Citrus Sinensis ID: 031813

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150--
Protein Sequence
MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR
Secondary Structure (PSIPRED)
cccccccccHHHHHHccccccccEEEEEEEcccccccHHHHHHHHHHHccccccccccccHHHHHHHHHHHHccccccccHHHHHccccccccccEEEEHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHEEEEcccccccccHHHHHHHccHHHHHHHHHHHHHccccHcHccccccHHHHHHHHHHHHcHHHccccHHHHccccccccccccEEEccHHHHHHHHHHHHHHHHHHHcccHHccccEEcccccccccccccEEEEEccc
Coil and Loop (DISEMBL)
MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVanprqfkipdwflnrqkdykdgkysQVVSNALDMKLRDDLERLKKIRNhrglrhywglrvrgqhtkttgrrgktvgvskkr
Flexible Loop (DISEMBL)
MSLVANEDFQHILRVlntnvdgkqKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANprqfkipdwflnrqkdykdgkySQVVSNALDMKLRDDLERLKKirnhrglrhywglrvrgqhtkttgrrgktvgvskkr
Low Complexity Region (SEG)
MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHtkttgrrgktvgvSKKR
Disordered region (IsUnstruct)
*******DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG*******************
Disordered Region (DISOPRED)
*****NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVG*****
Disordered Region (DISEMBL)
MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQH*****************
Disordered Region (DISPRO)
*SLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQ********GKTV******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	152	2.2.26 [Sep-21-2011]
P34788	152	40S ribosomal protein S18	yes	no	1.0	1.0	0.973	1e-83
Q8ISP0	152	40S ribosomal protein S18	N/A	no	1.0	1.0	0.782	1e-68
Q8IT98	152	40S ribosomal protein S18	N/A	no	1.0	1.0	0.763	1e-67
Q8JGS9	152	40S ribosomal protein S18	yes	no	1.0	1.0	0.736	1e-64
P62271	152	40S ribosomal protein S18	yes	no	1.0	1.0	0.730	4e-64
P62272	152	40S ribosomal protein S18	yes	no	1.0	1.0	0.730	4e-64
P62270	152	40S ribosomal protein S18	yes	no	1.0	1.0	0.730	4e-64
P62269	152	40S ribosomal protein S18	yes	no	1.0	1.0	0.730	4e-64
A5JST6	152	40S ribosomal protein S18	N/A	no	1.0	1.0	0.730	4e-64
Q5TJE9	152	40S ribosomal protein S18	yes	no	1.0	1.0	0.730	4e-64

>sp|P34788|RS18_ARATH 40S ribosomal protein S18 OS=Arabidopsis thaliana GN=RPS18A PE=1 SV=1

 Score =  307 bits (787), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 148/152 (97%), Positives = 151/152 (99%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLVANE+FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS
Sbjct: 1   MSLVANEEFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
           AAE+DNLM +VANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH
Sbjct: 61  AAEIDNLMTIVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR
Sbjct: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152

Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA.
Arabidopsis thaliana (taxid: 3702)

>sp|Q8ISP0|RS18_BRABE 40S ribosomal protein S18 OS=Branchiostoma belcheri GN=RPS18 PE=2 SV=1

 Score =  258 bits (658), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 119/152 (78%), Positives = 140/152 (92%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLV  E FQHILRV+NTN+DG++KIMFALTSIKG+GRR +NIVCKKAD+D++KRAGELS
Sbjct: 1   MSLVIPEKFQHILRVMNTNIDGRRKIMFALTSIKGVGRRYSNIVCKKADIDLSKRAGELS 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
             E++ L+ ++ NPRQ+KIPDWFLNRQKD KDGKYSQV++N+LD KLR+DLERLKKIR H
Sbjct: 61  DEEVERLITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVMANSLDNKLREDLERLKKIRAH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRHYWGLRVRGQHTKTTGRRG+TVGVSKK+
Sbjct: 121 RGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK 152

Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA.

Branchiostoma belcheri (taxid: 7741)

>sp|Q8IT98|RS18_ARGIR 40S ribosomal protein S18 OS=Argopecten irradians GN=RPS18 PE=2 SV=1

 Score =  254 bits (649), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 116/152 (76%), Positives = 140/152 (92%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           M+L+  E FQHILRV+NTN+DGK+KIMFA+T+IKG+GRR AN+VCKKADVD+ KRAGELS
Sbjct: 1   MALIIPEKFQHILRVMNTNIDGKRKIMFAMTAIKGMGRRYANVVCKKADVDITKRAGELS 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
             E++ ++ +++NPRQ+KIP+WFLNRQKD KDGKYSQV+SNALD KLR+DLERLKKIR H
Sbjct: 61  EDEIERVITIMSNPRQYKIPNWFLNRQKDVKDGKYSQVMSNALDNKLREDLERLKKIRAH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRHYWGLRVRGQHTKTTGRRG+TVGV+KK+
Sbjct: 121 RGLRHYWGLRVRGQHTKTTGRRGRTVGVAKKK 152

Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA.

Aequipecten irradians (taxid: 31199)

>sp|Q8JGS9|RS18_DANRE 40S ribosomal protein S18 OS=Danio rerio GN=rps18 PE=2 SV=1

 Score =  244 bits (623), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 112/152 (73%), Positives = 137/152 (90%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLV  E FQHILRVLNTN+DG++KI FA+T+IKG+GRR A++V +KAD+D+NKRAGEL+
Sbjct: 1   MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLNKRAGELT 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
             E++ ++ ++ NPRQ+KIPDWFLNRQKD KDGKYSQV++N LD KLR+DLERLKKIR H
Sbjct: 61  EDEVERVVTIMQNPRQYKIPDWFLNRQKDIKDGKYSQVLANGLDNKLREDLERLKKIRAH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRH+WGLRVRGQHTKTTGRRG+TVGVSKK+
Sbjct: 121 RGLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK 152

Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA (By similarity). Plays an essential role in early embryonic development.

Danio rerio (taxid: 7955)

>sp|P62271|RS18_RAT 40S ribosomal protein S18 OS=Rattus norvegicus GN=Rps18 PE=1 SV=3

 Score =  243 bits (619), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 111/152 (73%), Positives = 136/152 (89%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLV  E FQHILRVLNTN+DG++KI FA+T+IKG+GRR A++V +KAD+D+ KRAGEL+
Sbjct: 1   MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELT 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
             E++ ++ ++ NPRQ+KIPDWFLNRQKD KDGKYSQV++N LD KLR+DLERLKKIR H
Sbjct: 61  EDEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRH+WGLRVRGQHTKTTGRRG+TVGVSKK+
Sbjct: 121 RGLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK 152

Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA.

Rattus norvegicus (taxid: 10116)

>sp|P62272|RS18_PIG 40S ribosomal protein S18 OS=Sus scrofa GN=RPS18 PE=2 SV=3

 Score =  243 bits (619), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 111/152 (73%), Positives = 136/152 (89%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLV  E FQHILRVLNTN+DG++KI FA+T+IKG+GRR A++V +KAD+D+ KRAGEL+
Sbjct: 1   MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELT 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
             E++ ++ ++ NPRQ+KIPDWFLNRQKD KDGKYSQV++N LD KLR+DLERLKKIR H
Sbjct: 61  EDEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRH+WGLRVRGQHTKTTGRRG+TVGVSKK+
Sbjct: 121 RGLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK 152

Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA.

Sus scrofa (taxid: 9823)

>sp|P62270|RS18_MOUSE 40S ribosomal protein S18 OS=Mus musculus GN=Rps18 PE=1 SV=3

 Score =  243 bits (619), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 111/152 (73%), Positives = 136/152 (89%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLV  E FQHILRVLNTN+DG++KI FA+T+IKG+GRR A++V +KAD+D+ KRAGEL+
Sbjct: 1   MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELT 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
             E++ ++ ++ NPRQ+KIPDWFLNRQKD KDGKYSQV++N LD KLR+DLERLKKIR H
Sbjct: 61  EDEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRH+WGLRVRGQHTKTTGRRG+TVGVSKK+
Sbjct: 121 RGLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK 152

Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA.

Mus musculus (taxid: 10090)

>sp|P62269|RS18_HUMAN 40S ribosomal protein S18 OS=Homo sapiens GN=RPS18 PE=1 SV=3

 Score =  243 bits (619), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 111/152 (73%), Positives = 136/152 (89%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLV  E FQHILRVLNTN+DG++KI FA+T+IKG+GRR A++V +KAD+D+ KRAGEL+
Sbjct: 1   MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELT 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
             E++ ++ ++ NPRQ+KIPDWFLNRQKD KDGKYSQV++N LD KLR+DLERLKKIR H
Sbjct: 61  EDEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRH+WGLRVRGQHTKTTGRRG+TVGVSKK+
Sbjct: 121 RGLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK 152

Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA.

Homo sapiens (taxid: 9606)

>sp|A5JST6|RS18_CAPHI 40S ribosomal protein S18 OS=Capra hircus GN=RPS18 PE=2 SV=1

 Score =  243 bits (619), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 111/152 (73%), Positives = 136/152 (89%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLV  E FQHILRVLNTN+DG++KI FA+T+IKG+GRR A++V +KAD+D+ KRAGEL+
Sbjct: 1   MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELT 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
             E++ ++ ++ NPRQ+KIPDWFLNRQKD KDGKYSQV++N LD KLR+DLERLKKIR H
Sbjct: 61  EDEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRH+WGLRVRGQHTKTTGRRG+TVGVSKK+
Sbjct: 121 RGLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK 152

Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA.

Capra hircus (taxid: 9925)

>sp|Q5TJE9|RS18_CANFA 40S ribosomal protein S18 OS=Canis familiaris GN=RPS18 PE=1 SV=3

 Score =  243 bits (619), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 111/152 (73%), Positives = 136/152 (89%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLV  E FQHILRVLNTN+DG++KI FA+T+IKG+GRR A++V +KAD+D+ KRAGEL+
Sbjct: 1   MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELT 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
             E++ ++ ++ NPRQ+KIPDWFLNRQKD KDGKYSQV++N LD KLR+DLERLKKIR H
Sbjct: 61  EDEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRH+WGLRVRGQHTKTTGRRG+TVGVSKK+
Sbjct: 121 RGLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK 152

Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA.

Canis familiaris (taxid: 9615)

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	152
449443847	152	PREDICTED: 40S ribosomal protein S18-lik	1.0	1.0	0.986	3e-82
255566712	152	40S ribosomal protein S18, putative [Ric	1.0	1.0	0.980	5e-82
296085211	912	unnamed protein product [Vitis vinifera]	1.0	0.166	0.960	6e-82
15219950	152	40S ribosomal protein S18 [Arabidopsis t	1.0	1.0	0.973	9e-82
224085191	152	predicted protein [Populus trichocarpa]	1.0	1.0	0.973	1e-81
296081217	194	unnamed protein product [Vitis vinifera]	1.0	0.783	0.960	3e-81
13877525	152	S18.A ribosomal protein [Arabidopsis tha	1.0	1.0	0.967	3e-81
255559398	152	40S ribosomal protein S18, putative [Ric	1.0	1.0	0.973	5e-81
225432662	152	PREDICTED: 40S ribosomal protein S18-lik	1.0	1.0	0.960	1e-80
247421835	152	S18.A ribosomal protein [Jatropha curcas	1.0	1.0	0.967	1e-80

>gi|449443847|ref|XP_004139687.1| PREDICTED: 40S ribosomal protein S18-like [Cucumis sativus] gi|449525091|ref|XP_004169553.1| PREDICTED: 40S ribosomal protein S18-like [Cucumis sativus]

 Score =  308 bits (790), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 150/152 (98%), Positives = 151/152 (99%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRR ANIVCKKADVDMNKRAGEL+
Sbjct: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRFANIVCKKADVDMNKRAGELT 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
           AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH
Sbjct: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR
Sbjct: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255566712|ref|XP_002524340.1| 40S ribosomal protein S18, putative [Ricinus communis] gi|223536431|gb|EEF38080.1| 40S ribosomal protein S18, putative [Ricinus communis]

 Score =  308 bits (789), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 149/152 (98%), Positives = 151/152 (99%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRR ANIVCKKADVDMNKRAGEL+
Sbjct: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRFANIVCKKADVDMNKRAGELT 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
           AAELDNLMV+VANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH
Sbjct: 61  AAELDNLMVIVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR
Sbjct: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296085211|emb|CBI28706.3| unnamed protein product [Vitis vinifera]

 Score =  308 bits (788), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 146/152 (96%), Positives = 151/152 (99%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLVANE+FQHILRVLNTNVDGKQKIMFALTSIKGIGRR ANIVCKKADVDMNKRAGELS
Sbjct: 761 MSLVANEEFQHILRVLNTNVDGKQKIMFALTSIKGIGRRFANIVCKKADVDMNKRAGELS 820

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
           AAEL+NLMV+VANPRQFKIPDWFLNR+KDYKDG+YSQVVSNALDMKLRDDLERLKKIRNH
Sbjct: 821 AAELENLMVIVANPRQFKIPDWFLNRKKDYKDGRYSQVVSNALDMKLRDDLERLKKIRNH 880

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR
Sbjct: 881 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 912

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15219950|ref|NP_173692.1| 40S ribosomal protein S18 [Arabidopsis thaliana] gi|15234790|ref|NP_192718.1| 40S ribosomal protein S18 [Arabidopsis thaliana] gi|18399100|ref|NP_564434.1| 40S ribosomal protein S18 [Arabidopsis thaliana] gi|297809155|ref|XP_002872461.1| hypothetical protein ARALYDRAFT_489832 [Arabidopsis lyrata subsp. lyrata] gi|297845304|ref|XP_002890533.1| hypothetical protein ARALYDRAFT_472522 [Arabidopsis lyrata subsp. lyrata] gi|297851838|ref|XP_002893800.1| hypothetical protein ARALYDRAFT_473557 [Arabidopsis lyrata subsp. lyrata] gi|464707|sp|P34788.1|RS18_ARATH RecName: Full=40S ribosomal protein S18 gi|10086474|gb|AAG12534.1|AC015446_15 ribosomal protein S18 [Arabidopsis thaliana] gi|10092450|gb|AAG12853.1|AC079286_10 40S ribosomal protein S18; 25853-24673 [Arabidopsis thaliana] gi|14423408|gb|AAK62386.1|AF386941_1 S18.A ribosomal protein [Arabidopsis thaliana] gi|15724158|gb|AAL06471.1|AF411781_1 At1g22780/T22J18_5 [Arabidopsis thaliana] gi|405613|emb|CAA80684.1| ribosomal protein S18A [Arabidopsis thaliana] gi|434343|emb|CAA82273.1| S18 ribosomal protein [Arabidopsis thaliana] gi|434345|emb|CAA82274.1| S18 ribosomal protein [Arabidopsis thaliana] gi|434906|emb|CAA82275.1| S18 ribosomal protein [Arabidopsis thaliana] gi|2505871|emb|CAA72909.1| ribosomal protein S18A [Arabidopsis thaliana] gi|3287678|gb|AAC25506.1| Match to ribosomal S18 gene mRNA gb|Z28701, DNA gb|Z23165 from A. thaliana. ESTs gb|T21121, gb|Z17755, gb|R64776 and gb|R30430 come from this gene [Arabidopsis thaliana] gi|4538910|emb|CAB39647.1| S18.A ribosomal protein [Arabidopsis thaliana] gi|7267675|emb|CAB78103.1| S18.A ribosomal protein [Arabidopsis thaliana] gi|14334584|gb|AAK59471.1| putative ribosomal protein S18 [Arabidopsis thaliana] gi|17979113|gb|AAL47500.1| putative ribosomal protein S18 [Arabidopsis thaliana] gi|21555397|gb|AAM63849.1| ribosomal protein S18, putative [Arabidopsis thaliana] gi|21592452|gb|AAM64403.1| ribosomal protein S18, putative [Arabidopsis thaliana] gi|21593027|gb|AAM64976.1| ribosomal protein S18, putative [Arabidopsis thaliana] gi|30102858|gb|AAP21347.1| At4g09800 [Arabidopsis thaliana] gi|56236126|gb|AAV84519.1| At1g22780 [Arabidopsis thaliana] gi|98961089|gb|ABF59028.1| At1g22780 [Arabidopsis thaliana] gi|145713244|gb|ABP96570.1| pointed first leaf [Arabidopsis thaliana] gi|145713246|gb|ABP96571.1| pointed first leaf [Arabidopsis thaliana] gi|145713248|gb|ABP96572.1| pointed first leaf [Arabidopsis thaliana] gi|145713250|gb|ABP96573.1| pointed first leaf [Arabidopsis thaliana] gi|145713252|gb|ABP96574.1| pointed first leaf [Arabidopsis thaliana] gi|145713254|gb|ABP96575.1| pointed first leaf [Arabidopsis thaliana] gi|145713256|gb|ABP96576.1| pointed first leaf [Arabidopsis thaliana] gi|145713258|gb|ABP96577.1| pointed first leaf [Arabidopsis thaliana] gi|145713260|gb|ABP96578.1| pointed first leaf [Arabidopsis thaliana] gi|145713262|gb|ABP96579.1| pointed first leaf [Arabidopsis thaliana] gi|145713264|gb|ABP96580.1| pointed first leaf [Arabidopsis thaliana] gi|145713266|gb|ABP96581.1| pointed first leaf [Arabidopsis thaliana] gi|145713268|gb|ABP96582.1| pointed first leaf [Arabidopsis thaliana] gi|145713270|gb|ABP96583.1| pointed first leaf [Arabidopsis thaliana] gi|145713272|gb|ABP96584.1| pointed first leaf [Arabidopsis thaliana] gi|145713274|gb|ABP96585.1| pointed first leaf [Arabidopsis thaliana] gi|145713276|gb|ABP96586.1| pointed first leaf [Arabidopsis thaliana] gi|145713278|gb|ABP96587.1| pointed first leaf [Arabidopsis thaliana] gi|145713280|gb|ABP96588.1| pointed first leaf [Arabidopsis thaliana] gi|145713282|gb|ABP96589.1| pointed first leaf [Arabidopsis thaliana] gi|145713284|gb|ABP96590.1| pointed first leaf [Arabidopsis thaliana] gi|297318298|gb|EFH48720.1| hypothetical protein ARALYDRAFT_489832 [Arabidopsis lyrata subsp. lyrata] gi|297336375|gb|EFH66792.1| hypothetical protein ARALYDRAFT_472522 [Arabidopsis lyrata subsp. lyrata] gi|297339642|gb|EFH70059.1| hypothetical protein ARALYDRAFT_473557 [Arabidopsis lyrata subsp. lyrata] gi|332192166|gb|AEE30287.1| 40S ribosomal protein S18 [Arabidopsis thaliana] gi|332193538|gb|AEE31659.1| 40S ribosomal protein S18 [Arabidopsis thaliana] gi|332657400|gb|AEE82800.1| 40S ribosomal protein S18 [Arabidopsis thaliana]

 Score =  307 bits (787), Expect = 9e-82,   Method: Compositional matrix adjust.
 Identities = 148/152 (97%), Positives = 151/152 (99%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLVANE+FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS
Sbjct: 1   MSLVANEEFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
           AAE+DNLM +VANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH
Sbjct: 61  AAEIDNLMTIVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR
Sbjct: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224085191|ref|XP_002307515.1| predicted protein [Populus trichocarpa] gi|222856964|gb|EEE94511.1| predicted protein [Populus trichocarpa]

 Score =  306 bits (785), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 148/152 (97%), Positives = 150/152 (98%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRR +NIVCKKADVDMNKRAGELS
Sbjct: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRFSNIVCKKADVDMNKRAGELS 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
           AAELDNLM +VANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH
Sbjct: 61  AAELDNLMTIVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR
Sbjct: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296081217|emb|CBI18243.3| unnamed protein product [Vitis vinifera]

 Score =  306 bits (783), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 146/152 (96%), Positives = 151/152 (99%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLVANE+FQHILRVLNTNVDGKQKIMFALTSIKGIGRR ANIVCKKADVDMNKRAGELS
Sbjct: 43  MSLVANEEFQHILRVLNTNVDGKQKIMFALTSIKGIGRRFANIVCKKADVDMNKRAGELS 102

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
           AAEL+NLMV+VANPRQFKIPDWFLNR+KDYKDG+YSQVVSNALDMKLRDDLERLKKIRNH
Sbjct: 103 AAELENLMVIVANPRQFKIPDWFLNRKKDYKDGRYSQVVSNALDMKLRDDLERLKKIRNH 162

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR
Sbjct: 163 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 194

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|13877525|gb|AAK43840.1|AF370463_1 S18.A ribosomal protein [Arabidopsis thaliana] gi|17978783|gb|AAL47385.1| S18.A ribosomal protein [Arabidopsis thaliana]

 Score =  305 bits (782), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 147/152 (96%), Positives = 150/152 (98%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLVANE+FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK DVDMNKRAGELS
Sbjct: 1   MSLVANEEFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKTDVDMNKRAGELS 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
           AAE+DNLM +VANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH
Sbjct: 61  AAEIDNLMTIVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR
Sbjct: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559398|ref|XP_002520719.1| 40S ribosomal protein S18, putative [Ricinus communis] gi|223540104|gb|EEF41681.1| 40S ribosomal protein S18, putative [Ricinus communis] gi|313586541|gb|ADR71281.1| 40S ribosomal protein S18A [Hevea brasiliensis]

 Score =  305 bits (780), Expect = 5e-81,   Method: Compositional matrix adjust.
 Identities = 148/152 (97%), Positives = 149/152 (98%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRR ANIVCKKADVDMNKRAGELS
Sbjct: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRFANIVCKKADVDMNKRAGELS 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
           A ELD LMV+VANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH
Sbjct: 61  AEELDKLMVIVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR
Sbjct: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225432662|ref|XP_002282412.1| PREDICTED: 40S ribosomal protein S18-like [Vitis vinifera] gi|225460586|ref|XP_002262702.1| PREDICTED: 40S ribosomal protein S18-like [Vitis vinifera] gi|359479621|ref|XP_003632303.1| PREDICTED: 40S ribosomal protein S18-like [Vitis vinifera]

 Score =  304 bits (778), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 146/152 (96%), Positives = 151/152 (99%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLVANE+FQHILRVLNTNVDGKQKIMFALTSIKGIGRR ANIVCKKADVDMNKRAGELS
Sbjct: 1   MSLVANEEFQHILRVLNTNVDGKQKIMFALTSIKGIGRRFANIVCKKADVDMNKRAGELS 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
           AAEL+NLMV+VANPRQFKIPDWFLNR+KDYKDG+YSQVVSNALDMKLRDDLERLKKIRNH
Sbjct: 61  AAELENLMVIVANPRQFKIPDWFLNRKKDYKDGRYSQVVSNALDMKLRDDLERLKKIRNH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR
Sbjct: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|247421835|gb|ACS96445.1| S18.A ribosomal protein [Jatropha curcas]

 Score =  303 bits (777), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 147/152 (96%), Positives = 149/152 (98%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLVANE+FQHILRVLNTNVDGKQKIMFALTSIKGIGRR ANIVCKKADVDMNKRAGELS
Sbjct: 1   MSLVANEEFQHILRVLNTNVDGKQKIMFALTSIKGIGRRFANIVCKKADVDMNKRAGELS 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
           A ELD LMV+VANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH
Sbjct: 61  AEELDKLMVIVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR
Sbjct: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	152
TAIR|locus:2199670	152	PFL "POINTED FIRST LEAVES" [Ar	1.0	1.0	0.888	8e-69
TAIR|locus:2009066	152	AT1G34030 [Arabidopsis thalian	1.0	1.0	0.888	8e-69
TAIR|locus:2005541	152	RPS18C "S18 ribosomal protein"	1.0	1.0	0.888	8e-69
UNIPROTKB|Q8H590	152	OJ1656_E11.104 "Putative ribos	1.0	1.0	0.796	2e-63
UNIPROTKB|Q8H588	148	OJ1656_E11.108 "Putative ribos	0.960	0.986	0.808	2.1e-61
UNIPROTKB|A8HVP2	153	RPS18 "Ribosomal protein S18"	0.993	0.986	0.668	1.9e-53
ZFIN|ZDB-GENE-020419-20	152	rps18 "ribosomal protein S18"	1.0	1.0	0.657	8e-53
UNIPROTKB|Q90YQ5	152	rps18 "40S ribosomal protein S	1.0	1.0	0.651	2.7e-52
UNIPROTKB|Q3T0R1	152	RPS18 "40S ribosomal protein S	1.0	1.0	0.651	3.5e-52
UNIPROTKB|Q5TJE9	152	RPS18 "40S ribosomal protein S	1.0	1.0	0.651	3.5e-52

TAIR|locus:2199670 PFL "POINTED FIRST LEAVES" [Arabidopsis thaliana (taxid:3702)]

 Score = 698 (250.8 bits), Expect = 8.0e-69, P = 8.0e-69
 Identities = 135/152 (88%), Positives = 138/152 (90%)

