Citrus Sinensis ID: 033150

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120------
MVQTLAMPVAPALSVICNGHNNNLLTNASLSFPVSKQPQYPGLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLVIIPYFFVRGTF
ccccccccccccccccccccccccccccEEEccccccccccccEEEEEEEEccccccccEEEEEEEEEEcccHHHHHHHHHHccccccccccccHHHHHHHHHHHHccccccccHHHHHccccccc
ccHHHHccccHHHHHHHccccccccccccEEEccccccccccEEEEEEEEEEcccccccEEEEEEEEEEccccHHHHHHHHHccccccccccccHHHHHHHHHHHHccEEEccEEEEEEEEEEccc
mvqtlampvaPALSVICnghnnnlltnaslsfpvskqpqypglsiqcarvggveipnnkriEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGdlviipyffvrgtf
MVQTLAMPVAPALSVICNGHNNNLLTNASLSFPVSKQPQYPGLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKMenkitkdmseeeLITIRDEVSKYMIEGDLVIIPYFFVRGTF
MVQTLAMPVAPALSVICNGHNNNLLTNASLSFPVSKQPQYPGLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLVIIPYFFVRGTF
*******PVAPALSVICNGHNNNLLTNASLSFPVSKQPQYPGLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLVIIPYFFVR***
*********APALSVI*****************************QCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLVIIPYFFVRGT*
MVQTLAMPVAPALSVICNGHNNNLLTNASLSFPVSKQPQYPGLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLVIIPYFFVRGTF
************L****N*******TNASLSFPVSKQPQYPGLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLVIIPYFFVRGTF
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooo
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MVQTLAMPVAPALSVICNGHNNNLLTNASLSFPVSKQPQYPGLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLVIIPYFFVRGTF
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query126 2.2.26 [Sep-21-2011]
P42732169 30S ribosomal protein S13 no no 0.904 0.674 0.728 2e-43
P82163145 30S ribosomal protein S13 N/A no 0.619 0.537 0.612 7e-24
B5EM96118 30S ribosomal protein S13 yes no 0.523 0.559 0.550 7e-14
B7J4A1118 30S ribosomal protein S13 yes no 0.523 0.559 0.550 7e-14
Q9RDV8124 30S ribosomal protein S13 yes no 0.531 0.540 0.544 1e-13
Q8LPW2148 Small ribosomal subunit p no no 0.484 0.412 0.524 3e-13
Q8EUD6124 30S ribosomal protein S13 yes no 0.531 0.540 0.558 8e-13
P47421124 30S ribosomal protein S13 yes no 0.531 0.540 0.529 5e-12
B3PMM3122 30S ribosomal protein S13 yes no 0.531 0.549 0.573 7e-12
P38017119 30S ribosomal protein S13 N/A no 0.531 0.563 0.544 8e-12
>sp|P42732|RR13_ARATH 30S ribosomal protein S13, chloroplastic OS=Arabidopsis thaliana GN=RPS13 PE=2 SV=1 Back     alignment and function desciption
 Score =  174 bits (440), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 83/114 (72%), Positives = 95/114 (83%)

Query: 1   MVQTLAMPVAPALSVICNGHNNNLLTNASLSFPVSKQPQYPGLSIQCARVGGVEIPNNKR 60
           M Q +AMPVA +LS+ICN   +N L+  +L+ P S  P    LSI+CARVGGVEIP NKR
Sbjct: 1   MAQMVAMPVAHSLSLICNWAKSNPLSRNTLALPASNTPNKQSLSIRCARVGGVEIPANKR 60

