Psyllid ID: psy17134

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------9
Protein Sequence
MPLWAILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTPGDIEPEAVAEQEGEGDEIDFNKL
Secondary Structure (PSIPRED)
ccccccccccccHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHEEccHHHHHHHHHHHHHccccccccccEccHHHHHHHHHHHHHHHHcccccEEEccHHccccccccccccHccccccHHcccc
Coil and Loop (DISEMBL)
mplwaillfpkRKRQLVVSLLERacvkpvlrpyqlSVQEFGQICLAYRDMCeempglyeytledtpgdiepeavaeqegegdeidfnkl
Flexible Loop (DISEMBL)
mplwaillfpkrkrQLVVSLLERAcvkpvlrpyqlsVQEFGQICLAYRDMCEEMPGLYEYTLEDTPGDIEPEAvaeqegegdeidfnkl
Low Complexity Region (SEG)
MPLWAILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTPGDIEPEAVAEQEGEGDEIDFNKL
Disordered region (IsUnstruct)
**LWAILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTL***************************
Disordered Region (DISOPRED)
*PLWAILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTL**********************DFNKL
Disordered Region (DISEMBL)
MPLWAILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTPGDIEPEA****************
Disordered Region (DISPRO)
MPLWAILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPLWAILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTPGDIEPEAVAEQEGEGDEIDFNKL
Positional Conservation
no confident homologs detected

---

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	89	2.2.26 [Sep-21-2011]
Q2TBQ0	341	Mitochondrial dimethylade	yes	N/A	0.651	0.170	0.440	9e-07
Q8WVM0	346	Dimethyladenosine transfe	yes	N/A	0.651	0.167	0.423	2e-06
Q2PG46	345	Dimethyladenosine transfe	N/A	N/A	0.820	0.211	0.350	3e-06
Q28HM1	346	Dimethyladenosine transfe	yes	N/A	0.876	0.225	0.316	4e-06
Q8JZM0	345	Dimethyladenosine transfe	yes	N/A	0.820	0.211	0.350	4e-06
Q811P6	345	Dimethyladenosine transfe	yes	N/A	0.831	0.214	0.346	5e-06
Q7T0W5	344	Dimethyladenosine transfe	N/A	N/A	0.617	0.159	0.410	7e-06
Q5R4V9	343	Dimethyladenosine transfe	yes	N/A	0.651	0.169	0.423	1e-05

>sp|Q2TBQ0|TFB1M_BOVIN Mitochondrial dimethyladenosine transferase 1 OS=Bos taurus GN=TFB1M PE=2 SV=2

 Score = 52.4 bits (124), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 35/59 (59%), Gaps = 1/59 (1%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLED 64
           +LFP+ +R +    LLE A V P LRP QL+V  F  +C  YR MC+E P L+ Y   +
Sbjct: 266 MLFPEARRLESTGKLLELADVDPTLRPTQLTVSHFKSLCDVYRKMCDEDPHLFAYNFRE 324

S-adenosyl-L-methionine-dependent methyltransferase which specifically dimethylates mitochondrial 12S rRNA at the conserved stem loop. Also required for basal transcription of mitochondrial DNA, probably via its interaction with POLRMT and TFAM. Stimulates transcription independently of the methyltransferase activity.
Bos taurus (taxid: 9913)
EC: 2EC: .EC: 1EC: .EC: 1EC: .EC: -

>sp|Q8WVM0|TFB1M_HUMAN Dimethyladenosine transferase 1, mitochondrial OS=Homo sapiens GN=TFB1M PE=1 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 35/59 (59%), Gaps = 1/59 (1%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLED 64
           +LFP+ +R +    LLE A + P LRP QLS+  F  +C  YR MC+E P L+ Y   +
Sbjct: 266 MLFPEAQRLESTGRLLELADIDPTLRPRQLSISHFKSLCDVYRKMCDEDPQLFAYNFRE 324

S-adenosyl-L-methionine-dependent methyltransferase which specifically dimethylates mitochondrial 12S rRNA at the conserved stem loop. Also required for basal transcription of mitochondrial DNA, probably via its interaction with POLRMT and TFAM. Stimulates transcription independently of the methyltransferase activity.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: -

>sp|Q2PG46|TFB1M_MACFA Dimethyladenosine transferase 1, mitochondrial OS=Macaca fascicularis GN=TFB1M PE=2 SV=1

 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 4/77 (5%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
           +LFP+ +R +    LLE A + P LRP QLS+  F  +C  YR MC+E P L+ Y   + 
Sbjct: 266 MLFPEAQRLENTGRLLELADIDPTLRPRQLSISHFKSLCEVYRRMCDEDPQLFAYNFRE- 324

Query: 66  PGDIEPEAVAEQEGEGD 82
             ++    + ++E + D
Sbjct: 325 --ELRQRKIKKKEKQDD 339

S-adenosyl-L-methionine-dependent methyltransferase which specifically dimethylates mitochondrial 12S rRNA at the conserved stem loop. Also required for basal transcription of mitochondrial DNA, probably via its interaction with POLRMT and TFAM. Stimulates transcription independently of the methyltransferase activity.

Macaca fascicularis (taxid: 9541)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: -

>sp|Q28HM1|TFB1M_XENTR Dimethyladenosine transferase 1, mitochondrial OS=Xenopus tropicalis GN=tfb1m PE=2 SV=1

 Score = 50.4 bits (119), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
           +LFP+  R +    +L  A V P LRP +L++  F ++C  YR+MC++ P L+ Y   + 
Sbjct: 266 ILFPEESRLKCTEQMLRLADVDPTLRPTELTMTHFKKLCNVYREMCDQNPNLFAYNFREE 325

Query: 66  PGDIEPEAVAEQEGEGDEI 84
               + +    +EGE D++
Sbjct: 326 LRMRKLQGKTTEEGEEDDL 344

S-adenosyl-L-methionine-dependent methyltransferase which specifically dimethylates mitochondrial 12S rRNA at the conserved stem loop. Also required for basal transcription of mitochondrial DNA. Stimulates transcription independently of the methyltransferase activity.

Xenopus tropicalis (taxid: 8364)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: -

>sp|Q8JZM0|TFB1M_MOUSE Dimethyladenosine transferase 1, mitochondrial OS=Mus musculus GN=Tfb1m PE=2 SV=1

 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 4/77 (5%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
           +LFP+ +R +    LL+ A + P LRP  LS+  F  +C  YR MC+E P L+ Y   + 
Sbjct: 266 MLFPEAQRLESTGRLLQLADIDPTLRPTHLSLMHFKSLCDVYRKMCDEDPQLFTYNFRE- 324

Query: 66  PGDIEPEAVAEQEGEGD 82
             +++ +    QE +GD
Sbjct: 325 --ELKQKKSKGQEKDGD 339

S-adenosyl-L-methionine-dependent methyltransferase which specifically dimethylates mitochondrial 12S rRNA at the conserved stem loop. Also required for basal transcription of mitochondrial DNA, probably via its interaction with POLRMT and TFAM. Stimulates transcription independently of the methyltransferase activity.

Mus musculus (taxid: 10090)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: -

>sp|Q811P6|TFB1M_RAT Dimethyladenosine transferase 1, mitochondrial OS=Rattus norvegicus GN=Tfb1m PE=2 SV=1

 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 4/78 (5%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
           +LFP+ +R +    LL+ A + P LRP  LS+  F  +C  YR MC+E P L+ Y   + 
Sbjct: 266 MLFPEAQRLESTGRLLQLADIDPTLRPTHLSLMHFKSLCDVYRKMCDEDPQLFAYNFRE- 324

Query: 66  PGDIEPEAVAEQEGEGDE 83
             +++ +    QE +GD 
Sbjct: 325 --ELKQKKRKGQEKDGDS 340

S-adenosyl-L-methionine-dependent methyltransferase which specifically dimethylates mitochondrial 12S rRNA at the conserved stem loop. Also required for basal transcription of mitochondrial DNA, probably via its interaction with POLRMT and TFAM. Stimulates transcription independently of the methyltransferase activity.

Rattus norvegicus (taxid: 10116)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: -

>sp|Q7T0W5|TFB1M_XENLA Dimethyladenosine transferase 1, mitochondrial OS=Xenopus laevis GN=tfb1m PE=2 SV=1

 Score = 49.3 bits (116), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 35/56 (62%), Gaps = 1/56 (1%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYT 61
           +LFP+  R QL   +L  A V P LRP +L++  F ++C  YR+MC++ P L+ Y 
Sbjct: 266 ILFPEEIRIQLTEQMLRLADVDPTLRPTELTMTHFKKLCNVYREMCDQNPHLFSYN 321

S-adenosyl-L-methionine-dependent methyltransferase which specifically dimethylates mitochondrial 12S rRNA at the conserved stem loop. Also required for basal transcription of mitochondrial DNA. Stimulates transcription independently of the methyltransferase activity.

Xenopus laevis (taxid: 8355)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: -

>sp|Q5R4V9|TFB1M_PONAB Dimethyladenosine transferase 1, mitochondrial OS=Pongo abelii GN=TFB1M PE=2 SV=1

 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLED 64
           +LFP+ +R +    LLE A V P LRP Q S+  F  +C  YR MC+E P L+ Y   +
Sbjct: 266 MLFPEAQRLESTGRLLELADVDPTLRPCQPSISHFKSLCDVYRKMCDEDPQLFAYNFRE 324

S-adenosyl-L-methionine-dependent methyltransferase which specifically dimethylates mitochondrial 12S rRNA at the conserved stem loop. Also required for basal transcription of mitochondrial DNA, probably via its interaction with POLRMT and TFAM. Stimulates transcription independently of the methyltransferase activity.