Query:     1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
             MSLVANE+FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS
Sbjct:     1 MSLVANEEFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60

Query:    61 AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
             AAE+DNLM +VANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH
Sbjct:    61 AAEIDNLMTIVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120

Query:   121 RGLRHYWGLRVRGQHXXXXXXXXXXXXXSKKR 152
             RGLRHYWGLRVRGQH             SKKR
Sbjct:   121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=IBA

GO:0005618 "cell wall" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

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

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0006413 "translational initiation" evidence=TAS

TAIR|locus:2009066 AT1G34030 [Arabidopsis thaliana (taxid:3702)]

 Score = 698 (250.8 bits), Expect = 8.0e-69, P = 8.0e-69
 Identities = 135/152 (88%), Positives = 138/152 (90%)

Query:     1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
             MSLVANE+FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS
Sbjct:     1 MSLVANEEFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60

Query:    61 AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
             AAE+DNLM +VANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH
Sbjct:    61 AAEIDNLMTIVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120

Query:   121 RGLRHYWGLRVRGQHXXXXXXXXXXXXXSKKR 152
             RGLRHYWGLRVRGQH             SKKR
Sbjct:   121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA;ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=IBA

GO:0005886 "plasma membrane" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0016020 "membrane" evidence=IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005829 "cytosol" evidence=RCA

GO:0009506 "plasmodesma" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0001510 "RNA methylation" evidence=RCA

TAIR|locus:2005541 RPS18C "S18 ribosomal protein" [Arabidopsis thaliana (taxid:3702)]

 Score = 698 (250.8 bits), Expect = 8.0e-69, P = 8.0e-69
 Identities = 135/152 (88%), Positives = 138/152 (90%)

Query:     1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
             MSLVANE+FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS
Sbjct:     1 MSLVANEEFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60

Query:    61 AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
             AAE+DNLM +VANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH
Sbjct:    61 AAEIDNLMTIVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120

Query:   121 RGLRHYWGLRVRGQHXXXXXXXXXXXXXSKKR 152
             RGLRHYWGLRVRGQH             SKKR
Sbjct:   121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA;ISS;TAS

GO:0015935 "small ribosomal subunit" evidence=ISS;TAS

GO:0042254 "ribosome biogenesis" evidence=IBA

GO:0005730 "nucleolus" evidence=IDA

GO:0005773 "vacuole" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

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

GO:0005829 "cytosol" evidence=RCA

GO:0009506 "plasmodesma" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0001510 "RNA methylation" evidence=RCA

UNIPROTKB|Q8H590 OJ1656_E11.104 "Putative ribosomal protein S18A" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 647 (232.8 bits), Expect = 2.0e-63, P = 2.0e-63
 Identities = 121/152 (79%), Positives = 132/152 (86%)

Query:     1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
             MSL+A EDFQHILR+LNTNVDGKQKIMFALTSIKG+GRR +NI CKKAD+DMNKRAGEL+
Sbjct:     1 MSLIAGEDFQHILRLLNTNVDGKQKIMFALTSIKGVGRRFSNIACKKADIDMNKRAGELT 60

Query:    61 AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
               EL+ LM VVANPRQFK+PDWFLNR+KDYKDG++SQVVSNALDMKLRDDLERLKKIRNH
Sbjct:    61 PEELERLMTVVANPRQFKVPDWFLNRKKDYKDGRFSQVVSNALDMKLRDDLERLKKIRNH 120

Query:   121 RGLRHYWGLRVRGQHXXXXXXXXXXXXXSKKR 152
             RGLRHYWGLRVRGQH             SKKR
Sbjct:   121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152

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

GO:0005829 "cytosol" evidence=IBA

GO:0006412 "translation" evidence=IBA

GO:0015935 "small ribosomal subunit" evidence=IBA

GO:0042254 "ribosome biogenesis" evidence=IBA

UNIPROTKB|Q8H588 OJ1656_E11.108 "Putative ribosomal protein S18" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 628 (226.1 bits), Expect = 2.1e-61, P = 2.1e-61
 Identities = 118/146 (80%), Positives = 127/146 (86%)

Query:     7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 66
             EDFQHILR+LNTNVDGKQKIMFALTSIKGIGRR +NI CKKAD+DMNKRAGEL+  EL+ 
Sbjct:     3 EDFQHILRLLNTNVDGKQKIMFALTSIKGIGRRFSNIACKKADIDMNKRAGELTPEELER 62

Query:    67 LMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHY 126
             LM VVANPRQFK+PDWFLNR+KDYKDG++SQVVSNALDMKLRDDLERLKKIRNHRGLRHY
Sbjct:    63 LMTVVANPRQFKVPDWFLNRKKDYKDGRFSQVVSNALDMKLRDDLERLKKIRNHRGLRHY 122

Query:   127 WGLRVRGQHXXXXXXXXXXXXXSKKR 152
             WGLRVRGQH             SKKR
Sbjct:   123 WGLRVRGQHTKTTGRRGKTVGVSKKR 148

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

GO:0005829 "cytosol" evidence=IBA

GO:0006412 "translation" evidence=IBA

GO:0015935 "small ribosomal subunit" evidence=IBA

GO:0042254 "ribosome biogenesis" evidence=IBA

UNIPROTKB|A8HVP2 RPS18 "Ribosomal protein S18" [Chlamydomonas reinhardtii (taxid:3055)]

 Score = 553 (199.7 bits), Expect = 1.9e-53, P = 1.9e-53
 Identities = 101/151 (66%), Positives = 123/151 (81%)

Query:     2 SLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSA 61
             SLV  +DFQHILR+LNTNVDGK KIM+A+T+I+GIGRR +N+VCKKA+VD+ KRAGE SA
Sbjct:     3 SLVQGDDFQHILRLLNTNVDGKNKIMYAMTAIRGIGRRFSNLVCKKAEVDLRKRAGECSA 62

Query:    62 AELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHR 121
              EL+ +M +VANPR +KIPDWFLNRQKD+K G++SQ+ S+ LD  +RDDLERLKKIRNHR
Sbjct:    63 DELERMMGIVANPRAYKIPDWFLNRQKDHKTGRFSQLTSSQLDTVMRDDLERLKKIRNHR 122

Query:   122 GLRHYWGLRVRGQHXXXXXXXXXXXXXSKKR 152
             GLRHYWGLRVRGQH             +KK+
Sbjct:   123 GLRHYWGLRVRGQHTKTTGRAGKTVGVAKKK 153

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

GO:0005829 "cytosol" evidence=IBA

GO:0006412 "translation" evidence=IBA

GO:0015935 "small ribosomal subunit" evidence=IBA

GO:0042254 "ribosome biogenesis" evidence=IBA

ZFIN|ZDB-GENE-020419-20 rps18 "ribosomal protein S18" [Danio rerio (taxid:7955)]

 Score = 547 (197.6 bits), Expect = 8.0e-53, P = 8.0e-53
 Identities = 100/152 (65%), Positives = 124/152 (81%)

Query:     1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
             MSLV  E FQHILRVLNTN+DG++KI FA+T+IKG+GRR A++V +KAD+D+NKRAGEL+
Sbjct:     1 MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLNKRAGELT 60

Query:    61 AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
               E++ ++ ++ NPRQ+KIPDWFLNRQKD KDGKYSQV++N LD KLR+DLERLKKIR H
Sbjct:    61 EDEVERVVTIMQNPRQYKIPDWFLNRQKDIKDGKYSQVLANGLDNKLREDLERLKKIRAH 120

Query:   121 RGLRHYWGLRVRGQHXXXXXXXXXXXXXSKKR 152
             RGLRH+WGLRVRGQH             SKK+
Sbjct:   121 RGLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK 152

GO:0003723 "RNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0006412 "translation" evidence=IEA;IBA

GO:0015935 "small ribosomal subunit" evidence=IBA

GO:0042254 "ribosome biogenesis" evidence=IBA

GO:0005829 "cytosol" evidence=IBA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0051726 "regulation of cell cycle" evidence=IMP

UNIPROTKB|Q90YQ5 rps18 "40S ribosomal protein S18" [Ictalurus punctatus (taxid:7998)]

 Score = 542 (195.9 bits), Expect = 2.7e-52, P = 2.7e-52
 Identities = 99/152 (65%), Positives = 124/152 (81%)

Query:     1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
             MSLV  E FQHILRVLNTN+DG++KI FA+T+IKG+GRR A++V +KAD+D++KRAGEL+
Sbjct:     1 MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLSKRAGELT 60

Query:    61 AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
               E++ ++ ++ NPRQ+KIPDWFLNRQKD KDGKYSQV++N LD KLR+DLERLKKIR H
Sbjct:    61 EDEVERVVTIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAH 120

Query:   121 RGLRHYWGLRVRGQHXXXXXXXXXXXXXSKKR 152
             RGLRH+WGLRVRGQH             SKK+
Sbjct:   121 RGLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK 152

GO:0015935 "small ribosomal subunit" evidence=ISS

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

UNIPROTKB|Q3T0R1 RPS18 "40S ribosomal protein S18" [Bos taurus (taxid:9913)]

 Score = 541 (195.5 bits), Expect = 3.5e-52, P = 3.5e-52
 Identities = 99/152 (65%), Positives = 123/152 (80%)

Query:     1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
             MSLV  E FQHILRVLNTN+DG++KI FA+T+IKG+GRR A++V +KAD+D+ KRAGEL+
Sbjct:     1 MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELT 60

Query:    61 AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
               E++ ++ ++ NPRQ+KIPDWFLNRQKD KDGKYSQV++N LD KLR+DLERLKKIR H
Sbjct:    61 EDEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAH 120

Query:   121 RGLRHYWGLRVRGQHXXXXXXXXXXXXXSKKR 152
             RGLRH+WGLRVRGQH             SKK+
Sbjct:   121 RGLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK 152

GO:0015935 "small ribosomal subunit" evidence=ISS;IBA

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

GO:0042254 "ribosome biogenesis" evidence=IBA

GO:0006412 "translation" evidence=IBA

GO:0005829 "cytosol" evidence=IBA

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

GO:0019843 "rRNA binding" evidence=IEA

UNIPROTKB|Q5TJE9 RPS18 "40S ribosomal protein S18" [Canis lupus familiaris (taxid:9615)]

 Score = 541 (195.5 bits), Expect = 3.5e-52, P = 3.5e-52
 Identities = 99/152 (65%), Positives = 123/152 (80%)

Query:     1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
             MSLV  E FQHILRVLNTN+DG++KI FA+T+IKG+GRR A++V +KAD+D+ KRAGEL+
Sbjct:     1 MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELT 60

Query:    61 AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
               E++ ++ ++ NPRQ+KIPDWFLNRQKD KDGKYSQV++N LD KLR+DLERLKKIR H
Sbjct:    61 EDEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAH 120

Query:   121 RGLRHYWGLRVRGQHXXXXXXXXXXXXXSKKR 152
             RGLRH+WGLRVRGQH             SKK+
Sbjct:   121 RGLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK 152

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

GO:0015935 "small ribosomal subunit" evidence=ISS;IBA

GO:0042254 "ribosome biogenesis" evidence=IBA

GO:0006412 "translation" evidence=IBA

GO:0005829 "cytosol" evidence=IBA

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

GO:0019843 "rRNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q97B96	RS13_THEVO	No assigned EC number	0.3809	0.9605	0.8538	yes	no
Q90YQ5	RS18_ICTPU	No assigned EC number	0.7302	1.0	1.0	N/A	no
A5JST6	RS18_CAPHI	No assigned EC number	0.7302	1.0	1.0	N/A	no
P49202	RS18_CHLRE	No assigned EC number	0.7350	0.9934	0.9869	N/A	no
Q869U7	RS18_DICDI	No assigned EC number	0.6556	0.9934	0.9805	yes	no
Q962R1	RS18_SPOFR	No assigned EC number	0.7105	1.0	1.0	N/A	no
Q3T0R1	RS18_BOVIN	No assigned EC number	0.7302	1.0	1.0	yes	no
Q9V1A0	RS13_PYRAB	No assigned EC number	0.4275	0.9539	0.9797	yes	no
O26141	RS13_METTH	No assigned EC number	0.4178	0.9605	0.9798	yes	no
A1RT04	RS13_PYRIL	No assigned EC number	0.3673	0.9605	0.9542	yes	no
Q2NFZ3	RS13_METST	No assigned EC number	0.4362	0.9802	0.9738	yes	no
Q8PV19	RS13_METMA	No assigned EC number	0.4285	0.9605	0.9012	yes	no
P48151	RS18_ENTHI	No assigned EC number	0.6013	1.0	0.9806	N/A	no
A5UN52	RS13_METS3	No assigned EC number	0.4166	0.9473	0.9795	yes	no
P54019	RS13_METJA	No assigned EC number	0.4285	0.9671	0.98	yes	no
Q46GC7	RS13_METBF	No assigned EC number	0.4285	0.9605	0.9012	yes	no
A0B9L1	RS13_METTP	No assigned EC number	0.4413	0.9473	0.9056	yes	no
A2BK76	RS13_HYPBU	No assigned EC number	0.4324	0.9736	0.9801	yes	no
Q9YB60	RS13_AERPE	No assigned EC number	0.4066	0.9868	1.0	yes	no
Q12ZR6	RS13_METBU	No assigned EC number	0.4026	0.9736	1.0	yes	no
Q2FT96	RS13_METHJ	No assigned EC number	0.4013	0.9605	0.9668	yes	no
A3DMQ3	RS13_STAMF	No assigned EC number	0.4133	0.9868	0.9933	yes	no
A3CWH6	RS13_METMJ	No assigned EC number	0.3904	0.9539	0.9731	yes	no
Q8U0E2	RS13_PYRFU	No assigned EC number	0.4344	0.9539	0.9797	yes	no
O27999	RS13_ARCFU	No assigned EC number	0.4027	0.9407	0.9794	yes	no
Q8JGS9	RS18_DANRE	No assigned EC number	0.7368	1.0	1.0	yes	no
P62269	RS18_HUMAN	No assigned EC number	0.7302	1.0	1.0	yes	no
A3MUT0	RS13_PYRCJ	No assigned EC number	0.3630	0.9539	0.9477	yes	no
Q8ISP0	RS18_BRABE	No assigned EC number	0.7828	1.0	1.0	N/A	no
Q3IQT9	RS13_NATPD	No assigned EC number	0.4027	0.9407	0.8411	yes	no
Q6KZP8	RS13_PICTO	No assigned EC number	0.3877	0.9671	0.9303	yes	no
Q8IT98	RS18_ARGIR	No assigned EC number	0.7631	1.0	1.0	N/A	no
Q5JJF1	RS13_PYRKO	No assigned EC number	0.4149	0.9671	0.9865	yes	no
O74021	RS13_PYRHO	No assigned EC number	0.4413	0.9539	0.9797	yes	no
P34788	RS18_ARATH	No assigned EC number	0.9736	1.0	1.0	yes	no
Q5TJE9	RS18_CANFA	No assigned EC number	0.7302	1.0	1.0	yes	no
O94754	RS18_SCHPO	No assigned EC number	0.7171	1.0	1.0	yes	no
Q8SRP2	RS18_ENCCU	No assigned EC number	0.4344	0.9539	0.9477	yes	no
P0CX55	RS18A_YEAST	No assigned EC number	0.6666	0.9342	0.9726	yes	no
P0CX56	RS18B_YEAST	No assigned EC number	0.6666	0.9342	0.9726	yes	no
Q8ZTV0	RS13_PYRAE	No assigned EC number	0.3605	0.9605	0.9605	yes	no
Q9HJD6	RS13_THEAC	No assigned EC number	0.3605	0.9605	0.8538	yes	no
P62271	RS18_RAT	No assigned EC number	0.7302	1.0	1.0	yes	no
P62270	RS18_MOUSE	No assigned EC number	0.7302	1.0	1.0	yes	no
P41094	RS18_DROME	No assigned EC number	0.7039	1.0	1.0	yes	no
P62272	RS18_PIG	No assigned EC number	0.7302	1.0	1.0	yes	no
A2SSW0	RS13_METLZ	No assigned EC number	0.3973	0.9736	0.9866	yes	no
Q8TVC1	RS13_METKA	No assigned EC number	0.4304	0.9802	0.9867	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	fgenesh2_kg.1__3511__AT1G34030.1	annotation not avaliable (152 aa)
		(Arabidopsis lyrata)
Predicted Functional Partners:
	fgenesh2_kg.6__1496__AT5G15200.1	annotation not avaliable (198 aa)	•			•	•	•	•		0.928
	fgenesh2_kg.7__3438__AT5G39850.1	annotation not avaliable (197 aa)	•			•	•	•	•		0.927
	fgenesh2_kg.6__1842__AT2G09990.1	annotation not avaliable (146 aa)	•			•	•	•	•		0.879
	fgenesh2_kg.3__384__AT3G04230.1	annotation not avaliable (146 aa)	•			•	•	•	•		0.875
	fgenesh2_kg.3__1244__AT3G11940.2	annotation not avaliable (207 aa)				•	•	•	•		0.813
	fgenesh2_kg.6__206__AT5G02960.1	annotation not avaliable (142 aa)				•	•	•	•		0.810
	fgenesh2_kg.4__1779__AT2G37270.2	annotation not avaliable (207 aa)				•	•	•	•		0.808
	fgenesh2_kg.7__621__AT4G34670.1	annotation not avaliable (262 aa)				•	•	•	•		0.806
	fgenesh2_kg.3__991__AT3G09680.1	annotation not avaliable (142 aa)				•	•	•	•		0.802
	scaffold_502339.1	annotation not avaliable (149 aa)	•			•	•		•		0.798

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	152
PTZ00134	154	PTZ00134, PTZ00134, 40S ribosomal protein S18; Pro	3e-93
PRK04053	149	PRK04053, rps13p, 30S ribosomal protein S13P; Revi	5e-60
TIGR03629	144	TIGR03629, arch_S13P, archaeal ribosomal protein S	8e-54
pfam00416	106	pfam00416, Ribosomal_S13, Ribosomal protein S13/S1	2e-42
COG0099	121	COG0099, RpsM, Ribosomal protein S13 [Translation,	7e-40
PRK05179	122	PRK05179, rpsM, 30S ribosomal protein S13; Validat	4e-16
TIGR03631	113	TIGR03631, bact_S13, 30S ribosomal protein S13	9e-16
CHL00137	122	CHL00137, rps13, ribosomal protein S13; Validated	2e-08

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

 Score =  266 bits (682), Expect = 3e-93
 Identities = 108/152 (71%), Positives = 133/152 (87%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           ++L   +DFQHILR+LNTNVDGK+K+ +ALT+IKGIGRR A +VCKKA +D+ KRAGEL+
Sbjct: 3   LTLEKADDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELT 62

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
           A E++ ++ ++ANP QFKIPDWFLNRQ+D KDGK S + SN LD KLR+DLERLKKIR H
Sbjct: 63  AEEIEKIVEIIANPLQFKIPDWFLNRQRDPKDGKNSHLTSNMLDTKLREDLERLKKIRLH 122

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRH+WGLRVRGQHTKTTGRRG+TVGVS+K+
Sbjct: 123 RGLRHHWGLRVRGQHTKTTGRRGRTVGVSRKK 154

Length = 154

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

 Score =  181 bits (463), Expect = 5e-60
 Identities = 65/148 (43%), Positives = 104/148 (70%)

Query: 5   ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAEL 64
             E+F++I+R+  T++DG + + +ALT IKGIGRR A  + +K  +D N + G LS  E+
Sbjct: 2   MEEEFKYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEI 61

Query: 65  DNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLR 124
           + +   + +P +  IP W LNR+KDY+ G+   ++ + L + +R+D+ R+KKIR++RG+R
Sbjct: 62  EKIEEALEDPAEEGIPSWMLNRRKDYETGEDLHLIGSDLILTVREDINRMKKIRSYRGIR 121

Query: 125 HYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           H  GL+VRGQ T++TGR G TVGVS+K+
Sbjct: 122 HELGLKVRGQRTRSTGRTGGTVGVSRKK 149

Length = 149

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

 Score =  166 bits (422), Expect = 8e-54
 Identities = 70/145 (48%), Positives = 106/145 (73%), Gaps = 1/145 (0%)

Query: 8   DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67
           +F++I+R+ +T++DG + + +ALT IKGIGRR A  + +K  VD N + G L   E++ L
Sbjct: 1   EFKYIVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKL 60

Query: 68  MVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYW 127
              V N  ++ IP W LNR+KDY+ G+   ++ + LDM +R+D+ R+KKIR++RG+RH  
Sbjct: 61  EEAVEN-YEYGIPSWLLNRRKDYETGEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHEL 119

Query: 128 GLRVRGQHTKTTGRRGKTVGVSKKR 152
           GL+VRGQ TK+TGRRG+TVGVS+K+
Sbjct: 120 GLKVRGQRTKSTGRRGRTVGVSRKK 144

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

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

 Score =  136 bits (344), Expect = 2e-42
 Identities = 63/129 (48%), Positives = 78/129 (60%), Gaps = 23/129 (17%)

Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+LNTN+DG +KI  ALT IKGIGRR AN + KKA VD +KR GEL+  E+D +  +++N
Sbjct: 1   RILNTNLDGNKKIEIALTYIKGIGRRKANQILKKAGVDKDKRVGELTEEEIDRIRDIISN 60

Query: 74  PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
                                   VV N L  K+R+D+ERLKKIR +RGLRH  GL VRG
Sbjct: 61  -----------------------YVVENDLRRKIRNDIERLKKIRCYRGLRHIRGLPVRG 97

Query: 134 QHTKTTGRR 142
           Q TKT  R 
Sbjct: 98  QRTKTNART 106

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

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

 Score =  129 bits (328), Expect = 7e-40
 Identities = 52/143 (36%), Positives = 76/143 (53%), Gaps = 24/143 (16%)

Query: 12  ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71
           + R+   ++ G ++++ ALT I GIGRR A  +CKKA +D +KR GEL+  E++ L   +
Sbjct: 1   MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAI 60

Query: 72  ANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRV 131
            N                        +V   L  ++R D++RL KI  +RG+RH  GL V
Sbjct: 61  QN----------------------KYLVEGDLRREVRMDIKRLMKIGCYRGIRHRRGLPV 98

Query: 132 RGQHTKTTGRR--GKTVGVSKKR 152
           RGQ TKT  R   G   GV+KK+
Sbjct: 99  RGQRTKTNARTRKGPRKGVAKKK 121

Length = 121

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

 Score = 69.3 bits (171), Expect = 4e-16
 Identities = 47/143 (32%), Positives = 70/143 (48%), Gaps = 28/143 (19%)

Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+   ++   ++++ ALT I GIGR  A  +   A +D + R  +L+  ELD +   +  
Sbjct: 3   RIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEI-- 60

Query: 74  PRQFKIPDWFLNRQKDYK-DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVR 132
                         K+YK +G   + VS  +++K      RL  I  +RGLRH  GL VR
Sbjct: 61  -------------DKNYKVEGDLRREVS--MNIK------RLMDIGCYRGLRHRRGLPVR 99

Query: 133 GQHTKTTGR--RG--KTVGVSKK 151
           GQ TKT  R  +G  KT+   KK
Sbjct: 100 GQRTKTNARTRKGPRKTIAGKKK 122

Length = 122

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

 Score = 68.3 bits (168), Expect = 9e-16
 Identities = 43/129 (33%), Positives = 64/129 (49%), Gaps = 24/129 (18%)

Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+   ++   +++  ALT I GIGR  A  + +KA +D +KR  +L+  EL+ +   +  
Sbjct: 1   RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEI-- 58

Query: 74  PRQFKIPDWFLNRQKDYK-DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVR 132
                        +  YK +G   + VS  L++K      RL  I  +RGLRH  GL VR
Sbjct: 59  -------------EAKYKVEGDLRREVS--LNIK------RLMDIGCYRGLRHRRGLPVR 97

Query: 133 GQHTKTTGR 141
           GQ TKT  R
Sbjct: 98  GQRTKTNAR 106

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

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

 Score = 49.3 bits (118), Expect = 2e-08
 Identities = 41/132 (31%), Positives = 65/132 (49%), Gaps = 26/132 (19%)

Query: 24  QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWF 83
           ++I +ALT I GIG   A  + +KA++D + R  +L+  ++  L  ++            
Sbjct: 13  KRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREII------------ 60

Query: 84  LNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGR-- 141
              +++Y+       V   L      +++RL +I  +RG RH  GL VRGQ T+T  R  
Sbjct: 61  ---EENYQ-------VEGDLRRFESLNIKRLMEINCYRGRRHRLGLPVRGQRTRTNARTR 110

