Citrus Sinensis ID: 030809

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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-
Protein Sequence
MTMSLSIASTTTITFPTEPFSKIPKSTFNGVQIRQSWPIRTPLRFATSSSGSRGSSAVVMMAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQEEEAAAEAEKSA
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccHHcHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccEEEEEccccEEcccccccccccccccccEEEcccccccccccHccccccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MTMSLSIastttitfptepfskipkstfngvqirqswpirtplrfatsssgsrgsSAVVMMAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEEGINKRLSRKLDrqwkksivvrpppslkkLQEEEAAAEAEKSA
Flexible Loop (DISEMBL)
mtmslsiastttitfptepfskipKSTFNGVQIRQSWPIRTPlrfatsssgsrgssaVVMMAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRlqksvrnefkssefrrmRRRIarmltvkrereleeginkrlsrkldrqwkksivvrpppslkklqEEEAaaeaeksa
Low Complexity Region (SEG)
MTMSLSIASTTTITFPTEPFSKIPKSTFNGVQIRQSWPIRTPLRFATsssgsrgssAVVMMAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFrrmrrriarmLTVKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQeeeaaaeaeKSA
Disordered region (IsUnstruct)
*************************STFNGVQIRQSWPIRTPL***************************************VVDLKGELFMLRLQ***************************************************************************
Disordered Region (DISOPRED)
***************************FNGVQIRQSWPI****************************MKEIRAKTTEEINEEVVDLKGELFMLRLQKSV********FRRMRRRIARMLTVK*************************************************
Disordered Region (DISEMBL)
*********TTTITFPTEPFSKIPKSTFNGVQIRQSWPIRTPLRF************VVMMAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEEGINKRLSRKLDRQWKKSIVVRPPPS*****************
Disordered Region (DISPRO)
*TMSLSIASTTTITFPTEPFSKIPKSTFNGVQIRQSWPIRTPLRFATS*****GSSA**********MKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQEEEA********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTMSLSIASTTTITFPTEPFSKIPKSTFNGVQIRQSWPIRTPLRFATSSSGSRGSSAVVMMAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQEEEAAAEAEKSA
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	171	2.2.26 [Sep-21-2011]
Q9FJP3	173	50S ribosomal protein L29	yes	no	0.906	0.895	0.641	4e-44
Q9SWI6	161	50S ribosomal protein L29	N/A	no	0.906	0.962	0.573	4e-39
B1WQR8	78	50S ribosomal protein L29	yes	no	0.374	0.820	0.409	8e-07
Q67JV1	70	50S ribosomal protein L29	yes	no	0.350	0.857	0.516	4e-06
B8HMR2	74	50S ribosomal protein L29	yes	no	0.315	0.729	0.370	1e-05
Q8DMM4	70	50S ribosomal protein L29	yes	no	0.339	0.828	0.362	2e-05
O46902	65	50S ribosomal protein L29	yes	no	0.298	0.784	0.450	2e-05
B2ITP7	75	50S ribosomal protein L29	yes	no	0.327	0.746	0.428	2e-05
B7K240	78	50S ribosomal protein L29	yes	no	0.356	0.782	0.393	3e-05
Q49ZG0	69	50S ribosomal protein L29	yes	no	0.362	0.898	0.467	3e-05

>sp|Q9FJP3|RK29_ARATH 50S ribosomal protein L29, chloroplastic OS=Arabidopsis thaliana GN=RPL29 PE=1 SV=1

 Score =  176 bits (447), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 102/159 (64%), Positives = 123/159 (77%), Gaps = 4/159 (2%)

Query: 3   MSLSIAS--TTTITFPTEPFSKIPKSTFNGVQIRQSWPIRTPLRFATSSSGSRGSSAVVM 60
           +SLSIA+  T  I       +    S+F+GV+I+     R P   A + S S    +VVM
Sbjct: 2   LSLSIATPGTAAIFRRGTASATSTSSSFHGVRIQHQVSARVPA--AATISSSSPKPSVVM 59

Query: 61  MAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLT 120
           M+KRE E+KEIR+KTTE++ EEVVDLKGELFMLRLQKS RNEFKSS+FRRM++++ARMLT
Sbjct: 60  MSKREAELKEIRSKTTEQLQEEVVDLKGELFMLRLQKSARNEFKSSDFRRMKKQVARMLT 119

Query: 121 VKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQ 159
           VKRERE++EGI KRLSRKLDRQWKKSIV RPPPSLKKLQ
Sbjct: 120 VKREREIKEGIKKRLSRKLDRQWKKSIVPRPPPSLKKLQ 158

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SWI6|RK29_MAIZE 50S ribosomal protein L29, chloroplastic OS=Zea mays GN=RPL29 PE=2 SV=1

 Score =  160 bits (405), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 94/164 (57%), Positives = 124/164 (75%), Gaps = 9/164 (5%)

Query: 2   TMSLSIASTTTITFPTEPFSKIPKSTFNGVQIRQSWPIRTPLRFATSSSGSRGS----SA 57
           TMSL+ AS    + P    ++ P + F  +++  +    T  RFA  +  S+ +    +A
Sbjct: 3   TMSLAAASPLA-SIPRGIAAQAPCAAFLSIRLGGA----TATRFAGLAVASQPAERRAAA 57

Query: 58  VVMMAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIAR 117
           +V MAKRE+E++EIRA TTE++ EEVVDLKGELF+LRL++S R EFK+SEF RMR+RIAR
Sbjct: 58  MVAMAKREQELEEIRAMTTEQMEEEVVDLKGELFLLRLKRSARQEFKNSEFSRMRKRIAR 117

Query: 118 MLTVKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQEE 161
           MLTVKRERE+E+GINKRLSRKLDR+WK+SIVVRPPPSL+  +EE
Sbjct: 118 MLTVKREREIEQGINKRLSRKLDRKWKQSIVVRPPPSLRGNKEE 161

Zea mays (taxid: 4577)

>sp|B1WQR8|RL29_CYAA5 50S ribosomal protein L29 OS=Cyanothece sp. (strain ATCC 51142) GN=rpmC PE=3 SV=1

 Score = 53.1 bits (126), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 45/66 (68%), Gaps = 2/66 (3%)

Query: 68  MKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKREREL 127
           ++E+R  + EE+ EE++  K ELF LR Q++ R    + EF+  R R+A++LT++RER+L
Sbjct: 6   IEEVRQLSDEELAEEIIATKRELFDLRFQQATRQLENTHEFKHTRHRMAQLLTIERERQL 65

Query: 128 EEGINK 133
              IN+
Sbjct: 66  --NINQ 69

Cyanothece sp. (strain ATCC 51142) (taxid: 43989)

>sp|Q67JV1|RL29_SYMTH 50S ribosomal protein L29 OS=Symbiobacterium thermophilum (strain T / IAM 14863) GN=rpmC PE=3 SV=1

 Score = 50.8 bits (120), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 40/60 (66%)

Query: 68  MKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKREREL 127
           +KEIR  +TEEI  +V +LK ELF LR Q +V N   ++  R +RR IA+  TV REREL
Sbjct: 3   VKEIREMSTEEIKAKVAELKEELFNLRFQLAVNNLENTARIREVRRAIAQCKTVIREREL 62

Symbiobacterium thermophilum (taxid: 2734)

>sp|B8HMR2|RL29_CYAP4 50S ribosomal protein L29 OS=Cyanothece sp. (strain PCC 7425 / ATCC 29141) GN=rpmC PE=3 SV=1

 Score = 49.3 bits (116), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 38/54 (70%)

Query: 68  MKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTV 121
           MK++   +  E+  +++DLK +LF LRLQK+ R E K  +F+ +R ++A+++T+
Sbjct: 6   MKDLLDLSDAEVETQILDLKRQLFQLRLQKATRQEVKPHQFKHLRHQLAQLMTL 59

Cyanothece sp. (strain PCC 7425 / ATCC 29141) (taxid: 395961)

>sp|Q8DMM4|RL29_THEEB 50S ribosomal protein L29 OS=Thermosynechococcus elongatus (strain BP-1) GN=rpmC PE=3 SV=1

 Score = 48.5 bits (114), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 40/58 (68%)

Query: 68  MKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRER 125
           MK++R  + +E+++ +  +K ELF LR +K+ R E K  +F+ +R  +A++LT++ ER
Sbjct: 6   MKDLRQLSDQEVSDRIAAIKKELFDLRFKKATRQEVKPHQFKHLRHELAQLLTLENER 63

Thermosynechococcus elongatus (strain BP-1) (taxid: 197221)

>sp|O46902|RK29_GUITH 50S ribosomal protein L29, chloroplastic OS=Guillardia theta GN=rpl29 PE=3 SV=1

 Score = 48.5 bits (114), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 36/51 (70%)

Query: 75  TTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRER 125
           T  +IN+ V+ LK ELF LRLQK+ R E K   F++ ++ IA++LT+K ++
Sbjct: 14  TDTDINDTVLKLKKELFELRLQKATRQEIKPHLFKQKKKLIAKLLTIKSKK 64

Guillardia theta (taxid: 55529)

>sp|B2ITP7|RL29_NOSP7 50S ribosomal protein L29 OS=Nostoc punctiforme (strain ATCC 29133 / PCC 73102) GN=rpmC PE=3 SV=1

 Score = 48.5 bits (114), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 40/56 (71%)

Query: 70  EIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRER 125
           E R  + E++++E+V +K +LF LRLQK+ R   K  +FR+ R R+A++LT++ ER
Sbjct: 8   EARELSDEKLSDEIVAIKRQLFQLRLQKATRQLEKPHQFRQARHRLAQLLTLETER 63

Nostoc punctiforme (strain ATCC 29133 / PCC 73102) (taxid: 63737)

>sp|B7K240|RL29_CYAP8 50S ribosomal protein L29 OS=Cyanothece sp. (strain PCC 8801) GN=rpmC PE=3 SV=1

 Score = 48.1 bits (113), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 41/61 (67%)

Query: 68  MKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKREREL 127
           +++ R    EE+ EE++  K +LF LR QK+     K+ EF+  R R+A+++TV+RER+L
Sbjct: 6   IEDARKLNDEELVEEILAAKRQLFTLRFQKATNRLEKTHEFKHTRHRLAQLMTVERERQL 65

Query: 128 E 128
           +
Sbjct: 66  Q 66

Cyanothece sp. (strain PCC 8801) (taxid: 41431)

>sp|Q49ZG0|RL29_STAS1 50S ribosomal protein L29 OS=Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229) GN=rpmC PE=3 SV=1

 Score = 47.8 bits (112), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/62 (46%), Positives = 40/62 (64%)

Query: 69  KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELE 128
           KEIR  TT EI E++   K ELF LR Q +     +++  R +R+ IAR+ TV RERE+E
Sbjct: 4   KEIRDLTTSEIEEQIKSSKEELFNLRFQLATGQLEETARIRTVRKTIARLKTVAREREIE 63

Query: 129 EG 130
           +G
Sbjct: 64  QG 65

Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229) (taxid: 342451)