Pongo abelii (taxid: 9601)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: -

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	89
417399311	345	Putative ribosomal rna adenine dimethyla	0.831	0.214	0.384	7e-06
410960296	345	PREDICTED: mitochondrial dimethyladenosi	0.831	0.214	0.397	8e-06
73946166	345	PREDICTED: dimethyladenosine transferase	0.831	0.214	0.397	1e-05
118088399	350	PREDICTED: dimethyladenosine transferase	0.865	0.22	0.353	2e-05
190360597	340	dimethyladenosine transferase 1, mitocho	0.651	0.170	0.457	2e-05
432111751	345	Dimethyladenosine transferase 1, mitocho	0.831	0.214	0.397	3e-05
194227549	348	PREDICTED: mitochondrial dimethyladenosi	0.831	0.212	0.384	3e-05
328699806	352	PREDICTED: ribosomal RNA small subunit m	0.685	0.173	0.435	3e-05
355723907	347	transcription factor B1, mitochondrial [	0.831	0.213	0.397	3e-05
328909245	329	dimethyladenosine transferase 1 mitochon	0.719	0.194	0.4	3e-05

>gi|417399311|gb|JAA46678.1| Putative ribosomal rna adenine dimethylase [Desmodus rotundus]

 Score = 54.7 bits (130), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 45/78 (57%), Gaps = 4/78 (5%)

Query: 7   LLFPK-RKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
           +LFP+ ++R+    LL+ A V P LRP QLSV  F  +C  YR+MC++ P L+ Y   + 
Sbjct: 266 MLFPEAQRRESTGKLLQMAEVDPTLRPTQLSVSHFRSLCDVYREMCDKDPRLFAYNFRE- 324

Query: 66  PGDIEPEAVAEQEGEGDE 83
             + +     +QE EGD 
Sbjct: 325 --ERKKNKCKDQEQEGDR 340

Source: Desmodus rotundus

Species: Desmodus rotundus

Genus: Desmodus

Family: Phyllostomidae

Order: Chiroptera

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|410960296|ref|XP_003986729.1| PREDICTED: mitochondrial dimethyladenosine transferase 1-like [Felis catus]

 Score = 54.3 bits (129), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 43/78 (55%), Gaps = 4/78 (5%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
           +LFP+ +R +    LLE A V P LRP QLSV  F  +C  YR MC+E P L+ Y   + 
Sbjct: 266 MLFPEVQRVESTEKLLELADVDPTLRPSQLSVSHFKSLCDVYRKMCDEDPHLFTYNFRE- 324

Query: 66  PGDIEPEAVAEQEGEGDE 83
             +++      QE E D+
Sbjct: 325 --ELKQNKSKNQERENDK 340

Source: Felis catus

Species: Felis catus

Genus: Felis

Family: Felidae

Order: Carnivora

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|73946166|ref|XP_533459.2| PREDICTED: dimethyladenosine transferase 1, mitochondrial [Canis lupus familiaris]

 Score = 53.9 bits (128), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 42/78 (53%), Gaps = 4/78 (5%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
           +LFP+  R +    LLE A V P LRP QLSV  F  +C  YR MC+E P L+ Y   + 
Sbjct: 266 MLFPQIHRVESTGKLLELADVDPTLRPSQLSVSHFKSLCDVYRKMCDEDPHLFAYNFRE- 324

Query: 66  PGDIEPEAVAEQEGEGDE 83
             +++      QE E D+
Sbjct: 325 --ELKQNKSKNQEKEDDK 340

Source: Canis lupus familiaris

Species: Canis lupus

Genus: Canis

Family: Canidae

Order: Carnivora

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|118088399|ref|XP_426165.2| PREDICTED: dimethyladenosine transferase 1, mitochondrial [Gallus gallus]

 Score = 53.5 bits (127), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 46/82 (56%), Gaps = 5/82 (6%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
           +LFP+R+R +    L+  A V P LRP+QL++  F  +C  YR MC+E P L+ Y   + 
Sbjct: 266 ILFPERERLKKTEQLMMAADVDPTLRPFQLTMAHFRNLCNTYRKMCDEDPSLFAYNYREE 325

Query: 66  PGDIE----PEAVAEQEGEGDE 83
            G  +    PE++ + E   +E
Sbjct: 326 LGQTKRKHSPESIDQLEQTKEE 347

Source: Gallus gallus

Species: Gallus gallus

Genus: Gallus

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|190360597|ref|NP_001121947.1| dimethyladenosine transferase 1, mitochondrial [Sus scrofa] gi|186886356|gb|ACC93577.1| CGI-75 protein [Sus scrofa]

 Score = 53.5 bits (127), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/59 (45%), Positives = 35/59 (59%), Gaps = 1/59 (1%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLED 64
           +LFP+ +R +    LLE A V P LRP QLSV  F  +C  YR MC+E P L+ Y   +
Sbjct: 266 MLFPEAQRMERTGKLLESADVDPTLRPTQLSVSHFQSLCDVYRKMCDEDPHLFAYNFRE 324

Source: Sus scrofa

Species: Sus scrofa

Genus: Sus

Family: Suidae

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|432111751|gb|ELK34796.1| Dimethyladenosine transferase 1, mitochondrial [Myotis davidii]

 Score = 52.8 bits (125), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 43/78 (55%), Gaps = 4/78 (5%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
           +LFP+ +R +    LL+ A V P LRP QLSV  F  +C  YR MC+E P L+ Y   + 
Sbjct: 266 MLFPEAQRLERTGRLLQWADVDPTLRPCQLSVSHFKSLCDVYRRMCDEDPHLFAYNFRE- 324

Query: 66  PGDIEPEAVAEQEGEGDE 83
             +++    A QE E D 
Sbjct: 325 --ELKKNKRAGQEREADR 340

Source: Myotis davidii

Species: Myotis davidii

Genus: Myotis

Family: Vespertilionidae

Order: Chiroptera

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|194227549|ref|XP_001493452.2| PREDICTED: mitochondrial dimethyladenosine transferase 1-like [Equus caballus]

 Score = 52.8 bits (125), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 43/78 (55%), Gaps = 4/78 (5%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
           +LFP+ +R +    LL+ A V P LRP QLSV  F  +C  YR MC+E P L+ Y   + 
Sbjct: 266 MLFPEAQRLESTGKLLQLADVDPTLRPSQLSVSHFKSLCDVYRKMCDEDPHLFAYNFRE- 324

Query: 66  PGDIEPEAVAEQEGEGDE 83
             +++      QE E +E
Sbjct: 325 --ELKQNKSKNQEKEDEE 340

Source: Equus caballus

Species: Equus caballus

Genus: Equus

Family: Equidae

Order: Perissodactyla

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|328699806|ref|XP_003241051.1| PREDICTED: ribosomal RNA small subunit methyltransferase A-like [Acyrthosiphon pisum]

 Score = 52.8 bits (125), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/62 (43%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 8   LFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTP 66
           LFPK  R QL   LL  A ++P  RP+QL+V EFG+I  AY ++C+E P   +Y      
Sbjct: 268 LFPKPVREQLASELLTAAAIEPSTRPFQLTVSEFGRISEAYMNICKEKPDYMKYNYRGQK 327

Query: 67  GD 68
            D
Sbjct: 328 SD 329

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|355723907|gb|AES08046.1| transcription factor B1, mitochondrial [Mustela putorius furo]

 Score = 52.8 bits (125), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 43/78 (55%), Gaps = 4/78 (5%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
           +LFP+ +R +    LLE A V P LRP QLSV  F  +C  YR MC+E P L+ Y   + 
Sbjct: 272 MLFPEVERVESTGKLLELADVDPTLRPTQLSVSHFKSLCDVYRKMCDEDPLLFAYNFRE- 330

Query: 66  PGDIEPEAVAEQEGEGDE 83
             +++      QE E D+
Sbjct: 331 --ELKQNKSKNQEKEDDK 346

Source: Mustela putorius furo

Species: Mustela putorius

Genus: Mustela

Family: Mustelidae

Order: Carnivora

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|328909245|gb|AEB61290.1| dimethyladenosine transferase 1 mitochondrial-like protein, partial [Equus caballus]

 Score = 52.8 bits (125), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/65 (40%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 7   LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
           +LFP+ +R +    LL+ + V P LRP QLSV  F  +C  YR MC+E P L+ Y   + 
Sbjct: 246 MLFPEAQRVESTGKLLQLSDVDPTLRPSQLSVSHFKSLCDVYRKMCDEDPHLFAYNFREN 305

Query: 66  PGDIE 70
              I+
Sbjct: 306 SSKIK 310

Source: Equus caballus

Species: Equus caballus

Genus: Equus

Family: Equidae

Order: Perissodactyla

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	89
UNIPROTKB|E1BWX0	350	TFB1M "Uncharacterized protein	0.876	0.222	0.364	3e-08
UNIPROTKB|I3LVN4	245	TFB1M "Uncharacterized protein	0.651	0.236	0.457	5.5e-08
UNIPROTKB|E2RQC3	345	TFB1M "Uncharacterized protein	0.831	0.214	0.397	1e-07
UNIPROTKB|Q8WVM0	346	TFB1M "Dimethyladenosine trans	0.898	0.231	0.345	1.3e-07
UNIPROTKB|Q2TBQ0	341	TFB1M "Mitochondrial dimethyla	0.651	0.170	0.440	2.8e-07
MGI|MGI:2146851	345	Tfb1m "transcription factor B1	0.820	0.211	0.350	6e-07
RGD|727795	345	Tfb1m "transcription factor B1	0.820	0.211	0.350	7.7e-07

UNIPROTKB|E1BWX0 TFB1M "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 133 (51.9 bits), Expect = 3.0e-08, P = 3.0e-08
 Identities = 31/85 (36%), Positives = 47/85 (55%)

Query:     7 LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
             +LFP+R+R +    L+  A V P LRP+QL++  F  +C  YR MC+E P L+ Y   + 
Sbjct:   266 ILFPERERLKKTEQLMMAADVDPTLRPFQLTMAHFRNLCNTYRKMCDEDPSLFAYNYREE 325

Query:    66 PGDIE----PEAV--AEQEGEGDEI 84
              G  +    PE++   EQ  E D +
Sbjct:   326 LGQTKRKHSPESIDQLEQTKEEDHL 350

GO:0000179 "rRNA (adenine-N6,N6-)-dimethyltransferase activity" evidence=IEA

GO:0042645 "mitochondrial nucleoid" evidence=IEA

UNIPROTKB|I3LVN4 TFB1M "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 127 (49.8 bits), Expect = 5.5e-08, P = 5.5e-08
 Identities = 27/59 (45%), Positives = 35/59 (59%)