Query: 142 RG--KTVGVSKK 151
           RG  KTV   KK
Sbjct: 111 RGAKKTVAGKKK 122

Length = 122

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	152
PTZ00134	154	40S ribosomal protein S18; Provisional	100.0
PRK04053	149	rps13p 30S ribosomal protein S13P; Reviewed	100.0
TIGR03629	144	arch_S13P archaeal ribosomal protein S13P. This mo	100.0
COG0099	121	RpsM Ribosomal protein S13 [Translation, ribosomal	100.0
KOG3311	152	consensus Ribosomal protein S18 [Translation, ribo	100.0
PRK05179	122	rpsM 30S ribosomal protein S13; Validated	100.0
CHL00137	122	rps13 ribosomal protein S13; Validated	100.0
TIGR03631	113	bact_S13 30S ribosomal protein S13. This model des	100.0
PF00416	107	Ribosomal_S13: Ribosomal protein S13/S18; InterPro	100.0
COG1389	538	DNA topoisomerase VI, subunit B [DNA replication,	98.88
PRK04184	535	DNA topoisomerase VI subunit B; Validated	98.83
TIGR01052	488	top6b DNA topoisomerase VI, B subunit. This model	98.8
PF06831	92	H2TH: Formamidopyrimidine-DNA glycosylase H2TH dom	97.37
PRK01103	274	formamidopyrimidine/5-formyluracil/ 5-hydroxymethy	97.24
PRK14810	272	formamidopyrimidine-DNA glycosylase; Provisional	96.65
PRK14811	269	formamidopyrimidine-DNA glycosylase; Provisional	96.63
PRK10445	263	endonuclease VIII; Provisional	96.61
PRK13945	282	formamidopyrimidine-DNA glycosylase; Provisional	96.5
TIGR00577	272	fpg formamidopyrimidine-DNA glycosylase (fpg). All	96.45
PRK14867	659	DNA topoisomerase VI subunit B; Provisional	96.22
PRK14868	795	DNA topoisomerase VI subunit B; Provisional	95.63
COG0266	273	Nei Formamidopyrimidine-DNA glycosylase [DNA repli	94.64
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	94.17
PF05833	455	FbpA: Fibronectin-binding protein A N-terminus (Fb	93.93
TIGR00275	400	flavoprotein, HI0933 family. The model when search	92.72
PF11798	32	IMS_HHH: IMS family HHH motif; InterPro: IPR024728	90.39
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	90.07
PRK00274	272	ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1	89.14
PF10391	52	DNA_pol_lambd_f: Fingers domain of DNA polymerase	88.17
smart00278	26	HhH1 Helix-hairpin-helix DNA-binding motif class 1	87.79
COG0030	259	KsgA Dimethyladenosine transferase (rRNA methylati	87.57
PRK02515	132	psbU photosystem II complex extrinsic protein prec	86.16
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	85.89
COG3743	133	Uncharacterized conserved protein [Function unknow	85.74
PF09239	160	Topo-VIb_trans: Topoisomerase VI B subunit, transd	85.37
KOG3311	152	consensus Ribosomal protein S18 [Translation, ribo	85.34
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	85.13
PF03486	409	HI0933_like: HI0933-like protein; InterPro: IPR004	84.51
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	84.15
PRK14604	195	ruvA Holliday junction DNA helicase RuvA; Provisio	83.92
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	83.75
TIGR00755	253	ksgA dimethyladenosine transferase. Alternate name	83.64
PF00398	262	RrnaAD: Ribosomal RNA adenine dimethylase; InterPr	83.52
COG0632	201	RuvA Holliday junction resolvasome, DNA-binding su	83.24
PRK14602	203	ruvA Holliday junction DNA helicase RuvA; Provisio	82.75
TIGR03252	177	uncharacterized HhH-GPD family protein. This model	82.24
COG1293	564	Predicted RNA-binding protein homologous to eukary	81.85

>PTZ00134 40S ribosomal protein S18; Provisional

Probab=100.00  E-value=7e-65  Score=389.36  Aligned_cols=152  Identities=72%  Similarity=1.163  Sum_probs=146.8

Q ss_pred             CCCC--CccccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCcc
Q 031813            1 MSLV--ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFK   78 (152)
Q Consensus         1 ~~~~--~~~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~   78 (152)
                      |+++  ++++|+|||||+|||||++|+|.+||++|||||..+|.+||++|||||++++++||++|++.|.++|++|.+|.
T Consensus         1 ~~~~~~~~~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~   80 (154)
T PTZ00134          1 MSLTLEKADDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFK   80 (154)
T ss_pred             CCccccchhhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCC
Confidence            4455  33589999999999999999999999999999999999999999999999999999999999999999987899


Q ss_pred             CCccccCccCCCCCCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031813           79 IPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR  152 (152)
Q Consensus        79 ip~w~~nr~~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~gv~~~k  152 (152)
                      +|+||+||++|+.||+|.|+||+||++.+++||+||++|+||||+||++||||||||||||||||+++||++||
T Consensus        81 iP~w~~nr~kd~~tG~d~h~i~~dL~~~~~~dI~Rl~~I~sYRG~RH~~GLpVRGQRTkTnaR~g~~~gv~~kk  154 (154)
T PTZ00134         81 IPDWFLNRQRDPKDGKNSHLTSNMLDTKLREDLERLKKIRLHRGLRHHWGLRVRGQHTKTTGRRGRTVGVSRKK  154 (154)
T ss_pred             CChhHhhccccccccchhhhhHHHHHHHHHHHHHHHHHhcchheeecccCCccCCccCCCCCccccccceeccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999997

>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed

Probab=100.00  E-value=7.6e-64  Score=382.12  Aligned_cols=147  Identities=44%  Similarity=0.804  Sum_probs=144.9

Q ss_pred             ccccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccC
Q 031813            6 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLN   85 (152)
Q Consensus         6 ~~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~n   85 (152)
                      +++|++|+||+|||||++|+|.+||++|||||+++|.+||+++||||++++++||++|+++|.++|++|+.+.+|+||+|
T Consensus         3 ~~~~~~m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~N   82 (149)
T PRK04053          3 EEEFKYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWMLN   82 (149)
T ss_pred             hhhhhhhHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhhhc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999888999999999


Q ss_pred             ccCCCCCCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031813           86 RQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR  152 (152)
Q Consensus        86 r~~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~gv~~~k  152 (152)
                      |++|+.||++.|+||+||++.+++||+||++|+||||+||.+||||||||||||||||+++||+|||
T Consensus        83 r~~d~~tg~~~~~ie~dLr~~~~~~I~rl~~I~syRG~RH~~GLPVRGQRTrTNaRtg~~~gv~~kk  149 (149)
T PRK04053         83 RRKDYETGEDLHLIGSDLILTVREDINRMKKIRSYRGIRHELGLKVRGQRTRSTGRTGGTVGVSRKK  149 (149)
T ss_pred             cccccccCccceEehHHHHHHHHHHHHHHHHhcceeeecccCCCCCCCCcCCCCCcCCCccccccCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999997

>TIGR03629 arch_S13P archaeal ribosomal protein S13P

Probab=100.00  E-value=5.3e-63  Score=375.85  Aligned_cols=144  Identities=49%  Similarity=0.880  Sum_probs=141.8

Q ss_pred             ccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCcc
Q 031813            8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQ   87 (152)
Q Consensus         8 ~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~   87 (152)
                      +|+||+||+|+|||++|+|.+||++|||||+.+|.+||+++|||+++++++||++|+++|.++|++ ..|.+|+||+||+
T Consensus         1 ~~~~m~rI~~~~i~~~k~v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~-~~~~iP~w~~Nr~   79 (144)
T TIGR03629         1 EFKYIVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVEN-YEYGIPSWLLNRR   79 (144)
T ss_pred             CcceeeeeeCccCCCCCEEEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHh-ccccCCHHHhhcc
Confidence            589999999999999999999999999999999999999999999999999999999999999998 6799999999999


Q ss_pred             CCCCCCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031813           88 KDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR  152 (152)
Q Consensus        88 ~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~gv~~~k  152 (152)
                      +|+.||++.|+||+||++.+++||+||++|+||||+||.+||||||||||||||||+++||++||
T Consensus        80 ~d~~tg~~~~~ie~dL~~~~~~dI~rl~~I~~yRG~RH~~gLpVRGQRTrTNaRtg~~~gv~~kk  144 (144)
T TIGR03629        80 KDYETGEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVRGQRTKSTGRRGRTVGVSRKK  144 (144)
T ss_pred             cccccCccceEehHHHHHHHHHHHHHHHHhcceeeeeccCCCCCCCCcCCCCCcCCCccccccCC
Confidence            99999999999999999999999999999999999999999999999999999999999999997

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

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

Probab=100.00  E-value=4e-51  Score=299.67  Aligned_cols=119  Identities=44%  Similarity=0.701  Sum_probs=115.1

Q ss_pred             hhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCC
Q 031813           12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYK   91 (152)
Q Consensus        12 ~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~   91 (152)
                      |+||+|+|||++|.|.+|||+|||||..+|.+||+++||||++++++|||||+++|.+++++                  
T Consensus         1 maRIagvdip~~K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~~------------------   62 (121)
T COG0099           1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQN------------------   62 (121)
T ss_pred             CceecccCCCCCceEeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHHh------------------
Confidence            79999999999999999999999999999999999999999999999999999999999986                  


Q ss_pred             CCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCC--ccceeeeccC
Q 031813           92 DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRR--GKTVGVSKKR  152 (152)
Q Consensus        92 sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart--~~~~gv~~~k  152 (152)
                          .|+||.||++++++||+||++|+||||+||..|||||||||+|||||  |.++||.+||
T Consensus        63 ----~~~vegDLr~~v~~dIkRl~~i~~YRGiRH~~GLpVRGQrTktnaRtrkG~~~~v~~KK  121 (121)
T COG0099          63 ----KYLVEGDLRREVRMDIKRLMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKGVAKKK  121 (121)
T ss_pred             ----cCeehhHHHHHHHHHHHHHHHhhhhhhhhhhcCCCCCCcccCccccccCCCccccccCC
Confidence                23569999999999999999999999999999999999999999999  9999999987

>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=2e-49  Score=300.45  Aligned_cols=152  Identities=70%  Similarity=1.140  Sum_probs=150.4

Q ss_pred             CCCCCccccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCC
Q 031813            1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIP   80 (152)
Q Consensus         1 ~~~~~~~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip   80 (152)
                      |||+-++.||+|+||++++++++++|.|||++|||||...|..+|+++|+++.+++++|+++|++.+..++++|..|.+|
T Consensus         1 msl~~~~~~q~i~~il~~~~dg~~~V~fAl~~i~Gig~~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~d~~~~~~~   80 (152)
T KOG3311|consen    1 MSLVIPEAFQHILRILNTNVDGKRKVTFALTSIKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQILNDPRQYKIP   80 (152)
T ss_pred             CceecchhHHHHHHHHccCCCCCceeEEEEEEEeeechhhhhhhhhhcCcchhhhhccccHHHHHHHHHHhcCHHHhcCc
Confidence            89999889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCccCCCCCCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031813           81 DWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR  152 (152)
Q Consensus        81 ~w~~nr~~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~gv~~~k  152 (152)
                      .|++|+++|..+|+..|++.++++..++++|+|++++.||||+||.+|||||||||+|||+.|++|||++||
T Consensus        81 ~~~l~rq~~~~dG~~~~l~~~~ld~r~r~~ieRlkki~~~RG~rh~~gl~vRGQ~Tkt~~~~gk~v~Vs~Kk  152 (152)
T KOG3311|consen   81 DWFLNRQKDIIDGKVNHLLGNGLDTRLRADIERLKKIRCHRGLRHFWGLRVRGQRTKTNGRRGKTVGVSGKK  152 (152)
T ss_pred             hHHHHhhcccccCccccccchhhhhHHHHHHHHHhhhcccccceeccCCcccCccccccccccceeeecccC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999997

>PRK05179 rpsM 30S ribosomal protein S13; Validated

Probab=100.00  E-value=8.1e-48  Score=285.53  Aligned_cols=111  Identities=34%  Similarity=0.527  Sum_probs=107.6

Q ss_pred             hhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCC
Q 031813           12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYK   91 (152)
Q Consensus        12 ~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~   91 (152)
                      ||||+|||||++|+|.+||++|||||..+|.+||+++||||++++++|+++|++.|.++|+++  |              
T Consensus         1 MvrI~~~~l~~~k~v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~~--~--------------   64 (122)
T PRK05179          1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKN--Y--------------   64 (122)
T ss_pred             CceecCccCCCCcEEEeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhh--c--------------
Confidence            899999999999999999999999999999999999999999999999999999999999873  3              


Q ss_pred             CCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCcc
Q 031813           92 DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGK  144 (152)
Q Consensus        92 sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~  144 (152)
                            .+|+||++.+++||+||++|+||||+||++|||||||||||||||++
T Consensus        65 ------~i~~dL~~~~~~dI~rl~~I~sYRG~RH~~gLPVRGQRT~TNart~k  111 (122)
T PRK05179         65 ------KVEGDLRREVSMNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRK  111 (122)
T ss_pred             ------cchHHHHHHHHHHHHHHHHhcceeeeecccCCCCCCCcCCccccccC
Confidence                  36999999999999999999999999999999999999999999998

>CHL00137 rps13 ribosomal protein S13; Validated

Probab=100.00  E-value=7.3e-48  Score=285.74  Aligned_cols=111  Identities=31%  Similarity=0.499  Sum_probs=107.4

Q ss_pred             hhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCC
Q 031813           12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYK   91 (152)
Q Consensus        12 ~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~   91 (152)
                      ||||+||+||++|+|.+||++|||||..+|.+||+++||||++++++||++|+++|.++|++  +|.             
T Consensus         1 mvrI~~~~i~~~k~v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~--~~~-------------   65 (122)
T CHL00137          1 MVRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIEE--NYQ-------------   65 (122)
T ss_pred             CceEcCccCCCCCEeeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHHH--hCc-------------
Confidence            79999999999999999999999999999999999999999999999999999999999986  353             


Q ss_pred             CCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCcc
Q 031813           92 DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGK  144 (152)
Q Consensus        92 sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~  144 (152)
                             +|+||++.+++||+||++|+||||+||.+|||||||||||||||++
T Consensus        66 -------i~~dL~~~~~~dI~rl~~I~sYRG~RH~~gLPVRGQRT~tNarT~k  111 (122)
T CHL00137         66 -------VEGDLRRFESLNIKRLMEINCYRGRRHRLGLPVRGQRTRTNARTRR  111 (122)
T ss_pred             -------chHHHHHHHHHHHHHHHHhCchhcccccCCCCCCCCcCCccccccC
Confidence                   5999999999999999999999999999999999999999999997

>TIGR03631 bact_S13 30S ribosomal protein S13

Probab=100.00  E-value=2e-46  Score=274.81  Aligned_cols=111  Identities=35%  Similarity=0.519  Sum_probs=106.4

Q ss_pred             hhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCCCC
Q 031813           14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDG   93 (152)
Q Consensus        14 ri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg   93 (152)
                      ||+|+|||++|+|.+||++|||||..+|.+||+++||||++++++|+++|++.|.++|+++  |                
T Consensus         1 ri~~~~l~~~k~v~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~~~--~----------------   62 (113)
T TIGR03631         1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEAK--Y----------------   62 (113)
T ss_pred             CcCCccCCCCCEEeeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhc--C----------------
Confidence            7999999999999999999999999999999999999999999999999999999999873  3                


Q ss_pred             chhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccce
Q 031813           94 KYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTV  146 (152)
Q Consensus        94 ~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~  146 (152)
                          .||+||++.+++||+||++|+||||+||++|||||||||||||||++..
T Consensus        63 ----~i~~~L~~~~~~dI~rl~~I~syRG~RH~~gLpVRGQRT~TNart~k~~  111 (113)
T TIGR03631        63 ----KVEGDLRREVSLNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGP  111 (113)
T ss_pred             ----cchHHHHHHHHHHHHHHHHhcceeccccccCCCCCCCcCCccccccCCC
Confidence                3699999999999999999999999999999999999999999999853

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.

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

Probab=100.00  E-value=2.4e-46  Score=271.72  Aligned_cols=107  Identities=45%  Similarity=0.768  Sum_probs=101.7

Q ss_pred             hhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCCCC
Q 031813           14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDG   93 (152)
Q Consensus        14 ri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg   93 (152)
                      ||+||+||++|+|.+||++|||||+.+|.+||+++||+|+.++++|+++|+++|.++|++                    
T Consensus         1 rI~~~~l~~~k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~--------------------   60 (107)
T PF00416_consen    1 RILGTNLPGNKPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEK--------------------   60 (107)
T ss_dssp             ETTTTCE-TSSBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHT--------------------
T ss_pred             CcCCCcCCCCcchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHH--------------------
Confidence            799999999999999999999999999999999999999999999999999999999987                    


Q ss_pred             chhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCC
Q 031813           94 KYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRR  142 (152)
Q Consensus        94 ~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart  142 (152)
                        .|++|+||++.+++||+||++|+||||+||.+|||||||||||||||
T Consensus        61 --~~~i~~~L~~~~~~~i~rl~~i~syRG~RH~~gLpvRGQRT~tNarT  107 (107)
T PF00416_consen   61 --NHLIENDLKRQVRENIKRLKKIKSYRGIRHRKGLPVRGQRTKTNART  107 (107)
T ss_dssp             --HSTCHHHHHHHHHHHHHHHHHHTTHHHHHHHHTSBSSSSTSSSSSHH
T ss_pred             --hccccchHHHHHHHHHHHHHHHHHhhcchhhCCCCCCCCCCCCCCCC
Confidence              24579999999999999999999999999999999999999999986

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 ....

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

Probab=98.88  E-value=1.1e-09  Score=96.49  Aligned_cols=103  Identities=19%  Similarity=0.292  Sum_probs=89.0

Q ss_pred             cccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCC----HHHHHHHHHHHhCCCCccCCcc
Q 031813            7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS----AAELDNLMVVVANPRQFKIPDW   82 (152)
Q Consensus         7 ~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls----~~ei~~L~~~l~~~~~~~ip~w   82 (152)
                      +++..|++    .-+..+.-.|+..+|..||..+|..+|+.+|++|++.+.+|+    .+|..+|.+++.+   |.    
T Consensus       244 ~~L~~M~~----~T~~~tv~~fL~sef~rig~~ta~e~~e~~g~~~~~~p~~L~~~~~~eea~~lv~a~~~---~~----  312 (538)
T COG1389         244 DTLKKMAH----RTRRSTVREFLVSEFSRIGEKTADELLEYAGFDPDKKPRELTKKKTREEAEKLVEAFKK---MK----  312 (538)
T ss_pred             HHHHHHHH----HhhhhhHHHHHHHHHHHhhhhhHHHHHHHhcCCcccCHHHhhcccCHHHHHHHHHHHHh---Cc----
Confidence            34555555    234455568889999999999999999999999999999999    9999999999987   53    


Q ss_pred             ccCccCCCCCCchhhhhhhhHHHHHHh----hhhhhhccceeec
Q 031813           83 FLNRQKDYKDGKYSQVVSNALDMKLRD----DLERLKKIRNHRG  122 (152)
Q Consensus        83 ~~nr~~D~~sg~~~~lie~~L~~~~~~----~I~rl~~i~syRG  122 (152)
                      |+.|+.|++||++.++|+.+|+..++.    .+.|  +.+.|+|
T Consensus       313 fm~Pptd~LsPIGee~ie~gLk~~~~pefv~avTR--kPkvy~G  354 (538)
T COG1389         313 FMAPPTDGLSPIGEELIEKGLKSILNPEFVAAVTR--KPKVYRG  354 (538)
T ss_pred             ccCCCccccCcccHHHHHHHHHHhcCchheeeecc--CccccCC
Confidence            366799999999999999999999977    6788  9999999

>PRK04184 DNA topoisomerase VI subunit B; Validated

Probab=98.83  E-value=4.3e-09  Score=94.68  Aligned_cols=91  Identities=21%  Similarity=0.329  Sum_probs=80.4

Q ss_pred             CeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCCCCchhhhhhhh
Q 031813           23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNA  102 (152)
Q Consensus        23 ~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg~~~~lie~~  102 (152)
                      .....|+-.+|..||..+|..||+.+|+++++++.+|+++|+..|.+++.+   +++    +.|+.||+||++.++|+.+
T Consensus       256 ~~l~~fL~~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~---~~~----~~pp~~~lspige~~i~~g  328 (535)
T PRK04184        256 RTLKEFLVEEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKK---YKF----MAPPTACLSPIGEELIEKG  328 (535)
T ss_pred             CCHHHHHHHhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHh---ccC----cCCCCccCCCCCHHHHHHH
Confidence            455688889999999999999999999999999999999999999999997   543    4557789999999999999


Q ss_pred             HHHHHHh----hhhhhhccceeec
Q 031813          103 LDMKLRD----DLERLKKIRNHRG  122 (152)
Q Consensus       103 L~~~~~~----~I~rl~~i~syRG  122 (152)
                      |+..++.    .+.|  +.+.|+|
T Consensus       329 l~~~~~p~f~~~~tr--~p~~y~g  350 (535)
T PRK04184        329 LKKILKPEFVAAVTR--KPKVYSG  350 (535)
T ss_pred             HHHhcCccEEEEecc--CCcccCC
Confidence            9998877    4566  8888886

>TIGR01052 top6b DNA topoisomerase VI, B subunit

Probab=98.80  E-value=6.1e-09  Score=92.86  Aligned_cols=102  Identities=18%  Similarity=0.275  Sum_probs=85.0

Q ss_pred             ccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCC---CCCCCCCCCHHHHHHHHHHHhCCCCccCCcccc
Q 031813            8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD---MNKRAGELSAAELDNLMVVVANPRQFKIPDWFL   84 (152)
Q Consensus         8 ~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~---~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~   84 (152)
                      +++.|++-..    ......|+..+|..||..+|..||+.+|++   +++++.+|+++|+..|.+++.+   .++    +
T Consensus       236 ~l~~m~~~t~----~~~l~~fL~~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~~---~~~----~  304 (488)
T TIGR01052       236 DLKSMARSTR----ASTLRSFLVSEFSRIGEKKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFKE---MKF----M  304 (488)
T ss_pred             HHHHHHHhcC----cccHHHHHHHhhcccCHHHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHHh---cCC----C
Confidence            4455544332    245557888999999999999999999999   9999999999999999999987   332    4


Q ss_pred             CccCCCCCCchhhhhhhhHHHHHHh----hhhhhhccceeec
Q 031813           85 NRQKDYKDGKYSQVVSNALDMKLRD----DLERLKKIRNHRG  122 (152)
Q Consensus        85 nr~~D~~sg~~~~lie~~L~~~~~~----~I~rl~~i~syRG  122 (152)
                      .|+.||+||++.++|+.+|+..++.    .+.|  +.+.|+|
T Consensus       305 ~P~~~~lspige~~i~~gl~~~~~p~f~~~~tr--~p~~y~g  344 (488)
T TIGR01052       305 APPTDGLSPIGEENIEKGLKEILQPEFVGAVTR--SPKTYRG  344 (488)
T ss_pred             CCCccccCCCCHHHHHHHHHHhcCccEEEEecc--CCccccC
Confidence            5688999999999999999998777    4667  8888987

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

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

Probab=97.37  E-value=0.0002  Score=50.57  Aligned_cols=52  Identities=29%  Similarity=0.376  Sum_probs=42.8

Q ss_pred             CCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        22 ~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+++|..+|   +-|.|||...|.+||-++||+|..++++|+++|+..|-+.+..
T Consensus        22 ~~~~ik~~LlDQ~~iaGiGNiy~~EiLf~a~i~P~~~~~~L~~~~~~~l~~~~~~   76 (92)
T PF06831_consen   22 RRRPIKAALLDQSVIAGIGNIYADEILFRAGIHPERPASSLSEEELRRLHEAIKR   76 (92)
T ss_dssp             CCSBHHHHHHCTTTSTT--HHHHHHHHHHTTB-TTSBGGGSHHHHHHHHHHHHHH
T ss_pred             CcchHHHHHhCCCccccCcHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence            467777666   4599999999999999999999999999999999998887754

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

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

Probab=97.24  E-value=0.00041  Score=57.61  Aligned_cols=53  Identities=30%  Similarity=0.369  Sum_probs=48.6

Q ss_pred             CCCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           21 DGKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        21 ~~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      ..+..|.-+|   +-+-|||...|.+||-++||+|..++++||++|++.|-+.+.+
T Consensus       153 ~~~~~Ik~~LLDQ~~iaGiGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~~  208 (274)
T PRK01103        153 KKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKA  208 (274)
T ss_pred             cCCccHHHHhhcCCeEecccHhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence            3567888889   8899999999999999999999999999999999999888765

>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional

Probab=96.65  E-value=0.003  Score=52.52  Aligned_cols=52  Identities=25%  Similarity=0.337  Sum_probs=45.1

Q ss_pred             CCeeheeehhc---ccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           22 GKQKIMFALTS---IKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        22 ~~k~v~~aL~~---i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+.+|..+|..   |-|||...|.+||-++||+|..++++||++|++.|.+++.+
T Consensus       153 ~~~~ik~~Lldq~viaGiGNiya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~~  207 (272)
T PRK14810        153 RKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGE  207 (272)
T ss_pred             CCccHHHHhhcCceeccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHHH
Confidence            45667777755   49999999999999999999999999999999999887654

>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional

Probab=96.63  E-value=0.0032  Score=52.32  Aligned_cols=51  Identities=20%  Similarity=0.234  Sum_probs=44.3

Q ss_pred             Ceeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           23 KQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        23 ~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      +++|.-+|   +-|-|||...|.+||-.++|+|..++++||++|++.|-+.+..
T Consensus       143 ~~~Ik~~LlDQ~~iaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~  196 (269)
T PRK14811        143 ARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIRE  196 (269)
T ss_pred             CCcHHHHHhcCceeecccHHHHHHHHHHcCCCccCCcccCCHHHHHHHHHHHHH
Confidence            66776666   3489999999999999999999999999999999998766653

>PRK10445 endonuclease VIII; Provisional

Probab=96.61  E-value=0.0029  Score=52.34  Aligned_cols=51  Identities=22%  Similarity=0.298  Sum_probs=44.0

Q ss_pred             Ceeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           23 KQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        23 ~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      +++|.-+|   +-|-|||...|.+||-.++|+|..++++||++|++.|-+.+.+
T Consensus       151 ~~~IK~~LLDQ~~vaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~  204 (263)
T PRK10445        151 NRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLD  204 (263)
T ss_pred             cccHHHHHhcCCccccccHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHH
Confidence            45665555   3388999999999999999999999999999999999888765

>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional

Probab=96.50  E-value=0.0038  Score=52.10  Aligned_cols=52  Identities=27%  Similarity=0.347  Sum_probs=45.0

Q ss_pred             CCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        22 ~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      ...+|.-+|   +-|-|||...|.+||-.++|+|..++++||++|++.|.+.+..
T Consensus       163 ~~~~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~~  217 (282)
T PRK13945        163 RTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIE  217 (282)
T ss_pred             CCccHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence            356666555   3489999999999999999999999999999999998887764

>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg)

Probab=96.45  E-value=0.0041  Score=51.67  Aligned_cols=52  Identities=31%  Similarity=0.346  Sum_probs=45.2

Q ss_pred             CCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        22 ~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+.+|.-+|   +-|-|||...|.+||-.++|+|..++++||++|++.|-+.+.+
T Consensus       154 ~~~~Ik~~LlDQ~vvaGIGNiyadEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~  208 (272)
T TIGR00577       154 SKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLANSLSKEECELLHRAIKE  208 (272)
T ss_pred             CCCcHHHHHhcCCeEecccHHHHHHHHHHcCCCcchhhccCCHHHHHHHHHHHHH
Confidence            456666666   4488999999999999999999999999999999999888765

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).