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	171
330318596	178	50S ribosomal protein L29 [Camellia sine	0.912	0.876	0.743	2e-55
255584185	164	50S ribosomal protein L29, chloroplast p	0.941	0.981	0.725	5e-53
359485888	161	PREDICTED: 50S ribosomal protein L29, ch	0.935	0.993	0.738	3e-51
449438829	170	PREDICTED: 50S ribosomal protein L29, ch	0.906	0.911	0.677	5e-51
224096173	119	predicted protein [Populus trichocarpa]	0.678	0.974	0.905	1e-45
351725647	161	uncharacterized protein LOC100305741 [Gl	0.783	0.832	0.675	9e-45
297794125	172	hypothetical protein ARALYDRAFT_919853 [	0.754	0.75	0.727	4e-44
346473183	155	hypothetical protein [Amblyomma maculatu	0.725	0.8	0.694	5e-43
15238369	173	50S ribosomal protein L29 [Arabidopsis t	0.906	0.895	0.641	2e-42
388519129	165	unknown [Lotus japonicus]	0.801	0.830	0.637	5e-42

>gi|330318596|gb|AEC10965.1| 50S ribosomal protein L29 [Camellia sinensis]

 Score =  220 bits (560), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 119/160 (74%), Positives = 133/160 (83%), Gaps = 4/160 (2%)

Query: 3   MSLSIASTTTITFPTEP-FSKIPKSTFNGVQIRQSWPIRTPL--RFATSSSGSRGSSAVV 59
           +SLSIAS +++T P +P  S   KSTF+G++I    P RT L  R+  + S     S VV
Sbjct: 2   LSLSIASPSSVTLPPKPILSASSKSTFHGIRISHLCPARTALCARYVRNPSFF-FFSLVV 60

Query: 60  MMAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARML 119
           MMAKREEE+KEIR KTTEEINEE+VDLKGELFMLRLQKS RNEFKSSEFRRMR+RIARML
Sbjct: 61  MMAKREEELKEIRTKTTEEINEEIVDLKGELFMLRLQKSARNEFKSSEFRRMRKRIARML 120

Query: 120 TVKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQ 159
           TVKRERE+EEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQ
Sbjct: 121 TVKREREIEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQ 160

Source: Camellia sinensis

Species: Camellia sinensis

Genus: Camellia

Family: Theaceae

Order: Ericales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255584185|ref|XP_002532831.1| 50S ribosomal protein L29, chloroplast precursor, putative [Ricinus communis] gi|223527398|gb|EEF29538.1| 50S ribosomal protein L29, chloroplast precursor, putative [Ricinus communis]

 Score =  212 bits (539), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 124/171 (72%), Positives = 141/171 (82%), Gaps = 10/171 (5%)

Query: 3   MSLSIASTTTITFPTEPFSKIPKSTFNGVQIRQ--SWPIRTPLRFATSSSGSRGSSAVVM 60
           +SLSI S     F  +P S +PKS+F+G+QIR   S P+R P++   S SG      V+ 
Sbjct: 2   LSLSITS-----FSPKPLSPVPKSSFSGIQIRHTCSIPMRVPVKTTWSFSGK---PLVIT 53

Query: 61  MAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLT 120
           M+KR+EE+KEIR  +TE+INEEVVDLKGELFMLRLQKS RNEFKSSEFRRMR+RIARMLT
Sbjct: 54  MSKRQEELKEIREMSTEQINEEVVDLKGELFMLRLQKSARNEFKSSEFRRMRKRIARMLT 113

Query: 121 VKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQEEEAAAEAEKSA 171
           VKRERE+EEGINKRLSRK DRQWKKSIVVRPPPSLKKLQEEEAAAEAEKSA
Sbjct: 114 VKREREIEEGINKRLSRKFDRQWKKSIVVRPPPSLKKLQEEEAAAEAEKSA 164

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359485888|ref|XP_003633349.1| PREDICTED: 50S ribosomal protein L29, chloroplastic-like [Vitis vinifera]

 Score =  206 bits (524), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 124/168 (73%), Positives = 136/168 (80%), Gaps = 8/168 (4%)

Query: 3   MSLSIASTTTITFPTEPFSKIPKSTFNGVQIRQSWPIRTPLRFATSSSGSRGSSAVVMMA 62
            SLSIAS +++  P +  S  PKS+FNG        IR P     S      SS+VVMMA
Sbjct: 2   FSLSIASPSSLKIPPKTTSTFPKSSFNG--------IRIPTPNKPSFRSPSSSSSVVMMA 53

Query: 63  KREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVK 122
           KREEE+KEIRAKTTEE+NEE+VDLKGEL MLRLQKSVRNEFK SEF RMR+R+ARMLTVK
Sbjct: 54  KREEELKEIRAKTTEELNEEIVDLKGELLMLRLQKSVRNEFKPSEFGRMRKRVARMLTVK 113

Query: 123 RERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQEEEAAAEAEKS 170
           RERE+EEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQEEEAAAEAEKS
Sbjct: 114 REREIEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQEEEAAAEAEKS 161

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449438829|ref|XP_004137190.1| PREDICTED: 50S ribosomal protein L29, chloroplastic-like [Cucumis sativus] gi|449508367|ref|XP_004163294.1| PREDICTED: 50S ribosomal protein L29, chloroplastic-like [Cucumis sativus]

 Score =  205 bits (522), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 107/158 (67%), Positives = 133/158 (84%), Gaps = 3/158 (1%)

Query: 3   MSLSIAST-TTITFPTEPFSKIPKSTFNGVQIRQSWPIRTPLRFATSSSGSRGSSAVVMM 61
           ++LSIAS  +T+  P++  +   KS+FN +QIR  +  R P + AT+  G   +S+VVMM
Sbjct: 2   INLSIASLPSTLPIPSKFLNSTSKSSFNALQIRFPFSFRLPPKTATTGRGR--NSSVVMM 59

Query: 62  AKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTV 121
           AKRE+E+K+IR+KTTEEINEEV+DLKGEL MLRLQKS RNEFKSSEFRRMR+RI+RMLTV
Sbjct: 60  AKREDELKDIRSKTTEEINEEVIDLKGELLMLRLQKSARNEFKSSEFRRMRKRISRMLTV 119

Query: 122 KRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQ 159
           +RERE+EEG+ KRLSRKLDR+WKKSIVVRPPPSLKKL+
Sbjct: 120 RREREIEEGVGKRLSRKLDRKWKKSIVVRPPPSLKKLR 157

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224096173|ref|XP_002310561.1| predicted protein [Populus trichocarpa] gi|222853464|gb|EEE91011.1| predicted protein [Populus trichocarpa]

 Score =  187 bits (475), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 105/116 (90%), Positives = 112/116 (96%)

Query: 56  SAVVMMAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRI 115
           S+VVMMAK+EEE+KEIRAKTTEEINEEVVDLKGEL MLRLQKS RNEFKSSEFRRMR+RI
Sbjct: 4   SSVVMMAKKEEELKEIRAKTTEEINEEVVDLKGELLMLRLQKSTRNEFKSSEFRRMRKRI 63

Query: 116 ARMLTVKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQEEEAAAEAEKSA 171
           ARMLTVKRERE+ EG+ KRLSRKLDRQWK+SIVVRPPPSLKKLQEEEAAAEAEKSA
Sbjct: 64  ARMLTVKREREIVEGVGKRLSRKLDRQWKRSIVVRPPPSLKKLQEEEAAAEAEKSA 119

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725647|ref|NP_001236076.1| uncharacterized protein LOC100305741 [Glycine max] gi|255626497|gb|ACU13593.1| unknown [Glycine max]

 Score =  184 bits (468), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 100/148 (67%), Positives = 114/148 (77%), Gaps = 14/148 (9%)

Query: 12  TITFPTEPFSKIPKSTFNGVQIRQSWPIRTPLRFATSSSGSRGSSAVVMMAKREEEMKEI 71
           TI+F  +PF        NG+Q+R+S     P       +    S  VVMM+KR EE+KEI
Sbjct: 13  TISFLPKPF--------NGIQLRRSATCSIP------PTKCSASVPVVMMSKRTEELKEI 58

Query: 72  RAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEEGI 131
           R  TTE+INEEVVDLKGEL MLRLQKS RNEFKSSEF RMR+RIARMLTVKRERE+EEGI
Sbjct: 59  RQMTTEQINEEVVDLKGELVMLRLQKSARNEFKSSEFGRMRKRIARMLTVKREREIEEGI 118

Query: 132 NKRLSRKLDRQWKKSIVVRPPPSLKKLQ 159
           NKRLSRKLD++WKKSIVVRPPPSLKKL+
Sbjct: 119 NKRLSRKLDKKWKKSIVVRPPPSLKKLR 146

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297794125|ref|XP_002864947.1| hypothetical protein ARALYDRAFT_919853 [Arabidopsis lyrata subsp. lyrata] gi|297310782|gb|EFH41206.1| hypothetical protein ARALYDRAFT_919853 [Arabidopsis lyrata subsp. lyrata]

 Score =  182 bits (462), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 96/132 (72%), Positives = 112/132 (84%), Gaps = 3/132 (2%)

Query: 28  FNGVQIRQSWPIRTPLRFATSSSGSRGSSAVVMMAKREEEMKEIRAKTTEEINEEVVDLK 87
           F+GV+I+     R P   A + S SR  S VVMM+KRE E+KEIR+KTTE++ EEVVDLK
Sbjct: 29  FHGVRIQPQVSARVPA--AATISSSRKPS-VVMMSKREAELKEIRSKTTEQLQEEVVDLK 85

Query: 88  GELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEEGINKRLSRKLDRQWKKSI 147
           GELFMLRLQKS RNEFKSS+FRRM++++ARMLTVKRERE++EGI KRLSRKLDRQWKKSI
Sbjct: 86  GELFMLRLQKSARNEFKSSDFRRMKKQVARMLTVKREREIKEGIKKRLSRKLDRQWKKSI 145

Query: 148 VVRPPPSLKKLQ 159
           V RPPPSLKKLQ
Sbjct: 146 VPRPPPSLKKLQ 157

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|346473183|gb|AEO36436.1| hypothetical protein [Amblyomma maculatum]

 Score =  179 bits (453), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 91/131 (69%), Positives = 109/131 (83%), Gaps = 7/131 (5%)

Query: 26  STFNGVQIRQSWPIRTPLRFATSSSGSRGSSAVVMMAKREEEMKEIRAKTTEEINEEVVD 85
           S+FNG++IR +         +   S     +  + MAKREEE+K+IRAKTTEEINEE+VD
Sbjct: 15  SSFNGLRIRTAA-------ISIKPSPLFSPTKTIKMAKREEELKDIRAKTTEEINEEIVD 67

Query: 86  LKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEEGINKRLSRKLDRQWKK 145
           LKGELFMLRLQ+S RNEFKSSEFRRMR+R+ARMLTV+RERELEEGINKRLSRKLD++WK+
Sbjct: 68  LKGELFMLRLQRSARNEFKSSEFRRMRKRVARMLTVRRERELEEGINKRLSRKLDKKWKR 127

