Citrus Sinensis ID: 031757

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-------130-------140-------150---
MISLRNSVGMLSNVSRQLIQTISFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKKKPTR
cccccccccccccHHHHHHcccccccEEEEEEEEEcccccccccEEEEEEEEEcccHHHHHHHHHHccccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccc
ccccccccccccccccccccccccccEEEEEEEEEccccccccEEEEEEEEEEccccHHHHHHHHHcccccccHccccHHHHHHHHHHHHcccEcccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccc
mislrnsvGMLSNVSRQLIQTISFHGLRvqglrvgnteipndkrleTSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQcyrgirhsqglpcrgqrtstnartrkgkrvaipgkkkptr
MISLRNSVGMLSNVSRQLIQTISFHglrvqglrvgnteipndkrlETSLQHVYGIGRSRAHQILCDLNIGNKLTkeltgvelnslreevsryltgedlrrciKNDVERLVDIQCyrgirhsqglpcrgqrtstnartrkgkrvaipgkkkptr
MISLRNSVGMLSNVSRQLIQTISFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKKKPTR
***********SNVSRQLIQTISFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQCYRGIRHSQ*******************************
**************************LRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRV**********
MISLRNSVGMLSNVSRQLIQTISFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQCYRGIRHSQGL*****************************
************NVSRQLIQTISFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQCYRGIRHSQ*LPC***************************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MISLRNSVGMLSNVSRQLIQTISFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKKKPTR
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 ?
Query153 2.2.26 [Sep-21-2011]
Q9CA19154 Small ribosomal subunit p yes no 1.0 0.993 0.594 8e-49
Q8LPW2148 Small ribosomal subunit p no no 0.888 0.918 0.525 1e-34
P42732169 30S ribosomal protein S13 no no 0.738 0.668 0.557 5e-30
A5FZU3125 30S ribosomal protein S13 yes no 0.790 0.968 0.512 2e-26
A1KB04120 30S ribosomal protein S13 yes no 0.758 0.966 0.512 2e-26
B3PMM3122 30S ribosomal protein S13 yes no 0.764 0.959 0.533 2e-26
B3E854122 30S ribosomal protein S13 yes no 0.771 0.967 0.491 3e-26
Q6KI31122 30S ribosomal protein S13 yes no 0.764 0.959 0.516 5e-26
Q47J80120 30S ribosomal protein S13 yes no 0.764 0.975 0.483 5e-26
A9B434127 30S ribosomal protein S13 yes no 0.790 0.952 0.524 6e-26
>sp|Q9CA19|RT13_ARATH Small ribosomal subunit protein S13, mitochondrial OS=Arabidopsis thaliana GN=RPS13 PE=2 SV=1 Back     alignment and function desciption
 Score =  192 bits (487), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 91/153 (59%), Positives = 120/153 (78%)

Query: 1   MISLRNSVGMLSNVSRQLIQTISFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRA 60
           M+ LR S   L ++S+ L++ ++FHGLRVQG+RVGN E+PN+K L+T LQ VYGIGR ++
Sbjct: 1   MLGLRRSATTLFDISQSLLRNVTFHGLRVQGIRVGNAEVPNNKPLKTGLQEVYGIGRRKS 60

Query: 61  HQILCDLNIGNKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQCYRGIRH 120
           HQ+LC L I NKL ++LTG EL  LREEV ++  G++LRR + ++++RLV++ CYRG RH
Sbjct: 61  HQVLCHLGITNKLARDLTGKELIDLREEVGQHQHGDELRRRVGSEIQRLVEVDCYRGSRH 120

