Psyllid ID: psy13112

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300--
Protein Sequence
MTPPLRLESRDYVLSFHFFETRLRDDISFQERSQGSAKCDLMPTPRSPREREARPHAQPRKAPGSAQRDRKQGSAKRDPMHNPTKPQERVARPYMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRTAVLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIRYHEFDDDDQPYAVYK
Secondary Structure (PSIPRED)
cccccccccccEEEEEEEEHHHccccccHHHccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccEEccccccccccccccccccEEEEEccccccccccEEEEccccccccccEEEEEEEEEEEcccEEEccccEEEEEEEcccccccccccEEEEEccccccccccEEEEEcccccccccEEEEEEEEEEccccccccccccEEccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccEEEEcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccHHEEEEHHHHcccccccccEEccccccccccccccccHcHHccccccccccccccHHHHHccccccccccccccccccccccccccccEEccHHHHHHHccccEEEEccHHHccccccEEEEEccccccccEEEEEEEEEEEEcccccccccccEEEEEEHHHHHHcccccEEEEccHHHccccccEEEEcccccccccEEEEEEEEEEEEcccccccccccEEEEEcccHccccHHHHHHHHHccccHHccccccccccccccccccccccccEEEEEcccccccccEEEc
Coil and Loop (DISEMBL)
mtpplrlesrdyvLSFHFFetrlrddisfqersqgsakcdlmptprsprerearphaqprkapgsaqrdrkqgsakrdpmhnptkpqervarpymqprvantrnevryfpkftvmyahdpdkicktgdivlIEELPQKLTTLITHkvnkvvyplgditdpitgkkVVGLRvdlgkyfpkftvmyahdpdkicktgdivlIEELPQKLTTLITHkvnkvvyplgditdpitgkkVVGLRTAVLTADFYKELYELygknpqrkfdykkaprrgwqedkkdfthresyiryhefddddqpyavyk
Flexible Loop (DISEMBL)
mtpplrlesrdyVLSFHFFEtrlrddisfqersqgsakcdlmptprsprerearphaqprkapgsaqrdrkqgsakrdpmhnptkpqervarpymqprvantrnevrYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLithkvnkvvyplgditdpitgkkvvGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLithkvnkvvyplgditdpitgkkvvGLRTAVLTADFYKELYelygknpqrkfdykkaprrgwqedkkdfthRESYiryhefddddqpyavyk
Low Complexity Region (SEG)
MTPPLRLESRDYVLSFHFFETRLRDDISFQERSQGSAKCDLMPTPRSPREREARPHAQPRKAPGSAQRDRKQGSAKRDPMHNPTKPQERVARPYMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRTAVLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIRYHEFDDDDQPYAVYK
Disordered region (IsUnstruct)
**********DYVLSFHFFETRLRD****************************************************************************TRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRTAVLTADFYKELYELYGKNPQRKFDY*******************SYIRYHE************
Disordered Region (DISOPRED)
****LR*ESRDYVLSFHFFETRLRDDIS*********************************************************PQERVARPYMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRTAVLTADFYK**********************************ESYIRYHEFDDDD*P***Y*
Disordered Region (DISEMBL)
MTPPLRLESRDYVLSFHFFETRLRDDISFQERSQGSAKCD**********************************************QERVARPYMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRTAVLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIRYHEFDDDDQPYAVYK
Disordered Region (DISPRO)
****LRLESRDYVLSFHFFETRLRDDISFQER******C************************************************ERVARPYMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRTAVLTADFYKELYELYGKNPQRKFDYKKAPR****EDKKDFTHRESYIRYHEFDDDDQPYAVYK
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTPPLRLESRDYVLSFHFFETRLRDDISFQERSQGSAKCDLMPTPRSPREREARPHAQPRKAPGSAQRDRKQGSAKRDPMHNPTKPQERVARPYMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRTAVLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIRYHEFDDDDQPYAVYK
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	302	2.2.26 [Sep-21-2011]
P82916	130	28S ribosomal protein S17	yes	N/A	0.192	0.446	0.406	2e-07
Q9CQE3	120	28S ribosomal protein S17	yes	N/A	0.211	0.533	0.375	2e-06
Q9Y2R5	130	28S ribosomal protein S17	yes	N/A	0.192	0.446	0.390	2e-06
Q11189	160	Uncharacterized protein C	yes	N/A	0.205	0.387	0.343	0.0003

>sp|P82916|RT17_BOVIN 28S ribosomal protein S17, mitochondrial OS=Bos taurus GN=MRPS17 PE=1 SV=3

 Score = 57.0 bits (136), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/64 (40%), Positives = 40/64 (62%)

Query: 173 LGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGK 232
           L KYF K    +AHD  + C  GDIVL++ LP   T  + H++ ++V+ +G + DP+TGK
Sbjct: 39  LLKYFNKRKTYFAHDALQQCTVGDIVLLKALPVPRTKHVKHELAEIVFKVGQVVDPVTGK 98

Query: 233 KVVG 236
           +  G
Sbjct: 99  RCAG 102

Bos taurus (taxid: 9913)

>sp|Q9CQE3|RT17_MOUSE 28S ribosomal protein S17, mitochondrial OS=Mus musculus GN=Mrps17 PE=2 SV=1

 Score = 53.5 bits (127), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 38/64 (59%)

Query: 173 LGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGK 232
           L KYF K    +AHD  + C  GDIVL+  LP   +  + H++ ++++ +G + DP+TGK
Sbjct: 39  LLKYFNKRKTYFAHDALQQCSVGDIVLLRALPVPRSKHVKHELAEIIFKVGRVIDPVTGK 98

Query: 233 KVVG 236
              G
Sbjct: 99  PCAG 102

Mus musculus (taxid: 10090)

>sp|Q9Y2R5|RT17_HUMAN 28S ribosomal protein S17, mitochondrial OS=Homo sapiens GN=MRPS17 PE=2 SV=1

 Score = 53.5 bits (127), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 37/64 (57%)

Query: 173 LGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGK 232
           L KYF K    +AHD  + C  GDIVL+  LP      + H++ ++V+ +G + DP+TGK
Sbjct: 39  LLKYFNKRKTYFAHDALQQCTVGDIVLLRALPVPRAKHVKHELAEIVFKVGKVIDPVTGK 98

Query: 233 KVVG 236
              G
Sbjct: 99  PCAG 102

Homo sapiens (taxid: 9606)

>sp|Q11189|YPDA_CAEEL Uncharacterized protein C05D11.10 OS=Caenorhabditis elegans GN=C05D11.10 PE=4 SV=2

 Score = 46.2 bits (108), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 38/64 (59%), Gaps = 2/64 (3%)

Query: 173 LGKYFPKFTVMYAHDPDKICKTGDIVLIEEL--PQKLTTLITHKVNKVVYPLGDITDPIT 230
           L KYF +    +A D   +   GD VLI+++    +    ++H V++VV+  G+I DP+T
Sbjct: 47  LKKYFARSFDFWALDKTSLGNIGDTVLIKQIDGSSRPKANVSHAVDRVVFKFGNIVDPVT 106

Query: 231 GKKV 234
           G+K+
Sbjct: 107 GRKI 110

Caenorhabditis elegans (taxid: 6239)

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	302
274324145	166	28S ribosomal protein S17, mitochondrial	0.443	0.807	0.583	2e-35
91087591	159	PREDICTED: similar to GA18111-PA [Tribol	0.417	0.792	0.598	6e-34
195121120	155	GI19260 [Drosophila mojavensis] gi|19391	0.410	0.8	0.589	2e-32
195029111	155	GH21909 [Drosophila grimshawi] gi|193903	0.400	0.780	0.587	1e-31
24762582	155	mitochondrial ribosomal protein S17 [Dro	0.400	0.780	0.580	3e-31
195489551	155	GE11475 [Drosophila yakuba] gi|194178888	0.400	0.780	0.580	6e-31
125808890	155	GA18111 [Drosophila pseudoobscura pseudo	0.400	0.780	0.587	7e-31
194886187	155	GG19946 [Drosophila erecta] gi|190659754	0.400	0.780	0.580	7e-31
195383390	155	GJ22135 [Drosophila virilis] gi|19414520	0.400	0.780	0.580	8e-31
195341864	155	GM18264 [Drosophila sechellia] gi|195586	0.394	0.767	0.578	1e-30

>gi|274324145|ref|NP_001162111.1| 28S ribosomal protein S17, mitochondrial-like [Acyrthosiphon pisum] gi|193654931|ref|XP_001944690.1| PREDICTED: 28S ribosomal protein S17, mitochondrial-like isoform 1 [Acyrthosiphon pisum] gi|239791473|dbj|BAH72197.1| ACYPI008968 [Acyrthosiphon pisum]

 Score =  155 bits (393), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 80/137 (58%), Positives = 103/137 (75%), Gaps = 3/137 (2%)

Query: 165 KVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGD 224
           K + L  +L  YF K  V YAHDP++ CKTGD+VLI+EL +KLTT ITH+V KVVYPLGD
Sbjct: 30  KKLELDQNLLMYFHKDEVYYAHDPEQQCKTGDVVLIQELSEKLTTHITHQVLKVVYPLGD 89

Query: 225 ITDPITGKKVVGLRTA-VLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRE 283
           +TDPIT KKV  LR+  V   D  +E+  LYG   +R F+Y  AP+RGWQEDKKDF+H++
Sbjct: 90  VTDPITNKKVAALRSGTVCYRDDLEEIDNLYGLTKKR-FNYANAPKRGWQEDKKDFSHKK 148

Query: 284 SYIRYHEFDDDDQPYAV 300
           SYI+YHE  +++QPY+V
Sbjct: 149 SYIKYHE-SEEEQPYSV 164

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91087591|ref|XP_972027.1| PREDICTED: similar to GA18111-PA [Tribolium castaneum] gi|270009430|gb|EFA05878.1| hypothetical protein TcasGA2_TC008690 [Tribolium castaneum]

 Score =  150 bits (379), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 79/132 (59%), Positives = 96/132 (72%), Gaps = 6/132 (4%)

Query: 169 LRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDP 228
           L  +L  YF K   +YAHDP+KICKTGDIVLIE+LP K+T LITH V KVVYP+GDITDP
Sbjct: 34  LDTNLLMYFGKEEFVYAHDPNKICKTGDIVLIEQLPTKMTRLITHAVKKVVYPMGDITDP 93

Query: 229 ITGKKVVGLRTAVLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIRY 288
           +TGKKVV  +      DF   + ++YG+  +  F Y KAP RGWQEDKKDFTH ++YI+Y
Sbjct: 94  VTGKKVVAGK----YRDFVDSVNKVYGEK-EGAFKYDKAPPRGWQEDKKDFTHVQTYIKY 148

Query: 289 HEFDDDDQPYAV 300
           H+   DD PYAV
Sbjct: 149 HDSGKDD-PYAV 159

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195121120|ref|XP_002005069.1| GI19260 [Drosophila mojavensis] gi|193910137|gb|EDW09004.1| GI19260 [Drosophila mojavensis]

 Score =  145 bits (367), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 79/134 (58%), Positives = 97/134 (72%), Gaps = 10/134 (7%)

Query: 169 LRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDP 228
           L  +L  YF K T  +AHDP+K+CKTGD+VLI ELP++LT LITHKV KVVYPLGDITDP
Sbjct: 30  LDTNLNMYFKKDTFFFAHDPEKVCKTGDVVLIRELPERLTRLITHKVEKVVYPLGDITDP 89