Query: 146 SIVVRPPPSLK 156
           SIVVRPPPSL+
Sbjct: 128 SIVVRPPPSLR 138

Source: Amblyomma maculatum

Species: Amblyomma maculatum

Genus: Amblyomma

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|15238369|ref|NP_201325.1| 50S ribosomal protein L29 [Arabidopsis thaliana] gi|46397023|sp|Q9FJP3.1|RK29_ARATH RecName: Full=50S ribosomal protein L29, chloroplastic; AltName: Full=CL29; Flags: Precursor gi|189096148|pdb|3BBO|Z Chain Z, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome gi|10178184|dbj|BAB11658.1| 50S ribosomal protein L29 [Arabidopsis thaliana] gi|15028327|gb|AAK76640.1| putative 50S ribosomal protein L29 [Arabidopsis thaliana] gi|19310703|gb|AAL85082.1| putative 50S ribosomal protein L29 [Arabidopsis thaliana] gi|21553790|gb|AAM62883.1| 50S ribosomal protein L29 [Arabidopsis thaliana] gi|222424203|dbj|BAH20060.1| AT5G65220 [Arabidopsis thaliana] gi|332010642|gb|AED98025.1| 50S ribosomal protein L29 [Arabidopsis thaliana]

 Score =  176 bits (447), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 102/159 (64%), Positives = 123/159 (77%), Gaps = 4/159 (2%)

Query: 3   MSLSIAS--TTTITFPTEPFSKIPKSTFNGVQIRQSWPIRTPLRFATSSSGSRGSSAVVM 60
           +SLSIA+  T  I       +    S+F+GV+I+     R P   A + S S    +VVM
Sbjct: 2   LSLSIATPGTAAIFRRGTASATSTSSSFHGVRIQHQVSARVPA--AATISSSSPKPSVVM 59

Query: 61  MAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLT 120
           M+KRE E+KEIR+KTTE++ EEVVDLKGELFMLRLQKS RNEFKSS+FRRM++++ARMLT
Sbjct: 60  MSKREAELKEIRSKTTEQLQEEVVDLKGELFMLRLQKSARNEFKSSDFRRMKKQVARMLT 119

Query: 121 VKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQ 159
           VKRERE++EGI KRLSRKLDRQWKKSIV RPPPSLKKLQ
Sbjct: 120 VKREREIKEGIKKRLSRKLDRQWKKSIVPRPPPSLKKLQ 158

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388519129|gb|AFK47626.1| unknown [Lotus japonicus]

 Score =  175 bits (444), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 95/149 (63%), Positives = 114/149 (76%), Gaps = 12/149 (8%)

Query: 12  TITFPTEPFSKIP-KSTFNGVQIRQSWPIRTPLRFATSSSGSRGSSAVVMMAKREEEMKE 70
           T++F  +P   +P KS+FNG Q+R S     P         ++ + +VVMMAKRE E+K 
Sbjct: 13  TVSFLPKP---LPFKSSFNGNQLRHSATCSIP--------AAKRTVSVVMMAKREVELKA 61

Query: 71  IRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEEG 130
           IR  TTE+I EEV+DLKGELFMLRLQKS RNEFK S+F  MR+RIARMLTVKRERE+E G
Sbjct: 62  IREMTTEQIEEEVIDLKGELFMLRLQKSARNEFKPSDFGTMRKRIARMLTVKREREIEAG 121

Query: 131 INKRLSRKLDRQWKKSIVVRPPPSLKKLQ 159
           I KRLSRKLD++WK+SIVVRPPPSLKKLQ
Sbjct: 122 IGKRLSRKLDKKWKRSIVVRPPPSLKKLQ 150

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	171
TAIR|locus:2171835	173	AT5G65220 [Arabidopsis thalian	0.976	0.965	0.561	1.8e-39

TAIR|locus:2171835 AT5G65220 [Arabidopsis thaliana (taxid:3702)]

 Score = 421 (153.3 bits), Expect = 1.8e-39, P = 1.8e-39
 Identities = 96/171 (56%), Positives = 113/171 (66%)

Query:     3 MSLSIAST-TTITFPTEPFSKIP-KSTFNGVQIRQSWPIRTPLRFATXXXXXXXXXAVVM 60
             +SLSIA+  T   F     S     S+F+GV+I+     R P   A          +VVM
Sbjct:     2 LSLSIATPGTAAIFRRGTASATSTSSSFHGVRIQHQVSARVPA--AATISSSSPKPSVVM 59

Query:    61 MAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFXXXXXXXXXXLT 120
             M+KRE E+KEIR+KTTE++ EEVVDLKGELFMLRLQKS RNEFKSS+F          LT
Sbjct:    60 MSKREAELKEIRSKTTEQLQEEVVDLKGELFMLRLQKSARNEFKSSDFRRMKKQVARMLT 119

Query:   121 VKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQXXXXXXXXXKSA 171
             VKRERE++EGI KRLSRKLDRQWKKSIV RPPPSLKKLQ         ++A
Sbjct:   120 VKREREIKEGIKKRLSRKLDRQWKKSIVPRPPPSLKKLQEEEAAEEAAEAA 170


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.315   0.128   0.348    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      171       143   0.00091  102 3  10 22  0.46    31
                                                     30  0.48    33


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  579 (62 KB)
  Total size of DFA:  160 KB (2096 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  21.82u 0.08s 21.90t   Elapsed:  00:00:02
  Total cpu time:  21.82u 0.08s 21.90t   Elapsed:  00:00:02
  Start:  Thu May  9 22:33:50 2013   End:  Thu May  9 22:33:52 2013

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

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009295 "nucleoid" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0006354 "DNA-dependent transcription, elongation" evidence=RCA

GO:0042793 "transcription from plastid promoter" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

---

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)
Q9SWI6	RK29_MAIZE	No assigned EC number	0.5731	0.9064	0.9627	N/A	no
Q9FJP3	RK29_ARATH	No assigned EC number	0.6415	0.9064	0.8959	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	171
pfam00831	58	pfam00831, Ribosomal_L29, Ribosomal L29 protein	4e-16
cd00427	57	cd00427, Ribosomal_L29_HIP, Ribosomal L29 protein/	2e-15
PRK00306	66	PRK00306, PRK00306, 50S ribosomal protein L29; Rev	9e-15
COG0255	69	COG0255, RpmC, Ribosomal protein L29 [Translation,	3e-13
TIGR00012	55	TIGR00012, L29, ribosomal protein L29	8e-12
PRK00461	87	PRK00461, rpmC, 50S ribosomal protein L29; Reviewe	3e-11
CHL00154	67	CHL00154, rpl29, ribosomal protein L29; Validated	2e-09
PRK14549	69	PRK14549, PRK14549, 50S ribosomal protein L29P; Pr	2e-04

>gnl|CDD|201463 pfam00831, Ribosomal_L29, Ribosomal L29 protein

 Score = 68.3 bits (168), Expect = 4e-16
 Identities = 26/58 (44%), Positives = 36/58 (62%)

Query: 68  MKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRER 125
            KE+R  + EE+ E++ +LK ELF LR QK+          + +RR IAR+LTV RER
Sbjct: 1   AKELRELSDEELKEKLKELKKELFNLRFQKATGQLENPHRIKEVRRDIARILTVLRER 58

Length = 58

>gnl|CDD|238243 cd00427, Ribosomal_L29_HIP, Ribosomal L29 protein/HIP

 Score = 66.7 bits (164), Expect = 2e-15
 Identities = 24/57 (42%), Positives = 36/57 (63%)

Query: 69  KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRER 125
           KE+R K+ EE+ E++ +LK ELF LR QK+          R++R+ IAR+ TV  E+
Sbjct: 1   KELREKSDEELQEKLDELKKELFNLRFQKATGQLENPHRIRKVRKDIARIKTVLNEK 57

L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it participates in forming a protein ring that surrounds the polypeptide exit channel, providing structural support for the ribosome. L29 is involved in forming the translocon binding site, along with L19, L22, L23, L24, and L31e. In addition, L29 and L23 form the interaction site for trigger factor (TF) on the ribosomal surface, adjacent to the exit tunnel. L29 forms numerous interactions with L23 and with the 23S rRNA. In some eukaryotes, L29 is referred to as L35, which is distinct from L35 found in bacteria and some eukaryotes (primarily plastids and mitochondria). The mammalian homolog, HIP, is found on the surface of many tissues and cell lines. It is believed to play a role in cell adhesion and modulation of blood coagulation. It has also been shown to inhibit apoptosis in cancer cells. Length = 57

>gnl|CDD|178971 PRK00306, PRK00306, 50S ribosomal protein L29; Reviewed

 Score = 64.9 bits (159), Expect = 9e-15
 Identities = 29/62 (46%), Positives = 40/62 (64%)

Query: 69  KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELE 128
           KE+R  + EE+NE++++LK ELF LR QK+      +   R +RR IAR+ TV REREL 
Sbjct: 4   KELRELSVEELNEKLLELKKELFNLRFQKATGQLENTHRLREVRRDIARIKTVLRERELG 63

Query: 129 EG 130
             
Sbjct: 64  AA 65

Length = 66

>gnl|CDD|223333 COG0255, RpmC, Ribosomal protein L29 [Translation, ribosomal structure and biogenesis]

 Score = 61.2 bits (149), Expect = 3e-13
 Identities = 34/70 (48%), Positives = 43/70 (61%), Gaps = 4/70 (5%)

Query: 60  MMAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARML 119
           M AKR    KE+R K+ EE+ EE+ +LK ELF LR Q +          R +RR IAR+L
Sbjct: 1   MKAKR----KELREKSVEELEEELRELKKELFNLRFQLATGQLENPHRIREVRRDIARIL 56

Query: 120 TVKRERELEE 129
           TV RE+ELE 
Sbjct: 57  TVLREKELEA 66

Length = 69

>gnl|CDD|129124 TIGR00012, L29, ribosomal protein L29

 Score = 56.9 bits (138), Expect = 8e-12
 Identities = 26/55 (47%), Positives = 37/55 (67%)

Query: 70  EIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRE 124
           E+R K+ EE+ +++ +LK ELF LR QK+     K    R++RR IAR+LTV RE
Sbjct: 1   ELREKSKEELAKKLDELKKELFELRFQKATGQLAKPHRIRQVRRDIARLLTVLRE 55

This model describes a ribosomal large subunit protein, called L29 in prokaryotic (50S) large subunits and L35 in eukaryotic (60S) large subunits [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 55

>gnl|CDD|234773 PRK00461, rpmC, 50S ribosomal protein L29; Reviewed

 Score = 56.3 bits (136), Expect = 3e-11
 Identities = 29/82 (35%), Positives = 50/82 (60%)

Query: 67  EMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERE 126
             KE+R K+ EE+ + V++LK ELF LR + +  +  ++ + + +R+ IAR+LT+  ERE
Sbjct: 1   LFKELRKKSVEELEKLVIELKAELFTLRFKNATGSLDQTHKIKEIRKDIARILTILNERE 60

Query: 127 LEEGINKRLSRKLDRQWKKSIV 148
           LEE  N +  +K  ++  K   
Sbjct: 61  LEEKENNKEPKKNTKKAVKLAS 82

Length = 87

>gnl|CDD|177071 CHL00154, rpl29, ribosomal protein L29; Validated

 Score = 50.9 bits (122), Expect = 2e-09
 Identities = 23/57 (40%), Positives = 35/57 (61%)

Query: 69  KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRER 125
            +I   T  EI+EE++  K ELF LRL+K+ R  FK   F+  + R+A++LT+   R
Sbjct: 7   TDIIDLTDSEISEEIIKTKKELFDLRLKKATRQNFKPHLFKHKKHRLAQLLTLLSSR 63