Query: 121 SQGLPCRGQRTSTNARTRKGKRVAIPGKKKPTR 153
             GLPCRGQRTSTNART+KGK VAI GKKK  R
Sbjct: 121 RHGLPCRGQRTSTNARTKKGKAVAIAGKKKAPR 153
Located at the top of the head of the small subunit, it contacts several helices of the 18S rRNA.
Arabidopsis thaliana (taxid: 3702)
>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|P42732|RR13_ARATH 30S ribosomal protein S13, chloroplastic OS=Arabidopsis thaliana GN=RPS13 PE=2 SV=1 Back     alignment and function description
>sp|A5FZU3|RS13_ACICJ 30S ribosomal protein S13 OS=Acidiphilium cryptum (strain JF-5) GN=rpsM PE=3 SV=1 Back     alignment and function description
>sp|A1KB04|RS13_AZOSB 30S ribosomal protein S13 OS=Azoarcus sp. (strain BH72) GN=rpsM PE=3 SV=1 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|B3E854|RS13_GEOLS 30S ribosomal protein S13 OS=Geobacter lovleyi (strain ATCC BAA-1151 / DSM 17278 / SZ) GN=rpsM PE=3 SV=1 Back     alignment and function description
>sp|Q6KI31|RS13_MYCMO 30S ribosomal protein S13 OS=Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711) GN=rpsM PE=3 SV=1 Back     alignment and function description
>sp|Q47J80|RS13_DECAR 30S ribosomal protein S13 OS=Dechloromonas aromatica (strain RCB) GN=rpsM PE=3 SV=1 Back     alignment and function description
>sp|A9B434|RS13_HERA2 30S ribosomal protein S13 OS=Herpetosiphon aurantiacus (strain ATCC 23779 / DSM 785) GN=rpsM PE=3 SV=1 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 ?
Query153
118488715163 unknown [Populus trichocarpa] 0.908 0.852 0.690 5e-50
224066875163 predicted protein [Populus trichocarpa] 0.908 0.852 0.683 2e-49
15218103154 small ribosomal subunit protein S13 [Ara 1.0 0.993 0.594 5e-47
297842551154 hypothetical protein ARALYDRAFT_476938 [ 1.0 0.993 0.575 1e-45
351727919162 uncharacterized protein LOC100499902 [Gl 0.941 0.888 0.566 2e-40
255545528 290 30S ribosomal protein S13, putative [Ric 0.928 0.489 0.575 3e-40
388512017164 unknown [Lotus japonicus] 0.908 0.847 0.597 6e-40
388514311164 unknown [Lotus japonicus] 0.908 0.847 0.589 2e-39
351724017162 uncharacterized protein LOC100500355 [Gl 0.915 0.864 0.581 5e-38
225459459167 PREDICTED: 30S ribosomal protein S13, ch 0.954 0.874 0.568 8e-38
>gi|118488715|gb|ABK96168.1| unknown [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  202 bits (513), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 96/139 (69%), Positives = 119/139 (85%)

Query: 1   MISLRNSVGMLSNVSRQLIQTISFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRA 60
           M+ LR SV +L+ +++ L+Q  +F   RVQGLRVGNTEIPNDK+LE +LQ+++GIGR RA
Sbjct: 1   MLGLRGSVRLLTEINQSLLQNATFRCQRVQGLRVGNTEIPNDKKLEVALQYIHGIGRKRA 60

Query: 61  HQILCDLNIGNKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQCYRGIRH 120
           HQILC+L++ NK TK+LTG+ELNSLREEVS+YLTG DL R +K DV+RLVDI+CYRG RH
Sbjct: 61  HQILCELSLVNKPTKDLTGIELNSLREEVSKYLTGPDLARRVKADVQRLVDIECYRGYRH 120

Query: 121 SQGLPCRGQRTSTNARTRK 139
            +GLPCRGQRTSTNARTRK
Sbjct: 121 VEGLPCRGQRTSTNARTRK 139

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224066875|ref|XP_002302257.1| predicted protein [Populus trichocarpa] gi|222843983|gb|EEE81530.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|15218103|ref|NP_177898.1| small ribosomal subunit protein S13 [Arabidopsis thaliana] gi|32363391|sp|Q9CA19.1|RT13_ARATH RecName: Full=Small ribosomal subunit protein S13, mitochondrial; Short=mS13; Flags: Precursor gi|12323293|gb|AAG51625.1|AC012193_7 putative 30S ribosomal protein S13; 38847-37703 [Arabidopsis thaliana] gi|33589778|gb|AAQ22655.1| At1g77750 [Arabidopsis thaliana] gi|332197896|gb|AEE36017.1| small ribosomal subunit protein S13 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297842551|ref|XP_002889157.1| hypothetical protein ARALYDRAFT_476938 [Arabidopsis lyrata subsp. lyrata] gi|297334998|gb|EFH65416.1| hypothetical protein ARALYDRAFT_476938 [Arabidopsis lyrata subsp. lyrata] 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|255545528|ref|XP_002513824.1| 30S ribosomal protein S13, putative [Ricinus communis] gi|223546910|gb|EEF48407.1| 30S ribosomal protein S13, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|388512017|gb|AFK44070.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|388514311|gb|AFK45217.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|351724017|ref|NP_001236787.1| uncharacterized protein LOC100500355 [Glycine max] gi|255630109|gb|ACU15408.1| unknown [Glycine max] 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

