin Dependent Ribos		1e-05
1njm_T	237	The Crystal Structure Of The 50s Large Ribosomal Su		2e-05
1nkw_T	253	Crystal Structure Of The Large Ribosomal Subunit Fr		2e-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 = 75.1 bits (183), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 51/184 (27%), Positives = 97/184 (52%), Gaps = 10/184 (5%)
Query: 2   KIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILN 61
           ++ A+ R+ +  S    LR+ GK+PG++Y  + +  K+ ++        ++ + H  I+ 
Sbjct: 2   RLKAYYREGEKPS---ALRRAGKLPGVMYNRHLN-RKVYVDLVEFDKVFRQASIHHVIVL 57
Query: 62  LEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSC 121
               G+    L+R   L   ++   H DF  V +++ + + VPL F+ +   PA      
Sbjct: 58  ELPDGQSLPTLVRQVNLDKRRRRPEHVDFF-VLSDEPVEMYVPLRFVGT---PAGVRAGG 113
Query: 122 IISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIAT 181
           ++  +  D+ +   P+N+P+FIE+++  +E+  S+H SD+KLP GV +  S EE  TIA 
Sbjct: 114 VLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEE--TIAA 171
Query: 182 AIIP 185
            + P
Sbjct: 172 VVPP 175

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 51/184 (27%), Positives = 97/184 (52%), Gaps = 10/184 (5%)
Query: 2   KIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILN 61
           ++ A+ R+ +  S    LR+ GK+PG++Y  + +  K+ ++        ++ + H  I+ 
Sbjct: 4   RLKAYYREGEKPS---ALRRAGKLPGVMYNRHLN-RKVYVDLVEFDKVFRQASIHHVIVL 59
Query: 62  LEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSC 121
               G+    L+R   L   ++   H DF  V +++ + + VPL F+ +   PA      
Sbjct: 60  ELPDGQSLPTLVRQVNLDKRRRRPEHVDFF-VLSDEPVEMYVPLRFVGT---PAGVRAGG 115
Query: 122 IISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIAT 181
           ++  +  D+ +   P+N+P+FIE+++  +E+  S+H SD+KLP GV +  S EE  TIA 
Sbjct: 116 VLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEE--TIAA 173
Query: 182 AIIP 185
            + P
Sbjct: 174 VVPP 177

>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 = 75.1 bits (183), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 89/167 (53%), Gaps = 7/167 (4%)
Query: 19  LRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQL 78
           LR+ GK+PG++Y  + +  K+ ++        ++ + H  I+     G+    L+R   L
Sbjct: 18  LRRAGKLPGVMYNRHLN-RKVYVDLVEFDKVFRQASIHHVIVLELPDGQSLPTLVRQVNL 76
Query: 79  HAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKN 138
              ++   H DF  V +++ + + VPL F+ +   PA      ++  +  D+ +   P+N
Sbjct: 77  DKRRRRPEHVDFF-VLSDEPVEMYVPLRFVGT---PAGVRAGGVLQEIHRDILVKVSPRN 132
Query: 139 LPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIP 185
           +P+FIE+++  +E+  S+H SD+KLP GV +  S EE  TIA  + P
Sbjct: 133 IPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEE--TIAAVVPP 177

>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 = 74.7 bits (182), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 89/167 (53%), Gaps = 7/167 (4%)
Query: 19  LRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQL 78
           LR+ GK+PG++Y  + +  K+ ++        ++ + H  I+     G+    L+R   L
Sbjct: 16  LRRAGKLPGVMYNRHLN-RKVYVDLVEFDKVFRQASIHHVIVLELPDGQSLPTLVRQVNL 74
Query: 79  HAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKN 138
              ++   H DF  V +++ + + VPL F+ +   PA      ++  +  D+ +   P+N
Sbjct: 75  DKRRRRPEHVDFF-VLSDEPVEMYVPLRFVGT---PAGVRAGGVLQEIHRDILVKVSPRN 130
Query: 139 LPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIP 185
           +P+FIE+++  +E+  S+H SD+KLP GV +  S EE  TIA  + P
Sbjct: 131 IPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEE--TIAAVVPP 175

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

Iteration: 1
 Score = 74.3 bits (181), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 89/167 (53%), Gaps = 7/167 (4%)
Query: 19  LRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQL 78
           LR+ GK+PG++Y  + +  K+ ++        ++ + H  I+     G+    L+R   L
Sbjct: 18  LRRAGKLPGLMYNRHLN-RKVYVDLVEFDKVFRQASIHHVIVLELPDGQSLPTLVRQVNL 76
Query: 79  HAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKN 138
              ++   H DF  V +++ + + VPL F+ +   PA      ++  +  D+ +   P+N
Sbjct: 77  DKRRRRPEHVDFF-VLSDEPVEMYVPLRFVGT---PAGVRAGGVLQEIHRDILVKVSPRN 132
Query: 139 LPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIP 185
           +P+FIE+++  +E+  S+H SD+KLP GV +  S EE  TIA  + P
Sbjct: 133 IPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEE--TIAAVVPP 177