Length = 67

>gnl|CDD|237751 PRK14549, PRK14549, 50S ribosomal protein L29P; Provisional

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 23/62 (37%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 69  KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKS-SEFRRMRRRIARMLTVKREREL 127
            EIR  + EE  E++ +LK EL   R Q ++    ++    R +RR IAR+LT++RE++ 
Sbjct: 7   SEIREMSPEEREEKLEELKLELLKERAQAAMGGAPENPGRIREIRRTIARILTIQREKKR 66

Query: 128 EE 129
           E 
Sbjct: 67  EA 68

Length = 69

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	171
CHL00154	67	rpl29 ribosomal protein L29; Validated	99.89
PRK14549	69	50S ribosomal protein L29P; Provisional	99.88
COG0255	69	RpmC Ribosomal protein L29 [Translation, ribosomal	99.87
PRK00461	87	rpmC 50S ribosomal protein L29; Reviewed	99.86
PRK00306	66	50S ribosomal protein L29; Reviewed	99.86
PF00831	58	Ribosomal_L29: Ribosomal L29 protein; InterPro: IP	99.85
cd00427	57	Ribosomal_L29_HIP Ribosomal L29 protein/HIP. L29 i	99.82
TIGR00012	55	L29 ribosomal protein L29. called L29 in prokaryot	99.81
KOG3436	123	consensus 60S ribosomal protein L35 [Translation,	99.76
PF06984	87	MRP-L47: Mitochondrial 39-S ribosomal protein L47	96.35
KOG3331	213	consensus Mitochondrial/chloroplast ribosomal prot	94.48

>CHL00154 rpl29 ribosomal protein L29; Validated

Probab=99.89  E-value=6.8e-23  Score=145.26  Aligned_cols=62  Identities=37%  Similarity=0.579  Sum_probs=60.5

Q ss_pred             cChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHHHH
Q 030809           66 EEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKREREL  127 (171)
Q Consensus        66 mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrERel  127 (171)
                      |+++|||+||.+||.++|.++++|||+||||+++||++|||+|+.+|||||||+||++||..
T Consensus         4 mk~~elr~ls~~eL~~~l~elk~elf~LRfq~atgql~n~~~ir~~RrdIARikTil~ek~~   65 (67)
T CHL00154          4 PKITDIIDLTDSEISEEIIKTKKELFDLRLKKATRQNFKPHLFKHKKHRLAQLLTLLSSRLK   65 (67)
T ss_pred             CCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHHHHHHHHhc
Confidence            89999999999999999999999999999999999999999999999999999999999863

>PRK14549 50S ribosomal protein L29P; Provisional

Probab=99.88  E-value=1.6e-22  Score=143.60  Aligned_cols=67  Identities=37%  Similarity=0.483  Sum_probs=63.6

Q ss_pred             ccCCccChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhcc-CCCchhHHHHhHHHHHHHHHHHHHHHHh
Q 030809           61 MAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRN-EFKSSEFRRMRRRIARMLTVKRERELEE  129 (171)
Q Consensus        61 MsKr~mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgq-leNp~~IR~iRKdIARIlTVLrERel~e  129 (171)
                      |+.  |+++||++||.+||.++|.++++|||+||||+++|+ ++|||+|+.+||+||||+||++|++.++
T Consensus         1 M~~--mk~~elr~ls~~eL~~~l~elk~eLf~LR~q~~~~~~l~n~~~ir~~Rk~IARi~Tvl~ek~~~~   68 (69)
T PRK14549          1 MAI--LRASEIREMSPEEREEKLEELKLELLKERAQAAMGGAPENPGRIREIRRTIARILTIQREKKREA   68 (69)
T ss_pred             CCc--CcHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhCcCccccHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            554  999999999999999999999999999999999999 9999999999999999999999998653

>COG0255 RpmC Ribosomal protein L29 [Translation, ribosomal structure and biogenesis]

Probab=99.87  E-value=3.2e-22  Score=143.02  Aligned_cols=62  Identities=48%  Similarity=0.677  Sum_probs=59.6

Q ss_pred             HHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHHHHHhh
Q 030809           69 KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEEG  130 (171)
Q Consensus        69 kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrERel~e~  130 (171)
                      +|||+||.+||.++|.+|++|||+||||.++||++|||+|+.+|||||||+||++|+++...
T Consensus         6 ~elR~~s~eeL~~~l~eLK~ELf~LR~q~a~g~l~n~~~ir~vRr~IARi~Tv~~E~~~~~~   67 (69)
T COG0255           6 KELREKSVEELEEELRELKKELFNLRFQLATGQLENPHRIREVRRDIARILTVLREKELEAA   67 (69)
T ss_pred             HHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            69999999999999999999999999999999999999999999999999999999987543

>PRK00461 rpmC 50S ribosomal protein L29; Reviewed

Probab=99.86  E-value=1.1e-21  Score=145.53  Aligned_cols=75  Identities=37%  Similarity=0.593  Sum_probs=69.1

Q ss_pred             ChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHHHHHhhhhhHhhhHHHH
Q 030809           67 EMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEEGINKRLSRKLDR  141 (171)
Q Consensus        67 K~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrERel~e~~nkr~sRk~~r  141 (171)
                      +++|||+||.+||.++|.++++|||+||||+++|+++|||+|+.+||+||||+||++|+++++++|+..-....+
T Consensus         1 ~~~elR~lS~eEL~e~L~elkkELf~LR~q~atgql~n~~~ir~iRR~IARilTvl~Ek~~~~~~~~~~~~~~~~   75 (87)
T PRK00461          1 LFKELRKKSVEELEKLVIELKAELFTLRFKNATGSLDQTHKIKEIRKDIARILTILNERELEEKENNKEPKKNTK   75 (87)
T ss_pred             ChHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhCcccccHHHHHHHHHHHHHHHHHHHHHHHhhhcccchHHHHH
Confidence            368999999999999999999999999999999999999999999999999999999999999999765544443

>PRK00306 50S ribosomal protein L29; Reviewed

Probab=99.86  E-value=1.5e-21  Score=136.75  Aligned_cols=64  Identities=45%  Similarity=0.634  Sum_probs=61.9

Q ss_pred             cChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHHHHHh
Q 030809           66 EEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEE  129 (171)
Q Consensus        66 mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrERel~e  129 (171)
                      |+++|||+||.+||.++|.++++|||+|||++++|+++|||.|+.+||+||||+||++||+.+.
T Consensus         1 Mk~~elr~ls~~eL~~~l~~lkkeL~~lR~~~~~~~~~n~~~i~~~rk~IARi~Tvl~er~~~~   64 (66)
T PRK00306          1 MKAKELRELSVEELNEKLLELKKELFNLRFQKATGQLENTHRLREVRRDIARIKTVLRERELGA   64 (66)
T ss_pred             CCHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCcHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            6899999999999999999999999999999999999999999999999999999999998764

>PF00831 Ribosomal_L29: Ribosomal L29 protein; InterPro: IPR001854 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.85  E-value=2.1e-21  Score=133.11  Aligned_cols=58  Identities=47%  Similarity=0.654  Sum_probs=56.7

Q ss_pred             hHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHH
Q 030809           68 MKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRER  125 (171)
Q Consensus        68 ~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrER  125 (171)
                      ++|||+||.+||.++|.++++|||+||||+++|+++|||.|+.+||+||||+|+++||
T Consensus         1 ~~elr~ls~~eL~~~l~elk~eL~~Lr~q~~~~~l~n~~~ir~~Rr~IARi~Tvl~er   58 (58)
T PF00831_consen    1 AKELRELSDEELQEKLEELKKELFNLRFQKATGQLENPHRIREIRRDIARILTVLRER   58 (58)
T ss_dssp             CHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHSSSSCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHhcC
Confidence            4799999999999999999999999999999999999999999999999999999997

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 [, ]. Ribosomal protein L29 is one of the proteins from the large ribosomal subunit. L29 belongs to a family of ribosomal proteins of 63 to 138 amino-acid residues which, on the basis of sequence similarities [], groups: Red algal L29. Bacterial L29. Mammalian L35 Caenorhabditis elegans L35 (ZK652.4). Yeast L35. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1VSP_W 3MS1_Y 3MRZ_Y 3F1H_2 3PYT_Y 3PYO_Y 3D5D_2 3D5B_2 3PYR_Y 1VSA_W ....

>cd00427 Ribosomal_L29_HIP Ribosomal L29 protein/HIP

Probab=99.82  E-value=1.7e-20  Score=128.04  Aligned_cols=57  Identities=42%  Similarity=0.619  Sum_probs=55.4

Q ss_pred             HHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHH
Q 030809           69 KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRER  125 (171)
Q Consensus        69 kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrER  125 (171)
                      +|||+||.+||.++|.++++|||+||||+++|+++|||+|+.+||+||||+||++||
T Consensus         1 ~eir~ls~~eL~~~l~~l~~elf~Lr~q~~~~~~~~~~~~~~~Rr~IARi~Til~er   57 (57)
T cd00427           1 KELREKSDEELQEKLDELKKELFNLRFQKATGQLENPHRIRKVRKDIARIKTVLNEK   57 (57)
T ss_pred             ChHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCcCcHHHHHHHHHHHHHHHHHHcC
Confidence            489999999999999999999999999999999999999999999999999999985

L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it participates in forming a protein ring that surrounds the polypeptide exit channel, providing structural support for the ribosome. L29 is involved in forming the translocon binding site, along with L19, L22, L23, L24, and L31e. In addition, L29 and L23 form the interaction site for trigger factor (TF) on the ribosomal surface, adjacent to the exit tunnel. L29 forms numerous interactions with L23 and with the 23S rRNA. In some eukaryotes, L29 is referred to as L35, which is distinct from L35 found in bacteria and some eukaryotes (primarily plastids and mitochondria). The mammalian homolog, HIP, is found on the surface of many tissues and cell lines. It is believed to play a role in cell adhesion and modulat

>TIGR00012 L29 ribosomal protein L29

Probab=99.81  E-value=3.2e-20  Score=126.23  Aligned_cols=55  Identities=47%  Similarity=0.681  Sum_probs=53.7

Q ss_pred             HHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHH
Q 030809           70 EIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRE  124 (171)
Q Consensus        70 ELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrE  124 (171)
                      |||+||.+||.++|.++++|||+||||+++|+++|||+|+.+||+||||+||++|
T Consensus         1 elr~~s~~EL~~~l~~lr~eLf~Lr~~~~~~~~~~~~~i~~~Rk~IARi~Tvl~e   55 (55)
T TIGR00012         1 ELREKSKEELAKKLDELKKELFELRFQKATGQLAKPHRIRQVRRDIARLLTVLRE   55 (55)
T ss_pred             CHhhCCHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHHHHHhC
Confidence            6899999999999999999999999999999999999999999999999999985

called L29 in prokaryotic (50S) large subunits and L35 in eukaryotic (60S) large subunits.