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 ?
Query153
TAIR|locus:2203216154 AT1G77750 [Arabidopsis thalian 1.0 0.993 0.594 2e-47
TAIR|locus:2145618169 EMB3137 "EMBRYO DEFECTIVE 3137 0.830 0.751 0.566 4.6e-34
UNIPROTKB|A8JDP6164 PRPS13 "Plastid ribosomal prot 0.830 0.774 0.551 8.5e-33
UNIPROTKB|O66486126 rpsM "30S ribosomal protein S1 0.758 0.920 0.508 1.8e-25
UNIPROTKB|Q7NFF2127 rpsM "30S ribosomal protein S1 0.771 0.929 0.5 5.9e-25
UNIPROTKB|O06327124 rpsM "30S ribosomal protein S1 0.771 0.951 0.466 1.2e-24
UNIPROTKB|A9WH90127 rpsM "30S ribosomal protein S1 0.790 0.952 0.459 2e-24
UNIPROTKB|O86773126 rpsM "30S ribosomal protein S1 0.777 0.944 0.487 2e-24
UNIPROTKB|Q749B0122 rpsM "30S ribosomal protein S1 0.771 0.967 0.441 5.3e-24
UNIPROTKB|Q9RSJ9126 rpsM "30S ribosomal protein S1 0.790 0.960 0.439 5.3e-24
TAIR|locus:2203216 AT1G77750 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 496 (179.7 bits), Expect = 2.0e-47, P = 2.0e-47
 Identities = 91/153 (59%), Positives = 120/153 (78%)

Query:     1 MISLRNSVGMLSNVSRQLIQTISFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRA 60
             M+ LR S   L ++S+ L++ ++FHGLRVQG+RVGN E+PN+K L+T LQ VYGIGR ++
Sbjct:     1 MLGLRRSATTLFDISQSLLRNVTFHGLRVQGIRVGNAEVPNNKPLKTGLQEVYGIGRRKS 60

Query:    61 HQILCDLNIGNKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQCYRGIRH 120
             HQ+LC L I NKL ++LTG EL  LREEV ++  G++LRR + ++++RLV++ CYRG RH
Sbjct:    61 HQVLCHLGITNKLARDLTGKELIDLREEVGQHQHGDELRRRVGSEIQRLVEVDCYRGSRH 120

Query:   121 SQGLPCRGQRTSTNARTRKGKRVAIPGKKKPTR 153
               GLPCRGQRTSTNART+KGK VAI GKKK  R
Sbjct:   121 RHGLPCRGQRTSTNARTKKGKAVAIAGKKKAPR 153
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:0005739 "mitochondrion" evidence=ISM;IDA
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:0005763 "mitochondrial small ribosomal subunit" evidence=TAS
GO:0009507 "chloroplast" evidence=IDA
GO:0006354 "DNA-dependent transcription, elongation" evidence=RCA
TAIR|locus:2145618 EMB3137 "EMBRYO DEFECTIVE 3137" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|A8JDP6 PRPS13 "Plastid ribosomal protein S13" [Chlamydomonas reinhardtii (taxid:3055)] Back     alignment and assigned GO terms
UNIPROTKB|O66486 rpsM "30S ribosomal protein S13" [Aquifex aeolicus VF5 (taxid:224324)] Back     alignment and assigned GO terms
UNIPROTKB|Q7NFF2 rpsM "30S ribosomal protein S13" [Gloeobacter violaceus PCC 7421 (taxid:251221)] Back     alignment and assigned GO terms
UNIPROTKB|O06327 rpsM "30S ribosomal protein S13" [Mycobacterium tuberculosis (taxid:1773)] Back     alignment and assigned GO terms
UNIPROTKB|A9WH90 rpsM "30S ribosomal protein S13" [Chloroflexus aurantiacus J-10-fl (taxid:324602)] Back     alignment and assigned GO terms
UNIPROTKB|O86773 rpsM "30S ribosomal protein S13" [Streptomyces coelicolor A3(2) (taxid:100226)] Back     alignment and assigned GO terms
UNIPROTKB|Q749B0 rpsM "30S ribosomal protein S13" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
UNIPROTKB|Q9RSJ9 rpsM "30S ribosomal protein S13" [Deinococcus radiodurans R1 (taxid:243230)] 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