Query:     7 LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLED 64
             +LFP+ +R +    LLE A V P LRP QLSV  F  +C  YR MC+E P L+ Y   +
Sbjct:   171 MLFPEAQRMERTGKLLESADVDPTLRPTQLSVSHFQSLCDVYRKMCDEDPHLFAYNFRE 229

GO:0042645 "mitochondrial nucleoid" evidence=IEA

GO:0000179 "rRNA (adenine-N6,N6-)-dimethyltransferase activity" evidence=IEA

UNIPROTKB|E2RQC3 TFB1M "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 128 (50.1 bits), Expect = 1.0e-07, P = 1.0e-07
 Identities = 31/78 (39%), Positives = 42/78 (53%)

Query:     7 LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
             +LFP+  R +    LLE A V P LRP QLSV  F  +C  YR MC+E P L+ Y   + 
Sbjct:   266 MLFPQIHRVESTGKLLELADVDPTLRPSQLSVSHFKSLCDVYRKMCDEDPHLFAYNFRE- 324

Query:    66 PGDIEPEAVAEQEGEGDE 83
               +++      QE E D+
Sbjct:   325 --ELKQNKSKNQEKEDDK 340

GO:0042645 "mitochondrial nucleoid" evidence=IEA

GO:0000179 "rRNA (adenine-N6,N6-)-dimethyltransferase activity" evidence=IEA

UNIPROTKB|Q8WVM0 TFB1M "Dimethyladenosine transferase 1, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 127 (49.8 bits), Expect = 1.3e-07, P = 1.3e-07
 Identities = 29/84 (34%), Positives = 46/84 (54%)

Query:     7 LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
             +LFP+ +R +    LLE A + P LRP QLS+  F  +C  YR MC+E P L+ Y   + 
Sbjct:   266 MLFPEAQRLESTGRLLELADIDPTLRPRQLSISHFKSLCDVYRKMCDEDPQLFAYNFRE- 324

Query:    66 PGDIEPEAVAEQEGEGDEIDFNKL 89
               +++      +E E D+ +  +L
Sbjct:   325 --ELKRRKSKNEEKEEDDAENYRL 346

GO:0000179 "rRNA (adenine-N6,N6-)-dimethyltransferase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0042645 "mitochondrial nucleoid" evidence=IDA

UNIPROTKB|Q2TBQ0 TFB1M "Mitochondrial dimethyladenosine transferase 1" [Bos taurus (taxid:9913)]

 Score = 124 (48.7 bits), Expect = 2.8e-07, P = 2.8e-07
 Identities = 26/59 (44%), Positives = 35/59 (59%)

Query:     7 LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLED 64
             +LFP+ +R +    LLE A V P LRP QL+V  F  +C  YR MC+E P L+ Y   +
Sbjct:   266 MLFPEARRLESTGKLLELADVDPTLRPTQLTVSHFKSLCDVYRKMCDEDPHLFAYNFRE 324

GO:0042645 "mitochondrial nucleoid" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000179 "rRNA (adenine-N6,N6-)-dimethyltransferase activity" evidence=IEA

MGI|MGI:2146851 Tfb1m "transcription factor B1, mitochondrial" [Mus musculus (taxid:10090)]

 Score = 121 (47.7 bits), Expect = 6.0e-07, P = 6.0e-07
 Identities = 27/77 (35%), Positives = 43/77 (55%)

Query:     7 LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
             +LFP+ +R +    LL+ A + P LRP  LS+  F  +C  YR MC+E P L+ Y   + 
Sbjct:   266 MLFPEAQRLESTGRLLQLADIDPTLRPTHLSLMHFKSLCDVYRKMCDEDPQLFTYNFRE- 324

Query:    66 PGDIEPEAVAEQEGEGD 82
               +++ +    QE +GD
Sbjct:   325 --ELKQKKSKGQEKDGD 339

GO:0000154 "rRNA modification" evidence=IEA

GO:0000179 "rRNA (adenine-N6,N6-)-dimethyltransferase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0008649 "rRNA methyltransferase activity" evidence=IEA

GO:0016433 "rRNA (adenine) methyltransferase activity" evidence=IEA

GO:0016740 "transferase activity" evidence=IEA

GO:0032259 "methylation" evidence=IEA

GO:0042645 "mitochondrial nucleoid" evidence=ISO

RGD|727795 Tfb1m "transcription factor B1, mitochondrial" [Rattus norvegicus (taxid:10116)]

 Score = 120 (47.3 bits), Expect = 7.7e-07, P = 7.7e-07
 Identities = 27/77 (35%), Positives = 43/77 (55%)

Query:     7 LLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDT 65
             +LFP+ +R +    LL+ A + P LRP  LS+  F  +C  YR MC+E P L+ Y   + 
Sbjct:   266 MLFPEAQRLESTGRLLQLADIDPTLRPTHLSLMHFKSLCDVYRKMCDEDPQLFAYNFRE- 324

Query:    66 PGDIEPEAVAEQEGEGD 82
               +++ +    QE +GD
Sbjct:   325 --ELKQKKRKGQEKDGD 339


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.320   0.141   0.428    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       89        89   0.00091  102 3  11 22  0.49    29
                                                     29  0.50    30


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  7
  No. of states in DFA:  529 (56 KB)
  Total size of DFA:  113 KB (2077 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:04
  No. of threads or processors used:  24
  Search cpu time:  12.11u 0.06s 12.17t   Elapsed:  00:00:04
  Total cpu time:  12.11u 0.06s 12.17t   Elapsed:  00:00:08
  Start:  Thu Aug 15 13:14:46 2013   End:  Thu Aug 15 13:14:54 2013

GO:0000179 "rRNA (adenine-N6,N6-)-dimethyltransferase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0042645 "mitochondrial nucleoid" evidence=IEA;ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

No hit with e-value below 0.005

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	89
KOG0821|consensus	326		99.9
PRK00274	272	ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1	96.52
TIGR00755	253	ksgA dimethyladenosine transferase. Alternate name	95.24
PF00398	262	RrnaAD: Ribosomal RNA adenine dimethylase; InterPr	94.86
COG0030	259	KsgA Dimethyladenosine transferase (rRNA methylati	94.39
PF06831	92	H2TH: Formamidopyrimidine-DNA glycosylase H2TH dom	93.56
PTZ00338	294	dimethyladenosine transferase-like protein; Provis	93.55
COG0099	121	RpsM Ribosomal protein S13 [Translation, ribosomal	90.46
PRK14896	258	ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1	90.28
PRK01103	274	formamidopyrimidine/5-formyluracil/ 5-hydroxymethy	89.77
TIGR03631	113	bact_S13 30S ribosomal protein S13. This model des	89.71
CHL00137	122	rps13 ribosomal protein S13; Validated	89.65
PF00416	107	Ribosomal_S13: Ribosomal protein S13/S18; InterPro	88.97
PRK14810	272	formamidopyrimidine-DNA glycosylase; Provisional	88.9
PF05833	455	FbpA: Fibronectin-binding protein A N-terminus (Fb	88.61
PRK05179	122	rpsM 30S ribosomal protein S13; Validated	88.32
PTZ00134	154	40S ribosomal protein S18; Provisional	87.68
PF09645	110	F-112: F-112 protein; InterPro: IPR018601 This ent	86.03
TIGR03629	144	arch_S13P archaeal ribosomal protein S13P. This mo	85.69
PRK04053	149	rps13p 30S ribosomal protein S13P; Reviewed	85.3
PRK10445	263	endonuclease VIII; Provisional	85.26
PRK13945	282	formamidopyrimidine-DNA glycosylase; Provisional	85.18
PRK14811	269	formamidopyrimidine-DNA glycosylase; Provisional	85.17
PF09713	54	A_thal_3526: Plant protein 1589 of unknown functio	83.51
TIGR00577	272	fpg formamidopyrimidine-DNA glycosylase (fpg). All	82.46
PRK04184	535	DNA topoisomerase VI subunit B; Validated	81.78

>KOG0821|consensus

Probab=99.90  E-value=1.5e-24  Score=169.99  Aligned_cols=67  Identities=36%  Similarity=0.648  Sum_probs=65.0

Q ss_pred             ccccccCChhhH-HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCCCccccccCCCCCCC
Q psy17134          3 LWAILLFPKRKR-QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTPGDI   69 (89)
Q Consensus         3 ~g~~~LFP~~~R-elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~YdyR~~~~~~   69 (89)
                      ||++||||+++| |+|+.||++|+||||+||+|||+|||++||++|++||.++|++++||||.+|+..
T Consensus       257 rGl~TL~PeE~r~E~~~~Ll~~~~idpT~r~~~L~iEQf~~LAE~Y~E~c~~~p~~~ay~~r~~kn~e  324 (326)
T KOG0821|consen  257 RGLRTLFPEEQRLESTGRLLELADIDPTLRPRQLSIEQFKSLAEVYREMCDEDPQLFAYNFRKSKNEE  324 (326)
T ss_pred             ccccccCCHHHHHHHHHHHHHHhcCCCccCceeeeHHHHHHHHHHHHHHhccChhhhhhccccccccc
Confidence            899999999999 9999999999999999999999999999999999999999999999999998753

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

Probab=96.52  E-value=0.0027  Score=48.04  Aligned_cols=43  Identities=30%  Similarity=0.333  Sum_probs=34.5

Q ss_pred             ccccCChhhHHHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134          5 AILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRD   49 (89)
Q Consensus         5 ~~~LFP~~~Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~   49 (89)
                      ++.+||  ..+.+.++++.+|++|+.||-+||.++|.+|+.++..
T Consensus       228 l~~~~~--~~~~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~~  270 (272)
T PRK00274        228 LKNLFG--SKEKLEEALEAAGIDPNRRAETLSVEEFVRLANALAA  270 (272)
T ss_pred             HHhhcc--chHHHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHHh
Confidence            344555  1245678899999999999999999999999988764

>TIGR00755 ksgA dimethyladenosine transferase

Probab=95.24  E-value=0.026  Score=41.94  Aligned_cols=39  Identities=23%  Similarity=0.273  Sum_probs=30.5

Q ss_pred             ccccCChhhHHHHHHHHHhcCCCCCcccccccHHHHHHHHHH
Q psy17134          5 AILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLA   46 (89)
Q Consensus         5 ~~~LFP~~~Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~a   46 (89)
                      +..+||.   +.+..++..+++||+.||.+||++||.+|..+
T Consensus       214 l~~~~~~---~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~  252 (253)
T TIGR00755       214 LKQLLKA---SKLEEVLEQLGLDPTARAEQLSPEDFLRLANL  252 (253)
T ss_pred             Hhhhcch---hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHh
Confidence            3445553   23456788899999999999999999999764

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

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

Probab=94.86  E-value=0.037  Score=41.54  Aligned_cols=42  Identities=29%  Similarity=0.392  Sum_probs=33.5

Q ss_pred             ccccCChhhHHHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134          5 AILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRD   49 (89)
Q Consensus         5 ~~~LFP~~~Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~   49 (89)
                      ++.++|.   +-++.+++.|||+|+.|+-+||+++|.+|...+.+
T Consensus       221 L~~~~~~---~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~k  262 (262)
T PF00398_consen  221 LKSLFPG---EQLEELLEKAGIDPNARAEELSPEQFLKLFKYLNK  262 (262)
T ss_dssp             TTCTHHH---HHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHHH
T ss_pred             HhhhcCH---HHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhhC
Confidence            4445553   34567778899999999999999999999988764

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 ....