>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 = 72.8 bits (177), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 88/165 (53%), Gaps = 7/165 (4%)
Query: 19  LRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQL 78
           LR+ GK+PG++Y  + +  K+ ++        ++ + H  I+     G+    L+R   L
Sbjct: 18  LRRAGKLPGVMYNRHLN-RKVYVDLVEFDKVFRQASIHHVIVLELPDGQSLPTLVRQVNL 76
Query: 79  HAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKN 138
              ++   H DF  V +++ + + VPL F+ +   PA      ++  +  D+ +   P+N
Sbjct: 77  DKRRRRPEHVDFF-VLSDEPVEMYVPLRFVGT---PAGVRAGGVLQEIHRDILVKVSPRN 132
Query: 139 LPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAI 183
           +P+FIE+++  +E+  S+H SD+KLP GV +  S EE  TIA  +
Sbjct: 133 IPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEE--TIAAVV 175

>pdb|1B75|A Chain A, Solution Structure Of Ribosomal Protein L25 From Escherichia Coli Length = 94

Iteration: 1
 Score = 64.7 bits (156), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 32/86 (37%), Positives = 48/86 (55%)
Query: 8  RKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGK 67
          RK++G   SR LR   K P IIYGG + P+ I ++H+ + +   K  F+S +L + + GK
Sbjct: 9  RKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGK 68
Query: 68 VELVLLRNFQLHAYKKLVLHADFQRV 93
             V  ++ Q H YK  + H DF R 
Sbjct: 69 EIKVKAQDVQRHPYKPKLQHIDFVRA 94

>pdb|1D6K|A Chain A, Nmr Solution Structure Of The 5s Rrna E-LoopL25 COMPLEX Length = 94

Iteration: 1
 Score = 64.7 bits (156), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 32/86 (37%), Positives = 48/86 (55%)
Query: 8  RKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGK 67
          RK++G   SR LR   K P IIYGG + P+ I ++H+ + +   K  F+S +L + + GK
Sbjct: 9  RKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGK 68
Query: 68 VELVLLRNFQLHAYKKLVLHADFQRV 93
             V  ++ Q H YK  + H DF R 
Sbjct: 69 EIKVKAQDVQRHPYKPKLQHIDFVRA 94

>pdb|1PNU|T Chain T, Crystal Structure Of A Streptomycin Dependent Ribosome From Escherichia Coli, 50s Subunit Of 70s Ribosome. This File, 1pnu, Contains Only Molecules Of The 50s Ribosomal Subunit. The 30s Subunit, Mrna, P-Site Trna, And A-Site Trna Are In The Pdb File 1pns. Length = 173

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/140 (20%), Positives = 66/140 (47%), Gaps = 6/140 (4%)
Query: 37  VKISMNHNMIYHALKKETFHSSILNLEIYGKVEL-VLLRNFQLHAYKKLVLHADFQRVDT 95
           V  +++      A ++++  + + ++ + G      L++  Q+   K+  +H DF  V  
Sbjct: 30  VSFALDRKAFDRAFRQQS-TTGLFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTY 88
Query: 96  EKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYI-SCLPKNLPKFIEINLEKMEVNT 154
            + + V VP+H          ++   ++  V+ +L I +  P+ +P+ + +++ KM +  
Sbjct: 89  GEPVEVSVPVHTTGRSQG---EVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGD 145
Query: 155 SIHLSDIKLPRGVSVIHSTE 174
            I   DIKLP G ++    E
Sbjct: 146 HITAGDIKLPEGCTLAADPE 165

>pdb|1NJM|T Chain T, The Crystal Structure Of The 50s Large Ribosomal Subunit From Deinococcus Radiodurans Complexed With A Trna Acceptor Stem Mimic (Asm) And The Antibiotic Sparsomycin Length = 237

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/140 (20%), Positives = 66/140 (47%), Gaps = 6/140 (4%)
Query: 37  VKISMNHNMIYHALKKETFHSSILNLEIYGKVEL-VLLRNFQLHAYKKLVLHADFQRVDT 95
           V  +++      A ++++  + + ++ + G      L++  Q+   K+  +H DF  V  
Sbjct: 30  VSFALDRKAFDRAFRQQST-TGLFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTY 88
Query: 96  EKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYI-SCLPKNLPKFIEINLEKMEVNT 154
            + + V VP+H          ++   ++  V+ +L I +  P+ +P+ + +++ KM +  
Sbjct: 89  GEPVEVSVPVHTTGRSQG---EVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGD 145
Query: 155 SIHLSDIKLPRGVSVIHSTE 174
            I   DIKLP G ++    E
Sbjct: 146 HITAGDIKLPEGCTLAADPE 165

>pdb|1NKW|T Chain T, Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Length = 253

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/140 (20%), Positives = 66/140 (47%), Gaps = 6/140 (4%)
Query: 37  VKISMNHNMIYHALKKETFHSSILNLEIYGKVEL-VLLRNFQLHAYKKLVLHADFQRVDT 95
           V  +++      A ++++  + + ++ + G      L++  Q+   K+  +H DF  V  
Sbjct: 46  VSFALDRKAFDRAFRQQST-TGLFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTY 104
Query: 96  EKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYI-SCLPKNLPKFIEINLEKMEVNT 154
            + + V VP+H          ++   ++  V+ +L I +  P+ +P+ + +++ KM +  
Sbjct: 105 GEPVEVSVPVHTTGRSQG---EVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGD 161
Query: 155 SIHLSDIKLPRGVSVIHSTE 174
            I   DIKLP G ++    E
Sbjct: 162 HITAGDIKLPEGCTLAADPE 181