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q6KI31RS13_MYCMONo assigned EC number0.51690.76470.9590yesno
B1W3Y2RS13_STRGGNo assigned EC number0.50410.77770.9444yesno
Q9CA19RT13_ARATHNo assigned EC number0.59471.00.9935yesno
Q4A5I8RS13_MYCS5No assigned EC number0.50840.76470.9590yesno
B3PMM3RS13_MYCA5No assigned EC number0.53380.76470.9590yesno
A1KB04RS13_AZOSBNo assigned EC number0.51260.75810.9666yesno
A5FZU3RS13_ACICJNo assigned EC number0.51210.79080.968yesno
A9B434RS13_HERA2No assigned EC number0.52410.79080.9527yesno

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 ?
Query153
PRK05179122 PRK05179, rpsM, 30S ribosomal protein S13; Validat 5e-47
COG0099121 COG0099, RpsM, Ribosomal protein S13 [Translation, 3e-42
TIGR03631113 TIGR03631, bact_S13, 30S ribosomal protein S13 2e-39
pfam00416106 pfam00416, Ribosomal_S13, Ribosomal protein S13/S1 1e-35
CHL00137122 CHL00137, rps13, ribosomal protein S13; Validated 5e-30
PRK04053149 PRK04053, rps13p, 30S ribosomal protein S13P; Revi 2e-20
TIGR03629144 TIGR03629, arch_S13P, archaeal ribosomal protein S 2e-18
PTZ00134154 PTZ00134, PTZ00134, 40S ribosomal protein S18; Pro 1e-09
>gnl|CDD|235358 PRK05179, rpsM, 30S ribosomal protein S13; Validated Back     alignment and domain information 
 Score =  148 bits (376), Expect = 5e-47
 Identities = 61/120 (50%), Positives = 83/120 (69%), Gaps = 2/120 (1%)

Query: 33  RVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNI-GNKLTKELTGVELNSLREEVSR 91
           R+   +IP +KR+  +L ++YGIGR+RA +IL    I  +   K+LT  EL+ +REE+ +
Sbjct: 3   RIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDK 62

Query: 92  YLTGE-DLRRCIKNDVERLVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKKK 150
               E DLRR +  +++RL+DI CYRG+RH +GLP RGQRT TNARTRKG R  I GKKK
Sbjct: 63  NYKVEGDLRREVSMNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKTIAGKKK 122

Length = 122
>gnl|CDD|223177 COG0099, RpsM, Ribosomal protein S13 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|213840 TIGR03631, bact_S13, 30S ribosomal protein S13 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
>gnl|CDD|185469 PTZ00134, PTZ00134, 40S ribosomal protein S18; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 153
COG0099121 RpsM Ribosomal protein S13 [Translation, ribosomal 100.0
CHL00137122 rps13 ribosomal protein S13; Validated 100.0
PRK05179122 rpsM 30S ribosomal protein S13; Validated 100.0
TIGR03629144 arch_S13P archaeal ribosomal protein S13P. This mo 100.0
PRK04053149 rps13p 30S ribosomal protein S13P; Reviewed 100.0
PTZ00134154 40S ribosomal protein S18; Provisional 100.0
TIGR03631113 bact_S13 30S ribosomal protein S13. This model des 100.0
PF00416107 Ribosomal_S13: Ribosomal protein S13/S18; InterPro 100.0
KOG3311152 consensus Ribosomal protein S18 [Translation, ribo 100.0
PF0683192 H2TH: Formamidopyrimidine-DNA glycosylase H2TH dom 95.43
PRK01103274 formamidopyrimidine/5-formyluracil/ 5-hydroxymethy 94.61
PRK14810272 formamidopyrimidine-DNA glycosylase; Provisional 92.92
PRK14811269 formamidopyrimidine-DNA glycosylase; Provisional 92.45
PRK10445263 endonuclease VIII; Provisional 91.94
PF0063330 HHH: Helix-hairpin-helix motif; InterPro: IPR00044 91.8
PRK13945282 formamidopyrimidine-DNA glycosylase; Provisional 90.65
TIGR00577272 fpg formamidopyrimidine-DNA glycosylase (fpg). All 90.55
PRK02515132 psbU photosystem II complex extrinsic protein prec 89.92
PF05833 455 FbpA: Fibronectin-binding protein A N-terminus (Fb 89.05
KOG3311152 consensus Ribosomal protein S18 [Translation, ribo 87.51
PF1179832 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 87.27
PRK04184 535 DNA topoisomerase VI subunit B; Validated 86.26
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 85.48
COG3743133 Uncharacterized conserved protein [Function unknow 84.64
PF1039152 DNA_pol_lambd_f: Fingers domain of DNA polymerase 84.44
smart0027826 HhH1 Helix-hairpin-helix DNA-binding motif class 1 81.9
TIGR00275400 flavoprotein, HI0933 family. The model when search 80.73
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
Probab=100.00  E-value=1.1e-50  Score=304.79  Aligned_cols=119  Identities=49%  Similarity=0.813  Sum_probs=116.3