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

Probab=94.39  E-value=0.051  Score=42.46  Aligned_cols=32  Identities=28%  Similarity=0.384  Sum_probs=29.8

Q ss_pred             HHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134         18 VSLLERACVKPVLRPYQLSVQEFGQICLAYRD   49 (89)
Q Consensus        18 ~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~   49 (89)
                      .+++..+++||+.|+-+||+++|.+|+.+++.
T Consensus       225 ~~~l~~~~i~~~~R~e~ls~~~f~~L~~~l~~  256 (259)
T COG0030         225 EEVLEAAGIDPNARAENLSPEDFLKLANALKG  256 (259)
T ss_pred             HHHHHhcCCCcccChhhCCHHHHHHHHHHHhh
Confidence            48999999999999999999999999998765

>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=93.56  E-value=0.21  Score=32.91  Aligned_cols=38  Identities=24%  Similarity=0.259  Sum_probs=33.4

Q ss_pred             HHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134         16 LVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE   53 (89)
Q Consensus        16 lt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~   53 (89)
                      .+.|+|=.|+|+|......||-+++.+|+.+=++++++
T Consensus        43 y~~EiLf~a~i~P~~~~~~L~~~~~~~l~~~~~~vl~~   80 (92)
T PF06831_consen   43 YADEILFRAGIHPERPASSLSEEELRRLHEAIKRVLRE   80 (92)
T ss_dssp             HHHHHHHHTTB-TTSBGGGSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCccCccccCCHHHHHHHHHHHHHHHHH
Confidence            46788889999999999999999999999998888775

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 ....

>PTZ00338 dimethyladenosine transferase-like protein; Provisional

Probab=93.55  E-value=0.12  Score=40.29  Aligned_cols=34  Identities=21%  Similarity=0.442  Sum_probs=29.0

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRD   49 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~   49 (89)
                      +.....|..++++ +.||-+||+++|.+|+.+..+
T Consensus       255 ~~~~~~l~~~~~~-~~R~e~l~~~~f~~L~~~~~~  288 (294)
T PTZ00338        255 EFIAEILEDSGMF-EKRSVKLDIDDFLKLLLAFNK  288 (294)
T ss_pred             HHHHHHHHHcCCc-ccChhhCCHHHHHHHHHHHHH
Confidence            3445679999997 799999999999999998764

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

Probab=90.46  E-value=0.31  Score=34.82  Aligned_cols=34  Identities=18%  Similarity=0.205  Sum_probs=31.6

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYR   48 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~   48 (89)
                      -.|.+++..|||||..|.-+||-+|+.+|-++-.
T Consensus        28 ~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~   61 (121)
T COG0099          28 RRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQ   61 (121)
T ss_pred             HHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHH
Confidence            5688999999999999999999999999998876

>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional

Probab=90.28  E-value=0.46  Score=35.58  Aligned_cols=29  Identities=21%  Similarity=0.148  Sum_probs=23.6

Q ss_pred             HHHhc-CCCCCcccccccHHHHHHHHHHHH
Q psy17134         20 LLERA-CVKPVLRPYQLSVQEFGQICLAYR   48 (89)
Q Consensus        20 Ll~~A-dVDPtlRp~qLsv~ef~~Lc~aY~   48 (89)
                      ++..+ .++++.||.+||++||.+|+.++.
T Consensus       226 ~~~~~~~~~~~~R~e~L~~~~~~~l~~~~~  255 (258)
T PRK14896        226 VVEALPEELLNKRVFQLSPEEIAELANLLY  255 (258)
T ss_pred             HHHHcCCCCcCCCCccCCHHHHHHHHHHHH
Confidence            34555 466899999999999999998764

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

Probab=89.77  E-value=0.71  Score=35.39  Aligned_cols=39  Identities=23%  Similarity=0.140  Sum_probs=34.8

Q ss_pred             HHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhC
Q psy17134         16 LVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEM   54 (89)
Q Consensus        16 lt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~   54 (89)
                      .+.+.|=.|+|+|.++.-.||-+++.+|..+=++++++-
T Consensus       175 ya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~~vl~~a  213 (274)
T PRK01103        175 YADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEA  213 (274)
T ss_pred             HHHHHHHHcCCCccCccccCCHHHHHHHHHHHHHHHHHH
Confidence            467888899999999999999999999999988887764

>TIGR03631 bact_S13 30S ribosomal protein S13

Probab=89.71  E-value=0.57  Score=32.35  Aligned_cols=33  Identities=24%  Similarity=0.272  Sum_probs=30.7

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAY   47 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY   47 (89)
                      ..|..++..+||||..+.-+||-+|+.+|..+=
T Consensus        26 ~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l   58 (113)
T TIGR03631        26 TRARKILEKAGIDPDKRVKDLTEEELNAIREEI   58 (113)
T ss_pred             HHHHHHHHHhCcCcccccccCCHHHHHHHHHHH
Confidence            578899999999999999999999999999875

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.

>CHL00137 rps13 ribosomal protein S13; Validated

Probab=89.65  E-value=0.6  Score=32.75  Aligned_cols=34  Identities=18%  Similarity=0.284  Sum_probs=31.4

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYR   48 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~   48 (89)
                      ..|..++..+||||..+.-+||-+|+.+|..+=.
T Consensus        28 ~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~   61 (122)
T CHL00137         28 TSAKEILEKANIDPDIRTKDLTDEQISALREIIE   61 (122)
T ss_pred             HHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHH
Confidence            5788999999999999999999999999998764

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

Probab=88.97  E-value=0.83  Score=30.75  Aligned_cols=35  Identities=9%  Similarity=0.118  Sum_probs=30.7

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRD   49 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~   49 (89)
                      -.|..++..+||||..+--+||-+|+.+|..+-..
T Consensus        26 ~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~   60 (107)
T PF00416_consen   26 RKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEK   60 (107)
T ss_dssp             HHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHH
Confidence            56889999999999999999999999999987654

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 ....

>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional

Probab=88.90  E-value=0.94  Score=34.87  Aligned_cols=39  Identities=21%  Similarity=0.178  Sum_probs=34.3

Q ss_pred             HHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhC
Q psy17134         16 LVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEM   54 (89)
Q Consensus        16 lt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~   54 (89)
                      .+.++|=+|+|+|.++.-.||-+++.+|.++-+.++++-
T Consensus       174 ya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~~vl~~a  212 (272)
T PRK14810        174 YADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREA  212 (272)
T ss_pred             HHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHHHHHHHH
Confidence            467788889999999999999999999999888777663

>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=88.61  E-value=0.52  Score=37.59  Aligned_cols=51  Identities=22%  Similarity=0.204  Sum_probs=39.1

Q ss_pred             ccccCChhhHHHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCC
Q psy17134          5 AILLFPKRKRQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMP   55 (89)
Q Consensus         5 ~~~LFP~~~Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P   55 (89)
                      +...|+--...++.+++.+|+||+...+-+|+-+++..|+.++..++.+-.
T Consensus       193 L~~~~~G~~~~la~ei~~ra~i~~~~~~~~~~~~~~~~l~~~~~~l~~~l~  243 (455)
T PF05833_consen  193 LSKNFQGFGPELAEEILYRAGIDKNKKVEELSDEEIEKLFEAIRELLNELE  243 (455)
T ss_dssp             HHHHCTT--HHHHHHHHCCCTS-TTSBGGG--HHHHCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhHHHHHHHHHHHhCCCCccccccchhhhHHHHHHHHHHhhhhcc
Confidence            334455222389999999999999999999999999999999999998654

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.

>PRK05179 rpsM 30S ribosomal protein S13; Validated

Probab=88.32  E-value=0.81  Score=32.04  Aligned_cols=34  Identities=21%  Similarity=0.210  Sum_probs=31.3

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYR   48 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~   48 (89)
                      ..|..++..+||||+.+.-+||-+|+.+|..+=.
T Consensus        28 ~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~   61 (122)
T PRK05179         28 TRAKEILAAAGIDPDTRVKDLTDEELDKIREEID   61 (122)
T ss_pred             HHHHHHHHHhCcCcccccccCCHHHHHHHHHHHH
Confidence            5788999999999999999999999999998765

>PTZ00134 40S ribosomal protein S18; Provisional

Probab=87.68  E-value=0.93  Score=33.16  Aligned_cols=34  Identities=15%  Similarity=0.189  Sum_probs=31.3

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYR   48 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~   48 (89)
                      ..|..+++.+||||+.|.-+||-+|+.+|..+=.
T Consensus        41 ~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~   74 (154)
T PTZ00134         41 RFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIA   74 (154)
T ss_pred             HHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHh
Confidence            5788999999999999999999999999988764

>PF09645 F-112: F-112 protein; InterPro: IPR018601 This entry is represented by Sulfolobus virus-like particle SSV1, p11

Probab=86.03  E-value=0.51  Score=33.15  Aligned_cols=39  Identities=15%  Similarity=0.224  Sum_probs=25.2

Q ss_pred             cccccHHHHHHHHHHHHHHHHhCCCccccccCCCCCCCC
Q psy17134         32 PYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTPGDIE   70 (89)
Q Consensus        32 p~qLsv~ef~~Lc~aY~~~c~~~P~L~~YdyR~~~~~~~   70 (89)
                      -|+.|.+---.+-.+-+.||++||+.-.|++|+.|-.-+
T Consensus        30 qfeIS~s~Ay~I~~~lr~iCe~hq~eC~~~~k~rKtv~~   68 (110)
T PF09645_consen   30 QFEISYSRAYNIQRVLRKICEQHQDECEVQKKNRKTVFK   68 (110)
T ss_dssp             HH---HHHHHHHHHHHHHHHHH-TTTEEEEE-SS-EEEE
T ss_pred             HhccchhhhhHHHHHHHHHHHhCcchhhhhhccchHHHH
Confidence            345555555566677789999999999999999875543

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2VQC_A.