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	205
1feu_A	206	50S ribosomal protein L25; general stress protein	5e-54
2zjr_S	237	50S ribosomal protein L25; ribosome, large ribosom	4e-49
1b75_A	94	Protein (50S ribosomal protein L25); RNA-binding p	6e-35

>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 =  170 bits (433), Expect = 5e-54
 Identities = 48/200 (24%), Positives = 98/200 (49%), Gaps = 10/200 (5%)

Query: 1   MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSIL 60
            ++ A+ R+ +  S    LR+ GK+PG++Y  + +  K+ ++        ++ + H  I+
Sbjct: 3   YRLKAYYREGEKPS---ALRRAGKLPGLMYNRHLNR-KVYVDLVEFDKVFRQASIHHVIV 58

Query: 61  NLEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNS 120
                G+    L+R   L   ++   H DF  +  E  + + VPL F+ +     V+   
Sbjct: 59  LELPDGQSLPTLVRQVNLDKRRRRPEHVDFFVLSDE-PVEMYVPLRFVGT--PAGVRAGG 115

Query: 121 CIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIA 180
            ++  +  D+ +   P+N+P+FIE+++  +E+  S+H SD+KLP GV +      + TIA
Sbjct: 116 -VLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAV--SPEETIA 172

Query: 181 TAIIPVNTLESDNNSSIEKE 200
             + P +  +    ++ E  
Sbjct: 173 AVVPPEDVEKLAEEAAAEVA 192

>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 =  159 bits (403), Expect = 4e-49
 Identities = 34/179 (18%), Positives = 79/179 (44%), Gaps = 9/179 (5%)

Query: 16  SRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYG-KVELVLLR 74
            +       +  + Y   ++ V  +++      A ++++  + + ++ + G +    L++
Sbjct: 10  PKQKLDESMIAAVAYNK-ENNVSFALDRKAFDRAFRQQST-TGLFDITVEGGETFPALVK 67

Query: 75  NFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISC 134
             Q+   K+  +H DF  V   + + V VP+H      S        ++  V+ +L I  
Sbjct: 68  AVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGR--SQGEV-QGGLVDIVVHNLQIVA 124

Query: 135 L-PKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIPVNTLESD 192
             P+ +P+ + +++ KM +   I   DIKLP G ++    + + T+ + + P  T E  
Sbjct: 125 PGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLA--ADPELTVVSVLPPRLTAEEL 181

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

 Score =  118 bits (297), Expect = 6e-35
 Identities = 34/91 (37%), Positives = 50/91 (54%)

Query: 2  KIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILN 61
           I A  RK++G   SR LR   K P IIYGG + P+ I ++H+ + +   K  F+S +L 
Sbjct: 3  TINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLT 62

Query: 62 LEIYGKVELVLLRNFQLHAYKKLVLHADFQR 92
          + + GK   V  ++ Q H YK  + H DF R
Sbjct: 63 IVVDGKEIKVKAQDVQRHPYKPKLQHIDFVR 93

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	205
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	99.98
3lyw_A	90	YBBR family protein; structural genomics, PSI-2, p	94.37
2kq1_A	119	BH0266 protein; solution NESG, structural genomics	80.25

>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=3.6e-58  Score=385.79  Aligned_cols=176  Identities=26%  Similarity=0.526  Sum_probs=167.6

Q ss_pred             CEEEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEE-CCeEEEEEEEeEeec
Q psy8560           1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEI-YGKVELVLLRNFQLH   79 (205)
Q Consensus         1 ~~l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i-~G~~~~vlikevQ~~   79 (205)
                      ++|+|+.|+   |+++|||||+|+|||||||++.+ ++|+++.++|.+++++.+ .+++|+|++ +|+++.||+|++|+|
T Consensus         3 ~~l~a~~R~---k~aarrLRr~G~VPaVvYG~~~e-~~i~v~~~el~~~l~~~~-~~~vi~L~i~~G~~~~vlikdvQ~h   77 (206)
T 1feu_A            3 YRLKAYYRE---GEKPSALRRAGKLPGLMYNRHLN-RKVYVDLVEFDKVFRQAS-IHHVIVLELPDGQSLPTLVRQVNLD   77 (206)
T ss_dssp             EEEECEECS---SSCHHHHHHTTEEEEEEECSSCE-EEEEEEHHHHHHHHHHHT-TTSEEEEECTTSCEEEEEEEEEEEC
T ss_pred             eEEEEEEeC---ChHHHHHHHCCCceEEEEcCCce-EEEEEcHHHHHHHHhhcC-CcEEEEEEEcCCCEEEEEEEEeEeC
Confidence            368999999   88899999999999999999988 999999999999998765 478999999 999999999999999