Query: 229 ITGKKVV--GLRTAVLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYI 286
           I+GKKVV    R  +  A+      +L+GK+ ++ FDY KAP RG  E  KDFTH E+YI
Sbjct: 90  ISGKKVVVGKYREDIEMAN------QLFGKS-EKAFDYDKAPPRGRLEGTKDFTHGETYI 142

Query: 287 RYHEFDDDDQPYAV 300
           +YHE D  DQP+AV
Sbjct: 143 KYHE-DGKDQPFAV 155

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195029111|ref|XP_001987418.1| GH21909 [Drosophila grimshawi] gi|193903418|gb|EDW02285.1| GH21909 [Drosophila grimshawi]

 Score =  142 bits (359), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 77/131 (58%), Positives = 94/131 (71%), Gaps = 10/131 (7%)

Query: 172 DLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITG 231
           +L  YF K T  +AHDP K+CKTGD+VLI ELP+++T LITH V KVVYPLGDITDPITG
Sbjct: 33  NLNMYFKKDTFFFAHDPKKLCKTGDVVLIRELPERMTRLITHNVEKVVYPLGDITDPITG 92

Query: 232 KKVV--GLRTAVLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIRYH 289
           KKVV    R  +  A+      +L+GK+  + FDY+KAP RG  E  KDFTH E+YI+YH
Sbjct: 93  KKVVVGKYREDIEMAN------QLFGKSA-KGFDYEKAPPRGRLEGSKDFTHGETYIKYH 145

Query: 290 EFDDDDQPYAV 300
           E D  DQP+AV
Sbjct: 146 E-DGKDQPFAV 155

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24762582|ref|NP_525119.1| mitochondrial ribosomal protein S17 [Drosophila melanogaster] gi|7291756|gb|AAF47177.1| mitochondrial ribosomal protein S17 [Drosophila melanogaster] gi|19527541|gb|AAL89885.1| RE28524p [Drosophila melanogaster] gi|220948292|gb|ACL86689.1| mRpS17-PA [synthetic construct] gi|220957462|gb|ACL91274.1| mRpS17-PA [synthetic construct]

 Score =  141 bits (356), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 76/131 (58%), Positives = 94/131 (71%), Gaps = 10/131 (7%)

Query: 172 DLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITG 231
           +L  YF K    +AHDP K+CKTGD+VLI ELP++LT LITH V KVVYPLGDITDP+TG
Sbjct: 33  NLNMYFKKDEFYFAHDPQKVCKTGDVVLIRELPERLTRLITHNVEKVVYPLGDITDPLTG 92

Query: 232 KKVV--GLRTAVLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIRYH 289
           KKVV    R  +  A+      +L+GK+ ++ FDY+KAP RG  E  KDFTH E+YI+YH
Sbjct: 93  KKVVVGNYREDIEMAN------QLFGKS-EKAFDYEKAPPRGRLEGTKDFTHGETYIKYH 145

Query: 290 EFDDDDQPYAV 300
           E D  DQP+AV
Sbjct: 146 E-DGKDQPFAV 155

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195489551|ref|XP_002092787.1| GE11475 [Drosophila yakuba] gi|194178888|gb|EDW92499.1| GE11475 [Drosophila yakuba]

 Score =  140 bits (354), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 76/131 (58%), Positives = 94/131 (71%), Gaps = 10/131 (7%)

Query: 172 DLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITG 231
           +L  YF K    +AHDP K+CKTGD+VLI ELP++LT LITH V KVVYPLGDITDP+TG
Sbjct: 33  NLNMYFKKDEFYFAHDPQKVCKTGDVVLIRELPERLTRLITHNVEKVVYPLGDITDPLTG 92

Query: 232 KKVV--GLRTAVLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIRYH 289
           KKVV    R  +  A+      +L+GK+ ++ FDY+KAP RG  E  KDFTH E+YI+YH
Sbjct: 93  KKVVVGKYREDIEMAN------QLFGKS-EKAFDYEKAPPRGRLEGTKDFTHGETYIKYH 145

Query: 290 EFDDDDQPYAV 300
           E D  DQP+AV
Sbjct: 146 E-DGKDQPFAV 155

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125808890|ref|XP_001360909.1| GA18111 [Drosophila pseudoobscura pseudoobscura] gi|195153791|ref|XP_002017807.1| GL17109 [Drosophila persimilis] gi|54636081|gb|EAL25484.1| GA18111 [Drosophila pseudoobscura pseudoobscura] gi|194113603|gb|EDW35646.1| GL17109 [Drosophila persimilis]

 Score =  140 bits (353), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 77/131 (58%), Positives = 93/131 (70%), Gaps = 10/131 (7%)

Query: 172 DLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITG 231
           +L  YF K    +AHDP K+CKTGD+VLI ELP+++T LITH V KVVYPLGDITDPITG
Sbjct: 33  NLNMYFKKDDFYFAHDPQKVCKTGDVVLIRELPERMTRLITHAVEKVVYPLGDITDPITG 92

Query: 232 KKVV--GLRTAVLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIRYH 289
           KKVV    R  +  A+      EL+GK+ ++ FDY KAP RG  E  KDFTH E+YI+YH
Sbjct: 93  KKVVVGKYREDIEMAN------ELFGKS-KKSFDYDKAPPRGRLEGTKDFTHGETYIKYH 145

Query: 290 EFDDDDQPYAV 300
           E D  DQP+AV
Sbjct: 146 E-DGKDQPFAV 155

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194886187|ref|XP_001976567.1| GG19946 [Drosophila erecta] gi|190659754|gb|EDV56967.1| GG19946 [Drosophila erecta]

 Score =  140 bits (353), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 76/131 (58%), Positives = 94/131 (71%), Gaps = 10/131 (7%)

Query: 172 DLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITG 231
           +L  YF K    +AHDP K+CKTGD+VLI ELP++LT LITH V KVVYPLGDITDP+TG
Sbjct: 33  NLNMYFKKDEFYFAHDPQKVCKTGDVVLIRELPERLTRLITHNVEKVVYPLGDITDPLTG 92

Query: 232 KKVV--GLRTAVLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIRYH 289
           KKVV    R  +  A+      +L+GK+ ++ FDY+KAP RG  E  KDFTH E+YI+YH
Sbjct: 93  KKVVVGKYREDIEMAN------QLFGKS-EKGFDYEKAPPRGRLEGTKDFTHGETYIKYH 145

Query: 290 EFDDDDQPYAV 300
           E D  DQP+AV
Sbjct: 146 E-DGKDQPFAV 155

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195383390|ref|XP_002050409.1| GJ22135 [Drosophila virilis] gi|194145206|gb|EDW61602.1| GJ22135 [Drosophila virilis]

 Score =  140 bits (352), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 76/131 (58%), Positives = 94/131 (71%), Gaps = 10/131 (7%)

Query: 172 DLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITG 231
           +L  YF K T  +AHDP K+CKTGD+VLI ELP+++T LITH V KVVYPLGDITDPITG
Sbjct: 33  NLNMYFKKDTFYFAHDPQKLCKTGDVVLIRELPERMTRLITHSVEKVVYPLGDITDPITG 92

Query: 232 KKVV--GLRTAVLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIRYH 289
           KKVV    R  +  A+      +L+GK+  + FDY+KAP RG  E  KDFTH E+YI+YH
Sbjct: 93  KKVVVGKYREDIEMAN------QLFGKS-DKAFDYEKAPPRGRLEGTKDFTHGETYIKYH 145

Query: 290 EFDDDDQPYAV 300
           E D  +QP+AV
Sbjct: 146 E-DGTEQPFAV 155

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195341864|ref|XP_002037525.1| GM18264 [Drosophila sechellia] gi|195586325|ref|XP_002082928.1| GD24969 [Drosophila simulans] gi|194132375|gb|EDW53943.1| GM18264 [Drosophila sechellia] gi|194194937|gb|EDX08513.1| GD24969 [Drosophila simulans]

 Score =  139 bits (351), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 77/133 (57%), Positives = 93/133 (69%), Gaps = 14/133 (10%)

Query: 172 DLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITG 231
           +L  YF K    +AHDP K+CKTGD+VLI ELP++LT LITH V KVVYPLGDITDP+TG
Sbjct: 33  NLNMYFKKDEFYFAHDPQKVCKTGDVVLIRELPERLTRLITHNVEKVVYPLGDITDPLTG 92

Query: 232 KKVVGLRTAVLTADFYKELYE----LYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIR 287
           KKVV           Y+E  E    L+GK+ ++ FDY+KAP RG  E  KDFTH E+YI+
Sbjct: 93  KKVV--------VGKYREDIEMTNQLFGKS-EKAFDYEKAPPRGRLEGTKDFTHGETYIK 143

Query: 288 YHEFDDDDQPYAV 300
           YHE D  DQP+AV
Sbjct: 144 YHE-DGKDQPFAV 155

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by 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	302
PRK05610	84	PRK05610, rpsQ, 30S ribosomal protein S17; Reviewe	4e-04
TIGR03635	71	TIGR03635, S17_bact, 30S ribosomal protein S17	5e-04

>gnl|CDD|235532 PRK05610, rpsQ, 30S ribosomal protein S17; Reviewed

 Score = 38.2 bits (90), Expect = 4e-04
 Identities = 11/29 (37%), Positives = 15/29 (51%)

Query: 174 GKYFPKFTVMYAHDPDKICKTGDIVLIEE 202
           GK   +    +AHD +   K GD+V I E
Sbjct: 36  GKIVKRSKKYHAHDENNEAKIGDVVRIME 64

Length = 84

>gnl|CDD|213841 TIGR03635, S17_bact, 30S ribosomal protein S17

 Score = 37.5 bits (88), Expect = 5e-04
 Identities = 12/29 (41%), Positives = 16/29 (55%)

Query: 174 GKYFPKFTVMYAHDPDKICKTGDIVLIEE 202
           GK   +    +AHD +  CK GD+V I E
Sbjct: 31  GKIVKRTKKYHAHDENNECKVGDVVRIIE 59

This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 71

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	302
KOG3447|consensus	150		99.97
KOG3447|consensus	150		99.85
PRK05610	84	rpsQ 30S ribosomal protein S17; Reviewed	99.84
CHL00142	84	rps17 ribosomal protein S17; Validated	99.84
COG0186	87	RpsQ Ribosomal protein S17 [Translation, ribosomal	99.84
PRK08572	108	rps17p 30S ribosomal protein S17P; Reviewed	99.81
TIGR03630	102	arch_S17P archaeal ribosomal protein S17P. This mo	99.79
PF00366	69	Ribosomal_S17: Ribosomal protein S17; InterPro: IP	99.79
TIGR03635	71	S17_bact 30S ribosomal protein S17. This model des	99.78
COG0186	87	RpsQ Ribosomal protein S17 [Translation, ribosomal	99.77
PRK05610	84	rpsQ 30S ribosomal protein S17; Reviewed	99.76
CHL00142	84	rps17 ribosomal protein S17; Validated	99.76
PRK08572	108	rps17p 30S ribosomal protein S17P; Reviewed	99.71
PF00366	69	Ribosomal_S17: Ribosomal protein S17; InterPro: IP	99.7
TIGR03630	102	arch_S17P archaeal ribosomal protein S17P. This mo	99.69
PTZ00241	158	40S ribosomal protein S11; Provisional	99.69
TIGR03635	71	S17_bact 30S ribosomal protein S17. This model des	99.68
KOG1740|consensus	107		99.64
PTZ00241	158	40S ribosomal protein S11; Provisional	99.57
KOG1740|consensus	107		99.49
KOG1728|consensus	156		97.47
KOG1728|consensus	156		97.32
PF02080	71	TrkA_C: TrkA-C domain; InterPro: IPR006037 The reg	81.82

