Citrus Sinensis ID: 029900

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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-----
Protein Sequence
MALHCLSSSSCLTIQSKFKTLSLNNNSSSHSSFATFKSLCFSNKLSHNVFSTGSLTMSPIQRPMRHSVVCEAATKKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVEIHHGWYTPTPAETVQ
Secondary Structure (PSIPRED)
cccccccccccccccccHHHccccccccccccccHHccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
cccHEEccccHcccccccEEEEcccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHccccccccccccc
Coil and Loop (DISEMBL)
malhclsssscltiqskfktlslnnnssshssfATFKSLCFsnklshnvfstgsltmspiqrpmrhsVVCEAATKKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDglrkkpdaqpeevlPVEKLIAEAYSVIDKAVKvgtlhrntgaRRKSRLARRKKAVEihhgwytptpaetvq
Flexible Loop (DISEMBL)
malhclsssscLTIQSKFKTLSLNNNSSSHSSFATFKSLCFSNKLSHNVFSTGSLTMSPIQRPMRHSVVCEaatkkkadsaakrarqaekrriynksrksevktrMKKVLEaldglrkkpdaqpeevlPVEKLIAEAYSVIdkavkvgtlhrntgarrksrlarrkkaveihhgwytptpaetvq
Low Complexity Region (SEG)
MALHCLSSSSCLTIQskfktlslnnnssshssfatfkslCFSNKLSHNVFSTGSLTMSPIQRPMRHSVVCEaatkkkadsaakrarqaekrrIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGarrksrlarrkkaVEIHHGWYTPTPAETVQ
Disordered region (IsUnstruct)
********************************FATFKSLCFSNKLSHNVFST**************************************************************************VLPVEKLIAEAYSVIDKAVKVGTLHRN**************AVEIHHGWY*********
Disordered Region (DISOPRED)
********SSCLTIQSK********************************F***********RPM**********************QAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVEIHHGW**********
Disordered Region (DISEMBL)
********SSCLTIQSKFKTLSLN********FATFKSLCFSNKLSHNVFSTGSLTMSPIQRPMRHSVVC********************RRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRN**************AVEIHHGWYTPTPAETVQ
Disordered Region (DISPRO)
*******SSSCLTIQSKFKTLSLN******************************LTMSPIQRPMRHSVVCEAATKKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVEIHHGWYTPTP*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MALHCLSSSSCLTIQSKFKTLSLNNNSSSHSSFATFKSLCFSNKLSHNVFSTGSLTMSPIQRPMRHSVVCEAATKKKADSAAKRARQAEKRRIYNKSRxxxxxxxxxxxxxxxxxxxxxPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVEIHHGWYTPTPAETVQ
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	185	2.2.26 [Sep-21-2011]
Q9ASV6	202	30S ribosomal protein S20	yes	no	0.956	0.876	0.582	4e-53
B7JWV1	97	30S ribosomal protein S20	yes	no	0.475	0.907	0.488	4e-13
Q3M5D2	98	30S ribosomal protein S20	yes	no	0.481	0.908	0.505	4e-13
Q8YWL3	97	30S ribosomal protein S20	yes	no	0.481	0.917	0.505	5e-13
B1WZT9	97	30S ribosomal protein S20	yes	no	0.448	0.855	0.505	1e-12
Q8DJN4	98	30S ribosomal protein S20	yes	no	0.448	0.846	0.505	1e-12
Q7VA27	99	30S ribosomal protein S20	yes	no	0.432	0.808	0.465	1e-11
B7KG02	97	30S ribosomal protein S20	yes	no	0.443	0.845	0.488	2e-11
B0C2C8	94	30S ribosomal protein S20	yes	no	0.470	0.925	0.449	2e-11
P73336	97	30S ribosomal protein S20	N/A	no	0.448	0.855	0.435	4e-11

>sp|Q9ASV6|RR20_ARATH 30S ribosomal protein S20, chloroplastic OS=Arabidopsis thaliana GN=RPS20 PE=1 SV=1

 Score =  207 bits (526), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 116/199 (58%), Positives = 137/199 (68%), Gaps = 22/199 (11%)

Query: 3   LHCLSSSSCLTIQSKFKTLSLNN-----------NSSSHSSFATFKSLCFSNKLSHNVFS 51
           + CLSS  C T++S+FK LSL             N    S+  +       +      FS
Sbjct: 5   VQCLSS--CATLESQFKVLSLKGISCSSPSSSFSNRRGASATLSSSLSFSQSVSQCVAFS 62

Query: 52  TGSLTMSPIQRPMRHSVVCEAAT-KKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVL 110
           TG+L    +Q+PMR  +VCEAA   KKADSAAKRARQAEKRR+YNKS+KSE +TRMKKVL
Sbjct: 63  TGNLW---VQKPMRQLIVCEAAAPTKKADSAAKRARQAEKRRVYNKSKKSEARTRMKKVL 119

Query: 111 EALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVE 170
           EAL+GL+KK DAQ +E++ VEKLI EAYS IDKAVKV  LH+NTGARRKSRLARRKKAVE
Sbjct: 120 EALEGLKKKTDAQADEIVTVEKLIGEAYSAIDKAVKVKALHKNTGARRKSRLARRKKAVE 179

Query: 171 IHHGWYTP-----TPAETV 184
           IHHGWY P      P+E V
Sbjct: 180 IHHGWYVPDAAAAAPSEAV 198

Binds directly to 16S ribosomal RNA.
Arabidopsis thaliana (taxid: 3702)

>sp|B7JWV1|RS20_CYAP8 30S ribosomal protein S20 OS=Cyanothece sp. (strain PCC 8801) GN=rpsT PE=3 SV=1

 Score = 74.3 bits (181), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 44/90 (48%), Positives = 58/90 (64%), Gaps = 2/90 (2%)

Query: 80  SAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYS 139
           SA KR   AE+ R++NK+ KS V+T MKK  EA+      P   P+ +  VE+ ++ AYS
Sbjct: 6   SALKRIAVAERNRLHNKAYKSAVRTLMKKYFEAVQAYGNNPT--PDNLSVVEQCMSAAYS 63

Query: 140 VIDKAVKVGTLHRNTGARRKSRLARRKKAV 169
            IDKAVK   LHRN GAR+K+RLA+  K V
Sbjct: 64  KIDKAVKRHVLHRNNGARKKARLAKALKQV 93

Binds directly to 16S ribosomal RNA.

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

>sp|Q3M5D2|RS20_ANAVT 30S ribosomal protein S20 OS=Anabaena variabilis (strain ATCC 29413 / PCC 7937) GN=rpsT PE=3 SV=2

 Score = 74.3 bits (181), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 46/91 (50%), Positives = 56/91 (61%), Gaps = 2/91 (2%)

Query: 80  SAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYS 139
           SA KRA+ AE+ R+ NK+ KS VKT MK  L A+      P   PE     +  +A AYS
Sbjct: 7   SALKRAQIAERNRVRNKTYKSSVKTLMKNYLSAVQAYAANPT--PESKQEAQTRLAAAYS 64

Query: 140 VIDKAVKVGTLHRNTGARRKSRLARRKKAVE 170
            IDKAVK G LH N GAR+KSRLA + K +E
Sbjct: 65  RIDKAVKRGILHPNNGARKKSRLASKLKPIE 95

Binds directly to 16S ribosomal RNA.

Anabaena variabilis (strain ATCC 29413 / PCC 7937) (taxid: 240292)

>sp|Q8YWL3|RS20_NOSS1 30S ribosomal protein S20 OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rpsT PE=3 SV=1

 Score = 73.9 bits (180), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 46/91 (50%), Positives = 56/91 (61%), Gaps = 2/91 (2%)

Query: 80  SAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYS 139
           SA KRA+ AE+ R+ NK+ KS VKT MK  L A+      P   PE     +  +A AYS
Sbjct: 6   SALKRAQIAERNRVRNKTYKSSVKTLMKNYLSAVQAYAANPT--PESKQEAQTRLAAAYS 63

Query: 140 VIDKAVKVGTLHRNTGARRKSRLARRKKAVE 170
            IDKAVK G LH N GAR+KSRLA + K +E
Sbjct: 64  RIDKAVKRGILHPNNGARKKSRLASKLKPIE 94

Binds directly to 16S ribosomal RNA.

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

>sp|B1WZT9|RS20_CYAA5 30S ribosomal protein S20 OS=Cyanothece sp. (strain ATCC 51142) GN=rpsT PE=3 SV=1

 Score = 73.2 bits (178), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 43/85 (50%), Positives = 57/85 (67%), Gaps = 2/85 (2%)

Query: 80  SAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYS 139
           SA KR R +E+ R+ NKS KS V+T MKK L+A++     P   PE    V++ ++ AYS
Sbjct: 6   SALKRIRTSERNRLRNKSYKSAVRTLMKKYLQAVEEYAASPT--PENKAVVDQRMSAAYS 63

Query: 140 VIDKAVKVGTLHRNTGARRKSRLAR 164
            IDKAVK   LHRN GAR+K+RLA+
Sbjct: 64  KIDKAVKRSVLHRNNGARKKARLAK 88

Binds directly to 16S ribosomal RNA.

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

>sp|Q8DJN4|RS20_THEEB 30S ribosomal protein S20 OS=Thermosynechococcus elongatus (strain BP-1) GN=rpsT PE=3 SV=1

 Score = 72.8 bits (177), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 43/85 (50%), Positives = 56/85 (65%), Gaps = 2/85 (2%)

Query: 80  SAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYS 139
           SAAKRA+ AE+ R+ NK+ +S V+T +K  L A+      P   PE++  V   +  A+S
Sbjct: 6   SAAKRAQIAERNRLRNKAYRSAVRTLIKNYLNAISQYSTDPT--PEKLAEVHHRLNLAFS 63

Query: 140 VIDKAVKVGTLHRNTGARRKSRLAR 164
            IDKAVK G LHRNTGARRK+RL R
Sbjct: 64  KIDKAVKRGVLHRNTGARRKARLTR 88

Binds directly to 16S ribosomal RNA.

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

>sp|Q7VA27|RS20_PROMA 30S ribosomal protein S20 OS=Prochlorococcus marinus (strain SARG / CCMP1375 / SS120) GN=rpsT PE=3 SV=1

 Score = 69.3 bits (168), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 40/86 (46%), Positives = 57/86 (66%), Gaps = 6/86 (6%)

Query: 79  DSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKP--DAQPEEVLPVEKLIAE 136
           +SA KR + AE+ RI N++ KS ++T MK+  EA     +KP  DA+ +    ++  + +
Sbjct: 5   NSAKKRIQIAERNRIQNRTYKSAMRTLMKRCFEACGAYSEKPSEDAKKD----IQNSMND 60

Query: 137 AYSVIDKAVKVGTLHRNTGARRKSRL 162
           A+S IDKAVK G LHRNTGA +KSRL
Sbjct: 61  AFSKIDKAVKTGVLHRNTGANQKSRL 86

Binds directly to 16S ribosomal RNA.

Prochlorococcus marinus (strain SARG / CCMP1375 / SS120) (taxid: 167539)

>sp|B7KG02|RS20_CYAP7 30S ribosomal protein S20 OS=Cyanothece sp. (strain PCC 7424) GN=rpsT PE=3 SV=1

 Score = 68.9 bits (167), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 41/84 (48%), Positives = 56/84 (66%), Gaps = 2/84 (2%)

Query: 80  SAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYS 139
           SA KR + AE+ R+ NKS KS VKT MKK   A++  +  P  + ++   V++ ++ AYS
Sbjct: 6   SAIKRIQIAERNRLRNKSYKSAVKTLMKKYYAAVEDYKANPSEEAKK--AVDQAMSAAYS 63

Query: 140 VIDKAVKVGTLHRNTGARRKSRLA 163
            IDKAVK   LHRN GAR+KS+LA
Sbjct: 64  KIDKAVKCRILHRNNGARKKSQLA 87

Binds directly to 16S ribosomal RNA.

Cyanothece sp. (strain PCC 7424) (taxid: 65393)

>sp|B0C2C8|RS20_ACAM1 30S ribosomal protein S20 OS=Acaryochloris marina (strain MBIC 11017) GN=rpsT PE=3 SV=1

 Score = 68.6 bits (166), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 40/89 (44%), Positives = 56/89 (62%), Gaps = 2/89 (2%)

Query: 80  SAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYS 139
           SA KR   AE+ R+ NK+ KS +KT  K+   A+D  +  P    +++  ++  ++  YS
Sbjct: 6   SAKKRILIAERNRLQNKAYKSAIKTFTKRFQAAVDDYKSNP--SDDQLAAIQNEMSVTYS 63

Query: 140 VIDKAVKVGTLHRNTGARRKSRLARRKKA 168
            IDKAVKVG  HRNTGAR+K+ LAR  KA
Sbjct: 64  KIDKAVKVGVFHRNTGARKKAGLARILKA 92

Binds directly to 16S ribosomal RNA.

Acaryochloris marina (strain MBIC 11017) (taxid: 329726)

>sp|P73336|RS20_SYNY3 30S ribosomal protein S20 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=rpsT PE=3 SV=1

 Score = 67.8 bits (164), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 37/85 (43%), Positives = 55/85 (64%), Gaps = 2/85 (2%)

Query: 80  SAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYS 139
           SA KR   AE+ R+ NKS KS +KT MKK  ++++     P+  PE++  +   +A A+S
Sbjct: 6   SALKRIEIAERNRLQNKSYKSAIKTLMKKTFQSVEAYASDPN--PEKLDTINTSMAAAFS 63

Query: 140 VIDKAVKVGTLHRNTGARRKSRLAR 164
            IDKAVK   +H+N  AR+K+RLA+
Sbjct: 64  KIDKAVKCKVIHKNNAARKKARLAK 88

Binds directly to 16S ribosomal RNA.

Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

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	185
225461526	183	PREDICTED: 30S ribosomal protein S20, ch	0.983	0.994	0.721	2e-66
255582939	185	30S ribosomal protein S20, putative [Ric	0.940	0.940	0.747	4e-65
449456625	184	PREDICTED: 30S ribosomal protein S20, ch	0.929	0.934	0.693	4e-61
388516539	177	unknown [Lotus japonicus] gi|388517753|g	0.935	0.977	0.689	2e-57
351725205	180	uncharacterized protein LOC100499656 [Gl	0.783	0.805	0.736	3e-53
363807978	164	uncharacterized protein LOC100786192 [Gl	0.762	0.859	0.744	5e-52
297830074	197	hypothetical protein ARALYDRAFT_897793 [	0.924	0.868	0.607	1e-51
15232515	202	30S ribosomal protein S20 [Arabidopsis t	0.956	0.876	0.582	2e-51
312281953	209	unnamed protein product [Thellungiella h	0.924	0.818	0.594	4e-51
224128071	182	predicted protein [Populus trichocarpa]	0.670	0.681	0.808	3e-50

>gi|225461526|ref|XP_002285149.1| PREDICTED: 30S ribosomal protein S20, chloroplastic [Vitis vinifera] gi|302142967|emb|CBI20262.3| unnamed protein product [Vitis vinifera]

 Score =  256 bits (655), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 132/183 (72%), Positives = 149/183 (81%), Gaps = 1/183 (0%)

Query: 1   MALHCLSSSSCLTIQSKFKTLSLNNNSSSHSSFATFKSLCFSNKLSHNVFSTGSLTMSPI 60
           MA   +  + CL + SKF+ LSLN +SSS  S   F SL FS+ LS  VFS G L++S I
Sbjct: 1   MAGAAIGVAHCLALPSKFRILSLNASSSSSCSV-PFTSLGFSSNLSQTVFSKGRLSISTI 59

Query: 61  QRPMRHSVVCEAATKKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKP 120
           + P  HS+VC+AA  +KADSAAKR RQAEKRRIYNK+RKSE++TRMKKVLE LDGL+KKP
Sbjct: 60  RGPTHHSIVCDAAPMRKADSAAKRVRQAEKRRIYNKARKSEIRTRMKKVLEELDGLKKKP 119