>KOG3436 consensus 60S ribosomal protein L35 [Translation, ribosomal structure and biogenesis]

Probab=99.76  E-value=3.5e-18  Score=133.54  Aligned_cols=97  Identities=35%  Similarity=0.422  Sum_probs=90.5

Q ss_pred             ccCCccChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccC-CCchhHHHHhHHHHHHHHHHHHHHHHhhhh-------
Q 030809           61 MAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNE-FKSSEFRRMRRRIARMLTVKRERELEEGIN-------  132 (171)
Q Consensus        61 MsKr~mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgql-eNp~~IR~iRKdIARIlTVLrERel~e~~n-------  132 (171)
                      |++  ++..|||+.+.+||.++|+||+.||+.||+++.+|+. ++.+.|+.+||+|||++||+||++.++.+.       
T Consensus         1 M~k--ik~~eLr~~~ke~L~~ql~dLK~ELa~LRv~K~tgg~~~klskik~vrKsiArvLTVine~~k~~lr~~yk~~k~   78 (123)
T KOG3436|consen    1 MAK--IKARELRGKSKEQLLKQLDDLKVELAQLRVAKVTGGAASKLSKIKVVRKSIARVLTVINEKQKEELREAYKGKKY   78 (123)
T ss_pred             Ccc--hhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhhccchhhhHHHHHHHHHHHHHHHHhhhhhHHHHHHHhhcccc
Confidence            565  8999999999999999999999999999999999984 689999999999999999999999999888       


Q ss_pred             --hHhhhHHHHHHhhhhccCCCCcchhchH
Q 030809          133 --KRLSRKLDRQWKKSIVVRPPPSLKKLQE  160 (171)
Q Consensus       133 --kr~sRk~~r~~K~s~~~~ppp~~~~~~~  160 (171)
                        +.+..+..|+|.+.++-. ++||+..++
T Consensus        79 ~p~dLr~KktRa~rr~ltk~-~~slkt~kq  107 (123)
T KOG3436|consen   79 LPKDLRPKKTRAIRRRLTKH-QLSLKTEKQ  107 (123)
T ss_pred             cchhhhHHHHHHHHHhcccc-chhHhHHHH
Confidence              799999999999999888 899999883

>PF06984 MRP-L47: Mitochondrial 39-S ribosomal protein L47 (MRP-L47); InterPro: IPR010729 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.35  E-value=0.011  Score=44.11  Aligned_cols=62  Identities=19%  Similarity=0.289  Sum_probs=43.9

Q ss_pred             CccChHHHhcCCHHHHHHH---HHHHHHHHHHhHHHH--hhccCCCchhHHHHhHHHHHHHHHHHHH
Q 030809           64 REEEMKEIRAKTTEEINEE---VVDLKGELFMLRLQK--SVRNEFKSSEFRRMRRRIARMLTVKRER  125 (171)
Q Consensus        64 r~mK~kELR~LS~eEL~ek---L~ELKkELf~LRfQk--atgqleNp~~IR~iRKdIARIlTVLrER  125 (171)
                      |.=.+.|||.+|.+||.+.   +..-+.-|.-.+...  ......++.++..+|+.-+||++||+||
T Consensus        21 R~Wt~~ELR~KS~eDLHkLWyv~lKERN~L~T~~~e~~r~~~~~~~~~r~~kV~~sM~~Ik~Vl~ER   87 (87)
T PF06984_consen   21 RAWTAEELRRKSFEDLHKLWYVCLKERNMLLTEEYEARRQGEGMPSPERLEKVRKSMARIKHVLTER   87 (87)
T ss_pred             CcccHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHhcC
Confidence            4678999999999999984   222233332112111  1122689999999999999999999986

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 represents the N-terminal region (approximately 8 residues) of the eukaryotic mitochondrial 39-S ribosomal protein L47 (MRP-L47). Mitochondrial ribosomal proteins (MRPs) are the counterparts of the cytoplasmic ribosomal proteins, in that they fulfil similar functions in protein biosynthesis. However, they are distinct in number, features and primary structure [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005761 mitochondrial ribosome

>KOG3331 consensus Mitochondrial/chloroplast ribosomal protein L4/L29 [Translation, ribosomal structure and biogenesis]

Probab=94.48  E-value=0.23  Score=42.60  Aligned_cols=65  Identities=18%  Similarity=0.169  Sum_probs=51.7

Q ss_pred             cChHHHhcCCHHHHHHHHHHHH---HHHHHhHHH--HhhccCCCchhHHHHhHHHHHHHHHHHHHHHHhh
Q 030809           66 EEMKEIRAKTTEEINEEVVDLK---GELFMLRLQ--KSVRNEFKSSEFRRMRRRIARMLTVKRERELEEG  130 (171)
Q Consensus        66 mK~kELR~LS~eEL~ekL~ELK---kELf~LRfQ--katgqleNp~~IR~iRKdIARIlTVLrERel~e~  130 (171)
                      -.+.|||=+|..||...-=.+-   .-|+..|-.  ...++..||-+|-.+|+...||.+|++||+++.-
T Consensus        66 W~aeELR~KS~nDLH~LWYvcLkErNmL~T~~~~~k~~~~~~PnpERi~kV~~TM~~I~~Vl~ER~~Ay~  135 (213)
T KOG3331|consen   66 WSAEELRLKSFNDLHKLWYVCLKERNMLATMRHELKNIVGSFPNPERIDKVRTTMWRIEHVLNERNLAYS  135 (213)
T ss_pred             cchHHHhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5899999999999998754443   334444433  3457789999999999999999999999998764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	171
3bbo_Z	173	Homology Model For The Spinach Chloroplast 50s Subu		6e-40

>pdb|3BBO|Z Chain Z, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 173

Iteration: 1
 Score =  159 bits (403), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 94/159 (59%), Positives = 110/159 (69%), Gaps = 4/159 (2%)
Query: 3   MSLSIAS--TTTITFPTEPFSKIPKSTFNGVQIRQSWPIRTPLRFATXXXXXXXXXAVVM 60
           +SLSIA+  T  I       +    S+F+GV+I+     R P   A          +VVM
Sbjct: 2   LSLSIATPGTAAIFRRGTASATSTSSSFHGVRIQHQVSARVPA--AATISSSSPKPSVVM 59
Query: 61  MAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFXXXXXXXXXXLT 120
           M+KRE E+KEIR+KTTE++ EEVVDLKGELFMLRLQKS RNEFKSS+F          LT
Sbjct: 60  MSKREAELKEIRSKTTEQLQEEVVDLKGELFMLRLQKSARNEFKSSDFRRMKKQVARMLT 119
Query: 121 VKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQ 159
           VKRERE++EGI KRLSRKLDRQWKKSIV RPPPSLKKLQ
Sbjct: 120 VKREREIKEGIKKRLSRKLDRQWKKSIVPRPPPSLKKLQ 158

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	171
3bbo_Z	173	Ribosomal protein L29; large ribosomal subunit, sp	5e-48
1r73_A	66	TM1492, 50S ribosomal protein L29; ribosome, struc	1e-12
3v2d_2	72	50S ribosomal protein L29; ribosome associated inh	1e-12
3r8s_Y	63	50S ribosomal protein L29; protein biosynthesis, R	2e-11
2zjr_V	67	50S ribosomal protein L29; ribosome, large ribosom	1e-10
1vq8_V	71	50S ribosomal protein L29P; ribosome 50S, protein-	1e-09
3iz5_C	389	60S ribosomal protein L3 (L3P); eukaryotic ribosom	2e-08
3jyw_X	86	60S ribosomal protein L35; eukaryotic ribosome, RA	1e-06
4a17_U	124	RPL35, 60S ribosomal protein L21; eukaryotic ribos	1e-05
2zkr_v	123	60S ribosomal protein L35; protein-RNA complex, 60	2e-05
3u5e_H	191	L8, RP24, YL11, 60S ribosomal protein L9-A; transl	2e-05

>3bbo_Z Ribosomal protein L29; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 173

 Score =  153 bits (386), Expect = 5e-48
 Identities = 106/171 (61%), Positives = 132/171 (77%), Gaps = 2/171 (1%)

Query: 1   MTMSLSIASTTTITFPTEPFSKIPKSTFNGVQIRQSWPIRTPLRFATSSSGSRGSSAVVM 60
           +++S++   T  I       +    S+F+GV+I+     R P   A + S S    +VVM
Sbjct: 2   LSLSIATPGTAAIFRRGTASATSTSSSFHGVRIQHQVSARVPA--AATISSSSPKPSVVM 59

Query: 61  MAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLT 120
           M+KRE E+KEIR+KTTE++ EEVVDLKGELFMLRLQKS RNEFKSS+FRRM++++ARMLT
Sbjct: 60  MSKREAELKEIRSKTTEQLQEEVVDLKGELFMLRLQKSARNEFKSSDFRRMKKQVARMLT 119

Query: 121 VKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQEEEAAAEAEKSA 171
           VKRERE++EGI KRLSRKLDRQWKKSIV RPPPSLKKLQEEEAA EA ++A
Sbjct: 120 VKREREIKEGIKKRLSRKLDRQWKKSIVPRPPPSLKKLQEEEAAEEAAEAA 170

>1r73_A TM1492, 50S ribosomal protein L29; ribosome, structural genomics, PSI, protein structure initiative, joint center for structural genomics; NMR {Thermotoga maritima} SCOP: a.2.2.1 Length = 66

 Score = 58.8 bits (143), Expect = 1e-12
 Identities = 21/59 (35%), Positives = 33/59 (55%)

Query: 69  KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKREREL 127
            E+R  T EE+   + + K +L  LR Q ++     +S  +  +R IAR+ T+ REREL
Sbjct: 4   SELRNYTDEELKNLLEEKKRQLMELRFQLAMGQLKNTSLIKLTKRDIARIKTILREREL 62

>3v2d_2 50S ribosomal protein L29; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_W 1vsa_W 2j03_2 2jl6_2 2jl8_2 2v47_2 2v49_2 2wdi_2 2wdj_2 2wdl_2 2wdn_2 2wh2_2 2wh4_2 2wrj_2 2wrl_2 2wro_2 2wrr_2 2x9s_2 2x9u_2 2xg0_2 ... Length = 72

 Score = 59.0 bits (143), Expect = 1e-12
 Identities = 20/71 (28%), Positives = 41/71 (57%)

Query: 60  MMAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARML 119
            +++  ++++E R  +  E+ + V + K EL  LR Q S+    ++ + R ++R+IAR+L
Sbjct: 2   KLSEVRKQLEEARKLSPVELEKLVREKKRELMELRFQASIGQLSQNHKIRDLKRQIARLL 61

Query: 120 TVKRERELEEG 130
           TV  E+  +  
Sbjct: 62  TVLNEKRRQNA 72

>3r8s_Y 50S ribosomal protein L29; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_W 1p86_W 1vs8_X 1vs6_X 2aw4_X 2awb_X 1vt2_Y 2i2v_Y 2j28_X 2i2t_Y* 2qao_X* 2qba_X* 2qbc_X* 2qbe_X 2qbg_X 2qbi_X* 2qbk_X* 2qov_X 2qox_X 2qoz_X* ... Length = 63

 Score = 55.3 bits (134), Expect = 2e-11
 Identities = 21/58 (36%), Positives = 37/58 (63%)

Query: 69  KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERE 126
           KE+R K+ EE+N E+++L  E F LR+Q +     +S   +++RR +AR+ T+  E+ 
Sbjct: 4   KELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKA 61