>KOG3447|consensus

Probab=99.97  E-value=8.2e-32  Score=230.49  Aligned_cols=141  Identities=28%  Similarity=0.374  Sum_probs=124.7

Q ss_pred             ccceeEEEeeEEeecCCccCCcccee--eecceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEE
Q psy13112        140 TTLITHKVNKVVYPLGDITDPITGKK--VVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNK  217 (302)
Q Consensus       140 SK~KtW~V~eIV~kaG~i~DPiTGK~--VVGLrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~e  217 (302)
                      |..--|.+-+||   |++..|-..-+  ..+|++||.|||+|++.|||||+..+|++||+|+|+++|.|+.++.+|.|.+
T Consensus         7 s~~~~~lmGk~i---g~~~q~~akVR~~r~eld~yL~kYf~k~~~yfAhD~~~~c~vGDtVLir~lp~r~t~~V~H~v~~   83 (150)
T KOG3447|consen    7 SVHAQWLMGKVI---GTKMQKTAKVRVTRLELDPYLLKYFNKRKTYFAHDALQQCTVGDTVLIRALPVRRTKHVKHEVAE   83 (150)
T ss_pred             ecccEEEEeeee---eccccccceeeeehhhcCHHHHHHhccccceeecchhhccccCCEEEEecCCcchhhhhhhhhHh
Confidence            555667777774   44444332222  3579999999999999999999999999999999999999999999999999


Q ss_pred             eeecCCCccCCCCCceeeccccccccHHH-HHHHHHHhcCCCCCCcccCCCCCCCcccccccCCCccceEee
Q psy13112        218 VVYPLGDITDPITGKKVVGLRTAVLTADF-YKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIRY  288 (302)
Q Consensus       218 IV~k~G~iiDPVTgK~vv~~~Y~~~~~D~-i~~~~~l~g~~~~~~f~y~ka~~rg~~e~~~dfth~~~y~ky  288 (302)
                      ||++.|+||||||||+|++++|    +|+ +++...++|++. ..|+|.+|+.||+.++..||+|.+.|++|
T Consensus        84 VVfk~G~IidPvTGkk~~~~ty----~e~~~~~~~~~~~k~~-k~l~~esa~~r~r~~~~irrleqEkeanv  150 (150)
T KOG3447|consen   84 VVFKVGKIIDPVTGKKCAGDTY----LESPLSKETTQLSKNL-KELNIESAQFRERRALQIRRLEQEKEANV  150 (150)
T ss_pred             heeecccccCCCcCccccCcch----hcchHHHHHHHhhhcc-cccchhhcChhhhhhhhhhhhhcccccCC
Confidence            9999999999999999999999    999 666677889988 99999999999999999999999999986

>KOG3447|consensus

Probab=99.85  E-value=5.6e-23  Score=176.37  Aligned_cols=77  Identities=38%  Similarity=0.622  Sum_probs=75.0

Q ss_pred             ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecCCccCCccceeeecce
Q psy13112         94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLR  170 (302)
Q Consensus        94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~VVGLr  170 (302)
                      -.|.|++++|+++|||+|++.|||||+..+|++||+|+|+++|.+++++.+|.|.+||++.|+|+||+|||+|++..
T Consensus        28 VR~~r~eld~yL~kYf~k~~~yfAhD~~~~c~vGDtVLir~lp~r~t~~V~H~v~~VVfk~G~IidPvTGkk~~~~t  104 (150)
T KOG3447|consen   28 VRVTRLELDPYLLKYFNKRKTYFAHDALQQCTVGDTVLIRALPVRRTKHVKHEVAEVVFKVGKIIDPVTGKKCAGDT  104 (150)
T ss_pred             eeeehhhcCHHHHHHhccccceeecchhhccccCCEEEEecCCcchhhhhhhhhHhheeecccccCCCcCccccCcc
Confidence            35889999999999999999999999999999999999999999999999999999999999999999999999988

>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed

Probab=99.84  E-value=5e-21  Score=151.36  Aligned_cols=60  Identities=20%  Similarity=0.191  Sum_probs=57.7

Q ss_pred             ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeec
Q psy13112         94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPL  154 (302)
Q Consensus        94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~ka  154 (302)
                      ..|+|+++||.|+||++++++|+||||+|+|++||+|+|.|| +||||+|+|.|.+|++++
T Consensus        24 V~v~r~~~h~kY~K~~~r~kk~~aHD~~n~~k~GD~V~I~e~-rPlSK~K~~~v~~i~~~~   83 (84)
T PRK05610         24 VLVERRVKHPLYGKIVKRSKKYHAHDENNEAKIGDVVRIMET-RPLSKTKRWRLVEIVEKA   83 (84)
T ss_pred             EEEEEEEEeccccEEEEcceEEEEECCCCCCCCCCEEEEEEc-ccCCCCEEEEEEEEEecc
Confidence            468999999999999999999999999999999999999999 999999999999999865

>CHL00142 rps17 ribosomal protein S17; Validated

Probab=99.84  E-value=6.2e-21  Score=151.18  Aligned_cols=62  Identities=19%  Similarity=0.192  Sum_probs=59.1

Q ss_pred             ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecCC
Q psy13112         94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGD  156 (302)
Q Consensus        94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~  156 (302)
                      ..|+|+++||.|+||++++++|+||||+|+|++||+|+|.|| +||||+|+|.|.+|++++-.
T Consensus        21 V~v~r~~~h~kY~K~~~r~kk~~aHDe~n~~~~GD~V~I~e~-RPlSKtK~~~v~~i~~~~~~   82 (84)
T CHL00142         21 VAVENRYKHPIYGKIITKTKKYLVHDEENECNIGDQVLIEET-RPLSKTKRWILKEILSKSSL   82 (84)
T ss_pred             EEEEEEEEcCcccEEEEeeEEEEEeCCCCCCCCCCEEEEEEc-CCCCCcEEEEEEEEEEeeec
Confidence            468999999999999999999999999999999999999999 99999999999999998754

>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]

Probab=99.84  E-value=4.8e-21  Score=153.30  Aligned_cols=61  Identities=25%  Similarity=0.177  Sum_probs=58.6

Q ss_pred             ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecC
Q psy13112         94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  155 (302)
Q Consensus        94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG  155 (302)
                      -.|+++.+||.|+||++++++|+||||+|+|++||+|.|.|| |||||+|+|.|.+|++.++
T Consensus        26 V~ve~~~~hp~Y~K~v~r~kK~~aHde~~~~k~GD~V~I~Et-RPLSKtK~~~vv~i~~~a~   86 (87)
T COG0186          26 VEVERKVYHPKYGKYVRRSKKYHAHDECNEAKVGDIVRIAET-RPLSKTKRFVVVEIVEKAV   86 (87)
T ss_pred             EEEEEEEecccceEEEEEEeeeEeecccccCCCCCEEEEEEc-cccCCcceEEEEEEeeecc
Confidence            358999999999999999999999999999999999999999 9999999999999999875

>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed

Probab=99.81  E-value=6e-20  Score=151.67  Aligned_cols=60  Identities=22%  Similarity=0.153  Sum_probs=57.8

Q ss_pred             ceeeeeeeccccceEEeeeceEEeeCCC-CCCCCCCEEEEeecCcccccceeEEEeeEEeec
Q psy13112         94 YMQPRVANTRNEVRYFPKFTVMYAHDPD-KICKTGDIVLIEELPQKLTTLITHKVNKVVYPL  154 (302)
Q Consensus        94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~-N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~ka  154 (302)
                      ..|+|+++||.|+||++++++|+||||+ |+|++||+|+|.|| |||||+|+|.|.+|++++
T Consensus        47 V~v~r~~~hpkY~K~i~r~kky~aHDe~cn~~kvGD~V~I~E~-RPiSKtK~w~v~~i~~~~  107 (108)
T PRK08572         47 VEREYLHYVPKYERYEKRRSRIHAHNPPCIDAKVGDKVKIAEC-RPLSKTKSFVVVEKKERA  107 (108)
T ss_pred             EEEEEEEecCCccEEEEEeeeEEEECCCCCCCCCCCEEEEEEc-CCCCCceEEEEEEEEEcC
Confidence            5689999999999999999999999999 99999999999999 999999999999999875

>TIGR03630 arch_S17P archaeal ribosomal protein S17P

Probab=99.79  E-value=1.5e-19  Score=148.09  Aligned_cols=57  Identities=28%  Similarity=0.282  Sum_probs=54.9

Q ss_pred             ceeeeeeeccccceEEeeeceEEeeCCC-CCCCCCCEEEEeecCcccccceeEEEeeEE
Q psy13112         94 YMQPRVANTRNEVRYFPKFTVMYAHDPD-KICKTGDIVLIEELPQKLTTLITHKVNKVV  151 (302)
Q Consensus        94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~-N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV  151 (302)
                      ..|+|+++||.|+||++++++|+||||+ |+|++||+|+|.|| |||||+|+|.|.+|+
T Consensus        45 V~V~r~~~hpkY~K~i~r~kky~aHDe~cn~~kvGD~V~I~E~-RPlSKtK~w~vv~i~  102 (102)
T TIGR03630        45 VEREYLYYDRKYERYERRRSKIHAHNPPCIDVKEGDIVIIGET-RPLSKTKSFVVLGKV  102 (102)
T ss_pred             EEEEEEEecCCccEEEEEeeeEEEECCCCCCCCCCCEEEEEEc-CCCCCceEEEEEEeC
Confidence            4689999999999999999999999999 99999999999999 999999999999985

This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.

>PF00366 Ribosomal_S17: Ribosomal protein S17; InterPro: IPR000266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.79  E-value=1.5e-19  Score=137.75  Aligned_cols=55  Identities=27%  Similarity=0.383  Sum_probs=52.5

Q ss_pred             eeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeE
Q psy13112         95 MQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKV  150 (302)
Q Consensus        95 ~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eI  150 (302)
                      .|+|+++||.|+|+++++++|+||||+|+|++||+|+|.|| +||||+|+|.|.+|
T Consensus        15 ~v~~~~~~~ky~K~~~~~kk~~aHD~~~~~~vGD~V~I~e~-rPiSk~K~~~v~~v   69 (69)
T PF00366_consen   15 RVERLVYHPKYKKYIKRTKKYMAHDENNICKVGDKVRIREC-RPISKTKRFVVVEV   69 (69)
T ss_dssp             EEEEEEEETTTEEEEEEEEEEEEE-TTSSSTTTSEEEEEEE-EEEETTEEEEEEEE
T ss_pred             EEEEEEEcceEeeccCccccEEEeCCccCCCCCCEEEEEee-eccCCcEeEEEEEC
Confidence            58899999999999999999999999999999999999999 99999999999986

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 [, ]. The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [] has revealed that S17 has virtually no groups exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_Q 2VHP_Q 3BBN_Q 2QAL_Q 3OAR_Q 1VS5_Q 3KC4_Q 2AW7_Q 3E1C_J 2AVY_Q ....