>PRK14867 DNA topoisomerase VI subunit B; Provisional

Probab=96.22  E-value=0.0066  Score=56.40  Aligned_cols=82  Identities=13%  Similarity=0.127  Sum_probs=61.0

Q ss_pred             hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCCCCchhhhhhhhHHHHHHh-
Q 031813           31 TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRD-  109 (152)
Q Consensus        31 ~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg~~~~lie~~L~~~~~~-  109 (152)
                      ..+-++-...+..+-+.+.=-+++.+.+|+++|+..|.+++.+   ..+    +.|+.||+||++..+|+.+| ..+++ 
T Consensus       409 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~a~~~---~~~----~aP~t~~LsPige~~i~~gl-~~~~pe  480 (659)
T PRK14867        409 KDKAMVSDEELEKYRKEIKDLLKKNPKEMTWKEAELIVNVLQD---MDF----MAPSTTGLRPIGAENIEKSL-ETLEPD  480 (659)
T ss_pred             hhhhhhhhhhhhhhhhhhhhhccCChhhCCHHHHHHHHHHHHh---cCC----CCCCccccCCCCHHHHHHHH-HhcCcc
Confidence            3344444444444444332236889999999999999999987   332    45588999999999999999 88777 


Q ss_pred             ---hhhhhhccceeec
Q 031813          110 ---DLERLKKIRNHRG  122 (152)
Q Consensus       110 ---~I~rl~~i~syRG  122 (152)
                         .+.|  +.+.|+|
T Consensus       481 f~~a~tR--~p~~y~g  494 (659)
T PRK14867        481 FLKTLTR--KPKTYKG  494 (659)
T ss_pred             eEEEecc--CcccccC
Confidence               5677  8889987

>PRK14868 DNA topoisomerase VI subunit B; Provisional

Probab=95.63  E-value=0.022  Score=53.81  Aligned_cols=54  Identities=15%  Similarity=0.216  Sum_probs=42.5

Q ss_pred             CHHHHHHHHHHHhCCCCccCCccccCccCCCCCCchhhhhhhhHHHHHHh----hhhhhhccceeec
Q 031813           60 SAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRD----DLERLKKIRNHRG  122 (152)
Q Consensus        60 s~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg~~~~lie~~L~~~~~~----~I~rl~~i~syRG  122 (152)
                      +.++...|.+++.+   ..|    +.|+.||+||++..+|+.+|+..++.    .+.|  +.+.|+|
T Consensus       482 ~~~~a~~L~~am~~---~~~----~aP~t~cLsPIgee~i~~Gl~k~~~peF~aa~TR--~p~vy~G  539 (795)
T PRK14868        482 DRDAASDLLEAMRE---TDI----IAPPTDCLSPISAELVEAGLRKEFDADFYAAATR--DAEVHGG  539 (795)
T ss_pred             CHHHHHHHHHHHHh---cCC----CCCCccccCcCCHHHHHHHHHhhcCcceEEEecc--CCcccCC
Confidence            46677778888876   322    45688999999999999999998777    4566  7888876

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

Probab=94.64  E-value=0.053  Score=45.54  Aligned_cols=59  Identities=25%  Similarity=0.361  Sum_probs=46.9

Q ss_pred             hcCcccCCCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           15 VLNTNVDGKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        15 i~~~~l~~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      +...-...++.|.-+|   +-+-|||...|.++|-++||+|.+..++|+.+|+..|.+++..
T Consensus       147 l~~~l~~~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~~  208 (273)
T COG0266         147 LAEKLAKKKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQLALLHEAIKD  208 (273)
T ss_pred             HHHHHhcCccchHHHhhcCCceecccHHHHHHHHHHcCCCcccCccccCHHHHHHHHHHHHH
Confidence            3333344455565555   4489999999999999999999999999999998888777653

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

Probab=94.17  E-value=0.041  Score=31.14  Aligned_cols=18  Identities=33%  Similarity=0.565  Sum_probs=15.2

Q ss_pred             ehhcccccCHHHHHHHHH
Q 031813           29 ALTSIKGIGRRLANIVCK   46 (152)
Q Consensus        29 aL~~i~GIG~~~A~~Ic~   46 (152)
                      .|.+++|||+++|..|+.
T Consensus        12 eL~~lpGIG~~tA~~I~~   29 (30)
T PF00633_consen   12 ELMKLPGIGPKTANAILS   29 (30)
T ss_dssp             HHHTSTT-SHHHHHHHHH
T ss_pred             HHHhCCCcCHHHHHHHHh
Confidence            588999999999999975

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

>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=93.93  E-value=0.023  Score=49.74  Aligned_cols=51  Identities=29%  Similarity=0.503  Sum_probs=35.0

Q ss_pred             CCeeheeeh-hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHh
Q 031813           22 GKQKIMFAL-TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA   72 (152)
Q Consensus        22 ~~k~v~~aL-~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~   72 (152)
                      +...+.-+| ..+.|+|+..|..+|.++|++++..+.+++++++..|.+.+.
T Consensus       185 ~~~~l~~~L~~~~~G~~~~la~ei~~ra~i~~~~~~~~~~~~~~~~l~~~~~  236 (455)
T PF05833_consen  185 KEKTLVKALSKNFQGFGPELAEEILYRAGIDKNKKVEELSDEEIEKLFEAIR  236 (455)
T ss_dssp             CG-BHHHHHHHHCTT--HHHHHHHHCCCTS-TTSBGGG--HHHHCHHHHHHH
T ss_pred             CcccHHHHHHHHHHHhHHHHHHHHHHHhCCCCccccccchhhhHHHHHHHHH
Confidence            344454444 556699999999999999999999999999998776555543

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.

>TIGR00275 flavoprotein, HI0933 family

Probab=92.72  E-value=0.093  Score=45.40  Aligned_cols=51  Identities=24%  Similarity=0.423  Sum_probs=44.4

Q ss_pred             CCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+++.+...|..+  +-.+.+..||+.+||++++++++|+++|++.|.+.|.+
T Consensus       281 ~~~~~~~~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~  331 (400)
T TIGR00275       281 NPKKTVKNILKGL--LPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKN  331 (400)
T ss_pred             ChhhhHHHHhhhh--hhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhC
Confidence            3466666666644  78999999999999999999999999999999999987

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

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

Probab=90.39  E-value=0.19  Score=28.62  Aligned_cols=22  Identities=23%  Similarity=0.496  Sum_probs=15.7

Q ss_pred             eehhcccccCHHHHHHHHHHcCC
Q 031813           28 FALTSIKGIGRRLANIVCKKADV   50 (152)
Q Consensus        28 ~aL~~i~GIG~~~A~~Ic~~lgi   50 (152)
                      ..+++|.|||+.++..+ +++||
T Consensus        11 lpi~~~~GIG~kt~~kL-~~~GI   32 (32)
T PF11798_consen   11 LPIRKFWGIGKKTAKKL-NKLGI   32 (32)
T ss_dssp             SBGGGSTTS-HHHHHHH-HCTT-
T ss_pred             CCHHhhCCccHHHHHHH-HHccC
Confidence            36789999999999984 44443

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

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

Probab=90.07  E-value=0.042  Score=35.28  Aligned_cols=26  Identities=27%  Similarity=0.404  Sum_probs=21.5

Q ss_pred             heeehhcccccCHHHHHHHHHHcCCCC
Q 031813           26 IMFALTSIKGIGRRLANIVCKKADVDM   52 (152)
Q Consensus        26 v~~aL~~i~GIG~~~A~~Ic~~lgi~~   52 (152)
                      ++..|.+|.|||+.+|..+.+. |+..
T Consensus         3 ~~~~L~~I~Gig~~~a~~L~~~-G~~t   28 (60)
T PF14520_consen    3 VFDDLLSIPGIGPKRAEKLYEA-GIKT   28 (60)
T ss_dssp             HHHHHHTSTTCHHHHHHHHHHT-TCSS
T ss_pred             HHHhhccCCCCCHHHHHHHHhc-CCCc
Confidence            4567899999999999999876 7664

...

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

Probab=89.14  E-value=0.43  Score=39.28  Aligned_cols=52  Identities=23%  Similarity=0.281  Sum_probs=41.4

Q ss_pred             CCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      -..|.+.-+|..+.+. ...+..+++.+|++++.++.+|+.+|+.+|.+.+..
T Consensus       219 ~rrk~l~~~l~~~~~~-~~~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~~  270 (272)
T PRK00274        219 QRRKTLRNNLKNLFGS-KEKLEEALEAAGIDPNRRAETLSVEEFVRLANALAA  270 (272)
T ss_pred             chHHHHHHHHHhhccc-hHHHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHHh
Confidence            3466677777776542 345678899999999999999999999999988764

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

Probab=88.17  E-value=0.41  Score=30.39  Aligned_cols=22  Identities=23%  Similarity=0.314  Sum_probs=15.9

Q ss_pred             ehhcccccCHHHHHHHHHHcCCC
Q 031813           29 ALTSIKGIGRRLANIVCKKADVD   51 (152)
Q Consensus        29 aL~~i~GIG~~~A~~Ic~~lgi~   51 (152)
                      .+++|+|||+.+|....+ .|+.
T Consensus         3 ~f~~I~GVG~~tA~~w~~-~G~r   24 (52)
T PF10391_consen    3 LFTGIWGVGPKTARKWYA-KGIR   24 (52)
T ss_dssp             HHHTSTT--HHHHHHHHH-TT--
T ss_pred             chhhcccccHHHHHHHHH-hCCC
Confidence            478999999999999987 7754

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

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

Probab=87.79  E-value=0.49  Score=25.43  Aligned_cols=20  Identities=25%  Similarity=0.434  Sum_probs=16.9

Q ss_pred             ehhcccccCHHHHHHHHHHc
Q 031813           29 ALTSIKGIGRRLANIVCKKA   48 (152)
Q Consensus        29 aL~~i~GIG~~~A~~Ic~~l   48 (152)
                      .|.++.|||..+|..|+...
T Consensus         2 ~L~~i~GiG~k~A~~il~~~   21 (26)
T smart00278        2 ELLKVPGIGPKTAEKILEAX   21 (26)
T ss_pred             hhhhCCCCCHHHHHHHHHhc
Confidence            36789999999999998643

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

Probab=87.57  E-value=0.44  Score=39.69  Aligned_cols=48  Identities=23%  Similarity=0.295  Sum_probs=42.5

Q ss_pred             CCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      ...|.+.-+|..+++     ...+|+.+|++++.++.+||.+|+-.|.+++..
T Consensus       209 ~RRKtl~n~l~~~~~-----~~~~l~~~~i~~~~R~e~ls~~~f~~L~~~l~~  256 (259)
T COG0030         209 QRRKTLRNNLKNLFG-----LEEVLEAAGIDPNARAENLSPEDFLKLANALKG  256 (259)
T ss_pred             hhhHHHHHHHHhhhh-----HHHHHHhcCCCcccChhhCCHHHHHHHHHHHhh
Confidence            346778888888777     899999999999999999999999999998864

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

Probab=86.16  E-value=0.58  Score=35.33  Aligned_cols=59  Identities=20%  Similarity=0.161  Sum_probs=44.2

Q ss_pred             hcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCC---CCCCCCCCCHHHHHHHHHHHhC
Q 031813           15 VLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD---MNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        15 i~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~---~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      -.+.-||-|..-...|+.++|||+..|.+|++.-.+.   .-..+..+++.|.+.|.+..++
T Consensus        48 ~~~~kIdiN~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V~GIgekqk~~l~k~~~~  109 (132)
T PRK02515         48 EFGEKIDLNNSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNLPGLSERQKELLEANLDN  109 (132)
T ss_pred             hcCCcccCCccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcCCCCCHHHHHHHHHhhcc
Confidence            3566677677777789999999999999999632221   2235667899999999998876

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=85.89  E-value=0.5  Score=37.45  Aligned_cols=22  Identities=18%  Similarity=0.344  Sum_probs=18.9

Q ss_pred             eehhcccccCHHHHHHHHHHcC
Q 031813           28 FALTSIKGIGRRLANIVCKKAD   49 (152)
Q Consensus        28 ~aL~~i~GIG~~~A~~Ic~~lg   49 (152)
                      -+|++++|||+++|.+||-.|.
T Consensus       108 ~~L~~vpGIGkKtAerIilELk  129 (188)
T PRK14606        108 EGLSKLPGISKKTAERIVMELK  129 (188)
T ss_pred             HHHhhCCCCCHHHHHHHHHHHH
Confidence            4789999999999999996553

>COG3743 Uncharacterized conserved protein [Function unknown]

Probab=85.74  E-value=0.58  Score=35.36  Aligned_cols=44  Identities=18%  Similarity=0.222  Sum_probs=39.3

Q ss_pred             eehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHh
Q 031813           28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA   72 (152)
Q Consensus        28 ~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~   72 (152)
                      --|+.|.|||+..+.. +..+||-....+-.+|..|+..+..+|+
T Consensus        67 DDLt~I~GIGPk~e~~-Ln~~GI~tfaQIAAwt~~di~~id~~l~  110 (133)
T COG3743          67 DDLTRISGIGPKLEKV-LNELGIFTFAQIAAWTRADIAWIDDYLN  110 (133)
T ss_pred             ccchhhcccCHHHHHH-HHHcCCccHHHHHhcCHHHHHHHHhhcC
Confidence            4589999999998765 5789999999999999999999999985

>PF09239 Topo-VIb_trans: Topoisomerase VI B subunit, transducer; InterPro: IPR015320 DNA topoisomerases regulate the number of topological links between two DNA strands (i

Probab=85.37  E-value=0.35  Score=37.62  Aligned_cols=35  Identities=17%  Similarity=0.208  Sum_probs=21.0

Q ss_pred             ccCCCCCCchhhhhhhhHHHHHHhh----hhhhhccceeec
Q 031813           86 RQKDYKDGKYSQVVSNALDMKLRDD----LERLKKIRNHRG  122 (152)
Q Consensus        86 r~~D~~sg~~~~lie~~L~~~~~~~----I~rl~~i~syRG  122 (152)
                      |+.||+||++.++|+.+|+..++.+    ++|  +.+.|+|
T Consensus         1 P~~~cLsPiGe~~i~~Gl~k~l~pefv~avtR--~p~vy~G   39 (160)
T PF09239_consen    1 PPTDCLSPIGEELIEKGLKKELNPEFVAAVTR--KPSVYSG   39 (160)
T ss_dssp             --SCCS----HHHHHHHHHHHC--SEEEEEE-----EEETT
T ss_pred             CCCcccCccCHHHHHHHHHHhcCccEEEEEcc--CCceecC
Confidence            4789999999999999999999884    566  7788876

e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. This entry represents subunit B of topoisomerase VI, an ATP-dependent type IIB enzyme. Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A 2Q2E_B.

>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]

Probab=85.34  E-value=0.14  Score=39.53  Aligned_cols=46  Identities=13%  Similarity=-0.084  Sum_probs=39.0

Q ss_pred             hhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccce
Q 031813           99 VSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTV  146 (152)
Q Consensus        99 ie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~  146 (152)
                      +.+|.+.+..+++....++.+|.|-  ..+||+.||.|+.|+.+.+.+
T Consensus        70 i~~d~~~~~~~~~~l~rq~~~~dG~--~~~l~~~~ld~r~r~~ieRlk  115 (152)
T KOG3311|consen   70 ILNDPRQYKIPDWFLNRQKDIIDGK--VNHLLGNGLDTRLRADIERLK  115 (152)
T ss_pred             HhcCHHHhcCchHHHHhhcccccCc--cccccchhhhhHHHHHHHHHh
Confidence            4456677777899999999999999  999999999999998776543

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=85.13  E-value=0.57  Score=37.04  Aligned_cols=21  Identities=24%  Similarity=0.371  Sum_probs=18.3

Q ss_pred             eehhcccccCHHHHHHHHHHc
Q 031813           28 FALTSIKGIGRRLANIVCKKA   48 (152)
Q Consensus        28 ~aL~~i~GIG~~~A~~Ic~~l   48 (152)
                      -+|++++|||+++|.+|+-.|
T Consensus       108 ~~L~~vpGIGkKtAeRIilEL  128 (183)
T PRK14601        108 SVLKKVPGIGPKSAKRIIAEL  128 (183)
T ss_pred             HHHhhCCCCCHHHHHHHHHHH
Confidence            478999999999999999554

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

Probab=84.51  E-value=1.5  Score=38.58  Aligned_cols=51  Identities=27%  Similarity=0.394  Sum_probs=44.8

Q ss_pred             CCCeeheeehhcccccCHHHHHHHHHHcCC-CCCCCCCCCCHHHHHHHHHHHhC
Q 031813           21 DGKQKIMFALTSIKGIGRRLANIVCKKADV-DMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi-~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+++.+...|..+  +-.+.+..+|+.+++ ++++++.+|+++++..|.+.|.+
T Consensus       288 ~~~~~~~~~l~~~--lp~rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk~  339 (409)
T PF03486_consen  288 NPKRTLKNFLKGL--LPKRLALALLKRAGIKDPDKKVSELSKKERNRLANLLKR  339 (409)
T ss_dssp             TTTSBHHHHHTTT--S-HHHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHHC
T ss_pred             HHhhHHHHHHHHH--hHHHHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHHh
Confidence            4577788888876  899999999999999 99999999999999999999987

; PDB: 2I0Z_A 3V76_A 2GQF_A.

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=84.15  E-value=0.67  Score=36.97  Aligned_cols=21  Identities=33%  Similarity=0.504  Sum_probs=18.1

Q ss_pred             eehhcccccCHHHHHHHHHHc
Q 031813           28 FALTSIKGIGRRLANIVCKKA   48 (152)
Q Consensus        28 ~aL~~i~GIG~~~A~~Ic~~l   48 (152)
                      .+|++++|||+++|.+||-.|
T Consensus       107 ~~L~kvpGIGkKtAerIilEL  127 (197)
T PRK14603        107 RLLTSASGVGKKLAERIALEL  127 (197)
T ss_pred             HHHhhCCCCCHHHHHHHHHHH
Confidence            478999999999999999543

>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=83.92  E-value=0.69  Score=36.85  Aligned_cols=21  Identities=24%  Similarity=0.433  Sum_probs=18.4

Q ss_pred             eehhcccccCHHHHHHHHHHc
Q 031813           28 FALTSIKGIGRRLANIVCKKA   48 (152)
Q Consensus        28 ~aL~~i~GIG~~~A~~Ic~~l   48 (152)
                      .+|++++|||+++|.+|+-.|
T Consensus       108 ~~L~kvpGIGkKtAerIilEL  128 (195)
T PRK14604        108 ARLARVPGIGKKTAERIVLEL  128 (195)
T ss_pred             HHHhhCCCCCHHHHHHHHHHH
Confidence            479999999999999999554

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=83.75  E-value=0.71  Score=36.99  Aligned_cols=21  Identities=29%  Similarity=0.501  Sum_probs=18.3

Q ss_pred             eehhcccccCHHHHHHHHHHc
Q 031813           28 FALTSIKGIGRRLANIVCKKA   48 (152)
Q Consensus        28 ~aL~~i~GIG~~~A~~Ic~~l   48 (152)
                      -+|++++|||+++|.+|+-.|
T Consensus       107 ~~L~~vpGIGkKtAeRIIlEL  127 (196)
T PRK13901        107 ELISKVKGIGNKMAGKIFLKL  127 (196)
T ss_pred             HHHhhCCCCCHHHHHHHHHHH
Confidence            478999999999999999554

>TIGR00755 ksgA dimethyladenosine transferase

Probab=83.64  E-value=1.1  Score=36.29  Aligned_cols=58  Identities=17%  Similarity=0.228  Sum_probs=42.8

Q ss_pred             cchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHH
Q 031813            9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVV   70 (152)
Q Consensus         9 ~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~   70 (152)
                      |.++++.+  ---..|.+.-+|..+.+-  ..+..+++.+|+++++++.+||.+|+..|.+.
T Consensus       195 ~~~~~~~~--F~~rrk~l~~~l~~~~~~--~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~  252 (253)
T TIGR00755       195 FEKLLKAA--FSQRRKTLRNNLKQLLKA--SKLEEVLEQLGLDPTARAEQLSPEDFLRLANL  252 (253)
T ss_pred             HHHHHHHH--HccchHHHHHHHhhhcch--hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHh
Confidence            55555542  234567777778776442  34567888999999999999999999998765

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=83.52  E-value=0.46  Score=38.83  Aligned_cols=62  Identities=24%  Similarity=0.307  Sum_probs=48.7

Q ss_pred             cccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHh
Q 031813            7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA   72 (152)
Q Consensus         7 ~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~   72 (152)
                      +.|.++++.+=.  -..|.+.-+|..+++  ...+..+.+.+||+++.++.+|+.+|+.+|-++|+
T Consensus       200 ~~~~~~~~~~F~--~rrk~l~~~L~~~~~--~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~  261 (262)
T PF00398_consen  200 DAFEYFVRQLFS--QRRKTLRNSLKSLFP--GEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLN  261 (262)
T ss_dssp             HHHHHHHHHHHT--TTTSBHHHHTTCTHH--HHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh--CcchHHHHHHhhhcC--HHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhh
Confidence            356677765533  578888888887753  44456777789999999999999999999999875

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 ....