>2zjr_V 50S ribosomal protein L29; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: a.2.2.1 PDB: 1nwx_W* 1nwy_W* 1sm1_W* 1xbp_W* 2aar_W 2d3o_W 2zjp_V* 2zjq_V 1nkw_W 3cf5_V* 3dll_V* 3pio_V* 3pip_V* 1pnu_W 1pny_W 1vor_Y 1vou_Y 1vow_Y 1voy_Y 1vp0_Y Length = 67

 Score = 53.6 bits (129), Expect = 1e-10
 Identities = 17/62 (27%), Positives = 29/62 (46%)

Query: 69  KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELE 128
            E+R     +  +E+   K EL  LR Q +     +    R++RR +A++ TVK E   +
Sbjct: 4   SEMRNLQATDFAKEIDARKKELMELRFQAAAGQLAQPHRVRQLRREVAQLNTVKAELARK 63

Query: 129 EG 130
             
Sbjct: 64  GE 65

>1vq8_V 50S ribosomal protein L29P; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: a.2.2.1 PDB: 1vq4_V* 1vq5_V* 1vq6_V* 1vq7_V* 1s72_V* 1vq9_V* 1vqk_V* 1vql_V* 1vqm_V* 1vqn_V* 1vqo_V* 1vqp_V* 1yhq_V* 1yi2_V* 1yij_V* 1yit_V* 1yj9_V* 1yjn_V* 1yjw_V* 2otj_V* ... Length = 71

 Score = 51.2 bits (123), Expect = 1e-09
 Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 69  KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEF-KSSEFRRMRRRIARMLTVKREREL 127
           +EIR  T  E   E+ DLK EL   R  ++           + +R+ IAR+ T++ E   
Sbjct: 7   QEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTIQGEEGD 66

Query: 128 EE 129
            +
Sbjct: 67  LQ 68

>3jyw_X 60S ribosomal protein L35; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} Length = 86

 Score = 43.8 bits (103), Expect = 1e-06
 Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 2/61 (3%)

Query: 69  KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELE 128
            E+R K+ E++  ++VDLK EL  L++QK  R      + + +R+ IA +LTV  E++  
Sbjct: 6   YELRTKSKEQLASQLVDLKKELAELKVQKLSRP--SLPKIKTVRKSIACVLTVINEQQAA 63

Query: 129 E 129
            
Sbjct: 64  A 64

>4a17_U RPL35, 60S ribosomal protein L21; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_U 4a1c_U 4a1e_U Length = 124

 Score = 41.8 bits (98), Expect = 1e-05
 Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 69  KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRN-EFKSSEFRRMRRRIARMLTVKREREL 127
            ++R +T E++  E+  L+ EL  LR+ K       K      +R+ IA+ LT+  E+  
Sbjct: 8   FKLRTQTEEQLVGELGKLQTELSQLRIAKIAGGTANKLGRIGIVRKAIAKYLTIINEKRR 67

Query: 128 EE 129
           + 
Sbjct: 68  QA 69

>2zkr_v 60S ribosomal protein L35; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 123

 Score = 41.1 bits (96), Expect = 2e-05
 Identities = 23/62 (37%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 69  KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEF-KSSEFRRMRRRIARMLTVKREREL 127
           +++R K  EE+ +++ DLK EL  LR+ K       K S+ R +R+ IAR+LTV  + + 
Sbjct: 7   RDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTVINQTQK 66

Query: 128 EE 129
           E 
Sbjct: 67  EN 68

>3u5e_H L8, RP24, YL11, 60S ribosomal protein L9-A; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3izc_F 1s1i_H 3izs_F* 3j16_F 3o5h_I 3o58_I 3u5i_H 3jyw_H Length = 191

 Score = 41.1 bits (96), Expect = 2e-05
 Identities = 1/61 (1%), Positives = 6/61 (9%), Gaps = 2/61 (3%)

Query: 69  KEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELE 128
           ++               +   +                            + V       
Sbjct: 7   EQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLK--HIDVTFTKVNNQLIKVAVHNGGRKH 64

Query: 129 E 129
            
Sbjct: 65  V 65

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	171
3bbo_Z	173	Ribosomal protein L29; large ribosomal subunit, sp	100.0
1vq8_V	71	50S ribosomal protein L29P; ribosome 50S, protein-	99.91
3v2d_2	72	50S ribosomal protein L29; ribosome associated inh	99.9
3j21_W	72	50S ribosomal protein L29P; archaea, archaeal, KIN	99.9
1r73_A	66	TM1492, 50S ribosomal protein L29; ribosome, struc	99.9
2zjr_V	67	50S ribosomal protein L29; ribosome, large ribosom	99.89
4a17_U	124	RPL35, 60S ribosomal protein L21; eukaryotic ribos	99.89
3iz5_c	124	60S ribosomal protein L35 (L29P); eukaryotic ribos	99.89
2zkr_v	123	60S ribosomal protein L35; protein-RNA complex, 60	99.88
3r8s_Y	63	50S ribosomal protein L29; protein biosynthesis, R	99.88
3u5e_h	120	60S ribosomal protein L35-A, 60S ribosomal protein	99.87
3jyw_X	86	60S ribosomal protein L35; eukaryotic ribosome, RA	99.84

>3bbo_Z Ribosomal protein L29; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=100.00  E-value=4.3e-56  Score=361.84  Aligned_cols=167  Identities=63%  Similarity=0.897  Sum_probs=63.8

Q ss_pred             ccccccccccccccCCCCC--CCCCCCCccccccccccccccccccccCCCCCCCCceeeeccCCccChHHHhcCCHHHH
Q 030809            2 TMSLSIASTTTITFPTEPF--SKIPKSTFNGVQIRQSWPIRTPLRFATSSSGSRGSSAVVMMAKREEEMKEIRAKTTEEI   79 (171)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~MsKr~mK~kELR~LS~eEL   79 (171)
                      ++||++|+|++.+++|+|+  ++.|+++||||||+|+  +.|++.....-....+.+.||||+|..++++|||+||.+||
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~vmMAK~~~Ka~ELR~lS~eEL   78 (173)
T 3bbo_Z            1 MLSLSIATPGTAAIFRRGTASATSTSSSFHGVRIQHQ--VSARVPAAATISSSSPKPSVVMMSKREAELKEIRSKTTEQL   78 (173)
T ss_dssp             ---------------------------------------------------------------CCSSCHHHHHHSCHHHH
T ss_pred             CcccccCCCcccccCCCccccCCCCcccceeeeecCc--ccccccccccccCCccccchhccccccCCHHHHHhCCHHHH
Confidence            5899999999999999997  4799999999999998  66667322111122479999999986689999999999999


Q ss_pred             HHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHHHHHhhhhhHhhhHHHHHHhhhhccCCCCcchhch
Q 030809           80 NEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEEGINKRLSRKLDRQWKKSIVVRPPPSLKKLQ  159 (171)
Q Consensus        80 ~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrERel~e~~nkr~sRk~~r~~K~s~~~~ppp~~~~~~  159 (171)
                      .++|.+|++|||+||||+++||++||++|+.+|||||||+||++||+++++.|+++||+++|+||++++|||||||++||
T Consensus        79 ~ekL~eLKkELFnLRfQkATGQLeNpsrIR~VRRdIARIkTVLrErel~~~~~kr~SRk~~~~~k~s~~~~ppp~~~~~~  158 (173)
T 3bbo_Z           79 QEEVVDLKGELFMLRLQKSARNEFKSSDFRRMKKQVARMLTVKREREIKEGIKKRLSRKLDRQWKKSIVPRPPPSLKKLQ  158 (173)
T ss_dssp             HHHHHHHTTHHHHHHHHHHHCCCSCHHHHHHHHHHHHHHHHHHHHSCC--------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHhhhcccccCCCchhhhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhh
Q 030809          160 EEEAAAEAEKS  170 (171)
Q Consensus       160 ~~~~~~~~~~~  170 (171)
                      |||+|+||+++
T Consensus       159 ~~~~~~~~~~~  169 (173)
T 3bbo_Z          159 EEEAAEEAAEA  169 (173)
T ss_dssp             -----------
T ss_pred             hHHHHHHHHhh
Confidence            99999999886

>1vq8_V 50S ribosomal protein L29P; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: a.2.2.1 PDB: 1vq4_V* 1vq5_V* 1vq6_V* 1vq7_V* 1s72_V* 1vq9_V* 1vqk_V* 1vql_V* 1vqm_V* 1vqn_V* 1vqo_V* 1vqp_V* 1yhq_V* 1yi2_V* 1yij_V* 1yit_V* 1yj9_V* 1yjn_V* 1yjw_V* 2otj_V* ...

Probab=99.91  E-value=1.8e-24  Score=153.46  Aligned_cols=68  Identities=28%  Similarity=0.336  Sum_probs=62.5

Q ss_pred             ccCCccChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhh-ccCCCchhHHHHhHHHHHHHHHHHHHHHHhh
Q 030809           61 MAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSV-RNEFKSSEFRRMRRRIARMLTVKRERELEEG  130 (171)
Q Consensus        61 MsKr~mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkat-gqleNp~~IR~iRKdIARIlTVLrERel~e~  130 (171)
                      |++  |+++|||+||.+||.++|.+|++|||+||||+++ |+++|||+|+.+||+||||+||++|++.++.
T Consensus         1 Ma~--mk~~elr~~s~~EL~~~l~elk~ELf~LR~q~atggql~n~~~ir~vRr~IARi~Tvl~er~~~~~   69 (71)
T 1vq8_V            1 MTV--LHVQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTIQGEEGDLQE   69 (71)
T ss_dssp             -CC--SCHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHHHHHHHHHTC---
T ss_pred             CCC--CCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCccChHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            776  9999999999999999999999999999999999 7999999999999999999999999987643

>3v2d_2 50S ribosomal protein L29; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_W 1vsa_W 2j03_2 2jl6_2 2jl8_2 2v47_2 2v49_2 2wdi_2 2wdj_2 2wdl_2 2wdn_2 2wh2_2 2wh4_2 2wrj_2 2wrl_2 2wro_2 2wrr_2 2x9s_2 2x9u_2 2xg0_2 ...