Q ss_pred             ccCCceeEEEEEEeCCCCeEEEEEeEEEEecCCCcceeeCCeEEEEEecEEEEEEeCCCCCceEEEeccCCCCCCeEEEe
Q psy8560          80 AYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLS  159 (205)
Q Consensus        80 pv~~~i~HvDF~~v~~~~~v~v~VPI~~~Ge~~~~gvk~~GG~l~~~~~~i~V~~~p~~IPe~I~vDvs~L~iGd~i~v~  159 (205)
                      |+|+.++|+|||++++ ++|+++|||+|+|+  ++|+| .||+|++.+++|+|+|+|.+||++|+||||+|++||+||++
T Consensus        78 pv~~~i~HvDF~~v~~-~~v~v~VPv~~~G~--~~gvk-~GG~l~~~~~~v~V~~~p~~IPe~I~VDvs~L~iGdsi~v~  153 (206)
T 1feu_A           78 KRRRRPEHVDFFVLSD-EPVEMYVPLRFVGT--PAGVR-AGGVLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHAS  153 (206)
T ss_dssp             SSSSCEEEEEEEECCS-SCEEEEEEEEEESC--CHHHH-TTCEEEECCSEEEEEECGGGCCSCEEEECTTCCTTEEEEGG
T ss_pred             CCCCCeEEEEEEEECC-EEEEEEeeEEEEcC--ccccc-CceEEEEEEeEEEEEEcHHHCCccEEEEcccCCCCCEEEEe
Confidence            9999999999999999 99999999999996  68999 89999999999999999999999999999999999999999


Q ss_pred             ccCCCCCeEEeccCCCCceEEEEECccc
Q psy8560         160 DIKLPRGVSVIHSTEEDPTIATAIIPVN  187 (205)
Q Consensus       160 Dl~lp~gv~~~~~~d~~~vV~sv~~~~~  187 (205)
                      ||+||+|+++..  |+|++||+|..|+.
T Consensus       154 Dl~lP~gv~~~~--d~d~~V~~V~~~~~  179 (206)
T 1feu_A          154 DLKLPPGVELAV--SPEETIAAVVPPED  179 (206)
T ss_dssp             GSCCCTTCEESS--CTTCEEEEEECSSS
T ss_pred             eccCCCCcEEcC--CCCcEEEEEeCCCc
Confidence            999999999773  89999999999984

>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=7.1e-57  Score=383.65  Aligned_cols=176  Identities=21%  Similarity=0.409  Sum_probs=165.0

Q ss_pred             EeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECC-eEEEEEEEeEeecccCCce
Q psy8560           7 ERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYG-KVELVLLRNFQLHAYKKLV   85 (205)
Q Consensus         7 ~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G-~~~~vlikevQ~~pv~~~i   85 (205)
                      .|+.+||+++||| |+|+||||||| +.+|++|+++.++|.+++++.+ .+++|+|+++| ++++||+|++|+||+|+++
T Consensus         2 ~R~~~GKgaaRrL-r~G~VPaVvYG-g~e~v~i~v~~~el~k~l~~~~-~~~li~L~IdG~~~~~vliKdvQ~hPvk~~i   78 (237)
T 2zjr_S            2 ELTAKPRTPKQKL-DESMIAAVAYN-KENNVSFALDRKAFDRAFRQQS-TTGLFDITVEGGETFPALVKAVQMDKRKRAP   78 (237)
T ss_dssp             CCCBCCSCCHHHH-SSSCCCEEEES-SSCCCCCBCCHHHHHHHHHHHT-TSCCCBCCCTTCCCCBCCEEEEEECSSSCCE
T ss_pred             cccccCcHHHHHH-hCCCCCEEEeC-CCCCEEEEECHHHHHHHHHhcC-CcEEEEEEECCceeEEEEEEEEEecCCCCCe
Confidence            5999999999999 99999999999 8999999999999999998755 47899999999 9889999999999999999


Q ss_pred             eEEEEEEeCCCCeEEEEEeEEEEecCCCcceeeCCeEEEEEecEEEEEE-eCCCCCceEEEeccCCCCCCeEEEeccCCC
Q psy8560          86 LHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISC-LPKNLPKFIEINLEKMEVNTSIHLSDIKLP  164 (205)
Q Consensus        86 ~HvDF~~v~~~~~v~v~VPI~~~Ge~~~~gvk~~GG~l~~~~~~i~V~~-~p~~IPe~I~vDvs~L~iGd~i~v~Dl~lp  164 (205)
                      +|+|||+++++++|+++|||+|+|+  ++|+| +||+|++.+++|+|+| +|.+||++|+||||+|++||+||++||+||
T Consensus        79 lHVDF~~V~~~ekV~v~VPV~~vGe--~~GvK-~GGvL~~~~~eveV~~~lP~~IPe~IeVDVs~LeiGdsI~v~DL~LP  155 (237)
T 2zjr_S           79 IHVDFYMVTYGEPVEVSVPVHTTGR--SQGEV-QGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLP  155 (237)
T ss_dssp             EEEEEECCCSSCCCEEEEECEEESC--CTTTT-TTSEEECSCSEEEEECCCTTCCCSCCEEECTTCCSSCEEETTTSCCS
T ss_pred             EEEEEEEECCCCEEEEEEeEEEecC--Ccccc-CCcEEEEEEeEEEEEEeCHHHCCccEEEEcccCCCCCEEEeeeccCC
Confidence            9999999999999999999999996  68999 8999999999999999 999999999999999999999999999999


Q ss_pred             CCeEEeccCCCCceEEEEECcccccc
Q psy8560         165 RGVSVIHSTEEDPTIATAIIPVNTLE  190 (205)
Q Consensus       165 ~gv~~~~~~d~~~vV~sv~~~~~~~~  190 (205)
                      +|+++..  |++++||+|..|+.+.+
T Consensus       156 eGv~l~~--d~d~vVvsV~~p~~~~e  179 (237)
T 2zjr_S          156 EGCTLAA--DPELTVVSVLPPRLTAE  179 (237)
T ss_dssp             TTCCCCS--CTTCEEEEEECCC----
T ss_pred             CCcEEcC--CCCcEEEEEEcCCCCCC
Confidence            9999763  79999999999986544

>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=99.98  E-value=7.5e-34  Score=211.16  Aligned_cols=93  Identities=37%  Similarity=0.574  Sum_probs=88.5

Q ss_pred             CEEEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecc
Q psy8560           1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHA   80 (205)
Q Consensus         1 ~~l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~p   80 (205)
                      ++|+|+.|+.+||+++|+||++|+|||||||++.+|++|+++.++|.+++++.++.+++|+|+++|+++.|++||+|+||
T Consensus         2 ~~l~a~~R~~~Gk~~arrLRr~G~vPaVvYG~~~e~~~i~v~~~~~~~~l~~~~~~~~~i~L~i~G~~~~vlikdvQ~hp   81 (94)
T 1b75_A            2 FTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRHP   81 (94)
T ss_dssp             CCEEECSSCCSSSSSSSSTTTTTBCCEEEECSSSCCEEECCBSHHHHHHHTTTHHHHTCEEEEESSCEEEECCSEEECCS
T ss_pred             eEEEEEEecccCChHHHHHHHCCCceEEEECCCCCCEEEEECHHHHHHHHhccCcceEEEEEEECCEEEEEEEEEEEeCC
Confidence            47999999999999999999999999999999999999999999999999887766789999999999999999999999


Q ss_pred             cCCceeEEEEEEe
Q psy8560          81 YKKLVLHADFQRV   93 (205)
Q Consensus        81 v~~~i~HvDF~~v   93 (205)
                      +++.++|+|||+|
T Consensus        82 ~~~~i~HvDF~~v   94 (94)
T 1b75_A           82 YKPKLQHIDFVRA   94 (94)
T ss_dssp             SSCCCCEEEEEBC
T ss_pred             CCCCeEEEEEEEC
Confidence            9999999999985

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

Probab=94.37  E-value=0.18  Score=36.30  Aligned_cols=74  Identities=8%  Similarity=0.125  Sum_probs=47.5

Q ss_pred             EEEEeEEEEecCCCcceeeCCeEEEEEecEEEEEEe--CCCC-Cc--eEEEeccCCCCCC-eEEEeccCCCCCeEEeccC
Q psy8560         100 HVKVPLHFINSEISPAVKLNSCIISNVISDLYISCL--PKNL-PK--FIEINLEKMEVNT-SIHLSDIKLPRGVSVIHST  173 (205)
Q Consensus       100 ~v~VPI~~~Ge~~~~gvk~~GG~l~~~~~~i~V~~~--p~~I-Pe--~I~vDvs~L~iGd-~i~v~Dl~lp~gv~~~~~~  173 (205)
                      +.+|||.|.|.+  .|..     +.....+++|+..  ...+ +.  ...||+|++..|+ .+.|. +.+|.|+++.. .
T Consensus         4 tytVPv~~~Nlp--~~~~-----v~~~~~tV~V~v~G~r~~~~~~di~A~VDLsg~~~G~~~~~V~-v~~P~G~~lv~-v   74 (90)
T 3lyw_A            4 TLTLSLIAKNTP--ANSM-----IMTKLPSVRVKTEGYNPSINVNELFAYVDLSGSEPGEHDYEVK-VEPIPNIKIVE-I   74 (90)
T ss_dssp             EEEEEEEEESCC--TTEE-----ECSCCCEEEEEEEECCTTCCSTTCEEEEECTTCCSEEEEEECE-ECCCTTEEEEE-E
T ss_pred             eEEeeEEEeeCC--CCcE-----EecCCCEEEEEEEecCcCCChHHEEEEEECcCCCCCcEeEEEE-EECCCCCEEEE-E
Confidence            579999999964  3332     2333346665553  3222 11  4689999999998 44455 89999999443 3


Q ss_pred             CCCceEEEE
Q psy8560         174 EEDPTIATA  182 (205)
Q Consensus       174 d~~~vV~sv  182 (205)
                      .|+.+-..+
T Consensus        75 sP~~V~~~~   83 (90)
T 3lyw_A           75 SPRVVTLQL   83 (90)
T ss_dssp             ESSEEEEEE
T ss_pred             ccceEEEEe
Confidence            677766554

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

Probab=80.25  E-value=15  Score=26.83  Aligned_cols=79  Identities=9%  Similarity=0.019  Sum_probs=51.9

Q ss_pred             CeEEEEEeEEEEecCCCcceeeCCeEEEEEecEEEEEEeC--C---CC---Cc--eEEEeccCCCCCC---eEEEeccCC
Q psy8560          97 KKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLP--K---NL---PK--FIEINLEKMEVNT---SIHLSDIKL  163 (205)
Q Consensus        97 ~~v~v~VPI~~~Ge~~~~gvk~~GG~l~~~~~~i~V~~~p--~---~I---Pe--~I~vDvs~L~iGd---~i~v~Dl~l  163 (205)
                      ...-..|||.+.+.+       .|-.+...-.+++|....  .   .+   ++  ...+|+|+|..|.   .+.+.  .+
T Consensus         8 ~~~~~~VPV~v~~~~-------~~~~v~~~p~~V~V~l~G~~~~l~~~~~~~~~i~~~vDLs~l~~G~~~vpv~v~--~l   78 (119)
T 2kq1_A            8 NLSLGELELTVLYDE-------ERYDIVEQTETVQVDLEGPRGVLTVFRFARPSYEVFVDLTEAGEGSHTVDVEHR--GF   78 (119)
T ss_dssp             EEEEEEEEEEEECCT-------TTCEEEECCCEEEEEEEECHHHHHHHTTSCCCCEEEEECTTCCBEEEEEECEEE--SS
T ss_pred             eEEEEEeeEEEEECC-------CCEEEECCCCEEEEEEEECHHHhhhccccccCEEEEEECccCCCCeEEEEEEEe--cC
Confidence            445678999999853       234444445566665532  1   11   22  5689999999997   44444  48


Q ss_pred             CCCeEEeccCCCCceEEEEECcc
Q psy8560         164 PRGVSVIHSTEEDPTIATAIIPV  186 (205)
Q Consensus       164 p~gv~~~~~~d~~~vV~sv~~~~  186 (205)
                      |+|+++..  +|..+-+++....
T Consensus        79 p~~v~v~v--~P~~V~V~i~~~~   99 (119)
T 2kq1_A           79 PGDLAVTV--EPRMARVQLEERQ   99 (119)
T ss_dssp             CTTSEEEE--SCCEEEEEEESCC
T ss_pred             CCCeEEEE--cCCEEEEEEEEEE
Confidence            99999543  6888888887543

---

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	205
d1feua_	185	b.53.1.1 (A:) Ribosomal protein TL5 (general stres	2e-29
d2zjrs1	175	b.53.1.1 (S:1-175) Ribosomal protein TL5 (general	5e-29
d1dfup_	94	b.53.1.1 (P:) Ribosomal protein L25 {Escherichia c	2e-22

>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 =  105 bits (264), Expect = 2e-29
 Identities = 45/184 (24%), Positives = 92/184 (50%), Gaps = 10/184 (5%)

Query: 2   KIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILN 61
           ++ A+ R+ +  S    LR+ GK+PG++Y  + +  K+ ++        ++ + H  I+ 
Sbjct: 4   RLKAYYREGEKPS---ALRRAGKLPGLMYNRHLN-RKVYVDLVEFDKVFRQASIHHVIVL 59

Query: 62  LEIYGKVELVLLRNFQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSC 121
               G+    L+R   L   ++   H DF    +++ + + VPL F+ +           
Sbjct: 60  ELPDGQSLPTLVRQVNLDKRRRRPEHVDFFV-LSDEPVEMYVPLRFVGTPA---GVRAGG 115

Query: 122 IISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIAT 181
           ++  +  D+ +   P+N+P+FIE+++  +E+  S+H SD+KLP GV +      + TIA 
Sbjct: 116 VLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAV--SPEETIAA 173

Query: 182 AIIP 185
            + P
Sbjct: 174 VVPP 177

>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 =  104 bits (260), Expect = 5e-29
 Identities = 29/170 (17%), Positives = 70/170 (41%), Gaps = 5/170 (2%)

Query: 16  SRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRN 75
            +       +  + Y   ++ V  +++      A ++++           G+    L++ 
Sbjct: 10  PKQKLDESMIAAVAYNK-ENNVSFALDRKAFDRAFRQQSTTGLFDITVEGGETFPALVKA 68

Query: 76  FQLHAYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCL 135
            Q+   K+  +H DF  V   + + V VP+H               I+ + +    ++  
Sbjct: 69  VQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGRSQGEVQGGLVDIVVHNL--QIVAPG 126

Query: 136 PKNLPKFIEINLEKMEVNTSIHLSDIKLPRGVSVIHSTEEDPTIATAIIP 185
           P+ +P+ + +++ KM +   I   DIKLP G ++    + + T+ + + P
Sbjct: 127 PRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLA--ADPELTVVSVLPP 174

>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 = 85.0 bits (210), Expect = 2e-22
 Identities = 34/91 (37%), Positives = 50/91 (54%)

Query: 2  KIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILN 61
           I A  RK++G   SR LR   K P IIYGG + P+ I ++H+ + +   K  F+S +L 
Sbjct: 3  TINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLT 62