>TIGR03635 S17_bact 30S ribosomal protein S17

Probab=99.78  E-value=2.1e-19  Score=138.22  Aligned_cols=52  Identities=23%  Similarity=0.294  Sum_probs=50.5

Q ss_pred             eeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEE
Q psy13112         95 MQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKV  147 (302)
Q Consensus        95 ~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V  147 (302)
                      .|+|++.||.|+||++++++|+||||+|.|++||+|+|.|| +||||+|+|.|
T Consensus        20 ~v~~~~~h~ky~k~~~r~kk~~aHD~~~~~k~GD~V~I~ec-rPlSK~K~~~~   71 (71)
T TIGR03635        20 LVERRVKHPLYGKIVKRTKKYHAHDENNECKVGDVVRIIET-RPLSKTKRWRL   71 (71)
T ss_pred             EEEEEEEeccccEEEEccEEEEEECCCCCCCCCCEEEEEEc-CCcCCceEeEC
Confidence            58899999999999999999999999999999999999999 99999999986

This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.

>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]

Probab=99.77  E-value=5e-19  Score=141.73  Aligned_cols=53  Identities=30%  Similarity=0.305  Sum_probs=50.5

Q ss_pred             eeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCC
Q psy13112        170 RVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  223 (302)
Q Consensus       170 rp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G  223 (302)
                      -|.|+||+++++||+||||+|+|++||+|.|.|| |||||+|+|.|++|++.++
T Consensus        34 hp~Y~K~v~r~kK~~aHde~~~~k~GD~V~I~Et-RPLSKtK~~~vv~i~~~a~   86 (87)
T COG0186          34 HPKYGKYVRRSKKYHAHDECNEAKVGDIVRIAET-RPLSKTKRFVVVEIVEKAV   86 (87)
T ss_pred             cccceEEEEEEeeeEeecccccCCCCCEEEEEEc-cccCCcceEEEEEEeeecc
Confidence            4689999999999999999999999999999999 7999999999999999865

>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed

Probab=99.76  E-value=8.5e-19  Score=138.72  Aligned_cols=74  Identities=23%  Similarity=0.200  Sum_probs=59.0

Q ss_pred             EEEeeEEeecCCccCCccceeeec---ceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeec
Q psy13112        145 HKVNKVVYPLGDITDPITGKKVVG---LRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYP  221 (302)
Q Consensus       145 W~V~eIV~kaG~i~DPiTGK~VVG---Lrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k  221 (302)
                      ..+..+|-.. .+ | .|....|.   ..+.|+||++++++|+||||+|+|++||+|+|.|| |||||+|+|.|.+|+.+
T Consensus         7 ~~l~G~Vvs~-km-~-KTvvV~v~r~~~h~kY~K~~~r~kk~~aHD~~n~~k~GD~V~I~e~-rPlSK~K~~~v~~i~~~   82 (84)
T PRK05610          7 KTLQGRVVSD-KM-D-KTIVVLVERRVKHPLYGKIVKRSKKYHAHDENNEAKIGDVVRIMET-RPLSKTKRWRLVEIVEK   82 (84)
T ss_pred             CEEEEEEEcc-cC-C-ceEEEEEEEEEEeccccEEEEcceEEEEECCCCCCCCCCEEEEEEc-ccCCCCEEEEEEEEEec
Confidence            3455555544 22 2 45443332   45699999999999999999999999999999999 79999999999999986


Q ss_pred             C
Q psy13112        222 L  222 (302)
Q Consensus       222 ~  222 (302)
                      +
T Consensus        83 ~   83 (84)
T PRK05610         83 A   83 (84)
T ss_pred             c
Confidence            4

>CHL00142 rps17 ribosomal protein S17; Validated

Probab=99.76  E-value=1e-18  Score=138.55  Aligned_cols=54  Identities=26%  Similarity=0.337  Sum_probs=50.7

Q ss_pred             eeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCCC
Q psy13112        170 RVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGD  224 (302)
Q Consensus       170 rp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G~  224 (302)
                      .+.|+||++++++|+||||+|+|++||+|+|.|| |||||+|+|.|++|+.++-.
T Consensus        29 h~kY~K~~~r~kk~~aHDe~n~~~~GD~V~I~e~-RPlSKtK~~~v~~i~~~~~~   82 (84)
T CHL00142         29 HPIYGKIITKTKKYLVHDEENECNIGDQVLIEET-RPLSKTKRWILKEILSKSSL   82 (84)
T ss_pred             cCcccEEEEeeEEEEEeCCCCCCCCCCEEEEEEc-CCCCCcEEEEEEEEEEeeec
Confidence            4689999999999999999999999999999999 79999999999999988643

>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed

Probab=99.71  E-value=1.4e-17  Score=137.63  Aligned_cols=51  Identities=24%  Similarity=0.212  Sum_probs=49.0

Q ss_pred             eecceeeeeeeeEEeeCCC-CCCCCCCEEEEeecCCCcCcceeEEEEEeeecC
Q psy13112        171 VDLGKYFPKFTVMYAHDPD-KICKTGDIVLIEELPQKLTTLITHKVNKVVYPL  222 (302)
Q Consensus       171 p~y~K~ikRskKY~AHDen-N~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~  222 (302)
                      +.|+||++++++|+||||+ |+|++||+|+|.|| |||||+|+|.|++|+.++
T Consensus        56 pkY~K~i~r~kky~aHDe~cn~~kvGD~V~I~E~-RPiSKtK~w~v~~i~~~~  107 (108)
T PRK08572         56 PKYERYEKRRSRIHAHNPPCIDAKVGDKVKIAEC-RPLSKTKSFVVVEKKERA  107 (108)
T ss_pred             CCccEEEEEeeeEEEECCCCCCCCCCCEEEEEEc-CCCCCceEEEEEEEEEcC
Confidence            6899999999999999999 99999999999999 799999999999999874

>PF00366 Ribosomal_S17: Ribosomal protein S17; InterPro: IPR000266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.70  E-value=1.5e-17  Score=126.78  Aligned_cols=49  Identities=31%  Similarity=0.443  Sum_probs=45.8

Q ss_pred             ceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEe
Q psy13112        169 LRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKV  218 (302)
Q Consensus       169 Lrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eI  218 (302)
                      ..+.|+|+++++++|+||||+|+|++||+|+|+|| +||||+|+|.|.+|
T Consensus        21 ~~~ky~K~~~~~kk~~aHD~~~~~~vGD~V~I~e~-rPiSk~K~~~v~~v   69 (69)
T PF00366_consen   21 YHPKYKKYIKRTKKYMAHDENNICKVGDKVRIREC-RPISKTKRFVVVEV   69 (69)
T ss_dssp             EETTTEEEEEEEEEEEEE-TTSSSTTTSEEEEEEE-EEEETTEEEEEEEE
T ss_pred             EcceEeeccCccccEEEeCCccCCCCCCEEEEEee-eccCCcEeEEEEEC
Confidence            46789999999999999999999999999999999 79999999999986

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 [, ]. The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [] has revealed that S17 has virtually no groups exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_Q 2VHP_Q 3BBN_Q 2QAL_Q 3OAR_Q 1VS5_Q 3KC4_Q 2AW7_Q 3E1C_J 2AVY_Q ....

>TIGR03630 arch_S17P archaeal ribosomal protein S17P

Probab=99.69  E-value=3.6e-17  Score=134.20  Aligned_cols=49  Identities=29%  Similarity=0.329  Sum_probs=46.6

Q ss_pred             eeecceeeeeeeeEEeeCCC-CCCCCCCEEEEeecCCCcCcceeEEEEEee
Q psy13112        170 RVDLGKYFPKFTVMYAHDPD-KICKTGDIVLIEELPQKLTTLITHKVNKVV  219 (302)
Q Consensus       170 rp~y~K~ikRskKY~AHDen-N~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV  219 (302)
                      .+.|+|+++++++|+||||+ |.|++||+|+|.|| |||||+|+|.|++|+
T Consensus        53 hpkY~K~i~r~kky~aHDe~cn~~kvGD~V~I~E~-RPlSKtK~w~vv~i~  102 (102)
T TIGR03630        53 DRKYERYERRRSKIHAHNPPCIDVKEGDIVIIGET-RPLSKTKSFVVLGKV  102 (102)
T ss_pred             cCCccEEEEEeeeEEEECCCCCCCCCCCEEEEEEc-CCCCCceEEEEEEeC
Confidence            45899999999999999999 99999999999999 799999999999985

This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.

>PTZ00241 40S ribosomal protein S11; Provisional

Probab=99.69  E-value=6.1e-17  Score=141.40  Aligned_cols=59  Identities=22%  Similarity=0.215  Sum_probs=56.0

Q ss_pred             eeeeeeeccccceEEeeeceEEeeC-CCCCCCCCCEEEEeecCcccccceeEEEeeEEeec
Q psy13112         95 MQPRVANTRNEVRYFPKFTVMYAHD-PDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPL  154 (302)
Q Consensus        95 ~VeR~vkHp~YkKy~kKskKY~AHD-e~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~ka  154 (302)
                      .|+++.+||.|+||++++++|+||| |.|.|++||+|.|.|| |||||+|+|.|.+|+.++
T Consensus        87 ~ve~~~~h~kY~K~~kr~kk~~aHd~~~~~~kvGD~V~I~Ec-RPLSKTKrf~Vv~V~~~~  146 (158)
T PTZ00241         87 RRDYLHYVKKYNRYEKRHKNIPVHCSPCFDVKEGDIVVVGQC-RPLSKTVRFNVLKVEKNE  146 (158)
T ss_pred             EEEEEEecCccceEEEeeecEEEeCCccCCCCCCCEEEEEEc-CCCCCceeEEEEEEEecc
Confidence            5678999999999999999999998 5899999999999999 999999999999999875

>TIGR03635 S17_bact 30S ribosomal protein S17

Probab=99.68  E-value=2.8e-17  Score=126.46  Aligned_cols=66  Identities=27%  Similarity=0.281  Sum_probs=52.1

Q ss_pred             EEeeEEeecCCccCCccceeee---cceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEE
Q psy13112        146 KVNKVVYPLGDITDPITGKKVV---GLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKV  215 (302)
Q Consensus       146 ~V~eIV~kaG~i~DPiTGK~VV---GLrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V  215 (302)
                      .+..+|-... + | .|....|   ...+.|+|+++++++|+||||+|.|++||+|+|.|| |||||+|+|.|
T Consensus         3 ~l~G~Vvs~k-m-~-KTvvV~v~~~~~h~ky~k~~~r~kk~~aHD~~~~~k~GD~V~I~ec-rPlSK~K~~~~   71 (71)
T TIGR03635         3 TLQGVVVSDK-M-D-KTIVVLVERRVKHPLYGKIVKRTKKYHAHDENNECKVGDVVRIIET-RPLSKTKRWRL   71 (71)
T ss_pred             EEEEEEEccc-C-C-ceEEEEEEEEEEeccccEEEEccEEEEEECCCCCCCCCCEEEEEEc-CCcCCceEeEC
Confidence            4555555442 2 2 4554333   245689999999999999999999999999999999 79999999986

This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.