Probab=99.90  E-value=3.4e-24  Score=152.50  Aligned_cols=68  Identities=29%  Similarity=0.458  Sum_probs=64.0

Q ss_pred             ccCCccChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHHHHH
Q 030809           61 MAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELE  128 (171)
Q Consensus        61 MsKr~mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrERel~  128 (171)
                      ||...|+++|||++|.+||.++|.+|++|||+||||+++||++||++|+.+||+||||+||++|++++
T Consensus         3 ~~~~~mK~~elr~~s~eEL~~~L~elk~ELf~LR~q~atgql~n~~~ir~vRr~IARi~Tvl~er~~~   70 (72)
T 3v2d_2            3 LSEVRKQLEEARKLSPVELEKLVREKKRELMELRFQASIGQLSQNHKIRDLKRQIARLLTVLNEKRRQ   70 (72)
T ss_dssp             HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTTCCCCTTHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccccCCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHhc
Confidence            44445899999999999999999999999999999999999999999999999999999999999864

>3j21_W 50S ribosomal protein L29P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=99.90  E-value=1.7e-23  Score=148.94  Aligned_cols=65  Identities=31%  Similarity=0.364  Sum_probs=62.8

Q ss_pred             cChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhcc-CCCchhHHHHhHHHHHHHHHHHHHHHHhh
Q 030809           66 EEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRN-EFKSSEFRRMRRRIARMLTVKRERELEEG  130 (171)
Q Consensus        66 mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgq-leNp~~IR~iRKdIARIlTVLrERel~e~  130 (171)
                      |+++|||+||.+||.++|.+|++|||+||||+++|| ++|||+|+.+||+||||+||++|++++..
T Consensus         1 MK~~elr~~s~~EL~~~L~elk~ELf~LR~q~atgq~l~n~~~ir~vRr~IARi~Tvl~er~~~~~   66 (72)
T 3j21_W            1 MKPSEIREMSIEEIDAKIRELRLQLAKERGLLTMGTSLENPMVIRNLRRDIARLLTIKKEKLRERE   66 (72)
T ss_dssp             CCHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHCCSSCCSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            789999999999999999999999999999999999 99999999999999999999999998654

>1r73_A TM1492, 50S ribosomal protein L29; ribosome, structural genomics, PSI, protein structure initiative, joint center for structural genomics; NMR {Thermotoga maritima} SCOP: a.2.2.1

Probab=99.90  E-value=8.3e-24  Score=148.06  Aligned_cols=63  Identities=33%  Similarity=0.418  Sum_probs=61.0

Q ss_pred             cChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHHHHH
Q 030809           66 EEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELE  128 (171)
Q Consensus        66 mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrERel~  128 (171)
                      |+++|||+||.+||.++|.+|++|||+||||+++|+++|||+|+.+||+||||+||++|++++
T Consensus         1 MK~~elr~~s~~EL~~~l~elk~ELf~LR~q~atgql~n~~~ir~vRr~IARi~Tvl~er~~~   63 (66)
T 1r73_A            1 MKASELRNYTDEELKNLLEEKKRQLMELRFQLAMGQLKNTSLIKLTKRDIARIKTILRERELG   63 (66)
T ss_dssp             CCCSHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CChHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHccCccCcHHHHHHHHHHHHHHHHHHHHHhh
Confidence            678999999999999999999999999999999999999999999999999999999999863

>2zjr_V 50S ribosomal protein L29; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: a.2.2.1 PDB: 1nwx_W* 1nwy_W* 1sm1_W* 1xbp_W* 2aar_W 2d3o_W 2zjp_V* 2zjq_V 1nkw_W 3cf5_V* 3dll_V* 3pio_V* 3pip_V* 1pnu_W 1pny_W 1vor_Y 1vou_Y 1vow_Y 1voy_Y 1vp0_Y

Probab=99.89  E-value=6.6e-24  Score=148.95  Aligned_cols=64  Identities=27%  Similarity=0.344  Sum_probs=61.8

Q ss_pred             cChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHHHHHh
Q 030809           66 EEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEE  129 (171)
Q Consensus        66 mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrERel~e  129 (171)
                      |+++|||+||.+||.++|.+|++|||+||||+++|+++|||+|+.+||+||||+||++|++.+.
T Consensus         1 Mk~~elr~~s~~EL~~~l~elk~ELf~LR~q~atgql~n~~~ir~vRr~IARi~Tvl~er~~~~   64 (67)
T 2zjr_V            1 MKPSEMRNLQATDFAKEIDARKKELMELRFQAAAGQLAQPHRVRQLRREVAQLNTVKAELARKG   64 (67)
T ss_dssp             CCSTTTTTSCHHHHHHHHHTHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHHHHHTTTT
T ss_pred             CCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            6789999999999999999999999999999999999999999999999999999999998764

>4a17_U RPL35, 60S ribosomal protein L21; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_U 4a1c_U 4a1e_U

Probab=99.89  E-value=1.5e-23  Score=163.02  Aligned_cols=88  Identities=25%  Similarity=0.246  Sum_probs=79.2

Q ss_pred             eccCCccChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhc-cCCCchhHHHHhHHHHHHHHHHHHHHHHhhhh------
Q 030809           60 MMAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVR-NEFKSSEFRRMRRRIARMLTVKRERELEEGIN------  132 (171)
Q Consensus        60 ~MsKr~mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatg-qleNp~~IR~iRKdIARIlTVLrERel~e~~n------  132 (171)
                      ||++  |+++|||+||.+||.++|.+|+.|||+||||+++| +++||++|+.+|||||||+||++|++.++...      
T Consensus         1 M~~~--mKa~ELR~~s~eEL~~~L~eLK~ELf~LRfq~atggqlen~~rIr~vRRdIARi~Tvl~er~~~~lr~~yk~kk   78 (124)
T 4a17_U            1 MDKS--VRVFKLRTQTEEQLVGELGKLQTELSQLRIAKIAGGTANKLGRIGIVRKAIAKYLTIINEKRRQAVKDQFKGKS   78 (124)
T ss_dssp             -CCC--CCHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCS
T ss_pred             CCcc--cCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhcCccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence            4554  99999999999999999999999999999999999 89999999999999999999999999988765      


Q ss_pred             --------------------hHhhhHHHHHHhhhhcc
Q 030809          133 --------------------KRLSRKLDRQWKKSIVV  149 (171)
Q Consensus       133 --------------------kr~sRk~~r~~K~s~~~  149 (171)
                                          ++.++++.+++|+..+.
T Consensus        79 ~~P~dlr~kktra~rr~Lt~~e~~~kt~k~~~k~~~f  115 (124)
T 4a17_U           79 LKPLDIRVKKTRAIRRKLTKKQREAVLVKTQKKLNNF  115 (124)
T ss_dssp             SCCTTTSCCSCHHHHHSCCHHHHHCCCHHHHHHHHHT
T ss_pred             CCCcccCchHHHHHHHHcCHHHHhhhhHHHHHHHHhC
Confidence                                37788888888776553

>2zkr_v 60S ribosomal protein L35; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}

Probab=99.88  E-value=2.7e-23  Score=161.32  Aligned_cols=86  Identities=34%  Similarity=0.388  Sum_probs=59.2

Q ss_pred             ccCCccChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhcc-CCCchhHHHHhHHHHHHHHHHHHHHHHhhhh-------
Q 030809           61 MAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRN-EFKSSEFRRMRRRIARMLTVKRERELEEGIN-------  132 (171)
Q Consensus        61 MsKr~mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgq-leNp~~IR~iRKdIARIlTVLrERel~e~~n-------  132 (171)
                      |++  |+++|||+||.+||.++|.+|++|||+||||+++|| ++|||+|+.+|||||||+||++|++.++..+       
T Consensus         1 Ma~--mK~~ELR~~s~eEL~~~L~eLK~ELf~LRfq~atgq~len~~rir~vRrdIARI~Tvl~er~~~~lr~~yk~kk~   78 (123)
T 2zkr_v            1 MAK--IKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTVINQTQKENLRKFYKGKKY   78 (123)
T ss_dssp             -----CCHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHTCSCCCHHHHHHHHHHHHHHHHHHHHC--------------
T ss_pred             CCC--CCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence            775  999999999999999999999999999999999995 8999999999999999999999999876544       


Q ss_pred             -------------------hHhhhHHHHHHhhhhc
Q 030809          133 -------------------KRLSRKLDRQWKKSIV  148 (171)
Q Consensus       133 -------------------kr~sRk~~r~~K~s~~  148 (171)
                                         ++.++++.+++|+..+
T Consensus        79 ~p~dlr~k~tra~rr~Lt~~~~~~kt~k~~~k~~~  113 (123)
T 2zkr_v           79 KPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERL  113 (123)
T ss_dssp             -----------------------------------
T ss_pred             CCcccchHHHHHHHHHcCHHHHhhccHHHHHHHHh
Confidence                               2667777777766554

>3r8s_Y 50S ribosomal protein L29; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_W 1p86_W 1vs8_X 1vs6_X 2aw4_X 2awb_X 1vt2_Y 2i2v_Y 2j28_X 2i2t_Y* 2qao_X* 2qba_X* 2qbc_X* 2qbe_X 2qbg_X 2qbi_X* 2qbk_X* 2qov_X 2qox_X 2qoz_X* ...

Probab=99.88  E-value=6.8e-24  Score=147.33  Aligned_cols=61  Identities=34%  Similarity=0.507  Sum_probs=59.6

Q ss_pred             cChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHHH
Q 030809           66 EEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERE  126 (171)
Q Consensus        66 mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrERe  126 (171)
                      |+++|||+||.+||.++|.+|++|||+||||+++|+++||++|+.+||+||||+||++|++
T Consensus         1 MK~~elr~~s~~EL~~~l~elk~Elf~LR~q~atgql~n~~~ir~vRr~IARi~Tvl~er~   61 (63)
T 3r8s_Y            1 MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKA   61 (63)
T ss_dssp             CCGGGTTSCHHHHHHHHHHHHTHHHHHHHHHHHTTCCSCGGGTHHHHHHHHHHHHTTTSST
T ss_pred             CCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCcHHHHHHHHHHHHHHHHHHHhh
Confidence            7899999999999999999999999999999999999999999999999999999999875

>3u5e_h 60S ribosomal protein L35-A, 60S ribosomal protein L33-A; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 1s1i_X 2wwa_N 2ww9_N 3izc_c 3izs_c 2wwb_N 3o5h_c 3o58_c 3u5i_h 4b6a_h

Probab=99.87  E-value=3e-22  Score=154.91  Aligned_cols=85  Identities=34%  Similarity=0.416  Sum_probs=77.5

Q ss_pred             ccCCccChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHHHHHhhhh--------
Q 030809           61 MAKREEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEEGIN--------  132 (171)
Q Consensus        61 MsKr~mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrERel~e~~n--------  132 (171)
                      |++  |+++|||+||.+||.++|.+|+.|||+||||+++||+  |++|+.+|||||||+||++|++.++..+        
T Consensus         1 Ma~--mK~~ELR~~s~eEL~~~L~eLK~ELf~LRfq~atgql--~~~Ir~vRR~IARi~Tvl~er~~~~lr~~yk~kk~~   76 (120)
T 3u5e_h            1 MAG--VKAYELRTKSKEQLASQLVDLKKELAELKVQKLSRPS--LPKIKTVRKSIACVLTVINEQQREAVRQLYKGKKYQ   76 (120)
T ss_dssp             -CC--CCHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHTTSSC--CTHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSSCC
T ss_pred             CCc--CCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHCCc--chhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCC
Confidence            776  9999999999999999999999999999999999999  9999999999999999999999988765        


Q ss_pred             ------------------hHhhhHHHHHHhhhhcc
Q 030809          133 ------------------KRLSRKLDRQWKKSIVV  149 (171)
Q Consensus       133 ------------------kr~sRk~~r~~K~s~~~  149 (171)
                                        ++.+.++.+++|+..+.
T Consensus        77 p~dlr~kktra~rr~Lt~~~~~~kt~k~~~k~~~~  111 (120)
T 3u5e_h           77 PKDLRAKKTRALRRALTKFEASQVTEKQRKKQIAF  111 (120)
T ss_dssp             CTTTSCCSCHHHHSSCCSHHHHCCCHHHHHHHHHS
T ss_pred             CcccCchHHHHHHHHcCHHHHhhhhHHHHHHHHhC
Confidence                              37888888888876553

>3jyw_X 60S ribosomal protein L35; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}