Query: 61  IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDL 114
           IEYSLQYIHG+GRTRARQILVDL+MENKITKDM+EEELI +RDEVSKYMIEGDL
Sbjct: 61  IEYSLQYIHGIGRTRARQILVDLQMENKITKDMAEEELIILRDEVSKYMIEGDL 114
Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA.
Arabidopsis thaliana (taxid: 3702)
>sp|P82163|RR13_SPIOL 30S ribosomal protein S13, chloroplastic OS=Spinacia oleracea GN=RPS13 PE=1 SV=2 Back     alignment and function description
>sp|B5EM96|RS13_ACIF5 30S ribosomal protein S13 OS=Acidithiobacillus ferrooxidans (strain ATCC 53993) GN=rpsM PE=3 SV=1 Back     alignment and function description
>sp|B7J4A1|RS13_ACIF2 30S ribosomal protein S13 OS=Acidithiobacillus ferrooxidans (strain ATCC 23270 / DSM 14882 / NCIB 8455) GN=rpsM PE=3 SV=1 Back     alignment and function description
>sp|Q9RDV8|RS13_MYCGA 30S ribosomal protein S13 OS=Mycoplasma gallisepticum (strain R(low / passage 15 / clone 2)) GN=rpsM PE=3 SV=3 Back     alignment and function description
>sp|Q8LPW2|RT13_SOYBN Small ribosomal subunit protein S13, mitochondrial OS=Glycine max GN=RSP13 PE=3 SV=1 Back     alignment and function description
>sp|Q8EUD6|RS13_MYCPE 30S ribosomal protein S13 OS=Mycoplasma penetrans (strain HF-2) GN=rpsM PE=3 SV=1 Back     alignment and function description
>sp|P47421|RS13_MYCGE 30S ribosomal protein S13 OS=Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195) GN=rpsM PE=3 SV=2 Back     alignment and function description
>sp|B3PMM3|RS13_MYCA5 30S ribosomal protein S13 OS=Mycoplasma arthritidis (strain 158L3-1) GN=rpsM PE=3 SV=1 Back     alignment and function description
>sp|P38017|RS13_MYCSP 30S ribosomal protein S13 OS=Mycoplasma sp. GN=rpsM PE=3 SV=2 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query126
312985275168 chloroplast 30S ribosomal protein S13 [H 0.976 0.732 0.733 2e-45
186522813128 30S ribosomal protein S13 [Arabidopsis t 0.920 0.906 0.732 2e-42
18417346169 30S ribosomal protein S13 [Arabidopsis t 0.904 0.674 0.728 2e-41
224066873168 predicted protein [Populus trichocarpa] 0.896 0.672 0.719 2e-40
224082224168 predicted protein [Populus trichocarpa] 0.896 0.672 0.728 3e-40
225459459167 PREDICTED: 30S ribosomal protein S13, ch 0.896 0.676 0.701 2e-39
11276604197 ribosomal protein S13-like protein F18O2 0.968 0.619 0.614 3e-39
388512017164 unknown [Lotus japonicus] 0.880 0.676 0.701 3e-39
351727919162 uncharacterized protein LOC100499902 [Gl 0.865 0.672 0.692 3e-39
388514311164 unknown [Lotus japonicus] 0.880 0.676 0.701 3e-39
>gi|312985275|gb|ADR30788.1| chloroplast 30S ribosomal protein S13 [Hevea brasiliensis] Back     alignment and taxonomy information
 Score =  186 bits (473), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 91/124 (73%), Positives = 103/124 (83%), Gaps = 1/124 (0%)

Query: 1   MVQTLAMPVAPALSVICNGHNNNLLTNASLSFPVSKQPQYPGLSIQCARVGGVEIPNNKR 60
           M QTLAMPVAP+LS+ICNG  NN L+   +S P+S  P+  GLSIQCARVGGVEIPNNKR
Sbjct: 1   MAQTLAMPVAPSLSLICNGWRNNSLSTF-VSLPISNPPKIHGLSIQCARVGGVEIPNNKR 59

Query: 61  IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLVIIPYF 120
           +EYSLQYIHGVGR+RARQIL DL M+NKITKD+SEEELIT+RDEVSKYMIEGDL      
Sbjct: 60  VEYSLQYIHGVGRSRARQILSDLSMQNKITKDLSEEELITLRDEVSKYMIEGDLRRFNAL 119

Query: 121 FVRG 124
            +RG
Sbjct: 120 NIRG 123

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|186522813|ref|NP_001119224.1| 30S ribosomal protein S13 [Arabidopsis thaliana] gi|332004634|gb|AED92017.1| 30S ribosomal protein S13 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|18417346|ref|NP_568299.1| 30S ribosomal protein S13 [Arabidopsis thaliana] gi|1173194|sp|P42732.1|RR13_ARATH RecName: Full=30S ribosomal protein S13, chloroplastic; AltName: Full=CS13; Flags: Precursor gi|16767|emb|CAA79013.1| chloroplast 30S ribosomal protein S13 [Arabidopsis thaliana] gi|662869|emb|CAA88028.1| chloroplast ribosomal protein S13 [Arabidopsis thaliana] gi|1107483|emb|CAA63021.1| 30S ribosomal protein S13 [Arabidopsis thaliana] gi|1515107|emb|CAA60413.1| plastid ribosomal protein S13 [Arabidopsis thaliana] gi|14517397|gb|AAK62589.1| AT5g14320/F18O22_110 [Arabidopsis thaliana] gi|15450549|gb|AAK96452.1| AT5g14320/F18O22_110 [Arabidopsis thaliana] gi|332004633|gb|AED92016.1| 30S ribosomal protein S13 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|224066873|ref|XP_002302256.1| predicted protein [Populus trichocarpa] gi|118488232|gb|ABK95935.1| unknown [Populus trichocarpa] gi|222843982|gb|EEE81529.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224082224|ref|XP_002306609.1| predicted protein [Populus trichocarpa] gi|222856058|gb|EEE93605.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225459459|ref|XP_002285833.1| PREDICTED: 30S ribosomal protein S13, chloroplastic [Vitis vinifera] gi|302141873|emb|CBI19076.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|11276604|pir||T48605 ribosomal protein S13-like protein F18O22.110 [imported] - Arabidopsis thaliana gi|7573457|emb|CAB87771.1| ribosomal protein precursor-like [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|388512017|gb|AFK44070.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|351727919|ref|NP_001237689.1| uncharacterized protein LOC100499902 [Glycine max] gi|255627531|gb|ACU14110.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|388514311|gb|AFK45217.1| unknown [Lotus japonicus] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query126
TAIR|locus:2145618169 EMB3137 "EMBRYO DEFECTIVE 3137 0.904 0.674 0.728 4.8e-39
UNIPROTKB|Q0DPA4203 Os03g0704000 "Os03g0704000 pro 0.698 0.433 0.666 5.6e-29
UNIPROTKB|A8JDP6164 PRPS13 "Plastid ribosomal prot 0.611 0.469 0.532 5.4e-15
TAIR|locus:2203216154 AT1G77750 [Arabidopsis thalian 0.746 0.610 0.347 1.5e-12
UNIPROTKB|P20282121 rpsM "30S ribosomal protein S1 0.531 0.553 0.485 5e-12
TIGR_CMR|CHY_2284123 CHY_2284 "ribosomal protein S1 0.523 0.536 0.428 4.5e-11
TIGR_CMR|BA_0135121 BA_0135 "ribosomal protein S13 0.531 0.553 0.441 5.8e-11
TIGR_CMR|CJE_1764121 CJE_1764 "ribosomal protein S1 0.523 0.545 0.442 5.8e-11
UNIPROTKB|O06327124 rpsM "30S ribosomal protein S1 0.531 0.540 0.434 7.4e-11
UNIPROTKB|Q749B0122 rpsM "30S ribosomal protein S1 0.531 0.549 0.434 1.2e-10
TAIR|locus:2145618 EMB3137 "EMBRYO DEFECTIVE 3137" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 417 (151.9 bits), Expect = 4.8e-39, P = 4.8e-39
 Identities = 83/114 (72%), Positives = 95/114 (83%)

Query:     1 MVQTLAMPVAPALSVICNGHNNNLLTNASLSFPVSKQPQYPGLSIQCARVGGVEIPNNKR 60
             M Q +AMPVA +LS+ICN   +N L+  +L+ P S  P    LSI+CARVGGVEIP NKR
Sbjct:     1 MAQMVAMPVAHSLSLICNWAKSNPLSRNTLALPASNTPNKQSLSIRCARVGGVEIPANKR 60

Query:    61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDL 114
             IEYSLQYIHG+GRTRARQILVDL+MENKITKDM+EEELI +RDEVSKYMIEGDL
Sbjct:    61 IEYSLQYIHGIGRTRARQILVDLQMENKITKDMAEEELIILRDEVSKYMIEGDL 114
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:0005840 "ribosome" evidence=IEA
GO:0006412 "translation" evidence=IEA;ISS
GO:0009507 "chloroplast" evidence=ISM;IDA
GO:0015935 "small ribosomal subunit" evidence=ISS
GO:0042254 "ribosome biogenesis" evidence=IBA
GO:0009941 "chloroplast envelope" evidence=IDA
GO:0009570 "chloroplast stroma" evidence=IDA
GO:0006354 "DNA-dependent transcription, elongation" evidence=RCA
GO:0009773 "photosynthetic electron transport in photosystem I" evidence=RCA
GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA
GO:0019684 "photosynthesis, light reaction" evidence=RCA
GO:0035304 "regulation of protein dephosphorylation" evidence=RCA
UNIPROTKB|Q0DPA4 Os03g0704000 "Os03g0704000 protein" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
UNIPROTKB|A8JDP6 PRPS13 "Plastid ribosomal protein S13" [Chlamydomonas reinhardtii (taxid:3055)] Back     alignment and assigned GO terms
TAIR|locus:2203216 AT1G77750 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|P20282 rpsM "30S ribosomal protein S13" [Bacillus subtilis subsp. subtilis str. 168 (taxid:224308)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_2284 CHY_2284 "ribosomal protein S13" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TIGR_CMR|BA_0135 BA_0135 "ribosomal protein S13" [Bacillus anthracis str. Ames (taxid:198094)] Back     alignment and assigned GO terms
TIGR_CMR|CJE_1764 CJE_1764 "ribosomal protein S13/S18" [Campylobacter jejuni RM1221 (taxid:195099)] Back     alignment and assigned GO terms
UNIPROTKB|O06327 rpsM "30S ribosomal protein S13" [Mycobacterium tuberculosis (taxid:1773)] Back     alignment and assigned GO terms
UNIPROTKB|Q749B0 rpsM "30S ribosomal protein S13" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query126
PRK05179122 PRK05179, rpsM, 30S ribosomal protein S13; Validat 6e-27
TIGR03631113 TIGR03631, bact_S13, 30S ribosomal protein S13 1e-25
COG0099121 COG0099, RpsM, Ribosomal protein S13 [Translation, 6e-24
pfam00416106 pfam00416, Ribosomal_S13, Ribosomal protein S13/S1 8e-24
CHL00137122 CHL00137, rps13, ribosomal protein S13; Validated 3e-18
PRK04053149 PRK04053, rps13p, 30S ribosomal protein S13P; Revi 4e-05
TIGR03629144 TIGR03629, arch_S13P, archaeal ribosomal protein S 4e-05
>gnl|CDD|235358 PRK05179, rpsM, 30S ribosomal protein S13; Validated Back     alignment and domain information 
 Score = 96.3 bits (241), Expect = 6e-27
 Identities = 34/69 (49%), Positives = 50/69 (72%), Gaps = 2/69 (2%)

Query: 48  ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVS 106
           AR+ GV+IP NKR+  +L YI+G+GRTRA++IL    +  +   KD+++EEL  IR+E+ 
Sbjct: 2   ARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEID 61

Query: 107 K-YMIEGDL 114
           K Y +EGDL
Sbjct: 62  KNYKVEGDL 70

Length = 122
>gnl|CDD|213840 TIGR03631, bact_S13, 30S ribosomal protein S13 Back     alignment and domain information
>gnl|CDD|223177 COG0099, RpsM, Ribosomal protein S13 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|144128 pfam00416, Ribosomal_S13, Ribosomal protein S13/S18 Back     alignment and domain information
>gnl|CDD|177059 CHL00137, rps13, ribosomal protein S13; Validated Back     alignment and domain information
>gnl|CDD|235215 PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed Back     alignment and domain information
>gnl|CDD|213839 TIGR03629, arch_S13P, archaeal ribosomal protein S13P Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 126
COG0099121 RpsM Ribosomal protein S13 [Translation, ribosomal 99.94
CHL00137122 rps13 ribosomal protein S13; Validated 99.92
PRK05179122 rpsM 30S ribosomal protein S13; Validated 99.92
TIGR03629144 arch_S13P archaeal ribosomal protein S13P. This mo 99.91
PRK04053149 rps13p 30S ribosomal protein S13P; Reviewed 99.91
PTZ00134154 40S ribosomal protein S18; Provisional 99.9
TIGR03631113 bact_S13 30S ribosomal protein S13. This model des 99.89
PF00416107 Ribosomal_S13: Ribosomal protein S13/S18; InterPro 99.88
KOG3311152 consensus Ribosomal protein S18 [Translation, ribo 99.59
PRK01103274 formamidopyrimidine/5-formyluracil/ 5-hydroxymethy 95.99
PF0683192 H2TH: Formamidopyrimidine-DNA glycosylase H2TH dom 95.98
PRK14810272 formamidopyrimidine-DNA glycosylase; Provisional 94.72
PRK14811269 formamidopyrimidine-DNA glycosylase; Provisional 94.13
PRK10445263 endonuclease VIII; Provisional 93.68
PRK13945282 formamidopyrimidine-DNA glycosylase; Provisional 93.56
TIGR00577272 fpg formamidopyrimidine-DNA glycosylase (fpg). All 93.26
PF0063330 HHH: Helix-hairpin-helix motif; InterPro: IPR00044 93.21
PF1179832 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 92.25
PF05833 455 FbpA: Fibronectin-binding protein A N-terminus (Fb 92.19
PRK04184 535 DNA topoisomerase VI subunit B; Validated 91.83
PF1039152 DNA_pol_lambd_f: Fingers domain of DNA polymerase 90.05
PRK02515132 psbU photosystem II complex extrinsic protein prec 90.03
COG3743133 Uncharacterized conserved protein [Function unknow 88.56
COG0266273 Nei Formamidopyrimidine-DNA glycosylase [DNA repli 87.91
smart0027826 HhH1 Helix-hairpin-helix DNA-binding motif class 1 87.15
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 87.07
PRK14606188 ruvA Holliday junction DNA helicase RuvA; Provisio 86.26
TIGR00275400 flavoprotein, HI0933 family. The model when search 85.9
PF1457990 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI 85.29
PRK14601183 ruvA Holliday junction DNA helicase RuvA; Provisio 85.06
PRK14603197 ruvA Holliday junction DNA helicase RuvA; Provisio 84.84
PRK14604195 ruvA Holliday junction DNA helicase RuvA; Provisio 84.73
PRK14602203 ruvA Holliday junction DNA helicase RuvA; Provisio 83.75
PF1282664 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS 83.59
COG0632201 RuvA Holliday junction resolvasome, DNA-binding su 83.14
PRK13901196 ruvA Holliday junction DNA helicase RuvA; Provisio 83.07
TIGR01052 488 top6b DNA topoisomerase VI, B subunit. This model 82.94
PRK00274272 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 82.65
PRK14600186 ruvA Holliday junction DNA helicase RuvA; Provisio 80.48
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
Probab=99.94  E-value=2.2e-27  Score=174.91  Aligned_cols=78  Identities=38%  Similarity=0.684  Sum_probs=75.9

Q ss_pred             EEEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHh-hccccccchhhhcccccc
Q 033150           47 CARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS-KYMIEGDLVIIPYFFVRG  124 (126)
Q Consensus        47 MvrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~-~~~Ie~dLrR~i~~nI~~  124 (126)
                      |+||+|+|||++|+|.+|||+|||||+++|..||+++||+ +++++||||||+++|+++|+ .|+||+||++++++||+.
T Consensus         1 maRIagvdip~~K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~~~~~vegDLr~~v~~dIkR   80 (121)
T COG0099           1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQNKYLVEGDLRREVRMDIKR   80 (121)
T ss_pred             CceecccCCCCCceEeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHHhcCeehhHHHHHHHHHHHH
Confidence            8999999999999999999999999999999999999999 99999999999999999999 599999999999999973

>CHL00137 rps13 ribosomal protein S13; Validated Back     alignment and domain information
>PRK05179 rpsM 30S ribosomal protein S13; Validated Back     alignment and domain information
>TIGR03629 arch_S13P archaeal ribosomal protein S13P Back     alignment and domain information
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed Back     alignment and domain information
>PTZ00134 40S ribosomal protein S18; Provisional Back     alignment and domain information
>TIGR03631 bact_S13 30S ribosomal protein S13 Back     alignment and domain information
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated Back     alignment and domain information
>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 Back     alignment and domain information
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional Back     alignment and domain information
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional Back     alignment and domain information
>PRK10445 endonuclease VIII; Provisional Back     alignment and domain information
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional Back     alignment and domain information
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg) Back     alignment and domain information
>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 [, , ] Back     alignment and domain information
>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 [] Back     alignment and domain information
>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 Back     alignment and domain information
>PRK04184 DNA topoisomerase VI subunit B; Validated Back     alignment and domain information
>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 Back     alignment and domain information
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional Back     alignment and domain information
>COG3743 Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair] Back     alignment and domain information
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1 Back     alignment and domain information
>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 Back     alignment and domain information
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>TIGR00275 flavoprotein, HI0933 family Back     alignment and domain information
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A Back     alignment and domain information
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B Back     alignment and domain information
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>TIGR01052 top6b DNA topoisomerase VI, B subunit Back     alignment and domain information
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed Back     alignment and domain information
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query126
3bbn_M145 Homology Model For The Spinach Chloroplast 30s Subu 5e-25
3ofo_M114 Crystal Structure Of The E. Coli Ribosome Bound To 2e-09
2gy9_M115 Structure Of The 30s Subunit Of A Pre-Translocation 2e-09
3fih_M113 Ternary Complex-Bound E.Coli 70s Ribosome. This Ent 2e-09
1p6g_M117 Real Space Refined Coordinates Of The 30s Subunit F 2e-09
1vs5_M118 Crystal Structure Of The Bacterial Ribosome From Es 2e-09
3mr8_M117 Recognition Of The Amber Stop Codon By Release Fact 1e-08
1i94_M125 Crystal Structures Of The Small Ribosomal Subunit W 1e-08
1fjg_M126 Structure Of The Thermus Thermophilus 30s Ribosomal 1e-08
3pyn_M116 Crystal Structure Of A Complex Containing Domain 3 1e-08
>pdb|3BBN|M Chain M, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 145 Back     alignment and structure 
Iteration: 1

 Score =  108 bits (271), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 49/80 (61%), Positives = 67/80 (83%), Gaps = 2/80 (2%)
Query: 27  NASLSFPVSKQPQ--YPGLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLK 84
           ++S+SFP  K+    + GL I+C R+GGVEIPN+KR+EYSLQYIHG+GR+R+RQIL+DL 
Sbjct: 24  SSSVSFPAPKKGGIGHGGLQIECIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLN 83
Query: 85  MENKITKDMSEEELITIRDE 104
            +NK+TKD+SEEE+I +R E
Sbjct: 84  FDNKVTKDLSEEEVIILRKE 103
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>pdb|1I94|M Chain M, Crystal Structures Of The Small Ribosomal Subunit With Tetracycline, Edeine And If3 Length = 125 Back     alignment and structure
>pdb|1FJG|M Chain M, Structure Of The Thermus Thermophilus 30s Ribosomal Subunit In Complex With The Antibiotics Streptomycin, Spectinomycin, And Paromomycin Length = 126 Back     alignment and structure
>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 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query126
3bbn_M145 Ribosomal protein S13; small ribosomal subunit, sp 4e-35
3r8n_M114 30S ribosomal protein S13; protein biosynthesis, R 6e-33
2vqe_M126 30S ribosomal protein S13, 30S ribosomal protein S 5e-30
2xzm_M155 RPS18E; ribosome, translation; 3.93A {Tetrahymena 1e-17
3iz6_M152 40S ribosomal protein S18 (S13P); eukaryotic ribos 2e-17
3u5c_S146 40S ribosomal protein S18-A, 40S ribosomal protein 2e-17
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 145 Back     alignment and structure
 Score =  117 bits (295), Expect = 4e-35
 Identities = 48/100 (48%), Positives = 71/100 (71%), Gaps = 3/100 (3%)

Query: 5   LAMPVAPALSVICNGHNNNLLTNASLSFPVSKQPQYPGLSIQCARVGGVEIPNNKRIEYS 64
           +++P+A +   +     ++   + S   P      + GL I+C R+GGVEIPN+KR+EYS
Sbjct: 7   VSVPIATSSLPLSARGRSS---SVSFPAPKKGGIGHGGLQIECIRIGGVEIPNHKRVEYS 63

Query: 65  LQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDE 104
           LQYIHG+GR+R+RQIL+DL  +NK+TKD+SEEE+I +R E
Sbjct: 64  LQYIHGIGRSRSRQILLDLNFDNKVTKDLSEEEVIILRKE 103
>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 Back     alignment and structure
>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_M Length = 155 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query126
3bbn_M145 Ribosomal protein S13; small ribosomal subunit, sp 99.93
2xzm_M155 RPS18E; ribosome, translation; 3.93A {Tetrahymena 99.92
3u5c_S146 40S ribosomal protein S18-A, 40S ribosomal protein 99.92
2vqe_M126 30S ribosomal protein S13, 30S ribosomal protein S 99.91
3iz6_M152 40S ribosomal protein S18 (S13P); eukaryotic ribos 99.91
3r8n_M114 30S ribosomal protein S13; protein biosynthesis, R 99.91
3j20_O148 30S ribosomal protein S13P; archaea, archaeal, KIN 99.91
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 93.36
3arc_U97 Photosystem II 12 kDa extrinsic protein; PSII, mem 92.92
1ee8_A266 MUTM (FPG) protein; beta sandwich, zinc finger, he 92.6
1k82_A268 Formamidopyrimidine-DNA glycosylase; protein-DNA c 92.57
2xzf_A271 Formamidopyrimidine-DNA glycosylase; hydrolase-DNA 92.49
3u6p_A273 Formamidopyrimidine-DNA glycosylase; DNA glycosyla 92.48
1k3x_A262 Endonuclease VIII; hydrolase/DNA, hydrolase-DNA co 92.37
3w0f_A287 Endonuclease 8-like 3; helix two turns helix, zinc 92.33
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 92.01
3twl_A310 Formamidopyrimidine-DNA glycosylase 1; helix two t 92.01
3vk8_A295 Probable formamidopyrimidine-DNA glycosylase; DNA 91.87
1s5l_U134 Photosystem II 12 kDa extrinsic protein; photosynt 90.95
1mu5_A 471 Type II DNA topoisomerase VI subunit B; GHKL ATPas 90.94
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 89.34
2duy_A75 Competence protein comea-related protein; helix-ha 86.35
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 85.89
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 84.33
3fut_A271 Dimethyladenosine transferase; methyltransferase, 84.21
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
Probab=99.93  E-value=4.4e-29  Score=187.82  Aligned_cols=107  Identities=48%  Similarity=0.830  Sum_probs=63.0

Q ss_pred             ccccccccCcceeeeecCccCCcccccceecccccCCCCC--cceeeEEEecCccCCCCeEEEEeeccccccCHHHHHHH
Q 033150            2 VQTLAMPVAPALSVICNGHNNNLLTNASLSFPVSKQPQYP--GLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQI   79 (126)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~MvrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~I   79 (126)
                      .|++|||++|.++-+|+-|.     |-+++.+...+++|+  ++++||+||+|+|||++|+|.+|||+|||||+++|.+|
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~m~RI~gvdlp~~K~v~~aLt~IyGIG~~~A~~I   78 (145)
T 3bbn_M            4 LSMVSVPIATSSLPLSARGR-----SSSVSFPAPKKGGIGHGGLQIECIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQI   78 (145)
T ss_dssp             ------------------------------------------------CCCSSSCCCCSSBTTTGGGGSTTCCSSTTTGG
T ss_pred             ccccccccccccchhhhcCC-----CCccccccCCchhhhcccchhheeeEeCcccCCCCEEEEeeeeecCccHHHHHHH
Confidence            58899999999999997544     456678888999999  99999999999999999999999999999999999999


Q ss_pred             HHHhCCCccccCCCCHHHHHHHHHHHhhccccccchhhhccccc
Q 033150           80 LVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLVIIPYFFVR  123 (126)
Q Consensus        80 C~klGI~~~kv~~LteeQI~~L~~~I~~~~Ie~dLrR~i~~nI~  123 (126)
                      |+++||++++++||||+|+++|+++          ||++++||+
T Consensus        79 ~~~~gI~~~rv~~Lte~ei~~l~~~----------Rr~v~~nIk  112 (145)
T 3bbn_M           79 LLDLNFDNKVTKDLSEEEVIILRKE----------KRFNRVAIE  112 (145)
T ss_dssp             GTTTTCCSCBTTSCCSSTTHHHHSS----------CCCCSTTTH
T ss_pred             HHHcCCCceEcCCCCHHHHHHHHHH----------HHHHHHHHH
Confidence            9999999889999999999999976          788888886
>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_M Back     alignment and structure
>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 Back     alignment and structure
>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* ... Back     alignment and structure
>3iz6_M 40S ribosomal protein S18 (S13P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Back     alignment and structure
>3j20_O 30S ribosomal protein S13P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>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* Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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* Back     alignment and structure
>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* ... Back     alignment and structure
>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* Back     alignment and structure
>3w0f_A Endonuclease 8-like 3; helix two turns helix, zinc finger, DNA binding, hydrolase; 2.00A {Mus musculus} Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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* Back     alignment and structure
>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} Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus} SCOP: a.60.2.7 Back     alignment and structure
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Back     alignment and structure
>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* Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 126
d2gy9m1114 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escheri 9e-21
d2uubm1125 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus 1e-18
>d2gy9m1 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia coli [TaxId: 562]} Length = 114 Back     information, alignment and structure

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 = 78.7 bits (194), Expect = 9e-21
 Identities = 28/68 (41%), Positives = 48/68 (70%), Gaps = 1/68 (1%)

