Psyllid ID: psy8858

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-
Protein Sequence
MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLRK
Secondary Structure (PSIPRED)
cccEEcccccccccEEEEEEEEEcccHHHHHHHHHHHccccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEcccccccEEEEEEEEEEccccHHHHHHHHHHcccccccHccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHccccc
Coil and Loop (DISEMBL)
mtrivginipnnqhIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLScyrgirhrkslpcrgqrtrtnartrkgprRAAQSLRK
Flexible Loop (DISEMBL)
mtrivginipnnqhiiIGLTAIYGIGRSRAKKICevtkisttkkikdlndnelEKLREEISKfiiegdlrrefSMNIKRLIdlscyrgirhrkslpcrgqrtrtnartrkgprraaqslrk
Low Complexity Region (SEG)
MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLRK
Disordered region (IsUnstruct)
***IVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLSCYRGIRHR*****************************
Disordered Region (DISOPRED)
MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAA*****
Disordered Region (DISEMBL)
MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQ*********************
Disordered Region (DISPRO)
*TRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRK*LP*************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLRK
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	121	2.2.26 [Sep-21-2011]
A4G9R6	121	30S ribosomal protein S13	yes	N/A	1.0	1.0	0.776	2e-53
A6T3I1	121	30S ribosomal protein S13	yes	N/A	1.0	1.0	0.768	2e-53
Q13TJ3	121	30S ribosomal protein S13	yes	N/A	1.0	1.0	0.735	3e-49
B2T728	121	30S ribosomal protein S13	yes	N/A	1.0	1.0	0.727	3e-49
Q2SU50	121	30S ribosomal protein S13	yes	N/A	1.0	1.0	0.710	1e-48
Q63Q34	121	30S ribosomal protein S13	yes	N/A	1.0	1.0	0.710	1e-48
A3NEF6	121	30S ribosomal protein S13	yes	N/A	1.0	1.0	0.710	1e-48
Q3JMT6	121	30S ribosomal protein S13	yes	N/A	1.0	1.0	0.710	1e-48
A3P090	121	30S ribosomal protein S13	yes	N/A	1.0	1.0	0.710	1e-48
A1V880	121	30S ribosomal protein S13	yes	N/A	1.0	1.0	0.710	1e-48

>sp|A4G9R6|RS13_HERAR 30S ribosomal protein S13 OS=Herminiimonas arsenicoxydans GN=rpsM PE=3 SV=1

 Score =  207 bits (526), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 94/121 (77%), Positives = 111/121 (91%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+N+PN+QH +IGLTAIYGIGR RA+KIC+ T + TTKK+KDL+D+ELEKLR+EI
Sbjct: 1   MARIAGVNVPNHQHTVIGLTAIYGIGRPRAQKICDATGVLTTKKVKDLDDSELEKLRDEI 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
           +KFI+EGDLRRE SMNIKRL+DL CYRG+RHRK LPCRGQRTRTNARTRKGPR+AAQSL+
Sbjct: 61  AKFIVEGDLRREISMNIKRLMDLGCYRGMRHRKGLPCRGQRTRTNARTRKGPRKAAQSLK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.
Herminiimonas arsenicoxydans (taxid: 204773)

>sp|A6T3I1|RS13_JANMA 30S ribosomal protein S13 OS=Janthinobacterium sp. (strain Marseille) GN=rpsM PE=3 SV=1

 Score =  207 bits (526), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 93/121 (76%), Positives = 110/121 (90%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+N+PN+QH +IGLTAIYGIGR R++KIC+   + TTKK+KDL+DNELEKLR+EI
Sbjct: 1   MARIAGVNVPNHQHTVIGLTAIYGIGRPRSQKICDTAGVPTTKKVKDLDDNELEKLRDEI 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
           +KFI+EGDLRRE SMNIKRL+DL CYRG+RHRK LPCRGQRTRTNARTRKGPR+AAQSL+
Sbjct: 61  AKFIVEGDLRRELSMNIKRLMDLGCYRGMRHRKGLPCRGQRTRTNARTRKGPRKAAQSLK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.

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

>sp|Q13TJ3|RS13_BURXL 30S ribosomal protein S13 OS=Burkholderia xenovorans (strain LB400) GN=rpsM PE=3 SV=1

 Score =  193 bits (490), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 89/121 (73%), Positives = 105/121 (86%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QH  IGLTAIYGIGR+R++ IC    ++ +KK+KDLND +LEKLREE+
Sbjct: 1   MARIAGVNIPNHQHTEIGLTAIYGIGRTRSRDICVAAGVAFSKKVKDLNDADLEKLREEV 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
            KFI+EGDLRRE +MNIKRL+DL CYRG+RHRK LP RGQRTRTNARTRKGPRRAAQSL+
Sbjct: 61  GKFIVEGDLRRETTMNIKRLMDLGCYRGVRHRKGLPLRGQRTRTNARTRKGPRRAAQSLK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.

Burkholderia xenovorans (strain LB400) (taxid: 266265)

>sp|B2T728|RS13_BURPP 30S ribosomal protein S13 OS=Burkholderia phytofirmans (strain DSM 17436 / PsJN) GN=rpsM PE=3 SV=1

 Score =  193 bits (490), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 88/121 (72%), Positives = 105/121 (86%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QH  IGLTAIYG+GR+R++ IC    ++ +KK+KDLND +LEKLREE+
Sbjct: 1   MARIAGVNIPNHQHTEIGLTAIYGVGRTRSRDICVAAGVAFSKKVKDLNDADLEKLREEV 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
            KFI+EGDLRRE +MNIKRL+DL CYRG+RHRK LP RGQRTRTNARTRKGPRRAAQSL+
Sbjct: 61  GKFIVEGDLRRETTMNIKRLMDLGCYRGVRHRKGLPLRGQRTRTNARTRKGPRRAAQSLK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.

Burkholderia phytofirmans (strain DSM 17436 / PsJN) (taxid: 398527)

>sp|Q2SU50|RS13_BURTA 30S ribosomal protein S13 OS=Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301) GN=rpsM PE=3 SV=1

 Score =  191 bits (485), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 86/121 (71%), Positives = 105/121 (86%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QH  IGLTAI+GIGR+RA+ IC  + ++ +KK+KDL D +LEKLREE+
Sbjct: 1   MARIAGVNIPNHQHTEIGLTAIFGIGRTRARSICVASGVAFSKKVKDLTDADLEKLREEV 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
            KF++EGDLRRE +MNIKRL+DL CYRG+RHRK LP RGQRTRTNARTRKGPRRAAQ+L+
Sbjct: 61  GKFVVEGDLRREVTMNIKRLMDLGCYRGVRHRKGLPMRGQRTRTNARTRKGPRRAAQALK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.

Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301) (taxid: 271848)

>sp|Q63Q34|RS13_BURPS 30S ribosomal protein S13 OS=Burkholderia pseudomallei (strain K96243) GN=rpsM PE=3 SV=1

 Score =  191 bits (485), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 86/121 (71%), Positives = 105/121 (86%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QH  IGLTAI+GIGR+RA+ IC  + ++ +KK+KDL D +LEKLREE+
Sbjct: 1   MARIAGVNIPNHQHTEIGLTAIFGIGRTRARSICVASGVAFSKKVKDLTDADLEKLREEV 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
            KF++EGDLRRE +MNIKRL+DL CYRG+RHRK LP RGQRTRTNARTRKGPRRAAQ+L+
Sbjct: 61  GKFVVEGDLRREVTMNIKRLMDLGCYRGVRHRKGLPLRGQRTRTNARTRKGPRRAAQALK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.

Burkholderia pseudomallei (strain K96243) (taxid: 272560)

>sp|A3NEF6|RS13_BURP6 30S ribosomal protein S13 OS=Burkholderia pseudomallei (strain 668) GN=rpsM PE=3 SV=1

 Score =  191 bits (485), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 86/121 (71%), Positives = 105/121 (86%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QH  IGLTAI+GIGR+RA+ IC  + ++ +KK+KDL D +LEKLREE+
Sbjct: 1   MARIAGVNIPNHQHTEIGLTAIFGIGRTRARSICVASGVAFSKKVKDLTDADLEKLREEV 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
            KF++EGDLRRE +MNIKRL+DL CYRG+RHRK LP RGQRTRTNARTRKGPRRAAQ+L+
Sbjct: 61  GKFVVEGDLRREVTMNIKRLMDLGCYRGVRHRKGLPLRGQRTRTNARTRKGPRRAAQALK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.

Burkholderia pseudomallei (strain 668) (taxid: 320373)

>sp|Q3JMT6|RS13_BURP1 30S ribosomal protein S13 OS=Burkholderia pseudomallei (strain 1710b) GN=rpsM PE=3 SV=1

 Score =  191 bits (485), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 86/121 (71%), Positives = 105/121 (86%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QH  IGLTAI+GIGR+RA+ IC  + ++ +KK+KDL D +LEKLREE+
Sbjct: 1   MARIAGVNIPNHQHTEIGLTAIFGIGRTRARSICVASGVAFSKKVKDLTDADLEKLREEV 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
            KF++EGDLRRE +MNIKRL+DL CYRG+RHRK LP RGQRTRTNARTRKGPRRAAQ+L+
Sbjct: 61  GKFVVEGDLRREVTMNIKRLMDLGCYRGVRHRKGLPLRGQRTRTNARTRKGPRRAAQALK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.

Burkholderia pseudomallei (strain 1710b) (taxid: 320372)

>sp|A3P090|RS13_BURP0 30S ribosomal protein S13 OS=Burkholderia pseudomallei (strain 1106a) GN=rpsM PE=3 SV=1

 Score =  191 bits (485), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 86/121 (71%), Positives = 105/121 (86%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QH  IGLTAI+GIGR+RA+ IC  + ++ +KK+KDL D +LEKLREE+
Sbjct: 1   MARIAGVNIPNHQHTEIGLTAIFGIGRTRARSICVASGVAFSKKVKDLTDADLEKLREEV 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
            KF++EGDLRRE +MNIKRL+DL CYRG+RHRK LP RGQRTRTNARTRKGPRRAAQ+L+
Sbjct: 61  GKFVVEGDLRREVTMNIKRLMDLGCYRGVRHRKGLPLRGQRTRTNARTRKGPRRAAQALK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.

Burkholderia pseudomallei (strain 1106a) (taxid: 357348)

>sp|A1V880|RS13_BURMS 30S ribosomal protein S13 OS=Burkholderia mallei (strain SAVP1) GN=rpsM PE=3 SV=1

 Score =  191 bits (485), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 86/121 (71%), Positives = 105/121 (86%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QH  IGLTAI+GIGR+RA+ IC  + ++ +KK+KDL D +LEKLREE+
Sbjct: 1   MARIAGVNIPNHQHTEIGLTAIFGIGRTRARSICVASGVAFSKKVKDLTDADLEKLREEV 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
            KF++EGDLRRE +MNIKRL+DL CYRG+RHRK LP RGQRTRTNARTRKGPRRAAQ+L+
Sbjct: 61  GKFVVEGDLRREVTMNIKRLMDLGCYRGVRHRKGLPLRGQRTRTNARTRKGPRRAAQALK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.

Burkholderia mallei (strain SAVP1) (taxid: 320388)

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	121
340785619	121	30S ribosomal protein S13 [Collimonas fu	1.0	1.0	0.785	7e-52
134096299	121	30S ribosomal protein S13 [Herminiimonas	1.0	1.0	0.776	8e-52
152980690	121	30S ribosomal protein S13 [Janthinobacte	1.0	1.0	0.768	9e-52
399017011	121	30S ribosomal protein S13 [Herbaspirillu	1.0	1.0	0.760	5e-51
427399570	121	30S ribosomal protein S13 [Massilia timo	1.0	1.0	0.760	8e-51
445494445	121	30S ribosomal protein S13 [Janthinobacte	1.0	1.0	0.760	3e-50
300309479	121	30S ribosomal protein S13 [Herbaspirillu	1.0	1.0	0.752	6e-50
237747387	121	30S ribosomal subunit protein S13 [Oxalo	1.0	1.0	0.760	1e-49
237749537	121	30S ribosomal subunit protein S13 [Oxalo	1.0	1.0	0.743	6e-49
83748172	121	SSU ribosomal protein S13P [Ralstonia so	1.0	1.0	0.727	4e-48

>gi|340785619|ref|YP_004751084.1| 30S ribosomal protein S13 [Collimonas fungivorans Ter331] gi|340550886|gb|AEK60261.1| SSU ribosomal protein S13p (S18e) [Collimonas fungivorans Ter331]

 Score =  207 bits (527), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 95/121 (78%), Positives = 111/121 (91%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QH +IGLTAIYG+GR RA++IC+ T I TTKKIKDL+DNELEKLR+EI
Sbjct: 1   MARIAGVNIPNHQHTVIGLTAIYGVGRPRAQEICDSTGILTTKKIKDLDDNELEKLRDEI 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
           +KF++EGDLRRE SMNIKRL+DL CYRG+RHRK LPCRGQRTRTNARTRKGPR+AAQSL+
Sbjct: 61  AKFVVEGDLRRELSMNIKRLMDLGCYRGMRHRKGLPCRGQRTRTNARTRKGPRKAAQSLK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Source: Collimonas fungivorans Ter331

Species: Collimonas fungivorans

Genus: Collimonas

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|134096299|ref|YP_001101374.1| 30S ribosomal protein S13 [Herminiimonas arsenicoxydans] gi|158706238|sp|A4G9R6.1|RS13_HERAR RecName: Full=30S ribosomal protein S13 gi|133740202|emb|CAL63253.1| 30S ribosomal subunit protein S13 [Herminiimonas arsenicoxydans]

 Score =  207 bits (526), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 94/121 (77%), Positives = 111/121 (91%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+N+PN+QH +IGLTAIYGIGR RA+KIC+ T + TTKK+KDL+D+ELEKLR+EI
Sbjct: 1   MARIAGVNVPNHQHTVIGLTAIYGIGRPRAQKICDATGVLTTKKVKDLDDSELEKLRDEI 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
           +KFI+EGDLRRE SMNIKRL+DL CYRG+RHRK LPCRGQRTRTNARTRKGPR+AAQSL+
Sbjct: 61  AKFIVEGDLRREISMNIKRLMDLGCYRGMRHRKGLPCRGQRTRTNARTRKGPRKAAQSLK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Source: Herminiimonas arsenicoxydans

Species: Herminiimonas arsenicoxydans

Genus: Herminiimonas

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|152980690|ref|YP_001355078.1| 30S ribosomal protein S13 [Janthinobacterium sp. Marseille] gi|158706240|sp|A6T3I1.1|RS13_JANMA RecName: Full=30S ribosomal protein S13 gi|151280767|gb|ABR89177.1| small subunit ribosomal protein S13 [Janthinobacterium sp. Marseille]

 Score =  207 bits (526), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 93/121 (76%), Positives = 110/121 (90%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+N+PN+QH +IGLTAIYGIGR R++KIC+   + TTKK+KDL+DNELEKLR+EI
Sbjct: 1   MARIAGVNVPNHQHTVIGLTAIYGIGRPRSQKICDTAGVPTTKKVKDLDDNELEKLRDEI 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
           +KFI+EGDLRRE SMNIKRL+DL CYRG+RHRK LPCRGQRTRTNARTRKGPR+AAQSL+
Sbjct: 61  AKFIVEGDLRRELSMNIKRLMDLGCYRGMRHRKGLPCRGQRTRTNARTRKGPRKAAQSLK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Source: Janthinobacterium sp. Marseille

Species: Janthinobacterium sp. Marseille

Genus: Janthinobacterium

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|399017011|ref|ZP_10719212.1| 30S ribosomal protein S13 [Herbaspirillum sp. CF444] gi|398104341|gb|EJL94483.1| 30S ribosomal protein S13 [Herbaspirillum sp. CF444]

 Score =  204 bits (519), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 92/121 (76%), Positives = 109/121 (90%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QH +IGLTAIYG+GR RA++IC  T + T KK+KDL+DNELEKLR+EI
Sbjct: 1   MARIAGVNIPNHQHTVIGLTAIYGVGRPRAEEICVATGVPTNKKVKDLDDNELEKLRDEI 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
           +KF++EGDLRRE SMNIKRL+DL CYRG+RHRK LPCRGQRTRTNARTRKGPR+AAQSL+
Sbjct: 61  AKFVVEGDLRRELSMNIKRLMDLGCYRGMRHRKGLPCRGQRTRTNARTRKGPRKAAQSLK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Source: Herbaspirillum sp. CF444

Species: Herbaspirillum sp. CF444

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|427399570|ref|ZP_18890808.1| 30S ribosomal protein S13 [Massilia timonae CCUG 45783] gi|425721332|gb|EKU84245.1| 30S ribosomal protein S13 [Massilia timonae CCUG 45783]

 Score =  203 bits (517), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 92/121 (76%), Positives = 109/121 (90%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QH +IGLTAIYGIGR R++KIC+ T I+T KK+KDL+DNELEKLR+E+
Sbjct: 1   MARIAGVNIPNHQHTVIGLTAIYGIGRPRSQKICDATGIATNKKVKDLDDNELEKLRDEV 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
            KF++EGDLRRE SMNIKRL+DL CYRG+RHRK LP RGQRTRTNARTRKGPR+AAQSL+
Sbjct: 61  GKFVVEGDLRRELSMNIKRLMDLGCYRGMRHRKGLPVRGQRTRTNARTRKGPRKAAQSLK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Source: Massilia timonae CCUG 45783

Species: Massilia timonae

Genus: Massilia

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|445494445|ref|ZP_21461489.1| 30S ribosomal protein S13 [Janthinobacterium sp. HH01] gi|444790606|gb|ELX12153.1| 30S ribosomal protein S13 [Janthinobacterium sp. HH01]

 Score =  201 bits (512), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 92/121 (76%), Positives = 108/121 (89%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QH +IGLTAIYG+GR RAK IC  T I+T KK+KDL+D+ELEKLR+E+
Sbjct: 1   MARIAGVNIPNHQHTVIGLTAIYGVGRPRAKFICAATGIATNKKVKDLDDSELEKLRDEV 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
           +KFI+EGDLRRE SMNIKRL+DL CYRG+RHRK LP RGQRTRTNARTRKGPR+AAQSL+
Sbjct: 61  AKFIVEGDLRRELSMNIKRLMDLGCYRGMRHRKGLPVRGQRTRTNARTRKGPRKAAQSLK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Source: Janthinobacterium sp. HH01

Species: Janthinobacterium sp. HH01

Genus: Janthinobacterium

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|300309479|ref|YP_003773571.1| 30S ribosomal protein S13 [Herbaspirillum seropedicae SmR1] gi|409408724|ref|ZP_11257159.1| 30S ribosomal protein S13 [Herbaspirillum sp. GW103] gi|415943234|ref|ZP_11556034.1| 30S ribosomal protein S13 [Herbaspirillum frisingense GSF30] gi|300072264|gb|ADJ61663.1| 30S ribosomal subunit S13 protein [Herbaspirillum seropedicae SmR1] gi|386432046|gb|EIJ44874.1| 30S ribosomal protein S13 [Herbaspirillum sp. GW103] gi|407758750|gb|EKF68534.1| 30S ribosomal protein S13 [Herbaspirillum frisingense GSF30]

 Score =  201 bits (510), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 91/121 (75%), Positives = 107/121 (88%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QH +IGLTAIYGIGR RA+ IC  T + T KK+KDL+DNELEKLR+EI
Sbjct: 1   MARIAGVNIPNHQHTVIGLTAIYGIGRPRAQDICAATGVPTNKKVKDLDDNELEKLRDEI 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
           +KF++EGDLRRE SMNIKRL+DL CYRG+RHR+ LP RGQRTRTNARTRKGPR+AAQSL+
Sbjct: 61  AKFVVEGDLRRELSMNIKRLMDLGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKAAQSLK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Source: Herbaspirillum seropedicae SmR1

Species: Herbaspirillum seropedicae

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|237747387|ref|ZP_04577867.1| 30S ribosomal subunit protein S13 [Oxalobacter formigenes HOxBLS] gi|229378738|gb|EEO28829.1| 30S ribosomal subunit protein S13 [Oxalobacter formigenes HOxBLS]

 Score =  200 bits (508), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 92/121 (76%), Positives = 108/121 (89%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QHI+IGLTAIYGIGR RA+ IC  T ++ TKK+KDL+D+ELEKLREEI
Sbjct: 1   MARIAGVNIPNHQHIVIGLTAIYGIGRPRAEDICAATGVAPTKKVKDLDDSELEKLREEI 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
            KF+IEGDLRRE SM+IKRL+DL CYRG+RHR+ LP RGQRTRTNARTRKGPR+AAQSL+
Sbjct: 61  DKFVIEGDLRREVSMSIKRLMDLGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKAAQSLK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Source: Oxalobacter formigenes HOxBLS

Species: Oxalobacter formigenes

Genus: Oxalobacter

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|237749537|ref|ZP_04580017.1| 30S ribosomal subunit protein S13 [Oxalobacter formigenes OXCC13] gi|229380899|gb|EEO30990.1| 30S ribosomal subunit protein S13 [Oxalobacter formigenes OXCC13]

 Score =  197 bits (502), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 90/121 (74%), Positives = 108/121 (89%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QHI+IGLTAI+GIGR RA++IC  T +  TKK+KDL+DN+LEKLR+EI
Sbjct: 1   MARIAGVNIPNHQHIVIGLTAIFGIGRPRAEEICAATGVDPTKKVKDLDDNDLEKLRDEI 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
            KF+IEGDLRRE SM+IKRL+DL CYRG+RHR+ LP RGQRTRTNARTRKGPR+AAQSL+
Sbjct: 61  GKFVIEGDLRREVSMSIKRLMDLGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKAAQSLK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Source: Oxalobacter formigenes OXCC13

Species: Oxalobacter formigenes

Genus: Oxalobacter

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|83748172|ref|ZP_00945199.1| SSU ribosomal protein S13P [Ralstonia solanacearum UW551] gi|207744553|ref|YP_002260945.1| 30s ribosomal protein s13 [Ralstonia solanacearum IPO1609] gi|300702803|ref|YP_003744404.1| 30S ribosomal protein S13 [Ralstonia solanacearum CFBP2957] gi|386332170|ref|YP_006028339.1| 30S ribosomal protein S13 [Ralstonia solanacearum Po82] gi|421890471|ref|ZP_16321330.1| 30S ribosomal subunit protein S13 [Ralstonia solanacearum K60-1] gi|421895877|ref|ZP_16326276.1| 30s ribosomal protein s13 [Ralstonia solanacearum MolK2] gi|83725140|gb|EAP72291.1| SSU ribosomal protein S13P [Ralstonia solanacearum UW551] gi|206587042|emb|CAQ17626.1| 30s ribosomal protein s13 [Ralstonia solanacearum MolK2] gi|206595959|emb|CAQ62886.1| 30s ribosomal protein s13 [Ralstonia solanacearum IPO1609] gi|299070465|emb|CBJ41760.1| 30S ribosomal subunit protein S13 [Ralstonia solanacearum CFBP2957] gi|334194618|gb|AEG67803.1| 30S ribosomal protein S13 [Ralstonia solanacearum Po82] gi|378964182|emb|CCF98078.1| 30S ribosomal subunit protein S13 [Ralstonia solanacearum K60-1]

 Score =  194 bits (494), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 88/121 (72%), Positives = 106/121 (87%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+NIPN+QH +IGLTA+YGIGRSRA+KICEVT + T KK+KDL D +LEKLR+E+
Sbjct: 1   MARIAGVNIPNHQHTVIGLTAVYGIGRSRARKICEVTGVPTNKKVKDLTDADLEKLRDEV 60

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
           +KF +EGDLRRE +MNIKRL+DL CYRG+RHRK LP RGQRTRTNARTRKGPR+A  +L+
Sbjct: 61  NKFTVEGDLRRETTMNIKRLMDLGCYRGVRHRKGLPMRGQRTRTNARTRKGPRKAGVALK 120

Query: 121 K 121
           K
Sbjct: 121 K 121

Source: Ralstonia solanacearum UW551

Species: Ralstonia solanacearum

Genus: Ralstonia

Family: Burkholderiaceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	121
TIGR_CMR|SO_0253	118	SO_0253 "ribosomal protein S13	0.942	0.966	0.657	1.4e-39
TIGR_CMR|CPS_0623	118	CPS_0623 "ribosomal protein S1	0.942	0.966	0.649	1.9e-37
UNIPROTKB|A6UZL0	118	rpsM "30S ribosomal protein S1	0.942	0.966	0.614	3.9e-37
UNIPROTKB|P0A7S9	118	rpsM [Escherichia coli K-12 (t	0.942	0.966	0.587	1.2e-35
UNIPROTKB|Q9KP05	118	rpsM "30S ribosomal protein S1	0.942	0.966	0.605	2.4e-35
TIGR_CMR|VC_2574	118	VC_2574 "ribosomal protein S13	0.942	0.966	0.605	2.4e-35
TIGR_CMR|CHY_2284	123	CHY_2284 "ribosomal protein S1	1.0	0.983	0.573	6.7e-33
TIGR_CMR|CBU_0260	119	CBU_0260 "ribosomal protein S1	0.958	0.974	0.603	8.5e-33
TIGR_CMR|SPO_0509	122	SPO_0509 "ribosomal protein S1	1.0	0.991	0.549	4.7e-32
UNIPROTKB|O66486	126	rpsM "30S ribosomal protein S1	1.0	0.960	0.540	2e-31

TIGR_CMR|SO_0253 SO_0253 "ribosomal protein S13" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 422 (153.6 bits), Expect = 1.4e-39, P = 1.4e-39
 Identities = 75/114 (65%), Positives = 98/114 (85%)

Query:     1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
             M RI GINIP+ +H +I LTAI+GIGR+RA+ IC  T I+ T KIK+L++ +++ LREE+
Sbjct:     1 MARIAGINIPDQKHTVIALTAIFGIGRTRARAICAATSIAETAKIKELSEAQIDTLREEV 60

Query:    61 SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
             +K+++EGDLRRE SMNIKRL+DL CYRG+RHR+SLP RGQRT+TNARTRKGPR+
Sbjct:    61 AKYLVEGDLRREISMNIKRLMDLGCYRGLRHRRSLPLRGQRTKTNARTRKGPRK 114

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|CPS_0623 CPS_0623 "ribosomal protein S13" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 402 (146.6 bits), Expect = 1.9e-37, P = 1.9e-37
 Identities = 74/114 (64%), Positives = 93/114 (81%)

Query:     1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
             M RI GINIP+ +H +I +TAIYGIG +RAK IC  T I+ + KI +L++ +++ LR E+
Sbjct:     1 MARIAGINIPDRKHAVIAITAIYGIGATRAKAICAATGIAESTKISELDEAKIDLLRAEV 60