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

Probab=83.24  E-value=0.79  Score=36.86  Aligned_cols=21  Identities=33%  Similarity=0.498  Sum_probs=18.1

Q ss_pred             eehhcccccCHHHHHHHHHHc
Q 031813           28 FALTSIKGIGRRLANIVCKKA   48 (152)
Q Consensus        28 ~aL~~i~GIG~~~A~~Ic~~l   48 (152)
                      -+|++++|||+++|.+||-.|
T Consensus       108 ~~L~k~PGIGkKtAerivleL  128 (201)
T COG0632         108 KALSKIPGIGKKTAERIVLEL  128 (201)
T ss_pred             HhhhcCCCCCHHHHHHHHHHH
Confidence            478999999999999999654

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=82.75  E-value=0.82  Score=36.58  Aligned_cols=21  Identities=33%  Similarity=0.509  Sum_probs=17.9

Q ss_pred             eehhcccccCHHHHHHHHHHc
Q 031813           28 FALTSIKGIGRRLANIVCKKA   48 (152)
Q Consensus        28 ~aL~~i~GIG~~~A~~Ic~~l   48 (152)
                      -+|++++|||+++|.+|+-.|
T Consensus       109 ~~L~~ipGIGkKtAerIilEL  129 (203)
T PRK14602        109 AALTRVSGIGKKTAQHIFLEL  129 (203)
T ss_pred             HHHhcCCCcCHHHHHHHHHHH
Confidence            468999999999999999443

>TIGR03252 uncharacterized HhH-GPD family protein

Probab=82.24  E-value=0.74  Score=36.38  Aligned_cols=29  Identities=17%  Similarity=0.331  Sum_probs=24.3

Q ss_pred             CCCeeheeehhcccccCHHHHHHHHHHcC
Q 031813           21 DGKQKIMFALTSIKGIGRRLANIVCKKAD   49 (152)
Q Consensus        21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg   49 (152)
                      ++...+...|.+++|||+.+|.-+|..||
T Consensus       108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~  136 (177)
T TIGR03252       108 PDGKELLRRLKALPGFGKQKAKIFLALLG  136 (177)
T ss_pred             CCcHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            55666667899999999999999987665

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

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

Probab=81.85  E-value=1.5  Score=40.18  Aligned_cols=51  Identities=22%  Similarity=0.289  Sum_probs=45.1

Q ss_pred             CeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        23 ~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      ..-+..++..+.|+|.-.|..+|-++|+++.....++.++++..+...+.+
T Consensus       185 ~~~~~~~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~~~  235 (564)
T COG1293         185 GADIVRLLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREALEE  235 (564)
T ss_pred             chHHHHHHHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHHHh
Confidence            344567788999999999999999999999999999999999999887654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	152
3iz6_M	152	Localization Of The Small Subunit Ribosomal Protein		2e-69
2zkq_m	152	Structure Of A Mammalian Ribosomal 40s Subunit With		9e-57
3izb_M	146	Localization Of The Small Subunit Ribosomal Protein		1e-49
3zey_M	153	High-resolution Cryo-electron Microscopy Structure		2e-45
1s1h_M	132	Structure Of The Ribosomal 80s-Eef2-Sordarin Comple		2e-45
3jyv_M	130	Structure Of The 40s Rrna And Proteins And PE TRNA		1e-44
2xzm_M	155	Crystal Structure Of The Eukaryotic 40s Ribosomal S		8e-40
3j20_O	148	Promiscuous Behavior Of Proteins In Archaeal Riboso		2e-26
3ofo_M	114	Crystal Structure Of The E. Coli Ribosome Bound To		9e-05
1p6g_M	117	Real Space Refined Coordinates Of The 30s Subunit F		9e-05
2gy9_M	115	Structure Of The 30s Subunit Of A Pre-Translocation		9e-05
1vs5_M	118	Crystal Structure Of The Bacterial Ribosome From Es		1e-04
3fih_M	113	Ternary Complex-Bound E.Coli 70s Ribosome. This Ent		1e-04
1i94_M	125	Crystal Structures Of The Small Ribosomal Subunit W		5e-04
1fjg_M	126	Structure Of The Thermus Thermophilus 30s Ribosomal		6e-04
3pyn_M	116	Crystal Structure Of A Complex Containing Domain 3		6e-04
3mr8_M	117	Recognition Of The Amber Stop Codon By Release Fact		6e-04

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

Iteration: 1
 Score =  257 bits (657), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 121/152 (79%), Positives = 133/152 (87%)
Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSL+A E+FQHILRVLNTNVDGKQKIMFALTSIKG+GRR +NIVCKKAD+DMNKRAGELS
Sbjct: 1   MSLIAGEEFQHILRVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELS 60
Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
           A E+D LM VV NPRQFK+PDWFLNR+KDYKDG++SQVVSNA+DMKLRDDLERLKKIRNH
Sbjct: 61  AEEMDRLMAVVHNPRQFKVPDWFLNRKKDYKDGRFSQVVSNAVDMKLRDDLERLKKIRNH 120
Query: 121 RGLRHYWGLRVRGQHXXXXXXXXXXXXXSKKR 152
           RGLRHYWG+RVRGQH             SKKR
Sbjct: 121 RGLRHYWGVRVRGQHTKTTGRRGKTVGVSKKR 152

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

Iteration: 1
 Score =  215 bits (547), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 99/152 (65%), Positives = 123/152 (80%)
Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSLV  E FQHILRVLNTN+DG++KI FA+T+IKG+GRR A++V +KAD+D+ KRAGEL+
Sbjct: 1   MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELT 60
Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
             E++ ++ ++ NPRQ+KIPDWFLNRQKD KDGKYSQV++N LD KLR+DLERLKKIR H
Sbjct: 61  EDEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAH 120
Query: 121 RGLRHYWGLRVRGQHXXXXXXXXXXXXXSKKR 152
           RGLRH+WGLRVRGQH             SKK+
Sbjct: 121 RGLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK 152

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

Iteration: 1
 Score =  191 bits (485), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 89/137 (64%), Positives = 111/137 (81%), Gaps = 2/137 (1%)
Query: 1   MSLVANE--DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGE 58
           MSLV  E   FQHILR+LNTNVDG  KI++ALT+IKG+GRR +N+VCKKADVD++KRAGE
Sbjct: 1   MSLVVQEQGSFQHILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGE 60
Query: 59  LSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118
           L+  EL+ ++ ++ NP  +KIP WFLNRQ D  DGK    ++N ++ KLRDDLERLKKIR
Sbjct: 61  LTQEELERIVQIMQNPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIR 120
Query: 119 NHRGLRHYWGLRVRGQH 135
            HRG+RH+WGLRVRGQH
Sbjct: 121 AHRGIRHFWGLRVRGQH 137

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

Iteration: 1
 Score =  177 bits (449), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 82/136 (60%), Positives = 108/136 (79%), Gaps = 1/136 (0%)
Query: 1   MSL-VANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGEL 59
           MSL + +E FQHI+R+LNTNV+GK+K+ FAL  +KGIG R A +VCKKA VD+ +RAG L
Sbjct: 1   MSLTLQSESFQHIVRLLNTNVEGKRKVPFALRMVKGIGIRFAYMVCKKAGVDVERRAGTL 60
Query: 60  SAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRN 119
           S  EL+ +  V+A+P +FKIP+WFLNRQ+D K GK   + S+ +D +LR+DLERL+KIR 
Sbjct: 61  SPEELEKISEVIADPAKFKIPEWFLNRQRDPKTGKTEHLTSSMVDTRLREDLERLRKIRA 120
Query: 120 HRGLRHYWGLRVRGQH 135
           HRG+RH +GLRVRGQH
Sbjct: 121 HRGVRHAYGLRVRGQH 136

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

Iteration: 1
 Score =  177 bits (448), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 80/123 (65%), Positives = 102/123 (82%)
Query: 13  LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72
           LR+LNTNVDG  KI++ALT+IKG+GRR +N+VCKKADVD++KRAGEL+  EL+ ++ ++ 
Sbjct: 1   LRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIMQ 60
Query: 73  NPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVR 132
           NP  +KIP WFLNRQ D  DGK    ++N ++ KLRDDLERLKKIR HRG+RH+WGLRVR
Sbjct: 61  NPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRAHRGIRHFWGLRVR 120
Query: 133 GQH 135
           GQH
Sbjct: 121 GQH 123

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

Iteration: 1
 Score =  175 bits (443), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 79/122 (64%), Positives = 101/122 (82%)
Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+LNTNVDG  KI++ALT+IKG+GRR +N+VCKKADVD++KRAGEL+  EL+ ++ ++ N
Sbjct: 1   RLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIMQN 60
Query: 74  PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
           P  +KIP WFLNRQ D  DGK    ++N ++ KLRDDLERLKKIR HRG+RH+WGLRVRG
Sbjct: 61  PTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRAHRGIRHFWGLRVRG 120
Query: 134 QH 135
           QH
Sbjct: 121 QH 122

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

Iteration: 1
 Score =  159 bits (401), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 75/137 (54%), Positives = 99/137 (72%), Gaps = 2/137 (1%)
Query: 1   MSLVANE--DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGE 58
           MS V  +  DF++I R+LNTN+DGK+    ALT I+GIGRR A I+CK   +D N RAG 
Sbjct: 1   MSFVIEKESDFKYIHRILNTNIDGKRITPIALTGIRGIGRRFAYIICKVLKIDPNARAGL 60
Query: 59  LSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118
           L+  + + +  ++A+P    IP W LNR  D+KDGK  Q+ SN LD K+R+DLERLKKI+
Sbjct: 61  LTEDQCNKITDLIADPEAHGIPTWLLNRINDFKDGKNYQMASNTLDTKMREDLERLKKIK 120
Query: 119 NHRGLRHYWGLRVRGQH 135
           +HRGLRH+WGL+VRGQH
Sbjct: 121 SHRGLRHFWGLKVRGQH 137

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

Iteration: 1
 Score =  114 bits (285), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 53/127 (41%), Positives = 87/127 (68%)
Query: 8   DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67
           +F+HI+RV   ++DG +++ +ALT+IKGIG   A +VC+ A +D   +AG L+  ++  +
Sbjct: 3   NFRHIVRVAGVDLDGNKQLRWALTAIKGIGINFATMVCRVAGLDPFMKAGYLTDEQVKKI 62
Query: 68  MVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYW 127
             ++A+P    IP W +NR KDY+ G+   +++  LDM +R+D+ RL++IR +RG+RH  
Sbjct: 63  EEILADPVAHGIPRWAVNRPKDYETGRDLHLITAKLDMAIREDIMRLRRIRAYRGIRHEL 122
Query: 128 GLRVRGQ 134
           GL VRGQ
Sbjct: 123 GLPVRGQ 129

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 34/121 (28%), Positives = 54/121 (44%), Gaps = 23/121 (19%)
Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+   N+   +  + ALTSI G+G+  +  +   A +  + +  ELS  ++D L   VA 
Sbjct: 2   RIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA- 60
Query: 74  PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
             +F                    VV   L  ++   ++RL  +  +RGLRH  GL VRG
Sbjct: 61  --KF--------------------VVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRG 98
Query: 134 Q 134
           Q
Sbjct: 99  Q 99

>pdb|1P6G|M Chain M, Real Space Refined Coordinates Of The 30s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 117

Iteration: 1
 Score = 42.7 bits (99), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 34/121 (28%), Positives = 54/121 (44%), Gaps = 23/121 (19%)
Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+   N+   +  + ALTSI G+G+  +  +   A +  + +  ELS  ++D L   VA 
Sbjct: 2   RIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA- 60
Query: 74  PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
             +F                    VV   L  ++   ++RL  +  +RGLRH  GL VRG
Sbjct: 61  --KF--------------------VVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRG 98
Query: 134 Q 134
           Q
Sbjct: 99  Q 99

>pdb|2GY9|M Chain M, Structure Of The 30s Subunit Of A Pre-Translocational E. Coli Ribosome Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1056 Length = 115

Iteration: 1
 Score = 42.4 bits (98), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 34/121 (28%), Positives = 54/121 (44%), Gaps = 23/121 (19%)
Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+   N+   +  + ALTSI G+G+  +  +   A +  + +  ELS  ++D L   VA 
Sbjct: 2   RIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA- 60
Query: 74  PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
             +F                    VV   L  ++   ++RL  +  +RGLRH  GL VRG
Sbjct: 61  --KF--------------------VVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRG 98
Query: 134 Q 134
           Q
Sbjct: 99  Q 99

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 34/121 (28%), Positives = 54/121 (44%), Gaps = 23/121 (19%)
Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+   N+   +  + ALTSI G+G+  +  +   A +  + +  ELS  ++D L   VA 
Sbjct: 3   RIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA- 61
Query: 74  PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
             +F                    VV   L  ++   ++RL  +  +RGLRH  GL VRG
Sbjct: 62  --KF--------------------VVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRG 99
Query: 134 Q 134
           Q
Sbjct: 100 Q 100

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 34/121 (28%), Positives = 54/121 (44%), Gaps = 23/121 (19%)
Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+   N+   +  + ALTSI G+G+  +  +   A +  + +  ELS  ++D L   VA 
Sbjct: 2   RIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA- 60
Query: 74  PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
             +F                    VV   L  ++   ++RL  +  +RGLRH  GL VRG
Sbjct: 61  --KF--------------------VVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRG 98
Query: 134 Q 134
           Q
Sbjct: 99  Q 99

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 34/122 (27%), Positives = 52/122 (42%), Gaps = 22/122 (18%)
Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+    +   +++  ALT I GIG+  A    +K  ++   R  +L+ AE+  L   V N
Sbjct: 2   RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVEN 61
Query: 74  PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
                   W L                  L  ++  +++RL  I  +RGLRH  GL VRG
Sbjct: 62  -------TWKL---------------EGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRG 99
Query: 134 QH 135
           Q 
Sbjct: 100 QR 101

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 34/124 (27%), Positives = 53/124 (42%), Gaps = 22/124 (17%)
Query: 12  ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71
           + R+    +   +++  ALT I GIG+  A    +K  ++   R  +L+ AE+  L   V
Sbjct: 1   MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYV 60
Query: 72  ANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRV 131
            N        W L                  L  ++  +++RL  I  +RGLRH  GL V
Sbjct: 61  EN-------TWKL---------------EGELRAEVAANIKRLMDIGCYRGLRHRRGLPV 98
Query: 132 RGQH 135
           RGQ 
Sbjct: 99  RGQR 102

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 34/121 (28%), Positives = 52/121 (42%), Gaps = 22/121 (18%)
Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+    +   +++  ALT I GIG+  A    +K  ++   R  +L+ AE+  L   V N
Sbjct: 2   RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVEN 61
Query: 74  PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
                   W L                  L  ++  +++RL  I  +RGLRH  GL VRG
Sbjct: 62  -------TWKL---------------EGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRG 99
Query: 134 Q 134
           Q
Sbjct: 100 Q 100

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 34/121 (28%), Positives = 52/121 (42%), Gaps = 22/121 (18%)
Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+    +   +++  ALT I GIG+  A    +K  ++   R  +L+ AE+  L   V N
Sbjct: 2   RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVEN 61
Query: 74  PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
                   W L                  L  ++  +++RL  I  +RGLRH  GL VRG
Sbjct: 62  -------TWKL---------------EGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRG 99
Query: 134 Q 134
           Q
Sbjct: 100 Q 100

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	152
3iz6_M	152	40S ribosomal protein S18 (S13P); eukaryotic ribos	7e-86
2xzm_M	155	RPS18E; ribosome, translation; 3.93A {Tetrahymena	7e-83
3u5c_S	146	40S ribosomal protein S18-A, 40S ribosomal protein	8e-77
2vqe_M	126	30S ribosomal protein S13, 30S ribosomal protein S	7e-18
3r8n_M	114	30S ribosomal protein S13; protein biosynthesis, R	1e-17
3bbn_M	145	Ribosomal protein S13; small ribosomal subunit, sp	3e-14

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

 Score =  247 bits (632), Expect = 7e-86
 Identities = 134/152 (88%), Positives = 146/152 (96%)

Query: 1   MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
           MSL+A E+FQHILRVLNTNVDGKQKIMFALTSIKG+GRR +NIVCKKAD+DMNKRAGELS
Sbjct: 1   MSLIAGEEFQHILRVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELS 60

Query: 61  AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
           A E+D LM VV NPRQFK+PDWFLNR+KDYKDG++SQVVSNA+DMKLRDDLERLKKIRNH
Sbjct: 61  AEEMDRLMAVVHNPRQFKVPDWFLNRKKDYKDGRFSQVVSNAVDMKLRDDLERLKKIRNH 120

Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           RGLRHYWG+RVRGQHTKTTGRRGKTVGVSKKR
Sbjct: 121 RGLRHYWGVRVRGQHTKTTGRRGKTVGVSKKR 152

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

 Score =  239 bits (612), Expect = 7e-83
 Identities = 84/154 (54%), Positives = 109/154 (70%), Gaps = 2/154 (1%)

Query: 1   MSLVA--NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGE 58
           MS V     DF++I R+LNTN+DGK+    ALT I+GIGRR A I+CK   +D N RAG 
Sbjct: 1   MSFVIEKESDFKYIHRILNTNIDGKRITPIALTGIRGIGRRFAYIICKVLKIDPNARAGL 60

Query: 59  LSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118
           L+  + + +  ++A+P    IP W LNR  D+KDGK  Q+ SN LD K+R+DLERLKKI+
Sbjct: 61  LTEDQCNKITDLIADPEAHGIPTWLLNRINDFKDGKNYQMASNTLDTKMREDLERLKKIK 120

Query: 119 NHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
           +HRGLRH+WGL+VRGQHTKT+GR G   GV +K 
Sbjct: 121 SHRGLRHFWGLKVRGQHTKTSGRHGVVCGVVRKN 154

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

 Score =  224 bits (572), Expect = 8e-77
 Identities = 96/145 (66%), Positives = 118/145 (81%), Gaps = 2/145 (1%)

Query: 1   MSLVANE--DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGE 58
           MSLV  E   FQHILR+LNTNVDG  KI++ALT+IKG+GRR +N+VCKKADVD++KRAGE
Sbjct: 1   MSLVVQEQGSFQHILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGE 60

Query: 59  LSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118
           L+  EL+ ++ ++ NP  +KIP WFLNRQ D  DGK    ++N ++ KLRDDLERLKKIR
Sbjct: 61  LTQEELERIVQIMQNPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIR 120

Query: 119 NHRGLRHYWGLRVRGQHTKTTGRRG 143
            HRG+RH+WGLRVRGQHTKTTGRR 
Sbjct: 121 AHRGIRHFWGLRVRGQHTKTTGRRR 145

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

 Score = 73.7 bits (182), Expect = 7e-18
 Identities = 41/142 (28%), Positives = 64/142 (45%), Gaps = 26/142 (18%)

Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+    +   +++  ALT I GIG+  A    +K  ++   R  +L+ AE+  L   V  
Sbjct: 3   RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYV-- 60

Query: 74  PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
                        +  +K       +   L  ++  +++RL  I  +RGLRH  GL VRG
Sbjct: 61  -------------ENTWK-------LEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRG 100

Query: 134 QHTKTTGR--RG--KTVGVSKK 151
           Q T+T  R  +G  KTV   KK
Sbjct: 101 QRTRTNARTRKGPRKTVAGKKK 122

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

 Score = 64.7 bits (158), Expect = 3e-14
 Identities = 35/128 (27%), Positives = 54/128 (42%), Gaps = 34/128 (26%)

Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+    +   +++ ++L  I GIGR  +  +    + D NK   +LS  E+  L      
Sbjct: 48  RIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFD-NKVTKDLSEEEVIIL------ 100

Query: 74  PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
            R+         R              N + ++      RLK+IR +RG+RH  GL VRG
Sbjct: 101 -RK-------EKRF-------------NRVAIE------RLKEIRCYRGIRHKLGLPVRG 133

Query: 134 QHTKTTGR 141
           Q TK   R
Sbjct: 134 QRTKNNCR 141

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	152
3iz6_M	152	40S ribosomal protein S18 (S13P); eukaryotic ribos	100.0
2xzm_M	155	RPS18E; ribosome, translation; 3.93A {Tetrahymena	100.0
3j20_O	148	30S ribosomal protein S13P; archaea, archaeal, KIN	100.0
3u5c_S	146	40S ribosomal protein S18-A, 40S ribosomal protein	100.0
2vqe_M	126	30S ribosomal protein S13, 30S ribosomal protein S	100.0
3r8n_M	114	30S ribosomal protein S13; protein biosynthesis, R	100.0
3bbn_M	145	Ribosomal protein S13; small ribosomal subunit, sp	100.0
1mu5_A	471	Type II DNA topoisomerase VI subunit B; GHKL ATPas	98.74
2zbk_B	530	Type 2 DNA topoisomerase 6 subunit B; DNA binding	98.25
1ee8_A	266	MUTM (FPG) protein; beta sandwich, zinc finger, he	96.25
1k3x_A	262	Endonuclease VIII; hydrolase/DNA, hydrolase-DNA co	96.24
3u6p_A	273	Formamidopyrimidine-DNA glycosylase; DNA glycosyla	96.21
2xzf_A	271	Formamidopyrimidine-DNA glycosylase; hydrolase-DNA	96.21
1k82_A	268	Formamidopyrimidine-DNA glycosylase; protein-DNA c	96.21
3twl_A	310	Formamidopyrimidine-DNA glycosylase 1; helix two t	96.08
3w0f_A	287	Endonuclease 8-like 3; helix two turns helix, zinc	96.02
3vk8_A	295	Probable formamidopyrimidine-DNA glycosylase; DNA	96.01
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	92.94
3fut_A	271	Dimethyladenosine transferase; methyltransferase,	92.37
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	92.2
2q2e_B	621	Type 2 DNA topoisomerase 6 subunit B; DNA-binding,	91.99
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	90.51
1tdh_A	364	NEI endonuclease VIII-like 1; helix two turns heli	89.77
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	89.69
1z00_B	84	DNA repair endonuclease XPF; helix-hairpin-helix,	89.23
1qyr_A	252	KSGA, high level kasugamycin resistance protein, S	88.6
3arc_U	97	Photosystem II 12 kDa extrinsic protein; PSII, mem	86.23
1s5l_U	134	Photosystem II 12 kDa extrinsic protein; photosynt	85.88
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	85.85
2duy_A	75	Competence protein comea-related protein; helix-ha	85.46
3ftd_A	249	Dimethyladenosine transferase; KSGA, rossmann-like	85.36
3uzu_A	279	Ribosomal RNA small subunit methyltransferase A; s	82.32
3tqs_A	255	Ribosomal RNA small subunit methyltransferase A; p	80.8
3fhg_A	207	Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel	80.35

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

Probab=100.00  E-value=1.8e-68  Score=407.34  Aligned_cols=152  Identities=88%  Similarity=1.364  Sum_probs=150.6

Q ss_pred             CCCCCccccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCC
Q 031813            1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIP   80 (152)
Q Consensus         1 ~~~~~~~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip   80 (152)
                      |||+..|+||||+||+|||||++|+|.+|||+|||||+.+|..||+++||||++++++||++|+++|.++|++|.+|.||
T Consensus         1 ~~~~~~~~~~~m~RI~g~~i~~~k~v~~ALt~I~GIG~~~A~~I~~~~gid~~~r~g~Lt~~ei~~l~~~i~~~~~~~ip   80 (152)
T 3iz6_M            1 MSLIAGEEFQHILRVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELSAEEMDRLMAVVHNPRQFKVP   80 (152)
T ss_dssp             CCCCTTCSCCCCCCTTTTCCCCSSBHHHHHTTSTTCCHHHHHHHHHHHTCCSSSBTTTSCHHHHHHHHHHHHSCSSCCCC
T ss_pred             CCcccHHHHHHHHHHcCCcCCCCcEeHhhhhhccCcCHHHHHHHHHHcCCCCCcEeCcCCHHHHHHHHHHHHhhcccCcc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999889999


Q ss_pred             ccccCccCCCCCCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031813           81 DWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR  152 (152)
Q Consensus        81 ~w~~nr~~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~gv~~~k  152 (152)
                      +||+|||+|+.||++.|++|+||++.+++||+||++|+||||+||.+||||||||||||||||+||||+|||
T Consensus        81 ~w~lNr~kD~~~G~~~~li~~dL~~~~~~dI~RL~~I~~yRG~RH~~GLpVRGQrTkTnaRtg~tvgv~kkk  152 (152)
T 3iz6_M           81 DWFLNRKKDYKDGRFSQVVSNAVDMKLRDDLERLKKIRNHRGLRHYWGVRVRGQHTKTTGRRGKTVGVSKKR  152 (152)
T ss_dssp             CCSCSCCCSCCCCSCCTTCTHHHHHHHHHHHHHHHHHTCHHHHHHHHTCCSSCCCCSSCCHHHHCSCCSSCC
T ss_pred             hhhhhhhcccCCcceeeechhHHHHHHHHhHHHHhhhheeecccccCCCCcCCcCCcCCCCCceecceecCC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999997

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

Probab=100.00  E-value=1.5e-67  Score=403.37  Aligned_cols=152  Identities=55%  Similarity=0.947  Sum_probs=149.3