Query: 48  ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVS 106
           AR+ G+ IP++K    +L  I+GVG+TR++ IL    + E+    ++SE ++ T+RDEV+
Sbjct: 1   ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA 60

Query: 107 KYMIEGDL 114
           K+++EGDL
Sbjct: 61  KFVVEGDL 68
>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus thermophilus [TaxId: 274]} Length = 125 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query126
d2gy9m1114 Ribosomal protein S13 {Escherichia coli [TaxId: 56 99.91
d2uubm1125 Ribosomal protein S13 {Thermus thermophilus [TaxId 99.9
d2hkja178 Topoisomerase VI-B subunit middle domain {Archaeon 97.82
d1k82a188 DNA repair protein MutM (Fpg) {Escherichia coli [T 96.72
d1k3xa189 Endonuclease VIII {Escherichia coli [TaxId: 562]} 96.66
d1tdza188 DNA repair protein MutM (Fpg) {Lactococcus lactis 96.63
d1ee8a189 DNA repair protein MutM (Fpg) {Thermus thermophilu 96.57
d1r2za194 DNA repair protein MutM (Fpg) {Bacillus stearother 96.48
d2bcqa257 DNA polymerase lambda {Human (Homo sapiens) [TaxId 96.06
d1jmsa360 Terminal deoxynucleotidyl transferase {Mouse (Mus 95.5
d2fmpa257 DNA polymerase beta {Human (Homo sapiens) [TaxId: 95.43
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 95.31
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 94.62
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 94.45
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 94.04
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 93.43
d2axtu198 Photosystem II 12 kDa extrinsic protein PsbU {Ther 93.05
d2i0za2169 Flavoprotein BC4706 {Bacillus cereus [TaxId: 1396] 92.32
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 92.31
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 92.0
d2gqfa2148 Hypothetical protein HI0933 {Haemophilus influenza 91.38
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 90.83
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 89.8
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 86.99
d1tdha1115 Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapi 83.84
>d2gy9m1 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
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=99.91  E-value=3.1e-26  Score=163.56  Aligned_cols=77  Identities=35%  Similarity=0.588  Sum_probs=74.7

Q ss_pred             EEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhhccccccchhhhcccccc
Q 033150           48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSKYMIEGDLVIIPYFFVRG  124 (126)
Q Consensus        48 vrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~~~Ie~dLrR~i~~nI~~  124 (126)
                      .||+|+|||++|+|.+|||+|||||+++|.+||+++||| ++++++||++|++.|+++|++|.+|+||++.+++||+.
T Consensus         1 aRI~g~dip~~K~v~~ALt~I~GIG~~~A~~Ic~~lgid~~~kv~~Lt~~qi~~l~~~i~~~~i~~~L~~~~~~dI~r   78 (114)
T d2gy9m1           1 ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKR   78 (114)
T ss_dssp             CCCSSSCCCCSSBHHHHHTTSSSCCHHHHHHHHHHHTCCTTSBTTSCCHHHHHHHHHHHHSSCCSHHHHHHHHHHHHH
T ss_pred             CcccCccCCCCCEEEEEeeeeeCcCHHHHHHHHHHcCCCcccccCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            489999999999999999999999999999999999999 99999999999999999999999999999999999973
>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2hkja1 a.156.1.3 (A:229-306) Topoisomerase VI-B subunit middle domain {Archaeon Sulfolobus shibatae [TaxId: 2286]} Back     information, alignment and structure
>d1k82a1 a.156.1.2 (A:129-216) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1k3xa1 a.156.1.2 (A:125-213) Endonuclease VIII {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1tdza1 a.156.1.2 (A:132-219) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]} Back     information, alignment and structure
>d1ee8a1 a.156.1.2 (A:122-210) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1r2za1 a.156.1.2 (A:135-228) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jmsa3 a.60.12.1 (A:243-302) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2fmpa2 a.60.12.1 (A:92-148) DNA polymerase beta {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Back     information, alignment and structure
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]} Back     information, alignment and structure
>d2i0za2 e.74.1.1 (A:193-361) Flavoprotein BC4706 {Bacillus cereus [TaxId: 1396]} Back     information, alignment and structure
>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} Back     information, alignment and structure
>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2gqfa2 e.74.1.1 (A:195-342) Hypothetical protein HI0933 {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1tdha1 a.156.1.2 (A:132-246) Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure