Citrus Sinensis ID: 025898

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240------
Protein Sequence
MSSGVVYLVMGNLFFIVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAEMHGYDEEEDDIDYDDEEYDDEYDDGEGDEMDDNVDDDFEHGFSIVNVDDNEGEDSNDRSANISTIGRSNLRAEKVSR
Secondary Structure (PSIPRED)
ccccEEEEEEccEEEEEEEcccccccccccccccccHHHHHHHHHHHHHHccccccccccccEEEEEccccHHHHHHHHHHHHHHHHHcccEEEEEccccccccccccccccEEEEEEEEEEccccHHHHHHHHHcccccEEEEEEEEEccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccHHHcccc
Secondary Structure Prediction (SSPRO)
ccccEEEEEHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHccccccHHHccEEEEEEEEccccHHHHHHHHHHHHHHHHHcccEEEEEcccccHHcccHHHHHHHHHHEEEEEcccHHHHHHHHHHccHcHHHHHHHEEEccccccccccccHHHHHHHHccccccHHcccccccHHccccccccccccHccccccccccccEEEEEcccccccccccHHHHHcccccccEEEEEccc
Coil and Loop (DISEMBL)
MSSGVVYLVMGNLFFIVCYKKKVqedgralpefaddEEEKLYESLNIELESELNVERRRHYEVVYLIHEKyeedvgsvNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKrdkaitedcppppefhtlraemhgydeeeddidyddeeyddeyddgegdemddnvdddfeHGFSivnvddnegedsndrsanistigrsnlraekvsr
Flexible Loop (DISEMBL)
MSSGVVYLVMGNLFFIVCYKKKVQEDGRALPEFADDEEEKLYESLNieleselnverRRHYEVVYLIHekyeedvgsvneKVQDflrekkgrvwrlndwglrRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVikrdkaitedcppppEFHTLRAEMHGYDEEEDDIDYDDEEYDDEYDDGEGDEMDDNVDDDFEHGFSIvnvddnegedsndrsanistigrsnlraekvsr
Low Complexity Region (SEG)
MSSGVVYLVMGNLFFIVCYKKKVQEDGRALPEFADDEEEKlyeslnieleselnVERRRHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAEMHgydeeeddidyddeeyddeyddgegdemddnvdddfeHGFSIVNVDDNEGEDSNDRSANISTIGRSNLRAEKVSR
Disordered region (IsUnstruct)
****VVYLVMGNLFFIVCYKKKVQE***************LYESLNIELESELNVERRRHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAIT********************************************************************************************
Disordered Region (DISOPRED)
***GVVYLVMGNLFFIVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKA***************************************************************************************R*E****
Disordered Region (DISEMBL)
MSSGVVYLVMGNLFFIVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAEMHGYDEEEDDIDYDDEEYDDEYDDGEGDEMDDNVDDDFEHGFSIVNVDDNEGEDSNDRSANISTIGRSNLRAEKVSR
Disordered Region (DISPRO)
**SGVVYLVMGNLFFIVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDK***************************************************VDDDFEHGFSIVNVDDN*********A*ISTIGRSNLR******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSGVVYLVMGNLFFIVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIxxxxxxxxxxxxxxxxxxxxxKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAEMHGYDEEEDDIDYDDEEYDDEYDDGEGDEMDDNVDDDFEHGFSIVNVDDNEGEDSNDRSANISTIGRSNLRAEKVSR
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	246	2.2.26 [Sep-21-2011]
Q0VMF9	113	30S ribosomal protein S6	yes	no	0.406	0.884	0.43	2e-19
Q0ADI6	144	30S ribosomal protein S6	yes	no	0.581	0.993	0.303	7e-19
Q82XQ6	146	30S ribosomal protein S6	yes	no	0.406	0.684	0.38	7e-19
O07813	122	30S ribosomal protein S6	yes	no	0.406	0.819	0.41	9e-19
Q5F925	122	30S ribosomal protein S6	yes	no	0.406	0.819	0.41	9e-19
A1KUF0	122	30S ribosomal protein S6	yes	no	0.406	0.819	0.41	1e-18
Q9JU24	122	30S ribosomal protein S6	yes	no	0.406	0.819	0.41	1e-18
A9LZQ3	122	30S ribosomal protein S6	yes	no	0.406	0.819	0.41	1e-18
Q7NRY7	124	30S ribosomal protein S6	yes	no	0.406	0.806	0.41	1e-18
Q9JZ29	122	30S ribosomal protein S6	yes	no	0.406	0.819	0.4	2e-18

>sp|Q0VMF9|RS6_ALCBS 30S ribosomal protein S6 OS=Alcanivorax borkumensis (strain SK2 / ATCC 700651 / DSM 11573) GN=rpsF PE=3 SV=1

 Score = 95.9 bits (237), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 43/100 (43%), Positives = 64/100 (64%)

Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYEVV+L+H    E V ++ E+    + + KG + R+ DWG R+LAY I K  KAHY++
Sbjct: 2   RHYEVVFLVHPDQSEQVSAMVERYSAIVTDGKGTIHRVEDWGRRQLAYPINKIHKAHYVM 61

Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
           +N E + + + + +     ++ VIRHLVI+RD AITE  P
Sbjct: 62  LNIECDGETLGELENTFRFNDAVIRHLVIRRDNAITEPSP 101

Binds together with S18 to 16S ribosomal RNA.
Alcanivorax borkumensis (strain SK2 / ATCC 700651 / DSM 11573) (taxid: 393595)

>sp|Q0ADI6|RS6_NITEC 30S ribosomal protein S6 OS=Nitrosomonas eutropha (strain C91) GN=rpsF PE=3 SV=1

 Score = 94.4 bits (233), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 50/165 (30%), Positives = 82/165 (49%), Gaps = 22/165 (13%)

Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+++++H    E V ++ E+  + + E+ G + RL DWG R+L Y IQK  KAHYIL
Sbjct: 2   RHYEIIFIVHPDQSEQVSAMIERYSNMITERSGGIHRLEDWGRRQLTYPIQKLHKAHYIL 61

Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAEMHGYDEEED 178
           MN E + + +N+ +     ++ ++RHLVI+ +  +T   P                    
Sbjct: 62  MNIECDQESLNELEHSFKFNDAILRHLVIRMNGPVTTPSP-------------------- 101

Query: 179 DIDYDDEEYDDEYDDGEGDEMDDNVDDDFEHGFSIVNVDDNEGED 223
            +  DD+   DE   G       NV DD   G  +V  ++N+ + 
Sbjct: 102 -MMQDDKSKPDENSRGTAAP-TVNVADDSASGAQVVAAEENDTQS 144

Binds together with S18 to 16S ribosomal RNA.

Nitrosomonas eutropha (strain C91) (taxid: 335283)

>sp|Q82XQ6|RS6_NITEU 30S ribosomal protein S6 OS=Nitrosomonas europaea (strain ATCC 19718 / NBRC 14298) GN=rpsF PE=3 SV=1

 Score = 94.4 bits (233), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 38/100 (38%), Positives = 63/100 (63%)

Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+V+++H    E V ++ E+  + +  + G++ RL DWG R+L Y IQK  KAHY+L
Sbjct: 2   RHYEIVFIVHPDQSEQVSAMTERYSNIVTGRSGKIHRLEDWGRRQLTYPIQKLHKAHYVL 61

Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
           MN E + + +N+ +     ++ ++RHLVI+ +  IT   P
Sbjct: 62  MNIECDQESLNELEHSFKFNDAILRHLVIRMNGPITTPSP 101

Binds together with S18 to 16S ribosomal RNA.

Nitrosomonas europaea (strain ATCC 19718 / NBRC 14298) (taxid: 228410)

>sp|O07813|RS6_NEIGO 30S ribosomal protein S6 OS=Neisseria gonorrhoeae GN=rpsF PE=3 SV=1

 Score = 94.0 bits (232), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 41/100 (41%), Positives = 62/100 (62%)

Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+V+++H    E V ++ E+ +  + E  G++ RL DWG R+LAY I K  KAHY+L
Sbjct: 2   RHYEIVFIVHPDQSEQVPAMVERYKTMITEANGKIHRLEDWGRRQLAYPINKIHKAHYVL 61

Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
           MN E   + + + +T    ++ V+RHL IK   A+TE  P
Sbjct: 62  MNIETTPEVVGELETAFRFNDAVLRHLTIKTKHAVTEASP 101

Binds together with S18 to 16S ribosomal RNA.

Neisseria gonorrhoeae (taxid: 485)

>sp|Q5F925|RS6_NEIG1 30S ribosomal protein S6 OS=Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) GN=rpsF PE=3 SV=1

 Score = 94.0 bits (232), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 41/100 (41%), Positives = 62/100 (62%)

Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+V+++H    E V ++ E+ +  + E  G++ RL DWG R+LAY I K  KAHY+L
Sbjct: 2   RHYEIVFIVHPDQSEQVPAMVERYKTMITEANGKIHRLEDWGRRQLAYPINKIHKAHYVL 61

Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
           MN E   + + + +T    ++ V+RHL IK   A+TE  P
Sbjct: 62  MNIETTPEVVGELETAFRFNDAVLRHLTIKTKHAVTEASP 101

Binds together with S18 to 16S ribosomal RNA.

Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (taxid: 242231)

>sp|A1KUF0|RS6_NEIMF 30S ribosomal protein S6 OS=Neisseria meningitidis serogroup C / serotype 2a (strain ATCC 700532 / FAM18) GN=rpsF PE=3 SV=1

 Score = 93.6 bits (231), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 41/100 (41%), Positives = 62/100 (62%)

Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+V+++H    E V ++ E+ +  + E  G++ RL DWG R+LAY I K  KAHY+L
Sbjct: 2   RHYEIVFIVHPDQSEQVPAMVERYKTMIAEANGKIHRLEDWGRRQLAYPINKIHKAHYVL 61

Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
           MN E   + + + +T    ++ V+RHL IK   A+TE  P
Sbjct: 62  MNIETTPEVVEELETAFRFNDAVLRHLTIKTKHAVTEASP 101

Binds together with S18 to 16S ribosomal RNA.

Neisseria meningitidis serogroup C / serotype 2a (strain ATCC 700532 / FAM18) (taxid: 272831)

>sp|Q9JU24|RS6_NEIMA 30S ribosomal protein S6 OS=Neisseria meningitidis serogroup A / serotype 4A (strain Z2491) GN=rpsF PE=3 SV=1

 Score = 93.6 bits (231), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 41/100 (41%), Positives = 62/100 (62%)

Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+V+++H    E V ++ E+ +  + E  G++ RL DWG R+LAY I K  KAHY+L
Sbjct: 2   RHYEIVFIVHPDQSEQVPAMVERYKTMIAEANGKIHRLEDWGRRQLAYPINKIHKAHYVL 61

Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
           MN E   + + + +T    ++ V+RHL IK   A+TE  P
Sbjct: 62  MNIETTPEVVEELETAFRFNDAVLRHLTIKTKHAVTEASP 101

Binds together with S18 to 16S ribosomal RNA.

Neisseria meningitidis serogroup A / serotype 4A (strain Z2491) (taxid: 122587)

>sp|A9LZQ3|RS6_NEIM0 30S ribosomal protein S6 OS=Neisseria meningitidis serogroup C (strain 053442) GN=rpsF PE=3 SV=1

 Score = 93.6 bits (231), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 41/100 (41%), Positives = 62/100 (62%)

Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+V+++H    E V ++ E+ +  + E  G++ RL DWG R+LAY I K  KAHY+L
Sbjct: 2   RHYEIVFIVHPDQSEQVPAMVERYKTMIAEANGKIHRLEDWGRRQLAYPINKIHKAHYVL 61

Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
           MN E   + + + +T    ++ V+RHL IK   A+TE  P
Sbjct: 62  MNIETTPEVVEELETAFRFNDAVLRHLTIKTKHAVTEASP 101

Binds together with S18 to 16S ribosomal RNA.

Neisseria meningitidis serogroup C (strain 053442) (taxid: 374833)

>sp|Q7NRY7|RS6_CHRVO 30S ribosomal protein S6 OS=Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757) GN=rpsF PE=3 SV=1

 Score = 93.2 bits (230), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 41/100 (41%), Positives = 66/100 (66%)

Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+V+++H    E V ++ E+ +  +   +G++ RL DWG R+LAY IQK  KAHY+L
Sbjct: 2   RHYEIVFIVHPDQSEQVPAMIERYKGMVLAAEGKIHRLEDWGRRQLAYPIQKLHKAHYVL 61

Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
           MN E +A+ + + +     ++ V+RHL IK D+AI++  P
Sbjct: 62  MNVECQAETLAEIEHAFKFNDAVLRHLTIKMDRAISDASP 101

Binds together with S18 to 16S ribosomal RNA.

Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757) (taxid: 243365)

>sp|Q9JZ29|RS6_NEIMB 30S ribosomal protein S6 OS=Neisseria meningitidis serogroup B (strain MC58) GN=rpsF PE=3 SV=1

 Score = 93.2 bits (230), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 40/100 (40%), Positives = 62/100 (62%)

Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+V+++H    E V ++ E+ +  + E  G++ RL DWG R+LAY I K  KAHY+L
Sbjct: 2   RHYEIVFIVHPDQSEQVPAMVERYKTMIAEANGKIHRLEDWGRRQLAYPINKIHKAHYVL 61

Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
           MN E   + + + +T    ++ ++RHL IK   A+TE  P
Sbjct: 62  MNIETTPEVVEELETAFRFNDAILRHLTIKTKHAVTEASP 101

Binds together with S18 to 16S ribosomal RNA.

Neisseria meningitidis serogroup B (strain MC58) (taxid: 122586)

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	246
224099095	319	predicted protein [Populus trichocarpa]	0.869	0.670	0.668	1e-74
225432037	301	PREDICTED: uncharacterized protein LOC10	0.882	0.720	0.653	1e-68
449462132	318	PREDICTED: uncharacterized protein LOC10	0.747	0.578	0.646	8e-65
357161663	302	PREDICTED: uncharacterized protein LOC10	0.861	0.701	0.597	4e-64
326492696	303	predicted protein [Hordeum vulgare subsp	0.703	0.570	0.655	9e-63
356555979	323	PREDICTED: uncharacterized protein LOC10	0.621	0.473	0.718	5e-62
388521055	307	unknown [Lotus japonicus]	0.630	0.504	0.709	4e-61
108862831	317	ribosomal protein S6 containing protein,	0.890	0.690	0.539	8e-61
222617304	257	hypothetical protein OsJ_36520 [Oryza sa	0.626	0.599	0.714	1e-60
194701658	310	unknown [Zea mays] gi|223975025|gb|ACN31	0.634	0.503	0.711	3e-60

>gi|224099095|ref|XP_002311372.1| predicted protein [Populus trichocarpa] gi|222851192|gb|EEE88739.1| predicted protein [Populus trichocarpa]

 Score =  285 bits (729), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 149/223 (66%), Positives = 176/223 (78%), Gaps = 9/223 (4%)

Query: 16  IVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEEDV 75
           I+  +KK QEDGR LPEFAD EEEKL+E LN+EL+SEL VER RHYEVVYLIHEK++E+V
Sbjct: 90  ILLKEKKAQEDGRVLPEFADAEEEKLFEFLNLELQSELKVERLRHYEVVYLIHEKHDEEV 149

Query: 76  GSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTML 135
           GS+NEKVQDF+REKKGR+WR NDWG+RRLAYKIQKAK AHYILMNFELEA+WINDFK ML
Sbjct: 150 GSLNEKVQDFVREKKGRIWRFNDWGMRRLAYKIQKAKNAHYILMNFELEARWINDFKNML 209

Query: 136 DKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAEMHGYDEEEDDIDYD--DEEYDDEYDD 193
           DKDE+VIRHLVIKRD+AITEDCPPPPEFHTL+  M   D EED +DYD  DE YD++ + 
Sbjct: 210 DKDERVIRHLVIKRDEAITEDCPPPPEFHTLQGGMDNND-EEDGLDYDDNDEAYDEDLEV 268

Query: 194 ------GEGDEMDDNVDDDFEHGFSIVNVDDNEGEDSNDRSAN 230
                 G+GDE + +V     HG+   +  +NE   S   SA+
Sbjct: 269 EAEAVYGDGDEAEGSVSVISLHGYKEDDDGNNEVRHSKFASAS 311

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225432037|ref|XP_002273724.1| PREDICTED: uncharacterized protein LOC100243195 [Vitis vinifera] gi|296083213|emb|CBI22849.3| unnamed protein product [Vitis vinifera]

 Score =  265 bits (678), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 151/231 (65%), Positives = 178/231 (77%), Gaps = 14/231 (6%)

Query: 16  IVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEEDV 75
           ++  +KK QEDG  LPEFAD EEE+LYE LN++LES+LNVER RHYEVVYLIHEK++E+V
Sbjct: 85  VLLKEKKAQEDGSFLPEFADAEEEELYEFLNLQLESDLNVERMRHYEVVYLIHEKHDEEV 144

Query: 76  GSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTML 135
            +VN KVQDF+REKKG++WRLNDWGLRRLAYKIQKAK AHYILMNFELEA+WINDFKTML
Sbjct: 145 ENVNSKVQDFIREKKGKLWRLNDWGLRRLAYKIQKAKNAHYILMNFELEAQWINDFKTML 204

Query: 136 DKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAEMHGYDEEEDDIDYDDEEYDDEYDDGE 195
           D+DE+VIRHLVIKRD+AITEDCPPPPEFHTLRA       ++ D + DD +YDDE D   
Sbjct: 205 DQDERVIRHLVIKRDEAITEDCPPPPEFHTLRA-----GTDDYDDEEDDVDYDDEDDWDG 259

Query: 196 GDEMDDNVDDDFEHGFSIVNVDDNEGEDSNDRSANISTIGRSNLRAEKVSR 246
             E+D N        +S   VD     +S+DR      +GR NLRAEKV R
Sbjct: 260 EGEVDSN-------SYSDDVVDVIVPVNSDDRED--KNVGRRNLRAEKVGR 301

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462132|ref|XP_004148795.1| PREDICTED: uncharacterized protein LOC101219911 [Cucumis sativus] gi|449511877|ref|XP_004164078.1| PREDICTED: uncharacterized LOC101219911 [Cucumis sativus]

 Score =  252 bits (644), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 128/198 (64%), Positives = 156/198 (78%), Gaps = 14/198 (7%)

Query: 16  IVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEEDV 75
           ++  +KKV EDG+ LPEFAD EEEKLYE LN++LESE  VE+ RHYE+V+LIHEK  E+V
Sbjct: 91  VLLKEKKVAEDGQFLPEFADAEEEKLYEYLNLQLESESKVEQMRHYEIVFLIHEKNAEEV 150

Query: 76  GSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTML 135
            SV EKVQ FLREKKG++WRL+DWG+RRLAYKI+KAK AHYILMNFELEAKWIN+FK+ML
Sbjct: 151 ESVIEKVQGFLREKKGKLWRLSDWGMRRLAYKIKKAKYAHYILMNFELEAKWINEFKSML 210

Query: 136 DKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAEM----------HGYDEEEDDIDYDDE 185
           D DE+VIRHLVIKRD AITEDCPPPPEFHTLRA +                +D++++DDE
Sbjct: 211 DMDERVIRHLVIKRDTAITEDCPPPPEFHTLRAGIDDDDDNEEDDMDDYNSDDEMEWDDE 270

Query: 186 EYDDEYDDGEGDEMDDNV 203
              D+YD+G    +DD +
Sbjct: 271 AELDDYDEG----LDDGI 284

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357161663|ref|XP_003579164.1| PREDICTED: uncharacterized protein LOC100824031 [Brachypodium distachyon]

 Score =  250 bits (639), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 132/221 (59%), Positives = 166/221 (75%), Gaps = 9/221 (4%)

Query: 16  IVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEEDV 75
           ++  KKKV+EDG   PEFAD EEEKLYE LNIELES LN++R RHYEVVYLIHE   E+V
Sbjct: 74  VLLRKKKVKEDGETSPEFADAEEEKLYEFLNIELESGLNLQRMRHYEVVYLIHEDRVEEV 133

Query: 76  GSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTML 135
             V  KVQDF+REKKGR+WR+N+WGLRRLAYKI+KA  A+Y+LMNFE++AK+INDFKT+L
Sbjct: 134 EDVMSKVQDFIREKKGRIWRVNNWGLRRLAYKIKKATHANYVLMNFEIQAKYINDFKTLL 193

Query: 136 DKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAEMHGYDEEEDDIDYDDEEYDDEYDDGE 195
           DKDE++IRHLV+K+D+AITEDCPPPPEFH +R E +  DE    +D + E+ +D YD+ E
Sbjct: 194 DKDERIIRHLVMKQDEAITEDCPPPPEFHAMRTEQYMDDEY---VDEEVEKVEDGYDEDE 250

Query: 196 GDEMDDNVDDDFEHG-----FSIVNVDDNEGEDSNDRSANI 231
             E   NVD+ FE G       +  VDD+  ED   R+  +
Sbjct: 251 L-ESSGNVDNAFEDGDEPEMILVDEVDDDNAEDLRRRNRKV 290

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326492696|dbj|BAJ90204.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  246 bits (627), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 122/186 (65%), Positives = 149/186 (80%), Gaps = 13/186 (6%)

Query: 16  IVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEEDV 75
           ++  KKKV+EDG ALPEFAD EEEKLYE LNI+LES LN++R RHYEVVYLIHE   E+V
Sbjct: 76  VLLRKKKVKEDGEALPEFADAEEEKLYELLNIQLESGLNLQRMRHYEVVYLIHEDRVEEV 135

Query: 76  GSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTML 135
             V  KVQDF+REKKGR+WR+N+WGLRRLAYKI+KA  A+YILMNFE++A+ INDFKT+L
Sbjct: 136 EDVVSKVQDFIREKKGRIWRVNNWGLRRLAYKIKKATHANYILMNFEIQAQSINDFKTLL 195

Query: 136 DKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAEMHGYDEEEDDIDYDDEEYDDEYDDGE 195
           DKDE++IRHLV+KRD+AITEDCPPPPEFH +R++             DDE  D+EY  G+
Sbjct: 196 DKDERIIRHLVMKRDEAITEDCPPPPEFHAMRSQQ-----------LDDEYIDEEY--GK 242

Query: 196 GDEMDD 201
            D+ DD
Sbjct: 243 ADDADD 248

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356555979|ref|XP_003546305.1| PREDICTED: uncharacterized protein LOC100790128 [Glycine max]

 Score =  243 bits (620), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 110/153 (71%), Positives = 140/153 (91%)

Query: 16  IVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEEDV 75
           ++  K+ V+E+G+ LPEF D EE +L+E+L +EL+S+++VE  RHYEV+YLIHEK+EE+V
Sbjct: 100 VLLKKRTVEEEGKLLPEFEDAEERQLFEALMLELDSDMDVEILRHYEVMYLIHEKHEEEV 159

Query: 76  GSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTML 135
            +VNEK+QDFLREKKG+VWRLNDWG+RRLAYKI+KA  AHY+L+NFEL+AK+INDFKT+L
Sbjct: 160 AAVNEKIQDFLREKKGQVWRLNDWGMRRLAYKIKKANNAHYMLINFELDAKYINDFKTLL 219

Query: 136 DKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRA 168
           D+DE+VIRHLVIKRD+AITEDCPPPPEFHTLRA
Sbjct: 220 DQDERVIRHLVIKRDEAITEDCPPPPEFHTLRA 252

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388521055|gb|AFK48589.1| unknown [Lotus japonicus]

 Score =  240 bits (612), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 110/155 (70%), Positives = 136/155 (87%)

Query: 16  IVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEEDV 75
           ++  KK V+EDG  LPEF D EE KL+ESL +E++S+LNVE  RHYE+VYLIHEK+EE+V
Sbjct: 92  VLLKKKIVEEDGEFLPEFEDAEERKLFESLMLEMDSDLNVELLRHYEIVYLIHEKHEEEV 151

Query: 76  GSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTML 135
            +VNEK+QDFLREKKG VWR +DWG+R LAYKI+KA KAHYILMN E++AK+IN+FKT+L
Sbjct: 152 AAVNEKIQDFLREKKGTVWRFSDWGMRTLAYKIKKANKAHYILMNIEMDAKYINEFKTLL 211

Query: 136 DKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAEM 170
           D+DE+VIRHLV+KRD+AITEDCPPPPEFHTL A +
Sbjct: 212 DQDERVIRHLVVKRDEAITEDCPPPPEFHTLGASV 246

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|108862831|gb|ABA98957.2| ribosomal protein S6 containing protein, expressed [Oryza sativa Japonica Group]

 Score =  239 bits (610), Expect = 8e-61,   Method: Compositional matrix adjust.
 Identities = 131/243 (53%), Positives = 172/243 (70%), Gaps = 24/243 (9%)

Query: 16  IVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEEDV 75
           ++  KK V++DG+  PEFAD +EEKLYE LNI++ES+LN++R RHYEVVYLIHE   E+V
Sbjct: 87  VLLRKKMVKDDGQVAPEFADADEEKLYEFLNIQMESDLNLKRMRHYEVVYLIHEDRVEEV 146

Query: 76  GSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTML 135
             V  KVQDF+REKKGR+WRLN+WGLRRLAYKI+KA+ A+YILMNFE++AK+INDFKT+L
Sbjct: 147 EDVVSKVQDFVREKKGRIWRLNNWGLRRLAYKIKKARHANYILMNFEIQAKYINDFKTLL 206

Query: 136 DKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAEMH------------GYDEEEDDIDYD 183
           DKDE++IRHLV+KRD+AITEDC PPPEFHTLRA+              G +E+E + D+D
Sbjct: 207 DKDERIIRHLVMKRDEAITEDCSPPPEFHTLRAQQQYMDDEYIDDEDDGKEEQEPEEDWD 266

Query: 184 DEEYDDEYDDGEGDEMDDNVDDDFEHGFSIVNVDDNEGEDSNDRSANISTIGRSNLRAEK 243
           D+        GE +      DD+ E    I+ VD+ E +++ +      T+      AEK
Sbjct: 267 DK--------GEMENAGYEDDDEPE----IILVDEVERDNNENIRRRNRTMKVEKYAAEK 314

Query: 244 VSR 246
           V R
Sbjct: 315 VLR 317

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222617304|gb|EEE53436.1| hypothetical protein OsJ_36520 [Oryza sativa Japonica Group]

 Score =  238 bits (608), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 110/154 (71%), Positives = 137/154 (88%)

Query: 16  IVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEEDV 75
           ++  KK V++DG+  PEFAD +EEKLYE LNI++ES+LN++R RHYEVVYLIHE   E+V
Sbjct: 87  VLLRKKMVKDDGQVAPEFADADEEKLYEFLNIQMESDLNLKRMRHYEVVYLIHEDRVEEV 146