Query: 121 DAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVEIHHGWYTPTP 180
           DAQ EEVLP+EKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVEIHHGWYTP P
Sbjct: 120 DAQAEEVLPIEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVEIHHGWYTPAP 179

Query: 181 AET 183
             T
Sbjct: 180 PVT 182

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255582939|ref|XP_002532240.1| 30S ribosomal protein S20, putative [Ricinus communis] gi|223528058|gb|EEF30134.1| 30S ribosomal protein S20, putative [Ricinus communis]

 Score =  252 bits (644), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 130/174 (74%), Positives = 151/174 (86%)

Query: 9   SSCLTIQSKFKTLSLNNNSSSHSSFATFKSLCFSNKLSHNVFSTGSLTMSPIQRPMRHSV 68
           SSC ++ +K K+LSL   SSS  ++   +SL FS+ +SH+VF+ G L+MS ++RP+ HS+
Sbjct: 8   SSCFSVPTKLKSLSLTTTSSSTITYPALRSLSFSSAISHDVFNKGCLSMSIVKRPIGHSI 67

Query: 69  VCEAATKKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVL 128
           VCEAA KK+ADSAAKRARQAEKRRIY+K+ KSEV+TRMKKVLEALD LRKK DAQ EEVL
Sbjct: 68  VCEAAPKKRADSAAKRARQAEKRRIYHKAHKSEVRTRMKKVLEALDDLRKKSDAQAEEVL 127

Query: 129 PVEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVEIHHGWYTPTPAE 182
           P+EKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVEIHHGWYTP PAE
Sbjct: 128 PIEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVEIHHGWYTPAPAE 181

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449456625|ref|XP_004146049.1| PREDICTED: 30S ribosomal protein S20, chloroplastic-like [Cucumis sativus] gi|449507080|ref|XP_004162928.1| PREDICTED: 30S ribosomal protein S20, chloroplastic-like [Cucumis sativus]

 Score =  239 bits (609), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 122/176 (69%), Positives = 142/176 (80%), Gaps = 4/176 (2%)

Query: 10  SCLTIQSKFKTLSLNN---NSSSHSSFATFKSLCFSNKLSHNVFSTGSLTMSPIQRPMRH 66
           +C ++ SKF  LSLN    +  +  S +T +SL FS+ +S + FS G L+M   +R  R+
Sbjct: 7   TCFSLSSKFGNLSLNGFSSSIPAAPSSSTLRSLSFSSNISLSAFSNGCLSMRKTERLHRY 66

Query: 67  SVVCEAATKKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEE 126
           SVVCEAA K K DSAAKRARQAEKRRIYNK+RKSE+KTRMKKVLEALDGL+KK +AQ EE
Sbjct: 67  SVVCEAAPKSKVDSAAKRARQAEKRRIYNKARKSEIKTRMKKVLEALDGLKKKAEAQSEE 126

Query: 127 VLPVEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVEIHHGWYTP-TPA 181
           VLP+E LIAEAYSVIDKAV+ GTLHRNT ARRKSRLARRKKAVEIHHGWYTP +PA
Sbjct: 127 VLPIETLIAEAYSVIDKAVRAGTLHRNTAARRKSRLARRKKAVEIHHGWYTPDSPA 182

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388516539|gb|AFK46331.1| unknown [Lotus japonicus] gi|388517753|gb|AFK46938.1| unknown [Lotus japonicus]

 Score =  227 bits (578), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 122/177 (68%), Positives = 140/177 (79%), Gaps = 4/177 (2%)

Query: 8   SSSCLTIQSKFKTLSLNNNSSSHSSFATFKSLCFSNKLSHNVFSTGSLTMSPIQRPMRHS 67
           S S LT+ SKF+ LS  ++SSS  S +   S C    +SH VFS GSL++SP+QR  R  
Sbjct: 5   SCSWLTLPSKFRDLSPASSSSSSISNSASLSFC--RNISHTVFSQGSLSLSPVQR--RTL 60

Query: 68  VVCEAATKKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEV 127
           VVCE  TKKK DSA KRARQAEKRRIYNK+RKSE+KTRMKKVLEAL+ L+KK DAQPEE+
Sbjct: 61  VVCEVVTKKKVDSAIKRARQAEKRRIYNKARKSEIKTRMKKVLEALESLKKKSDAQPEEI 120

Query: 128 LPVEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVEIHHGWYTPTPAETV 184
           LP+EKLI EAYSVIDKA++VGTLHRNTG  RKSRLARRKK VEIHHGWYTP    +V
Sbjct: 121 LPIEKLIGEAYSVIDKAIRVGTLHRNTGGHRKSRLARRKKVVEIHHGWYTPVSDGSV 177

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725205|ref|NP_001237852.1| uncharacterized protein LOC100499656 [Glycine max] gi|255625577|gb|ACU13133.1| unknown [Glycine max]

 Score =  213 bits (542), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 109/148 (73%), Positives = 121/148 (81%), Gaps = 3/148 (2%)

Query: 38  SLCFSNKLSHNVFSTG-SLTMSPIQRPMRHSVVCEAATKKKADSAAKRARQAEKRRIYNK 96
           SL FS  LS   FS G SL++S + R  R SVVCEAA KKK DSA KRARQAEK R+YNK
Sbjct: 35  SLSFSRNLSRPFFSKGNSLSLSTVLR--RASVVCEAAPKKKVDSAVKRARQAEKHRVYNK 92

Query: 97  SRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGA 156
           +RKSE+KTR KKVLEAL+ L+KK DAQ EE+LP+EKLI EAYS+IDKAV+VGTLHRNTGA
Sbjct: 93  ARKSEIKTRTKKVLEALEVLKKKSDAQAEEILPIEKLIGEAYSIIDKAVRVGTLHRNTGA 152

Query: 157 RRKSRLARRKKAVEIHHGWYTPTPAETV 184
            RKSRLARRKKAVEIHHGWYTP P   V
Sbjct: 153 NRKSRLARRKKAVEIHHGWYTPAPEAIV 180

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807978|ref|NP_001241947.1| uncharacterized protein LOC100786192 [Glycine max] gi|255640470|gb|ACU20521.1| unknown [Glycine max]

 Score =  209 bits (531), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 108/145 (74%), Positives = 122/145 (84%), Gaps = 4/145 (2%)

Query: 41  FSNKLSHNVFSTGS-LTMSPIQRPMRHSVVCEAATKKKADSAAKRARQAEKRRIYNKSRK 99
           FS  LSH +FS G+ L++S  QR  R SVVCEAA KK  DSA KRARQAEKRR+YNK+RK
Sbjct: 23  FSRNLSHPLFSQGNCLSLSTAQR--RASVVCEAAPKK-VDSAVKRARQAEKRRVYNKARK 79

Query: 100 SEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGARRK 159
           SE+KTR KKVLEAL+ L+KK DAQ EE+L +EKLI EAYS+IDKAV+VGTLHRNTGA RK
Sbjct: 80  SEIKTRTKKVLEALEVLKKKQDAQAEEILSIEKLIGEAYSIIDKAVRVGTLHRNTGANRK 139

Query: 160 SRLARRKKAVEIHHGWYTPTPAETV 184
           SRLARRKKAVEIHHGWYTPTP  +V
Sbjct: 140 SRLARRKKAVEIHHGWYTPTPEASV 164

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297830074|ref|XP_002882919.1| hypothetical protein ARALYDRAFT_897793 [Arabidopsis lyrata subsp. lyrata] gi|297328759|gb|EFH59178.1| hypothetical protein ARALYDRAFT_897793 [Arabidopsis lyrata subsp. lyrata]

 Score =  207 bits (528), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 113/186 (60%), Positives = 133/186 (71%), Gaps = 15/186 (8%)

Query: 3   LHCLSSSSCLTIQSKFKTLSLN---------NNSSSHSSFATFKSLCFSNKLSHNVFSTG 53
           + CLSS  C T++S+FK LSL          N     S+  +       +      FS+G
Sbjct: 5   VQCLSS--CATLESQFKVLSLKGISSSSSFSNRRGGASATLSSSLSFSQSVSQCVAFSSG 62