Query: 62 LEIYGKVELVLLRNFQLHAYKKLVLHADFQR 92
          + + GK   V  ++ Q H YK  + H DF R
Sbjct: 63 IVVDGKEIKVKAQDVQRHPYKPKLQHIDFVR 93

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	205
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	100.0

>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-56  Score=366.51  Aligned_cols=180  Identities=25%  Similarity=0.518  Sum_probs=165.5

Q ss_pred             CEEEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEE-CCeEEEEEEEeEeec
Q psy8560           1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEI-YGKVELVLLRNFQLH   79 (205)
Q Consensus         1 ~~l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i-~G~~~~vlikevQ~~   79 (205)
                      ++|+|+.|+..|+   ++|||+|+|||||||++. +.+++++.++|.++++..++ ++++.|.+ ||+++.||+|++|+|
T Consensus         3 ~~l~a~~Re~~~~---~~LRr~G~VPaViYG~~~-~~~i~v~~~e~~k~~~~~~~-~~~i~l~~~dg~~~~vlikevQ~~   77 (185)
T d1feua_           3 YRLKAYYREGEKP---SALRRAGKLPGLMYNRHL-NRKVYVDLVEFDKVFRQASI-HHVIVLELPDGQSLPTLVRQVNLD   77 (185)
T ss_dssp             EEEECEECSSSCH---HHHHHTTEEEEEEECSSC-EEEEEEEHHHHHHHHHHHTT-TSEEEEECTTSCEEEEEEEEEEEC
T ss_pred             EEEEEEEecCCCc---hHHHhCCCceEEEECCCC-CcCEEecchHHHhHhhhhhc-cceEEEEeecchhhhheeeeeEec
Confidence            4799999997665   469999999999999875 58999999999999998876 46777888 899999999999999


Q ss_pred             ccCCceeEEEEEEeCCCCeEEEEEeEEEEecCCCcceeeCCeEEEEEecEEEEEEeCCCCCceEEEeccCCCCCCeEEEe
Q psy8560          80 AYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCLPKNLPKFIEINLEKMEVNTSIHLS  159 (205)
Q Consensus        80 pv~~~i~HvDF~~v~~~~~v~v~VPI~~~Ge~~~~gvk~~GG~l~~~~~~i~V~~~p~~IPe~I~vDvs~L~iGd~i~v~  159 (205)
                      |++++++|+|||+++ +++|+++|||+|+|+  |+|+| .||+|++.+++|+|+|+|++||++|+||||+|++||+||++
T Consensus        78 pv~~~i~HvDF~~v~-~~~v~v~VPv~~~G~--~~gvk-~GG~l~~~~~~i~v~~~p~~IPe~i~VDvs~L~igd~i~v~  153 (185)
T d1feua_          78 KRRRRPEHVDFFVLS-DEPVEMYVPLRFVGT--PAGVR-AGGVLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHAS  153 (185)
T ss_dssp             SSSSCEEEEEEEECC-SSCEEEEEEEEEESC--CHHHH-TTCEEEECCSEEEEEECGGGCCSCEEEECTTCCTTEEEEGG
T ss_pred             ccccceeEEEEeecc-CceEEEEeceEEeec--ccccc-cccEEEEEEeeeEEEeeccCCCeEEEEEcccCCCCCeEEEE
Confidence            999999999999986 999999999999995  79999 89999999999999999999999999999999999999999


Q ss_pred             ccCCCCCeEEeccCCCCceEEEEECccccccC
Q psy8560         160 DIKLPRGVSVIHSTEEDPTIATAIIPVNTLES  191 (205)
Q Consensus       160 Dl~lp~gv~~~~~~d~~~vV~sv~~~~~~~~~  191 (205)
                      ||++|+|+++..  +++++||+|.+|+.+++.
T Consensus       154 Dl~lp~gv~~~~--d~~~~vv~v~~p~~~ee~  183 (185)
T d1feua_         154 DLKLPPGVELAV--SPEETIAAVVPPEDVEKL  183 (185)
T ss_dssp             GSCCCTTCEESS--CTTCEEEEEECSSSSSCC
T ss_pred             eecCCCCcEEcc--CCCCeEEEEeCCCccccc
Confidence            999999999774  899999999999975443

>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=2.2e-55  Score=358.67  Aligned_cols=173  Identities=20%  Similarity=0.420  Sum_probs=161.4

Q ss_pred             CEEEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECC-eEEEEEEEeEeec
Q psy8560           1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYG-KVELVLLRNFQLH   79 (205)
Q Consensus         1 ~~l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G-~~~~vlikevQ~~   79 (205)
                      |+|+|++|+      +|++|++|+||||+||++ +++++++++++|.++++..+ .+++|+|+++| ++++||+|++|+|
T Consensus         1 ~~l~a~~r~------~k~~R~~G~VPaViYG~~-~~~~i~v~~~~l~k~l~~~~-~~~li~l~i~g~~~~~vlikevQ~~   72 (175)
T d2zjrs1           1 MELTAKPRT------PKQKLDESMIAAVAYNKE-NNVSFALDRKAFDRAFRQQS-TTGLFDITVEGGETFPALVKAVQMD   72 (175)
T ss_dssp             CCCCBCCSC------CHHHHSSSCCCEEEESSS-CCCCCBCCHHHHHHHHHHHT-TSCCCBCCCTTCCCCBCCEEEEEEC
T ss_pred             CeeEeccch------HHHHhhCCCCCEEEECCC-CCEEEEEcHHHHHHHHHhcC-cceEEEEEecCCceEEEEehhhhhh
Confidence            467777774      689999999999999976 89999999999999999776 57899999987 6789999999999