Probab=99.84  E-value=3.9e-22  Score=146.73  Aligned_cols=66  Identities=32%  Similarity=0.441  Sum_probs=62.8

Q ss_pred             ccChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHHHHHhhhh
Q 030809           65 EEEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEEGIN  132 (171)
Q Consensus        65 ~mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrERel~e~~n  132 (171)
                      +|+++|||+||.+||.++|.+|++|||+||||+++||+  |++|+.+|||||||+||++|+++++..+
T Consensus         2 ~MKa~ELR~~S~eEL~~~L~eLK~ELf~LRfq~atgql--p~rIr~vRRdIARikTvl~er~~~~lr~   67 (86)
T 3jyw_X            2 GVKAYELRTKSKEQLASQLVDLKKELAELKVQKLSRPS--LPKIKTVRKSIACVLTVINEQQAAAAAA   67 (86)
T ss_dssp             CSCHHHHHTSCHHHHHHHHHHHTTTHHHHHHHHHTCCC--HHHHTCCSTTTHHHHTTTTHHHHHHHSS
T ss_pred             CCCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHCCC--chHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            49999999999999999999999999999999999999  9999999999999999999999877543

---

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	171
d1r73a_	66	a.2.2.1 (A:) Ribosomal protein L29 (L29p) {Thermot	6e-15
d2gycw1	60	a.2.2.1 (W:1-60) Ribosomal protein L29 (L29p) {Esc	9e-14
d2zjrv1	66	a.2.2.1 (V:1-66) Ribosomal protein L29 (L29p) {Dei	1e-13
d1vqov1	65	a.2.2.1 (V:1-65) Ribosomal protein L29 (L29p) {Arc	2e-12
d2j0121	51	a.2.2.1 (2:12-62) Ribosomal protein L29 (L29p) {Th	8e-12

>d1r73a_ a.2.2.1 (A:) Ribosomal protein L29 (L29p) {Thermotoga maritima [TaxId: 2336]} Length = 66

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Thermotoga maritima [TaxId: 2336]

 Score = 63.8 bits (156), Expect = 6e-15
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 68  MKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKREREL 127
             E+R  T EE+   + + K +L  LR Q ++     +S  +  +R IAR+ T+ REREL
Sbjct: 3   ASELRNYTDEELKNLLEEKKRQLMELRFQLAMGQLKNTSLIKLTKRDIARIKTILREREL 62

Query: 128 EEGINK 133
             GI +
Sbjct: 63  --GIRR 66

>d2gycw1 a.2.2.1 (W:1-60) Ribosomal protein L29 (L29p) {Escherichia coli [TaxId: 562]} Length = 60

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Escherichia coli [TaxId: 562]

 Score = 60.4 bits (147), Expect = 9e-14
 Identities = 21/58 (36%), Positives = 37/58 (63%)

Query: 68  MKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRER 125
            KE+R K+ EE+N E+++L  E F LR+Q +     +S   +++RR +AR+ T+  E+
Sbjct: 3   AKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEK 60

>d2zjrv1 a.2.2.1 (V:1-66) Ribosomal protein L29 (L29p) {Deinococcus radiodurans [TaxId: 1299]} Length = 66

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Deinococcus radiodurans [TaxId: 1299]

 Score = 60.4 bits (147), Expect = 1e-13
 Identities = 17/63 (26%), Positives = 29/63 (46%)

Query: 68  MKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKREREL 127
             E+R     +  +E+   K EL  LR Q +     +    R++RR +A++ TVK E   
Sbjct: 3   PSEMRNLQATDFAKEIDARKKELMELRFQAAAGQLAQPHRVRQLRREVAQLNTVKAELAR 62

Query: 128 EEG 130
           +  
Sbjct: 63  KGE 65

>d1vqov1 a.2.2.1 (V:1-65) Ribosomal protein L29 (L29p) {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 65

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Archaeon Haloarcula marismortui [TaxId: 2238]

 Score = 57.3 bits (139), Expect = 2e-12
 Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 68  MKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEF-KSSEFRRMRRRIARMLTVKRER 125
           ++EIR  T  E   E+ DLK EL   R  ++           + +R+ IAR+ T++ E 
Sbjct: 5   VQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTIQGEE 63

>d2j0121 a.2.2.1 (2:12-62) Ribosomal protein L29 (L29p) {Thermus thermophilus [TaxId: 274]} Length = 51

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Thermus thermophilus [TaxId: 274]

 Score = 55.0 bits (133), Expect = 8e-12
 Identities = 18/51 (35%), Positives = 30/51 (58%)

Query: 70  EIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLT 120
           E R  +  E+ + V + K EL  LR Q S+    ++ + R ++R+IAR+LT
Sbjct: 1   EARKLSPVELEKLVREKKRELMELRFQASIGQLSQNHKIRDLKRQIARLLT 51

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	171
d2zjrv1	66	Ribosomal protein L29 (L29p) {Deinococcus radiodur	99.88
d1r73a_	66	Ribosomal protein L29 (L29p) {Thermotoga maritima	99.88
d2gycw1	60	Ribosomal protein L29 (L29p) {Escherichia coli [Ta	99.88
d1vqov1	65	Ribosomal protein L29 (L29p) {Archaeon Haloarcula	99.87
d2j0121	51	Ribosomal protein L29 (L29p) {Thermus thermophilus	99.68

>d2zjrv1 a.2.2.1 (V:1-66) Ribosomal protein L29 (L29p) {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Deinococcus radiodurans [TaxId: 1299]

Probab=99.88  E-value=1.2e-23  Score=145.36  Aligned_cols=64  Identities=27%  Similarity=0.344  Sum_probs=61.9

Q ss_pred             cChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHHHHHh
Q 030809           66 EEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELEE  129 (171)
Q Consensus        66 mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrERel~e  129 (171)
                      |+++|||+||.+||.++|.++++|||+||||+++||++|||+|+.+||+||||+||++|+.++.
T Consensus         1 MK~~elr~~s~~eL~~~l~~lk~elf~LRfq~~tgql~n~~~ik~~Rk~IARi~Tvl~er~~~~   64 (66)
T d2zjrv1           1 MKPSEMRNLQATDFAKEIDARKKELMELRFQAAAGQLAQPHRVRQLRREVAQLNTVKAELARKG   64 (66)
T ss_dssp             CCSTTTTTSCHHHHHHHHHTHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHHHHHTTTT
T ss_pred             CCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHCCCcchHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            7899999999999999999999999999999999999999999999999999999999998754

>d1r73a_ a.2.2.1 (A:) Ribosomal protein L29 (L29p) {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Thermotoga maritima [TaxId: 2336]

Probab=99.88  E-value=3e-23  Score=143.45  Aligned_cols=63  Identities=33%  Similarity=0.418  Sum_probs=61.4

Q ss_pred             cChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHHHHH
Q 030809           66 EEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRERELE  128 (171)
Q Consensus        66 mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrERel~  128 (171)
                      |+++|||+||.+||.++|.++++|||+||||+++|+++|||+|+.+||+||||+||++||+++
T Consensus         1 MK~~elr~ls~~eL~~~l~~l~~el~~LRfq~~~gql~~~~~i~~~Rk~IARi~Tvl~er~~~   63 (66)
T d1r73a_           1 MKASELRNYTDEELKNLLEEKKRQLMELRFQLAMGQLKNTSLIKLTKRDIARIKTILRERELG   63 (66)
T ss_dssp             CCCSHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHHHHHHHhc
Confidence            789999999999999999999999999999999999999999999999999999999999874

>d2gycw1 a.2.2.1 (W:1-60) Ribosomal protein L29 (L29p) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Escherichia coli [TaxId: 562]

Probab=99.88  E-value=1.6e-23  Score=142.38  Aligned_cols=60  Identities=35%  Similarity=0.515  Sum_probs=58.9

Q ss_pred             cChHHHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHHHHHHH
Q 030809           66 EEMKEIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLTVKRER  125 (171)
Q Consensus        66 mK~kELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlTVLrER  125 (171)
                      |+++|||+||.+||.++|.++++|||+||||+++||++|||+|+.+||+||||+||++||
T Consensus         1 Mk~~elr~ls~~eL~~~l~~l~~el~~lRfq~~~gql~~~~~i~~~Rk~IARi~Tvl~ek   60 (60)
T d2gycw1           1 MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEK   60 (60)
T ss_dssp             CCHHHHHHSCHHHHHHHHHHHHHHHHHCCCSTTTCSSCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHHHhcC
Confidence            789999999999999999999999999999999999999999999999999999999985

>d1vqov1 a.2.2.1 (V:1-65) Ribosomal protein L29 (L29p) {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=99.87  E-value=1.9e-22  Score=139.07  Aligned_cols=61  Identities=31%  Similarity=0.400  Sum_probs=59.3

Q ss_pred             cChHHHhcCCHHHHHHHHHHHHHHHHHhH-HHHhhccCCCchhHHHHhHHHHHHHHHHHHHH
Q 030809           66 EEMKEIRAKTTEEINEEVVDLKGELFMLR-LQKSVRNEFKSSEFRRMRRRIARMLTVKRERE  126 (171)
Q Consensus        66 mK~kELR~LS~eEL~ekL~ELKkELf~LR-fQkatgqleNp~~IR~iRKdIARIlTVLrERe  126 (171)
                      |+++|||+||.+||.++|.+|++|||+|| ||+++|+++|||+|+.+||+||||+||++||.
T Consensus         3 mK~~elr~ls~~eL~~~l~elk~El~~LR~~q~~~gql~~~~~ik~~Rk~IARi~Tvl~ek~   64 (65)
T d1vqov1           3 LHVQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTIQGEEG   64 (65)
T ss_dssp             SCHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHHHHHHhc
Confidence            79999999999999999999999999999 79999999999999999999999999999984

>d2j0121 a.2.2.1 (2:12-62) Ribosomal protein L29 (L29p) {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Thermus thermophilus [TaxId: 274]

Probab=99.68  E-value=4.4e-20  Score=122.20  Aligned_cols=51  Identities=35%  Similarity=0.492  Sum_probs=49.3

Q ss_pred             HHhcCCHHHHHHHHHHHHHHHHHhHHHHhhccCCCchhHHHHhHHHHHHHH
Q 030809           70 EIRAKTTEEINEEVVDLKGELFMLRLQKSVRNEFKSSEFRRMRRRIARMLT  120 (171)
Q Consensus        70 ELR~LS~eEL~ekL~ELKkELf~LRfQkatgqleNp~~IR~iRKdIARIlT  120 (171)
                      |||+||.+||.++|.++++|||+||||+++||++|||+|+.+||+||||+|
T Consensus         1 EiR~ls~~eL~~~l~elk~el~~LRfq~atgql~n~~~ik~~rk~IARi~T   51 (51)
T d2j0121           1 EARKLSPVELEKLVREKKRELMELRFQASIGQLSQNHKIRDLKRQIARLLT   51 (51)
T ss_dssp             CCTTTHHHHHHHHHHHHHHHSSSSCCTTSSTTTGGGTTSSSSSCCCCCCC-
T ss_pred             ChhhCCHHHHHHHHHHHHHHHHHHHHHHHHCCCcchHHHHHHHHHHHHhcC
Confidence            689999999999999999999999999999999999999999999999988