>KOG1740|consensus

Probab=99.64  E-value=1.2e-17  Score=137.62  Aligned_cols=63  Identities=19%  Similarity=0.247  Sum_probs=60.6

Q ss_pred             ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecCCc
Q psy13112         94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDI  157 (302)
Q Consensus        94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i  157 (302)
                      ..|+|+++||.|++|++++.+|+|||+.|+|++||.|.|+.| |||||+|.|.+.+||.+++.+
T Consensus        20 V~V~rl~~n~~ynryv~~~~kymahD~~n~cnvGD~Vrleps-RPlSk~K~f~i~eII~~a~r~   82 (107)
T KOG1740|consen   20 VRVDRLFFNPKYNRYVKRTSKYMAHDDKNQCNVGDRVRLEPS-RPLSKTKHFIIAEIIKKARRY   82 (107)
T ss_pred             EEeeeccccHHHHHHHHHhhheeecCccccccccceEEeccC-CcccccceeehHHHHHHHhhh
Confidence            368999999999999999999999999999999999999999 999999999999999998875

>PTZ00241 40S ribosomal protein S11; Provisional

Probab=99.57  E-value=3.2e-15  Score=130.70  Aligned_cols=51  Identities=24%  Similarity=0.260  Sum_probs=48.3

Q ss_pred             eecceeeeeeeeEEeeC-CCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecC
Q psy13112        171 VDLGKYFPKFTVMYAHD-PDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPL  222 (302)
Q Consensus       171 p~y~K~ikRskKY~AHD-enN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~  222 (302)
                      +.|+||++|+++|+||| |.|.|++||+|.|.|| |||||+|+|.|++|+.++
T Consensus        95 ~kY~K~~kr~kk~~aHd~~~~~~kvGD~V~I~Ec-RPLSKTKrf~Vv~V~~~~  146 (158)
T PTZ00241         95 KKYNRYEKRHKNIPVHCSPCFDVKEGDIVVVGQC-RPLSKTVRFNVLKVEKNE  146 (158)
T ss_pred             CccceEEEeeecEEEeCCccCCCCCCCEEEEEEc-CCCCCceeEEEEEEEecc
Confidence            48999999999999998 5899999999999999 799999999999999875

>KOG1740|consensus

Probab=99.49  E-value=1.7e-15  Score=125.06  Aligned_cols=63  Identities=21%  Similarity=0.265  Sum_probs=56.1

Q ss_pred             Cccceeee---cceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCC
Q psy13112        160 PITGKKVV---GLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  223 (302)
Q Consensus       160 PiTGK~VV---GLrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G  223 (302)
                      +.|.+.-|   .+++.|++|++++.+|+|||+.|+|++||.|.|+.| |||||+|+|++.+||.+++
T Consensus        15 qKTv~V~V~rl~~n~~ynryv~~~~kymahD~~n~cnvGD~Vrleps-RPlSk~K~f~i~eII~~a~   80 (107)
T KOG1740|consen   15 QKTVKVRVDRLFFNPKYNRYVKRTSKYMAHDDKNQCNVGDRVRLEPS-RPLSKTKHFIIAEIIKKAR   80 (107)
T ss_pred             CceeEEEeeeccccHHHHHHHHHhhheeecCccccccccceEEeccC-CcccccceeehHHHHHHHh
Confidence            45655544   367899999999999999999999999999999999 7999999999999999854

>KOG1728|consensus

Probab=97.47  E-value=6.1e-05  Score=66.20  Aligned_cols=64  Identities=27%  Similarity=0.294  Sum_probs=52.4

Q ss_pred             CCceeeeeeec--cccceEEeeeceEEeeC-CCCC-CCCCCEEEEeecCcccccceeEEEeeEEeecCC
Q psy13112         92 RPYMQPRVANT--RNEVRYFPKFTVMYAHD-PDKI-CKTGDIVLIEELPQKLTTLITHKVNKVVYPLGD  156 (302)
Q Consensus        92 ~~~~VeR~vkH--p~YkKy~kKskKY~AHD-e~N~-cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~  156 (302)
                      |--+|.|-++|  +.|+.|=++.+.+-||= |-.. .++||+|.|-|| +||||++++.|.+++..+|.
T Consensus        82 rTIvvrrdYlHy~~KY~ryekrHkN~svh~SPcFrdi~~gDiVtvGec-rPLSKtvrfnVLkv~k~~g~  149 (156)
T KOG1728|consen   82 RTIVVRRDYLHYIKKYNRYEKRHKNMSVHVSPCFRDIQEGDIVTVGEC-RPLSKTVRFNVLKVIKAAGS  149 (156)
T ss_pred             EEEEEEhhhhhHhHHhhHHHHhccCCccccchhhhccccCCEEEEeec-ccccceEEEEEEEEeecCCC
Confidence            45566677777  56777888888888884 3333 789999999999 99999999999999998876

>KOG1728|consensus

Probab=97.32  E-value=0.00015  Score=63.87  Aligned_cols=46  Identities=28%  Similarity=0.358  Sum_probs=36.5

Q ss_pred             eeeeeEEeeC-CCCC-CCCCCEEEEeecCCCcCcceeEEEEEeeecCCC
Q psy13112        178 PKFTVMYAHD-PDKI-CKTGDIVLIEELPQKLTTLITHKVNKVVYPLGD  224 (302)
Q Consensus       178 kRskKY~AHD-enN~-ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G~  224 (302)
                      +|.+.+-||= |-.. .++||+|.|-|| |||||++++.|.+++..+|.
T Consensus       102 krHkN~svh~SPcFrdi~~gDiVtvGec-rPLSKtvrfnVLkv~k~~g~  149 (156)
T KOG1728|consen  102 KRHKNMSVHVSPCFRDIQEGDIVTVGEC-RPLSKTVRFNVLKVIKAAGS  149 (156)
T ss_pred             HhccCCccccchhhhccccCCEEEEeec-ccccceEEEEEEEEeecCCC
Confidence            4555555663 2233 789999999999 79999999999999998763

>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus

Probab=81.82  E-value=3.6  Score=29.45  Aligned_cols=53  Identities=23%  Similarity=0.322  Sum_probs=31.7

Q ss_pred             eeEEeecCCccCCccceeeec--ceeecce---eeeeeeeEEeeCCCCCCCCCCEEEEeec
Q psy13112        148 NKVVYPLGDITDPITGKKVVG--LRVDLGK---YFPKFTVMYAHDPDKICKTGDIVLIEEL  203 (302)
Q Consensus       148 ~eIV~kaG~i~DPiTGK~VVG--Lrp~y~K---~ikRskKY~AHDenN~ckvGDiV~I~Ec  203 (302)
                      .++.-..+.   |.-|+.+..  ++..++-   -+.|...+..=+++-..+.||+|.|.-.
T Consensus         2 ~e~~V~~~s---~~~gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~   59 (71)
T PF02080_consen    2 VEVRVPENS---PLVGKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGD   59 (71)
T ss_dssp             EEEE--TTB---TTTTEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEE
T ss_pred             EEEEECCCC---CCCCCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEEC
Confidence            344444555   677888877  3332222   2356677777788999999999999977

The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	302
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.2 bits (93), Expect = 6e-04
 Identities = 49/318 (15%), Positives = 80/318 (25%), Gaps = 118/318 (37%)

Query: 18  FFETRLRDDISFQERSQGSAKCDLMPTPRSPREREARPHAQPRKAPGSAQRDRKQGSAKR 77
           F E  LR +  F           LM    SP + E R   QP           +    +R
Sbjct: 82  FVEEVLRINYKF-----------LM----SPIKTEQR---QP-------SMMTRMYIEQR 116

Query: 78  DPMHNPTKPQERVARPYMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQ 137
           D ++                      N+ + F K+ V                   +L Q
Sbjct: 117 DRLY----------------------NDNQVFAKYNVSRLQ------------PYLKLRQ 142

Query: 138 KLTTLITHKVNKVVY-PLGDITDPITGKKVVGL------RVDLGKYFPKF--TVMYAHDP 188
            L  L   K N ++   LG      +GK  V L      +V     F  F   +   + P
Sbjct: 143 ALLELRPAK-NVLIDGVLG------SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSP 195

Query: 189 DKI---------------CKTGD-----IVLIEELPQKLTTLITHKVNKVVYP-----LG 223
           + +                   D      + I  +  +L  L+  K     Y      L 
Sbjct: 196 ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK----PYENCLLVLL 251

Query: 224 DITDPITGKKV-VGLRTAVLTADFYKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHR 282
           ++ +        +  +  + T            K                       T  
Sbjct: 252 NVQNAKAWNAFNLSCKILLTTRF----------KQVTDFLSAATTTHISLDHHSMTLTPD 301

Query: 283 ES---YIRYHEFDDDDQP 297
           E     ++Y +    D P
Sbjct: 302 EVKSLLLKYLDCRPQDLP 319

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	302
1qd7_I	89	S17 ribosomal protein; 30S ribosomal subunit, low	99.87
3r8n_Q	80	30S ribosomal protein S17; protein biosynthesis, R	99.86
2vqe_Q	105	30S ribosomal protein S17; tRNA-binding, rRNA-bind	99.85
3bbn_Q	142	Ribosomal protein S17; small ribosomal subunit, sp	99.83
3j20_R	113	30S ribosomal protein S17P; archaea, archaeal, KIN	99.81
1qd7_I	89	S17 ribosomal protein; 30S ribosomal subunit, low	99.79
3r8n_Q	80	30S ribosomal protein S17; protein biosynthesis, R	99.78
2xzm_Q	157	Ribosomal protein S17 containing protein; ribosome	99.77
3u5c_L	156	RP41, S18, YS12, 40S ribosomal protein S11-A; tran	99.77
2vqe_Q	105	30S ribosomal protein S17; tRNA-binding, rRNA-bind	99.76
2zkq_q	158	40S ribosomal protein S11E; protein-RNA complex, 4	99.75
3bbn_Q	142	Ribosomal protein S17; small ribosomal subunit, sp	99.73
3j20_R	113	30S ribosomal protein S17P; archaea, archaeal, KIN	99.72
3iz6_P	161	40S ribosomal protein S11 (S17P); eukaryotic ribos	99.68
2xzm_Q	157	Ribosomal protein S17 containing protein; ribosome	99.68
3u5c_L	156	RP41, S18, YS12, 40S ribosomal protein S11-A; tran	99.68
2zkq_q	158	40S ribosomal protein S11E; protein-RNA complex, 4	99.65
3iz6_P	161	40S ribosomal protein S11 (S17P); eukaryotic ribos	99.58

>1qd7_I S17 ribosomal protein; 30S ribosomal subunit, low resolution model, ribosome; 5.50A {Thermus thermophilus} SCOP: i.1.1.3 PDB: 1eg0_G 1rip_A

Probab=99.87  E-value=2.3e-22  Score=159.70  Aligned_cols=62  Identities=19%  Similarity=0.116  Sum_probs=59.3

Q ss_pred             ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecCC
Q psy13112         94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGD  156 (302)
Q Consensus        94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~  156 (302)
                      -.|+|+++||+|+||++++++|+||||+|+|++||+|+|.|| +||||+|+|.|.+|++++..
T Consensus        20 V~ve~~~~hp~Y~K~~kr~kk~~aHDe~n~~k~GD~V~I~E~-RPlSKtK~~~vv~iv~~a~~   81 (89)
T 1qd7_I           20 VLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMET-RPLSATKRFRLVEIVEKAVR   81 (89)
T ss_pred             EEEEEEEEcCccceEEeccEEEEEeCCccCCCCCCEEEEEEc-ccCCCCEEEEEEEEEeecee
Confidence            368999999999999999999999999999999999999999 99999999999999998764

>2vqe_Q 30S ribosomal protein S17; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: b.40.4.5 PDB: 1gix_T* 1hnw_Q* 1hnx_Q* 1hnz_Q* 1hr0_Q 1ibk_Q* 1ibl_Q* 1ibm_Q 1jgo_T* 1jgp_T* 1jgq_T* 1ml5_T* 1xmo_Q* 1xmq_Q* 1xnq_Q* 1xnr_Q* 1yl4_T 2b64_Q* 2b9m_Q* 2b9o_Q* ...