Query: 76  GSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTML 135
             V  KVQDF+REKKGR+WRLN+WGLRRLAYKI+KA+ A+YILMNFE++AK+INDFKT+L
Sbjct: 147 EDVVSKVQDFVREKKGRIWRLNNWGLRRLAYKIKKARHANYILMNFEIQAKYINDFKTLL 206

Query: 136 DKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAE 169
           DKDE++IRHLV+KRD+AITEDC PPPEFHTLRA+
Sbjct: 207 DKDERIIRHLVMKRDEAITEDCSPPPEFHTLRAQ 240

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|194701658|gb|ACF84913.1| unknown [Zea mays] gi|223975025|gb|ACN31700.1| unknown [Zea mays] gi|414878109|tpg|DAA55240.1| TPA: ribosomal protein S6 containing protein [Zea mays]

 Score =  237 bits (605), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 111/156 (71%), Positives = 138/156 (88%)

Query: 16  IVCYKKKVQEDGRALPEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEEDV 75
           ++  KK V+EDG+  PEFAD +EEKLY+ LNIELES+LN++R RHYEVVYLIHE   E+V
Sbjct: 81  VLLRKKMVREDGQVSPEFADADEEKLYDFLNIELESDLNLKRMRHYEVVYLIHEDRVEEV 140

Query: 76  GSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTML 135
            +V  KVQDF+REKKGR+WRLN+WGLRRLAYKI+KA  A+YILMNFE+E+++INDFKT+L
Sbjct: 141 ENVVSKVQDFIREKKGRIWRLNNWGLRRLAYKIKKATHANYILMNFEIESRYINDFKTLL 200

Query: 136 DKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAEMH 171
           DKDE++IRHLV+KRD+AITEDCPPPP FHTLRA+ +
Sbjct: 201 DKDERIIRHLVMKRDEAITEDCPPPPVFHTLRAQQY 236

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

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	246
TAIR|locus:2086112	314	RFC3 "REGULATOR OF FATTY-ACID	0.621	0.487	0.647	5.4e-55
TIGR_CMR|CBU_0864	127	CBU_0864 "ribosomal protein S6	0.394	0.763	0.453	1.9e-19
TIGR_CMR|SO_3930	131	SO_3930 "ribosomal protein S6"	0.406	0.763	0.41	9.5e-18
TIGR_CMR|CPS_0415	143	CPS_0415 "ribosomal protein S6	0.406	0.699	0.38	1.2e-17
UNIPROTKB|Q9KUZ2	122	rpsF "30S ribosomal protein S6	0.394	0.795	0.381	6.7e-17
TIGR_CMR|VC_0366	122	VC_0366 "ribosomal protein S6"	0.394	0.795	0.381	6.7e-17
UNIPROTKB|P02358	135	rpsF [Escherichia coli K-12 (t	0.406	0.740	0.39	1.4e-16
TIGR_CMR|CHY_0035	96	CHY_0035 "ribosomal protein S6	0.378	0.968	0.340	1.4e-14
TIGR_CMR|GSU_0665	117	GSU_0665 "ribosomal protein S6	0.406	0.854	0.306	3.5e-11
TIGR_CMR|BA_5723	96	BA_5723 "ribosomal protein S6"	0.378	0.968	0.297	9.4e-11

TAIR|locus:2086112 RFC3 "REGULATOR OF FATTY-ACID COMPOSITION 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 549 (198.3 bits), Expect = 5.4e-55, Sum P(2) = 5.4e-55
 Identities = 99/153 (64%), Positives = 125/153 (81%)

Query:    16 IVCYKKKVQEDGRALPEFADDEEEKXXXXXXXXXXXXXXVERRRHYEVVYLIHEKYEEDV 75
             I+  +KK+ E+G  LPEFAD EE++               ER RHYEVVYLIHEK+ E+V
Sbjct:    78 ILLKEKKIDEEGDLLPEFADAEEKELYQFLDLQLQSDLNEERMRHYEVVYLIHEKHAEEV 137

Query:    76 GSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTML 135
              S+N+KVQD+L+EKKG+VWR +DWG+RRLAYKIQKA+ AHYILMNFE+EAK++N+FK +L
Sbjct:   138 ESINQKVQDYLKEKKGKVWRFSDWGMRRLAYKIQKAENAHYILMNFEIEAKYLNEFKGLL 197

Query:   136 DKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRA 168
             D DE+VIRHLV+KRD+AITEDCPPPPEFH++RA
Sbjct:   198 DSDERVIRHLVMKRDEAITEDCPPPPEFHSVRA 230

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

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0019843 "rRNA binding" evidence=IEA

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0019243 "methylglyoxal catabolic process to D-lactate" evidence=RCA

TIGR_CMR|CBU_0864 CBU_0864 "ribosomal protein S6" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 44/97 (45%), Positives = 63/97 (64%)

Query:    59 RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
             RHYE+V L+H      V ++ E+ Q  ++EK G+V RL DWG R+LAY I K  KAHY+L
Sbjct:     2 RHYEIVILVHPDQSSQVPAMVERYQSMIKEKDGKVHRLEDWGRRQLAYSIDKVHKAHYLL 61

Query:   119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITE 155
             MN E +   I++ +     ++ VIR L++KRD AIT+
Sbjct:    62 MNIESDQGVISELENAFRYNDAVIRSLILKRDHAITK 98

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

TIGR_CMR|SO_3930 SO_3930 "ribosomal protein S6" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 41/100 (41%), Positives = 62/100 (62%)

Query:    59 RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
             RHYE+V+++H    E V  + E+    + E  G++ RL DWG R+LAY IQ   KAHY+L
Sbjct:     2 RHYEIVFMVHPDQSEQVPGMIERYTGAITEANGKIHRLEDWGRRQLAYPIQDLHKAHYVL 61

Query:   119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
             MN E  A+ I + +T    ++ V+R++V++   AITE  P
Sbjct:    62 MNVEAPAETIEELETAFRFNDAVLRNMVMRTKGAITEASP 101

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|CPS_0415 CPS_0415 "ribosomal protein S6" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 215 (80.7 bits), Expect = 1.2e-17, P = 1.2e-17
 Identities = 38/100 (38%), Positives = 62/100 (62%)

Query:    59 RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
             RHYE+V+++H    E V  + ++  D +   +G++ RL DWG R+LAY I K  KAHY+L
Sbjct:     2 RHYEIVFMVHPDQSEQVSGMIQRYTDLINAAEGKIHRLEDWGRRQLAYPINKLHKAHYVL 61

Query:   119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
             MN E     I++ +T    ++ VIR+++++   A+TE  P
Sbjct:    62 MNIEAPQVVIDELETAFRYNDVVIRNMIMRTKDAVTEASP 101

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

UNIPROTKB|Q9KUZ2 rpsF "30S ribosomal protein S6" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 208 (78.3 bits), Expect = 6.7e-17, P = 6.7e-17
 Identities = 37/97 (38%), Positives = 61/97 (62%)

Query:    59 RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
             RHYE+V+++H    E V  + E+    + E  G++ RL DWG R+LAY I K  KAHY+L
Sbjct:     2 RHYEIVFMVHPDQSEQVAGMIERYTGSITEAGGKIHRLEDWGRRQLAYPINKLHKAHYVL 61

Query:   119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITE 155
             MN E +   +++ +T    ++ V+R+++++   AITE
Sbjct:    62 MNVEADQAVVDELETAFRFNDAVLRNMIMRTKAAITE 98

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|VC_0366 VC_0366 "ribosomal protein S6" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 208 (78.3 bits), Expect = 6.7e-17, P = 6.7e-17
 Identities = 37/97 (38%), Positives = 61/97 (62%)

Query:    59 RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
             RHYE+V+++H    E V  + E+    + E  G++ RL DWG R+LAY I K  KAHY+L
Sbjct:     2 RHYEIVFMVHPDQSEQVAGMIERYTGSITEAGGKIHRLEDWGRRQLAYPINKLHKAHYVL 61

Query:   119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITE 155
             MN E +   +++ +T    ++ V+R+++++   AITE
Sbjct:    62 MNVEADQAVVDELETAFRFNDAVLRNMIMRTKAAITE 98

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

GO:0006412 "translation" evidence=ISS

UNIPROTKB|P02358 rpsF [Escherichia coli K-12 (taxid:83333)]

 Score = 205 (77.2 bits), Expect = 1.4e-16, P = 1.4e-16
 Identities = 39/100 (39%), Positives = 61/100 (61%)

Query:    59 RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
             RHYE+V+++H    E V  + E+    +   +G++ RL DWG R+LAY I K  KAHY+L
Sbjct:     2 RHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVL 61

Query:   119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
             MN E   + I++ +T    ++ VIR +V++   A+TE  P
Sbjct:    62 MNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASP 101

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0006412 "translation" evidence=IEA

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

GO:0019843 "rRNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

TIGR_CMR|CHY_0035 CHY_0035 "ribosomal protein S6" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 32/94 (34%), Positives = 62/94 (65%)

Query:    59 RHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYI 117
             R YEV+Y++H + + E   S+ E+ +  + ++ G V +++ WG RR AY+I+K ++ +Y+
Sbjct:     3 RQYEVMYILHPELDAEKTESIIERFKGMIEQEGGEVTKIDRWGKRRFAYEIKKLREGYYV 62

Query:   118 LMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDK 151
             +MNF+ +A+   +   +L   + V+RH+VI+ DK
Sbjct:    63 VMNFKAKAETAQELDRLLRISDDVVRHIVIREDK 96

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|GSU_0665 GSU_0665 "ribosomal protein S6" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 154 (59.3 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 31/101 (30%), Positives = 57/101 (56%)

Query:    59 RHYEVVYLIH-EKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYI 117
             R YE + ++  E  ++++  +  KV D +   KG + RL DWG+R+LAY ++K+ +  Y 
Sbjct:     3 RMYETIVIVQPELGDDELKGLTAKVTDIIGSFKGVLHRLEDWGVRKLAYPVKKSVRGRYY 62

Query:   118 LMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
              + F+ +A  I + +  L  D+KV+R+  +K +K      P
Sbjct:    63 YVRFDGDAPLIAELERRLRLDDKVLRYQSVKLEKEAAAPAP 103

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

GO:0006412 "translation" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

TIGR_CMR|BA_5723 BA_5723 "ribosomal protein S6" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 150 (57.9 bits), Expect = 9.4e-11, P = 9.4e-11
 Identities = 28/94 (29%), Positives = 53/94 (56%)

Query:    59 RHYEVVYLIHEKYEEDVG-SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYI 117
             R YE++Y+I    EE+   ++ E+    L      +    +WG RRLAY+I   ++  Y+
Sbjct:     2 RKYEIMYIIRPGVEEEAQKALVERFAGVLTNNGAEIINTKEWGKRRLAYEINDLREGFYM 61

Query:   118 LMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDK 151
             ++N    A+ IN+F  +   +E ++RH+V+K ++
Sbjct:    62 ILNVNANAEAINEFDRLAKINEDILRHIVVKEEE 95

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

GO:0006412 "translation" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	246
PRK00453	108	PRK00453, rpsF, 30S ribosomal protein S6; Reviewed	6e-27
pfam01250	92	pfam01250, Ribosomal_S6, Ribosomal protein S6	1e-25
COG0360	112	COG0360, RpsF, Ribosomal protein S6 [Translation,	6e-25
TIGR00166	93	TIGR00166, S6, ribosomal protein S6	2e-21
CHL00123	97	CHL00123, rps6, ribosomal protein S6; Validated	7e-12
PRK14074	257	PRK14074, rpsF, 30S ribosomal protein S6; Provisio	3e-04
pfam03115	787	pfam03115, Astro_capsid, Astrovirus capsid protein	0.003
pfam02724	583	pfam02724, CDC45, CDC45-like protein	0.004

>gnl|CDD|179034 PRK00453, rpsF, 30S ribosomal protein S6; Reviewed

 Score = 99.5 bits (249), Expect = 6e-27
 Identities = 35/98 (35%), Positives = 59/98 (60%), Gaps = 1/98 (1%)

Query: 59  RHYEVVYLIH-EKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYI 117
           R YE+V+++  +  EE V ++ E+ +  + E  G + ++ DWG RRLAY I K +K HY+
Sbjct: 2   RKYEIVFILRPDLSEEQVKALVERFKGVITENGGTIHKVEDWGRRRLAYPINKLRKGHYV 61

Query: 118 LMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITE 155
           L+NFE     I + + +   +E V+R L +K ++A  E
Sbjct: 62  LLNFEAPPAAIAELERLFRINEDVLRFLTVKVEEAEEE 99

Length = 108

>gnl|CDD|216388 pfam01250, Ribosomal_S6, Ribosomal protein S6

 Score = 96.0 bits (240), Expect = 1e-25
 Identities = 33/92 (35%), Positives = 58/92 (63%), Gaps = 1/92 (1%)

Query: 59  RHYEVVYLIH-EKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYI 117
           R YE ++++  +  EE+V ++ EK +  + E  G V ++ DWG R+LAY I+K ++ +Y+
Sbjct: 1   RKYETMFILRPDLSEEEVKALIEKYKKLIEENGGEVVKVEDWGKRKLAYPIKKKREGYYV 60

Query: 118 LMNFELEAKWINDFKTMLDKDEKVIRHLVIKR 149
           L+NFE E + I + +  L  +E V+R L +K 
Sbjct: 61  LINFEAEPEAIAELERRLRINEDVLRFLTVKL 92

Length = 92

>gnl|CDD|223437 COG0360, RpsF, Ribosomal protein S6 [Translation, ribosomal structure and biogenesis]