Q ss_pred             eeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh-hccchHHHHHHHHHhHHH
Q 031757           31 GLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVS-RYLTGEDLRRCIKNDVER  108 (153)
Q Consensus        31 ~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~-~~~i~~dL~~~~~~dI~r  108 (153)
                      |+||+|+|||++|.|.+|||+|||||.++|..||+++||| ++++++|||+|+++|.++++ .|++|+||++++++||+|
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            7999999999999999999999999999999999999999 77999999999999999999 799999999999999999


Q ss_pred             HHhhhhccCCccCCCCccCCccccccccCCCCccccccCCC
Q 031757          109 LVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKK  149 (153)
Q Consensus       109 L~~I~sYRG~RH~~GLPVRGQRTrTNarTak~~~~gv~~kk  149 (153)
                      |++|+||||+||.+|||||||||||||||+||.++||++||
T Consensus        81 l~~i~~YRGiRH~~GLpVRGQrTktnaRtrkG~~~~v~~KK  121 (121)
T COG0099          81 LMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKGVAKKK  121 (121)
T ss_pred             HHHhhhhhhhhhhcCCCCCCcccCccccccCCCccccccCC
Confidence            99999999999999999999999999999999999988875

>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
>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
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated 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
>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
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional Back     alignment and domain information
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg) Back     alignment and domain information
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional 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
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis] 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
>PRK04184 DNA topoisomerase VI subunit B; Validated 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
>COG3743 Uncharacterized conserved protein [Function unknown] 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
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1 Back     alignment and domain information
>TIGR00275 flavoprotein, HI0933 family 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 ?
Query153
3bbn_M145 Homology Model For The Spinach Chloroplast 30s Subu 2e-26
1fjg_M126 Structure Of The Thermus Thermophilus 30s Ribosomal 3e-24
1i94_M125 Crystal Structures Of The Small Ribosomal Subunit W 3e-24
1vs5_M118 Crystal Structure Of The Bacterial Ribosome From Es 3e-23
1p6g_M117 Real Space Refined Coordinates Of The 30s Subunit F 3e-23
2gy9_M115 Structure Of The 30s Subunit Of A Pre-Translocation 4e-23
3ofo_M114 Crystal Structure Of The E. Coli Ribosome Bound To 5e-23
3fih_M113 Ternary Complex-Bound E.Coli 70s Ribosome. This Ent 5e-23
3pyn_M116 Crystal Structure Of A Complex Containing Domain 3 9e-22
3mr8_M117 Recognition Of The Amber Stop Codon By Release Fact 9e-22
3j20_O148 Promiscuous Behavior Of Proteins In Archaeal Riboso 3e-08
2zkq_m152 Structure Of A Mammalian Ribosomal 40s Subunit With 2e-06
3iz6_M152 Localization Of The Small Subunit Ribosomal Protein 5e-06
3izb_M146 Localization Of The Small Subunit Ribosomal Protein 5e-05
1s1h_M132 Structure Of The Ribosomal 80s-Eef2-Sordarin Comple 5e-05
2xzm_M155 Crystal Structure Of The Eukaryotic 40s Ribosomal S 6e-05
3zey_M153 High-resolution Cryo-electron Microscopy Structure 1e-04
3jyv_M130 Structure Of The 40s Rrna And Proteins And PE TRNA 2e-04
>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 =  114 bits (285), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 61/119 (51%), Positives = 81/119 (68%), Gaps = 10/119 (8%)
Query: 22  ISFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVE 81
           I   GL+++ +R+G  EIPN KR+E SLQ+++GIGRSR+ QIL DLN  NK+TK+L+  E
Sbjct: 37  IGHGGLQIECIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFDNKVTKDLSEEE 96
Query: 82  LNSLREEVSRYLTGEDLRRCIKNDVERLVDIQCYRGIRHSQGLPCRGQRTSTNARTRKG 140
           +  LR+E          +R  +  +ERL +I+CYRGIRH  GLP RGQRT  N RT KG
Sbjct: 97  VIILRKE----------KRFNRVAIERLKEIRCYRGIRHKLGLPVRGQRTKNNCRTLKG 145
>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|1I94|M Chain M, Crystal Structures Of The Small Ribosomal Subunit With Tetracycline, Edeine And If3 Length = 125 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|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|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|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|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|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
>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|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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>pdb|3ZEY|M Chain M, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 153 Back     alignment and structure
>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 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 ?
Query153
2vqe_M126 30S ribosomal protein S13, 30S ribosomal protein S 4e-51
3r8n_M114 30S ribosomal protein S13; protein biosynthesis, R 5e-48
3bbn_M145 Ribosomal protein S13; small ribosomal subunit, sp 2e-43
2xzm_M155 RPS18E; ribosome, translation; 3.93A {Tetrahymena 6e-36
3iz6_M152 40S ribosomal protein S18 (S13P); eukaryotic ribos 8e-36
3u5c_S146 40S ribosomal protein S18-A, 40S ribosomal protein 1e-34
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-07
>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M* 1xmq_M* ... Length = 126 Back     alignment and structure
 Score =  158 bits (402), Expect = 4e-51
 Identities = 58/123 (47%), Positives = 79/123 (64%), Gaps = 2/123 (1%)