>TIGR03629 arch_S13P archaeal ribosomal protein S13P

Probab=85.69  E-value=1.2  Score=32.09  Aligned_cols=45  Identities=13%  Similarity=0.127  Sum_probs=37.0

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCCCccc
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYE   59 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~   59 (89)
                      ..|..+++.+||||+.+.-+||-+|+.+|..+=...-...|+.+.
T Consensus        32 ~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~iP~w~~   76 (144)
T TIGR03629        32 RFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVENYEYGIPSWLL   76 (144)
T ss_pred             HHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHhccccCCHHHh
Confidence            578899999999999999999999999999887663334565443

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=85.30  E-value=1.5  Score=31.84  Aligned_cols=48  Identities=19%  Similarity=0.179  Sum_probs=36.9

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHH-HHHhCCCccccccC
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRD-MCEEMPGLYEYTLE   63 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~-~c~~~P~L~~YdyR   63 (89)
                      ..|..+++.+||||..+.-+||-+|+.+|..+=.+ .-...|..+ ||.|
T Consensus        36 ~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~-~Nr~   84 (149)
T PRK04053         36 RTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWM-LNRR   84 (149)
T ss_pred             HHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhh-hccc
Confidence            56889999999999999999999999999987643 223445443 5533

>PRK10445 endonuclease VIII; Provisional

Probab=85.26  E-value=2  Score=32.93  Aligned_cols=37  Identities=19%  Similarity=0.214  Sum_probs=34.1

Q ss_pred             HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134         17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE   53 (89)
Q Consensus        17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~   53 (89)
                      +.|.|=.|+|+|.++.-.||-+++.+|..+=++++..
T Consensus       172 adEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~vl~~  208 (263)
T PRK10445        172 RVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRL  208 (263)
T ss_pred             HHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHHHHHH
Confidence            5778889999999999999999999999999988877

>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional

Probab=85.18  E-value=2  Score=33.23  Aligned_cols=37  Identities=16%  Similarity=0.145  Sum_probs=34.2

Q ss_pred             HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134         17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE   53 (89)
Q Consensus        17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~   53 (89)
                      +.|.|=.|+|+|..+.-.||-+++.+|..+=++++..
T Consensus       185 a~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~~vl~~  221 (282)
T PRK13945        185 ADESLFKAGIHPTTPAGQLKKKQLERLREAIIEVLKT  221 (282)
T ss_pred             HHHHHHHcCCCccCccccCCHHHHHHHHHHHHHHHHH
Confidence            5678889999999999999999999999999998887

>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional

Probab=85.17  E-value=2  Score=33.05  Aligned_cols=38  Identities=24%  Similarity=0.225  Sum_probs=34.1

Q ss_pred             HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhC
Q psy17134         17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEM   54 (89)
Q Consensus        17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~   54 (89)
                      +.|.|=.|+|+|.++.-.||-+++.+|..+=++++..-
T Consensus       164 adEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~vl~~a  201 (269)
T PRK14811        164 ADESLWRARIHPARPATSLKAPEARRLYRAIREVMAEA  201 (269)
T ss_pred             HHHHHHHcCCCccCCcccCCHHHHHHHHHHHHHHHHHH
Confidence            57788899999999999999999999999888887763

>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length

Probab=83.51  E-value=0.66  Score=28.85  Aligned_cols=37  Identities=22%  Similarity=0.481  Sum_probs=29.8

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCCCccc-cccC
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPGLYE-YTLE   63 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~L~~-YdyR   63 (89)
                      |....|.+.|+|+|....            .+++++-+++|+.|. |..|
T Consensus        17 E~v~~L~~~a~I~P~~T~------------~VW~~Le~eN~eFF~aY~~r   54 (54)
T PF09713_consen   17 ECVRALQKQANIEPVFTS------------TVWQKLEKENPEFFKAYYTR   54 (54)
T ss_pred             HHHHHHHHHcCCChHHHH------------HHHHHHHHHCHHHHHHhhcC
Confidence            778888899999997653            489999999999885 5443

It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.

>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg)

Probab=82.46  E-value=2.7  Score=32.30  Aligned_cols=40  Identities=20%  Similarity=0.161  Sum_probs=35.5

Q ss_pred             HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCCC
Q psy17134         17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMPG   56 (89)
Q Consensus        17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P~   56 (89)
                      +.|.|=.|+|+|.++.-.||-+++.+|..+=++.++.-=.
T Consensus       176 adEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~vL~~ai~  215 (272)
T TIGR00577       176 ADEVLFRAGIHPERLANSLSKEECELLHRAIKEVLRKAIE  215 (272)
T ss_pred             HHHHHHHcCCCcchhhccCCHHHHHHHHHHHHHHHHHHHH
Confidence            5678889999999999999999999999999988876444

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).

>PRK04184 DNA topoisomerase VI subunit B; Validated

Probab=81.78  E-value=2  Score=36.79  Aligned_cols=41  Identities=22%  Similarity=0.382  Sum_probs=36.8

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCC
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMP   55 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P   55 (89)
                      ..|.++++.||+||..+|-.||-++..+|.+|.+++..-.|
T Consensus       272 ~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~p  312 (535)
T PRK04184        272 KTADEILEKAGLDPNKKPKELTREELERLVEAFKKYKFMAP  312 (535)
T ss_pred             HHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHhccCcCC
Confidence            77899999999999999999999999999999998754444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	89
3fut_A	271	Dimethyladenosine transferase; methyltransferase,	97.16
1qyr_A	252	KSGA, high level kasugamycin resistance protein, S	96.93
1qam_A	244	ERMC' methyltransferase; rRNA methyltransferase ER	96.88
3ftd_A	249	Dimethyladenosine transferase; KSGA, rossmann-like	96.75
3tqs_A	255	Ribosomal RNA small subunit methyltransferase A; p	96.61
3uzu_A	279	Ribosomal RNA small subunit methyltransferase A; s	96.53
1yub_A	245	Ermam, rRNA methyltransferase; MLS antibiotics; NM	96.45
3gru_A	295	Dimethyladenosine transferase; rossman fold, ribos	95.59
1zq9_A	285	Probable dimethyladenosine transferase; SGC, struc	95.58
2h1r_A	299	Dimethyladenosine transferase, putative; SGC toron	94.65
3r8n_M	114	30S ribosomal protein S13; protein biosynthesis, R	94.1
3j20_O	148	30S ribosomal protein S13P; archaea, archaeal, KIN	91.96
3u5c_S	146	40S ribosomal protein S18-A, 40S ribosomal protein	91.89
2vqe_M	126	30S ribosomal protein S13, 30S ribosomal protein S	91.62
3iz6_M	152	40S ribosomal protein S18 (S13P); eukaryotic ribos	91.59
2xzm_M	155	RPS18E; ribosome, translation; 3.93A {Tetrahymena	91.47
1i4w_A	353	Mitochondrial replication protein MTF1; mitochondr	89.25
2cmx_A	118	ORF F-112, F112, hypothetical 13.2 kDa protein; su	85.85
3twl_A	310	Formamidopyrimidine-DNA glycosylase 1; helix two t	85.71
2xzf_A	271	Formamidopyrimidine-DNA glycosylase; hydrolase-DNA	85.4
3u6p_A	273	Formamidopyrimidine-DNA glycosylase; DNA glycosyla	85.22
1k3x_A	262	Endonuclease VIII; hydrolase/DNA, hydrolase-DNA co	85.03
1ee8_A	266	MUTM (FPG) protein; beta sandwich, zinc finger, he	84.99
1k82_A	268	Formamidopyrimidine-DNA glycosylase; protein-DNA c	84.79
3vk8_A	295	Probable formamidopyrimidine-DNA glycosylase; DNA	82.06

>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=97.16  E-value=0.00033  Score=52.24  Aligned_cols=36  Identities=17%  Similarity=0.264  Sum_probs=31.8

Q ss_pred             HHHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134         14 RQLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRD   49 (89)
Q Consensus        14 Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~   49 (89)
                      ++...++|..+||||+.||.+||++||.+|+.+|++
T Consensus       234 ~~~~~~~l~~~~i~~~~R~e~Ls~~~f~~L~~~~~~  269 (271)
T 3fut_A          234 KARVEEALRALGLPPRVRAEELDLEAFRRLREGLEG  269 (271)
T ss_dssp             HHHHHHHHHHTTCCTTCCGGGCCHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHCCcCCCCChhhCCHHHHHHHHHHHHh
Confidence            355678899999999999999999999999999854

>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=96.93  E-value=0.00098  Score=48.84  Aligned_cols=32  Identities=22%  Similarity=0.400  Sum_probs=28.8

Q ss_pred             HHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134         18 VSLLERACVKPVLRPYQLSVQEFGQICLAYRD   49 (89)
Q Consensus        18 ~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~   49 (89)
                      .+.|..+||||+.||-+||++||.+|+.++.+
T Consensus       219 ~~~l~~~~i~~~~R~e~Ls~~~f~~l~~~~~~  250 (252)
T 1qyr_A          219 VEVLTGMGIDPAMRAENISVAQYCQMANYLAE  250 (252)
T ss_dssp             HHHHHHTTCCTTSBGGGSCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCCCChHHCCHHHHHHHHHHHHh
Confidence            45688999999999999999999999999864