Probab=99.85  E-value=1.6e-21  Score=158.85  Aligned_cols=62  Identities=21%  Similarity=0.176  Sum_probs=59.2

Q ss_pred             ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecCC
Q psy13112         94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGD  156 (302)
Q Consensus        94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~  156 (302)
                      ..|+|+++||+|+||++++++|+||||+|+|++||+|+|.|| +||||+|+|.|.+|++++..
T Consensus        21 V~ver~~~hpkY~K~~kr~kk~~aHDe~n~~k~GD~V~I~E~-RPlSKtKr~~vv~iv~~a~~   82 (105)
T 2vqe_Q           21 VLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIES-RPISKRKRFRVLRLVESGRM   82 (105)
T ss_dssp             EEEEEEEECTTTCCEEEEEEEEEEECTTCCCCTTCEEEEEEE-EEEETTEEEEEEEEEECCCH
T ss_pred             EEEEEEEEcCccceEEecceEEEEECCCCCCCCCCEEEEEEc-ccCCCCEEEEEEEEeecccc
Confidence            358899999999999999999999999999999999999999 99999999999999998763

>3bbn_Q Ribosomal protein S17; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1

Probab=99.83  E-value=4.9e-21  Score=163.33  Aligned_cols=61  Identities=23%  Similarity=0.217  Sum_probs=58.8

Q ss_pred             ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecC
Q psy13112         94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  155 (302)
Q Consensus        94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG  155 (302)
                      ..|+|+++||+|+||++++++|+||||+|+|++||+|+|.|| +||||+|+|.|++|++++.
T Consensus        78 V~Ver~~~hpkY~K~vkr~kKy~AHDe~n~~kvGD~V~I~E~-RPLSKtKrw~VveIveka~  138 (142)
T 3bbn_Q           78 VEVVRLAPHPKYKRRVRMKKKYQAHDPDNQFKVGDVVRLEKS-RPISKTKSFVALPVIARAA  138 (142)
T ss_dssp             EEEEEEEECSSSCSEEEEEEEEEEECTTCCCCTTEEEEEEEC-CCSSSSCCEEECCCSEEEC
T ss_pred             EEEEEEEEcCccccEEecceEEEEECCCCCCCCCCEEEEEEc-cCCCCcEEEEEEEEEeccc
Confidence            468999999999999999999999999999999999999999 9999999999999999875

>3j20_R 30S ribosomal protein S17P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=99.81  E-value=3e-20  Score=153.21  Aligned_cols=61  Identities=25%  Similarity=0.170  Sum_probs=58.5

Q ss_pred             ceeeeeeeccccceEEeeeceEEeeCC-CCCCCCCCEEEEeecCcccccceeEEEeeEEeecC
Q psy13112         94 YMQPRVANTRNEVRYFPKFTVMYAHDP-DKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  155 (302)
Q Consensus        94 ~~VeR~vkHp~YkKy~kKskKY~AHDe-~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG  155 (302)
                      ..|+|+++||+|+||++++++|+|||| +|+|++||+|.|.|| +||||+|+|.|.+|+++|.
T Consensus        49 V~ve~~~~hpkY~K~~kr~kk~~aHDe~~n~~~vGD~V~I~E~-RPlSKtKr~~vv~i~~~a~  110 (113)
T 3j20_R           49 VERQYYFYLNKYERYELRRSKIHAHNPPCINAKVGDKVLIAET-RPLSKTKHFVVVAVLERAE  110 (113)
T ss_dssp             EEEEEEEEETTTTEEEEEEEEEEEECCTTSCCCTTSEEEEEEC-SCSSSSEEEEEEEECCCCC
T ss_pred             EEEEEEEEcCcccEEEECceEEEEECCCCCCCCCCCEEEEEec-ccCCCcEeEEEEEEEeccc
Confidence            467899999999999999999999999 899999999999999 9999999999999999874

>1qd7_I S17 ribosomal protein; 30S ribosomal subunit, low resolution model, ribosome; 5.50A {Thermus thermophilus} SCOP: i.1.1.3 PDB: 1eg0_G 1rip_A

Probab=99.79  E-value=7.5e-20  Score=145.30  Aligned_cols=54  Identities=26%  Similarity=0.203  Sum_probs=51.1

Q ss_pred             ceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCC
Q psy13112        169 LRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  223 (302)
Q Consensus       169 Lrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G  223 (302)
                      ..|+|+||++++++|+||||+|+|++||+|+|.|| |||||+|+|.|++|++++.
T Consensus        27 ~hp~Y~K~~kr~kk~~aHDe~n~~k~GD~V~I~E~-RPlSKtK~~~vv~iv~~a~   80 (89)
T 1qd7_I           27 KHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMET-RPLSATKRFRLVEIVEKAV   80 (89)
T ss_pred             EcCccceEEeccEEEEEeCCccCCCCCCEEEEEEc-ccCCCCEEEEEEEEEeece
Confidence            34699999999999999999999999999999999 7999999999999999865

>2xzm_Q Ribosomal protein S17 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_Q

Probab=99.77  E-value=3.3e-19  Score=154.12  Aligned_cols=59  Identities=19%  Similarity=0.191  Sum_probs=56.2

Q ss_pred             eeeeeeeccccceEEeeeceEEeeC-CCCCCCCCCEEEEeecCcccccceeEEEeeEEeec
Q psy13112         95 MQPRVANTRNEVRYFPKFTVMYAHD-PDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPL  154 (302)
Q Consensus        95 ~VeR~vkHp~YkKy~kKskKY~AHD-e~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~ka  154 (302)
                      .|+++++||+|+||++++++|+||| |+|+|++||+|+|.|| |||||+|+|.|++|++++
T Consensus        86 ~ve~~~~hpkY~K~vkr~kKy~AHDee~n~~kvGD~V~I~Ec-RPLSKtKrw~Vv~I~~ka  145 (157)
T 2xzm_Q           86 RRDYLHYVRKYNRYEKRHRNIPVHISPCFSVKEGDILVAGQC-RPISKTVRFNALQVVPNE  145 (157)
T ss_dssp             EEEEEEEETTTTEEEEEEEEEEEECCTTSCCCTTCEEEEEEC-CCCSSSCCEEEEEECCCC
T ss_pred             EEEEEEecCccceEeecceeEEEECCCCCCCCCCCEEEEEEc-CCCCCcEEEEEEEEEecc
Confidence            3888999999999999999999999 6899999999999999 999999999999999875

>3u5c_L RP41, S18, YS12, 40S ribosomal protein S11-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_P 3o30_F 3o2z_F 3u5g_L 3jyv_Q* 1s1h_Q

Probab=99.77  E-value=3.8e-19  Score=153.63  Aligned_cols=60  Identities=18%  Similarity=0.203  Sum_probs=57.3

Q ss_pred             eeeeeeeccccceEEeeeceEEeeCC-CCCCCCCCEEEEeecCcccccceeEEEeeEEeecC
Q psy13112         95 MQPRVANTRNEVRYFPKFTVMYAHDP-DKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  155 (302)
Q Consensus        95 ~VeR~vkHp~YkKy~kKskKY~AHDe-~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG  155 (302)
                      .|+++.+||+|+||++++++|+|||| +|+|++||+|+|.|| +||||+|+|.|++|++++|
T Consensus        87 ~ve~~~~hpkY~K~vkr~kKy~AHDe~~n~~kvGD~V~I~Ec-RPLSKtKrw~Vv~Iv~ka~  147 (156)
T 3u5c_L           87 RRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVGDIVTVGQC-RPISKTVRFNVVKVSAAAG  147 (156)
T ss_dssp             EEEEEEEEGGGTEEEEEEEEEEEECCTTSCCCTTCEEEEEEE-EEEETTEEEEEEEECCCCS
T ss_pred             EEEEEeecCccceEEECceEEEEECCCcCcCCCCCEEEEEec-ccCCCcEeEEEEEEEecCC
Confidence            47789999999999999999999998 689999999999999 9999999999999999986

>2vqe_Q 30S ribosomal protein S17; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: b.40.4.5 PDB: 1gix_T* 1hnw_Q* 1hnx_Q* 1hnz_Q* 1hr0_Q 1ibk_Q* 1ibl_Q* 1ibm_Q 1jgo_T* 1jgp_T* 1jgq_T* 1ml5_T* 1xmo_Q* 1xmq_Q* 1xnq_Q* 1xnr_Q* 1yl4_T 2b64_Q* 2b9m_Q* 2b9o_Q* ...

Probab=99.76  E-value=4.3e-19  Score=144.64  Aligned_cols=54  Identities=26%  Similarity=0.282  Sum_probs=51.0

Q ss_pred             ceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCC
Q psy13112        169 LRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  223 (302)
Q Consensus       169 Lrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G  223 (302)
                      ..++|+||++++++|+||||+|+|++||+|+|.|| |||||+|+|.|++|++++.
T Consensus        28 ~hpkY~K~~kr~kk~~aHDe~n~~k~GD~V~I~E~-RPlSKtKr~~vv~iv~~a~   81 (105)
T 2vqe_Q           28 PHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIES-RPISKRKRFRVLRLVESGR   81 (105)
T ss_dssp             ECTTTCCEEEEEEEEEEECTTCCCCTTCEEEEEEE-EEEETTEEEEEEEEEECCC
T ss_pred             EcCccceEEecceEEEEECCCCCCCCCCEEEEEEc-ccCCCCEEEEEEEEeeccc
Confidence            34699999999999999999999999999999999 8999999999999999865

>2zkq_q 40S ribosomal protein S11E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 3jyv_Q* 1s1h_Q

Probab=99.75  E-value=8e-19  Score=151.84  Aligned_cols=60  Identities=23%  Similarity=0.234  Sum_probs=52.9

Q ss_pred             eeeeeeeccccceEEeeeceEEeeCCC-C-CCCCCCEEEEeecCcccccceeEEEeeEEeecC
Q psy13112         95 MQPRVANTRNEVRYFPKFTVMYAHDPD-K-ICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  155 (302)
Q Consensus        95 ~VeR~vkHp~YkKy~kKskKY~AHDe~-N-~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG  155 (302)
                      .|+++++||+|+||++++++|+||||+ | +|++||+|+|.|| |||||+|+|.|++|+..+|
T Consensus        89 ~ve~~~~hpkY~K~vkr~kKy~AHDe~~n~~~kvGD~V~I~E~-RPLSKtKrw~Vv~I~~~~~  150 (158)
T 2zkq_q           89 RRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIGDIVTVGEC-RPLSKTVRFNVLKVTKAAG  150 (158)
T ss_dssp             EEEEECSSTTCCCEEEEEEEECCBCCSSCCCC-CCCEEEEECC-SCSSSCC-CEEEEEEEC--
T ss_pred             EEEEEEecCccceeeecceeEEEECCcccCcCCCCCEEEEEEc-cccCCcEEEEEEEEecCCC
Confidence            388899999999999999999999986 4 8999999999999 9999999999999998665