Query: 33  RVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNI-GNKLTKELTGVELNSLREEVSR 91
           R+   EIP +KR++ +L ++YGIG++RA + L    I      K+LT  E+  LRE V  
Sbjct: 3   RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVEN 62

Query: 92  YLTGE-DLRRCIKNDVERLVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKKK 150
               E +LR  +  +++RL+DI CYRG+RH +GLP RGQRT TNARTRKG R  + GKKK
Sbjct: 63  TWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKK 122

Query: 151 PTR 153
             R
Sbjct: 123 APR 125
>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
>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
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query153
2xzm_M155 RPS18E; ribosome, translation; 3.93A {Tetrahymena 100.0
3iz6_M152 40S ribosomal protein S18 (S13P); eukaryotic ribos 100.0
2vqe_M126 30S ribosomal protein S13, 30S ribosomal protein S 100.0
3j20_O148 30S ribosomal protein S13P; archaea, archaeal, KIN 100.0
3u5c_S146 40S ribosomal protein S18-A, 40S ribosomal protein 100.0
3r8n_M114 30S ribosomal protein S13; protein biosynthesis, R 100.0
3bbn_M145 Ribosomal protein S13; small ribosomal subunit, sp 100.0
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 91.12
3u6p_A273 Formamidopyrimidine-DNA glycosylase; DNA glycosyla 90.76
3twl_A310 Formamidopyrimidine-DNA glycosylase 1; helix two t 90.52
1ee8_A266 MUTM (FPG) protein; beta sandwich, zinc finger, he 89.94
2xzf_A271 Formamidopyrimidine-DNA glycosylase; hydrolase-DNA 89.84
1k82_A268 Formamidopyrimidine-DNA glycosylase; protein-DNA c 89.77
1k3x_A262 Endonuclease VIII; hydrolase/DNA, hydrolase-DNA co 89.73
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 89.27
3w0f_A287 Endonuclease 8-like 3; helix two turns helix, zinc 88.98
3vk8_A295 Probable formamidopyrimidine-DNA glycosylase; DNA 88.47
3arc_U97 Photosystem II 12 kDa extrinsic protein; PSII, mem 87.7
1s5l_U134 Photosystem II 12 kDa extrinsic protein; photosynt 86.69
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 85.45
1mu5_A 471 Type II DNA topoisomerase VI subunit B; GHKL ATPas 83.53
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligome 82.67
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-bindin 80.65
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 80.61
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 80.08
>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_M Back     alignment and structure
Probab=100.00  E-value=4.2e-52  Score=324.25  Aligned_cols=131  Identities=31%  Similarity=0.387  Sum_probs=122.7

Q ss_pred             eeeeeccCCccccceeeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh-
Q 031757           14 VSRQLIQTISFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVSR-   91 (153)
Q Consensus        14 ~~~~~~~~~~~~~i~~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~-   91 (153)
                      ||+..++.++|||+    +||+|||||++|+|.+|||+|||||+++|..||+++||| ++++++||++|+++|.++|++ 
T Consensus         1 m~~~~~~~~~f~~m----~RI~g~~l~~~k~v~~aLt~I~GIG~~~A~~I~~~~gid~~~r~~~Lt~~ei~~l~~~i~~p   76 (155)
T 2xzm_M            1 MSFVIEKESDFKYI----HRILNTNIDGKRITPIALTGIRGIGRRFAYIICKVLKIDPNARAGLLTEDQCNKITDLIADP   76 (155)
T ss_dssp             CCCCSSTTTSSCSC----CEETTTEECCSSCHHHHHTTSTTCCHHHHHHHHHHTTCCSSSCSSCSCHHHHHHHHHHHHSH
T ss_pred             CCccccchHhhhhh----HheeCccCCCCCEEEEeeecccccCHHHHHHHHHHcCCCcccccccCCHHHHHHHHHHHhCc
Confidence            45555444589999    999999999999999999999999999999999999999 779999999999999999986 


Q ss_pred             ----------------------ccchHHHHHHHHHhHHHHHhhhhccCCccCCCCccCCccccccccCCCCccccccCCC
Q 031757           92 ----------------------YLTGEDLRRCIKNDVERLVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKK  149 (153)
Q Consensus        92 ----------------------~~i~~dL~~~~~~dI~rL~~I~sYRG~RH~~GLPVRGQRTrTNarTak~~~~gv~~kk  149 (153)
                                            |.+|+||++++++||+||++|+||||+||.+|||||||||||||||  +.++||++||
T Consensus        77 ~~~~iP~w~lNr~kD~~~G~~~~~ie~dLr~~~~~dI~Rl~~I~~yRG~RH~~GLpVRGQRTkTnaRt--g~tvGv~kkk  154 (155)
T 2xzm_M           77 EAHGIPTWLLNRINDFKDGKNYQMASNTLDTKMREDLERLKKIKSHRGLRHFWGLKVRGQHTKTSGRH--GVVCGVVRKN  154 (155)
T ss_dssp             HHHCCCGGGCSEEEETTTEEEECCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHTCCSSSCCCSSSSCS--SCCCSSCCCC
T ss_pred             cccCCCHHHhhcccccCCCceeEEecHHHHHHHHHhHHHHhhhceeeeeecccCCCcCCcCCccCCCC--cccccccccC
Confidence                                  8999999999999999999999999999999999999999999999  7799999998


Q ss_pred             C
Q 031757          150 K  150 (153)
Q Consensus       150 ~  150 (153)
                      +
T Consensus       155 ~  155 (155)
T 2xzm_M          155 K  155 (155)
T ss_dssp             -
T ss_pred             C
Confidence            5
>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
>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
>3j20_O 30S ribosomal protein S13P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} 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
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} 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
>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
>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
>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
>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
>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
>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
>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
>3w0f_A Endonuclease 8-like 3; helix two turns helix, zinc finger, DNA binding, hydrolase; 2.00A {Mus musculus} 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
>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
>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
>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
>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
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2 Back     alignment and structure
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A 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
>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

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 153
d2uubm1125 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus 2e-38
d2gy9m1114 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escheri 6e-36
>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus thermophilus [TaxId: 274]} Length = 125 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: Thermus thermophilus [TaxId: 274]

 Score =  125 bits (315), Expect = 2e-38
 Identities = 58/123 (47%), Positives = 79/123 (64%), Gaps = 2/123 (1%)

Query: 33  RVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNI-GNKLTKELTGVELNSLREEVSR 91
           R+   EIP +KR++ +L ++YGIG++RA + L    I      K+LT  E+  LRE V  
Sbjct: 2   RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVEN 61

Query: 92  YLTGE-DLRRCIKNDVERLVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKKK 150
               E +LR  +  +++RL+DI CYRG+RH +GLP RGQRT TNARTRKG R  + GKKK
Sbjct: 62  TWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKK 121