Query:    61 SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
              KF +EGDLRRE SMNIKRL+DL CYRGIRHR+SLP RGQRT+TNARTRKGPR+
Sbjct:    61 DKFTVEGDLRREVSMNIKRLMDLGCYRGIRHRRSLPLRGQRTKTNARTRKGPRK 114

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

GO:0006412 "translation" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

UNIPROTKB|A6UZL0 rpsM "30S ribosomal protein S13" [Pseudomonas aeruginosa PA7 (taxid:381754)]

 Score = 399 (145.5 bits), Expect = 3.9e-37, P = 3.9e-37
 Identities = 70/114 (61%), Positives = 92/114 (80%)

Query:     1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
             M RI G+NIP+N+H +I LT IYG+GR+ A+ IC  T ++   KIKDL+D ++++LR E+
Sbjct:     1 MARIAGVNIPDNKHTVISLTYIYGVGRTTAQNICAATGVNPAAKIKDLSDEQIDQLRNEV 60

Query:    61 SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
             +K   EGDLRRE +MNIKRL+DL CYRG+RHR+ LP RGQRT+TNARTRKGPR+
Sbjct:    61 AKHTTEGDLRREINMNIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK 114

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

GO:0005829 "cytosol" evidence=IBA

GO:0006412 "translation" evidence=IBA

GO:0015935 "small ribosomal subunit" evidence=IBA

GO:0042254 "ribosome biogenesis" evidence=IBA

UNIPROTKB|P0A7S9 rpsM [Escherichia coli K-12 (taxid:83333)]

 Score = 385 (140.6 bits), Expect = 1.2e-35, P = 1.2e-35
 Identities = 67/114 (58%), Positives = 94/114 (82%)

Query:     1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
             M RI GINIP+++H +I LT+IYG+G++R+K I     I+   KI +L++ +++ LR+E+
Sbjct:     1 MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEV 60

Query:    61 SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
             +KF++EGDLRRE SM+IKRL+DL CYRG+RHR+ LP RGQRT+TNARTRKGPR+
Sbjct:    61 AKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK 114

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

GO:0006412 "translation" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0042254 "ribosome biogenesis" evidence=IBA

GO:0019843 "rRNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000049 "tRNA binding" evidence=IEA

UNIPROTKB|Q9KP05 rpsM "30S ribosomal protein S13" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 382 (139.5 bits), Expect = 2.4e-35, P = 2.4e-35
 Identities = 69/114 (60%), Positives = 94/114 (82%)

Query:     1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
             M RI GINIP+++H +I LTAIYGIG++R+K I     I+ + KI +L + ++++LR+ +
Sbjct:     1 MARIAGINIPDHKHAVIALTAIYGIGKTRSKAILADLGIAESVKISELTEEQIDQLRDGV 60

Query:    61 SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
             +K+ +EGDLRRE SMNIKRL+DL CYRG+RHR+SLP RGQRT+TNARTRKGPR+
Sbjct:    61 AKYTVEGDLRREVSMNIKRLMDLGCYRGLRHRRSLPLRGQRTKTNARTRKGPRK 114

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|VC_2574 VC_2574 "ribosomal protein S13" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 382 (139.5 bits), Expect = 2.4e-35, P = 2.4e-35
 Identities = 69/114 (60%), Positives = 94/114 (82%)

Query:     1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
             M RI GINIP+++H +I LTAIYGIG++R+K I     I+ + KI +L + ++++LR+ +
Sbjct:     1 MARIAGINIPDHKHAVIALTAIYGIGKTRSKAILADLGIAESVKISELTEEQIDQLRDGV 60

Query:    61 SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
             +K+ +EGDLRRE SMNIKRL+DL CYRG+RHR+SLP RGQRT+TNARTRKGPR+
Sbjct:    61 AKYTVEGDLRREVSMNIKRLMDLGCYRGLRHRRSLPLRGQRTKTNARTRKGPRK 114

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|CHY_2284 CHY_2284 "ribosomal protein S13" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 359 (131.4 bits), Expect = 6.7e-33, P = 6.7e-33
 Identities = 70/122 (57%), Positives = 90/122 (73%)

Query:     1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
             M RI G+++P ++ + I LT IYGIGR  A  I + T I+   ++KDL + E+ KLR+EI
Sbjct:     1 MARIAGVDLPRDKRVEIALTYIYGIGRPTANVILKKTGINPDTRVKDLTEEEVAKLRDEI 60

Query:    61 SK-FIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSL 119
              K + +EG+LRRE ++NIKRLI++ CYRGIRHRK LP RGQRTRTNARTRKGPRR     
Sbjct:    61 EKNYKVEGELRREVALNIKRLIEIGCYRGIRHRKGLPVRGQRTRTNARTRKGPRRTVGVK 120

Query:   120 RK 121
             RK
Sbjct:   121 RK 122

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|CBU_0260 CBU_0260 "ribosomal protein S13/S18" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 358 (131.1 bits), Expect = 8.5e-33, P = 8.5e-33
 Identities = 70/116 (60%), Positives = 86/116 (74%)

Query:     3 RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK 62
             RI G+NIP  +H  I L AIYGIG SRA +IC+  KI    K+KDL++ EL+ LR E+ K
Sbjct:     4 RIAGVNIPVQKHARIALQAIYGIGNSRALEICKEAKIDPATKVKDLSEAELDALRTEVGK 63

Query:    63 FIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQS 118
             F +EGDLRRE SM+IKR +DL  Y GIRHR+ LP RGQRTR+NARTRKG R+  +S
Sbjct:    64 FSVEGDLRRERSMDIKRKMDLGAYEGIRHRRGLPLRGQRTRSNARTRKGKRKPIRS 119

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

TIGR_CMR|SPO_0509 SPO_0509 "ribosomal protein S13" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 67/122 (54%), Positives = 87/122 (71%)

Query:     1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
             M RI G+NIP  + + I LT I GIG + AK ICE   I  T+++ +L+D E+  +RE I
Sbjct:     1 MARIAGVNIPTAKRVPIALTYITGIGNTSAKAICEAVGIDATRRVNELSDAEILAIREHI 60

Query:    61 -SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSL 119
              + + +EGDLRRE  MNIKRL+DL CYRG+RHR++LP RGQRT TNARTRKGP +A    
Sbjct:    61 DANYSVEGDLRREVQMNIKRLMDLGCYRGLRHRRNLPVRGQRTHTNARTRKGPAKAIAGK 120

Query:   120 RK 121
             +K
Sbjct:   121 KK 122

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

GO:0006412 "translation" evidence=ISS

GO:0042255 "ribosome assembly" evidence=ISS

UNIPROTKB|O66486 rpsM "30S ribosomal protein S13" [Aquifex aeolicus VF5 (taxid:224324)]

 Score = 345 (126.5 bits), Expect = 2.0e-31, P = 2.0e-31
 Identities = 66/122 (54%), Positives = 89/122 (72%)

Query:     1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
             M RI G+++PNN+ + + LT IYGIG SRA++ICE T I  TK++ +L  +EL  LR+ I
Sbjct:     1 MARIAGVDLPNNKRLEVALTYIYGIGWSRAREICEKTGIPCTKRVGELTPDELNTLRKFI 60

Query:    61 SK-FIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSL 119
              + + +EGDLRRE  +NIK+L D+ CYRGIRH + LP RGQ+TRTNARTRKG R+     
Sbjct:    61 DENYKVEGDLRREVQLNIKKLKDMGCYRGIRHARGLPVRGQQTRTNARTRKGKRKTVGGT 120

Query:   120 RK 121
             +K
Sbjct:   121 KK 122

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

GO:0005829 "cytosol" evidence=IBA

GO:0006412 "translation" evidence=IBA

GO:0015935 "small ribosomal subunit" evidence=IBA

GO:0042254 "ribosome biogenesis" evidence=IBA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
B2UEJ6	RS13_RALPJ	No assigned EC number	0.7107	1.0	1.0	yes	N/A
B2T728	RS13_BURPP	No assigned EC number	0.7272	1.0	1.0	yes	N/A
B1JU45	RS13_BURCC	No assigned EC number	0.6942	1.0	1.0	yes	N/A
A1KB04	RS13_AZOSB	No assigned EC number	0.6695	0.9504	0.9583	yes	N/A
B2JI42	RS13_BURP8	No assigned EC number	0.7272	1.0	1.0	yes	N/A
B1XSS4	RS13_POLNS	No assigned EC number	0.6528	1.0	1.0	yes	N/A
Q7VTA8	RS13_BORPE	No assigned EC number	0.6859	1.0	1.0	yes	N/A
B4E5E3	RS13_BURCJ	No assigned EC number	0.7024	1.0	1.0	yes	N/A
B3R7E6	RS13_CUPTR	No assigned EC number	0.7024	1.0	1.0	yes	N/A
Q39KE4	RS13_BURS3	No assigned EC number	0.6942	1.0	1.0	yes	N/A
A1W330	RS13_ACISJ	No assigned EC number	0.6776	1.0	1.0	yes	N/A
A3NEF6	RS13_BURP6	No assigned EC number	0.7107	1.0	1.0	yes	N/A
A0K3P8	RS13_BURCH	No assigned EC number	0.6942	1.0	1.0	yes	N/A
Q62GM8	RS13_BURMA	No assigned EC number	0.7107	1.0	1.0	yes	N/A
Q46WG6	RS13_CUPPJ	No assigned EC number	0.6942	1.0	1.0	yes	N/A
Q0BJ23	RS13_BURCM	No assigned EC number	0.7107	1.0	1.0	yes	N/A
Q7WRA0	RS13_BORBR	No assigned EC number	0.6859	1.0	1.0	yes	N/A
B1YRQ2	RS13_BURA4	No assigned EC number	0.7107	1.0	1.0	yes	N/A
Q1BRX1	RS13_BURCA	No assigned EC number	0.6942	1.0	1.0	yes	N/A
A3MRX7	RS13_BURM7	No assigned EC number	0.7107	1.0	1.0	yes	N/A
A1TJT9	RS13_ACIAC	No assigned EC number	0.6859	1.0	1.0	yes	N/A
Q2SU50	RS13_BURTA	No assigned EC number	0.7107	1.0	1.0	yes	N/A
B9MBV9	RS13_ACIET	No assigned EC number	0.6776	1.0	1.0	yes	N/A
Q5P310	RS13_AROAE	No assigned EC number	0.6695	0.9504	0.9583	yes	N/A
C5CQ78	RS13_VARPS	No assigned EC number	0.6942	1.0	1.0	yes	N/A
A4SUY3	RS13_POLSQ	No assigned EC number	0.6694	1.0	1.0	yes	N/A
Q47J80	RS13_DECAR	No assigned EC number	0.6695	0.9504	0.9583	yes	N/A
Q2L248	RS13_BORA1	No assigned EC number	0.6694	1.0	1.0	yes	N/A
A1V880	RS13_BURMS	No assigned EC number	0.7107	1.0	1.0	yes	N/A
Q3SLM7	RS13_THIDA	No assigned EC number	0.7043	0.9504	0.9745	yes	N/A
A6T3I1	RS13_JANMA	No assigned EC number	0.7685	1.0	1.0	yes	N/A
A3P090	RS13_BURP0	No assigned EC number	0.7107	1.0	1.0	yes	N/A
Q12G80	RS13_POLSJ	No assigned EC number	0.6942	1.0	1.0	yes	N/A
A1WK95	RS13_VEREI	No assigned EC number	0.6694	1.0	1.0	yes	N/A
A4JAR3	RS13_BURVG	No assigned EC number	0.7107	1.0	1.0	yes	N/A
Q0K642	RS13_CUPNH	No assigned EC number	0.6942	1.0	1.0	yes	N/A
A9IHS0	RS13_BORPD	No assigned EC number	0.6694	1.0	1.0	yes	N/A
A4G9R6	RS13_HERAR	No assigned EC number	0.7768	1.0	1.0	yes	N/A
Q63Q34	RS13_BURPS	No assigned EC number	0.7107	1.0	1.0	yes	N/A
Q2YAX5	RS13_NITMU	No assigned EC number	0.6610	0.9752	0.944	yes	N/A
Q1LI60	RS13_RALME	No assigned EC number	0.7024	1.0	1.0	yes	N/A
A2S7J9	RS13_BURM9	No assigned EC number	0.7107	1.0	1.0	yes	N/A
Q7W2D2	RS13_BORPA	No assigned EC number	0.6859	1.0	1.0	yes	N/A
Q13TJ3	RS13_BURXL	No assigned EC number	0.7355	1.0	1.0	yes	N/A
A9ADL6	RS13_BURM1	No assigned EC number	0.7024	1.0	1.0	yes	N/A
A1VJ37	RS13_POLNA	No assigned EC number	0.6942	1.0	1.0	yes	N/A
Q3JMT6	RS13_BURP1	No assigned EC number	0.7107	1.0	1.0	yes	N/A
C1DAU0	RS13_LARHH	No assigned EC number	0.7105	0.9421	0.95	yes	N/A
Q21QP6	RS13_RHOFD	No assigned EC number	0.6859	1.0	1.0	yes	N/A
Q8XV35	RS13_RALSO	No assigned EC number	0.7107	1.0	1.0	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	121
PRK05179	122	PRK05179, rpsM, 30S ribosomal protein S13; Validat	2e-66
TIGR03631	113	TIGR03631, bact_S13, 30S ribosomal protein S13	2e-60
COG0099	121	COG0099, RpsM, Ribosomal protein S13 [Translation,	4e-52
CHL00137	122	CHL00137, rps13, ribosomal protein S13; Validated	2e-41
pfam00416	106	pfam00416, Ribosomal_S13, Ribosomal protein S13/S1	9e-37
PRK04053	149	PRK04053, rps13p, 30S ribosomal protein S13P; Revi	2e-20
TIGR03629	144	TIGR03629, arch_S13P, archaeal ribosomal protein S	1e-19
PTZ00134	154	PTZ00134, PTZ00134, 40S ribosomal protein S18; Pro	3e-09

>gnl|CDD|235358 PRK05179, rpsM, 30S ribosomal protein S13; Validated

 Score =  196 bits (500), Expect = 2e-66
 Identities = 73/122 (59%), Positives = 93/122 (76%), Gaps = 1/122 (0%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G++IP N+ ++I LT IYGIGR+RAK+I     I    ++KDL D EL+K+REEI
Sbjct: 1   MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEI 60

Query: 61  SK-FIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSL 119
            K + +EGDLRRE SMNIKRL+D+ CYRG+RHR+ LP RGQRT+TNARTRKGPR+     
Sbjct: 61  DKNYKVEGDLRREVSMNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKTIAGK 120

Query: 120 RK 121
           +K
Sbjct: 121 KK 122

Length = 122

>gnl|CDD|213840 TIGR03631, bact_S13, 30S ribosomal protein S13

 Score =  180 bits (459), Expect = 2e-60
 Identities = 71/113 (62%), Positives = 91/113 (80%), Gaps = 1/113 (0%)

Query: 3   RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI-S 61
           RI G++IPNN+ + I LT IYGIGR+RA+KI E   I   K++KDL + EL  +REEI +
Sbjct: 1   RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEA 60

Query: 62  KFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
           K+ +EGDLRRE S+NIKRL+D+ CYRG+RHR+ LP RGQRT+TNARTRKGPR+
Sbjct: 61  KYKVEGDLRREVSLNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK 113

This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 113

>gnl|CDD|223177 COG0099, RpsM, Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]

 Score =  159 bits (405), Expect = 4e-52
 Identities = 67/117 (57%), Positives = 91/117 (77%), Gaps = 1/117 (0%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G++IP N+ ++I LT IYGIGR RAK+IC+   I   K++ +L + E+E+LR+ I
Sbjct: 1   MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAI 60

Query: 61  -SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAA 116
            +K+++EGDLRRE  M+IKRL+ + CYRGIRHR+ LP RGQRT+TNARTRKGPR+  
Sbjct: 61  QNKYLVEGDLRREVRMDIKRLMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKGV 117

Length = 121

>gnl|CDD|177059 CHL00137, rps13, ribosomal protein S13; Validated

 Score =  132 bits (335), Expect = 2e-41
 Identities = 61/115 (53%), Positives = 80/115 (69%), Gaps = 1/115 (0%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+++P N+ I   LT IYGIG + AK+I E   I    + KDL D ++  LRE I
Sbjct: 1   MVRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREII 60

Query: 61  -SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
              + +EGDLRR  S+NIKRL++++CYRG RHR  LP RGQRTRTNARTR+G ++
Sbjct: 61  EENYQVEGDLRRFESLNIKRLMEINCYRGRRHRLGLPVRGQRTRTNARTRRGAKK 115

Length = 122

>gnl|CDD|144128 pfam00416, Ribosomal_S13, Ribosomal protein S13/S18

 Score =  120 bits (303), Expect = 9e-37
 Identities = 47/106 (44%), Positives = 73/106 (68%)

Query: 3   RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK 62
           RI+  N+  N+ I I LT I GIGR +A +I +   +   K++ +L + E++++R+ IS 
Sbjct: 1   RILNTNLDGNKKIEIALTYIKGIGRRKANQILKKAGVDKDKRVGELTEEEIDRIRDIISN 60

Query: 63  FIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNART 108
           +++E DLRR+   +I+RL  + CYRG+RH + LP RGQRT+TNART
Sbjct: 61  YVVENDLRRKIRNDIERLKKIRCYRGLRHIRGLPVRGQRTKTNART 106

This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes. Length = 106

>gnl|CDD|235215 PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed

 Score = 79.9 bits (198), Expect = 2e-20
 Identities = 41/132 (31%), Positives = 57/132 (43%), Gaps = 29/132 (21%)

Query: 3   RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS- 61
           RI G ++   + +   LT I GIGR  A+ I     +    K+  L+D E+EK+ E +  
Sbjct: 11  RIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALED 70

Query: 62  ----------------------KFIIEGDL---RREFSMNIKRLIDLSCYRGIRHRKSLP 96
                                   +I  DL    RE   +I R+  +  YRGIRH   L 
Sbjct: 71  PAEEGIPSWMLNRRKDYETGEDLHLIGSDLILTVRE---DINRMKKIRSYRGIRHELGLK 127

Query: 97  CRGQRTRTNART 108
            RGQRTR+  RT
Sbjct: 128 VRGQRTRSTGRT 139

Length = 149

>gnl|CDD|213839 TIGR03629, arch_S13P, archaeal ribosomal protein S13P

 Score = 77.7 bits (192), Expect = 1e-19
 Identities = 38/130 (29%), Positives = 56/130 (43%), Gaps = 22/130 (16%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           + RI   ++  N+ +   LT I GIGR  A+ I     +    K+  L+D E+EKL E +
Sbjct: 5   IVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAV 64

Query: 61  SKF----------------------IIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCR 98
             +                      +I  DL      +I R+  +  YRGIRH   L  R
Sbjct: 65  ENYEYGIPSWLLNRRKDYETGEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVR 124

Query: 99  GQRTRTNART 108
           GQRT++  R 
Sbjct: 125 GQRTKSTGRR 134

This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 144

>gnl|CDD|185469 PTZ00134, PTZ00134, 40S ribosomal protein S18; Provisional

 Score = 51.6 bits (124), Expect = 3e-09
 Identities = 36/130 (27%), Positives = 57/130 (43%), Gaps = 23/130 (17%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           + RI+  N+   + +   LTAI GIGR  A  +C+   I  TK+  +L   E+EK+ E I
Sbjct: 14  ILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEII 73

Query: 61  S-----------------------KFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPC 97
           +                         +    L  +   +++RL  +  +RG+RH   L  
Sbjct: 74  ANPLQFKIPDWFLNRQRDPKDGKNSHLTSNMLDTKLREDLERLKKIRLHRGLRHHWGLRV 133

Query: 98  RGQRTRTNAR 107
           RGQ T+T  R
Sbjct: 134 RGQHTKTTGR 143

Length = 154

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	121
CHL00137	122	rps13 ribosomal protein S13; Validated	100.0
COG0099	121	RpsM Ribosomal protein S13 [Translation, ribosomal	100.0
PRK05179	122	rpsM 30S ribosomal protein S13; Validated	100.0
TIGR03631	113	bact_S13 30S ribosomal protein S13. This model des	100.0
TIGR03629	144	arch_S13P archaeal ribosomal protein S13P. This mo	100.0
PRK04053	149	rps13p 30S ribosomal protein S13P; Reviewed	100.0
PF00416	107	Ribosomal_S13: Ribosomal protein S13/S18; InterPro	100.0
PTZ00134	154	40S ribosomal protein S18; Provisional	100.0
KOG3311|consensus	152		100.0
PF06831	92	H2TH: Formamidopyrimidine-DNA glycosylase H2TH dom	97.71
PRK01103	274	formamidopyrimidine/5-formyluracil/ 5-hydroxymethy	97.35
PRK04184	535	DNA topoisomerase VI subunit B; Validated	97.32
PRK14810	272	formamidopyrimidine-DNA glycosylase; Provisional	97.02
PRK14811	269	formamidopyrimidine-DNA glycosylase; Provisional	96.93
PRK10445	263	endonuclease VIII; Provisional	96.9
PRK13945	282	formamidopyrimidine-DNA glycosylase; Provisional	96.82
TIGR00577	272	fpg formamidopyrimidine-DNA glycosylase (fpg). All	96.8
TIGR01052	488	top6b DNA topoisomerase VI, B subunit. This model	96.66
COG1389	538	DNA topoisomerase VI, subunit B [DNA replication,	96.06
COG0266	273	Nei Formamidopyrimidine-DNA glycosylase [DNA repli	95.49
PF05833	455	FbpA: Fibronectin-binding protein A N-terminus (Fb	95.26
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	94.94
TIGR00275	400	flavoprotein, HI0933 family. The model when search	93.39
KOG3311|consensus	152		93.32
PF11798	32	IMS_HHH: IMS family HHH motif; InterPro: IPR024728	92.63
PF10391	52	DNA_pol_lambd_f: Fingers domain of DNA polymerase	91.53
PRK00274	272	ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1	91.29
PF03486	409	HI0933_like: HI0933-like protein; InterPro: IPR004	91.19
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	90.98
smart00278	26	HhH1 Helix-hairpin-helix DNA-binding motif class 1	90.09
PRK02515	132	psbU photosystem II complex extrinsic protein prec	90.02
COG0030	259	KsgA Dimethyladenosine transferase (rRNA methylati	89.23
TIGR00755	253	ksgA dimethyladenosine transferase. Alternate name	87.57
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	87.18
COG3743	133	Uncharacterized conserved protein [Function unknow	86.48
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	86.45
PRK13844	200	recombination protein RecR; Provisional	85.69
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	85.67
TIGR00615	195	recR recombination protein RecR. This family is ba	85.52
PRK14604	195	ruvA Holliday junction DNA helicase RuvA; Provisio	85.47
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	85.18
TIGR03252	177	uncharacterized HhH-GPD family protein. This model	84.74
PRK14602	203	ruvA Holliday junction DNA helicase RuvA; Provisio	84.54
PRK00076	196	recR recombination protein RecR; Reviewed	84.51
PF09883	225	DUF2110: Uncharacterized protein conserved in arch	84.5
COG0632	201	RuvA Holliday junction resolvasome, DNA-binding su	84.41
COG0353	198	RecR Recombinational DNA repair protein (RecF path	84.15
PF00398	262	RrnaAD: Ribosomal RNA adenine dimethylase; InterPr	83.94
PF14579	90	HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI	83.82
COG1293	564	Predicted RNA-binding protein homologous to eukary	83.6
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	80.88
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	80.39
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	80.36
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	80.04

>CHL00137 rps13 ribosomal protein S13; Validated

Probab=100.00  E-value=4.9e-55  Score=307.78  Aligned_cols=121  Identities=51%  Similarity=0.852  Sum_probs=118.1

Q ss_pred             CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH-hhcccchhhHHHHHHHHHH
Q psy8858           1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI-SKFIIEGDLRREFSMNIKR   79 (121)
Q Consensus         1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l-~~~~i~~~L~~~~~~~I~r   79 (121)
                      ||||+|+|||++|+|.+||++|||||+++|.+||+.+||||++++++|+++|+++|.++| ++|.+|+||++.+++||+|
T Consensus         1 mvrI~~~~i~~~k~v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~r   80 (122)
T CHL00137          1 MVRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIEENYQVEGDLRRFESLNIKR   80 (122)
T ss_pred             CceEcCccCCCCCEeeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHHHhCcchHHHHHHHHHHHHH
Confidence            899999999999999999999999999999999999999999999999999999999999 5799999999999999999


Q ss_pred             HHhhccccccccCCCCCcCCccccccccccCCCCcccccccC
Q psy8858          80 LIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLRK  121 (121)
Q Consensus        80 l~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~~  121 (121)
                      |++|+||||+||.+|||||||||||||||+|+++++++++++
T Consensus        81 l~~I~sYRG~RH~~gLPVRGQRT~tNarT~k~~~~~~~~kk~  122 (122)
T CHL00137         81 LMEINCYRGRRHRLGLPVRGQRTRTNARTRRGAKKTVAGKKK  122 (122)
T ss_pred             HHHhCchhcccccCCCCCCCCcCCccccccCCCcccccccCC
Confidence            999999999999999999999999999999999999997664

>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=4.3e-55  Score=304.51  Aligned_cols=120  Identities=56%  Similarity=1.053  Sum_probs=117.5

Q ss_pred             CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh-hcccchhhHHHHHHHHHH
Q psy8858           1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS-KFIIEGDLRREFSMNIKR   79 (121)
Q Consensus         1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~-~~~i~~~L~~~~~~~I~r   79 (121)
                      |+||+|+|||++|.|.+|||+|||||..+|.+||+++||||++++++|||+|+++|.++++ .|.+|+||++++++||+|
T Consensus         1 maRIagvdip~~K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~~~~~vegDLr~~v~~dIkR   80 (121)
T COG0099           1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQNKYLVEGDLRREVRMDIKR   80 (121)
T ss_pred             CceecccCCCCCceEeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHHhcCeehhHHHHHHHHHHHH
Confidence            8999999999999999999999999999999999999999999999999999999999995 999999999999999999


Q ss_pred             HHhhccccccccCCCCCcCCccccccccccCCCCccccccc
Q psy8858          80 LIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR  120 (121)
Q Consensus        80 l~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~  120 (121)
                      |++|+||||+||.+|||||||||+|||||+|+++++++++|
T Consensus        81 l~~i~~YRGiRH~~GLpVRGQrTktnaRtrkG~~~~v~~KK  121 (121)
T COG0099          81 LMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKGVAKKK  121 (121)
T ss_pred             HHHhhhhhhhhhhcCCCCCCcccCccccccCCCccccccCC
Confidence            99999999999999999999999999999999999987765

>PRK05179 rpsM 30S ribosomal protein S13; Validated

Probab=100.00  E-value=1.1e-54  Score=305.94  Aligned_cols=121  Identities=60%  Similarity=1.047  Sum_probs=118.0

Q ss_pred             CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh-hcccchhhHHHHHHHHHH
Q psy8858           1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS-KFIIEGDLRREFSMNIKR   79 (121)
Q Consensus         1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~-~~~i~~~L~~~~~~~I~r   79 (121)
                      ||||+|+|||++|+|.+||++|||||+.+|.+||+++||||++++++|+++|+++|.++|+ +|.+|+||++.+++||+|
T Consensus         1 MvrI~~~~l~~~k~v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~r   80 (122)
T PRK05179          1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKNYKVEGDLRREVSMNIKR   80 (122)
T ss_pred             CceecCccCCCCcEEEeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhhccchHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999995 599999999999999999


Q ss_pred             HHhhccccccccCCCCCcCCccccccccccCCCCcccccccC
Q psy8858          80 LIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLRK  121 (121)
Q Consensus        80 l~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~~  121 (121)
                      |++|+||||+||.+|||||||||||||||+|+++++++++++
T Consensus        81 l~~I~sYRG~RH~~gLPVRGQRT~TNart~k~~~~~~~~kk~  122 (122)
T PRK05179         81 LMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKTIAGKKK  122 (122)
T ss_pred             HHHhcceeeeecccCCCCCCCcCCccccccCCccccccccCC
Confidence            999999999999999999999999999999999999987764

>TIGR03631 bact_S13 30S ribosomal protein S13

Probab=100.00  E-value=2.3e-51  Score=285.87  Aligned_cols=112  Identities=63%  Similarity=1.100  Sum_probs=109.1

Q ss_pred             eeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH-hhcccchhhHHHHHHHHHHHH
Q psy8858           3 RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI-SKFIIEGDLRREFSMNIKRLI   81 (121)
Q Consensus         3 ~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l-~~~~i~~~L~~~~~~~I~rl~   81 (121)
                      ||+|+|+|++|+|.+||++|||||+.+|.+||+++||||++++++|+++|+++|.++| ++|.+|+||++.+++||+||+
T Consensus         1 ri~~~~l~~~k~v~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~~~~~i~~~L~~~~~~dI~rl~   80 (113)
T TIGR03631         1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEAKYKVEGDLRREVSLNIKRLM   80 (113)
T ss_pred             CcCCccCCCCCEEeeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999999999999999999999999 679999999999999999999


Q ss_pred             hhccccccccCCCCCcCCccccccccccCCCCc
Q psy8858          82 DLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR  114 (121)
Q Consensus        82 ~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~  114 (121)
                      +|+||||+||.+|||||||||||||||+|+.++
T Consensus        81 ~I~syRG~RH~~gLpVRGQRT~TNart~k~~~~  113 (113)
T TIGR03631        81 DIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK  113 (113)
T ss_pred             HhcceeccccccCCCCCCCcCCccccccCCCCC
Confidence            999999999999999999999999999998753

This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.