>3bbn_Q Ribosomal protein S17; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1

Probab=99.73  E-value=1.4e-18  Score=148.23  Aligned_cols=81  Identities=19%  Similarity=0.101  Sum_probs=60.2

Q ss_pred             cccceeEEEeeEEeecCCccCCccceeeec---ceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEE
Q psy13112        139 LTTLITHKVNKVVYPLGDITDPITGKKVVG---LRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKV  215 (302)
Q Consensus       139 LSK~KtW~V~eIV~kaG~i~DPiTGK~VVG---Lrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V  215 (302)
                      ++-.-+..+..+|-.. .| | .|....|.   ..++|+||++++++|+||||+|+|++||+|+|.|| |||||+|+|.|
T Consensus        55 lsvrg~k~l~G~VVS~-KM-d-KTIvV~Ver~~~hpkY~K~vkr~kKy~AHDe~n~~kvGD~V~I~E~-RPLSKtKrw~V  130 (142)
T 3bbn_Q           55 PVIRAMKTMQGRVVCA-TS-D-KTVAVEVVRLAPHPKYKRRVRMKKKYQAHDPDNQFKVGDVVRLEKS-RPISKTKSFVA  130 (142)
T ss_dssp             -----CCEEEEEEEEC-CS-T-TEEEEEEEEEEECSSSCSEEEEEEEEEEECTTCCCCTTEEEEEEEC-CCSSSSCCEEE
T ss_pred             ccccceEEEEEEEEEc-cC-C-ceEEEEEEEEEEcCccccEEecceEEEEECCCCCCCCCCEEEEEEc-cCCCCcEEEEE
Confidence            4444423444554442 22 3 55444443   34699999999999999999999999999999999 79999999999


Q ss_pred             EEeeecCC
Q psy13112        216 NKVVYPLG  223 (302)
Q Consensus       216 ~eIV~k~G  223 (302)
                      ++|++++.
T Consensus       131 veIveka~  138 (142)
T 3bbn_Q          131 LPVIARAA  138 (142)
T ss_dssp             CCCSEEEC
T ss_pred             EEEEeccc
Confidence            99999865

>3j20_R 30S ribosomal protein S17P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=99.72  E-value=5e-18  Score=140.03  Aligned_cols=53  Identities=26%  Similarity=0.236  Sum_probs=50.2

Q ss_pred             eeecceeeeeeeeEEeeCC-CCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCC
Q psy13112        170 RVDLGKYFPKFTVMYAHDP-DKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  223 (302)
Q Consensus       170 rp~y~K~ikRskKY~AHDe-nN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G  223 (302)
                      .+.|+||++++++|+|||| +|+|++||+|+|.|| |||||+|+|.|++|++++.
T Consensus        57 hpkY~K~~kr~kk~~aHDe~~n~~~vGD~V~I~E~-RPlSKtKr~~vv~i~~~a~  110 (113)
T 3j20_R           57 LNKYERYELRRSKIHAHNPPCINAKVGDKVLIAET-RPLSKTKHFVVVAVLERAE  110 (113)
T ss_dssp             ETTTTEEEEEEEEEEEECCTTSCCCTTSEEEEEEC-SCSSSSEEEEEEEECCCCC
T ss_pred             cCcccEEEECceEEEEECCCCCCCCCCCEEEEEec-ccCCCcEeEEEEEEEeccc
Confidence            3589999999999999999 899999999999999 7999999999999999864

>3iz6_P 40S ribosomal protein S11 (S17P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=99.68  E-value=1.3e-18  Score=150.90  Aligned_cols=59  Identities=22%  Similarity=0.194  Sum_probs=33.7

Q ss_pred             eeeeeeeccccceEEeeeceEEeeCC-CCCCCCCCEEEEeecCcccccceeEEEeeEEeec
Q psy13112         95 MQPRVANTRNEVRYFPKFTVMYAHDP-DKICKTGDIVLIEELPQKLTTLITHKVNKVVYPL  154 (302)
Q Consensus        95 ~VeR~vkHp~YkKy~kKskKY~AHDe-~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~ka  154 (302)
                      .|+++++||+|+||++++++|+|||| +|+|++||+|+|.|| +||||+|+|.|++|++++
T Consensus        88 ~ve~~~~hpkY~K~vkr~kKy~AHDe~~n~~kvGD~V~I~Ec-RPLSKtKrw~Vv~Iv~~~  147 (161)
T 3iz6_P           88 RRNYLHFVKKYQRYEKRHSNIPAHVSPCFRVKEGDHVIIGQC-RPLSKTVRFNVLKVIPAG  147 (161)
T ss_dssp             ECTTCCCCSSCEEEEEECCCSSSSCCEEEEECCCCCC------------------------
T ss_pred             EEEEEEecCccceEEECceeEEEECCCCCcCCCCCEEEEEec-cCCCCcEeEEEEEEEecC
Confidence            46788999999999999999999998 799999999999999 999999999999999985

>2xzm_Q Ribosomal protein S17 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_Q

Probab=99.68  E-value=2.8e-17  Score=142.08  Aligned_cols=51  Identities=18%  Similarity=0.217  Sum_probs=48.6

Q ss_pred             eecceeeeeeeeEEeeC-CCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecC
Q psy13112        171 VDLGKYFPKFTVMYAHD-PDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPL  222 (302)
Q Consensus       171 p~y~K~ikRskKY~AHD-enN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~  222 (302)
                      ++|+||++|+++|+||| |+|+|++||+|+|.|| |||||+|+|.|++|+.++
T Consensus        94 pkY~K~vkr~kKy~AHDee~n~~kvGD~V~I~Ec-RPLSKtKrw~Vv~I~~ka  145 (157)
T 2xzm_Q           94 RKYNRYEKRHRNIPVHISPCFSVKEGDILVAGQC-RPISKTVRFNALQVVPNE  145 (157)
T ss_dssp             TTTTEEEEEEEEEEEECCTTSCCCTTCEEEEEEC-CCCSSSCCEEEEEECCCC
T ss_pred             CccceEeecceeEEEECCCCCCCCCCCEEEEEEc-CCCCCcEEEEEEEEEecc
Confidence            68999999999999999 6899999999999999 799999999999999874

>3u5c_L RP41, S18, YS12, 40S ribosomal protein S11-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_P 3o30_F 3o2z_F 3u5g_L 3jyv_Q* 1s1h_Q

Probab=99.68  E-value=2.5e-17  Score=142.36  Aligned_cols=52  Identities=19%  Similarity=0.264  Sum_probs=49.9

Q ss_pred             eecceeeeeeeeEEeeCC-CCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCC
Q psy13112        171 VDLGKYFPKFTVMYAHDP-DKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  223 (302)
Q Consensus       171 p~y~K~ikRskKY~AHDe-nN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G  223 (302)
                      +.|+||++++++|+|||| +|.|++||+|+|.|| |||||+|+|.|++|++++|
T Consensus        95 pkY~K~vkr~kKy~AHDe~~n~~kvGD~V~I~Ec-RPLSKtKrw~Vv~Iv~ka~  147 (156)
T 3u5c_L           95 PKYNRYEKRHKNVPVHVSPAFRVQVGDIVTVGQC-RPISKTVRFNVVKVSAAAG  147 (156)
T ss_dssp             GGGTEEEEEEEEEEEECCTTSCCCTTCEEEEEEE-EEEETTEEEEEEEECCCCS
T ss_pred             CccceEEECceEEEEECCCcCcCCCCCEEEEEec-ccCCCcEeEEEEEEEecCC
Confidence            689999999999999998 689999999999999 7999999999999999986

>2zkq_q 40S ribosomal protein S11E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 3jyv_Q* 1s1h_Q

Probab=99.65  E-value=7.3e-17  Score=139.62  Aligned_cols=52  Identities=23%  Similarity=0.270  Sum_probs=45.3

Q ss_pred             eecceeeeeeeeEEeeCCC-C-CCCCCCEEEEeecCCCcCcceeEEEEEeeecCC
Q psy13112        171 VDLGKYFPKFTVMYAHDPD-K-ICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  223 (302)
Q Consensus       171 p~y~K~ikRskKY~AHDen-N-~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G  223 (302)
                      ++|+||++|+++|+||||+ | +|++||+|+|.|| |||||+|+|.|++|+...|
T Consensus        97 pkY~K~vkr~kKy~AHDe~~n~~~kvGD~V~I~E~-RPLSKtKrw~Vv~I~~~~~  150 (158)
T 2zkq_q           97 RKYNRFEKRHKNMSVHLSPCFRDVQIGDIVTVGEC-RPLSKTVRFNVLKVTKAAG  150 (158)
T ss_dssp             TTCCCEEEEEEEECCBCCSSCCCC-CCCEEEEECC-SCSSSCC-CEEEEEEEC--
T ss_pred             CccceeeecceeEEEECCcccCcCCCCCEEEEEEc-cccCCcEEEEEEEEecCCC
Confidence            6899999999999999986 4 7999999999999 7999999999999998654

>3iz6_P 40S ribosomal protein S11 (S17P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=99.58  E-value=9.4e-17  Score=139.31  Aligned_cols=51  Identities=24%  Similarity=0.234  Sum_probs=26.9

Q ss_pred             eecceeeeeeeeEEeeCC-CCCCCCCCEEEEeecCCCcCcceeEEEEEeeecC
Q psy13112        171 VDLGKYFPKFTVMYAHDP-DKICKTGDIVLIEELPQKLTTLITHKVNKVVYPL  222 (302)
Q Consensus       171 p~y~K~ikRskKY~AHDe-nN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~  222 (302)
                      +.|+||++++++|+|||| +|.|++||+|+|.|| |||||+|+|.|++|++++
T Consensus        96 pkY~K~vkr~kKy~AHDe~~n~~kvGD~V~I~Ec-RPLSKtKrw~Vv~Iv~~~  147 (161)
T 3iz6_P           96 KKYQRYEKRHSNIPAHVSPCFRVKEGDHVIIGQC-RPLSKTVRFNVLKVIPAG  147 (161)
T ss_dssp             SSCEEEEEECCCSSSSCCEEEEECCCCCC------------------------
T ss_pred             CccceEEECceeEEEECCCCCcCCCCCEEEEEec-cCCCCcEeEEEEEEEecC
Confidence            689999999999999998 799999999999999 799999999999999984

---

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	302
d2uubq1	100	b.40.4.5 (Q:2-101) Ribosomal protein S17 {Thermus	1e-04
d2uubq1	100	b.40.4.5 (Q:2-101) Ribosomal protein S17 {Thermus	0.001
d2gy9q1	78	b.40.4.5 (Q:5-82) Ribosomal protein S17 {Escherich	4e-04
d1ripa_	81	b.40.4.5 (A:) Ribosomal protein S17 {Bacillus stea	8e-04

>d2uubq1 b.40.4.5 (Q:2-101) Ribosomal protein S17 {Thermus thermophilus [TaxId: 274]} Length = 100

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Thermus thermophilus [TaxId: 274]

 Score = 38.2 bits (89), Expect = 1e-04
 Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 173 LGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVV 219
            GK   +     AHDP++  K GD+V I E    ++     +V ++V
Sbjct: 31  YGKVIKRSKKYLAHDPEEKYKLGDVVEIIESR-PISKRKRFRVLRLV 76