Query: 151 PTR 153
             R
Sbjct: 122 APR 124
>d2gy9m1 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia coli [TaxId: 562]} Length = 114 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 ?
Query153
d2uubm1125 Ribosomal protein S13 {Thermus thermophilus [TaxId 100.0
d2gy9m1114 Ribosomal protein S13 {Escherichia coli [TaxId: 56 100.0
d2hkja178 Topoisomerase VI-B subunit middle domain {Archaeon 97.41
d1k3xa189 Endonuclease VIII {Escherichia coli [TaxId: 562]} 96.07
d1r2za194 DNA repair protein MutM (Fpg) {Bacillus stearother 95.82
d1ee8a189 DNA repair protein MutM (Fpg) {Thermus thermophilu 95.77
d1tdza188 DNA repair protein MutM (Fpg) {Lactococcus lactis 95.69
d1k82a188 DNA repair protein MutM (Fpg) {Escherichia coli [T 95.61
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 94.79
d2bcqa257 DNA polymerase lambda {Human (Homo sapiens) [TaxId 94.49
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 94.34
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 94.09
d2fmpa257 DNA polymerase beta {Human (Homo sapiens) [TaxId: 93.39
d1jmsa360 Terminal deoxynucleotidyl transferase {Mouse (Mus 92.23
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 92.04
d2axtu198 Photosystem II 12 kDa extrinsic protein PsbU {Ther 91.84
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 91.79
d2i0za2169 Flavoprotein BC4706 {Bacillus cereus [TaxId: 1396] 89.58
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 89.2
d2gqfa2148 Hypothetical protein HI0933 {Haemophilus influenza 88.74
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 88.17
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 86.11
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 82.95
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 82.79
>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus thermophilus [TaxId: 274]} 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: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=9.6e-51  Score=304.57  Aligned_cols=121  Identities=46%  Similarity=0.781  Sum_probs=116.8

Q ss_pred             eEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh-ccchHHHHHHHHHhHHHH
Q 031757           32 LRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVSR-YLTGEDLRRCIKNDVERL  109 (153)
Q Consensus        32 vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~-~~i~~dL~~~~~~dI~rL  109 (153)
                      .||+|+|||++|+|++|||+|||||+++|.+||+++||| +.++++||++|++.|.+++++ |.+|+||++.+++||+||
T Consensus         1 aRI~g~di~~~K~v~~ALt~I~GIG~~~A~~Ic~~lgId~~~k~~~Lt~~qi~~I~~~i~~~~~i~~~L~~~~~~dIkrl   80 (125)
T d2uubm1           1 ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRL   80 (125)
T ss_dssp             CCCSTTCCCCSSBHHHHHTTSTTCCHHHHHHHHHTTTCCTTSBGGGCCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHHH
T ss_pred             CcccCccCCCCCEEEEeeeeeeCcCHHHHHHHHHHcCCCcccccccccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHH
Confidence            489999999999999999999999999999999999999 668999999999999999985 999999999999999999


Q ss_pred             HhhhhccCCccCCCCccCCccccccccCCCCccccccCCCCCC
Q 031757          110 VDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKKKPT  152 (153)
Q Consensus       110 ~~I~sYRG~RH~~GLPVRGQRTrTNarTak~~~~gv~~kk~~~  152 (153)
                      ++|+||||+||.+|||||||||||||||+|+.++||.+||+.+
T Consensus        81 ~~i~~yRG~RH~~gLpvRGQRT~tN~rt~kg~~~~v~~kk~~~  123 (125)
T d2uubm1          81 MDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAP  123 (125)
T ss_dssp             HHTTCHHHHHHHHTCCSSSCCCSSCCHHHHCSCCCCCCCSSSC
T ss_pred             HHhhhhhhhhhcCCCCCCCCCCCCCccccCCCccccccccCCC
Confidence            9999999999999999999999999999999999999988865
>d2gy9m1 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia coli [TaxId: 562]} 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
>d1k3xa1 a.156.1.2 (A:125-213) Endonuclease VIII {Escherichia coli [TaxId: 562]} 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
>d1ee8a1 a.156.1.2 (A:122-210) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]} 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
>d1k82a1 a.156.1.2 (A:129-216) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]} 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
>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]} 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
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} 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
>d1jmsa3 a.60.12.1 (A:243-302) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]} 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
>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]} 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
>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
>d2gqfa2 e.74.1.1 (A:195-342) Hypothetical protein HI0933 {Haemophilus influenzae [TaxId: 727]} 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
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]} 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
>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure