Citrus Sinensis ID: 040909

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
Protein Sequence
MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI
Secondary Structure (PSIPRED)
ccccccccEEEEEEEEEEEEEEcccccccccEEEEEEEccccHHHHHHcccccEEEEEEEEEEEEcccccEEEEEEcccccccccccEEEEEEEEccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEEEEEEEEccccccccccEEEEEEEccccHHHHHccccccEEEEEEEEEEcccccccEEEEEEcccccHHHcccEEEEEEccccc
Coil and Loop (DISEMBL)
mvkgrqgeriKLYVRGTILgykrsksnqypntsliqikgvnikeeaktkkngthyrcIWGKvarshsnsgvvrakfksnlppksvgdrvrvfmypnni
Flexible Loop (DISEMBL)
mvkgrqgeriklyvrgtilgykrsksnqypntsliqikgvnikeeaktkkngthyRCIWGKvarshsnsgvvrakfksnlppksvgdrvrvfmypnni
Low Complexity Region (SEG)
MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI
Disordered region (IsUnstruct)
*********IKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKNGTHYRCIWGKVARS*********************************
Disordered Region (DISOPRED)
*************VRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK**KNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI
Disordered Region (DISEMBL)
********RIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI
Disordered Region (DISPRO)
*******ERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNN*
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	98	2.2.26 [Sep-21-2011]
Q9C912	112	60S ribosomal protein L35	yes	no	1.0	0.875	0.75	4e-42
Q9LMK0	112	60S ribosomal protein L35	yes	no	1.0	0.875	0.741	7e-42
Q9FZH0	111	60S ribosomal protein L35	no	no	0.989	0.873	0.729	1e-40
P51422	111	60S ribosomal protein L35	yes	no	0.989	0.873	0.720	2e-40
Q55BN7	105	60S ribosomal protein L35	yes	no	0.897	0.838	0.446	4e-20
P41056	107	60S ribosomal protein L33	yes	no	0.938	0.859	0.452	2e-18
P05744	107	60S ribosomal protein L33	yes	no	0.938	0.859	0.443	4e-18
Q9USX4	108	60S ribosomal protein L33	yes	no	0.928	0.842	0.457	1e-17
P0DJ22	113	60S ribosomal protein L35	N/A	no	0.877	0.761	0.383	7e-17
P49180	124	60S ribosomal protein L35	yes	no	0.897	0.709	0.416	9e-17

>sp|Q9C912|R35A3_ARATH 60S ribosomal protein L35a-3 OS=Arabidopsis thaliana GN=RPL35AC PE=3 SV=1

 Score =  169 bits (429), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 84/112 (75%), Positives = 92/112 (82%), Gaps = 14/112 (12%)

Query: 1   MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------A 46
           MVKGRQGER++LYVRGTILGYKRSKSNQYPNTSL+QI+GVN +EE              A
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLVQIEGVNTQEEVNWYKGKRMAYIYKA 60

Query: 47  KTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           KTKKNG+HYRCIWGKV R H NSGVVRAKF SNLPPKS+G RVRVFMYP+NI
Sbjct: 61  KTKKNGSHYRCIWGKVTRPHGNSGVVRAKFTSNLPPKSMGSRVRVFMYPSNI 112

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LMK0|R35A1_ARATH 60S ribosomal protein L35a-1 OS=Arabidopsis thaliana GN=RPL35AA PE=3 SV=1

 Score =  169 bits (427), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 83/112 (74%), Positives = 91/112 (81%), Gaps = 14/112 (12%)

Query: 1   MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------A 46
           MVKGRQGER++LYVRGTILGYKRSKSNQYPNTSL+Q++GVN  EE              A
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLVQVEGVNTTEEVSWYKGKRMAYIYKA 60

Query: 47  KTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           KTKKNG+HYRCIWGKV R H NSGVVRAKF SNLPPKS+G RVRVFMYP+NI
Sbjct: 61  KTKKNGSHYRCIWGKVTRPHGNSGVVRAKFTSNLPPKSMGSRVRVFMYPSNI 112

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FZH0|R35A2_ARATH 60S ribosomal protein L35a-2 OS=Arabidopsis thaliana GN=RPL35AB PE=3 SV=1

 Score =  164 bits (415), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 81/111 (72%), Positives = 91/111 (81%), Gaps = 14/111 (12%)

Query: 2   VKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------AK 47
           +KGRQGER++LYVRGT+LGYKRSKSNQYPNTSLIQI+GVN +EE              AK
Sbjct: 1   MKGRQGERVRLYVRGTVLGYKRSKSNQYPNTSLIQIEGVNTQEEVNWYKGKRLAYIYKAK 60

Query: 48  TKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           TKKNG+HYRCIWGKV R H NSGVVR+KF SNLPPKS+G RVRVFMYP+NI
Sbjct: 61  TKKNGSHYRCIWGKVTRPHGNSGVVRSKFTSNLPPKSMGARVRVFMYPSNI 111

Arabidopsis thaliana (taxid: 3702)

>sp|P51422|R35A4_ARATH 60S ribosomal protein L35a-4 OS=Arabidopsis thaliana GN=RPL35AD PE=3 SV=2

 Score =  164 bits (414), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 80/111 (72%), Positives = 91/111 (81%), Gaps = 14/111 (12%)

Query: 2   VKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------AK 47
           +KGRQGER++LYVRGT+LGYKRSKSNQYPNTSL+QI+GVN +EE              AK
Sbjct: 1   MKGRQGERVRLYVRGTVLGYKRSKSNQYPNTSLVQIEGVNTQEEVNWYKGKRLAYIYKAK 60

Query: 48  TKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           TKKNG+HYRCIWGKV R H NSGVVR+KF SNLPPKS+G RVRVFMYP+NI
Sbjct: 61  TKKNGSHYRCIWGKVTRPHGNSGVVRSKFTSNLPPKSMGARVRVFMYPSNI 111

Arabidopsis thaliana (taxid: 3702)

>sp|Q55BN7|RL35A_DICDI 60S ribosomal protein L35a OS=Dictyostelium discoideum GN=rpl35a PE=3 SV=1

 Score = 96.7 bits (239), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 46/103 (44%), Positives = 70/103 (67%), Gaps = 15/103 (14%)

Query: 11  KLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEA---------------KTKKNGTHY 55
           K+Y +G +LGY+RS++ QYPN SLI+I+GV  +E++               K+ KN T +
Sbjct: 3   KIYSKGVVLGYRRSQATQYPNISLIKIEGVVSREDSTFYLGKKVCLVSKVSKSAKNPTGH 62

Query: 56  RCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           +  WGK+ ++H +SGVV+A+F  NLPPK++G  VRV +YP+NI
Sbjct: 63  KISWGKICKTHGSSGVVQARFARNLPPKAMGAPVRVMLYPSNI 105

The protein was found to bind to both initiator and elongator tRNAs and consequently was assigned to the P site or P and A site.

Dictyostelium discoideum (taxid: 44689)

>sp|P41056|RL33B_YEAST 60S ribosomal protein L33-B OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPL33B PE=1 SV=2

 Score = 91.3 bits (225), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 48/106 (45%), Positives = 65/106 (61%), Gaps = 14/106 (13%)

Query: 7   GERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK--------------TKKNG 52
            E  +LYV+G  L Y+RSK    PN SLI+I+GV   +EA+               +  G
Sbjct: 2   AESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQEAQFYLGKRIAYVYRASKEVRG 61

Query: 53  THYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           +  R +WGKV R+H NSGVVRA F++NLP K+ G  VR+F+YP+NI
Sbjct: 62  SKIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 107

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|P05744|RL33A_YEAST 60S ribosomal protein L33-A OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPL33A PE=1 SV=3

 Score = 89.7 bits (221), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 47/106 (44%), Positives = 65/106 (61%), Gaps = 14/106 (13%)

Query: 7   GERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK--------------TKKNG 52
            E  +LYV+G  L Y+RSK    PN SLI+I+GV   ++A+               +  G
Sbjct: 2   AESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVRG 61

Query: 53  THYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           +  R +WGKV R+H NSGVVRA F++NLP K+ G  VR+F+YP+NI
Sbjct: 62  SKIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 107

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q9USX4|RL33A_SCHPO 60S ribosomal protein L33-A OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpl33a PE=3 SV=2

 Score = 88.2 bits (217), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 49/107 (45%), Positives = 66/107 (61%), Gaps = 16/107 (14%)

Query: 6   QGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKT----------KKN---- 51
           QG R  LYV+   L ++RSK   +P TSL++I+G + KEEA+           K N    
Sbjct: 4   QGHR--LYVKAKHLSFQRSKHVIHPGTSLVKIEGCDSKEEAQFYLGKRICFVYKSNKPVR 61

Query: 52  GTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           G+  R IWG V+R H NSGVVRA+F  NLPPK+ G  +RV +YP+N+
Sbjct: 62  GSKIRVIWGTVSRPHGNSGVVRARFTHNLPPKTFGASLRVMLYPSNV 108

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|P0DJ22|RL35A_TETTS 60S ribosomal protein L35a OS=Tetrahymena thermophila (strain SB210) GN=RPL35A PE=1 SV=1

 Score = 85.9 bits (211), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 38/99 (38%), Positives = 62/99 (62%), Gaps = 13/99 (13%)

Query: 11  KLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK-------------TKKNGTHYRC 57
           +L+V+    G++RSK  Q  N +L++++ VN KE+                KKNG++YR 
Sbjct: 13  RLWVKAAFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQKKNGSNYRT 72

Query: 58  IWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPN 96
           IWG++ ++H N+GV  A+F  NLPP+++G  +RV +YPN
Sbjct: 73  IWGRIGKAHGNNGVAVARFAHNLPPQAIGSVLRVMLYPN 111

Tetrahymena thermophila (strain SB210) (taxid: 312017)

>sp|P49180|RL35A_CAEEL 60S ribosomal protein L35a OS=Caenorhabditis elegans GN=rpl-33 PE=1 SV=3

 Score = 85.5 bits (210), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 45/108 (41%), Positives = 62/108 (57%), Gaps = 20/108 (18%)

Query: 11  KLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEA----------------KTKKNG-- 52
           +LYV+    G+KR    Q  +TSL++++GV  KE+A                KT K G  
Sbjct: 17  RLYVKAIFTGFKRGLRTQSEHTSLLKLEGVFNKEDAGFYAGKRVVYLYKAHNKTLKTGHT 76

Query: 53  --THYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
             T  R IWGK+ R H N+G VRAKF  N+PP ++G R+RV +YP+NI
Sbjct: 77  VATRTRAIWGKITRPHGNAGAVRAKFHHNIPPSALGKRIRVLLYPSNI 124

Caenorhabditis elegans (taxid: 6239)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	98
449465053	446	PREDICTED: probable sugar phosphate/phos	1.0	0.219	0.75	3e-42
313586489	112	60S ribosomal protein L35aA [Hevea brasi	1.0	0.875	0.776	7e-42
13430186	112	ribosomal protein L33 [Castanea sativa]	1.0	0.875	0.767	5e-41
449531591	112	PREDICTED: 60S ribosomal protein L35a-1-	1.0	0.875	0.75	6e-41
209967441	112	60S ribosomal protein L35a [Vernicia for	1.0	0.875	0.767	7e-41
359807265	112	uncharacterized protein LOC100800463 [Gl	1.0	0.875	0.758	8e-41
224112609	112	predicted protein [Populus trichocarpa]	1.0	0.875	0.75	1e-40
15221191	112	60S ribosomal protein L35a-3 [Arabidopsi	1.0	0.875	0.75	1e-40
388522301	112	unknown [Medicago truncatula]	1.0	0.875	0.75	2e-40
224101037	112	predicted protein [Populus trichocarpa]	1.0	0.875	0.758	2e-40

>gi|449465053|ref|XP_004150243.1| PREDICTED: probable sugar phosphate/phosphate translocator At3g11320-like [Cucumis sativus]

 Score =  175 bits (444), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 84/112 (75%), Positives = 93/112 (83%), Gaps = 14/112 (12%)

Query: 1   MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------A 46
           MVKGRQGER++LY RGTILGYKRSKSNQYPNTSL+QI+GVN K+E              A
Sbjct: 1   MVKGRQGERVRLYTRGTILGYKRSKSNQYPNTSLLQIEGVNSKDEVSWYQGKRLAYIYKA 60

Query: 47  KTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           K KKNG+HYRCIWGKVAR H NSG+VRAKFKSNLPPKS+GDRVRVFMYP+NI
Sbjct: 61  KVKKNGSHYRCIWGKVARPHGNSGIVRAKFKSNLPPKSMGDRVRVFMYPSNI 112

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|313586489|gb|ADR71255.1| 60S ribosomal protein L35aA [Hevea brasiliensis]

 Score =  174 bits (440), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 87/112 (77%), Positives = 93/112 (83%), Gaps = 14/112 (12%)

Query: 1   MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------A 46
           MVKGRQGER++LYVRGTILGYKRSKSNQYPNTSLIQI+GVN KEE              A
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEEVAWYAGKRMAYIYKA 60

Query: 47  KTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           K KKNG+HYRCIWGKV R H NSGVVRAKFKSNLPPKS+GDRVRVFMYP+NI
Sbjct: 61  KVKKNGSHYRCIWGKVTRPHGNSGVVRAKFKSNLPPKSMGDRVRVFMYPSNI 112

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|13430186|gb|AAK25760.1|AF334840_1 ribosomal protein L33 [Castanea sativa]

 Score =  171 bits (433), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 86/112 (76%), Positives = 93/112 (83%), Gaps = 14/112 (12%)

Query: 1   MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------A 46
           MVKGRQGER++LYVRGTILGYKRSKSNQYPNTSLIQI+GVN KEE              A
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEEVGWYAGKRMAYVYKA 60

Query: 47  KTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           K KK+G+HYRCIWGKVAR H NSGVVRAKFKSNLPPKS+G RVRVFMYP+NI
Sbjct: 61  KVKKDGSHYRCIWGKVARPHGNSGVVRAKFKSNLPPKSMGARVRVFMYPSNI 112

Source: Castanea sativa

Species: Castanea sativa

Genus: Castanea

Family: Fagaceae

Order: Fagales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449531591|ref|XP_004172769.1| PREDICTED: 60S ribosomal protein L35a-1-like [Cucumis sativus]

 Score =  171 bits (433), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 84/112 (75%), Positives = 93/112 (83%), Gaps = 14/112 (12%)

Query: 1   MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------A 46
           MVKGRQGER++LY RGTILGYKRSKSNQYPNTSL+QI+GVN K+E              A
Sbjct: 1   MVKGRQGERVRLYTRGTILGYKRSKSNQYPNTSLLQIEGVNSKDEVSWYQGKRLAYIYKA 60

Query: 47  KTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           K KKNG+HYRCIWGKVAR H NSG+VRAKFKSNLPPKS+GDRVRVFMYP+NI
Sbjct: 61  KVKKNGSHYRCIWGKVARPHGNSGIVRAKFKSNLPPKSMGDRVRVFMYPSNI 112

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|209967441|gb|ACJ02349.1| 60S ribosomal protein L35a [Vernicia fordii]

 Score =  171 bits (432), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 86/112 (76%), Positives = 92/112 (82%), Gaps = 14/112 (12%)

Query: 1   MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------A 46
           MVKGRQGER++LYVRGTILGYKRSKSNQYPNTSLIQI+GVN KEE              A
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEEVGWYAGKRMAYIYKA 60

Query: 47  KTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           K KKNG+HYRCIWGKV R H NSGVVRAKFKSNLPPKS+G RVRVFMYP+NI
Sbjct: 61  KVKKNGSHYRCIWGKVTRPHGNSGVVRAKFKSNLPPKSMGARVRVFMYPSNI 112

Source: Vernicia fordii

Species: Vernicia fordii

Genus: Vernicia

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359807265|ref|NP_001241369.1| uncharacterized protein LOC100800463 [Glycine max] gi|255637727|gb|ACU19186.1| unknown [Glycine max]

 Score =  170 bits (431), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 85/112 (75%), Positives = 92/112 (82%), Gaps = 14/112 (12%)

Query: 1   MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------A 46
           MVKGRQGER++LYVRGTILGYKRSKSNQYPNTSLIQI+GVN KEE              A
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNAKEEVAWYAGKKMAYIYKA 60

Query: 47  KTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           K KKNG+HYRCIWGKV R H NSG+VRAKFKSNLPPKS+G RVRVFMYP+NI
Sbjct: 61  KVKKNGSHYRCIWGKVTRPHGNSGIVRAKFKSNLPPKSMGARVRVFMYPSNI 112

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224112609|ref|XP_002316240.1| predicted protein [Populus trichocarpa] gi|118482276|gb|ABK93065.1| unknown [Populus trichocarpa] gi|222865280|gb|EEF02411.1| predicted protein [Populus trichocarpa]

 Score =  170 bits (430), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 84/112 (75%), Positives = 92/112 (82%), Gaps = 14/112 (12%)

Query: 1   MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------A 46
           MVKGRQGER++LYVRGTILGYKRSKSNQYPNTSL+Q++GVN KEE              A
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLVQVEGVNTKEEVAWYAGKRMAYIYKA 60

Query: 47  KTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           K KKNG+HYRCIWGKV R H NSGVVRAKFKSNLPPKS+G RVRVFMYP+NI
Sbjct: 61  KVKKNGSHYRCIWGKVTRPHGNSGVVRAKFKSNLPPKSMGARVRVFMYPSNI 112

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15221191|ref|NP_177567.1| 60S ribosomal protein L35a-3 [Arabidopsis thaliana] gi|297842177|ref|XP_002888970.1| 60S ribosomal protein L35a [Arabidopsis lyrata subsp. lyrata] gi|75169629|sp|Q9C912.1|R35A3_ARATH RecName: Full=60S ribosomal protein L35a-3 gi|12324899|gb|AAG52401.1|AC020579_3 putative ribosomal protein; 23489-24540 [Arabidopsis thaliana] gi|13878115|gb|AAK44135.1|AF370320_1 putative ribosomal protein [Arabidopsis thaliana] gi|17104787|gb|AAL34282.1| putative ribosomal protein [Arabidopsis thaliana] gi|21554085|gb|AAM63166.1| putative ribosomal protein [Arabidopsis thaliana] gi|297334811|gb|EFH65229.1| 60S ribosomal protein L35a [Arabidopsis lyrata subsp. lyrata] gi|332197451|gb|AEE35572.1| 60S ribosomal protein L35a-3 [Arabidopsis thaliana]

 Score =  169 bits (429), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 84/112 (75%), Positives = 92/112 (82%), Gaps = 14/112 (12%)

Query: 1   MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------A 46
           MVKGRQGER++LYVRGTILGYKRSKSNQYPNTSL+QI+GVN +EE              A
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLVQIEGVNTQEEVNWYKGKRMAYIYKA 60

Query: 47  KTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           KTKKNG+HYRCIWGKV R H NSGVVRAKF SNLPPKS+G RVRVFMYP+NI
Sbjct: 61  KTKKNGSHYRCIWGKVTRPHGNSGVVRAKFTSNLPPKSMGSRVRVFMYPSNI 112

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388522301|gb|AFK49212.1| unknown [Medicago truncatula]

 Score =  169 bits (429), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 84/112 (75%), Positives = 91/112 (81%), Gaps = 14/112 (12%)

Query: 1   MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------A 46
           MVKGRQGER++LYVRGTILGYKRSK NQYPNTSL+QI+GVN KEE              A
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKVNQYPNTSLVQIEGVNTKEEVAWYAGKKMAYIYKA 60

Query: 47  KTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           K KKNGTHYRCIWGKV R H NSG+VRAKFKSNLPPKS+G RVRVFMYP+NI
Sbjct: 61  KVKKNGTHYRCIWGKVTRPHGNSGIVRAKFKSNLPPKSMGSRVRVFMYPSNI 112

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224101037|ref|XP_002312115.1| predicted protein [Populus trichocarpa] gi|118488215|gb|ABK95927.1| unknown [Populus trichocarpa] gi|222851935|gb|EEE89482.1| predicted protein [Populus trichocarpa]