>d2uubq1 b.40.4.5 (Q:2-101) Ribosomal protein S17 {Thermus thermophilus [TaxId: 274]} Length = 100

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Thermus thermophilus [TaxId: 274]

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 107 RYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVV 151
           +   +     AHDP++  K GD+V I E    ++     +V ++V
Sbjct: 33  KVIKRSKKYLAHDPEEKYKLGDVVEIIESR-PISKRKRFRVLRLV 76

>d2gy9q1 b.40.4.5 (Q:5-82) Ribosomal protein S17 {Escherichia coli [TaxId: 562]} Length = 78

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Escherichia coli [TaxId: 562]

 Score = 36.2 bits (84), Expect = 4e-04
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 173 LGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVV 219
            GK+  + T ++ HD +  C  GD+V I E    L+   +  + +VV
Sbjct: 29  YGKFIKRTTKLHVHDENNECGIGDVVEIRECR-PLSKTKSWTLVRVV 74

>d1ripa_ b.40.4.5 (A:) Ribosomal protein S17 {Bacillus stearothermophilus [TaxId: 1422]} Length = 81

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 35.4 bits (82), Expect = 8e-04
 Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 1/47 (2%)

Query: 173 LGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVV 219
            GK         AHD     K GDIV I E    L+     ++ ++V
Sbjct: 31  YGKRVKYSKKYKAHDEHNEAKVGDIVKIMETR-PLSATKRFRLVEIV 76

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	302
d2gy9q1	78	Ribosomal protein S17 {Escherichia coli [TaxId: 56	99.85
d2uubq1	100	Ribosomal protein S17 {Thermus thermophilus [TaxId	99.82
d1ripa_	81	Ribosomal protein S17 {Bacillus stearothermophilus	99.79
d2gy9q1	78	Ribosomal protein S17 {Escherichia coli [TaxId: 56	99.76
d2uubq1	100	Ribosomal protein S17 {Thermus thermophilus [TaxId	99.73
d1ripa_	81	Ribosomal protein S17 {Bacillus stearothermophilus	99.71
d1p3ha_	99	Chaperonin-10 (GroES) {Mycobacterium tuberculosis	81.01

>d2gy9q1 b.40.4.5 (Q:5-82) Ribosomal protein S17 {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Escherichia coli [TaxId: 562]

Probab=99.85  E-value=1.2e-21  Score=149.90  Aligned_cols=60  Identities=22%  Similarity=0.290  Sum_probs=58.2

Q ss_pred             ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeec
Q psy13112         94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPL  154 (302)
Q Consensus        94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~ka  154 (302)
                      ..|+|+++||.|+||++++++|+||||+|.|++||+|.|.|| +||||+|+|.|.+|+++|
T Consensus        18 V~v~r~~~h~ky~K~~~~~kky~aHDe~~~~~~GD~V~I~e~-rPlSK~K~~~v~~iv~ka   77 (78)
T d2gy9q1          18 VAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIREC-RPLSKTKSWTLVRVVEKA   77 (78)
T ss_dssp             EEEEEEEECSSSCCEEEEEEEEEEECTTCCCCTTCEEEEEEC-SCSSSSCCEEEEEEEESC
T ss_pred             EEEEEEEEcCccCEEEEeeEEEEEECCCCCCccccEEEEEEc-CcCCCcEEEEEEEEEecc
Confidence            468999999999999999999999999999999999999999 999999999999999986

>d2uubq1 b.40.4.5 (Q:2-101) Ribosomal protein S17 {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Thermus thermophilus [TaxId: 274]

Probab=99.82  E-value=6e-21  Score=152.23  Aligned_cols=62  Identities=21%  Similarity=0.176  Sum_probs=59.2

Q ss_pred             ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecCC
Q psy13112         94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGD  156 (302)
Q Consensus        94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~  156 (302)
                      ..|+|+++||.|+||++++++|+||||+|.|++||+|.|.|| +||||+|+|.|.+||+++..
T Consensus        20 V~v~r~~~h~ky~K~~~r~kk~~vHD~~n~~k~GD~V~I~e~-rPlSK~K~~~v~~Iv~ka~~   81 (100)
T d2uubq1          20 VLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIES-RPISKRKRFRVLRLVESGRM   81 (100)
T ss_dssp             EEEEEEEEETTTEEEEEEEEEEEEECTTCCCCTTCEEEEEEE-EEEETTEEEEEEEEEECCCH
T ss_pred             EEEEEEEeccccCEEEEeeEEEEEECCCCCCCCCCEEEEEEC-cCCCCceEEEEEEEEeccCC
Confidence            468999999999999999999999999999999999999999 99999999999999998763

>d1ripa_ b.40.4.5 (A:) Ribosomal protein S17 {Bacillus stearothermophilus [TaxId: 1422]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.79  E-value=1.5e-21  Score=150.45  Aligned_cols=60  Identities=20%  Similarity=0.127  Sum_probs=58.0

Q ss_pred             eeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecC
Q psy13112         95 MQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  155 (302)
Q Consensus        95 ~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG  155 (302)
                      .|+|+++||.|+||++++++|+||||+|.|++||+|+|.|| +||||+|+|.|.+|+++|-
T Consensus        21 ~v~r~~~~~ky~K~~kr~kk~~aHd~~~~~~~GD~V~I~e~-rPlSK~K~~~v~~Ii~ka~   80 (81)
T d1ripa_          21 LVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMET-RPLSATKRFRLVEIVEKAV   80 (81)
T ss_dssp             CBCCSCCCSCSSSCCCCSBCCCCCCCSTTCSSCEECCBCCC-CCSSSCCCCCCCCCBSSSC
T ss_pred             EEEEEEEcCccCEEEEeeEEEEEECCCCCCccCCEEEEEEc-cCCCCCeeEEEEEEehHhC
Confidence            68899999999999999999999999999999999999999 9999999999999999874

>d2gy9q1 b.40.4.5 (Q:5-82) Ribosomal protein S17 {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Escherichia coli [TaxId: 562]

Probab=99.76  E-value=2.8e-19  Score=136.73  Aligned_cols=53  Identities=26%  Similarity=0.382  Sum_probs=50.4

Q ss_pred             ceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecC
Q psy13112        169 LRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPL  222 (302)
Q Consensus       169 Lrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~  222 (302)
                      ..+.|+|+++++++|+||||+|.|++||+|.|.|| |||||+|+|.|.+|++++
T Consensus        25 ~h~ky~K~~~~~kky~aHDe~~~~~~GD~V~I~e~-rPlSK~K~~~v~~iv~ka   77 (78)
T d2gy9q1          25 KHPIYGKFIKRTTKLHVHDENNECGIGDVVEIREC-RPLSKTKSWTLVRVVEKA   77 (78)
T ss_dssp             ECSSSCCEEEEEEEEEEECTTCCCCTTCEEEEEEC-SCSSSSCCEEEEEEEESC
T ss_pred             EcCccCEEEEeeEEEEEECCCCCCccccEEEEEEc-CcCCCcEEEEEEEEEecc
Confidence            45689999999999999999999999999999999 799999999999999986

>d2uubq1 b.40.4.5 (Q:2-101) Ribosomal protein S17 {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Thermus thermophilus [TaxId: 274]

Probab=99.73  E-value=1.2e-18  Score=138.83  Aligned_cols=54  Identities=26%  Similarity=0.282  Sum_probs=51.0

Q ss_pred             ceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCC
Q psy13112        169 LRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  223 (302)
Q Consensus       169 Lrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G  223 (302)
                      ..+.|+||++++++|+||||+|.|++||+|.|.|| |||||+|+|.|.+|+.++.
T Consensus        27 ~h~ky~K~~~r~kk~~vHD~~n~~k~GD~V~I~e~-rPlSK~K~~~v~~Iv~ka~   80 (100)
T d2uubq1          27 PHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIES-RPISKRKRFRVLRLVESGR   80 (100)
T ss_dssp             EETTTEEEEEEEEEEEEECTTCCCCTTCEEEEEEE-EEEETTEEEEEEEEEECCC
T ss_pred             eccccCEEEEeeEEEEEECCCCCCCCCCEEEEEEC-cCCCCceEEEEEEEEeccC
Confidence            45689999999999999999999999999999999 7999999999999999854

>d1ripa_ b.40.4.5 (A:) Ribosomal protein S17 {Bacillus stearothermophilus [TaxId: 1422]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.71  E-value=2.5e-19  Score=137.98  Aligned_cols=54  Identities=26%  Similarity=0.203  Sum_probs=50.9

Q ss_pred             ceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCC
Q psy13112        169 LRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG  223 (302)
Q Consensus       169 Lrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G  223 (302)
                      ..+.|+|+++++++|+||||+|.|++||+|+|.|| +||||+|+|.|++|++++-
T Consensus        27 ~~~ky~K~~kr~kk~~aHd~~~~~~~GD~V~I~e~-rPlSK~K~~~v~~Ii~ka~   80 (81)
T d1ripa_          27 KHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMET-RPLSATKRFRLVEIVEKAV   80 (81)
T ss_dssp             CCSCSSSCCCCSBCCCCCCCSTTCSSCEECCBCCC-CCSSSCCCCCCCCCBSSSC
T ss_pred             EcCccCEEEEeeEEEEEECCCCCCccCCEEEEEEc-cCCCCCeeEEEEEEehHhC
Confidence            45689999999999999999999999999999999 7999999999999999863

>d1p3ha_ b.35.1.1 (A:) Chaperonin-10 (GroES) {Mycobacterium tuberculosis [TaxId: 1773]}

class: All beta proteins
fold: GroES-like
superfamily: GroES-like
family: GroES
domain: Chaperonin-10 (GroES)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=81.01  E-value=1.9  Score=31.64  Aligned_cols=62  Identities=19%  Similarity=0.135  Sum_probs=33.4

Q ss_pred             CCCEEEEeecCcccccceeEEEeeEEeecCCccCCccceeeecceeecceeeeeeeeEEe-eCC---CCCCCCCCEEEEe
Q psy13112        126 TGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYA-HDP---DKICKTGDIVLIE  201 (302)
Q Consensus       126 iGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~VVGLrp~y~K~ikRskKY~A-HDe---nN~ckvGDiV~I~  201 (302)
                      +||.|+|+.. ..-.+++.-.+.    +...-..|..|+.|+.+.           -.+. +.+   -..|++||+|++.
T Consensus         8 lgdrVLVk~~-~~~~kT~gGIiL----p~~~~~~~~~G~VvavG~-----------g~~~~~~~~~~~~~vk~GD~Vl~~   71 (99)
T d1p3ha_           8 LEDKILVQAN-EAETTTASGLVI----PDTAKEKPQEGTVVAVGP-----------GRWDEDGEKRIPLDVAEGDTVIYS   71 (99)
T ss_dssp             CTTEEEEEEC-CCCCBCTTSCBC----CCSSCCSEEEEEEEEECC-----------CEECSSSSCEECCSCCTTCEEEEE
T ss_pred             cCCEEEEEEc-chhcccccceEe----ccccccCceEEEEEEECC-----------ceEcCCCCEecCCeeecCCEEEEc
Confidence            6999999876 333444433222    221112344455444443           2222 222   1259999999999


Q ss_pred             ec
Q psy13112        202 EL  203 (302)
Q Consensus       202 Ec  203 (302)
                      +.
T Consensus        72 ~~   73 (99)
T d1p3ha_          72 KY   73 (99)
T ss_dssp             CT
T ss_pred             cc
Confidence            76