>1qam_A ERMC' methyltransferase; rRNA methyltransferase ERMC', cofactor analogs; 2.20A {Bacillus subtilis} SCOP: c.66.1.24 PDB: 1qan_A* 1qao_A* 1qaq_A* 2erc_A

Probab=96.88  E-value=0.00044  Score=49.60  Aligned_cols=32  Identities=9%  Similarity=0.077  Sum_probs=29.0

Q ss_pred             HHHHhcCCCCCcccccccHHHHHHHHHHHHHH
Q psy17134         19 SLLERACVKPVLRPYQLSVQEFGQICLAYRDM   50 (89)
Q Consensus        19 ~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~   50 (89)
                      +++..+|+||+.||-+||++||.+|+.+|..+
T Consensus       211 ~~~~~~~~~~~~r~e~l~~~~~~~l~~~~~~~  242 (244)
T 1qam_A          211 QFNNSLKHAGIDDLNNISFEQFLSLFNSYKLF  242 (244)
T ss_dssp             HHHHHHHHHTCSCTTSCCHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCCCCCCceeCCHHHHHHHHHHHHHh
Confidence            46788999999999999999999999999764

>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=96.75  E-value=0.0012  Score=48.03  Aligned_cols=29  Identities=31%  Similarity=0.399  Sum_probs=27.3

Q ss_pred             HHHhcCCCCCcccccccHHHHHHHHHHHH
Q psy17134         20 LLERACVKPVLRPYQLSVQEFGQICLAYR   48 (89)
Q Consensus        20 Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~   48 (89)
                      .|..++|||+.||-+||+++|.+|+.++.
T Consensus       217 ~l~~~~i~~~~r~e~l~~~~f~~l~~~~~  245 (249)
T 3ftd_A          217 LLKEAGINPDARVEQLSLEDFFKLYRLIE  245 (249)
T ss_dssp             HHHHTTCCTTCCGGGCCHHHHHHHHHHHH
T ss_pred             HHHHCCCCCCCChhhCCHHHHHHHHHHHH
Confidence            68899999999999999999999999985

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

Probab=96.61  E-value=0.0012  Score=48.60  Aligned_cols=28  Identities=29%  Similarity=0.428  Sum_probs=26.0

Q ss_pred             HHHhcCCCCCcccccccHHHHHHHHHHH
Q psy17134         20 LLERACVKPVLRPYQLSVQEFGQICLAY   47 (89)
Q Consensus        20 Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY   47 (89)
                      .|+.++|||+.||-+||++||.+|+.+|
T Consensus       227 ~l~~~~i~~~~R~e~Ls~~~f~~L~~~~  254 (255)
T 3tqs_A          227 QWPLLEINPQLRPQELTVEDFVKISNIL  254 (255)
T ss_dssp             GTGGGTCCTTSCGGGSCHHHHHHHHHHH
T ss_pred             HHHHCCcCCCCCceeCCHHHHHHHHHHh
Confidence            4688999999999999999999999886

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

Probab=96.53  E-value=0.0014  Score=48.89  Aligned_cols=30  Identities=13%  Similarity=0.157  Sum_probs=27.4

Q ss_pred             HHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134         20 LLERACVKPVLRPYQLSVQEFGQICLAYRD   49 (89)
Q Consensus        20 Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~   49 (89)
                      .|..++|||+.||-+||++||.+|+.+++.
T Consensus       245 ~l~~~~i~~~~R~e~Ls~~~f~~L~~~~~~  274 (279)
T 3uzu_A          245 DFDALGFDLARRAEDIGVDEYVRVAQAVAS  274 (279)
T ss_dssp             CTTTTTCCTTSBGGGCCHHHHHHHHHHHHH
T ss_pred             HHHHCCcCCCCCceeCCHHHHHHHHHHHHH
Confidence            567889999999999999999999999864

>1yub_A Ermam, rRNA methyltransferase; MLS antibiotics; NMR {Streptococcus pneumoniae} SCOP: c.66.1.24

Probab=96.45  E-value=0.001  Score=47.11  Aligned_cols=33  Identities=9%  Similarity=-0.058  Sum_probs=30.3

Q ss_pred             HHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134         21 LERACVKPVLRPYQLSVQEFGQICLAYRDMCEE   53 (89)
Q Consensus        21 l~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~   53 (89)
                      ++.++++|..||-+||+++|.+|+..|..+|.+
T Consensus       212 ~~~~~~~~~~r~~~l~~~~f~~l~~~~~~~~~~  244 (245)
T 1yub_A          212 HQAMKHAKVNNLSTITYEQVLSIFNSYLLFNGR  244 (245)
T ss_dssp             HHHHHHTTCSCTTSCCSHHHHHHHHHHHHHTTC
T ss_pred             HHHcCCCCCCChhhCCHHHHHHHHHHHHHhcCC
Confidence            378899999999999999999999999988864

>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=95.59  E-value=0.0071  Score=45.59  Aligned_cols=40  Identities=15%  Similarity=0.226  Sum_probs=34.1

Q ss_pred             HHHHHHHHhc-----CCCC--CcccccccHHHHHHHHHHHHHHHHhC
Q psy17134         15 QLVVSLLERA-----CVKP--VLRPYQLSVQEFGQICLAYRDMCEEM   54 (89)
Q Consensus        15 elt~~Ll~~A-----dVDP--tlRp~qLsv~ef~~Lc~aY~~~c~~~   54 (89)
                      +.+.++|..+     ++||  +.||-+||+++|.+|+.++.+..++.
T Consensus       246 ~~~~~~l~~~~~~~~~~~~~~~~R~e~Ls~~~f~~L~~~~~~~~~~~  292 (295)
T 3gru_A          246 DEMKKILEDFLNTNSEIKNLINEKVFKLSVKDIVNLSNEFYRFLQNR  292 (295)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHTSBGGGSCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhhhcccCCCccccCChhhCCHHHHHHHHHHHHHhhhcc
Confidence            4566778887     8899  99999999999999999998777653

>1zq9_A Probable dimethyladenosine transferase; SGC, structural genomics, structural genomics consortium; HET: SAM; 1.90A {Homo sapiens} SCOP: c.66.1.24

Probab=95.58  E-value=0.013  Score=42.94  Aligned_cols=33  Identities=9%  Similarity=0.240  Sum_probs=28.7

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYR   48 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~   48 (89)
                      +...+.|..++++ +.||-+||+++|.+|+.++.
T Consensus       246 ~~~~~~l~~~~~~-~~R~e~l~~~~f~~l~~~~~  278 (285)
T 1zq9_A          246 DKIQQILTSTGFS-DKRARSMDIDDFIRLLHGFN  278 (285)
T ss_dssp             HHHHHHHHHHTCT-TCBGGGCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCC-CCChhhCCHHHHHHHHHHHH
Confidence            4456789999998 67999999999999999874

>2h1r_A Dimethyladenosine transferase, putative; SGC toronto dimethyladenosine transferase, structural genomics, structural genomics consortium; 1.89A {Plasmodium falciparum}

Probab=94.65  E-value=0.045  Score=40.34  Aligned_cols=34  Identities=18%  Similarity=0.315  Sum_probs=29.1

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRD   49 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~   49 (89)
                      +...+.|+.+++++ .||-+||+++|.+|+.++.+
T Consensus       258 ~~~~~~l~~~~~~~-~R~e~l~~~~f~~l~~~~~~  291 (299)
T 2h1r_A          258 KYCLDVLEHLDMCE-KRSINLDENDFLKLLLEFNK  291 (299)
T ss_dssp             HHHHHHHHHTTCTT-CBGGGCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCC-CChhhCCHHHHHHHHHHHHh
Confidence            44566789999987 69999999999999998864

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

Probab=91.96  E-value=0.19  Score=35.56  Aligned_cols=44  Identities=14%  Similarity=0.166  Sum_probs=35.6

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHH-hCCCcc
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCE-EMPGLY   58 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~-~~P~L~   58 (89)
                      -.|..+++.|||||+.|.-+||-+|+.+|..+-....+ .-|..|
T Consensus        34 ~~A~~I~~~~gid~~~r~g~Lt~~ei~~i~~~i~~~~~~~iP~w~   78 (148)
T 3j20_O           34 NFATMVCRVAGLDPFMKAGYLTDEQVKKIEEILADPVAHGIPRWA   78 (148)
T ss_dssp             HHHHHHHHHHTCCSSSCTTBCCHHHHHHHHHHHHCHHHHCCCTTT
T ss_pred             HHHHHHHHHhCCCCCceeccCCHHHHHHHHHHHhcccccCCChhh
Confidence            56789999999999999999999999999988765432 245433

>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=91.89  E-value=0.19  Score=35.46  Aligned_cols=34  Identities=21%  Similarity=0.177  Sum_probs=30.7

Q ss_pred             HHHHHHHHHhcCCCCCcccccccHHHHHHHHHHH
Q psy17134         14 RQLVVSLLERACVKPVLRPYQLSVQEFGQICLAY   47 (89)
Q Consensus        14 Relt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY   47 (89)
                      +-.|..+++.|||||+.|.-+||-+|+.+|..+=
T Consensus        40 ~~~A~~I~~~~gid~~~r~g~Lt~~ei~~l~~~i   73 (146)
T 3u5c_S           40 RRYSNLVCKKADVDLHKRAGELTQEELERIVQIM   73 (146)
T ss_dssp             HHHHHHHHHHHTCCTTSCSSSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCceeccCCHHHHHHHHHHH
Confidence            3578999999999999999999999999998763

>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=91.62  E-value=0.15  Score=35.20  Aligned_cols=34  Identities=18%  Similarity=0.160  Sum_probs=30.9

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYR   48 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~   48 (89)
                      -.|..+++.|||||+.|.-+||-+|+.+|..+-.
T Consensus        28 ~~A~~I~~~~gi~~~~r~~~Lt~~ei~~l~~~i~   61 (126)
T 2vqe_M           28 ARAKEALEKTGINPATRVKDLTEAEVVRLREYVE   61 (126)
T ss_dssp             HHHHHHTTTTTCCTTSBGGGCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCcccccCcCCHHHHHHHHHHHH
Confidence            3578999999999999999999999999998765

>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=91.59  E-value=0.21  Score=35.44  Aligned_cols=33  Identities=15%  Similarity=0.163  Sum_probs=29.7

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAY   47 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY   47 (89)
                      -.|..+++.|||||+.|.-+||-+|+.+|..+=
T Consensus        39 ~~A~~I~~~~gid~~~r~g~Lt~~ei~~l~~~i   71 (152)
T 3iz6_M           39 RFSNIVCKKADIDMNKRAGELSAEEMDRLMAVV   71 (152)
T ss_dssp             HHHHHHHHHHTCCSSSBTTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCcEeCcCCHHHHHHHHHHH
Confidence            457889999999999999999999999998753

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

Probab=91.47  E-value=0.27  Score=34.99  Aligned_cols=44  Identities=14%  Similarity=0.149  Sum_probs=35.9

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHH-HHhCCCcc
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDM-CEEMPGLY   58 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~-c~~~P~L~   58 (89)
                      -.|..+++.|||||+.|.-+||-+|+.+|..+...- --..|..|
T Consensus        41 ~~A~~I~~~~gid~~~r~~~Lt~~ei~~l~~~i~~p~~~~iP~w~   85 (155)
T 2xzm_M           41 RFAYIICKVLKIDPNARAGLLTEDQCNKITDLIADPEAHGIPTWL   85 (155)
T ss_dssp             HHHHHHHHHTTCCSSSCSSCSCHHHHHHHHHHHHSHHHHCCCGGG
T ss_pred             HHHHHHHHHcCCCcccccccCCHHHHHHHHHHHhCccccCCCHHH
Confidence            467899999999999999999999999999887642 22456544

>1i4w_A Mitochondrial replication protein MTF1; mitochondrial transcription factor, transcription initiation; 2.60A {Saccharomyces cerevisiae} SCOP: c.66.1.24

Probab=89.25  E-value=0.19  Score=39.06  Aligned_cols=43  Identities=16%  Similarity=0.075  Sum_probs=29.5

Q ss_pred             cccccCChhhHHHHHHHHH-hcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134          4 WAILLFPKRKRQLVVSLLE-RACVKPVLRPYQLSVQEFGQICLAYRD   49 (89)
Q Consensus         4 g~~~LFP~~~Relt~~Ll~-~AdVDPtlRp~qLsv~ef~~Lc~aY~~   49 (89)
                      .++.|+|.+ .+...+.+. .+++  ..||.+||++||.+|+.+|.+
T Consensus       289 ~L~~l~~~~-~~~l~~~l~~~~~i--~~R~e~Ls~e~f~~L~~~~~~  332 (353)
T 1i4w_A          289 VMDSLGHGG-QQYFNSRITDKDLL--KKCPIDLTNDEFIYLTKLFME  332 (353)
T ss_dssp             GGGGSSTTH-HHHHTTTCCCCTTT--SSCGGGCCHHHHHHHHHHHHT
T ss_pred             HHHhhcccc-HHHHHHHhhhhcCc--ccChhhCCHHHHHHHHHHHHh
Confidence            466677742 221122333 5666  499999999999999999963

>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=85.71  E-value=1.3  Score=33.78  Aligned_cols=37  Identities=16%  Similarity=0.267  Sum_probs=33.6

Q ss_pred             HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134         17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE   53 (89)
Q Consensus        17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~   53 (89)
                      +.|.|=+|+|+|.+..-.||-+++.+|..+-++++.+
T Consensus       189 adEiLf~AgIhP~~~a~~Ls~~e~~~L~~~i~~vL~~  225 (310)
T 3twl_A          189 ADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVIEK  225 (310)
T ss_dssp             HHHHHHHTTCCTTSBGGGCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHHHHHH
Confidence            5678888999999999999999999999999988865

>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=85.40  E-value=1.5  Score=32.65  Aligned_cols=37  Identities=16%  Similarity=0.088  Sum_probs=33.9

Q ss_pred             HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134         17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE   53 (89)
Q Consensus        17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~   53 (89)
                      +.|.|=+|+|+|.+..-.||-+++.+|..+=++++.+
T Consensus       174 adEiLf~a~I~P~~~a~~Ls~~~~~~L~~~i~~vL~~  210 (271)
T 2xzf_A          174 VDEVLWLAKIHPEKETNQLIESSIHLLHDSIIEILQK  210 (271)
T ss_dssp             HHHHHHHTTCCTTCBGGGCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHHHHHH
Confidence            5778889999999999999999999999999988864

>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=85.22  E-value=1.4  Score=32.85  Aligned_cols=37  Identities=24%  Similarity=0.125  Sum_probs=34.5

Q ss_pred             HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134         17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE   53 (89)
Q Consensus        17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~   53 (89)
                      +.|.|=+|+|+|.+..-.||-+++.+|..+=++++.+
T Consensus       176 a~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~vL~~  212 (273)
T 3u6p_A          176 VDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGE  212 (273)
T ss_dssp             HHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCccCccccCCHHHHHHHHHHHHHHHHH
Confidence            5678889999999999999999999999999999887

>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=85.03  E-value=1.5  Score=32.45  Aligned_cols=39  Identities=10%  Similarity=0.052  Sum_probs=34.9

Q ss_pred             HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhCC
Q psy17134         17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEMP   55 (89)
Q Consensus        17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~P   55 (89)
                      +.|.|=+|+|+|.+..-.||-+++.+|..+=+..+.+--
T Consensus       171 adEiLf~a~I~P~~~a~~Ls~~~~~~L~~~i~~vl~~ai  209 (262)
T 1k3x_A          171 RVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSY  209 (262)
T ss_dssp             HHHHHHHHTCCSSCCGGGSCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHHHHHHHH
Confidence            578888999999999999999999999999988887643

>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=84.99  E-value=1.6  Score=32.52  Aligned_cols=38  Identities=24%  Similarity=0.233  Sum_probs=34.7

Q ss_pred             HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhC
Q psy17134         17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEM   54 (89)
Q Consensus        17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~   54 (89)
                      +.|.|=+|+|+|.+..-.||-+++.+|..+=++++.+-
T Consensus       164 a~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~vL~~a  201 (266)
T 1ee8_A          164 ADEALFRARLSPFRPARSLTEEEARRLYRALREVLAEA  201 (266)
T ss_dssp             HHHHHHHTTCCSSSBGGGCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCCCcccCCHHHHHHHHHHHHHHHHHH
Confidence            57788899999999999999999999999999988764

>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=84.79  E-value=1.6  Score=32.51  Aligned_cols=38  Identities=16%  Similarity=0.065  Sum_probs=34.6

Q ss_pred             HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHhC
Q psy17134         17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEEM   54 (89)
Q Consensus        17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~~   54 (89)
                      +.|.|=+|+|+|.+..-.||-+++.+|..+=++++.+-
T Consensus       171 a~EiLf~a~I~P~~~a~~Ls~~~~~~L~~~i~~vL~~a  208 (268)
T 1k82_A          171 ASESLFAAGIHPDRLASSLSLAECELLARVIKAVLLRS  208 (268)
T ss_dssp             HHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCCCcccCCHHHHHHHHHHHHHHHHHH
Confidence            57788899999999999999999999999999888764

>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=82.06  E-value=2.3  Score=32.19  Aligned_cols=36  Identities=22%  Similarity=0.188  Sum_probs=33.6

Q ss_pred             HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHH
Q psy17134         17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCE   52 (89)
Q Consensus        17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~   52 (89)
                      +.|.|=+|+|+|.+..-.||-+++.+|..+=+.++.
T Consensus       176 a~EiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~vL~  211 (295)
T 3vk8_A          176 VAEILYRAKIDPHKLGSNLTDQEIENLWYWIKYETK  211 (295)
T ss_dssp             HHHHHHHTTBCTTCBGGGCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCccCccccCCHHHHHHHHHHHHHHHH
Confidence            567888999999999999999999999999999887

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	89
d2hkja1	78	Topoisomerase VI-B subunit middle domain {Archaeon	96.87
d1qyra_	252	High level kasugamycin resistance protein KsgA {Es	96.71
d1i4wa_	322	Transcription factor sc-mtTFB {Baker's yeast (Sacc	96.32
d1zq9a1	278	Probable dimethyladenosine transferase {Human (Hom	96.03
d1tdza1	88	DNA repair protein MutM (Fpg) {Lactococcus lactis	94.72
d1k82a1	88	DNA repair protein MutM (Fpg) {Escherichia coli [T	94.31
d1ee8a1	89	DNA repair protein MutM (Fpg) {Thermus thermophilu	94.26
d1k3xa1	89	Endonuclease VIII {Escherichia coli [TaxId: 562]}	93.97
d1qama_	235	rRNA adenine dimethylase {Bacillus subtilis, Ermc'	93.94
d1r2za1	94	DNA repair protein MutM (Fpg) {Bacillus stearother	93.86
d2gy9m1	114	Ribosomal protein S13 {Escherichia coli [TaxId: 56	90.93
d2uubm1	125	Ribosomal protein S13 {Thermus thermophilus [TaxId	89.93
d2i0za2	169	Flavoprotein BC4706 {Bacillus cereus [TaxId: 1396]	84.75

>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=96.87  E-value=0.00057  Score=41.11  Aligned_cols=36  Identities=19%  Similarity=0.292  Sum_probs=33.3

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDM   50 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~   50 (89)
                      ..|.+++..|+|+|..++-.||-+++.+|+.+-+++
T Consensus        40 ~~a~Eil~~agi~P~~~~~~L~~~e~~~L~~air~~   75 (78)
T d2hkja1          40 TTADKILELAGLKPNKKVKNLTEEEITRLVETFKKY   75 (78)
T ss_dssp             HHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhCCCcccccccCCHHHHHHHHHHHhhh
Confidence            678999999999999999999999999999997754

>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=96.71  E-value=0.00078  Score=48.34  Aligned_cols=31  Identities=19%  Similarity=0.377  Sum_probs=29.0

Q ss_pred             HHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134         19 SLLERACVKPVLRPYQLSVQEFGQICLAYRD   49 (89)
Q Consensus        19 ~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~   49 (89)
                      +.++.+||||+.||-+||++||.+|+.+|++
T Consensus       220 ~~l~~~~i~~~~R~e~Ls~~~~~~L~~~l~~  250 (252)
T d1qyra_         220 EVLTGMGIDPAMRAENISVAQYCQMANYLAE  250 (252)
T ss_dssp             HHHHHTTCCTTSBGGGSCHHHHHHHHHHHHH
T ss_pred             HHHHHCCCCcccChhhCCHHHHHHHHHHHHh
Confidence            5788999999999999999999999999986

>d1i4wa_ c.66.1.24 (A:) Transcription factor sc-mtTFB {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

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: Transcription factor sc-mtTFB
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.32  E-value=0.0015  Score=47.79  Aligned_cols=43  Identities=14%  Similarity=0.016  Sum_probs=35.2

Q ss_pred             ccccccCChhhHHHHHHHHHhcCCCCCc---ccccccHHHHHHHHHHHHHH
Q psy17134          3 LWAILLFPKRKRQLVVSLLERACVKPVL---RPYQLSVQEFGQICLAYRDM   50 (89)
Q Consensus         3 ~g~~~LFP~~~Relt~~Ll~~AdVDPtl---Rp~qLsv~ef~~Lc~aY~~~   50 (89)
                      .++++++|.     +.+++..+++++.+   ||.+||++||.+|+.+|.++
T Consensus       273 ~~L~~l~p~-----~~~~l~~~~~~~~~~~~Rpe~Ls~~~~~~L~~~~~kw  318 (322)
T d1i4wa_         273 TVMDSLGHG-----GQQYFNSRITDKDLLKKCPIDLTNDEFIYLTKLFMEW  318 (322)
T ss_dssp             TGGGGSSTT-----HHHHHTTTCCCCTTTSSCGGGCCHHHHHHHHHHHHTC
T ss_pred             HHHHHhCcc-----hHHHHHHhCCCcchhhcChhhCCHHHHHHHHHHHHhc
Confidence            467788885     45678888888854   99999999999999999753

>d1zq9a1 c.66.1.24 (A:36-313) Probable dimethyladenosine transferase {Human (Homo sapiens) [TaxId: 9606]}

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: Probable dimethyladenosine transferase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.03  E-value=0.0028  Score=46.11  Aligned_cols=43  Identities=9%  Similarity=0.274  Sum_probs=36.1

Q ss_pred             ccCChhhH--HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHH
Q psy17134          7 LLFPKRKR--QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDM   50 (89)
Q Consensus         7 ~LFP~~~R--elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~   50 (89)
                      ++.|+...  +-..++|+.+|+++ .||-+||+++|.+|+.+|.+.
T Consensus       229 ~~rpe~l~~~~~i~~~l~~~g~~~-~RaE~Ls~~~f~~L~~~l~~~  273 (278)
T d1zq9a1         229 IIIPEDFSIADKIQQILTSTGFSD-KRARSMDIDDFIRLLHGFNAE  273 (278)
T ss_dssp             CCCCTTCCHHHHHHHHHHHHTCTT-CBGGGCCHHHHHHHHHHHHTT
T ss_pred             ccCcccccHHHHHHHHHHhcCCCc-CChhhCCHHHHHHHHHHHHHc
Confidence            35676654  66788999999986 599999999999999999865

>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=94.72  E-value=0.034  Score=34.02  Aligned_cols=38  Identities=16%  Similarity=0.086  Sum_probs=35.0

Q ss_pred             HHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134         16 LVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE   53 (89)
Q Consensus        16 lt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~   53 (89)
                      .+.|.|=.|+|+|.++.-+||-.++.+|+.+=+.++++
T Consensus        42 y~~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~vl~~   79 (88)
T d1tdza1          42 YVDEVLWLAKIHPEKETNQLIESSIHLLHDSIIEILQK   79 (88)
T ss_dssp             HHHHHHHHTTCCTTCBGGGCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCccchhhHcCHHHHHHHHHHHHHHHHH
Confidence            46788999999999999999999999999999998875

>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=94.31  E-value=0.047  Score=33.39  Aligned_cols=38  Identities=16%  Similarity=0.077  Sum_probs=34.4

Q ss_pred             HHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134         16 LVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE   53 (89)
Q Consensus        16 lt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~   53 (89)
                      .+.+.|=.|+|+|..++-.||-+++.+|+.+=++++.+
T Consensus        42 y~~EiLf~a~I~P~~~~~~L~~~~~~~L~~~i~~vl~~   79 (88)
T d1k82a1          42 YASESLFAAGIHPDRLASSLSLAECELLARVIKAVLLR   79 (88)
T ss_dssp             HHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCccChHHHCCHHHHHHHHHHHHHHHHH
Confidence            36788999999999999999999999999998888765

>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=94.26  E-value=0.051  Score=33.21  Aligned_cols=38  Identities=24%  Similarity=0.239  Sum_probs=35.0

Q ss_pred             HHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134         16 LVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE   53 (89)
Q Consensus        16 lt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~   53 (89)
                      .+.|.|=.|+|+|..+.-.||-+++.+|+.+=++++.+
T Consensus        42 y~~EiLf~a~I~P~~~~~~Ls~~e~~~L~~~i~~vl~~   79 (89)
T d1ee8a1          42 YADEALFRARLSPFRPARSLTEEEARRLYRALREVLAE   79 (89)
T ss_dssp             HHHHHHHHTTCCSSSBGGGCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCccchhhhCCHHHHHHHHHHHHHHHHH
Confidence            46788999999999999999999999999999998876

>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=93.97  E-value=0.059  Score=32.69  Aligned_cols=38  Identities=13%  Similarity=0.128  Sum_probs=34.5

Q ss_pred             HHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134         16 LVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE   53 (89)
Q Consensus        16 lt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~   53 (89)
                      .+.|+|=.|+|+|.++.-+||-+++.+|..+=.++++.
T Consensus        46 ~~~EiL~~a~i~P~~~~~~L~~~~~~~L~~~~~~v~~~   83 (89)
T d1k3xa1          46 LRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRF   83 (89)
T ss_dssp             HHHHHHHHHTCCSSCCGGGSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcccccCchhhCCHHHHHHHHHHHHHHHHH
Confidence            46788889999999999999999999999999888875

>d1qama_ c.66.1.24 (A:) rRNA adenine dimethylase {Bacillus subtilis, Ermc' [TaxId: 1423]}

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: rRNA adenine dimethylase
species: Bacillus subtilis, Ermc' [TaxId: 1423]

Probab=93.94  E-value=0.033  Score=38.86  Aligned_cols=31  Identities=16%  Similarity=0.246  Sum_probs=27.1

Q ss_pred             HHHHHHhcCCCCCcccccccHHHHHHHHHHHHHH
Q psy17134         17 VVSLLERACVKPVLRPYQLSVQEFGQICLAYRDM   50 (89)
Q Consensus        17 t~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~   50 (89)
                      -...++.+|+|   ||-+||++||.+|+.+|+..
T Consensus       203 l~~~l~~~~i~---r~e~Ls~ee~~~L~~~~~~~  233 (235)
T d1qama_         203 FNNSLKHAGID---DLNNISFEQFLSLFNSYKLF  233 (235)
T ss_dssp             HHHHHHHHTCS---CTTSCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCC---ChHhCCHHHHHHHHHHHHhh
Confidence            45678999999   58999999999999999864

>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=93.86  E-value=0.063  Score=33.13  Aligned_cols=38  Identities=24%  Similarity=0.121  Sum_probs=35.2

Q ss_pred             HHHHHHHhcCCCCCcccccccHHHHHHHHHHHHHHHHh
Q psy17134         16 LVVSLLERACVKPVLRPYQLSVQEFGQICLAYRDMCEE   53 (89)
Q Consensus        16 lt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~~c~~   53 (89)
                      .+.|.|=.|+|+|.+..-.||-+++.+|..+=++++.+
T Consensus        42 y~~EiLf~a~I~P~~~~~~Ls~~e~~~L~~~~~~vl~~   79 (94)
T d1r2za1          42 YVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGE   79 (94)
T ss_dssp             HHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999999876

>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=90.93  E-value=0.16  Score=32.23  Aligned_cols=34  Identities=12%  Similarity=0.049  Sum_probs=30.6

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYR   48 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~   48 (89)
                      -.|..++..+||||..+.-+||-+|+..|.....
T Consensus        27 ~~A~~Ic~~lgid~~~kv~~Lt~~qi~~l~~~i~   60 (114)
T d2gy9m1          27 TRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA   60 (114)
T ss_dssp             HHHHHHHHHHTCCTTSBTTSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCcccccCcccHHHHHHHHHHHH
Confidence            4678999999999999999999999999987653

>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=89.93  E-value=0.18  Score=32.47  Aligned_cols=33  Identities=18%  Similarity=0.161  Sum_probs=29.7

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAY   47 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY   47 (89)
                      -.|..++..+||||..+.-+||-+|+..|...=
T Consensus        27 ~~A~~Ic~~lgId~~~k~~~Lt~~qi~~I~~~i   59 (125)
T d2uubm1          27 ARAKEALEKTGINPATRVKDLTEAEVVRLREYV   59 (125)
T ss_dssp             HHHHHHHHTTTCCTTSBGGGCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCcccccccccHHHHHHHHHHH
Confidence            468899999999999999999999999998743

>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=84.75  E-value=0.44  Score=30.85  Aligned_cols=35  Identities=14%  Similarity=0.248  Sum_probs=32.1

Q ss_pred             HHHHHHHHhcCCCCCcccccccHHHHHHHHHHHHH
Q psy17134         15 QLVVSLLERACVKPVLRPYQLSVQEFGQICLAYRD   49 (89)
Q Consensus        15 elt~~Ll~~AdVDPtlRp~qLsv~ef~~Lc~aY~~   49 (89)
                      .++..+++.++|||...--+||-++.++|+..-+.
T Consensus       118 ~l~~~ll~~~~i~~~~~~~~ls~~~~~~L~~~Lk~  152 (169)
T d2i0za2         118 RYFLFLLEKNEIDGSEQAGQVSHEKIRALVKDFKE  152 (169)
T ss_dssp             HHHHHHHHHTTCCTTSBGGGSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCcccCCHHHCCHHHHHHHHHHHhC
Confidence            68899999999999999999999999999987654