Q ss_pred             ccCCceeEEEEEEeCCCCeEEEEEeEEEEecCCCcceeeCCeEEEEEecEEEEEEe-CCCCCceEEEeccCCCCCCeEEE
Q psy8560          80 AYKKLVLHADFQRVDTEKKIHVKVPLHFINSEISPAVKLNSCIISNVISDLYISCL-PKNLPKFIEINLEKMEVNTSIHL  158 (205)
Q Consensus        80 pv~~~i~HvDF~~v~~~~~v~v~VPI~~~Ge~~~~gvk~~GG~l~~~~~~i~V~~~-p~~IPe~I~vDvs~L~iGd~i~v  158 (205)
                      |++++++|+|||+++++++|+++|||+|+|+  |+|+| .||+|++.+++|++.|. |++||++|++|||+|++||+||+
T Consensus        73 pv~~~i~HvDF~~v~~~~~i~v~VPi~~~G~--~~gvk-~Gg~l~~~~~~i~v~~~~P~~IP~~i~vDvs~L~iGd~i~v  149 (175)
T d2zjrs1          73 KRKRAPIHVDFYMVTYGEPVEVSVPVHTTGR--SQGEV-QGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITA  149 (175)
T ss_dssp             SSSCCEEEEEEECCCSSCCCEEEEECEEESC--CTTTT-TTSEEECSCSEEEEECCCTTCCCSCCEEECTTCCSSCEEET
T ss_pred             hccCceeEEEEEecCCCcEEEEEEEEEeecc--ccccc-ccceeeeeehhhhhhccChhhCCceEEecchhccCCCeEEE
Confidence            9999999999999999999999999999996  68999 89999999999999995 99999999999999999999999


Q ss_pred             eccCCCCCeEEeccCCCCceEEEEECcc
Q psy8560         159 SDIKLPRGVSVIHSTEEDPTIATAIIPV  186 (205)
Q Consensus       159 ~Dl~lp~gv~~~~~~d~~~vV~sv~~~~  186 (205)
                      +||++|+|+++..  |+|.+||+|.+||
T Consensus       150 ~Dl~lp~gv~~~~--d~~~~v~~V~~pr  175 (175)
T d2zjrs1         150 GDIKLPEGCTLAA--DPELTVVSVLPPR  175 (175)
T ss_dssp             TTSCCSTTCCCCS--CTTCEEEEEECCC
T ss_pred             EeecCCCCcEEcc--CCCcEEEEEeCCC
Confidence            9999999999763  8999999999986

>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=100.00  E-value=1.5e-33  Score=207.84  Aligned_cols=92  Identities=37%  Similarity=0.580  Sum_probs=89.0

Q ss_pred             CEEEEEEeCCCCchHHHHHHHcCCeeEEEecCCCCceEEEEeHHHHHHHhhcCCcceEEEEEEECCeEEEEEEEeEeecc
Q psy8560           1 MKIIAFERKKKGTSFSRNLRKIGKVPGIIYGGNKDPVKISMNHNMIYHALKKETFHSSILNLEIYGKVELVLLRNFQLHA   80 (205)
Q Consensus         1 ~~l~a~~R~~~Gk~~ar~LRr~G~IPaViYG~~~e~~~i~v~~~e~~k~~~~~~~~~~vi~L~i~G~~~~vlikevQ~~p   80 (205)
                      ++|+|++|+.+||+++|+||++|+|||||||++.+|++++++.++|.+++++.++.+.+++|+++|+++.|++||+|+||
T Consensus         2 ~~L~a~~R~~~Gk~~~r~lRr~G~vPaViYG~~~~~~~i~v~~~~l~~~l~~~~~~~~~i~l~~~g~~~~vlikevQ~~p   81 (94)
T d1dfup_           2 FTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRHP   81 (94)
T ss_dssp             CEEECEECSCCSHHHHHHHHHTTEEEEEEECSSSCCEEEEEEHHHHHHHTTSGGGGTSCBEEEETTEECCEEEEEEEECS
T ss_pred             eEEEEEEeccCCcHHHHHHHHcCCccEEEECCCCCCcEEEecHHHHhhhhcccccccceEEEEECCeEEEeeheeeeecC
Confidence            58999999999999999999999999999999999999999999999999987777889999999999999999999999


Q ss_pred             cCCceeEEEEEE
Q psy8560          81 YKKLVLHADFQR   92 (205)
Q Consensus        81 v~~~i~HvDF~~   92 (205)
                      ++++++|||||+
T Consensus        82 v~~~i~HvDF~r   93 (94)
T d1dfup_          82 YKPKLQHIDFVR   93 (94)
T ss_dssp             SSSCEEEEEEEE
T ss_pred             CCCCEEEEeeec
Confidence            999999999998