Q ss_pred             CCCCCcc--ccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCcc
Q 031813            1 MSLVANE--DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFK   78 (152)
Q Consensus         1 ~~~~~~~--~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~   78 (152)
                      |||+..|  +||||+||+|||||++|.|.+||++|||||+.+|..||+++||||++++++||++|+++|.++|++|.+|.
T Consensus         1 m~~~~~~~~~f~~m~RI~g~~l~~~k~v~~aLt~I~GIG~~~A~~I~~~~gid~~~r~~~Lt~~ei~~l~~~i~~p~~~~   80 (155)
T 2xzm_M            1 MSFVIEKESDFKYIHRILNTNIDGKRITPIALTGIRGIGRRFAYIICKVLKIDPNARAGLLTEDQCNKITDLIADPEAHG   80 (155)
T ss_dssp             CCCCSSTTTSSCSCCEETTTEECCSSCHHHHHTTSTTCCHHHHHHHHHHTTCCSSSCSSCSCHHHHHHHHHHHHSHHHHC
T ss_pred             CCccccchHhhhhhHheeCccCCCCCEEEEeeecccccCHHHHHHHHHHcCCCcccccccCCHHHHHHHHHHHhCccccC
Confidence            8888666  89999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccccCccCCCCCCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031813           79 IPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR  152 (152)
Q Consensus        79 ip~w~~nr~~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~gv~~~k  152 (152)
                      ||+||+|||+|+.||++.|++|+||++.+++||+||++|+||||+||.+||||||||||||||||++|||+|||
T Consensus        81 iP~w~lNr~kD~~~G~~~~~ie~dLr~~~~~dI~Rl~~I~~yRG~RH~~GLpVRGQRTkTnaRtg~tvGv~kkk  154 (155)
T 2xzm_M           81 IPTWLLNRINDFKDGKNYQMASNTLDTKMREDLERLKKIKSHRGLRHFWGLKVRGQHTKTSGRHGVVCGVVRKN  154 (155)
T ss_dssp             CCGGGCSEEEETTTEEEECCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHTCCSSSCCCSSSSCSSCCCSSCCCC
T ss_pred             CCHHHhhcccccCCCceeEEecHHHHHHHHHhHHHHhhhceeeeeecccCCCcCCcCCccCCCCcccccccccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999997

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

Probab=100.00  E-value=1.5e-66  Score=395.25  Aligned_cols=146  Identities=43%  Similarity=0.795  Sum_probs=144.0

Q ss_pred             cccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCc
Q 031813            7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNR   86 (152)
Q Consensus         7 ~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr   86 (152)
                      ++||||+||+|||||++|.|.+|||+|||||..+|..||+++||||++++++||++|+++|.++|++|.+|+||+||+||
T Consensus         2 ~~~~~m~RI~g~~i~~~k~v~~aLt~I~GIG~~~A~~I~~~~gid~~~r~g~Lt~~ei~~i~~~i~~~~~~~iP~w~lNr   81 (148)
T 3j20_O            2 ANFRHIVRVAGVDLDGNKQLRWALTAIKGIGINFATMVCRVAGLDPFMKAGYLTDEQVKKIEEILADPVAHGIPRWAVNR   81 (148)
T ss_dssp             CCBCSCEECSSSCEECSSCHHHHHHHSTTCCHHHHHHHHHHHTCCSSSCTTBCCHHHHHHHHHHHHCHHHHCCCTTTSSE
T ss_pred             hhhhHhHHHcCccCCCCCEehhhhhhccCcCHHHHHHHHHHhCCCCCceeccCCHHHHHHHHHHHhcccccCCChhhhcc
Confidence            67999999999999999999999999999999999999999999999999999999999999999998788999999999


Q ss_pred             cCCCCCCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031813           87 QKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR  152 (152)
Q Consensus        87 ~~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~gv~~~k  152 (152)
                      |+|+.||++.|++|+||++.+++||+||++|+||||+||.+||||||||||||||||+||||+|||
T Consensus        82 ~kD~~~G~~~~~ve~dL~~~~~~dI~RL~~I~~yRG~RH~~GLpVRGQrTkTnaR~g~tvgv~kkk  147 (148)
T 3j20_O           82 PKDYETGRDLHLITAKLDMAIREDIMRLRRIRAYRGIRHELGLPVRGQRTRSNFRRGQTVGVSRKK  147 (148)
T ss_dssp             EEETTTEEEECCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHTCCSSSCCCSSCSCSSCCCCCSSCC
T ss_pred             cCCCCCCceeEEechHHHHHHHHHHHHHHHhCcEEeecccCCCcCCCCCCcCCCCcCcccceeccC
Confidence            999999999999999999999999999999999999999999999999999999999999999997

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

Probab=100.00  E-value=8e-64  Score=379.51  Aligned_cols=144  Identities=67%  Similarity=1.124  Sum_probs=140.3

Q ss_pred             CCCCCcc--ccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCcc
Q 031813            1 MSLVANE--DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFK   78 (152)
Q Consensus         1 ~~~~~~~--~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~   78 (152)
                      |||+..|  +||||+||+|||||++|.|.+|||+|||||..+|..||+++||||++++++||++|+++|.++|++|.+|+
T Consensus         1 ~~~~~~~~~~~~~~~RI~g~~i~~~k~v~~ALt~I~GIG~~~A~~I~~~~gid~~~r~g~Lt~~ei~~l~~~i~~~~~~~   80 (146)
T 3u5c_S            1 MSLVVQEQGSFQHILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIMQNPTHYK   80 (146)
T ss_dssp             -CCCCCCCSCCCSSBCCTTSCBCSSSCTTTTGGGSTTCCHHHHHHHHHHHTCCTTSCSSSCCHHHHHHHHHHHTCTTTTT
T ss_pred             CCccCCCHHHhhhhhhhcCccCCCCcchHhhHhhhcCCCHHHHHHHHHHcCCCCCceeccCCHHHHHHHHHHHHhhcccC
Confidence            8999766  89999999999999999999999999999999999999999999999999999999999999999998899


Q ss_pred             CCccccCccCCCCCCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCcc
Q 031813           79 IPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGK  144 (152)
Q Consensus        79 ip~w~~nr~~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~  144 (152)
                      ||+||+|||+|+.||++.|++|+||++.+++||+||++|+||||+||.+||||||||||||||+|+
T Consensus        81 iP~w~lNR~kD~~~G~~~~lie~dL~~~~~~dI~RL~~I~~yRG~RH~~GLpVRGQrTkTnaR~g~  146 (146)
T 3u5c_S           81 IPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRAHRGIRHFWGLRVRGQHTKTTGRRRA  146 (146)
T ss_dssp             CCSTTCTBCSCSSSCCCBCCCTHHHHHHHHHHHHHHHHHTCHHHHHHHTTCCCSCCCCSSSCCSCC
T ss_pred             ccHHHhhhhhcccccchheeehHHHHHHHHHhhHHHHhhceeeeecccCCCCCCccCCCcCCCCCC
Confidence            999999999999999999999999999999999999999999999999999999999999999985

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

Probab=100.00  E-value=1.4e-48  Score=289.63  Aligned_cols=111  Identities=32%  Similarity=0.483  Sum_probs=106.2

Q ss_pred             hhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCC
Q 031813           12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYK   91 (152)
Q Consensus        12 ~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~   91 (152)
                      |+||+|||||++|.|.+||++|||||..+|..||+++||||++++++||++|+++|.++|++  +|              
T Consensus         1 m~rI~g~~i~~~k~v~~aLt~I~GIG~~~A~~I~~~~gi~~~~r~~~Lt~~ei~~l~~~i~~--~~--------------   64 (126)
T 2vqe_M            1 MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVEN--TW--------------   64 (126)
T ss_dssp             -CCCSTTCCCCSSBHHHHHTTSSSCCSHHHHHHTTTTTCCTTSBGGGCCHHHHHHHHHHHHT--TS--------------
T ss_pred             CceEeCccCCCCcEeeeehhccccccHHHHHHHHHHcCCCcccccCcCCHHHHHHHHHHHHH--hC--------------
Confidence            89999999999999999999999999999999999999999999999999999999999986  24              


Q ss_pred             CCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCcc
Q 031813           92 DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGK  144 (152)
Q Consensus        92 sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~  144 (152)
                            ++|+||++++++||+||++|+||||+||.+|||||||||||||||++
T Consensus        65 ------~ve~dLrr~~~~nIkRL~~I~~YRG~RH~~GLPVRGQRTkTNaRTrk  111 (126)
T 2vqe_M           65 ------KLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRK  111 (126)
T ss_dssp             ------CCHHHHHHHHHHHHHHHHHTTCHHHHHHHTTCCSSSCCCSSCCHHHH
T ss_pred             ------cchhHHHHHHHHHHHHHHHHHHHhhhhhccCCcCCCccCccccccCC
Confidence                  35999999999999999999999999999999999999999999976

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

Probab=100.00  E-value=2.4e-44  Score=271.47  Aligned_cols=109  Identities=31%  Similarity=0.397  Sum_probs=92.3

Q ss_pred             CCCCccccc------hhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCC
Q 031813            2 SLVANEDFQ------HILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPR   75 (152)
Q Consensus         2 ~~~~~~~~~------~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~   75 (152)
                      |....++||      ||+||+|||||++|.|.+||++|||||..+|.+||+++|| +++++++|||+|+++|.++     
T Consensus        30 ~~~~~~~~~~~~~~~~m~RI~gvdlp~~K~v~~aLt~IyGIG~~~A~~I~~~~gI-~~~rv~~Lte~ei~~l~~~-----  103 (145)
T 3bbn_M           30 PAPKKGGIGHGGLQIECIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNF-DNKVTKDLSEEEVIILRKE-----  103 (145)
T ss_dssp             -----------------CCCSSSCCCCSSBTTTGGGGSTTCCSSTTTGGGTTTTC-CSCBTTSCCSSTTHHHHSS-----
T ss_pred             ccCCchhhhcccchhheeeEeCcccCCCCEEEEeeeeecCccHHHHHHHHHHcCC-CceEcCCCCHHHHHHHHHH-----
Confidence            334557899      8999999999999999999999999999999999999999 7999999999999998875     


Q ss_pred             CccCCccccCccCCCCCCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCcc
Q 031813           76 QFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGK  144 (152)
Q Consensus        76 ~~~ip~w~~nr~~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~  144 (152)
                                                  ++++++||+||++|+||||+||.+|||||||||||||||.|
T Consensus       104 ----------------------------Rr~v~~nIkRL~~I~~YRGlRH~~GLPVRGQRTkTNaRTrK  144 (145)
T 3bbn_M          104 ----------------------------KRFNRVAIERLKEIRCYRGIRHKLGLPVRGQRTKNNCRTLK  144 (145)
T ss_dssp             ----------------------------CCCCSTTTHHHHCCCCSCCTTTTTTCCSSSCCTTTCCCSSC
T ss_pred             ----------------------------HHHHHHHHHHHhhhceEeeeecccCCcCCCccCccccccCC
Confidence                                        11246899999999999999999999999999999999976

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

Probab=98.74  E-value=8.1e-09  Score=90.29  Aligned_cols=107  Identities=20%  Similarity=0.267  Sum_probs=86.1

Q ss_pred             ccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCcc
Q 031813            8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQ   87 (152)
Q Consensus         8 ~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~   87 (152)
                      ++-.+++++...=..-....|...+|.+||..+|.+||+.+|++|++++.+|+++|+..|.+++.+   ++  . +++|+
T Consensus       238 ~l~~~~~~~~~~~~~~~~~~fl~~~f~~v~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~~--~-~~~p~  311 (471)
T 1mu5_A          238 DREEIKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK---YE--D-FRSPS  311 (471)
T ss_dssp             CHHHHHHHSTTCSSCCBHHHHHTTSSSSCCHHHHHHHHHHTTCCTTSBGGGCCTTHHHHHHHHHHH---CC--C-CCCCC
T ss_pred             hHHHHHHHHHhcCCCcchHHhhhccccccCHHHHHHHHHhcCCCCCCChhhcCHHHHHHHHHHHHh---cc--C-ccCCC
Confidence            344455555332222245567778899999999999999999999999999999999999999987   42  1 25679


Q ss_pred             CCCCCCchhhhhhhhHHHHHHhh----hhhhhccceeec
Q 031813           88 KDYKDGKYSQVVSNALDMKLRDD----LERLKKIRNHRG  122 (152)
Q Consensus        88 ~D~~sg~~~~lie~~L~~~~~~~----I~rl~~i~syRG  122 (152)
                      .||+||.+.++++.+|++.++.+    ++|  ..+.|+|
T Consensus       312 ~~~lspig~~~~~~g~~~~~~~~f~~~~~r--~~~~~~g  348 (471)
T 1mu5_A          312 ADSLSVIGEDLIELGLKKIFNPDFAASITR--KPKAYQG  348 (471)
T ss_dssp             STTCCCCCHHHHHHHHHHHHCCSEEEEEEC--CCEEETT
T ss_pred             ccccCcCCHHHHHhhhhhccCceEEEEEec--CCceecC
Confidence            99999999999999999998886    566  7788887

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

Probab=98.25  E-value=7.8e-07  Score=78.84  Aligned_cols=90  Identities=18%  Similarity=0.223  Sum_probs=78.9

Q ss_pred             eeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCcc-CCccccCccCCCCCCchhhhhhhh
Q 031813           24 QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFK-IPDWFLNRQKDYKDGKYSQVVSNA  102 (152)
Q Consensus        24 k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~-ip~w~~nr~~D~~sg~~~~lie~~  102 (152)
                      ....|+-..+.++|..+|..||..+|++++.++.+|+.+|+..+.+++.+   ++ +    ++++.||+||.+.++++.+
T Consensus       253 ~l~~fl~~~ft~~g~~~a~~~~~~~gl~~~~~~~~l~~~~~~~ll~a~~~---~k~~----~~P~~~~lspig~~~~~~g  325 (530)
T 2zbk_B          253 TIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK---DEDF----RSPSADSLSVIGEDLIELG  325 (530)
T ss_dssp             BHHHHHHTTSTTCCHHHHHHHHHHTTCCSSCBSSCCCHHHHHHHHHHHHH---CCCC----CCCCSTTCCCCCTTHHHHH
T ss_pred             eeHhhhcCccccccHHHHHHHHHhhCCCCCCCcccCCHHHHHHHHHHHHh---ccCC----CCCCccccCcCCHHHHHhh
Confidence            34467778899999999999999999999999999999999999999986   54 3    5679999999999999999


Q ss_pred             HHHHHHhh----hhhhhccceeec
Q 031813          103 LDMKLRDD----LERLKKIRNHRG  122 (152)
Q Consensus       103 L~~~~~~~----I~rl~~i~syRG  122 (152)
                      |+..++.+    ++|  ..+.|+|
T Consensus       326 ~~~~~~~~f~~~~~r--~~~~~~g  347 (530)
T 2zbk_B          326 LKKIFNPDFAASITR--KPKAYQG  347 (530)
T ss_dssp             TTTTTCCSEEEEEEC--CCEEETT
T ss_pred             HHhhcCceEEEEEcc--CCceecC
Confidence            99888876    566  7788887

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

Probab=96.25  E-value=0.0047  Score=50.06  Aligned_cols=52  Identities=17%  Similarity=0.179  Sum_probs=45.0

Q ss_pred             CCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        22 ~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+.+|.-+|   +-|-|||...|.++|-.+||+|..++++||++|++.|-+.+..
T Consensus       142 ~~~~IK~~LlDQ~~vaGiGNiYa~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~  196 (266)
T 1ee8_A          142 SARPLKALLLDQRLAAGVGNIYADEALFRARLSPFRPARSLTEEEARRLYRALRE  196 (266)
T ss_dssp             CCSBHHHHHHHSSSSTTCCHHHHHHHHHHTTCCSSSBGGGCCHHHHHHHHHHHHH
T ss_pred             CCccHHHHHhccCccccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHHH
Confidence            356776666   3489999999999999999999999999999999998887754

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

Probab=96.24  E-value=0.0047  Score=49.90  Aligned_cols=50  Identities=24%  Similarity=0.308  Sum_probs=43.8

Q ss_pred             eeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           24 QKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        24 k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+|..+|   +-|-|||...|.++|-.+||+|..++++||++|++.|-+.+..
T Consensus       151 ~~Ik~~LLDQ~vvaGiGNiYadEiLf~a~I~P~~~a~~Ls~~~~~~L~~~i~~  203 (262)
T 1k3x_A          151 RQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLE  203 (262)
T ss_dssp             SCHHHHTTCTTTSBTCCHHHHHHHHHHHTCCSSCCGGGSCHHHHHHHHHHHHH
T ss_pred             ccHHHHHhcCCeeecccHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHH
Confidence            5666565   3379999999999999999999999999999999999888764

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

Probab=96.21  E-value=0.0048  Score=50.20  Aligned_cols=52  Identities=21%  Similarity=0.257  Sum_probs=45.6

Q ss_pred             CCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        22 ~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+.+|.-+|   +-|-|||...|.+||-.+||+|..++++||++|++.|-+.+..
T Consensus       154 ~~~~IK~~LlDQ~~vaGiGNiYa~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~  208 (273)
T 3u6p_A          154 TKRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVA  208 (273)
T ss_dssp             CCSBHHHHHHCTTTSTTCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHH
T ss_pred             CcchHHHHHhcCCccccccHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence            466676666   4499999999999999999999999999999999999888764

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

Probab=96.21  E-value=0.0049  Score=50.01  Aligned_cols=52  Identities=21%  Similarity=0.230  Sum_probs=45.1

Q ss_pred             CCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        22 ~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+.+|.-+|   +-|-|||...|.++|-.+||+|..++++||++|++.|-+.+..
T Consensus       152 ~~~~IK~~LLDQ~vvaGiGNiYadEiLf~a~I~P~~~a~~Ls~~~~~~L~~~i~~  206 (271)
T 2xzf_A          152 STKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSIIE  206 (271)
T ss_dssp             CCSBHHHHHHTSSSSSCCCHHHHHHHHHHTTCCTTCBGGGCCHHHHHHHHHHHHH
T ss_pred             CCccHHHHHhcCCeecccChhHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHH
Confidence            356676666   3489999999999999999999999999999999998887754

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

Probab=96.21  E-value=0.0048  Score=50.04  Aligned_cols=52  Identities=27%  Similarity=0.223  Sum_probs=45.2

Q ss_pred             CCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        22 ~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+.+|.-+|   +-|-|||...|.++|-.+||+|..++++||++|++.|-+.+..
T Consensus       149 ~~~~IK~~LlDQ~~vaGiGNiYa~EiLf~a~I~P~~~a~~Ls~~~~~~L~~~i~~  203 (268)
T 1k82_A          149 KKTAIKPWLMDNKLVVGVGNIYASESLFAAGIHPDRLASSLSLAECELLARVIKA  203 (268)
T ss_dssp             CCSBHHHHHTCTTTCSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHhcCCeeeccCchHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHHH
Confidence            356776666   4489999999999999999999999999999999999887754

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

Probab=96.08  E-value=0.0063  Score=50.42  Aligned_cols=52  Identities=27%  Similarity=0.277  Sum_probs=45.1

Q ss_pred             CCeeheeehh---cccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           22 GKQKIMFALT---SIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        22 ~~k~v~~aL~---~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+.+|.-+|-   -|-|||...|.+||-++||+|..++++||++|++.|-+.+..
T Consensus       167 ~~~~IK~~LLDQ~vvaGIGNiYadEiLf~AgIhP~~~a~~Ls~~e~~~L~~~i~~  221 (310)
T 3twl_A          167 KKITIKPLLLDQGYISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKE  221 (310)
T ss_dssp             CCSBHHHHHHCTTTSBSCCHHHHHHHHHHTTCCTTSBGGGCCHHHHHHHHHHHHH
T ss_pred             CcchHHHHHhcCccccCCcHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHH
Confidence            4667766663   389999999999999999999999999999999999887754

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

Probab=96.02  E-value=0.0065  Score=50.04  Aligned_cols=51  Identities=14%  Similarity=0.193  Sum_probs=45.2

Q ss_pred             Ceeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           23 KQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        23 ~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      +.+|..+|   +-|-|||...|.++|-.+||+|..++++||++|++.|.+.+.+
T Consensus       174 ~~~IK~~LLDQ~viaGiGNIYa~EiLf~AgI~P~~~~~~Ls~~~~~~L~~ai~~  227 (287)
T 3w0f_A          174 DRMLCDVLLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQACHLVKMTRD  227 (287)
T ss_dssp             SSBHHHHHHCTTTSTTCCHHHHHHHHHHHTCCTTCBGGGSCHHHHHHHHHHHHH
T ss_pred             cccHHHHHhcCCccccccHHHHHHHHHHccCCccCccccCCHHHHHHHHHHHHH
Confidence            44666555   4489999999999999999999999999999999999999875

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

Probab=96.01  E-value=0.0064  Score=50.02  Aligned_cols=52  Identities=27%  Similarity=0.333  Sum_probs=44.9

Q ss_pred             CCeeheeeh---hc-ccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           22 GKQKIMFAL---TS-IKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        22 ~~k~v~~aL---~~-i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+.+|.-+|   +- |-|||...|.+||-.+||+|..++++||++|++.|-+.+..
T Consensus       153 ~~~~Ik~~LLDQ~~~vaGIGNiYa~EiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~  208 (295)
T 3vk8_A          153 YKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIKY  208 (295)
T ss_dssp             CCSBHHHHHHCSSSSCBCCCHHHHHHHHHHTTBCTTCBGGGCCHHHHHHHHHHHHH
T ss_pred             cCchHHHHHhcCCcccccccHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence            455666555   33 89999999999999999999999999999999999888754

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

Probab=92.94  E-value=0.046  Score=34.78  Aligned_cols=37  Identities=16%  Similarity=0.223  Sum_probs=31.6

Q ss_pred             ehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHH
Q 031813           29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL   67 (152)
Q Consensus        29 aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L   67 (152)
                      .|.+|+|||+..+..+++.+|  .-..+.+.|.+|+..+
T Consensus         5 ~L~~IpGIG~kr~~~LL~~Fg--s~~~i~~As~eeL~~v   41 (63)
T 2a1j_A            5 FLLKMPGVNAKNCRSLMHHVK--NIAELAALSQDELTSI   41 (63)
T ss_dssp             HHHTSTTCCHHHHHHHHHHCS--SHHHHHTCCHHHHHHH
T ss_pred             HHHcCCCCCHHHHHHHHHHcC--CHHHHHHCCHHHHHHH
Confidence            578999999999999999988  4566778888888776

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

Probab=92.37  E-value=0.12  Score=41.54  Aligned_cols=63  Identities=13%  Similarity=0.136  Sum_probs=50.0

Q ss_pred             ccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813            8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus         8 ~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .|.++|+.+  .--..|.+..+|..+ |.+...+..+++.+||++++++.+||.+|+..|.+++++
T Consensus       207 ~~~~~v~~~--F~~rrKtL~n~L~~~-~~~~~~~~~~l~~~~i~~~~R~e~Ls~~~f~~L~~~~~~  269 (271)
T 3fut_A          207 GLFRLVEAA--FGKRRKTLLNALAAA-GYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLEG  269 (271)
T ss_dssp             HHHHHHHHH--TSSTTSCHHHHHHHT-TCCHHHHHHHHHHTTCCTTCCGGGCCHHHHHHHHHHHC-
T ss_pred             HHHHHHHHH--HhcCCcHHHHHHHhh-cCCHHHHHHHHHHCCcCCCCChhhCCHHHHHHHHHHHHh
Confidence            466666642  233578888888775 457788889999999999999999999999999998864

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

Probab=92.20  E-value=0.05  Score=35.56  Aligned_cols=33  Identities=18%  Similarity=0.265  Sum_probs=21.9

Q ss_pred             CcccCCCeeheeehhcccccCHHHHHHHHHHcC
Q 031813           17 NTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD   49 (152)
Q Consensus        17 ~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg   49 (152)
                      |.-++.+......|..|+|||+.+|..|++.+|
T Consensus        13 ~~~~~~~~~~~~~L~~I~gIG~~~A~~Ll~~fg   45 (78)
T 1kft_A           13 GLVPRGSHMNTSSLETIEGVGPKRRQMLLKYMG   45 (78)
T ss_dssp             ----------CCGGGGCTTCSSSHHHHHHHHHS
T ss_pred             hHHHhHHHHHHHHHhcCCCCCHHHHHHHHHHcC
Confidence            445666777888999999999999999999986

>2q2e_B Type 2 DNA topoisomerase 6 subunit B; DNA-binding, SPO11, ATPase; 4.00A {Methanosarcina mazei}

Probab=91.99  E-value=0.032  Score=50.30  Aligned_cols=87  Identities=23%  Similarity=0.235  Sum_probs=67.5

Q ss_pred             eeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCCCCchhhhhhhhHHHH
Q 031813           27 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMK  106 (152)
Q Consensus        27 ~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg~~~~lie~~L~~~  106 (152)
                      .|+-......|..+++.+|+..++.+.....+|+.+++.....++-+   ..+    .+|+.|+++|.+..+++..|...
T Consensus       260 sFvN~i~T~~GGr~in~~~~~~~l~k~~~~~~lt~dDiregL~avis---vki----~~Pqtk~l~pige~~i~~~l~~~  332 (621)
T 2q2e_B          260 PFLRYSFCKIGLLTAEEICKAAGLDPEIDPHALGRHEARKLIEAFEK---VKI----MAPPTDCLSPIGEDLIYRGLEKE  332 (621)
T ss_dssp             CTTSSSSCC--CHHHHHHHHTTTCCTTSCSSSCCSSSSTTTTHHHHT---SCC----SCCCSTTCCCCCHHHHHHHHHHH
T ss_pred             EEeCCcccCCCHHHHHHHHHHhCccccccCCCCCHHHHHhhcEEEEE---EEC----CCCCccccChhHHHHHHHHHHHh
Confidence            34334455667799999999999987656678999999888888765   444    57899999999999999999998


Q ss_pred             HHhhh----hhhhccceeec
Q 031813          107 LRDDL----ERLKKIRNHRG  122 (152)
Q Consensus       107 ~~~~I----~rl~~i~syRG  122 (152)
                      ++.+.    +|  .++.|+|
T Consensus       333 ~~p~f~~~~~r--~p~~~~g  350 (621)
T 2q2e_B          333 TTVDFIATSTR--KPAVYSG  350 (621)
T ss_dssp             SCCSEEECCBC--CCEEETT
T ss_pred             cChheEEEEec--CccccCC
Confidence            88753    45  7788887

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

Probab=90.51  E-value=0.11  Score=32.92  Aligned_cols=51  Identities=10%  Similarity=0.169  Sum_probs=35.6

Q ss_pred             eeheeehhcccccCHHHHHHHHHHcCC-------CC--CCCCCCCCHHHHHHHHHHHhCC
Q 031813           24 QKIMFALTSIKGIGRRLANIVCKKADV-------DM--NKRAGELSAAELDNLMVVVANP   74 (152)
Q Consensus        24 k~v~~aL~~i~GIG~~~A~~Ic~~lgi-------~~--~~~~~~Ls~~ei~~L~~~l~~~   74 (152)
                      ..+..+|+.|+|||..+|..|++.+|=       ++  -..+..+.+.....|..+++++
T Consensus        10 ~~~~~~L~~i~giG~~~a~~Ll~~fgs~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~~~   69 (75)
T 1x2i_A           10 ERQRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAP   69 (75)
T ss_dssp             HHHHHHHTTSTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSC
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHHhCc
Confidence            345678999999999999999998762       11  1234445666667777777663

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

Probab=89.77  E-value=0.035  Score=47.03  Aligned_cols=40  Identities=23%  Similarity=0.234  Sum_probs=34.7

Q ss_pred             Ceeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHH
Q 031813           23 KQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAA   62 (152)
Q Consensus        23 ~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~   62 (152)
                      +.+|..+|   +-|-|||...|.+||-.+||+|...+++|+++
T Consensus       158 ~~~IK~~LLDQ~vVAGIGNIYadEiLF~AgIhP~r~a~~Ls~~  200 (364)
T 1tdh_A          158 DRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEA  200 (364)
T ss_dssp             GSBHHHHTTCTTTSTTCCHHHHHHHHHHHTCCTTSBHHHHHGG
T ss_pred             cccHHHHHhcCCeeeccchHHHHHHHHHCcCCCCCChhhcCHH
Confidence            56666555   34899999999999999999999999999886

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

Probab=89.69  E-value=0.22  Score=33.14  Aligned_cols=50  Identities=14%  Similarity=0.217  Sum_probs=35.2

Q ss_pred             eheeehhcccccCHHHHHHHHHHcCC-------CCC--CCCCCCCHHHHHHHHHHHhCC
Q 031813           25 KIMFALTSIKGIGRRLANIVCKKADV-------DMN--KRAGELSAAELDNLMVVVANP   74 (152)
Q Consensus        25 ~v~~aL~~i~GIG~~~A~~Ic~~lgi-------~~~--~~~~~Ls~~ei~~L~~~l~~~   74 (152)
                      .+..+|..|+|||..+|..|++.+|=       ++.  ..+..+.+....+|.++++++
T Consensus        16 ~~~~~L~~IpgIG~~~A~~Ll~~fgsl~~l~~a~~~eL~~i~GIG~~~a~~I~~~l~~~   74 (89)
T 1z00_A           16 RVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEP   74 (89)
T ss_dssp             HHHHHHTTSSSCCHHHHHHHHHHTCBHHHHHHCCHHHHHTSTTCCHHHHHHHHHHHHSC
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHCCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence            45678999999999999999998761       110  133345566667777777764

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

Probab=89.23  E-value=0.12  Score=34.87  Aligned_cols=43  Identities=14%  Similarity=0.126  Sum_probs=33.4

Q ss_pred             CeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHH
Q 031813           23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL   67 (152)
Q Consensus        23 ~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L   67 (152)
                      |......|..|+|||...+..|++.+|  .-..+.+.|.+||..+
T Consensus        13 N~~~~s~L~~IpGIG~kr~~~LL~~Fg--Sl~~i~~AS~eEL~~v   55 (84)
T 1z00_B           13 NPGPQDFLLKMPGVNAKNCRSLMHHVK--NIAELAALSQDELTSI   55 (84)
T ss_dssp             CHHHHHHHHTCSSCCHHHHHHHHHHSS--CHHHHHHSCHHHHHHH
T ss_pred             cccHHHHHHhCCCCCHHHHHHHHHHcC--CHHHHHHCCHHHHHHH
Confidence            344566789999999999999999988  3455666777777765

>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=88.60  E-value=0.34  Score=38.29  Aligned_cols=57  Identities=18%  Similarity=0.109  Sum_probs=44.1

Q ss_pred             ccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHh
Q 031813            8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA   72 (152)
Q Consensus         8 ~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~   72 (152)
                      .|..+|+.+  .-.-.|.+.-+|..+++      ..+++.+|++|+.++.+||.+|+..|.+.+.
T Consensus       193 ~~~~~v~~~--F~~rrK~l~n~l~~~~~------~~~l~~~~i~~~~R~e~Ls~~~f~~l~~~~~  249 (252)
T 1qyr_A          193 VLSRITTEA--FNQRRKTIRNSLGNLFS------VEVLTGMGIDPAMRAENISVAQYCQMANYLA  249 (252)
T ss_dssp             HHHHHHHHH--HHTTTSBHHHHTTTTCC------HHHHHHTTCCTTSBGGGSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHH--HHhCCcHHHHHHhhhhh------HHHHHHcCCCCCCChHHCCHHHHHHHHHHHH
Confidence            355555443  23457888888877654      5578899999999999999999999998875

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

Probab=86.23  E-value=0.57  Score=32.37  Aligned_cols=54  Identities=17%  Similarity=0.177  Sum_probs=39.6

Q ss_pred             cCCCeeheeehhcccccCHHHHHHHHHHcCCCC---CCCCCCCCHHHHHHHHHHHhC
Q 031813           20 VDGKQKIMFALTSIKGIGRRLANIVCKKADVDM---NKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        20 l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~---~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      ++-|..-.-.|+.++|||+.+|.+|.+.=.+..   -..+.-+.+..+++|..++..
T Consensus        18 vdiNtAs~~eL~~lpGIG~~~A~~IV~~GpF~s~edL~~V~Gig~~~~e~l~~~l~~   74 (97)
T 3arc_U           18 IDLNNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLEH   74 (97)
T ss_dssp             EETTTSCGGGGGGSTTCTTHHHHHHHHHCCCSSGGGGGGCTTCCHHHHHHHHHTGGG
T ss_pred             eeCCcCCHHHHhHCCCCCHHHHHHHHHcCCCCCHHHHHhccCCCHHHHHHHHHHhce
Confidence            344444556789999999999999999422222   224666789999999998875

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

Probab=85.88  E-value=0.5  Score=34.73  Aligned_cols=54  Identities=19%  Similarity=0.194  Sum_probs=38.9

Q ss_pred             cCCCeeheeehhcccccCHHHHHHHHHHcC---CCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           20 VDGKQKIMFALTSIKGIGRRLANIVCKKAD---VDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        20 l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg---i~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      |+=|..=...|+.++|||+..|.+|.+--.   ++.-..+..+++.+.+.|.+..++
T Consensus        55 IniNtA~~~eL~~LpGiGp~~A~~II~~GpF~svedL~~V~GIg~k~~e~l~~~~~~  111 (134)
T 1s5l_U           55 IDLNNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLEH  111 (134)
T ss_dssp             EETTTSCGGGGGGSTTCTHHHHHHHHHTCCCSSGGGGGGCTTCCHHHHHHHHHHHTT
T ss_pred             eeCcccCHHHHHHCCCCCHHHHHHHHHcCCCCCHHHHHhCCCCCHHHHHHHHHhhcc
Confidence            333444456788999999999999995322   222335666789999999998876

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

Probab=85.85  E-value=0.32  Score=32.56  Aligned_cols=26  Identities=12%  Similarity=0.235  Sum_probs=22.8

Q ss_pred             eeheeehhcccccCHHHHHHHHHHcC
Q 031813           24 QKIMFALTSIKGIGRRLANIVCKKAD   49 (152)
Q Consensus        24 k~v~~aL~~i~GIG~~~A~~Ic~~lg   49 (152)
                      ..+..+|+.|.|||..+|..|++.+|
T Consensus        28 ~~~~~~L~~IpgIG~~~A~~Ll~~fg   53 (91)
T 2a1j_B           28 SRVTECLTTVKSVNKTDSQTLLTTFG   53 (91)
T ss_dssp             HHHHHHHTTSTTCCHHHHHHHHHHHS
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHCC
Confidence            34567899999999999999999987

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

Probab=85.46  E-value=0.36  Score=31.06  Aligned_cols=28  Identities=21%  Similarity=0.264  Sum_probs=22.0

Q ss_pred             CCeeheeehhcccccCHHHHHHHHHHcC
Q 031813           22 GKQKIMFALTSIKGIGRRLANIVCKKAD   49 (152)
Q Consensus        22 ~~k~v~~aL~~i~GIG~~~A~~Ic~~lg   49 (152)
                      -|..-...|..++|||..+|..|.+...
T Consensus        21 iN~a~~~~L~~ipGIG~~~A~~Il~~r~   48 (75)
T 2duy_A           21 LNEASLEELMALPGIGPVLARRIVEGRP   48 (75)
T ss_dssp             TTTCCHHHHTTSTTCCHHHHHHHHHTCC
T ss_pred             hhhCCHHHHHhCCCCCHHHHHHHHHHcc
Confidence            3333455688999999999999999763

>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=85.36  E-value=0.59  Score=36.72  Aligned_cols=54  Identities=13%  Similarity=0.277  Sum_probs=42.6

Q ss_pred             ccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813            8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus         8 ~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .|.++|+.+  .--..|.+.-+|..+          .++.+||+|++++.+||-+|+..|.+++.+
T Consensus       193 ~~~~~v~~~--F~~rrk~l~~~l~~~----------~l~~~~i~~~~r~e~l~~~~f~~l~~~~~~  246 (249)
T 3ftd_A          193 NYKKFLTKI--FQNRRKVLRKKIPEE----------LLKEAGINPDARVEQLSLEDFFKLYRLIED  246 (249)
T ss_dssp             HHHHHHHHH--HSSTTSCGGGTSCHH----------HHHHTTCCTTCCGGGCCHHHHHHHHHHHHC
T ss_pred             HHHHHHHHH--HhCcChhHHHHHHHH----------HHHHCCCCCCCChhhCCHHHHHHHHHHHHH
Confidence            355666552  233477777777764          689999999999999999999999999875

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

Probab=82.32  E-value=0.28  Score=39.45  Aligned_cols=58  Identities=12%  Similarity=0.172  Sum_probs=45.8

Q ss_pred             ccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813            8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus         8 ~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .|.++|+.+  .-...|.+.-+|..+.+      ..+++.+||++++++.+||.+|+..|.+++++
T Consensus       217 ~~~~~v~~~--F~~rrK~l~n~L~~~~~------~~~l~~~~i~~~~R~e~Ls~~~f~~L~~~~~~  274 (279)
T 3uzu_A          217 VLGEVVTAA--FSQRRKMLRNTLGGYRD------LVDFDALGFDLARRAEDIGVDEYVRVAQAVAS  274 (279)
T ss_dssp             HHHHHHHHH--GGGTTSBHHHHTGGGTT------TCCTTTTTCCTTSBGGGCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHH--HhccChHHHHHHHhhcC------HHHHHHCCcCCCCCceeCCHHHHHHHHHHHHH
Confidence            466777653  33457888888887754      35678899999999999999999999998864

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

Probab=80.80  E-value=0.45  Score=37.66  Aligned_cols=56  Identities=11%  Similarity=0.176  Sum_probs=42.5

Q ss_pred             ccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHH
Q 031813            8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV   71 (152)
Q Consensus         8 ~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l   71 (152)
                      .|.++|+.+  .--..|.+.-+|..+++      ...++.+||++++++.+||.+|+..|.+++
T Consensus       199 ~~~~~v~~~--F~~rrK~l~~~L~~~~~------~~~l~~~~i~~~~R~e~Ls~~~f~~L~~~~  254 (255)
T 3tqs_A          199 QLSHVVKEA--FSYRRKTVGNALKKLIN------PSQWPLLEINPQLRPQELTVEDFVKISNIL  254 (255)
T ss_dssp             HHHHHHHHH--HHSTTSCHHHHTTTTCC------GGGTGGGTCCTTSCGGGSCHHHHHHHHHHH
T ss_pred             HHHHHHHHH--HHccChHHHHHHhhhCC------HHHHHHCCcCCCCCceeCCHHHHHHHHHHh
Confidence            466666652  23347788888877653      135688999999999999999999998876

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

Probab=80.35  E-value=1.4  Score=33.86  Aligned_cols=43  Identities=19%  Similarity=0.158  Sum_probs=31.3

Q ss_pred             eheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHH
Q 031813           25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV   71 (152)
Q Consensus        25 ~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l   71 (152)
                      ...-.|.+++|||+.||..||..+|. +..-+-   |..+.++..-+
T Consensus       114 ~~~~~L~~lpGIG~kTA~~il~~~~~-~~~~~v---D~~v~Ri~~rl  156 (207)
T 3fhg_A          114 LARERLLNIKGIGMQEASHFLRNVGY-FDLAII---DRHIIDFMRRI  156 (207)
T ss_dssp             HHHHHHTTSTTCCHHHHHHHHHHTTC-CSSCCC---CHHHHHHHHHT
T ss_pred             HHHHHHHcCCCcCHHHHHHHHHHhCC-CCccee---cHHHHHHHHHc
Confidence            45667889999999999999987777 333333   46677766654

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	152
d2uubm1	125	a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus	5e-33
d2gy9m1	114	a.156.1.1 (M:1-114) Ribosomal protein S13 {Escheri	7e-32

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

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

 Score =  111 bits (278), Expect = 5e-33
 Identities = 39/141 (27%), Positives = 63/141 (44%), Gaps = 24/141 (17%)

Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+    +   +++  ALT I GIG+  A    +K  ++   R  +L+ AE+  L      
Sbjct: 2   RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRL------ 55

Query: 74  PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
            R++    W L                  L  ++  +++RL  I  +RGLRH  GL VRG
Sbjct: 56  -REYVENTWKL---------------EGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRG 99

Query: 134 QHTKTTGR--RGKTVGVSKKR 152
           Q T+T  R  +G    V+ K+
Sbjct: 100 QRTRTNARTRKGPRKTVAGKK 120

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

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

 Score =  107 bits (270), Expect = 7e-32
 Identities = 36/131 (27%), Positives = 56/131 (42%), Gaps = 23/131 (17%)

Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
           R+   N+   +  + ALTSI G+G+  +  +   A +  + +  ELS  ++D        
Sbjct: 2   RIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQID-------- 53

Query: 74  PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
                            +D     VV   L  ++   ++RL  +  +RGLRH  GL VRG
Sbjct: 54  ---------------TLRDEVAKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRG 98

Query: 134 QHTKTTGRRGK 144
           Q TKT  R  K
Sbjct: 99  QRTKTNARTRK 109

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	152
d2uubm1	125	Ribosomal protein S13 {Thermus thermophilus [TaxId	100.0
d2gy9m1	114	Ribosomal protein S13 {Escherichia coli [TaxId: 56	100.0
d2hkja1	78	Topoisomerase VI-B subunit middle domain {Archaeon	98.61
d1k3xa1	89	Endonuclease VIII {Escherichia coli [TaxId: 562]}	97.77
d1r2za1	94	DNA repair protein MutM (Fpg) {Bacillus stearother	97.7
d1ee8a1	89	DNA repair protein MutM (Fpg) {Thermus thermophilu	97.65
d1k82a1	88	DNA repair protein MutM (Fpg) {Escherichia coli [T	97.62
d1tdza1	88	DNA repair protein MutM (Fpg) {Lactococcus lactis	97.61
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	95.83
d1tdha1	115	Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapi	95.33
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	95.18
d2fmpa2	57	DNA polymerase beta {Human (Homo sapiens) [TaxId:	94.41
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	94.13
d2bcqa2	57	DNA polymerase lambda {Human (Homo sapiens) [TaxId	93.92
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	93.88
d1jmsa3	60	Terminal deoxynucleotidyl transferase {Mouse (Mus	93.6
d2i0za2	169	Flavoprotein BC4706 {Bacillus cereus [TaxId: 1396]	93.44
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	93.19
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	92.99
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	92.69
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	92.22
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	91.39
d2gqfa2	148	Hypothetical protein HI0933 {Haemophilus influenza	91.31
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	91.16
d2axtu1	98	Photosystem II 12 kDa extrinsic protein PsbU {Ther	90.97
d1b43a1	120	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr	87.45
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	87.38
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	85.86
d2duya1	65	Uncharacterized protein TTHA1967 {Thermus thermoph	85.37
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	85.34
d1qyra_	252	High level kasugamycin resistance protein KsgA {Es	85.15
d1ul1x1	140	Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo	82.96

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

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

Probab=100.00  E-value=7.5e-50  Score=294.73  Aligned_cols=118  Identities=32%  Similarity=0.476  Sum_probs=112.7

Q ss_pred             hhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCCC
Q 031813           13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKD   92 (152)
Q Consensus        13 vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~s   92 (152)
                      .||+|||||++|+|.+||++|||||+++|.+||+.+||||++++++||++|++.|.++++++  |               
T Consensus         1 aRI~g~di~~~K~v~~ALt~I~GIG~~~A~~Ic~~lgId~~~k~~~Lt~~qi~~I~~~i~~~--~---------------   63 (125)
T d2uubm1           1 ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENT--W---------------   63 (125)
T ss_dssp             CCCSTTCCCCSSBHHHHHTTSTTCCHHHHHHHHHTTTCCTTSBGGGCCHHHHHHHHHHHHHH--S---------------
T ss_pred             CcccCccCCCCCEEEEeeeeeeCcCHHHHHHHHHHcCCCcccccccccHHHHHHHHHHHhhh--h---------------
Confidence            48999999999999999999999999999999999999999999999999999999999862  2               


Q ss_pred             CchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCC--ccceeeeccC
Q 031813           93 GKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRR--GKTVGVSKKR  152 (152)
Q Consensus        93 g~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart--~~~~gv~~~k  152 (152)
                           ++|++|++.+.+||+||++|+||||+||.+|||||||||||||||  |.++||.+||
T Consensus        64 -----~i~~~L~~~~~~dIkrl~~i~~yRG~RH~~gLpvRGQRT~tN~rt~kg~~~~v~~kk  120 (125)
T d2uubm1          64 -----KLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKK  120 (125)
T ss_dssp             -----CCTTHHHHHHHHHHHHHHHTTCHHHHHHHHTCCSSSCCCSSCCHHHHCSCCCCCCCS
T ss_pred             -----hhHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCCCCCCCCCccccCCCcccccccc
Confidence                 469999999999999999999999999999999999999999997  7899999986

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

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

Probab=100.00  E-value=1.8e-47  Score=277.94  Aligned_cols=110  Identities=35%  Similarity=0.515  Sum_probs=105.6

Q ss_pred             hhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCCC
Q 031813           13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKD   92 (152)
Q Consensus        13 vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~s   92 (152)
                      .||+|+|||++|+|.+||++|||||..+|.+||+.+||||++++++||++|++.|.+++++   +               
T Consensus         1 aRI~g~dip~~K~v~~ALt~I~GIG~~~A~~Ic~~lgid~~~kv~~Lt~~qi~~l~~~i~~---~---------------   62 (114)
T d2gy9m1           1 ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAK---F---------------   62 (114)
T ss_dssp             CCCSSSCCCCSSBHHHHHTTSSSCCHHHHHHHHHHHTCCTTSBTTSCCHHHHHHHHHHHHS---S---------------
T ss_pred             CcccCccCCCCCEEEEEeeeeeCcCHHHHHHHHHHcCCCcccccCcccHHHHHHHHHHHHh---c---------------
Confidence            4899999999999999999999999999999999999999999999999999999999986   3               


Q ss_pred             CchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccc
Q 031813           93 GKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKT  145 (152)
Q Consensus        93 g~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~  145 (152)
                           ++|++|++.+++||+||++|+||||+||++|||||||||||||||+|.
T Consensus        63 -----~i~~~L~~~~~~dI~rl~~I~~yrG~RH~~gLpvRGQrT~tNart~k~  110 (114)
T d2gy9m1          63 -----VVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKG  110 (114)
T ss_dssp             -----CCSHHHHHHHHHHHHHTTTTTCHHHHHHHCCSCCCCCCSSSSCHHHHC
T ss_pred             -----ccHHHHHHHHHHHHHHHHHhccceeeeccCCCCCCCCCCCCCccccCC
Confidence                 358999999999999999999999999999999999999999999873

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

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

Probab=98.61  E-value=1.5e-08  Score=66.70  Aligned_cols=64  Identities=19%  Similarity=0.305  Sum_probs=51.3

Q ss_pred             cccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813            7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus         7 ~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      ++|+.|++=..   ..-+...+.-+.|.|||...|.+||..+||+|.+++++|+++|+..|.+++.+
T Consensus        11 ~~l~~~l~~~~---~~ik~~l~lq~~f~GvGn~~a~Eil~~agi~P~~~~~~L~~~e~~~L~~air~   74 (78)
T d2hkja1          11 EEIKILINNLK---RDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK   74 (78)
T ss_dssp             HHHHHHHHTCS---SCCBHHHHHHHHSSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC---CcchHHHHHHHHhcccCHHHHHHHHHHhCCCcccccccCCHHHHHHHHHHHhh
Confidence            44555554332   22345556667789999999999999999999999999999999999999987

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

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

Probab=97.77  E-value=1.5e-05  Score=53.17  Aligned_cols=52  Identities=23%  Similarity=0.295  Sum_probs=45.5

Q ss_pred             CCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        22 ~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+++|.-+|   +-|-|||...+.+||-.++|+|..++++|+++|++.|-+.+..
T Consensus        25 ~~~~Ik~~LlDQ~~~aGIGN~~~~EiL~~a~i~P~~~~~~L~~~~~~~L~~~~~~   79 (89)
T d1k3xa1          25 RNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLE   79 (89)
T ss_dssp             TTSCHHHHTTCTTTSBTCCHHHHHHHHHHHTCCSSCCGGGSCHHHHHHHHHHHHH
T ss_pred             ccchHHHHHhcCccccccCcHHHHHHHHHhcccccCchhhCCHHHHHHHHHHHHH
Confidence            456776665   4499999999999999999999999999999999999888753

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

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

Probab=97.70  E-value=2.5e-05  Score=52.75  Aligned_cols=53  Identities=21%  Similarity=0.255  Sum_probs=47.0

Q ss_pred             CCCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           21 DGKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        21 ~~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      ..+.+|.-+|   +-+-|||...+.+||-.++|+|.+++++|+++|+..|-+.+..
T Consensus        20 ~~~~~ik~~LlDQ~~~aGiGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~L~~~~~~   75 (94)
T d1r2za1          20 KTKRSVKALLLDQTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVA   75 (94)
T ss_dssp             TCCSBHHHHHHCTTTSSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHH
T ss_pred             cCCccHHHHHHhccccCCcccHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHH
Confidence            3567887777   6689999999999999999999999999999999999887753

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

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

Probab=97.65  E-value=2.9e-05  Score=51.86  Aligned_cols=52  Identities=17%  Similarity=0.179  Sum_probs=45.0

Q ss_pred             CCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        22 ~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+.+|.-+|   .-|-|||...+.+||-.++|+|..++++|+++|++.|-+.+..
T Consensus        21 ~~~~ik~~LlDQ~~iaGiGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~L~~~i~~   75 (89)
T d1ee8a1          21 SARPLKALLLDQRLAAGVGNIYADEALFRARLSPFRPARSLTEEEARRLYRALRE   75 (89)
T ss_dssp             CCSBHHHHHHHSSSSTTCCHHHHHHHHHHTTCCSSSBGGGCCHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHhccccCCCCcHHHHHHHHHHHcCccchhhhCCHHHHHHHHHHHHH
Confidence            355665555   4589999999999999999999999999999999999888754

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

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

Probab=97.62  E-value=3.1e-05  Score=51.63  Aligned_cols=52  Identities=27%  Similarity=0.223  Sum_probs=45.6

Q ss_pred             CCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        22 ~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+.+|..+|   +-|-|||...+.+||-.+||+|.+++++|+++|+..|-+.+..
T Consensus        21 ~~~~ik~~LlDQ~~iaGiGN~y~~EiLf~a~I~P~~~~~~L~~~~~~~L~~~i~~   75 (88)
T d1k82a1          21 KKTAIKPWLMDNKLVVGVGNIYASESLFAAGIHPDRLASSLSLAECELLARVIKA   75 (88)
T ss_dssp             CCSBHHHHHTCTTTCSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHccccccccchHHHHHHHHHHCCCccChHHHCCHHHHHHHHHHHHH
Confidence            466776555   4489999999999999999999999999999999999988764

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

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

Probab=97.61  E-value=3.5e-05  Score=51.40  Aligned_cols=52  Identities=21%  Similarity=0.230  Sum_probs=45.4

Q ss_pred             CCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        22 ~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .++.|.-+|   +-|.|||...|.+||-.++|+|..++++|+++|+..|-+.+..
T Consensus        21 ~~~~ik~~LldQ~~iaGIGNiy~~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~   75 (88)
T d1tdza1          21 STKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSIIE   75 (88)
T ss_dssp             CCSBHHHHHHTSSSSSCCCHHHHHHHHHHTTCCTTCBGGGCCHHHHHHHHHHHHH
T ss_pred             ccccHHHHHHhccccCCcChHHHHHHHHHHHcCccchhhHcCHHHHHHHHHHHHH
Confidence            356776666   4589999999999999999999999999999999999887753

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

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

Probab=95.83  E-value=0.0018  Score=40.61  Aligned_cols=23  Identities=35%  Similarity=0.626  Sum_probs=21.0

Q ss_pred             eeehhcccccCHHHHHHHHHHcC
Q 031813           27 MFALTSIKGIGRRLANIVCKKAD   49 (152)
Q Consensus        27 ~~aL~~i~GIG~~~A~~Ic~~lg   49 (152)
                      .++|+.|+|||+.+|..|++.+|
T Consensus        12 ~~~L~~IpgIG~~~a~~L~~~F~   34 (70)
T d2bgwa1          12 LYILQSFPGIGRRTAERILERFG   34 (70)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHHHS
T ss_pred             HHHHcCCCCcCHHHHHHHHHHhC
Confidence            45799999999999999999987

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

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

Probab=95.33  E-value=0.00074  Score=46.98  Aligned_cols=63  Identities=16%  Similarity=0.073  Sum_probs=43.6

Q ss_pred             ccchhhhhcCcccCCCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHH
Q 031813            8 DFQHILRVLNTNVDGKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVV   70 (152)
Q Consensus         8 ~~~~~vri~~~~l~~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~   70 (152)
                      +|...+.-.-..-..+++|..+|   .-|-|||...+.+||-.++|+|..++.+|+++|...|.+.
T Consensus        12 ~f~~~~~~~~~~k~~~~~i~~~LldQ~~~aGiGN~~~~EiLf~a~i~P~~~~~~l~~~~~~~l~~~   77 (115)
T d1tdha1          12 QFRESVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSP   77 (115)
T ss_dssp             HHHHHHHHTTTSGGGGSBHHHHTTCTTTSTTCCHHHHHHHHHHHTCCTTSBHHHHHGGGC-----C
T ss_pred             chhHHHHHHHhhcccCCcHHHHHhccchhccccHHHHHHHHHHcCCCCCCchhhcCHHHHhHHHhh
Confidence            45544433323334456675555   4499999999999999999999999999999998887553

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

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

Probab=95.18  E-value=0.0028  Score=40.58  Aligned_cols=50  Identities=14%  Similarity=0.197  Sum_probs=33.0

Q ss_pred             eheeehhcccccCHHHHHHHHHHcCC---------CCCCCCCCCCHHHHHHHHHHHhCC
Q 031813           25 KIMFALTSIKGIGRRLANIVCKKADV---------DMNKRAGELSAAELDNLMVVVANP   74 (152)
Q Consensus        25 ~v~~aL~~i~GIG~~~A~~Ic~~lgi---------~~~~~~~~Ls~~ei~~L~~~l~~~   74 (152)
                      .+..+|+.|+|||...|..+++.+|=         +.-..+..+.+.-...|.+++.+|
T Consensus        16 ~~~~~L~~I~gIg~~~a~~L~~~F~s~~~i~~A~~eeL~~i~GiG~~~A~~i~~~f~~p   74 (78)
T d2a1jb1          16 RVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEP   74 (78)
T ss_dssp             HHHHHHTTSTTCCHHHHHHHHHHHSSHHHHHSCCHHHHHTSSSCCSHHHHHHHHHHHSC
T ss_pred             HHHHHhcCCCCcCHHHHHHHHHHhCCcHHHHhhhHHHHHHhhhhhHHHHHHHHHHHcCc
Confidence            45678999999999999999999871         111133334444455555555553

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

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

Probab=94.41  E-value=0.008  Score=36.64  Aligned_cols=23  Identities=26%  Similarity=0.365  Sum_probs=20.0

Q ss_pred             eehhcccccCHHHHHHHHHHcCCC
Q 031813           28 FALTSIKGIGRRLANIVCKKADVD   51 (152)
Q Consensus        28 ~aL~~i~GIG~~~A~~Ic~~lgi~   51 (152)
                      ..|++|+|||+.+|..+.+. |+.
T Consensus         7 ~~l~~I~GvGp~~A~~l~~~-Gi~   29 (57)
T d2fmpa2           7 NFLTRVSGIGPSAARKFVDE-GIK   29 (57)
T ss_dssp             HHHTTSTTCCHHHHHHHHHT-TCC
T ss_pred             HHHhccccccHHHHHHHHHh-CCC
Confidence            46899999999999999865 874

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

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

Probab=94.13  E-value=0.0072  Score=36.88  Aligned_cols=38  Identities=18%  Similarity=0.277  Sum_probs=30.0

Q ss_pred             ehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHH
Q 031813           29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL   67 (152)
Q Consensus        29 aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L   67 (152)
                      +|.+|+|||+.+|..+.+. |+..-..+-+.+.+|+.++
T Consensus         2 ~L~~i~GIG~~~a~~L~~~-g~~sv~~l~~a~~~eL~~i   39 (61)
T d1pzna1           2 SIEDLPGVGPATAEKLREA-GYDTLEAIAVASPIELKEV   39 (61)
T ss_dssp             CSSCCTTCCHHHHHHHHTT-TCCSHHHHHTCCHHHHHHH
T ss_pred             ccccCCCCCHHHHHHHHHh-cCCCHHHHHhCCHHHHHHC
Confidence            6889999999999999865 6666666677777777654

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

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

Probab=93.92  E-value=0.01  Score=36.18  Aligned_cols=26  Identities=15%  Similarity=0.310  Sum_probs=21.5

Q ss_pred             eheeehhcccccCHHHHHHHHHHcCCC
Q 031813           25 KIMFALTSIKGIGRRLANIVCKKADVD   51 (152)
Q Consensus        25 ~v~~aL~~i~GIG~~~A~~Ic~~lgi~   51 (152)
                      ++-..+++|+|||+++|..+.+. |+.
T Consensus         5 ~~l~~ft~I~GvGp~~A~~l~~~-Gi~   30 (57)
T d2bcqa2           5 PVLELFSNIWGAGTKTAQMWYQQ-GFR   30 (57)
T ss_dssp             HHHHHHHTSTTCCHHHHHHHHHT-TCC
T ss_pred             HHHHHHhccccccHHHHHHHHHh-CCC
Confidence            44557899999999999999875 764

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

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

Probab=93.88  E-value=0.022  Score=35.25  Aligned_cols=49  Identities=10%  Similarity=0.116  Sum_probs=33.6

Q ss_pred             heeehhcccccCHHHHHHHHHHcCC---------CCCCCCCCCCHHHHHHHHHHHhCC
Q 031813           26 IMFALTSIKGIGRRLANIVCKKADV---------DMNKRAGELSAAELDNLMVVVANP   74 (152)
Q Consensus        26 v~~aL~~i~GIG~~~A~~Ic~~lgi---------~~~~~~~~Ls~~ei~~L~~~l~~~   74 (152)
                      ..+.|+.|+|||..+|..|++.+|=         ..-..+..+.+.-.+.|.+++.+|
T Consensus         8 ~~~~L~~I~gIG~~~a~~L~~~f~s~~~i~~As~eeL~~i~GIG~~~A~~I~~~~~~~   65 (68)
T d1x2ia1           8 QRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAP   65 (68)
T ss_dssp             HHHHHTTSTTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSC
T ss_pred             HHHHHcCCCCcCHHHHHHHHHHcCCHHHHHHhHHHHHHhCCCcCHHHHHHHHHHHhch
Confidence            3467899999999999999998871         111234445556666666666653

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

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

Probab=93.60  E-value=0.014  Score=35.83  Aligned_cols=24  Identities=21%  Similarity=0.253  Sum_probs=20.6

Q ss_pred             eeehhcccccCHHHHHHHHHHcCCC
Q 031813           27 MFALTSIKGIGRRLANIVCKKADVD   51 (152)
Q Consensus        27 ~~aL~~i~GIG~~~A~~Ic~~lgi~   51 (152)
                      ...|++|+|||+++|..+.++ |+.
T Consensus         7 l~~f~~I~GvGp~~A~~l~~~-Gi~   30 (60)
T d1jmsa3           7 FKLFTSVFGVGLKTAEKWFRM-GFR   30 (60)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHT-TCC
T ss_pred             HHHHhccccccHHHHHHHHHh-CCC
Confidence            456899999999999999876 874

>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=93.44  E-value=0.033  Score=39.74  Aligned_cols=51  Identities=22%  Similarity=0.283  Sum_probs=45.0

Q ss_pred             CCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+++.+...|..  -+..+.+..+|+.+|+++++++++|+++++.+|.+.|.+
T Consensus       102 ~~~~~~~~~l~~--~lp~~l~~~ll~~~~i~~~~~~~~ls~~~~~~L~~~Lk~  152 (169)
T d2i0za2         102 DPKKGIKNVLKG--YVPERYFLFLLEKNEIDGSEQAGQVSHEKIRALVKDFKE  152 (169)
T ss_dssp             STTSBHHHHTTT--SSCHHHHHHHHHHTTCCTTSBGGGSCHHHHHHHHHHHHH
T ss_pred             ccchhHhhhccc--ccchHHHHHHHHHcCCcccCCHHHCCHHHHHHHHHHHhC
Confidence            456677776665  378899999999999999999999999999999999987

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

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

Probab=93.19  E-value=0.021  Score=34.73  Aligned_cols=38  Identities=16%  Similarity=0.242  Sum_probs=30.2

Q ss_pred             ehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHH
Q 031813           29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLM   68 (152)
Q Consensus        29 aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~   68 (152)
                      .|.+|+|||...+..+++.+|  .-..+.+.|.+|+..+.
T Consensus         4 ~L~~iPGIg~~~~~~Ll~~f~--Si~~l~~As~~eL~~v~   41 (62)
T d2a1ja1           4 FLLKMPGVNAKNCRSLMHHVK--NIAELAALSQDELTSIL   41 (62)
T ss_dssp             HHHTSTTCCHHHHHHHHHHCS--SHHHHHTCCHHHHHHHH
T ss_pred             HHhcCCCCCHHHHHHHHHHhc--cHHHHHhCCHHHHHHCc
Confidence            478999999999999998887  34566677777776654

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

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

Probab=92.99  E-value=0.013  Score=35.66  Aligned_cols=36  Identities=19%  Similarity=0.257  Sum_probs=27.3

Q ss_pred             hhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHH
Q 031813           30 LTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN   66 (152)
Q Consensus        30 L~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~   66 (152)
                      |+.|+|||+.+|..+.+. |+..-..+.+.+.+|+.+
T Consensus         1 L~~IpGIG~~~a~~L~~~-G~~tv~~l~~a~~eeL~~   36 (60)
T d2i1qa1           1 LTDLPGVGPSTAEKLVEA-GYIDFMKIATATVGELTD   36 (60)
T ss_dssp             CTTSTTCCHHHHHHHHHH-TCCSHHHHHTCCHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHc-cCCCHHHHHhCCHHHHHH
Confidence            678999999999998876 666666666666666544

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

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

Probab=92.69  E-value=0.025  Score=35.71  Aligned_cols=22  Identities=36%  Similarity=0.477  Sum_probs=18.5

Q ss_pred             eehhcccccCHHHHHHHHHHcC
Q 031813           28 FALTSIKGIGRRLANIVCKKAD   49 (152)
Q Consensus        28 ~aL~~i~GIG~~~A~~Ic~~lg   49 (152)
                      -+|++++|||+++|.+||-.|.
T Consensus        44 ~~L~~vpGIG~KtA~rIi~eLk   65 (71)
T d1bvsa2          44 ASLTRVPGIGRRGAERIVLELA   65 (71)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHSS
T ss_pred             HHhhcCCCCCHHHHHHHHHHHH
Confidence            4688999999999999987654

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

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

Probab=92.22  E-value=0.03  Score=35.51  Aligned_cols=22  Identities=41%  Similarity=0.549  Sum_probs=18.3

Q ss_pred             eehhcccccCHHHHHHHHHHcC
Q 031813           28 FALTSIKGIGRRLANIVCKKAD   49 (152)
Q Consensus        28 ~aL~~i~GIG~~~A~~Ic~~lg   49 (152)
                      -+|++++|||.++|.+||-.|.
T Consensus        45 ~~L~~vpGIG~KtA~rIi~eLk   66 (73)
T d1ixra1          45 RLLTSASGVGRRLAERIALELK   66 (73)
T ss_dssp             HHHTTSTTCCHHHHHHHHHHHT
T ss_pred             HHhhcCCCCCHHHHHHHHHHHH
Confidence            4688999999999999987763

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

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

Probab=91.39  E-value=0.029  Score=33.51  Aligned_cols=35  Identities=20%  Similarity=0.330  Sum_probs=25.2

Q ss_pred             ehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHH
Q 031813           29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD   65 (152)
Q Consensus        29 aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~   65 (152)
                      .|.+|+|||+.+|..+++.+| + -..+.+-+.+|+.
T Consensus         3 ~L~~I~gVG~~~a~~L~~~F~-s-~~~i~~As~eeL~   37 (56)
T d1kfta_           3 SLETIEGVGPKRRQMLLKYMG-G-LQGLRNASVEEIA   37 (56)
T ss_dssp             GGGGCTTCSSSHHHHHHHHHS-C-HHHHHHCCHHHHT
T ss_pred             CcccCCCccHHHHHHHHHHhC-C-HHHHHHhhHHHHH
Confidence            588999999999999999987 2 2233334444443

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

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

Probab=91.31  E-value=0.088  Score=36.79  Aligned_cols=50  Identities=16%  Similarity=0.271  Sum_probs=43.7

Q ss_pred             CCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .+++.+.-.|..+  +-.+.+..+|+..++ +++++++|+++|+..|.+.|.+
T Consensus        84 ~~kk~i~~~L~~~--lPkrl~~~ll~~~~~-~~~~~~~lsk~~~~~L~~~Lk~  133 (148)
T d2gqfa2          84 SPKQMLKTILVRL--LPKKLVELWIEQGIV-QDEVIANISKVRVKNLVDFIHH  133 (148)
T ss_dssp             CTTSBHHHHHTTT--SCHHHHHHHHHTTSS-CCCBGGGCCHHHHHHHHHHHHC
T ss_pred             hhhhhHHHHHHHH--hHHHHHHHHHHHcCc-ccchHHHCCHHHHHHHHHHHhC
Confidence            6678888888765  789999999998665 6899999999999999999987

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

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

Probab=91.16  E-value=0.046  Score=35.04  Aligned_cols=21  Identities=29%  Similarity=0.401  Sum_probs=17.5

Q ss_pred             eehhcccccCHHHHHHHHHHc
Q 031813           28 FALTSIKGIGRRLANIVCKKA   48 (152)
Q Consensus        28 ~aL~~i~GIG~~~A~~Ic~~l   48 (152)
                      -+|++++|||+++|.+|+-.|
T Consensus        44 ~~L~~vpGIG~KtA~rIi~eL   64 (78)
T d1cuka2          44 GALVKLPGIGKKTAERLIVEM   64 (78)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHH
T ss_pred             HHhhcCCCCCHHHHHHHHHHH
Confidence            368899999999999998665

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

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

Probab=90.97  E-value=0.062  Score=35.87  Aligned_cols=58  Identities=17%  Similarity=0.188  Sum_probs=43.4

Q ss_pred             cCcccCCCeeheeehhcccccCHHHHHHHHHHcC---CCCCCCCCCCCHHHHHHHHHHHhC
Q 031813           16 LNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD---VDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus        16 ~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg---i~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      .|.-|+-|..-...|..++|||+.+|.+|++-=.   ++.-..+.-+++..++.|..+++.
T Consensus        15 ~g~kidlN~As~~eL~~lpGIg~~~A~~Iv~~gpf~s~edL~~V~GIg~~~~e~lk~yl~~   75 (98)
T d2axtu1          15 YGEKIDLNNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLEH   75 (98)
T ss_dssp             BTTBEESSSSCGGGGTTSTTCTHHHHHHHHHSCCCSSGGGGGGCTTCCTTHHHHHHHHGGG
T ss_pred             cCCceecccccHHHHHHhhhhcHHHHHHHHHcCCcCCHHHHhhCCCCCHHHHHHHHHHHhc
Confidence            3445666777788899999999999999996311   112235666799999999999875

>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=87.45  E-value=0.12  Score=35.25  Aligned_cols=60  Identities=22%  Similarity=0.293  Sum_probs=41.1

Q ss_pred             ccccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCC
Q 031813            6 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANP   74 (152)
Q Consensus         6 ~~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~   74 (152)
                      .|+|=.+.-++|+|-..        ..|+|||+.+|..+.++.| +.........+.....+.+++.+|
T Consensus         3 ~eqfIdl~iL~G~DY~~--------~gI~GIGpktAlklikk~~-~~~~~~~~~~~~~~~~~~~~f~~p   62 (120)
T d1b43a1           3 REKLIELAILVGTDYNP--------GGIKGIGLKKALEIVRHSK-DPLAKFQKQSDVDLYAIKEFFLNP   62 (120)
T ss_dssp             HHHHHHHHHHHCCTTST--------TCSTTCCHHHHHHHHHTCS-SGGGGTGGGCSSCHHHHHHHHHSC
T ss_pred             HHHHHHHHHHhCCCCCc--------ccCCCcCHHHHHHHHHHhC-CHHHHHHhccccchHHHHHHhcCC
Confidence            46788888899988642        3499999999999999876 222223333344455666777765

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

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

Probab=87.38  E-value=0.096  Score=32.87  Aligned_cols=26  Identities=35%  Similarity=0.548  Sum_probs=21.6

Q ss_pred             eeheeehhcccccCHHHHHHHHHHcC
Q 031813           24 QKIMFALTSIKGIGRRLANIVCKKAD   49 (152)
Q Consensus        24 k~v~~aL~~i~GIG~~~A~~Ic~~lg   49 (152)
                      +.++..|.++.|||+.+|..||..++
T Consensus         5 r~~F~~Li~V~GIGpK~Al~iLs~~~   30 (71)
T d1bvsa2           5 RDLFLALLSVSGVGPRLAMATLAVHD   30 (71)
T ss_dssp             HHHHHHHHTSSSCCHHHHHHHHHHSC
T ss_pred             HHHHHHHhccCCcCHHHHHHHHHhCC
Confidence            45667899999999999999986654

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

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

Probab=85.86  E-value=0.13  Score=32.45  Aligned_cols=26  Identities=19%  Similarity=0.284  Sum_probs=21.3

Q ss_pred             eeheeehhcccccCHHHHHHHHHHcC
Q 031813           24 QKIMFALTSIKGIGRRLANIVCKKAD   49 (152)
Q Consensus        24 k~v~~aL~~i~GIG~~~A~~Ic~~lg   49 (152)
                      +.++..|.++.|||+.+|..|+..++
T Consensus         6 r~lF~~Li~V~GIGpk~Al~iLs~~~   31 (73)
T d1ixra1           6 LALFELLLSVSGVGPKVALALLSALP   31 (73)
T ss_dssp             HHHHHHHHSSSCCCHHHHHHHHHHSC
T ss_pred             HHHHHHHhccCCcCHHHHHHHHHHcc
Confidence            44567889999999999999986543

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

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

Probab=85.37  E-value=0.12  Score=31.48  Aligned_cols=51  Identities=20%  Similarity=0.233  Sum_probs=32.6

Q ss_pred             CCCeeheeehhcccccCHHHHHHHHHHcC---CCCCCCCCCCCHHHHHHHHHHH
Q 031813           21 DGKQKIMFALTSIKGIGRRLANIVCKKAD---VDMNKRAGELSAAELDNLMVVV   71 (152)
Q Consensus        21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg---i~~~~~~~~Ls~~ei~~L~~~l   71 (152)
                      |=|..-...|..++|||..+|.+|.+.=.   ++.-..+.-+++..+++|..+|
T Consensus        10 diNtA~~~eL~~lpgig~~~A~~Iv~~R~f~s~edL~~v~gi~~~~~~~i~~~l   63 (65)
T d2duya1          10 SLNEASLEELMALPGIGPVLARRIVEGRPYARVEDLLKVKGIGPATLERLRPYL   63 (65)
T ss_dssp             ETTTCCHHHHTTSTTCCHHHHHHHHHTCCCSSGGGGGGSTTCCHHHHHHHGGGE
T ss_pred             ccccCCHHHHHHCCCCCHHHHHHHHHcCCCCCHHHHHhCCCCCHHHHHHHHHHc
Confidence            33455556788999999999999997532   2222344445666666665443

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

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

Probab=85.34  E-value=0.13  Score=32.72  Aligned_cols=26  Identities=19%  Similarity=0.354  Sum_probs=21.3

Q ss_pred             eeheeehhcccccCHHHHHHHHHHcC
Q 031813           24 QKIMFALTSIKGIGRRLANIVCKKAD   49 (152)
Q Consensus        24 k~v~~aL~~i~GIG~~~A~~Ic~~lg   49 (152)
                      +.++..|.++.|||+++|..|+..++
T Consensus         5 r~~F~~Li~V~GIGpK~Al~iLs~~~   30 (78)
T d1cuka2           5 RTLFKELIKTNGVGPKLALAILSGMS   30 (78)
T ss_dssp             HHHHHHHHHSSSCCHHHHHHHHHHSC
T ss_pred             HHHHHHHHccCCccHHHHHHHHHhCC
Confidence            44567889999999999999986553

>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=85.15  E-value=0.32  Score=36.86  Aligned_cols=57  Identities=18%  Similarity=0.131  Sum_probs=41.1

Q ss_pred             cchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813            9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN   73 (152)
Q Consensus         9 ~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~   73 (152)
                      |..+++.+  .-.-.|.+.-+|..+..      ..+++.+|++++.|+.+||.+|+-+|.+++++
T Consensus       194 ~~~~~~~~--F~~rRK~l~~~L~~~~~------~~~l~~~~i~~~~R~e~Ls~~~~~~L~~~l~~  250 (252)
T d1qyra_         194 LSRITTEA--FNQRRKTIRNSLGNLFS------VEVLTGMGIDPAMRAENISVAQYCQMANYLAE  250 (252)
T ss_dssp             HHHHHHHH--HHTTTSBHHHHTTTTCC------HHHHHHTTCCTTSBGGGSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HccchHHHHHHHhhhcc------HHHHHHCCCCcccChhhCCHHHHHHHHHHHHh
Confidence            44455432  12245666666655443      35789999999999999999999999999864

>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.96  E-value=0.26  Score=33.71  Aligned_cols=36  Identities=28%  Similarity=0.409  Sum_probs=28.2

Q ss_pred             CccccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcC
Q 031813            5 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD   49 (152)
Q Consensus         5 ~~~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg   49 (152)
                      +.|+|-.|.=+.|+|-         +..|+|||..+|..++.+.|
T Consensus         2 ~~~q~id~~~L~GsD~---------~pgv~gIG~ktA~kli~~~~   37 (140)
T d1ul1x1           2 NQEQFVDLCILLGSDY---------CESIRGIGPKRAVDLIQKHK   37 (140)
T ss_dssp             CHHHHHHHHHHHHCSS---------SCCCTTCCHHHHHHHHHHSS
T ss_pred             CHHHHHHHHHHhCCCC---------CCCCCCccHHHHHHHHHHhC
Confidence            3467888888888442         44799999999999998865