 Score = 94.6 bits (236), Expect = 6e-25
 Identities = 42/101 (41%), Positives = 64/101 (63%), Gaps = 1/101 (0%)

Query: 59  RHYEVVYLIH-EKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYI 117
           R YE+V+++  +  EE V ++ EK +  L    G + ++ DWG RRLAY I+K ++ HY+
Sbjct: 1   RKYEIVFIVRPDLSEEQVAALVEKYKGVLTNNGGEIHKVEDWGKRRLAYPIKKLREGHYV 60

Query: 118 LMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
           LMNFE E   I + + +L  +E V+RHL+IK +KA  E  P
Sbjct: 61  LMNFEAEPAAIAELERLLRINEDVLRHLIIKVEKAKEELSP 101

Length = 112

>gnl|CDD|129270 TIGR00166, S6, ribosomal protein S6

 Score = 85.1 bits (211), Expect = 2e-21
 Identities = 36/93 (38%), Positives = 55/93 (59%)

Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+++L+     E+V    E+ +  +      + R  DWG RRLAY I+K  +AHY+L
Sbjct: 1   RHYEIIFLVRPTLSEEVKGQIERYKKVITLNGAEIVRSEDWGKRRLAYPIKKQLRAHYVL 60

Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDK 151
           MNF  EA+ I +F+     ++ VIR L+IK + 
Sbjct: 61  MNFSGEAQVIKEFERTARINDNVIRSLIIKLEH 93

The ribosomal protein S6 ortholog family, including yeast MRP17, shows more than two-fold length variation from 95 residues in Bacillus subtilis to 215 in Mycoplasma pneumoniae. This length variation comes primarily from poorly conserved C-terminal extensions that are particularly long in the Mycoplasmas. MRP17 protein is a component of the small ribosomal subunit in mitochondria, and is shown here to be an ortholog of S6 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 93

>gnl|CDD|177046 CHL00123, rps6, ribosomal protein S6; Validated

 Score = 59.6 bits (145), Expect = 7e-12
 Identities = 29/89 (32%), Positives = 47/89 (52%), Gaps = 1/89 (1%)

Query: 61  YEVVYLIHEKY-EEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILM 119
           YE +YL+     EE++    E  +  LR++  +   + + G R+L+YKI K +   YI M
Sbjct: 8   YETMYLLKPDLNEEELLKWIENYKKLLRKRGAKNISVQNRGKRKLSYKINKYEDGIYIQM 67

Query: 120 NFELEAKWINDFKTMLDKDEKVIRHLVIK 148
           N+    K +N  +  L  DE V+R+L  K
Sbjct: 68  NYSGNGKLVNSLEKALKLDENVLRYLTFK 96

Length = 97

>gnl|CDD|172564 PRK14074, rpsF, 30S ribosomal protein S6; Provisional

 Score = 40.7 bits (95), Expect = 3e-04
 Identities = 19/53 (35%), Positives = 29/53 (54%)

Query: 99  WGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDK 151
           WGL   AY I K K  HY +M     +  +++F   +  +E +IRHL ++ DK
Sbjct: 187 WGLLDFAYPINKMKSGHYCIMCISSTSSIMDEFVRRMKLNENIIRHLSVQVDK 239

Length = 257

>gnl|CDD|217373 pfam03115, Astro_capsid, Astrovirus capsid protein precursor

 Score = 38.2 bits (89), Expect = 0.003
 Identities = 27/113 (23%), Positives = 44/113 (38%), Gaps = 34/113 (30%)

Query: 159 PPPEFHTLRAEMHG--------------------YDEEEDDIDYDDEEYDDEYDDGEGDE 198
           PPP    +  EM                       D  ED I  ++ + +DE  + E DE
Sbjct: 629 PPPAASQIYFEMRTSLPQSRAELSGLEERAVEDAPDPYEDLISLEETDTEDESTEDEDDE 688

Query: 199 MDDNVDDDFEHGFSIVNVDDNEGEDS--NDRSANISTI---GRSNLRAEKVSR 246
           +D          F + +   +E ED   N+R   +ST+   G S  RA ++++
Sbjct: 689 LDR---------FDLHDSSGSEPEDDDENNRVTLLSTLINQGMSVERATRITK 732

This product is encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The 87kD precursor protein undergoes an intracellular cleavage to form a 79kD protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion. Length = 787

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 37.7 bits (88), Expect = 0.004
 Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 6/68 (8%)

Query: 173 YDEEEDDIDYDDEEYDDEYDDGEGDEMDDNVDDDFEHGFSIVNVDDNEGEDSNDRSANIS 232
            +EE  D    D+ Y D  +D + DE  D  D++          +D+E +D +D   +I+
Sbjct: 106 IEEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSKS------EDDEDDDDDDDDDDIA 159

Query: 233 TIGRSNLR 240
           T  RS  R
Sbjct: 160 TRERSLER 167

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	246
CHL00123	97	rps6 ribosomal protein S6; Validated	99.97
PRK00453	108	rpsF 30S ribosomal protein S6; Reviewed	99.97
COG0360	112	RpsF Ribosomal protein S6 [Translation, ribosomal	99.96
TIGR00166	93	S6 ribosomal protein S6. MRP17 protein is a compon	99.96
PF01250	92	Ribosomal_S6: Ribosomal protein S6; InterPro: IPR0	99.95
PRK14074	257	rpsF 30S ribosomal protein S6; Provisional	99.83
KOG4708	141	consensus Mitochondrial ribosomal protein MRP17 [T	99.67
PRK14074	257	rpsF 30S ribosomal protein S6; Provisional	97.17
KOG1832	1516	consensus HIV-1 Vpr-binding protein [Cell cycle co	90.15
PF09026	101	CENP-B_dimeris: Centromere protein B dimerisation	88.28
KOG1832	1516	consensus HIV-1 Vpr-binding protein [Cell cycle co	82.98
PF04931	784	DNA_pol_phi: DNA polymerase phi; InterPro: IPR0070	82.93
PF11705	233	RNA_pol_3_Rpc31: DNA-directed RNA polymerase III s	82.67

>CHL00123 rps6 ribosomal protein S6; Validated

Probab=99.97  E-value=2.7e-30  Score=202.76  Aligned_cols=94  Identities=30%  Similarity=0.525  Sum_probs=90.3

Q ss_pred             ccccceeEEEEecCCCh-hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHH
Q 025898           56 ERRRHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTM  134 (246)
Q Consensus        56 ~~Mr~YEim~ILrp~~e-Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~  134 (246)
                      .+|++||+|+|++|+++ +++++++++++++|+++||+|+++++||.|+|||||+|+++|||++++|.++|++|++|++.
T Consensus         3 ~~mr~YE~~~Il~p~l~e~~~~~~~~~~~~~i~~~gg~i~~~~~wG~r~LAY~I~k~~~G~Yv~~~f~~~~~~i~eler~   82 (97)
T CHL00123          3 SKLNKYETMYLLKPDLNEEELLKWIENYKKLLRKRGAKNISVQNRGKRKLSYKINKYEDGIYIQMNYSGNGKLVNSLEKA   82 (97)
T ss_pred             CcccceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEeecCeeeeEEcCCCCEEEEEEEEEEECHHHHHHHHHH
Confidence            36899999999999985 47999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hCCCCCeeEEEEEee
Q 025898          135 LDKDEKVIRHLVIKR  149 (246)
Q Consensus       135 Lrlde~VLR~mVVK~  149 (246)
                      |+++++|||||++|.
T Consensus        83 lri~e~VlR~m~vk~   97 (97)
T CHL00123         83 LKLDENVLRYLTFKK   97 (97)
T ss_pred             hCCCCCeEEEEEEeC
Confidence            999999999999973

>PRK00453 rpsF 30S ribosomal protein S6; Reviewed

Probab=99.97  E-value=9.3e-30  Score=201.50  Aligned_cols=104  Identities=34%  Similarity=0.662  Sum_probs=98.1

Q ss_pred             ccceeEEEEecCCCh-hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhC
Q 025898           58 RRHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLD  136 (246)
Q Consensus        58 Mr~YEim~ILrp~~e-Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lr  136 (246)
                      ||+||+|+|++|..+ +++++++++++++|.++||+|+.+++||.|+|||+|+|+++|+|++|+|.++|+++++|++.|+
T Consensus         1 M~~YE~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~i~~~~~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~l~   80 (108)
T PRK00453          1 MRKYEIVFILRPDLSEEQVKALVERFKGVITENGGTIHKVEDWGRRRLAYPINKLRKGHYVLLNFEAPPAAIAELERLFR   80 (108)
T ss_pred             CCceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEecccccccceEcCCCcEEEEEEEEEEeCHHHHHHHHHHhC
Confidence            899999999999974 5799999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeeEEEEEeecCCCCCCCCCCC
Q 025898          137 KDEKVIRHLVIKRDKAITEDCPPPP  161 (246)
Q Consensus       137 lde~VLR~mVVK~de~i~e~~p~~p  161 (246)
                      +|++|||||++|+++......+..+
T Consensus        81 ~~~~VlR~~~vk~~~~~~~~~~~~~  105 (108)
T PRK00453         81 INEDVLRFLTVKVEEAEEEPSPMMK  105 (108)
T ss_pred             CCCCeEEEEEEEecccccccChhhh
Confidence            9999999999999988776665543

>COG0360 RpsF Ribosomal protein S6 [Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=5.1e-30  Score=207.31  Aligned_cols=103  Identities=40%  Similarity=0.727  Sum_probs=98.2

Q ss_pred             cceeEEEEecCCCh-hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhCC
Q 025898           59 RHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDK  137 (246)
Q Consensus        59 r~YEim~ILrp~~e-Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lrl  137 (246)
                      ++||+|||++|+.+ +++++.+++++++|+++||+|.++++||.|+|||||+|+++|||++|+|+|+|+++++|+|.|++
T Consensus         1 ~~YEi~~iv~p~~see~~~~~ve~~~~~l~~~gg~i~~~e~wG~R~LAY~IkK~~~g~Y~l~~f~~~~~~i~Eler~~ri   80 (112)
T COG0360           1 RKYEIVFIVRPDLSEEQVAALVEKYKGVLTNNGGEIHKVEDWGKRRLAYPIKKLREGHYVLMNFEAEPAAIAELERLLRI   80 (112)
T ss_pred             CceEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEehhhhhhhhcceecccceEEEEEEEEEcCHHHHHHHHHHhcc
Confidence            46999999999987 57999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeeEEEEEeecCCCCCCCCCCC
Q 025898          138 DEKVIRHLVIKRDKAITEDCPPPP  161 (246)
Q Consensus       138 de~VLR~mVVK~de~i~e~~p~~p  161 (246)
                      |++|||||++|.+...+..+|+.+
T Consensus        81 n~~VlR~liik~~~~~~~~~~~~~  104 (112)
T COG0360          81 NEDVLRHLIIKVEKAKEELSPMLK  104 (112)
T ss_pred             chhhheeeEEEechhhcccchhhh
Confidence            999999999999999888877754

>TIGR00166 S6 ribosomal protein S6

Probab=99.96  E-value=4.4e-29  Score=192.99  Aligned_cols=92  Identities=39%  Similarity=0.709  Sum_probs=88.9

Q ss_pred             cceeEEEEecCCChhhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhCCC
Q 025898           59 RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKD  138 (246)
Q Consensus        59 r~YEim~ILrp~~eEei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lrld  138 (246)
                      ++||+|+|++|..++++++++++++++|.++||+|+++++||.|+|||||+|+++|+|++|+|+++|+++++|++.|+++
T Consensus         1 ~~YE~~~Il~p~~~~~~~~~~~~~~~~i~~~gg~i~~~~~~G~r~LaY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lr~~   80 (93)
T TIGR00166         1 RHYEIIFLVRPTLSEEVKGQIERYKKVITLNGAEIVRSEDWGKRRLAYPIKKQLRAHYVLMNFSGEAQVIKEFERTARIN   80 (93)
T ss_pred             CceeEEEEECCCCcHHHHHHHHHHHHHHHhCCCEEEEEEeecceecceEcCCCceEEEEEEEEEeCHHHHHHHHHHhcCC
Confidence            57999999999987669999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCeeEEEEEeec
Q 025898          139 EKVIRHLVIKRD  150 (246)
Q Consensus       139 e~VLR~mVVK~d  150 (246)
                      ++|||||++|++
T Consensus        81 ~~VlR~~~vk~~   92 (93)
T TIGR00166        81 DNVIRSLIIKLE   92 (93)
T ss_pred             cCeEEEEEEEec
Confidence            999999999974

MRP17 protein is a component of the small ribosomal subunit in mitochondria, and is shown here to be an ortholog of S6.

>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.95  E-value=8e-28  Score=184.35  Aligned_cols=91  Identities=34%  Similarity=0.718  Sum_probs=86.6

Q ss_pred             cceeEEEEecCCCh-hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhCC
Q 025898           59 RHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDK  137 (246)
Q Consensus        59 r~YEim~ILrp~~e-Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lrl  137 (246)
                      |.||+|+|++|..+ ++++++++++.++|.++||+|+.+++||.|+|||||+|+.+|+|++++|+++|+++++|++.|++
T Consensus         1 r~YE~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~v~~~~~~G~r~LaY~i~k~~~G~Y~~~~f~~~~~~i~el~~~l~~   80 (92)
T PF01250_consen    1 RKYELMFILRPDLSEEEIKKLIERVKKIIEKNGGVVRSVENWGKRRLAYPIKKQKEGHYFLFNFDASPSAIKELERKLRL   80 (92)
T ss_dssp             EEEEEEEEE-TTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEEESSEETTECEEEEEEEEEEESTTHHHHHHHHHHT
T ss_pred             CceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEeecccccCCCCCCEEEEEEEEEEeCHHHHHHHHHHhcC
Confidence            68999999999975 47999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeeEEEEEee
Q 025898          138 DEKVIRHLVIKR  149 (246)
Q Consensus       138 de~VLR~mVVK~  149 (246)
                      +++|||||++|.
T Consensus        81 ~~~VlR~~~vK~   92 (92)
T PF01250_consen   81 DEDVLRYLIVKK   92 (92)
T ss_dssp             STTEEEEEEEE-
T ss_pred             CCCeEEEEEEeC
Confidence            999999999984

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....

>PRK14074 rpsF 30S ribosomal protein S6; Provisional

Probab=99.83  E-value=1.4e-20  Score=169.24  Aligned_cols=89  Identities=22%  Similarity=0.378  Sum_probs=83.4

Q ss_pred             hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhCCCCCeeEEEEEeecCC
Q 025898           73 EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKA  152 (246)
Q Consensus        73 Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lrlde~VLR~mVVK~de~  152 (246)
                      ++++++++++.++|+++|  +.++++||+|+|||||+|+++|+|++++|.++|++|++|+|.+|++++|||||++|++++
T Consensus       163 DQveevvEkik~iIe~~G--iikvE~WGkRkLAYpIkK~~eGyYvL~nFeAep~aIaELER~lRInE~VIRfLtVKlDe~  240 (257)
T PRK14074        163 NQSNKTLEMLLKNIEASG--LIKYEYWGLLDFAYPINKMKSGHYCIMCISSTSSIMDEFVRRMKLNENIIRHLSVQVDKF  240 (257)
T ss_pred             HHHHHHHHHHHHHHHhcC--eeehHhhcchhhccccCCCCeEEEEEEEEEcCHHHHHHHHHHhcCccceeeEEEEeeccc
Confidence            567788999999999995  569999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCc
Q 025898          153 ITEDCPPPPEF  163 (246)
Q Consensus       153 i~e~~p~~p~f  163 (246)
                      ...++|+.++.
T Consensus       241 ~~~pSpimkk~  251 (257)
T PRK14074        241 FEGKSYMMNKQ  251 (257)
T ss_pred             cccCChhhhhh
Confidence            99999987653

>KOG4708 consensus Mitochondrial ribosomal protein MRP17 [Translation, ribosomal structure and biogenesis]

Probab=99.67  E-value=2.1e-17  Score=138.19  Aligned_cols=97  Identities=25%  Similarity=0.396  Sum_probs=88.9

Q ss_pred             cccceeEEEEecCCChhhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCC----CCeeEEEEEEEEeCcchHHHHH
Q 025898           57 RRRHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQK----AKKAHYILMNFELEAKWINDFK  132 (246)
Q Consensus        57 ~Mr~YEim~ILrp~~eEei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK----~~~G~Yvl~~F~a~psaI~ELe  132 (246)
                      .|+.||+++|+++...++.+.++.+..+.+-..||.|+.++++|.|.|+|+|+|    |..|+||+|.|.++|++..++.
T Consensus         2 lmp~yelali~~~~~rpela~~l~rt~~~lid~ngVvrdveslG~r~Lpy~i~K~~~~h~~g~~f~m~f~ss~~v~~ei~   81 (141)
T KOG4708|consen    2 LMPLYELALITRSLSRPELAKLLARTGGHLIDRNGVVRDVESLGKRELPYKIKKLDQRHYRGQHFLMTFYSSPAVQSEIK   81 (141)
T ss_pred             cchHHHHHHHhcccCCHHHHHHHHHHhhHHhhcCCeEeechhcchhhhcchHHHhcCccccceEEEEeecCCHHHHHHHH
Confidence            599999999999998777777777777777778899999999999999999996    5689999999999999999999


Q ss_pred             HHhCCCCCeeEEEEEeecCCC
Q 025898          133 TMLDKDEKVIRHLVIKRDKAI  153 (246)
Q Consensus       133 r~Lrlde~VLR~mVVK~de~i  153 (246)
                      +.|+.+.+|||+++||++...
T Consensus        82 ~~l~~D~dviR~~IVKv~~~~  102 (141)
T KOG4708|consen   82 RILKRDPDVIRWLIVKVDDIK  102 (141)
T ss_pred             HHHhcChhhHHhhheeccccc
Confidence            999999999999999999853

>PRK14074 rpsF 30S ribosomal protein S6; Provisional

Probab=97.17  E-value=0.00036  Score=63.92  Aligned_cols=46  Identities=15%  Similarity=0.234  Sum_probs=43.4

Q ss_pred             ccceeEEEEecCCChh-hHHHHHHHHHHHHhhCCCEEEEEEeeeccc
Q 025898           58 RRHYEVVYLIHEKYEE-DVGSVNEKVQDFLREKKGRVWRLNDWGLRR  103 (246)
Q Consensus        58 Mr~YEim~ILrp~~eE-ei~~liekv~~iI~k~GG~I~~vedwG~Rr  103 (246)
                      |+.||.+||.+++++. ++..+++.+..+|.++||.|...+.||.+.
T Consensus         1 m~lYE~~fIa~q~ls~~q~e~l~e~~~~~l~~~~~~v~~~e~wG~~~   47 (257)
T PRK14074          1 MNLYEFTFIAQQGLLQQEVEEMVQELAVLLKNIKADVMFQQIKGILE   47 (257)
T ss_pred             CCccceeeeecccccHHHHHHHHHHHHHHHHhcCCeeehhhhhhhhh
Confidence            8999999999999865 799999999999999999999999999865

>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]

Probab=90.15  E-value=0.22  Score=53.54  Aligned_cols=40  Identities=8%  Similarity=0.155  Sum_probs=22.7

Q ss_pred             EEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHH
Q 025898           92 RVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFK  132 (246)
Q Consensus        92 ~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELe  132 (246)
                      .|++.+.|..|.+--- .....=.-..+.|+..+..+=...
T Consensus      1281 VIINSEIwD~RTF~lL-h~VP~Ldqc~VtFNstG~VmYa~~ 1320 (1516)
T KOG1832|consen 1281 VIINSEIWDMRTFKLL-HSVPSLDQCAVTFNSTGDVMYAML 1320 (1516)
T ss_pred             EEeechhhhhHHHHHH-hcCccccceEEEeccCccchhhhh
Confidence            5788899999865321 011122335667777766554443

>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box

Probab=88.28  E-value=0.14  Score=41.33  Aligned_cols=17  Identities=24%  Similarity=0.472  Sum_probs=0.0

Q ss_pred             CCccccccccCCCCCcc
Q 025898          161 PEFHTLRAEMHGYDEEE  177 (246)
Q Consensus       161 p~f~s~~~~~~~~~~~~  177 (246)
                      |.||-+....|.+.|.+
T Consensus         1 ~~~~~~eg~~dse~dsd   17 (101)
T PF09026_consen    1 PTLHFLEGEEDSESDSD   17 (101)
T ss_dssp             -----------------
T ss_pred             CceeecccCcccccccc
Confidence            34566666665444443

CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.

>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]

Probab=82.98  E-value=0.67  Score=50.06  Aligned_cols=9  Identities=11%  Similarity=0.003  Sum_probs=3.9

Q ss_pred             CCceEEEec
Q 025898          209 HGFSIVNVD  217 (246)
Q Consensus       209 ~~~~~~~~~  217 (246)
                      +++..+.+|
T Consensus      1460 Gd~~d~~~D 1468 (1516)
T KOG1832|consen 1460 GDEADILID 1468 (1516)
T ss_pred             cccccCCCC
Confidence            344444444

>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar

Probab=82.93  E-value=1.1  Score=46.69  Aligned_cols=13  Identities=15%  Similarity=0.478  Sum_probs=5.8

Q ss_pred             HhCCCCCeeEEEE
Q 025898          134 MLDKDEKVIRHLV  146 (246)
Q Consensus       134 ~Lrlde~VLR~mV  146 (246)
                      .|......||.++
T Consensus       597 lls~~s~llR~~~  609 (784)
T PF04931_consen  597 LLSQPSALLRKVS  609 (784)
T ss_pred             HHhCcchHHHHHH
Confidence            3444444555443

The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent

>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2

Probab=82.67  E-value=1.2  Score=39.91  Aligned_cols=25  Identities=32%  Similarity=0.708  Sum_probs=14.1

Q ss_pred             cCcCCCCCCCCCCCC-CCCCCCCCce
Q 025898          188 DDEYDDGEGDEMDDN-VDDDFEHGFS  212 (246)
Q Consensus       188 ~~~~~~~~~~~~~~~-~~~~~~~~~~  212 (246)
                      ++++++++++++.+| ..+-||.++.
T Consensus       194 dee~~dee~e~~~DYna~~YFDnGed  219 (233)
T PF11705_consen  194 DEEFEDEEDEDDDDYNAENYFDNGED  219 (233)
T ss_pred             ccccchhhhccCCCcchhccCCCCCc
Confidence            444434444445556 6667776666

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	246
1p6g_F	135	Real Space Refined Coordinates Of The 30s Subunit F		3e-17
3sfs_F	131	Crystal Structure Of Release Factor Rf3 Trapped In		3e-17
3fih_F	100	Ternary Complex-Bound E.Coli 70s Ribosome. This Ent		2e-16
2gy9_F	95	Structure Of The 30s Subunit Of A Pre-Translocation		9e-15
2j5a_A	110	Folding Of S6 Structures With Divergent Amino-Acid		3e-09
3r3t_A	99	Crystal Structure Of 30s Ribosomal Protein S From B		2e-08

>pdb|1P6G|F Chain F, Real Space Refined Coordinates Of The 30s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 135

Iteration: 1
 Score = 85.1 bits (209), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 39/100 (39%), Positives = 61/100 (61%)
Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+V+++H    E V  + E+    +   +G++ RL DWG R+LAY I K  KAHY+L
Sbjct: 2   RHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVL 61
Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
           MN E   + I++ +T    ++ VIR +V++   A+TE  P
Sbjct: 62  MNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASP 101

>pdb|3SFS|F Chain F, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp State On A Rotated Conformation Of The Ribosome Length = 131

Iteration: 1
 Score = 85.1 bits (209), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 39/100 (39%), Positives = 61/100 (61%)
Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+V+++H    E V  + E+    +   +G++ RL DWG R+LAY I K  KAHY+L
Sbjct: 2   RHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVL 61
Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCP 158
           MN E   + I++ +T    ++ VIR +V++   A+TE  P
Sbjct: 62  MNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASP 101

>pdb|3FIH|F Chain F, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry Consists Of The 30s Subunit, Trnas And The Ternary Complex. Length = 100

Iteration: 1
 Score = 82.0 bits (201), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/97 (39%), Positives = 60/97 (61%)
Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+V+++H    E V  + E+    +   +G++ RL DWG R+LAY I K  KAHY+L
Sbjct: 2   RHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVL 61
Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITE 155
           MN E   + I++ +T    ++ VIR +V++   A+TE
Sbjct: 62  MNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTE 98

>pdb|2GY9|F Chain F, Structure Of The 30s Subunit Of A Pre-Translocational E. Coli Ribosome Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1056 Length = 95

Iteration: 1
 Score = 77.0 bits (188), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 36/94 (38%), Positives = 57/94 (60%)
Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+V+++H    E V  + E+    +   +G++ RL DWG R+LAY I K  KAHY+L
Sbjct: 2   RHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVL 61
Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKA 152
           MN E   + I++ +T    ++ VIR +V++   A
Sbjct: 62  MNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHA 95

>pdb|2J5A|A Chain A, Folding Of S6 Structures With Divergent Amino-Acid Composition: Pathway Flexibility Within Partly Overlapping Foldons Length = 110

Iteration: 1
 Score = 58.9 bits (141), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/92 (38%), Positives = 54/92 (58%), Gaps = 2/92 (2%)
Query: 59  RHYEVVYLIHEKY-EEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYI 117
           R+YE V+ +     EE++    E+V++F+++K G +    DWG+R+LAY IQK   A Y 
Sbjct: 8   RYYETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARYF 67
Query: 118 LMNFELEAKWI-NDFKTMLDKDEKVIRHLVIK 148
           L+ F+ E   + N+    L  DE VIR L I+
Sbjct: 68  LVQFKTENPQLPNELDFQLKIDEDVIRWLNIQ 99

>pdb|3R3T|A Chain A, Crystal Structure Of 30s Ribosomal Protein S From Bacillus Anthracis Length = 99

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 51/94 (54%), Gaps = 1/94 (1%)
Query: 59  RHYEVVYLIHEKYEEDVG-SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYI 117
           R YE+ Y+I    EE+   ++ E+    L      +    +WG RRLAY+I   ++  Y 
Sbjct: 5   RKYEIXYIIRPGVEEEAQKALVERFAGVLTNNGAEIINTKEWGKRRLAYEINDLREGFYX 64
Query: 118 LMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDK 151
           ++N    A+ IN+F  +   +E ++RH+V+K ++
Sbjct: 65  ILNVNANAEAINEFDRLAKINEDILRHIVVKEEE 98

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	246
3r8n_F	100	30S ribosomal protein S6; protein biosynthesis, RN	1e-33
3i1m_F	135	30S ribosomal protein S6; ribosome structure, prot	7e-32
1cqm_A	101	Ribosomal protein S6; alzheimer disease, oligomeri	7e-27
2j5a_A	110	30S ribosomal protein S6; ribonucleoprotein, RIBO	1e-26
3r3t_A	99	30S ribosomal protein S6; structural genomics, cen	6e-26
1vmb_A	140	30S ribosomal protein S6; TM0603, structural genom	1e-23
3bbn_F	168	Ribosomal protein S6; small ribosomal subunit, spi	5e-22
2kjw_A	96	TS9, 30S ribosomal protein S6; S6 permutant, solut	3e-09

>3i1m_F 30S ribosomal protein S6; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1p6g_F 1p87_F* 1vs7_F* 2avy_F 2aw7_F 1vs5_F 2i2u_F 2i2p_F* 2qan_F* 2qb9_F* 2qbb_F* 2qbd_F 2qbf_F 2qbh_F* 2qbj_F* 2qou_F* 2qow_F* 2qoy_F* 2qp0_F* 2vho_F ... Length = 135

 Score =  112 bits (283), Expect = 7e-32
 Identities = 43/134 (32%), Positives = 70/134 (52%)

Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+V+++H    E V  + E+    +   +G++ RL DWG R+LAY I K  KAHY+L
Sbjct: 2   RHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVL 61

Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITEDCPPPPEFHTLRAEMHGYDEEED 178
           MN E   + I++ +T    ++ VIR +V++   A+TE  P        R     +  E  
Sbjct: 62  MNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANETA 121

Query: 179 DIDYDDEEYDDEYD 192
           D     +  ++E +
Sbjct: 122 DDAEAGDSEEEEEE 135

>1cqm_A Ribosomal protein S6; alzheimer disease, oligomerization; 1.65A {Thermus thermophilus} SCOP: d.58.14.1 PDB: 1cqn_A 1qjh_A 1ris_A 1fka_F 1gix_I* 1hnw_F* 1hnx_F* 1hnz_F* 1hr0_F 1i94_F* 1i95_F* 1i96_F* 1i97_F* 1ibk_F* 1ibl_F* 1ibm_F 1j5e_F 1jgo_I* 1jgp_I* 1jgq_I* ... Length = 101

 Score = 98.8 bits (247), Expect = 7e-27
 Identities = 26/98 (26%), Positives = 45/98 (45%), Gaps = 1/98 (1%)

Query: 59  RHYEVVYLIHEKYEED-VGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYI 117
           R YEV  +++   ++  +    E +Q  L     RV ++   GLRRLAY I K  + +++
Sbjct: 2   RRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVAILGLRRLAYPIAKDPQGYFL 61

Query: 118 LMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITE 155
               E+    +ND    L   + V R +V+K  +    
Sbjct: 62  WYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLA 99

>2j5a_A 30S ribosomal protein S6; ribonucleoprotein, RIBO protein S6, RNA-binding, rRNA-binding, protein folding; 2.3A {Aquifex aeolicus} SCOP: d.58.14.1 Length = 110

 Score = 98.9 bits (247), Expect = 1e-26
 Identities = 35/99 (35%), Positives = 57/99 (57%), Gaps = 2/99 (2%)

Query: 59  RHYEVVYLIH-EKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYI 117
           R+YE V+ +     EE++    E+V++F+++K G +    DWG+R+LAY IQK   A Y 
Sbjct: 8   RYYETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARYF 67

Query: 118 LMNFELE-AKWINDFKTMLDKDEKVIRHLVIKRDKAITE 155
           L+ F+ E  +  N+    L  DE VIR L I+  ++  +
Sbjct: 68  LVQFKTENPQLPNELDFQLKIDEDVIRWLNIQIKESEVK 106

>3r3t_A 30S ribosomal protein S6; structural genomics, center for structural genomics of infec diseases, csgid, beta-barrel, cytosol; 2.30A {Bacillus anthracis} Length = 99

 Score = 96.5 bits (241), Expect = 6e-26
 Identities = 28/94 (29%), Positives = 53/94 (56%), Gaps = 1/94 (1%)

Query: 59  RHYEVVYLIHEKYEED-VGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYI 117
           R YE++Y+I    EE+   ++ E+    L      +    +WG RRLAY+I   ++  Y+
Sbjct: 5   RKYEIMYIIRPGVEEEAQKALVERFAGVLTNNGAEIINTKEWGKRRLAYEINDLREGFYM 64

Query: 118 LMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDK 151
           ++N    A+ IN+F  +   +E ++RH+V+K ++
Sbjct: 65  ILNVNANAEAINEFDRLAKINEDILRHIVVKEEE 98

>1vmb_A 30S ribosomal protein S6; TM0603, structural genomics, JCSG, structure initiative, PSI, joint center for structural GENO translation; 1.70A {Thermotoga maritima} SCOP: d.58.14.1 Length = 140

 Score = 91.7 bits (228), Expect = 1e-23
 Identities = 22/99 (22%), Positives = 52/99 (52%), Gaps = 2/99 (2%)

Query: 59  RHYEVVYLIH-EKYEEDVGSVNEKVQDFLREK-KGRVWRLNDWGLRRLAYKIQKAKKAHY 116
           R YE +++I     EE+  ++ E+V+  + E+ KG++ ++   G+R+ AY+I+K  +  Y
Sbjct: 19  RIYESMFIIAPNVPEEERENLVERVKKIIEERVKGKIDKVERMGMRKFAYEIKKFNEGDY 78

Query: 117 ILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITE 155
            ++ F  + + + + +       ++IR    +R     +
Sbjct: 79  TVIYFRCDGQNLQELENFYRVTPEIIRWQTFRRFDLEKK 117

>3bbn_F Ribosomal protein S6; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 168

 Score = 88.4 bits (219), Expect = 5e-22
 Identities = 23/103 (22%), Positives = 46/103 (44%), Gaps = 10/103 (9%)

Query: 59  RHYEVVYLIH-EKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKA--- 114
           R YE + ++  +  E++  ++ +K ++ L         + + G+  LAY I++  KA   
Sbjct: 63  RQYETMAVLRPDMTEDERLTLTQKYEELLVAGGAMYVEVFNRGVIPLAYSIKRKNKAGET 122

Query: 115 ------HYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDK 151
                  Y+L  +  + + I+  +  L  D+ VIR    K  K
Sbjct: 123 NNYLDGIYLLFTYFTKPESISPLEAALVTDDDVIRSSSFKIRK 165

>2kjw_A TS9, 30S ribosomal protein S6; S6 permutant, solution structure, backbone dynamics, folding, ribonucleoprotein, RNA-binding, rRNA-binding; NMR {Thermus thermophilus} Length = 96

 Score = 52.3 bits (125), Expect = 3e-09
 Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 31  PEFADDEEEKLYESLNIELESELNVERRRHYEVVYLIHEKYEED-VGSVNEKVQDFLREK 89
            +  +D   +L    N+     +       YEV  +++   ++  +    E +Q  L   
Sbjct: 16  EDRVNDLARELRIRDNVRRVMVVASTTPGRYEVNIVLNPNLDQSQLALEKEIIQRALENY 75

Query: 90  KGRVWRLNDWGLRRLAYKIQK 110
             RV ++ + GLRRLAY I K
Sbjct: 76  GARVEKVEELGLRRLAYPIAK 96

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	246
1cqm_A	101	Ribosomal protein S6; alzheimer disease, oligomeri	99.98
3r8n_F	100	30S ribosomal protein S6; protein biosynthesis, RN	99.97
3i1m_F	135	30S ribosomal protein S6; ribosome structure, prot	99.97
2j5a_A	110	30S ribosomal protein S6; ribonucleoprotein, RIBO	99.97
3r3t_A	99	30S ribosomal protein S6; structural genomics, cen	99.96
1vmb_A	140	30S ribosomal protein S6; TM0603, structural genom	99.96
3bbn_F	168	Ribosomal protein S6; small ribosomal subunit, spi	99.95
2kjw_A	96	TS9, 30S ribosomal protein S6; S6 permutant, solut	99.62
3zzp_A	77	TS9, ribosomal protein S6; protein folding, RNA-bi	99.05
2kjw_A	96	TS9, 30S ribosomal protein S6; S6 permutant, solut	98.76
3zzp_A	77	TS9, ribosomal protein S6; protein folding, RNA-bi	97.93

>1cqm_A Ribosomal protein S6; alzheimer disease, oligomerization; 1.65A {Thermus thermophilus} SCOP: d.58.14.1 PDB: 1cqn_A 1qjh_A 1ris_A 1fka_F 1gix_I* 1hnw_F* 1hnx_F* 1hnz_F* 1hr0_F 1i94_F* 1i95_F* 1i96_F* 1i97_F* 1ibk_F* 1ibl_F* 1ibm_F 1j5e_F 1jgo_I* 1jgp_I* 1jgq_I* ...

Probab=99.98  E-value=2.4e-32  Score=213.85  Aligned_cols=99  Identities=26%  Similarity=0.414  Sum_probs=93.9

Q ss_pred             ccceeEEEEecCCC-hhhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhC
Q 025898           58 RRHYEVVYLIHEKY-EEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLD  136 (246)
Q Consensus        58 Mr~YEim~ILrp~~-eEei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lr  136 (246)
                      ||+||+|+|++|++ ++++++++++++++|+++||+|+++++||.|+|||+|+|+++|||++|+|.|+|+++++|++.|+
T Consensus         1 M~~YE~~~Il~p~l~~e~~~~~~~~~~~~i~~~gg~i~~~e~wG~R~LAY~I~k~~~G~Y~l~~f~a~~~~i~eler~lr   80 (101)
T 1cqm_A            1 MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVAILGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELR   80 (101)
T ss_dssp             CEEEEEEEEECTTCCHHHHHHHHHHHHHHHHHTTCEEEEEEEEEEEEEEEEETTEEEEEEEEEEEEECHHHHHHHHHHHH
T ss_pred             CCceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEeecCcccccCcCCCCEEEEEEEEEEeChHHHHHHHHHhc
Confidence            89999999999997 46899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeeEEEEEeecCCCCCC
Q 025898          137 KDEKVIRHLVIKRDKAITED  156 (246)
Q Consensus       137 lde~VLR~mVVK~de~i~e~  156 (246)
                      +|++|||||++|++++.+++
T Consensus        81 ~~~~VlR~l~vk~~~~~~~~  100 (101)
T 1cqm_A           81 IRDNVRRVMVVKSQEPFLAN  100 (101)
T ss_dssp             TSTTEEEEEEEECSSCCC--
T ss_pred             CCcceEEEEEEEecccccCC
Confidence            99999999999999876654

>3i1m_F 30S ribosomal protein S6; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1p6g_F 1p87_F* 1vs7_F* 2avy_F 2aw7_F 1vs5_F 2i2u_F 2i2p_F* 2qan_F* 2qb9_F* 2qbb_F* 2qbd_F 2qbf_F 2qbh_F* 2qbj_F* 2qou_F* 2qow_F* 2qoy_F* 2qp0_F* 2vho_F ...

Probab=99.97  E-value=1.8e-32  Score=226.05  Aligned_cols=107  Identities=36%  Similarity=0.661  Sum_probs=98.7

Q ss_pred             ccceeEEEEecCCChhhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhCC
Q 025898           58 RRHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDK  137 (246)
Q Consensus        58 Mr~YEim~ILrp~~eEei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lrl  137 (246)
                      ||+||+|||++|+++++++++++++.++|+++||+|+++++||.|+|||+|+|+++|||++|+|.|+|+++++|++.|++
T Consensus         1 Mr~YE~~~Il~P~~~e~v~~~ve~~~~~I~~~GG~I~~ve~wG~R~LAY~I~K~~~G~Y~l~~f~a~~~~i~ELer~lri   80 (135)
T 3i1m_F            1 MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRF   80 (135)
T ss_dssp             CCEECBEEEECSTTTTSHHHHHHHHHHHHHHTTCEECCCEEEEEECCSSCTTSSSCEEEEECCEECCTTHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCchHHHHHHHHHHHHHHHHCCCEEEEEEeeccccCceEcCCCCeEEEEEEEEEeCHHHHHHHHHHhcC
Confidence            89999999999998878999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeeEEEEEeecCCCCCCCCCCCCcc
Q 025898          138 DEKVIRHLVIKRDKAITEDCPPPPEFH  164 (246)
Q Consensus       138 de~VLR~mVVK~de~i~e~~p~~p~f~  164 (246)
                      |++|||||++|+++..+++||+.+...
T Consensus        81 ~e~VLR~livk~d~~~~~~s~~~~~~~  107 (135)
T 3i1m_F           81 NDAVIRSMVMRTKHAVTEASPMVKAKD  107 (135)
T ss_dssp             CSSEESCCBCCCSSCCCSCC-------
T ss_pred             CCCeEEEEEEEeccCccCCChhhhhhh
Confidence            999999999999999999999986654

>2j5a_A 30S ribosomal protein S6; ribonucleoprotein, RIBO protein S6, RNA-binding, rRNA-binding, protein folding; 2.3A {Aquifex aeolicus} SCOP: d.58.14.1

Probab=99.97  E-value=5.1e-31  Score=209.55  Aligned_cols=97  Identities=34%  Similarity=0.599  Sum_probs=93.0

Q ss_pred             cccceeEEEEecCCCh-hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEe-CcchHHHHHHH
Q 025898           57 RRRHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFEL-EAKWINDFKTM  134 (246)
Q Consensus        57 ~Mr~YEim~ILrp~~e-Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a-~psaI~ELer~  134 (246)
                      .||+||+|+|++|+++ ++++++++++.++|+++||+|+++++||.|+|||+|+|+++|||++++|.| +|+++++|++.
T Consensus         6 ~M~~YE~~~Il~p~l~~e~~~~~v~~~~~~i~~~Gg~i~~~e~wG~R~LAY~I~K~~~G~Y~l~~f~a~~~~~i~eler~   85 (110)
T 2j5a_A            6 TLRYYETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARYFLVQFKTENPQLPNELDFQ   85 (110)
T ss_dssp             SCEEEEEEEEECTTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEECSSCSSSCSEEEEEEEEEEESCTTHHHHHHHH
T ss_pred             CCCcceEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEeecCcccccCcCCCCEEEEEEEEEEeCCHHHHHHHHHH
Confidence            5999999999999975 579999999999999999999999999999999999999999999999999 99999999999


Q ss_pred             hCCCCCeeEEEEEeecCCC
Q 025898          135 LDKDEKVIRHLVIKRDKAI  153 (246)
Q Consensus       135 Lrlde~VLR~mVVK~de~i  153 (246)
                      |++|++|||||++|+++..
T Consensus        86 lr~~e~VlR~livk~~~~~  104 (110)
T 2j5a_A           86 LKIDEDVIRWLNIQIKESE  104 (110)
T ss_dssp             HHHCTTEEEEEEEEECGGG
T ss_pred             hCCCcCeEEEEEEEccccc
Confidence            9999999999999998654

>3r3t_A 30S ribosomal protein S6; structural genomics, center for structural genomics of infec diseases, csgid, beta-barrel, cytosol; 2.30A {Bacillus anthracis}

Probab=99.96  E-value=8.4e-32  Score=210.30  Aligned_cols=96  Identities=29%  Similarity=0.635  Sum_probs=91.4

Q ss_pred             ccccceeEEEEecCCCh-hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHH
Q 025898           56 ERRRHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTM  134 (246)
Q Consensus        56 ~~Mr~YEim~ILrp~~e-Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~  134 (246)
                      +.||+||+|+|++|+++ ++++++++++.++|+++||+|+++++||.|+|||+|+|+++|||++++|.|+|+++++|++.
T Consensus         2 ~~M~~YE~~~Il~p~~~~e~~~~~~~~~~~~i~~~gg~i~~~e~wG~R~LAY~I~k~~~G~Y~l~~f~a~~~~i~eler~   81 (99)
T 3r3t_A            2 NAMRKYEIMYIIRPGVEEEAQKALVERFAGVLTNNGAEIINTKEWGKRRLAYEINDLREGFYMILNVNANAEAINEFDRL   81 (99)
T ss_dssp             -CCCCCCCCCCCCTTSCHHHHHHHHHHHHHHHHTTTCCCCCCCCCCSCCCCCCCCCCCCSCCCCCCCCCCHHHHHHHHHH
T ss_pred             CCCcceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEeeccccCcCcCCCCEEEEEEEEEEeCHHHHHHHHHH
Confidence            46999999999999985 57999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hCCCCCeeEEEEEeecC
Q 025898          135 LDKDEKVIRHLVIKRDK  151 (246)
Q Consensus       135 Lrlde~VLR~mVVK~de  151 (246)
                      |+++++|||||++|+++
T Consensus        82 lr~~~~VlR~livk~~~   98 (99)
T 3r3t_A           82 AKINEDILRHIVVKEEE   98 (99)
T ss_dssp             HHHCTTCCCCCCCCCC-
T ss_pred             hcCCCCeEEEEEEEecC
Confidence            99999999999999875

>1vmb_A 30S ribosomal protein S6; TM0603, structural genomics, JCSG, structure initiative, PSI, joint center for structural GENO translation; 1.70A {Thermotoga maritima} SCOP: d.58.14.1

Probab=99.96  E-value=1.3e-30  Score=216.25  Aligned_cols=107  Identities=20%  Similarity=0.446  Sum_probs=96.9

Q ss_pred             hhccccceeEEEEecCCCh-hhHHHHHHHHHHHHhhC-CCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHH
Q 025898           54 NVERRRHYEVVYLIHEKYE-EDVGSVNEKVQDFLREK-KGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDF  131 (246)
Q Consensus        54 ~~~~Mr~YEim~ILrp~~e-Eei~~liekv~~iI~k~-GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~EL  131 (246)
                      -...||+||+|||++|+++ ++++++++++.++|+++ ||+|+++++||+|+|||||+|+++|+|++|+|.|+|++|++|
T Consensus        14 ~~~~Mr~YE~~~Il~P~l~ee~v~~~ve~~~~~I~~~~GG~I~~ve~wG~R~LAY~I~K~~~G~Yvl~~f~a~~~~i~EL   93 (140)
T 1vmb_A           14 AYVKERIYESMFIIAPNVPEEERENLVERVKKIIEERVKGKIDKVERMGMRKFAYEIKKFNEGDYTVIYFRCDGQNLQEL   93 (140)
T ss_dssp             ---CCEEEEEEEEECTTSCHHHHHHHHHHHHHHHHHTTCCEEEEEEEEEEEEEEEEETTEEEEEEEEEEEEECSSSTHHH
T ss_pred             cccccccceEEEEECCCCCHHHHHHHHHHHHHHHHhcCCCEEEEEEeecCcccccccCCCCEEEEEEEEEEECHHHHHHH
Confidence            3456999999999999975 57999999999999999 999999999999999999999999999999999999999999


Q ss_pred             HHHhCCCCCeeEEEEEeecCCCCCCCCCC
Q 025898          132 KTMLDKDEKVIRHLVIKRDKAITEDCPPP  160 (246)
Q Consensus       132 er~Lrlde~VLR~mVVK~de~i~e~~p~~  160 (246)
                      ++.||+|++|||||++|+++.....+++.
T Consensus        94 er~lri~e~VLR~livK~~~~~~~~s~~~  122 (140)
T 1vmb_A           94 ENFYRVTPEIIRWQTFRRFDLEKKERKAQ  122 (140)
T ss_dssp             HHHHHTCTTEEEEEEEECHHHHHHHHHHH
T ss_pred             HHHhcCCcceeEEEEEEecccccchhhhh
Confidence            99999999999999999987655544443

>3bbn_F Ribosomal protein S6; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=99.95  E-value=2.2e-28  Score=208.58  Aligned_cols=96  Identities=21%  Similarity=0.342  Sum_probs=91.3

Q ss_pred             cccceeEEEEecCCCh-hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCC---------eeEEEEEEEEeCcc
Q 025898           57 RRRHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAK---------KAHYILMNFELEAK  126 (246)
Q Consensus        57 ~Mr~YEim~ILrp~~e-Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~---------~G~Yvl~~F~a~ps  126 (246)
                      .||+||+|+|++|+++ ++++++++++.++|+++||+|+++++||+|+|||+|+|++         +|+|++|+|.|+|+
T Consensus        61 ~Mr~YE~m~IlrPdl~eeev~alver~~~iI~~~GG~I~~ve~WG~RrLAY~IkK~~kgg~~~~h~eG~Yvlm~F~a~p~  140 (168)
T 3bbn_F           61 GLRQYETMAVLRPDMTEDERLTLTQKYEELLVAGGAMYVEVFNRGVIPLAYSIKRKNKAGETNNYLDGIYLLFTYFTKPE  140 (168)
T ss_dssp             -CEEEEEEEEECTTSCHHHHHSTTHHHHHHHTTTSCEEEEEEEEEECCCSSCTTSCSSSCSSCCCCCCEEEEEEEEECTT
T ss_pred             CCCceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEecccccccceeccCcccccccccceEEEEEEEEEeCHH
Confidence            4999999999999975 5799999999999999999999999999999999999998         79999999999999


Q ss_pred             hHHHHHHHhCCCCCeeEEEEEeecCC
Q 025898          127 WINDFKTMLDKDEKVIRHLVIKRDKA  152 (246)
Q Consensus       127 aI~ELer~Lrlde~VLR~mVVK~de~  152 (246)
                      +|++|++.|++|++|||||++|+++.
T Consensus       141 ~I~ELeR~Lride~VLR~liVK~d~~  166 (168)
T 3bbn_F          141 SISPLEAALVTDDDVIRSSSFKIRKR  166 (168)
T ss_dssp             SSHHHHHHHHTSSCCSEEECCBCCSC
T ss_pred             HHHHHHHHhcCCcCeeEEEEEecccc
Confidence            99999999999999999999998854

>2kjw_A TS9, 30S ribosomal protein S6; S6 permutant, solution structure, backbone dynamics, folding, ribonucleoprotein, RNA-binding, rRNA-binding; NMR {Thermus thermophilus}

Probab=99.62  E-value=1.1e-16  Score=125.35  Aligned_cols=57  Identities=30%  Similarity=0.452  Sum_probs=53.2

Q ss_pred             hhccccceeEEEEecCCCh-hhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCC
Q 025898           54 NVERRRHYEVVYLIHEKYE-EDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQK  110 (246)
Q Consensus        54 ~~~~Mr~YEim~ILrp~~e-Eei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK  110 (246)
                      .+++||+||+|||++|+++ +++++++++++++|+++||+|.++++||+|+|||||+|
T Consensus        39 ~~e~Mr~YE~m~Il~P~l~ee~~~~~ve~~~~iI~~~gG~i~~ve~WG~R~LAY~I~K   96 (96)
T 2kjw_A           39 ASTTPGRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAK   96 (96)
T ss_dssp             ECSSSSCEEEEEECCSSCCHHHHHHHHHHHHHHHHHHTCCCSCCEECCCCCCCCSCCC
T ss_pred             ehhhhhhhheeeeeCCCCCHHHHHHHHHHHHHHHHhCCCEEEEEeccccccccccCCC
Confidence            4556999999999999985 57999999999999999999999999999999999997

>3zzp_A TS9, ribosomal protein S6; protein folding, RNA-binding; 0.96A {Thermus thermophilus}

Probab=99.05  E-value=1.1e-10  Score=87.72  Aligned_cols=42  Identities=17%  Similarity=0.237  Sum_probs=38.8

Q ss_pred             CCeeEEEEEEEEeCcchHHHHHHHhCCCCCeeEEEEEeecCC
Q 025898          111 AKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKA  152 (246)
Q Consensus       111 ~~~G~Yvl~~F~a~psaI~ELer~Lrlde~VLR~mVVK~de~  152 (246)
                      +++|||++++|.|+|+++++|+|.||++++|||||++|.+++
T Consensus         2 k~~G~Yvl~~~~a~~~~i~Eler~~rine~VlR~l~vr~d~~   43 (77)
T 3zzp_A            2 DPQGYTTWYQVEMPEDRVNDLARELRIRDNVRRVMVVASTTP   43 (77)
T ss_dssp             --CTTEEEEEEECCHHHHHHHHHHHHTSTTEEEEEEEECSST
T ss_pred             CceEEEEEEEEEeCHhHHHHHHHHhCCCHHHHHHHHHhccCC
Confidence            468999999999999999999999999999999999998865

>2kjw_A TS9, 30S ribosomal protein S6; S6 permutant, solution structure, backbone dynamics, folding, ribonucleoprotein, RNA-binding, rRNA-binding; NMR {Thermus thermophilus}

Probab=98.76  E-value=1.4e-09  Score=84.96  Aligned_cols=40  Identities=18%  Similarity=0.332  Sum_probs=38.9

Q ss_pred             CCeeEEEEEEEEeCcchHHHHHHHhCCCCCeeEEEEEeec
Q 025898          111 AKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRD  150 (246)
Q Consensus       111 ~~~G~Yvl~~F~a~psaI~ELer~Lrlde~VLR~mVVK~d  150 (246)
                      +++|||++++|+|+|+++++|+|.+|++++|||||+++++
T Consensus         2 ~~~g~Y~~~~~~a~~~~v~eler~~r~~e~vlR~l~v~~e   41 (96)
T 2kjw_A            2 DPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVAST   41 (96)
T ss_dssp             TTSCCCEEECCCCCHHHHHHHHHHHHHCTTCSEEEEEECS
T ss_pred             CceEEEEEEEeecChhHHHHHHHHhccchhhhhhhheehh
Confidence            5789999999999999999999999999999999999998

>3zzp_A TS9, ribosomal protein S6; protein folding, RNA-binding; 0.96A {Thermus thermophilus}

Probab=97.93  E-value=6.1e-06  Score=61.82  Aligned_cols=38  Identities=16%  Similarity=0.250  Sum_probs=34.1

Q ss_pred             hhccccceeEEEEecCCChh-hHHHHHHHHHHHHhhCCC
Q 025898           54 NVERRRHYEVVYLIHEKYEE-DVGSVNEKVQDFLREKKG   91 (246)
Q Consensus        54 ~~~~Mr~YEim~ILrp~~eE-ei~~liekv~~iI~k~GG   91 (246)
                      +.+..|+||+|||++|++++ ++++++++++++|+++||
T Consensus        39 r~d~~r~YE~m~Il~P~l~ee~~~~~vek~~~~i~~~Gg   77 (77)
T 3zzp_A           39 ASTTPGRYEVNIVLNPNLDQSQLQNEKEIIQRALENYGA   77 (77)
T ss_dssp             ECSSTTEEEEEEEECTTCCHHHHHHHHHHHHHHHHHHTC
T ss_pred             hccCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHhcCC
Confidence            45568999999999999865 799999999999999987

---

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	246
d2qalf1	100	d.58.14.1 (F:1-100) Ribosomal protein S6 {Escheric	8e-27
d1vmba_	107	d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga ma	3e-22
d1loua_	97	d.58.14.1 (A:) Ribosomal protein S6 {Thermus therm	6e-22
d2j5aa1	106	d.58.14.1 (A:3-108) Ribosomal protein S6 {Aquifex	5e-19

>d2qalf1 d.58.14.1 (F:1-100) Ribosomal protein S6 {Escherichia coli [TaxId: 562]} Length = 100

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Escherichia coli [TaxId: 562]

 Score = 97.5 bits (243), Expect = 8e-27
 Identities = 38/98 (38%), Positives = 60/98 (61%)

Query: 59  RHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYIL 118
           RHYE+V+++H    E V  + E+    +   +G++ RL DWG R+LAY I K  KAHY+L
Sbjct: 2   RHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVL 61

Query: 119 MNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKAITED 156
           MN E   + I++ +T    ++ VIR +V++   A+TE 
Sbjct: 62  MNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEA 99

>d1vmba_ d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga maritima [TaxId: 2336]} Length = 107

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Thermotoga maritima [TaxId: 2336]

 Score = 86.0 bits (213), Expect = 3e-22
 Identities = 22/98 (22%), Positives = 52/98 (53%), Gaps = 2/98 (2%)

Query: 57  RRRHYEVVYLIH-EKYEEDVGSVNEKVQDFLREK-KGRVWRLNDWGLRRLAYKIQKAKKA 114
           + R YE +++I     EE+  ++ E+V+  + E+ KG++ ++   G+R+ AY+I+K  + 
Sbjct: 1   KERIYESMFIIAPNVPEEERENLVERVKKIIEERVKGKIDKVERMGMRKFAYEIKKFNEG 60

Query: 115 HYILMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDKA 152
            Y ++ F  + + + + +       ++IR    +R   
Sbjct: 61  DYTVIYFRCDGQNLQELENFYRVTPEIIRWQTFRRFDL 98

>d1loua_ d.58.14.1 (A:) Ribosomal protein S6 {Thermus thermophilus [TaxId: 274]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Thermus thermophilus [TaxId: 274]

 Score = 84.9 bits (210), Expect = 6e-22
 Identities = 25/94 (26%), Positives = 44/94 (46%), Gaps = 1/94 (1%)

Query: 59  RHYEVVYLIH-EKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYI 117
           R YEV  +++    +  +    E +Q        RV ++ + GLRRLAY I K  + +++
Sbjct: 2   RRYEVNIVLNPNLDQSQLALEKEIIQRAAENYGARVEKVEELGLRRLAYPIAKDPQGYFL 61

Query: 118 LMNFELEAKWINDFKTMLDKDEKVIRHLVIKRDK 151
               E+    +ND    L   + V R +V+K  +
Sbjct: 62  WYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQE 95

>d2j5aa1 d.58.14.1 (A:3-108) Ribosomal protein S6 {Aquifex aeolicus [TaxId: 63363]} Length = 106

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Aquifex aeolicus [TaxId: 63363]

 Score = 77.5 bits (191), Expect = 5e-19
 Identities = 35/99 (35%), Positives = 57/99 (57%), Gaps = 2/99 (2%)

Query: 59  RHYEVVYLIH-EKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYI 117
           R+YE V+ +     EE++    E+V++F+++K G +    DWG+R+LAY IQK   A Y 
Sbjct: 6   RYYETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARYF 65

Query: 118 LMNFELE-AKWINDFKTMLDKDEKVIRHLVIKRDKAITE 155
           L+ F+ E  +  N+    L  DE VIR L I+  ++  +
Sbjct: 66  LVQFKTENPQLPNELDFQLKIDEDVIRWLNIQIKESEVK 104

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	246
d1loua_	97	Ribosomal protein S6 {Thermus thermophilus [TaxId:	99.97
d2qalf1	100	Ribosomal protein S6 {Escherichia coli [TaxId: 562	99.97
d2j5aa1	106	Ribosomal protein S6 {Aquifex aeolicus [TaxId: 633	99.96
d1vmba_	107	Ribosomal protein S6 {Thermotoga maritima [TaxId:	99.95
d1sc6a3	84	Phosphoglycerate dehydrogenase, regulatory (C-term	80.81

>d1loua_ d.58.14.1 (A:) Ribosomal protein S6 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Thermus thermophilus [TaxId: 274]

Probab=99.97  E-value=6.2e-31  Score=201.73  Aligned_cols=95  Identities=26%  Similarity=0.442  Sum_probs=92.2

Q ss_pred             ccceeEEEEecCCChh-hHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhC
Q 025898           58 RRHYEVVYLIHEKYEE-DVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLD  136 (246)
Q Consensus        58 Mr~YEim~ILrp~~eE-ei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lr  136 (246)
                      |++||+++|++|++++ +++++++++.++|+++||+|.++++||.|+|||||+|+++|+|++++|+++|+++++|++.|+
T Consensus         1 M~~YE~~~i~~p~l~~~~~~~~~~~~~~~i~~~gg~i~~~e~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~l~   80 (97)
T d1loua_           1 MRRYEVNIVLNPNLDQSQLALEKEIIQRAAENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELR   80 (97)
T ss_dssp             CEEEEEEEEECTTCCHHHHHHHHHHHHHHHHHTTCEEEEEEEEEEEEEEEEETTEEEEEEEEEEEEECGGGHHHHHHHHH
T ss_pred             CCcceEEEEECCCCCHHHHHHHHHHHHHHHHhCCCEEEEEeeeEEEeccccccccceeEEEEEEEEeCHHHHHHHHHHhc
Confidence            8999999999999865 799999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeeEEEEEeecCC
Q 025898          137 KDEKVIRHLVIKRDKA  152 (246)
Q Consensus       137 lde~VLR~mVVK~de~  152 (246)
                      ++++|||||++|++++
T Consensus        81 l~~~VlR~l~vk~~e~   96 (97)
T d1loua_          81 IRDNVRRVMVVKSQEP   96 (97)
T ss_dssp             TSTTEEEEEEEECSSC
T ss_pred             CCcCeEEEEEEEecCC
Confidence            9999999999999875

>d2qalf1 d.58.14.1 (F:1-100) Ribosomal protein S6 {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Escherichia coli [TaxId: 562]

Probab=99.97  E-value=1.5e-31  Score=206.37  Aligned_cols=100  Identities=38%  Similarity=0.707  Sum_probs=96.6

Q ss_pred             ccceeEEEEecCCChhhHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhCC
Q 025898           58 RRHYEVVYLIHEKYEEDVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDK  137 (246)
Q Consensus        58 Mr~YEim~ILrp~~eEei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lrl  137 (246)
                      ||+||+|+|++|+++++++++++++.++|+++||+|.++++||.|+|||||+|+++|+|++++|.++|++|++|++.|++
T Consensus         1 M~~YE~~~Il~p~~~e~~~~~~~~~~~~i~~~gg~v~~~~~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~l~~   80 (100)
T d2qalf1           1 MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRF   80 (100)
T ss_dssp             CCEECEEEEECGGGTTHHHHHHHHHHHHHHHTTCCCCCCCCCBSCBCSSCTTSCSBCBBCCCCEECCHHHHHHHHHHTTS
T ss_pred             CCcceEEEEECCCcHHHHHHHHHHHHHHHHhCCCEEEEEeeeeeeecccccccCCeeEEEEEEEecCHHHHHHHHHHhcC
Confidence            99999999999998778999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeeEEEEEeecCCCCCCC
Q 025898          138 DEKVIRHLVIKRDKAITEDC  157 (246)
Q Consensus       138 de~VLR~mVVK~de~i~e~~  157 (246)
                      +++|||||++|+++..++++
T Consensus        81 ~~~VlR~l~vk~~~~~~e~S  100 (100)
T d2qalf1          81 NDAVIRSMVMRTKHAVTEAS  100 (100)
T ss_dssp             CTTEEEEEECCCSSCCCSCC
T ss_pred             ccCeeEEEEEEeccCcCCCC
Confidence            99999999999998877654

>d2j5aa1 d.58.14.1 (A:3-108) Ribosomal protein S6 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.96  E-value=5e-30  Score=199.92  Aligned_cols=100  Identities=34%  Similarity=0.590  Sum_probs=94.2

Q ss_pred             hccccceeEEEEecCCChh-hHHHHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeC-cchHHHHH
Q 025898           55 VERRRHYEVVYLIHEKYEE-DVGSVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELE-AKWINDFK  132 (246)
Q Consensus        55 ~~~Mr~YEim~ILrp~~eE-ei~~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~-psaI~ELe  132 (246)
                      .+.||+||+|+|++|.+++ +++++++++.++|+++||+|..+++||.|+|||||+|+++|+|++++|.++ |+++++|+
T Consensus         2 ~k~Mr~YE~~~Il~p~l~~~~~~~~~~~~~~~i~~~gg~i~~~~~wG~r~LAY~Ikk~~~G~Y~~~~f~~~~~~~i~el~   81 (106)
T d2j5aa1           2 YKTLRYYETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARYFLVQFKTENPQLPNELD   81 (106)
T ss_dssp             CCSCEEEEEEEEECTTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEECSSCSSSCSEEEEEEEEEEESCTTHHHHHH
T ss_pred             cCccccccEEEEECCCCCHHHHHHHHHHHHHHHHHCCCeEEEEecceeechhhhhhhccceEEEEEEEEECcHHHHHHHH
Confidence            4689999999999999864 799999999999999999999999999999999999999999999999996 78899999


Q ss_pred             HHhCCCCCeeEEEEEeecCCCC
Q 025898          133 TMLDKDEKVIRHLVIKRDKAIT  154 (246)
Q Consensus       133 r~Lrlde~VLR~mVVK~de~i~  154 (246)
                      +.|+++++|||||++|+++...
T Consensus        82 ~~l~l~~~VlR~l~vkl~~~~~  103 (106)
T d2j5aa1          82 FQLKIDEDVIRWLNIQIKESEV  103 (106)
T ss_dssp             HHHHHCTTEEEEEEEEECGGGC
T ss_pred             HHhCCCcCeeEEEEEEecchhc
Confidence            9999999999999999987644

>d1vmba_ d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Thermotoga maritima [TaxId: 2336]

Probab=99.95  E-value=4e-29  Score=195.30  Aligned_cols=94  Identities=22%  Similarity=0.519  Sum_probs=90.0

Q ss_pred             ccceeEEEEecCCCh-hhHHHHHHHHHHHHhhC-CCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHh
Q 025898           58 RRHYEVVYLIHEKYE-EDVGSVNEKVQDFLREK-KGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTML  135 (246)
Q Consensus        58 Mr~YEim~ILrp~~e-Eei~~liekv~~iI~k~-GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~L  135 (246)
                      ||.||+|+|++|+++ +++++++++++++|+++ ||+|..+++||.|+|||||+|+++|||++++|.++|+++++|++.|
T Consensus         2 ~R~YE~~~Il~p~l~~~~~~~~~~~~~~~i~~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~l   81 (107)
T d1vmba_           2 ERIYESMFIIAPNVPEEERENLVERVKKIIEERVKGKIDKVERMGMRKFAYEIKKFNEGDYTVIYFRCDGQNLQELENFY   81 (107)
T ss_dssp             CEEEEEEEEECTTSCHHHHHHHHHHHHHHHHHTTCCEEEEEEEEEEEEEEEEETTEEEEEEEEEEEEECSSSTHHHHHHH
T ss_pred             CceeEEEEEECCCCCHHHHHHHHHHHHHHHHhcCCCEEEEEEeeeeeccceEcCCCcEEEEEEEEEEECHHHHHHHHHHh
Confidence            899999999999985 47999999999999886 9999999999999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEEEeecC
Q 025898          136 DKDEKVIRHLVIKRDK  151 (246)
Q Consensus       136 rlde~VLR~mVVK~de  151 (246)
                      +++++|||||++|+++
T Consensus        82 ~l~~~VlR~livk~~~   97 (107)
T d1vmba_          82 RVTPEIIRWQTFRRFD   97 (107)
T ss_dssp             HTCTTEEEEEEEECHH
T ss_pred             cCCcCeEEEEEEEccc
Confidence            9999999999999764

>d1sc6a3 d.58.18.1 (A:327-410) Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
domain: Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
species: Escherichia coli [TaxId: 562]

Probab=80.81  E-value=5  Score=27.46  Aligned_cols=60  Identities=10%  Similarity=0.112  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHhhCCCEEEEEEeeeccccccccCCCCeeEEEEEEEEeCcchHHHHHHHhCCCCCeeEEEE
Q 025898           77 SVNEKVQDFLREKKGRVWRLNDWGLRRLAYKIQKAKKAHYILMNFELEAKWINDFKTMLDKDEKVIRHLV  146 (246)
Q Consensus        77 ~liekv~~iI~k~GG~I~~vedwG~RrLAY~IkK~~~G~Yvl~~F~a~psaI~ELer~Lrlde~VLR~mV  146 (246)
                      .++.++.++|.+.|.+|..... |         ...++-|.++.++.+.....++-..++.-+.|+|.-+
T Consensus        23 Gvla~I~~~l~~~~iNI~~~~~-~---------~~~~~~~a~~~i~~D~~~~~~v~~~i~~l~~Vi~vR~   82 (84)
T d1sc6a3          23 GVLTALNKIFAEQGVNIAAQYL-Q---------TSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARL   82 (84)
T ss_dssp             THHHHHHHHHHHTTCEEEEEEE-E---------ECSSEEEEEEEEECCHHHHHHHHHHHHTSTTEEEEEE
T ss_pred             CHHHHHHHHHHHcCCCHHHhcc-c---------cCCCCcEEEEEEECCCCCHHHHHHHHHCCCCEEEEEE
Confidence            4688999999999999987654 2         3356778999999988888888888888899998754