>TIGR03629 arch_S13P archaeal ribosomal protein S13P

Probab=100.00  E-value=1.1e-49  Score=287.34  Aligned_cols=118  Identities=32%  Similarity=0.537  Sum_probs=111.3

Q ss_pred             CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh------------------
Q psy8858           1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK------------------   62 (121)
Q Consensus         1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~------------------   62 (121)
                      |+||+|+|||++|+|.+||++|||||+.+|.+||+++||||++++++||++|+++|.++|++                  
T Consensus         5 m~rI~~~~i~~~k~v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~iP~w~~Nr~~d~~t   84 (144)
T TIGR03629         5 IVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVENYEYGIPSWLLNRRKDYET   84 (144)
T ss_pred             eeeeeCccCCCCCEEEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHhccccCCHHHhhccccccc
Confidence            89999999999999999999999999999999999999999999999999999999999964                  


Q ss_pred             ----cccchhhHHHHHHHHHHHHhhccccccccCCCCCcCCccccccccccCCCCccccccc
Q psy8858          63 ----FIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR  120 (121)
Q Consensus        63 ----~~i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~  120 (121)
                          |.+|+||++++++||+||++|+||||+||.+|||||||||||||||++  ..+|++||
T Consensus        85 g~~~~~ie~dL~~~~~~dI~rl~~I~~yRG~RH~~gLpVRGQRTrTNaRtg~--~~gv~~kk  144 (144)
T TIGR03629        85 GEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVRGQRTKSTGRRGR--TVGVSRKK  144 (144)
T ss_pred             CccceEehHHHHHHHHHHHHHHHHhcceeeeeccCCCCCCCCcCCCCCcCCC--ccccccCC
Confidence                679999999999999999999999999999999999999999998864  45566654

This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.

>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed

Probab=100.00  E-value=1.1e-49  Score=288.62  Aligned_cols=118  Identities=33%  Similarity=0.531  Sum_probs=111.0

Q ss_pred             CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh-------------------
Q psy8858           1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS-------------------   61 (121)
Q Consensus         1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~-------------------   61 (121)
                      ||||+|+|||++|+|.+||++|||||+++|.+||+.+||||++++++|+++|+++|.++|+                   
T Consensus         9 m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~Nr~~d~~   88 (149)
T PRK04053          9 IVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWMLNRRKDYE   88 (149)
T ss_pred             hHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhhhccccccc
Confidence            8999999999999999999999999999999999999999999999999999999999994                   


Q ss_pred             ----hcccchhhHHHHHHHHHHHHhhccccccccCCCCCcCCccccccccccCCCCccccccc
Q psy8858          62 ----KFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR  120 (121)
Q Consensus        62 ----~~~i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~  120 (121)
                          ++.+|+||++.+++||+||++|+||||+||.+|||||||||||||||.  ++.+|+.+|
T Consensus        89 tg~~~~~ie~dLr~~~~~~I~rl~~I~syRG~RH~~GLPVRGQRTrTNaRtg--~~~gv~~kk  149 (149)
T PRK04053         89 TGEDLHLIGSDLILTVREDINRMKKIRSYRGIRHELGLKVRGQRTRSTGRTG--GTVGVSRKK  149 (149)
T ss_pred             cCccceEehHHHHHHHHHHHHHHHHhcceeeecccCCCCCCCCcCCCCCcCC--CccccccCC
Confidence                467999999999999999999999999999999999999999999886  455566554

>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=100.00  E-value=5.3e-50  Score=276.38  Aligned_cols=106  Identities=58%  Similarity=0.943  Sum_probs=102.2

Q ss_pred             eeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh-cccchhhHHHHHHHHHHHH
Q psy8858           3 RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK-FIIEGDLRREFSMNIKRLI   81 (121)
Q Consensus         3 ~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~-~~i~~~L~~~~~~~I~rl~   81 (121)
                      ||+|++||++|+|.+||++|||||+++|.+||+.+||+|++++++|+++|+++|.++|.+ |.+++||++.+.+||+||+
T Consensus         1 rI~~~~l~~~k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~~~~i~~~L~~~~~~~i~rl~   80 (107)
T PF00416_consen    1 RILGTNLPGNKPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEKNHLIENDLKRQVRENIKRLK   80 (107)
T ss_dssp             ETTTTCE-TSSBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHTHSTCHHHHHHHHHHHHHHHH
T ss_pred             CcCCCcCCCCcchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHHhccccchHHHHHHHHHHHHH
Confidence            799999999999999999999999999999999999999999999999999999999965 9999999999999999999


Q ss_pred             hhccccccccCCCCCcCCccccccccc
Q psy8858          82 DLSCYRGIRHRKSLPCRGQRTRTNART  108 (121)
Q Consensus        82 ~i~~yRG~RH~~gLpVRGQRT~tNart  108 (121)
                      +|+||||+||.+|||||||||||||||
T Consensus        81 ~i~syRG~RH~~gLpvRGQRT~tNarT  107 (107)
T PF00416_consen   81 KIKSYRGIRHRKGLPVRGQRTKTNART  107 (107)
T ss_dssp             HHTTHHHHHHHHTSBSSSSTSSSSSHH
T ss_pred             HHHHhhcchhhCCCCCCCCCCCCCCCC
Confidence            999999999999999999999999987

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 S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....

>PTZ00134 40S ribosomal protein S18; Provisional

Probab=100.00  E-value=7.2e-49  Score=285.55  Aligned_cols=118  Identities=31%  Similarity=0.494  Sum_probs=110.1

Q ss_pred             CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh---cc-------------
Q psy8858           1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK---FI-------------   64 (121)
Q Consensus         1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~---~~-------------   64 (121)
                      ||||+|+|||++|+|.+||++|||||+.+|.+||+++||||++++++|+++|+++|.++|++   |.             
T Consensus        14 mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~nr~kd~~   93 (154)
T PTZ00134         14 ILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKIPDWFLNRQRDPK   93 (154)
T ss_pred             hhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCCCChhHhhcccccc
Confidence            89999999999999999999999999999999999999999999999999999999999954   53             


Q ss_pred             -------cchhhHHHHHHHHHHHHhhccccccccCCCCCcCCccccccccccCCCCccccccc
Q psy8858          65 -------IEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR  120 (121)
Q Consensus        65 -------i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~  120 (121)
                             +|+||++.+++||+||++|+||||+||.+|||||||||||||||++  ..+|+++|
T Consensus        94 tG~d~h~i~~dL~~~~~~dI~Rl~~I~sYRG~RH~~GLpVRGQRTkTnaR~g~--~~gv~~kk  154 (154)
T PTZ00134         94 DGKNSHLTSNMLDTKLREDLERLKKIRLHRGLRHHWGLRVRGQHTKTTGRRGR--TVGVSRKK  154 (154)
T ss_pred             ccchhhhhHHHHHHHHHHHHHHHHHhcchheeecccCCccCCccCCCCCcccc--ccceeccC
Confidence                   6999999999999999999999999999999999999999997764  45566554

>KOG3311|consensus

Probab=100.00  E-value=1.7e-35  Score=213.09  Aligned_cols=118  Identities=29%  Similarity=0.568  Sum_probs=108.4

Q ss_pred             CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh---cc-------------
Q psy8858           1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK---FI-------------   64 (121)
Q Consensus         1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~---~~-------------   64 (121)
                      |++|+|++++++++|.|||++|||||...|..+|+++|||+.+++++|+++|++.+.+++++   |.             
T Consensus        12 i~~il~~~~dg~~~V~fAl~~i~Gig~~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~d~~~~~~~~~~l~rq~~~~   91 (152)
T KOG3311|consen   12 ILRILNTNVDGKRKVTFALTSIKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQILNDPRQYKIPDWFLNRQKDII   91 (152)
T ss_pred             HHHHHccCCCCCceeEEEEEEEeeechhhhhhhhhhcCcchhhhhccccHHHHHHHHHHhcCHHHhcCchHHHHhhcccc
Confidence            57899999999999999999999999999999999999999999999999999999999853   21             


Q ss_pred             -------cchhhHHHHHHHHHHHHhhccccccccCCCCCcCCccccccccccCCCCccccccc
Q psy8858          65 -------IEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR  120 (121)
Q Consensus        65 -------i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~  120 (121)
                             +.+.++...+++|+||++|.||||+||.+|||||||||+|||  ++++..+|++||
T Consensus        92 dG~~~~l~~~~ld~r~r~~ieRlkki~~~RG~rh~~gl~vRGQ~Tkt~~--~~gk~v~Vs~Kk  152 (152)
T KOG3311|consen   92 DGKVNHLLGNGLDTRLRADIERLKKIRCHRGLRHFWGLRVRGQRTKTNG--RRGKTVGVSGKK  152 (152)
T ss_pred             cCccccccchhhhhHHHHHHHHHhhhcccccceeccCCcccCccccccc--cccceeeecccC
Confidence                   356788999999999999999999999999999999999999  666677788775

>PF06831 H2TH: Formamidopyrimidine-DNA glycosylase H2TH domain; InterPro: IPR015886 This entry represents a helix-2turn-helix DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents

Probab=97.71  E-value=3.6e-05  Score=51.58  Aligned_cols=50  Identities=30%  Similarity=0.408  Sum_probs=41.5

Q ss_pred             Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      +++|..+|   +-+.|||...+.+||-.+||+|..++.+|+++|+..|.+.+.
T Consensus        23 ~~~ik~~LlDQ~~iaGiGNiy~~EiLf~a~i~P~~~~~~L~~~~~~~l~~~~~   75 (92)
T PF06831_consen   23 RRPIKAALLDQSVIAGIGNIYADEILFRAGIHPERPASSLSEEELRRLHEAIK   75 (92)
T ss_dssp             CSBHHHHHHCTTTSTT--HHHHHHHHHHTTB-TTSBGGGSHHHHHHHHHHHHH
T ss_pred             cchHHHHHhCCCccccCcHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHH
Confidence            45666666   679999999999999999999999999999999999988874

Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger []. This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006289 nucleotide-excision repair; PDB: 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A 2F5P_A ....

>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated

Probab=97.35  E-value=0.00024  Score=55.88  Aligned_cols=51  Identities=24%  Similarity=0.288  Sum_probs=46.9

Q ss_pred             CCeeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          11 NNQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        11 ~~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      .+..|.-+|   +-+.|||.-.|.+||-.+||+|..++++||++|++.|.+.+.
T Consensus       154 ~~~~Ik~~LLDQ~~iaGiGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~  207 (274)
T PRK01103        154 KKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIK  207 (274)
T ss_pred             CCccHHHHhhcCCeEecccHhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHH
Confidence            456788888   889999999999999999999999999999999999998884

>PRK04184 DNA topoisomerase VI subunit B; Validated

Probab=97.32  E-value=0.00025  Score=60.86  Aligned_cols=53  Identities=26%  Similarity=0.333  Sum_probs=47.9

Q ss_pred             CeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc
Q psy8858          12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI   64 (121)
Q Consensus        12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~   64 (121)
                      .....|+-.+|..||..+|.+||..+|++|++++.+|+++|++.|.++|+++.
T Consensus       256 ~~l~~fL~~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~  308 (535)
T PRK04184        256 RTLKEFLVEEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKKYK  308 (535)
T ss_pred             CCHHHHHHHhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHhcc
Confidence            34456777899999999999999999999999999999999999999997764

>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional

Probab=97.02  E-value=0.00094  Score=52.62  Aligned_cols=51  Identities=22%  Similarity=0.281  Sum_probs=44.3

Q ss_pred             CCeeeeeehh---cccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          11 NNQHIIIGLT---AIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        11 ~~k~v~~aLt---~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      .+.+|.-+|-   -|.|||.-.|.+||-.+||+|..++++||++|++.|.+.+.
T Consensus       153 ~~~~ik~~Lldq~viaGiGNiya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~  206 (272)
T PRK14810        153 RKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIG  206 (272)
T ss_pred             CCccHHHHhhcCceeccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHH
Confidence            3455666664   35999999999999999999999999999999999999874

>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional

Probab=96.93  E-value=0.0014  Score=51.56  Aligned_cols=50  Identities=18%  Similarity=0.218  Sum_probs=43.9

Q ss_pred             Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      +.+|.-+|   +-|-|||.-.|.+||-.+||+|..++++||++|++.|.+.+.
T Consensus       143 ~~~Ik~~LlDQ~~iaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~  195 (269)
T PRK14811        143 ARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIR  195 (269)
T ss_pred             CCcHHHHHhcCceeecccHHHHHHHHHHcCCCccCCcccCCHHHHHHHHHHHH
Confidence            45566666   568999999999999999999999999999999999988773

>PRK10445 endonuclease VIII; Provisional

Probab=96.90  E-value=0.0015  Score=51.16  Aligned_cols=50  Identities=24%  Similarity=0.302  Sum_probs=43.9

Q ss_pred             Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      +++|.-+|   +-+-|||.-.|.+||-.+||+|..++++||++|++.|.+.+.
T Consensus       151 ~~~IK~~LLDQ~~vaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~  203 (263)
T PRK10445        151 NRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALL  203 (263)
T ss_pred             cccHHHHHhcCCccccccHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHH
Confidence            44555555   468899999999999999999999999999999999999884

>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional

Probab=96.82  E-value=0.0017  Score=51.35  Aligned_cols=50  Identities=30%  Similarity=0.370  Sum_probs=43.8

Q ss_pred             Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      ..+|.-+|   +-|-|||.-.|.+||-.+||+|..++++||++|++.|.+.+.
T Consensus       164 ~~~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~  216 (282)
T PRK13945        164 TRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAII  216 (282)
T ss_pred             CccHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHH
Confidence            44555555   568999999999999999999999999999999999988873

>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg)

Probab=96.80  E-value=0.0018  Score=50.96  Aligned_cols=50  Identities=24%  Similarity=0.304  Sum_probs=43.8

Q ss_pred             Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      +.+|.-+|   +-|-|||.-.|.+||-.++|+|..++.+||++|++.|.+.+.
T Consensus       155 ~~~Ik~~LlDQ~vvaGIGNiyadEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~  207 (272)
T TIGR00577       155 KRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLANSLSKEECELLHRAIK  207 (272)
T ss_pred             CCcHHHHHhcCCeEecccHHHHHHHHHHcCCCcchhhccCCHHHHHHHHHHHH
Confidence            44555555   568899999999999999999999999999999999998884

All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>TIGR01052 top6b DNA topoisomerase VI, B subunit

Probab=96.66  E-value=0.0023  Score=54.52  Aligned_cols=52  Identities=23%  Similarity=0.256  Sum_probs=46.6

Q ss_pred             CeeeeeehhcccccCHHHHHHHHHHhCCC---CCcccCCCCHHHHHHHHHHHhhc
Q psy8858          12 NQHIIIGLTAIYGIGRSRAKKICEVTKIS---TTKKIKDLNDNELEKLREEISKF   63 (121)
Q Consensus        12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~---p~~~~~~Ls~~qi~~L~~~l~~~   63 (121)
                      .....|+-.+|..||..+|.+||..+|++   |++.+.+|+++|++.|.++|++.
T Consensus       247 ~~l~~fL~~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~~~  301 (488)
T TIGR01052       247 STLRSFLVSEFSRIGEKKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFKEM  301 (488)
T ss_pred             ccHHHHHHHhhcccCHHHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHHhc
Confidence            34456677899999999999999999999   99999999999999999999654

This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).

>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]

Probab=96.06  E-value=0.0045  Score=52.52  Aligned_cols=52  Identities=25%  Similarity=0.282  Sum_probs=46.9

Q ss_pred             eeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCC----HHHHHHHHHHHhhcc
Q psy8858          13 QHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLN----DNELEKLREEISKFI   64 (121)
Q Consensus        13 k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls----~~qi~~L~~~l~~~~   64 (121)
                      +.-.|...+|.-||..+|..+|+.+|++|++.+.+|+    ++|.+.|.+++++|.
T Consensus       257 tv~~fL~sef~rig~~ta~e~~e~~g~~~~~~p~~L~~~~~~eea~~lv~a~~~~~  312 (538)
T COG1389         257 TVREFLVSEFSRIGEKTADELLEYAGFDPDKKPRELTKKKTREEAEKLVEAFKKMK  312 (538)
T ss_pred             hHHHHHHHHHHHhhhhhHHHHHHHhcCCcccCHHHhhcccCHHHHHHHHHHHHhCc
Confidence            3345777899999999999999999999999999999    999999999997664

>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]

Probab=95.49  E-value=0.022  Score=45.30  Aligned_cols=51  Identities=25%  Similarity=0.326  Sum_probs=43.9

Q ss_pred             CCeeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          11 NNQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        11 ~~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      .+++|.-+|   +-+-|||.-.|.++|-.+||+|....++|+++|+..|.+++.
T Consensus       154 ~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~  207 (273)
T COG0266         154 KKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQLALLHEAIK  207 (273)
T ss_pred             CccchHHHhhcCCceecccHHHHHHHHHHcCCCcccCccccCHHHHHHHHHHHH
Confidence            344455555   568999999999999999999999999999999999888874

>PF05833 FbpA: Fibronectin-binding protein A N-terminus (FbpA); InterPro: IPR008616 This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein, the C-terminal region is IPR008532 from INTERPRO

Probab=95.26  E-value=0.0067  Score=50.27  Aligned_cols=48  Identities=33%  Similarity=0.505  Sum_probs=35.7

Q ss_pred             eeeeeeh-hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858          13 QHIIIGL-TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI   60 (121)
Q Consensus        13 k~v~~aL-t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l   60 (121)
                      ..+.-+| ..+.|+|+..|..+|.++|++++..+.++++++++.|.+.+
T Consensus       187 ~~l~~~L~~~~~G~~~~la~ei~~ra~i~~~~~~~~~~~~~~~~l~~~~  235 (455)
T PF05833_consen  187 KTLVKALSKNFQGFGPELAEEILYRAGIDKNKKVEELSDEEIEKLFEAI  235 (455)
T ss_dssp             -BHHHHHHHHCTT--HHHHHHHHCCCTS-TTSBGGG--HHHHCHHHHHH
T ss_pred             ccHHHHHHHHHHHhHHHHHHHHHHHhCCCCccccccchhhhHHHHHHHH
Confidence            3444555 45569999999999999999999999999999999888877

Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host [].; PDB: 3DOA_A 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A.

>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]

Probab=94.94  E-value=0.021  Score=30.72  Aligned_cols=18  Identities=33%  Similarity=0.438  Sum_probs=15.2

Q ss_pred             ehhcccccCHHHHHHHHH
Q psy8858          18 GLTAIYGIGRSRAKKICE   35 (121)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~   35 (121)
                      .|.+++|||+++|..|+.
T Consensus        12 eL~~lpGIG~~tA~~I~~   29 (30)
T PF00633_consen   12 ELMKLPGIGPKTANAILS   29 (30)
T ss_dssp             HHHTSTT-SHHHHHHHHH
T ss_pred             HHHhCCCcCHHHHHHHHh
Confidence            578999999999999975

The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....

>TIGR00275 flavoprotein, HI0933 family

Probab=93.39  E-value=0.069  Score=43.77  Aligned_cols=50  Identities=16%  Similarity=0.205  Sum_probs=41.4

Q ss_pred             eeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc
Q psy8858          13 QHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI   64 (121)
Q Consensus        13 k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~   64 (121)
                      +.+...|..+  +-...+..||+.+||++++++.+|+++|++.|.+.|++|.
T Consensus       284 ~~~~~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~~~  333 (400)
T TIGR00275       284 KTVKNILKGL--LPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKNWP  333 (400)
T ss_pred             hhHHHHhhhh--hhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhCCE
Confidence            3444444432  7789999999999999999999999999999999997765

The model when searched with a partial length search brings in proteins with a dinucleotide-binding motif (Rossman fold) over the initial 40 residues of the model, including oxidoreductases and dehydrogenases. Partially characterized members include an FAD-binding protein from Bacillus cereus and flavoprotein HI0933 from Haemophilus influenzae.

>KOG3311|consensus

Probab=93.32  E-value=0.019  Score=41.97  Aligned_cols=47  Identities=19%  Similarity=0.024  Sum_probs=42.6

Q ss_pred             cchhhHHHHHHHHHHHHhhccccccccCCCCCcCCccccccccccCCCC
Q psy8858          65 IEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPR  113 (121)
Q Consensus        65 i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~  113 (121)
                      +.+|.+.+...|+..+.++.+|.|.  ..+||+.||.|+.|+.++|.++
T Consensus        70 i~~d~~~~~~~~~~l~rq~~~~dG~--~~~l~~~~ld~r~r~~ieRlkk  116 (152)
T KOG3311|consen   70 ILNDPRQYKIPDWFLNRQKDIIDGK--VNHLLGNGLDTRLRADIERLKK  116 (152)
T ss_pred             HhcCHHHhcCchHHHHhhcccccCc--cccccchhhhhHHHHHHHHHhh
Confidence            6678888899999999999999999  9999999999999999988554

>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []

Probab=92.63  E-value=0.08  Score=28.71  Aligned_cols=20  Identities=30%  Similarity=0.566  Sum_probs=15.1

Q ss_pred             ehhcccccCHHHHHHHHHHhC
Q psy8858          18 GLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      .+++++|||+.++..+ +.+|
T Consensus        12 pi~~~~GIG~kt~~kL-~~~G   31 (32)
T PF11798_consen   12 PIRKFWGIGKKTAKKL-NKLG   31 (32)
T ss_dssp             BGGGSTTS-HHHHHHH-HCTT
T ss_pred             CHHhhCCccHHHHHHH-HHcc
Confidence            5789999999999884 4444

This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....

>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains

Probab=91.53  E-value=0.15  Score=30.75  Aligned_cols=22  Identities=32%  Similarity=0.498  Sum_probs=15.9

Q ss_pred             ehhcccccCHHHHHHHHHHhCCC
Q psy8858          18 GLTAIYGIGRSRAKKICEVTKIS   40 (121)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~lGi~   40 (121)
                      .+++|+|||+.+|....+ .|+.
T Consensus         3 ~f~~I~GVG~~tA~~w~~-~G~r   24 (52)
T PF10391_consen    3 LFTGIWGVGPKTARKWYA-KGIR   24 (52)
T ss_dssp             HHHTSTT--HHHHHHHHH-TT--
T ss_pred             chhhcccccHHHHHHHHH-hCCC
Confidence            468999999999999997 7755

There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....

>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed

Probab=91.29  E-value=0.19  Score=39.20  Aligned_cols=49  Identities=14%  Similarity=0.356  Sum_probs=37.4

Q ss_pred             CeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      .|.+..+|..+++. ...+..+++.+|++|+.++.+|+.+|+..|.+.+.
T Consensus       221 rk~l~~~l~~~~~~-~~~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~  269 (272)
T PRK00274        221 RKTLRNNLKNLFGS-KEKLEEALEAAGIDPNRRAETLSVEEFVRLANALA  269 (272)
T ss_pred             HHHHHHHHHhhccc-hHHHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHH
Confidence            34445555555432 34567889999999999999999999999988874

>PF03486 HI0933_like: HI0933-like protein; InterPro: IPR004792 This is a family of conserved hypothetical proteins that may include proteins with a dinucleotide-binding motif (Rossman fold), including oxidoreductases and dehydrogenases

Probab=91.19  E-value=0.3  Score=40.64  Aligned_cols=52  Identities=17%  Similarity=0.272  Sum_probs=43.0

Q ss_pred             CCeeeeeehhcccccCHHHHHHHHHHhCC-CCCcccCCCCHHHHHHHHHHHhhcc
Q psy8858          11 NNQHIIIGLTAIYGIGRSRAKKICEVTKI-STTKKIKDLNDNELEKLREEISKFI   64 (121)
Q Consensus        11 ~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi-~p~~~~~~Ls~~qi~~L~~~l~~~~   64 (121)
                      +++.+...|..+  +-...+..+|+.+++ +++.++.+++++++..|.+.|++|.
T Consensus       289 ~~~~~~~~l~~~--lp~rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk~~~  341 (409)
T PF03486_consen  289 PKRTLKNFLKGL--LPKRLALALLKRAGIKDPDKKVSELSKKERNRLANLLKRFP  341 (409)
T ss_dssp             TTSBHHHHHTTT--S-HHHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHHCEE
T ss_pred             HhhHHHHHHHHH--hHHHHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHHhCc
Confidence            455566666655  788999999999999 9999999999999999999997765

; PDB: 2I0Z_A 3V76_A 2GQF_A.