 Score =  169 bits (428), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 85/112 (75%), Positives = 91/112 (81%), Gaps = 14/112 (12%)

Query: 1   MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------A 46
           MVKGRQGER++LYVRGTILGYKRSKSNQYPNTSLIQI+GVN KEE              A
Sbjct: 1   MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLIQIEGVNTKEEVAWYAGKRMAYIYKA 60

Query: 47  KTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           K KK G+HYRCIWGKV R H NSGVVRAKFKSNLPPKS+G RVRVFMYP+NI
Sbjct: 61  KVKKQGSHYRCIWGKVTRPHGNSGVVRAKFKSNLPPKSMGTRVRVFMYPSNI 112

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	98
TAIR|locus:2019627	112	AT1G74270 [Arabidopsis thalian	1.0	0.875	0.75	1.1e-39
TAIR|locus:2007422	112	AT1G07070 [Arabidopsis thalian	1.0	0.875	0.741	2.3e-39
TAIR|locus:2033548	111	AT1G41880 [Arabidopsis thalian	0.989	0.873	0.729	2.6e-38
TAIR|locus:2078991	111	AT3G55750 [Arabidopsis thalian	0.989	0.873	0.720	3.4e-38
GENEDB_PFALCIPARUM|PF11_0438	140	PF11_0438 "Ribosomal protein,	0.928	0.65	0.523	8.7e-24
UNIPROTKB|Q8IHT9	140	PF11_0438 "60S ribosomal prote	0.928	0.65	0.523	8.7e-24
DICTYBASE|DDB_G0270424	105	rpl35a "S60 ribosomal protein	0.897	0.838	0.446	3.1e-19
UNIPROTKB|F1NQ35	113	RPL35A "Uncharacterized protei	0.489	0.424	0.62	5e-19
WB|WBGene00004447	124	rpl-33 [Caenorhabditis elegans	0.571	0.451	0.516	1.3e-18
RGD|628793	110	Rpl35a "ribosomal protein L35a	0.489	0.436	0.62	2.1e-18

TAIR|locus:2019627 AT1G74270 [Arabidopsis thaliana (taxid:3702)]

 Score = 423 (154.0 bits), Expect = 1.1e-39, P = 1.1e-39
 Identities = 84/112 (75%), Positives = 92/112 (82%)

Query:     1 MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------A 46
             MVKGRQGER++LYVRGTILGYKRSKSNQYPNTSL+QI+GVN +EE              A
Sbjct:     1 MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLVQIEGVNTQEEVNWYKGKRMAYIYKA 60

Query:    47 KTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
             KTKKNG+HYRCIWGKV R H NSGVVRAKF SNLPPKS+G RVRVFMYP+NI
Sbjct:    61 KTKKNGSHYRCIWGKVTRPHGNSGVVRAKFTSNLPPKSMGSRVRVFMYPSNI 112

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

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0022625 "cytosolic large ribosomal subunit" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

TAIR|locus:2007422 AT1G07070 [Arabidopsis thaliana (taxid:3702)]

 Score = 420 (152.9 bits), Expect = 2.3e-39, P = 2.3e-39
 Identities = 83/112 (74%), Positives = 91/112 (81%)

Query:     1 MVKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------A 46
             MVKGRQGER++LYVRGTILGYKRSKSNQYPNTSL+Q++GVN  EE              A
Sbjct:     1 MVKGRQGERVRLYVRGTILGYKRSKSNQYPNTSLVQVEGVNTTEEVSWYKGKRMAYIYKA 60

Query:    47 KTKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
             KTKKNG+HYRCIWGKV R H NSGVVRAKF SNLPPKS+G RVRVFMYP+NI
Sbjct:    61 KTKKNGSHYRCIWGKVTRPHGNSGVVRAKFTSNLPPKSMGSRVRVFMYPSNI 112

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

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0022625 "cytosolic large ribosomal subunit" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2033548 AT1G41880 [Arabidopsis thaliana (taxid:3702)]

 Score = 410 (149.4 bits), Expect = 2.6e-38, P = 2.6e-38
 Identities = 81/111 (72%), Positives = 91/111 (81%)

Query:     2 VKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------AK 47
             +KGRQGER++LYVRGT+LGYKRSKSNQYPNTSLIQI+GVN +EE              AK
Sbjct:     1 MKGRQGERVRLYVRGTVLGYKRSKSNQYPNTSLIQIEGVNTQEEVNWYKGKRLAYIYKAK 60

Query:    48 TKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
             TKKNG+HYRCIWGKV R H NSGVVR+KF SNLPPKS+G RVRVFMYP+NI
Sbjct:    61 TKKNGSHYRCIWGKVTRPHGNSGVVRSKFTSNLPPKSMGARVRVFMYPSNI 111

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

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0016020 "membrane" evidence=IDA

GO:0022625 "cytosolic large ribosomal subunit" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

TAIR|locus:2078991 AT3G55750 [Arabidopsis thaliana (taxid:3702)]

 Score = 409 (149.0 bits), Expect = 3.4e-38, P = 3.4e-38
 Identities = 80/111 (72%), Positives = 91/111 (81%)

Query:     2 VKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------AK 47
             +KGRQGER++LYVRGT+LGYKRSKSNQYPNTSL+QI+GVN +EE              AK
Sbjct:     1 MKGRQGERVRLYVRGTVLGYKRSKSNQYPNTSLVQIEGVNTQEEVNWYKGKRLAYIYKAK 60

Query:    48 TKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
             TKKNG+HYRCIWGKV R H NSGVVR+KF SNLPPKS+G RVRVFMYP+NI
Sbjct:    61 TKKNGSHYRCIWGKVTRPHGNSGVVRSKFTSNLPPKSMGARVRVFMYPSNI 111

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

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0022625 "cytosolic large ribosomal subunit" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

GENEDB_PFALCIPARUM|PF11_0438 PF11_0438 "Ribosomal protein, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 273 (101.2 bits), Expect = 8.7e-24, P = 8.7e-24
 Identities = 55/105 (52%), Positives = 73/105 (69%)

Query:     8 ERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEA------------KTKKN--GT 53
             + ++LY +G ILGYKRS+ NQ PN +LI IK VN K+ A            +T K+  G 
Sbjct:    36 QAVRLYEKGVILGYKRSQRNQDPNFTLISIKNVNTKKHAQFYVGKRVAYVYRTTKHHDGV 95

Query:    54 HYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
               +CIWGKV R+H NSGV+RAKFK+++PPK+ GDRVR+ MYP+NI
Sbjct:    96 KIKCIWGKVCRTHGNSGVIRAKFKTHIPPKAFGDRVRILMYPSNI 140

GO:0015934 "large ribosomal subunit" evidence=ISS

UNIPROTKB|Q8IHT9 PF11_0438 "60S ribosomal protein L35Ae, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 273 (101.2 bits), Expect = 8.7e-24, P = 8.7e-24
 Identities = 55/105 (52%), Positives = 73/105 (69%)

Query:     8 ERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEA------------KTKKN--GT 53
             + ++LY +G ILGYKRS+ NQ PN +LI IK VN K+ A            +T K+  G 
Sbjct:    36 QAVRLYEKGVILGYKRSQRNQDPNFTLISIKNVNTKKHAQFYVGKRVAYVYRTTKHHDGV 95

Query:    54 HYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
               +CIWGKV R+H NSGV+RAKFK+++PPK+ GDRVR+ MYP+NI
Sbjct:    96 KIKCIWGKVCRTHGNSGVIRAKFKTHIPPKAFGDRVRILMYPSNI 140

GO:0015934 "large ribosomal subunit" evidence=ISS

DICTYBASE|DDB_G0270424 rpl35a "S60 ribosomal protein L35a" [Dictyostelium discoideum (taxid:44689)]

 Score = 230 (86.0 bits), Expect = 3.1e-19, P = 3.1e-19
 Identities = 46/103 (44%), Positives = 70/103 (67%)

Query:    11 KLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEA---------------KTKKNGTHY 55
             K+Y +G +LGY+RS++ QYPN SLI+I+GV  +E++               K+ KN T +
Sbjct:     3 KIYSKGVVLGYRRSQATQYPNISLIKIEGVVSREDSTFYLGKKVCLVSKVSKSAKNPTGH 62

Query:    56 RCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
             +  WGK+ ++H +SGVV+A+F  NLPPK++G  VRV +YP+NI
Sbjct:    63 KISWGKICKTHGSSGVVQARFARNLPPKAMGAPVRVMLYPSNI 105

GO:0006412 "translation" evidence=IEA;ISS

GO:0005840 "ribosome" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000049 "tRNA binding" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|F1NQ35 RPL35A "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 165 (63.1 bits), Expect = 5.0e-19, Sum P(2) = 5.0e-19
 Identities = 31/50 (62%), Positives = 39/50 (78%)

Query:    49 KKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
             K N T  R IWGKV R+H NSG+VRAKF+SNLP K++G R+RV +YP+ I
Sbjct:    66 KPNRT--RVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 113

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

GO:0006412 "translation" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0022625 "cytosolic large ribosomal subunit" evidence=IEA

GO:0042273 "ribosomal large subunit biogenesis" evidence=IEA

WB|WBGene00004447 rpl-33 [Caenorhabditis elegans (taxid:6239)]

 Score = 163 (62.4 bits), Expect = 1.3e-18, Sum P(2) = 1.3e-18
 Identities = 31/60 (51%), Positives = 39/60 (65%)

Query:    43 KEEAKTKKNG----THYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
             K   KT K G    T  R IWGK+ R H N+G VRAKF  N+PP ++G R+RV +YP+NI
Sbjct:    65 KAHNKTLKTGHTVATRTRAIWGKITRPHGNAGAVRAKFHHNIPPSALGKRIRVLLYPSNI 124

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

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0040017 "positive regulation of locomotion" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

RGD|628793 Rpl35a "ribosomal protein L35a" [Rattus norvegicus (taxid:10116)]

 Score = 165 (63.1 bits), Expect = 2.1e-18, Sum P(2) = 2.1e-18
 Identities = 31/50 (62%), Positives = 39/50 (78%)

Query:    49 KKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
             K N T  R IWGKV R+H NSG+VRAKF+SNLP K++G R+RV +YP+ I
Sbjct:    63 KPNKT--RVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