Query: 54  SLTMSPIQRPMRHSVVCEAAT-KKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEA 112
           +L    +Q+P R  +VCEAA   KKADSAAKRARQAEKRRIYNKS+KSE +TRMKKVLEA
Sbjct: 63  NLW---VQKPTRQLIVCEAAAPTKKADSAAKRARQAEKRRIYNKSKKSEARTRMKKVLEA 119

Query: 113 LDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVEIH 172
           L+GL+KK DAQP+E++ VEKLI EAYS IDKAVKV  LH+NTGARRKSRLARRKKAVEIH
Sbjct: 120 LEGLKKKTDAQPDEIVTVEKLIGEAYSAIDKAVKVKALHKNTGARRKSRLARRKKAVEIH 179

Query: 173 HGWYTP 178
           HGWY P
Sbjct: 180 HGWYVP 185

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15232515|ref|NP_188137.1| 30S ribosomal protein S20 [Arabidopsis thaliana] gi|75308015|sp|Q9ASV6.1|RR20_ARATH RecName: Full=30S ribosomal protein S20, chloroplastic; Flags: Precursor gi|188036221|pdb|3BBN|T Chain T, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome. gi|13605653|gb|AAK32820.1|AF361807_1 AT3g15190/F4B12_10 [Arabidopsis thaliana] gi|13899121|gb|AAK48982.1|AF370555_1 Unknown protein [Arabidopsis thaliana] gi|15777889|gb|AAL05905.1| AT3g15190/F4B12_10 [Arabidopsis thaliana] gi|18377542|gb|AAL66937.1| unknown protein [Arabidopsis thaliana] gi|21592469|gb|AAM64420.1| 30S ribosomal protein S20 [Arabidopsis thaliana] gi|332642109|gb|AEE75630.1| 30S ribosomal protein S20 [Arabidopsis thaliana]

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 116/199 (58%), Positives = 137/199 (68%), Gaps = 22/199 (11%)

Query: 3   LHCLSSSSCLTIQSKFKTLSLNN-----------NSSSHSSFATFKSLCFSNKLSHNVFS 51
           + CLSS  C T++S+FK LSL             N    S+  +       +      FS
Sbjct: 5   VQCLSS--CATLESQFKVLSLKGISCSSPSSSFSNRRGASATLSSSLSFSQSVSQCVAFS 62

Query: 52  TGSLTMSPIQRPMRHSVVCEAAT-KKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVL 110
           TG+L    +Q+PMR  +VCEAA   KKADSAAKRARQAEKRR+YNKS+KSE +TRMKKVL
Sbjct: 63  TGNLW---VQKPMRQLIVCEAAAPTKKADSAAKRARQAEKRRVYNKSKKSEARTRMKKVL 119

Query: 111 EALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVE 170
           EAL+GL+KK DAQ +E++ VEKLI EAYS IDKAVKV  LH+NTGARRKSRLARRKKAVE
Sbjct: 120 EALEGLKKKTDAQADEIVTVEKLIGEAYSAIDKAVKVKALHKNTGARRKSRLARRKKAVE 179

Query: 171 IHHGWYTP-----TPAETV 184
           IHHGWY P      P+E V
Sbjct: 180 IHHGWYVPDAAAAAPSEAV 198

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312281953|dbj|BAJ33842.1| unnamed protein product [Thellungiella halophila]

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 116/195 (59%), Positives = 135/195 (69%), Gaps = 24/195 (12%)

Query: 3   LHCLSSSSCLTIQSKFKTLSLNN----------------NSSSHSSFATFKSLCFSNKLS 46
           + CLSS  C  + SKFK LSL                   S+   S AT  S    ++  
Sbjct: 5   VQCLSS--CAALDSKFKVLSLKGISSSFSSASASSSSSSFSTRRGSSATLGSSLSYSQSV 62

Query: 47  HN--VFSTGSLTMSPIQRPMRHSVVCEAAT-KKKADSAAKRARQAEKRRIYNKSRKSEVK 103
                FS+G+L    +Q+PMR  +VCEAA   KKADSAAKRARQAEKRR+YNKS+KSE +
Sbjct: 63  SQCIAFSSGNLR---VQKPMRQLIVCEAAAPTKKADSAAKRARQAEKRRLYNKSKKSEAR 119

Query: 104 TRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLA 163
           TRMKKVLEAL+GL+KK DAQP+E++ VEKLI EAYS IDKAVKV  LH+NTGARRKSRLA
Sbjct: 120 TRMKKVLEALEGLKKKADAQPDEIVTVEKLIGEAYSAIDKAVKVRALHKNTGARRKSRLA 179

Query: 164 RRKKAVEIHHGWYTP 178
           RRKKAVEIHHGWY P
Sbjct: 180 RRKKAVEIHHGWYVP 194

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224128071|ref|XP_002329074.1| predicted protein [Populus trichocarpa] gi|222869743|gb|EEF06874.1| predicted protein [Populus trichocarpa]

 Score =  203 bits (516), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 101/125 (80%), Positives = 112/125 (89%), Gaps = 1/125 (0%)

Query: 53  GSLTMSPIQRPMRH-SVVCEAATKKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLE 111
           G L+M   QR + + S+VCE+  KKKADSA KR RQAEKRR+YNK+RKSEVKTRMKKVLE
Sbjct: 48  GCLSMRTTQRSIHNFSIVCESTPKKKADSAEKRTRQAEKRRVYNKARKSEVKTRMKKVLE 107

Query: 112 ALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAVEI 171
           ALD L+KKP+AQ EEVLP+EKLIAEAYSVIDKA+KVGTLHRNTGARRKSRLARRKKAVEI
Sbjct: 108 ALDDLKKKPEAQFEEVLPIEKLIAEAYSVIDKAIKVGTLHRNTGARRKSRLARRKKAVEI 167

Query: 172 HHGWY 176
           HHGWY
Sbjct: 168 HHGWY 172

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	185
TAIR|locus:2083661	202	PRPS20 "plastid ribosomal prot	0.745	0.683	0.503	1.8e-30

TAIR|locus:2083661 PRPS20 "plastid ribosomal protein S20" [Arabidopsis thaliana (taxid:3702)]

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 72/143 (50%), Positives = 86/143 (60%)

Query:    41 FSNKLSHNV-FSTGSLTMSPIQRPMRHSVVCEXXX-XXXXXXXXXXXXXXXXXXIYNKSR 98
             FS  +S  V FSTG+L    +Q+PMR  +VCE                      +YNKS+
Sbjct:    51 FSQSVSQCVAFSTGNLW---VQKPMRQLIVCEAAAPTKKADSAAKRARQAEKRRVYNKSK 107

Query:    99 KSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGXXX 158
             KSE +TRMKKVLEAL+GL+KK DAQ +E++ VEKLI EAYS IDKAVKV  LH+NTG   
Sbjct:   108 KSEARTRMKKVLEALEGLKKKTDAQADEIVTVEKLIGEAYSAIDKAVKVKALHKNTGARR 167

Query:   159 XXXXXXXXXXVEIHHGWYTPTPA 181
                       VEIHHGWY P  A
Sbjct:   168 KSRLARRKKAVEIHHGWYVPDAA 190


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        0.316   0.129   0.377    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      185       127   0.00091  102 3  11 22  0.39    31
                                                     29  0.40    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:  556 (59 KB)
  Total size of DFA:  125 KB (2081 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:  12.00u 0.17s 12.17t   Elapsed:  00:00:01
  Total cpu time:  12.00u 0.17s 12.17t   Elapsed:  00:00:01
  Start:  Tue May 21 01:20:31 2013   End:  Tue May 21 01:20:32 2013

GO:0003723 "RNA binding" evidence=IEA

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:0009570 "chloroplast stroma" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0006364 "rRNA processing" evidence=RCA

GO:0015995 "chlorophyll biosynthetic process" 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)
Q9ASV6	RR20_ARATH	No assigned EC number	0.5829	0.9567	0.8762	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	185
PRK00239	88	PRK00239, rpsT, 30S ribosomal protein S20; Reviewe	2e-21
COG0268	88	COG0268, RpsT, Ribosomal protein S20 [Translation,	1e-17
CHL00102	93	CHL00102, rps20, ribosomal protein S20	8e-16
pfam01649	84	pfam01649, Ribosomal_S20p, Ribosomal protein S20	1e-15
TIGR00029	87	TIGR00029, S20, ribosomal protein S20	5e-12

>gnl|CDD|178943 PRK00239, rpsT, 30S ribosomal protein S20; Reviewed

 Score = 83.3 bits (207), Expect = 2e-21
 Identities = 41/90 (45%), Positives = 53/90 (58%), Gaps = 9/90 (10%)

Query: 80  SAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYS 139
           SA KR RQ EKRR+ NKSRKS V+T +KKV  A+    K+           E+ +  A S
Sbjct: 6   SAKKRIRQNEKRRLRNKSRKSRVRTAIKKVEAAIAAGDKEA---------AEEALKAAQS 56

Query: 140 VIDKAVKVGTLHRNTGARRKSRLARRKKAV 169
            IDKA   G +H+N  AR+KSRLA +  A+
Sbjct: 57  KIDKAASKGVIHKNKAARKKSRLAAKVNAL 86

Length = 88

>gnl|CDD|223346 COG0268, RpsT, Ribosomal protein S20 [Translation, ribosomal structure and biogenesis]

 Score = 73.5 bits (181), Expect = 1e-17
 Identities = 38/90 (42%), Positives = 53/90 (58%), Gaps = 9/90 (10%)

Query: 80  SAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYS 139
           SA KRARQ+EKRR+ NKSRKS ++T +KKV  A++           +    +  + EA  
Sbjct: 6   SAKKRARQSEKRRLRNKSRKSALRTAIKKVEAAIEA---------GDKEAAKAALKEAQK 56

Query: 140 VIDKAVKVGTLHRNTGARRKSRLARRKKAV 169
            IDKA   G +H+N  AR+KSRLA +   +
Sbjct: 57  KIDKAASKGVIHKNKAARKKSRLAAKLNKL 86

Length = 88

>gnl|CDD|214366 CHL00102, rps20, ribosomal protein S20

 Score = 69.0 bits (169), Expect = 8e-16
 Identities = 38/90 (42%), Positives = 56/90 (62%), Gaps = 2/90 (2%)

Query: 80  SAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYS 139
           SA KR + +E+ R+ NK+ KS VKT +KK L+ L+  +  P+        V++ ++  YS
Sbjct: 6   SAIKRIKISERNRLRNKAYKSSVKTLIKKYLKNLEDYKTSPN--SNNKKKVQETLSSVYS 63

Query: 140 VIDKAVKVGTLHRNTGARRKSRLARRKKAV 169
            IDKAVK G  H+NT AR+KS+LA+  K  
Sbjct: 64  KIDKAVKKGVFHKNTAARKKSKLAKALKKS 93

Length = 93

>gnl|CDD|216626 pfam01649, Ribosomal_S20p, Ribosomal protein S20

 Score = 68.2 bits (167), Expect = 1e-15
 Identities = 40/86 (46%), Positives = 52/86 (60%), Gaps = 9/86 (10%)

Query: 80  SAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYS 139
           SA KR RQ EKRR+ NKS KS+++T +KKV EA++   K             + + E  S
Sbjct: 5   SAKKRIRQNEKRRLRNKSYKSKMRTLIKKVREAIEAGEKDKAK---------EALKEVQS 55

Query: 140 VIDKAVKVGTLHRNTGARRKSRLARR 165
            IDKA K G +H+NT AR+KSRLA  
Sbjct: 56  KIDKAAKKGVIHKNTAARKKSRLAAI 81

Bacterial ribosomal protein S20 interacts with 16S rRNA. Length = 84

>gnl|CDD|211539 TIGR00029, S20, ribosomal protein S20

 Score = 58.7 bits (142), Expect = 5e-12
 Identities = 34/84 (40%), Positives = 50/84 (59%), Gaps = 9/84 (10%)

Query: 80  SAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYS 139
           SA KR RQ EKRR++N S+KS++KT +KKV  A+            +    ++   EA  
Sbjct: 6   SAEKRIRQNEKRRLHNASQKSKMKTIIKKVYAAIAA---------GDKDKAQEAFKEAAK 56

Query: 140 VIDKAVKVGTLHRNTGARRKSRLA 163
            +D+A + G +H+N  AR+KSRLA
Sbjct: 57  KLDRAARKGIIHKNKAARKKSRLA 80

This family consists of bacterial (and chloroplast) examples of the bacteria ribosomal small subunit protein S20 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 87

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	185
CHL00102	93	rps20 ribosomal protein S20	100.0
TIGR00029	87	S20 ribosomal protein S20. This family consists of	99.98
PRK00239	88	rpsT 30S ribosomal protein S20; Reviewed	99.97
COG0268	88	RpsT Ribosomal protein S20 [Translation, ribosomal	99.97
PF01649	84	Ribosomal_S20p: Ribosomal protein S20; InterPro: I	99.97

>CHL00102 rps20 ribosomal protein S20

Probab=100.00  E-value=1.3e-32  Score=208.06  Aligned_cols=92  Identities=41%  Similarity=0.578  Sum_probs=87.6

Q ss_pred             ccCchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhccCCCCCCCCccchHHHHHHHHHHHHHHHHhhhCcchhhh
Q 029900           75 KKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNT  154 (185)
Q Consensus        75 maniKSA~KRiRq~eKrRlrNrs~KS~vRT~iKKv~~AIeagdk~~~a~a~d~~~A~~~l~~a~S~IDKAakKGVIHKNt  154 (185)
                      |||++||+||+||+|++|+||++++|+|||+||+|+++|++|++.+  +++|.++|+++|..+++.||+|++|||||+|+
T Consensus         1 MaN~kSa~KR~rq~ekrr~rN~~~kS~~rT~iKk~~~ai~~~~~~~--~~~d~~~a~~~l~~a~s~iDkaa~KGviHkN~   78 (93)
T CHL00102          1 MANNKSAIKRIKISERNRLRNKAYKSSVKTLIKKYLKNLEDYKTSP--NSNNKKKVQETLSSVYSKIDKAVKKGVFHKNT   78 (93)
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccC--CcccHHHHHHHHHHHHHHHHHHHHcCCcchhH
Confidence            8999999999999999999999999999999999999999987654  46889999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHH
Q 029900          155 GARRKSRLARRKKA  168 (185)
Q Consensus       155 AARKKSRLakkin~  168 (185)
                      |+|+||||+++|+.
T Consensus        79 AaRkKSRL~k~v~~   92 (93)
T CHL00102         79 AARKKSKLAKALKK   92 (93)
T ss_pred             HHHHHHHHHHHhcc
Confidence            99999999999874

>TIGR00029 S20 ribosomal protein S20

Probab=99.98  E-value=3.1e-32  Score=203.69  Aligned_cols=86  Identities=40%  Similarity=0.494  Sum_probs=82.6

Q ss_pred             ccCchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhccCCCCCCCCccchHHHHHHHHHHHHHHHHhhhCcchhhh
Q 029900           75 KKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNT  154 (185)
Q Consensus        75 maniKSA~KRiRq~eKrRlrNrs~KS~vRT~iKKv~~AIeagdk~~~a~a~d~~~A~~~l~~a~S~IDKAakKGVIHKNt  154 (185)
                      |||++||+||+||+|++|++|++++|+|||+||+|+.+|++||         .++|+++|..+++.||+|++|||||+|+
T Consensus         1 MaN~kSa~KR~r~~~krr~~N~~~kS~~kT~iKk~~~ai~~~d---------~~~a~~~l~~a~s~iDkaa~KgviHkN~   71 (87)
T TIGR00029         1 MANIKSAEKRIRQNEKRRLHNASQKSKMKTIIKKVYAAIAAGD---------KDKAQEAFKEAAKKLDRAARKGIIHKNK   71 (87)
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---------HHHHHHHHHHHHHHHHHHHHCCCcchhH
Confidence            8999999999999999999999999999999999999999865         4679999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q 029900          155 GARRKSRLARRKKAV  169 (185)
Q Consensus       155 AARKKSRLakkin~l  169 (185)
                      |+|+||||++.|+++
T Consensus        72 AaRkKSrL~k~v~~~   86 (87)
T TIGR00029        72 AARKKSRLAAQLNKL   86 (87)
T ss_pred             HHHHHHHHHHHHhhc
Confidence            999999999999975

This family consists of bacterial (and chloroplast) examples of the bacteria ribosomal small subunit protein S20.

>PRK00239 rpsT 30S ribosomal protein S20; Reviewed

Probab=99.97  E-value=7.7e-32  Score=201.71  Aligned_cols=87  Identities=46%  Similarity=0.546  Sum_probs=83.1

Q ss_pred             ccCchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhccCCCCCCCCccchHHHHHHHHHHHHHHHHhhhCcchhhh
Q 029900           75 KKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNT  154 (185)
Q Consensus        75 maniKSA~KRiRq~eKrRlrNrs~KS~vRT~iKKv~~AIeagdk~~~a~a~d~~~A~~~l~~a~S~IDKAakKGVIHKNt  154 (185)
                      |+|++||+||+||++++|++|++++|+|||+||+|+.+|++||         .++|+++|..+++.||+|++|||||+|+
T Consensus         1 MaN~kSa~KR~r~~~krr~~N~~~kS~~kT~iKk~~~ai~~~~---------~~~a~~~~~~a~s~iDka~~KgiiHkN~   71 (88)
T PRK00239          1 MANIKSAKKRIRQNEKRRLRNKSRKSRVRTAIKKVEAAIAAGD---------KEAAEEALKAAQSKIDKAASKGVIHKNK   71 (88)
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC---------HHHHHHHHHHHHHHHHHHHHCCCcchhH
Confidence            8999999999999999999999999999999999999999754         4789999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH
Q 029900          155 GARRKSRLARRKKAVE  170 (185)
Q Consensus       155 AARKKSRLakkin~l~  170 (185)
                      |+|+||||+++|+++.
T Consensus        72 AaRkKSrL~~~~~~~~   87 (88)
T PRK00239         72 AARKKSRLAAKVNALA   87 (88)
T ss_pred             HHHHHHHHHHHHHhhc
Confidence            9999999999999863

>COG0268 RpsT Ribosomal protein S20 [Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=9.4e-32  Score=202.19  Aligned_cols=87  Identities=44%  Similarity=0.546  Sum_probs=83.4

Q ss_pred             ccCchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhccCCCCCCCCccchHHHHHHHHHHHHHHHHhhhCcchhhh
Q 029900           75 KKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNT  154 (185)
Q Consensus        75 maniKSA~KRiRq~eKrRlrNrs~KS~vRT~iKKv~~AIeagdk~~~a~a~d~~~A~~~l~~a~S~IDKAakKGVIHKNt  154 (185)
                      |+||+||+||+||+|+||+||+++||+|||+||+|+++|+.||         ++.|+++|..+++.||++++|||||+|+
T Consensus         1 MAN~~SA~KR~r~~~krr~rN~~~kS~~rT~iKk~~~ai~~gd---------~~~A~~~l~~a~~~idkaa~KGvihkN~   71 (88)
T COG0268           1 MANIKSAKKRARQSEKRRLRNKSRKSALRTAIKKVEAAIEAGD---------KEAAKAALKEAQKKIDKAASKGVIHKNK   71 (88)
T ss_pred             CCChHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHcCC---------HHHHHHHHHHHHHHHHHHHHcCcccccH
Confidence            8999999999999999999999999999999999999999864         4789999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH
Q 029900          155 GARRKSRLARRKKAVE  170 (185)
Q Consensus       155 AARKKSRLakkin~l~  170 (185)
                      |+|+||||+.++|++.
T Consensus        72 AaR~kSRLa~~~~~~~   87 (88)
T COG0268          72 AARKKSRLAAKLNKLA   87 (88)
T ss_pred             HHHHHHHHHHHHhhhc
Confidence            9999999999999874

>PF01649 Ribosomal_S20p: Ribosomal protein S20; InterPro: IPR002583 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.97  E-value=2.1e-30  Score=192.26  Aligned_cols=84  Identities=48%  Similarity=0.630  Sum_probs=77.0

Q ss_pred             cCchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhccCCCCCCCCccchHHHHHHHHHHHHHHHHhhhCcchhhhH
Q 029900           76 KKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTG  155 (185)
Q Consensus        76 aniKSA~KRiRq~eKrRlrNrs~KS~vRT~iKKv~~AIeagdk~~~a~a~d~~~A~~~l~~a~S~IDKAakKGVIHKNtA  155 (185)
                      ||++||+||+||++++|++|++++|+|||+||+|+++|++||         .++|+++|..+++.||+|+++||||+|+|
T Consensus         1 aN~kSa~KR~r~~~krr~~Nr~~kS~~rT~iKk~~~ai~~~~---------~~~a~~~l~~a~s~iDka~~kgiihkN~A   71 (84)
T PF01649_consen    1 ANIKSAKKRIRQNEKRRARNRSRKSRVRTAIKKFREAIEAGD---------KEEAKELLRKAYSAIDKAAKKGIIHKNKA   71 (84)
T ss_dssp             ---SSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----------HHHHHHHHHHHHHHHHHHHHHSSSTTTHH
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccC---------hHHHHHHHHHHHHHHHHHHHcCCcchhHH
Confidence            699999999999999999999999999999999999999865         46799999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 029900          156 ARRKSRLARRKKA  168 (185)
Q Consensus       156 ARKKSRLakkin~  168 (185)
                      +|+||||++.||+
T Consensus        72 aRkKSRL~~~~nK   84 (84)
T PF01649_consen   72 ARKKSRLAKKLNK   84 (84)
T ss_dssp             HHHHHHHHHHCHT
T ss_pred             HHHHHHHHHHhcC
Confidence            9999999999874

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 family consists of bacterial (and chloroplast) examples of the ribosomal small subunit protein S20. Bacterial ribosomal protein S20 forms part of the 30S ribosomal subunit, and interacts with 16S rRNA.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1I94_T 1FJG_T 4DH9_T 3KNJ_T 3TVG_W 3UYF_W 3V28_T 3KIS_t 3HUY_T 1HNX_T ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	185
3bbn_T	202	Homology Model For The Spinach Chloroplast 30s Subu		2e-32

>pdb|3BBN|T Chain T, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 202

Iteration: 1
 Score =  134 bits (338), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 70/142 (49%), Positives = 84/142 (59%), Gaps = 9/142 (6%)
Query: 49  VFSTGSLTMSPIQRPMRHSVVCEXXX-XXXXXXXXXXXXXXXXXXIYNKSRKSEVKTRMK 107
            FSTG+L    +Q+PMR  +VCE                      +YNKS+KSE +TRMK
Sbjct: 60  AFSTGNLW---VQKPMRQLIVCEAAAPTKKADSAAKRARQAEKRRVYNKSKKSEARTRMK 116
Query: 108 KVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGXXXXXXXXXXXX 167
           KVLEAL+GL+KK DAQ +E++ VEKLI EAYS IDKAVKV  LH+NTG            
Sbjct: 117 KVLEALEGLKKKTDAQADEIVTVEKLIGEAYSAIDKAVKVKALHKNTGARRKSRLARRKK 176
Query: 168 XVEIHHGWYTP-----TPAETV 184
            VEIHHGWY P      P+E V
Sbjct: 177 AVEIHHGWYVPDAAAAAPSEAV 198

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	185
3bbn_T	202	Ribosomal protein S20; small ribosomal subunit, sp	1e-39
2vqe_T	106	30S ribosomal protein S20; tRNA-binding, rRNA-bind	3e-27
3r8n_T	85	30S ribosomal protein S20; protein biosynthesis, R	3e-20
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

>3bbn_T Ribosomal protein S20; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 202

 Score =  132 bits (334), Expect = 1e-39
 Identities = 116/194 (59%), Positives = 133/194 (68%), Gaps = 13/194 (6%)

Query: 1   MALHCLSSSSCLTIQSKFKTLSLNNNSSSH----------SSFATFKSLCFSNKLSHNV- 49
           MA      SSC T++S+FK LSL   S S           +S     SL FS  +S  V 
Sbjct: 1   MATIVQCLSSCATLESQFKVLSLKGISCSSPSSSFSNRRGASATLSSSLSFSQSVSQCVA 60

Query: 50  FSTGSLTMSPIQRPMRHSVVCEAATKKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKV 109
           FSTG+L +    R  +  V   AA  KKADSAAKRARQAEKRR+YNKS+KSE +TRMKKV
Sbjct: 61  FSTGNLWVQKPMR--QLIVCEAAAPTKKADSAAKRARQAEKRRVYNKSKKSEARTRMKKV 118

Query: 110 LEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAV 169
           LEAL+GL+KK DAQ +E++ VEKLI EAYS IDKAVKV  LH+NTGARRKSRLARRKKAV
Sbjct: 119 LEALEGLKKKTDAQADEIVTVEKLIGEAYSAIDKAVKVKALHKNTGARRKSRLARRKKAV 178

Query: 170 EIHHGWYTPTPAET 183
           EIHHGWY P  A  
Sbjct: 179 EIHHGWYVPDAAAA 192

>2vqe_T 30S ribosomal protein S20; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.7.6.1 PDB: 1gix_W* 1hnw_T* 1hnx_T* 1hnz_T* 1hr0_T 1j5e_T 1jgo_W* 1jgp_W* 1jgq_W* 1ml5_W* 1yl4_W 2b64_T* 2b9m_T* 2b9o_T* 2f4v_T* 2ow8_u* 2qnh_u* 2uxb_T* 1fjg_T* 2uxd_T* ... Length = 106

 Score = 98.2 bits (245), Expect = 3e-27
 Identities = 38/99 (38%), Positives = 56/99 (56%), Gaps = 9/99 (9%)

Query: 71  EAATKKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPV 130
                K+  SA KR RQ+ KRR+ NK++KS +KT  KK ++     + +           
Sbjct: 2   AQKKPKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAVQLAQEGKAE---------EA 52

Query: 131 EKLIAEAYSVIDKAVKVGTLHRNTGARRKSRLARRKKAV 169
            K++ +A S+IDKA K  TLH+N  ARRKSRL R+ + +
Sbjct: 53  LKIMRKAESLIDKAAKGSTLHKNAAARRKSRLMRKVRQL 91

>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 = 39.8 bits (92), Expect = 3e-04
 Identities = 27/214 (12%), Positives = 56/214 (26%), Gaps = 64/214 (29%)

Query: 5   CLSSSSCLT--IQSKFKT----LSLNNNSSSHSSFATFKSLCFSNKLSHNVFSTGSLTMS 58
            ++   CL+  +Q K       L+L N +S  +     + L +  ++  N  S    + +
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLY--QIDPNWTSRSDHSSN 222

Query: 59  PIQRPMRHSVVCEAATKKKADSAAKRARQAEKRRIYNKS--------RKSEVK------- 103
              R                 S     R+  K + Y                        
Sbjct: 223 IKLR---------------IHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCK 267

Query: 104 ----TRMKKVLEALDGLRKKP-----------DAQPEEVL------PVEKLIAEAYSVID 142
               TR K+V + L                    + + +L        + L  E  +   
Sbjct: 268 ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNP 327

Query: 143 KAVK-VGTLHRNTGAR----RKSRLARRKKAVEI 171
           + +  +    R+  A     +     +    +E 
Sbjct: 328 RRLSIIAESIRDGLATWDNWKHVNCDKLTTIIES 361

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	185
3bbn_T	202	Ribosomal protein S20; small ribosomal subunit, sp	100.0
2vqe_T	106	30S ribosomal protein S20; tRNA-binding, rRNA-bind	100.0
3r8n_T	85	30S ribosomal protein S20; protein biosynthesis, R	99.97

>3bbn_T Ribosomal protein S20; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=100.00  E-value=2.5e-57  Score=380.40  Aligned_cols=176  Identities=67%  Similarity=0.937  Sum_probs=97.9

Q ss_pred             ccccccccccccccchhhhcccccCCCCCCcc----------ccccceeeeccccccc-cccCccccccccCCCcceeee
Q 029900            2 ALHCLSSSSCLTIQSKFKTLSLNNNSSSHSSF----------ATFKSLCFSNKLSHNV-FSTGSLTMSPIQRPMRHSVVC   70 (185)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~f~~~~~~~~-~s~~~~~~~~~~~~~~~~~~~   70 (185)
                      +++||+  +||+||++|++|||++++||+.++          ..+++|+|+++|+|++ |++|.+++.++.|+   .|||
T Consensus         4 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fs~s~~~~~~~~~~~~~~~~~~r~---~~v~   78 (202)
T 3bbn_T            4 IVQCLS--SCATLESQFKVLSLKGISCSSPSSSFSNRRGASATLSSSLSFSQSVSQCVAFSTGNLWVQKPMRQ---LIVC   78 (202)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhhhh--hhhcCchhhheeeecccccCCcccccCCcccCccccccccchhhhcccceeeccccccccccccc---eeEE
Confidence            467877  999999999999999999777221          3488999999999999 99999999999988   4999


Q ss_pred             hh-hcccCchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhccCCCCCCCCccchHHHHHHHHHHHHHHHHhhhCc
Q 029900           71 EA-ATKKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGT  149 (185)
Q Consensus        71 ~~-~~maniKSA~KRiRq~eKrRlrNrs~KS~vRT~iKKv~~AIeagdk~~~a~a~d~~~A~~~l~~a~S~IDKAakKGV  149 (185)
                      |+ ++|+|+|||+||+||+|+||+||+++||+|||+||||+++|++++..++++++|+++|+++|..+++.||||++|||
T Consensus        79 ~a~~~~aN~KSAkKRiRqneKRRlrNka~KS~vRTaIKKv~~AIea~~~~~~~~~gDke~A~~al~~A~s~IDKAa~KGV  158 (202)
T 3bbn_T           79 EAAAPTKKADSAAKRARQAEKRRVYNKSKKSEARTRMKKVLEALEGLKKKTDAQADEIVTVEKLIGEAYSAIDKAVKVKA  158 (202)
T ss_dssp             -CCCSSCCCCCSSHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHTTCCCCCCSSSCCCHHHHHHHHHHHHHTTSSSSSS
T ss_pred             eccccccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCcCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence            99 99999999999999999999999999999999999999999997766677789999999999999999999999999


Q ss_pred             chhhhHHHHHHHHHHHHHHHHHhhCcCCCCCCC
Q 029900          150 LHRNTGARRKSRLARRKKAVEIHHGWYTPTPAE  182 (185)
Q Consensus       150 IHKNtAARKKSRLakkin~l~~~~g~~~p~~~~  182 (185)
                      ||+|+|+|+||||+++||++.++||||+|+|+.
T Consensus       159 IHKNkAARKKSRLak~vnal~~~~g~y~pa~~~  191 (202)
T 3bbn_T          159 LHKNTGARRKSRLARRKKAVEIHHGWYVPDAAA  191 (202)
T ss_dssp             SCTTHHHHHHHHHTTHHHHSSCC----------
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHhCCCCCCccc
Confidence            999999999999999999999999999999764

>2vqe_T 30S ribosomal protein S20; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.7.6.1 PDB: 1gix_W* 1hnw_T* 1hnx_T* 1hnz_T* 1hr0_T 1j5e_T 1jgo_W* 1jgp_W* 1jgq_W* 1ml5_W* 1yl4_W 2b64_T* 2b9m_T* 2b9o_T* 2f4v_T* 2ow8_u* 2qnh_u* 2uxb_T* 1fjg_T* 2uxd_T* ...

Probab=100.00  E-value=8.8e-34  Score=218.04  Aligned_cols=91  Identities=42%  Similarity=0.472  Sum_probs=83.3

Q ss_pred             hcccCchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhccCCCCCCCCccchHHHHHHHHHHHHHHHHhhhCcchh
Q 029900           73 ATKKKADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHR  152 (185)
Q Consensus        73 ~~maniKSA~KRiRq~eKrRlrNrs~KS~vRT~iKKv~~AIeagdk~~~a~a~d~~~A~~~l~~a~S~IDKAakKGVIHK  152 (185)
                      .+|+||+||+||+||+|++|+||+++||+|||+||+|+++|++||         .++|+++|..+++.||++++|||||+
T Consensus         4 k~MAN~KSA~KRirq~ekrr~rNka~kS~~rT~iKkv~~Ai~~gd---------k~~A~~~l~~a~s~iDkaa~KGviHK   74 (106)
T 2vqe_T            4 KKPKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAVQLAQEGK---------AEEALKIMRKAESLIDKAAKGSTLHK   74 (106)
T ss_dssp             ----CCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC---------HHHHHHHHHHHHHHHHHHTTTTSSCT
T ss_pred             ccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC---------HHHHHHHHHHHHHHHHHHHHcCCccH
Confidence            689999999999999999999999999999999999999999865         47899999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHHHh
Q 029900          153 NTGARRKSRLARRKKAVEIH  172 (185)
Q Consensus       153 NtAARKKSRLakkin~l~~~  172 (185)
                      |+|+|+||||+++||.+...
T Consensus        75 N~AARkKSRLak~v~~l~~~   94 (106)
T 2vqe_T           75 NAAARRKSRLMRKVRQLLEA   94 (106)
T ss_dssp             THHHHHHHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHHHHhcc
Confidence            99999999999999998763

---

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	185
d2uubt1	99	a.7.6.1 (T:8-106) Ribosomal protein S20 {Thermus t	2e-22
d2gy9t1	83	a.7.6.1 (T:4-86) Ribosomal protein S20 {Escherichi	2e-20

>d2uubt1 a.7.6.1 (T:8-106) Ribosomal protein S20 {Thermus thermophilus [TaxId: 274]} Length = 99

class: All alpha proteins
fold: Spectrin repeat-like
superfamily: Ribosomal protein S20
family: Ribosomal protein S20
domain: Ribosomal protein S20
species: Thermus thermophilus [TaxId: 274]

 Score = 84.4 bits (209), Expect = 2e-22
 Identities = 37/93 (39%), Positives = 55/93 (59%), Gaps = 9/93 (9%)

Query: 77  KADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAE 136
           +  SA KR RQ+ KRR+ NK++KS +KT  KK ++     + +            K++ +
Sbjct: 1   RNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAIQLAQEGKAE---------EALKIMRK 51

Query: 137 AYSVIDKAVKVGTLHRNTGARRKSRLARRKKAV 169
           A S+IDKA K  TLH+N  ARRKSRL R+ + +
Sbjct: 52  AESLIDKAAKGSTLHKNAAARRKSRLMRKVRQL 84

>d2gy9t1 a.7.6.1 (T:4-86) Ribosomal protein S20 {Escherichia coli [TaxId: 562]} Length = 83

class: All alpha proteins
fold: Spectrin repeat-like
superfamily: Ribosomal protein S20
family: Ribosomal protein S20
domain: Ribosomal protein S20
species: Escherichia coli [TaxId: 562]

 Score = 78.5 bits (194), Expect = 2e-20
 Identities = 29/90 (32%), Positives = 46/90 (51%), Gaps = 9/90 (10%)

Query: 80  SAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYS 139
           SA KRA Q+EK R +N SR+S ++T +KKV  A++   K            +K   E   
Sbjct: 2   SAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKA---------AAQKAFNEMQP 52

Query: 140 VIDKAVKVGTLHRNTGARRKSRLARRKKAV 169
           ++D+    G +H+N  AR K+ L  +   +
Sbjct: 53  IVDRQAAKGLIHKNKAARHKANLTAQINKL 82

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	185
d2gy9t1	83	Ribosomal protein S20 {Escherichia coli [TaxId: 56	99.96
d2uubt1	99	Ribosomal protein S20 {Thermus thermophilus [TaxId	99.95

>d2gy9t1 a.7.6.1 (T:4-86) Ribosomal protein S20 {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Spectrin repeat-like
superfamily: Ribosomal protein S20
family: Ribosomal protein S20
domain: Ribosomal protein S20
species: Escherichia coli [TaxId: 562]

Probab=99.96  E-value=1.1e-29  Score=185.04  Aligned_cols=82  Identities=34%  Similarity=0.447  Sum_probs=78.6

Q ss_pred             hhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhccCCCCCCCCccchHHHHHHHHHHHHHHHHhhhCcchhhhHHHH
Q 029900           79 DSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGARR  158 (185)
Q Consensus        79 KSA~KRiRq~eKrRlrNrs~KS~vRT~iKKv~~AIeagdk~~~a~a~d~~~A~~~l~~a~S~IDKAakKGVIHKNtAARK  158 (185)
                      |||+||+||++++|++|++++|+|||+||+|+++|++||         .++|+++|..+++.||+|++|||||+|+|+|+
T Consensus         1 KSA~Kr~rq~~kr~~~N~~~kS~~rT~iKk~~~ai~~~d---------~~~a~~~~~~a~s~iDkaa~KgiiHkN~AaRk   71 (83)
T d2gy9t1           1 KSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGD---------KAAAQKAFNEMQPIVDRQAAKGLIHKNKAARH   71 (83)
T ss_dssp             CCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC---------HHHHHHHHHTTHHHHHHHHHTTTTCHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC---------HHHHHHHHHHHHHHHHHHHHCCCcchhHHHHH
Confidence            699999999999999999999999999999999999864         47899999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 029900          159 KSRLARRKKAV  169 (185)
Q Consensus       159 KSRLakkin~l  169 (185)
                      ||||++.||++
T Consensus        72 kSRL~k~v~~~   82 (83)
T d2gy9t1          72 KANLTAQINKL   82 (83)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhc
Confidence            99999999987

>d2uubt1 a.7.6.1 (T:8-106) Ribosomal protein S20 {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Spectrin repeat-like
superfamily: Ribosomal protein S20
family: Ribosomal protein S20
domain: Ribosomal protein S20
species: Thermus thermophilus [TaxId: 274]

Probab=99.95  E-value=6e-29  Score=186.93  Aligned_cols=88  Identities=43%  Similarity=0.494  Sum_probs=82.6

Q ss_pred             chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhccCCCCCCCCccchHHHHHHHHHHHHHHHHhhhCcchhhhHHH
Q 029900           78 ADSAAKRARQAEKRRIYNKSRKSEVKTRMKKVLEALDGLRKKPDAQPEEVLPVEKLIAEAYSVIDKAVKVGTLHRNTGAR  157 (185)
Q Consensus        78 iKSA~KRiRq~eKrRlrNrs~KS~vRT~iKKv~~AIeagdk~~~a~a~d~~~A~~~l~~a~S~IDKAakKGVIHKNtAAR  157 (185)
                      +.||+||+||+++||+||++++|+|||+||+|+.+|++||         .++|+++|..+++.||+|++|||||+|+|+|
T Consensus         2 ~~SA~KRiRq~~krr~rN~~~kS~~kT~iKk~~~ai~~~d---------~e~A~~~l~~a~s~iDKAakKgiiHkN~AaR   72 (99)
T d2uubt1           2 NLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAIQLAQEGK---------AEEALKIMRKAESLIDKAAKGSTLHKNAAAR   72 (99)
T ss_dssp             CCSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTC---------HHHHHHHHHHHHHHHHHHTTSSTTCSHHHHH
T ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccC---------HHHHHHHHHHHHHHHHHHHhCCCCCcchHHH
Confidence            4799999999999999999999999999999999998754         5789999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhC
Q 029900          158 RKSRLARRKKAVEIHHG  174 (185)
Q Consensus       158 KKSRLakkin~l~~~~g  174 (185)
                      +||||+++||.+....+
T Consensus        73 kKSRL~k~v~~l~~~a~   89 (99)
T d2uubt1          73 RKSRLMRKVRQLLEAAG   89 (99)
T ss_dssp             HHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHHHHhhhc
Confidence            99999999999987654