>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A

Probab=90.98  E-value=0.035  Score=33.80  Aligned_cols=26  Identities=42%  Similarity=0.571  Sum_probs=21.2

Q ss_pred             eeeehhcccccCHHHHHHHHHHhCCCC
Q psy8858          15 IIIGLTAIYGIGRSRAKKICEVTKIST   41 (121)
Q Consensus        15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p   41 (121)
                      ++-+|.+|.|||+..|..+.+. |+..
T Consensus         3 ~~~~L~~I~Gig~~~a~~L~~~-G~~t   28 (60)
T PF14520_consen    3 VFDDLLSIPGIGPKRAEKLYEA-GIKT   28 (60)
T ss_dssp             HHHHHHTSTTCHHHHHHHHHHT-TCSS
T ss_pred             HHHhhccCCCCCHHHHHHHHhc-CCCc
Confidence            3457889999999999999877 7664

...

>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1

Probab=90.09  E-value=0.27  Score=25.11  Aligned_cols=20  Identities=40%  Similarity=0.453  Sum_probs=16.9

Q ss_pred             ehhcccccCHHHHHHHHHHh
Q psy8858          18 GLTAIYGIGRSRAKKICEVT   37 (121)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~l   37 (121)
                      .|.+++|||..+|..|+...
T Consensus         2 ~L~~i~GiG~k~A~~il~~~   21 (26)
T smart00278        2 ELLKVPGIGPKTAEKILEAX   21 (26)
T ss_pred             hhhhCCCCCHHHHHHHHHhc
Confidence            36799999999999998743

>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional

Probab=90.02  E-value=0.21  Score=35.77  Aligned_cols=62  Identities=18%  Similarity=0.254  Sum_probs=44.3

Q ss_pred             CccCCCCeeeeeehhcccccCHHHHHHHHHHhCCC---CCcccCCCCHHHHHHHHHHHhhcccch
Q psy8858           6 GINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKIS---TTKKIKDLNDNELEKLREEISKFIIEG   67 (121)
Q Consensus         6 ~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~---p~~~~~~Ls~~qi~~L~~~l~~~~i~~   67 (121)
                      +.-++-|..-.-+|..++|||+.+|..|++--.+.   .-..+.-+++.|.+.|.+...+|.+..
T Consensus        50 ~~kIdiN~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V~GIgekqk~~l~k~~~~ftV~~  114 (132)
T PRK02515         50 GEKIDLNNSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNLPGLSERQKELLEANLDNFTVTE  114 (132)
T ss_pred             CCcccCCccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcCCCCCHHHHHHHHHhhcceeeCC
Confidence            44455556666678999999999999999632222   123466678888999988887776543

>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]

Probab=89.23  E-value=0.25  Score=39.06  Aligned_cols=46  Identities=15%  Similarity=0.374  Sum_probs=39.6

Q ss_pred             CCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          11 NNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        11 ~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      ..|.+..+|+..++     ..++|..+|+|++.++.+|+.+|+-.|.+.+.
T Consensus       210 RRKtl~n~l~~~~~-----~~~~l~~~~i~~~~R~e~ls~~~f~~L~~~l~  255 (259)
T COG0030         210 RRKTLRNNLKNLFG-----LEEVLEAAGIDPNARAENLSPEDFLKLANALK  255 (259)
T ss_pred             hhHHHHHHHHhhhh-----HHHHHHhcCCCcccChhhCCHHHHHHHHHHHh
Confidence            35666677777776     88999999999999999999999999999884

>TIGR00755 ksgA dimethyladenosine transferase

Probab=87.57  E-value=0.43  Score=36.64  Aligned_cols=46  Identities=13%  Similarity=0.237  Sum_probs=35.1

Q ss_pred             CeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHH
Q psy8858          12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREE   59 (121)
Q Consensus        12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~   59 (121)
                      .|.+..+|..+++-  ..+..+++.+|+++++++.+|+.+|+..|.+.
T Consensus       207 rk~l~~~l~~~~~~--~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~  252 (253)
T TIGR00755       207 RKTLRNNLKQLLKA--SKLEEVLEQLGLDPTARAEQLSPEDFLRLANL  252 (253)
T ss_pred             hHHHHHHHhhhcch--hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHh
Confidence            45556666665432  34567888899999999999999999998765

Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=87.18  E-value=0.4  Score=36.04  Aligned_cols=22  Identities=32%  Similarity=0.465  Sum_probs=18.7

Q ss_pred             eehhcccccCHHHHHHHHHHhC
Q psy8858          17 IGLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      -+|++++|||+++|.+||-.|-
T Consensus       108 ~~L~~vpGIGkKtAerIilELk  129 (188)
T PRK14606        108 EGLSKLPGISKKTAERIVMELK  129 (188)
T ss_pred             HHHhhCCCCCHHHHHHHHHHHH
Confidence            3689999999999999996543

>COG3743 Uncharacterized conserved protein [Function unknown]

Probab=86.48  E-value=0.64  Score=33.32  Aligned_cols=43  Identities=23%  Similarity=0.288  Sum_probs=38.4

Q ss_pred             ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      -||.|.|||+.... .+..+||.....+-.+|..|+..+.++|.
T Consensus        68 DLt~I~GIGPk~e~-~Ln~~GI~tfaQIAAwt~~di~~id~~l~  110 (133)
T COG3743          68 DLTRISGIGPKLEK-VLNELGIFTFAQIAAWTRADIAWIDDYLN  110 (133)
T ss_pred             cchhhcccCHHHHH-HHHHcCCccHHHHHhcCHHHHHHHHhhcC
Confidence            58999999998765 67899999999999999999999999883

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=86.45  E-value=0.46  Score=35.61  Aligned_cols=21  Identities=33%  Similarity=0.363  Sum_probs=18.1

Q ss_pred             eehhcccccCHHHHHHHHHHh
Q psy8858          17 IGLTAIYGIGRSRAKKICEVT   37 (121)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~l   37 (121)
                      -+|++++|||+++|.+|+-.|
T Consensus       108 ~~L~~vpGIGkKtAeRIilEL  128 (183)
T PRK14601        108 SVLKKVPGIGPKSAKRIIAEL  128 (183)
T ss_pred             HHHhhCCCCCHHHHHHHHHHH
Confidence            368999999999999999554

>PRK13844 recombination protein RecR; Provisional

Probab=85.69  E-value=1.3  Score=33.73  Aligned_cols=72  Identities=15%  Similarity=0.217  Sum_probs=48.6

Q ss_pred             eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc-------------------cchhhHH----
Q psy8858          15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI-------------------IEGDLRR----   71 (121)
Q Consensus        15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~-------------------i~~~L~~----   71 (121)
                      +.-+|++++|||+++|..+.-.+=        +.++++++.|.+.|.+..                   |=+|-.|    
T Consensus        13 LI~~l~~LPGIG~KsA~Rla~~lL--------~~~~~~~~~la~~i~~~~~~i~~C~~C~~lte~~~C~IC~d~~Rd~~~   84 (200)
T PRK13844         13 VIESLRKLPTIGKKSSQRLALYLL--------DKSPETAIAIANSLLDATANIKKCVYCQALTEDDVCNICSNTNRDDTK   84 (200)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHHHHHhCCcCCCCCCCCCCCCCCCCCCCCCCCCE
Confidence            456789999999999999985542        345778888888873321                   1011111    


Q ss_pred             ----HHHHHHHHHHhhccccccccCCC
Q psy8858          72 ----EFSMNIKRLIDLSCYRGIRHRKS   94 (121)
Q Consensus        72 ----~~~~~I~rl~~i~~yRG~RH~~g   94 (121)
                          +--.|+.-+-+.+.|+|.=|-+|
T Consensus        85 iCVVE~~~Dv~aiE~t~~y~G~YhVL~  111 (200)
T PRK13844         85 LCIIESMLDMIAIEEAGIYRGKYFVLN  111 (200)
T ss_pred             EEEECCHHHHHHHHhhCccceEEEEcc
Confidence                12346667778899999999875

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=85.67  E-value=0.53  Score=35.58  Aligned_cols=21  Identities=29%  Similarity=0.316  Sum_probs=17.9

Q ss_pred             eehhcccccCHHHHHHHHHHh
Q psy8858          17 IGLTAIYGIGRSRAKKICEVT   37 (121)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~l   37 (121)
                      .+|++++|||+++|.+||-.|
T Consensus       107 ~~L~kvpGIGkKtAerIilEL  127 (197)
T PRK14603        107 RLLTSASGVGKKLAERIALEL  127 (197)
T ss_pred             HHHhhCCCCCHHHHHHHHHHH
Confidence            368999999999999999443

>TIGR00615 recR recombination protein RecR

Probab=85.52  E-value=1.7  Score=33.01  Aligned_cols=77  Identities=25%  Similarity=0.295  Sum_probs=51.2

Q ss_pred             eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc-------------------cchhhHH----
Q psy8858          15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI-------------------IEGDLRR----   71 (121)
Q Consensus        15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~-------------------i~~~L~~----   71 (121)
                      +..+|++++|||+++|..+.-.+=        ..+++++..|.++|.+..                   |=+|-.+    
T Consensus         9 Li~~l~~LPGIG~KsA~RlA~~ll--------~~~~~~~~~la~ai~~~~~~i~~C~~C~~lse~~~C~IC~d~~Rd~~~   80 (195)
T TIGR00615         9 LIESLKKLPGIGPKSAQRLAFHLL--------KRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRDNSV   80 (195)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCCCCCCCCCCCE
Confidence            456789999999999999975443        335678888888773321                   1011111    


Q ss_pred             ----HHHHHHHHHHhhccccccccCCC---CCcCC
Q psy8858          72 ----EFSMNIKRLIDLSCYRGIRHRKS---LPCRG   99 (121)
Q Consensus        72 ----~~~~~I~rl~~i~~yRG~RH~~g---LpVRG   99 (121)
                          +--.|+.-+-+.+.|+|.=|-+|   -|.-|
T Consensus        81 iCVVE~~~Dv~aiE~~~~y~G~YhVL~G~iSPldg  115 (195)
T TIGR00615        81 ICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDG  115 (195)
T ss_pred             EEEECCHHHHHHHHhhCccceEEEEccCccCccCC
Confidence                12346667778899999999987   55554

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=85.47  E-value=0.55  Score=35.47  Aligned_cols=21  Identities=29%  Similarity=0.419  Sum_probs=18.2

Q ss_pred             eehhcccccCHHHHHHHHHHh
Q psy8858          17 IGLTAIYGIGRSRAKKICEVT   37 (121)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~l   37 (121)
                      .+|++++|||+++|.+|+-.|
T Consensus       108 ~~L~kvpGIGkKtAerIilEL  128 (195)
T PRK14604        108 ARLARVPGIGKKTAERIVLEL  128 (195)
T ss_pred             HHHhhCCCCCHHHHHHHHHHH
Confidence            468999999999999999554

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=85.18  E-value=0.58  Score=35.55  Aligned_cols=21  Identities=29%  Similarity=0.249  Sum_probs=18.1

Q ss_pred             eehhcccccCHHHHHHHHHHh
Q psy8858          17 IGLTAIYGIGRSRAKKICEVT   37 (121)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~l   37 (121)
                      -+|++++|||.++|.+|+-.|
T Consensus       107 ~~L~~vpGIGkKtAeRIIlEL  127 (196)
T PRK13901        107 ELISKVKGIGNKMAGKIFLKL  127 (196)
T ss_pred             HHHhhCCCCCHHHHHHHHHHH
Confidence            368999999999999999554

>TIGR03252 uncharacterized HhH-GPD family protein

Probab=84.74  E-value=0.39  Score=35.97  Aligned_cols=29  Identities=24%  Similarity=0.492  Sum_probs=23.8

Q ss_pred             CCCeeeeeehhcccccCHHHHHHHHHHhC
Q psy8858          10 PNNQHIIIGLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus        10 ~~~k~v~~aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      |+...+.-.|.+++|||+.+|..++..||
T Consensus       108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~  136 (177)
T TIGR03252       108 PDGKELLRRLKALPGFGKQKAKIFLALLG  136 (177)
T ss_pred             CCcHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            44555567799999999999999998766

This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=84.54  E-value=0.64  Score=35.26  Aligned_cols=21  Identities=33%  Similarity=0.450  Sum_probs=17.8

Q ss_pred             eehhcccccCHHHHHHHHHHh
Q psy8858          17 IGLTAIYGIGRSRAKKICEVT   37 (121)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~l   37 (121)
                      -+|++++|||+++|.+|+-.|
T Consensus       109 ~~L~~ipGIGkKtAerIilEL  129 (203)
T PRK14602        109 AALTRVSGIGKKTAQHIFLEL  129 (203)
T ss_pred             HHHhcCCCcCHHHHHHHHHHH
Confidence            368999999999999999443

>PRK00076 recR recombination protein RecR; Reviewed

Probab=84.51  E-value=1.9  Score=32.74  Aligned_cols=77  Identities=23%  Similarity=0.349  Sum_probs=50.9

Q ss_pred             eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc-------------------cchhhHH----
Q psy8858          15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI-------------------IEGDLRR----   71 (121)
Q Consensus        15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~-------------------i~~~L~~----   71 (121)
                      +..+|++++|||+++|..+.-.+=        ..+++++..|.+.|.+..                   |=.|=.|    
T Consensus         9 Li~~l~~LPGIG~KsA~Rla~~ll--------~~~~~~~~~la~~i~~~~~~i~~C~~C~~lse~~~C~IC~d~~Rd~~~   80 (196)
T PRK00076          9 LIEALRKLPGIGPKSAQRLAFHLL--------QRDREDVLRLAQALEEAKEKIKHCSVCGNLTEQDPCEICSDPRRDQSL   80 (196)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHHHHHcCCcCCCCCCcCCCCcCCCCCCCCCCCCE
Confidence            455789999999999999986543        335778888888773321                   1001011    


Q ss_pred             ----HHHHHHHHHHhhccccccccCCC---CCcCC
Q psy8858          72 ----EFSMNIKRLIDLSCYRGIRHRKS---LPCRG   99 (121)
Q Consensus        72 ----~~~~~I~rl~~i~~yRG~RH~~g---LpVRG   99 (121)
                          +--.|+.-+-+.+.|+|.=|-+|   -|.-|
T Consensus        81 icVVE~~~Dv~aiE~s~~y~G~YhVL~G~ispl~g  115 (196)
T PRK00076         81 ICVVESPADVLAIERTGEYRGLYHVLGGLLSPLDG  115 (196)
T ss_pred             EEEECCHHHHHHHHhhCcCceEEEEecCCcCCCCC
Confidence                12346666778899999999987   45444

>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function

Probab=84.50  E-value=1.6  Score=33.82  Aligned_cols=67  Identities=13%  Similarity=0.184  Sum_probs=52.1

Q ss_pred             CeeeeeehhcccccCHHHHHHHHHHhCCCCCcc------------cCCCCHHHHHHHHHHHhh----cccchhhHHHHHH
Q psy8858          12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKK------------IKDLNDNELEKLREEISK----FIIEGDLRREFSM   75 (121)
Q Consensus        12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~------------~~~Ls~~qi~~L~~~l~~----~~i~~~L~~~~~~   75 (121)
                      ...+..--..++|+|+....+|..++|+=++.+            ...|+++|++.|-++.+.    ..+.+.-+.+++.
T Consensus        96 G~~~~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~~~~~rltd~q~d~l~~W~~~~~drl~Vnsatr~ev~~  175 (225)
T PF09883_consen   96 GIFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDGIEARLTDEQVDRLYEWTRDGTDRLNVNSATRSEVRA  175 (225)
T ss_pred             cccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEcccCcccccCHHHHHHHHHHhhCCCCeEEEecccHHHHHH
Confidence            445555556788999999999999999999988            567999999999999943    4566666666665


Q ss_pred             HHH
Q psy8858          76 NIK   78 (121)
Q Consensus        76 ~I~   78 (121)
                      -++
T Consensus       176 aln  178 (225)
T PF09883_consen  176 ALN  178 (225)
T ss_pred             HHH
Confidence            544

>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]

Probab=84.41  E-value=0.68  Score=35.29  Aligned_cols=21  Identities=33%  Similarity=0.453  Sum_probs=18.4

Q ss_pred             eehhcccccCHHHHHHHHHHh
Q psy8858          17 IGLTAIYGIGRSRAKKICEVT   37 (121)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~l   37 (121)
                      -+|++++|||.++|.+||-.|
T Consensus       108 ~~L~k~PGIGkKtAerivleL  128 (201)
T COG0632         108 KALSKIPGIGKKTAERIVLEL  128 (201)
T ss_pred             HhhhcCCCCCHHHHHHHHHHH
Confidence            468999999999999999654

>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]

Probab=84.15  E-value=1.6  Score=33.31  Aligned_cols=78  Identities=22%  Similarity=0.321  Sum_probs=53.6

Q ss_pred             eeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc-------------------cchhhHH---
Q psy8858          14 HIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI-------------------IEGDLRR---   71 (121)
Q Consensus        14 ~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~-------------------i~~~L~~---   71 (121)
                      .+..+|.+++|||+++|..+.--+-        ..++++++.|.++|.+..                   |=+|=.+   
T Consensus         9 ~LI~~l~kLPGvG~KsA~R~AfhLL--------~~~~~~~~~la~al~~a~~~i~~C~~C~~~te~d~C~ICsd~~Rd~~   80 (198)
T COG0353           9 KLIDALKKLPGVGPKSAQRLAFHLL--------QRDREDVERLAKALLEAKENIKHCSVCGNLTESDPCDICSDESRDKS   80 (198)
T ss_pred             HHHHHHhhCCCCChhHHHHHHHHHH--------ccCHHHHHHHHHHHHHHHhcCccccccCCcCCCCcCcCcCCcccCCc
Confidence            3556889999999999999985543        446788888888883321                   1011111   


Q ss_pred             -----HHHHHHHHHHhhccccccccCCC---CCcCC
Q psy8858          72 -----EFSMNIKRLIDLSCYRGIRHRKS---LPCRG   99 (121)
Q Consensus        72 -----~~~~~I~rl~~i~~yRG~RH~~g---LpVRG   99 (121)
                           +--.|+..+-+.+.|+|.=|-.|   -|.-|
T Consensus        81 ~icVVe~p~Dv~a~E~~~~f~G~YhVL~G~lspl~g  116 (198)
T COG0353          81 QLCVVEEPKDVLALEKTGEFRGLYHVLGGLLSPLDG  116 (198)
T ss_pred             eEEEEcchHHHHHHHHhcccCeeEEEecCccCcccC
Confidence                 12457778889999999999887   44444

>PF00398 RrnaAD: Ribosomal RNA adenine dimethylase; InterPro: IPR001737 This family of proteins include rRNA adenine dimethylases (e

Probab=83.94  E-value=0.62  Score=36.08  Aligned_cols=50  Identities=12%  Similarity=0.258  Sum_probs=38.9

Q ss_pred             CCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          10 PNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        10 ~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      ...|.+..+|+.+++  ...+..+.+.+||+++.++.+|+.+|+..|.++|+
T Consensus       212 ~rrk~l~~~L~~~~~--~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~  261 (262)
T PF00398_consen  212 QRRKTLRNSLKSLFP--GEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLN  261 (262)
T ss_dssp             TTTSBHHHHTTCTHH--HHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHH
T ss_pred             CcchHHHHHHhhhcC--HHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhh
Confidence            345667777776643  34456777779999999999999999999998874

g. KsgA) and the Erythromycin resistance methylases (Erm). The bacterial enzyme KsgA catalyses the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaea, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In Saccharomyces cerevisiae (Baker's yeast), and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. The best conserved region in these enzymes is located in the N-terminal section and corresponds to a region that is probably involved in S-adenosyl methionine (SAM) binding domain. The crystal structure of KsgA from Escherichia coli has been solved to a resolution of 2.1A. It bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to the yeast mitochondrial transcription factor, sc-mtTFB []. The Erm family of RNA methyltransferases, which methylate a single adenosine base in 23S rRNA confer resistance to the MLS-B group of antibiotics. Despite their sequence similarity, the two enzyme families have strikingly different levels of regulation that remain to be elucidated. Other orthologs, of this family include the yeast and Homo sapiens (Human) mitochondrial transcription factors (MTF1 and h-mtTFB respectively), which are nuclear encoded []. Human-mtTFB is able to stimulate transcription in vitro independently of its S-adenosylmethionine binding and rRNA methyltransferase activity [].; GO: 0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity, 0008649 rRNA methyltransferase activity, 0000154 rRNA modification; PDB: 3FTF_A 3R9X_B 3FTE_A 3FTC_A 3FTD_A 3GRY_A 3FYC_A 3GRU_A 3FYD_A 3GRV_A ....

>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A

Probab=83.82  E-value=1.2  Score=29.12  Aligned_cols=26  Identities=42%  Similarity=0.626  Sum_probs=22.0

Q ss_pred             eeeeeehhcccccCHHHHHHHHHHhC
Q psy8858          13 QHIIIGLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus        13 k~v~~aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      ..|.++|+.|+|||...|..|++.-.
T Consensus        23 ~~Ir~gl~~Ikglg~~~a~~I~~~R~   48 (90)
T PF14579_consen   23 NAIRLGLSAIKGLGEEVAEKIVEERE   48 (90)
T ss_dssp             TEEE-BGGGSTTS-HHHHHHHHHHHH
T ss_pred             CEEeehHhhcCCCCHHHHHHHHHhHh
Confidence            68999999999999999999998764

>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]

Probab=83.60  E-value=1.2  Score=38.76  Aligned_cols=46  Identities=26%  Similarity=0.409  Sum_probs=41.1

Q ss_pred             eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858          15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI   60 (121)
Q Consensus        15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l   60 (121)
                      +..++..+.|+|.-.|+++|.++|+++.....++.++++..+...+
T Consensus       188 ~~~~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~  233 (564)
T COG1293         188 IVRLLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREAL  233 (564)
T ss_pred             HHHHHHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHH
Confidence            3456778999999999999999999999999999999999997755

>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A

Probab=80.88  E-value=1.6  Score=26.35  Aligned_cols=20  Identities=45%  Similarity=0.604  Sum_probs=17.6

Q ss_pred             ehhcccccCHHHHHHHHHHh
Q psy8858          18 GLTAIYGIGRSRAKKICEVT   37 (121)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~l   37 (121)
                      .|..++|||+.+|..|+..+
T Consensus        39 ~L~~i~Gig~~~a~~i~~~~   58 (60)
T PF14520_consen   39 ELAEIPGIGEKTAEKIIEAA   58 (60)
T ss_dssp             HHHTSTTSSHHHHHHHHHHH
T ss_pred             HHhcCCCCCHHHHHHHHHHH
Confidence            47889999999999999765

...

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=80.39  E-value=0.55  Score=35.34  Aligned_cols=34  Identities=15%  Similarity=0.246  Sum_probs=21.4

Q ss_pred             eCccCCCCeeeeeehhcccccCHHHHHHHHHHhC
Q psy8858           5 VGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus         5 ~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      +|-.=...+.++..|.++.|||+++|..|+..++
T Consensus        61 yGF~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~   94 (194)
T PRK14605         61 FGFATTEELSLFETLIDVSGIGPKLGLAMLSAMN   94 (194)
T ss_pred             eCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHhCC
Confidence            3444444555666667777777777777776554

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=80.36  E-value=1.1  Score=33.63  Aligned_cols=18  Identities=39%  Similarity=0.534  Sum_probs=16.0

Q ss_pred             ehhcccccCHHHHHHHHH
Q psy8858          18 GLTAIYGIGRSRAKKICE   35 (121)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~   35 (121)
                      +|++++|||.++|..|+-
T Consensus       109 ~L~~vpGIGkKtAerIil  126 (194)
T PRK14605        109 LLSTIPGIGKKTASRIVL  126 (194)
T ss_pred             HHHhCCCCCHHHHHHHHH
Confidence            589999999999999763

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=80.04  E-value=1.2  Score=33.46  Aligned_cols=20  Identities=25%  Similarity=0.381  Sum_probs=16.8

Q ss_pred             eehhcccccCHHHHHHHHHHh
Q psy8858          17 IGLTAIYGIGRSRAKKICEVT   37 (121)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~l   37 (121)
                      .+| +++|||.++|.+|+-.|
T Consensus       108 ~~L-~vpGIGkKtAerIilEL  127 (186)
T PRK14600        108 AAL-KVNGIGEKLINRIITEL  127 (186)
T ss_pred             hhe-ECCCCcHHHHHHHHHHH
Confidence            467 89999999999999544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	121
1vs5_M	118	Crystal Structure Of The Bacterial Ribosome From Es		2e-39
3fih_M	113	Ternary Complex-Bound E.Coli 70s Ribosome. This Ent		1e-38
3ofo_M	114	Crystal Structure Of The E. Coli Ribosome Bound To		1e-38
2gy9_M	115	Structure Of The 30s Subunit Of A Pre-Translocation		1e-38
1p6g_M	117	Real Space Refined Coordinates Of The 30s Subunit F		1e-38
1fjg_M	126	Structure Of The Thermus Thermophilus 30s Ribosomal		4e-33
1i94_M	125	Crystal Structures Of The Small Ribosomal Subunit W		2e-32
3mr8_M	117	Recognition Of The Amber Stop Codon By Release Fact		4e-32
3pyn_M	116	Crystal Structure Of A Complex Containing Domain 3		4e-32
3bbn_M	145	Homology Model For The Spinach Chloroplast 30s Subu		2e-14
3j20_O	148	Promiscuous Behavior Of Proteins In Archaeal Riboso		9e-11
1s1h_M	132	Structure Of The Ribosomal 80s-Eef2-Sordarin Comple		3e-06
3izb_M	146	Localization Of The Small Subunit Ribosomal Protein		3e-06
3jyv_M	130	Structure Of The 40s Rrna And Proteins And PE TRNA		3e-06
2zkq_m	152	Structure Of A Mammalian Ribosomal 40s Subunit With		7e-06
3iz6_M	152	Localization Of The Small Subunit Ribosomal Protein		9e-06
2xzm_M	155	Crystal Structure Of The Eukaryotic 40s Ribosomal S		2e-05
3zey_M	153	High-resolution Cryo-electron Microscopy Structure		2e-04

>pdb|1VS5|M Chain M, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With The Antibiotic Kasugamyin At 3.5a Resolution. This File Contains The 30s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. Length = 118

Iteration: 1
 Score =  156 bits (395), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 67/114 (58%), Positives = 94/114 (82%)
Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI GINIP+++H +I LT+IYG+G++R+K I     I+   KI +L++ +++ LR+E+
Sbjct: 1   MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEV 60
Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
           +KF++EGDLRRE SM+IKRL+DL CYRG+RHR+ LP RGQRT+TNARTRKGPR+
Sbjct: 61  AKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK 114

>pdb|3FIH|M Chain M, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry Consists Of The 30s Subunit, Trnas And The Ternary Complex. Length = 113

Iteration: 1
 Score =  154 bits (390), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 66/113 (58%), Positives = 93/113 (82%)
Query: 2   TRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61
            RI GINIP+++H +I LT+IYG+G++R+K I     I+   KI +L++ +++ LR+E++
Sbjct: 1   ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA 60
Query: 62  KFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
           KF++EGDLRRE SM+IKRL+DL CYRG+RHR+ LP RGQRT+TNARTRKGPR+
Sbjct: 61  KFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK 113

>pdb|3OFO|M Chain M, Crystal Structure Of The E. Coli Ribosome Bound To Erythromycin. This File Contains The 30s Subunit Of The First 70s Ribosome. Length = 114

Iteration: 1
 Score =  154 bits (389), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 66/113 (58%), Positives = 93/113 (82%)
Query: 2   TRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61
            RI GINIP+++H +I LT+IYG+G++R+K I     I+   KI +L++ +++ LR+E++
Sbjct: 1   ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA 60
Query: 62  KFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
           KF++EGDLRRE SM+IKRL+DL CYRG+RHR+ LP RGQRT+TNARTRKGPR+
Sbjct: 61  KFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK 113

>pdb|2GY9|M Chain M, 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 = 115

Iteration: 1
 Score =  154 bits (389), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 66/113 (58%), Positives = 93/113 (82%)
Query: 2   TRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61
            RI GINIP+++H +I LT+IYG+G++R+K I     I+   KI +L++ +++ LR+E++
Sbjct: 1   ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA 60
Query: 62  KFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
           KF++EGDLRRE SM+IKRL+DL CYRG+RHR+ LP RGQRT+TNARTRKGPR+
Sbjct: 61  KFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK 113

>pdb|1P6G|M Chain M, 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 = 117

Iteration: 1
 Score =  154 bits (389), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 66/113 (58%), Positives = 93/113 (82%)
Query: 2   TRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61
            RI GINIP+++H +I LT+IYG+G++R+K I     I+   KI +L++ +++ LR+E++
Sbjct: 1   ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA 60
Query: 62  KFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
           KF++EGDLRRE SM+IKRL+DL CYRG+RHR+ LP RGQRT+TNARTRKGPR+
Sbjct: 61  KFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK 113

>pdb|1FJG|M Chain M, Structure Of The Thermus Thermophilus 30s Ribosomal Subunit In Complex With The Antibiotics Streptomycin, Spectinomycin, And Paromomycin Length = 126

Iteration: 1
 Score =  135 bits (341), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 64/122 (52%), Positives = 89/122 (72%), Gaps = 1/122 (0%)
Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+ IP N+ + + LT IYGIG++RAK+  E T I+   ++KDL + E+ +LRE +
Sbjct: 1   MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYV 60
Query: 61  -SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSL 119
            + + +EG+LR E + NIKRL+D+ CYRG+RHR+ LP RGQRTRTNARTRKGPR+     
Sbjct: 61  ENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGK 120
Query: 120 RK 121
           +K
Sbjct: 121 KK 122

>pdb|1I94|M Chain M, Crystal Structures Of The Small Ribosomal Subunit With Tetracycline, Edeine And If3 Length = 125

Iteration: 1
 Score =  133 bits (335), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 63/121 (52%), Positives = 88/121 (72%), Gaps = 1/121 (0%)
Query: 2   TRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI- 60
            RI G+ IP N+ + + LT IYGIG++RAK+  E T I+   ++KDL + E+ +LRE + 
Sbjct: 1   ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVE 60
Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120
           + + +EG+LR E + NIKRL+D+ CYRG+RHR+ LP RGQRTRTNARTRKGPR+     +
Sbjct: 61  NTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKK 120
Query: 121 K 121
           K
Sbjct: 121 K 121

>pdb|3MR8|M Chain M, Recognition Of The Amber Stop Codon By Release Factor Rf1. This Entry 3mr8 Contains 30s Ribosomal Subunit. The 50s Ribosomal Subunit Can Be Found In Pdb Entry 3ms1. Molecule B In The Same Asymmetric Unit Is Deposited As 3mrz (50s) And 3ms0 (30s). Length = 117

Iteration: 1
 Score =  132 bits (333), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 62/114 (54%), Positives = 86/114 (75%), Gaps = 1/114 (0%)
Query: 2   TRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI- 60
            RI G+ IP N+ + + LT IYGIG++RAK+  E T I+   ++KDL + E+ +LRE + 
Sbjct: 1   ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVE 60
Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
           + + +EG+LR E + NIKRL+D+ CYRG+RHR+ LP RGQRTRTNARTRKGPR+
Sbjct: 61  NTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRK 114

>pdb|3PYN|M Chain M, Crystal Structure Of A Complex Containing Domain 3 From The Psiv Igr Ires Rna Bound To The 70s Ribosome. This File Contains The 30s Subunit Of The First 70s Ribosome. Length = 116

Iteration: 1
 Score =  132 bits (333), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 62/114 (54%), Positives = 86/114 (75%), Gaps = 1/114 (0%)
Query: 2   TRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI- 60
            RI G+ IP N+ + + LT IYGIG++RAK+  E T I+   ++KDL + E+ +LRE + 
Sbjct: 1   ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVE 60
Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
           + + +EG+LR E + NIKRL+D+ CYRG+RHR+ LP RGQRTRTNARTRKGPR+
Sbjct: 61  NTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRK 114

>pdb|3BBN|M Chain M, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 145

Iteration: 1
 Score = 74.3 bits (181), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 46/110 (41%), Positives = 69/110 (62%), Gaps = 13/110 (11%)
Query: 3   RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKI-KDLNDNELEKLREEIS 61
           RI G+ IPN++ +   L  I+GIGRSR+++I  +  ++   K+ KDL++ E+  LR+E  
Sbjct: 48  RIGGVEIPNHKRVEYSLQYIHGIGRSRSRQI--LLDLNFDNKVTKDLSEEEVIILRKE-- 103
Query: 62  KFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKG 111
                   +R   + I+RL ++ CYRGIRH+  LP RGQRT+ N RT KG
Sbjct: 104 --------KRFNRVAIERLKEIRCYRGIRHKLGLPVRGQRTKNNCRTLKG 145

>pdb|3J20|O Chain O, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (30s Ribosomal Subunit) Length = 148

Iteration: 1
 Score = 62.0 bits (149), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 40/130 (30%), Positives = 62/130 (47%), Gaps = 23/130 (17%)
Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           + R+ G+++  N+ +   LTAI GIG + A  +C V  +    K   L D +++K+ E +
Sbjct: 7   IVRVAGVDLDGNKQLRWALTAIKGIGINFATMVCRVAGLDPFMKAGYLTDEQVKKIEEIL 66
Query: 61  SKFIIEGDLR------------REFSM-----------NIKRLIDLSCYRGIRHRKSLPC 97
           +  +  G  R            R+  +           +I RL  +  YRGIRH   LP 
Sbjct: 67  ADPVAHGIPRWAVNRPKDYETGRDLHLITAKLDMAIREDIMRLRRIRAYRGIRHELGLPV 126
Query: 98  RGQRTRTNAR 107
           RGQRTR+N R
Sbjct: 127 RGQRTRSNFR 136

>pdb|1S1H|M Chain M, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From Yeast Obtained By Docking Atomic Models For Rna And Protein Components Into A 11.7 A Cryo-Em Map. This File, 1s1h, Contains 40s Subunit. The 60s Ribosomal Subunit Is In File 1s1i Length = 132

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 59/130 (45%), Gaps = 23/130 (17%)
Query: 3   RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI-- 60
           R++  N+  N  I+  LT I G+GR  +  +C+   +   K+  +L   ELE++ + +  
Sbjct: 2   RLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIMQN 61
Query: 61  -------SKFI--------------IEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRG 99
                  + F+              +  ++  +   +++RL  +  +RGIRH   L  RG
Sbjct: 62  PTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRAHRGIRHFWGLRVRG 121
Query: 100 QRTRTNARTR 109
           Q T+T  R R
Sbjct: 122 QHTKTTGRRR 131

>pdb|3IZB|M Chain M, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 146

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 59/130 (45%), Gaps = 23/130 (17%)
Query: 3   RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI-- 60
           R++  N+  N  I+  LT I G+GR  +  +C+   +   K+  +L   ELE++ + +  
Sbjct: 16  RLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIMQN 75
Query: 61  -------SKFI--------------IEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRG 99
                  + F+              +  ++  +   +++RL  +  +RGIRH   L  RG
Sbjct: 76  PTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRAHRGIRHFWGLRVRG 135
Query: 100 QRTRTNARTR 109
           Q T+T  R R
Sbjct: 136 QHTKTTGRRR 145

>pdb|3JYV|M Chain M, Structure Of The 40s Rrna And Proteins And PE TRNA FOR EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution Length = 130

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 59/130 (45%), Gaps = 23/130 (17%)
Query: 3   RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI-- 60
           R++  N+  N  I+  LT I G+GR  +  +C+   +   K+  +L   ELE++ + +  
Sbjct: 1   RLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIMQN 60
Query: 61  -------SKFI--------------IEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRG 99
                  + F+              +  ++  +   +++RL  +  +RGIRH   L  RG
Sbjct: 61  PTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRAHRGIRHFWGLRVRG 120
Query: 100 QRTRTNARTR 109
           Q T+T  R R
Sbjct: 121 QHTKTTGRRR 130

>pdb|2ZKQ|MM Chain m, Structure Of A Mammalian Ribosomal 40s Subunit Within An 80s Complex Obtained By Docking Homology Models Of The Rna And Proteins Into An 8.7 A Cryo-Em Map Length = 152

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 59/130 (45%), Gaps = 23/130 (17%)
Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL---- 56
           + R++  NI   + I   +TAI G+GR  A  +     I  TK+  +L ++E+E++    
Sbjct: 12  ILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIM 71
Query: 57  ----REEISKF---------------IIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPC 97
               + +I  +               ++   L  +   +++RL  +  +RG+RH   L  
Sbjct: 72  QNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRV 131
Query: 98  RGQRTRTNAR 107
           RGQ T+T  R
Sbjct: 132 RGQHTKTTGR 141

>pdb|3IZ6|M Chain M, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 152

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 32/128 (25%), Positives = 59/128 (46%), Gaps = 23/128 (17%)
Query: 3   RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS- 61
           R++  N+   Q I+  LT+I G+GR  +  +C+   I   K+  +L+  E+++L   +  
Sbjct: 14  RVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELSAEEMDRLMAVVHN 73
Query: 62  --KF-IIEGDLRRE-------FSMNIKRLIDLSC------------YRGIRHRKSLPCRG 99
             +F + +  L R+       FS  +   +D+              +RG+RH   +  RG
Sbjct: 74  PRQFKVPDWFLNRKKDYKDGRFSQVVSNAVDMKLRDDLERLKKIRNHRGLRHYWGVRVRG 133
Query: 100 QRTRTNAR 107
           Q T+T  R
Sbjct: 134 QHTKTTGR 141

>pdb|2XZM|M Chain M, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit In Complex With Initiation Factor 1. This File Contains The 40s Subunit And Initiation Factor For Molecule 1 Length = 155

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 37/128 (28%), Positives = 58/128 (45%), Gaps = 23/128 (17%)
Query: 3   RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK 62
           RI+  NI   +   I LT I GIGR  A  IC+V KI    +   L +++  K+ + I+ 
Sbjct: 16  RILNTNIDGKRITPIALTGIRGIGRRFAYIICKVLKIDPNARAGLLTEDQCNKITDLIAD 75
Query: 63  FIIEG----------DLR--REFSM-----------NIKRLIDLSCYRGIRHRKSLPCRG 99
               G          D +  + + M           +++RL  +  +RG+RH   L  RG
Sbjct: 76  PEAHGIPTWLLNRINDFKDGKNYQMASNTLDTKMREDLERLKKIKSHRGLRHFWGLKVRG 135
Query: 100 QRTRTNAR 107
           Q T+T+ R
Sbjct: 136 QHTKTSGR 143

>pdb|3ZEY|M Chain M, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 153

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 36/130 (27%), Positives = 59/130 (45%), Gaps = 23/130 (17%)
Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           + R++  N+   + +   L  + GIG   A  +C+   +   ++   L+  ELEK+ E I
Sbjct: 13  IVRLLNTNVEGKRKVPFALRMVKGIGIRFAYMVCKKAGVDVERRAGTLSPEELEKISEVI 72
Query: 61  ---SKF-IIEGDLRRE------------FSM-------NIKRLIDLSCYRGIRHRKSLPC 97
              +KF I E  L R+             SM       +++RL  +  +RG+RH   L  
Sbjct: 73  ADPAKFKIPEWFLNRQRDPKTGKTEHLTSSMVDTRLREDLERLRKIRAHRGVRHAYGLRV 132
Query: 98  RGQRTRTNAR 107
           RGQ T T+ R
Sbjct: 133 RGQHTCTSGR 142

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	121
3r8n_M	114	30S ribosomal protein S13; protein biosynthesis, R	6e-65
2vqe_M	126	30S ribosomal protein S13, 30S ribosomal protein S	1e-63
3bbn_M	145	Ribosomal protein S13; small ribosomal subunit, sp	5e-53
3u5c_S	146	40S ribosomal protein S18-A, 40S ribosomal protein	4e-47
3iz6_M	152	40S ribosomal protein S18 (S13P); eukaryotic ribos	6e-45
2xzm_M	155	RPS18E; ribosome, translation; 3.93A {Tetrahymena	1e-43

>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M* 1xmq_M* ... Length = 126

 Score =  188 bits (480), Expect = 1e-63
 Identities = 64/122 (52%), Positives = 88/122 (72%), Gaps = 1/122 (0%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           M RI G+ IP N+ + + LT IYGIG++RAK+  E T I+   ++KDL + E+ +LRE +
Sbjct: 1   MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYV 60

Query: 61  SK-FIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSL 119
              + +EG+LR E + NIKRL+D+ CYRG+RHR+ LP RGQRTRTNARTRKGPR+     
Sbjct: 61  ENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGK 120

Query: 120 RK 121
           +K
Sbjct: 121 KK 122

>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 145

 Score =  162 bits (412), Expect = 5e-53
 Identities = 45/111 (40%), Positives = 63/111 (56%), Gaps = 11/111 (9%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
             RI G+ IPN++ +   L  I+GIGRSR+++I         K  KDL++ E+  LR   
Sbjct: 46  CIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFDN-KVTKDLSEEEVIILR--- 101

Query: 61  SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKG 111
                    +R   + I+RL ++ CYRGIRH+  LP RGQRT+ N RT KG
Sbjct: 102 -------KEKRFNRVAIERLKEIRCYRGIRHKLGLPVRGQRTKNNCRTLKG 145

>3u5c_S 40S ribosomal protein S18-A, 40S ribosomal protein S17-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_M 3o30_L 3o2z_L 3u5g_S 1s1h_M 3jyv_M* 2zkq_m Length = 146

 Score =  147 bits (373), Expect = 4e-47
 Identities = 31/132 (23%), Positives = 57/132 (43%), Gaps = 23/132 (17%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           + R++  N+  N  I+  LT I G+GR  +  +C+   +   K+  +L   ELE++ + +
Sbjct: 14  ILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIM 73

Query: 61  S-----------------------KFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPC 97
                                      +  ++  +   +++RL  +  +RGIRH   L  
Sbjct: 74  QNPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRAHRGIRHFWGLRV 133

Query: 98  RGQRTRTNARTR 109
           RGQ T+T  R R
Sbjct: 134 RGQHTKTTGRRR 145

>3iz6_M 40S ribosomal protein S18 (S13P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Length = 152

 Score =  142 bits (359), Expect = 6e-45
 Identities = 29/133 (21%), Positives = 58/133 (43%), Gaps = 23/133 (17%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           + R++  N+   Q I+  LT+I G+GR  +  +C+   I   K+  +L+  E+++L   +
Sbjct: 12  ILRVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELSAEEMDRLMAVV 71

Query: 61  SKF-----------------------IIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPC 97
                                     ++   +  +   +++RL  +  +RG+RH   +  
Sbjct: 72  HNPRQFKVPDWFLNRKKDYKDGRFSQVVSNAVDMKLRDDLERLKKIRNHRGLRHYWGVRV 131

Query: 98  RGQRTRTNARTRK 110
           RGQ T+T  R  K
Sbjct: 132 RGQHTKTTGRRGK 144

>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_M Length = 155

 Score =  139 bits (352), Expect = 1e-43
 Identities = 35/133 (26%), Positives = 56/133 (42%), Gaps = 23/133 (17%)

Query: 1   MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60
           + RI+  NI   +   I LT I GIGR  A  IC+V KI    +   L +++  K+ + I
Sbjct: 14  IHRILNTNIDGKRITPIALTGIRGIGRRFAYIICKVLKIDPNARAGLLTEDQCNKITDLI 73

Query: 61  SKF-----------------------IIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPC 97
           +                         +    L  +   +++RL  +  +RG+RH   L  
Sbjct: 74  ADPEAHGIPTWLLNRINDFKDGKNYQMASNTLDTKMREDLERLKKIKSHRGLRHFWGLKV 133

Query: 98  RGQRTRTNARTRK 110
           RGQ T+T+ R   
Sbjct: 134 RGQHTKTSGRHGV 146

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	121
2vqe_M	126	30S ribosomal protein S13, 30S ribosomal protein S	100.0
3r8n_M	114	30S ribosomal protein S13; protein biosynthesis, R	100.0
2xzm_M	155	RPS18E; ribosome, translation; 3.93A {Tetrahymena	100.0
3j20_O	148	30S ribosomal protein S13P; archaea, archaeal, KIN	100.0
3iz6_M	152	40S ribosomal protein S18 (S13P); eukaryotic ribos	100.0
3u5c_S	146	40S ribosomal protein S18-A, 40S ribosomal protein	100.0
3bbn_M	145	Ribosomal protein S13; small ribosomal subunit, sp	100.0
1mu5_A	471	Type II DNA topoisomerase VI subunit B; GHKL ATPas	96.86
1k3x_A	262	Endonuclease VIII; hydrolase/DNA, hydrolase-DNA co	96.73
1ee8_A	266	MUTM (FPG) protein; beta sandwich, zinc finger, he	96.72
1k82_A	268	Formamidopyrimidine-DNA glycosylase; protein-DNA c	96.71
2xzf_A	271	Formamidopyrimidine-DNA glycosylase; hydrolase-DNA	96.7
3u6p_A	273	Formamidopyrimidine-DNA glycosylase; DNA glycosyla	96.69
3w0f_A	287	Endonuclease 8-like 3; helix two turns helix, zinc	96.63
3twl_A	310	Formamidopyrimidine-DNA glycosylase 1; helix two t	96.56
3vk8_A	295	Probable formamidopyrimidine-DNA glycosylase; DNA	96.53
2zbk_B	530	Type 2 DNA topoisomerase 6 subunit B; DNA binding	94.29
3fut_A	271	Dimethyladenosine transferase; methyltransferase,	92.92
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	92.88
1tdh_A	364	NEI endonuclease VIII-like 1; helix two turns heli	92.32
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	92.22
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	91.42
1qyr_A	252	KSGA, high level kasugamycin resistance protein, S	91.23
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	89.24
1z00_B	84	DNA repair endonuclease XPF; helix-hairpin-helix,	89.23
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	87.7
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	87.44
3ftd_A	249	Dimethyladenosine transferase; KSGA, rossmann-like	86.44
3fhf_A	214	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	86.29
2duy_A	75	Competence protein comea-related protein; helix-ha	86.08
3fhg_A	207	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	86.03
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	85.8
3uzu_A	279	Ribosomal RNA small subunit methyltransferase A; s	85.77
3tqs_A	255	Ribosomal RNA small subunit methyltransferase A; p	83.85
3gru_A	295	Dimethyladenosine transferase; rossman fold, ribos	81.41
3vdp_A	212	Recombination protein RECR; zinc finger, DNA repai	81.1
3v76_A	417	Flavoprotein; structural genomics, PSI-biology, NE	80.76
2edu_A	98	Kinesin-like protein KIF22; kinesin-like DNA bindi	80.16
3n0u_A	219	Probable N-glycosylase/DNA lyase; structural genom	80.07

>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M* 1xmq_M* ...

Probab=100.00  E-value=2.1e-56  Score=314.79  Aligned_cols=121  Identities=53%  Similarity=0.934  Sum_probs=117.6

Q ss_pred             CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh-hcccchhhHHHHHHHHHH
Q psy8858           1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS-KFIIEGDLRREFSMNIKR   79 (121)
Q Consensus         1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~-~~~i~~~L~~~~~~~I~r   79 (121)
                      |+||+|+|||++|.|++||++|||||+++|..||+.+||||++++++||++|+++|.++|+ +|.+|+||++++++||+|
T Consensus         1 m~rI~g~~i~~~k~v~~aLt~I~GIG~~~A~~I~~~~gi~~~~r~~~Lt~~ei~~l~~~i~~~~~ve~dLrr~~~~nIkR   80 (126)
T 2vqe_M            1 MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKR   80 (126)
T ss_dssp             -CCCSTTCCCCSSBHHHHHTTSSSCCSHHHHHHTTTTTCCTTSBGGGCCHHHHHHHHHHHHTTSCCHHHHHHHHHHHHHH
T ss_pred             CceEeCccCCCCcEeeeehhccccccHHHHHHHHHHcCCCcccccCcCCHHHHHHHHHHHHHhCcchhHHHHHHHHHHHH
Confidence            8999999999999999999999999999999999999999999999999999999999996 699999999999999999


Q ss_pred             HHhhccccccccCCCCCcCCccccccccccCCCCcccccccC
Q psy8858          80 LIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLRK  121 (121)
Q Consensus        80 l~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~~  121 (121)
                      |++|+||||+||.+|||||||||||||||+|+++++|+++||
T Consensus        81 L~~I~~YRG~RH~~GLPVRGQRTkTNaRTrkg~~~~v~~kkk  122 (126)
T 2vqe_M           81 LMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKK  122 (126)
T ss_dssp             HHHTTCHHHHHHHTTCCSSSCCCSSCCHHHHCSCCCCCCCCS
T ss_pred             HHHHHHHhhhhhccCCcCCCccCccccccCCCcccccccccC
Confidence            999999999999999999999999999999999999998775

>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_M

Probab=100.00  E-value=3.6e-51  Score=296.84  Aligned_cols=119  Identities=30%  Similarity=0.432  Sum_probs=112.1

Q ss_pred             CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh------------------
Q psy8858           1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK------------------   62 (121)
Q Consensus         1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~------------------   62 (121)
                      |+||+|||||++|+|.+|||+|||||+.+|..||+++||||++++++||++|+++|.++|++                  
T Consensus        14 m~RI~g~~l~~~k~v~~aLt~I~GIG~~~A~~I~~~~gid~~~r~~~Lt~~ei~~l~~~i~~p~~~~iP~w~lNr~kD~~   93 (155)
T 2xzm_M           14 IHRILNTNIDGKRITPIALTGIRGIGRRFAYIICKVLKIDPNARAGLLTEDQCNKITDLIADPEAHGIPTWLLNRINDFK   93 (155)
T ss_dssp             CCEETTTEECCSSCHHHHHTTSTTCCHHHHHHHHHHTTCCSSSCSSCSCHHHHHHHHHHHHSHHHHCCCGGGCSEEEETT
T ss_pred             hHheeCccCCCCCEEEEeeecccccCHHHHHHHHHHcCCCcccccccCCHHHHHHHHHHHhCccccCCCHHHhhcccccC
Confidence            89999999999999999999999999999999999999999999999999999999999965                  


Q ss_pred             -----cccchhhHHHHHHHHHHHHhhccccccccCCCCCcCCccccccccccCCCCcccccccC
Q psy8858          63 -----FIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLRK  121 (121)
Q Consensus        63 -----~~i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~~  121 (121)
                           |.+|+||++++++||+||++|+||||+||.+|||||||||||||||++  ..+|.++||
T Consensus        94 ~G~~~~~ie~dLr~~~~~dI~Rl~~I~~yRG~RH~~GLpVRGQRTkTnaRtg~--tvGv~kkk~  155 (155)
T 2xzm_M           94 DGKNYQMASNTLDTKMREDLERLKKIKSHRGLRHFWGLKVRGQHTKTSGRHGV--VCGVVRKNK  155 (155)
T ss_dssp             TEEEECCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHTCCSSSCCCSSSSCSSC--CCSSCCCC-
T ss_pred             CCceeEEecHHHHHHHHHhHHHHhhhceeeeeecccCCCcCCcCCccCCCCcc--cccccccCC
Confidence                 789999999999999999999999999999999999999999999986  335666654

>3j20_O 30S ribosomal protein S13P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=100.00  E-value=9.8e-51  Score=292.65  Aligned_cols=119  Identities=34%  Similarity=0.561  Sum_probs=111.4

Q ss_pred             CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh---c--------------
Q psy8858           1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK---F--------------   63 (121)
Q Consensus         1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~---~--------------   63 (121)
                      |+||+|||||++|+|.+|||+|||||+++|..||+++||||++++++||++|+++|.++|++   |              
T Consensus         7 m~RI~g~~i~~~k~v~~aLt~I~GIG~~~A~~I~~~~gid~~~r~g~Lt~~ei~~i~~~i~~~~~~~iP~w~lNr~kD~~   86 (148)
T 3j20_O            7 IVRVAGVDLDGNKQLRWALTAIKGIGINFATMVCRVAGLDPFMKAGYLTDEQVKKIEEILADPVAHGIPRWAVNRPKDYE   86 (148)
T ss_dssp             CEECSSSCEECSSCHHHHHHHSTTCCHHHHHHHHHHHTCCSSSCTTBCCHHHHHHHHHHHHCHHHHCCCTTTSSEEEETT
T ss_pred             hHHHcCccCCCCCEehhhhhhccCcCHHHHHHHHHHhCCCCCceeccCCHHHHHHHHHHHhcccccCCChhhhcccCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999954   3              


Q ss_pred             ------ccchhhHHHHHHHHHHHHhhccccccccCCCCCcCCccccccccccCCCCcccccccC
Q psy8858          64 ------IIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLRK  121 (121)
Q Consensus        64 ------~i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~~  121 (121)
                            .+|+||++++++||+||++|+||||+||.+|||||||||||||||++  ..+|.++|+
T Consensus        87 ~G~~~~~ve~dL~~~~~~dI~RL~~I~~yRG~RH~~GLpVRGQrTkTnaR~g~--tvgv~kkk~  148 (148)
T 3j20_O           87 TGRDLHLITAKLDMAIREDIMRLRRIRAYRGIRHELGLPVRGQRTRSNFRRGQ--TVGVSRKKK  148 (148)
T ss_dssp             TEEEECCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHTCCSSSCCCSSCSCSSC--CCCCSSCCC
T ss_pred             CCceeEEechHHHHHHHHHHHHHHHhCcEEeecccCCCcCCCCCCcCCCCcCc--ccceeccCC
Confidence                  68999999999999999999999999999999999999999999765  555666653

>3iz6_M 40S ribosomal protein S18 (S13P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=100.00  E-value=4.2e-50  Score=290.43  Aligned_cols=110  Identities=27%  Similarity=0.530  Sum_probs=105.6

Q ss_pred             CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh---ccc------------
Q psy8858           1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK---FII------------   65 (121)
Q Consensus         1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~---~~i------------   65 (121)
                      |+||+|||||++|+|.+|||+|||||+.+|..||+++||||++++++||++|+++|.++|++   |.|            
T Consensus        12 m~RI~g~~i~~~k~v~~ALt~I~GIG~~~A~~I~~~~gid~~~r~g~Lt~~ei~~l~~~i~~~~~~~ip~w~lNr~kD~~   91 (152)
T 3iz6_M           12 ILRVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELSAEEMDRLMAVVHNPRQFKVPDWFLNRKKDYK   91 (152)
T ss_dssp             CCCTTTTCCCCSSBHHHHHTTSTTCCHHHHHHHHHHHTCCSSSBTTTSCHHHHHHHHHHHHSCSSCCCCCCSCSCCCSCC
T ss_pred             HHHHcCCcCCCCcEeHhhhhhccCcCHHHHHHHHHHcCCCCCcEeCcCCHHHHHHHHHHHHhhcccCcchhhhhhhcccC
Confidence            89999999999999999999999999999999999999999999999999999999999953   654            


Q ss_pred             --------chhhHHHHHHHHHHHHhhccccccccCCCCCcCCccccccccccC
Q psy8858          66 --------EGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRK  110 (121)
Q Consensus        66 --------~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRGQRT~tNart~k  110 (121)
                              ++||++++++||+||++|+||||+||.+|||||||||||||||++
T Consensus        92 ~G~~~~li~~dL~~~~~~dI~RL~~I~~yRG~RH~~GLpVRGQrTkTnaRtg~  144 (152)
T 3iz6_M           92 DGRFSQVVSNAVDMKLRDDLERLKKIRNHRGLRHYWGVRVRGQHTKTTGRRGK  144 (152)
T ss_dssp             CCSCCTTCTHHHHHHHHHHHHHHHHHTCHHHHHHHHTCCSSCCCCSSCCHHHH
T ss_pred             CcceeeechhHHHHHHHHhHHHHhhhheeecccccCCCCcCCcCCcCCCCCce
Confidence                    599999999999999999999999999999999999999999963

>3u5c_S 40S ribosomal protein S18-A, 40S ribosomal protein S17-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_M 3o30_L 3o2z_L 3u5g_S 1s1h_M 3jyv_M* 2zkq_m

Probab=100.00  E-value=1.4e-49  Score=286.10  Aligned_cols=110  Identities=29%  Similarity=0.552  Sum_probs=105.9

Q ss_pred             CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh---hccc------------
Q psy8858           1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS---KFII------------   65 (121)
Q Consensus         1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~---~~~i------------   65 (121)
                      |+||+|||||++|+|.+|||+|||||+.+|..||+++||||++++++||++|+++|.++|+   +|.|            
T Consensus        14 ~~RI~g~~i~~~k~v~~ALt~I~GIG~~~A~~I~~~~gid~~~r~g~Lt~~ei~~l~~~i~~~~~~~iP~w~lNR~kD~~   93 (146)
T 3u5c_S           14 ILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIMQNPTHYKIPAWFLNRQNDIT   93 (146)
T ss_dssp             SBCCTTSCBCSSSCTTTTGGGSTTCCHHHHHHHHHHHTCCTTSCSSSCCHHHHHHHHHHHTCTTTTTCCSTTCTBCSCSS
T ss_pred             hhhhcCccCCCCcchHhhHhhhcCCCHHHHHHHHHHcCCCCCceeccCCHHHHHHHHHHHHhhcccCccHHHhhhhhccc
Confidence            8999999999999999999999999999999999999999999999999999999999995   3554            


Q ss_pred             --------chhhHHHHHHHHHHHHhhccccccccCCCCCcCCccccccccccC
Q psy8858          66 --------EGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRK  110 (121)
Q Consensus        66 --------~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRGQRT~tNart~k  110 (121)
                              |+||++++++||+||++|+||||+||.+|||||||||||||||.+
T Consensus        94 ~G~~~~lie~dL~~~~~~dI~RL~~I~~yRG~RH~~GLpVRGQrTkTnaR~g~  146 (146)
T 3u5c_S           94 DGKDYHTLANNVESKLRDDLERLKKIRAHRGIRHFWGLRVRGQHTKTTGRRRA  146 (146)
T ss_dssp             SCCCBCCCTHHHHHHHHHHHHHHHHHTCHHHHHHHTTCCCSCCCCSSSCCSCC
T ss_pred             ccchheeehHHHHHHHHHhhHHHHhhceeeeecccCCCCCCccCCCcCCCCCC
Confidence                    999999999999999999999999999999999999999999864

>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=100.00  E-value=1.5e-46  Score=269.02  Aligned_cols=100  Identities=46%  Similarity=0.734  Sum_probs=95.5

Q ss_pred             CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcccchhhHHHHHHHHHHH
Q psy8858           1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRL   80 (121)
Q Consensus         1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~i~~~L~~~~~~~I~rl   80 (121)
                      |+||+|||||++|.|.+||++|||||+.+|.+||+++|| |++++++|+|+|+++|.++          ++++.+||+||
T Consensus        46 m~RI~gvdlp~~K~v~~aLt~IyGIG~~~A~~I~~~~gI-~~~rv~~Lte~ei~~l~~~----------Rr~v~~nIkRL  114 (145)
T 3bbn_M           46 CIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNF-DNKVTKDLSEEEVIILRKE----------KRFNRVAIERL  114 (145)
T ss_dssp             -CCCSSSCCCCSSBTTTGGGGSTTCCSSTTTGGGTTTTC-CSCBTTSCCSSTTHHHHSS----------CCCCSTTTHHH
T ss_pred             eeeEeCcccCCCCEEEEeeeeecCccHHHHHHHHHHcCC-CceEcCCCCHHHHHHHHHH----------HHHHHHHHHHH
Confidence            899999999999999999999999999999999999999 7999999999999999876          66689999999


Q ss_pred             HhhccccccccCCCCCcCCccccccccccCC
Q psy8858          81 IDLSCYRGIRHRKSLPCRGQRTRTNARTRKG  111 (121)
Q Consensus        81 ~~i~~yRG~RH~~gLpVRGQRT~tNart~k~  111 (121)
                      ++|+||||+||.+|||||||||||||||+|+
T Consensus       115 ~~I~~YRGlRH~~GLPVRGQRTkTNaRTrKg  145 (145)
T 3bbn_M          115 KEIRCYRGIRHKLGLPVRGQRTKNNCRTLKG  145 (145)
T ss_dssp             HCCCCSCCTTTTTTCCSSSCCTTTCCCSSCC
T ss_pred             hhhceEeeeecccCCcCCCccCccccccCCC
Confidence            9999999999999999999999999999875

>1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae} SCOP: a.156.1.3 d.14.1.3 d.122.1.2 PDB: 1mx0_A* 1z5b_A* 1z5a_A* 1z59_A* 1z5c_A* 2hkj_A*

Probab=96.86  E-value=0.00093  Score=55.14  Aligned_cols=51  Identities=27%  Similarity=0.422  Sum_probs=45.7

Q ss_pred             eeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc
Q psy8858          14 HIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI   64 (121)
Q Consensus        14 ~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~   64 (121)
                      ...|...++.+||..+|.+||+.+|++|++++.+|+++|+..|.++|+++.
T Consensus       255 ~~~fl~~~f~~v~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  305 (471)
T 1mu5_A          255 IKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYE  305 (471)
T ss_dssp             HHHHHTTSSSSCCHHHHHHHHHHTTCCTTSBGGGCCTTHHHHHHHHHHHCC
T ss_pred             hHHhhhccccccCHHHHHHHHHhcCCCCCCChhhcCHHHHHHHHHHHHhcc
Confidence            344555789999999999999999999999999999999999999997664

>1k3x_A Endonuclease VIII; hydrolase/DNA, hydrolase-DNA complex; HET: BRU PED; 1.25A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1k3w_A* 1q39_A 2ea0_A* 2oq4_A* 1q3c_A 2opf_A* 1q3b_A*

Probab=96.73  E-value=0.0019  Score=49.45  Aligned_cols=50  Identities=22%  Similarity=0.262  Sum_probs=44.0

Q ss_pred             eeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh
Q psy8858          13 QHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK   62 (121)
Q Consensus        13 k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~   62 (121)
                      .+|.-+|   +-|-|||.-.|.++|-.+||+|...+++||++|++.|.+.+..
T Consensus       151 ~~Ik~~LLDQ~vvaGiGNiYadEiLf~a~I~P~~~a~~Ls~~~~~~L~~~i~~  203 (262)
T 1k3x_A          151 RQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLE  203 (262)
T ss_dssp             SCHHHHTTCTTTSBTCCHHHHHHHHHHHTCCSSCCGGGSCHHHHHHHHHHHHH
T ss_pred             ccHHHHHhcCCeeecccHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHH
Confidence            5566666   4569999999999999999999999999999999999998843

>1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken STR genomics/proteomics initiative, RSGI, structural genomics; 1.90A {Thermus thermophilus} SCOP: a.156.1.2 b.113.1.1 g.39.1.8

Probab=96.72  E-value=0.0019  Score=49.60  Aligned_cols=50  Identities=16%  Similarity=0.226  Sum_probs=44.1

Q ss_pred             Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      +.+|.-+|   +-|-|||.-.|.++|-.+||+|...+++|+++|++.|.+.+.
T Consensus       143 ~~~IK~~LlDQ~~vaGiGNiYa~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~  195 (266)
T 1ee8_A          143 ARPLKALLLDQRLAAGVGNIYADEALFRARLSPFRPARSLTEEEARRLYRALR  195 (266)
T ss_dssp             CSBHHHHHHHSSSSTTCCHHHHHHHHHHTTCCSSSBGGGCCHHHHHHHHHHHH
T ss_pred             CccHHHHHhccCccccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHH
Confidence            34555555   578999999999999999999999999999999999999884

>1k82_A Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8

Probab=96.71  E-value=0.002  Score=49.57  Aligned_cols=51  Identities=22%  Similarity=0.155  Sum_probs=44.7

Q ss_pred             Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh
Q psy8858          12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK   62 (121)
Q Consensus        12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~   62 (121)
                      +.+|.-+|   +-|-|||.-.|.++|-.+||+|...+++|+++|++.|.+.+..
T Consensus       150 ~~~IK~~LlDQ~~vaGiGNiYa~EiLf~a~I~P~~~a~~Ls~~~~~~L~~~i~~  203 (268)
T 1k82_A          150 KTAIKPWLMDNKLVVGVGNIYASESLFAAGIHPDRLASSLSLAECELLARVIKA  203 (268)
T ss_dssp             CSBHHHHHTCTTTCSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHH
T ss_pred             CCcHHHHHhcCCeeeccCchHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHHH
Confidence            44555566   5789999999999999999999999999999999999998843

>2xzf_A Formamidopyrimidine-DNA glycosylase; hydrolase-DNA complex; HET: VET; 1.80A {Lactococcus lactis subsp} PDB: 1pm5_A* 1xc8_A* 1pji_A* 2xzu_A* 3c58_A* 1tdz_A* 1nnj_A 1kfv_A 1pjj_A*

Probab=96.70  E-value=0.002  Score=49.58  Aligned_cols=51  Identities=22%  Similarity=0.314  Sum_probs=44.5

Q ss_pred             Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh
Q psy8858          12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK   62 (121)
Q Consensus        12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~   62 (121)
                      +.+|.-+|   +-|-|||.-.|.++|-.+||+|...+++|+++|++.|.+.+..
T Consensus       153 ~~~IK~~LLDQ~vvaGiGNiYadEiLf~a~I~P~~~a~~Ls~~~~~~L~~~i~~  206 (271)
T 2xzf_A          153 TKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSIIE  206 (271)
T ss_dssp             CSBHHHHHHTSSSSSCCCHHHHHHHHHHTTCCTTCBGGGCCHHHHHHHHHHHHH
T ss_pred             CccHHHHHhcCCeecccChhHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHH
Confidence            34555555   5689999999999999999999999999999999999998843

>3u6p_A Formamidopyrimidine-DNA glycosylase; DNA glycosylase, DNA repair, sequence context; HET: DNA 08Q; 1.60A {Geobacillus stearothermophilus} PDB: 3u6d_A* 3u6c_A* 3u6l_A* 3u6m_A* 3u6o_A* 3u6e_A* 3u6q_A* 3u6s_A* 3gp1_A* 3sbj_A* 2f5q_A* 2f5s_A* 3gq4_A* 3gpy_A* 2f5n_A 2f5o_A 2f5p_A 3sau_A* 3sar_A* 3sav_A* ...

Probab=96.69  E-value=0.0021  Score=49.60  Aligned_cols=51  Identities=22%  Similarity=0.279  Sum_probs=44.9

Q ss_pred             Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh
Q psy8858          12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK   62 (121)
Q Consensus        12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~   62 (121)
                      +.+|.-+|   +-|-|||.-.|.++|-.+||+|...+++|+++|++.|.+.+..
T Consensus       155 ~~~IK~~LlDQ~~vaGiGNiYa~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~  208 (273)
T 3u6p_A          155 KRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVA  208 (273)
T ss_dssp             CSBHHHHHHCTTTSTTCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHH
T ss_pred             cchHHHHHhcCCccccccHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence            45555556   5789999999999999999999999999999999999998843

>3w0f_A Endonuclease 8-like 3; helix two turns helix, zinc finger, DNA binding, hydrolase; 2.00A {Mus musculus}

Probab=96.63  E-value=0.0024  Score=49.84  Aligned_cols=52  Identities=15%  Similarity=0.183  Sum_probs=46.1

Q ss_pred             Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhc
Q psy8858          12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKF   63 (121)
Q Consensus        12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~   63 (121)
                      +.+|..+|   +-|-|||...+.++|-.+||+|...+++|+++|++.|.+.+...
T Consensus       174 ~~~IK~~LLDQ~viaGiGNIYa~EiLf~AgI~P~~~~~~Ls~~~~~~L~~ai~~V  228 (287)
T 3w0f_A          174 DRMLCDVLLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQACHLVKMTRDF  228 (287)
T ss_dssp             SSBHHHHHHCTTTSTTCCHHHHHHHHHHHTCCTTCBGGGSCHHHHHHHHHHHHHH
T ss_pred             cccHHHHHhcCCccccccHHHHHHHHHHccCCccCccccCCHHHHHHHHHHHHHH
Confidence            34566666   67899999999999999999999999999999999999999655

>3twl_A Formamidopyrimidine-DNA glycosylase 1; helix two turns helix, zinc-LESS finger, hydrolase, DNA DAMA repair, DNA-binding, glycosidase, lyase; 1.70A {Arabidopsis thaliana} PDB: 3twm_A* 3twk_A

Probab=96.56  E-value=0.0028  Score=49.81  Aligned_cols=50  Identities=24%  Similarity=0.238  Sum_probs=44.0

Q ss_pred             Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      +.+|.-+|   +-|-|||.-.|.++|-.+||+|...+++|+++|++.|.+.+.
T Consensus       168 ~~~IK~~LLDQ~vvaGIGNiYadEiLf~AgIhP~~~a~~Ls~~e~~~L~~~i~  220 (310)
T 3twl_A          168 KITIKPLLLDQGYISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIK  220 (310)
T ss_dssp             CSBHHHHHHCTTTSBSCCHHHHHHHHHHTTCCTTSBGGGCCHHHHHHHHHHHH
T ss_pred             cchHHHHHhcCccccCCcHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHH
Confidence            45565556   468999999999999999999999999999999999998884

>3vk8_A Probable formamidopyrimidine-DNA glycosylase; DNA glycosylase, hneil1 ortholog, DNA lesion, thymine glycol zincless finger; HET: DNA CTG; 2.00A {Acanthamoeba polyphaga mimivirus} PDB: 3vk7_A* 3a42_A 3a46_A* 3a45_A*

Probab=96.53  E-value=0.0027  Score=49.51  Aligned_cols=50  Identities=30%  Similarity=0.266  Sum_probs=43.9

Q ss_pred             Ceeeeeeh---hc-ccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          12 NQHIIIGL---TA-IYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        12 ~k~v~~aL---t~-I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      +.+|.-+|   +- |-|||...|.++|-.+||+|...+++|+++|++.|.+.+.
T Consensus       154 ~~~Ik~~LLDQ~~~vaGIGNiYa~EiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~  207 (295)
T 3vk8_A          154 KQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIK  207 (295)
T ss_dssp             CSBHHHHHHCSSSSCBCCCHHHHHHHHHHTTBCTTCBGGGCCHHHHHHHHHHHH
T ss_pred             CchHHHHHhcCCcccccccHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHH
Confidence            44555556   34 8999999999999999999999999999999999999884

>2zbk_B Type 2 DNA topoisomerase 6 subunit B; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae}

Probab=94.29  E-value=0.056  Score=45.21  Aligned_cols=50  Identities=28%  Similarity=0.381  Sum_probs=44.6

Q ss_pred             eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc
Q psy8858          15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI   64 (121)
Q Consensus        15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~   64 (121)
                      .-|.-..+-++|...|..+|+.+|++|+.++.+|+++|+..+.+++.+++
T Consensus       255 ~~fl~~~ft~~g~~~a~~~~~~~gl~~~~~~~~l~~~~~~~ll~a~~~~k  304 (530)
T 2zbk_B          255 KEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKDE  304 (530)
T ss_dssp             HHHHHTTSTTCCHHHHHHHHHHTTCCSSCBSSCCCHHHHHHHHHHHHHCC
T ss_pred             HhhhcCccccccHHHHHHHHHhhCCCCCCCcccCCHHHHHHHHHHHHhcc
Confidence            34555779999999999999999999999999999999999999996554

>3fut_A Dimethyladenosine transferase; methyltransferase, dimethyltransferase, dual-specific methyltransferase, 16S rRNA methyltransferase; 1.52A {Thermus thermophilus} PDB: 3fuu_A* 3fuv_A 3fuw_A* 3fux_A*

Probab=92.92  E-value=0.092  Score=40.04  Aligned_cols=49  Identities=16%  Similarity=0.356  Sum_probs=41.5

Q ss_pred             CCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858          11 NNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI   60 (121)
Q Consensus        11 ~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l   60 (121)
                      ..|.+..+|..+ |.+...+..+++.+||+|+.++.+|+.+|+..|.+.+
T Consensus       219 rrKtL~n~L~~~-~~~~~~~~~~l~~~~i~~~~R~e~Ls~~~f~~L~~~~  267 (271)
T 3fut_A          219 RRKTLLNALAAA-GYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGL  267 (271)
T ss_dssp             TTSCHHHHHHHT-TCCHHHHHHHHHHTTCCTTCCGGGCCHHHHHHHHHHH
T ss_pred             CCcHHHHHHHhh-cCCHHHHHHHHHHCCcCCCCChhhCCHHHHHHHHHHH
Confidence            456777778664 4567778899999999999999999999999998877

>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A*

Probab=92.88  E-value=0.064  Score=32.35  Aligned_cols=37  Identities=16%  Similarity=0.311  Sum_probs=30.6

Q ss_pred             ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858          18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL   56 (121)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L   56 (121)
                      .|.+|+|||+..+..+++.+|  .-..+.+.|.+|+..+
T Consensus         5 ~L~~IpGIG~kr~~~LL~~Fg--s~~~i~~As~eeL~~v   41 (63)
T 2a1j_A            5 FLLKMPGVNAKNCRSLMHHVK--NIAELAALSQDELTSI   41 (63)
T ss_dssp             HHHTSTTCCHHHHHHHHHHCS--SHHHHHTCCHHHHHHH
T ss_pred             HHHcCCCCCHHHHHHHHHHcC--CHHHHHHCCHHHHHHH
Confidence            578999999999999999988  2346677788888766

>1tdh_A NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS finger, hydrolase; 2.10A {Homo sapiens} SCOP: a.156.1.2 b.113.1.1 g.39.1.8

Probab=92.32  E-value=0.016  Score=46.55  Aligned_cols=40  Identities=23%  Similarity=0.235  Sum_probs=35.2

Q ss_pred             Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHH
Q psy8858          12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDN   51 (121)
Q Consensus        12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~   51 (121)
                      +.+|.-+|   +-|-|||...|.++|-.+||+|...+++|+++
T Consensus       158 ~~~IK~~LLDQ~vVAGIGNIYadEiLF~AgIhP~r~a~~Ls~~  200 (364)
T 1tdh_A          158 DRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEA  200 (364)
T ss_dssp             GSBHHHHTTCTTTSTTCCHHHHHHHHHHHTCCTTSBHHHHHGG
T ss_pred             cccHHHHHhcCCeeeccchHHHHHHHHHCcCCCCCChhhcCHH
Confidence            45566666   57899999999999999999999999999987

>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3

Probab=92.22  E-value=0.044  Score=33.97  Aligned_cols=33  Identities=18%  Similarity=0.257  Sum_probs=21.8

Q ss_pred             CccCCCCeeeeeehhcccccCHHHHHHHHHHhC
Q psy8858           6 GINIPNNQHIIIGLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus         6 ~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      |.-+..+......|..|+|||+.+|..|++.+|
T Consensus        13 ~~~~~~~~~~~~~L~~I~gIG~~~A~~Ll~~fg   45 (78)
T 1kft_A           13 GLVPRGSHMNTSSLETIEGVGPKRRQMLLKYMG   45 (78)
T ss_dssp             ----------CCGGGGCTTCSSSHHHHHHHHHS
T ss_pred             hHHHhHHHHHHHHHhcCCCCCHHHHHHHHHHcC
Confidence            345566777888999999999999999999986

>3arc_U Photosystem II 12 kDa extrinsic protein; PSII, membrane-protein complex, transmembrane alpha-helix, E transport, photosynthesis; HET: OEX CLA PHO BCR PL9 SQD LMG UNL LMT HTG DGD LHG HEM; 1.90A {Thermosynechococcus vulcanus} PDB: 3bz1_U* 2axt_U* 3bz2_U* 3kzi_U* 3prq_U* 3prr_U* 3a0b_U* 3a0h_U*

Probab=91.42  E-value=0.14  Score=33.71  Aligned_cols=58  Identities=21%  Similarity=0.264  Sum_probs=42.5

Q ss_pred             CCCeeeeeehhcccccCHHHHHHHHHHhCCCC---CcccCCCCHHHHHHHHHHHhhcccch
Q psy8858          10 PNNQHIIIGLTAIYGIGRSRAKKICEVTKIST---TKKIKDLNDNELEKLREEISKFIIEG   67 (121)
Q Consensus        10 ~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p---~~~~~~Ls~~qi~~L~~~l~~~~i~~   67 (121)
                      +-|..-.-.|+.++|||+.+|..|.+.=++..   -..+.-+.+..+++|..++..|.++.
T Consensus        19 diNtAs~~eL~~lpGIG~~~A~~IV~~GpF~s~edL~~V~Gig~~~~e~l~~~l~~f~v~~   79 (97)
T 3arc_U           19 DLNNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLEHFTVTE   79 (97)
T ss_dssp             ETTTSCGGGGGGSTTCTTHHHHHHHHHCCCSSGGGGGGCTTCCHHHHHHHHHTGGGEECCC
T ss_pred             eCCcCCHHHHhHCCCCCHHHHHHHHHcCCCCCHHHHHhccCCCHHHHHHHHHHhceeEecC
Confidence            33444456789999999999999999422221   22455678999999999998887743

>1qyr_A KSGA, high level kasugamycin resistance protein, S-adenosylMet; adenosine dimethyltransferase, rRNA modification, transferase, translation; 2.10A {Escherichia coli} SCOP: c.66.1.24 PDB: 4adv_V 3tpz_A

Probab=91.23  E-value=0.16  Score=38.17  Aligned_cols=45  Identities=7%  Similarity=0.165  Sum_probs=36.6

Q ss_pred             CCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          11 NNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        11 ~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      ..|.+..+|+.+++      ..++..+||+|+.++.+||.+|+-.|.+.+.
T Consensus       205 rrK~l~n~l~~~~~------~~~l~~~~i~~~~R~e~Ls~~~f~~l~~~~~  249 (252)
T 1qyr_A          205 RRKTIRNSLGNLFS------VEVLTGMGIDPAMRAENISVAQYCQMANYLA  249 (252)
T ss_dssp             TTSBHHHHTTTTCC------HHHHHHTTCCTTSBGGGSCHHHHHHHHHHHH
T ss_pred             CCcHHHHHHhhhhh------HHHHHHcCCCCCCChHHCCHHHHHHHHHHHH
Confidence            35667777766553      5578899999999999999999999998873

>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus}

Probab=89.24  E-value=0.32  Score=33.92  Aligned_cols=55  Identities=22%  Similarity=0.297  Sum_probs=39.8

Q ss_pred             CeeeeeehhcccccCHHHHHHHHHHhCC---CCCcccCCCCHHHHHHHHHHHhhcccc
Q psy8858          12 NQHIIIGLTAIYGIGRSRAKKICEVTKI---STTKKIKDLNDNELEKLREEISKFIIE   66 (121)
Q Consensus        12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi---~p~~~~~~Ls~~qi~~L~~~l~~~~i~   66 (121)
                      |..=.-.|+.++|||+.+|..|.+--.+   +.-..+.-+++.+.+.|.+...+|.+.
T Consensus        58 NtA~~~eL~~LpGiGp~~A~~II~~GpF~svedL~~V~GIg~k~~e~l~~~~~~~tv~  115 (134)
T 1s5l_U           58 NNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLEHFTVT  115 (134)
T ss_dssp             TTSCGGGGGGSTTCTHHHHHHHHHTCCCSSGGGGGGCTTCCHHHHHHHHHHHTTEECC
T ss_pred             cccCHHHHHHCCCCCHHHHHHHHHcCCCCCHHHHHhCCCCCHHHHHHHHHhhcceeec
Confidence            3444556889999999999999953222   223356667899999999988777663

>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A*

Probab=89.23  E-value=0.17  Score=32.36  Aligned_cols=40  Identities=15%  Similarity=0.192  Sum_probs=30.6

Q ss_pred             eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858          15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL   56 (121)
Q Consensus        15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L   56 (121)
                      ....|..|+|||+..+..|++.+|=  -..+.+.|.+|+..+
T Consensus        16 ~~s~L~~IpGIG~kr~~~LL~~FgS--l~~i~~AS~eEL~~v   55 (84)
T 1z00_B           16 PQDFLLKMPGVNAKNCRSLMHHVKN--IAELAALSQDELTSI   55 (84)
T ss_dssp             HHHHHHTCSSCCHHHHHHHHHHSSC--HHHHHHSCHHHHHHH
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHcCC--HHHHHHCCHHHHHHH
Confidence            3456889999999999999998872  235666677777655

>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5

Probab=87.70  E-value=0.19  Score=31.74  Aligned_cols=25  Identities=8%  Similarity=0.201  Sum_probs=22.0

Q ss_pred             eeeeehhcccccCHHHHHHHHHHhC
Q psy8858          14 HIIIGLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus        14 ~v~~aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      .+..+|..|+|||+.+|..|++.+|
T Consensus        16 ~~~~~L~~IpgIG~~~A~~Ll~~fg   40 (89)
T 1z00_A           16 RVTECLTTVKSVNKTDSQTLLTTFG   40 (89)
T ss_dssp             HHHHHHTTSSSCCHHHHHHHHHHTC
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHCC
Confidence            3456789999999999999999886

>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5

Probab=87.44  E-value=0.2  Score=31.85  Aligned_cols=25  Identities=8%  Similarity=0.201  Sum_probs=22.1

Q ss_pred             eeeeehhcccccCHHHHHHHHHHhC
Q psy8858          14 HIIIGLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus        14 ~v~~aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      .+..+|..|.|||+.+|..|++.+|
T Consensus        29 ~~~~~L~~IpgIG~~~A~~Ll~~fg   53 (91)
T 2a1j_B           29 RVTECLTTVKSVNKTDSQTLLTTFG   53 (91)
T ss_dssp             HHHHHHTTSTTCCHHHHHHHHHHHS
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHCC
Confidence            3557899999999999999999987

>3ftd_A Dimethyladenosine transferase; KSGA, rossmann-like fold, RNA methyltransferase, mtase, anti resistance, methyltransferase, RNA-binding; 1.44A {Aquifex aeolicus} PDB: 3ftc_A 3fte_A 3ftf_A* 3r9x_B*

Probab=86.44  E-value=0.48  Score=35.27  Aligned_cols=40  Identities=13%  Similarity=0.165  Sum_probs=33.0

Q ss_pred             CeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      .|.+..+|..+          .+..+||+|+.++.+|+.+|+..|.+.+.
T Consensus       206 rk~l~~~l~~~----------~l~~~~i~~~~r~e~l~~~~f~~l~~~~~  245 (249)
T 3ftd_A          206 RKVLRKKIPEE----------LLKEAGINPDARVEQLSLEDFFKLYRLIE  245 (249)
T ss_dssp             TSCGGGTSCHH----------HHHHTTCCTTCCGGGCCHHHHHHHHHHHH
T ss_pred             ChhHHHHHHHH----------HHHHCCCCCCCChhhCCHHHHHHHHHHHH
Confidence            45566666553          68899999999999999999999998873

>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase; 2.00A {Methanocaldococcus jannaschii} PDB: 3knt_A*

Probab=86.29  E-value=1.3  Score=32.69  Aligned_cols=25  Identities=24%  Similarity=0.127  Sum_probs=20.6

Q ss_pred             eeeehh-cccccCHHHHHHHHHHhCC
Q psy8858          15 IIIGLT-AIYGIGRSRAKKICEVTKI   39 (121)
Q Consensus        15 v~~aLt-~I~GIG~~~A~~Ic~~lGi   39 (121)
                      ..-.|. +++|||+.+|..|+..+|.
T Consensus       122 ~re~Ll~~LpGVG~KTA~~vL~~~g~  147 (214)
T 3fhf_A          122 AREFLVRNIKGIGYKEASHFLRNVGY  147 (214)
T ss_dssp             HHHHHHHHSTTCCHHHHHHHHHHTTC
T ss_pred             HHHHHHHhCCCCCHHHHHHHHHHcCC
Confidence            334577 9999999999999987776

>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus} SCOP: a.60.2.7

Probab=86.08  E-value=0.58  Score=28.47  Aligned_cols=27  Identities=33%  Similarity=0.397  Sum_probs=21.5

Q ss_pred             CeeeeeehhcccccCHHHHHHHHHHhC
Q psy8858          12 NQHIIIGLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus        12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      |..-...|..++|||+.+|..|.+...
T Consensus        22 N~a~~~~L~~ipGIG~~~A~~Il~~r~   48 (75)
T 2duy_A           22 NEASLEELMALPGIGPVLARRIVEGRP   48 (75)
T ss_dssp             TTCCHHHHTTSTTCCHHHHHHHHHTCC
T ss_pred             hhCCHHHHHhCCCCCHHHHHHHHHHcc
Confidence            333445688999999999999999763

>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus}

Probab=86.03  E-value=0.56  Score=34.23  Aligned_cols=25  Identities=24%  Similarity=0.169  Sum_probs=21.2

Q ss_pred             eeeehhcccccCHHHHHHHHHHhCC
Q psy8858          15 IIIGLTAIYGIGRSRAKKICEVTKI   39 (121)
Q Consensus        15 v~~aLt~I~GIG~~~A~~Ic~~lGi   39 (121)
                      ..-.|.+++|||+.+|..||..+|.
T Consensus       115 ~~~~L~~lpGIG~kTA~~il~~~~~  139 (207)
T 3fhg_A          115 ARERLLNIKGIGMQEASHFLRNVGY  139 (207)
T ss_dssp             HHHHHTTSTTCCHHHHHHHHHHTTC
T ss_pred             HHHHHHcCCCcCHHHHHHHHHHhCC
Confidence            4556889999999999999987676

>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5

Probab=85.80  E-value=0.29  Score=29.35  Aligned_cols=26  Identities=4%  Similarity=0.054  Sum_probs=22.2

Q ss_pred             eeeeeehhcccccCHHHHHHHHHHhC
Q psy8858          13 QHIIIGLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus        13 k~v~~aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      .....+|+.|+|||..+|..|++.+|
T Consensus        10 ~~~~~~L~~i~giG~~~a~~Ll~~fg   35 (75)
T 1x2i_A           10 ERQRLIVEGLPHVSATLARRLLKHFG   35 (75)
T ss_dssp             HHHHHHHTTSTTCCHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHcC
Confidence            34566789999999999999999876

>3uzu_A Ribosomal RNA small subunit methyltransferase A; ssgcid, seattle structural genomics center for infectio disease; 1.75A {Burkholderia pseudomallei}

Probab=85.77  E-value=0.15  Score=38.85  Aligned_cols=45  Identities=7%  Similarity=0.118  Sum_probs=35.9

Q ss_pred             CCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          11 NNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        11 ~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      ..|.+..+|..+++      ..++..+||+|+.++.+||.+|+..|.+++.
T Consensus       229 rrK~l~n~L~~~~~------~~~l~~~~i~~~~R~e~Ls~~~f~~L~~~~~  273 (279)
T 3uzu_A          229 RRKMLRNTLGGYRD------LVDFDALGFDLARRAEDIGVDEYVRVAQAVA  273 (279)
T ss_dssp             TTSBHHHHTGGGTT------TCCTTTTTCCTTSBGGGCCHHHHHHHHHHHH
T ss_pred             cChHHHHHHHhhcC------HHHHHHCCcCCCCCceeCCHHHHHHHHHHHH
Confidence            35666677766544      3467889999999999999999999999873

>3tqs_A Ribosomal RNA small subunit methyltransferase A; protein synthesis; 1.98A {Coxiella burnetii} SCOP: c.66.1.0

Probab=83.85  E-value=0.28  Score=36.84  Aligned_cols=43  Identities=9%  Similarity=0.165  Sum_probs=33.7

Q ss_pred             CeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858          12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI   60 (121)
Q Consensus        12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l   60 (121)
                      .|.+..+|..+++      ...++.+||+|+.++.+||.+|+..|.+++
T Consensus       212 rK~l~~~L~~~~~------~~~l~~~~i~~~~R~e~Ls~~~f~~L~~~~  254 (255)
T 3tqs_A          212 RKTVGNALKKLIN------PSQWPLLEINPQLRPQELTVEDFVKISNIL  254 (255)
T ss_dssp             TSCHHHHTTTTCC------GGGTGGGTCCTTSCGGGSCHHHHHHHHHHH
T ss_pred             ChHHHHHHhhhCC------HHHHHHCCcCCCCCceeCCHHHHHHHHHHh
Confidence            4566666766543      134688999999999999999999998875

>3gru_A Dimethyladenosine transferase; rossman fold, ribosomal assem adenosyl-L-methionine, rRNA, methyltransferase, RNA-binding processing; HET: AMP; 1.60A {Methanocaldococcus jannaschii} PDB: 3grr_A* 3grv_A* 3gry_A* 3fyd_A 3fyc_A*

Probab=81.41  E-value=0.55  Score=36.10  Aligned_cols=51  Identities=22%  Similarity=0.262  Sum_probs=42.3

Q ss_pred             CCeeeeeehhccc---ccCHHHHHHHHHHh-----CCCC--CcccCCCCHHHHHHHHHHHh
Q psy8858          11 NNQHIIIGLTAIY---GIGRSRAKKICEVT-----KIST--TKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        11 ~~k~v~~aLt~I~---GIG~~~A~~Ic~~l-----Gi~p--~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      ..|.+..+|.+..   |+....+..+++.+     |+++  +.++.+||.+|+..|.+++.
T Consensus       226 rrK~l~n~L~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~R~e~Ls~~~f~~L~~~~~  286 (295)
T 3gru_A          226 RNKSVRKALIDSSKELNYNKDEMKKILEDFLNTNSEIKNLINEKVFKLSVKDIVNLSNEFY  286 (295)
T ss_dssp             TTSBHHHHHHHTGGGGTCCHHHHHHHHHHHHTTCHHHHHHHTSBGGGSCHHHHHHHHHHHH
T ss_pred             CchHHHHHHhhhhccccCCHHHHHHHHHHhhhcccCCCccccCChhhCCHHHHHHHHHHHH
Confidence            4677888887653   45577788889998     8998  99999999999999999883

>3vdp_A Recombination protein RECR; zinc finger, DNA repair, DNA binding; 2.45A {Thermoanaerobacter tengcongensis} PDB: 3vdu_A 3ve5_D

Probab=81.10  E-value=1.9  Score=32.08  Aligned_cols=72  Identities=22%  Similarity=0.373  Sum_probs=48.2

Q ss_pred             eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc-----------c-ch-------hhHH----
Q psy8858          15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI-----------I-EG-------DLRR----   71 (121)
Q Consensus        15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~-----------i-~~-------~L~~----   71 (121)
                      +.-+|++++|||+++|..+.-.+=        .-+++++..|.++|.+..           + +.       |=++    
T Consensus        24 LI~~l~~LPGIG~KsA~RlA~hLL--------~~~~~~~~~La~al~~~~~~i~~C~~C~nlte~~~C~IC~d~~Rd~~~   95 (212)
T 3vdp_A           24 LIEELSKLPGIGPKTAQRLAFFII--------NMPLDEVRSLSQAIIEAKEKLRYCKICFNITDKEVCDICSDENRDHST   95 (212)
T ss_dssp             HHHHHHTSTTCCHHHHHHHHHHHT--------TSCHHHHHHHHHHHHHHHHHCEECTTTCCEESSSSCHHHHCTTSEEEE
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHHHHHhCCcCCCCCCCCCCCcCCCCCCCCCCCCE
Confidence            445789999999999999985442        335788888888883321           0 00       0000    


Q ss_pred             ----HHHHHHHHHHhhccccccccCCC
Q psy8858          72 ----EFSMNIKRLIDLSCYRGIRHRKS   94 (121)
Q Consensus        72 ----~~~~~I~rl~~i~~yRG~RH~~g   94 (121)
                          +--.|+.-+-+.+.|+|.=|-+|
T Consensus        96 iCVVE~~~Dv~aiE~t~~y~G~YhVLg  122 (212)
T 3vdp_A           96 ICVVSHPMDVVAMEKVKEYKGVYHVLH  122 (212)
T ss_dssp             EEEESSHHHHHHHHTTSCCCEEEEECS
T ss_pred             EEEECCHHHHHHHHhhCccceEEEecC
Confidence                01235666778899999999887

>3v76_A Flavoprotein; structural genomics, PSI-biology, NEW YORK structural genomi research consortium, nysgrc; HET: FDA; 2.51A {Sinorhizobium meliloti}

Probab=80.76  E-value=1.8  Score=34.41  Aligned_cols=51  Identities=22%  Similarity=0.351  Sum_probs=40.9

Q ss_pred             CeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhccc
Q psy8858          12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFII   65 (121)
Q Consensus        12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~i   65 (121)
                      ++.+...|..  .+....+..+++.+++ +++++.+|+++++..|.+.|+.+.+
T Consensus       299 ~~~~~~~l~~--~lp~~~~~~~~~~~~~-~~~~~~~~~~~~~~~l~~~l~~~~~  349 (417)
T 3v76_A          299 RQAVQTALAD--ILPRRLAQFFADEAKL-TGRMLADLSDKTIDALASSIQVWAV  349 (417)
T ss_dssp             SSBHHHHHTT--TSCHHHHHHHHHHTTC-TTCBGGGCCHHHHHHHHHHHHSEEE
T ss_pred             hhhHHHHHHH--HhhHHHHHHHHHhcCC-CCCchhhCCHHHHHHHHHHhcCCEE
Confidence            3444444443  3778899999999999 9999999999999999999977653

>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7

Probab=80.16  E-value=2.6  Score=26.93  Aligned_cols=21  Identities=24%  Similarity=0.278  Sum_probs=18.7

Q ss_pred             eehhcccccCHHHHHHHHHHh
Q psy8858          17 IGLTAIYGIGRSRAKKICEVT   37 (121)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~l   37 (121)
                      ..|..|+|||...|..|++..
T Consensus        40 ~~L~~ipGIG~~~A~~Il~~r   60 (98)
T 2edu_A           40 RDLRSLQRIGPKKAQLIVGWR   60 (98)
T ss_dssp             HHHHHSTTCCHHHHHHHHHHH
T ss_pred             HHHHHCCCCCHHHHHHHHHHH
Confidence            357899999999999999886

>3n0u_A Probable N-glycosylase/DNA lyase; structural genomics, ISFI, DNA repair, 8-oxoguanine, base EX repair, PSI-2, protein structure initiative; 1.50A {Thermotoga maritima}

Probab=80.07  E-value=1  Score=33.39  Aligned_cols=25  Identities=24%  Similarity=0.163  Sum_probs=20.6

Q ss_pred             eeehh-cccccCHHHHHHHHHHhCCC
Q psy8858          16 IIGLT-AIYGIGRSRAKKICEVTKIS   40 (121)
Q Consensus        16 ~~aLt-~I~GIG~~~A~~Ic~~lGi~   40 (121)
                      .-.|. +++|||+.+|..+|..+|..
T Consensus       128 r~~L~~~l~GVG~kTA~~vL~~~g~~  153 (219)
T 3n0u_A          128 REFLVRNAKGIGWKEASHFLRNTGVE  153 (219)
T ss_dssp             HHHHHHHSTTCCHHHHHHHHHTTTCC
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHcCCC
Confidence            34577 99999999999999767763

---

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	121
d2gy9m1	114	a.156.1.1 (M:1-114) Ribosomal protein S13 {Escheri	6e-44
d2uubm1	125	a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus	4e-40
d2hkja1	78	a.156.1.3 (A:229-306) Topoisomerase VI-B subunit m	0.003

>d2gy9m1 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia coli [TaxId: 562]} Length = 114

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Ribosomal protein S13
domain: Ribosomal protein S13
species: Escherichia coli [TaxId: 562]

 Score =  137 bits (346), Expect = 6e-44
 Identities = 66/112 (58%), Positives = 93/112 (83%)

Query: 3   RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK 62
           RI GINIP+++H +I LT+IYG+G++R+K I     I+   KI +L++ +++ LR+E++K
Sbjct: 2   RIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAK 61

Query: 63  FIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114
           F++EGDLRRE SM+IKRL+DL CYRG+RHR+ LP RGQRT+TNARTRKGPR+
Sbjct: 62  FVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK 113

>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus thermophilus [TaxId: 274]} Length = 125

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Ribosomal protein S13
domain: Ribosomal protein S13
species: Thermus thermophilus [TaxId: 274]

 Score =  128 bits (322), Expect = 4e-40
 Identities = 63/120 (52%), Positives = 87/120 (72%), Gaps = 1/120 (0%)

Query: 3   RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREE-IS 61
           RI G+ IP N+ + + LT IYGIG++RAK+  E T I+   ++KDL + E+ +LRE   +
Sbjct: 2   RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVEN 61

Query: 62  KFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLRK 121
            + +EG+LR E + NIKRL+D+ CYRG+RHR+ LP RGQRTRTNARTRKGPR+     +K
Sbjct: 62  TWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKK 121

>d2hkja1 a.156.1.3 (A:229-306) Topoisomerase VI-B subunit middle domain {Archaeon Sulfolobus shibatae [TaxId: 2286]} Length = 78

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Topoisomerase VI-B subunit middle domain
domain: Topoisomerase VI-B subunit middle domain
species: Archaeon Sulfolobus shibatae [TaxId: 2286]

 Score = 32.1 bits (73), Expect = 0.003
 Identities = 14/41 (34%), Positives = 23/41 (56%)

Query: 24 GIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI 64
           IG + A KI E+  +   KK+K+L + E+ +L E   K+ 
Sbjct: 36 SIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYE 76

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	121
d2uubm1	125	Ribosomal protein S13 {Thermus thermophilus [TaxId	100.0
d2gy9m1	114	Ribosomal protein S13 {Escherichia coli [TaxId: 56	100.0
d2hkja1	78	Topoisomerase VI-B subunit middle domain {Archaeon	98.63
d1k3xa1	89	Endonuclease VIII {Escherichia coli [TaxId: 562]}	97.95
d1r2za1	94	DNA repair protein MutM (Fpg) {Bacillus stearother	97.85
d1ee8a1	89	DNA repair protein MutM (Fpg) {Thermus thermophilu	97.85
d1k82a1	88	DNA repair protein MutM (Fpg) {Escherichia coli [T	97.85
d1tdza1	88	DNA repair protein MutM (Fpg) {Lactococcus lactis	97.82
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	95.47
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	95.43
d2i0za2	169	Flavoprotein BC4706 {Bacillus cereus [TaxId: 1396]	95.41
d2fmpa2	57	DNA polymerase beta {Human (Homo sapiens) [TaxId:	95.38
d2bcqa2	57	DNA polymerase lambda {Human (Homo sapiens) [TaxId	95.34
d1tdha1	115	Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapi	95.34
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	95.08
d1jmsa3	60	Terminal deoxynucleotidyl transferase {Mouse (Mus	95.01
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	93.83
d2gqfa2	148	Hypothetical protein HI0933 {Haemophilus influenza	93.83
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	93.14
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	92.99
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	92.9
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	92.78
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	92.21
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	92.14
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	90.5
d1qyra_	252	High level kasugamycin resistance protein KsgA {Es	89.57
d1vdda_	199	Recombination protein RecR {Deinococcus radioduran	87.78
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	86.14
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	83.93
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	83.93
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	81.54

>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Ribosomal protein S13
domain: Ribosomal protein S13
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=4.6e-54  Score=301.32  Aligned_cols=120  Identities=53%  Similarity=0.931  Sum_probs=116.7

Q ss_pred             ceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH-hhcccchhhHHHHHHHHHHH
Q psy8858           2 TRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI-SKFIIEGDLRREFSMNIKRL   80 (121)
Q Consensus         2 v~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l-~~~~i~~~L~~~~~~~I~rl   80 (121)
                      .||+|+|||++|+|.+||++|||||+++|.+||+.+||||++++++||++|++.|.+++ ++|.+|+||++.+.+||+||
T Consensus         1 aRI~g~di~~~K~v~~ALt~I~GIG~~~A~~Ic~~lgId~~~k~~~Lt~~qi~~I~~~i~~~~~i~~~L~~~~~~dIkrl   80 (125)
T d2uubm1           1 ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRL   80 (125)
T ss_dssp             CCCSTTCCCCSSBHHHHHTTSTTCCHHHHHHHHHTTTCCTTSBGGGCCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHHH
T ss_pred             CcccCccCCCCCEEEEeeeeeeCcCHHHHHHHHHHcCCCcccccccccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHH
Confidence            48999999999999999999999999999999999999999999999999999999999 57999999999999999999


Q ss_pred             HhhccccccccCCCCCcCCccccccccccCCCCcccccccC
Q psy8858          81 IDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLRK  121 (121)
Q Consensus        81 ~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~~  121 (121)
                      ++|+||||+||.+|||||||||||||||+|+.+++|+++|+
T Consensus        81 ~~i~~yRG~RH~~gLpvRGQRT~tN~rt~kg~~~~v~~kk~  121 (125)
T d2uubm1          81 MDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKK  121 (125)
T ss_dssp             HHTTCHHHHHHHHTCCSSSCCCSSCCHHHHCSCCCCCCCSS
T ss_pred             HHhhhhhhhhhcCCCCCCCCCCCCCccccCCCccccccccC
Confidence            99999999999999999999999999999999999998875

>d2gy9m1 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Ribosomal protein S13
domain: Ribosomal protein S13
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1.8e-53  Score=294.17  Aligned_cols=114  Identities=58%  Similarity=1.077  Sum_probs=111.5

Q ss_pred             ceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcccchhhHHHHHHHHHHHH
Q psy8858           2 TRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLI   81 (121)
Q Consensus         2 v~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~i~~~L~~~~~~~I~rl~   81 (121)
                      .||+|+|||++|+|.+||++|||||+.+|.+||+.+||||++++++||++|++.|.+++.+|.+++||++.+++||+||+
T Consensus         1 aRI~g~dip~~K~v~~ALt~I~GIG~~~A~~Ic~~lgid~~~kv~~Lt~~qi~~l~~~i~~~~i~~~L~~~~~~dI~rl~   80 (114)
T d2gy9m1           1 ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKRLM   80 (114)
T ss_dssp             CCCSSSCCCCSSBHHHHHTTSSSCCHHHHHHHHHHHTCCTTSBTTSCCHHHHHHHHHHHHSSCCSHHHHHHHHHHHHHTT
T ss_pred             CcccCccCCCCCEEEEEeeeeeCcCHHHHHHHHHHcCCCcccccCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHH
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccccccCCCCCcCCccccccccccCCCCcc
Q psy8858          82 DLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRA  115 (121)
Q Consensus        82 ~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~  115 (121)
                      +|+||||+||.+|||||||||||||||+|+++++
T Consensus        81 ~I~~yrG~RH~~gLpvRGQrT~tNart~k~~~k~  114 (114)
T d2gy9m1          81 DLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKP  114 (114)
T ss_dssp             TTTCHHHHHHHCCSCCCCCCSSSSCHHHHCSCCC
T ss_pred             HhccceeeeccCCCCCCCCCCCCCccccCCCCCC
Confidence            9999999999999999999999999999988763

>d2hkja1 a.156.1.3 (A:229-306) Topoisomerase VI-B subunit middle domain {Archaeon Sulfolobus shibatae [TaxId: 2286]}

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Topoisomerase VI-B subunit middle domain
domain: Topoisomerase VI-B subunit middle domain
species: Archaeon Sulfolobus shibatae [TaxId: 2286]

Probab=98.63  E-value=2.2e-08  Score=62.59  Aligned_cols=44  Identities=32%  Similarity=0.574  Sum_probs=41.9

Q ss_pred             hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhc
Q psy8858          20 TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKF   63 (121)
Q Consensus        20 t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~   63 (121)
                      +.|.|||...|.+||..+||+|++++++|+++|++.|.+.+++|
T Consensus        32 ~~f~GvGn~~a~Eil~~agi~P~~~~~~L~~~e~~~L~~air~~   75 (78)
T d2hkja1          32 NEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKY   75 (78)
T ss_dssp             HHSSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHHC
T ss_pred             HHhcccCHHHHHHHHHHhCCCcccccccCCHHHHHHHHHHHhhh
Confidence            67889999999999999999999999999999999999999765

>d1k3xa1 a.156.1.2 (A:125-213) Endonuclease VIII {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Middle domain of MutM-like DNA repair proteins
domain: Endonuclease VIII
species: Escherichia coli [TaxId: 562]

Probab=97.95  E-value=4.4e-06  Score=53.05  Aligned_cols=51  Identities=24%  Similarity=0.276  Sum_probs=45.1

Q ss_pred             CCeeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          11 NNQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        11 ~~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      .+++|.-+|   +-+.|||...+.+||-.++|+|..++++|+++|++.|.+.+.
T Consensus        25 ~~~~Ik~~LlDQ~~~aGIGN~~~~EiL~~a~i~P~~~~~~L~~~~~~~L~~~~~   78 (89)
T d1k3xa1          25 RNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALL   78 (89)
T ss_dssp             TTSCHHHHTTCTTTSBTCCHHHHHHHHHHHTCCSSCCGGGSCHHHHHHHHHHHH
T ss_pred             ccchHHHHHhcCccccccCcHHHHHHHHHhcccccCchhhCCHHHHHHHHHHHH
Confidence            345666666   578999999999999999999999999999999999998873

>d1r2za1 a.156.1.2 (A:135-228) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Middle domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.85  E-value=8.6e-06  Score=52.30  Aligned_cols=51  Identities=22%  Similarity=0.285  Sum_probs=45.2