GO:0000049 "tRNA binding" evidence=TAS

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

GO:0005739 "mitochondrion" evidence=ISO

GO:0005840 "ribosome" evidence=TAS

GO:0006364 "rRNA processing" evidence=ISO

GO:0006412 "translation" evidence=IEA

GO:0022625 "cytosolic large ribosomal subunit" evidence=ISO

GO:0042273 "ribosomal large subunit biogenesis" evidence=ISO

---

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)
Q9C912	R35A3_ARATH	No assigned EC number	0.75	1.0	0.875	yes	no
Q9FZH0	R35A2_ARATH	No assigned EC number	0.7297	0.9897	0.8738	no	no
P41056	RL33B_YEAST	No assigned EC number	0.4528	0.9387	0.8598	yes	no
Q9LMK0	R35A1_ARATH	No assigned EC number	0.7410	1.0	0.875	yes	no
Q9USX4	RL33A_SCHPO	No assigned EC number	0.4579	0.9285	0.8425	yes	no
Q55BN7	RL35A_DICDI	No assigned EC number	0.4466	0.8979	0.8380	yes	no
P05744	RL33A_YEAST	No assigned EC number	0.4433	0.9387	0.8598	yes	no
P51422	R35A4_ARATH	No assigned EC number	0.7207	0.9897	0.8738	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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	Length	Definition	E-value
Query	98
PTZ00041	120	PTZ00041, PTZ00041, 60S ribosomal protein L35a; Pr	4e-38
pfam01247	95	pfam01247, Ribosomal_L35Ae, Ribosomal protein L35A	5e-37
COG2451	100	COG2451, COG2451, Ribosomal protein L35AE/L33A [Tr	9e-26
PRK04337	87	PRK04337, PRK04337, 50S ribosomal protein L35Ae; V	7e-13

>gnl|CDD|240239 PTZ00041, PTZ00041, 60S ribosomal protein L35a; Provisional

 Score =  123 bits (311), Expect = 4e-38
 Identities = 57/105 (54%), Positives = 74/105 (70%), Gaps = 14/105 (13%)

Query: 8   ERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEA--------------KTKKNGT 53
           + ++LYV+   LGYKRSK NQYPN +L++I+GVN +E+A              K  KNGT
Sbjct: 16  KPVRLYVKAVFLGYKRSKVNQYPNVALLKIEGVNTREDARFYLGKRVAYVYKAKKLKNGT 75

Query: 54  HYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
            +R IWGK+ R H NSGVVRA+F  NLPPK++G RVRVF+YP+NI
Sbjct: 76  KFRAIWGKITRPHGNSGVVRARFNKNLPPKAIGSRVRVFLYPSNI 120

Length = 120

>gnl|CDD|189906 pfam01247, Ribosomal_L35Ae, Ribosomal protein L35Ae

 Score =  119 bits (301), Expect = 5e-37
 Identities = 53/95 (55%), Positives = 65/95 (68%), Gaps = 14/95 (14%)

Query: 12 LYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEA--------------KTKKNGTHYRC 57
          LYV+   LGY+R K NQ+PNTSL++I+GVN KE+A              K KKNG+  R 
Sbjct: 1  LYVKAVFLGYRRGKRNQHPNTSLLKIEGVNTKEDAQFYLGKRVAYVYKAKKKKNGSKIRV 60

Query: 58 IWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVF 92
          IWGKV R H NSGVVRAKF+ NLPP+++G RVRV 
Sbjct: 61 IWGKVTRPHGNSGVVRAKFRRNLPPQAMGARVRVM 95

Length = 95

>gnl|CDD|225295 COG2451, COG2451, Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]

 Score = 91.4 bits (227), Expect = 9e-26
 Identities = 46/101 (45%), Positives = 65/101 (64%), Gaps = 13/101 (12%)

Query: 8   ERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEA----------KTKKNGTHYRC 57
           E  +L ++G +L Y+RSK  Q+PN SLI+I+GV+  EEA          K + +G   R 
Sbjct: 3   EGHRLRIKGVVLSYRRSKRTQHPNVSLIKIEGVDSPEEAQFYLGKRVCYKYRSSG---RV 59

Query: 58  IWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           I GKV R+H NSG VRA+F+ NLP +++G  V V +YP+NI
Sbjct: 60  IKGKVVRTHGNSGAVRARFERNLPGQALGTSVEVKLYPSNI 100

Length = 100

>gnl|CDD|179831 PRK04337, PRK04337, 50S ribosomal protein L35Ae; Validated

 Score = 58.1 bits (141), Expect = 7e-13
 Identities = 32/87 (36%), Positives = 46/87 (52%), Gaps = 12/87 (13%)

Query: 14 VRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKT---------KKNGTHYRCIWGKVAR 64
          ++G IL Y+R K+ QY    +I+  GV+ +EEA              G  Y    GK+ R
Sbjct: 3  MKGVILSYRRGKNTQYNRQVIIKPLGVDDREEAAKLIGRKVIWKDPTGNKYV---GKIVR 59

Query: 65 SHSNSGVVRAKFKSNLPPKSVGDRVRV 91
           H N G VRA+FK  LP +++GD V +
Sbjct: 60 VHGNRGEVRARFKPGLPGQALGDYVEI 86

Length = 87

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	98
PTZ00041	120	60S ribosomal protein L35a; Provisional	100.0
KOG0887	111	consensus 60S ribosomal protein L35A/L37 [Translat	100.0
PF01247	95	Ribosomal_L35Ae: Ribosomal protein L35Ae; InterPro	100.0
COG2451	100	Ribosomal protein L35AE/L33A [Translation, ribosom	100.0
PRK04337	87	50S ribosomal protein L35Ae; Validated	100.0
PF09853	53	DUF2080: Putative transposon-encoded protein (DUF2	95.93
PF01782	84	RimM: RimM N-terminal domain; InterPro: IPR002676	89.61
PRK00122	172	rimM 16S rRNA-processing protein RimM; Provisional	89.02
PRK14594	166	rimM 16S rRNA-processing protein RimM; Provisional	88.66
PF01782	84	RimM: RimM N-terminal domain; InterPro: IPR002676	87.74
TIGR02273	165	16S_RimM 16S rRNA processing protein RimM. This fa	86.85
PRK14593	184	rimM 16S rRNA-processing protein RimM; Provisional	83.83
PRK14592	165	rimM 16S rRNA-processing protein RimM; Provisional	83.81
PRK14591	169	rimM 16S rRNA-processing protein RimM; Provisional	81.88
TIGR02273	165	16S_RimM 16S rRNA processing protein RimM. This fa	81.18

>PTZ00041 60S ribosomal protein L35a; Provisional

Probab=100.00  E-value=2e-53  Score=302.35  Aligned_cols=96  Identities=59%  Similarity=1.118  Sum_probs=89.3

Q ss_pred             CCCCCceeceEEEEEEEeeecccCCCCCCeeEEEecCccchHHhh--------------hcCCCceeeEEEeEEEeecCC
Q 040909            3 KGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK--------------TKKNGTHYRCIWGKVARSHSN   68 (98)
Q Consensus         3 ~~~~~~~~Rly~kg~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak--------------~~~~~~k~RviwGKV~r~HGn   68 (98)
                      +++..++.|||+||+|+|||||++||+|||||||||||+++|||.              +.++++++|+|||||+|+|||
T Consensus        11 ~~~~~~~~Rly~kgv~lgYkRg~~nQ~~~~aLlKieGV~~~~~a~fYlGKrvayvyka~~~~~~~k~RviwGKVtR~HGn   90 (120)
T PTZ00041         11 TNRKKKPVRLYVKAVFLGYKRSKVNQYPNVALLKIEGVNTREDARFYLGKRVAYVYKAKKLKNGTKFRAIWGKITRPHGN   90 (120)
T ss_pred             ccCCcCCcceEEEEEEEEeccccccCCCceEEEEecCcCChhhhHhhccceEEEEEcCccccCCcceeEEEEEEEcccCC
Confidence            345566899999999999999999999999999999999999954              345688999999999999999


Q ss_pred             CceEEEEeCCCCCccCCCCeEEEEEeecCC
Q 040909           69 SGVVRAKFKSNLPPKSVGDRVRVFMYPNNI   98 (98)
Q Consensus        69 sGvVrAkF~~nLPp~AiG~~VrVmLyps~i   98 (98)
                      ||+|||+|++||||||||++||||||||+|
T Consensus        91 sGvVrAkF~~nLPp~A~G~~VrVmlyPs~i  120 (120)
T PTZ00041         91 SGVVRARFNKNLPPKAIGSRVRVFLYPSNI  120 (120)
T ss_pred             CcEEEEEeCCCCChHHcCCeEEEEEccCCC
Confidence            999999999999999999999999999997

>KOG0887 consensus 60S ribosomal protein L35A/L37 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.3e-49  Score=278.71  Aligned_cols=96  Identities=66%  Similarity=1.061  Sum_probs=90.3

Q ss_pred             CCCCCceeceEEEEEEEeeecccCCCCCCeeEEEecCccchHHhh--------------hcCCCceeeEEEeEEEeecCC
Q 040909            3 KGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK--------------TKKNGTHYRCIWGKVARSHSN   68 (98)
Q Consensus         3 ~~~~~~~~Rly~kg~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak--------------~~~~~~k~RviwGKV~r~HGn   68 (98)
                      +..|.+.+|||+||+|+||+||+++|+|||+|||||||+++|||.              ...+++++|+|||||||+|||
T Consensus         2 k~~~~e~~rl~vk~~~~~~kr~~r~~~~~t~llkIEGv~skeEa~fYlGkR~~yvYKa~~~~~~~k~RvIWGkVTr~HGN   81 (111)
T KOG0887|consen    2 KGMMGERGRLYVKGTFLGYKRGKRNQHPNTSLLKIEGVYSKEEASFYLGKRCVYVYKAKPEVRGSKTRVIWGKVTRPHGN   81 (111)
T ss_pred             CCcccccceeEeeeEEeeeeecccccCCCcEEEEEecccchhhhheeecCcEEEEEecCCCCCCceEEEEEEEEecccCC
Confidence            566788899999999999999999999999999999999999954              334679999999999999999


Q ss_pred             CceEEEEeCCCCCccCCCCeEEEEEeecCC
Q 040909           69 SGVVRAKFKSNLPPKSVGDRVRVFMYPNNI   98 (98)
Q Consensus        69 sGvVrAkF~~nLPp~AiG~~VrVmLyps~i   98 (98)
                      ||+|||+|.+||||+|||++||||||||+|
T Consensus        82 sG~VrAkF~~Nlp~Ka~G~rvrVmLYps~i  111 (111)
T KOG0887|consen   82 SGVVRAKFTSNLPPKAMGHRVRVMLYPSNI  111 (111)
T ss_pred             cceEEEEeccCCChhHcCcEEEEEEecccC
Confidence            999999999999999999999999999998

>PF01247 Ribosomal_L35Ae: Ribosomal protein L35Ae; InterPro: IPR001780 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=100.00  E-value=4.7e-46  Score=255.70  Aligned_cols=81  Identities=67%  Similarity=1.117  Sum_probs=73.5

Q ss_pred             eEEEEEEEeeecccCCCCCCeeEEEecCccchHHhh--------------hcCCCceeeEEEeEEEeecCCCceEEEEeC
Q 040909           12 LYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK--------------TKKNGTHYRCIWGKVARSHSNSGVVRAKFK   77 (98)
Q Consensus        12 ly~kg~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak--------------~~~~~~k~RviwGKV~r~HGnsGvVrAkF~   77 (98)
                      ||+||+|+|||||++||+|||||||||||+++|||.              +.++++++|+|||||+|+|||||+|||+|+
T Consensus         1 ly~kgv~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrv~yvyk~~~~~~~~k~r~iwGkV~r~HGnsGvVrAkF~   80 (95)
T PF01247_consen    1 LYVKGVFLGYKRGKRNQHPNTALLKIEGVNTKEDAQFYLGKRVAYVYKAKNKKNGSKGRVIWGKVTRPHGNSGVVRAKFK   80 (95)
T ss_dssp             -EEEEEEEEEEEETSTTCEEEEEEEESS-STCHHHHTTTT-EEEEEECE-SSSTTECSEEEEEEEEEESTTTTEEEEEES
T ss_pred             CeeeEEEEeecccccccCCCeeEEeecCccCHHHHHhhcCcEEEEEEecccccCCCcEeEEEEEEEeEEcCCCEEEEEeC
Confidence            899999999999999999999999999999999964              345688999999999999999999999999


Q ss_pred             CCCCccCCCCeEEEE
Q 040909           78 SNLPPKSVGDRVRVF   92 (98)
Q Consensus        78 ~nLPp~AiG~~VrVm   92 (98)
                      +||||||||++||||
T Consensus        81 ~nLP~~a~G~~VrVm   95 (95)
T PF01247_consen   81 KNLPPQAIGSRVRVM   95 (95)
T ss_dssp             S--STTGCSSEEEEE
T ss_pred             CCCChHHcCCEEEeC
Confidence            999999999999998

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The ribosomal L35A eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of: Vertebrate L35A. Caenorhabditis elegans L35A (F10E7.7). Saccharomyces cerevisiae L37A/L37B (Rp47). Plant L35A. Pyrococcus woesei L35A homologue []. These proteins have 87 to 110 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_j 2LP6_A 1SQR_A 4A18_H 4A1D_H 4A19_H 4A1B_H 3IZS_j.

>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.6e-42  Score=239.26  Aligned_cols=93  Identities=47%  Similarity=0.738  Sum_probs=85.7

Q ss_pred             CCceeceEEEEEEEeeecccCCCCCCeeEEEecCccchHHhhhcCC-------CceeeEEEeEEEeecCCCceEEEEeCC
Q 040909            6 QGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKN-------GTHYRCIWGKVARSHSNSGVVRAKFKS   78 (98)
Q Consensus         6 ~~~~~Rly~kg~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak~~~~-------~~k~RviwGKV~r~HGnsGvVrAkF~~   78 (98)
                      |.+..|+++||+|+|||||+++|||+++|||||||+|+|||.....       .+..|||||+|+|+|||||+|||+|.+
T Consensus         1 ~~~~~r~~ikgv~lsyrR~k~~q~P~~~liKi~gv~s~~eA~~y~gk~v~yk~~~~G~Vi~G~V~R~HGnsGaVrarF~~   80 (100)
T COG2451           1 MAEGHRLRIKGVVLSYRRSKRTQHPNVSLIKIEGVDSPEEAQFYLGKRVCYKYRSSGRVIKGKVVRTHGNSGAVRARFER   80 (100)
T ss_pred             CCccceEEEeeEEEEEEecccccCCceEEEEEecCCCHHHHHhhhccEEEEEeCCCCcEEEEEEEEecCCcceEEEEecC
Confidence            3456899999999999999999999999999999999999986532       344699999999999999999999999


Q ss_pred             CCCccCCCCeEEEEEeecCC
Q 040909           79 NLPPKSVGDRVRVFMYPNNI   98 (98)
Q Consensus        79 nLPp~AiG~~VrVmLyps~i   98 (98)
                      ||||||+|+.|+||||||+|
T Consensus        81 ~LP~qa~G~~v~v~ly~~~~  100 (100)
T COG2451          81 NLPGQALGTSVEVKLYPSNI  100 (100)
T ss_pred             CCCchhcCcEEEEEEccCCC
Confidence            99999999999999999986

>PRK04337 50S ribosomal protein L35Ae; Validated

Probab=100.00  E-value=1e-41  Score=231.28  Aligned_cols=79  Identities=38%  Similarity=0.612  Sum_probs=71.9

Q ss_pred             EEEEEEeeecccCCCCCCeeEEEecCccchHHhhhcCCC------ceeeEEEeEEEeecCCCceEEEEeCCCCCccCCCC
Q 040909           14 VRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKNG------THYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGD   87 (98)
Q Consensus        14 ~kg~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak~~~~~------~k~RviwGKV~r~HGnsGvVrAkF~~nLPp~AiG~   87 (98)
                      +||+|+|||||++||+|||||||||||+++|||+.....      ...|+|||||||+|||||+|||+|++||||||||+
T Consensus         3 ~kgv~~gykRg~~nQ~~~~aLlkiegv~~~~~a~fylGKrv~yvyk~grviwGKItR~HGnsGvVrAkF~~nLP~~a~G~   82 (87)
T PRK04337          3 MKGVILSYRRGKNTQYNRQVIIKPLGVDDREEAAKLIGRKVIWKDPTGNKYVGKIVRVHGNRGEVRARFKPGLPGQALGD   82 (87)
T ss_pred             ceEEEEEeccccCccCCceEEEEEcCcCCHHHHHhhcCceEEEEeCCCCEEEEEEEeeeCCCceEEEEECCCCChHHcCC
Confidence            699999999999999999999999999999998865321      12489999999999999999999999999999999


Q ss_pred             eEEEE
Q 040909           88 RVRVF   92 (98)
Q Consensus        88 ~VrVm   92 (98)
                      +|||.
T Consensus        83 ~vrv~   87 (87)
T PRK04337         83 YVEII   87 (87)
T ss_pred             EEEeC
Confidence            99983

>PF09853 DUF2080: Putative transposon-encoded protein (DUF2080); InterPro: IPR019205 This entry, found in various hypothetical archaeal proteins, has no known function

Probab=95.93  E-value=0.016  Score=36.41  Aligned_cols=34  Identities=26%  Similarity=0.471  Sum_probs=27.9

Q ss_pred             EEEeEEEeecCCCceEEEEeCCCCCccCCCCeEEEEEee
Q 040909           57 CIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYP   95 (98)
Q Consensus        57 viwGKV~r~HGnsGvVrAkF~~nLPp~AiG~~VrVmLyp   95 (98)
                      +++++|+ +||||    |++..+||+.-+|.++.|.+..
T Consensus        17 ~~~~~vk-~~Gns----a~v~p~lPkeyiGK~v~iiil~   50 (53)
T PF09853_consen   17 TFIGVVK-PFGNS----ARVYPSLPKEYIGKKVIIIILE   50 (53)
T ss_pred             EEEEEEE-ecCcc----eeEcCCCChHHcCcEEEEEEeC
Confidence            5667766 99999    5677999999999999887643

>PF01782 RimM: RimM N-terminal domain; InterPro: IPR002676 The RimM protein is essential for efficient processing of 16S rRNA []

Probab=89.61  E-value=0.45  Score=30.32  Aligned_cols=28  Identities=18%  Similarity=0.445  Sum_probs=22.8

Q ss_pred             EeEEEeecCCCceEEEEeCCCCCccCCC
Q 040909           59 WGKVARSHSNSGVVRAKFKSNLPPKSVG   86 (98)
Q Consensus        59 wGKV~r~HGnsGvVrAkF~~nLPp~AiG   86 (98)
                      -|+|.+|||-.|-|++..-.+.|.....
T Consensus         2 vG~I~~~hGlkG~vkv~~~td~~~~~~~   29 (84)
T PF01782_consen    2 VGRIGKPHGLKGEVKVRPFTDFPERLFN   29 (84)
T ss_dssp             EEEEEEEETTTTEEEEEE-SSSGGGGGG
T ss_pred             EEEECCCEecCEEEEEEEecCCHHHHcC
Confidence            3999999999999999999887765443

The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes [].; GO: 0006364 rRNA processing; PDB: 2QGG_A 3A1P_C 2DOG_A 2DYI_A 3H9N_A 2F1L_A.

>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional

Probab=89.02  E-value=0.48  Score=34.46  Aligned_cols=30  Identities=23%  Similarity=0.403  Sum_probs=26.2

Q ss_pred             eEEEeEEEeecCCCceEEEEeCCCCCccCC
Q 040909           56 RCIWGKVARSHSNSGVVRAKFKSNLPPKSV   85 (98)
Q Consensus        56 RviwGKV~r~HGnsGvVrAkF~~nLPp~Ai   85 (98)
                      .+..|+|++|||-.|-|+++.-...|...+
T Consensus         7 ~v~iG~i~~~hGlkGevkv~~~td~p~~~~   36 (172)
T PRK00122          7 LLVVGKIVSAHGIKGEVKVKSFTDFPERIF   36 (172)
T ss_pred             eEEEEEEECCCcccEEEEEEEecCCHHHHc
Confidence            477899999999999999999988886544

>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional

Probab=88.66  E-value=0.44  Score=34.80  Aligned_cols=27  Identities=22%  Similarity=0.086  Sum_probs=23.6

Q ss_pred             EEEeEEEeecCCCceEEEEeCCCCCcc
Q 040909           57 CIWGKVARSHSNSGVVRAKFKSNLPPK   83 (98)
Q Consensus        57 viwGKV~r~HGnsGvVrAkF~~nLPp~   83 (98)
                      ++.|+|++|||=.|-|+++.-..-|+.
T Consensus         2 ~~iG~I~~~hGlkGevkV~~~td~~~~   28 (166)
T PRK14594          2 FVKGIILSSYGINGYAKVKSISNNFCD   28 (166)
T ss_pred             EEEEEEECceeeeEEEEEEEccCCHHH
Confidence            578999999999999999988776655

>PF01782 RimM: RimM N-terminal domain; InterPro: IPR002676 The RimM protein is essential for efficient processing of 16S rRNA []

Probab=87.74  E-value=1.7  Score=27.65  Aligned_cols=31  Identities=10%  Similarity=0.253  Sum_probs=22.1

Q ss_pred             EEEEeeecccCCCCCCeeEEEecCccchHHhhhcCC
Q 040909           16 GTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKN   51 (98)
Q Consensus        16 g~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak~~~~   51 (98)
                      -.+.+++     .+.+..|++++||+|+++|...++
T Consensus        45 ~~v~~~~-----~~~~~~i~~~~gi~~r~~Ae~l~g   75 (84)
T PF01782_consen   45 LKVESVR-----PHGKSLIVKFEGIDDREAAEALRG   75 (84)
T ss_dssp             EEEEEEE-----EETTEEEEEETT--SHHHHHTTTT
T ss_pred             EEEEEEE-----EeCCEEEEEEcCCCCHHHHHhhCC
Confidence            4555555     337899999999999999987654

The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes [].; GO: 0006364 rRNA processing; PDB: 2QGG_A 3A1P_C 2DOG_A 2DYI_A 3H9N_A 2F1L_A.

>TIGR02273 16S_RimM 16S rRNA processing protein RimM

Probab=86.85  E-value=1.1  Score=32.30  Aligned_cols=30  Identities=23%  Similarity=0.385  Sum_probs=25.5

Q ss_pred             EEEeEEEeecCCCceEEEEeCCCCCccCCC
Q 040909           57 CIWGKVARSHSNSGVVRAKFKSNLPPKSVG   86 (98)
Q Consensus        57 viwGKV~r~HGnsGvVrAkF~~nLPp~AiG   86 (98)
                      +..|+|++|||=.|-|+++.-...|...+.
T Consensus         2 v~iG~I~~~hGlkGevkv~~~td~p~~~~~   31 (165)
T TIGR02273         2 LVVGKIGGPHGIKGEVKVKSFTDFPESLFD   31 (165)
T ss_pred             EEEEEEECCcccCEEEEEEEcCCCHHHHcC
Confidence            467999999999999999998888875543

This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide.

>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional

Probab=83.83  E-value=1.1  Score=33.11  Aligned_cols=29  Identities=17%  Similarity=0.347  Sum_probs=25.0

Q ss_pred             EEEeEEEeecCCCceEEEEeCCCCCccCC
Q 040909           57 CIWGKVARSHSNSGVVRAKFKSNLPPKSV   85 (98)
Q Consensus        57 viwGKV~r~HGnsGvVrAkF~~nLPp~Ai   85 (98)
                      +..|+|+++||-.|-|++..-..-|....
T Consensus         5 i~iG~I~~~hGikGevkv~~~td~pe~~~   33 (184)
T PRK14593          5 LLVGRIGKSVGLNGGLKLHLESDFPECLK   33 (184)
T ss_pred             EEEEEEECCEeeeEEEEEEECCCCHHHhc
Confidence            56799999999999999999988777543

>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional

Probab=83.81  E-value=1.3  Score=32.12  Aligned_cols=29  Identities=21%  Similarity=0.240  Sum_probs=25.1

Q ss_pred             EEEeEEEeecCCCceEEEEeCCCCCccCC
Q 040909           57 CIWGKVARSHSNSGVVRAKFKSNLPPKSV   85 (98)
Q Consensus        57 viwGKV~r~HGnsGvVrAkF~~nLPp~Ai   85 (98)
                      +..|+|++|||=.|-|+++.-+.-|....
T Consensus         3 v~iG~I~~~hGlkGevkv~~~td~p~~~~   31 (165)
T PRK14592          3 ICLGVITSPHGIKGHVKIKTFTEDPENIS   31 (165)
T ss_pred             EEEEEEECCCccCEEEEEEECCCCHHHhc
Confidence            56799999999999999999988777543

>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional

Probab=81.88  E-value=1.9  Score=31.45  Aligned_cols=29  Identities=10%  Similarity=-0.094  Sum_probs=25.3

Q ss_pred             eEEEeEEEeecCCCceEEEEeCCCCCccC
Q 040909           56 RCIWGKVARSHSNSGVVRAKFKSNLPPKS   84 (98)
Q Consensus        56 RviwGKV~r~HGnsGvVrAkF~~nLPp~A   84 (98)
                      -+..|+|.+|||=.|-|+++.-...|...
T Consensus         5 ~v~vG~I~~~hGlkGevkv~~~td~p~~~   33 (169)
T PRK14591          5 FVEIAKIGATYKLNGELNLYPLANSIETL   33 (169)
T ss_pred             EEEEEEEeCCccccEEEEEEECCCCHHHh
Confidence            46789999999999999999988877744

>TIGR02273 16S_RimM 16S rRNA processing protein RimM

Probab=81.18  E-value=1.3  Score=31.98  Aligned_cols=20  Identities=20%  Similarity=0.458  Sum_probs=17.1

Q ss_pred             CCCeeEEEecCccchHHhhh
Q 040909           29 YPNTSLIQIKGVNIKEEAKT   48 (98)
Q Consensus        29 ~~~~aLlKieGV~~k~~Ak~   48 (98)
                      +.+..||+++|++|+++|..
T Consensus        55 ~~~~~lv~f~gi~~~~~Ae~   74 (165)
T TIGR02273        55 QNNKLIVKFEGIDDREAAEA   74 (165)
T ss_pred             ECCEEEEEECCCCCHHHHHH
Confidence            35578999999999999875

This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	98
3izr_j	111	Localization Of The Large Subunit Ribosomal Protein		1e-36
3izs_j	107	Localization Of The Large Subunit Ribosomal Protein		3e-19
4a18_H	113	T.Thermophila 60s Ribosomal Subunit In Complex With		5e-18
3zf7_l	149	High-resolution Cryo-electron Microscopy Structure		5e-13
1sqr_A	95	Solution Structure Of The 50s Ribosomal Protein L35		5e-09
3j21_c	87	Promiscuous Behavior Of Proteins In Archaeal Riboso		1e-08

>pdb|3IZR|JJ Chain j, Localization Of The Large Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 111

Iteration: 1
 Score =  147 bits (372), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 74/111 (66%), Positives = 86/111 (77%), Gaps = 14/111 (12%)
Query: 2   VKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------AK 47
           +KGRQG+R++LYVRGTILGYKRSKSNQY NTSL+QI+GVN KEE              AK
Sbjct: 1   MKGRQGQRVRLYVRGTILGYKRSKSNQYENTSLLQIEGVNTKEEVGWYAGKRIAYVYKAK 60
Query: 48  TKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           TK N +  RCIWGKV R H NSGVVRAKF+SNLPP S+G +VRVFMYP++I
Sbjct: 61  TKSNDSTIRCIWGKVTRPHGNSGVVRAKFRSNLPPTSMGKKVRVFMYPSSI 111

>pdb|3IZS|JJ Chain j, Localization Of The Large Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 107

Iteration: 1
 Score = 89.7 bits (221), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/106 (44%), Positives = 65/106 (61%), Gaps = 14/106 (13%)
Query: 7   GERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK--------------TKKNG 52
            E  +LYV+G  L Y+RSK    PN SLI+I+GV   ++A+               +  G
Sbjct: 2   AESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVRG 61
Query: 53  THYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           +  R +WGKV R+H NSGVVRA F++NLP K+ G  VR+F+YP+NI
Sbjct: 62  SKIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 107

>pdb|4A18|H Chain H, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 1 Length = 113

Iteration: 1
 Score = 85.9 bits (211), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 38/99 (38%), Positives = 62/99 (62%), Gaps = 13/99 (13%)
Query: 11  KLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK-------------TKKNGTHYRC 57
           +L+V+    G++RSK  Q  N +L++++ VN KE+                KKNG++YR 
Sbjct: 13  RLWVKAAFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQKKNGSNYRT 72
Query: 58  IWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPN 96
           IWG++ ++H N+GV  A+F  NLPP+++G  +RV +YPN
Sbjct: 73  IWGRIGKAHGNNGVAVARFAHNLPPQAIGSVLRVMLYPN 111

>pdb|3ZF7|LL Chain l, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 149

Iteration: 1
 Score = 69.3 bits (168), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 38/113 (33%), Positives = 59/113 (52%), Gaps = 25/113 (22%)
Query: 11  KLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEA------------------------ 46
           +LY++GT+ GY R    Q  NT+L++I+ VN  E+A                        
Sbjct: 37  RLYMKGTLAGYTRGLHGQNKNTALVRIENVNTTEDAKWYVGKRVCYVYHGYKIKRCVRWS 96
Query: 47  KTKKNGTHYRCIWGKVARSHSNSGVVRAKFK-SNLPPKSVGDRVRVFMYPNNI 98
           K     ++ R IWG++ R H  SG VR KF  S++P  ++G R+RV++YP+ I
Sbjct: 97  KAPARRSNTRAIWGRITRPHGTSGTVRVKFNGSSVPASAIGRRIRVYLYPSRI 149

>pdb|1SQR|A Chain A, Solution Structure Of The 50s Ribosomal Protein L35ae From Pyrococcus Furiosus. Northeast Structural Genomics Consortium Target Pfr48. Length = 95

Iteration: 1
 Score = 56.2 bits (134), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 12/91 (13%)
Query: 12 LYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKNGTHYRCIW---------GKV 62
          + ++G +L Y+RSK NQ+ N  +I+   VN +EEA +K  G     +W         GK+
Sbjct: 1  MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEA-SKLIGR--LVLWKSPSGKILKGKI 57
Query: 63 ARSHSNSGVVRAKFKSNLPPKSVGDRVRVFM 93
           R H   G VRA+F+  LP +++GD V + +
Sbjct: 58 VRVHGTKGAVRARFEKGLPGQALGDYVEIVL 88

>pdb|3J21|CC Chain c, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Proteins) Length = 87

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 32/89 (35%), Positives = 50/89 (56%), Gaps = 12/89 (13%)
Query: 12 LYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKNGTHYRCIW---------GKV 62
          + ++G +L Y+RSK NQ+ N  +I+   VN +EEA +K  G     +W         GK+
Sbjct: 1  MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEA-SKLIGR--LVLWKSPSGKILKGKI 57
Query: 63 ARSHSNSGVVRAKFKSNLPPKSVGDRVRV 91
           R H   G VRA+F+  LP +++GD V +
Sbjct: 58 VRVHGTKGAVRARFEKGLPGQALGDYVEI 86

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	98
3iz5_J	166	60S ribosomal protein L12 (L11P); eukaryotic ribos	5e-38
3izc_j	107	60S ribosomal protein RPL33 (L35AE); eukaryotic ri	9e-37
4a18_H	113	RPL35A; ribosome, eukaryotic initiation factor 6,	2e-34
1sqr_A	95	50S ribosomal protein L35AE; PFR48, structure, aut	3e-34

>4a18_H RPL35A; ribosome, eukaryotic initiation factor 6, EIF6, transla large ribosomal subunit, rRNA; 3.52A {Tetrahymena thermophila} PDB: 4a19_H 4a1b_H 4a1d_H Length = 113

 Score =  113 bits (284), Expect = 2e-34
 Identities = 38/105 (36%), Positives = 62/105 (59%), Gaps = 13/105 (12%)

Query: 5   RQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK-------------TKKN 51
                 +L+V+    G++RSK  Q  N +L++++ VN KE+                KKN
Sbjct: 7   SPVAPTRLWVKAAFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQKKN 66

Query: 52  GTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPN 96
           G++YR IWG++ ++H N+GV  A+F  NLPP+++G  +RV +YPN
Sbjct: 67  GSNYRTIWGRIGKAHGNNGVAVARFAHNLPPQAIGSVLRVMLYPN 111

>1sqr_A 50S ribosomal protein L35AE; PFR48, structure, autostructure, northeast structural genomics consortium, beta-barrel; NMR {Pyrococcus furiosus} SCOP: b.43.3.3 PDB: 2lp6_A Length = 95

 Score =  112 bits (281), Expect = 3e-34
 Identities = 29/93 (31%), Positives = 50/93 (53%), Gaps = 6/93 (6%)

Query: 12 LYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEA------KTKKNGTHYRCIWGKVARS 65
          + ++G +L Y+RSK NQ+ N  +I+   VN +EEA               + + GK+ R 
Sbjct: 1  MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSGKILKGKIVRV 60

Query: 66 HSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
          H   G VRA+F+  LP +++GD V + +  ++ 
Sbjct: 61 HGTKGAVRARFEKGLPGQALGDYVEIVLEHHHH 93

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	98
3iz5_j	111	60S ribosomal protein L35A (L35AE); eukaryotic rib	100.0
3izc_j	107	60S ribosomal protein RPL33 (L35AE); eukaryotic ri	100.0
4a18_H	113	RPL35A; ribosome, eukaryotic initiation factor 6,	100.0
1sqr_A	95	50S ribosomal protein L35AE; PFR48, structure, aut	100.0
3j21_c	87	50S ribosomal protein L35AE; archaea, archaeal, KI	100.0
3h9n_A	177	Ribosome maturation factor RIMM; structural genomi	81.48
2dyi_A	162	Probable 16S rRNA-processing protein RIMM; ribosom	80.28

>4a18_H RPL35A; ribosome, eukaryotic initiation factor 6, EIF6, transla large ribosomal subunit, rRNA; 3.52A {Tetrahymena thermophila} PDB: 4a19_H 4a1b_H 4a1d_H

Probab=100.00  E-value=5.7e-53  Score=296.55  Aligned_cols=90  Identities=41%  Similarity=0.865  Sum_probs=85.1

Q ss_pred             ceeceEEEEEEEeeecccCCCCCCeeEEEecCccchHHhhhc-------------CCCceeeEEEeEEEeecCCCceEEE
Q 040909            8 ERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTK-------------KNGTHYRCIWGKVARSHSNSGVVRA   74 (98)
Q Consensus         8 ~~~Rly~kg~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak~~-------------~~~~k~RviwGKV~r~HGnsGvVrA   74 (98)
                      +++|||+||+|+|||||++||+|||||||||||+++|||...             ..++++|+|||||||+|||||+|||
T Consensus        10 ~~~rly~Kgv~lgYkRg~~nQ~~~taLlKIeGV~~~~~a~fylGKrvayvykak~~~g~k~RviwGKVtR~HGnsGvVrA   89 (113)
T 4a18_H           10 APTRLWVKAAFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQKKNGSNYRTIWGRIGKAHGNNGVAVA   89 (113)
T ss_dssp             CSCCCCEEEEEEEEEEETTEEEEEEEEEEETTCCSHHHHHTTTTCEEEEEEEEEEETTEEEEEEEEEEEEEETTTTEEEE
T ss_pred             ccceeEEEEEEEecccccCCCCCCeEEEEEcCcCCHHHHHhhcCCeEEEEEecCCCCCCeEEEEEEEEEeeeCCCCeEEE
Confidence            779999999999999999999999999999999999996532             1578999999999999999999999


Q ss_pred             EeCCCCCccCCCCeEEEEEeecC
Q 040909           75 KFKSNLPPKSVGDRVRVFMYPNN   97 (98)
Q Consensus        75 kF~~nLPp~AiG~~VrVmLyps~   97 (98)
                      +|++||||||||++||||||||+
T Consensus        90 kF~~nLP~kA~G~~VrVmLyPs~  112 (113)
T 4a18_H           90 RFAHNLPPQAIGSVLRVMLYPNR  112 (113)
T ss_dssp             EESSCCCGGGGGSEEEEECCCCC
T ss_pred             EeCCCCChHHcCCeEEEEEecCC
Confidence            99999999999999999999997

>1sqr_A 50S ribosomal protein L35AE; PFR48, structure, autostructure, northeast structural genomics consortium, beta-barrel; NMR {Pyrococcus furiosus} SCOP: b.43.3.3 PDB: 2lp6_A

Probab=100.00  E-value=1.4e-44  Score=247.67  Aligned_cols=82  Identities=35%  Similarity=0.576  Sum_probs=73.7

Q ss_pred             EEEEEEEeeecccCCCCCCeeEEEecCccchHHhhhcCCC------ceeeEEEeEEEeecCCCceEEEEeCCCCCccCCC
Q 040909           13 YVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKNG------THYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVG   86 (98)
Q Consensus        13 y~kg~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak~~~~~------~k~RviwGKV~r~HGnsGvVrAkF~~nLPp~AiG   86 (98)
                      |+||+|+|||||++||+|||||||||||+++|||+...+.      ...|+|||||||||||||+|||+|++||||||||
T Consensus         2 ~~Kgv~lgYkRg~~nQ~~~~aLlkIegV~~k~~a~fYlGKrvayvyka~rviwGKVtR~HGnsGvVrAkF~~nLP~kA~G   81 (95)
T 1sqr_A            2 RIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSGKILKGKIVRVHGTKGAVRARFEKGLPGQALG   81 (95)
T ss_dssp             CCEEEEEEEECCSSSSSCCEEEEEESCCCCHHHHHHHTTCEEEECCSTTCCEEEEEEEESSSSSCEEEECSSCCSSSCTT
T ss_pred             eeeEEEEeeccccCcCCCceEEEEEcCCCCHHHHHhhcCCeEEEEECCCCEEEEEEEeeeCCCCEEEEEeCCCCChHHcC
Confidence            7899999999999999999999999999999998864321      1229999999999999999999999999999999


Q ss_pred             CeEEEEEe
Q 040909           87 DRVRVFMY   94 (98)
Q Consensus        87 ~~VrVmLy   94 (98)
                      ++|||||-
T Consensus        82 ~~VrVml~   89 (95)
T 1sqr_A           82 DYVEIVLE   89 (95)
T ss_dssp             CEEECC--
T ss_pred             CEEEEEEe
Confidence            99999984

>3j21_c 50S ribosomal protein L35AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} PDB: 1sqr_A 2lp6_A

Probab=100.00  E-value=3.3e-42  Score=232.70  Aligned_cols=78  Identities=37%  Similarity=0.618  Sum_probs=71.7

Q ss_pred             EEEEEEeeecccCCCCCCeeEEEecCccchHHhhhcCC------CceeeEEEeEEEeecCCCceEEEEeCCCCCccCCCC
Q 040909           14 VRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKN------GTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGD   87 (98)
Q Consensus        14 ~kg~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak~~~~------~~k~RviwGKV~r~HGnsGvVrAkF~~nLPp~AiG~   87 (98)
                      +||+|+|||||++||+|||||||||||+++|||....+      ....++|||||||+|||||+|||+|++||||||||+
T Consensus         3 ~Kg~~~gykRg~~nQ~~~taLlkieGV~~~~~a~fylGKrvayv~~~g~~iwGKVtr~HGnsGvVrAkF~~nLP~~a~G~   82 (87)
T 3j21_c            3 IKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSGKILKGKIVRVHGTKGAVRARFEKGLPGQALGD   82 (87)
T ss_dssp             EEEEEEEESCCSSCCCTTCEEEEESSCCSHHHHGGGTTCEEEECCSSSCCEEEEEEEECCSSSCEEEEESSCCCSSCSCC
T ss_pred             eeEEEEecccccCcCCCCeEEEEEcCcCCHHHHHhhcCceEEEEeCCCCEEEEEEEeeeCCCCeEEEEeCCCCChHHcCC
Confidence            79999999999999999999999999999999886532      123469999999999999999999999999999999


Q ss_pred             eEEE
Q 040909           88 RVRV   91 (98)
Q Consensus        88 ~VrV   91 (98)
                      +|||
T Consensus        83 ~Vri   86 (87)
T 3j21_c           83 YVEI   86 (87)
T ss_dssp             EECC
T ss_pred             eEEe
Confidence            9997

>3h9n_A Ribosome maturation factor RIMM; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.70A {Haemophilus influenzae}

Probab=81.48  E-value=1.8  Score=30.82  Aligned_cols=29  Identities=14%  Similarity=0.088  Sum_probs=24.3

Q ss_pred             eEEEeEEEeecCCCceEEEEeCCCCCccC
Q 040909           56 RCIWGKVARSHSNSGVVRAKFKSNLPPKS   84 (98)
Q Consensus        56 RviwGKV~r~HGnsGvVrAkF~~nLPp~A   84 (98)
                      ++..|+|.++||-.|-|++.-.+.-|-..
T Consensus         2 ~v~vG~I~~~hGikGevkv~~~Td~pe~~   30 (177)
T 3h9n_A            2 IEVVGKLGSTYGIRGWLRIYSSTEQAESI   30 (177)
T ss_dssp             EEEEEEEEEECSSSSCEEEEECSSSSGGG
T ss_pred             EEEEEEEeCCCccCEEEEEEECCCCHHHh
Confidence            46779999999999999998877777643

>2dyi_A Probable 16S rRNA-processing protein RIMM; ribosomal protein S19, PRC-barrel, STRU genomics, NPPSFA; 2.00A {Thermus thermophilus} PDB: 3a1p_A 2dog_A

Probab=80.28  E-value=1.4  Score=31.03  Aligned_cols=22  Identities=14%  Similarity=0.058  Sum_probs=18.9

Q ss_pred             EEEeEEEeecCCCceEEEEeCCC
Q 040909           57 CIWGKVARSHSNSGVVRAKFKSN   79 (98)
Q Consensus        57 viwGKV~r~HGnsGvVrAkF~~n   79 (98)
                      +..|+|.++||-.|-|++ |--.
T Consensus         4 v~vG~I~~~hGikGevkv-~td~   25 (162)
T 2dyi_A            4 VEIGRFGAPYALKGGLRF-RGEP   25 (162)
T ss_dssp             EEEEEEEEECSSSSCEEE-EECG
T ss_pred             EEEEEEeCCCccCeEEEE-EEch
Confidence            567999999999999999 6553

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	98
d1sqra_	87	b.43.3.3 (A:) Ribosomal protein L35ae {Pyrococcus	1e-32

>d1sqra_ b.43.3.3 (A:) Ribosomal protein L35ae {Pyrococcus furiosus [TaxId: 2261]} Length = 87

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Ribosomal protein L35ae
domain: Ribosomal protein L35ae
species: Pyrococcus furiosus [TaxId: 2261]

 Score =  106 bits (267), Expect = 1e-32
 Identities = 29/86 (33%), Positives = 47/86 (54%), Gaps = 6/86 (6%)

Query: 12 LYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEA------KTKKNGTHYRCIWGKVARS 65
          + ++G +L Y+RSK NQ+ N  +I+   VN +EEA               + + GK+ R 
Sbjct: 1  MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSGKILKGKIVRV 60

Query: 66 HSNSGVVRAKFKSNLPPKSVGDRVRV 91
          H   G VRA+F+  LP +++GD V +
Sbjct: 61 HGTKGAVRARFEKGLPGQALGDYVEI 86

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	98
d1sqra_	87	Ribosomal protein L35ae {Pyrococcus furiosus [TaxI	100.0
d1wb1a2	79	Elongation factor SelB, domains 2 and 4 {Methanoco	89.44
d2f1la2	89	16S rRNA processing protein RimM, N-terminal domai	88.93
d2f1la2	89	16S rRNA processing protein RimM, N-terminal domai	86.72

>d1sqra_ b.43.3.3 (A:) Ribosomal protein L35ae {Pyrococcus furiosus [TaxId: 2261]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Ribosomal protein L35ae
domain: Ribosomal protein L35ae
species: Pyrococcus furiosus [TaxId: 2261]

Probab=100.00  E-value=9.9e-46  Score=248.31  Aligned_cols=81  Identities=36%  Similarity=0.602  Sum_probs=76.4

Q ss_pred             eEEEEEEEeeecccCCCCCCeeEEEecCccchHHhhhcC------CCceeeEEEeEEEeecCCCceEEEEeCCCCCccCC
Q 040909           12 LYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKK------NGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSV   85 (98)
Q Consensus        12 ly~kg~~lgykRg~~~Q~~~~aLlKieGV~~k~~Ak~~~------~~~k~RviwGKV~r~HGnsGvVrAkF~~nLPp~Ai   85 (98)
                      ||+||+|+|||||++||+|||||||||||+++|||+...      ..++.|+|||||||+|||||+|||+|++|||||||
T Consensus         1 lyvKgv~~gykRg~~nq~~~~~Llkiegv~~k~~a~fylGKrv~y~~~~~r~iwGKVtr~HGnsGvVrAkF~~nLP~qa~   80 (87)
T d1sqra_           1 MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSGKILKGKIVRVHGTKGAVRARFEKGLPGQAL   80 (87)
T ss_dssp             CCCEEEEEEEECCSSSSSCCEEEEEESCCCCHHHHHHHTTCEEEECCSTTCCEEEEEEEESSSSSCEEEECSSCCSSSCT
T ss_pred             CeEEEEEEEeccccccCCCCEEEEEEcCcCCHHHHHhhcCcEEEEECCCCcEEEeeEeeecCCCceEEEEecCCCChHHc
Confidence            799999999999999999999999999999999988653      35677999999999999999999999999999999


Q ss_pred             CCeEEEE
Q 040909           86 GDRVRVF   92 (98)
Q Consensus        86 G~~VrVm   92 (98)
                      |++||||
T Consensus        81 G~~VrVm   87 (87)
T d1sqra_          81 GDYVEIV   87 (87)
T ss_dssp             TCEEECC
T ss_pred             CCEEEeC
Confidence            9999998

>d1wb1a2 b.43.3.1 (A:390-468) Elongation factor SelB, domains 2 and 4 {Methanococcus maripaludis [TaxId: 39152]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor SelB, domains 2 and 4
species: Methanococcus maripaludis [TaxId: 39152]

Probab=89.44  E-value=0.04  Score=34.57  Aligned_cols=48  Identities=21%  Similarity=0.304  Sum_probs=33.5

Q ss_pred             EEEecCccchH-HhhhcCCC---ceeeEEEeEEEeecCCCceEEEEeCCCCC
Q 040909           34 LIQIKGVNIKE-EAKTKKNG---THYRCIWGKVARSHSNSGVVRAKFKSNLP   81 (98)
Q Consensus        34 LlKieGV~~k~-~Ak~~~~~---~k~RviwGKV~r~HGnsGvVrAkF~~nLP   81 (98)
                      +.=|||...-+ .|.+.+..   ....-|||||.-+||..|.+.|-|.-|.-
T Consensus        14 r~~IegLA~sK~~aEkLIGe~v~i~~k~i~Gkik~TfGTkG~l~adF~geV~   65 (79)
T d1wb1a2          14 RTVIDGLAQSKVAAEKLIGEEISIEGKDIVGKIKGTFGTKGLLTAEFSGNVE   65 (79)
T ss_dssp             CCEETTSCSSHHHHHHSCSCCCEETTTCCCBCCCCCBTTTTBBCCCBSSCCC
T ss_pred             cEEeeecccchhHHHhhcCcEEEecCCceEEEEeccccCceEEEEEeccccC
Confidence            34477775444 45555431   12234899999999999999999998764

>d2f1la2 b.43.3.4 (A:7-95) 16S rRNA processing protein RimM, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: RimM N-terminal domain-like
domain: 16S rRNA processing protein RimM, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=88.93  E-value=0.11  Score=31.01  Aligned_cols=26  Identities=23%  Similarity=0.271  Sum_probs=21.5

Q ss_pred             CCCCCCeeEEEecCccchHHhhhcCC
Q 040909           26 SNQYPNTSLIQIKGVNIKEEAKTKKN   51 (98)
Q Consensus        26 ~~Q~~~~aLlKieGV~~k~~Ak~~~~   51 (98)
                      .+++.+..+++++||+|+|+|...++
T Consensus        52 ~~~~~~~~~vk~~~i~~r~~Ae~l~g   77 (89)
T d2f1la2          52 GRLHGKVLAAKLKGLDDREEARTFTG   77 (89)
T ss_dssp             EEEETTEEEEEETTCCSHHHHHTTTT
T ss_pred             EEecccEEEEEEcCCCCHHHHHHhCC
Confidence            34566789999999999999998755

>d2f1la2 b.43.3.4 (A:7-95) 16S rRNA processing protein RimM, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: RimM N-terminal domain-like
domain: 16S rRNA processing protein RimM, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=86.72  E-value=0.67  Score=27.26  Aligned_cols=25  Identities=16%  Similarity=0.137  Sum_probs=21.4

Q ss_pred             EEEeEEEeecCCCceEEEEeCCCCC
Q 040909           57 CIWGKVARSHSNSGVVRAKFKSNLP   81 (98)
Q Consensus        57 viwGKV~r~HGnsGvVrAkF~~nLP   81 (98)
                      +..|+|.+|||=.|-|+..--..-|
T Consensus         3 i~iGki~~~hGlkG~vki~~~t~~~   27 (89)
T d2f1la2           3 VVIGKIVSVYGIRGEVKVYSFTDPL   27 (89)
T ss_dssp             EEEEEEEEEETTTTEEEEEECSSSG
T ss_pred             EEEEEEeCCEeeeEEEEEEECCCCH
Confidence            6789999999999999988776644