Q ss_pred             CCeeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          11 NNQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        11 ~~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      .+.+|.-+|   +-+-|||...+.+||-.++|+|..++.+|+++|+..|.+.+.
T Consensus        21 ~~~~ik~~LlDQ~~~aGiGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~L~~~~~   74 (94)
T d1r2za1          21 TKRSVKALLLDQTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMV   74 (94)
T ss_dssp             CCSBHHHHHHCTTTSSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHH
T ss_pred             CCccHHHHHHhccccCCcccHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHH
Confidence            455666666   678999999999999999999999999999999999998873

>d1ee8a1 a.156.1.2 (A:122-210) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Middle domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Thermus thermophilus [TaxId: 274]

Probab=97.85  E-value=1.1e-05  Score=51.24  Aligned_cols=49  Identities=16%  Similarity=0.232  Sum_probs=42.9

Q ss_pred             eeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          13 QHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        13 k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      .+|.-+|   +-|.|||...+.+||-.+||+|..++++|+++|++.|.+.+.
T Consensus        23 ~~ik~~LlDQ~~iaGiGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~L~~~i~   74 (89)
T d1ee8a1          23 RPLKALLLDQRLAAGVGNIYADEALFRARLSPFRPARSLTEEEARRLYRALR   74 (89)
T ss_dssp             SBHHHHHHHSSSSTTCCHHHHHHHHHHTTCCSSSBGGGCCHHHHHHHHHHHH
T ss_pred             CcHHHHHHhccccCCCCcHHHHHHHHHHHcCccchhhhCCHHHHHHHHHHHH
Confidence            4444444   578999999999999999999999999999999999999884

>d1k82a1 a.156.1.2 (A:129-216) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Middle domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Escherichia coli [TaxId: 562]

Probab=97.85  E-value=1.2e-05  Score=51.09  Aligned_cols=50  Identities=22%  Similarity=0.161  Sum_probs=44.0

Q ss_pred             Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      +.+|.-+|   +-|-|||...+.+||-.+||+|..++++|+++|+..|.+.+.
T Consensus        22 ~~~ik~~LlDQ~~iaGiGN~y~~EiLf~a~I~P~~~~~~L~~~~~~~L~~~i~   74 (88)
T d1k82a1          22 KTAIKPWLMDNKLVVGVGNIYASESLFAAGIHPDRLASSLSLAECELLARVIK   74 (88)
T ss_dssp             CSBHHHHHTCTTTCSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHH
T ss_pred             CchHHHHHHccccccccchHHHHHHHHHHCCCccChHHHCCHHHHHHHHHHHH
Confidence            44555555   578999999999999999999999999999999999999884

>d1tdza1 a.156.1.2 (A:132-219) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]}

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Middle domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Lactococcus lactis [TaxId: 1358]

Probab=97.82  E-value=1.3e-05  Score=50.90  Aligned_cols=50  Identities=22%  Similarity=0.312  Sum_probs=43.5

Q ss_pred             Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      ++.|.-+|   +-|.|||...+.+||-.++|+|..++.+|+++|+..|.+.+.
T Consensus        22 ~~~ik~~LldQ~~iaGIGNiy~~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~   74 (88)
T d1tdza1          22 TKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSII   74 (88)
T ss_dssp             CSBHHHHHHTSSSSSCCCHHHHHHHHHHTTCCTTCBGGGCCHHHHHHHHHHHH
T ss_pred             cccHHHHHHhccccCCcChHHHHHHHHHHHcCccchhhHcCHHHHHHHHHHHH
Confidence            34455455   578999999999999999999999999999999999998874

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Aeropyrum pernix [TaxId: 56636]

Probab=95.47  E-value=0.0029  Score=37.60  Aligned_cols=38  Identities=29%  Similarity=0.364  Sum_probs=27.2

Q ss_pred             eeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHH
Q psy8858          16 IIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEK   55 (121)
Q Consensus        16 ~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~   55 (121)
                      .++|+.|+|||+.+|..|++.+| + -..+..-+.+|+..
T Consensus        12 ~~~L~~IpgIG~~~a~~L~~~F~-s-~~~l~~As~eeL~~   49 (70)
T d2bgwa1          12 LYILQSFPGIGRRTAERILERFG-S-LERFFTASKAEISK   49 (70)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHHHS-S-HHHHTTCCHHHHHH
T ss_pred             HHHHcCCCCcCHHHHHHHHHHhC-C-HHHHHHcCHHHHHc
Confidence            35789999999999999999988 2 23344445555443

>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.43  E-value=0.0052  Score=35.63  Aligned_cols=39  Identities=23%  Similarity=0.332  Sum_probs=30.4

Q ss_pred             ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHH
Q psy8858          18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLR   57 (121)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~   57 (121)
                      +|.+|+|||+.+|..+.+. |+..-..+-+.+++|+..+.
T Consensus         2 ~L~~i~GIG~~~a~~L~~~-g~~sv~~l~~a~~~eL~~i~   40 (61)
T d1pzna1           2 SIEDLPGVGPATAEKLREA-GYDTLEAIAVASPIELKEVA   40 (61)
T ss_dssp             CSSCCTTCCHHHHHHHHTT-TCCSHHHHHTCCHHHHHHHH
T ss_pred             ccccCCCCCHHHHHHHHHh-cCCCHHHHHhCCHHHHHHCC
Confidence            6889999999999999866 66666667777777776543

>d2i0za2 e.74.1.1 (A:193-361) Flavoprotein BC4706 {Bacillus cereus [TaxId: 1396]}

class: Multi-domain proteins (alpha and beta)
fold: HI0933 insert domain-like
superfamily: HI0933 insert domain-like
family: HI0933 insert domain-like
domain: Flavoprotein BC4706
species: Bacillus cereus [TaxId: 1396]

Probab=95.41  E-value=0.011  Score=40.26  Aligned_cols=53  Identities=11%  Similarity=0.164  Sum_probs=43.9

Q ss_pred             CCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhccc
Q psy8858          11 NNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFII   65 (121)
Q Consensus        11 ~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~i   65 (121)
                      +++.+...|..  -+....+..+|+.+|+++++++.+|+++++.+|.+.|++|.+
T Consensus       103 ~~~~~~~~l~~--~lp~~l~~~ll~~~~i~~~~~~~~ls~~~~~~L~~~Lk~~~l  155 (169)
T d2i0za2         103 PKKGIKNVLKG--YVPERYFLFLLEKNEIDGSEQAGQVSHEKIRALVKDFKEFTV  155 (169)
T ss_dssp             TTSBHHHHTTT--SSCHHHHHHHHHHTTCCTTSBGGGSCHHHHHHHHHHHHHEEE
T ss_pred             cchhHhhhccc--ccchHHHHHHHHHcCCcccCCHHHCCHHHHHHHHHHHhCCEe
Confidence            44455555544  377899999999999999999999999999999999987754

>d2fmpa2 a.60.12.1 (A:92-148) DNA polymerase beta {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: DNA polymerase beta
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.38  E-value=0.0034  Score=36.45  Aligned_cols=23  Identities=39%  Similarity=0.437  Sum_probs=19.9

Q ss_pred             eehhcccccCHHHHHHHHHHhCCC
Q psy8858          17 IGLTAIYGIGRSRAKKICEVTKIS   40 (121)
Q Consensus        17 ~aLt~I~GIG~~~A~~Ic~~lGi~   40 (121)
                      -.|++|||||+.+|..+.+. |+.
T Consensus         7 ~~l~~I~GvGp~~A~~l~~~-Gi~   29 (57)
T d2fmpa2           7 NFLTRVSGIGPSAARKFVDE-GIK   29 (57)
T ss_dssp             HHHTTSTTCCHHHHHHHHHT-TCC
T ss_pred             HHHhccccccHHHHHHHHHh-CCC
Confidence            35799999999999999875 875

>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: DNA polymerase lambda
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.34  E-value=0.0018  Score=37.61  Aligned_cols=26  Identities=15%  Similarity=0.273  Sum_probs=21.7

Q ss_pred             eeeeehhcccccCHHHHHHHHHHhCCC
Q psy8858          14 HIIIGLTAIYGIGRSRAKKICEVTKIS   40 (121)
Q Consensus        14 ~v~~aLt~I~GIG~~~A~~Ic~~lGi~   40 (121)
                      ++.-.+++|||||+++|..+.+. |+.
T Consensus         5 ~~l~~ft~I~GvGp~~A~~l~~~-Gi~   30 (57)
T d2bcqa2           5 PVLELFSNIWGAGTKTAQMWYQQ-GFR   30 (57)
T ss_dssp             HHHHHHHTSTTCCHHHHHHHHHT-TCC
T ss_pred             HHHHHHhccccccHHHHHHHHHh-CCC
Confidence            45567899999999999999876 865

>d1tdha1 a.156.1.2 (A:132-246) Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Middle domain of MutM-like DNA repair proteins
domain: Endonuclease VIII-like 1 (NEIL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.34  E-value=0.00097  Score=43.96  Aligned_cols=48  Identities=19%  Similarity=0.124  Sum_probs=37.2

Q ss_pred             eeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858          13 QHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI   60 (121)
Q Consensus        13 k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l   60 (121)
                      ++|.-+|   .-|-|||...+.++|-.++|+|..++.+|+++|...|.+..
T Consensus        28 ~~i~~~LldQ~~~aGiGN~~~~EiLf~a~i~P~~~~~~l~~~~~~~l~~~~   78 (115)
T d1tdha1          28 RPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPE   78 (115)
T ss_dssp             SBHHHHTTCTTTSTTCCHHHHHHHHHHHTCCTTSBHHHHHGGGC-----CC
T ss_pred             CcHHHHHhccchhccccHHHHHHHHHHcCCCCCCchhhcCHHHHhHHHhhH
Confidence            4455555   57899999999999999999999999999999998876653

>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=95.08  E-value=0.0074  Score=34.89  Aligned_cols=36  Identities=33%  Similarity=0.381  Sum_probs=27.5

Q ss_pred             hhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHH
Q psy8858          19 LTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEK   55 (121)
Q Consensus        19 Lt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~   55 (121)
                      |++|+|||+.++..+.+. |+..-..+-+.+.+++..
T Consensus         1 L~~IpGIG~~~a~~L~~~-G~~tv~~l~~a~~eeL~~   36 (60)
T d2i1qa1           1 LTDLPGVGPSTAEKLVEA-GYIDFMKIATATVGELTD   36 (60)
T ss_dssp             CTTSTTCCHHHHHHHHHH-TCCSHHHHHTCCHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHc-cCCCHHHHHhCCHHHHHH
Confidence            678999999999998876 676666666666666543

>d1jmsa3 a.60.12.1 (A:243-302) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: Terminal deoxynucleotidyl transferase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.01  E-value=0.0042  Score=36.34  Aligned_cols=24  Identities=21%  Similarity=0.393  Sum_probs=20.7

Q ss_pred             eeehhcccccCHHHHHHHHHHhCCC
Q psy8858          16 IIGLTAIYGIGRSRAKKICEVTKIS   40 (121)
Q Consensus        16 ~~aLt~I~GIG~~~A~~Ic~~lGi~   40 (121)
                      ...|++|||||+++|..+.+. |+.
T Consensus         7 l~~f~~I~GvGp~~A~~l~~~-Gi~   30 (60)
T d1jmsa3           7 FKLFTSVFGVGLKTAEKWFRM-GFR   30 (60)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHT-TCC
T ss_pred             HHHHhccccccHHHHHHHHHh-CCC
Confidence            446899999999999999877 875

>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: PsbU-like
domain: Photosystem II 12 kDa extrinsic protein PsbU
species: Thermosynechococcus elongatus [TaxId: 146786]

Probab=93.83  E-value=0.022  Score=36.22  Aligned_cols=58  Identities=22%  Similarity=0.288  Sum_probs=42.4

Q ss_pred             cCCCCeeeeeehhcccccCHHHHHHHHHHhCC---CCCcccCCCCHHHHHHHHHHHhhccc
Q psy8858           8 NIPNNQHIIIGLTAIYGIGRSRAKKICEVTKI---STTKKIKDLNDNELEKLREEISKFII   65 (121)
Q Consensus         8 ~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi---~p~~~~~~Ls~~qi~~L~~~l~~~~i   65 (121)
                      -++-|..-...|..++|||+.+|..|++-=.+   +.-..+.-+++.+++.|..++..|.+
T Consensus        18 kidlN~As~~eL~~lpGIg~~~A~~Iv~~gpf~s~edL~~V~GIg~~~~e~lk~yl~~f~~   78 (98)
T d2axtu1          18 KIDLNNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLEHFTV   78 (98)
T ss_dssp             BEESSSSCGGGGTTSTTCTHHHHHHHHHSCCCSSGGGGGGCTTCCTTHHHHHHHHGGGEEC
T ss_pred             ceecccccHHHHHHhhhhcHHHHHHHHHcCCcCCHHHHhhCCCCCHHHHHHHHHHHhccee
Confidence            35556667778999999999999999963111   12235556689999999999876654

>d2gqfa2 e.74.1.1 (A:195-342) Hypothetical protein HI0933 {Haemophilus influenzae [TaxId: 727]}

class: Multi-domain proteins (alpha and beta)
fold: HI0933 insert domain-like
superfamily: HI0933 insert domain-like
family: HI0933 insert domain-like
domain: Hypothetical protein HI0933
species: Haemophilus influenzae [TaxId: 727]

Probab=93.83  E-value=0.027  Score=37.55  Aligned_cols=53  Identities=11%  Similarity=0.142  Sum_probs=43.2

Q ss_pred             CCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhccc
Q psy8858          10 PNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFII   65 (121)
Q Consensus        10 ~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~i   65 (121)
                      .+++.|.-.|..+  +-.+.+..+|+..++ +++++.+|+++|+..|.+.|++|.+
T Consensus        84 ~~kk~i~~~L~~~--lPkrl~~~ll~~~~~-~~~~~~~lsk~~~~~L~~~Lk~~~~  136 (148)
T d2gqfa2          84 SPKQMLKTILVRL--LPKKLVELWIEQGIV-QDEVIANISKVRVKNLVDFIHHWEF  136 (148)
T ss_dssp             CTTSBHHHHHTTT--SCHHHHHHHHHTTSS-CCCBGGGCCHHHHHHHHHHHHCEEE
T ss_pred             hhhhhHHHHHHHH--hHHHHHHHHHHHcCc-ccchHHHCCHHHHHHHHHHHhCCEE
Confidence            4566676677655  688999999997655 7899999999999999999977653

>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Mycobacterium leprae [TaxId: 1769]

Probab=93.14  E-value=0.018  Score=34.57  Aligned_cols=20  Identities=40%  Similarity=0.522  Sum_probs=16.2

Q ss_pred             ehhcccccCHHHHHHHHHHh
Q psy8858          18 GLTAIYGIGRSRAKKICEVT   37 (121)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~l   37 (121)
                      +|++++|||+++|..||-.|
T Consensus        45 ~L~~vpGIG~KtA~rIi~eL   64 (71)
T d1bvsa2          45 SLTRVPGIGRRGAERIVLEL   64 (71)
T ss_dssp             HHHTSTTCCHHHHHHHHHHS
T ss_pred             HhhcCCCCCHHHHHHHHHHH
Confidence            57888888888888888655

>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=92.99  E-value=0.021  Score=34.41  Aligned_cols=21  Identities=38%  Similarity=0.431  Sum_probs=17.4

Q ss_pred             ehhcccccCHHHHHHHHHHhC
Q psy8858          18 GLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      +|++++|||.++|..||-.|.
T Consensus        46 ~L~~vpGIG~KtA~rIi~eLk   66 (73)
T d1ixra1          46 LLTSASGVGRRLAERIALELK   66 (73)
T ss_dssp             HHTTSTTCCHHHHHHHHHHHT
T ss_pred             HhhcCCCCCHHHHHHHHHHHH
Confidence            578899999999999887763

>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.90  E-value=0.03  Score=32.22  Aligned_cols=38  Identities=16%  Similarity=0.284  Sum_probs=29.5

Q ss_pred             ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHH
Q psy8858          18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLR   57 (121)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~   57 (121)
                      .|.+|+|||...+..+++.+|  .-..+.+.|.+|+..+.
T Consensus         4 ~L~~iPGIg~~~~~~Ll~~f~--Si~~l~~As~~eL~~v~   41 (62)
T d2a1ja1           4 FLLKMPGVNAKNCRSLMHHVK--NIAELAALSQDELTSIL   41 (62)
T ss_dssp             HHHTSTTCCHHHHHHHHHHCS--SHHHHHTCCHHHHHHHH
T ss_pred             HHhcCCCCCHHHHHHHHHHhc--cHHHHHhCCHHHHHHCc
Confidence            378999999999999998877  23456677777776654

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.78  E-value=0.016  Score=32.93  Aligned_cols=35  Identities=17%  Similarity=0.353  Sum_probs=25.5

Q ss_pred             ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHH
Q psy8858          18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELE   54 (121)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~   54 (121)
                      .|.+|+|||+.+|..+++.+| + -..+.+-+.+|+.
T Consensus         3 ~L~~I~gVG~~~a~~L~~~F~-s-~~~i~~As~eeL~   37 (56)
T d1kfta_           3 SLETIEGVGPKRRQMLLKYMG-G-LQGLRNASVEEIA   37 (56)
T ss_dssp             GGGGCTTCSSSHHHHHHHHHS-C-HHHHHHCCHHHHT
T ss_pred             CcccCCCccHHHHHHHHHHhC-C-HHHHHHhhHHHHH
Confidence            589999999999999999988 2 2234444555543

>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.21  E-value=0.022  Score=34.22  Aligned_cols=25  Identities=8%  Similarity=0.201  Sum_probs=22.5

Q ss_pred             eeeeehhcccccCHHHHHHHHHHhC
Q psy8858          14 HIIIGLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus        14 ~v~~aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      .+..+|+.|.|||+..|..+++.+|
T Consensus        16 ~~~~~L~~I~gIg~~~a~~L~~~F~   40 (78)
T d2a1jb1          16 RVTECLTTVKSVNKTDSQTLLTTFG   40 (78)
T ss_dssp             HHHHHHTTSTTCCHHHHHHHHHHHS
T ss_pred             HHHHHhcCCCCcCHHHHHHHHHHhC
Confidence            3567899999999999999999988

>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Escherichia coli [TaxId: 562]

Probab=92.14  E-value=0.032  Score=33.99  Aligned_cols=20  Identities=25%  Similarity=0.454  Sum_probs=16.2

Q ss_pred             ehhcccccCHHHHHHHHHHh
Q psy8858          18 GLTAIYGIGRSRAKKICEVT   37 (121)
Q Consensus        18 aLt~I~GIG~~~A~~Ic~~l   37 (121)
                      +|++++|||.++|..|+-.|
T Consensus        45 ~L~~vpGIG~KtA~rIi~eL   64 (78)
T d1cuka2          45 ALVKLPGIGKKTAERLIVEM   64 (78)
T ss_dssp             HHHTSTTCCHHHHHHHHHHH
T ss_pred             HhhcCCCCCHHHHHHHHHHH
Confidence            57888888888888888665

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=90.50  E-value=0.056  Score=31.58  Aligned_cols=24  Identities=4%  Similarity=0.026  Sum_probs=21.5

Q ss_pred             eeeehhcccccCHHHHHHHHHHhC
Q psy8858          15 IIIGLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus        15 v~~aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      ..+.|+.|+|||+.+|..|.+.+|
T Consensus         8 ~~~~L~~I~gIG~~~a~~L~~~f~   31 (68)
T d1x2ia1           8 QRLIVEGLPHVSATLARRLLKHFG   31 (68)
T ss_dssp             HHHHHTTSTTCCHHHHHHHHHHHC
T ss_pred             HHHHHcCCCCcCHHHHHHHHHHcC
Confidence            346789999999999999999987

>d1qyra_ c.66.1.24 (A:) High level kasugamycin resistance protein KsgA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: rRNA adenine dimethylase-like
domain: High level kasugamycin resistance protein KsgA
species: Escherichia coli [TaxId: 562]

Probab=89.57  E-value=0.13  Score=37.06  Aligned_cols=31  Identities=3%  Similarity=0.111  Sum_probs=28.2

Q ss_pred             HHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858          31 KKICEVTKISTTKKIKDLNDNELEKLREEIS   61 (121)
Q Consensus        31 ~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~   61 (121)
                      .++++.+|++|+.++.+|+.+|+-.|.+++.
T Consensus       219 ~~~l~~~~i~~~~R~e~Ls~~~~~~L~~~l~  249 (252)
T d1qyra_         219 VEVLTGMGIDPAMRAENISVAQYCQMANYLA  249 (252)
T ss_dssp             HHHHHHTTCCTTSBGGGSCHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCcccChhhCCHHHHHHHHHHHH
Confidence            3578899999999999999999999999884

>d1vdda_ e.49.1.1 (A:) Recombination protein RecR {Deinococcus radiodurans [TaxId: 1299]}

class: Multi-domain proteins (alpha and beta)
fold: Recombination protein RecR
superfamily: Recombination protein RecR
family: Recombination protein RecR
domain: Recombination protein RecR
species: Deinococcus radiodurans [TaxId: 1299]

Probab=87.78  E-value=0.24  Score=34.83  Aligned_cols=72  Identities=22%  Similarity=0.299  Sum_probs=48.3

Q ss_pred             eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc------------cc-------hhhHH----
Q psy8858          15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI------------IE-------GDLRR----   71 (121)
Q Consensus        15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~------------i~-------~~L~~----   71 (121)
                      +..+|++++|||+++|..+.-.+=        ..+++++..|.+.|.+..            .+       +|-.+    
T Consensus        10 LI~~l~kLPGIG~KsA~Rla~~LL--------~~~~~~~~~l~~~l~~~~~~I~~C~~C~~l~e~~~C~iC~d~~Rd~~~   81 (199)
T d1vdda_          10 LIRELSRLPGIGPKSAQRLAFHLF--------EQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRT   81 (199)
T ss_dssp             HHHHHHTSTTCCHHHHHHHHHHHS--------SSCHHHHHHHHHHHHHHHHHCEECSSSCCEESSSSCHHHHCSSSCTTE
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHHHHHhhCCCCCCCccccCCCcccccCcCCCcce
Confidence            456789999999999999986542        345778888888873321            00       00000    


Q ss_pred             ----HHHHHHHHHHhhccccccccCCC
Q psy8858          72 ----EFSMNIKRLIDLSCYRGIRHRKS   94 (121)
Q Consensus        72 ----~~~~~I~rl~~i~~yRG~RH~~g   94 (121)
                          +--.|+.-+-+.+.|+|+=|.+|
T Consensus        82 iCVVE~~~Dl~~iE~t~~y~G~YhVL~  108 (199)
T d1vdda_          82 ICVVEEPGDVIALERSGEYRGLYHVLH  108 (199)
T ss_dssp             EEEESSHHHHHHTTTTSSCCSEEEECS
T ss_pred             EEEEecHHHHHHHHhcccchhhhhhhc
Confidence                01346666777889999999875

>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Mycobacterium leprae [TaxId: 1769]

Probab=86.14  E-value=0.088  Score=31.35  Aligned_cols=26  Identities=19%  Similarity=0.374  Sum_probs=21.3

Q ss_pred             eeeeeehhcccccCHHHHHHHHHHhC
Q psy8858          13 QHIIIGLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus        13 k~v~~aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      +.++..|.++.|||+++|..||..++
T Consensus         5 r~~F~~Li~V~GIGpK~Al~iLs~~~   30 (71)
T d1bvsa2           5 RDLFLALLSVSGVGPRLAMATLAVHD   30 (71)
T ss_dssp             HHHHHHHHTSSSCCHHHHHHHHHHSC
T ss_pred             HHHHHHHhccCCcCHHHHHHHHHhCC
Confidence            34566789999999999999997654

>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=83.93  E-value=0.13  Score=30.79  Aligned_cols=26  Identities=15%  Similarity=0.161  Sum_probs=21.0

Q ss_pred             eeeeeehhcccccCHHHHHHHHHHhC
Q psy8858          13 QHIIIGLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus        13 k~v~~aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      +.++..|.++.|||+++|-.|+..++
T Consensus         6 r~lF~~Li~V~GIGpk~Al~iLs~~~   31 (73)
T d1ixra1           6 LALFELLLSVSGVGPKVALALLSALP   31 (73)
T ss_dssp             HHHHHHHHSSSCCCHHHHHHHHHHSC
T ss_pred             HHHHHHHhccCCcCHHHHHHHHHHcc
Confidence            34556788999999999999996554

>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Escherichia coli [TaxId: 562]

Probab=83.93  E-value=0.12  Score=31.23  Aligned_cols=26  Identities=19%  Similarity=0.197  Sum_probs=21.1

Q ss_pred             eeeeeehhcccccCHHHHHHHHHHhC
Q psy8858          13 QHIIIGLTAIYGIGRSRAKKICEVTK   38 (121)
Q Consensus        13 k~v~~aLt~I~GIG~~~A~~Ic~~lG   38 (121)
                      +.++..|.++.|||+++|-.|+..++
T Consensus         5 r~~F~~Li~V~GIGpK~Al~iLs~~~   30 (78)
T d1cuka2           5 RTLFKELIKTNGVGPKLALAILSGMS   30 (78)
T ss_dssp             HHHHHHHHHSSSCCHHHHHHHHHHSC
T ss_pred             HHHHHHHHccCCccHHHHHHHHHhCC
Confidence            34556789999999999999997654

>d2duya1 a.60.2.7 (A:11-75) Uncharacterized protein TTHA1967 {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: ComEA-like
domain: Uncharacterized protein TTHA1967
species: Thermus thermophilus [TaxId: 274]

Probab=81.54  E-value=0.21  Score=28.81  Aligned_cols=47  Identities=32%  Similarity=0.422  Sum_probs=29.4

Q ss_pred             CeeeeeehhcccccCHHHHHHHHHHhCCC---CCcccCCCCHHHHHHHHH
Q psy8858          12 NQHIIIGLTAIYGIGRSRAKKICEVTKIS---TTKKIKDLNDNELEKLRE   58 (121)
Q Consensus        12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~---p~~~~~~Ls~~qi~~L~~   58 (121)
                      |..-...|..++|||..+|..|.+.=.+.   .-..+.-++++.++.|..
T Consensus        12 NtA~~~eL~~lpgig~~~A~~Iv~~R~f~s~edL~~v~gi~~~~~~~i~~   61 (65)
T d2duya1          12 NEASLEELMALPGIGPVLARRIVEGRPYARVEDLLKVKGIGPATLERLRP   61 (65)
T ss_dssp             TTCCHHHHTTSTTCCHHHHHHHHHTCCCSSGGGGGGSTTCCHHHHHHHGG
T ss_pred             ccCCHHHHHHCCCCCHHHHHHHHHcCCCCCHHHHHhCCCCCHHHHHHHHH
Confidence            45555678899999999999999753221   122333345555555543